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https://f1000research.com/articles/11-1229/v1
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28 Oct 22
|
{
"type": "Case Report",
"title": "Case Report: A pericardial effusion secondary to cardiac desmoplastic small round cell tumor ",
"authors": [
"Nehemias Guevara",
"Jane Atallah",
"Mailing Flores Chang",
"Steven Epstein",
"Rocco Lafaro",
"Ilmana Fulger",
"Jane Atallah",
"Mailing Flores Chang",
"Steven Epstein",
"Rocco Lafaro",
"Ilmana Fulger"
],
"abstract": "Desmoplastic small round cell tumor (DSRCT) is an aggressive malignancy usually described in the abdomen and pelvis of adolescent males but rarely in the chest. A 71-year-old male presented with chest pain and was found to have pericardial effusion with cardiac tamponade. He underwent pericardiocentesis and pericardial window. Pericardial fluid and cardiac biopsy results confirmed DSRCT. The patient received the P6 protocol with a good but brief response. He had multiple hospitalizations in the following months for pericardial fluid recollection. Repeat imaging showed mediastinal metastasis. He is currently undergoing second-line chemotherapy treatment. We describe a unique case of primary DSRCT invading the pericardium and myocardium and exhibiting extensive mediastinal metastasis. This is the fourth report of cardiac DSRCT in the literature.",
"keywords": [
"desmoplastic small round blue cell tumours",
"s: malignant pericardial effusion",
"primary cardiac tumor",
"mediastinal metastasis",
"cardiac sarcoma",
"cardiac malignancy"
],
"content": "Introduction\n\nDesmoplastic small round cell tumor (DSRCT) is an extremely rare and aggressive malignancy. It was first described in 1987 in young males involving the scrotum and abdomen.1 The origin of this tumor is still unknown, and it tends to present as an intra-abdominal or retroperitoneal mass.2 It is thought that DSRCT has a mesothelial origin, but an epithelial origin has also been hypothesized.2\n\nAccording to the National Cancer Institute database, not more than 200-450 cases have been published since this entity was first described. In addition, few cases of DSRCT have been reported as chest masses, among which three were described to have a primary cardiac origin,3,4 with one presenting in a pediatric age group.5\n\nHere, we describe a case of a primary DSRCT affecting the pericardium and myocardium of a 71-year-old male patient and the treatment he received based on the most updated evidence. To the best of our knowledge, only three cases of cardiac DSRCT have been reported in the English literature. Nevertheless, clinicians should be aware of such tumors to prompt early diagnosis and avoid treatment delays.\n\n\nCase presentation\n\nA 71-year-old male, a retired mechanic, with a history of hypertension, dyslipidemia, diabetes mellitus, chronic hepatitis C infection related to remote intravenous drug use, splenectomy for traumatic splenic rupture, former smoker, and chronic T cell large granular lymphocyte (T-LGL) leukemia diagnosed two years prior, presented with complaints of shortness of breath and chest pain. The electrocardiogram showed low voltage tracing suggestive of pericardial effusion. He was found to have a large anterior and posterior pericardial effusion with diastolic collapse on echocardiography suggesting cardiac tamponade. Computed tomography (CT) chest demonstrated moderate pericardial and pleural effusions with enlarged mediastinal lymph nodes (LN), the largest measuring 2.3 × 2.2 cm, and a right infra-hilar node 2.1 × 1.5 cm, without axillary or another lymphadenopathy. The patient underwent pericardiocentesis followed by anterior thoracotomy to create a pericardial window with a biopsy of pericardial and myocardial mass.\n\nPathologic evaluation of pericardial fluid and surgical biopsy, including histological, immunohistochemical (IHC), and cytogenetic analyses, were performed. Cytology of the pericardial fluid showed sheets of atypical lymphocytes, suspicious for the lymphoproliferative disorder. Flow cytometry was negative for B or T cell lymphoma, T- LGL only comprised 2.7% of the cells, and CD56 (+) cells comprised 8%. The surgical biopsy consisted of multiple pieces of grey tan myocardial tissue, measuring 0.4 cm in greatest dimension, and two pieces of pick tan pericardial tissue, measuring up to 1 cm. Histologically, sheets of atypical, small, round to oval cells embedded in a dense stroma were noted. Immunohistochemical stains showed diffuse positivity for epithelial membrane antigen EMA, cytokeratin AE1/AE3, and Wt-1c, with focal positivity for desmin (peri-nuclear), CD99, and Fli-1 (shown in Figure 1). MOC31, TTF-1, and synaptophysin stains were negative. Cytogenetic analysis demonstrated EWSR1:WT1 fusion. The fluorescence in situ hybridization (FISH) study was positive for a rearrangement involving the EWSR1 gene at chromosome 22q12 (39% of cells). The morphological features, as well as the IHC profile, supported the diagnosis of DSRCT.\n\nOriginal magnification (A/D) × 40; (B/C) × 4.\n\nPretreatment staging positron emission tomography (PET)/CT (shown in Figure 2) revealed moderate to large nonmetabolic pericardial effusion with abnormal enhancement of the myocardium and multiple metastatic hypermetabolic mediastinal and left supraclavicular lymphadenopathy. The patient completed a modified P6 outpatient regimen with cycles 1,2,3, and 6 of cyclophosphamide, doxorubicin, and vincristine and cycles 4, 5, and 7 with ifosfamide and etoposide. He tolerated chemotherapy well over four months without noted toxicities or dose delays. Follow-up CT chest/abdomen/pelvis without contrast showed significant improvement in the generalized mediastinal lymphadenopathy and pericardial effusion, reflecting a good response to treatment.\n\nThe relative paucity of tumor-free myocardium uptake compared to presumed regions of disease. Avid tracer uptake to numerous metastatic lymph nodes, including retrocrural lymph node (white arrow) and to both adrenal glands (black arrows).\n\nThe patient overall maintained good functional capacity and reported biking daily; however, he continued to present to the ED intermittently with complaints of pleuritic chest pain and dyspnea. Repeat CTA two months later showed disease progression with enlarged lymph nodes in the right mediastinum and a 2 cm pathologic lymph node in the lateral left epicardial fat pad that had previously measured 1 cm. The tumor was best characterized on magnetic resonance imaging (MRI) chest/thorax as an enhancing 3.7 cm infiltrative mass lesion about the anterior pericardium with likely infiltration of the adjacent right ventricular wall apex and numerous (more than 10) adjacent enhancing nodules seen involving the cardio-phrenic fat anteriorly, the largest on the right measured 2.1 × 1.9 × 2.1 cm, and the largest on the left 2.2 × 1.4 × 2.2 cm, which appeared contiguous with right periapical infiltrative pericardial mass (shown in Figure 3). The large pericardial effusion persisted, measuring up to 2.8 mm in maximum width without tamponade physiology. The patient received colchicine with an improvement in symptoms.\n\nThe patient presented again with complaints of abdominal pain and diarrhea two weeks after completing one cycle of second-line treatment with Irinotecan (20 mg/m2/day) and Temozolomide (100 mg/m2/day). As a result, he underwent urgent pericardiocentesis for early tamponade found on follow-up echo, followed by a repeat pericardial window.\n\nInterval PET/CT revealed worsening disease with disseminated supraclavicular, mediastinal, and hilar lymphadenopathy with an invasion of the chest wall and possible invasion of the right ventricle (shown in Figure 4). The patient understood his poor prognosis and opted for completing two cycles of second-line chemotherapy. To date, it has been a total of 19 months since diagnosis.\n\n\nDiscussion\n\nDSRCT is a rare and highly malignant sarcoma commonly found in the abdomen, retroperitoneum, and pelvis, predominantly in adolescent males.6–8 Patients often present with symptoms related to abdominal distention, as the disease is often multifocal, with extensive lesions found in the peritoneum and mesentery.6,7,9 Concurrent sites of distant metastases at presentation commonly involve lymph nodes, the liver, and the lungs.6–10 Few cases of primary DSRCT have been reported in the lungs and pleura,11–13 with fewer reports of mediastinal cases.6,14,15 However, primary cardiac DSRCT is highly uncommon, with only three cases published in the literature.5–7\n\nHistologically, DSRCT is characterized by nests of small, round, ovoid, or spindled cells embedded in an abundant desmoplastic fibrous stroma.16 Epithelial (keratin and epithelial membrane antigen EMA), mesenchymal (vimentin and desmin), and neural (CD56 and neuron-specific enolase NSE) markers are expressed on immunohistochemical staining of neoplastic cells, suggesting evidence of divergent differentiation.17 Immunohistochemical positivity for desmin, Wilms tumor 1 (WT1), keratin, and NSE is seen in the review of 32 tumors.1 In an analysis of 39 tumors with the histologic pattern of the desmoplastic small round cell, cytokeratin (PCK) is expressed in 95% of tumors, EMA in 96%, desmin in 100%, NSE in 72%, and WT1 in 89%.18 In our case, tumor cells show positive markers for desmin, WT1, PCK AE1/AE3, EMA, CD99, and CD56 consistent with immunohistochemical features of DSRCT. Also, the perinuclear dot-like pattern of desmin immunoreactivity is distinctive for DSRCT.19 The EWSR1:WT1 fusion protein, resulting from a reciprocal translocation between Ewing sarcoma RNA binding protein 1 (EWSR1) and Wilms tumor one gene (WT1) t(11;22) (p13;q12),20 constitutes the molecular hallmark of DSRCT.21 EWSR1:WT1 protein is thought to drive cell proliferation by acting through WT1 protein, a transcription factor involved in mesenchymal to epithelial differentiation during development.22 The observed immunoreactivity to the C-terminal region of WT1, present in our case, is diagnostic of DSRCT over Ewing sarcoma/primitive neuroectodermal tumor (EWS/PNET), which carries a similar EWSR gene rearrangement.23\n\nImaging studies regarding DSRCT can overlap with other aggressive peritoneal malignancies, such as neuroblastoma, malignant lymphoma, rhabdomyosarcoma, Ewing sarcoma, Wilms tumor, primitive neuroectodermal tumor, anaplastic synovial sarcoma.\n\nOf the 400 DSRCT cases reported in the literature, roughly 200 are published in the radiology literature.24\n\nCT and MRI are complementary studies in the setting of DSRCT; a retrospective study showed the peritoneal/omental masses with no identifiable origin of the tumor itself in 94% of the cases; furthermore, the majority (80%) demonstrating large (>5 cm) dominant soft-tissue deposit and multiple smaller foci25\n\nCT and MRI typically demonstrated a heterogeneous soft-tissue enhancement with cystic degeneration; calcification is not a standard characteristic and is present only in 20% of the cases. Distant metastasis was seen in 25% of the cases; locally advanced disease was most familiar with further complications. These same characteristics have been seen in similar studies.15,26,27 Although CT scans in cardiac cases have yet to be completely documented, two of the three published cases had CTs prior to any intervention. The common findings were large pericardial effusion, mediastinal lymphadenopathy, and a heart mass. In all the cases, DSRCT was never the first diagnosis to be considered.5–7,28,29\n\nCases involving the mediastinum, and pleura, such as mesothelioma and localized fibrous tumors, make it hard to consider DSRCT as a possible diagnosis.\n\nMesothelioma usually presents as a unilateral pleural effusion, with thickening of the mediastinal pleura and circumferential/nodular pleural thickening with interlobar fissure as well; this can be seen in the image studies as an enhancement. On the other hand, fibrous tumors present as a homogeneous mass with intermediate to high attenuation on unenhanced CT scans.12–29\n\nMRI has been useful in delineating the extension of the disease, including local invasion of osseous anatomical structures if surgical resection is being considered. MRI of DSRCTs often demonstrates high signal intensity on T2 weighted sequences vs. hypo- or iso-intensity relative to skeletal muscle on T1 weighted images. Heterogeneous T1 and T2 signal patterns and heterogeneous enhancement following gadolinium administration are attributed to fibrous stroma and internal degeneration, including necrosis, hemorrhage, and calcification.12,15,26,28,30\n\nRegarding cardiac tumor involvement, the data for the utility of PET/CT as a diagnostic tool is limited, even unavailable. PET/CT shows the intensity of fluorodeoxyglucose (FDG) uptake, and the maximum standardized uptake value of the masses remains variable and is frequently as high as 12, indicating intensely avid hypermetabolism. PET/CT has no value in diagnosing DSRCT.30 However, PET/CT has been used to follow DSRCT lesions after the surgical or chemotherapeutic intervention, to verify tumor response to therapy, and to assess patient outcomes based on the changes in metabolic activity of lesions during therapy.26–30\n\nThere is no standard therapeutic regimen for DSRCT. The literature recommends various treatments, including multiple-agent chemotherapy, adjuvant radiotherapy, surgical procedures, and targeted drug therapy. In our index patient, the treatment was with chemotherapy utilizing the P6 regimen (consisting of seven courses of chemotherapy) with cycles 1,2,3 and 6 of cyclophosphamide (4200 mg/m2), doxorubicin (75 mg/m2), vincristine, and cycles 4, 5 and 7 with Ifosfamide (9 mg/m2) and Etoposide (500 mg/m2).\n\nDue to the tumor's location, it becomes challenging to propose surgical management. However, the P6 regimen combined with debulking surgical and radiation therapy approaches is the best treatment strategy,31 which is well described in a review of 12 patients by Hassan et al. treated at the Mayo Clinic. Hassan et al. reported that the medical survival of patients managed with surgical resection was 34 months, compared with the ones that underwent biopsy alone were 14 months.32 Furthermore, T. Lal et al. compared the 3-year survival of the surgery group and the non-surgery group; 58% survived in the surgery group, while there was no survivor in the group that did not have surgery.15 Hence, it was proposed that effective cytoreduction and tumor resection would benefit patients without metastasis.\n\nJin et al. described the medical management for mediastinal DSRCT in a 51-year-old male patient who was treated with cyclophosphamide combined with doxorubicin and vincristine chemotherapy for four cycles. Repeat imaging showed distant metastasis, for which the patient was started on ifosfamide (9 g/m2) + etoposide (500 g/m2) every two weeks for three cycles. Subsequently, cyclophosphamide (200 g/m2) + adriamycin (75 g/m2) + vincristine (1.4 g/m2) were used for maintenance treatment for 4 cycles. Radiotherapy (a total of 70Gy of mediastinal Y field radiation) was administered. Nonetheless, there was no improvement; the patient had a total survival period of 17 months.15\n\nTherapies for DSRCT are more limited due to surgical resection and radiotherapy difficulties. In addition, patients have progress of disease despite maximal chemotherapy. This should prompt further research into more effective chemotherapeutic options.\n\n\nConclusion\n\nDSRCT is a rare and highly malignant sarcoma commonly found in the abdomen, retroperitoneum, and pelvis, predominantly in adolescent males. Patients often present with symptoms related to abdominal distention, as the disease is often multifocal, with extensive lesions found in the peritoneum and mesentery. Concurrent sites of distant metastases at presentation commonly involve lymph nodes, the liver, and the lungs. Few cases of primary DSRCT have been reported in the lungs and pleura, with fewer reports of mediastinal cases. However, primary cardiac DSRCT is exceptionally uncommon, with only three cases published in the literature.\n\n\nConsent\n\nInformed written consent was obtained from the patient to publish this case report and the accompanying images.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nReisner D: A Case of Desmoplastic Small Round Cell Tumor. J. Radiol. Case Rep. 2015; 9: 1–7. PubMed Abstract | Publisher Full Text\n\nSesterhenn I, Davis CJ, Mostofi FK: Undifferentiated malignant epithelial tumors involving serosal surfaces of scrotum and abdomen in young males. J. Urol. 1987; 137. Publisher Full Text\n\nLayfield LJ, Lenarsky C: Desmoplastic small cell tumors of the peritoneum coexpressing mesenchymal and epithelial markers. Am. J. Clin. Pathol. 1991; 96: 536–543. PubMed Abstract | Publisher Full Text\n\nLettieri CK, Garcia-Filion P, Hingorani P: Incidence and outcomes of desmoplastic small round cell tumor: results from the surveillance, epidemiology, and end results database. J. Cancer Epidemiol. 2014; 2014: 680126. PubMed Abstract | Publisher Full Text\n\nRomanos-Sirakis EC: A primary cardiac sarcoma with features of a desmoplastic small round cell tumor in an adolescent male. J. Pediatr. Hematol. Oncol. 2010; 32: 236–239. PubMed Abstract | Publisher Full Text\n\nYin K: Cardiac desmoid tumour. Eur. J. Cardiothorac. Surg. 2018; 53: 1292. PubMed Abstract | Publisher Full Text\n\nGeorge S: Malignant small round cell tumor of the heart: a diagnostic dilemma. Cardiovasc. Pathol. 2007; 16: 56–58. PubMed Abstract | Publisher Full Text\n\nLae ME: Desmoplastic small round cell tumor: a clinicopathologic, immunohistochemical, and molecular study of 32 tumors. Am. J. Surg. Pathol. 2002; 26: 823–835. Publisher Full Text\n\nLi G: Primary abdominopelvic desmoplastic small round cell tumor: CT and correlated clinicopathologic 6 of 7 features. Eur. Rev. Med. Pharmacol. Sci. 2014; 18: 2670–2677. PubMed Abstract\n\nHayes-Jordan A, Anderson PM: The diagnosis and management of desmoplastic small round cell tumor: a review. Curr. Opin. Oncol. 2011; 23: 385–389. Publisher Full Text\n\nIkeue T: Desmoplastic Small Round Cell Tumor of the Pleura Successfully Treated with a Lower Dose of Pazopanib. Intern. Med. 2016; 55: 2463–2467. PubMed Abstract | Publisher Full Text\n\nFois AG: Desmoplastic small round cell tumors of the pleura: a review of the clinical literature. Multidiscip. Respir. Med. 2017; 12: 22. PubMed Abstract | Publisher Full Text\n\nCao Y: Desmoplastic small round cell tumor: A case report of a rare differential diagnosis of solid tumors of the pleura. Oncol. Lett. 2015; 10: 2991–2995. PubMed Abstract | Publisher Full Text\n\nNayak HK: Mediastinal mass-a rare presentation of desmoplastic small round cell tumour. BMJ Case Rep. 2011; 2011: bcr1020115042. PubMed Abstract | Publisher Full Text\n\nJin D: Mediastinal desmoplastic small round cell tumor. Medicine (Baltimore). 2020; 99: e22921. PubMed Abstract | Publisher Full Text\n\nGerald WL, Rosai J: Case 2. Desmoplastic small cell tumor with divergent differentiation. Pediatr. Pathol. 1989; 9: 177–183. PubMed Abstract | Publisher Full Text\n\nGerald WL, Rosai J: Desmoplastic small cell tumor with multi-phenotypic differentiation. Zentralbl. Pathol. 1993; 139: 141–151. PubMed Abstract\n\nOrdonez NG: Desmoplastic small round cell tumor: I: a histopathologic study of 39 cases with emphasis on unusual histological patterns. Am. J. Surg. Pathol. 1998; 22: 1303–1313. Publisher Full Text\n\nYin WH: Desmoplastic small round cell tumor of the submandibular gland--a rare but distinctive primary salivary gland neoplasm. Hum. Pathol. 2010; 41: 438–442. PubMed Abstract | Publisher Full Text\n\nSawyer JR, Tryka AF, Lewis JM: A novel reciprocal chromosome translocation t(11;22)(p13;q12) in an intraabdominal desmoplastic small round-cell tumor. Am. J. Surg. Pathol. 1992, 16: 411–416. Publisher Full Text\n\nGerald WL, Rosai J, Ladanyi M: Characterization of the genomic breakpoint and chimeric transcripts in the EWS-WT1 gene fusion of desmoplastic small round cell tumor. Proc. Natl. Acad. Sci. U. S. A. 1995; 92: 1028–1032. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee SB: The EWS-WT1 translocation product induces PDGFA in desmoplastic small round-cell tumour. NatGenet. 1997; 17: 309–313. PubMed Abstract | Publisher Full Text\n\nHill DA: WT1 staining reliably differentiates desmoplastic small round cell tumor from Ewing sarcoma/primitive neuroectodermal tumor. An immunohistochemical and molecular diagnostic study. Am. J. Clin. Pathol. 2000; 114: 345–353. PubMed Abstract | Publisher Full Text\n\nZhang WD: MRI, and FDG-PET/CT imaging findings of abdominopelvic desmoplastic small round cell tumors: correlation with histopathologic findings. Eur. J. Radiol. 2011; 80: 269–273. PubMed Abstract | Publisher Full Text\n\nThomas R: Desmoplastic small round cell tumour: the radiological, pathological and clinical features. Insights Imaging. 2013; 4: 111–118. PubMed Abstract | Publisher Full Text\n\nMorani AC: Desmoplastic Small Round Cell Tumor: Imaging Pattern of Disease at Presentation. AJR Am. J. Roentgenol. 2019; 212: W45–w54. Publisher Full Text\n\nArora VC: Characteristic imaging features of desmoplastic small round cell tumour. Pediatr. Radiol. 2013; 43: 93–102. PubMed Abstract | Publisher Full Text\n\nSuhag S, Byrd RH, Jaiswal K: Rare Case of Thoracic Desmoplastic Small Round Cell Tumor in a Three-Year-Old Boy. J. Oncol. Pract. 2019; 15: 617–620. PubMed Abstract | Publisher Full Text\n\nBian Y: Effusion cytology of desmoplastic small round cell tumor of the pleura. A case report. Acta Cytol. 1993; 37: 77–82. PubMed Abstract\n\nKis B: Imaging of desmoplastic small round cell tumour in adults. Br. J. Radiol. 2012; 85: 187–192. PubMed Abstract | Publisher Full Text\n\nJayakrishnan T: Desmoplastic Small Round-cell Tumor: Retrospective Review of Institutional Data and Literature Review. Anticancer Res. 2021; 41: 3859–3866. PubMed Abstract | Publisher Full Text\n\nMello CA: Desmoplastic Small Round Cell Tumor: A Review of Main Molecular Abnormalities and Emerging Therapy. Cancers (Basel). 2021; 13. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "171650",
"date": "25 May 2023",
"name": "Fernand Bteich",
"expertise": [
"Reviewer Expertise Broad exposure to all sorts of tumors in an academic setting",
"including sarcomas and mediastinal tumors."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI think this case report is well-written and informative. It provides a good overview of DSRCT, a rare tumor and an orphan disease, including its clinical presentation, diagnosis, and treatment.\nDiagnosis is made with convincing pathologic review and immunohistochemistry biomarkers. The authors also do a solid job of reviewing the literature on cardiac DSRCT. I would recommend this case report to anyone interested in learning more about this tumor. This adds to literature by describing a rare presentation of the disease in an old gentleman. It shows that, despite advanced age, multi-modal chemotherapy can be administered and achieve some degree of disease control.\nRecommendations/questions:\nSome attention can be paid to a few sentence structures.\n\nWould avoid brand names of medications such as \"Adriamycin\".\n\nWould elaborate on any role for NGS and targeted therapies as well as immunotherapy in the discussion part of the case report.\n\nAny link between patient's T-LGL and his diagnosis of DSRCT?\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "265984",
"date": "06 May 2024",
"name": "Madelyn Espinosa-Cotton",
"expertise": [
"Reviewer Expertise DSRCT in general",
"T cell bispecific antibodies",
"radioimmunotherapy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting case of cardiac DSRCT, which is an unusual presentation of this disease. Also unusual is the patient's age, since DSRCT is typically seen in adolescents and young adults. The case report is well written and sufficient details are given regarding diagnosis and treatment.\n\nThis is the second case I know of in which a patient previously treated for another malignancy developed DSRCT. It would be useful to include any cytotoxic treatments the patient in this report received for his T-LCL, as they could potentially have contributed to his development of DSRCT. I would also like to see the authors discuss any other case reports in which DSRCT is a secondary malignancy.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1229
|
https://f1000research.com/articles/8-1755/v1
|
15 Oct 19
|
{
"type": "Brief Report",
"title": "Influence of delivery mode on maternal mental status one month after delivery at a perinatal center in Japan: A cross-sectional study",
"authors": [
"Shunji Suzuki"
],
"abstract": "Background: Maternal mental status has been thought to be affected by the delivery modes. We examined the influence of delivery modes on the mental status of women who delivered at our institute in Japan. Methods: Data were collected from the medical charts of 645 primiparous women without a history of mental disorders who delivered singleton babies and underwent a 1-month postpartum check-up at our institute from September 2018 to June 2019. The maternal mental status was examined based on the scores of the Edinburgh Postnatal Depression Scale (EPDS) and the Mother-Infant Bonding Scale (MIBS). Results: The rate of high scores of the EPDS and the MIBS in women choosing elective cesarean section were higher than in women with vaginal delivery and emergency cesarean section. Conclusion: A fulfilling birth-plan and birth-review may also be necessary for women choosing elective cesarean section.",
"keywords": [
"maternal mental status",
"elective cesarean section",
"birth-review"
],
"content": "Introduction\n\nMaternal mental status has been thought to be affected by the delivery modes because childbirth is an important event for both the mother and child, and it influences early mother-infant interaction1,2. In this study, we examined the influence of delivery modes on the mental status of women who delivered at our institute in Japan.\n\n\nMethods\n\nThe protocol for this study was approved by the Ethics Committee of the Japanese Red Cross Katsushika Maternity Hospital. In addition, informed consent concerning analysis from a retrospective database was obtained from all subjects. In our institute, cesarean section is not performed without medical indication because cesarean section on maternal request for pain relief has not been generally recognized in Japan.\n\nData were collected from the medical charts of 645 primiparous women without a history of mental disorders who delivered singleton babies and underwent a 1-month postpartum check-up at our institute from September 2018 to June 2019. Of the 645 primiparous women, 389 women (60.3%) had vaginal deliveries, 80 (12.4%) had elective cesarean deliveries, and 176 (27.3%) had emergent cesarean deliveries. In this study, demographic data included maternal age. The maternal mental status was examined based on the scores of the Edinburgh Postnatal Depression Scale (EPDS) and the Mother-Infant Bonding Scale (MIBS), and the time required for psychiatric counseling by our midwives. Women with the EPDS ≥ 9 points, those with the MIBS ≥ 3 points, and the time required for psychiatric counseling ≥ 25 minutes were diagnosed with mental problems.\n\nData are presented as mean ± SD or number (%). SPSS Statistics software version 20 (IBM Corp., Armonk, NY, USA) was used for statistical analyses. For statistical analysis, the Χ2 test for categorical variables and the Student’s t-test for continuous variables were used. Differences with p < 0.05 were considered significant.\n\n\nResults\n\nTable 1 shows the clinical description of primiparous women and the results of mental problems. The rates of high scores of the EPDS and the MIBS were higher in the emergency cesarean group than vaginal delivery group; in addition, the rate of high scores of the EPDS and the MIBS and a long time for psychiatric counseling in women choosing elective cesarean section were higher than in women with vaginal delivery and emergency cesarean section, as shown in Table 1.\n\nData are presented as mean ± SD or number (%).\n\nEPDS, Edinburgh Postnatal Depression Scale; MIBS, Mother-Infant Bonding Scale.\n\n*P vs. vaginal delivery group.\n\n#P vs. vaginal and emergency cesarean delivery groups.\n\n\nDiscussion\n\nThis may be the first report to indicating that women received elective cesarean section are more prone to have mental problems. Although we predicted that the highest frequency of mental problems would be in the emergent cesarean delivery group, the women choosing elective cesarean delivery actually had the most mental problems. The reason for the results is not clear; however, based on the records of psychiatric counseling, it may be because there was no birth-plan or birth-review for women scheduled for elective cesarean delivery. In our institute, a birth-plan has been carried out for all pregnant women scheduled for vaginal delivery, and a birth-review that takes a long time during hospitalization has been performed especially for mothers undergoing emergency caesarean section in order to recover from the trauma of the sudden departure from normal labor3. This is because a birth-review is one of the concrete measures to learn about the ‘bruising’ of labor and promptly affirm the experience of delivery3,4. A mother’s thought during birth-review about the experience of childbirth has been suggested to help express feelings of embarrassment and provide an opportunity to reconstruct the facts. On the other hand, pregnant woman scheduled to undergo elective cesarean section are given an explanation and birth-review of cesarean section solely from a surgical perspective. The absence of an adequate birth-plan or birth-review may lead to mental problems in postpartum women who receive elective cesarean section.\n\nWe understand the small sample size for statistical analyses as one of serious limitations in this study. However, a fulfilling birth-plan and birth-review may also be necessary for women choosing elective cesarean section.\n\n\nData availability\n\nFigshare: delivery mode and maternal mental status. https://doi.org/10.6084/m9.figshare.9956690.v15.\n\nThis project contains data on the delivery method, EPDS and MIBS scores and counselling time for each participant.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe author wishes to thank all patients for their collaboration.\n\n\nReferences\n\nPilch D: [The influence of birth modus on the emotional state of the mother, bonding, and the newborn's neurobehavioural state]. Pomeranian J Life Sci. 2015; 61(3): 249–256. PubMed Abstract\n\nRowe-Murray HJ, Fisher JR: Operative intervention in delivery is associated with compromised early mother-infant interaction. BJOG. 2001; 108(10): 1068–1075. PubMed Abstract | Publisher Full Text\n\nNakamura M: Review of literature on birth review (Childbirth recall) of child-rearing period (in Japanease). Seisen J Nurs Stud. 2018; 7: 29–34. Reference Source\n\nRubin R: Attainment of the maternal role. 2. Models and referrants. Nurs Res. 1967; 16(4): 342–346. PubMed Abstract\n\nSuzuki S: delivery mode and maternal mental status. figshare. Dataset. 2019."
}
|
[
{
"id": "63674",
"date": "08 Jun 2020",
"name": "Tuğba Kınay",
"expertise": [
"Reviewer Expertise obstetrics and gynecology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to evaluate this report. The paper is about the effect of delivery mode on the postpartum mental status of women. The results of the study indicate that the women who underwent elective cesarean delivery had higher scores of the EPDS and MIBS than women with vaginal delivery and emergent cesarean delivery. I have the following comment: In discussion section, the author state that – \"We understand the small sample size for statistical analyses as one of serious limitations in this study. However, a fulfilling birth-plan and birth-review may also be necessary for women choosing elective cesarean section.\" I don’t think that the current study based on its methodology can support that statement .The conclusion paragraph including main outcomes of the study should be rewritten.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/8-1755
|
https://f1000research.com/articles/11-1226/v1
|
27 Oct 22
|
{
"type": "Research Article",
"title": "Impact of a pulmonary rehabilitation program on social disadvantage and physical activity data of postCOVID19 patients: A North-African pilot study",
"authors": [
"Wafa BENZARTI",
"Emna TOULGUI",
"Amine Ghram",
"Chiraz RAHMANI",
"Sana AISSA",
"Ines GHANNOUCHI",
"Imene GARGOURI",
"Amani SAYHI",
"Asma KNAZ",
"Walid OUANES",
"Sonia JEMNI",
"Helmi Ben Saad",
"Wafa BENZARTI",
"Emna TOULGUI",
"Amine Ghram",
"Chiraz RAHMANI",
"Sana AISSA",
"Ines GHANNOUCHI",
"Imene GARGOURI",
"Amani SAYHI",
"Asma KNAZ",
"Walid OUANES",
"Sonia JEMNI"
],
"abstract": "Background\nIn addition to the cardiorespiratory, muscular, and neurological manifestations, coronavirus disease 2019 (COVID-19) alters patients’ health-related quality of life (HRQoL), induces a large variety of psychiatric manifestations, and reduces mobility and motor activity. Several studies have raised the impact of a pulmonary rehabilitation program (PRP) on social disadvantage (e.g., HRQoL, anxiety, depression) and physical activity of COVID-19 patients, but very few have been performed in low-income countries. This study aimed to investigate the impact of a PRP on post-COVID-19 HRQoL, hospital anxiety and depression (HAD), and physical activity in Tunisian post-COVID19-patients. Methods This was a cross-sectional study in an outpatient care setting. Patients with post-COVID-19 were included. They completed an interview (including three questionnaires) before and after a PRP (three sessions/week for four weeks, each session was 70 minutes in duration, PRP items: aerobic cycle endurance, strength training, and education). The VQ11 questionnaire assessed functional dimension, psychological dimension, relational dimension, and total score; HAD appraised depression and anxiety; and Voorrips physical activity assessed daily activity, physical activity, leisure activity, and total scores. Data were expressed as mean±standard deviation in PRP change (PRP change=after-PRP values − before-PRP values). Results In total, 14 moderate to severe post-COVID-19 patients (61±4 years) were included. The PRP significantly improved the i) functional, psychological, and relational dimensions, and the VQ11 total score by 1.79±1.58 (p=0.0033), 2.00±2.15 (p=0.0108), 1.57±1.50 (p=0.0077), and 5.36±3.97 (p=0.0015), respectively; ii) HAD anxiety and depression scores by 2.07±2.40 (p=0.0076), and 2.57±3.08 (p=0.0058); and iii) physical activity and total scores by 1.75±2.44 (p=0.0251), and 1.78±2.65 (p=0.0341), respectively. Conclusion The PRP improved HRQoL, HAD, and physical activity of Tunisian post-COVID-19 patients.",
"keywords": [
"Handicap",
"Health Status",
"North Africa",
"Physical Rehabilitation",
"SARS-Cov-2"
],
"content": "Abbreviations list\n\naPRP: after pulmonary rehabilitation program\n\nBMI: body mass index\n\nbPRP: before pulmonary rehabilitation program\n\nEQ 5 D: Euroqol five domains\n\nEQ-5D-5L: Euroqol five domains 5 levels\n\nGAD-7: generalized anxiety disorder-7 questionnaire\n\nHAD: hospital anxiety and depression\n\nHR: heart rate\n\nHRQoL: health-related quality of life\n\nPRP: pulmonary rehabilitation program\n\nRT-PCR: reverse transcriptase-polymerase chain reaction\n\nSAS: self-rating anxiety scale\n\nSD: standard deviation\n\nSDS: self-rating depression scale\n\nVAS: visual analogue scale\n\n\nIntroduction\n\nCoronavirus disease 2019 (COVID-19) is an infectious disease involving the respiratory system and several extra pulmonary organs.1 COVID-19 has clinically diverse manifestation ranging from asymptomatic presentation to critical illness.2 In people recovering from COVID-19, there is some concern regarding the potential long-term sequelae and associated impairment of functional capacity since clinical sequelae may persist after acute-COVID-19.3 According to one guideline (www.nice.org.uk/guidance/ng188 2020), signs and symptoms of COVID-19 from 4 to 12 weeks after the onset of the first symptoms are defined as “ongoing symptomatic COVID-19”, while COVID-19 sequelae that last >12 weeks are summarized by terms such as “post-COVID-19 syndrome”, “long-COVID-19”, or “post-acute sequelae of infection by severe acute respiratory syndrome coronavirus 2”.4 The main manifestations reported by patients are organic such as chest pain, breathlessness, fatigue, and reduced mobility.3\n\nIn post-COVID-19 patients, psychological manifestations are noted.5–8 Indeed, COVID-19 was reported to alter health-related quality of life (HRQoL).5–9 Three months after symptom onset, around 75% of hospitalized COVID-19 patients identify unusual patient-reported outcomes, with 33% of patients identifying at least moderate deficiencies in major dimensions of HRQoL.8 The relationship between COVID-19 and altered HRQoL could be related to severity at admission, hypoxaemia, systemic inflammation, respiratory support during hospitalization, and lack of contact with family and loved ones during quarantine or hospitalization.10,11 Persistent symptoms post-acute phase could explain the persistence of a poor HRQoL.12 COVID-19 was reported to possibly lead to symptoms of depression and anxiety, and lack of motivation.5–9 Among the described health problems of post-COVID-19, neuropsychological impairments are common (47%), with a high prevalence of psychological disorders such as augmented levels of stress, anxiety, and depression.13–16 Since HRQoL is a multidimensional concept that includes domains related to physical, mental, emotional, and social functioning, it is important to focus on and improve it.17\n\nDuring the virus’s speedy spread in the absence of a COVID-19 vaccine, numerous states instigated restrictive procedures (e.g., stay-at-home instructions, closures of parks and fitness and recreation centers).18 These procedures led to a rise in physical inactivity, which is recognized as a risk factor for COVID-19 severity and mortality.18,19 COVID-19 patients have reduced mobility and motor activity, which leads to an increase in unhealthy lifestyle habits, raising the risk of diseases.20 In patients with chronic conditions, one clinical guideline recommend to increase their physical activity and emotional participation in everyday activities.21 Physical activity has been proven to be effective in improving both mental and physical health and continues to be the greatest method to preserve well-being of the body, to guarantee quotidian activities, and to preserve a good function of the cardiorespiratory and muscular chain.21,22 Thus, as in chronic cardiorespiratory diseases, COVID-19 patients could benefit from a pulmonary rehabilitation program (PRP).23,24\n\nThe European Respiratory Society taskforce recommends that COVID-19 patients with a need for rehabilitative interventions should receive a PRP.25 Most publications carried out in high-income countries investigated the impact of PRP on submaximal exercise data on COVID-19 patients.26–37 In COVID-19, a PRP is an excellent management axis, but studies related to its impact on patients’ social disadvantage or physical activity are scarce.24,26–29,31–34 Four systematic reviews demonstrated the feasibility and efficiency of a PRP in the management of post-COVID-19 patients.35–38 Almost all of the retained studies were performed in specialized rehabilitation units from high-income countries. In low-income countries, the potential benefit of a PRP after COVID-19 is unclear.\n\nSince no previous study from a low-income country raised the impact of an ambulatory PRP on HRQoL, psychological manifestation, and physical activity of COVID-19 patients, the aim of this cross-sectional study was to examine the impact of a PRP on social disadvantage (HRQoL, anxiety and depression), and physical activity of Tunisian COVID-19 patients. PRP will be considered ‘efficient’ if the PRP change (ΔPRP=after (aPRP) minus before (bPRP) PRP values) for the main outcome of this study (HRQoL total score) is statistically significant.\n\n\nMethods\n\nThe present study is part of a project including two parts. The first part aimed to evaluate the impact of a PRP on the 6-minute walk test performed by COVID-19 patients.24 Meanwhile, this research constitutes the second part of this project. Figure 1 details the project flowchart.\n\nCOVID-19: coronavirus disease 2019. PRP: pulmonary rehabilitation program.\n\nThis was a cross-sectional study conducted from 2nd February 2021 to 26th September 2021 by a multidisciplinary team including the department of pulmonology and department of physiology and functional explorations at the Farhat HACHED hospital, Sousse, Tunisia, and the department of physical medicine and rehabilitation at the Sahloul hospital, Sousse, Tunisia. During each study step, all recommended preventive measures to fight against COVID-19 transmission were applied. The study was conducted following the guidelines established by the STROBE statement.39\n\nThe target population was COVID-19 patients hospitalized (during February to June 2021) in the COVID-19 units of the aforementioned pulmonology and physical medicine departments. Only male COVID-19 patients aged > 50 years, with a chest-computed tomography during the hospitalization period showing an extensive/severe extent of parenchymal lung injury40 were included in this study. COVID-19 patients admitted into an intensive care unit were excluded. Absence during two or more exercise training sessions or the aPRP evaluation session was applied as an exclusion criterion.\n\nCOVID-19 diagnosis was confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR).41 All patients underwent chest-computed tomography. The following two classifications were applied: i) chest-computed tomography classification, which consisted of five levels based on the extent of parenchymal lung injury: absent or minimal (<10%), moderate (10–25%), extensive (25–50%), severe (50–75%), and critical (>75%),40 and ii) clinical classification (https://www.who.int/publications/i/item/WHO-2019-nCoV-clinical-2021-2), including four levels (mild, moderate, severe, and critical).\n\nThe PRP was ‘inspired’ from previous international recommendations for COVID-19 PRPs, and for the practice of physical activity in chronically ill patients aged >50 years.25,42–45 Once four to five consecutive patients agreed to participate in the PRP, they formed one group and began the PRP. Figure 2 summarizes the five phases of the study.\n\nThe first phase of the study (Figure 2) was a meeting between two physicians (ET and WB in the authors’ list) and a group of four to five patients. During this phase, the physicians explained the PRP content and its progress; and when applicable, they educated patients about how to manage some comorbidities such as diabetes mellitus and/or arterial hypertension, and encouraged smokers to stop smoking. The physicians also related psychological support, such as how to manage emotional distress and/or post-traumatic stress disorder, and how to cope with COVID-19.46 Moreover, the physicians also presented some nutritional advice47,48 and responded to patients’ inquiries. During the end of this phase, each patient was interviewed separately. The interview, which included four parts [detailed in the appendices A (French/Arabic version) and B (translated English version)], was prepared in local Arabic dialect, and questions were asked by the same trained physicians (ET and WB in the authors’ list). For each patient, the questions were repeated by the same interviewer bPRP and aPRP. The duration of the interview was approximately 30 minutes for each patient. The first part of the interview was derived from the American thoracic society questionnaire49 and was performed only bPRP. This first part involved clinical (schooling and socioeconomic levels, lifestyle habits, medical and surgical history) and COVID-19 (date of RT-PCR, hospitalization, number of days bPRP, imaging) data. Two schooling-levels were arbitrarily defined: low (illiterate and primary school) or high (secondary and university). The socioeconomic level was determined according to the patient’s profession, and two levels were defined: unfavorable or favorable. Cigarette smoking was evaluated in pack-years, and patients were classified into two groups: non-smoker (<five pack-years), and smoker (≥five pack-years). Hospital stay was the number of days of hospitalization for COVID-19 management. The number of days bPRP represented the number of days between COVID-19 diagnosis (day of RT-PCR) and the first day of the onset of exercise training. The second part of the interview concerned the evaluation of the HRQoL via the VQ11.50 VQ11 is a valid French questionnaire providing a reliable measure of HRQoL, which has been validated in patients with chronic respiratory conditions.50 The VQ11 includes 11 items divided into three components (functional=three questions; psychological=four questions; and relational=four questions), and its score ranges from 11 to 55.50 The VQ11 Arabic version was used.51 The third part of the interview aimed to determine the current presence of and tendency towards anxiety or depression at the time of evaluation via the hospital anxiety and depression (HAD) questionnaire.52 The latter includes 14 questions (score range 0–3); scored to separately estimate the anxiety and depressive status (seven questions each). The individual score for anxiety and depression subscales may vary from 0 to 21. The HAD Arabic version was used.53 A HAD anxiety or depression score ranging between 0 and 7 was considered to be normal, a score between 8 and 10 indicated borderline-abnormal (borderline case) anxiety or depression, and a score of 11 or more indicated abnormal (case) anxiety or depression.54 The fourth part of the interview concerned the Voorrips questionnaire,55 which objectively evaluated the level of physical activity. This questionnaire is reproducible, and its score is positively correlated with the 24-hour measurement of the physical activity quantified by the use of a pedometer.55 The Voorrips questionnaire includes 51 questions divided into three parts, evaluating the respondents’ daily sports and leisure physical activities. When added, the three parts give the total physical-activity score.55 The Arabic version of the Voorrips questionnaire is not yet validated, but it was used in previous Tunisian studies.56,57\n\nThe second phase of the study (Figure 2) was reserved to perform evaluations/tests to gather anthropometric data including age, height (cm), weight (kg), and body mass index (BMI, kg/m2), as well as spirometry, a 6-minute walk test, and handgrip strength. The data of the last three tests were explored in the first part of the project.24 The obesity status was noted, in which underweight is BMI<18.5 kg/m2, normal weight is BMI=18.5–24.9 kg/m2, overweight is BMI=25.0–29.9 kg/m2, and obesity is BMI≥30.0 kg/m2.58\n\nThe third phase of the study (Figure 2) was reserved for the exercise training, which consisted of three sessions per week for four weeks (12 sessions of 70 minutes each). Exercise training was performed in four groups of four or five patients. A typical exercise training session included the following five items (Figure 3):\n\ni) Item 1 involved warming-up for five minutes, including light exercises such as walking slowly, mobilization of cervical, lumbar spine, and peripheral joints.\n\nii) Item 2 was comprised of lower limbs strengthening for 45 minutes such as aerobic training on an ergocycle. The cycling intensity was standardized and personalized using a heart rate (HR) monitor. The HR target was the HR determined at the end of the 6-minute walk test (±5 bpm). The HR monitor alarms were set around the HR target. The patients were asked to gradually reach their HR targets during the first five minutes and to maintain pedaling for 10 minutes at this intensity. Then, they were asked to return to empty pedaling or walking at their own pace for five minutes. They were again asked to complete one cycle of 10 minutes of target HR training and five minutes of active recovery (e.g., empty pedaling or walking at their own pace). To complete this item, the last cycle involved seven minutes of target HR training and three minutes of active recovery.\n\niii) Item 3 was upper limbs strengthening for 10 minutes. Various muscle groups of the upper limbs performed sets of ten repetitions (e.g., raising and lowering shoulders, shoulder blade stabilization, bending and straightening elbows, raising arms). These exercises were performed without load during the first exercise training sessions, then with dumbbells of increasing weights along exercise training (https://www.respir-sud.com/english/rehabilitation/12/105/2/D%c3%a9monstration.html).\n\niv) Item 4 consisted of balance posture and proprioception exercises for five minutes. Several exercises were performed to improve balance posture, proprioception, coordination, and stability. Positions exercises included floor exercises, seated, and standing exercises and were varied between sessions. Exercises of increasing difficulty were performed along the exercise training, such as static and dynamic standing and walking exercises on a mat, as well as bipodal and unipodal exercises on an unstable platform (https://www.respir-sud.com/english/rehabilitation/12/105/2/D%c3%a9monstration.html).\n\nv) Item 5 was a five-minute relaxation session. Numerous exercises involving spine and limbs stretching (e.g., standing stretch, cat back exercises, sphinx position) and breathing exercises (e.g., controlled diaphragmatic breathing, coordination between inspiratory and expiratory times) were performed (https://www.respir-sud.com/english/rehabilitation/12/105/2/D%c3%a9monstration.html).\n\nHR: heart rate.\n\nDuring each exercise training session, therapeutic education was carried out to strengthen the patients’ adherence to the lifestyle counseling provided during the bPRP meeting, for example management of comorbidities, encouraging smoking cessation when applicable, psychological support, and nutritional counseling.47 All exercise training items were performed on patients not wearing a facemask.\n\nThe fourth phase (Figure 2) was reserved to evaluations/tests similar to the second phase. During the fifth phase (Figure 2), the following issues were tackled: patients’ feedback, questionnaires (as conducted during the first step, except the first part of the interview), checking the results of aPRP evaluations, and advising patients to continue exercise training.\n\nThe sample size was calculated according to this formulae59:\n\nQuantitative and categorical data were presented as mean±standard deviation (SD) 95% confidence interval and percentage, respectively. For each quantitative data including VQ11 scores (functional dimension, psychological dimension, relational dimension, total score), HAD anxiety and depression scores, Voorrips questionnaire (daily activity, physical activity, leisure activity, total score), a ΔPRP was calculated. The Wilcoxon matched pairs test and the one-sided chi squared test were used to compare the quantitative and categorical data bPRP and aPRP, respectively. PRP was considered ‘efficient’ if the ΔPRP change of the VQ11 total score (i.e., main outcome) is statistically significant. All statistical procedures were performed using statistical software (StatSoft, Inc. (2014). STATISTICA (data analysis software system), version 12. www.statsoft.com, 011after- PRPbefore-RRID: SCR_014213). The significance level was set at p<0.05.\n\n\nResults\n\nAmong the 68 COVID-19 patients discharged from COVID-19 hospital units, 18 volunteered to participate in the study. Among them, 14 patients completed the full PRP (Figure 1).\n\nThe mean±SD (95% confidence interval) of age, height, weight, and BMI were 61±4 (59 to 64) years, 1.70±0.04 (1.67 to 1.72) m, 89±16 (80 to 99) kg, and 31.0±5.2 (28.0 to 34.0) kg/m2, respectively. The frequencies of patients with normal weight, overweight, and obesity, were 7%, 50%, and 43%, respectively. The schooling and socioeconomic levels were low and unfavorable in 40% and 43% of patients, respectively, and 64% of patients were smokers (mean±SD of pack-years: 24±18 (8 to 39)). The frequencies of patients with diabetes mellitus, arterial hypertension, chronic obstructive pulmonary disease, dyslipidemia, and dysthyroidism, were 57%, 43%, 36%, 21%, and 7%, respectively. Table 1 details the COVID-19 data and severity classification of the 14 patients.\n\nTable 2 details the impact of PRP on HRQoL, HAD anxiety and depression scores, and physical activity scores. It concluded that the means of the functional, psychological, and relational dimensions, and the VQ11 total score decreased significantly by 1.79, 2.00, 1.57, and 5.36 points, respectively. Additionally, the means of the HAD anxiety and depression scores decreased significantly by 2.07 and 2.57 points and the percentage of COVID-19 patients with abnormal HAD anxiety decreased significantly from 21% to 0%. Furthermore, the means of the physical activity and total scores increased significantly by 1.75 and 1.78 points, respectively.\n\n* p value<0.05 (Wilcoxon matched pairs test or one-sided chi squared test): before-PRP vs. after-PRP.\n\n\nDiscussion\n\nThe present North African study demonstrated that a PRP improved HRQoL, HAD, and the physical activity of Tunisian COVID-19 patients. To the best of the authors’ knowledge, this is the first African and Arab study investigating the impact of a PRP on post-COVID-19 patients in terms of social disadvantages and physical activity. The methodology and main outcomes of some similar studies including a single group of COVID-19 patients, and case-control studies are detailed in Table 3 and Table 4, respectively.\n\na Median (minimum-maximum);\n\nb Mean ±SD;\n\nc Median (interquartile range).\n\n* p<0.05: before PRP vs. after PRP. For the study of Gloeckl et al.:\n\nα p<0.05 before PRP vs. after PRP for the group mild/moderate;\n\nβ p<0.05 before PRP vs. after PRP for the group severe/critical;\n\n¥ p<0.05 between-group difference mild/moderate vs. severe/critical for the same period.\n\na Mean±SD;\n\n* p<0.05;\n\nFor the study of Liu et al.:\n\nα p<0.05 before-PRP vs. after-PRP for the same group cases;\n\n¥ p<0.05 between-group difference cases vs. controls for the same period.\n\nFor the study of Spielmanns et al.:\n\nΔ p<0.05 before-PRP vs. after-PRP for the PG group;\n\nδ p<0.05 before-PRP vs. after-PRP for the LG group;\n\n£ p<0.05 between-group difference PG vs. LG for the same period.\n\nThe three dimensions (functional, psychological, and relational) and the total score of the VQ11 increased after the PRP, by 1.79, 2, 1.57, and 5.36 points, respectively (Table 2). These results are similar to those reported by Bouteleux et al.27 In the latter study, the mean±SD of the VQ11 total score and the functional dimension score were improved by four points, from 29±10 bPRP to 25±10 aPRP (p=0.041), and two points, from 10±3 bPRP to 8±3 aPRP (p<0.001) in mild COVID-19 outpatients. However, Bouteleux et al.27 reported no statistical changes in the psychological (from 11±4 bPRP to 10±4 aPRP (p=0.264)) and relational dimensions (from 9±4 bPRP to 8±4 aPRP (p=0.162)). Across similar studies, several assessment tools of HRQoL were used, including the Euroqol five domains (EQ 5D), EQ 5D five levels (EQ-5D-5L) visual analogue scale (VAS),26,28 or SF-36 scale.29,33 Betschart et al.26 reported a statistically significant improvement in HRQoL from a mean of 65% (bPRP) to 81% (aPRP) on the EQ-5D-5L VAS (0–100%, 100% representing “the best health you can imagine”). Gloeckl et al.29 noted that HRQoL was improved significantly only in patients with severe/critical COVID-19 (compared to mild/moderate COVID-19) in the mental component sum score of the SF-36 (from 38.5 bPRP to 52.9 aPRP points). Daynes et al.28 highlighted that the EQ 5D thermometer improved by 8±19 (p=0.05) after six weeks of a PRP using exercise and education. Liu et al.33 concluded that the eight dimensions of the SF-36 scores in elderly COVID-19 patients were statistically significant within the intervention group that underwent six weeks of a PRP, between the intervention and control groups.\n\nFrom a public health viewpoint, it is central to determine the level of HRQoL in order to suggest a theoretical base for the expansion of appropriate policies and courses to increase well-being and avoid the frequent difficulties related to HRQoL.60 HRQoL is an increasingly important health goal, and it is an independent predictor of health outcome.61 The effectiveness of a PRP in increasing physical performance and HRQoL could be explained by the improvement in dyspnea, lung function, or the 6-minute walk distance.62 Bardakci et al.62 noted that physical health parameters of SF-36 are lower in patients with a low 6-minute walk distance and low spirometry data. At the post-recovery stage, most COVID-19 patients retain an altered HRQoL, which poses challenges to patients, and health professionals,12 thus having a major impact on economic trends in almost all sectors.63 Predictors for COVID-19-induced deficits in HRQoL after hospitalization are yet to be determined in research.26\n\nAs done in some related studies27,28,32,34 (Table 3 and Table 4), anxiety and depression were evaluated using the HAD questionnaire.54 The means of the HAD anxiety and depression scores decreased significantly by 2.07, and 2.57 points, respectively, and the percentage of COVID-19 patients with abnormal HAD anxiety decreased significantly from 21% to 0%. These findings are different to these reported in some studies,27,28,32 where no improvement was noted in both HAD anxiety and depression scores (Table 3 and Table 4). First, in the study of Daynes et al.,28 the increases in the HAD anxiety and depression mean±SD scores by 0±4 (p=0.5) and 1±4 (p=0.1) were not statistically significant. Second, Bouteleux et al.27 reported that the increases in the mean±SD scores of HAD anxiety (from 8±3 bPRP to 8±0 aPRP, p=0.941) and depression (from 6±4 bPRP to 5±0 aPRP, p=0.306) were not statistically significant. Third, Puchner et al.32 noted that symptoms of depression and anxiety were not increased after multi-disciplinary inpatient PRP in 23 patients discharged after severe to critical COVID-19 infection. Other studies have used different scales, such as self-rating anxiety and depression scale (SAS, SDS, respectively)64 and the generalized anxiety disorder-7 questionnaire (GAD-7),65 and reported improvement only in anxiety.29,33 For instance, Gloeckl et al.,29 reported a slight but significant increase in the GAD-7 score by a median (interquartile range) of 1 (0–2, p=0.021) after three weeks of inpatient PRP in COVID-19 patients. In the study of Liu et al.,33 SAS and SDS scores decreased after six weeks of a PRP in the intervention group, but only anxiety was statistically significant within and between groups (intervention vs. control), and SDS scores were not statistically significant within or between groups.\n\nIn our study, the improvement in anxiety and depression status could be related to the psychological support provided during the PRP (e.g., management of emotional distress, post-traumatic stress disorder, and strategies for coping with COVID-19). Moreover, anxiety and depression have been linked to reduced HRQoL.66\n\nThe present study is the first to evaluate the impacts of a PRP on the physical activity of COVID-19 patients evaluated using a generic questionnaire55 (Table 2). In the literature, some related studies have evaluated the impacts of PRPs on functional impairment using some functional assessment scales including general scales (e.g., functional independence measure,33 functional assessment of chronic illness therapy)28 or specific scales (e.g., post-COVID-19 functional status scale26 (Table 3 and Table 4)), and have reported divergent conclusions. Indeed, Liu et al.33 did not note any improvement in the activities of daily living assessed by the functional independence measure scale.33 However, some authors reported an improvement in the functional status.26,28 In fact, symptoms such as dyspnea in chronic respiratory diseases could cause reductions in the activities of daily living, thus leading to dependence and disability.67 By improving these symptoms, a PRP in COVID-19 patients could restore their ability to take care of themselves.4,15,68 Physical activity continues to be the best method to preserve well-being, guarantee daily activities, and preserve good function of the cardiorespiratory and muscular chain.45 From a public health awareness perspective, it is vital to reconnoiter the level of physical activity in the interest of providing a theoretical foundation for the expansion of appropriate guidelines to ameliorate health and turn aside the numerous problems related to physical inactivity.60\n\nThe inconsistencies noted between our findings and these of some similar studies (Table 3 and Table 4) could be clarified by some points related to dissimilarities in:\n\ni) Study designs, including case control33 vs. prospective observational cohort29 studies.\n\nii) PRP locations, such as inpatient32 or outpatient26 PRP.\n\niii) Inclusion criteria, for example inclusion of COVID-19 patients of different ages e.g., elderly (≥ 65 years)33 or middle-aged (48±15 years)27], or both males and females.27,28\n\niv) COVID-19 patients’ profiles, including their comorbidities or lack of them and/or the disease severity stages, from mild/moderate to severe/critical.29\n\nv) PRP components, such as exercise training alone27 vs. exercise training and education.26,30\n\nvi) Durations and/or frequencies of PRP, for example two sessions per week and 16 sessions26 vs. five sessions per week and three sessions.29\n\nvii) Time periods between the diagnosis of COVID-19 and the beginning of PRP (e.g., late PRP for long-COVID-1928 vs. early PRP for acute COVID-1932).\n\nThe present study has two strong points and three main limitations. The first strong point was the fact that the study was led in an outpatient unit in a low-income country and the different components of a PRP were performed, including exercise training, education, and nutritional counseling. The second strong point was the calculation of the sample size according to a predictive formula.59 The first major limitation concerns the lack of a randomized COVID-19 control-group due to ethical considerations during the COVID-19 pandemic. Indeed, while few similar studies included a control group33,34 (Table 4), several other studies26–32 included only one group (Table 3). The lack of a control-group did not allow us to ‘affirm’ that our findings are solely attributable to the PRP. For that reason, we recognize that the positive impacts of the PRP could be interpreted as a natural remission of COVID-19. Nevertheless, the initial symptoms in our patients presented almost three months before the PRP (Table 1). Consequently, we relate these improvements principally to the impact of the PRP, which also comprised specific interventions focusing on disease management and coping with COVID-19 and its sequelae.29 The second limitation concerns the use of the VQ11 questionnaire to evaluate the HRQoL.27 The VQ11 is mainly validated in COPD patients and is not proposed for being used in the general population.50 However, the VQ11 is usually used in our departments,51 easily administered, and seems reliable with the indication of a PRP in our study as it precisely assesses the alteration of HRQoL related to respiratory disability.27 The third limitation involves the use of a non-validated Arabic version of the Voorrips questionnaire.55 However, the Arabic version of that questionnaire was previously used in some Tunisian studies.56,57 Future research to address the aforementioned limitations is needed.\n\n\nConclusion\n\nFour weeks of a PRP in post-COVID-19 patients is efficient even in a low-income country, such as Tunisia. This Tunisian study demonstrated that a PRP performed in patients with post-COVID-19 is associated with marked improvements in HRQoL, HAD anxiety and depression, and physical activity scores. Pulmonary rehabilitation has imposed itself as a standard of care for the treatment of post-COVID-19 patients. Future randomized studies are needed to assess the effectiveness and long-term benefits of PRP in post-COVID-19 patients.\n\n\nEthical approval\n\nThis study was approved by the ethics committee of Farhat HACHED Hospital (Approval number FH2502/2021).\n\n\nInformed consent\n\nWritten informed consent was obtained from all patients after receiving an explanation of the study.",
"appendix": "Data availability\n\nZenodo: Impact of a pulmonary rehabilitation program on social disadvantage and physical activity data of postCOVID19 patients: A North-African pilot study, https://doi.org/10.5281/zenodo.7191266. 69\n\nThe project contains the following underlying data:\n\n- [Data of 14 patients.xls] (Excel file including the numerical data of the 14 patients).\n\n- [Appendix A: Copy of the French/Arabic questionnaire] (Applied questionnaire).\n\n- [Appendix B: Copy of the translated English questionnaire] (Translated questionnaire).\n\nZenodo: STROBE checklist for ‘[Impact of a pulmonary rehabilitation program on social disadvantage and physical activity data of postCOVID19 patients: A North-African pilot study], https://doi.org/10.5281/zenodo.7191266. 69\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nXie Y, Xu E, Bowe B, et al.: Long-term cardiovascular outcomes of COVID-19. Nat. Med. 2022; 28(3): 583–590. PubMed Abstract | Publisher Full Text\n\nTsai PH, Lai WY, Lin YY, et al.: Clinical manifestation and disease progression in COVID-19 infection. J. Chin. Med. Assoc. 2021; 84(1): 3–8. Publisher Full Text\n\nLopez-Leon S, Wegman-Ostrosky T, Perelman C, et al.: More than 50 long-term effects of COVID-19: a systematic review and meta-analysis. Sci. Rep. 2021; 11(1): 16144. PubMed Abstract | Publisher Full Text\n\nGreenhalgh T, Knight M, A'Court C, et al.: Management of post-acute covid-19 in primary care. BMJ. 2020; 370: m3026. Publisher Full Text\n\nLiu C, Pan W, Li L, et al.: Prevalence of depression, anxiety, and insomnia symptoms among patients with COVID-19: A meta-analysis of quality effects model. J. Psychosom. Res. 2021; 147: 110516. PubMed Abstract | Publisher Full Text\n\nShanbehzadeh S, Tavahomi M, Zanjari N, et al.: Physical and mental health complications post-COVID-19: Scoping review. J. Psychosom. Res. 2021; 147: 110525. 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Med. 2021; 189: 106648.\n\nDaynes E, Gerlis C, Chaplin E, et al.: Early experiences of rehabilitation for individuals post-COVID to improve fatigue, breathlessness exercise capacity and cognition - A cohort study. Chron. Respir. Dis. 2021; 18: 14799731211015691.\n\nGloeckl R, Leitl D, Jarosch I, et al.: Benefits of pulmonary rehabilitation in COVID-19: a prospective observational cohort study. ERJ Open Res. 2021; 7(2): 00108–02021. PubMed Abstract | Publisher Full Text\n\nHermann M, Pekacka-Egli AM, Witassek F, et al.: Feasibility and efficacy of cardiopulmonary rehabilitation after COVID-19. Am. J. Phys. Med. Rehabil. 2020; 99(10): 865–869. PubMed Abstract | Publisher Full Text\n\nPiquet V, Luczak C, Seiler F, et al.: Do patients with COVID-19 benefit from rehabilitation? Functional outcomes of the first 100 patients in a COVID-19 rehabilitation unit. Arch. Phys. Med. Rehabil. 2021; 102(6): 1067–1074. PubMed Abstract | Publisher Full Text\n\nPuchner B, Sahanic S, Kirchmair R, et al.: Beneficial effects of multi-disciplinary rehabilitation in postacute COVID-19: an observational cohort study. Eur. J. Phys. Rehabil. Med. 2021; 57(2): 189–198. PubMed Abstract | Publisher Full Text\n\nLiu K, Zhang W, Yang Y, et al.: Respiratory rehabilitation in elderly patients with COVID-19: A randomized controlled study. Complement. Ther. Clin. Pract. 2020; 39: 101166. PubMed Abstract | Publisher Full Text\n\nSpielmanns M, Pekacka-Egli AM, Schoendorf S, et al.: Effects of a comprehensive pulmonary rehabilitation in severe post-COVID-19 patients. Int. J. Environ. Res. Public Health. 2021; 18(5): 2695. PubMed Abstract | Publisher Full Text\n\nChen H, Shi H, Liu X, et al.: Effect of pulmonary rehabilitation for patients with post-COVID-19: A systematic review and meta-analysis. Front. Med. (Lausanne). 2022; 9: 837420. PubMed Abstract | Publisher Full Text\n\nDemeco A, Marotta N, Barletta M, et al.: Rehabilitation of patients post-COVID-19 infection: a literature review. J. Int. Med. Res. 2020; 48(8): 300060520948382. PubMed Abstract | Publisher Full Text\n\nDixit S, Borghi-Silva A, Bairapareddy KC: Revisiting pulmonary rehabilitation during COVID-19 pandemic: a narrative review. Rev. Cardiovasc. Med. 2021; 22(2): 315–327. PubMed Abstract | Publisher Full Text\n\nPrabawa IMY, Silakarma D, Prabawa IPY, et al.: Physical rehabilitation therapy for long COVID-19 patient with respiratory sequelae: A systematic review. Open Access Maced. J. Med. Sci. 2022; 10(F): 468–474. Publisher Full Text\n\nvon Elm E , Altman DG, Egger M, et al.: The strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies. Int. J. Surg. 2014; 12(12): 1495–1499. Publisher Full Text\n\nRevel MP, Parkar AP, Prosch H, et al.: COVID-19 patients and the radiology department - advice from the European Society of Radiology (ESR) and the European Society of Thoracic Imaging (ESTI). Eur. Radiol. 2020; 30(9): 4903–4909. PubMed Abstract | Publisher Full Text\n\nJamil S, Mark N, Carlos G, et al.: Diagnosis and management of COVID-19 disease. Am. J. Respir. Crit. Care Med. 2020; 201(10): P19–P20. Publisher Full Text\n\nBarker-Davies RM, O'Sullivan O, Senaratne KPP, et al.: The Stanford Hall consensus statement for post-COVID-19 rehabilitation. Br. J. Sports Med. 2020; 54(16): 949–959. PubMed Abstract | Publisher Full Text\n\nZhao HM, Xie YX, Wang C, et al.: Recommendations for respiratory rehabilitation in adults with coronavirus disease 2019. Chin. Med. J. 2020; 133(13): 1595–1602. PubMed Abstract | Publisher Full Text\n\nCarda S, Invernizzi M, Bavikatte G, et al.: COVID-19 pandemic. What should physical and rehabilitation medicine specialists do? A clinician's perspective. Eur. J. Phys. Rehabil. Med. 2020; 56(4): 515–524. PubMed Abstract | Publisher Full Text\n\nNelson ME, Rejeski WJ, Blair SN, et al.: Physical activity and public health in older adults: recommendation from the American College of Sports Medicine and the American Heart Association. Circulation. 2007; 116(9): 1094–1105. Publisher Full Text\n\nSimpson R, Robinson L: Rehabilitation after critical illness in people with COVID-19 infection. Am. J. Phys. Med. Rehabil. 2020; 99(6): 470–474. PubMed Abstract | Publisher Full Text\n\nGhram A, Ayadi H, Knechtle B, et al.: What should a family physician know about nutrition and physical exercise rehabilitation' advices to communicate to 'long-term COVID-19' patients? Postgrad. Med. 2022; 134(2): 143–147. PubMed Abstract | Publisher Full Text\n\nToulgui E, Benzarti W, Ben SH: Comments about the “systematic review: Physical rehabilitation therapy for long COVID-19 patient with respiratory sequelae”. Open Access Maced. J. 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Publisher Full Text\n\nSerhier Z, Bendahhou K, Ben Abdelaziz A, et al.: Methodological sheet n degrees 1: How to calculate the size of a sample for an observational study? Tunis. Med. 2020; 98(1): 1–7. PubMed Abstract\n\nSaad H: Physical activity status of hookah smokers: an update. Egypt J. Chest Dis. Tuberc. 2022; 71(3): 395–398. Publisher Full Text\n\nAzpiazu Garrido M, Cruz Jentoft A, Villagrasa Ferrer JR, et al.: Quality of life in noninstitutionalized persons older than 65 years in two health care districts in Madrid. Aten. Primaria. 2003; 31(5): 285–292. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBardakci MI, Ozturk EN, Ozkarafakili MA, et al.: Evaluation of long-term radiological findings, pulmonary functions, and health-related quality of life in survivors of severe COVID-19. J. Med. Virol. 2021; 93(9): 5574–5581. PubMed Abstract | Publisher Full Text\n\nFerreira LN, Pereira LN, da Fe BM , et al.: Quality of life under the COVID-19 quarantine. Qual. Life Res. 2021; 30(5): 1389–1405. PubMed Abstract | Publisher Full Text\n\nGainotti G, Cianchetti C, Taramelli M, et al.: The guided self-rating anxiety-depression scale for use in clinical psychopharmacology. Act. Nerv. Super. (Praha). 1972; 14(1): 49–51. PubMed Abstract\n\nLowe B, Decker O, Muller S, et al.: Validation and standardization of the generalized anxiety disorder screener (GAD-7) in the general population. Med. Care. 2008; 46(3): 266–274. PubMed Abstract | Publisher Full Text\n\nRubio JM, Olfson M, Perez-Fuentes G, et al.: Effect of first episode axis I disorders on quality of life. J. Nerv. Ment. Dis. 2014; 202(4): 271–274. PubMed Abstract | Publisher Full Text\n\nCutaia M, Brehm R, Cohen M: The relationship of the BODE index to oxygen saturation during daily activities in patients with chronic obstructive pulmonary disease. Lung. 2011; 189(4): 269–277. 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}
|
[
{
"id": "160406",
"date": "03 Feb 2023",
"name": "Yacine Ouahchi",
"expertise": [
"Reviewer Expertise Lung function testing and sleep medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study reports the impact of a pulmonary rehabilitation program (PRP) on social disadvantage (HRQoL, anxiety and depression) and physical activity in Tunisian COVID-19 patients. The authors found that PRP improve HRQoL, HAD and physical activity in their studied population. The topic is interesting, because the results of this study add to our knowledge about the benefits of a PRP in COVID 19 patients. Moreover, this study is the first conducted in a low-income country, allowing doing comparisons with results of other studies in high-income countries.\nOverall, the manuscript is well written, with a perfect coherence between its different parts. I consider then that it may be indexed in the present form. Below are some comments:\nIntroduction The authors described clearly the COVID and the post COVID syndrome. The problem was also briefly and clearly defined as well as the aims of the study.\nMethods The study population was clearly defined with justifying the sample size. The study protocol comprised 5 phases which were clearly described in all what concerned evaluations and the exercise training session.\nResults Results were reported and resumed in a table showing the changes induced by PRP in HRQoL, HAD and physical activity scores in the studied population.\nDiscussion: The authors discussed the results and compared them to those of other studies. They also reported the strengths and limitations of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "9301",
"date": "06 Feb 2023",
"name": "Helmi BEN SAAD",
"role": "Author Response",
"response": "All the authors are very happy to note that the reviewer appreciated our paper. No action is needed from our side. Thanks"
}
]
},
{
"id": "190403",
"date": "04 Aug 2023",
"name": "Mehdi Martani",
"expertise": [
"Reviewer Expertise Pulmonary function testing - Respiratory physiology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read with great interest this article on the role of rehabilitation in improving quality of life and physical activity in Tunisian patients with COVID19 .\nThe problem addressed by the authors is of great importance, because the post COVID19 syndrome is a topical subject that remains until now poorly explored.\nSections of the article are clear, consistent and balanced.\nThe methodology of the study is very explicit with a detailed rehabilitation protocol.\n\nHowever, I have only one comment regarding the use of the VQ11 questionnaire to assess the quality of life of patients with COVID19, knowing this questionnaire was originally developed for the assessment of the quality of life of patients with COPD. My my concern is to have explanations or justifications regarding the use of the VQ11 questionnaire for the assessment of the quality of life of patients with post COVID-19 syndrome.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "10028",
"date": "07 Aug 2023",
"name": "Helmi BEN SAAD",
"role": "Author Response",
"response": "Thank you very much for your positive feedback. We really appreciate your comments. We found your following remark “I have only one comment regarding the use of the VQ11 questionnaire to assess the quality of life of patients with COVID19, knowing this questionnaire was originally developed for the assessment of the quality of life of patients with COPD. My my concern is to have explanations or justifications regarding the use of the VQ11 questionnaire for the assessment of the quality of life of patients with post COVID-19 syndrome” related to the use of the VQ11 in post COVID-19 syndrome very interesting and defendable. Below is our answer detailed into 3 points. Point 1. The VQ11 is validated in its Arabic version on COPD patients (please see our reference 51: Knaz H, Anane I, Guezguez F, et al. : Applicability of the Arabic version of the French quality of life' (QOL) questionnaire (VQ11) in Tunisian patients with chronic obstructive pulmonary disease. Rev. Mal. Respir. 2020; 37(9): 699–709.) Point 2. The VQ11 was previously used in a similar French study (please see our Reference number 27: Bouteleux B, Henrot P, Ernst R, et al.: Respiratory rehabilitation for Covid-19 related persistent dyspnoea: A one-year experience. Respir. Med. 2021; 189: 106648.) aiming to describe the clinical and functional characteristics of real-life patients referred to ambulatory respiratory rehabilitation following SARS-CoV-2 infection, and to describe the evolution of these patients over the course of rehabilitation. Therefore, it seems that the VQ11 can be applied in patients with COVID-19. Point 3. The following precautions were applied in our manuscript: In the Methods section, we have clearly noted that: “The second part of the interview concerned the evaluation of the HRQoL via the VQ11 (50). VQ11 is a valid French questionnaire providing a reliable measure of HRQoL, which has been validated in patients with chronic respiratory conditions(50). The VQ11 includes 11 items divided into three components (functional=three questions; psychological=four questions; and relational=four questions), and its score ranges from 11 to 55.50 The VQ11 Arabic version was used (51). In the subsection sample size, we have mentioned that the VQ11 was used in COVID-19 patients. We have noted that: According to a French study (27), the VQ11 total score of trained COVID-19 patients (N=39, mean age: 48 years) improved by 13.8%, from 29±10 bPRP to 25±10 aPRP (p=0.138). In the discussion section, we have described the French study (please see Table 3, Bouteleux (2021) [France] (27)). Moreover, we have considered your pertinent remark as a study limitation, and the following sentence exists in the paper: “The second limitation concerns the use of the VQ11 questionnaire to evaluate the HRQo (27). The VQ11 is mainly validated in COPD patients and is not proposed for being used in the general population (50). However, the VQ11 is usually used in our departments,51 easily administered, and seems reliable with the indication of a PRP in our study as it precisely assesses the alteration of HRQoL related to respiratory disability (27). In brief, thank you for your positive feedback. We hope that we have argued the use of the VQ11 in our study. Thank you."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1226
|
https://f1000research.com/articles/11-1225/v1
|
27 Oct 22
|
{
"type": "Research Article",
"title": "Evaluation of PD-L1 expression in vulvar cancer",
"authors": [
"Ghada Sahraoui",
"Marwa Manai",
"Rahma Yaïche",
"Lamia Charfi",
"Montassar Ghalleb",
"Hayet Douik",
"Karima Mrad",
"Raoudha Doghri",
"Marwa Manai",
"Rahma Yaïche",
"Lamia Charfi",
"Montassar Ghalleb",
"Hayet Douik",
"Karima Mrad",
"Raoudha Doghri"
],
"abstract": "Background: The PD-1/PD-L1 inhibitory immune checkpoint seems to have a significant prognostic impact in the evolution of certain cancers such as bronchopulmonary cancer, breast cancer, lymphomas etc. Indeed, it has been suggested that PD-L1 expression was associated with a worse prognosis due to its immunosuppressive activity within tumor tissue. Currently, the evaluation of the expression of these biomarkers is of increasing interest in gynecological cancers. Hence, we proposed to study the expression of PDL1 in vulvar cancer. Our aims were to study the expression profile of PD-L1 in vulvar cancer by immunohistochemistry and to correlate its expression with overall and relapse-free survival rates. Methods: This is a retrospective study conducted at the pathological anatomy and cytology department of the Saleh Azaiez Institute, Tunis, Tunisia involving 55 patients followed for vulvar cancer over a period of 13 years from 2008 to 2021. Clinicopathologic data was collected from medical records and pathology reports. Results: PD-L1 expression in vulvar squamous cell carcinoma was observed in 44% of cases. This expression was noted in 33% of cases in tumor cells and in 11% of cases in lymphocytes. The median follow-up period was 40 months. During this period, 30% of patients relapsed. For all recurrence cases, 77% were during the first two years. The overall survival rate was 68.4% at two years and 50.3% at five years. The recurrence-free survival rate was 63.8% at five years. Overall survival as well as recurrence-free survival were more reduced in the case of PD-L1 expression. However, this difference was not significant (p=0.07). Conclusions: These results, although insufficient, emphasize the prognostic value that PDL1 could play in vulvar cancer as described in the literature. Despite the low numbers and the unavailability of data for some cases, our results encourage carrying out this work on larger populations.",
"keywords": [
"vulvar cancer",
"squamous cell carcinoma",
"PD-L1",
"immunohistochemistry"
],
"content": "Introduction\n\nVulvar cancer accounts for 3–5% of all female genital malignancies.1 It mainly affects postmenopausal women over the age of 60 years.2\n\nSquamous cell carcinoma is the most frequent histological type with an incidence reported between two and seven per 100,000 women. Its particularity is that it can arise from pre-cancerous lesions or vulvar intraepithelial neoplasia.3\n\nRecently, immunotherapy has become one of the therapeutic bases in the management of some cancers by blocking of the PD-1/PD-L1 axis in solid tumors.4\n\nPD-L1 is a membranous protein of nucleated cells. It acts by binding to its PD-1 receptor located on T lymphocytes, inactivating its action. Until now, it played a key role in the treatment of bronchopulmonary cancers.5\n\nOur aims in this work were to study the immunohistochemical expression profile of PD-L1 in vulvar cancer and to correlate its expression with survival rates.\n\n\nMethods\n\nOur study was retrospective, and it was conducted at the Pathological Anatomy and Cytology Department of the Salah Azaiez Institute of Tunis in Tunisia. It involved 55 patients followed for vulvar cancer who underwent vulvectomy in Cancer Surgery Department from January 2008 to December 2021. Clinicopathologic data were collected from medical records and pathology reports, which were archived in the Salah Azaiez Institute (Cancer Surgery and Pathology departments).\n\nImmunohistochemical analysis was performed using an automaton (BOND-MAX, Leica Biosystems, Melbourne Pty Ltd). Immunohistochemical steps of the protocol were performed with EnVision FLEX visualization system (Dako) for 60 min, on a Lenovo Ideapad 3-15IIL05, Type 81 WE (Windows 10 Professional Version 21H1) connected to the automaton. Immunohistochemistry samples were imaged using an Olympus BX51 microscope with camera (Olympus U-TV0.63XC SN 1H50935 T7 TOKYO, JAPAN) with a 40× oil objective.\n\nThe main steps of immunohistochemistry were as follows:\n\nStep 1: Preparing the slides\n\nThe Tissue MicroArray (TMA) blocks were cut into 4 μm paraffin sections by a microtome and adhered to glass slides then incubated at 37°C overnight to remove excess paraffin and promote their attachment to the slides, then placed in a steam room.\n\nStep 2: Deparaffinization and rehydration\n\nWe started with deparaffinization of the slides by immersion in three baths of toluene for 5 min in each to eliminate the rest of the paraffin, then rehydration in alcohol for 10 min in three baths of decreasing concentration (100°, 95° and 85°). We rinsed with distilled water and then put them on a support.\n\nStep 3: Antigenic unmasking\n\nThe antigenic unmasking was carried out initially by heating in a water bath at 97°C for 40 min at pH 6 or pH 9.\n\nStep 4: Cooling the slides\n\nThe slides were allowed to cool and then rinsed with Tris Saline Buffer (TBS) for 5 min to remove traces of the unmasking solution.\n\nStep 5: Blocking antigenic sites\n\nTo block non-specific sites, we incubated the slides in hydrogen peroxide (H2O2) for 5 min then rinsed with TBS.\n\nStep 6: Adding the antibody\n\nThe antibody used was PD-L1, monoclonal Mouse (clone 22C3, Isotype: IgG1 kappa, Ref M3653, Batchcode 11146263). The concentration required was 1/50 and the manufacturing company was Dako (North America INC, 6392 Via Real, Carpinteria CA, 93013, USA). It was incubated in a humid tank for 1 hr to avoid the risk of tissue dehydration. It was then rinsed with TBS.\n\nStep 7: Revealing the antigen-antibody complex\n\nThe peroxidase activity was initiated by the addition of its DAB substrate in the presence of H2O2 for 10 min, the latter was oxidized by the peroxidase from which an insoluble brown precipitate was observed.\n\nStep 8: Microscopic observation\n\nA microscopic preparation was then ready for analysis by the pathologist.\n\nThe PD-L1 expression study was performed on 4-μm tissue sections cut from formalin-fixed, paraffin-embedded lymph node biopsies. Immunostaining by PD-L1 was considered positive in case of membrane labeling associated or not with cytoplasmic labeling. We considered the cut-off ≥5% of immunostained tumor cells and inflammatory immune cells6 (Figures 1–6). Recurrence was defined as tumor relapse in the first five years after treatment at any site: local recurrence, regional recurrence, and/or distant metastasis. All underlying data are provided.7\n\nStatistical analysis was performed using Microsoft Excel 2019 for Microsoft 365 MSO (Version 2208 Build 16.0.15601.20148) (RRID:SCR_016137) and SPSS software (version 20) (RRID:SCR_019096). Continuous data were summarized using descriptive statistics. Kaplan–Meier curves were plotted.\n\nWe respected ethical considerations in our work. We received ethical approval for this study from the ethics committee of Salah Azaiez Institute, Tunis. The ethics committee approval number is ISA/2021/12 dated 12th January 2021.\n\n\nResults\n\nThis study included 55 patients followed for vulvar cancer. All clinicopathological data are summarized in Table 1. The average age of our patients was 66 years with extremes of 45 and 91 years. The most affected age group was 70–79 years, which represented 31% of cases.\n\nThe disease was incidentally discovered in 31 (56%) cases. It was revealed by a vulvar pruritus in 23 (42%) cases. Pelvic pain associated with burning on urination was the chief complaint in one (2%) case. These symptoms evolved over a period ranging from one month to 15 years. Further paraclinical explorations such as chest standard radiography, abdomino-pelvic ultrasound, cervico-vaginal smear, mammography and abdomino-pelvic scanner did not reveal secondary localizations.\n\nMacroscopic characteristics\n\nWe had 54 surgical sections following vulvectomy and a single biopsy. The tumor was strictly lateral in 31 (56%) cases with the labia majora being the most common site, noted in 18 (58%) cases. The tumor was medial (clitoris, vulvar range and paraurethral) in seven (13%) cases and both medial and lateral in 17 (31%) cases. It was unifocal in 52 (95%) cases and multifocal in three (5%) cases. Macroscopic tumor size varied between 5 and 170 mm an average tumor size of 15 mm. In our study series, 15 (27) patients had a tumor larger than 30 mm. The tumor was ulcerated in 19 (34%) cases. The mean depth of invasion was 6 mm (range 1–30 mm).\n\nMicroscopic characteristics\n\nAll our cases corresponded to squamous cell carcinoma, well differentiated in 50 (91%) of cases. Vulvar intraepithelial neoplasia (VIN) was noted in 34 (62%) cases, lichen sclerosis in 27 (49%) cases and lichen planus in three (5%) cases.\n\nSurgical margins were free of invasion in 34 (62%) cases.\n\nInguinal dissection was performed in 51 (93%) cases and showed lymph node metastases in 17 (31%) cases.\n\nImmunohistochemical data\n\nPD-L1 immunostaining was as follows:\n\n• tumor cells = 18 cases (33%) with variable intensity;\n\n• lymphocytes = six cases (11%) with moderate intensity in all cases.\n\nFollow-up and survival\n\nThe median follow-up period was 39 months (ranging from 1 to 15 years). During follow-up, 25 (45%) patients had recurrence, which was local in seven (28%) cases, regional in three (12%) cases, loco-regional in 4% and distant in one (4%) case.\n\nThe OS rates were 58% at five years with a median period of eight years (Figure 7) and the RFS rate was 60% at five years with a median period of 96 months (Figure 8). Overall survival as well as recurrence-free survival were more reduced in case of PD-L1 expression. However, this difference was not significant (p = 0.8).\n\n\nDiscussion\n\nThe PD-1/PD-L1 inhibitory immune checkpoint seems to have a significant prognostic impact in the evolution of certain cancers (bronchopulmonary cancer, breast cancer, lymphomas, etc.).8–10 Indeed, it has been suggested that the expression of PD-L1 by tumor cells was associated with a worse prognosis due to its immunosuppressive activity within the tumor tissue.9 Some in vitro studies have demonstrated that the binding of PD-L1 to its PD-1 receptor negatively regulates the synthesis of IL-2 and IFN-γ. Therefore, suppression of the secretion of these cytokines leads to apoptosis of cytotoxic T cells.10–14\n\nAccording to some studies, the expression of PD-L1 in intra-tumoral lymphocytes may also play a role in immune suppression, even when it is not expressed by tumor cells.15–19 However, the expression of PD-L1 by tumor cells and/or the microenvironment varies according to tumor type and the prognostic implications remain controversial.20–25 In addition, the expression of PD-L1 by tumors suggests a possible prognostic impact and the possibility of immunotherapy via PD-1 blockade.26\n\nNumerous studies on different types of tumors (particularly lymphomas) have demonstrated that blocking PD-L1 improves the response of T lymphocytes and promotes antitumor activity. This suggests that these molecules represent potential biomarkers in certain tumors.27–29\n\nSeveral research studies have attempted to determine the prognostic factors of vulvar cancer in order to optimize therapeutic management. The expression of PDL1 in this type of neoplasia has not been previously studied in the literature, hence the interest of our work.\n\nIndeed, we observed PDL1 expression in vulvar squamous cell carcinoma in 44% of cases. This expression was noted in tumor cells in 33% of cases and in lymphocytes in 11% of cases.\n\nIn accordance with data from the literature, in the cases of our series expressing PDL1, there was a decrease in the rates of overall survival and survival without relapse (without being significant). This reflects a poorer prognosis for PDL1 positive tumors. These results are encouraging and encourage us to carry out this research work on a larger population.\n\nIt is true that the PDL1/PD1 checkpoint in cancers is a topical subject and there are many works that focus on it; nevertheless, our series concerns a cancer that is not yet treated, which is the cancer of the vulva. Our study could thus enrich the various works that have been devoted to the study of this regulatory checkpoint in gynecological cancers.\n\nThe main limitation of our study was the relatively small size of the study population, as well as missing data for a number of tumors. In addition, we could enrich our work with a more complete statistical study where we study the level of expression of PDL1 in relation to the various histoprognostic factors of vulvar tumors in order to better detect the prognostic role of PDL1 in this type of tumor.\n\nIn addition, our study was centralized on a single technique which was immunohistochemistry. A cytogenetic and molecular study, in addition to immunohistochemistry, could on the one hand catch up with the false negatives of the first technique, and, on the other hand, better characterize the ultrastructural profile of these tumors.\n\n\nConclusions\n\nIn summary, in accordance with data from the literature, in the cases of our series expressing PD-L1, we found histological factors of poor prognosis in the cases of PD-L1 plus at the level of the tumor cells. These results are encouraging and encourage us to carry out this research work on a larger population.\n\n\nConsent\n\nWritten informed consent for publication of the patients’ details and their images was obtained from the patients.",
"appendix": "Data availability\n\nZenodo: Underlying data for ‘Evaluation of PD-L1 expression in vulvar cancer’, https://doi.org/10.5281/zenodo.7195826. 7\n\nThis project contains the following underlying data:\n\n• Supplementary figures 1–6: The different figures provided are raw and unedited, uploaded as they were taken with our camera. They demonstrate various degree of intensity of PD-L1 expression in both tumor cells and lymphocytes.\n\n• Supplementary figures 7,8: These figures correspond to the Kaplan-Meier 5-year overall and relapse-free survival curves.\n\n• Data file 1: Table (1) raw clinicopathological data.xlsx. These data include age of anonymous patients at which cancer was diagnosed, symptomatology, the type of sample taken, tumor location, focality and size, the presence or absence of ulceration, hisological tumor type, immunostaining profile of tumor cells and lymphocytes, the percentage of PD-L1 expression and its variable intensity, margins status, inguinal dissection, lymph node metastasis status and recurrence at follow-up.\n\n• Data file 2: TMA protocol.xls This file contains the TMA protocol table explaining all the procedures.\n\n• Data file 3: Readme clinicopathological PD-L1 vulvar cancer_Data.txt\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nMerlo S: Modern treatment of vulvar cancer. Radiol. Oncol. 2020; 54(4): 371–376. PubMed Abstract | Publisher Full Text\n\nZongo N, Korsaga Somé N, Ouédraogo S, et al.: Cancer of the vulva: Diagnostic stages, treatment and survival in a country with limited resources (Burkina Faso). Bull. Cancer. 2019; 106(11): 1057–1063. PubMed Abstract | Publisher Full Text\n\nChokoeva AA, Tchernev G, Castelli E, et al.: Vulvar cancer: a review for dermatologists. Wien. Med. Wochenschr. 2015; 165(7-8): 164–177. PubMed Abstract | Publisher Full Text\n\nBalar AV, Weber JS: PD-1 and PD-L1 antibodies in cancer: current status and future directions. Cancer Immunol. Immunother. 2017; 66(5): 551–564. PubMed Abstract | Publisher Full Text\n\nCree IA, Booton R, Cane P, et al.: PD-L1 testing for lung cancer in the UK: recognizing the challenges for implementation. Histopathology. 2016; 69(2): 177–186. PubMed Abstract | Publisher Full Text\n\nFerreira CR, Manohar V, Zhao S, et al.: Genetic Subtypes of Systemic Anaplastic Large Cell Lymphoma Show Distinct Differences in PD-L1 Expression and Regulatory and Cytotoxic T Cells in the Tumor Microenvironment. Appl. Immunohistochem. Mol. Morphol. 2020; 28(1): 10–16. PubMed Abstract | Publisher Full Text\n\nSahraoui G, et al.:Evaluation of PD-L1 expression in vulvar cancer. [Dataset]. Zenodo. 2022. Publisher Full Text\n\nHind ZEA: Profil épidemio-clinique du cancer de la vulve. Thèse pour l’obtention du doctorat en médecine. Université Cadi Ayyad.2012.\n\nCanavan TP, Cohen D: Vulvar cancer. Am. Fam. Physician. 2002; 66(7): 1269–1274. PubMed Abstract\n\nTan A, Bieber AK, Stein JA, et al.: Diagnosis and management of vulvar cancer: A review. J. Am. Acad. Dermatol. 2019; 81(6): 1387–1396. Publisher Full Text\n\nWeinberg D, Gomez-Martinez RA: Vulvar Cancer. Obstet. Gynecol. Clin. N. Am. 2019; 46(1): 125–135. Publisher Full Text\n\nSingh N, Gilks CB: Vulval squamous cell carcinoma and its precursors. Histopathology. 2020; 76(1): 128–138. PubMed Abstract | Publisher Full Text\n\nWohlmuth C, Wohlmuth-Wieser I: Vulvar malignancies: an interdisciplinary perspective. J. Dtsch. Dermatol. Ges. 2019; 17(12): 1257–1276. PubMed Abstract | Publisher Full Text\n\nStroup AM, Harlan LC, Trimble EL: Demographic, clinical, and treatment trends among women diagnosed with vulvar cancer in the United States. Gynecol. Oncol. 2008; 108(3): 577–583. PubMed Abstract | Publisher Full Text\n\nRenati S, Henderson C, Aluko A, et al.: Basal cell carcinoma of the vulva: a case report and systematic review of the literature. Int. J. Dermatol. 2019; 58(8): 892–902. PubMed Abstract | Publisher Full Text\n\nPleunis N, Schuurman MS, Van Rossum MM, et al.: Rare vulvar malignancies; incidence, treatment and survival in the Netherlands. Gynecol. Oncol. 2016; 142(3): 440–445. Publisher Full Text\n\nKilts TP, Long B, Glasgow AE, et al.: Invasive vulvar extramammary Paget's disease in the United States. Gynecol. Oncol. 2020; 157(3): 649–655. PubMed Abstract | Publisher Full Text\n\nAlkatout I, Schubert M, Garbrecht N, et al.: Vulvar cancer: epidemiology, clinical presentation, and management options. Int. J. Women's Health. 2015; 7: 305–313. PubMed Abstract | Publisher Full Text\n\nDahbi Z, Elmejjatti F, Naciri F, et al.: Les traitements du cancer de la vulve: expérience du Centre d’Oncologie d’Oujda [Vulvar cancer treatment options: experience in the Oncology Center in Oujda]. Pan Afr. Med. J. 2018; 31: 182.\n\nSukswai N, Khoury JD: Immunohistochemistry Innovations for Diagnosis and Tissue-Based Biomarker Detection. Curr. Hematol. Malig. Rep. 2019; 14(5): 368–375. PubMed Abstract | Publisher Full Text\n\nCreager MD, Choi J, Hutcheson JD, et al.: 3.18 Immunohistochemistry. Comprehensive Biomaterials II. 2017; (3): 387–405. Publisher Full Text\n\nEclache V: L’expression de P53 permet de prédire l’évolution des patients présentant une myélodysplasie de faible risque avec délétion 5q. Hématologie. 2014; 20(3): 135–137.\n\nPoaty H, Bolenga Liboko A, Ondima I, et al.: Place de l’Immunohistochimie dans le Diagnostic des Cancers Colorectaux Héréditaires à Brazzaville. Health Sci. Dis. 2018 Jul. 1 [cited 2022 Sep. 20]; 19(3).\n\nSteele KE, Brown C: Multiplex Immunohistochemistry for Image Analysis of Tertiary Lymphoid Structures in Cancer. Methods Mol. Biol. 2018; 1845: 87–98. Publisher Full Text\n\nMahoney KM, Sun H, Liao X, et al.: PD-L1 Antibodies to Its Cytoplasmic Domain Most Clearly Delineate Cell Membranes in Immunohistochemical Staining of Tumor Cells. Cancer Immunol. Res. 2015; 3(12): 1308–1315. PubMed Abstract | Publisher Full Text\n\nGong J, Chehrazi-Raffle A, Reddi S, et al.: Development of PD-1 and PD-L1 inhibitors as a form of cancer immunotherapy: a comprehensive review of registration trials and future considerations. J. Immunother. Cancer. 2018; 6(1): 8. PubMed Abstract | Publisher Full Text\n\nChoschzick M, Gut A, Fink D: PD-L1 receptor expression in vulvar carcinomas is HPV-independent. Virchows Arch. 2018; 473(4): 513–516. PubMed Abstract | Publisher Full Text\n\nThangarajah F, Morgenstern B, Pahmeyer C, et al.: Clinical impact of PD-L1 and PD-1 expression in squamous cell cancer of the vulva. J. Cancer Res. Clin. Oncol. 2019; 145(6): 1651–1660. PubMed Abstract | Publisher Full Text\n\nKiyasu J, Miyoshi H, Hirata A, et al.: Expression of programmed cell death ligand 1 is associated with poor overall survival in patients with diffuse large B-cell lymphoma. Blood. 2015; 126(19): 2193–2201. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "227074",
"date": "11 May 2024",
"name": "Tao Chang",
"expertise": [
"Reviewer Expertise Gynecologic Oncology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The authors cited relatively insufficient literature on PDL1 expression in vulvar squamous cell carcinoma.\n2. Immunohistochemistry methodology description is more like an experimental report than a scientific paper, and some sentences are confusing, such as 'The PD-L1 expression study was performed on 4-μm tissue sections cut from formalin-fixed, paraffin-embedded lymph node biopsies'.\n\n3. Why was ≥5% chosen as the cutoff value for PDL1 expression? Since it was Dako's PDL1, why doesn't it use TPS and CPS as the scoring criteria?\n4. The research goal of this article is the correlation between PDL1 expression and prognosis of VSCC. The clinical data only has age but no information such as stage, grade, lymph node metastasis, etc., which is unreasonable.\n5. The KM graph is puzzling in single line form, why is there no comparison between PDL1 positive and negative?\n6. There are flaws in statistical methods and immunohistochemistry pictures.\nIn summary, the results of the article do not support the conclusion stated.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1225
|
https://f1000research.com/articles/11-1224/v1
|
27 Oct 22
|
{
"type": "Research Article",
"title": "Comparison of percentage excess weight loss and body composition after Roux-en-Y gastric bypass versus sleeve gastrectomy: A prospective study",
"authors": [
"Suwimol Sapwarobol",
"Juntagan Aiam-O-Ran",
"Junaida Astina",
"Juntagan Aiam-O-Ran",
"Junaida Astina"
],
"abstract": "Background: The aim of the present study was to evaluate the efficacy of Roux-en-Y gastric bypass (RYGB) vs. sleeve gastrectomy (SG) on glycemic control and blood lipid profile at preoperative (baseline), three and six months after surgery. Methods: In a prospective non-randomized design, 32 participants, SG (n = 11) and RYGB (n = 21) completed the study. Results: Results showed that fasting blood glucose (FBG) and Hemoglobin A1C (HbA1C) were significantly reduced from 113.55±30.18 mg/dL at baseline to 93.6±14.81 mg/dL at three months post operation following SG (p = 0.006). In addition, HbA1C decreased significantly in both groups at baseline, three- and six-months post operation (SG 6.41± 0.96, 5.4±0.36 and 5.28±0.57 % (p = 0.022) and RYGB 5.91± 0.94, 5.11± 0.57 and 4.96± 0.55% (p<0.001) respectively). Levels of high-density lipoprotein (HDL) were restored significantly in both groups at 6 months compared to three months post-surgery (SG 41.2± 9.99, 38.67±4.85 and 45.36± 6.22 (p = 0.023) and RYGB 42.67± 9.97, 36.58± 6.06 and 43.03± 6.66 (p =0.003) respectively), whereas there is no significant different in low-density lipoprotein and total cholesterol. Conclusions: Both bariatric surgery (SG and RYGB) improved glycemic control and blood lipid profile. Trial registration: The trial is registered with Thai Clinical Trials Registry (TCTR20210429004) April 29, 2021.",
"keywords": [
"Roux-en-Y gastric bypass",
"Sleeve gastrectomy",
"excess weight loss"
],
"content": "Introduction\n\nBariatric surgery is the last treatment option for morbid and severely obese patients (body mass index (BMI) ≥ 40 or a BMI ≥ 35 with serious comorbidities) who cannot achieve weight loss with non-surgical treatment. It has been considered a safe and effective treatment for obesity and its comorbidities in the long term.1 Currently, it is shown to reduce body weight, resulting in complete remission or significant improvement of type 2 diabetes mellitus and other metabolic abnormalities, including hyperlipidemia, obstructive sleep apnea, non-alcoholic fatty liver, and hypertension.1,2 Furthermore, the benefits of bariatric surgery include long-term weight loss, quality of life improvement, and the reduction of health care expenses.\n\nThe purpose of the bariatric procedure is to limit storage volume of the stomach and hinder nutrient absorption. There are many bariatric surgical procedures performed to achieve an ideal weight in patients, however, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) are the two most prevalent bariatric procedures.3 SG is performed by resection along the vertical axis of the stomach, creating a tubular stomach and limiting gastric volume to 60–100 ml with the preservation of the pylorus. Therefore, the continuity of the intestine remains intact. The target weight loss (%TWL) of SG is 25–30%. In contrast, the RYGB procedure divides the stomach into a proximal gastric pouch, which is 15–30 mL in volume, and a lower gastric remnant. The jejunum is divided 15 to 50 cm distally of the ligament of Trietz and the distal alimentary Roux limb is connected to the stomach pouch.4 The RYGB procedure reroutes the intestine so that nutrients bypass most of the stomach and the duodenum and flow directly into the jejunum.4\n\nWith a combination of restrictive and malabsorptive procedures in RYGB, patients tend to lose more weight than those who have undergone SG, at least within the first year follow up.5 Weight loss is the primary outcome used for assessing the success of the bariatric procedure. Percentage of excess weight loss (%EWL), the percentage of excess BMI loss (%EBMI loss), the percentage of total weight loss (%TWL), and the percentage of BMI loss (%BMIL) are also considered as indicators for the procedure’s effectiveness. However, the percentage of excess weight loss (%EWL) is used as one of the criteria for success in bariatric surgery.6\n\nFor the Asian and Pacific regions, the total number of bariatric surgery cases has increased rapidly from 2,770 to 46,110 over 10 years (2003–2013). Both RYGB and SG procedures were frequently used (25% and 49% respectively).7 In 2017, a total of 95,125 patients underwent bariatric surgery, including 68% SG, 19.5% RYGB, and 12.5% others. Similarly, in Thailand, patients who underwent bariatric surgery had SG, RYGB and other procedures: 56.4%, 40.5% and 3.1%, respectively.8\n\nStudies comparing weight loss and changes in body composition after SG and RYGB have been reported recently. Most of the studies have been conducted on Caucasians.9 However, changes in body composition and BMI are related to ethnic-specific factors. It has been found that Asians have a more significant response to metabolic risks than Caucasians with the same BMI, which may be due to the higher body fat in Asians and over-responsiveness to obesity.9,10 Thus, the efficacy results of body composition changes after bariatric surgery in Caucasians may not be applicable to Asian populations. In addition, studies comparing a RYGB and SG for Asian patients are limited. Therefore, the primary objective of this study was to investigate the impact of two different bariatric surgeries, RYGB and SG, on weight and body composition changes. The secondary objective was to observe the factors related to weight loss mechanisms in patients, including resting energy expenditure, diet intake, changes in hunger and desire for specific food types and physical activity (level and MET-min/week).\n\n\nMethods\n\nThe study was approved by the Institutional Review Board of Faculty of Medicine, Chulalongkorn University (IRB No. 345/60, COA No. 650/2017, August 10, 2017). Voluntary written informed consent was obtained from each participant prior to enrolment. The study was registered with Thai Clinical Trials Registry (TCTR20210429004) April 29, 2021. Due to being unaware of the requirement for registration, this study was registered retrospectively. All operations were performed with the laparoscopically standard technique.\n\nA total of 41 participants who had undergone RYGB and SG procedures during June 2019 to February 2020 at King Chulalongkorn Memorial hospital, Bangkok Thailand, were recruited into the study. Inclusion criteria included: older than 18 years-old, BMI over 35 kg/m2 or 32.5 kg/m2 with comorbidities, underwent first-time bariatric procedures. Patients who were taking medication known to influence body composition, having a pacemaker or other internally placed biomedical devices, having conditions associated with significant hydration changes and/or metabolic disturbances were excluded. The primary end point of this present study is the percentage of excess weight loss after bariatric surgery. Sample size calculation based on the previous study of Strain et al. (2009) that investigated the percentage of excess weight loss in morbidly obese patients who underwent RYGB and SG procedures.6 The minimum participants is 10 per arm, which will provide 80% power to a difference between two groups using a two-sided α of 0.05.\n\nA prospective non-randomized study was performed to compare the impact of RYGB and SG procedures on weight loss and body composition changes at preoperative (baseline), one, three and six months after surgery. Participants meeting the inclusion criteria were examined and underwent RYGB or SG based on their preferences.\n\nBody weight and body compositions were measured using a bioelectrical impedance analyzer (Inbody 720, Biospace Co., Ltd., Seoul, Korea). Participants were requested to avoid drinking water and other beverages for eight hours and to fast two hours before testing. On the clinic day at King Chulalongkorn Memorial Hospital, participants were requested to dress in light attire and go barefoot. In order to measure body compositions, eight polar electrodes were positioned, four electrodes on the tips of both toes and four electrodes on the fingertips of both hands. The electrical current was supplied to the front of both feet and the fingertips of both hands and voltage was then measured on the heel of both feet and the thenar portion of the palms of both hands. Body mass index (BMI) was calculated as weight/height2 (in kilograms per square meter). Percentage of excess weight loss (%EWL) and percentage of total weight loss (%TWL) have been calculated using the equations below.\n\nIdeal body weight is defined by the weight corresponding to a BMI of 23 kg/m2, the cut-off for defining obesity in Asian populations.10\n\nResting energy expenditure was measured by indirect calorimetry (Fitmate GS Desktop indirect calorimetry with canopy hood (Cosmed, Rome, Italy)). The portable indirect calorimetry assessed the concentration of oxygen that patients consumed by using an oxygen sensor. The oxygen concentration was calculated by using a fixed respiratory quotient (RQ) of 0.85 and Weir equation to assess resting energy expenditure.11\n\nAll biochemical parameters were examined at baseline (pre-operation), three, and six months after surgery by the Center for medical diagnostic laboratories, King Chulalongkorn Memorial Hospital, Bangkok, Thailand. At each clinic visit, blood samples of approximately 15 ml were taken from a vein puncture after an overnight fast of 10-12 h. Then, samples were separated into three tubes; sodium fluoride containing tubes for plasma glucose analysis, gel clot activator tubes for lipid profile, creatinine, serum glutamate-pyruvate transaminase (SGPT), serum glutamic oxaloacetic transaminase (SGOT) analysis and ethylenediaminetetraacetic acid (EDTA) containing tubes for HbA1C analysis. Blood samples were centrifuged at 3,000 rpm for 10 min and analyzed. Fasting plasma glucose was analyzed by hexokinase method using clinical chemistry analyzer (Beckman Coulter AU480). This assay is based on the phosphorylation of glucose by hexokinase (HK) in the presence of magnesium ions and adenosine triphosphate (ATP). Glucose-6-phosphate and adenosine diphosphate (ADP) produced by this reaction were then oxidized by glucose-6-phosphate dehydrogenase (G6P-DH) to gluconate-6-phosphate with the concurrent reduction of Nicotinamide adenine dinucleotide (NAD) to NAD + hydrogen (NADH). The Beckman Coulter analyzers automatically calculate the increase in absorbance at 340 nm, which is proportional to the glucose concentration in the blood sample. Cholesterol, triglyceride were examined using the enzymatic method (Beckman Coulter, USA). In this enzymatic method, esterified cholesterol is converted to cholesterol and fatty acids by cholesterol esterase. The cholesterol was converted to cholest-4-en-3-one and hydrogen peroxide by cholesterol oxidase. The hydrogen peroxide then reacts with 4-aminophenazone in the presence of peroxidase to produce a colored product. HbA1C were determined via the enzymatic method. The HbA1C assay consists of two analyses of glycated hemoglobin and total hemoglobin. These two concentrations were used to determine the HbA1C percentage. Liver function enzymes including SGOT and SGPT were analyzed using the NADH method. Serum glutamate-pyruvate transaminase catalyzes the transfer of the amino group from L-alanine to α-ketoglutarate, forming pyruvate and L-glutamate. Pyruvate is reduced to L-lactate while NADH is oxidized to NAD. The decrease in absorbance represents the oxidation of NADH to NAD. Serum glutamic oxaloacetic transaminase transfer amino acid group from L-aspartate to α-ketoglutarate, forming oxaloacetate and L-glutamate. Oxaloacetate is reduced to L-malate with the presence of NADH. In this reaction, NADH is oxidized to NAD. The decrease in absorbance represents the oxidation of NADH to NAD.\n\nPatients were asked to record their three-day food intake (two weekdays and one weekend day), as well as any dietary supplements during every follow-up. The three-day food record was assessed by a registered dietitian using INMUCAL-Nutrient Software Version 3 (developed by Institute of Nutrition, Mahidol University, Thailand).\n\nA minimum of 10 participants per arm provides 80% power to a difference between two groups using a two-sided 𝛼 of 0.05; there is an expected loss to follow-up rate of 30%. Thus, 13 participants per arm were required. Results were expressed as means and standard deviations (S.D.) for normal distribution data, and median and interquartile range (IQR) for non-normal distribution as well as frequencies as percentages. Continuous variables such as body weight outcomes, body composition, energy and macronutrients intake, resting energy expenditure, visual analog scale (VAS) of hunger and taste changes and blood chemistry were tested by a Mann-Whitney U test to compare surgical groups. Comparisons of time points were analyzed by using non-parametric one way repeated-measures ANOVA (Friedman’s test). A Chi-squared test was used to compare the frequencies between the two groups and McNemar’s test was used to compare the frequencies between the baseline and time points. Spearman’s correlation was used to assess the association between body weight and body composition outcomes as well as related factors. p-values < 0.05 were considered statistically significant. All analyses were performed using SPSS, version 16.0 (IBM, Chicago, IL, USA).\n\n\nResults\n\nA total of 32 participants (SG (n = 11, two female subjects, nine male subjects) and RYGB (n = 21, 14 female subjects, seven male subjects)) completed the six-month follow-up study (Figure 1).34\n\nSleeve gastrectomy (SG), Roux-en-Y gastric bypass (RYGB).\n\nBaseline characteristics of the SG and RYGB groups are shown in Table 1. There was no significant difference in sex, age, and waist to hip ratio (WHR) between groups. However, mean basal weight before surgery was significantly different according to the surgical procedure (SG (107.39 (15.59)) vs. RYGB (128.87 (19.22)), p = 0.0033). As a result, BMI (SG (40.42 (4.76)) vs. RYGB (46.40 (6.46)), p = 0.0027), fat mass (SG (52.56 (8.20)) vs. RYGB (65.28 (12.92)), p = 0.0033) and fat free mass (SG (54.95 (11.71)) vs. RYGB (64.24 (10.91)), p = 0.0069) were different between surgical procedures at baseline (Table 1). At the baseline, there were no significant differences in comorbidity including type II diabetes mellitus (DM), hypertension (HTN), dyslipidemia (DLP), non-alcoholic fatty live disease (NAFLD), and gastroesophageal reflux disease (GERD) however, there was a significant difference in obstructive Sleep apnea (OSA) between RYGB (95.24%) and SG (63.64%).\n\n* p-value ≤ 0.05 is considered statistically significant. Characteristics were compared between surgical methods.\n\nIn this six-month follow up study, significant weight loss was obtained after three and six months for both procedures. The body weight of subjects in both bariatric procedures were significantly reduced from the baseline, three months and six months: SG group (107.39 (15.39) kg, 90.42 (15.25) kg, and 81.70 (13.52) kg, (p < 0.001)); and RYGB group (128.87 (19.22) kg, 108.30 (17.82) kg and 99.77 (18.09) kg (p < 0.001)), respectively. When comparing the body weight of patients between groups, a significant difference was also found at three months (90.42 (15.25) kg vs. 108.30 (17.82) kg, p = 0.0083) and six months after surgery (81.70 (13.52) kg vs. 99.77 (18.09) kg, p = 0.0068). Similarly, BMI, WHR, and body composition, including fat mass, and fat-free mass were significantly decreased at three and six months following each SG and RYGB procedure, when compared to their baseline (all p ≤ 0.001) (Table 2).\n\n* Indicates significant differences between group at the same time point.\n\nThe %EWL and %TWL were reduced significantly after three and six months for both groups (p < 0.001, 0.003 in the SG group, and all p < 0.001 in the RYGB group, respectively). The %EWL and %TWL at three months between the two procedures were not different. However, the %EWL at six months was higher in the SG group than the RYGB group (58.35 (15.30) % vs. 46.54 (12.52) %, p = 0.0257) (Figure 2).\n\nEnergy and macronutrient intake including carbohydrate, protein, and fat were decreased significantly after three and six months of both procedures (p < 0.05). There was no significant difference in energy and macronutrient intake found when comparing the two groups at each follow-up month.\n\nFasting blood glucose significantly decreased from 113.55 (30.18) mg/dL at baseline to 93.60 (14.81) mg/dL at three months following SG treatment (p = 0.006). In addition, HbA1C was significantly lower at six months compared to the baseline in both groups (SG from 6.41 (0.96)% to 5.28 (0.57)%, p = 0.022; RYGB from 5.91(0.94)% to 4.96(0.55)%, p ≤ 0.001). Bariatric surgery also affected the lipid profile in both groups. Total cholesterol was significantly lower at three months (161.12 (38.41) mg/dL) compared to the baseline (186.32 (37.85) mg/dL) in RYGB group (p = 0.032). When compared between groups, total cholesterol at six months was significantly lower in the RYGB group (170.71 (30.38) mg/dL) compared to the SG group (200.09 (29.52) mg/dL), p = 0.020. HDL-cholesterol decreased at three months following both surgeries. HDL-cholesterol in the SG group decreased from 41.2 (9.99) mg/dL at baseline to 38.67 (4.85) mg/dL, while in the RYGB group it decreased from 42.67 (9.97) mg/dL at baseline to 36.58 (6.06) mg/dL at three months. However, HDL-cholesterol significantly restored after six months following both surgeries as HDL-cholesterol in SG and RYGB group at six months were 45.36 (6.22) mg/dL and 43.03 (6.66) mg/dL, respectively. There were no significant differences on HDL-cholesterol between groups. Triglyceride level was significantly lower at six months following both surgeries compared to baseline (SG group 156.5 (88.98) mg/dL at baseline to 72.09 (23.91) mg/dL at six months, p = 0.008, RYGB group 143.79 (56.6) mg/dL at baseline to 79.06 (28.63) mg/dL at six months, p ≤ 0.001).\n\nThe kidney function was not significantly affected by both surgeries as there were no differences in creatinine and eGFR values at any time points. Meanwhile, the SG group significantly decreased SGOT at month three and month six compared to the RYGB group (at month three, SGOT in SG vs. RYGB were 18.56 (5.53) units/L vs. 25.48 (9.98) units/L, p = 0.036; while at six months, SGOT in SG vs. RYGB were 17.00 (2.83) units/L vs. 21.33 (7.81) units/L, p = 0.039). Albumin level in RYGB was significantly lower in the RYGB group at baseline and six months compared to SG (at baseline were 4.02 (0.28) g/dL vs. 4.36 (0.31) g/dL for RYGB and SG, respectively, p = 0.005; while at six months were 3.89 (0.25) g/dL vs. 4.25 (0.25) g/dL for RYGB and SG, respectively, p = 0.006).\n\nIn the SG group, blood biochemical parameters including hemoglobin, hematocrit, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and mean corpuscular hemoglobin concentration (MCHC) were not changed significantly when compared between follow-up months (p > 0.05). Patients in the RYGB group showed a difference in MCV at three and six months (83.62 (7.03) fl at baseline vs. 83.46 (6.31) fl and 84.67 (6.46) fl, p = 0.012) and MCH was also higher at three and six months (26.92 (2.73) pg at baseline vs. 27.51 (2.41) pg and 27.42 (2.44) pg, p = 0.032). In addition, MCHC at three months (32.91 (0.79) g/dl) was higher than the baseline and six months after surgery (p = 0.003). When comparing blood biochemical parameters, including hemoglobin, hematocrit, MCV, MCH, and MCHC of patients between groups, no significant difference was presented at the three and six month follow-ups (p > 0.05).\n\nThe level of vitamin D was increased after six months when compared to the baseline both for the SG (22.93 (9.10) pg/ml vs. 34.47 (11.09) pg/ml, p = 0.008) and the RYGB group (18.84 (7.32) pg/ml vs. 28.81 (10.44) pg/ml, p = 0.002). Also, there was a reduction of folate levels six months post-surgery when compared to the baseline in the SG (11.49 (5.31) ng/ml vs. 5.77 (3.44) ng/ml, p = 0.024) and RYGB group (7.53 (4.81) ng/ml vs. 5.27 (3.15) ng/ml, p = 0.018). Additionally, only vitamin B12 levels were significantly different at six months when comparing procedures (533.55 (136.10) pg/ml vs. 351.89 (121.17) pg/ml, p ≤ 0.001).\n\nThe VAS scores of hungers and desires for specific types of patients were shown in Table 3. Patients in the SG group reported a significant increase in hunger (1.17 (0.98) vs. 3.00 (1.41), p = 0.028) and desire for sour food (0.67 (1.21) vs. 2.17 (0.98), p = 0.007) after the six-month follow-up. Meanwhile, patients in the RYGB group reported a higher score of desire for sour and fatty food after the six-month follow-up (1.71 (2.20) vs. 3.21 (2.22), p =0.007 and 0.43 (1.09) vs. 2.07 (2.27), p =0.010, respectively). No significant difference in hunger and desire for specific types between the two procedures was observed (p > 0.05) (Table 3).\n\n* P-value ≤ 0.05 is considered statistically significant.\n\n\nDiscussion\n\nIn the current study, we found that both the SG and RYGB procedures decreased the body weight, BMI, WHR, fat mass, and fat-free mass. Consequently, EWL was reduced at six months by 58.35% and 46.54% for SG and RYGB, respectively. A previous study reported that EWL at six months following SG and RYGB were 64% and 61% (p > 0.05).12 By contrast, Rondelli et al., reported that EWL in SG was lower compared to RYGB at the one-year follow-up (49% vs 61.5% for SG vs. RYGB, respectively, p = 0.001), however there was no significant difference of EWL between procedures at the two- and three-year follow-ups. A previous study reported several factors affecting the EWL in SG and RYGB, including the characteristics of patients, complications following the surgery, and the technical aspects regarding the surgery (the SG diameter, the volume of RYGB gastric pouch, and the Roux limb length, etc.)5\n\nThe weight reduction following SG and RYGB procedures is mediated by several mechanisms, including caloric restriction, hormonal, and neural factors in the gastrointestinal tract thus the food intake and appetite were reduced.13 Food intake could be the major player of weight loss in the short-term following SG and RYGB procedures. In the current study, the food intake of patients at six months following SG and RYGB procedures significantly decreased from the baseline by 66.4% (-1,216 kcal/day) and 52.7% (-855.4 kcal/day), respectively (p < 0.05). Furthermore, reduction of carbohydrate and fat intake were significantly decreased at the three and six months follow up for both groups when compared to each baseline (p < 0.05). For those patients who underwent SG, the carbohydrate and fat intake decreased by 209.01 g/day and 38.5 g/day at the six-month follow up, while in RYGB, the carbohydrate and fat intake decreased by 132.91 g/day and 30.1 g/day at the six-month follow up when compared to the baseline. A meta-analysis study revealed that RYGB decreased food intake by 1,215.16 kcal/day, while SG decreased 939.38 kcal/day. Janmohammadi et al., also showed that fat intake was decreased following RYGB and SG procedures by -1.91 g/day (95%CI −3.37 to −0.44, p = 0.78) and -2.83 g/day (95%CI −7.07 to 1.42, p = 0.19), respectively. Post-operative adverse effects on gastrointestinal symptoms, such as vomiting, nausea, aversion of food, and dumping syndrome may occur in patients who underwent bariatric surgery which decreased the food intake.14\n\nIn addition, resection of the stomach in SG limits the volume of food intake and increases the release of gut peptides hormones, including glucagon-like-peptide (GLP)-1 and peptide YY (PYY), which promotes satiety and thus reduces the food intake.13 In addition, several studies reported that other hormones, such as ghrelin, were changed following bariatric surgery. Ghrelin is a gut hormone that is positively associated with hunger. A previous study reported that the area under the curve of ghrelin was significantly lower by 77% for patients who underwent RYGB when compared to normal-weight controls.15 Similarly, Frühbeck et al., reported that ghrelin concentration decreased 24 h following RYGB surgery.16 Decreased ghrelin was accompanied by decreased hunger following SG and RYGB procedures.17–19\n\nIn the current study, we observed the favorable effects of both SG and RYGB on glucose profile. Fasting blood glucose was significantly decreased following SG treatment compared to the baseline, and both treatments significantly lowered the HbA1C compared to the baseline. Similarly, it was reported that SG and RYGB improved the glucose tolerance and decreased the fasting blood glucose report in in vitro and clinical studies.20–22 The improvement in blood glucose profile is possibly mediated through the increasing of GLP-1 following bariatric surgery treatment.21 GLP-1 is known to improve glucose tolerance by inhibiting β-cell apoptosis and stimulating insulin secretion.21\n\nBoth treatments significantly decreased triglyceride at six months compared to the baseline. Furthermore, RYGB also decreased the total cholesterol in the current study. However, there was no effect of SG on total cholesterol. A similar finding was observed in Liaskos’ study that showed RYGB is more effective in decreasing lipemia in non-diabetic obese patients.23 This malabsorptive nature of RYGB limits the lipid absorption and allows the greater reduction of total cholesterol level compared to SG procedure.23\n\nIn the current study we observed that liver function as indicated by liver enzymes, including SGOT and SGPT, were significantly lower following SG compared to RYGB. Previous studies also had similar findings that SG treatment decreased SGOT compared to other type of bariatric surgeries at six months24 and two years following surgery.25 The underlying mechanism of the increasing liver enzymes following RYGB remains unclear. However, it was thought that different mechanisms of bariatric surgery possess different effects on endocrine and physiological function in the gut.25 Further studies are needed to confirm the mechanism of liver enzyme reduction in different type of bariatric surgery.\n\nObesity is associated with vitamin D deficiency because of sequestration of vitamin D and other fat-soluble vitamins in adipose tissue.26 Furthermore, inadequate food intake and reduced absorption area of nutrients following SG and RYGB increases risk of micronutrient deficiency, including vitamin D deficiency.27 In the current study, the vitamin D levels for both groups at the six-month follow-up increased by 50.3% and 52.9% when compared to the baseline. In contrast, folate in both groups decreased by 49.8% and 30%. The increase of vitamin D in this current study could be mediated by the vitamin D supplementation following SG and RYGB procedures. Vitamin D supplementation is recommended for patients who underwent bariatric surgery. The dose may vary depending on the initial serum vitamin D in patients. It is recommended to take 3,000 IU/day of vitamin D, titrate to >30 mg/ml, to prevent the deficiency. In the presence of vitamin D deficiency, it is recommended to consume 50,000 IU of vitamin D once per week for eight weeks, followed by 1,500–2,000 IU/day for maintenance therapy.28,29\n\nReduction of serum folate in the current study may be due to inadequate intake of folic acid and vitamin B12. Lower serum vitamin B12 may lower serum folate since vitamin B12 is a coenzyme for folate activation. Additionally, both surgeries may reduce the area of folate absorption.27 The present study also found a reduction of folate among patients for both bariatric procedures. Folate is a water-soluble B-vitamin that functions as a coenzyme for purines and pyrimidines synthesis and amino acid conversion. Deficiency of this vitamin results in cell division and protein synthesis impairment.30 Folates are not synthesized by mammals but can be produced by gut microbes.31 It is also present in various types of food including liver, yeast, leafy vegetables, legumes, and fruits. Previous studies indicated that there are factors responsible for folate deficiency in bariatric patients which include eating behavior modification, inadequate dietary intake, malabsorption, gut microbiota diversity reduction, and poor compliance to vitamin supplementation.32,33 Providing sufficient vitamin supplementation may improve folate levels and prevent related complication from folate deficiency in post-operative patients.\n\nThis study enhances knowledge to the limited literature comparing RYGB and LSG regarding body composition changes in the Thai population. In this study, all participants meeting the inclusion criteria were included therefore, the results from this study can be extrapolated into the real-life Thai clinical setting. However, to respect patient right and autonomy, randomization was not feasible. With non-randomized design, selection bias may have occurred. In addition, this study did not examine the exercise patterns, which may confound the results.\n\n\nConclusions\n\nWeight loss was comparable between SG and RYGB groups at six months after surgery. Body compositions include body fat percentage and fat mass rapidly decreased during six months similarly for both procedures, and patients in the RYGB group lost more fat-free mass than the SG group at six months post-operation. In addition, no significant difference of hunger and desire for specific types of food between procedures was observed.",
"appendix": "Data availability\n\nFigshare: Results.xlsx. https://doi.org/10.6084/m9.figshare.20059715. 34\n\nThis project contains the following underlying data:\n\n- Body composition and laboratory data of both bariatric surgery (SG and RYGB) at preoperative, one, three and six months after surgery provided\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe author acknowledges the contributions of all participants for their enthusiasm and cooperation.\n\n\nReferences\n\nJensen MD, Ryan DH, Apovian CM, et al.: 2013 AHA/ACC/TOS guideline for the management of overweight and obesity in adults: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines and The Obesity Society. Circulation. 2014; 129(25 Suppl 2): S102–S138. 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N. Engl. J. Med. 2004; 350(3): 308–309. PubMed Abstract | Publisher Full Text\n\nMans E, Serra-Prat M, Palomera E, et al.: Sleeve gastrectomy effects on hunger, satiation, and gastrointestinal hormone and motility responses after a liquid meal test. Am. J. Clin. Nutr. 2015; 102(3): 540–547. PubMed Abstract | Publisher Full Text\n\nDirksen C, Jørgensen NB, Bojsen-Møller KN, et al.: Gut hormones, early dumping and resting energy expenditure in patients with good and poor weight loss response after Roux-en-Y gastric bypass. Int. J. Obes. 2013; 37(11): 1452–1459. PubMed Abstract | Publisher Full Text\n\nCushing CC, Benoit SC, Peugh JL, et al.: Longitudinal trends in hedonic hunger after Roux-en-Y gastric bypass in adolescents. Surg. Obes. Relat. Dis. 2014; 10(1): 125–130. PubMed Abstract | Publisher Full Text\n\nWallenius V, Dirinck E, Fändriks L, et al.: Glycemic Control after Sleeve Gastrectomy and Roux-En-Y Gastric Bypass in Obese Subjects with Type 2 Diabetes Mellitus. Obes. Surg. 2018; 28(6): 1461–1472. PubMed Abstract | Publisher Full Text\n\nLi L, Wang X, Bai L, et al.: The Effects of Sleeve Gastrectomy on Glucose Metabolism and Glucagon-Like Peptide 1 in Goto-Kakizaki Rats. J. Diabetes Res. 2018; 2018: 1082561.\n\nGudbrandsen OA, Dankel SN, Skumsnes L, et al.: Short-term effects of Vertical sleeve gastrectomy and Roux-en-Y gastric bypass on glucose homeostasis. Sci. Rep. 2019; 9(1): 14817. PubMed Abstract | Publisher Full Text\n\nLiaskos C, Koliaki C, Alexiadou K, et al.: Roux-en-Y Gastric Bypass Is More Effective than Sleeve Gastrectomy in Improving Postprandial Glycaemia and Lipaemia in Non-diabetic Morbidly Obese Patients: a Short-term Follow-up Analysis. Obes. Surg. 2018; 28(12): 3997–4005. PubMed Abstract | Publisher Full Text\n\nZadeh MHea: Changes in serum albumin and liver enzymes following three different types of bariatric surgery: six-month follow-up. Sao Paulo Med. J. 2021; 139: 598–606. 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PubMed Abstract | Publisher Full Text\n\nMechanick JI, Youdim A, Jones DB, et al.: Clinical practice guidelines for the perioperative nutritional, metabolic, and nonsurgical support of the bariatric surgery patient--2013 update: cosponsored by American Association of Clinical Endocrinologists, The Obesity Society, and American Society for Metabolic & Bariatric Surgery. Obesity (Silver Spring). 2013; 21 Suppl 1(0 1): S1–S27.\n\nVisentin MD-BN, Zhao R, Goldman ID: The intestinal absorption of folates. Annual review of physiology. Annu. Rev. Physiol. 2014; 76: 251–274. PubMed Abstract | Publisher Full Text\n\nLeBlanc JG, Milani C, de Giori GS , et al.: Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr. Opin. Biotechnol. 2013; 24(2): 160–168. PubMed Abstract | Publisher Full Text\n\nPatel JJ, Mundi MS, Hurt RT, et al.: Micronutrient Deficiencies After Bariatric Surgery: An Emphasis on Vitamins and Trace Minerals [Formula: see text]. Nutr. Clin. Pract. 2017; 32(4): 471–480. PubMed Abstract | Publisher Full Text\n\nCiobârcă D, Cătoi AF, Copăescu C, et al.: Bariatric Surgery in Obesity: Effects on Gut Microbiota and Micronutrient Status. Nutrients. 2020; 12(1). PubMed Abstract | Publisher Full Text\n\nSapwarobol S:Results.xlsx. figshare. [Dataset]. 2022. Publisher Full Text"
}
|
[
{
"id": "154380",
"date": "21 Nov 2022",
"name": "Gina Segovia-Siapco",
"expertise": [
"Reviewer Expertise Nutrition",
"nutritional epidemiology",
"dietary assessment methodology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript reports the results of a study that aimed to compare the expected post-surgery changes in anthropometric, biochemical, and clinical indicators of health, as well as appetite of those who underwent Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG). Subjects were followed up for 6 months and measurements were taken at baseline, 1, 3, and 6 months (p. 4) after surgery although comparison of results were only done for months 3 and 6 relative to baseline. The authors concluded that weight loss and decreases in %body fat and fat mass were similar between the two surgical groups, except that the RYGB group lost more fat-free mass. There were no differences in hunger and craving for specific types of foods.\nSome issues found in this manuscript are as follows:\nDiscrepancies between the objectives and conclusions stated in the Abstract and the body of the manuscript. Although the conclusions are consistent with the stated aim in the abstract, which is also the case for the manuscript, the authors should ensure that the abstract reflects what are presented in the manuscript.\n\nTable 3 that shows results of the visual analog scale (on hunger and taste preferences). There is no description in the methods section on how these were measured although something was mentioned in the data analysis section. Suggestion: add a subsection on “Measurement of Hunger and Food Cravings” or something similar in the Methods section.\n\nFigure 2 has asterisks (*) on top of the error bars but it is not clear from the figure what they signify. If the asterisks (*) indicate sig differences between the RYGB and SG groups, then the \"whiskers\" (SEM?) should not be touching. There is no explanation in the figure about this. Since figures and tables should be stand-alone, please add some explanations in the figure legend itself. Also, if there are errors in the error charts, those need to be corrected.\nHere are other relatively minor issues (page numbers refer to the pdf version of the article)\nUnder Participants subsection: --“... provide 80% power to a difference between two groups...” should have been “... provide 80% power to detect a significant difference between two groups...“\n\nUnder Study Design subsection --Second line – month 1 measurements are not shown in any of the tables. Please explain. --In the formula for %EWL: What is the Post-Op weight? Is this the weight right after surgery? These are not shown in the tables. Also, in the formula for %TWL: what is the \"starting weight\" and \"presenting weight\"?. Suggestion for both formulas: add a definition or explanation for each of the items in the formula.\n\nIn the Biochemical parameters subsection: --In general, please correct grammatical errors (inconsistent verb tenses) and punctuations. Some sentences can be stated more clearly. E.g., lines 13-15 of this subsection may be stated: “Cholesterol and triglycerides were examined using the enzymatic method (Beckman....) where cholesterol esterase converts esterified cholesterol to cholesterol and fatty acids.” Etc. --Vein puncture – did you mean “venipuncture”?\n\nIn the Statistical analysis subsection: --First line: “ . . . 80% power to a difference…” should be “ . . . 80% power to detect a difference…” First line: you have left a “?” – please supply the word.\n\nIn the Results Section: --Correct this: The description of the gender distribution of participants for the SG group is not consistent with what table 1 shows. --3rd paragraph lines 2-3: This is confusing since it sounds like there was already a reduction in weight at baseline. Maybe you meant this to be --\"For both bariatric procedures, there was loss in body weight over the 6-month period: from 107.4 (15.4) kg at baseline to ----- at month 3 and ---- at month 6 post-surgery for the SG group; and, from 128.9 (19.2) kg fat baseline to ___ at month 3 and ____ at month 6 post-surgery for the RYGB group.\" --On p. 8, second paragraph, last line: . . . differences were found. . . instead of “difference was presented”\n\nTable 3: --As mentioned earlier, there is no description of the tool (VAS) that was used to measure hunger and desire for specific foods in the Methods section. Please add that. --Also, provide information in the table on what the values represent (satiety?) and how the values are interpreted (e.g. what do higher values mean, etc.).\n\nIn the Discussion section: --p. 10, para 1, sentence 2 : “Consequently, EWL was reduced…” EWL stands for \"Extra Weight Loss\" and it (EWL) was greater at six months than at 3 months. This means that over time, more weight was lost, or weight loss increased but the sentence says “reduced”. Please clarify or correct, if it is an error. -- p. 10, para 1, sentence 4: It seems that there is a missing reference citation --p. 10. para 2. sentence 4: Needs to be corrected since you were negating what you meant by using both \"reduction\" and \"decreased\" in the same sentence. You can remove \"reduction of\". --p. 10, para 2, sentence 6: Where is the citation of the meta-analysis study in the 6th sentence of the second paragraph --p. 10: Third paragraph of the discussion section should still be part of the second paragraph since you are still explaining the possible mechanisms behind weight reduction following bariatric surgery. --In general, please check grammatical errors (i.e., verb tenses, sentence structures). --p. 11, para. 4, sentence 3: Are you referring to your results here or what literature says? In your results, the SGPT increased but also eventually decreased (at 6 months) for RYGB. Please clarify.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "232225",
"date": "19 Jan 2024",
"name": "Antonio D’Urso",
"expertise": [
"Reviewer Expertise gastrointestinal surgeryobesity surgery"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a nice study comparing results of bariatric surgery on Asian population even if these are very short term results that is known to be effective. The lack of randomization may affect selection and some results. Indications in Asian population are different from western countries. The IFSO and ASMBS published recently an update on indications for metabolic and bariatric surgery (Eisenberg D et al, 2023) [Ref 1]. Please update indications in the introduction section. Usually the biliary limb of a RYGB varies from 15 to 75 cm with the most common performed at 50 cm as reported in metanalysis of randomized trial. (Kamocka A et al, 2022)[Ref 2]. Please modify this point in the introduction section. Usually if a patient presents with GERD SG is not recommended, please explain which was the criteria to propose a SG to your patient with known GERD.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1224
|
https://f1000research.com/articles/11-1223/v1
|
27 Oct 22
|
{
"type": "Review",
"title": "Suicide in the geriatric population of South East Asia - contexts and attributes",
"authors": [
"Sujita Kumar Kar",
"S. M. Yasir Arafat",
"Nisha Mani Pandey",
"Russell Kabir",
"Shivangini Singh",
"S. M. Yasir Arafat",
"Nisha Mani Pandey",
"Russell Kabir",
"Shivangini Singh"
],
"abstract": "Suicide in the geriatric population is a significant problem. Increasing age, living alone, having a psychiatric illness and medical comorbidities have been identified as risk factors for suicide among the elderly population. The elderly population in South East Asia is rapidly growing and the number of elderly people with mental illness and/or medical comorbidities is also increasing. The factors and attributes of suicide may vary from region to region due to socio-cultural and geographic diversities. Understanding these factors may help in planning suicide prevention strategies for the elderly population. There is a dearth of studies assessing the demography, risk factors for, and prevention of suicide among the elderly population in South East Asia. We tried to observe and explain the challenging paradigms to excerpt attributes and the context of geriatric suicide. It is observed in this review that lack of social integration or interaction along with some psychiatric disorders leads to suicidal ideation and completed suicide in the elderly. South East Asia has unique characteristics in several aspects like religious and cultural diversity, poverty, unemployment, demographic structure of the region, migration, natural disasters and calamities, political environment, poor policy implementation, and easy access to suicide means (e.g. pesticides). Primary care physicians, specialized mental health support, gate-keeper training, means restriction, raising awareness, supportive family environment, and dedicated call centers could be potential areas for suicide prevention among the elderly people of the region. Further studies are warranted to formulate effective suicide prevention strategies.",
"keywords": [
"Geriatric suicide",
"South East Asia",
"Suicidal Behavior",
"Depression",
"Suicide prevention"
],
"content": "Introduction\n\nSuicide is described as an unforced and willing termination of one’s life, and it is a complex incident that suddenly ends the lifecycle. People (close ones to general population at large) are often unaware why someone committed suicide or ended their life. Thus, many times the surroundings explain the factors, features, reason, and conditions that led to the person’s suicide. One cannot establish or give a final statement on the issue as the person who did it, is not available to contribute to the investigation. It is challenging to gather thorough and reliable information because of the variety of interactions with the family and the contradictory information they may provide. The rate of suicide in the geriatric population is high and strategies are needed to address this. In order to gather more information on the topic and become aware of the issues, we need to carefully observe the factors and contexts of suicide in the geriatric population. We must be careful to explain these issues as when the suicidal individual is elderly it is more difficult to gather the data. However, based on the findings of some South East Asia (SEA) region-based researchers and a few other studies the authors tried to observe and explain the challenging paradigms to attributes and context of geriatric suicide.\n\nSuicide in the geriatric population is a significant problem. The geriatric population has unique issues like retirement, loss of job, dependency on others for daily needs, loss of spouse/close friends, medical illnesses, loneliness and isolation, which makes them vulnerable for enormous distress.1 Suicide is often multifactorial and the result of close, intense interaction between several biological, psychological and social factors.2 In a retrospective study over 37 years, it was found that negative mental state is an important predictor of suicide in elderly, whereas chronic medical illness and significant psychological distress are important predictors of suicide in older men.2\n\nAs per the report of the American Association for Marriage and Family Therapy (AAMFT), in the United States (US), suicide in older adults is responsible for 18% of all suicide related deaths, though older adults represent 12% of the US population.3 Increasing age, being separated from their spouse, and being a white male are important determinants of suicide in older adults.3 However, having a psychiatric illness, particularly depression, is also an important predictor of suicide in older adults.3 The elderly population in South East Asia is rapidly growing and the number of elderly people with mental illness and/or medical comorbidities is also increasing rapidly.4 Hence, it is anticipated that the number of suicides among the elderly population will grow significantly. So, it is obvious that the contexts and attributes of suicide in the elderly population will be different from that of adult population. The suicide rate in the South East Asia region was estimated to be 17.7 per 100,000 population.5 The rate of suicide in the elderly population and adolescents is found to be higher than the adult population and there is gross variation in the prevalence of suicide across the South Asian countries.5 Hanging is found to be the common mode of suicide in older adults.2\n\nIn the South East Asia region, the male to female suicide ratio is higher (close to 1) than the rest of the world (3:5).5 The factors and attributes of suicide may vary from region to region due to socio-cultural and geographic diversities. Understanding these factors may help in planning the suicide prevention strategy for elderly population.\n\n\nSuicide in South East Asia\n\nIt has been reported that 10% world’s suicides take place in India, Pakistan and Sri Lanka.6 Jordan et al.(2014) cited in their scoping review that the suicide rates in South Asia can be compared to the global average and it is men who commit suicide than the women.7 The suicide rate among the South Asian population ranges between 0.43/100000 to 331.0/100000 of the population and the rate varies between countries, and is mainly linked to the development levels (countries with different developmental indexes have different suicide rates; there is also significant regional variations).7 Various researchers conducted studies at various points of time in different regions and found gross variations in suicide rate.7 The prevalence rate of suicide in studies conducted in India ranges between 11.7 per 100000 population to 189.0 per 100000 population, whereas in Bangladesh (6.6 to 128.8 per 100000), Pakistan (1.1 to 14.9 per 100000), Nepal (7.0 per 100000) and Sri Lanka (19.6 to 24.1 per 100000) the rates are different, indicating the loco-regional variations.7\n\nArafat et al.(2021) shared that hanging and poisoning were the most common suicide methods in Bangladesh and India, and poisoning was the preferred method of suicide in Sri Lanka.8 However, their review concluded that hanging is the most common method of suicide in South Asia. In India, most suicides are reported as due to personal or social reasons, followed by health and other reasons.9 Chandrasekaran and Gnanaselane (2008) investigated the predictors of repeated suicide attempts of 348 samples from India and found that repeat suicide attempts are associated with depression, hopelessness and suicidal intent, and presence of major depression and social dissidence are predictive factors for repeat attempts.10\n\nA recent scoping review by Arafat et al. (2022) revealed that the prevalence of depression among fatal (37.3%) and nonfatal suicidal attempts (32.7%) in South Asian countries seems to be lower compared to other regions of the world.11 In another research, Arafat et al. found that the presence of preexisting psychiatric morbidities and stressful life events are the most common risk factors for suicide in South Asia.12\n\n\nEpidemiology of suicide in geriatric population\n\nThe rapid growth of the geriatric population is one of the important facts of the 21st century.13 Suicide among the elderly people is considered as a major public health concern and it is associated with complex underlying psychosocial, physical and mental health issues faced by the elderly population.14 Additionally, marital conflict, feelings of hopelessness due to being alone, and being a widow are the potential risk factors for suicide among the older population.15\n\nSuicidal behavior among elderly population is grossly under-studied in Bangladesh. One recent review identified only one study assessing the depression and suicidal thoughts among rural elderly people of Bangladesh.15 The study revealed that 23% of 625 participants had suicidal thoughts. The frequency of suicidal thoughts was significantly higher among illiterate persons, women, and those living without partners. Living with family members and having a good contact with them were identified as protective factors in Bangladesh.16 Amudhan et al. (2020) analysed the national mental health survey data from India and reported that India accounts for 26.6% of global suicide deaths, and that the prevalence was higher among those over 60 years of age.17 However, Philip et al. (2022) found that there is a slight modest increase in the suicidal rates among people 60 years and over and the rates were higher among elderly women compared to elderly men in India.18\n\nShoib et al. (2020) found that depression along with hopelessness are the key contributing factors of suicidal behaviours among the geriatric population in Kashmir, India.19 In Sri Lanka, about 23.6% of deaths among the elderly population were reported to be suicides.14\n\nIt is reported that among all World Health Organization (WHO) regions, the highest suicide rate occurs in the South East Asia region.20 A 37 year retrospective study that mined the data between 1979 and 2015 (from the records of autopsy and police reports of suicide) revealed that gender is a major risk of suicide in the elderly population with men being more affected than women, which was already reported in the younger group.21 This might be because women generally tend to express their feelings and try to vent their frustrations if someone asks generously and properly. Whereas men generally don’t wish to share their feelings and emotions due to their own habits and rules.22,23 Another attribute leading to suicide is advancement in age, which might be due to increasing degeneration and deterioration in bio-psycho-physical activities as well as a loss of individuality.24 The retrospective study revealed that as longevity increased, the shift in suicidal age was prominent as the affected group shifted from 60-69 years in 1990 to 70-79 years in 2015.21\n\nIn general, it is observed that the elderly had previously loved living in a joint family set-up.25 When they are suddenly confined to a room due to various reasons, or their social circle is restricted, or they have to migrate from one place to another place, or their partner dies, their entire way of living changes. Life-changing situations can adversely affect elderly populations. Some studies reported that India, Sri Lanka, Japan, Taiwan, and China have high suicidal rates in rural areas.26–29 In rural China, the suicide rate is reported to be 2-3 times higher than in urban areas, and the rate of suicide among residents of North China is quite high.26,28,30 It is reported that persistent loneliness leads to suicidal thoughts.31 It is also reported that those with economic difficulties have higher reported suicidality.32 Unfortunately, data related to suicide among economically dependent elderly people is not readily available.\n\nA study from China observed that a person with physical or mental health issues, especially with chronic illnesses and/or any sort of physical disabilities, is also at risk of suicide, and in certain conditions disturbed neurotransmitters (decreased level of serotonin) lead to suicide in older persons.33 Psychiatric morbidity is a major cause of suicide in the geriatric population. Among psychiatric disorders, mood disorders were found to be the most significant reason for attempting suicide.34 The same author reported that among the elderly, approximately 65% of all suicides were due to a psychiatric disorder.35 A review related to the psychological autopsy of the SEA region, which is related to suicide amongst the overall population, reports variable estimates for various countries ranging between as low as 5% to as high as 95%.12 It is also stated that around 5% of suicides may be committed due to sub-clinical conditions.36 It can be said that poor mental health conditions or persistent stress can lead to suicidal thoughts in each segment of the population, and thus in the elderly. Studies report that elderly people with mild dementia often commit suicide.37–39 The suicide rate among the patients with dementia (within in first year of diagnosis of dementia) is 26.42 per 100000 person a year.40\n\nIt is observed by the study that lack of social integration or interaction along with some psychiatric disorders leads to suicidal ideation and completed suicide in the elderly.41 An Indian study reveals that elderly people with past psychiatric history often make repeated attempts to commit suicide42; the study also states that, generally, elderly people who plan for suicide often have co-morbid physical illness, mental illness (particularly depression), and a family burden of psychiatric illness. A study from Korea reports that strong bonding and informal support play gatekeeper roles and help in preventing suicide.43 Another study from Sri Lanka reports that elderly people with a lower social network develop depressive symptoms which further leads to suicide.44 Some studies from China, Bangladesh, and Indonesia reveal that lack of friendship, less familial support, frequent harassment, quarrel among peers, worrying, loneliness, unhealthy dietary practices, alcohol use, and inactiveness can all lead to suicide or suicide attempts among youth and adults.45,46\n\nIn summary, it can be said that a male older adult, who has a dependency, resides in a rural area, has any ailment but especially psychiatric illness (depression) or a mild level of dementia or disability, has neither formal nor informal support, or lives alone, and feels withdrawn from society, is at risk of developing negative emotions and committing suicide, and such factors need to be taken care of.\n\n\nHow is South East Asia different from the rest of the world with respect to epidemiology, context and attributes of geriatric suicide?\n\nAs discussed above, given its high rate of suicide, South East Asia can be considered the hub of suicide. There are certain factors that make the South East Asian population unique and different from the rest of the world. These factors are:\n\n1. Religious and cultural diversity: South East Asia is the hub of multiple religious practices. Different religions have different notions related to suicide. Some religion condemn suicide considering it as a sin; whereas several religions glorify self-sacrifice. This largely influences the suicidal behavior.\n\n2. War and terrorism: War and terrorism are common in certain conflicting zones (Pakistan, Afghanistan, India, Sri Lanka, Myanmar) of South East Asia, which adversely affects the mental health of elderly population. Due to war and terrorism, there is significant disruption of social integrity, support systems, supply chaind and a spread of fear; which may attribute to mental illnesses and suicidal behavior.\n\n3. Poverty: In South East Asia, poverty is a major social challenge. Poverty is considered as an important indicator of mental health. It may adversely affect the mental health of the elderly population.\n\n4. Unemployment: Unemployment is a common challenge in the South East Asian countries and it is higher among the elderly population as there is gross lack of job opportunities for elderly people in this region.\n\n5. Population explosion: South East Asia contains a large percentage of the global population, including the population of elderly people. It is anticipated that over next few decades the population of elderly in South East Asia will grow exponentially, creating a major challenge for healthcare resources.\n\n6. Migration: Poverty, unemployment, war, terrorism and natural calamities are the major factors responsible for migration and displacement of elderly population in South East Asia. Migration may have several mental health implications.\n\n7. Natural disasters and calamities: Natural disasters and calamities hit the South East Asian countries very often causing devastation. The elderly population are among the worst sufferers. Mental health is seriously affected by the natural disasters and calamities.\n\n8. Political instability: Political instability produces significant social chaos, which is commonly seen in countries of South East Asia.\n\n9. Economic instability: Economic instability often results in poverty, price hikes, and unemployment, which significantly affect mental health.\n\n10. Poor policy implementation: Several policies do exist for the benefit of elderly population in South East Asian countries; however, due to poor implementation, the elderly population remains deprived from facilities and faces several challenges.\n\n11. Easy access to suicide means (e.g. pesticides): The selection of mode of suicide depends upon the access to the means readily available. In the South East Asian countries easy access to pesticides, and several other suicidal means, results in adoption of easy modes of suicide.\n\nMarriage, divorce, and alcohol consumption are other important determinants of suicide.47 The geriatric population is increasing globally, including in South-East Asian countries.48 It has been anticipated that the geriatric population of South-East Asia will rise exponentially by 2050, and thus the suicide rate and total number of suicides in the geriatric population will also increase.48\n\nResearch evidence suggest that during the period of economic crisis (1997-1998), there was an increase in suicide rates in most South East Asian countries.47 The increase in suicides cannot be exclusively attributed to the financial crisis, however. Evidence suggests that in South East Asia, affluent countries have a higher suicide rate,49 which indicates that there may be other attributing factors, specific to countries and regions, which are associated with suicide.\n\nGrief is an important modulating factor for suicidal behavior, and complicated grief is common following natural disasters. As South East Asian countries commonly encounter natural disasters, their significant impact on mental health and suicidal behavior cannot be ignored.50\n\nThe COVID-19 pandemic affected the elderly population significantly. Lockdown-related restrictions, medical morbidities, isolation, limited recreational opportunities, loss of spouse and fear of COVID-19 had a cumulative effect that affected the mental well-being of the elderly population significantly.51 There are significant regional variations in COVID-19 globally, and South East Asia was one of the worst affected regions. Comparisons of suicide rates between 1979 and 2014 revealed that Taiwan, Hong Kong, and Japan have lower male to female suicide rates in comparison to Australia and New Zealand in the adult population; however, in the elderly population the suicide rate varies across the countries.52 Similarly, there is also a difference in mode of suicide in different age groups, and across rural and urban areas.53\n\nFrom the research perspective, a significantly higher number of suicides are occurring in South East Asian countries; however, most researches on suicide are from developed countries like the USA, UK, Australia.48 Whatever research data exists, mostly are in reference to completed suicide.54 Though the number of suicide attempts are much higher than the number of completed suicides, the research on these population are sparse.\n\n\nPrevention of geriatric suicide\n\nPrevention of suicide among the geriatric population is still an untapped area in South Asia due to a dearth of studies assessing the risk factors for suicide in the region. Adequate research assessing the risk factors and effectiveness of interventions, identifying local resilience factors, trained manpower, funds, and proper services settings is necessary to prevent suicide in the geriatric age group in SEAR. Likewise in other age groups, the biopsychosocial approach could be attempted in SEAR countries.14 Medications can be considered to treat depression or psychiatric disorders as a biological approach, problem solving psychotherapy, cognitive behavior therapy, or other appropriate approach of psychotherapy can be used as a psychological approach, and finally managing social events and ensuring a supportive social environment can be targeted as a social approach.\n\nIdentification of psychiatric disorders, especially depression, would be an important prevention strategy in the region. It is well accepted that timely initiation of treatment of depressive disorders can prevent suicides.14 Although the psychological measures have shown efficacy in developed countries, studies are warranted in SEAR countries due to its different socio-demographic pattern, manpower, and social structure.14 In old age there are various forms of physical comorbidities for which older people attend health appointments more frequently than those of adult age. Therefore, regular screenings of depressive symptoms, any recent evidence of increased substance abuse, and suicidal thoughts would be able to identify the at-risk individuals earlier. Referring the risky individuals to the mental health services providers would help in suicide prevention.\n\nGeriatric psychiatry is yet to gain momentum in SEAR as a full-blown discipline. There is an extreme dearth of specialized services in countries like Bangladesh, Myanmar, Nepal, and North Korea. Therefore, in addition to the improvement of primary care settings, geriatric mental health services should be prioritized and empowered to treat psychiatric disorders and prevent suicides.\n\nLikewise in other groups, gatekeepers could play a vital role in suicide prevention in geriatric groups. Primary care physicians, caregivers in residential care homes, and close family members could act as gatekeepers. However, it is supposed to be challenging to provide trainings except to the primary care physicians because, due to cultural barriers, training to residential care homes and family members may face resistance. Multilayered suicide prevention strategies ensuring adequate co-ordination between universal, selected and targeted strategies could be attempted and tested.55,56\n\nMeans restriction is the restricting of access to potential methods of suicide. This includes the class I pesticide ban, creating barriers to open bridges, etc. Means restriction has been established to have a positive impact on suicide prevention.53 However, it should be contextualized based on country, culture, and methods. A previous study from Sri Lanka has shown that banning of lethal pesticides has reduced the suicide rate.14\n\nRaising awareness among the general population, family members, and caregivers in care homes regarding the risk factors and suicidal behavior in old age should be prioritized to prevent elderly suicide.57 It is important to consider that the residential care home service concept is different in western countries to SEAR countries. Improved mental health and suicide literacy and reduced stigma towards suicide would help to identify at-risk elder individuals.8,14\n\nElderly persons living in nuclear families with working sons/daughters and their spouses are alone for the whole day, especially in the cities of SEAR. Elders living alone with physical comorbidities are at a higher risk of suicide.34,56,58,59 Supportive communication among the family members is an important area to prevent suicide.\n\nA dedicated telephone help line has shown positive effects in suicide prevention among isolated elderly persons in Italy, which needs to be tested in a South Asian culture.14,56\n\n\nConclusion and future directions\n\nSuicide among the elderly population is a serious issue. Ageing, living alone, having a mental health condition, and having coexisting physical conditions have all been recognized as risk factors for suicide in the older population. In South East Asia, both the elderly population and the number of elderly people with mental illness and/or medical comorbidities are growing quickly. Due to geographic and socio-cultural differences, there may be regional variations in the causes and characteristics of suicide. Planning the elderly population's suicide prevention approach may be aided by having a better understanding of these issues. Studies investigating the demographics, risk factors, and prevention of suicide among the senior population in the area are scarce. Primary care doctors, specialized mental health support, gatekeeper training, means restriction, raising awareness, a supportive family environment, and a dedicated call center could be feasible strategies for preventing suicide among the elderly in the area. To develop successful suicide prevention techniques, additional research is required.",
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Lancet Psychiatry. 2020; 7: 41–51. PubMed Abstract | Publisher Full Text\n\nPhilip S, Mukherjee N, Shekhar A, et al.: Rise in suicide related deaths in minors during the pandemic in a LAMI country. Int. J. Soc. Psychiatry. 2022; 0(0). Publisher Full Text\n\nShoib S, Islam SMS, Arafat SY, et al.: Depression and suicidal ideation among the geriatric population of Kashmir, India. Int. J. Soc. Psychiatry. 2021; 67: 651–655. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Regional Office for South-East Asia. Regional Strategy on Preventing Suicide. World Health Organization;2018. Regional Office for South-East Asia.\n\nCrestani C, Masotti V, Corradi N, et al.: Suicide in the elderly: a 37-years retrospective study. Acta Bio-Medica. Atenei. Parm. 2019; 90: 68–76.\n\nKelly MM, Tyrka AR, Price LH, et al.: SEX DIFFERENCES IN THE USE OF COPING STRATEGIES: PREDICTORS OF ANXIETY AND DEPRESSIVE SYMPTOMS. Depress. Anxiety. 2008; 25: 839–846. PubMed Abstract | Publisher Full Text\n\nGoubet KE, Chrysikou EG: Emotion Regulation Flexibility: Gender Differences in Context Sensitivity and Repertoire. Front. Psychol. 2019; 10. PubMed Abstract | Publisher Full Text\n\nShah A, Bhat R, Zarate-Escudero S, et al.: Suicide rates in five-year age-bands after the age of 60 years: the international landscape. Aging Ment. Health. 2016; 20: 131–138. PubMed Abstract | Publisher Full Text\n\nLodhi FS, Rabbani U, Khan AA, et al.: Factors associated with quality of life among joint and nuclear families: a population-based study. BMC Public Health. 2021; 21: 234. PubMed Abstract | Publisher Full Text\n\nPhillips MR, Li X, Zhang Y: Suicide rates in China, 1995-99. Lancet Lond Engl. 2002; 359: 835–840. PubMed Abstract | Publisher Full Text\n\nGajalakshmi V, Peto R: Suicide rates in rural Tamil Nadu, South India: verbal autopsy of 39 000 deaths in 1997-98. Int. J. Epidemiol. 2007; 36: 203–207. PubMed Abstract | Publisher Full Text\n\nYip PS, Callanan C, Yuen HP: Urban/rural and gender differentials in suicide rates: east and west. J. Affect. Disord. 2000; 57: 99–106. PubMed Abstract | Publisher Full Text\n\nOtsu A, Araki S, Sakai R, et al.: Effects of urbanization, economic development, and migration of workers on suicide mortality in Japan. Soc. Sci. Med. 1982; 2004(58): 1137–1146.\n\nRebholz CM, Gu D, Yang W, et al.: Mortality from suicide and other external cause injuries in China: a prospective cohort study. BMC Public Health. 2011; 11: 56. PubMed Abstract | Publisher Full Text\n\nJeon G-S, Jang S-N, Rhee S-J, et al.: Gender differences in correlates of mental health among elderly Koreans. J. Gerontol. B Psychol. Sci. Soc. Sci. 2007; 62: S323–S329. PubMed Abstract | Publisher Full Text\n\nKim J, Lee Y-S, Lee J: Living Arrangements and Suicidal Ideation among the Korean Elderly. Aging Ment. Health. 2016; 20: 1305–1313. PubMed Abstract | Publisher Full Text\n\nDong X, Chang E-S, Zeng P, et al.: Suicide in the global chinese aging population: a review of risk and protective factors, consequences, and interventions. Aging Dis. 2015; 6: 121–130. PubMed Abstract | Publisher Full Text\n\nZhou L, Wang G, Jia C, et al.: Being left-behind, mental disorder, and elderly suicide in rural China: a case-control psychological autopsy study. Psychol. Med. 2019; 49: 458–464. PubMed Abstract | Publisher Full Text\n\nZhou M, Zhang Y, Wang L, et al.: Analysis of negative life events among 304 elderly suicide victims. Zhonghua Liu Xing Bing Xue Za Zhi Zhonghua Liuxingbingxue Zazhi. 2004; 25: 292–295. PubMed Abstract\n\nErnst C, Lalovic A, Lesage A, et al.: Suicide and no axis I psychopathology. BMC Psychiatry. 2004; 4: 7. PubMed Abstract | Publisher Full Text\n\nPurandare N, Voshaar RCO, Rodway C, et al.: Suicide in dementia: 9-year national clinical survey in England and Wales. Br. J. Psychiatry. 2009; 194: 175–180. PubMed Abstract | Publisher Full Text\n\nSchmutte T, Olfson M, Maust DT, et al.: Suicide risk in first year after dementia diagnosis in older adults. Alzheimers Dement. J. Alzheimers Assoc. 2022; 18: 262–271. PubMed Abstract | Publisher Full Text\n\nChoi JW, Lee KS, Han E: Suicide risk within 1 year of dementia diagnosis in older adults: a nationwide retrospective cohort study. J. Psychiatry Neurosci. JPN. 2021; 46: E119–E127. PubMed Abstract | Publisher Full Text\n\nSchmutte T, Olfson M, Maust DT, et al.: Suicide risk in first year after dementia diagnosis in older adults. Alzheimers Dement. 2022; 18: 262–271. PubMed Abstract | Publisher Full Text\n\nDuberstein PR, Conwell Y, Conner KR, et al.: Poor social integration and suicide: fact or artifact? A case-control study. Psychol. Med. 2004; 34: 1331–1337. Publisher Full Text\n\nSuresh Kumar PN, Anish PK, George B: Risk factors for suicide in elderly in comparison to younger age groups. Indian J. Psychiatry. 2015; 57: 249–254. PubMed Abstract | Publisher Full Text\n\nKwon H-J, Jeong J-U, Choi M: Social Relationships and Suicidal Ideation Among the Elderly Who Live Alone in Republic of Korea: A Logistic Model. Inq. J. Med. Care Organ. Provis. Financ. 2018; 55: 46958018774177.\n\nRasnayake S, Navratil P: Warning Signs of Elderly Suicide and Factors Affecting Professional Help-Seeking: Case of Sri Lanka. J. Popul. Soc. Stud. JPSS. 2023; 31: 1–19.\n\nMarthoenis M, Yasir Arafat SM: Rate and Associated Factors of Suicidal Behavior among Adolescents in Bangladesh and Indonesia: Global School-Based Student Health Survey Data Analysis. Scientifica. 2022; 2022: 1–7. Publisher Full Text\n\nPeltzer K, Pengpid S: Suicidal ideation and associated factors among students aged 13-15 years in Association of Southeast Asian Nations (ASEAN) member states, 2007-2013. Int. J. Psychiatry Clin. Pract. 2017; 21: 201–208. PubMed Abstract | Publisher Full Text\n\nChang S-S, Gunnell D, Sterne JAC, et al.: Was the economic crisis 1997–1998 responsible for rising suicide rates in East/Southeast Asia? A time–trend analysis for Japan, Hong Kong, South Korea, Taiwan, Singapore and Thailand. Soc. Sci. Med. 2009; 68: 1322–1331. PubMed Abstract | Publisher Full Text\n\nChiu HFK, Takahashi Y, Suh GH: Elderly suicide prevention in East Asia. Int. J. Geriatr. Psychiatry. 2003; 18: 973–976. Publisher Full Text\n\nLau BWK, Pritchard C: Suicide of older people in Asian societies: an international comparison. Australas. J. Ageing. 2001; 20: 196–203. Publisher Full Text\n\nKristensen P, Weisæth L, Heir T: Predictors of Complicated Grief After a Natural Disaster: A Population Study Two Years After the 2004 South-East Asian Tsunami. Death Stud. 2010; 34: 137–150. PubMed Abstract | Publisher Full Text\n\nDe Leo D: Late-life suicide in an aging world. Nat. Aging. 2022; 2: 7–12. Publisher Full Text\n\nSnowdon J, Chen Y-Y, Zhong B, et al.: A longitudinal comparison of age patterns and rates of suicide in Hong Kong, Taiwan and Japan and two Western countries. Asian J. Psychiatr. 2018; 31: 15–20. PubMed Abstract | Publisher Full Text\n\nLi M, Katikireddi SV: Urban-rural inequalities in suicide among elderly people in China: a systematic review and meta-analysis. Int. J. Equity Health. 2019; 18: 2. PubMed Abstract | Publisher Full Text\n\nSuh G-H, Gega L: Suicide attempts among the elderly in East Asia. Int. Psychogeriatr. 2017; 29: 707–708. Publisher Full Text\n\nSakashita T, Oyama H: Suicide Prevention Interventions and Their Linkages in Multilayered Approaches for Older Adults: A Review and Comparison. Front. Public Health. 2022; 10: 842193. PubMed Abstract | Publisher Full Text\n\nOyama H, Watanabe N, Ono Y, et al.: Community-based suicide prevention through group activity for the elderly successfully reduced the high suicide rate for females. Psychiatry Clin. Neurosci. 2005; 59: 337–344. PubMed Abstract | Publisher Full Text\n\nZalsman G, Hawton K, Wasserman D, et al.: Suicide prevention strategies revisited: 10-year systematic review. Lancet Psychiatry. 2016; 3: 646–659. PubMed Abstract | Publisher Full Text\n\nVirojanapa S, Taneepanichskul N: Suicidal Idea among The Elderly. J. Public Health Dev. 2020; 18: 102–109.\n\nSuh G-H, Gega L: Suicide attempts among the elderly in East Asia. Int. Psychogeriatr. 2017; 29: 707–708. Publisher Full Text"
}
|
[
{
"id": "176311",
"date": "15 Nov 2023",
"name": "Ravi Bhat",
"expertise": [
"Reviewer Expertise Psychogeriatrics"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article has many factual errors starting with the geographical area covered. South East Asian countries are Brunei, Burma (Myanmar), Cambodia, Timor-Leste, Indonesia, Laos, Malaysia, the Philippines, Singapore, Thailand and Vietnam (Southeast Asia - Wikipedia). However, the authors appear to be writing about evidence from South Asian countries or East Asian countries. Systematic reviews of suicide in older adults are not quoted (e.g., Barker et al., (2022)1 or Troya et al., (2019)2. The authors continue to use inappropriate words to describe the act of suicide, for example, \"are often unaware why someone committed suicide\" [my emphasis].\n\nIt was good to read the unique perspectives on suicide in older adults from South Asia. However, no evidence is cited for the points made.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? No\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1223
|
https://f1000research.com/articles/11-52/v1
|
17 Jan 22
|
{
"type": "Research Article",
"title": "Effects of Antigravity Treadmill Training on Gait and Balance in Patients with Diabetic Polyneuropathy: A Randomized Controlled Trial",
"authors": [
"Ashraf Abdelaal",
"Shamekh El-Shamy",
"Ashraf Abdelaal"
],
"abstract": "Background: Diabetic polyneuropathy (DPN) is the most prevalent consequence of diabetes mellitus, and it has a significant impact on the patient's health. This study aims to evaluate effects of antigravity treadmill training on gait and balance in patients with DPN. Methods: The study included 45 males with type 2 diabetes who were randomly assigned to one of two groups: the experimental group (n=23) or the control group (n=22). For a period of 12 weeks, the experimental group received antigravity treadmill training (75% weight bearing, 30 min per session, three times per week) combined with traditional physical therapy. During the same time period, the control group received only traditional physical therapy. The Biodex Balance System was used to assess postural stability indices, while the GAITRite Walkway System was used to assess spatiotemporal gait parameters. All measurements were obtained before and at the end of the study after 12 weeks of treatment. Results: The mean values of all measured variables improved significantly in both groups (P<0.05), with the experimental group showing significantly greater improvements than the control group. The post-treatment gait parameters (i.e., step length, step time, double support time, velocity, and cadence) were 61.3 cm, 0.49 sec, 0.25 sec, 83.09 cm/sec, and 99.78 steps/min as well as 56.14 cm, 0.55 sec, 0.29 sec, 75.73 cm/sec, and 88.14 steps/min for the experimental and control group, respectively. The post-treatment overall stability index was 0.32 and 0.70 for the experimental and control group, respectively. Conclusions: Antigravity treadmill training in combination with traditional physical therapy appears to be superior to traditional physical therapy alone in terms of gait and balance training. As a result, the antigravity treadmill has been found to be an effective device for the rehabilitation of DPN patients.",
"keywords": [
"Diabetic polyneuropathy",
"antigravity treadmill",
"traditional rehabilitation",
"gait",
"balance"
],
"content": "Introduction\n\nDiabetes mellitus (DM) is a long-term metabolic disorder that impairs the body's capacity to control blood glucose levels. DM is a major health concern, with an increase in the prevalence of type 2 DM (T2DM), which has been linked to lifestyle factors. Long-term microvascular and macrovascular complications are responsible for the disease's high morbidity and mortality, and they place patients and healthcare systems under a great deal of stress.1\n\nDiabetic polyneuropathy (DPN) is the most common complication. It's linked to having diabetes for a long time and having poor glycemic control, which causes a lot of pain and distress. Saudi Arabia is the largest country in the Middle East, occupying approximately four-fifths of the Arabian Peninsula and residences to over 33.3 million people. Diabetes affects approximately one-fourth of people above the age of 30.2\n\nDPN is a progressive degeneration of the peripheral nerves that affects the sensory, motor, and autonomic components of the nerves, causing loss of protective sensation, intrinsic foot muscle dysfunction, and foot anhydrosis.3 It leads to increased public health costs and has a significant impact on patient quality of life when not treated properly. Plantar ulceration and amputation, the disease's most fatal outcome, can still be avoided if proper measures are applied.4\n\nDPN affects the quantity and quality of sensory information used in gait generation and control, causing alterations in the sensory and motor control systems. Reduced range of motion, muscle strength, and changes in gait parameters are all linked to reduced mobility and impaired balance.5 In comparison to healthy controls, DPN patients exhibit a lower gait velocity, lower cadence, shorter stride length, longer stance time, and higher steps variability. These alterations in gait are more noticeable when walking on uneven surfaces. DPN patients exhibit a lower ankle moment and ankle power, as well as a different onset and cessation time of muscle activity than healthy controls.6\n\nDespite the fact that current physical therapy therapies can help patients with DPN improve their gait and balance, the effects are minor.7 In two systematic studies of DPN therapies, lower extremity strengthening was only given a fair recommendation.8,9 Other pain-relieving and function-improving therapies, such as electrotherapy and monochromatic light therapy, lacked sufficient evidence to be recommended.9 Salsabili et al.10 showed that following four weeks of task-oriented gait and balance training, Timed \"Up and Go\" scores and Falls Efficacy Scale scores improved.\n\nThe antigravity treadmill is a unique method of preserving a patient's body weight during treadmill training that was recently developed. An inflatable treadmill is included in this system. The patient is dressed in neoprene shorts that are zipped up within the bag. The air pressure in the bag, which acts as a lifting force on the body, determines how much body weight needs to be supported. The air pressure is equally distributed across the lower body, minimizing the pressure points found in traditional body weight support systems.11\n\nAbdelaal and El-shamy,12 concluded in a recent trial that a moderate intensity antigravity treadmill training can significantly improve gait, balance, and fall risk scores in patients with DPN. During this moderate intensity aerobic training in patients with DPN, the 75% weight bearing had more significant results than the 0 %, 25%, and 50% weight bearing on gait, balance, and fall risk scores. Therefore, using the lower body positive pressure (LBPP) technology for unweighting patients with DPN during antigravity treadmill training can provide a new treatment modality for patients with DPN.\n\nDespite the growing popularity of LBPP treadmills, it's unclear how valid the available scientific evidence to support their use in the rehabilitation of patients with DPN. The purpose of this study was therefore to investigate the effects of antigravity treadmill training on gait and balance in patients with DPN.\n\n\nMethods\n\nThis single-blind randomized controlled trial was designed to study the effects of antigravity treadmill training on gait and balance in patients with DPN. It was approved by the Ethical Committee of the Faculty of Applied Medical Sciences, Umm Al-Qura University (15-MED5221-10). This trial was registered in the ClinicalTrial.gov PRS No NCT05088993. Before signing an informed consent form accepting to participate in the study, all participants were given a full explanation of the study's procedures, hazards, and objectives.\n\n45 elderly Saudi men diagnosed with DPN are recruited from Umm Al-Qura University Medical Center, Makkah, Saudi Arabia, and referred to a physiotherapist, who performs the initial assessment. The inclusion criteria for this study were age between 60 to 80 years old; having uncontrolled T2DM more than 10 years, with DPN; glycosylated hemoglobin (HbA1c %) level between 7–11%, fasting blood glucose level of 7.0–11.1 mmol/L; treated only with oral hypoglycemic medications; able to walk independently with or without assistive devices; with normal nutritional status; cognitively competent and able to understand and follow instructions.\n\nThe exclusion criteria were patients with type 1 diabetes; younger than 60 or older than 80 years old; following diet regimen; patients with malnutrition (BMI<21 kg/m2 or with recent weight loss >5% body weight in the last month or >10% in six months); recently involved in an exercise training program within the last six months; underwent surgical intervention within the last six months; patients with feet ulcers; patients with serious cardiovascular insult or sever complications that can impact patient's safety, performance and affects study outcomes.\n\nThe proper sample size was calculated using G*Power for Windows (G*Power 3.1.3, RRID:SCR_013726) with estimated power (1-error probability) = 0.95, = 0.05. The effect size was 0.6 using one-way ANOVA with in-between interaction in two groups and two measurement intervals. A minimum of 40 patients was specified as a sample size for this study. An extra five participants were added above the required number to compensate any potential dropouts.\n\nPatients were randomly assigned to experimental (n = 23) and control (n = 22) therapy groups using an online randomization website (www.randomization.com) to prevent bias in the treatment assignment. Traditional physical therapy was delivered to the control group. The experimental group, on the other hand, received antigravity treadmill training in addition to the traditional program given to the control group. Both groups received the usual medical care during the study period. The therapists who performed the measurements and evaluated the results were blind of the groups' assignments. Figure 1 demonstrates the experimental design as a flow chart.\n\nPatients’ demographic data and clinical characteristics including age and diabetes duration in years were recorded, weight in kg and height in meter, body mass index (BMI; kg/m2), blood pressure (BP) in mmHg, and resting heart rate (HR). fasting blood glucose (FBG) level and glycosylated hemoglobin % (HbA1c) were evaluated according to the American Diabetes Association guidelines. Evaluation of the DPN was done using the Michigan neuropathy screening instrument. Nutritional status was evaluated by the Mini Nutritional Assessment scale according to exclude the patients with malnutrition. All previous demographic characteristics were evaluated under resting conditions at the beginning of the study. While other measurements, spatiotemporal gait parameters and postural stability indices were done at baseline (pre) and after 12 weeks of interventions (post).\n\nGait parameters were measured using the GAITRite Walkway System (GAITRite, CIR Systems, Sparta, NJ, USA). GAITRite is a 4.5-m computerized carpet with embedded sensors that activate when mechanical pressure is applied. Sensor activation timing and relative sensor distances were detected by the walkway. After that, the GAITRite version 4.7 application software analyzes spatial and temporal gait parameters for each footfall, as well as an overall range for each parameter. The system has been evaluated and proved to have high test-retest reliability.13 It was used in a previous DPN study.14 Each evaluation takes about 15 min to complete, which includes gait testing and data analysis using the manufacturer's software. The patients were tested at their maximum walking speed. Manually eliminated footfalls that were only partially captured. The average statistics from three walking trials were used in the analysis. Subjects were told to begin walking two meters before the edge of the mat and continue walking two meters beyond the end of the mat to avoid acceleration and deceleration changes.15 In this study, the therapist assessed step length (cm), step time (sec), double support time (sec), velocity (cm/sec), and cadence (steps/min).\n\nPostural stability indices were measured using the Biodex Balance System (BBS) (Biodex Medical System, Shirley, NY, USA). For evaluating balance, the BBS is a valid and reliable tool. The device includes a movable circular platform with a 20° tilt in a 360° range, as well as a computer software interface for objective balance testing and simultaneous movement in the anterior-posterior and medio-lateral directions. BBS provides a numerical stability index (SI) that displays postural instability around the body's center of gravity. The SI illustrates the patient's ability to control the platform's tilting angle and amount of motion. A lower SI score suggests more balance and stability, whereas a high SI score indicates higher movement, less stability, and a considerable deviation. The system provides 12 levels of stability, with level 1 allowing the most tilting and level 12 allowing the least tilting. One of the balance indices that's been measured was the antero-posterior stability index (APSI), medio-lateral stability index (MLSI), and overall stability index (OSI).\n\nAll patients were given an explanation of the evaluation procedure, as provided in the BBS operation manuals, prior to the postural stability test. Each patient was instructed to stand barefoot in the center of the locked platform and shift his feet to a position that would allow him to retain the cursor on the visual feedback screen in the center of the screen grid. The patient was told to hold his feet in that posture until the platform could be stabilized once he was in a centered position. The angles of the feet and heel coordinates were then recorded on the platform. These angles were entered into the BBS, and the test started. In order to keep the pointer centered when the platform got unstable, the patient was told to retain his focus on the screen. After that, the computer analyzes the patient's sway motions and reports on his or her ability to control platform variation while in a balanced position. A printout report, including APSI, MLSI, and OSI data was obtained at the end of each test trial. Three trials with one minute of rest between them were obtained for each patient, with the average of these trials being utilized for statistical analysis.16\n\nTraditional physical therapy program\n\nBoth groups received the same traditional physical therapy program for 12 weeks, three times a week, for 30 min each. The treatment session includes a set of exercises aimed at improving muscle strength, balance, and physical endurance, as well as specific gait training. Each session comprises three phases: warm-up, actual training, and cool-down. 5 min of gentle stretching exercises for the calf, hamstring, quadriceps, and iliopsoas muscles were included in the warm-up activities. The active phase lasted 20 min and was performed on a balance training mat with a high elasticity. Gait training including walking in all directions, weight shifting exercises, balance training exercises on the mat and balance board, and proprioceptive exercises in an open and closed chain were all part of the training phase. After the exercise, there was a 5-minute cool-down phase. During the cool-down phase, patients did deep breathing and static back extensor exercises in a reclined position.16 All of the patients were allowed to proceed with their usual leisure activities. They were asked to report any symptom or feeling of falling during the exercise session.\n\nAntigravity treadmill training\n\nAn AlterG treadmill (AlterG Pro 200, Alter G Inc, USA) was used to provide antigravity treadmill training to the patients in the experimental group. The AlterG allows the patient to change their body weight from 20% to 100% in 1% increments. The air pressure inside the LBPP chamber can be adjusted from 0 to 2.0 kPa above atmospheric pressure. By allowing full range of motion of the upper and lower body as well as a normal gait mechanism, the LBPP treadmills improve balance and strength, maintain patients in position, support patients laterally, and prevent falls. They are very comfortable to train in for long periods of time and have simple controls for adjusting body weight, speed, and inclination. The AlterG treadmill is comprised of two compressors, a protective transparent chamber, safety locks, and several sizes of pants. The treadmill is linked to the compressors, which employ a controller to control the pressure inside the chamber. The transparent material of the chamber allows the therapist to observe the patient walk on the treadmill and provide him with necessary feedback. The AlterG system's force plate was used to determine the patient's weight. The body weight support was set at 75% of body weight for each patient in this study, with a start speed of 0.1 m/sec. The treadmill speed was gradually increased until each patient's maximal walking capacity was reached without losing control of their lower limbs or treadmill track. For 12 weeks, a 30-minute gait training program was performed three times per week. As a warm-up, patients walked back and forth across the room for around five minutes. The inclination on the treadmill was set to zero degrees. The patients were told to maintain an upright posture on the treadmill belt with their feet flat on the belt, and they could stop the training by pressing the stop button.12\n\nData were tested for normality using the Shapiro–Wilk test. Data were presented as mean ± SD. Mean changes in gait parameters and postural stability indices dependent variables were analyzed using paired t-test to test within-groups assumptions. Between-groups assumptions were analyzed using one-way analysis of variance (ANOVA). The level of significance was set at P<0.05. Statistical analysis was performed using SPSS software (version 16.0; SPSS Inc, Chicago, IL) (RRID:SCR 019096).\n\n\nResults\n\nA total of 82 elderly Saudi men diagnosed with DPN were selected as potential participants for this study (Figure 1). 37 of the participants were excluded (29 not meeting the inclusion criteria, and eight refused to participate). This study included 45 men who were randomly assigned into two groups. There were no significant differences in mean age, height, BMI, diabetes duration, FBG, HbA1c, HR, systolic and diastolic blood pressure and nutritional status (P>0.05) between experimental and control group as shown in Table 1. Exercise compliance was 100% for all subjects after therapy.\n\n☼ Level of significance at P<0.05.\n\n* Significant.\n\n** Non-significant.\n\nThe mean values of gait parameters (step length (cm), step time (sec), double support time (sec), velocity (cm/sec), and cadence (steps/min) between the experimental and control groups were not significantly different at baseline (P>0.05) (Table 2). The mean values of gait parameters obtained at the baseline and post-treatment assessments, however, were significantly different (P<0.05). When compared to patients in the control group, patients in the experimental group showed improved gait parameters (Table 2).\n\n☼ Level of significance at P<0.05.\n\n* Significant.\n\n** Non-significant.\n\nThe mean values of the overall stability index, anteroposterior stability index, and mediolateral stability index between the experimental and control groups were not significantly different (P>0.05) at the beginning of the study (Table 3). Between the baseline and post-treatment examinations, there was a significant difference (P<0.05) in the mean stability indices. When compared to patients in the control group, patients in the experimental group showed improvements in postural stability indices (Table 3).\n\n☼ Level of significance at P<0.05.\n\n* Significant.\n\n** Non-significant.\n\n\nDiscussion\n\nThe findings of this study showed that a program combining antigravity treadmill training and traditional physical therapy improved gait parameters and balance performance more effectively than a traditional physical therapy program alone. After 12 weeks of treatment, both groups showed improvements in all measured variables. In the experimental group, however, there was a greater improvement.\n\nThe use of an antigravity treadmill, which is a device that adjusts the gravity experienced in the lower extremities during walking training by using a unique air pressure control system, resulted in significant improvements in gait parameters and postural stability in the experimental group. This reduces the patient's weight by 80%, allowing them to walk and run without having to bear their full weight. This device is also safe and effective for postoperative rehabilitation because of its precision control of up to 1% of body weight, allowing patients with lower limb injuries to rehabilitate without pain.17 Walking distance can be increased while keeping normal walking patterns, and walking activities can be done without affecting ankle and knee joint range of motion.18\n\nThe amount of impact on the knee is reduced when walking on an antigravity treadmill. According to a previous study, reducing gravity to 50% of body weight reduced force transmitted to the knee during early rehabilitation and reduced force transmitted to the knee.19 Furthermore, previous study has showed that utilizing an antigravity treadmill for muscular strength and aerobic training enhanced walking and dynamic balance while keeping the same kinetic movement as normal walking and reduced musculoskeletal system strain.20,21\n\nAntigravity treadmill training is used to prevent quadriceps muscle atrophy and strengthen muscles in patients with femoral fractures. It also allows for partial weight bearing initially, which may help with long-term gait stability.22 Kim et al., who used an antigravity treadmill to treat adults with femoral fractures, found that both groups improved in muscular strength and endurance activities following the intervention. Furthermore, at 60°/s of hip extensor and gluteus muscular activity, antigravity treadmill training improved muscle strength much more than traditional therapy. As a result, gait training by antigravity treadmill compensates for traditional rehabilitation therapies' limitations and provides a rehabilitation plan for patients with femoral fractures to ensure a stable and effective gait.23\n\nUnloading the body weight during walking has the potential to reduce muscular activity as measured by EMG and change the muscle activation pattern.24–26 Unweighing has also been shown in the literature to produce a reduction in muscle EMG activities that would be muscle specific. Unloading the body weight during running reduced EMG muscle activities in all muscle groups except hip adductors during the swing phase and hamstrings during the stance phase of the running cycle, according to Hunter et al..25 Unweighting has been shown to reduce cardiorespiratory and metabolic demands in previous research.27 Furthermore, cardiorespiratory and metabolic demands increased with increased walking speed and with lower unloading rate.28\n\nReduced gravity appears to delay chondrogenesis during the very early stages of cell condensation and cell binding, but has a lesser effect on cartilage growth and development at later stages of chondrogenesis, which is more relevant for rehabilitation, according to scientific data.29,30 Reduced gravity also decreases the extracellular matrix protein content as well as cell density in neocartilage, whereas increasing the ratio of collagen type II to type I expression.29 According to Wolf’s law, a certain load stimulates biological processes to strengthen, whereas overloading has a potentially negative or catabolic effect on tissues. Extrapolating this to antigravity training, it appears that load reduction is associated with the ability to exercise at higher intensities without the risk of negative or catabolic effects. This demonstrates that antigravity treadmills are successful in reducing ground reaction forces and peak knee joint moments in inverse relation to the applied upward body force.30\n\nThe antigravity treadmill has been used to treat many diseases. Berthelsen et al.,21 for example, conducted a study in 2014 investigating the use of an antigravity treadmill for ambulation training in muscular dystrophy patients. They found that 10-weeks of antigravity treadmill training improved walking capacity and balance statistically when compared to before training without causing muscle damage.21\n\nPositive outcomes of using AlterG in stroke patients with sequelae have been found in terms of walking speed, walking distance, and a reduction in risk of fall. Independence, mobility, and participation have all been linked to gait speed and endurance.31,32 In a patient with chronic stroke, training on a pressure-controlled treadmill was associated with enhanced gait parameters, reduced fall risk, increased participation, and reduced the self-perceived negative impact. These findings suggest that a pressure-controlled treadmill might be a reasonable alternative to body-weight-supported locomotor training.31 Popp et al. compared conventional therapy to antigravity treadmill treatment on chronic stroke patients, reporting a positive response and improvement in gait and endurance in the antigravity treadmill group.33\n\nThe antigravity treadmill provides a safe environment where the patient can retrain their gait and improve their balance by receiving positive biofeedback. There have been some case reports of antigravity treadmills having a positive effect in this population, but more research is required. In order to have a positive impact on the population's health, effective treatment approaches must be implemented in routine clinical practice.34\n\nThe findings of this study are similar to that of Sukonthamarn et al.,35 who found that after a one-month training program, both the intervention and control groups showed improvements in standing balance, motor power, six-minute walk distance, and the functional ambulatory category scale in subacute to chronic hemiparetic stroke patients within one year of onset. Furthermore, ambulation training using an antigravity treadmill in combination with traditional physiotherapy seems to be superior to traditional physiotherapy alone in terms of balance training. Lastly, the antigravity treadmill is a safe rehabilitative medical device that can help patients in achieving better clinical outcomes.35\n\nThe significant improvement in gait parameters and postural stability in the experimental group in this study is consistent with the findings of Miura et al.,36 who found that LBPP training could effectively increase exercise tolerance and physical performance in elderly patients.36 These findings reflect the safety and ease of use of such rehabilitation equipment that eliminates the risk of falling during aerobic treadmill training sessions.37\n\nAlterG's advantages over the suspension weight-loss system are primarily reflected in the patient's comfort during the weight-loss process.38 The force is evenly distributed throughout the human body's lower portion, and the patient has no sense of pressure. Furthermore, LBPP can improve venous return during walking, which lowers heart rate significantly.37 All of the aforementioned advantages of aerobic exercise are beneficial to patients with osteoarthritis, particularly those with cardiovascular disease and hypertension, promoting patient rehabilitation.39\n\nIn terms of limitations, the results of this study should be interpreted with caution because it only included male patients in a particular age range, and dietary regimens and routine activities were not properly monitored. Lack of follow-up data, limiting clinical application of our findings to the antigravity treadmill's short-term effects. It's also difficult to isolate the antigravity treadmill's effect in both groups because of the effect of the physical therapy program. The outcomes of this study are promising, but additional trials with fewer inclusion and exclusion criteria would produce more generalizable results. Long-term studies and a comparison to other harness systems are required. Future research on the antigravity treadmill's impact on muscle strength, energy expenditure, and quality of life in DPN patients could be extremely effective for patients.\n\n\nConclusions\n\nAntigravity treadmill training in combination with traditional physical therapy appears to be superior to traditional physical therapy alone in terms of gait and balance training. As a result, the antigravity treadmill has been found to be an effective device for the rehabilitation of DPN patients.\n\n\nData availability\n\nFigshare: Underlying data for ‘Effects of antigravity treadmill training on gait and balance in patients with diabetic polyneuropathy: A randomized controlled trial’.\n\nThe project contains the following underlying data:\n\n• Demographic characteristics raw data: https://figshare.com/s/2990d265a8bea78e4c27 DOI: 10.6084/m9.figshare.17053808\n\n• Gait parameters and postural stability: https://figshare.com/s/197dc8c07d05380056ea DOI: 10.6084/m9.figshare.17054036\n\n• Flow chart of the study: https://figshare.com/s/15128a129f514ba02d92 DOI: 10.6084/m9.figshare.17054045\n\n• Tables: https://figshare.com/s/10ee7a9d111b2c4487ee DOI: 10.6084/m9.figshare.17054057\n\nCONSORT Checklist: https://figshare.com/s/23df41d9235a4e2f1e5e DOI: 10.6084/m9.figshare.17054060\n\n\nAuthor contributions\n\nAshraf Abdelaal: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing-Original Draft Preparation, Writing-Review & Editing.\n\nShamekh El-Shamy: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Software, Supervision, Validation, Visualization, Writing-Original Draft Preparation, Writing-Review & Editing.",
"appendix": "Acknowledgments\n\nThis work was funded by grant number (15-MED5221-10) from the National Science, Technology and Innovation Plan (MAARIFAH), The King Abdul-Aziz City for Science and Technology (KACST), Kingdom of Saudi Arabia. We thank the Science and Technology Unit at Umm Al-Qura University for their continued logistics support.\n\n\nReferences\n\nDixon CJ, Knight T, Binns E, et al.: Clinical measures of balance in people with type two diabetes: A systematic literature review. Gait Posture 2017; 58: 325–332. Publisher Full Text\n\nAljohani M, Karam A, Alamri A, et al.: Diabetic neuropathy in Saudi Arabia: a comprehensive review for further actions. IJMDC. 2020; 4(11): 2008–2013. Publisher Full Text\n\nMustapa A, Justine M, Mohd Mustafah N, et al.: Postural Control and Gait Performance in the Diabetic Peripheral Neuropathy: A Systematic Review. Biomed. Res. Int. 2016; 2016: 1–14. Publisher Full Text\n\nJahantigh Akbari N, Hosseinifar M, Naimi SS, et al.: The efficacy of physiotherapy interventions in mitigating the symptoms and complications of diabetic peripheral neuropathy: A systematic review. J. Diabetes Metab. Disord. 2020; 19(2): 1995–2004. PubMed Abstract | Publisher Full Text\n\nMelese H, Alamer A, Hailu Temesgen M, et al.: Effectiveness of Exercise Therapy on Gait Function in Diabetic Peripheral Neuropathy Patients: A Systematic Review of Randomized Controlled Trials. Diabetes Metab. Syndr. Obes. 2020; 13: 2753–2764. PubMed Abstract | Publisher Full Text\n\nSuzuki K, Niitsu M, Kamo T, et al.: Effect of Exercise with Rhythmic Auditory Stimulation on Muscle Coordination and Gait Stability in Patients with Diabetic Peripheral Neuropathy: A Randomized Controlled Trial. OJTR. 2019; 07: 79–91. Publisher Full Text\n\nWrisley DM, McLean G, Hill JB, et al.: Long-Term Use of a Sensory Prosthesis Improves Function in a Patient with Peripheral Neuropathy: A Case Report. Front. Neurol. 2021; 12: 655963. PubMed Abstract | Publisher Full Text\n\nItes KI, Anderson EJ, Cahill ML, et al.: Balance interventions for diabetic peripheral neuropathy: a systematic review. J. Geriatr. Phys. Ther. 2011; 34(3): 109–116. Publisher Full Text\n\nTofthagen C, Visovsky C, Berry DL: Strength and balance training for adults with peripheral neuropathy and high risk of fall: current evidence and implications for future research. Oncol. Nurs. Forum 2012; 39(5): E416–E424. PubMed Abstract | Publisher Full Text\n\nSalsabili H, Bahrpeyma F, Esteki A: The effects of Task-Oriented Motor Training on gait characteristics of patients with type 2 diabetes neuropathy. J. Diabetes Metab. Disord. 2016; 15: 14. Publisher Full Text\n\nCornish S, Peeler J: The Effect of a Lower Body Positive Pressure Supported Treadmill Exercise Regime on Systemic Biomarkers of Inflammation and Cartilage Degradation in Individuals with Knee Osteoarthritis: A Pilot Study. International Journal of Kinesiology and Sports Science. 2021; 9(3): 18–27. Publisher Full Text\n\nAbdelaal AA, El-Shamy SM: Effect of lower body positive pressure aerobic training on fall risk in patients with diabetic polyneuropathy. Randomized controlled trial. Eur. J. Phys. Rehabil. Med. 2021 Oct 12; Publisher Full Text\n\nHollman JH, McDade EM, Petersen RC: Normative spatiotemporal gait parameters in older adults. Gait Posture 2011; 34(1): 111–118. PubMed Abstract | Publisher Full Text\n\nMenz HB, Lord SR, St George R, et al.: Walking stability and sensorimotor function in older people with diabetic peripheral neuropathy. Arch. Phys. Med. Rehabil. 2004; 85(2): 245–252. PubMed Abstract | Publisher Full Text\n\nVo ML, Chin RL, Miranda C, et al.: Changes in spatiotemporal gait parameters following intravenous immunoglobulin treatment for chronic inflammatory demyelinating polyneuropathy. Muscle Nerve. 2017; 56(4): 732–736. PubMed Abstract | Publisher Full Text\n\nIbrahim Z, Ali O, Moawd S, et al.: Low Vibrational Training as an Additional Intervention for Postural Balance, Balance Confidence and Functional Mobility in Type 2 Diabetic Patients with Lower Limb Burn Injury: A Randomized Clinical Trial. Diabetes Metab. Syndr. Obes. 2021; 14: 3617–3626. PubMed Abstract | Publisher Full Text\n\nSaxena A, Granot AJ: Use of an anti-gravity treadmill in the rehabilitation of the operated achilles tendon: A pilot study. J. Foot Ankle Surg. 2011; 50: 558–561. PubMed Abstract | Publisher Full Text\n\nGrabowski AM: Metabolic and biomechanical effects of velocity and weight support using a lower-body positive pressure device during walking. Arch. Phys. Med. Rehabil. 2010; 91: 951–957. PubMed Abstract | Publisher Full Text\n\nPatil S, Steklov N, Bugbee WD, et al.: Anti-gravity treadmills are effective in reducing knee forces. J. Orthop. Res. 2013; 31(5): 672–679. PubMed Abstract | Publisher Full Text\n\nMikami Y, Fukuhara K, Kawae T, et al.: The effect of anti-gravity treadmill training for prosthetic rehabilitation of a case with below-knee amputation. Prosthetics Orthot. Int. 2015; 39(6): 502–506. PubMed Abstract | Publisher Full Text\n\nBerthelsen MP, Husu E, Christensen SB, et al.: Anti-gravity training improves walking capacity and postural balance in patients with muscular dystrophy. Neuromuscul. Disord. 2014; 24(6): 492–498. PubMed Abstract | Publisher Full Text\n\nOh MK, Yoo JI, Byun H, et al.: Efficacy of Combined Antigravity Treadmill and Conventional Rehabilitation After Hip Fracture in Patients With Sarcopenia. J. Gerontol. A Biol. Sci. Med. Sci. 2020; 75(10): e173–e181. PubMed Abstract | Publisher Full Text\n\nKim P, Lee H, Choi W, et al.: Effect of 4 Weeks of Anti-Gravity Treadmill Training on Isokinetic Muscle Strength and Muscle Activity in Adults Patients with a Femoral Fracture: A Randomized Controlled Trial. Int. J. Environ. Res. Public Health 2020; 17(22): 8572. PubMed Abstract | Publisher Full Text\n\nDeffeyes JE, Karst GM, Stuberg WA, et al.: Coactivation of lower leg muscles during body weight-supported treadmill walking decreases with age in adolescents. Percept. Mot. Skills 2012; 115(1): 241–260. PubMed Abstract | Publisher Full Text\n\nHunter I, Seeley MK, Hopkins JT, et al.: EMG activity during positive-pressure treadmill running. J. Electromyogr. Kinesiol. 2014; 24(3): 348–352. PubMed Abstract | Publisher Full Text\n\nLiebenberg J, Scharf J, Forrest D, et al.: Determination of muscle activity during running at reduced body weight. J. Sports Sci. 2011; 29(2): 207–214. Publisher Full Text\n\nGrabowski AM: Metabolic and biomechanical effects of velocity and weight support using a lower-body positive pressure device during walking. Arch. Phys. Med. Rehabil. 2010; 91(6): 951–957. PubMed Abstract | Publisher Full Text\n\nSueyoshi T, Emoto G: The Effect of Anti-Gravity Treadmill on Balance in Acute Phase of Post-Operative Knee Rehabilitation. Asian J. Sports Med. 2018; 9(4): e59287.\n\nStamenković V, Keller G, Nesic D, et al.: Neocartilage formation in 1 g, simulated, and microgravity environments: implications for tissue engineering. Tissue Eng. Part A 2010; 16(5): 1729–1736. PubMed Abstract | Publisher Full Text\n\nDebecker N, Luyten M, Vandenabeele F, et al.: The effect of anti-gravity training after meniscal or chondral injury in the knee. A systematic review. Acta Orthop. Belg. 2020; 86(3): 422–433. PubMed Abstract\n\nLathan C, Myler A, Bagwell J, et al.: Pressure-controlled treadmill training in chronic stroke: a case study with AlterG. J. Neurol. Phys. Ther. 2015; 39(2): 127–133. PubMed Abstract | Publisher Full Text\n\nHoffman MD, Donaghe HE: Physiological responses to body weight–supported treadmill exercise in healthy adults. Arch. Phys. Med. Rehabil. 2011; 92: 960–966. PubMed Abstract | Publisher Full Text\n\nPopp H, Breen J, Ferlito T, et al.: Anti-gravity treadmill training leads to superior walking ability compared to conventional physical therapy in chronic community dwelling stroke survivors. Stroke. 2015; 46(Suppl-1): 46. Publisher Full Text\n\nCarmina MLM: Antigravity Treadmill for Rehabilitation of Stroke Survivors. Int. J. Neurorehabilitation. 2019; 6(2): 342.\n\nSukonthamarn K, Rerkmoung S, Konjen N, et al.: Effectiveness of Anti-Gravity Treadmill Training in Improving Walking Capacity and Balance in Hemiparetic Stroke Patients: A Randomized Controlled Trial. J. Med. Assoc. Thail. 2019; 102: 982–990.\n\nMiura M, Kohzuki M, Ito O, et al.: Acute and Chronic Effects of Lower Body Positive Pressure Exercise on the Very Elderly: A Pilot Study. Int. J. Phys. Med. Rehabil. 2013; 1: 173–177.\n\nCutuk A, Groppo ER, Quigley EJ, et al.: Ambulation in simulated fractional gravity using lower body positive pressure: cardiovascular safety and gait analyses. J. Appl. Physiol. 2006; 101(3): 771–777. PubMed Abstract | Publisher Full Text\n\nRuckstuhl H, Kho J, Weed M, et al.: Comparing two devices of suspended treadmill walking by varying body unloading and Froude number. Gait Posture. 2009; 30(4): 446–451. PubMed Abstract | Publisher Full Text\n\nKawae T, Mikami Y, Fukuhara K, et al.: Anti-gravity treadmill can promote aerobic exercise for lower limb osteoarthritis patients. J. Phys. Ther. Sci. 2017; 29(8): 1444–1448. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "125998",
"date": "16 Mar 2022",
"name": "Sobhy M Aly",
"expertise": [
"Reviewer Expertise physiotherapy- biomechanics-statistics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for inviting me to review this paper.\nThis research studies the effect of antigravity treadmill training on gait and balance in patients with diabetic polyneuropathy. Subjects were divided randomly into study and control groups. The study group received antigravity treadmill training and physiotherapy while the control group received the physiotherapy alone. The results explained improvement of both groups post-treatment with significant difference between groups post-treatment.\nMinor comments:\nTitle \"Effects\" should be changed to \"Effect\".\nResults In the abstract: no need to mention all these numbers, just mention if there was a significant difference between groups or not.\nKey words \"Traditional rehabilitation\" is inappropriate.\nSample size calculation This is inappropriate. Please revise the parameters for calculation, power and effect size.\nOutcome measures\nShould include only the outcome measures and not the baseline measures.\nEvaluation of spatiotemporal gait parameters \"computerized carpet with embedded sensors that activate...\" should be changed to \"activated\".\nFurthermore, why were patients tested at their maximum walking speed? The patients should be tested at their comfortable walking speed.\nTreatment interventions \"5 min of...\" should be changed to \"five\".\nStatistical analysis \"Between-groups assumptions were analyzed using one-way analysis of variance (ANOVA)\" should be changed to \"Between-groups comparisons...\".\nStatistical analysis is inappropriate. Either use paired and unpaired t-test or mixed model MANOVA. No need for between-groups ANOVA.\nResults \"...(P>0.05) between experimental and control group...\" should be changed to \"...between experimental and control group (P>0.05)...\"\n\"The mean values of gait parameters obtained at the baseline and post-treatment assessments, however, were significantly different (P<0.05). When compared to patients in the control group, patients in the experimental group showed improved gait parameters (Table 2).\" Please rephrase this section to better explain the results within groups and between groups.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7995",
"date": "23 Mar 2022",
"name": "Shamekh El-Shamy",
"role": "Author Response",
"response": "Thank for your valuable comments and I appreciate your time and effort. Authors reply to the reviewer’s comments point by point. Minor comments: Title \"Effects\" should be changed to \"Effect\". Author changed it to “Effect”. Results In the abstract: no need to mention all these numbers, just mention if there was a significant difference between groups or not. These numbers showed the significant improvement after the treatment. Key words \"Traditional rehabilitation\" is inappropriate. Author changed it to “Traditional treatment”. Sample size calculation This is inappropriate. Please revise the parameters for calculation, power and effect size. Author has revised the parameters and corrected it. Outcome measures Should include only the outcome measures and not the baseline measures. Author includes these measures to follow up the diabetic patients during the study. Evaluation of spatiotemporal gait parameters \"computerized carpet with embedded sensors that activate...\" should be changed to \"activated\". Author corrects it “activated” Furthermore, why were patients tested at their maximum walking speed? The patients should be tested at their comfortable walking speed. Author corrects it to “comfortable”. Treatment interventions \"5 min of...\" should be changed to \"five\". Author changes it to “five”. Statistical analysis \"Between-groups assumptions were analyzed using one-way analysis of variance (ANOVA)\" should be changed to \"Between-groups comparisons...\". Author changes it to \"Between-groups comparisons...\". Statistical analysis is inappropriate. Either use paired and unpaired t-test or mixed model MANOVA. No need for between-groups ANOVA. Author used paired and unpaired t-test. Results \"...(P>0.05) between experimental and control group...\" should be changed to \"...between experimental and control group (P>0.05)...\" Author changes it to “...between experimental and control group (P>0.05)...\" \"The mean values of gait parameters obtained at the baseline and post-treatment assessments, however, were significantly different (P<0.05). When compared to patients in the control group, patients in the experimental group showed improved gait parameters (Table 2).\" Please rephrase this section to better explain the results within groups and between groups. Author rephrases this section The mean values of gait parameters obtained at the baseline and post-treatment assessments were significantly different in the experimental and control group (P<0.05). The patients in the experimental group exhibited improvements in their gait parameters compared with patients in the control group (Table 2)."
}
]
}
] | 1
|
https://f1000research.com/articles/11-52
|
https://f1000research.com/articles/11-1219/v1
|
26 Oct 22
|
{
"type": "Research Article",
"title": "Factors associated with scientific production of professors working at a private university in Peru: An analytical cross-sectional study",
"authors": [
"Oriana Rivera-Lozada",
"ISABEL CRISTINA RIVERA-LOZADA",
"Cesar Antonio Bonilla-Asalde",
"ISABEL CRISTINA RIVERA-LOZADA",
"Cesar Antonio Bonilla-Asalde"
],
"abstract": "Objective: To estimate the association between the academic, personal, and work characteristics and scientific production of professors at a private university of Lima, Peru, in 2021. Methods: We undertook an observational, analytical, and cross-sectional study. The sample included 322 professors through simple random sampling. Two questionnaires were administered. The first gathered personal, academic, and work characteristics; while the second evaluated scientific production. The chi-squared test was used, with a significance level of p<0,05, to evaluate the association between the different characteristics and scientific production. A multiple logistic regression was analyzed through the Stepwise method to evaluate the relationship between the variables of exposure and scientific production. We calculated prevalence ratios (PRs) with their respective 95% confidence intervals (95% CI). Results: We analyzed 322 professors, 59,6% were male. Scientific production was associated with being registered in Renacyt (PR = 5,52; 95% CI: 2,14 to 4,23; p = <0.001), having a doctoral degree (PR = 2,45; 95% CI: 1,60 to 3,85; p = <0.001), having been a thesis advisor (PR = 3,83; 95% CI: 1,45 to 5,66; p = <0.001), having facilities to conduct research at the workplace (PR = 1,58; 95% CI: 1,12 to 2,47; p = 0.006), and having received training by the university (PR = 1,99; 95% CI: 1,55 to 2,56; p = 0,001). Conclusions: Scientific production was associated with being registered in Renacyt, having a doctoral degree, having been a thesis advisor, having facilities to conduct research at the workplace, and having being trained in research by the university. Hence, evaluation systems and the monitoring of university quality standards should be strengthened. In addition, it is necessary to undertake wider scope studies in order to enhance the strategies that promote professors’ research.",
"keywords": [
"Scientific production",
"Publication",
"Professors",
"Universities",
"Research Culture"
],
"content": "Introduction\n\nScientific production is one of the most important indicators of scientific and technological development.1 It is closely related to the economic and social development of a country or region,2,3 as it helps researchers disseminate knowledge through the publication of scientific articles in indexed journals. The countries that lead the scientific output rankings are the United States, China, and Great Britain; while in Latin America, Brazil, Mexico, and Argentina are in the top of the lists.4,5 In Peru, the efforts to reach scientific and technological development through the investment in education and research projects with a great impact are scarce. Thus, this country is in the 73rd place in terms of scientific production at a world level and in the eighth in Latina American.5\n\nIn the world, universities constitute the ideal environment for the generation of evidence through scientific research.6 They have a fundamental role in scientific production by promoting and producing new knowledge that help the countries’ development.7\n\nAmong the diverse strategies to promote research among professors and students,8 training, attracting, and retaining young researchers with aptitudes for research stand out, in addition to didactic techniques such as flipped classroom.9 Thus, universities seek to train future researchers during the undergraduate programs, where research is one of the most important pillars in the education of future professionals,10 particularly in the human medicine programs, and health sciences in general. This is intended to be replicated with greater demand and quality in the different postgraduate programs.1,9\n\nHowever, in developing countries and especially in Peru, universities do not fully comply with the function of training quality researchers.11,12 This is manifested through the low level of medicine scientific production, compared to medical scientific production of countries such as the United States3 or European countries.13 This could be explained by the limited available economic or human resources for research,14 a low level of research culture and deficient research training during the under- and postgraduate programs.15\n\nThis situation leads research and scientific production to be a matter of interest and concern within the Peruvian scientific community and the Government. Thus, in 2014, the Peruvian University Law 30220 was passed,16 which states that students should conduct research projects such as a thesis or a scientific article and this should be sustained and approved as a condition sine qua non to obtain their professional degree and finish satisfactorily the different postgraduate programs. This, in addition, is a basic condition of quality for the licensing of the different professional schools.1\n\nThe courses that include research activity have a clear objective: to guide students in their scientific education. This situation requires that responsible professors have sufficient research experience expressed in a significant number of publications in indexed journals that certify scientific suitability and novelty.17,18 Currently, there exists little available evidence that explores the scientific production of professors in Peru. In addition, this lack of evidence also includes scarce studies on factors associated with, particularly, the area of health sciences which reflects the current condition of the compliance of universities in terms of their scientific and training function, and offers truthful and pertinent information to implement programs and strategies that promote the scientific development of the country.\n\nTaking into account what we stated above, this research’s objective was to estimate the association between professor’s academic, personal and work characteristics and their scientific production at the Universidad Norbert Wiener, Lima, Peru, in 2021, as a first step to identify those factors that contribute or limit the development of scientific production in a higher education institution in the capital of the country.\n\n\nMethods\n\nWe undertook an observational, analytical, cross-sectional study. The population was made up of 663 professors of the Universidad Norbert Wiener during the first term of 2021, in Lima, Peru. We included both male and female professors that worked at the Universidad Norbert Wiener during the period of the study. Professors that did not want to participate or were not available to fill in the questionnaires during the period of the study were excluded.\n\nThe research instruments33 were developed by the researchers and were applied using the Google Forms (Google, 2022) tool, for which the link to the survey was sent by e-mail to the study participants. The data provided by the participants were collected in Google drive (Google, 2022).\n\nA sample size was determined by proportional allocation according to the size of the school of origin, resulting in a total of 332 university teachers, after applying the statistical formulas. The sampling was simple random probabilistic, since there was a list of all the university teachers.\n\nThe information on the included participants in this study was collected through two questionnaires. The first was oriented towards the identification of academic, work, and personal characteristics. The second gathered information about the scientific production of the evaluated professors. Data collection was carried out via email, using the drive tool between the months of September and December 2020.\n\nThe data collection instruments were developed by the research team and validated through the Aiken’s V coefficient with the participation of ten expert methodologists and experts on the subject, who assessed clarity, objectivity, being up-to-date, organization, sufficiency, adequacy, coherence, methodology, and pertinence of the instruments’ content.\n\nThe reliability of the instrument was evaluated through a pilot test that included 30 professors from Norbert Wiener University, who were randomly selected and did not enter the study. The instruments were sent by email using Google drive (Google), then both instruments were subjected to the Cronbach's alpha and KR-20 reliability tests according to the type of variable evaluated. We obtained a Cronbach's alpha coefficient of 0.85 for the instrument that evaluates scientific production and 0.88 for academic factors. In addition, we obtained a KR-20 coefficient of 0.82 for personal factors and 0.90 for work factors. For which the SPSS version 25.0 (IBM Corp, 2017) (RRID:SCR_016479) was used, whose license is from Norbert Wiener University.\n\nReliability was assessed through a pilot test that included 30 professors of the Universidad Norbert Wiener. Both instruments were subjected to the Cronbach’s alpha and KR-20 tests according to the type of variable evaluated. We obtained a Cronbach’s alpha coefficient of 0.85 for the instrument that assesses scientific production and 0.88 for the one about academic factors. In addition, we obtained a KR-20 coefficient of 0.82 for the personal factors and 0.90 for the work factors the results of the instrument reliability test were adequate; therefore, no changes were made to the instruments. Data from the pilot study cannot be shared in this study, as they are being used for another study that will analyze the psychometric properties of the instruments.\n\nThis study included professors of the Universidad Privada Norbert Wiener with socioeconomic characteristics that differ from the population of university teachers in Peru. However, this study is one of the first to evaluate professor’s scientific production and the possible associated factors, and it will serve as baseline for future studies with a wider scope.\n\nScientific production can be assessed in different ways that include journal type, H-index, language of publication, level of inter-institutional collaboration at a national as well as international level.\n\nOutcome variable: Scientific production\n\nProfessors’ scientific production was assessed as a dependent or outcome variable. This was defined as the number of publications (original article, review article, clinical case reports, books) in journals indexed in Scopus, Web of Science (WoS), Scielo, Latindex. In addition, the impact of publication through the H-index was reported. This information was obtained through the research instrument.\n\nVariables of exposure: Personal, academic and work characteristics\n\nProfessors’ personal, academic, and work characteristics were evaluated as well as the postgraduate programs studied, the level of English comprehension, database management, reference management, statistical software management, subscription to scientific journals, memberships in scientific societies or groups, research competencies, or thesis advising.\n\nFurthermore, work characteristics such as access to incentives, institutional support, infrastructure, and research funding were assessed, as well as administrative aspects such as employment category, contract type, and number of teaching and non-teaching hours.\n\nIn addition, we evaluated personal characteristics such as bio-social (gender, age, civil status, and children) and professional (profession, professional experience, teaching experience, or institutions where he/she worked) factors.\n\nThe obtained data were collected in the Excel 2010 (Microsoft, 2010) (RRID:SCR_016137) software and were analyzed with the SPSS program version 25.0. The descriptive results of the categorical variables were shown through absolute and relative frequencies; while for quantitative variables, we calculated measures of central tendency and dispersion.\n\nFor assessing the relationship between each exposure and outcome variables, we used bivariate analysis and the Chi-squared test with their respective p-values. We considered p<0.05 statistically significant. We calculated prevalence ratios (PRs) and their respective confidence interval at 95% for each relationship.\n\nAlso, in order to evaluate the relationship between the variables of exposure and scientific production, a multiple logistic regression analysis was performed using the Stepwise method, where step by step we added the indicators that showed a value of p<0.05 to the previous bivariate analysis. All statistical analyzes were performed using SPSS version 25.0 software licensed by Norbert Wiener University.\n\nThis study was carried out following the guidelines of the Declaration of Helsinki of 1964 and its subsequent modifications. In addition, the participants agreed to participate through written informed consent and we ensured the anonymity of the data obtained from each participant, so their integrity was not violated. This study was evaluated and approved by the Institutional Research Ethics Committee of the Norbert Wiener University. The approval number by the ethics committee was Exp. No 158-2020.\n\n\nResults\n\nThe information obtained from a total of 322 professors,33 allowed us to find that 59.6% (n=192) did not have publications in indexed journals and only 9.6% (n=31) had published six or more articles. By evaluating scientific production in different databases, we found that 13.4% (n=43) had a publication in Scopus, and 5.3% (n=17) had five or more. Also, 9.0% (n=29) had a publication in WoS and 3.1% (n=10) had four or more. In addition, 9.3% (n=30) had a publication in Scielo and 7.5% (n=24) had published four or more. We also found that 15.2% (n=49) published one or two papers in Latindex and 5% (n=16) had published five or more. On the other hand, 51.2% (n=165) did not have an H-index and 40.1% (n=129) did not know about this index. Moreover, 91.9% (n=296) had an H-index equal to 0, while 1.9% (n=6) had an H-index equal to or higher than 5 (Table 1).\n\nOf the 322 professors included in this study, 58.7% (n=189) belonged to the Faculty of Health Sciences; 6.8% (n=22), to Pharmacy and Biochemistry; 11.2% (n=36), to Engineering and Businesses; 9% (n=29), to Law and Political Sciences; and 14.3% (n=43), to the Postgraduate School.\n\nAmong the personal characteristics, we found that 59.3% (=191) were male and the median age was 48 (29-72 years old). We found that 16.8% of professors were registered in Renacyt (National Registry of Science, Technology and Technological Innovation), in which the most frequent category was Rostworowski III (3.4% n=11). Of the total, 98.4% stated that they had an interest in research and 50.3% (n=162) mentioned that they felt satisfaction due to research, but 62.7% (n=202) and 59.9% (n=193) indicated that economic aspects and workload, respectively, prevent them from conducting research. Through bivariate analysis, we could find an association between scientific production and belonging to the teaching staff of a postgraduate school (PR=2.05; 95% confidence interval: 1.38 to 3.04; p<0.001), being registered in DINA (PR=5.52; 95% confidence interval: 2.14 to 14.25; p<0.001) or in Renacyt (PR=2.39; 95% confidence interval: 1.92 to 2.98; p<0.001), and having received an award (RP=2.28; 95% confidence interval 1.81 to 2.88; p<0.001) or having being recognized for researching (PR=2.34; 95% confidence interval: 1.55 to 3.01; p<0.001) (Table 2).\n\n* P-value estimated through Chi-squared test, with a level of significance of p<0.05.\n\n** Universidad Norbert Wiener.\n\n† National Directory of Researchers and Innovators.\n\n‡ National Registry of Science, Technology and Technological Innovation.\n\nRegarding the academic characteristics, we found that 99.4% (n=320) had a postgraduate degree and the most frequent was the master’s degree (81.4% n=262). In addition, 43.8% (n=141) had a basic level of English; while 14.3% (n=46) had an advanced level. According to what was declared by the study participants in the research survey. Likewise, Of the total, 85.7% (n=276) reported that they use a database for doing research. Also, 50.6% (n=163) stated that they used Google Scholar; 47.5% (n=153) used Scopus; 73.3% (n=253) used Scielo; 50.6% (n=163) used Pubmed; and 41.6% (n=134) used Medline. In addition, 54.7% (n=176) reported that they used reference managers; while 68.6% (n=221) used statistical software. Bivariate analysis showed that having a master’s degree was associated with not having scientific production (PR=0.65; 95% confidence interval: 1.49 to 0.85; p=0.002). Furthermore, scientific production was associated with having a doctoral degree (PR=2.14; 95% confidence interval: 1.60 to 2.85; p<0.001), having an intermediate level of English (PR=1.35; 95% confidence interval: 1.01 to 1.82; =0.045), having knowledge of bibliographic search in databases (PR=2.93; 95% confidence interval: 1.46 to 5.87; =0.002), and knowing how to use any statistical software (PR=2.05; 95% confidence interval: 1.39 to 3.03; p<0.001). In addition, belonging to a scientific society (PR=2.05; 95% confidence interval: 1.75 to 2.88; p<0.001) or to a research group (PR=3.67; 95% confidence interval: 2.66 to 5.07; p<0.001), and being a thesis advisor in a master’s program (PR=1.91; 95% confidence interval: 1.48 to 2.47; p<0.001) or in a doctoral program (PR=1.95; 95% confidence interval: 1.49 to 2.55; p<0.001) were also associated with a better level of scientific production (Table 3).\n\n* P-value estimated through the Chi-squared test, with a level of significance of p<0.05.\n\nIn regard to work characteristics, only 5.9% (n=19) were professors with a permanent appointment and 76.7% (n=247) did not have a regulated teaching category. Also, 73.3% (n=236) indicated that the university did not grant them time for research and only 11.5% (n=37) dedicated 10 or more hours a week to research-related activities. In addition, 87.9% (n=283) had not received any funding for conducting research; 90.7% (n=292) had not received an incentive to publish; and 727% (n=234) had not received any support in the management of research projects. Bivariate analysis showed that scientific production was associated with having facilities to conduct research (PR=148; 95% confidence interval: 1.12 to 1.97; p=0.006) or having been trained in research (PR=1.55; 95% confidence interval: 1.12 to 2.13; p=0.008); and having received funding (PR=1.99; 95% confidence interval: 1.55 to 2.56; p<0.001) or a research incentive (PR=1.98; 95% confidence interval: 1.52 to 2.58; p<0.001) (Table 4).\n\n* P-value estimated through the Chi-squared test, with a level of significance of p<0.05.\n\nMultivariate analysis by scientific production in the study sample\n\nThrough multiple logistic regression analysis, using the Stepwise method, it was found that the main factors associated with scientific production were being registered in Renacyt (adjusted prevalence ratio (aPR)=5.52; 95% confidence interval: 2.14 to 4.23; p<0.001), having a doctoral degree (aPR=2.45; 95% confidence interval: 1.60 to 3.85; p<0.001), and having being a thesis advisor (aPR=3.83; 95% confidence interval: 1.45 to 5.66; p<0.001) (Table 5).\n\n* P-value estimated through multiple logistic regression using the Stepwise method, with a level of significance of p<0.05.\n\n** National Registry of Science, Technology and Technological Innovation.\n\n\nDiscussion\n\nThis study’s objective was to estimate the association between university teachers’ scientific production and their personal, academic, and work characteristics to give basic data that enable the implementation or modification of strategies that encourage professors to conduct research.\n\nScientific research is an essential and mandatory activity of universities, which, according to the legal Peruvian university framework,16 “are academic communities oriented towards research and teaching”. In addition to being an indicator for national and international licensing and accreditation processes, scientific production is the best way to measure research competencies in professors.18 This is why, it is indispensable for university teachers to be sufficiently trained, as they are the first contact that students will have with research19 and professors are who encourage them to do research in an adequate way.17\n\nHowever, this study found that barely 40% of professors have published a scientific article in indexed journals, and only 9.6% had more than six publications in those journals. In addition, 22.1% had, at least, a publication in Scopus and 20.5% in Scielo. These findings are similar to what was reported by previous studies such as the one by Alarcón-Ruiz,20 who found out, in 2018, that 26% of the assessed professors had a publication in Scopus over the last five years, while only 5% had a publication in the same database over the last two years. Chachaima-Mar J17 also reported similar percentages as this author found that only 14.6% of the sample had published in Scielo and 5.9%, in Scopus over the last three years, and LILACS was the most commonly used database (34.4%). Despite these similarities, it is possible to note that in our research we found a better percentage of professors with at least one published article in indexed journals. This evidences that this indicator has improved and that, if it continues in the subsequent years, it is possible to reverse the current situation in regard to professors’ scientific production in Peru.\n\nIn addition, a factor related to the number of publications is the H-index, which measures the impact of those publications. In this study, we found that only 8,7% of professors had an H-index, which coincides with what was reported in another study.21 These findings could be the reflection of the low level of culture of publication in the university community, despite the fact that conducting research, many times do not end up in publication due to the little initiative, training or funding, among others.22\n\nDefinitely, having teaching staff that do not publish indicates that these professors are not trained to teach research, for which it is crucial to study the factors involving the lack of scientific production of university teachers. Thus, this study found that receiving awards, incentives or funding for researching favors scientific production, as reported in other studies.14,23 This might be explained by the great economic expenses involving the process of developing a research project, its execution, and publication, which evidence that adequate and well-oriented funding of research activities would greatly contribute to the improvement of publication indexes in professors of Peruvian universities.\n\nHowever, we have to take into account that, although economic incentives motivate professors and increase publications in universities, it has been demonstrated that they can decrease the quality of the published articles, which increases plagiarism, salami sliced or redundant publications and generates authorship problems.24 This could be solved if incentives are directed to payment for publications in journals with a high impact factor, and with the implementation of surveillance to guarantee scientific integrity.\n\nIn addition, in our study, personal characteristics such as gender or civil status were not associated with scientific production, which coincides with what was reported with evidence.25,26 It is important to mention that significant differences have been reported in terms of female and male scientific production, highlighting the low level of representativity of female scientists in the published articles.27 This contrast could be due to the methodological or sample characteristics’ differences between the present study and the cited studies, although this found difference serves as the basis for questioning why there is still a low level of women’s scientific production. This led us to refocus on the existing gender gaps in the academic and scientific community.28 However, this is different when comparing women’s scientific production by academic areas as reported by Valdespinto-Aberti,29 who found female predominance in pediatrics publications, and by Holman et al.,27 who reported the predominance of female authors in nursing and obstetrician areas.\n\nIn this study we did not find an association between time working as a professor and scientific production, which is similar to what was reported by another study in 2018.26 This could be due to the fact that probably professionals’ research practice is, in many cases, related to pre-professional training. Therefore, independently from the time a professional is practicing as a professor, it will be more complicated that they conduct research if they have not been motivated during their university education. In addition, a study found that younger professors were the ones with the most of scientific production.25 This could probably be due to the fact that this group has a higher level of familiarity with technological resources currently available and which are used for research and by journals, which evidences that the time of teaching practice is not a relevant factor in scientific production.\n\nMoreover, we found that doctoral education is associated with a higher frequency of publications. This finding has already been reported in other studies, in which it was evidenced that the higher academic degree, the higher level of participation in research,28,29 which is related to the objective of doctoral education: to produce new knowledge from research. This shows the importance of scientific preparation in university teachers in order to improve indicators of scientific production. To this end, it is crucial to implement programs and strategies for the promotion and the following of research practices in professors.30,31\n\nThis study had some limitations: 1) the population included was comprised of professors of the Universidad Norbert Wiener, which could not be representative of the totality of the country in regard to socioeconomic characteristics; 2) Assessing scientific production has multiple nuances, which goes beyond the type of journal in which the professor publishes and the H-index, including also the published language and the level of inter-institutional collaboration nationally as well as intentionally; 3) Due to the fact that the instrument was created specifically for this study, it is not possible to directly compare the results with other studies that used instruments with different structure and content. Despite these limitations, this study is one of the first to focus the attention on specific population and, because of that, can serve as a basis for subsequent studies with a wider scope and for decision-making in regard to strategies, programs, and policies that seek to promote and strengthen research in university teachers.\n\n\nConclusions\n\nTo conclude, scientific production is related to being registered in Renacyt, having a doctoral degree, having been a thesis advisor, having facilities to conduct research activities at the workplace, and having been trained in research by the university. These findings are consistent with what was described in the literature and let us know the current situation of professors. Scientific production is low, which has an impact on the educational environment, since professors are not participating in one of the main functions of the university and are not contributing to the development of Peru. Therefore, it is necessary to reinforce the universities’ evaluation systems with respect to university quality standards that allow a better monitoring of professors’ research practice. In addition, wider scope studies should be conducted to know the current situation of professors’ scientific production and its associated factors at a national level. This will enable the implementation of strategies that promote research in professors in order to improve scientific production indicators.\n\n\nData availability\n\nZenodo: Factors associated with scientific production of professors working at a private university in Peru: An analytical cross-sectional study, https://doi.org/10.5281/zenodo.7067303.32\n\nThis project contains the following underlying data:\n\n- Factors associated with scientific production of professors working at a private university in Peru An analytical cross-sectional study.xlsx (All raw data collected).\n\nData from the pilot study cannot be shared in this study, as they are being used for another study that will analyze the psychometric properties of the instruments.\n\nZenodo: Instruments-Factors associated with scientific production of professors working at a private university in Peru: An analytical cross-sectional study, https://doi.org/10.5281/zenodo.7091241.33\n\n- This project contains the following extended data: Instrument.pdf (Combined questionnaires used in study).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nConsent\n\nWritten informed consent for publication of the participants details was obtained from the participants. The approval number by the ethics committee was Exp. No 158-2020.",
"appendix": "References\n\nMayta-Tristán P, Toro-Huamanchumo CJ, Alhuay-Quispe J, et al.: Producción científica y licenciamiento de escuelas de medicina en el Perú. Rev Peru Med Exp Salud Publica. May 13, 2019; 36(1): 106–115. PubMed Abstract | Publisher Full Text Reference Source\n\nYnalvez M, Shrum WM: Professional networks, scientific collaboration, and publication productivity in resource-constrained research institutions in a developing country. Res Policy. Match 1, 2011; 40(2): 204–216. Publisher Full Text\n\nLeon-Gonzales J, Socorro-Castro A, Caeceres-Mesa M, et al.: Producción científica en América Latina y el Caribe en el período 1996-2019. Rev Cuba Med Mil. 2020; 49(3): 573.Reference Source\n\nMorán-Mariños C, Montesinos-Segura R, Taype-Rondan A: Producción científica en educación médica en Latinoamérica en Scopus, 2011-2015. Educ Médica. March 1, 2019; 20: 10–15. Publisher Full Text\n\nScimago: Producción e impacto científico en el mundo.2019.Reference Source\n\nBarros-Bastidas C, Turpo GO: Training in research and its incidence in the scientific production of teachers in education of a public university of Ecuador. Publicaciones. 2020; 50(2): 167–185. Publisher Full Text Reference Source\n\nSola-Martínez T, Díaz IA, María J, et al.: Eficacia del método Flipped Classroom en la Universidad: Meta-Análisis de laproducción científica de impacto. Rev Iberoam sobre calidad, Efic y cambio en Educ. 2019; 17(1): 25.\n\nMamani-Benito O: The Thesis Supervisor as a Coach: an alternative to foster student scientific production. Rev Cuba Educ Médica Super. 2019; 33(1): 1590.Reference Source\n\nBarros-Bastidas C: Formación para la investigación desde eventos académicos y la producción científica de docentes universitarios. Rev Lasallista Investig. 2018; 15(2): 9. Publisher Full Text Reference Source\n\nCastro-Rodríguez Y: Factores que contribuyen en la producción científica estudiantil. El caso de Odontología en la Universidad Nacional Mayor de San Marcos, Perú. Educ Médica. March 1, 2019; 20: 49–58. Publisher Full Text\n\nLimaymanta CH, Zulueta-Rafael H, Restrepo-Arango C, et al.: Análisis bibliométrico y cienciométrico de la producción científica de Perú y Ecuador desde Web of Science (2009-2018). Inf Cult y Soc. December 1, 2020; 43: 31–52. Publisher Full Text Reference Source\n\nMamani-Benito O, Ventura-Leon J, Caycho-Rodriguez T: Publicación científica de docentes que conforman el jurado dictaminador de tesis en una Facultad de Ciencias de la Salud peruana. Rev Cuba Inf en Ciencias la Salud. 2019; 30(0): 1373.Reference Source\n\nCarvajal-Tapia AE, Carvajal-Rodríguez E, Carvajal-Tapia AE, et al.: Producción científica en ciencias de la salud en los países de América Latina, 2006-2015: análisis a partir de SciELO. Rev Interam Bibl. 2019; 42(1): 15–21. Publisher Full Text Reference Source\n\nMoquillaza-Alcántara VH: Producción científica asociada al gasto e inversión en investigación en universidades peruanas. An la Fac Med. March 27, 2019; 80(1): 56–59. Publisher Full Text Reference Source\n\nHerrera-Añazco P, Ortiz-Saavedra P, Taype-Rondán Á, et al.: Prevalencia y factores asociados a publicar artículos científicos durante la residencia médica en Perú. FEM Rev la Fund Educ Médica. 2018; 21(1): 9–16. Publisher Full Text Reference Source\n\nCongreso de la Republica del Perú: Ley No 30220. Perú.2014.\n\nChachaima-Mar JE, Fernández-Guzmán D, Atamari-Anahui N: Publicación científica de docentes de una escuela de medicina peruana: frecuencia y características asociadas. Educ Médica. September 1, 2019; 20: 2–9. Publisher Full Text\n\nBarros-Bastidas C, Turpo GO: La formación en investigación y su incidencia en la producción científica del profesorado de educación de una universidad pública de Ecuador. Publicaciones Fac Educ y Humanidades del Campus Melilla. 2020; 50(2): 167–185.Reference Source\n\nMejia CR, Valladares-Garrido MJ, Almanza-Mio C, et al.: Participación en una sociedad científica de estudiantes de Medicina asociada a la producción científica extracurricular en Latinoamérica. Educ Médica. March 1, 2019; 20: 99–103. Publisher Full Text\n\nAlarcon-Ruiz CA, Quezada MA: Publicación de artículos científicos por asesores de tesis de una Facultad de Medicina. Rev Medica Hered. 16 de octubre de 2018; 29(3): 152–152. Publisher Full Text Reference Source\n\nÑique-Carbajal C, Díaz-Manchay R, Sandoval-Abanto R, et al.: Producción científica de docentes de medicina y enfermería en Google Académico. FEM Rev la Fund Educ Médica. 2021; 24(1): 65–65. Publisher Full Text Reference Source\n\nPereyra-Elias R, Ng-Sueng LF, Toro-Polo LM, et al.: Baja publicación de los trabajos presentados a los Congresos de la Sociedad de Gastroenterología del Perú 1998-2008. Rev gastroeterologia del Peru. 2011; 31(2): 124–132.Reference Source\n\nEscobar-Perez B, Garcia-Meca E, Larran-Jorge M: Factores que influyen sobre la producción científica en Contabilidad en España: la opinión de los profesores universitarios de Contabilidad (II parte). Rev Española Doc Científica. 2014; 37(2): e047. Publisher Full Text Reference Source\n\nCarrell DT, Simoni M: Easier ways to get a publication: the problem of low quality scientific publications. Andrology. January 1, 2018; 6(1): 1–2. PubMed Abstract | Publisher Full Text\n\nPereyra-Elías R, Huaccho-Rojas JJ, Taype-Rondan Á, et al.: Publicación y factores asociados en docentes universitarios de investigación científica de escuelas de medicina del Perú. Rev Peru Med Exp Salud Publica. 2014; 31(3): 3–9.\n\nPulido-Mejia C, Mejia C: Publicación científica de los docentes de medicina en una universidad colombiana: características y factores asociados. Rev Cuba Educ Médica Super. 2018; 32(2): 1–9.Reference Source\n\nHolman L, Stuart-Fox D, Hauser CE: The gender gap in science: How long until women are equally represented? PLoS Biol. April 19, 2018; 16(4): e2004956. PubMed Abstract | Publisher Full Text\n\nAlgarra M, Serrano-Puche J, Rebolledo M: Woman in communication research in Spain: an analysis of scientific production (2007-2013). AdComunica. 2018; 15: 65–87. Publisher Full Text\n\nValdespino-Alberti AI, Alvarez Toca I, Sosa-Palacios O, et al.: Producción científica en la Revista Cubana de Pediatría durante el período 2005-2016. Rev Cuba Pediatr. 2019; 91(2): 571.Reference Source\n\nValles-Coral MA: Vista de modelo de gestión de la investigación para incrementar la producción científica de los docentes universitarios del Perú. Rev Investig Desarro e Innovación. 2019; 10(1): 67–78. Publisher Full Text Reference Source\n\nMillones-Gómez PA, Yangali-Vicente JS, Arispe-Alburqueque CM, et al.: Research policies and scientific production: A study of 94 Peruvian universities. PLoS One. May 1, 2021; 16(5): e0252410. PubMed Abstract | Publisher Full Text\n\nRivera-Lozada O, Bonilla-Asalde CA, Rivera-Lozada IC: Factors associated with scientific production of professors working at a private university in Peru: An analytical cross-sectional study. [Data]. Zenodo.2022. Publisher Full Text\n\nOriana R-L, Cristina R-LI, Antonio BAC: Instruments- Factors associated with scientific production of professors working at a private university in Peru: An analytical cross-sectional study. [Data]. Zenodo.2022. Publisher Full Text"
}
|
[
{
"id": "162954",
"date": "27 Apr 2023",
"name": "Salomon Huancahuire-Vega",
"expertise": [
"Reviewer Expertise Medical education and Public health"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study that measures the association of scientific production with certain personal, academic, and work characteristics of university professors. The study was carried out with professors from a private university in Lima. The manuscript is well organized and written. However, there are some issues that need to be clarified:\nIn the Methods section, design and population of the study subsection, it is mentioned that the study was carried out during the first term of 2021. However, in the Procedures subsection, they mention between September and December 2020. Correct the information.\nThe last two paragraphs of the Procedures section have the same information, that is, they are duplicated. Correct.\nAbout the variable Scientific production. Were editor-letters and editorials not considered publications?\nIf you have access to the databases, why didn't the researchers collect the scientific production data of the university professors directly from the databases? This form would have helped to reduce some memory bias of the participants when completing the questionnaires on scientific production.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "266037",
"date": "06 May 2024",
"name": "Jose Antonio Grandez Urbina",
"expertise": [
"Reviewer Expertise Health Sciences and Regenerative Medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article investigates the factors influencing scientific production among professors at Universidad Norbert Wiener in Lima, Peru, in 2021. It discusses the importance of scientific production for the development of universities and countries, particularly in the context of the Peruvian scientific community's concerns about low scientific output. The study aims to identify factors that contribute to or limit scientific production in higher education institutions. The research employs an observational, analytical, cross-sectional study design with a sample size of 322 university professors. Data collection involved questionnaires addressing academic, personal, and work characteristics, as well as scientific production. Statistical analysis included descriptive analysis, bivariate analysis, and multiple logistic regression.\nKey findings include:\nOnly 40% of professors had published scientific articles in indexed journals. Factors positively associated with scientific production include being registered in Renacyt, holding a doctoral degree, and being a thesis advisor. Personal, academic, and work characteristics such as gender, civil status, time working as a professor, and having a master's degree did not significantly influence scientific production. Challenges identified include limited funding, lack of incentives, and workload hindering research activities.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "266036",
"date": "24 May 2024",
"name": "Boris Salazar",
"expertise": [],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPeer Review of Oriana Rivera-Lozada, ISABEL CRISTINA RIVERA-LOZADA2, and Cesar Antonio Bonilla-Asalde, “Factors associated with scientific production of professors working at a private university in Peru: An analytical cross-sectional study”.\nThe article under review is an attempt to explore the statistical association between the academic, personal and work characteristics of a sample of 332 university teachers from a private university in Peru, and their scientific production. The authors are adamant about their motivations: they know how far from the world’s top-tier scientists’ outputs is the Peruvian scientific production –measured by the number of publications in peer-reviewed journals of the sample of teachers under study, and by their H-indexes— and how a huge share of that gap is related to the absence, in Peruvian universities, of serious and well-funded research training programs for young motivated undergraduate students. Would-be or future university teachers that did not learn from early youth the secrets of scientific research will be in no position to contribute to the training of an increasing number of future scientists in their countries.\nAs the authors avoided the difficulties of causal analysis, they concentrated their efforts in finding the most credible data to measure what they tagged as the “dependent or outcome variable”, that is, the scientific production of the sample of 332 university teachers from the Universidad Norbert Weiner. They had on their side the powerful indexes, processed and provided by different publishing and research organizations, that put into numbers the amount and impact of individual researchers’ scientific publications.\nWhat they denominated as “variables of exposure” were divided in two parts: those belonging to the individuals and those related to the institutional, academic, professional, occupational and working arrangements provided by the university and the Peruvian higher educational system. Regrettably the interactions between these two types of variables were not directly addressed by the authors.\nIn the first part the authors included “the level of English comprehension, database management, reference management, statistical software management, subscription to scientific journals, memberships in scientific societies or groups, research competencies, or thesis advising (p. 4).” These characteristics read as the research endowment of every university teacher: his or her capacities, abilities and competencies for conducting research. Are those endowments inherent to each individual, and to his or her decisions, or are they the result of paths forced upon them by forces beyond their control, including the incentives and institutional arrangements of Peruvian universities and university system?\nThe second part correspond to what they classified as the “work characteristics”: “access to incentives, institutional support, infrastructure, and research funding were assessed, as well as administrative aspects such as employment category, contract type, and number of teaching and non-teaching hours (idem)”. These, of course, reflect the institutional arrangements of both the University of reference and the Peruvian Higher Education system.\nA clear correlation between “the economic situation prevents me from research”, “family load prevents me for research”, heavy “work load prevents me from research” and not “receiving any funding for research”, on the one hand, and no scientific production was clearly detected, with “87.9% not having received any funds for conducting research” (p. 8).\n\nThey also found the 59.6% of the university teachers under study did not have any publication in indexed journals. This finding goes in line with an even more telling discovery: 40.1% of the teachers surveyed did not even know of the existence of the H-index! It is difficult to find a shaper signal of the separate existence of the university teachers surveyed in two different, unrelated worlds: one in which the H-index gives each one of them a place in a hierarchy, and another one in which that index does not even exist because it does not belong into the real lives of those university teachers.\nRegretfully, as I said before, these findings and the interactions between the institutional rules of individual universities and of the Peruvian Higher Education system and the personal traits of the university teachers were not fully exploited in the discussion section of the paper.\nThere is, however, a logistic regression of the professors’ personal academic and work characteristics and their scientific production (p.14) that in some way deals with the interaction issue I raised above. Because they estimated a logistic regression they found what type of characteristics, personal and work related, were probabilistically associated with having a higher scientific production output. It comes as no surprise that the teachers registered in Renacyt, having a doctoral degree, having been a thesis advisor, having facilities for research activities at work and having received training by the universities, are the ones with the highest scientific production in the sample of university teachers from the Norbert Weiner University.\nIt is pretty obvious that this group of teachers belong into the “fat tail” of the distribution of probability of the scientific production of the sample of reference: they are the few chosen, that with a smaller probability, have a large scientific production and an H-index larger that 6. Most of the remaining teachers in the sample have a large probability of having 0 or a very small scientific production. This is not a strange finding, only related to the Norbert Weiner’s teachers. On the contrary, it does reflect the world distribution of probability of the scientific production of university teachers. Only an elite of university teachers concentrates most of the world’s scientific production.\nMy humble recommendation is that the authors give some extra lines to the discussion of the interactions between university teachers’ personal and work traits and the institutional arrangements of the Norbert Weiner University and of the Peruvian University at large. A more nuanced discussion of the findings in page 14 will clearly improve the interpretation and discussion powers of the article.\nIt goes without saying that I recommend this article under review.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
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https://f1000research.com/articles/11-1219
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https://f1000research.com/articles/11-1217/v1
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25 Oct 22
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{
"type": "Research Article",
"title": "Indigenous astronomical knowledge based seasonal weather forecast: evidence from Borana Oromo pastoralists of Southern Ethiopia",
"authors": [
"Abera Bekele Dinsa",
"Feyera Senbeta Wakjira",
"Ermias Teferi Demmesie",
"Tamirat Tefera Negash",
"Feyera Senbeta Wakjira",
"Ermias Teferi Demmesie",
"Tamirat Tefera Negash"
],
"abstract": "Indigenous knowledge is still widely used by communities around the world to overcome social-ecological challenges. Borana Oromo pastoralists of Southern Ethiopia have been searching for future weather phenomena using their indigenous knowledge. This study examines indigenous knowledge-based seasonal weather forecasts through using observable physical and temporal patterns of astronomic objects. Data were generated through using focus group discussion, experimental knowledgeable groups and direct observation in the year 2021. The finding reveals that Borana Oromo pastoralists commonly define physical and temporal outlooks of the Moon that are changed and/ or displayed periodically within a range of varying contexts. The observation of the Moon features have been offering sufficient lapse time in a more than/within ahead of a season/ and is relatively more accurate than the other traditional forecasting objects. The study showed that both temporal and spatial dimensions of the forecasting were actually happened in Ganna (March to May rainfall), Adolessa dry season (June to September) and Hgayya rainfall (October to November) seasons of 2021. This indigenous weather forecasting practices are still regularly used in every livelihood decision making process. However, this indigenous weather knowledge of Borana Oromo pastoralists of Southern Ethiopia is not yet mainstreamed in the formal institutional structures. Curtailments of mobility, severity of drought, weakening of traditional institution, leaving of traditional life style and death of the knowledgeable elders are the major factors that are challenging the potential effects of the indigenous weather forecasting indicators of the features of moon in the study area.",
"keywords": [
"Astronomy Moon",
"Borana Oromo",
"Ethiopia",
"Weather Forecast",
"Indigenous Knowledge"
],
"content": "1. Introduction\n\nIndigenous knowledge (IK) is not a new concept (UNFCCC, 2013; Chand et al., 2014; Ibrahimm, 2020); it has been in existence ‘since humankind’ (Sillitoe and Sillitoe 2006; Bruchac, 2020). However, (World Bank, 2009; Tang, 2012) noted that IK is a wisdom that is unique to a given culture/society with in a given geographical area. In line with this, (SsetteeE, 2007; Fernandez, 2015) argued that IK is an essential survival mechanism: it is the sum total of knowledge and practices based on people’s accumulated experience in dealing with the problems related to all aspects of life system. In this regard, IK practices are not static traditions (Langill, 1999; SsetteeE, 2007; MoSTE, 2015); it is rather complex, holistic, dynamic/changing through adaptive responses to external and internal changes/shocks and have evolved throughout the generations from wisdom distilled in trial and error (Eyong, 2001; Mandaluyong & Donato-kinomis, 2016; Rahman & Rusli, 2017; Ibrahimm, 2020). These characteristics of IK are the driver in formulating cost-effective and participatory adaptation measures/to prepare and respond better to disaster risks (Theodory, 2016; Berkes et al., 2021). The logic behind this is that ‘intrinsic resilience’ is the outcome of indigenous adaptation practices (Kirmayer et al., 2011; Hiwasaki, 2014; Rustomjee, 2015).\n\nIn connection with this (Fernandez, 2015; MoSTE, 2015; Mandayulong et al., 2016; Nakashima et al., 2018), noted that the ancient human civilization/knowledge, technology and practices that are distilled through millennia of experimentations including fire making, domestication of animals and plants, knowledge on cultivation/husbandry, celestial knowledge and etc … which have still multi-dimensional effects on human wellbeing are rooted in IK. Even, in the age of the current modernization/globalization period, IK is functional in all fields of humanity and sustainability science in the forms of literary knowledge, languages, belief, arts, music, science, agriculture, ecological knowledge, engineering and governance, etc. (Eyong, 2001; Mandaluyong & Donato-kinomis, 2016; Lambert & Scott, 2019). Studies assert that IK has value, not only for the culture in which it evolves, but also for those who are striving to improve conditions in rural livelihoods (Apgar & Apgar, 2010; Nakashima et al., 2018; Panampitiya, 2019). Hence, IK cannot be separated into discrete disciplinary departments and time.\n\nPuffer & Associate (1995), Session et al. (2006), Mauro et al. (2010), Lunga (2014) explored that marginalization of the IK worldview was underway since the 12th century with the increasing dominance of the modernization values/cultures. In addition, lack of documentation, influence of modernization, departing of IK based life style and/or death are among the factors that are challenging IK (Saskato, 2010; Apgar & Apgar, 2010; IASG, 2014). However, recently, the role of IK in development is more recognized at all levels in response to increasing multi-hazard/disaster, climate variability and change and as a response to failure of the blue print development planning (UNFCCC, 2013; MoSTE, 2015; Theodory, 2016; David-Chavez, 2019).\n\nHistorically, prediction of seasonal weather and impending disasters have been an integral part of indigenous peoples’ adaptation and resilient strategies which are used to interpret observed natural signals to predict future weather patterns (Rahman & Rusli, 2017; Mosime, 2018; Šakić, 2020; Nyadzi et al., 2021). Still today, indigenous communities in different parts of the world have relied on IK weather forecasting in making agricultural practices, environmental conservation, governance, in disaster risk reduction measures; and to deal with continuum of dynamic aspects of social, political, economic, environmental and technological change in resilience process (Tang, 2012; Ibañez, 2014; Mandayulong et al., 2016; Nakashima, et al., 2018).\n\nIndigenous astronomy is about people’s relationships with the sky, not just about the sky (Willis & Ii, 2011; Lawrence, 2021a). Important aspect of indigenous astronomy is how knowledge about the sky is culturally encoded weather in every daily livelihood decision making (Scofield, 2010; Ruggles, 2015; Lee et al., 2020). Studies posited that even today, the use of indigenous astronomical seasonal weather forecasting information is functional in Africa (Angchok & Dubey, 2006; Holbrook, 2016; Mafongoya and Ajayi, 2017; Chang et al., 2019). In Uganda, Karamoja communities used star relationship with the moon to forecast future weather events (Okonya & Kroschel, 2013; Oruru et al., 2016). Holbrook, (2016) stated that in South Africa indigenous knowledge of changing seasons, lunar cycle, shape, location of the Moon and the stars are used to predict drought. In Zimbabwe, a set of the biotic and abiotic weather forecasting objects are used for agricultural practices (Jiri et al., 2015). Studies in Burkina Faso and Lesotho quoted in (Ifejika et al., 2009) examined that local forecasting knowledge seems to be less widely used than in the past.\n\nApparently, in rural areas of Ethiopia indigenous knowledge practices are still sustained/dominated in all aspects of life and livelihoods making (Workineh et al., 2010; Ibinarriaga, 2020). In connection with this, Borana pastoralists define outlooks of astronomic objects, observe atmospheric characteristics, read physical condition of biotic objects and rememorize the unique and known weather events in each Geda cycle, periodically in the process of future weather forecasting. However, studies and proper documentation have not yet been undertaken to preserve this invaluable indigenous weather indicating knowledge and practices of the Borana Oromo pastoralists. In addition, no area specific study is undertaken on practical experiences of community-based approaches vis-à-vis weather indicating features of the astronomic objects including moon in the study area. Hence, the objective of this paper is to examine indigenous astronomic seasonal weather forecasting knowledge and practices of Borana Oromo pastoralists of southern Ethiopia with insights on the weather indicating features of the Moon. This study is tried to answers three interrelated questions. 1) What are the future weather indicating features of the Moon in the study area?, 2) Is there sufficient lapse time between forecasting and occurrence of the weather events?, 3) Are indigenous weather forecasting practices currently being used by the study community in the process of the livelihood decision making?\n\nCognizant with the above narratives, several scholars have developed definitions of indigenous knowledge in respect of the aspect/contexts of the indigeneity matters consistent with the premise of the disciplines under concern. Hence, it is beyond the theme of this study to thoroughly deliver/articulate all existing debates in the literature. In this regard, owing to the fact that a given IK is embedded/is the reflection of a society within a given specific environmental/geographical area (Tang, 2012); it is better to highlight the definition of the phrase indigenous science and indigenous peoples separately before articulating the definition of the IK to more substantiate the topic under the study. In connection with this, it is believed that Indigenous science and indigenous peoples are the subset of the indigenous knowledge/both are encrusted in IK (Eyong, 2001; Lunga, 2014; Lambert & Scott, 2019). The existing literature classifies indigenous sciences as individual and social/cultural level definitions. In this regard, this study highlights on the social/cultural level, definitions which define indigenous science/ethno science as a culture/society dependent collective rational perceiving of a reality (Theodory, 2016; David-Chavez, 2019). Indigenous science classifies the objects, activities, and events within a given universe. Indigenous science interprets the local world cultural perspective of indigenous agriculture, astronomy, navigation, mathematics, medical practices, engineering, military science, architecture, and ecology, etc. (Scofield, 2010; Siseho, 2013; MoSTE, 2015; Holbrook, 2016; Panampitiya, 2019; Ibinarriaga, 2020). In addition, processes of science that include rational observation of natural events, classification, and problem solving are woven into all aspects of indigenous science (Langill, 1999; Rahman & Rusli, 2017; David-Chavez, 2019).\n\nApparently, it is also beyond the scope of this research to deliver the details of the social science disciplines perspectives scholars’ debate on the issues of the indigenous peoples. In line with this study, it is more applicable to use/adopt the development perspectives definition of the UNPFII studies cited in (UNFCCC, 2013; Rahman & Rusli, 2017; Šakić, 2020) and the World Bank studies cited in (Langill, 1999; Eyong, 2001; SsetteeE, 2007; Burgos-Ayala et al., 2020) that defines indigenous peoples as groups of native inhabitants having their own territory, languages, political system and self-rule, have historical continuity with their neighbors pre-settlers societies, with distinct social and cultural identity; resolve to maintain and reproduce their ancestral environments which are vulnerable/disadvantaged in the development process aftermath of the intrusion of the external cultures/actors. In connection with this (Rajasekaran, 1993; Panampitiya, 2019; Bruchac, 2020), posited that worldwide indigenous peoples speak ‘two-thirds of humankinds’ more than 7,000 known spoken languages and many of these languages are, currently, under use and/or spoken by very few peoples; it is expected that unless protection is maintained, 70 to 90 per cent of these languages will be lost by 2115.\n\nIn regard with this, before inception of defining the phrase indigenous knowledge having the highlight over view of the terms knowledge could help to understand the brief context of the IK. In line with this (Tang, 2012; IASG, 2014; Ibañez, 2014; Theodory, 2016; Aderemi, 2017; Mafongoya and Ajayi, 2017; Šakić, 2020), stated that knowledge is the awareness or understanding of a practical or theoretical thing or fact. It further stated that knowledge embraces knowledge of tools and techniques for assessment, acquisition, transformation, and utilization of resources in the locality (SsetteeE, 2007; Ibañez, 2014; Fernandez, 2015; Mandaluyong & Donato-kinomis, 2016; Ajagbe, 2018; Williams & Sikutshwa, 2020) also noted that it is indigenous because it differs from known forms of formal knowledge (scientific, Western, modern) in the contextual sense (as IK is deeply rooted in its environment, history, and new experiences) and the epistemological nature of IK is holistic. This kind of knowledge remains the information base for a society, which facilitates communication and livelihood decision-making (Apgar & Apgar, 2010; Nakashima et al., 2018; David-Chavez, 2019) attempted to isolate indigenous science from its holistic body of knowledge and reveals that indigenous knowledge bears both scientific and technological threads but in its creation and use it is simply practical/pragmatic knowledge and not ordinarily identified as a science. Thus, understanding and analysis of indigenous science tends to be done with reference to well-established Western modern science (WMS), which people are already familiar with (SsetteeE, 2007; Fernandez, 2015; Mandaluyong & Donato-kinomis, 2016). In synopsis with this, this study adopted, aggregated and synthesize IK definition of mainly IPBES, World Bank and UNPFII studies cited in (Langill, 1999; SsetteeE, 2007; Sirima, 2015) which stated that IK is a multifaceted array of area-specific knowledge; know how, practices, representation of identity and survival strategy, adaptive/dynamic with change and holistic in nature, intergenerational, and which guides societies in their interactions with their surrounding environment. Indigenous knowledge can help build resilience in three ways: increasing the range of available knowledge; providing the basis for adaptations; and enabling social practice and learning (Panampitiya, 2019; Berkes et al., 2021).\n\nAstronomically, theBorana zone is between 3° 31’ 31” to 6° 35’ 37” latitude and 36° 42’ 38” to 39° 45’15” E longitudes (Homann et al., 2008; Lemenih et al., 2011). It is in the southern part of the Oromia regional state Of Ethiopia. Yabello the capital town of Borana Zone is 570 km South of the capital city, Addis Ababa (Tura and Reddy, 2015). It borders Kenya in the South, Somali Regional State and Gudji Zone of Oromia in the East, and the Sidama Region, Southern Nations, Nationalities, and Peoples Region (SNNPR) in the north and west (Godana, 2016). The landscape of the Zone is mainly lowlands with slightly undulating peaks up to 2000 meters above sea level in some areas (Berhanu and Beyene; 2015). The land area is 63,939 km2 (Dalle, 2014; Dirriba et al., 2020). The projected population of the Borana Zone is 1,626,930 (male: 821,733; and female: 805,197) with the majority (97%) living in rural areas; Borana Oromo is the largest community in the area with interconnected Oromo groups of Garba and Burdji (Desta, 2006; Homann et al., 2008; Berhanu, 2011; Demisachew & Abiyot, 2019).\n\nSource: OPC, 2021.\n\nAgro-ecologically, it is semi-arid lowlands and frequently prone to devastating severe drought with an increasing trends (Ambelu, 2015). There are four locally defined seasons in which annual rainfall distribution and the dry period patterns of the study area are bimodal in character (Gebissa Takele, 2015). Mean annual rainfall of the area is between 400 to 700 mm (Berhanu, 2011). In the normal scenario, the long/main rain season (Ganna season rainfall) is between March and May; and the short rain season (Hagayya rainfall) is between September and November (Lemenih et al., 2011; Zewdie et al., 2015). The onset and cessation of both rainfall seasons are often irregular in duration; and are scattered in spatial coverage (Bule, 2021). The warm dry season (Bona Hagayya) is between December and February with high evapo-transpiration rate (Dalle, 2014); and the cool dry season (Bona Adoolessa) is between June and August (Lemenih et al., 2011).\n\nThe main important sources of livelihoods are pastoralism and/or livestock production; under semi-sedentary basis (Tadicha, 2015). Borana pastoralists are known worldwide due to the famous Boran cattle breeds (Desta, 2006). A periodical livestock mobility strategy is the common drought risk mitigation which allow Borana pastoralists to use ecologically/seasonally variable scarce communal natural resources (Mengistu, 2015). The holistic Oromo traditional administration, the Geda system, is still mainly functional among the Borana Oromo community of the Southern Ethiopia. In line with this, traditionally, in the Borana zone of Southern Ethiopia, indigenous weather forecasting knowledge practices and information are the driver/basis of livelihood decision making. Drought, scarcity of water, rangeland degradation, poor market system, lack of infrastructure, weak disaster preparedness, weak service delivery system/lack of strong institution, weakening of the customary indigenous system and lack of pastoral oriented development policy exacerbated the adverse effects of the drought in the area (Godana, 2016; Mohamed, 2019; Dirriba et al., 2020).\n\n\nMethods\n\nAll research subjects and variables under the study were purposively selected to directly reach/explore the major representative samples and quality data in the study area. To easily manage the demeanor of this study, 13 districts of the zone were grouped in to five clusters that were consist of Yabello, Teltele, Gomole, Dirre and Moyale which are based on the proximate of the district to each other for the purpose of this study. Primary data were generated through using focus group discussions, experimental groups, knowledgeable informants, and direct observation. In the present study, indigenous knowledge of astronomical seasonal weather representative variables of observable external physical features of the stars were mainly explored using well experienced elders in the community.\n\nData were collected through using focus group discussion participants, experimental groups and key informant interview participants that were held at the aforementioned clusters. Accordingly, five focus group discussions; each consists of 12 participants (8 males and 4 females) were participated in data generation. Regarding the experimental groups, five groups (clusters) each consists of 4 (a total of 20 participants) well experienced traditional astronomical weather forecasters were used for gathering data. In addition, 10 key knowledgeable informants (6 males and 4 females) were interviewed. During data collection, four local enumerators who have in-depth knowledge of variable under the study were participated in all the steps and phases of the data collection after receiving training on the topic and issues of the study. The first author has more than eight years career experiences and native with the same community in different geographical area. Selection of the participants and formation of the clusters were undertaken in collaboration with the relevant stakeholders/organizations including GOs, NGOs, and community based organization and community representatives.\n\nData were collected in three months lead time of each season. The data were collected in four subsequent rounds/seasons; starting from the seasons of Bona Hagaya (warm dry season of December to February), Ganna (main rainfall season of March to May), Bona Addolessa (cool dry season of June to August) and Roba Hagayyaa (small rainfall season of September to November) of 2021. According to the local calendar of the study area New Year is started on first day of December.\n\nThe details of the data were collected through reading physically/spatially and temporally varied multidimensional outlooks of the weather indicating features of the moon. In this regard, defining, reading and observation of the direction/inclination of the new Moon, cloud surrounding the moon/cloud not surrounding the moon and cloud pattern of the moon were done in the data collection process to know the upcoming season’s weather phenomena in the study area. In connection with this, Borana Oromo abstractly made sequential list of 27 traditional day patterns of the moon which are reconfigured/varied in chronological order with in each of the 12 moon/months of the year, moon day/the day on which new moon is re-emerged in the night sky and rainfall patterns of the moon day, etc. are used in the data collection process of this research. In this research, during defining, reading and observation; ratification of the projection/forecast (mainly normal occurrence of rainfall/severe drought) was established by the experimental groups/experienced traditional weather forecasters upon the interpretation of the future weather indicating features of the moon.\n\nIn connection with this, data were collected in three months lead time of Bona hagayyaa (dry season of December to February), Ganna rainfall season (main rainfall of March to April), Bona Addolessa (cool dry period of June to August) and Hagaya rainfall season (September to Mid-November) of 2021. Finally, verifications of the accuracy/occurrence of the future weather phenomena were done against the projection/established forecast of the future weather indicating features of the moon. In this study, only qualitative data were collected through using semi-structured questioners and open ended interview guides. Finally, data were analysed through using Bazeley (2009) methods of qualitative data analysis techniques.\n\n\n2. Results and discussion\n\nIt is identified through this study that indigenous weather forecasting knowledge is the fundamental driver of the livelihood decision making among Borana Oromo pastoralists of the Southern Ethiopia, since time immemorial. In this regard, in the process of making this in to effects; traditionally, indigenous Borana Oromo community could define, read, and interprets all objects in the easily observable/biosphere/and hardly accessible environment/Universe/to forecast current particular and future weather events in the process of making/ensuring drought resilience.\n\nIt is identified through this study that commonly practiced indigenous based weather forecast indicating objects that are exhibit change naturally with in a continuum of varying temporal/seasonal contexts that are, currently, in use by the study area communities are mainly categorized into astronomic objects, atmospheric characteristics, biotic objects and the Geda cycles/historical experiences.\n\nIn the process of weather forecasting; Borana Oromo pastoralists could regularly define multidimensional outlooks of the astronomic/celestial objects which are displaying varied indicators/signs with in a context of changing spatial and temporal patterns. In this regard, alignment/defect of the alignment/, direction, group formation, color/physical features, size, ray, type, and duration of the observation of the stars in the sky are used in weather forecasting. In connection with this, Borana pastoralists’ abstract sequential list of day patterns of the emerging of the new moon/moon day/, cloud formation/no cloud formation, inclination of each of the new emerging moon and colour pattern of the moon are defined and interpreted in the indigenous weather forecast process. In addition, ring formation, direction/position, size, partial or full eclipse (death) and color/physical features of the sun are regularly defined to indicate either of the fortune/wickedness of the forthcoming season. In addition, it is identified that they could make the prediction through defining characteristics/conditions of the biotic objects that are varying in alignment with temporal patterns and are influenced by the pulling effects of the tell-connections with in the Geo-space (wind circulation, cloud formation, temperatures and lightening with in the land, ocean and atmosphere) of the their environment. In line with this, pastotalists of the study area are accustomed in reading indicators such as Physical condition, physiological features, movement/flying patterns, rhythm/sound and smell of biotic objects; observing of cloud, wind, temperatures and lightening that are varying vis-a-vis with in the temporal and spatial contexts are used in the study area in weather forecasting. Weather Forecasting is also undertaken through using Geda Cycle. There are seven cycles in Geda system. Each cycle has completed in eight years and each cycle of the Geda has its own distinctive name. Each Geda cycle is known by its usual and unique expected weather events which are greatly known in that cycle. Hence, it is possible to forecast weather condition of the coming 40 years through using Geda cycles. This is in consistent with the Studies of (Bruchac, 2020; Zounon et al., 2020) noted that indigenous community in Zambia and Benin use plant, animal, historical experiences and astronomical elements to forecast weather. In Nigeria (JU 2018) argued IK indicators that are used to predict the severe drought are fruits drying/falling off from trees, increasing occurrence of termites, shedding of tree and appearance of rainbows.\n\nAs it is identified through this study, all members of the community have no skill of forecasting upcoming season of weather events from all objects at equal level. In this regard, one do have the skill of forecasting upcoming season of weather events via defining of astronomic objects, others have observe/interprets atmospheric objects/or read physical and physiological condition of biotic objects, etc. Even though, all fathers have shared/transfer/their skill of weather forecasting to all their children, including women without any gender restriction; all the children of a given household/family/do not have capacity, wish and interest to keep all the elements of forecasting signs equally at required level. In connection with this, there are few individuals in the community who are qualified in making accurate forecasting via using a given specific objects in the environment. Individuals those who are qualified in reading internal intestinal structures of livestock are locally called Uchu; those who are qualified in defining physical and temporal features of the moon are locally called ‘Ayyaantu; individuals those who are qualified in identifying the star moon-alignment are called Hedduu and those individuals who are qualified in rememorizing the known events in each Geda cycles are called Arga-dhageti. In this regard, in a village there is one trusted forecaster in each of the aforementioned capacity; an aggregate of total experienced forecaster might range up to 1% (one per cent) of the community in the study area. Although it is the driver of the livelihood decision making at the local level; IK weather forecasting of Borana pastoralists were not mainstreamed in the formal institutional structures.\n\n2.1.1 Weather indicating features of the Moon\n\nIt is identified through this study that, it is a widely common/accustomed/ ordinary traditional practice that any pastoralists in the study areas have regularly searching future outlooks of the seasonal weather phenomena, since time immemorial. In line with this, in the study area; one of the widely used practice of indigenous based weather indicating objects that are exhibit change naturally with in a continuum of varying temporal and/or seasonal and spatial contexts are observable external physical features of the moon. It is identified that Borana Oromo pastoralists regularly define/read physical and temporal outlooks of the moon that are changed and/or displayed periodically with in a range of varying contexts. This is in consistent with the Study in Botswana quoted in Lorreta (2014), posited that it was customary for the ancient people to align their sacred monuments with precise solar, lunar and stellar positions; (Lee et al. 2020) noted that Weather forecasting has been a tool of decision making since millennia. In connection with this Lawrence (2021a), also found that until about 350 years ago scientists and natural philosophers thought that the Sun, Moon and planets play an important role in modulating the weather on Earth.\n\nThe prediction that is set up via the observation of the moon would offer sufficient lapse time in a more than/within ahead of the three months lead time and is more accurate than the other traditional forecasting objects that are, currently, under use in the study area. In addition, this future seasonal weather indicating features of the moon would provide specific spatial dimensions of the weather events within and beyond the Borana zone area in all direction. Especially, future phenomena of the severity and physical distribution of drought; and location specific amount of rainfall in the Borana zone and its surrounding area is easily predicted by using seasonal weather indicating features of the moon. This is agreed with the finding of the Lawrence (2021b), which noted that many village level Astrologers (Pandits) are still predicting highly accurate weather with planet movements in advance of the occurrences of the events which allow people to prepare in disaster risk management.\n\nThese outlooks of the weather indicating features of the moon which are used for making seasonal weather forecasting by Borana pastoralists are categorized in to two major sets of the multidimensional distinctive interrelated patterns. These outlooks of the Moon includes: 1) weather indicating temporal patterns of the moon/patterns of the days of the emerging of the new Moon Locally called ayyaana Ji’aa)1, 2) Weather indicating physical pattern of the moon, In line with this, a physical pattern of the Moon entails four observable indicators during the dry season of Bona Adolessa and Bona Hagaya to make the probable clue of the upcoming rainfall season: Moon with tiny synthesized cloud, Moon with partially synthesized cloud, Moon without synthesized cloud and; the Color patterns of the observable external physical quality/dirtiness of the outlooks of the moon which are changed periodically. The weather phenomena indicating temporal patterns of the moon are categorized in to two interrelated patterns: 1) Day Patterns of the Moon, and 2) rainfall patterns of the day of the new moon. Study of Oruru et al. (2016), explored that indigenous people in Uganda observe moon and stars to predict weather changes.\n\nIn line with this, future weather indicating temporal patterns of the moon are categorized in to two interrelated patterns: 1) Day patterns of the Moon (Tables 1-12), and 2) rainfall patterns of the moon.\n\nDay patterns of the Moon: According to local calendar there are abstractly made 27 distinctive day patterns of a moon which are locally called Ayyaana. The main legends of the temporal patterns of the moon days are to ratify the days on which each new moon are emerging/re-emerging in the night sky. In the study area; each moon has distinctive temporal patterns. This study discover that Borana Oromo abstractly created astronomic based sequential list of 27 traditional temporal patterns of the moon is reconfigured/varied in chronological order with in each of the 12 moon/months of the year. This day/temporal patterns of a new moon have great influence on the upcoming season weather phenomena and livelihood decision making process. This is in consistent with the, Baki study in Botswana quoted in (Loretta, 2014) posited that celestial bodies are used for practical purposes such as timekeeping and in creating accurate calendar; is therefore fundamental in relation to the daily cycle of work as well as the annual round of agricultural activities. In similar with this, study in ancient weather forecasting de-signs (Beardmore, 2013) noted that astronomy, Weather and Calendars are the main methods of weather prediction in the ancient world.\n\nTable 1 discloses sequential lists of the days of a month which are the benchmark/point of a reference for the description of the next 12 Tables. Generation old knowledge of Borana Oromo abstractly created sequential list of 27 traditional day patterns that are derived/developed/based on the lunar cycles of the light and dark nights of the moon in the sky are depicted in the Table 1. These 27 days of a month that are traditionally derived from the lunar cycles of the moon which are reconfigured/varied in chronological order with in each of the 12 moons of the year are used for weather forecasting since time immemorial, in the study area (see all 12 tables).\n\nRemark1, First day of the new moon: As depicted in the Table 1, in the study area; the start/commence of the first day of each moon (in the column 3 of Table 1) begin from the first probable day/as listed in the column 2 of Table 1) on which each particular new moon is expected to re-emerge in the night sky. Out of 12 moons of the year; nine of them have nature driven two probable emerging days as listed in the column 2 of Table 1(which makes them 30 days per month) and three of them have three probable emerging days (which makes them 31 days per month). In this regard, in the study area; for the purpose of annual/monthly calendar commencements of the first date of the new moon are begin from the first probable day of their re-observation in the night sky. However, for the purpose of the seasonal calendar; commencements of the first date of the new moon are beginning from the first actual emerging day of their re-observation in the night sky. Study area community believes that the exact actual first date of the emergence of the new moon has great impact on the upcoming season weather phenomena.\n\nRemark 2, Full Dark Night of the Moon/End Date of each Moon: each moon of a year has one full dark night day. In this regard, there is no observable sign of moon in the night sky on full dark night sky day. This full dark night day is locally called Luwoo which is between the Diba of the current moon and the crescent of the next new moon. Traditionally, this day is expected as the driver of the terrifying events. Hence, it is not listed with in the nature driven locally created abstract sequence of the 27 dates of a moon; and it is silently over passed by the community in the study area. It is the end date of each moon; it is the 30th date for those of the moon having two probable emerging day; and 31st date for those of the moon having three probable emerging day.\n\nRemark 3, Double Count Dates: As stated in the remark one and two of this section; each 12 moon of a year has two/three probable emerging days. Local community believes that each moon of a year has emerging phase (1st to 15th dates) and hidden phase (16th to 30/31th dates) as depicted in the Tables 1–12. In this case, they believed that the first date of the emerging phase of each moon in the column 3 of Table 1 begin from the first probable emerging date that are listed orderly in the column two of Table 1. Similarly, the 30th/31st date of the final hidden phase of each moon is/was completed on the Luwoo day of each moon that was represented by the serial number 30/31 in the column 4 of the Tables 1–12 in this section. This implies that, 1 st, 2nd and 3rd dates are re-counted/double counted in the IK based calendar of the study area. Hence, this study constructed two columns of serial number in all 1–12 Tables that was derived from the benchmark Table 1, in this section. The serial numbers 1 to 27 were listed in the first column of the Tables to orderly count 1st to 27th dates in the emerging phase of the moon. The serial number 28, 29, 30/31were listed in the column 4 of all 1–12 Tables to re-count/double count hidden phase of the moon. This was due to the fact that the two/three probable emerging dates (represented by serial number 1 to 3) of the new moon in the column 2 of 1–12 Tables were recounted in the hidden phase of the dates (represented by the serial number 28 to 30/31) of the end of each moon.\n\nAs depicted here below; all the 12 Tables in this section/seasonal weather indicating temporal patterns of the moon/were derived from the Table 1.\n\nAs it is seen from Table 2, January moon is emerged on the day of Adula duraa. Lunar cycle of 1 st up to 15 thdates of the January moon (Adula duraa up to Maganata jarraa) are locally called the light/bright moon nights of the January Month2. Lunar cycle of the 16th up to 30th dates of the January moon (Maganata biritii up to Adula bal’aa) are locally called the dark moon nights of the January Month. When it is seen, literally January moon has only 29 days. However, it had 30 days. In this case, next to the day of Adula bal’aa/next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of January moon/30 st date of January month. In line with this, because of the January Moon has two probable emerging days which consists of Adula duraa and Adula bal’aa/serial number 1 to 2 in the emerging phase of the moon/the total dates of the January moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the January moon was observed on the date of the Adula bal’aa which was represented by the serial number 29 of the column 4 in the Table 2. The probability of the emerging of the January moon is on the day of Adula duraa (serial number 1) or Adula bal’aa (serial number 2). In this case, there is a common belief that when the January moon is emerged on the day of Adula duraa; the upcoming Ganna rain season (March to May) would be very little/the probability of severe drought would be very high. In the 2021, January moon was emerged on the day of Adula bal’aa instead of Adulaa duraa. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the January Moon of 2021 on the day of Adulaa duraa.\n\nThis is in agreement with the study of Lee et al. (2020) which noted that, the regularity of the motions of celestial objects enabled peoples around the world to create worldviews that is culturally organized systems of knowledge and generations of sky watchers, carefully tracking the positions of the heavenly bodies in order to understand how to conduct the human life on the earth. In addition, study quoted in Loretta (2014) noted that the perspective of the Mapuche people of Chile belief as natural forces govern and regulate the universe. It also stated that there is a very strong connection with nature and the environment in which one lives.\n\nAs it is seen from Table 3, February moon is emerged on the day of Garba Duraa. Lunar cycle of 1st up to 15th dates of the February moon (Garba Duraa up to Salban Duraa) are locally called the light/bright moon nights of the February Month3. Lunar cycle of the 16th up to 31st dates of the February moon (SalbanBall’aa up to Garba Dullacha) are locally called the dark moon nights of the February Month. When it is seen, literally February moon has only 30 days. However, it has 31 days. In this case, next to the day of Garba dullacha/next to serial number 30 in the hidden phase of the double counting within the column 4 of the Table 3/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of February moon/31st date of February month. In line with this, because of the February Moon has three probable emerging days which consists of Garba Duraa, Garba Bal’aa and Garba Dullacha/serial number 1 to 3 in the emerging phase of the moon/the total dates of the February moon are/were 31. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the February moon was on the day of the Garba Dullachaa which was represented by the serial number 30 of the column 4 in the Table 3. Finally, there was one full dark night on which there was completely no moon which is locally called Luwoo of the February moon or the 31st day of the February month. The probability of the emerging of the February moon is on the day of Garba Duraa, Garba Bal’aa and Garba Dullacha. In this case, when the February moon is emerged on the day of Garba Duraa the upcoming Ganna rainfall (March to May) would be very little/the probability of prolonged and severe drought in the Bona addolessa (December to February) would be very high. In the 2021, February moon was emerged on the day of Garba duraa instead of Garba Bal’aa. Furthermore, community believed that when the shower of rainfall is occurred on either days of Gardaduma, Sonsa, Ruruma, Lumasa, Gidada, Arba, Walla, Sorsa, Algajim and Ruda of the February month; the upcoming Ganna rainfall (March to May) would be very little. In this case, shower of rainfall was occurred on the day of Sonsa in February 2021. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the February Moon of 2021 on the day of Garba duraa and occurrence of shower of rainfall on the day of Sonsa.\n\nAs it is seen from Table 4, March moon is emerged on the day of Bita duraa. Lunar cycle of 1st up to 15th dates of the March moon (Bita duraa up to Gardaduma) are locally called the light/bright moon nights of the March Month4. Lunar cycle of the 16th up to 30th dates of the March moon (Sonsa up to Bita bal’aa) are locally called the dark moon nights of the March Month. When it is seen, literally March moon has only 29 days. However, it had 30 days. In this case, next to the day of Bita bal’aa/next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of March moon/30th date of March month. In line with this, because of the March Moon have two probable emerging days which consists of Bita duraa and Bita bal’aa/serial number 1 to 2 in the emerging phase of the moon/the total days of the March moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the March moon was observed on the day of the Bita bal’aa which was represented by the serial number 29 of the column 4 inthe Table 4. The probability of the emerging of the March moon is on the day of Bita duraa (serial number 1) or Bita bal’aa (serial number 2). In this case, there is a common belief that when the March moon is emerged on the day of Bita duraa; upcoming Ganna rain season (March to May) would be very little/the probability of prolonged and severe drought would be very high in the Bona Hagayyaa (dry season of December to February). In the 2021, March moon was emerged on the day of Bita duraa instead of Bita bal’aa. Furthermore, community believed that when the first shower rainfall is occurred on either days of Gardaduma, Sonsa, Ruruma, Lumasa, Gidada, Arba, Walla, Sorsa, Algajim and Ruda of the March month; the Ganna rainfall (March to May) would be very little in its entire dimension. In this case, first shower of 2021 Ganna rainfall (March to May) was occurred on the day of Gardaduma. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the March Moon of 2021 on the day of Bita duraa; and the occurrence of the first shower of 2021 Ganna rainfall (March to May) on the dates of Gardaduma.\n\nThis is in agreed with the study of Scofield (2010) in the ancient Greece weather forecasting de-signs. Hesiod used three counting traditions to describe the various points in the Moon's cycle that are favorable or unfavorable for one activity or another. He first counted the entire cycle, referring to the positive qualities of the first, fourth, and seventh days of the Moon for planting. The first day is being the day on which the crescent appears after the New Moon; about 1 to 15 days after the New Moon. He then shifted into another way of counting the cycle; stating that the sixteenth day of the mid-month is bad for plants. The second cycle is also the 16th day of the Moon/the day after the Full Moon. Study of Beardmore (2013) also supported this study which stated that Hesiod's good and bad days of the lunar month, appears to be a kind of indigenous Greek astrology that offered information for farmers. This justification illustrated as moon days are used for livelihood decision making in the ancient Greece, however, it is yet not stated the future temporal, spatial and features of the future/seasonal/weather indicating outlooks of the moon.\n\nAs it is seen from Table 5, April moon is emerged on the day of Sorsa. Lunar cycle of 1st up to 15th dates of the March moon (Sorsa up to Ruruma) are locally called the light/bright moon nights of the April Month5. Lunar cycle of the 16th up to 30th dates of the April moon (Lumasa up to Algajim) are locally called the dark moon nights of the April Month. When it is seen, literally April moon has only 29 days. However, it had 30 days. In this case, next to the day of Algajim/next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of April moon/30th date of April month. In line with this, because of the April Moon has two probable emerging days which consists of Sorsa and Algajim/serial number 1 to 2 in the emerging phase of the moon/the total days of the April moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the April moon was observed on the day of the Algajim which was represented by the serial number 29 of the column 4 in the Table 5. The probability of the emerging of the April moon is on the days of Sorsa (serial number 1) or Algajim (serial number 2). In this case, there is a common belief that when the April moon is emerged on the day of Sorsa; Ganna rain season (March to May) would be interupted/the probability of severe drought would be very high. In the 2021, April moon was emerged on the day of Sorsa instead of Algajim. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the April Moon of 2021 on the day of Sorsa\n\nAs it is seen from Table 6, May moon is emerged on the day of Arba. Lunar cycle of 1st up to 15th dates of the May moon (Arba up to Gidada) are locally called the light/bright moon nights of the May Month6. Lunar cycle of the 16th up to 30th dates of the May moon (Ruda up to Walla) are locally called the dark moon nights of the May Month. When it is seen, literally May moon has only 29 days. However, it had 30 days. In this case, next to the day of Walla/next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of May moon/30th date of May month. In line with this, because of the May Moon has two probable emerging days which consists of Arba and Walla/serial number 1 to 2 in the emerging phase of the moon/the total days of the May moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the May moon was observed on the day of the Walla which was represented by the serial number 29 of the column 4 in the Table 6. The probability of the emerging of the May moon is on the dates of Arba (serial number 1) or Walla (serial number 2). In this case, there is a common belief that when the May moon is emerged on the day of Sorsa; Ganna rain season (March to May) would be interrupted/the probability of severe drought would be very high. Even though, May moon of the 2021was emerged on its right day on Walla; Ganna rainfall (March to May) was very poor.\n\nAs it is seen from Table 7, June moon is emerged on the Day of Basa dura. Lunar cycle of 1st up to 15th dates of the June moon (Basa dura up to Areeri duraa) are locally called the light/bright moon nights of the June Month Lunar cycle of the 16th up to 30th dates of the June moon (Areeri bal’aa up to Basa bal’aa) are locally called the dark moon nights of the June Month. When it is seen, literally June moon has only 29 days. However, it had 30 days. In this case, next to the day of Basa bal’aa/next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of June moon/30 st date of June month. In line with this, because of the June Moon has two probable emerging days which consists of Basa dura and Basa bal’aa/serial number 1 to 2 in the emerging phase of the moon/the total days of the June moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the June moon was observed on the day of the Basa bal’aa which was represented by the serial number 29 of the column 4 in the Table 7. The probability of the emerging of the June moon is on the day of Basa dura (serial number 1) or Basa bal’aa (serial number 2). In this case, there is a common belief that when the June moon is emerged on the day of Basa dura; the upcoming Hagayyaa rain season (September to October) would be very little/the probability of severe drought would be very high. In the 2021, June moon was emerged on the day of Basa dura instead of Basa bal’aa. Hence, the study community believed that lack of Hagayya rain/severe and devastating drought of 2021/2022 were mainly caused by the nature driven anomalous of the emerging of the June Moon of 2021 on the day of Basa dura.\n\nAs it is seen from Table 8, July moon is emerged on the day of Maganata duraa. Lunar cycle of 1st up to 15th day of the July moon (Maganata duraa up to Adula duraa) are locally called the light/bright moon nights of the July Month Lunar cycle of the 16th up to 31st dates of the July moon (Adula bal’aa up to Maganata biritii) are locally called the dark moon nights of the July Month. When it is seen, literally July moon has only 30 days. However, it had 31 days. In this case, next to the day of Maganata biritii/next to serial number 30 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of July moon/31st date of July month. In line with this, because of the July Moon has three probable emerging days which consists of Maganata duraa, Maganata Jarraa and Maganata biritii/serial number 1 to 3 in the emerging phase of the moon/the total days of the July moon are/were 31. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the July moon was observed on the day of the Maganata biritii which was represented by the serial number 30 of the column 4 in the Table 8. The probability of the emerging of the July moon is on the day of Maganata duraa (serial number 1) or Maganata Jarraa (serial number 2) or Maganata biritii. In this case, there is a common belief that when the July moon is emerged on the day of Maganata duraa; the upcoming Hagayyaa rain season (September to October) would be very little/the probability of severe drought in the Bona Hagayyaa (December to February) would be very high. In the 2021, July moon was emerged on the day of Maganata duraa instead of Maganata Jarraa. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the July Moon of 2021 on the day of Maganata duraa.\n\nAs it is seen from Table 9, August moon is emerged on the day of Salban duraa. Lunar cycle of 1st up to 15th dates of the August moon (Salban duraa up to Garba bal’aa) are locally called the light/bright moon nights of the August Month Lunar cycle of the 16th up to 31st dates of the August moon (Garba dullacha up to Salbaan dullacha) are locally called the dark moon nights of the August Month. When it is seen, literally August moon has only 30 days. However, it had 31 dates. In this case, next to the day of Salbaan dullacha /next to serial number 30 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of August moon/31st date of August month. In line with this, because of the August Moon has three probable emerging days which consists of Salban duraaSalbaan bal’aa, and Salbaan dullacha/serial number 1 to 3 in the emerging phase of the moon with in the column 2/the total days of the August moon are/were 31. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the August moon was observed on the day of the Salbaan dullacha which was represented by the serial number 30 of the column 4 in the Table 9. The probability of the emerging of the August moon is on the day of Salban duraa (serial number 1) or Salbaan bal’aa (serial number 2) or Salbaandullacha (serial number 3). In this case, there is a common belief that when the August moon is emerged on the day of Salbanduraa; the upcoming Hagayyaa rainfall season (September to October) would be very little/the probability of severe drought would be very high. In the 2021, August moon was emerged on the day of Salban duraa instead of Salbaan bal’aa. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the August Moon of 2021 on the dates of Salban duraa. This is supported by the Study in India (Sankar et al. 2019) posited that Many village level Astrologers (Pandits) are still predicting highly accurate weather with planet movements. It also stated that the daily rainfall forecast through Astro-meteorology showed the highest forecast accuracy of 74–87 percent. Apparently study undertaken by Lawrence (2021b) explore that the repeated cycles of the sun, moon, and stars helped to regulate human activity as people strove to make sense of their world and to keep their actions in harmony with the cosmos as they perceived it. Study of (Scofield, 2010) found that early Greece use context of astrological features to best illustrate works and days, the cycle of the year, and the month in the process of agricultural activities.\n\nAs it is seen from Table 10, September moon is emerged on the day of Gardaduma. Lunar cycle of 1st up to 15th dates of the September moon (Gardaduma to Bita bal’aa) are locally called the light/bright moon nights of the September Month Lunar cycle of the 16th up to 30th dates of the September moon (Sorsa up to Sorsa) are locally called the dark moon nights of the September Month. When it is seen, literally September moon has only 29 days. However, it had 30 days. In this case, next to the day of Sonsa /next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of September moon/30th date of September month. In line with this, because of the September Moon has two probable emerging dates which consists of Gardaduma and Sonsa/serial number 1 to 2 in the emerging phase of the moon/the total days of the September moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the September moon was observed on the day of the Sonsa which was represented by the serial number 29 of the column 4 in the Table 10. The probability of the emerging of the September moon is on the day of Gardaduma (serial number 1) or Sonsa (serial number 2). In this case, there is a common belief that when the September moon is emerged on the day the upcoming of Gardaduma; Hagayyaa rain season (September to October) would be very little/the probability of severe drought would be very high.\n\nAs it is seen from Table 11, October moon is emerged on the day of Ruruma. Lunar cycle of 1st up to 15th dates of the October moon (Ruruma up to Algajim) are locally called the light/bright moon nights of the October Month7. Lunar cycle of the 16th up to 30th dates of the October moon (Arba up to Lumasa) are locally called the dark moon nights of the October Month. When it is seen, literally October moon has only 29 days. However, it had 30 days. In this case, next to the day of Lumasa/next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of October moon/30th date of October month. In line with this, because of the October Moon has two probable emerging days which consists of Ruruma and Lumasa/serial number 1 to 2 in the emerging phase of the moon/the total days of the October moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the October moon was observed on the day of the Lumasa which was represented by the serial number 29 of the column 4 in the Table 11. The probability of the emerging of the October moon is on the day of Ruruma (serial number 1) or Lumasa (serial number 2). In this case, there is a common belief that when the October moon is emerged on the day of Ruruma; Hagaya rain season (October to November) would be interrupted/the probability of severe drought in the Bona Hagayyaa (December to February) would be very high. In the 2021, October moon was emerged on the day of Ruruma instead of Lumasa. Furthermore, community believed that when the first shower of rainfall is occurred on either day of Gardaduma, Sonsa, Ruruma, Lumasa, Gidada, Arba, Walla, Sorsa, Algajim and Ruda of the October month; the Hagayyaa rainfall would be very little/interrupted early. Similarly, first shower of 2021 October rainfall was occurred on the day of Ruruma. Hence, the study community believed that severe and devastating drought of 2021/2022 was mainly caused by the nature driven anomalous of the emerging of the October Moon of 2021 on the day of Ruruma; and the occurrence of the first shower of 2021 Hagayya rainfall on the day of Arba. Study of Allen quoted in (Loretta, 2014) posited that indigenous peoples observations of the celestial objects give future clue of the seasonal patterns. This is exactly still functional among the Borana Oromo of Southern Ethiopia.\n\nAs it is seen from Table 12, November moon is emerged on the day of Gidada. Lunar cycle of 1st up to 15th dates of the November moon (Gidada up to Walla) are locally called the light/bright moon nights of the November Month8. Lunar cycle of the 16th up to 30th dates of the November moon (Basa dura up to Ruda) are locally called the dark moon nights of the November Month. When it is seen, literally November moon has only 29 days. However, it had 30 days. In this case, next to the day of Ruda /next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of November moon/30th date of November month. In line with this, because of the November Moon has two probable emerging days which consists of Gidada and Ruda/serial number 1 to 2 in the emerging phase of the moon/the total days of the November moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the November moon was observed on the day of the Ruda which was represented by the serial number 29 of the column 4 in the Table 12. The probability of the emerging of the October moon is on the day of Gidada (serial number 1) or Ruda (serial number 2). In this case, there is a common belief that when the November moon is emerged on the day of Gidada the probability of prolonged/severe drought in the Bona Hagayyaa (December to February) and the scarcity/interruption of rainfall in the upcoming Ganna season (March to May) would be very high in the study area. Hence, the study community believed that the devastating drought of the 2021/202 drought was caused by the anomalous of the emergence of the November moon on the day of Gidada. Similarly (Lehoux, 2021) found that in ancient Greek new and full moons were used to determine general weather conditions. Study of Mcmillan quoted in (Lorettaa, 2014) revealed that Batswana communities have prominent phonological markers of cultural astronomy that signal the change of the seasons; predict droughts as well as weather related diseases by watching the movements of celestial bodies.\n\nAs it is seen from Table 13, December moon is emerged on the day of Areeri duraa. Lunar cycle of 1st up to 15th dates of the December moon (Areeri duraa up to Basa bal’aa) are locally called the light/bright moon nights of the December Month9. Lunar cycle of the 16th up to 30th dates of the December moon (Maganata duraa up to Areeri bal’aa) are locally called the dark moon nights of the December Month. When it is seen, literally December moon has only 29 days. However, it had 30 days. In this case, next to the days of Areeri bal’aa /next to serial number 29 in the hidden phase of the double counting/ there was one full dark night without no sign of moon in the night sky which is locally called Luwoo of December moon/30th days of December month. In line with this, because of the December Moon has two probable emerging days which consists of Areeri duraa and Areeri bal’aa/serial number 1 to 2 in the emerging phase of the moon/the total days of the December moon are/were 30. The Diba (final hardly observable decreased margin in the hidden phase of the moon) of the December moon was observed on the day of the Areeri bal’aa which was represented by the serial number 29 of the column 4 in the Table 13. The probability of the emerging of the October moon is on the day of Areeri duraa (serial number 1) or Areeri bal’aa (serial number 2). In this case, there is a common belief that when the December moon is emerged on the day of Areeri duraa the probability of prolonged and severe drought would be very high in the Hagayya drought season (December to February) and scarcity of rainfall in the upcoming Ganna season (March to May). Hence, the study community believed that the devastating drought of the 2021/202 drought was mainly caused by the anomaly of the emerging of the December moon on the day of Areeri duraa Rainfall Patterns of the Day of New Moon: In the study area it is believed that day of a new moon has decisive factors on the amount and distribution of rainfall. In this case, when the first shower of rainfall is occurred on the day of Salbaan duraa; high rainfall will be expected in that whole season (see Tables 1–12). Similarly, when the first shower of rainfall is occurred on the day of Salban bal’aa, salban dullacha, Basa bal’aa, Areeri dura, Areeri bal’aa and Bitaa bal’aa; sufficient rainfall is expected in that whole season. Similarly, when the first shower is occurred on the day of Basaa duraa; there is no equal physical distribution of rainfall in that particular season for all area of Borana zone. Similarly, when the first shower is occurred on the days of sorsa, algajim, arba, walla, gardaduma, sonsa, ruruma, lumasa, gidada and ruda; rainfall is not sufficient in amount and physical distributions, in the study area.\n\nStudy in Botswana quoted in Loretta (2014) support this current study, disclose that the moon controlled the tides and regulate annual agricultural activities and production. It further stated that months are divided up according to the phases of the moon. The author of the ancient Greece De Signs of weather study quoted in Beardmore (2013) did sketch out a basic time-reckoning system/seasonal calendar that were based on a mixture of stellar, lunar and solar patterns. Astronomical time-reckoning which is tied to a seasonal structure, has been argued and demonstrated in works of (Scofield, 2010). It stated that the first method, used to describe the weather for each quarter of the year, utilizes horoscopes calculated for the new or full Moon that most closely precedes the equinoxes and solstices.\n\nIt is identified through this study that future weather indicating physical features of the Moon are categorized in to three distinctive interrelated features: 1) probable inclination/direction of the first date new moon and, 2) formation of the ring/cloud surrounding the moon, 3) Colour patterns of the moon.\n\nProbable Direction/Inclination of the first date new moon: In connection with this there are three predetermined probable direction of the first date new moon. In this case, 1) when the probable inclination of the first date new moon of December, January and February dry periods are towards south direction; the condition of the upcoming rainfall season is comparatively more favorable to the area in the South direction than elsewhere. In this regard, according to the local community; the benchmark/the reference area of the probable south ward inclination of the first day new moon is Dire district. The upcoming season rainfall will more favorable for the Dire district including the area towards south of Dire such as Moyale and Miyo than the districts of the Borana zone in the other three direction. The inclination of the first day new moon to this direction is mainly to signals Ganna rainfalls (March to May). During such inclination of the moon/towards Dire direction; Finna/condition is more very suitable for cattle in all the dry land areas of Borena. In this regard, in the last Bona Hagaya (December to February) and Bona Addolessa (June to September) of 2021 the first date new moon is not inclined into the southwards as the result Ganna (March to May) and Hagayya rainfall (October to November) of 2021 was very poor in the area south of Dirre district of the Borana zone. This is in consistent with the study of Lawrence (2021) argued there is universal belief that the planets, solar system and their movements around the Earth affected atmospheric conditions and weather.\n\nSimilarly, 2) when the probable inclination of the first date new moon of June, July and August (during early period of the drought season known as Bona Adolessa) are inclined towards North direction; the condition of the upcoming rainfall season will comparatively more favorable to the area in the North direction than elsewhere. In this regard, according to the local community; the local benchmark/the reference area of the probable North ward inclination of the first date new moon is Gomole district. The upcoming season rainfall will more favorable for the Gomole district including the area towards North of Gomole than the other districts of the Borana zone in three directions. This phenomenon was actually happened in Ganna and Hagayya rainfall season of 2021. Ganna and Hagayya rainfall season of 2021 was more favorable to Gomole and area to the North of Gomole district of Borana zone. In the study area, the inclination of the first date new moon towards north direction is mostly used to signals Hagaya rainfall season. In this regard, when the inclination is made towards north direction the upcoming season/condition will be more suitable for Goat and camel than cattle in all the dry land areas of Borena zone. Contrary to this, 3) When the first new moon is emerged towards East direction/upwards during the dry season of bona Adolessa/Bona Hagayya; the upcoming season rainfall will be delayed or the probability of severe drought will be high. Study in Tanzania (Elia 2014) revealed that when a half moon is constantly appearing in north direction it signals rainfall, however, it did not identified the time lapse between observing the indicating features of the moon and the occurrence of rainfall which is very mandatory in making early preparedness.\n\nTiny clouds surrounding the Moon: This study identified six predetermined probable direction through which tiny clouds are surrounding the moon. First) Moon is surrounded with a tiny synthesized cloud; during the dry season of the Bona Addolessa (June to September) and Bona Hagaya (December to February) moon is surrounded by a tiny synthesized cloud. The tiny cloud surrounding the moon is formed on the seventh date of new moon. This sign of the moon is indicating that the upcoming rainfall season will be very promising in its entire dimension i.e. rainfall will be very good in time of initiation, in amount and in physical patterns of distribution. In addition, it indicating that there will be favorable condition in the upcoming season which is locally called Finnaa (enough/sufficient amount of water, pasture and milk). Furthermore, it indicates that there will be no fear of risk of disease (both of human and livestock disease) outbreak and local conflict. The amount of rainfall in the upcoming season will be determined by the physical pattern/direction through which tiny cloud is formed around the moon in the night sky. In line with this, when the Moon is surrounded by tiny cloud while it is on the eastern, mid and western direction of the earth during the very early period of Bona Adolessa/Bona Hagaya it implies that the upcoming season rainfall will be high, medium and small, respectively. This is similar with the study quoted in Beardmore, (2013) which stated that the seemingly celestial is explained by Aristotle as being firmly terrestrial. In addition, the temporal pattern of the Danbala/tiny cloud that is surrounding the moon has its own implication on the upcoming season rainfall. For example, when the moon is surrounded by tiny cloud in October and in April; the upcoming rainfall season of the Ganna (end of February up to May) and Hagaya (end of September up to November) would be very promising in its entire dimension, respectively. Secondly, when a tiny cloud that has a gap/a get/is surrounding the moon during the dry period of Bona Adolessa (June to August) and Bona Hagaya (December to March) will indicating that the forthcoming season (rainfall season of October to November) and rainfall of (March to May) would be very promising, respectively.\n\nIn contrast, thirdly, when a tiny cloud is not surrounding the moon during the dry season of Bona Adolessa/Bona Hagaya/it is indicating that the upcoming rainfall season is too little/the probability of the occurrence of the prolonged drought would be very high. In addition, the moon is stunted/shirked/in physical appearance and looks like reddish in color. Fourthly, when a tiny segment of cloud is observed inside the moon during the dry season it implies that there will be normal occurrence of rainfall in the upcoming season. Fifthly, the direction on which cloud is constructed around the moon has decisive factors on the amount of rainfall of the upcoming season. When the moon is surrounded by (constructed) tiny cloud after 15th dates of new moon while it is on the eastern, mid of the sky and western direction during the dry season it is indicating that the upcoming season rainfall will be very promising, medium and small, respectively. Furthermore, when the moon is surrounded by tiny cloud in October it indicates that the upcoming rainfall season of the Ganna (end of February/March up to May) will be very good in its entire dimension. Similarly, when the moon is surrounded by tiny clouds while it is in the east, mid of the sky and west in April it is indicating that the upcoming rainfall season of the Hagaya (October to November) will be very good in its entire dimension. In contrary to this, study (Elia, 2014) in Tanzania argued that when the moon is surrounded by clouds, the villagers believe that rainfall will be small quantities.\n\nColor patterns of the Moon: In the study area it is believed that when the color of the moon looks white, big, shine, cloudy and shivering during the current particular period of the dry season; it is indicating that the upcoming rainfall season will promising in its all dimension. However, when the color of the moon is dirty and stunted during the current particular period of the dry season; it is indicating that the upcoming rainfall season will be very little. This phenomenon was actually happened in Hagayya and Adolessa dry season of 2021. Study in Tanzania (Lehoux 2021) revealed that the moon’s brightness and its haloes, taken just before and after its significant phases, give weather predictions. Similar studies (Elia 2014) In Tanzania revealed that when farmers observe a halo of light around the moon, they believe as it signifies that the moon is surrounded by water and that this forecasts rain. Study (Oruru et al., 2016) in Uganda among the Baganda clan expect sunshine when the moon is bright red in color. However, both of these studies were not identified the specified lapse time between the observations of the indicators and occurrence of the rainfall.\n\nIn this study it is identified that since time immemorial local community in the study area has far-fetched trust in the role of indigenous weather forecasting practices, especially, in the role of seasonal weather indicating features of the moon in drought resilience. Every daily livelihood activities: management of water and pasture land, mobility, herd splitting, herd diversification, social support and livestock selling and opportunistic crop farming are undertaken depending on the indigenous weather/drought forecasting information that are especially found through defining of weather indicating features of the moon. In addition, they commonly use and believe in its role of prediction/in disaster risk reduction such as drought, flood, disease/pest outbreak and local conflict. In this regard, forecasting based on the weather indicating features of the moon are more accurate and trusted in livelihood decision making process than the other aspects of the astronomic features and/or than the other aspects of the indigenous weather forecasting objects currently, under use in the study area. In line with this, although all members of the community (including children and women) could have basic skill of forecasting weather events; all have not equal capacity, i.e. there are differences among individuals in accuracy of forecasting. In line with this, individuals who have mastered in defining physical and temporal patterns of the moon in the process of forecasting future events including weathers are locally known as Ayyaantu. Currently, curtailments of mobility, severity of drought, weakening of traditional institution, leaving of traditional life style and death of the knowledgeable elders have challenged the potential effects of the indigenous weather forecasting indicators of the features of moon among Borana pastoralists.\n\nStudy of ancient Greece weather signs study (Beardmore 2013) disclose that popular-practical astronomy originating far back beyond the beginnings of writing, and having gained particular traction in Babylonia, where known to have taken place in systematic observations of celestial and meteorological phenomena. It further stated that astro-meteorology as being connected to the weather; it began life bound up with time-reckoning and specific activities. In this regard (Beardmore 2013) posited that regularities formed by the motions of celestial objects provided the necessary context upon which many structural symbolic patterns were built to regulate human activities on the earth.\n\n\n3. Conclusion and recommendation\n\nConclusion: It is identified through this study that since time immemorial indigenous astronomic weather forecasting knowledge is the driver of livelihood decision making among Borana Oromo Pastoralists of Southern Ethiopia. In this regard, physical and temporal and/or probable predetermined day patterns of the emerging of new moon are the main features of the moon that are commonly used by the local community in the process of indicating future weather phenomena. Day patterns of the emerging of new moon is relatively more accurate and is relatively widely used than the other features of moon in weather forecasting in the study area. The prediction that is displayed via the observation of the moon would offer sufficient lapse time in a more than/within ahead of the three months lead time which is sufficient for making early preparedness in advance of the occurrence of the weather/adverse events.\n\nRecommendation: Borana pastoralists have full trust in indigenous weather forecasting knowledge in leading vis-à-vis of their every daily livelihood activities. Hence, the following recommendations are mandatory in demonstrating the full potential of the indigenous knowledge weather forecasting knowledge:\n\n1. It is better to strengthening traditional institutions in order to regain and rehabilitate the full functional capacity of the indigenous weather forecasting knowledge,\n\n2. Borana pastoralists define outlooks of astronomic objects (sun, moon and stars), observe atmospheric characteristics (cloud, wind, temperature, rainfall and lightning), read physical condition of biotic objects (livestock, tree, wild life, birds, social insects, Reptiles etc.) and rememorize the unique and known events in each Geda cycles periodically in the process of future weather forecasting. In this regard, it is advisable to undertake detail in-depth study; and making documentation of the findings of each objects in order to preserve and use this body of knowledge in sustainable manner,\n\n3. It is better to acknowledge and mainstreaming the indigenous weather knowledge in to formal institutional structures and integrate with science to improve its applicability and role in drought resilience.\n\n\nData availability\n\nOSF: Underlying data for “Indigenous Astronomical Knowledge based Seasonal Weather Forecast: Evidence from Borana Oromo Pastoralists of Southern Ethiopia” https://doi.org/10.17605/OSF.IO/4K2QM; archived at https://archive.org/details/osf-registrations-4k2qm-v1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
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Publisher Full Text\n\n\nFootnotes\n\n1 The first day on which each new moon is emerging in the night sky is locally called ayyaana ji’aa.\n\n2 See remarks on the start and end of the counting of the moon dates of a month in this section.\n\n3 The day on which no sign of moon is observed in the night sky.\n\n4 See remarks on the start and end of the counting of the moon dates of a month in this section.\n\n5 See remarks on the start and end of the counting of the moon dates of a month in this section.\n\n6 See remarks on the start and end of the counting of the moon dates of a month in this section.\n\n7 See remarks on the start and end of the counting of the moon dates of a month in this section.\n\n8 See remarks on the start and end of the counting of the moon dates of a month in this section.\n\n9 See remarks on the start and end of the counting of the moon dates of a month in this section."
}
|
[
{
"id": "211167",
"date": "24 Oct 2023",
"name": "Hilding Neilson",
"expertise": [
"Reviewer Expertise Astronomy",
"Indigenous methodologies"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is a valuable discussion of Indigenous knowledges using the Lunar phases as a method for weather prediction. The authors demonstrate and reproduce local Indigenous knowledge for science. This work is important and I urge the journal to accept the article after revisions.\nSome comments:\nThere are grammar mistakes in the article that would benefit from editing.\n\nThere is a lot of information in the Tables indicating temporal patterns that could be represented by a plot or a few plots. The plots could illustrate the days that are double-counted, etc.\n\nThe authors discuss the 12 moons but since the time from New Moon to New Moon is 29.5 days then some years there will be a 13th Moon. How does this fit into the local knowledges?\n\nSimilarly, the timing of a Moon will vary throughout the month depending on the lunar cycle. That is, sometimes, New Moon will be in the beginning of a calendar month and sometimes in the middle of the month. How does this impact the description? By and large, this is not an issue with methodology, but defining the Moon as January Moon of March Moon could confuse the reader, perhaps it would be clearer if the authors write the Moon as the first Moon of the year, second Moon and so on.\n\nThe authors are inconsistent with using a capital 'I' and small 'i' when describing Indigenous peoples, methods, etc.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "211165",
"date": "01 Nov 2023",
"name": "Duane Hamacher",
"expertise": [
"Reviewer Expertise Cultural astronomy",
"Indigenous astronomy",
"Indigenous Science",
"Indigenous Knowledge",
"history and philosophy of science",
"astrophysics",
"ethnography"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis detailed paper dives into the astronomical knowledge of the Borana Oromo pastoralists of Ethiopia, with a focus on lunar calendar systems. It provides a useful and detailed ethnographic analysis of lunar calendars, focusing on a culture that has relatively little published about its star knowledge.\nThe paper goes into some depth, with a well-laid-out focus on lunar calendars and their link to seasonal calendars and weather forecasting, providing a substantial amount of detail and does so within the local cultural framework.\nParticular interest is given to forecasting techniques using the moon, such as haloes, cusp orientation (inclination of the Moon), clouds, and lunar location on the celestial dome. This is one of - if not the most - detailed studies of Indigenous lunar calendars and lunar astronomy in the literature. It represents an invaluable contribution to the study of cultural/Indigenous astronomy and presents a useful case study in cultural science focused ethnography.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "211170",
"date": "17 Dec 2023",
"name": "Jarita C Holbrook",
"expertise": [
"Reviewer Expertise Cultural Astronomy",
"African Indigenous Astronomy",
"Science & Technology Studies"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is a positive contribution to Indigenous weatherlore using the Moon. The social context and the demarkation of the types of expertise with their local names will be helpful for future researchers and those studying other peoples within the region. The authors smartly present three uses of the Moon: 1) on which day the new moon/first crescent falls 2) if and when clouds appear around the moon and 3) the appearance of the moon in terms of colour and 'shivering' (scintillation). There is always the issue of providing more common references (i.e. Gregorian Calendar Months) to understand lunar systems. This may be solved by referencing to other 13 month lunar calendars instead. It is significant that such complicated Indigenous logics are presented in the African context. Of interest is if there are associated tools or artefacts that aid in doing the calendar tasks correctly. The authors present the internal logic of whether the predictions were successful or not, this could be followed up by presenting the rainfall record for the region for 2021.\n\nThere are significant and distracting grammatical errors, thus this article could be improved by having a final grammar edit.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1217
|
https://f1000research.com/articles/8-189/v1
|
15 Feb 19
|
{
"type": "Research Article",
"title": "Correlation of cervical progesterone levels to plasma progesterone levels in normal pregnancy and preterm labor: A cross-sectional study",
"authors": [
"Yuyun Lisnawati",
"Noroyono Wibowo",
"Ana Mariana",
"Noroyono Wibowo",
"Ana Mariana"
],
"abstract": "Background: Theory of “functional progesterone withdrawal” explains the role of progesterone prior to delivery. Previous studies mentioned the existence of progesterone regulation in the cervix that plays a role in maintaining the integrity of the cervix and cervical ripening. Cervical progesterone levels relate to activities of progesterone at the cervix, compared to its amount in circulation. The objective of this study was to measure cervical mucus progesterone levels and its correlation to plasma progesterone levels in pregnancy. Methods: This was a cross sectional study conducted in January-September 2010 at Persahabatan Hospital. The subjects were pregnant woman in the 28th – 34th weeks of gestational age. In total, 72 subjects who met the criteria were divided into normal pregnancy group and preterm labor group. The cervical and plasma progesterone levels were measured using The Advia Centaur® Progesterone kit, which is a commercial immunoassay with direct chemiluminescence method. Results: There was positive correlation (r=0.539) between cervical progesterone levels with plasma progesterone levels in the preterm labor group. There was no correlation between cervical progesterone levels with plasma progesterone levels in the normal pregnancy group. Conclusion: This study showed that cervical progesterone levels could be measured through cervical mucus. A significant positive correlation was found by this study between cervical progesterone levels and plasma progesterone levels in the preterm labor group. This study is expected to provide new insights for understanding the metabolism and the role of progesterone in maintaining cervical integrity during pregnancy, and its relation to prevention of preterm birth.",
"keywords": [
"Cervical",
"Progesteron"
],
"content": "Introduction\n\nPreterm birth contributes long and short-term effects to neonatal health problems. The incidence of preterm birth has not shown a significant decline. About a decade ago, the incidence of preterm birth was reported around 12–13% in United States and 5–11% in developed countries1,2. In Indonesia the rate of preterm birth is 15.5% and is included in the group of 10 countries with the highest preterm birth according to the World Health Organization 20133.\n\nThe hormone progesterone maintains the continuity of pregnancy in order to prevent preterm labor that can cause preterm delivery. Progesterone is a steroid hormone which has important role of maintaining uterine quiescence until the pregnancy reaches term. A recent study stated that circulatory progesterone level in humans remains stable until placenta is born. Nevertheless, the role of progesterone in the onset of labor is still believed to occur through an indirect mechanism called “functional progesterone withdrawal”4,5.\n\nCirculation of progesterone hormones may enter the peripheral tissue such as salivary glands and cervix. Progesterone regulation also occurs in the uterus and cervix. The uterus produces 5α-reductase enzyme and 20α-hydroxysteroid dehydrogenase enzyme (20α-HSD) which converts progesterone into inactive metabolites and decreases the uterine quiescence6. Mahendroo et al.6 showed that in a term rat uterus with 5α-reductase deficiency, the uterus remains to contract although delivery does not happen because there was no cervix maturation.\n\nAndersson et al.7 showed that during pregnancy, cervical glandular epithelial cells produce 17β-hydroxysteroid dehydrogenase (17β-HSD) type 2 enzyme that converts estradiol to estrone and 20α-hydroxyprogesterone (20αP) to progesterone. Approaching delivery, regulation of 17β-HSD type 2 decreases and creates a state that supports cervical maturation. The data on the study by Andersson et al. supports the idea that cervical maturation and myometrial contraction in labor involves regulation of progesterone in the cervix and uterus through the complex relationship between cervical epithelial, stromal, and myometrium7.\n\nProgesterone plasma level is widely studied to monitor the function of the corpus luteum in secretory phase and the beginning of pregnancy. In later pregnancy, progesterone level monitoring is only done for individuals with a high risk of having abortus or preterm delivery, although the effectivity of its application in clinical practice remains controversial8.\n\nAssumption about the reduced quantity of plasma progesterone before delivery is now widely questioned. Currently, the role that progesterone plays before delivery is described as “progesterone functional withdrawal” theory. Prior studies mention that there is progesterone regulation in the cervix, which contributes to preserve cervical integrity as well as cervical maturation6,7. It is assumed that cervical progesterone levels reflect the target organ’s progesterone activity, i.e. the cervix, better than circulatory progesterone. Therefore, measuring cervical mucus progesterone during normal pregnancy and preterm delivery pregnancy needs to be explored. As far as we know, there has been no research that measures levels of progesterone in cervical mucus.\n\n\nMethods\n\nThis study was a cross-sectional correlation study conducted in January 2010 until September 2010 at Persahabatan General Hospital Jakarta, Indonesia.\n\nThe participants are subjects in the 28th – 34th weeks of pregnancy with a single and normal fetus. The subjects were divided into two groups, normal pregnancy and preterm labor, as described in the inclusion criteria.\n\nThe inclusion criteria for this study were as follows: (1) pregnant women at 28th – 34th weeks of pregnancy with single and normal fetus who attended at Persahabatan General Hospital, (2) subjects in normal pregnancy group had no contraction, (3) subjects in preterm labor group had minimal 4 contractions in 20 minutes that was proved by cardiotocography, without amniotic membrane ruptured or blood mucus in cervix, (4) subject willing to take part in research and sign informed consent. The exclusion criteria for this study were as follows: (1) respondents who does not meet the inclusion requirements for this study; and (2) respondents who not willing to be a participant in this study and incomplete of filling informed consent.\n\nTo anticipate differences in progesterone levels every week of gestational age, subgroup analysis was carried out based on gestational age. The subjects of the study were recruited according to three subgroup of gestational age in each group of normal pregnancy and preterm labor: (1) 28 (+0 days) up to 29 (+6 days) weeks, (2) 30 (+0 days) up to 31 (+6 days) weeks, and (3) 32 (+0 days) to 33 (+6 days) weeks.\n\nThe sample size was derived from the formula n= (Zα+Zβ0.5Inx[1+r1−r])2+3, a sample of at least 12 subjects in each subgroup is needed to detect a moderate correlation (r = 0.75) with 80% power and 5% confidence limit, calculated using the hypothesis test formula for Pearson correlation. Based on this calculation, we enrolled 72 participants, 36 subjects in the normal pregnancy group and 36 subjects in the preterm labor group.\n\nIn both group participants, they were given an explanation of the purpose and benefits of the study, and as asked to provide written consent to participate in the study. The written approval sheet was signed by the patient and the researcher. After the patients signed the written approval sheet and also have given the information by the researcher, maternal blood (5 mL) was collected from patients to measure progesterone and cervical plasma. The blood samples were centrifuged on 3000 rpm for 15 minutes to obtain the plasma/serum.\n\nCervical mucus was collected using prism shaped MQA ophthalmic sponge. The speculum was inserted inside the vagina on lithotomy position to visualize the cervix with enough lighting to inspect. The ophthalmic sponge was hold on the base of the prism using long forceps/tweezers and collection of cervical mucus was performed by inserting the ophthalmic sponge into the external orifice of the uterus and hold still for 60 seconds until the sponge absorbs the mucus. The sponge was removed gently and put inside a storage tube, a neutral vacuum tube filled with 1 cc of 0,9% NaCl to store the specimen. The tube was put inside a cooler (2–8°C) within 30 minutes of collection to prevent contamination and the tube was put inside a freezer within 4 hours after collection. Before processing, samples were centrifuged at 16000 g to obtain the supernatant (to separate sample from sponge)9.\n\nThe plasma blood and cervical mucus progesterone levels were measured using The Advia Centaur® Progesterone kit, which is a commercial immunoassay with direct chemiluminescence method. This kit has 0.21 µg/L (0.67 nmol/L) analytical sensitivity. The score used in the analysis were between 0.21 μg/L to 60.00 μg/L.\n\nAfter all the necessary data was collected, the data was coded on pre-arranged coding sheets by the principal investigator. Statistical analyses and data entry were performed using the Statistical Package for the Social Sciences (SPSS), version 20.0. We performed statistical analysis using a Spearman test for measures the correlation or the strength of association between cervical progesterone level and plasma progesterone level in normal pregnancy group and the preterm labor group. The results were presented in tables and figures.\n\nThis study was approved by The Ethics Committee of Persahabatan General Hospital (approval number 01/Diklit-RSP/Kom.Etik/II/2010). The research proposal was submitted and reviewed by the Research Committee, whereby permission was granted to conduct the research. A written letter of consent was submitted to the health institution to seek permission to conduct this study, which was also granted. Privacy and confidentiality of the clients' information was observed through the use of data collection with coded identification numbers. All prospective subjects received an explanation from the main researcher and additional researchers regarding the procedures for conducting research. The decision to follow or refuse to follow the research was taken by informed consent. All data will be kept confidential and the subject had the right to know all the results of the examination carried out.\n\n\nResults\n\nThis study enrolled a total of 72 pregnant women who met the study criteria. They were divided into two groups: 36 women in the normal pregnancy group and 36 women in the preterm labor group. Table 1 shows that there were no significant differences in age distribution, education level and working status between groups. Gestational age grouping was balanced evenly between the two groups.\n\nChi Square test; Unpaired T-test*\n\nData distribution of cervical progesterone levels in normal pregnancy group and preterm labor group were not normal due to extreme values. Table 2 shows that the median of the cervical progesterone level of normal pregnancy group was 1.74 ng/ml, which is lower than preterm labor group (median: 1.91 ng/ml). The range of progesterone levels in the preterm labor group was greater than in normal group. Plasma progesterone levels in both groups had normal data distribution. Mean value of normal pregnancy group was 174.52 ± 59.11 ng/ml, lower than preterm labor group (195.10 ± 82.21 ng/ml).\n\nThe correlation between cervical progesterone levels and plasma progesterone levels in normal pregnancy group were show using a scatter plot graph (Figure 1). Although schematically there was a trend of increasing relationship between cervical and plasma progesterone levels, the statistical test proved that there was no correlation between them (p=0.251; r=0.196). The correlation between cervical progesterone levels and plasma progesterone levels was more visible in the preterm labor group compared to the normal group (Figure 2). The test showed a significant correlation with moderate strength (p=0.001; r=0.539). This result indicated that elevated level of cervical progesterone was directly proportional to plasma progesterone level.\n\nSpearman correlation r = 0.196; p value = 0.251.\n\nSpearman correlation r = 0.539; p = 0.001\n\n\nDiscussion\n\nAs a pregnancy hormone, progesterone is not only metabolized in circulation, but also in the uterus. Previous studies have proven the existence of local regulation of progesterone in uterus and cervix. A term uterus produces an enzyme that convert progesterone into inactive metabolites and decreases the uterine quiescence6,7. In this study, the cervical progesterone level could be measured through the cervical mucus, which was collected using a prism shaped ophthalmic sponge. The data obtained from both groups had abnormal distribution. The range was quite large, especially in the preterm labor group with a median of 1.91 ng/ml (0.37–13.72). The existence of extreme values affected the distribution of data in both groups and caused abnormal data distribution. Some of the possible causes of this abnormal data distribution were bias, which could occur in collecting and processing samples; and examination methods, which still require correction and presence of cervical local factors (such as clinical or subclinical infection) that may affect the regulation of progesterone (which was not explored in this study).\n\nProgesterone is a hormone that plays a dominant role to keep the uterus quiescence during pregnancy. Circulatory progesterone level in humans remains elevated until birth, which refers to the notion of a \"functional progesterone withdrawal”, which occurs before delivery4,5. The definition may also apply to cervical progesterone. Progesterone is inactivated by local regulation of the cervix, not by the quantity of the progesterone hormone. The study by Andersson et al.7 was one study that proved the existence of progesterone inactivation in the uterus and cervix before delivery. Using immunohistochemical methods and quantitative real-time PCR, this study proved the existence of elevation of 20α-hydroxyprogesterone (20αP), an inactive metabolite of progesterone, just before delivery. This elevation was allegedly caused by decreasing concentrations of 17β-HSD type 2 enzyme in endocervical epithelial cells7. The method that we use was different from the methods above. We tried to measure progesterone level from cervical mucus by using competitive immunoassay with direct chemiluminescence method. This may be a limitation of our study.\n\nIn the present study, cervical progesterone levels in the normal group were lower than the preterm labor group. These results were inversely related to the expected hypothesis where cervical progesterone levels in preterm labor group were expected to be lower than the normal pregnancy group. The hypothesis, which was based on the assumption that the cervical mucus was similar with saliva and the study conducted by Connor et al.10 in which it was stated that salivary progesterone concentrations between 24 and 34 weeks of pregnancy were lower in pregnant women who experienced delivery before 34 weeks of gestation compared to pregnant women who experienced delivery after 37 weeks, were not proven in this study. The salivary progesterone levels in the study by Connor et al. were measured serially, while in this study progesterone level were measured one-time. Therefore, to get better data, serial measurements of cervical progesterone level using a good method in the pregnancy group might be needed.\n\nHigh cervical progesterone levels in the preterm labor group in the present study might be caused by an increase of progesterone metabolites in the cervix due to infection process. Infection rates contributed more than 30% as a cause of preterm labor. Mahendroo et al.6 showed conversion of progesterone into inactive metabolites by cervical enzymes before delivery in pregnant rats. Using radioimmunoassay examination technique (RIA), this study detected conversion of progesterone into 5a-pregnan-3,20-dione by steroid 5a-reductase, into 4-pregnen-20a-ol-3-one by 20a-hydroxysteroid dehydrogenase and into 5a-pregnan-3a, 20a-diol by the combined action of two enzymes with 3a-hydroxysteroid dehydrogenase. This present study used a competitive immunoassay technique with direct chemiluminescence method which did not differentiate active progesterone to its inactive metabolite produced in the cervix. Detected progesterone level in cervical mucus possibly includes progesterone and its inactive metabolites and therefore did not reflect the actual activity of cervical progesterone.\n\nIn the normal pregnancy group, although schematically there was a trend of increasing relationship between cervical and plasma progesterone level, the result generated by the correlation test showed that there was no significant correlation with weak strength. Thus, the elevation of plasma progesterone levels was not followed by elevation in plasma progesterone level. Different results were obtained in the preterm labor group: the relationship between cervical progesterone and plasma progesterone were more visible and the result obtained from the test showed a significant relationship as well as moderate correlation strength (r=0.539). This result indicated that the elevation of cervical progesterone level in the preterm labor group was directly proportional to plasma progesterone levels. Differences occurred in both groups require further study. Was it influenced by the regulation of local progesterone that occurs in the cervix? As known from previous studies, the regulation of cervical progesterone during pregnancy was different than before delivery. Would inflammation/infection in the cervix influence cervical and plasma progesterone level? A one-time sample collection was also thought to be possible factor influencing different results of both groups.\n\n\nConclusion\n\nCervical progesterone levels can measured through the cervical mucus. A significant positive correlation was only found between cervical progesterone level with plasma progesterone level in the preterm labor group. This study is expected to provide new insights for understanding the metabolism and the role of progesterone in maintaining cervical integrity during pregnancy, and its relation to prevention of preterm birth.\n\n\nData availability\n\nOpen Science Framework: Correlation of cervical progesterone levels to plasma progesterone levels in normal pregnancy and preterm labor: A cross-sectional study, https://doi.org/10.17605/OSF.IO/YDM9P11.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Grant information\n\nThis work is supported by Hibah PITTA 2018 funded by DRPM Universitas Indonesia No.5000/UN2.R3.1/HKP.05.00/2018.\n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\n\nAcknowledgements\n\nThis work was performed at the Department of Obstetrics and Gynecology, Persahabatan General Hospital Jakarta, Indonesia. The authors wish to thank all staff at the Persahabatan General Hospital Jakarta for supporting us regarding this study\n\n\nReferences\n\nGoldenberg RL, Culhane JF, Iams JD, et al.: Epidemiology and causes of preterm birth. Lancet. 2008; 371(9606): 75–84. PubMed Abstract | Publisher Full Text\n\nWen SW, Smith G, Yang Q, et al.: Epidemiology of preterm birth and neonatal outcome. Semin Fetal Neonatal Med. 2004; 9(6): 429–35. PubMed Abstract | Publisher Full Text\n\nWHO: Preterm Birth [Internet]. 2013; [updated November 2013; cited 2014 October 15]. Reference Source\n\nNorwitz ER, Robinson JN, Challis JR: The control of labor. N Engl J Med. 1999; 341(9): 660–6. PubMed Abstract | Publisher Full Text\n\nSfakianaki AK, Norwitz ER: Mechanisms of progesterone action in inhibiting prematurity. J Matern Fetal Neonatal Med. 2006; 19(12): 763–72. PubMed Abstract | Publisher Full Text\n\nMahendroo MS, Porter A, Russell DW, et al.: The parturition defect in steroid 5alpha-reductase type 1 knockout mice is due to impaired cervical ripening. Mol Endocrinol. 1999; 13(6): 981–92. PubMed Abstract | Publisher Full Text\n\nAndersson S, Minjarez D, Yost NP, et al.: Estrogen and progesterone metabolism in the cervix during pregnancy and parturition. J Clin Endocrinol Metab. 2008; 93(6): 2366–74. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThornton JG: Progesterone and preterm labor--still no definite answers. N Engl J Med. 2007; 357(5): 499–501. PubMed Abstract | Publisher Full Text\n\nCastle PE, Rodriguez AC, Bowman FP, et al.: Comparison of ophthalmic sponges for measurements of immune markers from cervical secretions. Clin Diagn Lab Immunol. 2004; 11(2): 399–405. PubMed Abstract | Publisher Full Text | Free Full Text\n\nConnor ML, Sanford LM, Howland BE: Saliva progesterone throughout the menstrual cycle and late pregnancy. Can J Physiol Pharmacol. 1982; 60(3): 410–3. PubMed Abstract | Publisher Full Text\n\nLisnawati Y: Correlation of Cervical Progesterone Levels to Plasma Progesterone Levels in Normal Pregnancy and Preterm Labor: A Cross-Sectional Study. OSF. 2019. http://www.doi.org/10.17605/OSF.IO/YDM9P"
}
|
[
{
"id": "89602",
"date": "28 Jul 2021",
"name": "Pei F. Lai",
"expertise": [
"Reviewer Expertise Progesterone and cAMP signalling in human myometrium during pregnancy and labour",
"with specific interest in preterm labour."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, the authors highlight that cervical progesterone action during human preterm labour is best characterised by profiling the local (rather systemic) availability of this steroid in pregnant women, which is attributed to the concept of functional progesterone withdrawal. Their aim was to determine whether the correlation in progesterone concentration between maternal peripheral blood plasma and cervical mucus is different between non-labouring and preterm labouring women, when analysed at 28-34 weeks of gestation.\nThe effort made to obtain preterm gestation-matched samples for comparison of non-labouring and labouring women was good. However, the authors need to present more measurements with statistical analyses for their sample groups to sufficiently establish the extent to which local (cervical) progesterone is more important than circulating (blood) progesterone in the manifestation of preterm labour. The relevance of their findings to the clinical efficacy of progesterone prophylaxis for preterm labour prevention (evaluated by several published clinical studies, refer to Romero et al., 20161 and EPPPIC Group, 20212) also requires more detailed consideration to improve the article.\n\nAdditionally, comments for each section of the article are as follows:\nIntroduction:\nLocalised regulation of progesterone metabolism is only one possibility for how functional progesterone withdrawal is mediated. The other (relatively more explored) possibility involves changes in tissue progesterone receptor expression/function irrespective of ligand concentration; this should be acknowledged with the inclusion of relevant references, though only needs to be mentioned briefly because it was not the focus of the authors’ study.\n\nIt would be helpful to explicitly state the hypothesis of the study in the Introduction (rather than give it first mention in the Discussion).\n\nMethods:\nFor the participant inclusion/exclusion criteria, please state whether tocolytics or steroids were administered prior to sample collection. Please also describe the method used to confirm absence of fetal membrane rupture.\n\nFurther detail should be added to Table 1 to make the data more valuable for potential future integration with similar datasets from other sources. For example, gravida, parity, ethnicity, body mass index, history of preterm birth, type of preterm labour (e.g. idiopathic, placental abruption, chorioamnionitis), Bishop score at time of sampling, gestation at fetal delivery, and mode of fetal delivery.\n\nPlease include a citation for the power calculation formula, to explain what each factor in the calculation represents (to help with interpretation by those who are unfamiliar with this specific formula).\n\nThe “300 rpm” centrifugation speed (in first paragraph of the ‘Data collection’ section) needs to be converted to standard relative centrifugal force (g unit).\n\nPlease state whether the blood serum or cervical mucus samples needed to be diluted prior to use at the immunoassay for quantifying their progesterone concentrations; also include mention of any control samples that were used to evaluate assay accuracy.\n\nResults:\nIt is stated in the Methods section that “To anticipate differences in progesterone levels every week of gestational age, subgroup analysis was carried out based on gestational age” – this subgroup consideration is not shown in the data presented, despite it being a good approach. The authors need to either include their findings from this subgroup analysis or explain why they decided not to proceed with it.\n\nFigures 1 and 2 show that progesterone concentrations, in both blood plasma and cervical mucus, for the two participant groups of interest were within very similar ranges to each other; this is in agreement with median values presented in Table 2. Can the authors comment on whether the wider min-max range for cervical mucus samples from the preterm labour group (shown in Table 2) was mostly attributed to the six samples that contained >6 ng/mL progesterone (shown in Figure 2)? Was there anything clinically distinct about these six women, when compared to the other 30 women in the preterm labour group?\n\nDiscussion & Conclusion:\n\nPossible explanations for abnormal data distribution for both participant groups are good. Can the authors add further comment with regards to possibility of infection for both groups of participants, especially whether it was a consideration for their inclusion/exclusion criteria for participant selection?\n\nProgesterone concentration in blood plasma from preterm pregnant women has been quantified in previous studies (e.g. Smith et al., 20093). The authors should add depth to their discussion by commenting on how comparable their dataset is to these previous studies; with consideration of any differences in participant demographics, clinical observations and sampling methodology.\n\nIn the third paragraph, the authors should be more cautious about their interpretation of differences in cervical progesterone concentration between their preterm labour and normal pregnancy groups, especially because they did not present statistical analysis outcome for the corresponding data (Table 2) that shows notable overlap of min-max ranges.\n\nThe authors should provide any technical information regarding cross-reactivity of the immunoassay (in the Methods section), which would help to judge to what extent we should be concerned about “Detected progesterone level in cervical mucus possibly includes progesterone and its inactive metabolites and therefore did not reflect the actual activity of cervical progesterone” (fourth paragraph). Additional assays (ideally using either a different immunoassay kit or methodology) with control samples (of metabolites) should have been undertaken to ascertain accuracy of progesterone quantification, where high cross-reactivity with its metabolites was likely to occur.\n\nThe following sentence needs correcting: “Thus, the elevation of plasma progesterone levels was not followed by elevation in plasma progesterone level” (fifth paragraph).\n\nThe last sentence of the Conclusion is an overstatement until more observations and findings are added to the article. If samples are still available for use, the authors should consider acquiring data for quantification of specific progesterone metabolites (such as those identified in references 6 and 7) to assess whether preterm labour is associated with changes in their concentrations more at the cervix than maternal blood.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "8844",
"date": "25 Oct 2022",
"name": "Yuyun Lisnawati",
"role": "Author Response",
"response": "1. We thank you for the comment and addition to our manuscript. We were also aware to the issues presented. We have added a comparison of both cervical and serum progesterone level between normal pregnancy and preterm labor. However, the resuls were not significant. We have also added the possible reason and the prior studies about the issue. 2. Added to the introduction section 3. The aim of the study and the hypothesis were added to the study. 4. In this study, the tests were performed prior to the tocolytics or steroid administration to ensure that those would not become confounding factors. Furthermore, the absence of fetal membrane rupture was proved by ultrasound examination. Added to the inclusion / exclusion criteria. 5. We agree to the comment. However, we are very sorry to tell you that the details to our demographic characteristics is currently very limited. Therefore, it cannot be added to Table 1. 6. Our calculation was based on the assumption that a moderate correlation would have moderate correlation with serum progesterone. We have changed the section accordingly. 7-8. Revised accordingly. 9. We are very sorry for the mistake in our wording. The sentence has been omitted as the correct process was the normal pregnancy group subjects were matched for age and gestational age to the preterm labor group. 10. We have also observed the phenomenon in our previous discussion. However, there were no clinically significant differences between the subjects and other subjects. 11. Added to the discussion section, especially on the infection being one of the confounding factors in this study. 12-13. Added to the respective section. 14. We are aware of the issue. However, there was no additional examination performed with the same sample. Therefore, we can only explain the issue as a limitation to our study and it should be performed in future studies. 15. Omitted. 16. We agree that the later part of our conclusion is an overstatement. Therefore, it was omitted"
}
]
},
{
"id": "127213",
"date": "21 Mar 2022",
"name": "Charles Bitamazire Businge",
"expertise": [
"Reviewer Expertise Obstetrics and Gynaecology",
"public health",
"micronutrients and cardiovascular disease"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors need to clearly state their hypothesis or study aims. They simply stated that measuring cervical mucus progesterone during normal pregnancy and preterm delivery pregnancy needs to be explored.\nIn paragraph six of the introduction, they noted that “It is assumed that cervical progesterone levels reflect the target organ’s progesterone activity, i.e., the cervix, better than circulatory progesterone”. Hence there seems to be an implied hypothesis that cervical progesterone among women with preterm labour will be lower than that of controls with normal pregnancy. However, the title of their research and the statistical approach used to calculate the sample size do not match with this implied aim/hypothesis. In the discussion, they did not put much emphasis on the correlation between serum and cervical progesterone (as the title suggests) but dwelt more on the difference between the measured levels of cervical progesterone of women with and without preterm birth. This mismatch needs to be addressed.\nAlso, in the introduction, the authors rightly observed that “Assumption about the reduced quantity of plasma progesterone before delivery is now widely questioned. Currently, the role that progesterone plays before delivery is described as “progesterone functional withdrawal” theory.” If their aim was to confirm or refute the hypothesis that it is the absolute reduction of progesterone in cervical stroma instead of ‘functional progesterone withdrawal’ that is crucial in the process of preterm labour, this needs to be clearly stated. In this case, they will use the Mann-Whitney U test to compare the serum progesterone levels and the cervical progesterone levels of the two groups (since the data is not normally distributed). They can then correlate the cervical and serum levels of each group as a secondary aim. This can then be followed by an appropriate discussion of the results as they relate to the aim of the study.\nThe unexpectedly higher levels of serum and cervical progesterone observed by the authors may be due to chance alone given the small sample size. Several related studies have reported that low serum progesterone is associated with preterm labour (Ku et al., 20181; Pratama et al., 20202).\nDespite having high serum and cervical progesterone, some women may be at increased risk of preterm labour due to increased metabolism of progesterone in the target tissues (Patil et al., 20203) or other mechanisms.\nThe authors concluded that their study was expected to provide new insights for understanding the metabolism and the role of progesterone in maintaining cervical integrity during pregnancy, and its relation to the prevention of preterm birth. However, there is no data from their study to support this statement.\nSeveral sentences require editing so as to improve on clarity.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8845",
"date": "25 Oct 2022",
"name": "Yuyun Lisnawati",
"role": "Author Response",
"response": "1. The aim of the study and the hypothesis were added to the study. 2. We thank you for the comment toward our manuscript. We are also aware to the problem and made the changes accordingly 3. The additional statistical test was performed in our study. However, there were no significant difference of both cervical and serum progesterone between study groups. We have also added the discussion to our discussion part. 4-5. Added to the respective section. 6. We are also aware to the issue. The statement has been omitted. 7. Various grammatical errors and confusing sentences were altered accordingly. We hope that our response will sufficiently address your concern toward our manuscript. If you have any other comment or recommendation, please let us know. We thank you once again for your cooperation. Sincerely yours, Yuyun Lisnawati"
}
]
}
] | 1
|
https://f1000research.com/articles/8-189
|
https://f1000research.com/articles/11-1215/v1
|
25 Oct 22
|
{
"type": "Research Article",
"title": "Paediatric critical COVID-19: clinical features and outcomes during five waves.",
"authors": [
"Sameh Ghorbel",
"Samia Tilouche",
"Saima Khenis",
"Manel Marzouk",
"Nejla Soyah",
"Amel Tej",
"Raoudha Kebaili",
"Maroua abdelbari",
"Hajer Benbelgacem",
"Jihene Bouguila",
"Houneida Zaghouani",
"Neila Hannachi",
"Abassi Bakir Dejla",
"Asma Ammar",
"Mansour Njah",
"Jalel Boukadida",
"Lamia Boughamoura",
"Sameh Ghorbel",
"Samia Tilouche",
"Saima Khenis",
"Manel Marzouk",
"Nejla Soyah",
"Amel Tej",
"Raoudha Kebaili",
"Maroua abdelbari",
"Hajer Benbelgacem",
"Jihene Bouguila",
"Houneida Zaghouani",
"Neila Hannachi",
"Abassi Bakir Dejla",
"Mansour Njah",
"Jalel Boukadida",
"Lamia Boughamoura"
],
"abstract": "Background: Data reported from several countries show that both children and adolescents accounted for less than 2% of symptomatic cases of Coronavirus disease 2019 (COVID-19). The study objective was to describe the clinical characteristics of children admitted to Tunisian paediatric intensive care units (PICU). Methods: This was a single centre observational retrospective study conducted in the PICU of the Farhat Hached tertiary teaching hospital in Sousse, Tunisia during the period from the March 1, 2020 to February 28, 2022. We included all children aged from one month to 15 years with recent severe or critical severe acute respiratory syndrome coronavirus 2. Infection was confirmed by the positivity of reverse transcriptase either for SARS-CoV2 or with presence of IgM antibodies. We included severe and critical forms of COVID-19 according to the World Health Organization (WHO) classification. Results: 26 patients were included. 16 (61%) were one year old or younger. 18 patients (69.2%) were male. The median age in our research series was six months [1-156 months]. 17 (65.3%) patients had morbidities including mainly cardiac and neurological diseases. Fever (88.4%) and tachypnea (80.8%) were the most common clinical signs. Leukocytosis, high level of C-reactive protein, D-dimer, troponin, and pro-B type natriuretic peptide levels were found in 17, 8, 10, 6, and 10 cases respectively. Seven patients were initially treated with high-flow nasal cannula and didn't need escalation. Three were intubated. Invasive mechanical ventilation was used in six cases. Antibiotics and corticosteroids were used in 84% and 42.3% of children. The median paediatric intensive care unit length-of-stay was 10.9 days. There were six deaths. Conclusion: Paediatricians should be vigilant to the different clinical manifestations of COVID-19 in children admitted in PICU. Special attention should be allocated to infants under one year of age, of the male gender, and for children with comorbidities.",
"keywords": [
"COVID-19",
"children",
"Critical Care",
"Paediatric Intensive Care Units"
],
"content": "Introduction\n\nOn January 30, 2020, the World Health Organization (WHO) reassessed the potential impact of COVID-19 on global public health and subsequently declared COVID-19 a public health emergency of international concern.1 This pandemic has caused a considerable number of hospitalizations among adults, especially in intensive care units, with many deaths were deplored, especially among the elderly population.1 Current research and data have proven that the clinical forms of paediatric cases are most often minor, moderate, or even asymptomatic,2 however, the disease can evolve into Acute Respiratory Distress Syndrome (ARDS), multi-organ dysfunction, and result in death in children.3 The first severe paediatric case published in China was of a one-year-old infant.4 Tunisian children were spared from severe forms during the first months of the pandemic. After two years of the evolution of the pandemic, publications concerned with severe paediatric forms, involving the vital prognosis, are scarce. The impact of comorbidities on the severity of infection is also controversial.\n\nTo our knowledge, this is the first publication concerned with severe and potentially fatal forms in a Tunisian paediatric population.\n\nThe objective of our study is to describe the clinical, biological, and therapeutic particularities of severe and critical SARS-CoV-2 infection among paediatric patients admitted in a Tunisian intensive care unit.\n\n\nMethods\n\nThis research received ethical approval from the Committee of Medical Ethics and research of the University hospital of Farhat Hached (Sousse/Tunisia) (approval number CER-26-2022).\n\nPersonal information collected would be kept strictly confidential and used solely for the purposes of this study. Consent was waived by the ethical committee as this was a retrospective and descriptive study with medical records.\n\nThis is an observational cross-sectional study conducted in the paediatric department of Farhat Hached hospital of Sousse in Tunisia. Data were collected retrospectively from medical records. We covered the period of two years (from March 1st to February 28th, 2022).\n\nOur hospital is a tertiary teaching hospital composed of 26 medical wards, four surgical wards, and nine laboratories. The paediatric department has a 42-bed capacity of hospitalisation, out of which 10 are dedicated to PICU.\n\nChildren were admitted through the local and regional emergency departments or regional hospital wards belonging to the centre region of Tunisia.\n\nWe included all children aged from one month to 15 years, who had revealed on admission or during the evolution, a severe or critical form of infection with SARS-CoV-2.\n\nCriteria for performing SARS-CoV-2 testing evolved during the study period but predominantly required a febrile respiratory illness, or/and atypical symptoms (acute abdominal pain, diarrhoea …), especially among children with comorbidities and those who require PICU admission.\n\nConfirmation was obtained either by the positivity of the nasopharyngeal reverse transcription-polymerase chain reaction (RT-PCR), and when outside the period of positivity for RT-PCR, using IgM and/or IgG antibodies positive against SARS-CoV-2.\n\nWe excluded patients whose diagnosis of Multisystem Inflammatory Syndrome in Children (MIS-C) was retained on admission.\n\nThe severity of COVID-19 infection was identified according to WHO classification5:\n\n• Severe disease: SpO2<90% on room air, signs of pneumonia, or signs of severe respiratory distress.\n\n• Critical disease: Requiring life-sustaining treatment, sepsis, or septic shock.\n\nWe collected different types of variables as detailed below:\n\n• Demographic variables: Sex, age.\n\n• Clinical variables: comorbidities, close contact tested positive for COVID-19, clinical symptoms at presentation, organ involvement, and dysfunction.\n\n• Biological variables: SARS-CoV-2 rapid test result, Nasopharyngeal RT – PCR, IgM against SARS-CoV-2, and blood tests results.\n\n• Radiological data: chest radiology, CT of the thorax, and echography result.\n\n• Therapeutic variables: type of respiratory support, adjuvant treatment, hemodynamic support, and pharmacological treatment.\n\n• Evolutionary variables: Acute Respiratory Distress Syndrome, Multisystem Inflammatory Syndrome in Children, and Healthcare Associated Infection.\n\nData analyses were performed by Microsoft Excel 2010 and results are presented as numbers (percentages) or median (interquartile ranges [IQRs]) as appropriate.\n\n\nResults\n\nDuring the study period, 125 children’s infected with SARS-CoV-2 were admitted to our department.31 Among these patients, 26 cases (20.8%) were identified as suffering from a severe or critical form of COVID-19. The median age in our series was six months [1-156 months]. 16 infants (61.5%) were under one year old and eight patients (30.7%) were school-age children and adolescents. There were two obese patients, at six and eight years old. Their body mass index (BMI) was 23 and 29 respectively. 17 (65.3%) patients had previous comorbidities. The median duration of symptoms before hospitalization was three days [one-10 days].\n\nThe most common symptoms at admission were fever in 23 cases (88.4%) and cough in 17 cases (65.4%). Polypnea, signs of struggles, and saturation of less than 90% on room air were observed in 21 (80.8%), 13 (50%), and 10 (42.3%) respectively.\n\nOther signs were found as hypotension in four cases (7.8%), tachycardia in nine cases (34.6%), seizures in four children (23.1%) and gastrointestinal symptoms in 11 patients (42.3%) (Table 1).\n\na A patient may have had multiple symptoms and/or comorbidities.\n\nDuring hospitalization, we collected 21 cases of respiratory distress (80.7%), six cases of shock (23%), four cases (15.3%) of heart failure (HF) including three cases occurring on congenital heart disease and one case of high abundance pericarditis complicated by tamponade in a 13-year-old child. Their evolution was rapidly favourable after emergency pericardial drainage, which brought back 700 ml.\n\nNeurological distress was the reason for admission for three patients: one case of status epilepticus, one case of SARS-CoV-2 co-infection with Neisseria meningitides serogroup B, and one case of fatal encephalitis. Two children were admitted with Diabetic ketoacidosis (DKA), which was inaugural in one case. Besides, we have two cases of haematological involvement: an autoimmune haemolytic anaemia and an acute haemolytic crisis in a patient with sickle cell disease (Table 2).\n\nThe diagnosis was confirmed by RT-PCR for 24 patients (92.3%). The other two cases were confirmed by detection of IgM antibodies in the presence of suggestive symptoms. A rapid antigen detection test was maintained for fifteen children before confirmation by RT-PCR and it was recorded positive in 13 cases (86.6%).\n\nChest radiography showed bilateral diffuse alveolar-interstitial infiltrate in nine cases (among 12 performed chest radiography).\n\nGround glass opacities were present in the chest-computed tomography (CT) of 11 patients.\n\nSpecialized echocardiography was performed in 11 cases. It showed a large circumferential pericardial effusion of 35 mm with tamponade in one case (Figure 1).\n\nAdditional laboratory and radiological findings are shown in Table 3.\n\nTwenty four patients (92.3%) required some type of ventilator support. Twelve patients (46.15%) were managed noninvasively. One patient was put on non-invasive ventilation (NIV) at Bilevel Positive Airway Pressure (BIPAP) and then put on high-flow nasal cannula oxygen therapy (HFNC). Ten other children had received HFNC, immediately in five cases and after standard oxygen therapy in five cases.\n\nMechanical ventilation (MV) was initiated in six cases (23%). Intubation was done on the day of admission for three patients. For the other children, it was done during the therapeutic escalation on the fourth, twelfth, and twenty-third days.\n\nAmong those requiring MV, the indication was severe ARDS in three cases, requiring conventional ventilation and then the use of high-frequency oscillation ventilation (HFO), and nitric oxide (NO) (n = 3). The mean duration of MV was nine days [1-27 days].\n\nAntibiotics and corticosteroids were administered to 22 (84%) and 11 (43%) patients respectively. Intravenous immunoglobulin therapies (Ig IV) were administered to five patients: one patient who had ataxia telangiectasia, one patient who had severe myocarditis, and three patients who had presented MIS-C criteria in the course of evolution.\n\nNo patient used specific SARS-CoV-2 treatments like Remdesivir or Hydroxychloroquine.\n\nIntratracheal surfactant instillation at the dose of 50 mg/kg X 3/day was performed in an ARDS that escaped other therapeutic alternatives with an initial good response to treatment (Table 4).\n\na A patient might have one or more complications.\n\nb Acute Respiratory Distress Syndrome.\n\nc Multisystem Inflammatory Syndrome in Children.\n\nd Healthcare Associated Infection.\n\ne Deep vein thrombosis.\n\nARDS was documented in four children (15.3%) of our sample and was severe in all four cases of them. One of these children was supported with NIV then HFNC, the second was initially supported with HFNC and he required escalation to invasive mechanical ventilation. The other two patients were supported at admission with invasive mechanical ventilation.\n\nDeaths occurred in six children, so the mortality rate was 23%. Five of them had comorbidities as congenital heart diseases, West syndrome, hypotrophy, and probable immune deficiency. Concerning the case of probable immune deficiency, we performed an immune assessment which showed a profound and persistent lymphopenia on all lymphocyte lineages with a normal mitogen response to PHA and very weak to anti-CD3, a normal NBT test.\n\nOne infant was hospitalized with critical form, encephalitis, and multisystem organ failure and died the same day (patient 4).\n\nThe role of SARS-CoV-2 in the outcome of (Patient 1, Patient 2, Patient 5, and Patient 6) is uncertain since the length of hospitalization is extended and the children presented other complications. Additional information is shown in Table 6.\n\na Ventricular Septal Defect.\n\nb Acute Respiratory Distress Syndrome.\n\nc Multisystem Inflammatory Syndrome in Children.\n\nd Deep vein thrombosis.\n\ne Healthcare Associated Infection.\n\nf Multi-visceral failure.\n\ng Paediatric intensive care units.\n\n\nDiscussion\n\nIn this study, we report the characteristics and clinical course of 26 severe and critically ill infants and children with COVID-19 hospitalized during the first two years of the pandemic at paediatric department of Farhat Hached Sousse Tunisia.\n\nThe first paediatric publications concluded that the disease was mild.2 Publications of severe and critical paediatric forms, involving the vital prognosis, are still rare. Thereupon, several studies were published in the west demonstrating the characteristics of children infected with COVID-19 and requiring intensive care.6–8 In our series, the percentage of children admitted to intensive care was 20.8% of the total number of children hospitalized for COVID-19. This percentage was higher than the rate reported in a series published earlier in China, which included 2,135 children. In the literature, the rate of admission to the PICU varies from 5.9 to 39% among hospitalized children.2,3,8\n\nAccording to our findings, Chinese publications settled that the majority of serious and critical cases were seen in children under the age of one year.2\n\nThis has important implications and requires amplified monitoring in children less than one year of age. However, we noted that the age group of one to five years was the less affected. This result was observed in North America.6 Consistent with other series, our study found that school-aged children and adolescents exceed 30% of patients hospitalized for COVID-19 in PICU.6,8\n\nWe noted in our series the predominance of the male gender. One key discovery in understanding the mechanism of SARS-CoV-2 infection involves the role of the transmembrane serine protease 2 (TMPRSS2), MPRSS2 is a critical factor enabling cellular infection by SARS-CoV-2. Some authors put forward the hypothesis that the modulation of its expression by sex steroids could contribute to the male predominance of severe infection.9 A preponderance of the male gender was noted in the paediatric series of Chao et al. (67.4%)7 and Shekermedian (80%)6 but Tsabouri et al., concluded that male sex is not an independent risk factor for severity in children.10\n\nMoreover, multicentre studies have described high rates of comorbidities in children hospitalized in PICU with COVID-19.11 Congenital heart disease was communal in our series, followed by neurological and endocrine aetiologies. These comorbidities were predominant in severe cases in the series of the literature.12,13 The hypotheses proposed to explain the severity of COVID-19 in children with congenital heart disease by: the destructive effect of COVID-19 on the heart,13 the poor prognosis of influenza and other viral respiratory diseases in these children,14 and the fact that many of these patients may have concomitant abnormalities in other organs, such as the lungs and kidneys.15 On the other hand, the severity of these forms in children who have neurologic disorders could be attributed to the decrease in muscle tone and strength, mobility alteration or structural conditions.16 Early studies have shown that individuals at high risk of metabolic dysfunction appeared at higher risk for complications, but the relationship between diabetes and COVID-19 is still not well understood. Instead, a new hypothesis has emerged, which suggests a bidirectional relationship between diabetes and COVID-19.17\n\nAs was expected, in our study, and in published studies, the most common presenting symptoms were fever followed by lower respiratory tract symptoms in more than 60% of children.8\n\nLikewise, COVID-19 can progress to ARDS and multi-organ dysfunction. To emphasize, respiratory and cardiovascular involvement were predominant in our series. In our series, we noted four cases (15.3%) of ARDS. This was similar to that observed in paediatric COVID-19 patients admitted to intensive care units in Brazil (13%).8 In our series, only one child did not need MV and was supported with NIV and HFNC. In general, SARS-CoV-2 ARDS is described as an atypical form of ARDS. The main characteristic is the dissociation between relatively well-preserved pulmonary compliance and the severity of hypoxemia.18 In our series, we found that respiratory and hemodynamic distress were the main indications for ICU hospitalization. Fisler et al., have found that hypoxia, hemodynamic instability, pneumonia, or ARDS were the most frequent indications for PICU admission.3\n\nPaying attention to the two cardiovascular manifestations of the patients of our series: Tamponnade and myocarditis. Pericarditis complicated by tamponade has been described even in children with COVID-19.19 The pathogenesis of tamponade secondary to COVID-19 is still unknown. Two mechanisms could be incriminated. The first one: cardiac affinity of the virus which could be explained by the direct binding of the S protein of SARS-CoV-2 to the human angiotensin converting enzyme 2 present in the human heart, allowing a cellular infection.20 The second mechanism: the cytokine storm triggered by an imbalanced response of type 1 and type 2 helper T cells.21\n\nMyocarditis is a cardiac manifestation that was also observed in our study. The mechanism of cardiac injury is not well defined, but it might be caused by direct myocardial infection, hypoxemia, and indirect injury due to systemic inflammatory response. Myocardial necrosis and endothelial involvement were found in biopsies performed in post-mortem. Given that, pathological processes included direct myocardial injury through virus binding to ACE2, systemic inflammation, and altered myocardial demand-supply ratio.22\n\nSince our series is unusual by the diversity of manifestations extrapulmonary, we have identified neurological symptoms, which ranged from non-specific or specific mild symptoms such as altered state of consciousness and seizures. For neurological distress, in the series of Qiu et al., refractory seizures were the main causes of admission to PICU.23 Two infants had encephalitis. An autopsy report has documented the presence of SARS-CoV-2 in the brain tissue of a COVID-19 patient. Thus, there is no definitive conclusion on the mechanisms of SARS-CoV-2 neuro-invasion. These proposed mechanisms include direct viral invasion, systemic blood circulation, or distribution of infected immune cells.24\n\nOne patient had a Meningococcal meningitis and COVID-19 co-infection.\n\nBacterial coinfection is more common in paediatrics, particularly for pneumococcus and meningococcus. The frequent carriage of the bacteria explains coinfection with meningococci at this age. However, the mechanism is not yet known. Bacterial co-infection with meningococcus was also reported in a 22-year-old woman.25\n\nIn our series, two children were hospitalized with severe DKA. A descriptive study carried out in Germany resolved that there was a significant increase in the frequency of diabetic decompensation in the area of COVID-19 in children newly diagnosed with type 1 diabetes.26 SARS-CoV-2 can trigger severe DKA for people with new-onset diabetes. However, at present, there is no perceptible evidence that SARS-CoV-2 induces type 1 diabetes.27\n\nManagement is essentially symptomatic. With the acquisition of experience in the management of COVID -19 patients, clinicians realized that the mortality on invasive ventilation was high and that when HFNC is used with precautions, it avoids intubation.28 Until now, the use of ONHD in case of ARDS complicating SARS-CoV-2 infection in children is exceptional. In a study carried out in the United States of America, seven children with ARDS were initially treated by HFNC, four had subsequently required mechanical ventilation.7 HFNC could have a central role in improving the disease. We need more data and guidelines. Patients treated with HFNC should be closely monitored to detect the need for therapeutic escalation and mechanical ventilation. Patients in our study did not receive Remdesivir or Tocilucimab. Remdesivir was not available in Tunisia and Tociluzimab did not have marketing authorization in paediatrics. We tried exogenous surfactant treatment for our 1-month-old patient with ARDS. In the literature, surfactant was effective in the treatment of ARDS in combination with other therapeutic measures.29,30\n\nMortality was marked high in our series (23%)compared with the initial paediatric reports.2,6–8\n\nOur study has important strengths. First, it is the first Tunisian paediatric series of severe and potentially fatal cases of COVID-19 reported. Secondly, this series is representative of the centre region of Tunisia, as our hospital covers most of the Tunisian central region.\n\nThe main limitation of our study was its cross-sectional design, which does not allow prospective surveillance of patients. Secondly, there is a diversity of factors explaining the severity of COVID-19, which can be related not only to patient-related factors but also to extrinsic factors.\n\n\nConclusion\n\nPaediatric patients represent a small percentage of all severe and critical SARS-CoV-2cases in the general population. Nevertheless, paediatricians must be vigilant. Our study highlighted the large spectrum of vital clinical presentations as well as the significant occurrence of potentially fatal paediatric cases.\n\nCareful monitoring and early intervention are necessary for an infant less than one year of age and in the presence of comorbidities. We hope that this series will help manage other similar patients with the same conditions. Prevention measures are also necessary to prevent the spread of COVID-19, with the need to protect children who are vulnerable and have comorbidities.",
"appendix": "Data availability\n\nZenodo: Paediatric critical COVID-19: clinical features and outcomes during five waves. https://doi.org/10.5281/zenodo.7133628. 31\n\nThis project contains the following underlying data:\n\n• Severe covid pediatric.sav (anonymised underlying data collected from patient records for this study)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nWorld Health Organisation (WHO): Coronavirus 2019(COVID-19), situation report-38.27 February 2020.Reference Source\n\nDong Y, Mo X, Hu Y: Epidemiological characteristics of 2143 pediatric patients with 2019 coronavirus disease in China. J. Emerg. Med. 2020; 58(4): 712–713.\n\nFisler G, Izard SM, Shah S, et al.: Characteristics and risk factors associated with critical illness in pediatric COVID-19. Ann. Intensive Care. 2020; 10(1): 171. PubMed Abstract | Publisher Full Text\n\nChen F, Sheng LZ, Rong ZF, et al.: First case of severe childhood novel coronavirus pneumonia in China. Chinese Journal of Pediatrics. 2020; 5–5.\n\nWorld helath Organisation (WHO): Orientations évolutives concernant la prise en charge clinique de la COVID-19.Reference Source\n\nShekerdemian LS, Mahmood NR, Wolfe KK, et al.: Characteristics and Outcomes of Children With Coronavirus Disease 2019 (COVID-19) Infection Admitted to US and Canadian Pediatric Intensive Care Units. JAMA Pediatr. 2020; 174(9): 868–873. PubMed Abstract | Publisher Full Text\n\nChao JY, Derespina KR, Herold BC, et al.: Clinical Characteristics and Outcomes of Hospitalized and Critically Ill Children and Adolescents with Coronavirus Disease 2019 at a Tertiary Care Medical Center in New York City. J. Pediatr. 2020; 223: 14–19.e2. 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Pediatr. 2020; 27(5): 235–238. PubMed Abstract | Publisher Full Text\n\nInciardi RM, Adamo M, Lupi L, et al.: Characteristics and outcomes of patients hospitalized for COVID-19 and cardiac disease in Northern Italy. Eur. Heart J. 2020; 41(19): 1821–1829. PubMed Abstract | Publisher Full Text\n\nGeskey JM, Cyran SE: Managing the Morbidity Associated with Respiratory Viral Infections in Children with Congenital Heart Disease. Int. J. Pediatr. 2012; 2012: e646780.\n\nRosa RCM, Rosa RFM, Zen PRG, et al.: Congenital heart defects and extracardiac malformations. Rev. Paul. Pediatr. juin. 2013; 31(2): 243–251. PubMed Abstract | Publisher Full Text\n\nWoodruff RC, Campbell AP, Taylor CA, et al.: Risk Factors for Severe COVID-19 in Children. Pediatrics. 2022; 149(1): e2021053418. PubMed Abstract | Publisher Full Text\n\nThe Lancet Diabetes Endocrinology null: COVID-19 and diabetes: a co-conspiracy? Lancet Diabetes Endocrinol. 2020; 8(10): 801. Publisher Full Text\n\nGattinoni L, Coppola S, Cressoni M, et al.: COVID-19 Does Not Lead to a « Typical » Acute Respiratory Distress Syndrome. Am. J. Respir. Crit. Care Med. 2020; 201(10): 1299–1300. PubMed Abstract | Publisher Full Text\n\nRaymond TT, Das A, Manzuri S, et al.: Pediatric COVID-19 and Pericarditis Presenting With Acute Pericardial Tamponade. World J. Pediatr. Congenit Heart Surg. 2020; 11(6): 802–804. PubMed Abstract | Publisher Full Text\n\nJin Y, Yang H, Ji W, et al.: Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses. 2020; 12(4): E372.\n\nWong CK, Lam CWK, Wu AKL, et al.: Plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome. Clin. Exp. Immunol. 2004; 136(1): 95–103. PubMed Abstract\n\nHaryalchi K, Olangian-Tehrani S, Asgari Galebin SM, et al.: The importance of myocarditis in Covid-19. Health Sci. Rep. 2022; 5(1): e488. PubMed Abstract | Publisher Full Text\n\nQiu H, Wu J, Hong L, et al.: Clinical and epidemiological features of 36 children with coronavirus disease 2019 (COVID-19) in Zhejiang, China: an observational cohort study. Lancet Infect. Dis. 2020; 20(6): 689–696. PubMed Abstract | Publisher Full Text\n\nGasmi A, Tippairote T, Mujawdiya PK, et al.: Neurological Involvements of SARS-CoV2 Infection. Mol. Neurobiol. 2021; 58(3): 944–949. PubMed Abstract | Publisher Full Text\n\nGallacher SD, Seaton A: Meningococcal meningitis and COVID-19 co-infection. BMJ Case Rep. 2020; 13(8): e237366. PubMed Abstract | Publisher Full Text\n\nKamrath C, Mönkemöller K, Biester T, et al.: Ketoacidosis in Children and Adolescents With Newly Diagnosed Type 1 Diabetes During the COVID-19 Pandemic in Germany. JAMA. 2020; 324(8): 801–804. PubMed Abstract | Publisher Full Text\n\nBoddu SK, Aurangabadkar G, Kuchay MS: New onset diabetes, type 1 diabetes and COVID-19. Diabetes Metab. Syndr. 2020; 14(6): 2211–2217. PubMed Abstract | Publisher Full Text\n\nRimensberger PC, Kneyber MCJ, Deep A, et al.: Caring for Critically Ill Children With Suspected or Proven Coronavirus Disease 2019 Infection: Recommendations by the Scientific Sections’ Collaborative of the European Society of Pediatric and Neonatal Intensive Care. Pediatr. Crit. Care Med. 2021; 22(1): 56–67. PubMed Abstract | Publisher Full Text\n\nCattel F, Giordano S, Bertiond C, et al.: Use of exogenous pulmonary surfactant in acute respiratory distress syndrome (ARDS): Role in SARS-CoV-2-related lung injury. Respir. Physiol. Neurobiol. 2021; 288: 103645. PubMed Abstract | Publisher Full Text\n\nVeldhuizen RAW, Zuo YY, Petersen NO, et al.: The COVID-19 pandemic: a target for surfactant therapy? Expert. Rev. Respir. Med. 2021; 15(5): 597–608. PubMed Abstract | Publisher Full Text\n\nSameh G, Samia T, Saima K, et al.:Paediatric critical COVID-19: clinical features and outcomes during five waves. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "155825",
"date": "02 Dec 2022",
"name": "Franco Diaz-Rubio",
"expertise": [
"Reviewer Expertise Pediatric Critical Care"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a small case series of a single PICU over two years, describing 26 patients.\nFirst, the title is misleading because it highlights “during five waves”. The authors don’t discuss this topic in the manuscript. Maybe “over the first two years of the pandemic” is more appropriate.\nBackground section:\nEssential references are missing (suggested references are listed below). Thus “publications concerned with severe paediatric forms, involving the vital prognosis, are scarce” is an overstatement.\n\nThe geographical location should not be the main objective of the research. Especially because the authors don’t discuss “particularities of severe and critical SARS-CoV-2 infection” … “in a Tunisian intensive care unit”.\n\nMethods:\nThe ethics statement is confusing. It seems to me that the study is a retrospective review of medical records. In most countries a specific informed consent is required for access to medical records by non-treating physicians, either for research or for clinical evaluations. If the IRB waived informed consent, please upload the full document. I know it may change in different countries and institutions.\n\nA “retrospective chart review” is probably more appropriate to describe the study.\n\nInstead of sample recruitment, I’d write inclusion criteria.\n\nAlso, exclusion criteria need to be clearly defined.\n\nPlease add the criteria used for MIS-C diagnosis.\n\nPlease add the authors' interpretation of IgM +/IgG+ and IgM-/IgG+ serology. Was there serology or multiple COVID-19 tests when initial rt-PCR was negative, and COVID-19 clinical suspicion persisted? Please clarify if SARS-CoV-2 rt-PCR or serology was taken when the rapid antigen test was positive or negative.\n\nThe statistical analysis is insufficient. Comparisons between groups are needed. i.e., dead vs. alive; shock vs. no-shock; vs. respiratory failure; critical vs. non-critical.\n\nThat would give an idea of the differences between clinical phenotypes.\n\nResults:\nOverall, case descriptions are very detailed, adding important information to the current knowledge. Table 6 is very informative.\n\nIn these case descriptions, I think there is an inadequate phenotype description.\n\nWhat were the diagnosis and the leading cause of admission to PICU? It seems that many patients developed MIS-C after admission. I would not classify these cases as complications.\n\nIt would be interesting to organize the cases in MIS-C vs. Respiratory failure vs. Neuro-COVID. (Similar to table 5) and analyze the differences in clinical presentation and outcomes.\n\nDiscussion:\nIt is well structured, and the authors explain the main findings of their study.\n\nAlthough, analytic results are mandatory to address differences and similarities with other large cohorts adequately.\n\nLimitations:\nPlease add the retrospective nature of the study - also, the risk of type II error due to a small number.\n\nMinor comments:\nLanguage editing is necessary. Wording and non-usual medical terms make the manuscript difficult to read.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "157116",
"date": "21 Dec 2022",
"name": "Philippe Jouvet",
"expertise": [
"Reviewer Expertise Pediatric Intensive Care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nS Ghorbel et al. Report a retrospective single center cohort study (n=26) in a Tunisia Pediatric Intensive Care study conducted on a 2 years period. They report a high mortality rate (6/26) and conclude that paediatricians should be vigilant to the different clinical manifestations of COVID-19 in children admitted in PICU with a special attention allocated to infants under one year of age, of the male gender, and for children with comorbidities. The authors wrote a very detailed report. However methodology, results and discussion need further work.\nMajor comments\nTitle: Change Title as it is a review on a 2 years period but no description of the different waves.\nAbstract: Specify if there was a protocol or not for the management of COVID patients in the PICU\nMethodology section:\nAuthors wrote page 3: ‘We included all children aged from one month to 15 years, who had revealed on admission or during the evolution, a severe or critical form of infection with SARS-CoV-2’. Is there any patient not admitted in PICU included in the study? It is unclear. Whatever the answer is, could you detail PICU admission criteria? This is crucial for reader. In North American PICUs, mortality rate in below 5%.\n\nThe management of the patients is difficult to compare as the resources available in the Tunisia PICU are not described. Can you detail a bit further the staff (no respiratory therapist, patient nurse ratio, …) , space and stuff (ECMO for example) available in the PICU. This will help in the interpretation and generalizability of the results.\n\nPlease report the population covered by your PICU. As far as reviewer knowledge is concerned, there is a few PICU in Tunisia with a large population covered making admission to PICU a challenge.\n\nResult section:\nIn Table 4, many treatments are reported but there is no protocol specified in the methodology section. Reviewer is surprised by the low rate of steroid used in this population compared to what is published. Reviewer is not sure that clonazepam and surfactant are specific treatments of COVID infection.\n\nLine 18 page 8 Surfactant therapy: ‘Intratracheal surfactant instillation at the dose of 50 mg/kg X 3/day was performed in an ARDS that escaped other therapeutic alternatives with an initial good response to treatment (Table 4)’. How many days? What does an initial good response means? Did the patient died? What were the other therapies? Reviewer is not sure that this case needs such an highlight\n\nData reported in Table 5 are not outcomes but rather complications. What was the ARDS definition used?\n\nLine 22 Page 11: the autopsy reports are not detailed in the result section, so they cannot be discussed. Please include them in the result section.\nMinor comments Add ‘2020’ to March 1st, line 28 page 3 Line 44 page 11: What does ONHD means?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1215
|
https://f1000research.com/articles/11-1212/v1
|
25 Oct 22
|
{
"type": "Research Article",
"title": "Survival rate of patients with combined hepatocellular cholangiocarcinoma receiving medical cannabis treatment: A retrospective, cohort comparative study",
"authors": [
"Narisara Phansila",
"Paopong Pansila",
"Adisorn Wongkongdech",
"Niruwan Turnbull",
"Mahalul Azam",
"Ranee Wongkongdech",
"Narisara Phansila",
"Paopong Pansila",
"Adisorn Wongkongdech",
"Niruwan Turnbull",
"Mahalul Azam"
],
"abstract": "Background: Cholangiocarcinoma (CCA) incidence in Northeastern Thailand is very high and a major cause of mortality. CCA patients typically have a poor prognosis and short-term survival rate due to late-stage diagnosis. Thailand is the first Southeast Asian country to approve medicinal cannabis treatment, especially for palliative care with advanced cancer patients. Methods: A retrospective cohort comparative study of survival rates among 491 newly diagnosed advanced CCA patients was carried out between September 1, 2019, and June 30, 2021. A total of 404 patients were in the standard palliative care pain management treatment group (ST), and 87 were in the medicinal cannabis treatment group (CT). Patients with CCA were recruited from four tertiary hospitals and two secondary hospitals in five provinces of Northeast Thailand. The cumulative survival rates were calculated by the Kaplan-Meier method, and independent prognostic factors were investigated using Cox regression. Results: For ST patients, there was a total follow-up time of 790 person-months, with a mortality rate of 48.35/100 person-months. For CT patients the total follow-up time was 476 person-months, with mortality rate of 10.9/ 100 person-months. The median survival time after registration at a palliative clinic was 0.83 months (95% CI: 0.71–0.95) for ST and 5.66 months (95% CI: 1.94–9.38) for CT. Multivariate analysis showed that CT treatment protocol was associated with a significantly better survival (P value <0.001; median time of CT, 5.66 months (95% CI: 1.94–9.38); median time of ST, 0.83 months (95% CI: 0.71–0.95). Therefore, CT had a reduced probability of dying from the disease (HRadj., 0.28 (95% CI: 0.20–0.37) Conclusions: The medical cannabis increased overall survival rates among CCA patients.",
"keywords": [
"Survival rate",
"medicinal cannabis",
"combined hepatocellular cholangiocarcinoma",
"cHCC-CC",
"palliative care",
"Northeastern Thailand"
],
"content": "Introduction\n\nCombined hepatocellular cholangiocarcinoma (cHCC-CC) is a rare, but severely aggressive primary liver cancer manifesting characteristics of both hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC). The incidence rate is approximately 0.59 per 1,000,000 populations worldwide1 but it is highly prevalent in Thailand.2 The highest reported CC incidence internationally is in northeastern Thailand, 118.5 per 100,000, in Khon Kaen Province, which is over 100 times higher than the global rate.3\n\nCC is generally asymptomatic in early stages and is usually diagnosed late when the disease has already metastasized. Late-stage diagnosis limits the effective therapeutic options and has an aggressive disease course4 and very poor prognosis,5 resulting in lower survival rates. Previous studies have shown the median post-diagnosis survival of CC patients to be about 9 months (95% CI: 7–11), with 1-, 3-, and 5-year survival rates at 43.4, 21.5, and 17.1%, respectively.1 Mean overall survival rate at 1-, 3-, and 5-year was 66.6, 41.5, and 32.7% for patients with transitional cHCC-CC, with median survival time from diagnosis 4.3 months (95% CI: 3.3–5.1),6 and after supportive treatment was 4 months.7 Survival time was increased among CC patients receiving surgery (an average of 29.38 months), best supportive treatment was 5.12 months and 13.38 months for chemotherapy patients.8\n\nAt present, medical cannabis products are in use in many countries.9 Cannabis as a palliative treatment for patients with cancer appears to be well-tolerated, effective and a safe pain-relief option with significant improvement in quality of life shown after 6 months of treatment.10 In patients with cancer, cannabinoids have mainly been used as part of palliative care to alleviate pain, relieve nausea and stimulate appetite.11 Thailand legalized medical cannabis in February 2019, becoming the first country in Southeast Asia to regulate medical treatment.12 Currently, there are two treatment options for palliative cancer patients in Thailand; the standard current treatment and the new cannabis treatment. However, to the best of our knowledge, no studies on the survival rate of patients treated with medicinal cannabis from the patients’ perspective have been carried out to date. The present study aims to compare survival rates in palliative cHCC-CC patients who were treated with standard treatment (ST) or cannabis treatment (CT) palliative care protocols.\n\n\nMethods\n\nThis study was reviewed and approved by the Mahasarakham University Human Research Ethics Committee (Reference No. 204/2563; approved on July 24, 2020), and Roi-Et Regional Hospital (Reference RE064/2563; approved on August 26, 2020), Buriram Regional Hospital Ethics Committee for Human Research, based on the Declaration of Helsinki and the ICH Good Clinical Practice Guidelines (Reference No. GCP0066/2563; approved on February 4, 2020). Because of its retrospective manner, informed consent was waived by the Roi-Et Regional Hospital and Buriram Regional Hospital. Data were collected from August 30, 2020, to June 30, 2021, which collected event data on 491 cases from September 1, 2019, to June 30, 2021.\n\nA retrospective cohort study was conducted with 491 cHCC-CC patients (404 received ST and 87 received CT), who were diagnosed at least by ultrasonography and treated by supportive treatment at a palliative care and/or cannabis care clinic between September 1, 2019, and June 30, 2021. Data were extracted from the four tertiary hospitals, and two secondary hospitals serving five provinces of northeastern Thailand (Roi-Et Regional Hospital, Buriram Regional Hospital, Surin Provincial Hospital, Sawang Dandin Crown Prince Hospital, Panna Nikhom Hospital and Pana Hospital).\n\nThe independent variables were age at registration (palliative clinic and/or cannabis clinic), sex, cancer treatment and period of diagnosis to registration. The dependent variable was the survival time of patients with cHCC-CC. In order to calculate survival time, the starting point was identified as the date of registration, and the follow-up period ended when a patient passed away or on completion of the study. Censored data were used for those still alive at the end of the study (June 30, 2021) or lost to follow-up. Death status on the cause of treatment was confirmed by linkage with the death certificates from the national statistics database and by a telephone call to the patient or public health officer in community health centers.\n\nStatistical analysis was performed with Stata (RRID:SCR_012763) version 15 (free alternative, Rstudio). Descriptive statistics were used to present baseline characteristics and clinical subject data. Frequency and percentages were constructed to describe categorical data and expressed as the means deviation (in SD) or medians with ranges to describe continuous data. The Kaplan-Meier method was used for observing survival duration with 95% confidence intervals (95% CI). Then between-group comparisons were evaluated using a log-rank test. The test for associations between the diverse covariates and survival rate was performed using the Cox proportional hazard regression model. The results were submitted as hazard ratios (HR) with 95% CI for HR. A p-value less than 0.05 is typically considered to be statistically significant.\n\n\nResults\n\nTable 1 shows the characteristics of the study participants.15,16 There were 491 patients (296 male subjects and 195 female subjects) with cHCC-CC; there were 404 in the ST group (242 male subjects and 162 female subjects) and 87 in the CT group (54 male participants and 33 female participants). The mean age of those in the ST group was 66.60 years old, and the mean age of the CT group was 65.64 years old. Most patients (43.38%) were 70 years of age. More than 71.53% in the ST received cancer chemotherapy and combinations, and 49.42% of the CT group also received palliative care. Mean point of diagnosis with advanced cHCC-CC to registration was 6.12 months for ST, and 5.46 months for CT. Most patients (38.49%) were registered at the palliative and/or cannabis care clinic, and 94.60% (ST) and 59.80% (CT) had passed away by the end of the study. The total follow-up time for ST patients was 790 person-months, with a mortality rate of 48.35/100 person-months. For the CT group follow-up was 476 person-months, with a mortality rate of 10.9./100 person-months for CT.\n\nST, standard palliative care pain management treatment group; CT, medicinal cannabis treatment group.\n\nThe survival rate data after registration at either the palliative or cannabis care clinic. The cumulative 3, 6, 9 and 12 months survival rates were 28.80% (95% CI: 24.72–32.99), 20.00% (95% CI: 16.35–23.92), 16.50% (95% CI: 12.86–20.55) and 15.75% (95% CI: 12.04–19.92) for ST, 60.48% (95% CI: 49.35–69.91), 48.63% (95% CI: 36.78–57.70), 35.73% (95% CI: 23.83–47.74) and 29.98% (95% CI: 18.15–42.73) for CT, respectively. The median duration of survival was 0.83 months (95% CI: 0.71–0.95) for ST and 5.66 months (95% CI: 1.94–9.38) for CT. None of the demographic factors were significantly associated with survival time for either ST or CT. Comparing ST with CT, there was a statistically significant difference in age, sex, cancer treatment and period diagnosis with advanced cHCC-CC to register factors (p-value<0.05). There were factors found that affected the survival of patients receiving palliative care for liver and bile duct cancer. The most significant treatment factor found was between those patients who received standard therapy and those who received medical cannabis. Those on standard therapy were 3.57% more at risk of death than those on cannabis.\n\nMultivariate analysis showed that CT treatment protocol was associated with improved patient survival, which was statistically significant (P value <0.001, the median time of CT, 5.66 months (95% CI: 1.94–9.38) and ST, 0.83 months (95% CI: 0.71–0.95), HRadj, 0.28 (95% CI: 0.20–0.37).\n\n\nDiscussion\n\nThe impact of two types of treatment that affect the survival of cHCC-CC patients who either had supportive treatment at palliative clinic or a cannabis clinic. CT was the most effective treatment, with an overall survival time of 5.66 months, while overall survival time was 0.83 months for ST. Meanwhile, the overall survival times are consistent with other findings for after supportive treatment7 where survival time was only 4.3 months post-diagnosis. Patients diagnosed at an advanced stage were twice as likely to pass away (HR: 1.8, 95% CI: 1.1–2.9).13 By contrast, patients with advanced cancer using cannabis showed a significantly decreased overall survival compared to non-users.14\n\nIn the univariate analysis, cancer treatment and period of diagnosis with advanced cHCC-CC to registration were associated with survival rate. It was found that the ST registered patients survived less than three months after being diagnosed with advanced-stage cHCC-CC. The reason for this might be that some patients had been consulting and were being cared for by an oncologist or other doctor rather than those patients who were registered for and receiving supportive treatment at a Palliative Clinic. Furthermore, most patients had been treated with a combination of surgery and chemotherapy, before being admitted to a Palliative Clinic. Although the registered patients at the Cannabis Clinic were >70 years old, they had no cancer treatment, only supportive treatment at the Cannabis Clinic. At the community hospitals where CT/MRI/biopsy/US have shown advanced organ metastases others who received treatment at a Cannabis clinic without waiting for a consultation with an oncologist were able to receive chemotherapy along with cannabis. This study has several limitations. A number of patients in the CT group dropped out before completion of the study. As a consequence, most patients suffering from advanced cancers and receiving heavy oncological treatments were older adults.\n\nPatients with CCA have poor prognosis and short-term survival at the time of diagnosis. Registration and decision-making at the standard and/or cannabis clinic in each hospital differs across physicians, patients, families, stages of disease, organ metastasis, methods of treatment, and severity of symptoms. To the best of our knowledge, this is the first study that has compared survival rate and quality of life of CHCA/CCA patients who received either ST or CT across tertiary and secondary hospitals and across five provinces. Medical cannabis used in this study were standardized cannabis preparations made by the Thailand Food and Drug Administration. The side effects, safety, benefits and harms of the cannabis produced have been reviewed and are considered appropriate patient treatment. Prescribing doctors are trained, registered prescribers of medical cannabis.\n\n\nAuthor contributions\n\nN.P., contributed to Conceptualization, Data Curation, Formal Analysis, Resources, Methodology, Investigation, Writing – Original Draft. P.P., and A.W., contributed to Methodology, Investigation, Resources, Validation, Formal Analysis, Visualization. N.T., contributed to Conceptualization, Investigation, Supervision, Visualization, Writing – Review & Editing. M.A., contributed to Investigation, Visualization, Writing – Review & Editing. R.W., contributed to Conceptualization, Project Administration, Methodology, Investigation, Writing – Review & Editing, Funding Acquisition, and Supervision.",
"appendix": "Data availability\n\nFigshare: Data_survival_cannabis. https://doi.org/10.6084/m9.figshare.20101193. 15\n\nFigshare: F1000_survival_table1_narisara_ranee. https://doi.org/10.6084/m9.figshare.20486913. 16\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to express the appreciation for all patients who participated in this research and the Hospital Center of Excellence Team (palliative clinic and cannabis clinic) for their invaluable help and encouragement throughout the course of this research. This research project was financially supported by Mahasarakham University. An earlier version of this article can be found on Research Square (doi: https://doi.org/10.21203/rs.3.rs-1030279/v1).\n\n\nReferences\n\nWang J, Li E, Yang H, et al.: Combined hepatocellular-cholangiocarcinoma: a population level analysis of incidence and mortality trends. World J. Surg. Oncol. 2019 Dec; 17(1): 43. PubMed Abstract | Publisher Full Text\n\nTitapun A, Pugkhem A, Luvira V, et al.: Outcome of curative resection for perihilar cholangiocarcinoma in Northeast Thailand. World J. Gastrointest. Oncol. 2015 Dec 15; 7(12): 503–512. PubMed Abstract | Publisher Full Text\n\nAlsaleh M, Leftley Z, Barbera TA, et al.: Cholangiocarcinoma: a guide for the nonspecialist. Int. J. Gen. Med. 2019; 12: 13–23. PubMed Abstract | Publisher Full Text\n\nBanales JM, Marin JJG, Lamarca A, et al.: Cholangiocarcinoma 2020: the next horizon in mechanisms and management. Nat. Rev. Gastroenterol. Hepatol. 2020 Sep; 17(9): 557–588. PubMed Abstract | Publisher Full Text\n\nLoosen SH, Gaisa NT, Schmeding M, et al.: Prolonged Survival of a Patient with Advanced-Stage Combined Hepatocellular-Cholangiocarcinoma. Case Rep. Gastroenterol. 2020 Dec 10; 14(3): 658–67. Page 13/16. PubMed Abstract | Publisher Full Text\n\nWoradet S, Promthet S, Songserm N, et al.: Factors affecting survival time of cholangiocarcinoma patients: a prospective study in Northeast Thailand. Asian Pac. J. Cancer Prev. 2013; 14(3): 1623–1627. PubMed Abstract | Publisher Full Text\n\nThunyaharn N, Promthet S, Wiangnon S, et al.: Survival of cholangiocarcinoma patients in northeastern Thailand after supportive treatment. Asian Pac. J. Cancer Prev. 2013; 14(11): 7029–7032. PubMed Abstract | Publisher Full Text\n\nChanchai C, Piyasatit P, Muntham D, et al.: Clinical Prognostic Factors and Treatment Outcomes for the Survival of Patients with Cholangiocarcinoma in the Eastern Region of Thailand. Asian Pac. J. Cancer Care. 2019 Aug 1; 4(4): 101–105. Publisher Full Text\n\nCarliner H, Brown QL, Sarvet AL, et al.: Cannabis use, attitudes, and legal status in the U.S.: A review. Prev. Med. 2017 Nov; 104: 13–23. PubMed Abstract | Publisher Full Text\n\nBar-Lev Schleider L, Mechoulam R, Lederman V, et al.: Prospective analysis of safety and efficacy of medical cannabis in large unselected population of patients with cancer. Eur. J. Intern. Med. 2018; 49: 37–43. PubMed Abstract | Publisher Full Text\n\nDariš B, Verboten MT, Knez Ž, Ferk P: Cannabinoids in cancer treatment: Therapeutic potential and legislation. Bosn. J. Basic Med. Sci. 2019 Feb; 19(1): 14–23. 1. PubMed Abstract | Publisher Full Text\n\nWorld Law Group: 2020 Global Cannabis Guide – Thailand.2020 Aug 28 [cited 2021 April 18]; 12(9).Reference Source\n\nWoradet S, Songserm N, Promthet S, et al.: Health-Related Quality of Life and Survival of Cholangiocarcinoma Patients in Northeastern Region of Thailand. PLoS One. 2016; 11(9): e0163448. PubMed Abstract | Publisher Full Text\n\nBar-Sela G, Cohen I, Campisi-Pinto S, et al.: Cannabis Consumption Used by Cancer Patients during Immunotherapy Correlates with Poor Clinical Outcome. Cancers (Basel). 2020 Aug 28 [cited 2021 May 15]; 12(9). PubMed Abstract | Publisher Full Text Reference Source\n\nPhansila N, Pansila P, Wongkongdech A, et al.:Data_survival_cannabis. figshare. [Dataset]. 2022. Publisher Full Text\n\nPhansila N:F1000_survival_table1_narisara_ranee. figshare. [Dataset]. 2022. Publisher Full Text"
}
|
[
{
"id": "170664",
"date": "01 Jun 2023",
"name": "Selamat Budijitno",
"expertise": [
"Reviewer Expertise Surgical Oncology",
"biomolecular",
"Immunology",
"epidemiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBased on the STROBE criteria, most of this research has fulfilled the criteria. In my opinion, there are several things that need to be improved so that this research is better:\nThere is no sufficient detail of the methods, especially on the eligibility criteria of participants, and the method of follow up that provided to allow replication by others.\n\nThere are no very important data as a confounder, namely the pain scale/level of pain on the criteria when matching participants.\n\nIt would be clearer if the authors can explain the relationship between pain levels, quality of life, and survival rates in biomolecular terms. Such as, for example, mutations in the NMDA receptor in chronic pain, which will produce P protein which can increase the risk of advanced metastasis, NMDA receptors stimulates the MAPK and CaMK pathways, leading to CREB activation in tumor cells. NMDAR-interacting proteins and the downstream signaling effectors display features in common between the neuronal and metastatic cancer processes, such as cell adhesion, migration, and survival.\n\nIn the results of the cohort study, it would be better if the authors can explain in the report the numbers of individuals at each stage of study – e.g., numbers potentially eligible, examined for eligibility, confirmed eligible, included in the study, completing follow-up, and the reason of dropped out participant.\n\nGive reasons for nonparticipation/dropped out participant in each stage. Consider use of a flow diagram.\nThank you.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "178384",
"date": "26 Jun 2023",
"name": "Nat Na-Ek",
"expertise": [
"Reviewer Expertise Clinical epidemiology",
"pharmacoepidemiology",
"and social epidemiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this piece of work on the benefits of medical cannabis in improving the survival rate of combined hepatocellular cholangiocarcinoma (cHCC-CC) patients is interesting. However, several issues need further clarification and improvements.\nMajor points:\nIt is important to recheck the accuracy of the provided data (https://doi.org/10.6084/m9.figshare.2010119). I noticed inconsistencies in the reported figures, such as the percentages of male and female patients and the number of patients receiving each treatment modality. Additionally, there was a coding issue with one patient receiving medical cannabis coded as 12 in the current treatment variable without an explanation. Addressing these inconsistencies is crucial for the reproducibility of the results.\n\nThe authors did not mention whether they performed a proportional hazards assumption test in the statistical analysis. Upon re-analysis, I found that the treatment variable violated this assumption, indicating that the hazard ratio was not constant at 0.28 across the entire follow-up time as reported. More importantly, the significant association between medical cannabis and survival rate was observed only in the early follow-up (3 months), not the whole study period.\nTherefore, it is important for the authors to conduct a re-analysis and introduce an interaction term between the treatment variable and time using the time-varying covariate (TVC) option in STATA. When reporting the hazard ratio, the authors should present it across the range of follow-up (e.g., within 10 months) to ensure validity and reliability. More details and examples can be found at Bellera et al. (2010)1.\n\nPlease avoid making causal claims in an observational study. For example, the sentence \"the medical cannabis increased overall survival rates among cHCC-CC patients\" (conclusion of the abstract) should be revised to \"the medical cannabis was associated with improved overall survival rates among cHCC-CC patients.\" This distinction is vital because several alternative explanations (e.g., bias, errors, confounding, effect modification, reverse causality) could account for the significant findings. For instance, patients who received medical cannabis might have been more closely monitored by physicians, or they might have had unobserved or unmeasured characteristics (residual confounders) that affected their prognosis positively. Additionally, there may have been discrepancies in the quality of care across different settings.\nTherefore, the authors should refrain from assuming causality to avoid exaggerating the significance of their results. It would be appropriate to include a cautionary statement in the discussion section, such as \"as this is an observational study, we cannot infer causality, and a randomised controlled trial is needed to establish the efficacy of medical cannabis in cancer patients.\"\n\nPlease provide justification and references for each covariate selected as adjusting factors in the analysis. Furthermore, clarify why certain continuous variables (e.g., age, disease duration after registration) were categorised instead of using them as continuous scales. Additionally, I recommend running the analysis with age as a quadratic term (age + age2), as it was found to be significantly associated with death, suggesting a non-linear relationship between age and mortality. Therefore, using a quadratic term for each continuous variable would be more appropriate as it preserves important information2.\n\nProvide more details about the medical cannabis used in the study, such as product details, dosage form, dose, and administration. This information is crucial for generalising the findings to a clinical setting and enabling reproducibility. Additionally, clarify what the standard treatment was in the study and whether it was consistent across different settings.\n\nIn the discussion section, provide more information about the individuals who were lost to follow-up and discuss how their exclusion might have influenced the findings. Is it possible to determine whether these patients were still alive at the end of the study or if they died soon after dropping out?\n\nDiscuss the potential impact of differences in the quality of care across settings on the survival rate of patients in the study. It would be helpful to perform a subgroup analysis according to settings and utilise the strata option in the Cox model.\nFurthermore, consider conducting subgroup analyses based on other variables such as sex, age group, and current treatment to assess whether effect modification plays a role in the findings. Sensitivity and subgroup analyses are necessary to ensure the robustness of the findings, particularly in an observational study.\n\nIn the discussion section, compare the survival rates of the study, particularly in the standard treatment group, with previous works. If applicable, discuss the reasons for any differences observed. This will help strengthen the external validity of the study.\nMinor issues:\nUse \"multivariable\" instead of \"multivariate\" when discussing regression models. The term \"multivariable\" refers to adding explanatory variables (X) in the regression model, while \"multivariate\" implies examining various outcomes (Y) simultaneously3.\n\nSpell \"proportional hazards regression\" with an \"s\" in \"hazards\" since the term \"proportional\" implies the existence of at least two hazards.\n\nBe aware of the term person-months as it is not a person per month, but it is rather the product of patients and their corresponding follow-up time. So, the unit of the incidence rate in your work should be written as “100 person-months” not “100 person/month”.\n\nTo improve clarity, consider splitting Table 1 into three separate tables. Table 1 should focus solely on the characteristics of included participants, allowing for inferential statistics (e.g., independent t-test, chi-squared test) to test the association between each characteristic and exposure status. Then, create Table 2 to present details of the outcome variable according to exposure status. Finally, present Table 3 as the main findings regarding the association between treatment and all-cause mortality, including both crude (unadjusted) and adjusted hazard ratios. Additionally, including a Kaplan-Meier plot with a risk table would aid in visualising the survival rates between patients receiving medical cannabis and those receiving standard treatment.\n\nIf possible, please discuss the potential biological mechanisms or underlying explanations of how medical cannabis can improve the survival rate of cHCC-CC patients.\nOverall, addressing these major and minor points will greatly enhance the clarity, validity, and reproducibility of your study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1212
|
https://f1000research.com/articles/11-1211/v1
|
25 Oct 22
|
{
"type": "Research Article",
"title": "Melan-A expression related to apoptosis of melanocytes in segmental and non-segmental vitiligo",
"authors": [
"Boedhy Setyanto",
"Handono Kalim",
"Sri Poeranto",
"Dhelya Widasmara",
"Handono Kalim",
"Sri Poeranto",
"Dhelya Widasmara"
],
"abstract": "Background\nVitiligo is a progressive depigmentation of the skin with unclear etiology. Cell-mediated immunity has been suggested to play an important role in the pathogenesis of vitiligo’s progression. Melan-A has a high affinity for specific CD8+ T cells and is one of the critical markers for detecting damage to melanocytes. Our study aims to demonstrate the differences in Melan-A expression associated with apoptosis of melanocytes in patients with segmental vitiligo (SV) and those with non-segmental vitiligo (NSV). Methods A cross-sectional study with 64 patients diagnosed with vitiligo, of whom 33 had NSV and 31 had SV. Skin biopsy and direct immunofluorescence were used to examine Melan-A, and the TUNEL staining method was performed to examine melanocyte apoptosis in both groups. Group comparisons were conducted using appropriate statistical methods. Results Melan-A expression was significantly higher in the NSV group than in the SV group, and there was a significant difference between the two groups (p=0.001). The median of melanocyte apoptosis in the NSV group was relatively higher than in the SV group, and a significant difference was found between the two groups (p=0.001). The Spearman’s rank correlation test between Melan-A expression and melanocyte apoptosis in the NSV group was 0.767 (76.7%) and showed a significant relationship (p<0.05). The same test in the SV group was 0.583 (58.3%) and showed a significant relationship (p<0.05). In both groups, the higher the Melan-A expression, the higher the melanocyte apoptosis. Conclusion Melan-A expression and melanocyte apoptosis are positively correlated. Higher Melan-A expression and melanocyte apoptosis in NSV indicates more severe vitiligo disease compared to SV.",
"keywords": [
"Melan-A",
"melanocyte apoptosis",
"segmental vitiligo",
"non-segmental vitiligo",
"disease severity"
],
"content": "1. Introduction\n\nVitiligo is a progressive pigmentation disorder due to the loss of cutaneous melanocytes. To date, the cause of this loss remains unclear. The prevalence of the disease is 0.5–2% of the worldwide population.1,2 In South Malang, Indonesia, of the 2,700 patients who visited the Dermatology and Venereology outpatient clinic at Kepanjen Hospital between 2015 and 2019, 187 had vitiligo, amounting to a prevalence of 7%. The peak occurrence of vitiligo is between the first and third decade of life.3\n\nVitiligo does not affect life expectancy, but it affects quality of life because it may cause the patient to feel inferior in their social environment and face stigma from society.4 The disease’s pathogenesis is not fully understood,5,6 and no single mechanism has fully been implicated in disease causation.3 There are 3 main hypotheses for the pathogenesis of vitiligo, namely genetic factors, oxidative stress, and autoimmunity.6–8\n\nClinically, vitiligo is divided into segmental vitiligo (SV) and non-segmental vitiligo (NSV), with the prevalence of SV being less than that of NSV. The course of SV is acute, appearing rapidly within a few weeks and stabilizing within 1–2 years.9 On the other hand, NSV is characterized by the expansion of lesions on both sides of the body, and the course of the disease is chronic and progressive throughout life.10 Diagnosis can be made by clinical examination and skin biopsy.11\n\nMelan-A/MART-1 (melanoma antigen recognized by T cell-1) is a protein with a high affinity for specific CD8+ T cells in perilesional skin and blood that has been detected in vitro and is associated with the extent and severity of vitiligo disease.12 It is one of the critical markers for detecting melanocyte cell damage or melanocyte apoptosis.13 Melan-A is found mainly in the perilesional zones.14 Recent studies have shown that circulating T lymphocytes are cytotoxic against Melan-A in most vitiligo patients, as a specific cellular immune response against melanocytes.15\n\nDepigmentation levels and vitiligo disease activity can be correlated with an increase in T cells expressing increased antigen-associated receptors.16 Various studies have shown the role of cytokines in the process of melanocyte cell damage.17 The notion that CD8+ T cells act as the final procedure in melanocyte destruction is extensive in the pathogenesis of vitiligo.18 This study aims to compare Melan-A expression and melanocyte apoptosis between SV and NSV and identify correlation between them.\n\n\n2. Methods\n\nThe number of research subjects was calculated using the Lameshow (Cochran) formula, where based on the calculation, the minimum number of samples required was 32 people for each group as research subjects. The subjects consisted of 64 patients diagnosed with vitiligo divided into two groups: the NSV group which contained 33 patients, and the SV group which consisted of 31 patients. All patients attended the Dermatology and Venereology outpatient clinic at Kanjuruan Kepanjen General Hospital during the period from 21st September 2021 to 22nd March 2022. Each patient’s vitiligo diagnosis was confirmed by anamnesis, clinical examination, and skin biopsy. Anamnesis identifies the presence of milky white patches. In clinical examinations, SV presents within a few weeks and stabilizes within 1–2 years.9 In contrast, NSV is characterized by the expansion of lesions on both sides of the body, and the disease is chronic and progressive throughout life. The skin biopsy shows if there are melanocytes at the lesion area in the epidermis.14\n\nThe patients included in this study were aged between 12 and 60 years and had no keloid history. Exclusion criteria included patients with diabetes mellitus, HIV, Cushing syndrome, active infection, trauma, and malignancy, as well as pregnant women, smokers, and those with too much sun exposure (all subjects in this study exposed to the sun less than 2 hours per day). The subjects were enrolled after providing informed consent and detailed demographic and clinical information alongside their family history of vitiligo.\n\nMelan-A expression and melanocyte apoptosis were examined by skin biopsy and direct immunofluorescence, followed by the terminal deoxynucleotidyl transferase-mediated d UTP nick-end labelling (TUNEL) method. We used the anti-Melan-A antibody kit from Santa Cruz (catalog number Sc-20032 PE). Double staining immunofluorescence was used to examine the co-distribution of Melan-A and melanocyte apoptosis in the same sample of cells. All skin biopsies were performed at the Dermatology and Venereology outpatient clinic at Kanjuruhan Kepanjen General Hospital, and the samples were given to the clinical pathology department, Faculty of Medicine, Universitas Brawijaya Malang, for further processing.\n\nSkin biopsies were taken in the following way. Perilesional vitiligo was disinfected with 70% alcohol, then 0.25 mL of lidocaine was applied to anesthetize the area to be biopsied. A skin biopsy with a diameter of 3 mm was performed using the punch biopsy method. The skin tissue from the biopsy was placed in an Eppendorf tube. After completion, the wound was cleaned with a 0.9% NaCl solution, a topical fucidic acid applied, and closed using sterile gauze. The tissue was cut to a thickness of 2–3 mm, before the tissue was given a code according to the researcher’s gross code and inserted into a cassette. The tissue was then processed using an Automatic Tissue Tex Processor tool for 90 minutes, according to the standards of the Anatomical Pathology Laboratory of the FKUB, until an alarm signaled completion. The process of blocking and cutting the tissue was performed, which the epidermis was removed from the Tissue Tex Processor machine. Then the tissue block was performed with paraffin according to the tissue code. The tissue was cut with a microtome tool with a thickness of 3–5 microns.\n\nThis was followed by hematoxylin and eosin (H&E) staining, which was conducted at the Patology Anatomy at the Faculty of Medicine, Universitas Brawijaya. There followed the deparaffination process. The tissue was placed into two tubes of xylol solution for 20 minutes each, after which it was placed into four tubes with ethanol absolute, 90%, 80%, 70%, each 1 mL for 3 minutes (hydration), and then in running water for 15 minutes. It was subsequently stained in Mayers hematoxylin for 1 minute and washed with 4–5 changes of tap water until blue stopped coming off the slides. The tissue was placed in 1% acid alcohol (1% HCl in 70% alcohol) twice for decolorization and rinsed in running tap water before counterstaining in eosin for 3–5 minutes. The slides were then dehydrated in an increasing concentration of ethanol (70%, 80%, 90%, 100%), each 1 mL and were put in two xylene baths for clearing, followed by the immunofluorescence process.\n\nThe immunofluorescence process was conducted in the biomedical laboratory at the Faculty of Medicine, Universitas Brawijaya. The slide was heated at 60°C for 60 minutes. Then the slide was immersed in the following solutions in sequence: xylol solution (pure, 1 mL) for 2×10 minutes, absolute ethanol (96%, 1 mL) for 2×10 minutes, 90% ethanol (1 mL) for 1×5 minutes, 80% ethanol (1 mL) for 1×5 minutes, 70% ethanol (1 mL) for 1×5 minutes, and sterile distilled water for 3×5 minutes. The antigen retrieval process was carried out with citrate buffer. The slide was first immersed in a chamber containing citrate buffer at pH 6.0 (Na citrate dehydrate 2.96 g + twin 20 0.5 mL dissolved in distilled water). The slide was then placed in a water bath at 95°C for 20 minutes. After removal from the water bath, we waited for approximately 20 minutes for it to come to room temperature. The slide was then washed with PBS for 3×5 minutes. After that, the slide was washed with PBS Triton-X 100 0.2% for 5×1 minute. The slide was incubated with 3% bovine serum albumin (BSA) for 30 minutes at room temperature, after which time the BSA solution was discarded. The slide was incubated with Melan-A antibody (Santa Cruz; catalog number Sc-20032 PE) 1:100 in the blocking buffer overnight at 4°C. After overnight incubation, the slide was washed with PBS for 3×5 minutes. Then the slide was incubated with DAPI 1:1000 for 5 minutes before washing the slide with PBS for 3×5 minutes.\n\nFurther, the slide was stained using the TUNEL method conducted at the Biomedical Laboratory, Faculty of Medicine, Universitas Brawijaya, Malang. Tissue pieces were incubated at a temperature of 21–37 °C for 15–30 minutes using a proteinase K working solution 15 μg/mL with concentration 100 μg/mL. Then, the slides were immersed in Tris-HCl (0.1 M, pH 7.5) containing 3% BSA and 20% normal bovine serum for 30 minutes at a temperature of 15–25 °C. Then the slides were rinsed with PBS at 15–25°C twice and the excess fluid was drained. Then 50 μL of the TUNEL reaction mixture was added to the section before being incubated for 60 minutes at 37°C in a humid and dark atmosphere. The slide was rinsed three times in PBS for 5 minutes each. Mounting medium was used to cover the slide followed by a cover slip. Melan-A expression (red color) and apoptosis of melanocyte expression (green color) were evaluated by an Olympus IX71 fluorescence microscope under 40× magnification. Photos were taken for documentation. The next process was to analyze the Melan-A expression and apoptosis of melanocyte using ImageJ software. The results of the two groups were then compared.\n\nData were analyzed using descriptive statistics to calculate the percentages, mean values, and standard deviations. Since the data were not normally distributed, we used the non-parametric Mann–Whitney u test. Student’s t-test and Spearman’s rank correlation were used to analyze the variance between the two groups and association among the variables. A p value less than 0.05 was considered statistically significant.\n\n\n3. Results\n\nThere were 64 patients with vitiligo included in this study, of whom 33 were in the NSV group and 31 in the SV group. The mean age was 22.32±9.20 years in the SV group and 44.79±11.24 years in NSV group. The subjects’ characteristics are presented in Table 1.\n\nIn Figure 1, the results of the Mann Whitney tests showed a p value of 0.001 (<α=0.05); thus, it can be concluded that there were differences between Melan-A expression in the NSV group and the SV group. the median of Melan-A expression was 16.27±8.16 pixels in the NSV group and 2.70±4.14 pixels in the SV group. Melan-A expression in the NSV group was relatively higher than in the SV group. We then used ImageJ software to calculate Melan-A expression and melanocyte apoptosis from qualitative to quantitative values. The mean result of Melan-A expression in the NSV group was 30.15 pixels and 2.60 pixels in the SV group.\n\nIn Figure 2, the results of the Mann Whitney tests showed a p value of 0.001 (<α=0.05); thus, it can be concluded that there were differences between melanocyte apoptosis in the VNS group and the VS group. The median of melanocyte apoptosis to be 26.45±8.16 pixels in the NSV group and 6.12±5.056 pixels in the SV group. Melanocyte apoptosis was higher in the NSV group than in the SV group. After analysis with ImageJ software, we identified the mean result of melanocyte apoptosis expression in the NSV group to be 51.23 and 5.07 pixels in the SV group.\n\nIn Figure 3, the results of the Spearman’s rank correlation test showed that the relationship between Melan-A expression and melanocyte apoptosis in the NSV group was 0.767 (76.7%) and significant (p<0.05). The relationship was positive; thus, the higher the expression of Melan-A, the higher the melanocyte apoptosis. Based on the results of the Spearman’s rank correlation test, the relationship between Melan-A expression and melanocyte apoptosis in the SV group was 0.583 (58.3%) and significant (p<0.05). The relationship was positive; thus, the higher the expression of Melan-A, the higher the melanocyte apoptosis.\n\nFigure 4 indicates that melanocyte apoptosis was more dominant in the NSV group than in the SV group, due to the possibility of redox balance disturbances and more severe melanocyte destruction.\n\n(a) The fluorescence feature of Melan-A (red color, shown with an orange arrow) and melanocyte apoptosis (green color, shown with a yellow arrow) in SV; (b) the fluorescence feature of Melan-A (red color, shown with an orange arrow) and melanocyte apoptosis (green color, shown with a yellow arrow) in NSV. All viewed by Olympus IX71 fluorescence microscope under 40× magnification.\n\n\n4. Discussion\n\nThis study provides important insights about the differences in Melan-A expression associated with apoptosis of melanocytes in SV and NSV patients. Several previous studies have described the role of Melan-A in vitiligo in general, but no studies have investigated the differences in Melan-A expression and melanocyte apoptosis and their correlation in SV and NSV patients. The progressive depigmentation of NSV and its unpredictable disease course highlights its research importance.\n\nThe Melan-A/MART-1 protein, which is located in the melanosome and plays a role in both protein formation and maturation,9,18,19 is one of the activation stimulants for CD8+ T cells, along with GP100 and tyrosinase. Melan-A has an important role in the expression, stabilization, transport, and processing of the melanosome in melanocytes. Melan-A is usually found in individuals who have HLAA2, although it can also be found in others, but the amount is only 1 in 1000 CD8+ T cells and in the naïve state.20,21 Several studies have shown better sensitivity and specificity of Melan-A as a marker of melanocytic differentiation, compared to markers S100 and HMB-45. The HMB45 marker is not specific for melanocytes because it can also be expressed by sweat gland cells and nonmelanocytic tumors. However, HMB45, which is a monoclonal antibody, reacts with a melanosomal protein (GP100) which can not only express activated melanocytes, but can also express fetal melanocytes, thereby confirming melanocyte activity. The S100 marker can also detect melanocyte activity but has the disadvantage of being able to react positively not only to melanocytes, but also to Langerhans cells, neurons, tissue, muscle cells, and apocrine glands. Circulating cytotoxic T lymphocytes are found in most vitiligo patients, where T cells express an increase in lymphocyte-associated antigen receptors, which in turn correlates with the degree of depigmentation and vitiligo disease activity.20,22 Histologically, Melan-A appears to be most dominant when located in perilesional zones.22–24 CD8+ T cells infiltrate the perilesional skin, where vitiligo is most active, and preferentially localize to the epidermis and dermis, adjacent to melanocyte.25\n\nThe increased amount of Melan-A can be caused by several factors, such as stress, ultraviolet exposure, pollution, and chemical materials that are immunogenic and have both autoreactivity and a high affinity for CD8+ T cells that destroy melanocytes, leading the process of apoptosis to occur.20,26–28 The presence of neoantigens resulting from damage to melanocytes activates pattern recognition receptors, in turn activating dendritic cells through damage-associated molecular patterns (DAMPs) followed by reactive CD8+ T cells that continuously destroy the melanocytes.18,29,30\n\nMelanocyte apoptosis is a programmed and schematic mechanism that occurs in vitiligo. DNA in melanocytes is cut into fragments with enzymes from endonuclease, which catalyze DNA. In electrophoresis, the melanocytes are seen to shrink, which indicates preparation for cell death. A typical feature of apoptosis is a “step ladder pattern”, whereby the cells appear wavy. In the end, the cells become fragmented and release apoptotic bodies.31–33 However, in addition to apoptosis, several authors have recently suggested that neoantigens can also be caused by another form of melanocyte cell death such as necroptosis, pyroptosis, ferroptosis, oxeiptosis, and parthanatos, which are characterized by an inflammatory process. Apoptosis that is too long can also cause necrosis and vice versa. In other words, it can be said that both prolonged apoptosis and necrosis can produce neoantigens and trigger autoimmunity.34\n\nThe autoimmune mechanism leading to apoptosis can be through either the extrinsic or intrinsic pathway. The extrinsic pathway occurs through FAS ligand and FAS receptors, as well as involving FAS-associated death domain (FAAD). The subsequent FAAD-like interleukin F-beta converting enzyme (FLICE) activates procaspase 8, converting it into caspase 8. Caspase 8 activates procaspase 3 to caspase 3, which in turn activates apoptosis.35,36 Furthermore, the extrinsic pathway also involves the movement of perforin and granzyme into cells. Perforin makes holes or pores in the surface of the target cell membrane, which, besides causing direct damage, also facilitates the entry of granzyme into the cell. Granzyme will stimulate the target cells to undergo apoptosis. The intrinsic pathway occurs in cells and involves pro-apoptotic factors such as Bax and Bak, as well as anti-apoptotic factors such as Bcl-2 and Bcl-xl, which affect the cytochrome. Then cell death can occur through caspases.37–39\n\nIn our study, it was found that there were differences between Melan-A expression in the NSV group and the SV group. The result of Melan-A expression in the NSV group was higher than in the SV group. Besides, we identified that melanocyte apoptosis in the NSV group was higher than in the SV group. In both groups, there was a positive correlation between Melan-A expression and melanocyte apoptosis; the higher Melan-A expression, the higher the melanocyte apoptosis. Our study shows that in NSV, Melan-A is more immunogenic, which causes more autoreactivity in CD8+ T cells. These specific CD8+ T cells secrete TNFα, IL6, IL8, perforin, and granzyme and induce endoplasmic reticulum-associated degradation (ERAD), which eventually causes melanocyte damage and cell death. It can increase the acceleration of the autoimmune process and the progression of vitiligo disease.12 It is said that Th1 and Th2 imbalances and Melan-A play a major role in the progression of SV to NSV.9 A descriptive study conducted by Vaniary et al., which evaluated the expression of Melan-A in vitiligo patients, found that the Melan-A expression on depigmented skins of vitiligo patients was below the average value, although this study did not compare Melan-A in vitiligo and in healthy skin.40 Our result is consistent with the study by Arora et al., which showed that an increase in Melan-A causes autoreactivity to CD8+ T cells and increasingly causes more severe damage to melanocytes.12 From the study conducted by Chen et al., the role of the role of CD8+ T cells as executors is explained by the high frequency of serum melanocyte-specific CD8+ T cells in vitiligo patients compared with healthy people. In addition, serum CD8+ T cell levels are also associated with disease severity.18 Altogether, these findings provide strong evidence that Melan-A expression correlates with melanocyte apoptosis in both NSV and SV. In addition, in NSV patients, there was an acceleration of the autoimmune process and progression of vitiligo disease, which was indicated by higher expression of Melan-A and melanocyte apoptosis than in SV.\n\n\n5. Conclusion\n\nIn conclusion, the expression of Melan-A in NSV is higher than in SV, and the apoptosis of melanocytes in NSV is higher than in SV. There is a positive correlation between Melan-A expression and melanocyte apoptosis. The higher Melan-A expression, the more melanocytes are undergoing apoptosis in NSV and SV. Future multicenter studies with larger sample sizes and correlations with other vitiligo biomarkers are necessary to fully understand the pathogenesis of NSV and SV.\n\n\nEthics\n\nThis research has been declared to be ethically feasible by Health Research Ethic Committee Faculty of Medicine Brawijaya University July 28th 2021 with number 218/EC/KEPK-S3/07/2021.\n\n\nInformed consent\n\nWritten informed consent for publication of the patients’ details was obtained from the participants or from the parents/guardians of participants under the age of 18.",
"appendix": "Data availability\n\nZenodo: Melan-A Expression Related to Apoptosis of Melanocytes in Segmental and Nonsegmental Vitiligo, https://doi.org/10.5281/zenodo.6997417.\n\nThe project contains the following underlying data:\n\n- Analysis Result.docx (analysis result data).\n\n- DAPI and Apoptosis SV (Immunofluorescence).\n\n- DAPI and Melan-A NSV (Immunofluorescence).\n\n- DAPI and Melan-A SV (Immunofluorescence).\n\n- DAPI and Apoptosis NSV (Immunofluorescence).\n\n- DAPI and Apoptosis SV (Immunofluorescence).\n\n- Data and Demographic.docx (demographic data of subjects)\n\n- Melan-A and Apoptosis SV (Immunofluorescence)\n\n- Melan-A and Apoptosis NSV (Immunofluorescence)\n\n- Result-2.docx (result data)\n\nFigshare: STROBE checklist for Melan-A expression related to apoptosis of melanocytes in segmental and non-segmental vitiligo, https://doi.org/10.6084/m9.figshare.21163072.v1. 41\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nHabib A: Clinical profile of segmental vitiligo in a group of Pakistani patients. Pak. Armed Forces Med. J. 2019; 69(3): 495–499.\n\nRelke N, Gooderham M: The use of Janus kinase inhibitors in vitiligo: a review of the literature. J. Cutan. Med. Surg. 2019; 23(3): 298–306. PubMed Abstract | Publisher Full Text\n\nKaragaiah P, Schwartz RA, Lotti T, et al.: Biologic and targeted therapeutics in vitiligo. J. Cosmet. Dermatol. 2022. PubMed Abstract | Publisher Full Text\n\nKang S, Amagai M, Bruckner A, et al.: Fitzpatrick’s dermatology. 9th ed.New York:McGraw-Hill;2019.\n\nDelmas V, Larue L: Melanocyte homeostasis in vitiligo. Vitiligo. 2019; 265–275. Publisher Full Text\n\nAbdel-Malek ZA, Jordan C, Ho T, et al.: The enigma and challenges of vitiligo pathophysiology and treatment. Pigment Cell Melanoma Res. 2020; 33(6): 778–787. PubMed Abstract | Publisher Full Text\n\nPicardo M: Pathophysiology overrview. Vitiligo. 2019; 189–192. Publisher Full Text\n\nHarris JE: What causes vitiligo? Vitiligo Clinic and Research. 1–2.\n\nBoniface K, Seneschal J, Picardo M, et al.: Vitiligo: focus on clinical aspects, immunopathogenesis, and therapy. Clin. Rev. Allergy Immunol. 2018; 54(1): 52–67. PubMed Abstract | Publisher Full Text\n\nHann S, Yu HS, Lan CCE, et al.: Segmental vitiligo. Vitiligo. 2019; 53–71. Publisher Full Text\n\nXie H, Zhou F, Liu L, et al.: Vitiligo: how do oxidative strss-induced autoantigens triger autoimmunity? J. Dermatol. Sci. 2016; 81(1): 3–9. PubMed Abstract | Publisher Full Text\n\nArora A, Kumaran M: Pathogenesis of vitiligo: an update. Pigment Int. 2017; 4(2): 65. Publisher Full Text\n\nKubanov A, Proshutinskala VV, Katunina O, et al.: Immununohistochemichal analysis of melanocyte content in different zones of vitiligo lesions using the Melan-A marker. Acta Derm. 2015; 25: 5–9. PubMed Abstract | Publisher Full Text\n\nCosta C, Kovacs D: Vitiligo: histopathology, including electron microscopy. Vitiligo.2019; 25–37. Publisher Full Text\n\nBabai S, Voisin AL, Bertin C, et al.: Le Louet H Occurrences and outcomes of immune checkpoint inhibitors-induced vitiligo in cancer patients: a retrospective cohort study. Drug Saf. 2019; 43: 111–117. PubMed Abstract | Publisher Full Text\n\nAwad SS, Tadros E: Understanding the role of lymphocytes in vitiligo. Int. J. Immunol. Immunother. 2021; 8: 60. Publisher Full Text\n\nPraharsini IGAA, Suryawati N, Indira IE, et al.: (2018). High level of tumor necrosis alpha and serum interferon gamma as risk factors for progression of vitiligo disease. Int. J. Health Sci. 2018; 2(2): 1–8.\n\nChen X, Guo W, Chang Y, et al.: Oxidative stress-induced IL-15 trans-presentation in keratinocytes contributes to CD8+ T cells activation via JAK-STAT pathway in vitiligo. Free Radic. Biol. Med. 2019; 139: 80–91. Publisher Full Text\n\nKundu RV, Mhlaba JM, Rangel SM, et al.: The convergence theory for vitiligo: a reappraisal. Exp. Dermatol. 2018. Publisher Full Text\n\nSpeeckaert R, Van Geel N: Vitiligo: an update on pathophysiology and treatment options, Article Reviews.2017; 18(June): 733–744. Publisher Full Text\n\nSpeeckaer R, Speeckaert M, De Schepper S, et al.: Biomarkers of disease activity in vitiligo: a systematic review. Autoimmun. Rev. 2017; 16(9): 937–945. PubMed Abstract | Publisher Full Text\n\nNa N, Park J: A new approach using a numerical diagnostic criterion for vitiligo diagnosis with HMB-45 and Melan-A staining. Int. J. Clin. Exp. Pathol. 2021; 14(8): 902–907. PubMed Abstract\n\nZhang L, Chen S, Kang Y, et al.: Association of clinical markers with disease progression in patiens with vitiligo from China. JAMA Dermatol. 2019; 156: 288. Publisher Full Text\n\nWebb KC, Henning SW, Le Poole IC: Immunity/Immunopathology. Vitiligo. 2019; 285–301. Publisher Full Text\n\nBerqvist C, Ezzdine K: Vitiligo: a review. Review Article of Dermatology. 2020; 1–22. Publisher Full Text\n\nIannella G, Greco A, Didona D, et al.: Vitiligo: pathogenesis, clinical variants and treatment approaches. Autoimmun. Rev. 2016; 15(December): 335–343. PubMed Abstract | Publisher Full Text\n\nRuiz-Argüelles A, Brito GJ, Reyes-Izquierdo P, et al.: Apoptosis of melanocytes in vitiligo results from antibody penetration. J. Autoimmun. 2017; 29(4): 281–286. Publisher Full Text\n\nFrisoli ML, Essien K, Harris JE: Vitiligo: mechanisms of pathogenesis and treatment. Annu. Rev. Immunol. 2020; 38(1): 621–648. Publisher Full Text\n\nSingh M, Kotnis A, Jadeja SD, et al.: Cytokines: the yin and yang of vitiligo pathogenesis. Expert. Rev. Clin. Immunol. 2018; 15: 177–188. PubMed Abstract | Publisher Full Text\n\nPark K, Lee SE, Shin K-O, et al.: Insights into the role of endoplasmic reticulum stress in skin function and assciated diseases. Review Article. FEBS J. 2019; 286: 413–425. PubMed Abstract | Publisher Full Text\n\nPatel S, Rauf A, Khan H, et al.: A holistic review on the autoimmune disease vitiligo with emphasis on the causal factors. Biomed. Pharmacother. 2017; 92: 501–508. PubMed Abstract | Publisher Full Text\n\nAvalos-Díaz E, Pérez-Pérez E, Rodríguez-Rodríguez M, et al.: Autoimmune vitiligo in rheumatic disease in the mestizo Mexican population. Biomed. Rep. 2016; 5(2): 176–180. PubMed Abstract | Publisher Full Text\n\nRodrigues M, Ezzedine K, Hamzavi I, et al.: New discoveries in the pathogenesis and classification of vitiligo. J. Am. Acad. Dermatol. 2017; 77(July): 1–13. PubMed Abstract | Publisher Full Text\n\nScaturro P, Pichlmair A: Oxeiptosis: a discreet way to respond to radicals. Curr. Opin. Immunol. 2019; 56: 37–43. PubMed Abstract | Publisher Full Text\n\nAbbas AK, Lichtman AH, Pillai S: Cellular and mollecular immunology. 9th ed.Winsland:Elsevier;2018.\n\nJimbo H, Nagai H, Fujiwara S, et al.: Fas-FasL interaction factor and interferon in Fas-mediated melanocyte apoptosis. Exp. Dermatol. 2019; 2019: 61–69. Publisher Full Text\n\nJohnson JD, Barnard DF, Kulp AC, et al.: Neuroendocrine regulation of brain cytokines after psychological stress. J. Endocr. Soc. 2019; 3(7): 1302–1320. PubMed Abstract | Publisher Full Text\n\nTang L, Li J, Fu W, et al.: Supression of FADS1 induces ROS generation, cell cycle arrest, and apoptosis in melanosit: Implications for votiligo. Research Paper.2019; 11(24). Publisher Full Text\n\nKiselevsky DB: Granzymes and Mitochondria. Biochem. Mosc. 2020; 85(2): 131–139. PubMed Abstract | Publisher Full Text\n\nVaniary TIN, Listiawan MY, Murtiastutik D: Expression of Melan-A in depigmented skin of vitiligo patients. Berkala Ilmu Kesehatan Kulit dan Kelamin. 2020; 32(1): 17–20. Publisher Full Text\n\nSetyanto B:Melan-A expression related to apoptosis of melanocytes in segmental and non-segmental vitiligo. figshare. [Dataset]. 2022. Publisher Full Text"
}
|
[
{
"id": "154147",
"date": "13 Dec 2022",
"name": "Afif Nurul Hidayati",
"expertise": [
"Reviewer Expertise Immunology",
"autoimmune diseases",
"immunocompromized condition",
"STI",
"HIV/AIDS"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate this manuscript. Melan-A/MART-1 (melanoma antigen recognized by T cell-1) is a protein with a high affinity for specific CD8+ T cells in perilesional skin and blood that has been detected in vitro and is associated with the extent and severity of vitiligo disease and one of the critical markers for detecting melanocyte cell damage or melanocyte apoptosis.\nI have some questions:\nYou have not conveyed the benefits of this research both for science and for the subjects.\n\nBased on the calculation of sample size that you mentioned, the minimum number of samples required was 32 people for each group as research subjects. The subjects of your research consisted of 64 patients diagnosed with vitiligo divided into two groups: the NSV group which contained 33 patients, BUT the SV group which consisted of 31 patients (why not 32 patients?)\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "193268",
"date": "06 Sep 2023",
"name": "Niharika Srivastava",
"expertise": [
"Reviewer Expertise Immunology",
"Dermatology",
"genetics."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nCongratulations on this piece of work. I found this study informative and precise. This study includes the correlation of MelanA and CD8+ cells in Non-Segmental and Segmental Vitiligo patients. The work is accurately presented and has cited recent literature from the year 2015-2022. The study also sounds technically appropriate. Since comparison between Melan A/CD8 expression in NSV and SV patients' skin has not been co-related in the previously reported literature. Therefore, the current study has new information to share. The Discussion conclusions were well explained and adequately supported by the results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1211
|
https://f1000research.com/articles/11-527/v1
|
16 May 22
|
{
"type": "Research Article",
"title": "Antiproliferative activity of standardized herbal phytopreparation from Asclepias subulata",
"authors": [
"Francisco Humberto González Gutiérrez",
"Luisa Alondra Rascón Valenzuela",
"Salvador Enrique Meneses Sagrero",
"Marcelo J. Dias-Silva",
"Olivia Valenzuela Antelo",
"Carlos Velazquez",
"Wagner Vilegas",
"Ramón Enrique Robles Zepeda",
"Francisco Humberto González Gutiérrez",
"Luisa Alondra Rascón Valenzuela",
"Salvador Enrique Meneses Sagrero",
"Marcelo J. Dias-Silva",
"Olivia Valenzuela Antelo",
"Carlos Velazquez",
"Wagner Vilegas"
],
"abstract": "Background: Several studies have shown that active compounds of Asclepias subulata (cardenolides) have antiproliferative effect on human cancer cells. Cardenolides isolated from A. subulata can be used as active chemical markers to elaborate phytopharmaceutical preparations. To evaluate the antiproliferative effect of a standardized extract of the aerial parts, based on Asclepias subulata cardenolides. Methods: Four standardized extracts were prepared by HPLC-DAD depending on the concentration of calotropin and the antiproliferative activity was measured for the MTT assay, on the A549, MCF-7, HeLa, PC3 and ARPE cell lines. The concentrations of calotropin used for the standardization of the extracts were 10, 7.6, 5 and 1 mg/dL. Results: Standardization of the A. subulata extract based on calotropin at 7.6 mg/g dry weight was achieved and the antiproliferative activity was evaluated over A549, HeLa and MCF-7 cell lines, obtaining proliferation percentages of 3.8 to 13.4%. Conclusions: The standardized extracts of A. subulata at different concentrations of calotropin showed antiproliferative activity against all the cell lines evaluated. The greatest effect was observed against the HeLa cell line.",
"keywords": [
"Asclepias subulate",
"Calotropin",
"Cardenolides",
"Standardized extract",
"Antiproliferative activity"
],
"content": "Introduction\n\nCancer continues to be the most aggressive disease and with a high mortality rate. World Health Organization (WHO) estimated that during 2015, 8.2 million people died due to this condition1 but the burden increased in 2018 to 18.1 million new cases and 9.6 million deaths.2 In recent years, there is an increasing interest in the study of natural resources for medicine, so research on the phytochemical, pharmacological and clinical validation of numerous active ingredients derived from natural products has been multiplied.3 Natural products have been considered as a significant source for the generation of pharmaceutical compounds such as analgesics, antifungals, antibiotics, and anticancer agents.3 Herbal medicine has become a non-toxic, safe and readily available source of compounds for cancer treatments2 and the design and research of standardized extracts (preparations obtained only from medicinal herbs that contains pharmacologically active components) can generate advances in the study of new therapies against cancer, reducing or avoiding the appearance of side effects3 since it has been proven that herbal medicine are a safe source, not toxic and readily available cancer treatment compounds.2\n\nAsclepias subulata (Asclepiadaceae) is a native plant from the Sonoran Desert in North America, which has been used in traditional medicine for the treatment of several diseases and cancer types.4 In our research group Rascon et al., 2015,5 were able to demonstrate the antiproliferative activity of the ethanolic extract of A. subulata the aerial parts of, obtaining results of IC50 of 0.4 and 8.4 μg/mL in A549 and HeLa respectively. In addition, they demonstrated the apoptotic activity of the plant extract. These authors also fractionated the extract to obtain the bioactive components, obtaining a new cardenolide 12,16-dihydroxycalotropin and three known compounds, calotropin, corotoxigenin 3-O-glucopyranoside and desglucuzarina. All these compounds showed high antiproliferative activity and selectivity in human cancer cells.4 Despite the most important use of the cardiac glycosides are on cardiac failures treatments,6,7 recent studies evidenced that cardenolides are also apoptosis inductors and growth-inhibitors against tumors in in vitro and in vivo models, with no significant toxicity on normal cells.6,8 These data stimulated us to generate a standardized extract of the aerial parts of A. subulata based on its most abundant cardenolides of the plant.\n\n\nMethods\n\nA. subulata (Decne., 1844) (Asclepiadaceae) was collected in an experimental area located in the Department of Agriculture and Livestock (DAL) of the University of Sonora, Mexico (29°03′18″ North latitude and 111°05′21″ West longitude). The taxonomic identification was carried out by Eng. Jesus Sanchez Escalante and deposited in the Herbarium of the University of Sonora with the voucher number USON-26395.\n\nThe aerial parts of A. subulata was dried at room temperature (25°C), in the shade and grounded with a Whiley mill (200 mesh) affording 300 g of the powder, that was macerated with 70% ethanol in a 1:10 w/v proportion with manual agitation for 10 days. The ethanolic extract was filtered and concentrated on a rotary evaporator at 40 °C under reduced pressure affording 172 g (57.4% rendimento) of the A. subulata etanolic extract (AsE).\n\nThe cardenolides were identified and isolated following the methodology described by Rascon et al., 2015.4 The standardization was performed using a High Performance Liquid Cromatograph (HPLC) (Jasco system compound of binary pump model PU-2086 Plus, São Paulo, SP, Brazil) coupled to a diode array detector (DAD) (Jasco MD-2018 Plus, São Paulo, SP, Brazil) and to an evaporative light scattering detector (ELSD) (Jasco ELS-2040, São Paulo, SP, Brazil). We use a Luna C18 (2) 100A column (250 × 21.2 mm d.i, 5 μm) (Phenomenex, CA, USA) with pre-column (4 × 3 mm d.i.) were used. A binary solvent system was used; solvent A (water with 0.1% formic acid); and solvent B (methanol with 0.1% formic acid) at a flow rate of 7 mL/min4. The run was monitored at 30 min. The identification of the chromatographic peaks was performed using addition of compound isolated in the previous step. ESI-IT-MS/MS spectra were obtained with a LTQXL Thermo Scientific spectrometer (ionization mode: negative or positive, scan range: 150–2000 m/z, voltage: –13 kV, heated capillary temperature: 280°C, sheathgas:10 μa, auxiliarygas:10 μa) (San Jose, CA, USA). The NMR experiments were performed on a Bruker Advance 600 MHz equipment, and the samples were processed using CD3OD as the solvent using one and 2D techniques (DEPTQ, HMBC, HSQC, and TOCSY) to confirmation of the structures of the isolated compounds. The calibration curve was prepared using the standard addition method, with seven different concentrations of calotropin (0.3-1 mg/mL) and the values were projected in graph using the PRISMA 5. Considering the IC50 of the in vitro antiproliferative activity observed in our previous works,5 four standardized extracts were prepared by HPLC-DAD depending on the concentration of calotropin and the antiproliferative. The concentrations of calotropin used for the standardization of the extracts were 10, 7.6, 5 and 1 mg/dL, taken by previous studies.4,5\n\nA549 (human alveolar adenocarcinoma) (ATCC number: CCL-185), PC-3 (human prostatic adenocarcinoma) (ATCC number: CRL-1435), LS180 (human colorectal adenocarcinoma) (ATCC number: CL-187), HeLa (human cervix adenocarcinoma) (ATCC: CCL-2), ARPE-19 (human retinal pigmented epithelium) (ATCC number: CRL-2302) cell lines were purchased from the American Type Culture Collection (ATCC, Rockville, MD, USA). The cell lines were maintained using Dulbecco’s Modified Eagle’s Medium culture medium supplemented 5% of fetal bovine serum. Cells were grown incubated at 37 °C in a humidified incubator with 5% of CO2.\n\nAntiproliferative activity was evaluated by the MTT reduction assay [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium] with some modifications.5 Briefly, the cells were added into a 96-well plate (1 × 104 cells per well in 50 μL of medium). After 24 h incubation at 37°C, were added 50 μL of medium containing different concentrations of standardized extracts: 10 mg/dL; 7.6 mg/dL; 5 mg/dL and 1 mg/dL (maximal DMSO concentration were of 2% v/v) and the cell cultures were incubated for 48 h. Doxorubicin was used as positive control. In the last 4 h of incubation time the cells where were washed with PBS 1X. Fresh culture medium (100 mL) and 10 μL of MTT solution (5 mg/mL) were added to each well. The formed formazan crystals were dissolved with 100 mL of acidic isopropyl alcohol. The absorbance of the samples was measured with an ELISA plate reader (iMark Microplate Absorbance Reader, Bio-Rad), The differences in means were analyzed using one-way analysis of variance (one-way ANOVA) followed by Tukey’s test (Sigma Stat 3; Systat Software Inc., CA, USA).\n\n\nResults\n\nThe AsE was prepared by maceration for 10 days with 70% ethanol, filtered and dried, were yielding of 172.1 g (57.4%). Fractionation of 5 g of AsE using gel permeation chromatography on an open column of Sephadex and further purification using a semipreparative HPLC-DAD system led to the isolation of the cardenolides (Figure 1), which were identified using NMR, Mass spectrometry and comparison to previous literature data.4 Total of 9 subfractions were obtained and then were analized for subjected thin layer chromatography (TLC) technique and HPLC to know the complexity of its compounds. Thus, fractions 3 (1167.2 mg) and 4 (576.6 mg) were selected, which gave us two signals called compound A and compound B, which also demonstrated that their maximum absorption points are between 210 and 225 nm, searching the literature for note that the signals that show a characteristic unique absorption maximum between 214 and 222 nm, corresponding to a functional group of unsaturated lactone and can be considered cardenolides;9 the structures were confirmed by NMR and agree with the data reported by the bibliography.4 The chromatographic profiles were optimized by means of analytical HPLC and subsequently the conditions used were extrapolated to a semi-preparative HPLC system using the ELSD as the main detector due to the low absorption in the UV-visible spectrum that the samples presented. This way it was possible to obtain compounds 1, 2 and 3. Compound 1 (Rt 17.4 min) was obtained as a fine white powder (32.8 mg). Its ESI-MS mass spectrum showed an [M-H]- ion at m/z 531; comparison with the literature allowed us to identify 1 as calotropin.4 Compound 2 (Rt 18.1 min) generated amorphous and colorless crystals with a weight of 21.2 mg, Its ESI-MS mass spectrum showed an [M-H]- ion at m/z 577; comparison with the literature allowed us to identify 2 as calactin.10 Compound 3 (RT 17.9 min) was obtained as a fine white powder (5 mg). Its ESI-MS mass spectrum showed the [M-H]- ion at m/z 547. MS3 fragmentarion of the precursos ion at m/z 547 led to the product iosn at m/z 529, 511 and 401, which are in accordance to Rascon et al; 2015.4 This compound corresponds to cardenolide 4′-hydroxy-7,8-dehydrocalotropin. All these compounds were also subjected to NMR analyses and compared to literature data4 in order to confirm their identities (see extended data for more information17). Continuing with the study, by means of mass spectrophotometry the identification of 11 compounds shown in Supplementary material 2 (see extended data17) was achieved.\n\nA: Calotropin (17.4 min), B: Calactin (18.1 min).\n\nPlants in a natural environment face different biological and ecological stimuli that mean that they do not provide secondary metabolites in a consistent way; since nature does not provide a product with consistent or standardized concentrations, it is necessary to perform a standardization of extracts that are required to be used in traditional medicine, but the standardization of an herbal product is complicated, starting from its cultivation, extraction, storage, etc.11 After the clean-up, the AsE was analysed using HPLC-DAD-ELSD (Figure 1). The chromatographic run was achieved in about 30 min, and led to a good resolution of the peaks assined to compounds 1 and 2, which ios essential for the standardization of the AsE. Standardization of the AsE led to the final concentration of 7.6 mg of calotropin per gram of AsE (Figure 2). Once this information was gathered, we were able to use three different concentrations of the extract based on calotropin and IC50 and the IC50 reports present in the previous studies: a low (1 mg/dL), a medium (5 mg/dL), a high (10 mg/dL) and a base 7.6 mg/dL that allowed us to continue with the evaluation of the extract in subsequent experiments.\n\nCalotropin was quantified using different concentrations (0.3-1 mg/mL) whit standard addition method by HPLC.\n\nAntiproliferative activity of the AsE\n\nThen, based on this result and on the IC50 and the IC50 reports reported in our previous studies we were able to investigate the antiproliferative activity of AsE using four different concentrations: 10 mg/dL (high); 7.6 mg/dl (base); 5 mg/dL (medium) and 1 mg/dL (low), which were evaluated in different cell lines (Table 1), HeLa being the most affected; a maximum of 10% proliferation was observed in all lines, which shows that the extract even in the low concentration of 1 mg/dL stops the growth of cancer cells in vitro.\n\na Statistically significant difference at p=0.05. ± Standard deviation.\n\nb There is no statistically significant difference p=0.05.\n\n\nDiscussion\n\nThe term cancer includes more than 100 different types of diseases that feature the accelerated and disorderly growth of cells with abnormal expressed genes that participate in the regulation of the cell cycle directly,12 with an incidence of 439.2 cases per 100 thousand inhabitants of which 163.5 will die from the disease.1 The generation of standardized extracts that support the treatments against this disease and given its high mortality and worldwide incidence is of vital importance. In the present work, it was standardized by HPLC-DAD technique, using calotropin as internal standard; the AsE at a concentration of 7.6 mg per dry gram of plant, which presented an antiproliferative activity of less than 1 μg/mL, showing a cytotoxic effect in different cell lines, the most sensitive lines were HeLa and A549, Table 2. The selectivity of the extract for cancer lines is evident when comparing the activity in Table 2, since the ARPE-19 line (non-cancerous line used as control) has a lower sensitivity than cancer lines, this can be tried to explain since the cancer cells, being in a state of massive and uncontrolled proliferation, need different signaling pathways to support their high proliferation metabolism, conveniently changing their energy production from one pathway to another, such as the overexpression of Na+/K+ pumps; epidermal growth receptors (EGFR), insulin receptors, etc.13 Therefore, it is hypothesized that the components present in the A. subulata extract could be inhibiting some growth receptors over-expressed in these cell lines, such as EGFR. Rascon et al, 2015 reported the antiproliferative activity by IC50 of a methanol extract in A549 (8.7 μg/mL) and HeLa (<0.4 μg/mL) cell lines;5 in the present study, an increase in activity was achieved following the activity patterns reported by Rascon et al. 2015 reporting the increase in antiproliferative activity when using an ethanolic fraction,5 which was verified by generating an ethanolic extract and observing the increase in antiproliferative activity at 0.23 μg/mL in A549 and 0.6 in HeLa, respectively, Table 1. This is due to the concentration of secondary metabolites (cardenolides) in this fraction. The comparison between the antiproliferative activity of a wild A. subulata extract and an extract from artificial culture is demonstrated by comparing the works of Bustamante et al., 2020 (IC50 0.8 μg/mL),14 Rascon et al., 2015 (IC50 8.7 μg/mL)5 and the present work (IC50 0.23 μg/mL); the wild plant, being in conditions of natural stress, does not modify the production of its secondary metabolites, but in a crop where these stress levels are varied, it can choose the best growing conditions for the plant was harvested and thus generate a better extract with better antiproliferative activity.14,15 In the study by Bustamante et al., 2020 showed a calotropin production (reference cardenolide) of 236. 97 μg/g in average of the generated crop,14 while in this study a concentration of 7.6 mg of calotropin per dry gram of plant is reported.\n\n* Positive control.\n\nThis high difference is being influenced by different biotic stress factors such as the herbalism of the plant by worms of the monarch butterfly and the false monarch at the time of the collection of the plant; Agrawal et al. 2014 established that the increase in the production of cardenolides in Asclepias sicaria and Asclepias halli when they are stimulated by herbalism of monarch butterfly worms, thus showing that the plant increases the production of cardenolides as a defense mechanism.15 The method of quantification of cardenolides is another factor to consider, for his part Bustamante et al., 2020 uses an external standardization pattern while in the present work an internal one was used, managing to eradicate the error of the matrix. It has been shown that the antiproliferative activity of the extracts from Asclepias subulata given by its bioactive principles the cardenolides such as: calotropin, calactin; 4′-hydroxy-7,8-dehydrocalotropin; identified in the plant (supplementary material 2)4 that can interact with the Na+/K+ pump and cell death receptors, caspase activation and mitochondrial membrane depolarization, among other signaling pathways for the generation of cellular apoptosis.8,16 Studies by Rascon et al. 2015 demonstrated that the Asclepias subulata extract could induce cell apoptosis through the activation of caspases 3, 8 and 9 and the depolarization of mitochondria, hypothesizing that the activation of apoptosis occurs intrinsically.4,5,8 More recent studies have shown that cardenolides can activate various metabolic pathways that induce apoptosis, the most defined mechanism being the interaction they have with the sodium potassium pump, since when interacting with it they generate a conformational change that induces the activation of the protein. c-Src tyrosine kinase, which interacts with the epidermal growth receptor (EGFR) and the activation of the Ras-Raf pathway by activating the protein by phosphorylation Ras which in turn initiates the downstream signaling pathway of Raf, Mek and Erk that leads to the production of reactive oxygen species and activation of pro-apoptotic proteins such as Bax and the decline of anti-apoptotic proteins of the BCL-2 family, the depolarization of the mitochondrial membrane and activation of caspases, activation of cycle arrest proteins in cells such as p53 and p21 that together act for the activation of cellular apoptosis.4,5,8,9 It is hypothesized that this pathway is the mechanism of action of the generated extract and to achieve its clarification it is of vital importance to evaluate the proteins involved such as p53, Bax, Ras, Raf among others to establish it.\n\n\nConclusions\n\nAn ethanolic extract of Asclepias subulata was generated with a concentration of 7.6 mg of calotropin per gram of dry weight with IC50 less than 1 μg/mL in different cell lines, presenting better activity in cell lines such as HeLa and A549, which places it as an extract with activity antiproliferative candidate for generation of phytopreparation against cancer.\n\n\nData availability\n\nOpen Science Framework: Antiproliferative activity of standardized herbal phytopreparation from Asclepias subulate, https://doi.org/10.17605/OSF.IO/NC5V3.17\n\nThis project contains the following underlying data:\n\n- Mass data.rar\n\n- Francisco_4′-hydroxy-7,8-dehydrocalotropin.zip\n\n- Francisco_Calactin.zip\n\n- Francisco_Calotropin.zip\n\n- Calibration curve data\n\nOpen Science Framework: Antiproliferative activity of standardized herbal phytopreparation from Asclepias subulate, https://doi.org/10.17605/OSF.IO/NC5V3.17\n\nThis project contains the following extended data:\n\n- Compounds identified by HPLC-MS from ethanolic extract of Asclepias subulata.docx\n\n- Spectrometric data from 1H-RMN y 13C-RMN for compounds A and B in CD3OH δ expressed in ppm.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nINEGI: “Statistics on … World Cancer Day (February 4)”. national data. National Institute of Statistics and Geography, Mexico. 2020. November 09 of 2021. Reference Source\n\nKhan T, Ali M, Khan A, et al.: Anticancer Plants: A Review of the Active Phytochemicals, Applications in Animal Models, and Regulatory Aspects. Biomolecules. 2020; 10(1): 47. PubMed Abstract | Publisher Full Text\n\nVidal M, Torres H, Hernandez S, et al.: Antiproliferative activity of standardized phytopreparations from Ibervillea sonorae (S. Watson) Greene. Steroids. 2021; 169: 108824. PubMed Abstract | Publisher Full Text\n\nRascón LA, Velazquez CA, Garibay A, et al.: Antiproliferative activity of cardenolide glycosides from Asclepias subulata. J. Ethnopharmacol. 2015; 171: 280–286. PubMed Abstract | Publisher Full Text\n\nRascón LA, Jimenez M, Velazquez CA, et al.: Antiproliferative and apoptotic activities of extracts of Asclepias subulata. Pharm. Biol. 2015; 53(12): 1741–1751. PubMed Abstract | Publisher Full Text\n\nWen S, Chen Y, Lu Y, et al.: Cardenolides from the Apocynaceae family and their anticancer activity. Fitoterapia. 2016; 112: 74–84. PubMed Abstract | Publisher Full Text\n\nNagy M: Cardiac Glycosides in Medicinal Plants. INTECH open science; World’s largest Science, Technology & Medicine Open Access book publisher. 2017; (2): 29–45. Publisher Full Text\n\nRascón LA, Velázquez C, Garibay A, et al.: Apoptotic activities of cardenolide glycosides from Asclepias subulata. J. Ethnopharmacol. 2016; 193: 303–311. PubMed Abstract | Publisher Full Text\n\nZüst T, Petschenka G, Hastings AP, et al.: Toxicity of Milkweed Leaves and Latex: Chromatographic Quantification Versus Biological Activity of Cardenolides in 16 Asclepias Species. J. Chem. Ecol. 2018; 45: 50–60. Publisher Full Text\n\nMohamed NH, Liu M, Alwahibi LH, et al.: Cytotoxic cardenolides from the latex of Calotropis procera. Bioorg. Med. Chem. Lett. 2015; 25: 4615–4620. PubMed Abstract | Publisher Full Text\n\nDelgado G, Romo A: Quality control of phytopharmaceuticals. Selected Topics in Chemistry of Natural Products (Spanish). First edition.DF, Mexico: National Autonomous University of Mexico; 2015; 435–474.\n\nYin H, Qu J, Peng Q, et al.: Molecular mechanisms of EBV-driven cell cycle progression and oncogenesis. Med. Microbiol. Immunol. 2018; 208: 573–583. PubMed Abstract | Publisher Full Text\n\nPeiris M, Martinez U, Pestell R, et al.: Cancer stem cell metabolism2. Breast Cancer Res. 2016; 18: 55. PubMed Abstract | Publisher Full Text\n\nBustamante HG, Lopez J, Rodríguez JC, et al.: Quantification of cardenolide glycosides and antiproliferative activity from a crop of the medicinal plant Asclepias subulata. Ind. Crop. Prod. 2020; 158: 112952. Publisher Full Text\n\nAgrawal A, Hastings A, Patrick E, et al.: Specificity of Herbivore-Induced Hormonal Signaling and Defensive Traits in Five Closely Related Milkweeds (Asclepias spp.). J ChemEcol. 2014; 40: 717–729. PubMed Abstract | Publisher Full Text\n\nNewman R, Yang P, Pawlus A, et al.: Cardial glycosides as novel cancer therapeutic agents. Mol. Interv. 2008; 8: 36–49. Publisher Full Text\n\nGonzalez Gutierrez FH: Antiproliferative activity of standardized herbal phytopreparation from Asclepias subulate [dataset].2022. Publisher Full Text"
}
|
[
{
"id": "137993",
"date": "07 Jun 2022",
"name": "Shadma Wahab",
"expertise": [
"Reviewer Expertise Isolation and Identification of natural products",
"Molecular Docking",
"anticancer",
"antifungal",
"antibacterial antidiabetic activities of plants and their constituents."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nActivity against cell proliferation of a standardized herbal Phyto preparation derived from Asclepias subulata has been reported in this study. After reviewing, I found the noticeable strengths in the article; however, the study needs Major revision before final acceptance. Further, my comments on the article are as follows:\nWhat is the rationale for selection for the proposed antiproliferative activity? The introduction section can be revised to justify the type of activity preferred and the rationale behind that.\n\nWhy has the author chosen aerial parts of A. subulata for antiproliferative activity?\n\nWhy was the maceration method selected to prepare the extract? Please put the appropriate reference for the chosen method.\n\nInformation on the chemicals used in the study is missing.\n\nWhy was the solvent ethanol selected as extracting solvent? Why not any other solvent?\n\nDiscussion should be the interpretation of the results, not just the explanation of the results. Hence must be result-oriented.\n\nPlease revise the conclusion section, and future recommendations should be included.\n\nAdd some recent references in the methodology part.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "8828",
"date": "25 Oct 2022",
"name": "Ramón Enrique Robles Zepeda",
"role": "Author Response",
"response": "Firstly, we would like to thank you for considering our work for indexing and secondly, thank you for your comments, which we allow ourselves to refute in some cases and follow up and change for your advice. Next, we present each of them: 1.- What is the rationale for selection for the proposed antiproliferative activity? The introduction section can be revised to justify the type of activity preferred and the rationale behind that. Thank you for considering the reading of the article and its corrections; Considering point number one, we allow ourselves to differ from your comment since the introduction is handled based on the collaborative work of our working group where the high antiproliferative activity of the phytopreparation is specified, which is reflected in articles cited in the publication, such as: Rascon et al 2015. 2.- Why has the author chosen aerial parts of A. subulata for antiproliferative activity? In consideration of this question, in our work we are trying to establish the potential of a phytopreparation of an endemic plant from the northwest of the state of Sonora; whereby; the total deforestation of the plant is not convenient for our future work; Likewise, it is known that the main secondary metabolites of the plant (cardenolides) are distributed in the aerial part of the plant, since they are used as a defense mechanism against predation. Agrawal A. Hastings A. Patrick E. Knight A. Specificity of Herbivore-Induced Hormonal Signaling and Defensive Traits in Five Closely Related Milkweeds (Asclepias spp.) J ChemEcol. 2014.1-13. Doi: 10.1007/s10886-014-0449-6. 3.- Why was the maceration method selected to prepare the extract? Please put the appropriate reference for the chosen method. I appreciate the correction of the bibliographic citation, which was added to the text, as well as the greater detail of the technique used. 4.- Information on the chemicals used in the study is missing. In consideration of this point, the information on each of the chemicals used in the study was added to the complementary material part, thanks for noting the lack of information. 5.- Why was the solvent ethanol selected as extracting solvent? Why not any other solvent? In our group, we worked with methanolic extracts of Asclepias subulata (Rascon et al. 2015), as well as its fractions with different solvents changing their polarity; It was observed that the one with the best biological activity was the ethanolic fraction, as well as in which the bioactive compounds were found, for this reason we worked with this fraction. Later, Bustamante et al., 2020, established the conditions to be able to work with the ethanolic extract and the concentration of the bioactive compounds. Based on these two works, the decision was made to work with the same ethanolic extract that are expressed in the work under review. 6.- Discussion should be the interpretation of the results, not just the explanation of the results. Hence must be result oriented. In reference to this point, the discussion was improved both in terms of writing and information. Thanks for your opinion. 7.- Please revise the conclusion section, and future recommendations should be included. Considering this point, the conclusion was modified giving a final point of recommendation following the mentioned point of view. An ethanolic extract of Asclepias subulata was generated with a concentration of 7.6 mg of calotropin per gram of dry weight with IC50 less than 1 μg/mL in different cell lines, presenting better activity in cell lines such as HeLa and A549, which places it as an extract with antiproliferative activity that is a candidate for the generation of a phytopreparation against cancer in the near future, it is recommended to evaluate the route of action both in vitro and in vivo to reinforce the acceptance and generation of the phytopreparation. 8. Add some recent references in the methodology part. 1.- Vidal M, Torres H, Hernandez S, et al.: Antiproliferative activity of standardized phytopreparations from Ibervillea sonorae (S. Watson) Greene. Steroids. 2021; 169: 108824. 2.- Wambua J, Wafula P, Muhoro J, Naulikha S.: In vitro anti-cancer efficacy and phyto-chemical screening of solvent extracts of Kigelia africana (Lam.) Benth. 2020; e04481. https://doi.org/10.1016/j.heliyon.2020.e04481"
}
]
},
{
"id": "139841",
"date": "21 Jun 2022",
"name": "Juan Carlos Sepúlveda-Arias",
"expertise": [
"Reviewer Expertise Biological activity of natural products",
"Immunomodulation",
"Immunology",
"Molecular Biology",
"Biotechnology."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGonzález Gutierrez et al. did evaluate the antiproliferative activity of a standardized ethanolic extract obtained from the aerial parts of Asclepias subulata. The extract was standardized base on different concentrations of calotropin. The work presented is part of a research line aimed at studying the composition and biological activity of extract obtained from Asclepias subulata from the región of Sonora, as evidenced by previous publications. I consider that the manuscript is important and interesting. However, I have some minor considerations:\nThe concentrations of calotropin in the extracts used for the standardization are presented in the abstract as 'mg/dL', in methods as 'mg/mL', and in the antiproliferative activity section also as 'mg/dL' - please correct.\n\nI suggest including in table 1 the Selectivity Index values.\n\nPlease include the number of experiments and replicates used to evaluate the antiproliferative activity. Also, I suggest revising the statistical analysis and considering using the Kruskal-Wallis test with Dunn´s post hoc test.\n\nPlease edit the language and grammar because some parts are difficult to follow (please revise the annotated copy of the article I have attached here).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8829",
"date": "25 Oct 2022",
"name": "Ramón Enrique Robles Zepeda",
"role": "Author Response",
"response": "Firstly, we would like to thank you for considering our work for indexing and secondly, thank you for your comments, which we allow ourselves to refute in some cases and follow up and change for your advice. Next, we present each of them: 1. The concentrations of calotropin in the extracts used for the standardization are resented in the abstract as 'mg/dL', in methods as 'mg/mL', and in the antiproliferative activity section also as 'mg/dL' - please correct. Thanks for the comments, regarding the different measurement units used, they are correct, to generate a phytopreparation with visualization to be used in in vivo models, it was necessary to use units of mg/dL, however in the in vitro evaluation and for the standardization of the phytopreparation it is necessary to use units in mg/mL. 2. I suggest including in table 1 the Selectivity Index values. It was included. 3. Please include the number of experiments and replicates used to evaluate the antiproliferative activity. Also, I suggest revising the statistical analysis and considering using the Kruskal-Wallis test with Dunn´s post hoc test. Thank you for noting the lack of information, this has already been attached (highlighted in red); Based on the statistical analysis, the analysis of variance test was carried out using the Tukey test, due to the type of study and the type of data generated. 4. Please edit the language and grammar because some parts are difficult to follow (please revise the annotated copy of the article I have attached here). Thank you for providing us with the language fixes, they were all taken into consideration and modified."
}
]
}
] | 1
|
https://f1000research.com/articles/11-527
|
https://f1000research.com/articles/11-1210/v1
|
25 Oct 22
|
{
"type": "Opinion Article",
"title": "Japanese norms in Japanese workplaces",
"authors": [
"Liang Morita"
],
"abstract": "Japan is known for its exclusionary tendencies and clearly delineated Japanese way of doing things. Seeing as its immigration law was amended in April 2019 to allow more migrant workers into the country, there is some urgency in studying these ethnocentric practices, which often lead to inequalities between Japanese and foreign employees at the workplace. The objective of this opinion piece is to help the reader understand the sociocultural context and rationale behind Japanese norms in blue- and white-collar workplaces, as well as foreign employees’ reactions and points of view. Such understanding will hopefully increase both Japanese and foreign employees’ willingness to accommodate each other, and reduce friction and conflict at the workplace.",
"keywords": [
"Japan",
"workplace",
"migrant workers",
"immigration"
],
"content": "1. Introduction\n\nThe COVID-19 pandemic has shown us that migrant workers are essential to economies around the world, although acknowledgement of this fact and respect for them are lacking (Cremers, 2022). Recent research on migrant workers in blue-collar workplaces in Europe has revealed inequalities between migrant workers and local workers (Dijkstra et al., 2020; Kraft, 2019a, 2019b; Lonsmann and Kraft, 2018). These inequalities include migrant workers being perceived as incompetent in spite of evidence that they perform their jobs well. The inequalities are mostly due to local co-workers and employers’ insistence on doing things their way. In Kraft’s work on a Norwegian construction site, for example, Polish workers’ abilities are often underestimated because they do not speak Norwegian and they work in ways that differ from Norwegian norms. These negative attitudes are exacerbated by racialised assumptions about migrant workers from lower-income countries being limited in what they can do (Liu-Farrer et al., 2021). A racial hierarchy exists in the minds of many of the stakeholders of cross-border migration, which assigns those who are white and from high-income European countries to the top of the hierarchy, while those of other races and from less wealthy parts of the world are destined for the bottom (Liu-Farrer et al., 2021).\n\nJapan is known for its exclusionary attitudes towards migrant workers (Doudou, 2006; Morita, 2015; Park, 2017)1, so it is reasonable to ask if Japanese co-workers and employers are also ethnocentric in the way they run the workplace. Since the Japanese immigration law was changed in April 2019 to accept more migrant workers, and more will arrive now that the stringent pandemic entry requirements have eased, there is some urgency in pursuing this line of research.\n\nCompared to many countries in Europe and North America, fewer studies of foreign employees in Japanese workplaces have been conducted. There are even fewer of migrant workers in blue-collar workplaces. However, one of the areas which has been relatively well-researched is Japanese-style human resource management (HRM) in white-collar workplaces (such as Maki et al., 2015; Sekiguchi et al., 2016; Froese et al., 2020); as well as foreign fresh graduates (FFGs) in Japanese companies (such as Conrad and Meyer-Ohle, 2019, 2020). The third area which has been studied is prejudice and discrimination faced by Nikkeijin (Japanese-Brazilians) in blue-collar workplaces (such as Morita, 2016, 2017c; Tsuda, 2009, 2021). Finally, there is a small number of publications on the ‘Japanese language only’ attitude in blue-collar workplaces (Morita, 2021a).\n\nThis opinion article will show that in all four types of research mentioned above, Japanese co-workers and employers are ethnocentric and they insist on doing things the Japanese way. Rather than being a theoretical study of Japanese workplace behaviour, the objective of this article to is help the reader understand, in practical ways and on the ground, the sociocultural context and rationale behind such behaviour, as well as foreign employees’ reactions and points of view. The author hopes that such understanding will eventually lead to an increase in both Japanese and foreigner employees’ willingness to accommodate each other, and therefore reduce friction and conflict at the workplace.\n\nThe case of Nikkeijin will be used here as an example of the analysis presented in this article. The Nikkeijin are descendants of Japanese emigrants who left Japan for better fortunes in the Americas. Most of them are Japanese-Brazilians who started to return to Japan in the late 1980s due to the economic downturn in Brazil and flourishing Japanese economy. They mostly took up unskilled positions in construction and manufacturing (Tsuda, 2021). Lawmakers created a new visa category, which is said to enable the Nikkeijin to return to the country of their ancestors in order to learn more about their ancestry. In reality, this is a visa which allows the Nikkeijin to live and work in Japan, and therefore alleviate the labour shortage. This is an exception made for the Nikkeijin, since Japan had not accepted unskilled foreign workers until then. The rationale behind this manoeuvre was that since the Nikkeijin were descendants of the Japanese, they should be able to fit into Japanese society without causing any damage to the homogeneity of the Japanese population. This reasoning was flawed, as lawmakers and other Japanese soon found out that the Nikkeijin were culturally Brazilian. Most of them did not speak Japanese, and they behaved fundamentally as Brazilians (Tsuda, 2009, 2021). The Japanese reacted negatively to this, and soon changed their perception of the Nikkeijin from ‘descendants of Japanese’ to ‘unskilled workers from a poor and undeveloped country’. Racist incidents against the Nikkeijin were common (Morita, 2015, 2017c; Tsuda, 2021). The Nikkeijin reacted to this prejudice and discrimination by withdrawing into their own community, avoiding contact with the wider Japanese society as much as they can.\n\nOne of the lessons we can learn from the case of the Nikkeijin is that many Japanese are quick to judge migrant workers based on an internalised hierarchy of countries, with the wealthiest at the top and the poorest at the bottom (Tsuda, 2021). They may be prejudiced against people from low-income countries, as they think of these countries as backward and unsophisticated. This should alert us to the possibility of similar prejudices against migrant workers from other low-income countries.\n\nThe Nikkeijin will be discussed in greater detail in Section 4. The next section (Section 2) will explain the Japanese tendency to clearly delineate the Japanese way of doing things vis-à-vis the rest of the world. This is followed by Section 3, which is on Japanese-style HRM in white-collar workplaces (including FFGs), after which the ‘Japanese language only’ attitude in blue-collar workplaces is discussed in Section 5. The article ends with discussion and concluding remarks in Section 6.\n\n\n2. The tendency to clearly delineate the Japanese way of doing things\n\nMany people around the world are ethnocentric to some degree, so it is no surprise that the Japanese are ethnocentric. However, the course of events that have shaped Japanese ethnocentricity is unique and interesting. The next few paragraphs will draw on Rivers’ (2018) work, which lays out the key developments of Japanese ethnocentricity, beginning at the Meiji Era.\n\nSince the Meiji Era (1868-1912), Japan has been troubled by a sense of insecurity and anxiety concerning its survival (Rivers, 2018). There has been an undercurrent of collective insecurity and anxiety about the country’s identity, as well as a narrative of the nation, people, and language being under a state of constant threat and danger from contamination or corruption. This insecurity and anxiety can be clearly seen at the end of the Second World War, when Japan was devastated and humiliated by the US army.\n\nThe Japanese lived with their national pride at a low ebb until the end of the 1960s, when a type of discourse known as Nihonjinron emerged to provide them with an identity that restored their pride (Rivers, 2018). Nihonjinron writing appeared in books and in articles in magazines, newspapers and elsewhere, emphasising the uniqueness of the Japanese. Japanese people, language, culture, and customs were said to be extremely unique, and a line was drawn between what was Japanese and what was not. This type of writing also stressed the strong connection between the Japanese and the land they occupy.\n\nPride in being Japanese swelled during the bubble economy years of the 1980s (Rivers, 2018). When the bubble burst in the 1990s, morale was once again low. In April 1999, right-wing politician Ishihara Shintaro was elected as Governor of Tokyo, and until he resigned in October 2012, he boosted national pride. One of Ishihara’s main campaign promises was to restore Japanese pride and confidence. He clearly distinguished what was Japanese from what was not, as well as established a belief in a strong and capable Japan. Ishihara brazenly labelled all migrant workers as criminals, as well as claimed that Japan was ethnically and culturally homogeneous, and would self-destruct if not consciously preserved.\n\nThis legacy of Nihonjinron and Ishihara has clearly delineated who and what is Japanese, versus who and what is not. In the present-day, everyday life, this has translated into the Japanese way of doing things versus the foreign (Morita, 2015, 2018). The following three examples (the first two from Nagy, 2012 and the third from Morita, 2015) illustrate this point.\n\nIn the context of interviewing Japanese respondents on whether to introduce multilingual services for foreign residents in Tokyo, a respondent pointed out that migrant workers should conduct their lives the Japanese way since they have come to Japan, and not expect the Japanese to accommodate them:\n\n‘It is natural that foreigners who come to Japan should do things the Japanese way. It’s strange that we provide special services for them. We should not give them any special treatment.’ (Nagy, 2012: 133)\n\nIn a different interview, the managing director of an organisation for cultural and international exchange in Tokyo emphasised to Nagy (2012: 132) that foreign residents must adapt to the Japanese way of life and not expect the Japanese to bend to their ways. Migrant workers must also minimise disruptions and disturbances to Japanese lives:\n\n‘Multicultural coexistence practices are not about creating a municipality that minorities want to come to; rather, it is about maintaining the integrity of the Japanese community, ensuring that the foreigners that do settle temporarily or for the long term don’t disrupt the traditional patterns of life. Multicultural coexistence programs provide foreign residents with knowledge about Japanese customs and manners so they can avoid causing problems with Japanese residents.’\n\n‘Multicultural coexistence’ refers to a government programme which helps foreign residents settle into their lives in Japan, mostly through the provision of multilingual services and Japanese language classes.\n\nIn the final example, a British resident who responded to Morita’s (2015: 18) questionnaire in her study of discrimination against foreign residents encountered confrontational behaviour when he did not conform to Japanese ways:\n\n‘I know that, in Nagoya, when I transgress a system even when that system is simply advisory like the date to pick up at the dry cleaners … they have been very confrontational. I assume this is based on the fact that I am foreign and must comply with Japanese rules to the very letter, but the exact rationale isn’t clear to me as I find it hard to see their point of view on this.’\n\nWhat the dry cleaners had failed to explain was that there was an unwritten rule requiring customers to pick up their dry cleaning as soon as it is ready, the reason being limited storage space in the shop. The British respondent had been accustomed to collecting his suits at his leisure and convenience, and was unaware of the Japanese norm.\n\nSections 3, 4 and 5 will show how this emphasis on Japanese norms manifests itself in both blue- and white-collar workplaces.\n\n\n3. Japanese-style human resource management in white-collar workplaces\n\nSekiguchi and his colleagues’ (Maki et al., 2015; Sekiguchi et al., 2016; Froese et al., 2020) comprehensive study of Japanese-style human resource management (HRM), together with Conrad and Meyer-Ohle’s (2019, 2020) focus on foreign fresh university graduates (FFGs) in Japanese companies, offer us an avenue to understanding the experiences of foreign employees in Japanese companies. They paint a picture of Japanese employers insisting on Japanese-style HRM, in spite of its obvious incompatibility with foreign employees (Sekiguchi et al., 2016; Froese et al., 2020). Nonetheless, these employees are expected to conform.\n\nSeveral characteristics of Japanese workplaces will be discussed in this section, beginning with seniority-based pay and promotion, and life-long employment, which are regarded as pillars of Japanese HRM (Froese et al., 2020). Japanese MNCs have tried to replace seniority-based earnings with Western-style performance- or merit-based criteria, but the changes have not been significant (Froese et al., 2020). Many foreign employees have not made plans to work in Japan for long periods of time, so salary increments and promotion calculated according to long-term employment are unattractive to them (Morita, 2018). For the same reason, starting salaries and the speed of career development can appear to be lower and slower when compared to other high-income countries. Long-term employment is the norm for core employees, the vast majority of whom are Japanese. Having said that, in order to reduce costs, companies have been hiring more fixed-term, contract-based Japanese employees. Its numbers have been increasing steadily (Froese et al., 2020).\n\nA common dissatisfaction with working in Japanese companies is that employees have little say in whereabouts they work in the company, both when they first enter the company and subsequently when they are moved to other departments (Conrad and Meyer-Ohler, 2019). Japanese companies usually hire their employees at entry level when they are fresh graduates, and from their point of view, gradually develop them by rotating them through different departments and positions in the company (Sekiguchi et al., 2016). New employees first participate in an orientation programme that introduces the company and teaches business manners and behaviour. After that, these employees are assigned their first positions, but continue to take part in regular centralised training programmes (Conrad and Meyer-Ohler, 2019). Human resource departments emphasise that companies have the freedom to place new employees wherever they want to, since they are not hired for specific positions. Many new employees are first posted to domestic sales, which companies claim is the best place for them to get to know the business (Conrad and Meyer-Ohler, 2019). After two to three years, these employees are usually rotated to a different department.\n\nFrom foreign employees’ point of view, their job descriptions are too broad and general (Conrad and Meyer-Ohle, 2019). Employers stress that they have the right to assign employees to wherever they see fit, and from their experience, those who have been rotated around the various departments of the company learn most and turn out to be the best employees.\n\nAnother characteristic of Japanese companies is having a collectivist culture which emphasises teamwork, consensus-building, and harmony. Companies also have a tendency to follow Confucian traditions, especially the hierarchy in which older people are respected (Froese et al., 2020; Sekiguchi et al., 2016). There is a tendency to form groups, and members make a distinction between who is ‘in’ and who is ‘out’, resulting in clearly delineated in-groups and out-groups. Only a small minority of Japanese multinational corporations (MNCs) use English as their working language (Yamao and Sekiguchi, 2015), and this reinforces in-groups consisting of Japanese-language speakers and out-groups made up of those who do not speak the language, inevitably, the migrant workers. This situation is compounded by the fact that company-specific knowledge and unwritten rules are encoded in Japanese, thereby exacerbating the disadvantage of foreign employees (Froese et al., 2020).\n\nTeamwork and consensus-building, while usually associated with positive effects, can work against foreign employees. In Hof and Tseng’s (2021) study, foreign employees were told that in every situation, they must report to, communicate with, and discuss matters with their teams. Unilateral decision-making is strongly discouraged. From the point of view of foreign employees, Japanese ideas of ‘teamwork’ and ‘consensus-building’ prolong and delay decision-making and decrease efficiency (Hof and Tseng, 2021). Foreign employees who flout the rules risk being reprimanded by their superiors, as seen in the case of a foreign employee in a construction firm. The employee thought her supervisor had given her clear instructions to address some issues in the morning meeting, and proceeded to do so unilaterally, only to be reprimanded afterwards. She was told she should have communicated with her team members and addressed the issues together before acting (Hof and Tseng, 2021).\n\nThere are a few more characteristics of Japanese workplaces which foreign employees are unaccustomed to, such as long working hours. In many cases, this is due to required socialising with clients or co-workers after business hours (Conrad and Meyer-Ohle, 2020). Spending time with co-workers is thought of as building camaraderie. Superiors and subordinates are also expected to socialise in order to build strong bonds between them (Froese et al., 2020). Foreign employees also have to adjust to very low levels of diversity in the workplace and company-specific practices, which they have to learn from scratch and may not be useful in other places of employment (Conrad and Meyer-Ohle, 2020).\n\nIn general, Japanese MNCs have not been successful in internationalising their management, and many still adopt an ethnocentric style (Sekiguchi et al., 2016). Although some companies, especially newer ones, are aggressively internationalising their HRM practices, many MNCs (such as large manufacturers) are hesitant or only doing so slowly. We can see how slowly internationalisation is proceeding from the experiences of FFGs. While many companies have made the initial job application easier by allowing online applications in English, the subsequent selection, socialisation, and training processes are very much the same as those for Japanese employees (Conrad and Meyer-Ohle, 2019).\n\nInstead of trying to accommodate foreign employees or work towards a compromise, Japanese employers have responded to their dissatisfaction by tightening their selection criteria. They show a preference for those who are most likely to accept Japanese-style HRM and are good cultural fits (Conrad and Meyer-Ohle, 2019, 2020; Maki et al., 2015). This defeats the very purpose of hiring foreign employees, which is to internationalise the company. Selecting only those who are like minded does very little towards representing the diversity found in the international markets for the firm’s products and services.\n\n\n4. Prejudice and discrimination against Nikkeijin (Japanese-Brazilians) in blue-collar workplaces\n\nIn the 1950s and 1960s, many Japanese left Japan for Latin America to seek better economic fortunes. The return migrants who started arriving in Japan in the late 1980s are descendants of these Japanese emigrants. The largest group among them are the Japanese-Brazilians, who mostly take up jobs as unskilled factory workers due to the economic crisis in Brazil and severe labour shortage in Japan (Tsuda, 2021).\n\nThe Japanese were initially enthusiastic about welcoming these Nikkeijin back to Japan, expecting them to be fluent in Japanese and well-versed in Japanese culture (Tsuda, 2009). When it transpired that they were culturally Brazilian and spoke little Japanese, the Japanese were disappointed and distanced themselves. The Nikkeijin were at first regarded as Japanese because of their descent, but were downgraded to part-Japanese after direct contact. As the Japanese saw more of them, their attitudes became negative (Morita, 2015).\n\nThe Nikkeijin suffer from discrimination and social class prejudice in their everyday life as well as at work (Morita, 2017c; Tsuda, 2009). The Japanese see Latin America countries as poor, low-status, backward and crime-ridden. In addition, the Nikkeijin are thought of as descendants of poor and uneducated Japanese of low social status who could not survive economically in Japan, and now it appears that these descendants could not make it in Latin American either (Tsuda, 2009).\n\nThere is considerable prejudice against the Nikkeijin based on negative evaluations of their Latin American behaviour (Tsuda, 2009). Their language and cultural differences are a stigma because they have failed to live up to Japanese expectations. Many Japanese measure migrant workers, or part-Japanese, against the highest standards in Japanese language and culture (Hein, 2012). In practice, few can live up to these standards. Migrant workers are expected to embrace Japanese language and culture without being accepted or treated as equals (Hein, 2012). This shows that many Japanese dictate the terms of what they think is appropriate language and cultural standards, with little consideration for migrant workers.\n\nCremers (2022) referred to Central and Eastern European workers in the Dutch labour market as being part of the ‘flexible layer’, which performs unattractive, temporary, and routine work under poor conditions. Recruitment for these jobs exploit legislative loopholes and do not uphold the principle of equal pay for equal work. The same can be said of the Nikkeijin. They are part of the flexible layer in the sense that they are hired when there is a surge in demand for manufacturers’ products, and let go when demand eases (Chiavacci, 2014). They are also the most flexible workers who can be employed at short notice. Although this flexibility is vital to Japanese manufacturers’ competitiveness and success, the Nikkeijin’s employment is extremely vulnerable to economic fluctuations, making it unstable and precarious (Takenoshita, 2015). The COVID pandemic has shown us just how vulnerable they are, as they are the first workers to be laid off. Although some Nikkeijin are employed directly by manufacturers, many are hired by dispatch agencies, which means their earnings are reduced due to agencies’ commissions. They have become indispensable to core sectors of the economy, as they are structurally embedded in key export industries such as automobiles and electronics (Chiavacci, 2014). However, this has come at a personal cost to them, because they are kept in their precarious positions where there is little opportunity for pay increments or full-time employment at dispatch agencies (Ogawa, 2011).\n\nMost Nikkeijin are in fact well-educated and come from a middle-class background (Tsuda, 2009). They worked as professionals or were business owners before coming to Japan. The most commonly offered reason as to why they have ended up in unskilled jobs in Japan is that they lack the Japanese credentials and language skills necessary for professional positions (Takenoshita, 2013). This may sound legitimate and unproblematic, but it reveals much more upon further examination.\n\nIf it is in fact Japanese credentials and language skills which are necessary for highly skilled positions, why is it that the Japanese-Americans are mostly successful in securing highly-skilled positions (Tsuda, 2021)? Most Japanese-Americans attend university in the US, and do not have a strong command of Japanese. The criteria used to define unskilled and highly-skilled migrants are not as objective and unproblematic as they may seem. A range of stakeholders, including national and local governments, employers, migration entrepreneurs and brokers, professional associations, media, and non-governmental organisations, shape and decide who highly-skilled migrants are (Liu-Farrer et al., 2021). Global inequalities as well as power relations between countries have an impact too, resulting in racialised assumptions playing a role instead of the criteria being objective measurements of migrants’ abilities. In South-to-North labour migration, it is usually taken for granted that immigrants from the South are unskilled migrants (Liu-Farrer et al., 2021). Many Japanese think of Brazil as poor and backward, while the US is wealthy and advanced. Labelling the Nikkeijin as unskilled migrants has more to do with Japanese perceptions of Brazil than what they are able or unable to do as workers.\n\nTsuda’s (2009) Japanese respondents thought little of their Nikkei co-workers’ work ethic and ability, and saw them as lazy, slow, irresponsible and careless at work. A Brazilian respondent in Oda’s (2010: 785) study confirmed this:\n\n‘At the company [where I work] we had to assemble a piece and some guy said we should do it this way. But when I look at the drawings, I could see he got it wrong. But he just took the drawings from my hands and ignored me. Why? Because I’m Brazilian! … Because I’m from the third world!’\n\nTsuda (2021) analysed the discrimination against the Nikkeijin as racism, or more specifically, co-ethnic racism. Strictly speaking, the Nikkeijin are of Japanese descent and therefore the same race, and the term ‘racism’ should not apply. Racism is defined as unequal treatment of other groups as inferior based on essentialised and apparently immutable differences, which produces systems of inequality and domination. This definition fits what the Nikkeijin suffer in Japan. Because their national differences are essentialised as immutable and inferior, these differences produce socioeconomic inequalities and hierarchies that are difficult to overcome (Tsuda, 2021).\n\nThese national differences are caused by entrenched global inequalities between developed and developing countries (Tsuda, 2021). These inequalities result from historical-structural forces acting over extended periods of time. In order to illustrate what he meant by ‘national differences’, Tsuda compared the Nikkeijin with the much smaller numbers of Americans of Japanese descent, or Japanese-Americans. In the system of hierarchical class stratification in Japan, Japanese-Americans are positioned much higher than the Nikkeijin because of the immense difference in international status between the US and Brazil.\n\nSince the migrant workers who are most likely to come to Japan are from low-income countries in Asia and therefore rank low in the class hierarchy, they are likely to experience similar discrimination and social class prejudice. This will be taken up again and discussed further in Section 6.\n\n\n5. The ‘Japanese language only’ attitude in blue-collar workplaces\n\nThis section focuses on another line of research which will help us understand what blue-collar workplaces are like for migrant workers. Although there is no official policy on working language in blue-collar workplaces, Morita (2021a) found that Japanese co-workers and employers expect Japanese only. Her research drew on Kusunoki’s (2018) study on foreign nurse trainees in Japanese hospitals, in which Japanese co-workers expected Japanese to be used not just with Japanese co-workers, but also among the trainees themselves. They also underrate the trainees’ Japanese skills, assuming that since they are Japanese, they have the right and authority to dictate the rules on language use and form judgements. This attitude of ‘in Japan we speak Japanese’ can be traced back to Nihinjinron writing (see Section 2), which emphasises the strong connection between the Japanese and the land they occupy.\n\nThree accounts of communication at blue-collar workplaces involving migrant workers are presented in Morita (2021a), in which Japanese co-workers also expect the Japanese language to be used. The first account describes a 2020 Tokyo Olympics construction site, where in spite of an acute labour shortage, migrant workers were assigned only menial tasks such as shifting raw materials. Labour Inspectors noted that the transportation of raw materials could have been carried out much more efficiently with forklifts or other equipment. Migrant workers would then be free to help alleviate the labour shortage. As to why migrant workers were told to move raw materials, given that their co-workers said that they did not speak Japanese and communication was a challenge, it was likely that they were labelled as non-Japanese speakers and seen as capable of menial work only (Morita, 2021a). This echoes Kraft’s (2019a, 2019b) findings concerning Polish workers at a Norwegian construction site, who were also perceived as non-Norwegian speakers and therefore had to be limited to simple tasks. Unlike Polish workers, the migrant workers in Japan had received at least several months’ Japanese language training. Their Japanese skills were clearly underrated, as well as their abilities as workers. The new visa for migrant workers which was introduced in April 2019 requires a pass in a Japanese language test. The test itself is, however, flawed due to its focus on Chinese characters (kanji) and grammar and unlikely to improve their communicative skills at the workplace (Morita, 2021b).\n\nAnother attitude which stood out in the analysis is that only the Japanese language can be used, and if the migrant workers do not speak Japanese, communication is not possible. Kraft (2019a, 2019b) has shown that communication is possible even when Polish workers do not speak Norwegian. It can be achieved with words and fragments of Norwegian, drawings, and gestures, provided both parties are willing to make the effort. Practically all Japanese learn English in middle school and high school, and should therefore be able to remember and use some English words and sentence fragments. When combined with Japanese, drawings, and gestures, communication should be possible to some extent, even if it is limited. The unwillingness to make the effort or consider alternative means of communication appear to be a greater barrier than the migrant workers’ lack of Japanese skills.\n\nThe second account concerns a Vietnamese worker at a Japanese construction firm who complained about having to perform decontamination work in Fukushima although it was not in his job description (Morita, 2021a). The owner of the business also expected only Japanese to be used, and was inconsistent in his opinion as to whether the Vietnamese worker spoke Japanese. It appeared that his judgement shifted depending on what was convenient for him. When he wanted to justify his decision to send the worker to Fukushima, he claimed that the worker did not speak Japanese, or else an explanation would have been provided. Later in the owner’s story, he described a conversation between himself and the worker, one that presumably took place in Japanese, in which he told the worker to return home to Vietnam if he did not want to perform the decontamination work. This shows that judgements on migrant workers’ Japanese abilities are not necessarily objective and consistent.\n\nThe third and final account is about a small Japanese business in which workers resisted the owner’s efforts to internationalise by refusing to use English with foreign co-workers at first, but later relented (Morita, 2021a). At the beginning, Japanese workers spoke Japanese with migrant workers and failed to communicate, resulting in frustration. They threatened to leave their jobs, and at least one of them did. The owner’s insistence on foreign employees being necessary for internationalisation and expansion eventually persuaded the workers to use English. This shows that at least some Japanese workers at the company did have sufficient English language skills to use it at work, despite frequent claims that they were incompetent in English.\n\n\n6. Discussion and concluding remarks\n\nThe presence of migrant workers in Japan should be understood in the context of them meeting the country’s labour needs due to its rapidly aging and declining population. Nihonjiron writing has entrenched the idea that Japan is for the Japanese only (see Section 2). Ishihara Shintaro (see Section 2) has made the idea of migrant workers worse by calling them criminals. While it is true that some migrant workers commit crimes, the media has blown these crimes out of proportion (Morita, 2017a, 2017b). The idea that migrant workers are opportunistic individuals who have come to Japan for the sole purpose of making money (Morita, 2021a) has also biased the Japanese into forgetting that migrant workers need to make a living and that they are humans.\n\nThe studies cited in the section on Japanese-style HRM (Section 3) have observed that when asked to accommodate foreign employees’ needs, human resource departments have flatly refused to do so. While it is true that Japanese-style HRM works well in the Japanese context, human resource employees may be unaware of the contextual differences outside Japan. If they were to develop some awareness and understanding of these differences and the resulting HRM practices, they may be more patient and able to empathise when handling foreign employees’ complaints. The inclusion of materials on foreign HRM practices in their training may be a wise move.\n\nConcerning the tendency to rank countries and their people according to their economic power (see Section 4), leaders and educators could encourage the public to be less materialistic. While the economic differences cannot be disputed, as people all are equal. The effects of prejudice and discrimination on their victims should also be made known. One of them is to cause the Nikkeijin to withdraw from Japanese society and form their own self-sufficient communities (Tsuda, 2009).\n\nBlue-collar Japanese workers could be reminded that migrant workers are in Japan to ease the labour shortage, and that it is to everyone’s advantage if they make an effort to communicate with them. This will hopefully increase Japanese workers’ willingness to make themselves understood and understand migrant workers. Terms such as ‘Cool Japan’ are popular with the Japanese and have become buzzwords. English-speaking business leaders such as Mikitani Hiroshi (of Rakuten) and Maezawa Yusaku (of Zozotown) could lead the way in encouraging the public to use some English, linking it to ‘Cool Japan’. The Emperor and Empress attended the recent funeral of Queen Elizabeth II, and were seen conversing with other foreign dignitaries in photographs and video footage. The fact that they both speak English could be highlighted.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgment\n\nThe authors would like to state that the previous version of this manuscript was published as a pre-print and available at SSRN: https://ssrn.com/abstract=4066871 or http://dx.doi.org/10.2139/ssrn.4066871.\n\n\nReferences\n\nChiavacci D: Indispensable future workforce or internal security threat? Securing Japan’s future and immigration.Vosse W, Drifte R, Blechinger-Talcott V, editors. Governing Insecurity in Japan: The Domestic Discourse and Policy Response. Abingdon:Routledge;2014; (pp. 115–140).\n\nConrad H, Meyer-Ohle H: Overcoming the ethnocentric firm? – foreign fresh university graduate employment in Japan as a new international human resource development method. Int. J. Hum. Resour. Manag. 2019; 30(17): 2525–2543.\n\nConrad H, Meyer-Ohle H: Training regimes and diversity: experiences of young foreign employees in Japanese headquarters. Work Employ. Soc. 2020.\n\nCremers J: Invisible but not unlimited – migrant workers and their working and living conditions. Transfer. 2022; 28(2): 285–289. Publisher Full Text\n\nDijkstra BE, Coler M, Redeker G: The multilingual workplace realities of Polish truckers: A case study in the Netherlands. Multilingua. 2020; 1–28.\n\nDoudou D: Racism, Racial Discrimination, Xenophobia and All Forms of Discrimination: Report of the Special Rapporteur on Contemporary Forms of Racism, Racial Discrimination, Xenophobia and Related Intolerance. Geneva:United Nations;2006.\n\nFroese FJ, Shen J, Sekiguchi T, et al.: Liability of Asianness? Global talent management challenges of Chinese, Japanese, and Korean multinationals. Hum. Resour. Manag. Rev. 2020; 30: 100776. Publisher Full Text\n\nHein P: Does ethnic origin determine integration success? A comparison of immigration policies in Germany and Japan. Asian Ethnicity. 2012; 13(2): 161–185. Publisher Full Text\n\nHof H, Tseng Y-F: When “global talents” struggle to become local workers: The new face of skilled migration to corporate Japan. Asian Pac. Migr. J. 2021; 29(4): 511–531. Publisher Full Text\n\nKraft K: Language policies and linguistic competence: New speakers in the Norwegian construction industry. Lang. Policy. 2019a; 18: 573–591. Publisher Full Text\n\nKraft K:Linguistic securitisation as a governmentality in the neoliberalising welfare state.Martin Rojo L, Del Percio A , editors. Language and Neoliberal Governmentality. Abingdon:Routledge;2019b; (pp. 29–48).\n\nKusunoki R:Japanese native speakers’ perceptions of non-native speakers: Communication between Japanese medical professionals and Economic Partnership Agreement (EPA) nurse trainees.Houghton SA, Hashimoto K, editors. Towards Post-Native-Speakerism: Dynamics and Shifts. Singapore:Springer;2018; (pp.113–127).\n\nLiu-Farrer G, Yeoh BS, Baas M: Social construction of skill: An analytical approach toward the question of skill in cross-border labour mobilities. J. Ethn. Migr. Stud. 2021; 47(10): 2237–2251. Publisher Full Text\n\nLonsmann D, Kraft K: Language policy and practice in multilingual production workplaces. Multilingua. 2018; 37(4): 403–427. Publisher Full Text\n\nMaki M, Ebisuya A, Sekiguchi T: Nihon kigyo honsha ni okeru jinji kokusaika no genjo to kadai [The internationalization of human resource practices in Japanese headquarters]. Multinational Enterprises. 2015; 8(1): 93–113.\n\nMorita L: Some manifestations of Japanese exclusionism. SAGE Open. July-September 2015; 5: 215824401560003–215824401560006. Publisher Full Text\n\nMorita L: A comparison of co-ethnic migrants in Japan and Singapore. Cogent Soc. Sci. 2016; 2(1189386): 1–17. Publisher Full Text\n\nMorita L: Why Japan isn’t more attractive to highly-skilled migrants. Cogent Soc. Sci. 2017a; 3(1306952): 1–12. Publisher Full Text\n\nMorita L: Why Japan needs English. Cogent Soc. Sci. 2017b; 3(1399783): 1–11. Publisher Full Text\n\nMorita L: The potential of bicultural Nikkeijin. Stud. Asian Soc. Sci. 2017c; 4(1): 21–31. Publisher Full Text\n\nMorita L: Does doing things the Japanese way attract highly-skilled migrants? Cogent Soc. Sci. 2018; 4(1430725): 1–12. Publisher Full Text\n\nMorita L: A preliminary study of Japanese co-workers’ attitudes towards migrant workers’ Japanese language skills in blue-collar workplaces. F1000 Res. 2021a; 10: 494. Publisher Full Text\n\nMorita L: Some doubts on the efficacy of the language requirement of the new blue-collar visas in Japan. SSRN. 2021b; 1–13. Publisher Full Text\n\nNagy SR: From temporary migrant to integrated resident: Local government approaches to migrant integration in the Tokyo Metropolis. Asien. 2012; 124: 115–136.\n\nOda E: Family narratives and transforming identities: Three generations of Japanese Brazilians living between Brazil, Japan and beyond. Soc. Identities. 2010; 16(6): 775–790. Publisher Full Text\n\nOgawa N: Population aging and immigration to Japan. Asian Pac. Migr. J. 2011; 20(2): 133–167. Publisher Full Text\n\nPark S: Inventing aliens: Immigration control, ‘xenophobia’ and racism in Japan. Race Class. 2017; 58(3): 64–80. Publisher Full Text\n\nRivers DJ:“Introverted psychosis” and the psychology of native-speaker interaction: Social representation, status and threat perception.Houghton SA, Rivers DJ, Hashimoto K, editors. Beyond Native-Speakerism: Current Explorations and Future Visions. New York:Routledge;2018; (pp. 59–81). Publisher Full Text\n\nSekiguchi T, Froese FJ, Iguchi C: International human resource management of Japanese multinational corporations: Challenges and future directions. Asian Bus. Manag. 2016; 15(2): 83–109. Publisher Full Text\n\nTakenoshita H: Labour market flexibilisation and the disadvantages of immigrant employment: Japanese-Brazilian immigrants in Japan. J. Ethn. Migr. Stud. 2013; 39(7): 1177–1195. Publisher Full Text\n\nTakenoshita H: Social capital and mental health among Brazilian immigrants in Japan. Jpn. J. Sociol. 2015; 24(1): 48–64. Publisher Full Text\n\nTsuda T:Japanese-Brazilian ethnic return migration and the making of Japan’s newest immigrant minority.Weiner M, editor. Japan’s Minorities: The Illusion of Homogeneity. Abingdon:Routledge;2009; (pp. 206–227).\n\nTsuda T: Racism without racial difference? Co-ethnic racism and national hierarchies among Nikkeijin ethnic return migrants in Japan. Ethn. Racial Stud. 2021; 1–21.\n\nYamao S, Sekiguchi T: Employee commitment to corporate globalization: The role of English language proficiency and human resource practices. J. World Bus. 2015; 50(1): 168–179. Publisher Full Text\n\n\nFootnotes\n\n1 Research on migrant workers is a relatively recent field, and while it is growing steadily, there is not exactly an abundance of studies to pick and choose from at the moment. I hope the reader will excuse me for citing my own work."
}
|
[
{
"id": "173795",
"date": "06 Jun 2023",
"name": "Stephen R Nagy",
"expertise": [
"Reviewer Expertise Previously I worked on migration but it is no longer my ares of focus"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author has skillfully investigated Japanese norms in the Japanese work place. Their literature review is robust and covers many of the key thinkers and writers on the topic.\n\nI would only suggest to improve the paper the author could have included more primary source material. They could have also used more Japanese language material to strengthen the comprehensiveness of the literature review.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "173793",
"date": "06 Jun 2023",
"name": "Md Jahangir Alam",
"expertise": [
"Reviewer Expertise Skills for employability"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWell articulated, but I advise the author to read the following papers to establish their argument (Alam et al., 20231 and Alam et al., 20222. The theoretical framework is not clear in this paper. The author might consider reading some articles to develop the theoretical framework.\nIf possible the author should separate the discussion and conclusion part for better understanding.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1210
|
https://f1000research.com/articles/8-1936/v1
|
20 Nov 19
|
{
"type": "Research Article",
"title": "How to promote ‘discipline without tough love’ during pregnancy: a randomized controlled trial",
"authors": [
"Shunji Suzuki"
],
"abstract": "Background: In Japan, the effect of education using the leaflet ‘Discipline Without Tough Love’ on mothers during caring for their infants have been reported. We examined the effect of this education on pregnant Japanese women. Methods: The present study was a prospective investigation of all Japanese women with singleton pregnancies who visited our hospital for a perinatal visit at 20-23 weeks’ gestation between November 2017 and March 2018 and gave birth at ≥ 37 weeks’ gestation at our hospital. We examined the maternal feelings (bonding situation) to babies of women who received the leaflet in comparison with that in women who did not receive it during the health check-up performed routinely at one month after delivery using the Japanese version of the Mother-to-Infant Bonding Scale. Results: There were no significant differences in maternal feelings for their babies between the two groups of women. Conclusions: We did not identify any effect of health consultations cased on ‘Discipline Without Tough Love’ during pregnancy on maternal feelings toward babies at one month after delivery. A further study to enlighten pregnant women about parenting without corporal punishment will be needed in Japan. Registration: Japan Registry of Clinical Trials 1030190112; registered on 5 October 2019.",
"keywords": [
"discipline without tough-love",
"education",
"pregnant women",
"Japan"
],
"content": "Introduction\n\nChildren can adapt themselves and their relationship with their caregivers (parents) in a way incomparable to any other stage of life. If children’s environment is negatively influenced, development of their brain may be impaired1–4. For example, Tomoda et al.2–4 observed that exposure to parental verbal abuse or interparental violence during childhood, leading to ‘multiple forms of childhood maltreatment’, is associated with the incidence of abnormality of the brain structure and/or mental disorders, such as reactive attachment disorders. Although whether spanking is helpful or harmful to children had continued to be a source of considerable debate, meta-analyses focused specifically on spanking representing about 160,000 children by Gershoff and Grogan-Kaylor5 indicated a link between spanking and an increased risk of detrimental child outcomes. In 2016, the rate of Japanese women mistreating their children was reported to be 6–37%6.\n\nBased on this background, in 2016 the Japanese Ministry of Health, Labour and Welfare conducted an enlightenment program to help avoid improper childrearing as ‘Discipline Without Tough Love: Strategy Of Zero Tough Love’ using the leaflet shown in Figure 16. In the leaflet, some of the text for parents is as follows: (1) do not use corporal punishment or ranting for parenting, (2) minimize irritated feelings and send out an ‘SOS’, and (3) support the growth of children while considering children’s emotions and behavior separately because children cannot express an ‘SOS’ by themselves, even if they fear their parents. In Japan, some regional reports concerning the effect of education using the leaflet on mothers during caring for their infants have already been published7. Although it has been considered that the gap between the ideal situation and reality of child rearing in women occurs mainly after childbirth, maternal mental and social conditions during pregnancy are now considered important factors associated with the possibility of subsequent child abuse8.\n\nThe commentaries are as follows: Parents sometimes may get irritated with their children’s attitude during childrearing. Parents sometimes may want to slap or shout at their children. At first glance, the acts of slapping and/or shouting may seem to be effective, but the children usually cannot understand why they were slapped or shouted at. In such situations, the children usually listen to their parents out of fear. Even if your intention regarding hitting and/or shouting is ‘tough love’ at the beginning, the acts may escalate to become abuse unintentionally. Let’s avoid ‘tough love’ leading to corporal punishment or verbal abuse. Let’s keep your emotions hidden from children to raise them healthily.\n\nIn the current study, therefore, we examined the effect of education using the leaflet ‘Discipline Without Tough Love’ on Japanese women during pregnancy.\n\n\nMethods\n\nThis study was conducted after receiving approval from the ethics committee of the Japanese Red Cross Katsushika Maternity Hospital (2017-002). This study was carried out in accordance with the Declaration of Helsinki. Written informed consent from each participant was obtained before enrolment. Blinding was performed in the clinicians responsible for one-month postpartum care.\n\nThe present study was a prospective investigation of all Japanese women with singleton pregnancies who visited our hospital for a perinatal visit at 20–23 weeks’ gestation between November 2017 and March 2018 and delivered a healthy neonate at ≥ 37 weeks’ gestation at our hospital. In this study, we excluded women with perinatal complications such as preterm delivery, low-birth-weight infant, and neonatal asphyxia requiring neonatal admission. This was because individual and important mental health care is needed for mothers whose babies have health problems9,10. When this study was planned, the required sample size was 762 participants for 90% power based on a previous observation in Japan11; the trial recruited 882 participants. In our institute, midwives carry out three health consultations during pregnancy to support the healthy lives of pregnant women. These consultations are at about 8–11, 20–23, and 34–36 weeks’ gestation. During the study period, at the second health consultation at 20–23 weeks’ gestation, the responsible midwife handed the leaflet directly to the pregnant women randomly selected with the comment of ‘a leaflet concerning the things to keep in mind for healthy childrearing after delivery’. In detail, pregnant women were randomly assigned to the two groups (with and without the leaflet) early in the morning on the day of health consultations using a web-based randomization system (Research Randomizer) stratified by parity (primipara vs. multipara) according to the computer-generated randomization code.\n\nIn this study, we examined the maternal feelings (bonding situation) toward babies of women who received the leaflet in comparison with that in women who did not receive it during the routine health check-up performed one month after delivery using the Japanese version of Mother-to-Infant Bonding Scale (MIBS-J), which is a simple self-administrated questionnaire designed to detect problems with a mother’s feelings towards her newborn baby12–15. If a score is higher than 3, there is a possibility that the mother will have problems regarding feelings for her baby. If at least one of the third and fifth questions of MIBS-J (third question: feel resentful toward my baby; fifth question: feel angry toward my baby) is ≥ 1, the possibility of feeling-related problems also existed11,15.\n\nThe items recorded as obstetric and perinatal characteristics that may affect the results were as follows: maternal age, parity, history of abortion, history of infertility treatment, economic problems, results of the modified Violence Against Women Screen (VAWS)16–18, results of the Whooley questions during the early pregnancy18,19, presence or absence of participation in a parents class, and delivery modes.\n\nThe modified VAWS is a Japanese screening instrument for intimate partner violence (IPV) to identify pregnant women who have experienced abuse based on scores using a 3-point Likert scale13–15. The total score ranges from 0–9; a score higher than 2 is positive for IPV. Whooley questions comprise a screening instrument for depression in the general adult population including pregnant and postpartum women17,20. If at least one of the two questions is ‘yes’, we diagnose the woman with depressive symptom.\n\nIf a pregnant woman was supported by the hospitalization assistance policy (HAP) system of the Japanese Child Welfare Government, we defined her as having economic problems21,22. The HAP system assists with delivery costs. The main objectives of the HAP system are to help pregnant women who: 1) receive livelihood protection because they are unable to maintain minimum living standards due to poverty, 2) live in households exempt from residence tax, and 3) live in households in which the income tax is less than ¥8,400 (=about $80 US) per year. In this study, the diagnosis of depression was performed by Japanese psychiatric specialists.\n\nThe parents’ class in our institute is a participatory group offering guidance in which pregnant women can learn about pregnancy, childbirth, and child rearing together with their partners23.\n\nIn Japan, women without obstetric complications can freely select their birthing facility even at late pregnancy. Our institute is one of the major perinatal centers in Tokyo, Japan (about 2,000 deliveries per year); however, medical care by psychiatrists is not carried out. Therefore, almost all pregnant women complicated by depression receive psychotherapy in nearby psychiatric clinics. Neonatal asphyxia was defined as a neonatal Apgar score at 1 or 5 min of < 7. Postpartum hemorrhage was defined as an estimated blood loss of ≥ 1,000 mL. In most cases, the gestational age was defined based on ultrasonography at 9–11 weeks of gestation. In cases with a delayed first visit, the gestational age was confirmed based on Neonatal Neurological Assessment.\n\nThe primary end point of was the effect of the leaflet ‘Discipline Without Tough -Love’ on the score of the MIBS-J in mothers at one month after delivery.\n\nData are expressed as the number (percentage). SPSS Statistics software version 20 (IBM Corp., Armonk, NY, USA) was used for statistical analyses. A chi-square test was used for categorical data, and a p-value < 0.05 was considered significant. Logistic regression analysis was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs).\n\n\nResults\n\nFigure 2 shows a flow diagram for the study. During the study period, 882 pregnant women visited our hospital for a perinatal visit and received the midwives’ health consultations at 20–23 weeks’ gestation. Ultimately, a randomized prospective study was conducted involving 334 women who received the consultations with the leaflet of ‘discipline without tough love’ and 320 women who received the standard consultations without the leaflet as a control group.\n\nTable 1 shows the characteristics of the two groups of women who examined their maternal feelings at one month after delivery using the MIBS-J as follows: those who received the consultations with the ‘discipline without tough love’ leaflet (n = 334), and those who received the standard consultations without the leaflet (n = 320). As shown in Table 1, there were no significant differences in the clinical characteristics such as maternal age, parity, history of infertility treatment, the rate of having economic problems, the rate of positive of the modified VAWS or the Whooleys’ question, or delivery modes between the two groups. These indicate that the randomization of this study was performed equally effectively. Individual-level results are available as Underlying data24.\n\nThe groups consist of those who received consultations with the leaflet of ‘discipline without tough love’ (n = 334), and those received standard consultations without the leaflet (n = 320).\n\nCI, confidence interval; VAWS, Violence Against Women Screen.\n\nTable 2 shows the results of maternal feelings for their babies at one month after delivery using the MIBS-J in the two groups as follows: those who received the consultations with the leaflet of ‘discipline without tough love’, and those who received the standard consultations without the leaflet. As shown in Table 2, there were no significant differences in the rate of score ≥ 3, or yes for the third or the fifth question of the MIBS-J indicating problems with maternal feelings between the two groups.\n\nThe groups consist of those who received consultations with the leaflet of ‘discipline without tough love’ (n = 334), and those received standard consultations without the leaflet (n = 320).\n\nCI, confidence interval.\n\n*Total score and the answer for the third and fifth question of the Japanese version of Mother-to-Infant Bonding Scale (MIBS-J).\n\nThe prevalence of women showing problems with maternal feelings in the control group was 15%. It is estimated that a definitive trial powered to detect the same difference in prevalence would require approximately 556 patients equally divided into the current two groups (two-tailed α = 0.05, β = 0.2), Therefore, the sample size of the current observation would be sufficient. There indicate that the awareness of ‘discipline without tough love’ through the leaflet during pregnancy was not very effective for the maternal feelings at one month after delivery.\n\n\nDiscussion\n\nUnfortunately, in the current study we could not identify any effect of our health consultations with the ‘discipline without tough love’ leaflet at 20–23 weeks’ gestation on maternal feelings for babies at one month after delivery in pregnant Japanese women, although the effect of education using the leaflet on mothers during childcare of their infants was observed based on some regional reports in Japan7. Because the current study is the first trial of the guidance concerning ‘discipline without tough love’ with the leaflet during pregnancy in Japan, a consideration of the guidance methods and/or the leaflet itself may be necessary in the future. However, the period of pregnancy may be too early to teach mothers about ideal childrearing. Alternatively, the timing of one month after delivery may have been too early to assess the problems with maternal feelings toward children. In Japan, the percentage of mothers guilty of child mistreatment has been reported to be about 37% with children aged 3 years old, but only 6% with children of 3–4 months6. Therefore, pregnant Japanese women may be less likely to abuse their children during pregnancy.\n\nAs mentioned in the Introduction, even ‘tough love’ such as rough words and/or striking will traumatize children, even when used as discipline1–4. Therefore, we hope to spread enlightenment to avoid ‘discipline with tough love’. Based on these goals, the current study was performed; however, we did not obtain the expected results. We will perform further studies to enlighten pregnant women about using ‘discipline without tough love’ in Japan.\n\nWe understand that there are some limitations in this study. A first limitation relates to the duration of the trial; the long-term impact of the leaflet cannot be addressed. Because, child abuse had been observed to increase with the age of children6. Therefore, further additional studies with long-term follow-up periods may be needed such as a study at two years after delivery using the MIBS-J. In this study, the intervention was carried out as planned; however, the subjects could not be blinded by receiving the leaflet. In addition, some regional differences of the number of child neglect and emotional abuse have been observed between urban areas and other areas in Japan24. For example, child neglect has been discovered higher in urban areas24. Therefore, the same results may not be able to be expected in other Japanese institutes.\n\nIn conclusion, we could not identify an effect of health consultations concerning ‘discipline without tough love’ during pregnancy on maternal feelings for babies at one month after delivery.\n\n\nData availability\n\nFigshare: Data for ‘How to promote ‘discipline without tough -love’ during pregnancy’. https://doi.org/10.6084/m9.figshare.10259672.v124.\n\nThis project contains data on maternal characteristics and effect of the leaflet on maternal feeling at one month after delivery.\n\nCONSORT checklist for ‘How to promote ‘discipline without tough love’ during pregnancy’. https://doi.org/10.6084/m9.figshare.10308275.v125.\n\nUnderlying data are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\nThe completed CONSORT checklist is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nTomoda A: Preliminary Evidence for Impaired Brain Activity of Neural Reward Processing in Children and Adolescents with Reactive Attachment Disorder. Yakugaku Zasshi. 2016; 136(5): 711–714. PubMed Abstract | Publisher Full Text\n\nTomoda A, Sheu YS, Rabi K, et al.: Exposure to parental verbal abuse is associated with increased gray matter volume in superior temporal gyrus. Neuroimage. 2011; 54 Suppl 1: S280–5286. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTomoda A, Suzuki H, Rabi K, et al.: Reduced prefrontal cortical gray matter volume in young adults exposed to harsh corporal punishment. Neuroimage. 2009; 47 Suppl 2: T66–T71. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFujisawa TX, Shimada K, Takiguchi S, et al.: Type and timing of childhood maltreatment and reduced visual cortex volume in children and adolescents with reactive attachment disorder. Neuroimage Clin. 2018; 20: 216–221. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGershoff ET, Grogan-Kaylor A: Spanking and child outcomes: Old controversies and new meta-analyses. J Fam Psychol. 2016; 30(4): 453–69. PubMed Abstract | Publisher Full Text\n\nMinistry of Health, Labor and Welfare: Measures to prevent child abuse (in Japanese). 2019. Reference Source\n\nKitazawa J, Tachibana Y, Yamazaki Y: Priority task strategy of healthy parents and children 21 (second edition) and ‘strategy of zero tough-love’ (in Japanese). Jpn J Public Health. 2017; 76: A124–A126.\n\nLukasse M, Schroll AM, Ryding EL, et al.: Prevalence of emotional, physical and sexual abuse among pregnant women in six European countries. Acta Obstet Gynecol Scand. 2014; 93(7): 669–677. PubMed Abstract | Publisher Full Text\n\nCherry AS, Mignogna MR, Roddenberry Vaz A, et al.: The contribution of maternal psychological functioning to infant length of stay in the Neonatal Intensive Care Unit. Int J Womens Health. 2016; 8: 233–42. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarris R, Gibbs D, Mangin-Heimos K, et al.: Maternal mental health during the neonatal period: Relationships to the occupation of parenting. Early Hum Dev. 2018; 120: 31–39. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYoshida K, Yamashita H, Conroy S, et al.: A Japanese version of Mother-to-Infant Bonding Scale: factor structure, longitudinal changes and links with maternal mood during the early postnatal period in Japanese mothers. Arch Womens Ment Health. 2012; 15(5): 343–52. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKamibeppu K, Furuta M, Yamashita H, et al.: Training health professionals to detect and support mothers at risk of postpartum depression or infant abuse in the community: a cross-sectional and a before and after study. Biosci Trends. 2009; 3(1): 17–24. PubMed Abstract\n\nWatanabe H: [Mother-infant mental health from viewpoint of relationship disturbance]. Seishin Shinkeigaku Zasshi. 2003; 105(9): 1151–4. PubMed Abstract\n\nKumar R: “Anybody’s child”: severe disorders of mother-to-infant bonding. Br J Psychiatry. 1997; 171: 175–81. PubMed Abstract | Publisher Full Text\n\nJapan Association of Obstetricians and Gynecologists: The Maternal Mental Health-care for Mother and Child (in Japanese). 2019. Reference Source\n\nKataoka Y, Yaji Y, Eto H, et al.: [Domestic violence against women during pregnancy]. Nihon Koshu Eisei Zasshi. 2005; 52(9): 785–95. PubMed Abstract\n\nKataoka Y, Imazeki M, Shinohara E: Survey of intimate partner violence before and during pregnancy among Japanese women. Jpn J Nurs Sci. 2016; 13(1): 189–95. PubMed Abstract | Publisher Full Text\n\nKataoka Y, Yaju Y, Eto H, et al.: Self-administered questionnaire versus interview as a screening method for intimate partner violence in the prenatal setting in Japan: a randomised controlled trial. BMC Pregnancy Childbirth. 2010; 10: 84. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWhooley MA, Avins AL, Miranda J, et al.: Case-finding instruments for depression. Two questions are as good as many. J Gen Intern Med. 1997; 12(7): 439–445. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe National Institute for Health and Care Excellence: Antenatal and postnatal mental health: clinical management and service guidance. Clinical guideline [CG192]. (Published date: December 2014, Last updated: June 2015). Reference Source\n\nHiraizumi Y, Suzuki S: The hospitalization assistance policy system in Japan. J Nippon Med Sch. 2011; 78(4): 267–269. PubMed Abstract | Publisher Full Text\n\nMinistry of Health, Labour and Welfare (Japan): Children and childrearing. 2019. Reference Source\n\nNakamura S, Hirai K, Nomachi N, et al.: Changes in the maternal body during pregnancy (in Japanese). Perinatal Care (Tokyo). 2015; 34 Summer: 78–81.\n\nSuzuki S: Data for 'How to promote ‘discipline without tough-love’ during pregnancy'. figshare. Dataset. 2019. http://www.doi.org/10.6084/m9.figshare.10259672.v1\n\nSuzuki S: CONSORT 2010 Checklist.doc. figshare. Dataset. 2019. http://www.doi.org/10.6084/m9.figshare.10308275.v1"
}
|
[
{
"id": "82574",
"date": "06 Apr 2021",
"name": "Hiroko Iwata",
"expertise": [
"Reviewer Expertise Reproductive health",
"Maternity",
"Parenthood",
"Nursing"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review your manuscript. I hope my comments below help you improve the paper.\nMethods:\nP3: Readers may want to know more about the intervention. Is it that a midwife handed the leaflet with/without explanations? Did you check if the women in the intervention group actually read the leaflet at some point of care?\n\nP4: Please provide reliability and validity information on MIBS-J.\n\nResults:\nP4: I wonder if randomization is conducted after obtaining informed consent from potential participants. Under “Study and participant background”, there is a description of “During the study period, 882 pregnant women visited our hospital for a perinatal visit”, and that figure 2 indicates all 882 women were assessed for eligibility. Did the author ensure voluntary participations?\n\nP4: Because both groups receive some kind of consultations, the author should provide brief contents of consultations in a control group. This is related with the impact of the intervention.\n\nP5: Table 1 needs to be revised appropriately. Table 1 looks like results of logistic regression, not just participants’ characteristics, however, the outcome is the score of the MIBS-J, which may be a continuous variable. It is really confusing. If the author used categorial data, not a continuous data (i.e., the score of the MIBS-J) when conducting logistic regression, you should say so in Methods section. Likewise, table 2 also needs to be revised.\n\nDiscussion:\nP7: What do you mean by “Therefore, pregnant Japanese women may be less likely to abuse their children during pregnancy”?\n\nStructure, grammar and style:\nFigure 2: Please correct “Analuzed” to “Analyzed”.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6580",
"date": "19 Apr 2021",
"name": "Shunji Suzuki",
"role": "Author Response",
"response": "April 11, 2021 Editorial office Dear Editors, I would like to thank you and Dr. Hiroko Iwata for the comments and critique of our manuscript entitled ‘How to promote ‘discipline without tough love’ during pregnancy: a randomized controlled trial. I have been able to respond positively to each suggestion and we believe the paper has been strengthened. The changes are highlighted with red color. To Dr. Hiroko Iwata, Thank you very much for your suggestions. I have been able to respond positively to your each suggestion. Methods 1: The midwives handed the leaflet with explanations what was written; however, we did not check whether or not the women in the intervention group actually read the leaflet. I have added these in the Methods & Discussion. Methods 2: I have provided the suggested information in Ref 11. Results 1: We ensured their voluntary participation by allowing them the freedom not to receive leaflets. I have added this in the Methods. Results 2: The midwives handed the leaflet with explanations what was written. That is, they explained about the child discipline to the pregnant women in the intervention group actively from them; however, we explained to the women in the control group only when asked. I have added these in the Methods. Results 3: Thank you very much for your suggestion. Because this is a prospective study, I have separated Table 1 to 2 tables (Table 1 & 2). Results 4: I have re-written to ‘Therefore, the pregnant Japanese women may not be possible to imagine that they may abuse their children’. Results 5: Thank you very much for your pointing out. Thank you very much for your excellent suggestions, again. I do hope and trust that with these changes the manuscript is now acceptable for indexing. Thank you for considering my paper. Sincerely yours, Shunji Suzuki, MD Department of Obstetrics and Gynecology, Japanese Red Cross Katsushika Maternity Hospital 5-11-12-2 Tateishi, Katsushika-ku, Tokyo 124-0012 Japan Tel: +81-3-3693-5211 Fax: +81-3-3694-8725 e-mail: czg83542@mopera.ne.jp"
}
]
}
] | 1
|
https://f1000research.com/articles/8-1936
|
https://f1000research.com/articles/11-360/v1
|
28 Mar 22
|
{
"type": "Research Article",
"title": "Automated segmentation of endometriosis using transfer learning technique",
"authors": [
"S. Visalaxi",
"T. Sudalaimuthu",
"T. Sudalaimuthu"
],
"abstract": "Background: This paper focuses on segmenting the exact location of endometriosis using the state-of-art technique known as U-Net. Endometriosis is a progressive disorder that has a significant impact on women. The lesion-like appearance that grows inside the uterus and sheds for every periodical cycle is known as endometriosis. If the lesion exists and is transferred to other locations in the women’s reproductive system, it may lead to a serious problem. Besides radiologists deep learning techniques exist for recognizing the presence and aggravation of endometriosis. Methods: The proposed method known as structural similarity analysis of endometriosis (SSAE) identifies the similarity between pathologically identified and annotated images obtained from standardized dataset known as GLENDA v1.5 by implementing two systematic approaches. The first approach is based on semantic segmentation and the second approach uses statistical analysis. Semantic segmentation is a cutting-edge technology for identifying exact locations by performing pixel-level classification. In semantic segmentation, U-Net is a transfer-learning architecture that works effectively for biomedical image classification. The SSAE implements the U-Net architecture for segmenting endometriosis based on the region of occurrence. The second approach proves the similarity between pathologically identified images and the corresponding annotated images using a statistical evaluation. Statistical analysis was performed using calculation of both the mean and standard deviation of all four regions by implementing systematic sampling procedure. Results: The SSAE obtains the intersection over union value of 0.72 and the F1 score of 0.74 for the trained dataset. The means of both the laparoscopic and annotated images for all regions were similar. Consequently, the SSAE facilitated the presence of abnormalities in a specific region. Conclusions: The proposed SSAE approach identifies the affected region using U-Net architecture and systematic sampling procedure.",
"keywords": [
"F1 Score",
"Intersection over Union",
"Segmentation",
"Systematic Sampling",
"U-Net"
],
"content": "Introduction\n\nEndometriosis is a common gynecological problem that occurs in women of aged 18 to 50 years.1 The lesion-like structure that underlines the uterus and other surrounding regions is referred to as endometriosis. Endometriosis along with the uterus affects other regions, including ovaries, peritoneum, and multiple locations known as deep infiltrating endometriosis.2 The most common practice for recognizing endometriosis is laparoscopy.\n\nDeep infiltrating endometriosis (DIE) is a serious concern among women of reproductive age. The DIE affects multiple regions including the uterus, ovaries, gall bladder, liver, and other abdominal regions. DIE also penetrates approximately 4 to 5 mm into the tissues.3,4 DIE is unpredictable at earlier stages and poses a great challenge for gynecologists.\n\nThe greatest problem with endometriosis is unbearable abdominal pain and infertility, which in turn leads to psychological depression and serious health issues includes dysmenorrhea, severe pelvic pain, dyspareunia, frequent urination.5 The advanced stages of endometriosis may lead to endometrial cancer, leading to further complications.6 Computerized diagnosis helps radiologists in identifying the exact location and also precisely recognize abnormalities. Various methods exist for identifying endometriosis including magnetic resonance imaging (MRI), transvaginal scanning (TVUS), and laparoscopic surgery. Among all laparoscopic surgery is considered the best practice to identify the exact location of endometriosis.7 The staging depends on the location and aggravation of the lesion spread across multiple locations. According to the stages of endometriosis, endometriosis is classified as (a) minimal endometriosis, (b) mild endometriosis, (c) advanced or deep endometriosis.\n\nThe proposed work implements the segmentation process using predicted pathological images from earlier work and the corresponding annotated images from the dataset. The proposed work known as structural similarity analysis of endometriosis was validated using two approaches. The first approach was semantic segmentation using U-Net and the second approach used statistical evaluation.\n\nDeep learning serves as a decision support system for radiologists. Deep learning is a state-of-the-art technique for recognizing the affected areas. Among the various deep learning networks, convolution neural networks (CNNs) play a vital role in processing biomedical images. CNNs perform various tasks including classification, prediction, localization, and segmentation. The CNN implements the segmentation process to recognize the pattern and identify the object. Segmentation analyzes the super pixel of each image and classifies them based on various criteria.\n\nSegmentation can be classified majorly into two types: a) instance segmentation, b) semantic segmentation. The combination of these two segmentations is known as panoptic Segmentation.8 Instance segmentation considers multiple objects in the same class in various instances. Semantic segmentation treats multiple objects in a single class as a single instance. Medical images invoke a semantic segmentation. Image segmentation can be implemented effectively using transfer learning architectures including Mask R-CNN, fully convolution neural network (F-CNN), and U-Net architecture.9 In this study, segmentation was used to predict the exact location of the endometriosis by implementing pixel classification.\n\nSemantic segmentation using the U-Net architecture was identified as a prominent segmentation process for biomedical images. U-Net is a transfer learning architecture that invokes CNN for implementing pixel classification. The U-Net architecture applies down sampling to extract more features from an image.10 Statistical analysis plays a predominant role in the validation and verification of medical datasets. The mean and standard deviation were used to analyze each value in the dataset and evaluate the difference in values.\n\n\nRelated studies\n\nLiterature studies used to analyze the similarity between two datasets based on deep learning techniques are discussed below.\n\nSegmentation plays a vital role in recognizing abnormalities. Suggested gonadotrophin releasing hormone is used to improve pregnancy rates in women with and without endometriosis.11 Endometriosis was predicted using the transfer-learning approach. ResNet50 classifies pathological and non-pathological endometriosis with an accuracy rate of 91%.12 Attribute description was developed through “pattern recognition and image processing techniques”. Ultrasonic images are used for extracting features, segmentation of images and so on.13 The segmentation of medical images was implemented using deep-learning techniques. A comparison was performed using supervised and weakly supervised learning techniques.14 Semantic segmentation in biomedical images was analyzed. Traditional segmentation loses pixel quality, whereas semantic segmentation processes preserve pixel quality through down-sampling process. Semantic segmentation invokes a CNN to maintain the pixel quality.15 The process known as automatic augmentation was implemented. The process involves the following steps: a) preprocessing of images b) detection of features c) mask generation d) mask processing and e) segmentation.16 Introduced image segmentation with discriminant analysis of dental radiographs. Because annotation was performed manually, the similarity between the overlapped region and the corresponding samples is preserved.17 The image segmentation was implemented on gastrointestinal images and later applied Machine learning algorithms for transparency.18 Hybrid segmentation known as a 3D residual network was used for identifying tumors in the kidney and liver. The Squeeze-excitation block along with the 3D RN, was used for segmenting the tumors.19 A convolution neural network (CNN) was used to segment skull regions from computed tomography (CT) images. The automated CNN outperforms well with a mean F1 score of 0.92 and a mean deviation of 1.2 mm±1.75 mm.20\n\nVarious architectures exist for semantic segmentation to identify abnormalities. Various learning architectures exist for implementing segmentation. The U-Net architecture plays a predominant role in medical imaging. The U-Net module was implemented for segmenting lung nodules. CT scan images of the lung were used for segmentation with an F1 score of 0.82 and an intersection over union (IOU) value of 0.752.21 A novel method was introduced known as the U-NET transformer that encodes the sequence of input and captures global multiscale information. Performance was evaluated using brain tumor and spleen segmentation tasks.22 The ensemble machine learning model was implemented for evaluating endometriosis. CA-CNN, DFKZnet, and 3D U-Net was adopted to validate the performance of the ensemble learning model.23 The ovaries were classified automatically based on K-means clustering and an artificial neural network using texture features. Three features autocorrelation, average of sum, variance of sum were used for ovarian detection.24 U-Net segmentation was implemented to identify uterine diseases using the MRI images. The mean F1 coefficient was 0.84 and the mean absolute distance was 18.5.25 Mi U-Net is a state-of-art technique that helps segment kidney stones from medical images. The Mi U-Net outperformed well in terms of qualitative and quantitative metrics.26 U-Net and DeeplabV3 segmentations were implemented to identify abnormalities in fetal echocardiograph. Among the two types of segmentation DeeplabV3 performs well and evaluation was performed based on the IOU, F1 Score.27 Docker-based deep learning outperforms other methods for segmenting biomedical images. DDeep3M works effectively on smaller and larger datasets.28 Mask RCNN segmentation was implemented for laparoscopic gynecological images. The model performed well with an accuracy of 95%.29\n\nFrom the literature review, various segmentation processes have been identified to recognize the aggravation of endometriosis. Segmentation was implemented by detecting features, K-means clustering, supervised machine learning algorithms, and neural network algorithms. Manually annotated images were also used to identify the overlapping regions, where pixel classification was not clear. A gap exists in the selection of annotated images and implementation of a suitable segmentation process. Hence the SSAE was implemented using two approaches to analyze the similarity between pathological images from earlier studies and their corresponding annotated images. Semantic segmentation along with U-Net plays a vital role in identifying abnormalities.\n\nSSAE implements a semantic segmentation process to recognize the location and aggravation of endometriosis. The SSAE uses both pathologically proven endometriosis images from an earlier work and the corresponding annotated images to perform the segmentation process.30 The statistical method was adopted as yet another validation procedure for analyzing similarities.\n\n\nMethods\n\nThis study took place in Jan 2022. Endometriosis was predicted in four regions of the reproductive system including ovary, uterus, peritoneum, deep infiltrating endometriosis (rectum, gall bladder). Laparoscopic images and annotated images of endometriosis were obtained from the standardized GLENDA v1.531 dataset. The dataset contains Laparoscopic images of both pathological and non-pathological identified endometriosis regions. Pathological lesions identified in laparoscopic images were used for segmentation process. In the proposed method 373 laparoscopic images and 628 corresponding annotated images were used for segmentation process.\n\nA recognized pathological report of endometriosis was selected for segmentation. The images were classified as pathological images and their corresponding annotated images. Table 1 shows the number of endometriosis images by affected region.\n\nEndometriosis is recognized at different location in a single pathological image. The pathologically affected images were identified from the dataset12 where the uterus is 17, Peritoneum is 257, Ovary is 53 and Deep infiltrating endometriosis is 55. These different locations were distributed into various annotated images for precise pixel classification. The endometriosis-affected uterus regions consisted of 17 raw images, and the lesions identified at multiple locations are distributed as 25 annotated images. Similarly, endometriosis affected peritoneum regions consist of 257 raw images in which the lesions identified at multiple locations are distributed as 489 annotated images. In addition, the endometriosis-affected ovary regions consisted of 53 raw images where the lesion identified at multiple locations is distributed as 54 annotated images.\n\nFinally, endometriosis affected deep infiltrating endometriosis (rectum, sigmoid) regions consisting of 55 raw images, where the lesions identified at multiple locations were distributed as 59 annotated images. The Structural similarity analysis of Endometriosis (SSAE) methodology is illustrated in the Figure 1.\n\nIOU=intersection over union.\n\nThe identified pathological and annotated image datasets were given as input for SSAE. SSAE was effectively implemented using semantic segmentation and statistical analysis. The performance of semantic segmentation was validated using Intersection over union (IOU) and F1 score. Similarly, the statistical performance was evaluated using the mean and standard deviation.\n\nThe semantic segmentation process ascertains the spread of endometriosis at multiple locations identified from pathologically proven images and mapped with annotated images. U-Net is a state-of-art technique for semantic segmentation to identify the images based on pixel classification.32 Semantic segmentation is a cutting-edge technology for recognizing the exact location of biomedical images. The steps involved in segmenting the laparoscopic images were as follows:\n\n1) Collection of Endometriosis Laparoscopic Image Dataset\n\n2) Identified Pathological Endometriosis Laparoscopic Images\n\n3) Identified Pathological Endometriosis Annotated Images\n\n4) Pre-processing of Images includes Augmentation.\n\n5) Applying Semantic Segmentation using U-Net Architecture.\n\n6) Performance validation of pixel classification using IOU, F1 score, IOU threshold, Jacard-Coefficient.\n\nThe steps are illustrated in Figure 2 as follows:\n\nThe obtained raw images and equivalent annotated images were preprocessed as follows. Preprocessing was performed effectively through augmentation. Preprocessing includes (a) rotation (b) horizontal shift (c) vertical shift (d) shear range, (e) zoom range. These augmentation processes increased the size of the training dataset. The various augmentation process performed for training data are as follows: a) rotation range as 15, b) shift range in width wise as 0.05, c) shift range in height wise as 0.05, d) shear range as 50, e) zoom range as 0.02 respectively. The training and test data was split as 70% and 30% for training and testing data. The segmentation process was implemented on the preprocessed images. The segmentation process implements pixel classification to ensure the aggravation of endometriosis at various locations. Various segmentation architecture processes have been proposed. The most effective U-Net architecture was implemented. U-Net is a convolution neural network architecture that was mainly developed to identify the precise location of the infected area.\n\nThe U-Net model was implemented with the following parameters: a) filter size as 64, b) Adam optimizer, c) loss function as binary cross entropy d) softmax as activation function. The training model was implemented with 20 epochs with 50 steps per epochs. From the targeted output, it was possible to identify the intensity of endometriosis in every region using pixel classification.33 Table 2 lists the various hyper parameters identified for execution. The model is available from GitHub and is archived with Zenodo.47\n\nIOU=intersection over union.\n\nThe performance of the proposed system was evaluated using various metrics as follows:\n\nThe IoU34 is calculated as the ratio of the overlapped area between the predicted and ground truth to the overall area between the predicted and targeted areas.\n\nWhere ∝∩ indicates the overlapped area and ∝∪ indicates the overall area.\n\nThe F1 Score35 is calculated as the ratio of the overlapped area multiplied by two to the total number of pixels in both images.\n\nWhere ∝∩ indicates the overlapped area and ρI denotes pixel of both the images.\n\nThe pathologically identified datasets and annotated datasets were used as inputs for statistical analysis.46 The statistical analysis was performed in Excel 2013. Systematic random sampling was performed to validate the pathologically identified images with annotated images. The pixel intensity of endometriosis affected four regions namely the uterus, ovary, peritoneum, and deep infiltrating (rectum) were calculated as follows:\n\nTo perform systematic sampling, population size, sample size, and starting point were calculated as follows:\n\nWhere K is the systematic sampling value, N is the number of images and n is the sample size taken. The starting point (Ø) was calculated based on the systematic sample value.\n\nThe random weight value is calculated using starting point value as follows:\n\nBy multiplying the random weight value with the corresponding identified pixel value (ρl) of laparoscopic images, the desired sampling value was obtained as follows.\n\nSimilarly, for annotated images, the sampling value was calculated as follows:\n\nwhere (ρA) represents the pixel value of annotated images. δL and δA represent the sampling values of pathologically identified and annotated images for the uterus, ovary, peritoneum, and deep infiltrating.\n\nThe mean and standard deviation of the sampling values30 for both pathologically identified and annotated images that included all four regions were calculated as follows:\n\nWhere λLi and μLi represent the mean and standard deviation for laparoscopic images of all four regions. Similarly for annotated images,\n\nWhere λAi and μAi represent the mean and standard deviation for annotated images of all four regions.\n\n\nResults\n\nThe pathologically identified images and their corresponding annotated images of endometriosis were considered as inputs for segmentation. The four regions including the ovary, uterus, peritoneum, and deep infiltrating endometriosis are involved in pixel classification. The pathologically identified images and annotated images were pre-processed. These preprocessing include rotation and shifting to increase the training size of the images. As a result, the pre-processed images were fed as input to the segmentation.\n\nSegmentation analyzes the pre-processed images pixel-by-pixel level. Semantic segmentation involves the classification of each pixel of an image into all classes. The U-Net architecture36 implements a down sampling technique to encode the input images to attribute representation at multiple levels.\n\nThe pathological37 and annotated images were provided as input for semantic segmentation using U-Net architecture. As a result of the segmentation process involving various parameters the ground truth area was identified which predicts the region of occurrence as a segmented output as illustrated in Figure 3.\n\nThe laparscopic images are taken from the GLENDA dataset under CC BY 4.0.31\n\nThe hyper parameters as mentioned were executed in the colab environment and the total number of parameters executed was 31,055,492 with trainable parameters as 31,043,716 and non-trainable parameters as 11,776.\n\nA careful investigation was performed by selecting the network parameters. Trials were carried out to identify the optimized parametric value. The filter size was identified based on trials with sizes as 16, 32 and 64 and it was found that a filter size 64 was the most optimized parameter values. The overlapping region was not sufficient for the lower bound values of filter sizes38 16 and 32. Similarly, the optimizers used for U-Net architectures were RMSprop, SGD, and Adam.39 Also the epoch sizes were chosen based on empirical analysis. The epoch size identified was 10, 20 and 30.The results obtained are illustrated in Figures 4-6.\n\nIOU=intersection over union.\n\nIOU=intersection over union.\n\nIOU=intersection over union.\n\nThe prediction area was evaluated using the following performance metrics: a) IOU b) F1 Score) with a filter size of 64, epochs of 20, and Adam optimizer was selected. Based on the execution with the identified hyper parameters the ground truth was predicted and the output image obtained was depicted in Figure 7.\n\nThe laparscopic images are taken from the GLENDA dataset under CC BY 4.0.31\n\nA comparison was made between the training IOU and validation IOU along with the epochs. The best identified parameters were executed and graph was illustrated in Figure 8.\n\nThe proposed methodology for segmenting the endometriosis to identify the similarity of pixels between pathological and annotated images was compared with other architectures. The various architectures used for analyzing the pathological and annotated images were fully conventional network and Mask RCNN. These architectures were compared based on their performance using overlapping regions. Table 3 presents the comparison was based on various metrics and comparison was illustrated in Figure 9.\n\nIOU=intersection over union.\n\nThe proposed SSAE method was compared with other existing methods, where the SSAE method performs well in terms of Intersection over Union and F1 Score. The comparison is illustrated in Table 4.\n\nSSAE=structural similarity analysis of endometriosis; IOU=intersection over union; MRI=magnetic resonance imaging.\n\nIn addition to the segmentation process, the intensity of endometriosis was identified using statistical analysis.40,41 The pixel intensity of affected regions was identified for both pathological and annotated images. Random sampling was applied to both the pathological images and annotated image pixel values. From the obtained values, the mean and standard deviation were calculated for both the pathological and annotated images for all four regions was listed in Table 4.\n\n\nDiscussion\n\nThe empirical analysis was performed to identify the hyper parameters for segmenting the exact location. Based on analysis, the Adam optimizer performs well for overlapping regions based on the performance of intersection over union. The next parameter was the loss function. The loss functions used in U-Net architectures are cross-entropy loss, focal loss, and IoU Loss.42 Cross-entropy performs well based on the overlapping region. The sizes of the epochs were 10, 20 and 30. It was identified that intersection over Union was obtained when the epoch size was 20. When the epoch size was 10, the performance of the IOU was not up to the level, whereas when the epoch size was 30, outliers were found to be detected.\n\nThe filter size was analyzed based on the performance of the SSAE method. When the filter size was 16, the obtained IOU was 0.48 and the F1 Score was 0.56. In addition, when the filter size was 32, the IOU was 0.65 and the F1 Score was 0.68. Finally, the best overlapping occurs when the filter size as 32 with IOU of 0.72 and F1 Score of 0.74 (Figure 4).\n\nThe optimizer plays an important role in identifying the segmented regions. Various optimizer were analyzed based on the performance of the SSAE method. First the U-Net optimizer known as RMSprop was used where the overlapping region was not clear with an IOU of 0.3 and a F1 Score of 0.35. The second optimizer identified was SGD (stochastic gradient descent), where the IOU was 0.48 and the F1 Score was 0.58. Finally, the best overlap occurs when the Adam optimizer was executed with an IOU of 0.72 and the F1 Score of 0.74 (Figure 5).\n\nAn epoch trains the data with the specified parameters with forward and backward passes. An epoch improves the quality of the metrics. In the given model, epoch size was determined based on the metric value obtained at the end of each pass. Initially 10 epochs were used where the model obtained an IOU of 0.58, F1 Score of 0.55. To fine tune the parameters, the epoch size was increased to 20 where the IOU was 0.72 and the F1 Score was 0.74. Finally, epoch size was tuned to 30, leading to overfitting. The epoch size of 20 outperformed well for the given model and all comparisons are illustrated in Figure 6.\n\nThe F1 Score is another method used to evaluate the pixel classification performance. The training and validation F1 Score was compared with those of epochs and graphical illustrations are presented in Figure 8.\n\nAmong all other architecture, structural similarity between pathological and annotated images was implemented with higher performance using U-Net with an IOU of 0.72 and F1 score of 0.74, where the fully conventional network contains an IOU of 0.68 and an F1 score of 0.74. In addition, the performance of Mask RCNN obtains an IOU of 0.71 and an F1 score of 0.73. A graphical representation of performance analysis of the various architectures is illustrated in Figure 9.\n\nThe proposed SSAE method was compared with existing methods that invoke segmentation process for identifying various disorder. The first method was proposed by Leibetseder.43 In this approach laparoscopic images of endometriosis was segmented using FCNN and Mask RCNN. This method obtained an IoU of 0.7 and F1 score of 0.73. Similarly, Giusti44 uses Magnetic resonance images for segmenting deep infiltrating endometriosis. The method obtains an IoU of 0.68 and F1 score of 0.7. Next method Ma45 uses Magnetic resonance images for segmenting gall bladder where the IoU obtained was 0.66 and F1 Score was 0.68. The SSAE method outperforms well as listed in Table 4.\n\nThe calculated values for the four regions are listed in Table 5. In the pathological images, the mean value for the uterus was 0.559 which was closer to the mean value of the uterus in the annotated images. In addition, the mean value of the peritoneum in the pathological images was 1.188 which was closer to the annotated image mean value of the peritoneum. The next region’s ovary mean value in the pathological image is 0.861 which is closer to the mean value of Ovary in the annotated images. Finally, the DIE mean value is 0.85 was closer to the mean value of DIE in the annotated images.\n\nDIE=Deep infiltrating endometriosis.\n\nSimilarly, the standard deviation of the uterus in a pathological image is 0.040, which is closer to the standard deviation of uterus in annotated images is 0.056. In addition, the standard deviation of the peritoneum in the pathological image is 0.0770 which was closer to annotated image standard deviation of peritoneum is 0.077. The standard deviation of the next region of the ovary in the pathological image is 0.056 which is closer to the standard deviation of ovary in the annotated images as 0.080. Finally, the standard deviation of DIE is 0.0544 which was closer to the standard deviation of DIE in annotated image of 0.060. Among the four regions, peritoneum has the major impact that was identified from the mean value obtained.\n\n\nConclusion\n\nEndometriosis is a disease that affects 1/15th of women in the reproductive age groups. The proposed SSAE system evaluates the aggravation of endometriosis at distinct locations namely the uterus, ovary, peritoneum, and rectum from pathologically proven and corresponding annotated images. The proposed work invokes the U-Net architecture for segmenting the endometriosis-affected regions for pixel-level classification. In addition to the segmentation process, system sampling was performed using the intensity of the pixel values from both the pathological and annotated images. Means and standard deviations were calculated as a result of the sampling process. The mean and standard deviation obtained for each region in the pathological images were similar to the mean and standard deviation of the annotated images. The statistical value obtained for the peritoneum was 1.188±0.0773 for pathological images which was similar to the value obtained for annotated images 1.2142±0.0770. Similarly, for the uterus the statistical value was 0.559±0.0404 in the pathological images as 0.566±0.0532 in the annotated images. Ovary the value in pathological images as 0.8613±0.0566 was identical to the statistical value of annotated ovarian images as 1.0921±0.0806. Finally, the peritoneum obtained the statistical value of 0.859±0.054 in the pathological images which was similar to annotated image value of 1.0040±0.0606. The proposed system obtains the IOU of 0.72 and an F1 score of 0.74.\n\n\nData availability\n\nThe standardized Endometriosis dataset was obtained from Glenda V1.5.31 The dataset holds around 25000 both pathological, non-pathological images, and annotated images. The dataset consists of four labels: Ovary, Peritoneum, Uterus and Deep Infiltrating Endometriosis.\n\nFigshare: Endometriosis Dataset Description and Mean Standard Calculation. https://doi.org/10.6084/m9.figshare.19330682.v1.46\n\nThis project contains the following underlying data:\n\n- DIE_Mean and Standard Deviation.csv\n\n- Ovary_ Mean and Standard Deviation.csv\n\n- Peritoneum_Mean and Standard Deviation.csv\n\n- Uterus_ Mean and Standard Deviation.csv\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nSoftware availability\n\nSource code available from: https://github.com/visalaxi/Automated-segmentation-of-Endometriosis-using-Transfer-Learning\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.6324521.47\n\nLicense: Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nGruber TM, Mechsner S: Pathogenesis of endometriosis: The origin of pain and subfertility. Cells. 2021; 10(6): 1381. PubMed Abstract | Publisher Full Text\n\nMarcellin L, Goffinet F, Azria E, et al.: Association between Endometriosis Phenotype and Preterm Birth in France. JAMA Netw. Open. 2022; 5(2): e2147788–e2147788. PubMed Abstract | Publisher Full Text\n\nKoppolu A, Maksym RB, Paskal W, et al.: Epithelial cells of deep infiltrating endometriosis harbor mutations in cancer driver genes. Cells. 2021; 10(4): 749. PubMed Abstract | Publisher Full Text\n\nD’Alterio MN, D’Ancona G, Raslan M, et al.: Management challenges of deep infiltrating endometriosis. Int. J. Fertil. Steril. 2021; 15(2): 88–94. PubMed Abstract | Publisher Full Text\n\nDelanerolle G, Ramakrishnan R, Hapangama D, et al.: A systematic review and meta-analysis of the Endometriosis and Mental-Health Sequelae; The ELEMI Project. Womens Health. 2021; 17: 174550652110197. 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PubMed Abstract | Publisher Full Text\n\nYan X, Tang H, Sun S, et al.: After-unet: Axial fusion transformer unet for medical image segmentation. Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision. 2022; (pp. 3971–3981).\n\nGüngör ND, Gürbüz T, Yurci A: Does Depot Analog Suppression Have Positive Effects on All Other Frozen-thawed Embryo Transfer Cycles in Addition to Endometriosis?. Ulutas Med. J. 2021; 7(1): 22–30. Publisher Full Text\n\nVisalaxi S, Muthu TS: Automated prediction of endometriosis using deep learning. Int. J. Nonlinear Anal. Appl. 2021; 12(2): 2403–2416.\n\nIsmail WZW: Automatic feature description of Endometrioma in Ultrasonic images of the ovary. Int. J. Integr. Eng. 2018; 10(1).\n\nLópez-Linares Román K, García Ocaña MI, Lete Urzelai N, et al.: Medical image segmentation using deep learning. Deep Learning in Healthcare. Cham: Springer; 2020; (pp. 17–31).\n\nBindhu V: Biomedical image analysis using semantic segmentation. 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Syst. 2020; 8(2-3): 75–85. Publisher Full Text\n\nKurata Y, Nishio M, Kido A, et al.: Automatic segmentation of the uterus on MRI using a convolutional neural network. Comput. Biol. Med. 2019; 114: 103438. PubMed Abstract | Publisher Full Text\n\nGupta S, Ali S, Goldsmith L, et al.: Mi-unet: Improved segmentation in ureteroscopy. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI). 2020, April; (pp. 212–216). IEEE.\n\nYang T, Han J, Zhu H, et al.: Segmentation of five components in four chamber view of fetal echocardiography. 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI). 2020, April; (pp. 1962–1965). IEEE.\n\nWu X, Chen S, Huang J, et al.: DDeep3M: Docker-powered deep learning for biomedical image segmentation. J. Neurosci. Methods. 2020; 342: 108804. PubMed Abstract | Publisher Full Text\n\nSouza CA, Menegatti JE, Pazello RT, et al.: Neural Network Image Segmentation Model for Laparoscopic Gynecological Surgeries. J. Minim. Invasive Gynecol. 2021; 28(11): S18. Publisher Full Text\n\nSimpson AL, Antonelli M, Bakas S, et al.: A large annotated medical image dataset for the development and evaluation of segmentation algorithms. arXiv preprint arXiv:1902.09063. 2019.\n\nLeibetseder A, Kletz S, Schoeffmann K, et al.: GLENDA: gynecologic laparoscopy endometriosis dataset. International Conference on Multimedia Modeling. Cham: Springer; 2020, January; (pp. 439–450).\n\nZhao X, Vemulapalli R, Mansfield PA, et al.: Contrastive Learning for Label Efficient Semantic Segmentation. Proceedings of the IEEE/CVF International Conference on Computer Vision. 2021; (pp. 10623–10633).\n\nYuan D, Shu X, Fan N, et al.: Accurate bounding-box regression with distance-IoU loss for visual tracking. J. Vis. Commun. Image Represent. 2022; 103428.\n\nGhosal S, Xie A, Shah P: Uncertainty quantified deep learning for predicting dice coefficient of digital histopathology image segmentation. arXiv preprint arXiv:2109.00115. 2021.\n\nAndrade C: Understanding the difference between standard deviation and standard error of the mean, and knowing when to use which. Indian J. Psychol. Med. 2020; 42(4): 409–410. PubMed Abstract | Publisher Full Text\n\nHammernik K, Knoll F, Rueckert D: Deep Learning for Parallel MRI Reconstruction: Overview, Challenges, and Opportunities. MAGNETOM Flash. 2019; 4: 10–15.\n\nSankaravadivel V, Thalavaipillai S: Symptoms based endometriosis prediction using machine learning. Bull. Electr. Eng. Inform. 2021; 10(6): 3102–3109. Publisher Full Text\n\nLu Y, Lu G, Zhou Y, et al.: Highly shared convolutional neural networks. Expert Syst. Appl. 2021; 175: 114782. Publisher Full Text\n\nMela CA, Liu Y: Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images. BMC Bioinform. 2021; 22(1): 1–30. Publisher Full Text\n\nWang Y, Zheng C, Peng H: Covariance Mean-to-Standard-Deviation Factor for Ultrasound Imaging. 2020 IEEE International Ultrasonics Symposium (IUS). 2020, September; (pp. 1–4). IEEE.\n\nSudalaimuthu T: Endometrium Phase prediction using K-means Clustering through the link of Diagnosis and procedure. 2021 8th International Conference on Signal Processing and Integrated Networks (SPIN). 2021, August; (pp. 1178–1181). IEEE.\n\nZhao B, Zhang X, Li Z, et al.: A multi-scale strategy for deep semantic segmentation with convolutional neural networks. Neurocomputing. 2019; 365: 273–284. Publisher Full Text\n\nLeibetseder A, Schoeffmann K, Keckstein J, et al.: Endometriosis detection and localization in laparoscopic gynecology. Multimed. Tools Appl. 2022; 81: 6191–6215. Publisher Full Text\n\nGiusti S, Forasassi F, Bastiani L, et al.: Anatomical localization of deep infiltrating endometriosis: 3D MRI reconstructions. Abdom. Imaging. 2012; 37(6): 1110–1121. PubMed Abstract | Publisher Full Text\n\nMa Z, Jorge RNM, Tavares JMR: Bladder wall segmentation in MR images. USNCCM-11-11th US National Congress of Computational Mechanics. 2011.\n\nVisalaxi S, Sudalaimuthu T: Endometriosis Dataset Description and Mean Standard Calculation. figshare. Dataset. 2022. Publisher Full Text\n\nVisalaxi S, Sudalaimuthu T: Automated Segmentation of Endometriosis using Transfer Learning.2022. Publisher Full Text"
}
|
[
{
"id": "129994",
"date": "13 Oct 2022",
"name": "S. Muthurajkumar",
"expertise": [
"Reviewer Expertise Cloud Computing",
"Machine Learning",
"Data Mining",
"Networking"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors proposed the work using segmentation process on images. Overall the article is a clear, concise and well written manuscript.\nIn the introduction part, the authors addresses two types of segmentation processes and identifies semantic segmentation as the prominent one for the proposed study. Various related studies were analyzed to choose U-Net architecture for performing segmentation. In the methodological section, the overview of steps involved in the segmentation process was elaborated. The reason for choosing appropriate hyper parameters was mentioned. Along with the segmentation process, statistical analysis were used for validation of locating endometriosis in distinct regions. The performance of the proposed approach was evaluated using the metrics a) intersection over union, b) F1 score, c) Mean and standard deviation. The result and discussion focus on the results obtained based on various dimensions. First various filter size was compared with the metric intersection over union. Next various epochs were compared with metrics intersection over union and F1 score. Finally, the optimizer was compared with metrics intersection over union and F1 score. Also, the training and testing score of intersection over union and F1 score was illustrated for the optimized epoch value. Finally, the U-Net architecture performance was compared with the metrics of fully conventional network and Mask R CNN for the identified dataset. At last the result obtained from metrics of various existing methods were compared with the proposed method. The conclusion section, provides an overview of the entire work with the results obtained using segmentation and statistical analysis process.\nThe authors addresses the major concern of endometriosis and states the solution by segmenting the regions affected by endometriosis. The proposed approach identifies the precise location of endometriosis by segmentation using cutting-edge technology. The authors therefore presented a concise need on the importance of anatomy-based analysis of endometriosis.\nThere are certain clarifications that need to be addressed by the author.\nEmphasize a short description on various types of segmentation process.\n\nHighlight the needs of three segmentation process for which the comparative study was performed.\n\nIn the implementation section, the reason for selecting systematic random sampling can be mentioned more appropriately.\n\nIn the conclusion section, the statistical sampling was written where, the semantic segmentation process could be more emphasized.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-360
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https://f1000research.com/articles/11-241/v1
|
28 Feb 22
|
{
"type": "Research Article",
"title": "Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills",
"authors": [
"Sebastian A. Medina-Ramirez",
"Ricardo Rojas-Humpire",
"Josue F. Canaza",
"Fiorella Hernandez",
"Salomón Huancahuire-Vega",
"Sebastian A. Medina-Ramirez",
"Ricardo Rojas-Humpire",
"Josue F. Canaza",
"Fiorella Hernandez"
],
"abstract": "Background: The measures taken to contain the COVID-19 pandemic, led to significant changes in university education, resulting in the new normal standard of virtual teaching in many undergraduate medical schools worldwide. Therefore, the aim of this paper was to determine the factors related to academic satisfaction with virtual teaching in medical students during the COVID-19 pandemic. Methods: A cross-sectional-analytical study was conducted on medical students at a private university in Peru, through self-reported questionnaires divided into sociodemographic data and variables of interest that could influence academic satisfaction during the pandemic. To evaluate possible factors related to academic satisfaction, stepwise regression models were performed for both sexes. Results: In total, data from 310 medical students, 117 males and 193 females, were analyzed. Academic satisfaction reached a score of 11.2 ± 2.9, which was similar in both sexes. The best regression model for males (AIC: 544.32; RMSE: 2.42; R2: 0.30) showed that adaptation to university life (favorable change) and depression (unfavorable change) explained 30% of changes in students' academic satisfaction. While in females (AIC: 907.59; RMSE: 2.49; R 2: 0.22) the model integrated favorable factors such as adjustment to college life and anxiety; while depression and poor sleep quality were unfavorable factors. Conclusion: Factors that contributed to academic satisfaction in medical students were determined in this study, which differed by gender. Thus, it is important to take into account the particularities of male and female medical students in order to improve their academic satisfaction during their university careers.",
"keywords": [
"COVID-19",
"Medical students",
"academic satisfaction",
"sleep",
"digital competencies"
],
"content": "Introduction\n\nOn March 11, 2020, the World Health Organization declared the outbreak of coronavirus disease (COVID-19) a pandemic. Since then, strict measures have been taken to contain the spread of the virus. Social distancing being the main one, has brought with it significant problems for education as it affects nearly 1.6 billion students worldwide.1 This posed a substantial challenge to medical education forcing an abrupt transition to online formats.2 Due to restrictions, there were limitations of access the suitable educational environments (such as laboratories, simulation rooms, and hospitals) leading to rapid transition to remote learning. As a result, there may be skills and health factors that would be impacting students' individual experience and perception of their academic environment.3 In addition, medical students, as well as other students in higher education, experience various difficulties that lead to a general feeling of dissatisfaction and frustration with online education.4\n\nAcademic satisfaction in academic environments through a socio-cognitive model has been highlighted in several studies due to its importance in finding external factors that could have an impact on students' overall academic satisfaction.5 In this model, cognitive, affective, and behavioral factors are considered due to students' perceptions of their performance contrary to other studies that focus on the subject's perception in the institutional context.6 Due to the COVID 19 pandemic, medical students in Peru have had no choice but to transition to remote education and it is not currently known how satisfied they are with their studies.\n\nIn addition, it is important to know the influence that the pandemic has on mental health in college students, previous studies have shown that there is an association with depression and anxiety.7 On the other hand, for the use of technology, the success of acquiring a good experience will depend on the learning obtained by using it, whether for academic or non-academic purposes.8 In the context of the pandemic, this could influence the experience of using and acquiring digital skills required for optimal learning. Factors such as mental health issues and the need to adapt to the digital environment could be contributing to perceptions of academic satisfaction.\n\nUnderstanding the factors that positively or negatively influence academic satisfaction could lead us to effectively assess the problem and design targeted interventions according to the needs of a specific group of individuals classified by gender, age or socio-demographic origin. In our study we included variables previously known to have some influence on students' academic satisfaction such as adaptability to university life, digital skills, sleep quality, anxiety and depression. The aim of this work was to determine the factors related to academic satisfaction in medical students during the COVID-19 pandemic.\n\n\nMethods\n\nThis analytical cross-sectional study was conducted in students of the Faculty of Medicine of the Universidad Peruana Unión belonging to the first to the seventh year of studies. Students were invited to complete an online survey, in which questionnaires related to academic satisfaction, adaptation to the university, digital skills, sleep quality, stress, depression and anxiety were applied. Likewise, a virtual meeting was held for each academic year and a reminder to complete the survey was sent, which was available for 5 weeks. This study was reviewed and approved by the ethics committee of the Universidad Peruana Unión before being conducted (2021-CEUPeU-0005).\n\nThrough a class briefing session per academic year, under the supervision of the academic area coordinator, all students were briefly informed of the purpose of the study and were given an average of 15 minutes to complete the questionnaire. Before completing the questionnaires, the participants who agreed to participate voluntarily gave their informed consent. Likewise, in the presentation, they were informed that the answers were confidential and that only the researchers had access to it for the purpose of this study.\n\nSocio-demographic aspects were considered in order to know the general information of the participants, and to measure the variables of interest we took into account five questionnaires, which are found in their completed version in extended data, and they are detailed below:\n\n1. Brief Scale of Satisfaction with Studies (EBSE): The EBSE is composed of 4 items, it is distributed in 2 factors: satisfaction with studies and negative affect. In this scale good internal consistency and reliability were evidenced (α=0.788). This scale reflects the satisfaction that the student has with respect to their performance and in general with their studies, distributed on a Likert scale of 5 options, ranging from strongly agree to strongly disagree.6\n\n2. Adaptability to university life: Developed by Baker and Sirik,9 and adapted by Rodriguez-Ayan and Sotelo. It is a questionnaire that aims to determine the degree of adaptation of students during their stay at the university. It measures 3 dimensions: social, academic and institutional. It consists of 11 items distributed on a 4-point Likert scale.10\n\n3. Pittsburgh Sleep Quality Index Questionnaire (PSQI): PSQI is a questionnaire used to measure sleep quality and its alterations in the last month.11 The questionnaire consists of 19 self-assessment questions that are used to obtain the overall score. Distributed in 7 items, which are: subjective sleep quality, latency, duration, efficiency, sleep disturbances, use of medication for sleep, and daytime dysfunction. In its original version this questionnaire has an internal consistency of (α=0.83), while the adapted version in the Peruvian population showed a lower consistency but was equally valid (α=0.564) and regarding construct validity, three factors were found that explain 60.2% of the total variance.12\n\n4. Digital skills: This questionnaire consists of 35 questions measured using a 5-point Likert scale. It is based on the digital skills matrix developed by the National Autonomous University of Mexico (UNAM), exploring the following categories: access to information, communication and collaboration, information security, information management, media management, hardware and virtual learning environments. With respect to its psychometric characteristics, the study conducted by Avitia et al. recorded a good internal consistency (α=0.95) in general, as well as in each of its categories.13\n\n5. Depression, anxiety and stress scale (DASS - 21): This questionnaire consists of 21 questions measured through a Likert scale from 0 to 3 points. It is divided into 3 dimensions which separately measures depression, stress and anxiety, each being composed of 7 items. In its Spanish version it has an acceptable internal validity, for stress (α=0.82), depression (α=0.84) and anxiety (α=0.70) and shows a good interrelation between the 3 factors evaluated by this scale.14\n\nData analysis was performed in the R programming language version 4.0.2. (https://www.rstudio.com/) (RRID:SCR_001905). The variables were ordered in graphs and tables taking into account their categorical nature expressed as absolute frequency and percentage (%), or numerical as mean ± standard deviation (SD). For the comparative analysis, the χ2 (chi-square) or Student's t-test was used according to the distribution of the variable. To establish the best model of factors related to academic satisfaction in medical students, stepwise regression models were performed with bidirectional elimination approach in the adjustment of independent variables, the best regression models were established based on Akaike's information criterion (AIC), root mean square error (RMSE), and R2. Multivariate regression models stratified by sex were obtained with their respective 95% confidence intervals (95%CI), a value of p<0.05 was considered statistically significant in the analyses.\n\n\nResults\n\nA total of 310 responses were obtained. The average age of the participants was 21.6 ± 3 years. The number of men was 117 (37.7%) and women 193 (62.3%). The total number of participants were divided into basic sciences (1st and 2nd academic year) and clinical sciences (3rd to 7th academic year), representing 42.3% and 57.7% respectively. It was found that half the participants belonged to the coastal region (52.9%), while those belonging to the highland region (21%) and those who were foreigners (20%) had similar proportion (Table 1).\n\nIn the assessment of emotional disorders, the presence of at least one emotional disorder was evident in more than half of the respondents. However, this differed according to sex and type of emotional disorder.\n\nIn women, 64%, 53% and 46% had stress, depression and anxiety respectively, finding that 55% (n=106) of the stressors (moderate or severe) belonged to the most worrying states. However, in men, of the 62% who had anxiety, 56% (n=66) presented the most worrying states, while 57% and 48% had depression and stress respectively (Figure 1).\n\nA general result and comparison were made according to scores obtained in men and women for digital skills, adaptation to university life and academic satisfaction.\n\nThe results showed that, for digital skills, both sexes had a high score (87.5 ± 22.6, p=0.012), meaning a good management of digital programs or applications in general. Minimal differences in scores were found, interestingly it was statistically significant for women and men respectively in the following components: virtual environments (10 vs. 8.1, p<0.001), media management (7.7 vs. 6.9, p=0.021) and information management (15.6 vs. 14.2, p=0.007). This shows that there is a greater knowledge about the organization and use of the applications necessary for academic activities. However, this is contrary with respect to the management of search engines and access to online information, as well as a basic knowledge of information security, such as clearing history and logging out of the electronic devices they use.\n\nOn the other hand, for adaptation to university life we found an overall result of 36.9 ± 6.5 and for academic satisfaction of 11.2 ± 2.9, which did not present important differences in scores according to sex and were not statistically significant. Therefore, it is evident that they have the same perception in the new virtual teaching.\n\nRegarding sleep quality, 83.9% (n=260) of the respondents had poor sleep quality, being the majority group in both sexes with this problem (163 women and 97 men), while only 16.1% (n=50) had good sleep quality (Table 2).\n\na Total scores.\n\n* p<0.05, statistically significant.\n\nThe generation of stepwise regression models to explain changes in academic satisfaction in medical students started from a factor pool of digital skills, adjustment to college life, emotional disturbance, and sleep quality for both males and females. The two-way elimination approach showed that for males the best model for academic satisfaction was at step 2 with the integration of adjustment to university life and depression (AIC: 544.32; RMSE: 2.42 and R2: 0.30), while for females the best model was at step 4 with the integration of adjustment to university life, depression, anxiety and sleep quality (AIC: 907.59; RMSE: 2.49 and R2: 0.22) (Table 3).\n\na Adaptation to university life.\n\nb Quality of sleep.\n\nThe resulting multivariate models for the students revealed that in males increased adjustment to college life (x1h) and decreased depression (x2h) explained 30% of the changes in academic satisfaction (yh), yh = 6.49 + 0.16(x1h) - 0.15(x2h). On the other hand, in females adaptation to college life (x1m) and anxiety (x2m) produced positive changes in academic satisfaction, unlike depression (x3m) and decreased sleep quality (x4m), which produced negative changes in academic satisfaction (ym), ym = 10.51 + 0.08(x1m) - 0.25(x2m) + 0.13(x3m) - 0.13(x4m) (Table 4).\n\na Adjustment to university life.\n\nb Quality of sleep.\n\n* p<0.05.\n\n** p<0.01 statistically significant.\n\n\nDiscussion\n\nEducation systems in all countries have been directly affected by the restrictions due to COVID-19, affecting about 1.57 billion students in 191 countries.15 Higher education institutions were forced to migrate to virtual means in order to continue academic activities. Pre-pandemic studies showed that distance learning in medical students could lead to an increase in knowledge, yet not be effective on academic satisfaction.16 Since student satisfaction is a way of addressing the quality of university services, knowing the factors that affect it has become vitally important for these institutions, especially under the remote modality in which they are currently being conducted. In this study, during the global pandemic contingency due to COVID-19, it was determined that the academic satisfaction of medical students of both sexes in the multivariate analysis was positively influenced by adequate adaptation to university life, and interestingly in women, by anxiety. On the other hand, poor sleep quality and depression had significant negative effects on academic satisfaction.\n\nAccording to Huebner and Gilman,17 student satisfaction is a multidimensional and complex affective variable that includes students' enjoyment and evaluation of their experiences in the educational environment. It has been verified that the difficulty of adaptation to the university environment is a factor that encourages student repetition and desertion and directly affects student satisfaction.18 This study has confirmed the positive influence of adaptation to university life on academic satisfaction in both male and female medical students. Similar results were reported for first-year university students, in which it was also shown that social support networks of family and faculty members could improve academic satisfaction related to adjustment to university life.19 Additionally, it has been verified that academic adjustment positively influenced the success of Netherlands university students. This success was measured in terms of their grades, number of credits earned, and intention to stay.20 In Peru, university education faces a high dropout rate; according to the government regulator, it was estimated that 27% of students who enter university studies drop out during the first year.21 This high dropout rate could be influenced by the difficulty of adapting to university life, which could lead to dissatisfaction and early abandonment.\n\nUnderstanding and meeting students' expectations to improve their satisfaction in academic life is a challenge for universities, as students bring in multiple expectations. Efforts are needed, especially because of the potential impact of academic satisfaction on students' psychological health and well-being.22 In this study it has been verified that depression negatively influences the academic satisfaction of male and female students. Depression is an important psychological problem for university students,23 and the exposure of medical students to depression during their university years has been previously related to their academic satisfaction.24\n\nHowever, due to the pandemic context, the levels of depression in medical students have increased, mainly due to the influence of isolation,25 which could generate academic problems and be reflected in their satisfaction. Universities should ensure that students have access to psychosocial services to help them cope with depression, mental distress and improve students' satisfaction with their studies.\n\nIt has been documented that the prevalence of anxiety symptoms in medical students is high.26 Additionally, it has been verified that the symptom of anxiety in medical students is associated with female gender and academic performance.27 Many papers show that lower academic satisfaction scores are strongly associated with psychological disorders such as anxiety, depression and stress.22 Interestingly, in this study it was found that anxiety positively influences academic satisfaction in female students. In that sense, in a study with Chilean medical students it was found that those who present high levels of motivation are also more stressed and suffer greater anxiety because they want to have good results.24\n\nIt has been shown that during the COVID-19 pandemic, the number of hours of sleep per night has varied among individuals, including students, which has been putting healthy lifestyles at risk.28 In addition, previous studies have shown that most medical students sleep less than 6 hours per night,29 and that sleep quality is a factor that directly affects academic performance and satisfaction with their studies.30 In this sense, in this study more than 80% of the students had poor sleep quality, and this variable was strongly associated and negatively influenced the academic satisfaction in both males and females. University students, mainly in health sciences such as medicine, should receive more knowledge about sleep hygiene to improve satisfaction with their studies.\n\nThis study had some limitations. The majority of medical students who responded to the survey were from the first years with a predominance of women and it was conducted in a single university center. However, there was participation of students from different regions of Peru including a considerable participation of students residing abroad. Additionally, there were no cut-off scores for most of the questionnaires used, however, most of these questionnaires have been previously used in the Latino population.31,32 On the other hand, we did not consider other specific factors by academic year, which could influence academic satisfaction, such as academic demand or clinical courses, because of which we could cover most common factors among medical students. However, future studies should consider these limitations and include these factors to have a better understanding of the outcome of academic satisfaction. Despite these limitations it is important to highlight the use of stepwise regression in uni- and multivariate models for the determination of the influence of each factor on academic satisfaction.\n\nIn conclusion, both sexes had a good organization and management of digital programs, the factors that influenced academic satisfaction for both sexes were adaptation to the university and depression. In addition, in women it influenced the quality of sleep and anxiety. The factors found in this study can suggest universities to implement programs to have a good mental health. In addition, this may help teachers to develop plans and strategies for adaptation to the university, in this way they could improve the academic satisfaction of medical students during their university career.\n\n\nData availability statement\n\nFigshare: “Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills” https://doi.org/10.6084/m9.figshare.19113827.v2.33\n\nFigshare: “Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills”\n\nThis project contains the following extended data: https://doi.org/10.6084/m9.figshare.19119353.v4.34\n\n\nReporting guidelines\n\nSTROBE checklist for “Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills” https://doi.org/10.6084/m9.figshare.19113959.35\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthor’s contribution\n\nMedina-Ramirez S.A: Conceptualization, Investigation, Software, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Rojas-Humpire R: Conceptualization, Investigation, Methodology, Software, Writing – Original Draft Preparation, Writing – Review & Editing; Canaza J.F: Conceptualization, Investigation, Methodology, Writing – Review & Editing; Hernandez F: Conceptualization, Investigation, Methodology, Writing – Review & Editing; Huancahuire-Vega S: Conceptualization, Investigation, Methodology, Supervision, Resources, Writing – Original Draft Preparation, Writing – Review & Editing.",
"appendix": "References\n\nGrupo de las Naciones Unidas para el Desarrollo Sostenible: GNUDS|Informe de políticas: Educación durante COVID-19 y más allá.Reference Source\n\nRose S: Medical Student Education in the Time of COVID-19. JAMA. 2020 Jun 2; 323(21): 2131–2132. Publisher Full Text\n\nKhan KW, Ramzan M, Zia Y, et al.: Factors Affecting Academic Performance of Medical Students. Life Sci. 2020 Feb 13; 1(1): 4–4. Publisher Full Text\n\nWatermeyer R, Crick T, Knight C, et al.: COVID-19 and digital disruption in UK universities: afflictions and affordances of emergency online migration. High Educ (Dordr). 2020 Jun 4; 81: 623–641. Publisher Full Text\n\nLent RW: Toward a Unifying Theoretical and Practical Perspective on Well-Being and Psychosocial Adjustment. J. Couns. Psychol. 2004; 51(4): 482–509. Publisher Full Text\n\nMerino-Soto C, Dominguez-Lara S, Fernández-Arata M: Validación inicial de una Escala Breve de Satisfacción con los Estudios en estudiantes universitarios de Lima. Educación Médica. 2017 Jan 1; 18(1): 74–77. Publisher Full Text\n\nPedraz-Petrozzi B, Krüger-Malpartida H, Arevalo-Flores M, et al.: Emotional Impact on Health Personnel, Medical Students, and General Population Samples During the COVID-19 Pandemic in Lima. Peru. Revista Colombiana de Psiquiatría (English ed). 2021 Jul 1; 50(3): 189–198. PubMed Abstract | Publisher Full Text\n\nRamírez Mera UN, Barragán López JF: Autopercepción de estudiantes universitarios sobre el uso de tecnologías digitales para el aprendizaje. Apertura (Guadalajara, Jal). 2018 Oct; 10(2): 94–109. Publisher Full Text\n\nBaker RW, Siryk B: Alienation and Freshman Transition into College. J. Coll. Stud. Pers. 1980 Sep; 21(5): 437–442.\n\nRodriguez-Ayan MN, Sotelo ME: Cuestionario de adaptación a la vida universitaria (CAVU): desarrollo, estructura factorial y validación inicial. Revista Argentina de Ciencias del Comportamiento. 2014 Dec 10; 6(3): 40–49.\n\nBuysse DJ, Reynolds CF, Monk TH, et al.: The Pittsburgh Sleep Quality Index: a new instrument for psychiatric practice and research. Psychiatry Res. 1989 May; 28(2): 193–213. PubMed Abstract | Publisher Full Text\n\nLuna Y, Robles-Arana Y: Ysela Agüero-Palacios. Validación del índice de calidad de sueño de Pittsburgh en una muestra peruana. Anales de. Salud Mental. 2015.\n\nAvitia Carlos P, Ramírez IU: Evaluación de la habilidad digital de los estudiantes universitarios: estado de ingreso y potencial educativo. Edutec Revista Electrónica de Tecnología Educativa. 2017 Dec 5; 61: a366–a366. Publisher Full Text\n\nBados A, Solanas A, Andrés R: Psychometric properties of the Spanish version of Depression, Anxiety and Stress Scales (DASS). Psicothema. 2005; 17(4): 679–683.\n\nGiannini S: COVID-19 y educación superior: de los efectos inmediatos al día después. Revista Latinoamericana de Educación Comparada: RELEC. 2020; 11(17): 1–57.\n\nSichani MM, Mobarakeh SR, Omid A: The effect of distance learning via SMS on academic achievement and satisfaction of medical students. J. Educ. Health Promot. 2018 Feb 9; 7: 29. Publisher Full Text\n\nHuebner ES, Gilman R: Students Who Like and Dislike School. Appl. Res. Qual. Life. 2006 Jul 1; 1(2): 139–150. Publisher Full Text\n\nGonzález LE, Uribe D: Estimaciones sobre la “repitencia” y deserción en la educación superior chilena. Consideraciones sobre sus implicaciones. Calidad en la Educación. 2002 May 30; (17): 75–90. Publisher Full Text\n\nAkanni AA, Oduaran CA: Perceived social support and life satisfaction among freshmen: Mediating roles of academic self-efficacy and academic adjustment. J. Psychol. Afr. 2018 Mar 4; 28(2): 89–93. Publisher Full Text\n\nVan Rooij ECM, Jansen EPWA, van de Grift WJCM : First-year university students’ academic success: the importance of academic adjustment. Eur. J. Psychol. Educ. 2018 Oct 1; 33(4): 749–767. Publisher Full Text\n\nEddaif B, Boriky D, Mustapha F, et al.: Transition from High-School to University: Obstacles and Difficulties. IOSR Journal of Research & Method in Education. 2017; 07: 33–37. Publisher Full Text\n\nFranzen J, Jermann F, Ghisletta P, et al.: Psychological Distress and Well-Being among Students of Health Disciplines: The Importance of Academic Satisfaction. Int. J. Environ. Res. Public Health. 2021 Feb 23; 18(4): 2151. PubMed Abstract | Publisher Full Text\n\nSahin Baltaci H, Kucuker D, Ozkilic I, et al.: Investigation of Variables Predicting Depression in College Students. Eurasian J. Educ. Res. Reference Source\n\nZugun-Eloae C, Iorga M, Gavrilescu I-M, et al.: Motivation, Stress and Satisfaction Among Medical Students. The Medical-Surgical Journal. 2016 Sep 30; 120(3): 688–693.\n\nMirhosseini S, Bazghaleh M, Basirinezhad MH, et al.: The relationship between depression and academic satisfaction in medical science students. J. Ment. Health Train. Educ. Pract. 2021; 16(2): 99–111. Publisher Full Text\n\nMirza AA, Baig M, Beyari GM, et al.: Depression and Anxiety Among Medical Students: A Brief Overview. AMEP. 2021 Apr 21; 12: 393–398. PubMed Abstract | Publisher Full Text\n\nMahroon ZA, Borgan SM, Kamel C, et al.: Factors Associated with Depression and Anxiety Symptoms Among Medical Students in Bahrain. Acad. Psychiatry. 2018 Feb 1; 42(1): 31–40. PubMed Abstract | Publisher Full Text\n\nEnriquez-Martinez OG, Martins MCT, Pereira TSS, et al.: Diet and Lifestyle Changes During the COVID-19 Pandemic in Ibero-American Countries: Argentina, Brazil, Mexico, Peru, and Spain. Front. Nutr. 2021 Jun 2; 8: 257. Publisher Full Text\n\nJohnson KM, Simon N, Wicks M, et al.: Amount of Sleep, Daytime Sleepiness, Hazardous Driving, and Quality of Life of Second Year Medical Students. Acad. Psychiatry. 2017 Oct 1; 41(5): 669–673. PubMed Abstract | Publisher Full Text\n\nÖrsal Ö, Örsal Ö, Alparslan G, et al.: Evaluation of the relation between quality of sleep and anxiety among university students. HealthMED. 2012 Jan 1; 6: 2244–2255.\n\nWolniczak I, Cáceres-DelAguila JA, Palma-Ardiles G, et al.: Association between Facebook dependence and poor sleep quality: a study in a sample of undergraduate students in Peru. PLoS One. 2013; 8(3): e59087. PubMed Abstract | Publisher Full Text\n\nDiaz-Godiño J, Fernández-Henriquez L, Peña-Pastor F, et al.: Lifestyles, Depression, Anxiety, and Stress as Risk Factors in Nursing Apprentices: A Logistic Regression Analysis of 1193 Students in Lima, Peru. J. Environ. Public Health. 2019 Nov 6; 2019: 1–7. Publisher Full Text\n\nMedina-Ramirez S: Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills. figshare. Dataset. 2022. Publisher Full Text\n\nMedina-Ramirez S: Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills. figshare. Dataset. 2022. Publisher Full Text\n\nMedina-Ramirez S: Online academic satisfaction during the COVID-19 pandemic in medical students: role of sleep, emotions, college adjustment, and digital skills. figshare. Dataset. 2022. Publisher Full Text"
}
|
[
{
"id": "127163",
"date": "26 Apr 2022",
"name": "Oriana Rivera Lozada",
"expertise": [
"Reviewer Expertise Public Health",
"epidemiology",
"infectious diseases and health education."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article addresses a very interesting topic for medical education today, such as the topic of satisfaction in times of Covid. The document is quite clear and concrete. However, it could be improved in some aspects:\n\nIntroduction: It is well structured, however, it can be strengthened with information from Peruvian studies that have been carried out (background).\nMethodology:\nAdd the reliability data of the instrument Adaptability to university life.\n\nSpecify sample and sampling data\n\nResults and Discussion: Add the biases of the study and what they did to control them. The discussion should strengthen with preferably national background.\nSpecify some interventions that can be proposed based on this research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8342",
"date": "10 Jun 2022",
"name": "Salomon Huancahuire-Vega",
"role": "Author Response",
"response": "Introduction: It is well structured, however, it can be strengthened with information from Peruvian studies that have been carried out (background). Thank you for your comment. We have added information about Peruvian studies: “In addition, their clinical practices were suspended as a protective measure. Under these conditions, it was determined in Peruvian health students that they had low levels of knowledge, risk perception attitudes, and preventive practices regarding COVID-19” Methodology: Add the reliability data of the instrument Adaptability to university life. Thank you for your comment. We have added reliability information about Adaptability to university life instrument: “Regarding its reliability evaluated by the test-retest procedure, a correlation of 0.821 was recorded, which implies a good reliability (greater than 0.8)” Specify sample and sampling data Thank you for your comment. We have added information about sampling data “Participants were selected by non-probability convenience sampling” Results and Discussion: Add the biases of the study and what they did to control them. The discussion should strengthen with preferably national background. Thank you for your comment. In the last part of the discussion we put a paragraph with the limitations and possible biases of the study, we also commented on explanations for each of them. “This study had some limitations. The majority of medical students who responded to the survey were from the first years with a predominance of women and it was conducted in a single university center. However, there was participation of students from different regions of Peru including a considerable participation of students residing abroad. Additionally, there were no cut-off scores for most of the questionnaires used, however, most of these questionnaires have been previously used in the Latino population. On the other hand, we did not consider other specific factors by academic year, which could influence academic satisfaction, such as academic demand or clinical courses, because of which we could cover most common factors among medical students. However, future studies should consider these limitations and include these factors to have a better understanding of the outcome of academic satisfaction. Despite these limitations it is important to highlight the use of stepwise regression in uni- and multivariate models for the determination of the influence of each factor on academic satisfaction” Specify some interventions that can be proposed based on this research. Thank you for your comment. Given that depression and anxiety influenced academic satisfaction, it is proposed that universities implement programs to monitor the mental health of students. These recommendations are at the end of the conclusion paragraph: “The factors found in this study can suggest universities to implement programs to have a good mental health. In addition, this may help teachers to develop plans and strategies for adaptation to the university, in this way they could improve the academic satisfaction of medical students during their university career”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-241
|
https://f1000research.com/articles/11-1018/v1
|
08 Sep 22
|
{
"type": "Review",
"title": "Genetics and functional significance of the understudied methamphetamine sensitive circadian oscillator (MASCO)",
"authors": [
"S K Tahajjul Taufique",
"David E Ehichioya",
"Julie S Pendergast",
"Shin Yamazaki",
"S K Tahajjul Taufique",
"David E Ehichioya",
"Julie S Pendergast"
],
"abstract": "The last 50 years have witnessed extraordinary discoveries in the field of circadian rhythms. However, there are still several mysteries that remain. One of these chronobiological mysteries is the circadian rhythm that is revealed by administration of stimulant drugs to rodents. Herein we describe the discovery of this circadian rhythm and its underlying oscillator, which is frequently called the methamphetamine-sensitive circadian oscillator, or MASCO. This oscillator is distinct from canonical circadian oscillators because it controls robust activity rhythms independently of the suprachiasmatic nucleus and canonical circadian genes are not essential for its timekeeping. We discuss these fundamental properties of MASCO and synthesize studies of strain, sex, and circadian gene mutations on MASCO. The anatomical loci of MASCO are not known, so it has not been possible thus far to discover its novel molecular timekeeping mechanism or its functional significance. However, studies in mutant mice suggest that genetic approaches can be used to identify the neural network involved in the rhythm generation of MASCO. We also discuss parallels between human and rodent studies that support our working hypothesis that a function of MASCO may be to regulate sleep-wake cycles.",
"keywords": [
"circadian",
"ultradian",
"infradian",
"dopamine",
"sleep",
"ADHD",
"N24SWD",
"psychostimulant"
],
"content": "Discovery of the extra-SCN pacemaker that is sensitive to methamphetamine\n\nThe mammalian circadian system is most often illustrated as a network of circadian clocks that is organized hierarchically. The primary central circadian pacemaker is in the suprachiasmatic nucleus (SCN) and it receives information from the retina and entrains to the light and dark cycle. Then the SCN coordinates the phases of oscillators in peripheral tissues. The molecular timekeeping mechanism in these circadian clocks is a transcriptional-translational feedback loop of canonical circadian genes (e.g., Bmal1, Clock, Period, Cryptochrome). This conceptualization of the mammalian circadian system has been carefully described many times.1–4 However, this is not a complete picture of the mammalian circadian system. There are also circadian pacemakers that control circadian rhythms of locomotor activity in rodents, but do not require the SCN or the canonical circadian molecular timekeeping mechanism. These extra-SCN circadian pacemakers are revealed by methamphetamine/amphetamine, restricted food availability (the food-entrainable oscillator or FEO), or other rewarding stimuli such as wheel-running activity and palatable meals.5 This review will focus on the mystifying circadian activity rhythm revealed by methamphetamine/amphetamine administration to rodents.\n\nThe effect of amphetamine treatment on circadian activity rhythms was first described in 1982 by Ikeda and Chiba.6 They studied the effects of several psychotropics on circadian locomotor activity rhythms in Fischer rats under light and dark conditions (LD). Cocaine, morphine, and FS-32 (a thymoleptic antidepressant discovered by Ikeda) did not robustly affect activity rhythms. In contrast, administering low-dose d-amphetamine (0.01%) in the drinking water had striking and reproducible effects on the locomotor activity rhythm. Upon amphetamine administration, a highly elevated activity bout appeared at the end of activity period (Stage I in Figure 1). This activity bout extended to the beginning of the light phase and then free-ran with a very long period (Stage II in Figure 1). Chronic amphetamine administration caused this newly emerged free-running rhythm to become dominant and the light-entrained activity rhythm controlled by the SCN was no longer visible (Stage III in Figure 1). The periods of the emergent activity rhythms were sometimes in the circabidian (period ~ two days) range of 48–55 h. Ikeda and Chiba observed the same phenomenon when rats were given amphetamine in their drinking water in constant darkness (DD). From those observations, Ikeda and Chiba proposed that there are at least two circadian oscillators underlying the circadian behavior rhythm in rats; one oscillator is more sensitive to amphetamine than the other.\n\nFigure reproduced from Ikeda and Chiba 19826 with permission of publisher.\n\nThe next seminal discovery was that the psychostimulant-induced activity rhythm was driven by a circadian oscillator located outside of the SCN. Ken-Ichi Honma’s group first showed that low-dose methamphetamine (0.01% or 0.005% in drinking water) had similar effects on activity rhythms in Wistar rats as d-amphetamine treatment in Fischer rats.7 Importantly, they also found that methamphetamine treatment revealed a long-period free-running activity rhythm in SCN-lesioned rats8 indicating that this rhythm is generated by an oscillator outside of the SCN. During the next decade, Honma’s lab established the foundational principles of the methamphetamine-revealed circadian oscillator. In summary, they found that this rhythm dissociated from the SCN-controlled rhythm and free-ran in LD and DD.7 The methamphetamine-revealed rhythm could also entrain to restricted feeding.9 They excluded the possibility that the rhythm was driven by the drinking rhythm by administering methamphetamine via subcutaneous, continuous delivery osmotic pumps.8 Honma and others reported that the methamphetamine-induced rhythm persisted for several cycles after withdrawing methamphetamine/amphetamine administration.8,10–14\n\nThree labs named the MA-induced oscillator in the early 2000’s. Ralph’s group named this oscillator the chemically-inducible oscillator (CIO).11 Honma’s group named it the methamphetamine-induced oscillator (MAO).15 Menaker’s group named it the methamphetamine-sensitive circadian oscillator (MASCO).10 These names reflected the distinct conceptualizations of the oscillator by each lab. The names CIO and MAO imply the oscillator is not rhythmic or functional without amphetamine/methamphetamine. MASCO implies the oscillator is functional without, but enhanced by, amphetamine/methamphetamine. Herein we will call the extra-SCN circadian oscillator/pacemaker revealed by amphetamine/methamphetamine MASCO because this name is widely used in recent publications and because we favor the hypothetical functionality implied by this name. There is no established name for the rhythm driven by MASCO. Therefore, we will call it the MASCO-driven rhythm. Storch’s group hypothesized that the MASCO-driven rhythm is the output of a so-called dopamine ultradian oscillator (DUO) whose period is elongated by methamphetamine.16\n\n\nCurrent model of SCN-MASCO coupling\n\nThe current working model of MASCO-SCN coupling was developed from studying the periods of activity rhythm(s) in DD and constant light (LL) (Figure 2A-E, Table 1). The SCN is a robust oscillator in DD, but a much weaker oscillator in LL because the phases of individual cellular oscillators become desynchronized in LL.17 These known differences in SCN oscillator amplitude were used to probe the relationship between the SCN and MASCO.10,18 The model presented here is based mainly on data collected from C57BL/6J mice, except where indicated (Figure 2A-E). For ease of discussion, we will refer to methamphetamine treatment, although some studies have been performed with amphetamine and methylphenidate with similar results.6,19\n\nThe effects of short-term methamphetamine administration on periods of activity rhythms in C57BL/6J (black font) and C3H (red font) mice are shown. Black arrows indicate coupling between oscillators. Gray arrows indicate strength of output. *Data taken from Pendergast et al. 2013. **Data taken from Tataroglu et al. 2006. See Table 1 for other studies. Figure modified from Yamazaki 201954 with permission.\n\na Amphetamine.\n\nFirst, we consider MASCO in the absence of the SCN (Figure 2A). Mice with SCN lesions and no methamphetamine treatment have arrhythmic or ultradian locomotor activity (i.e., there is no apparent MASCO output rhythm, but see later discussion about residual quasi-circadian rhythms in arrhythmic circadian mutant mice). Therefore, we hypothesize that MASCO is a weak oscillator without methamphetamine, so it alone cannot drive an output activity rhythm continuously. Methamphetamine treatment of SCN lesioned mice results in a robust free-running activity rhythm with a long period ranging from 26 h to 30 h. These data suggest that MASCO is a strong oscillator with a long period in the presence of methamphetamine.\n\nNext, we examine the putative relationship between the SCN and MASCO without methamphetamine treatment (Figure 2B, C). In DD, the SCN is a strong oscillator and MASCO is a weak oscillator, resulting in strong coupling of the SCN to MASCO (Figure 2B). The period of the activity rhythm, which may be an integration of the output of the coupled SCN and MASCO, is about 23.7 h. In LL, the amplitude of the SCN oscillator is weakened and the period lengthened, but we propose that the SCN oscillator is still stronger than MASCO in LL without methamphetamine treatment (Figure 2C). The period of the resulting activity rhythm is lengthened in LL, to about 26 h. Since MASCO is a very weak oscillator without methamphetamine treatment, there is only 1 rhythmic component in DD and LL in the absence of methamphetamine treatment.\n\nCoupling between the SCN and MASCO changes upon methamphetamine administration because methamphetamine treatment increases the amplitude of MASCO (Figure 2D, E). In DD, the SCN and MASCO are both strong oscillators during treatment with methamphetamine, resulting in strong bi-directional coupling between the two oscillators (Figure 2D). We propose that MASCO is a stronger oscillator than the SCN in the presence of methamphetamine. Upon methamphetamine treatment, there is one free-running activity rhythm with an ~24 h period (Figure 3A), which is slightly longer than the period without methamphetamine (23.6 h). However, prolonged methamphetamine administration induces two activity components, one rhythm driven by the SCN and another rhythm driven by MASCO. During this dissociation, the period of the MASCO-driven activity rhythm gets much longer, typically in the 26-30 h range, which approximates the period in SCN-lesioned animals administered methamphetamine. Occasionally, the MASCO-driven activity rhythm exhibits circabidian periods around 48 h during prolonged methamphetamine administration. This dissociation of SCN- and MASCO-driven rhythms can be also seen in LD conditions, suggesting that MASCO is not light-entrainable (Figure 3B). There is also evidence that MASCO can govern the SCN rhythm. in vivo multi-unit activity recordings from the SCN of freely behaving golden hamsters treated with methamphetamine showed that the SCN electrical activity rhythm “free-ran” in the LD cycle with a long period.20 During prolonged methamphetamine treatment the SCN-driven rhythm was no longer observed in LD and DD. These data suggest that with methamphetamine administration, MASCO can govern the SCN and the activity rhythm driven by coupled MASCO-SCN free-runs in LD. MASCO remains a very strong oscillator in LL, but the SCN oscillator amplitude weakens (Figure 2E). The period of the activity rhythm is longer in LL than in DD because the SCN period is longer and because the contribution of MASCO output to the activity rhythm is greater.\n\nA: Period lengthening of the activity rhythm during short-term methamphetamine administration. The rhythm is controlled by coupled SCN and MASCO in wild-type mice in DD. B: Dissociation of SCN and MASCO-driven activity rhythms by methamphetamine administration in a wild-type mouse in an LD cycle. C: The MASCO-driven activity rhythm in an SCN-lesioned wild-type mouse revealed by methamphetamine administration (NOTE: birhythmicity). D: Birhythmicity of the MASCO-driven activity rhythm in Per1/2 double knockout mice in DD. MA: methamphetamine administration. The actograms were generated from original data published in Pendergast et al., 201318 and 2014.55 The data are re-plotted with the same x-y scale, so the periods of the free-running rhythms can be compared by the angle of the slope. Figure modified from Yamazaki 201954 with permission.\n\nBackground strain also affects activity rhythm periods of mice treated with methamphetamine. The Menaker group treated C3H mice with methamphetamine and showed no effect on the period of the activity rhythm (red text in Figure 2).10 They therefore lesioned the SCN in C3H mice to study the MASCO. They found that SCN lesioned C3H mice administered methamphetamine had an activity rhythm period of 24.5 h, which was much shorter than the MASCO-driven rhythm in C57BL/6J mice. Thus, the lack of period changes in C3H mice upon methamphetamine treatment is likely because the period of MASCO is very close to the period of the SCN in this strain. However, they also reported two dissociated activity rhythms (23.5 h and ~29 h) in male C3H mice given a higher methamphetamine dose (0.0065–0.01%). This suggests that the period of MASCO in C3H mice can get longer during prolonged, higher doses of methamphetamine administration. The effects of prolonged methamphetamine administration and the influence of genes on the period of MASCO are further discussed in the next section.\n\n\nCanonical circadian genes are not essential for MASCO\n\nThe next surprising discovery about MASCO was that it can oscillate without the canonical circadian genes that are essential for rhythmicity in nearly all circadian oscillators. These studies were performed in circadian mutant mice in DD so the mice had no circadian activity rhythms (Table 2; most mutants exhibited ultradian rhythms). The first study was in arrhythmic ClockΔ19 mutant mice. Two independent laboratories showed that Clock Δ19 mutant mice expressed MASCO-driven activity rhythms upon amphetamine or methamphetamine administration.11,21 Similar results were later found in arrhythmic Cry1/2 double knockout mice, Bmal1 knockout mice, Per1/2 double knockout mice, and Per1/2/3 triple knockout mice.13,14,16,22 Collectively these studies demonstrate that the canonical circadian genes, which are essential for timekeeping in nearly all circadian clocks, are not required for MASCO to oscillate.\n\na Amphetamine.\n\nMASCO-driven activity rhythms in single circadian gene knockout mice have also been studied (Table 2). In these studies, the mice were SCN lesioned to remove the influence of the SCN (since we predict it is coupled to MASCO, see Figure 2) and the autonomous period of MASCO was measured. SCN-lesioned Npas2 knockout mice, as well as single Per1, Per2, or Per3 knockout mice had activity rhythms with 26–30 h periods when treated with methamphetamine (Table 2). The MASCO-driven behavior periods in these single mutant mice on the C57BL/6J background were similar to those observed in SCN-lesioned WT C57BL/6J mice, demonstrating that single gene knockouts do not have a discernible effect on the period of MASCO. Homozygous tau mutant mice exhibited a shortened free-running period (~20 h) in DD. SCN-lesioned homozygous tau mutant mice were arrhythmic in DD and methamphetamine administration revealed a MASCO-driven activity rhythm with a ~34 h period. These data showing that the tau mutation does not influence the period of MASCO in the same way it does the SCN period, suggests that the molecular timekeeping mechanism in MASCO is different from that in canonical circadian oscillators.14 It was also shown that methamphetamine induced a very long free-running period (~27 h) in heterozygous Gsk3β mutant mice in DD even though the mutation did not affect the circadian period in DD without methamphetamine).23 These data suggest that Gsk3β mutant mice have increased sensitivity to methamphetamine.\n\nNote that several studies have also been performed in single circadian gene mutant mice with intact SCN. These studies are difficult to interpret because the resulting locomotor activity is driven by coupled SCN and MASCO, and the mutation could affect one or both of these oscillators. For these reasons, studying the effects of single gene knockouts on MASCO during short-term methamphetamine administration must be performed in SCN lesioned animals (except Bmal1 KO mice with disabled circadian clocks, see Table 2). Alternatively, prolonged methamphetamine administration can reveal two independent free-running components – one from the SCN and another from MASCO. However, experiments designed to observe free-running periods of both rhythms with chronic methamphetamine treatment should be performed in DD.\n\n\nSudden period changes are a unique rhythmic property of MASCO\n\nMASCO-driven behavior rhythms in SCN-lesioned animals or in animals with genetically disabled SCN rhythmicity, where rhythms are solely driven by MASCO, are typically less stable than the rhythms of mice with intact SCN, where the rhythms are driven by coupled MASCO-SCN. Sudden period changes in the MASCO-driven circadian behavior rhythms in mice without functional SCN are often recorded. In some publications, the authors described the details of these spontaneous period changes (e.g., occurred after a cage change).13,18,21 But in most studies, the authors just reported the unstable nature of MASCO rhythmicity. In general, the MASCO-driven circadian rhythm is ~26–30 h in DD (occasionally rhythms with periods twice as long as a day, circabidian or much longer, infradian) were reported during prolonged methamphetamine administration, see below). Studies frequently report a zigzag pattern of activity (Figure 3C, D), where a long-period rhythm suddenly shifts to a short-period rhythm and then suddenly switches back to a longer period rhythm. We have observed this zigzag pattern in Per1/2 double knockout mice and SCN-lesioned wild type mice.18 We noticed that the period changes often coincided with the days we opened the light-tight boxes for visual inspection (note that we used an infrared viewer so mice were not exposed to visible light).18 This zigzag pattern can be interpreted as either two weakly coupled oscillators exhibiting relative coordination or a single oscillator showing birhythmicity, which is the two stable regimes of a limit cycle oscillator.24 Regardless of the underlying mechanism, this may be a unique characteristic of MASCO.\n\nThe period of the MASCO-driven behavior rhythm is also variable and generally becomes longer over the course of methamphetamine administration. Studies of prolonged methamphetamine administration to arrhythmic mutant mice and SCN-lesioned animals often report that the period of MASCO-driven behavior rhythm is circabidian or even much longer, infradian (one report showed that the period of the MASCO-driven activity rhythm reached ~100 h).13,14,16,21 In addition to period instability, a characteristic of MASCO is that its output rhythms often exceed the circadian range.\n\n\nGenetic factors that influence the period of MASCO\n\nAlthough most circadian mutations and genetic modification of circadian genes have no noticeable effects on MASCO, several genetic factors do affect MASCO. First, the period of MASCO differs by mouse strain. In C57BL/6J mice, methamphetamine treatment reveals an activity rhythm with a period much longer (26–30 h) than the SCN-controlled rhythm. In contrast, the period of the activity rhythm in C3H mice treated with methamphetamine is indistinguishable from the period of the rhythm without methamphetamine. There are three possible reasons that methamphetamine has no apparent effect on activity rhythms in C3H mice: (i) The animal is insensitive to methamphetamine; (ii) The animal has a MASCO with a short period, or; (iii) The animal does not have a functional MASCO. Studies in C3H mice, as we discussed previously, showed that they have a functional MASCO with a short period that is sensitive to methamphetamine.\n\nSecond, MASCO-driven rhythms are altered in some circadian mutant mice. Methamphetamine administration to Per2 knockout mice does not affect the period of the free-running rhythm in DD. A confusing result is that methamphetamine revealed a typical long period of MASCO in SCN-lesioned Per2 knockout mice. This excludes all three possible mechanisms described above. When methamphetamine was given to SCN-intact Per2 knockout mice in LL, two different free-running periods appeared, one was ~23 h and the other was ~30 h. It is known that LL does not affect the period of Per2 knockout mice (they lack a parametric light effect).25–27 Therefore, in LL, it is likely that the short period rhythm is driven by the SCN and the long period rhythm is driven by MASCO. In the case of Per2 knockout mice, it is likely that coupling between the SCN and MASCO is affected. To explain the MASCO rhythms in DD, we concluded that the MASCO driven rhythm was masked and therefore not expressed in the behavior rhythm. Methamphetamine also does not affect the periods of the MASCO-driven rhythms in Rev-Erbα knockout mice and in R6/2 and Q175 Huntington’s disease model mice.28–31 Because SCN lesions have not yet been performed in those mice, the cause of methamphetamine insensitivity is unknown.\n\nThird, some gene mutants affect the period of MASCO. Per1/2/3 triple knockout mice express a MASCO-driven circadian rhythm that has an ~20 h period. None of the SCN-lesioned single Per gene knockout mice (Per1 or Per2 or Per3) exhibited short-period MASCO-driven rhythms. Per1/2 double knockout mice exhibited activity rhythms that alternate between short and long periods. This zigzag pattern is commonly seen in the MASCO driven rhythm, so it is tempting to speculate that the period tends to be stable at the long period in most mutants, but at the short period in Per1/2/3 triple knockout mice, so Per1/2/3 triple knockout mice stably exhibit the shorter MASCO period.\n\n\nSex differences in MASCO-driven activity\n\nStudies of MASCO have been performed in both male and female rodents (Table 1). Honma’s group tested for sex differences in the response of activity rhythms to methamphetamine treatment. They housed rats in the LD cycle and administered methamphetamine. They found that the MASCO-driven activity rhythm typically dissociated from the SCN-driven rhythm in female rats, but they observed this dissociation less frequently in male rats.7 Therefore, Honma’s group used females for their MASCO studies. On the other hand, Menaker’s group observed period elongation by methamphetamine in both male and female mice in DD.10 They and others also observed that methamphetamine revealed MASCO-driven activity rhythms in both male and female SCN lesioned mice (Tables 1 and 2).10 Therefore, it is likely that MASCO is present in both sexes but coupling between the SCN and MASCO may be weaker in females, which is why the MASCO-driven rhythm dissociates more readily in females.\n\n\nRole of dopamine in MASCO\n\nA primary action of methamphetamine in the brain is to elevate extracellular monoamine neurotransmitters, dopamine, serotonin and norepinephrine, in synapses. Several studies have shown that using pharmacological or genetic models to change dopamine levels or signalling affects MASCO rhythms.\n\nThe pharmacological approach has been to treat animals with haloperidol which is a non-selective dopamine D2 receptor antagonist. Honma’s group demonstrated that injection of haloperidol produced phase-dependent shifts in MASCO-driven behavior rhythms in SCN-lesioned rats.32 Intramuscular injection of haloperidol offset the dissociated MASCO-driven activity component in rats.33 Chronically treating C57BL/6 wild-type and Bmal1 knockout mice with haloperidol shortened the period of the MASCO-driven activity rhythm.16 On the other hand, one study showed that haloperidol did not affect MASCO period in SCN-intact wild-type mice (CBA x C57BL/6J).30\n\nMASCO has also been studied in genetically modified mice with altered dopamine signalling. Sodium-dependent dopamine transporter (Slc6a3) knockout mice exhibited two activity components (~23.5 h and ~27 h) in DD without methamphetamine.16 R6/2 Huntington’s disease model mice have compromised dopamine signalling and MASCO-driven activity rhythms. However, when these mice were treated with L-dopa, the MASCO-driven activity rhythm was rescued.29 Together these studies suggest that the MASCO-driven circadian rhythm is revealed by increased dopamine signalling. However, it is possible that the monoamine serotonin also affects MASCO. The serotonin-specific reuptake inhibitor, paroxetine, is often used as an antidepressant in Huntington’s disease and also rescues the methamphetamine-insensitive phenotype in the R6/2 mouse model.30 Studying the MASCO-driven circadian behavior rhythm in dopamine receptor knockout mice will likely provide useful information about the specific role of dopamine in MASCO.\n\n\nIs MASCO an autonomous circadian oscillator in normal physiological conditions?\n\nIn the presence of methamphetamine, MASCO is a robust circadian oscillator. During prolonged chronic methamphetamine administration, MASCO can take over SCN function and control the locomotor activity rhythm. In SCN-lesioned animals, MASCO can at least partially substitute for the SCN and coordinate the phases of oscillators in peripheral tissues.34 MASCO also can drive core body temperature, feeding, drinking, and plasma corticosterone rhythms in SCN-lesioned rats.35 However, we do not know the nature of MASCO in the absence of methamphetamine treatment. It is possible that MASCO is a weak circadian oscillator and strongly coupled to the SCN, therefore we cannot observe the MASCO-driven rhythm in the absence of methamphetamine. When methamphetamine is administered, MASCO becomes a strong oscillator and eventually takes over SCN function. It is also possible that MASCO is not a circadian oscillator in the absence of methamphetamine. In the past, researchers have proposed that MASCO is a dopamine ultradian oscillator whose period is elongated by methamphetamine.16,36 It is also possible that MASCO is not any kind of oscillator without methamphetamine.\n\nThe anatomical location of MASCO has not yet been identified so it is not possible to collect biochemical and molecular measurements to determine whether MASCO is rhythmic in normal conditions (i.e., in the absence of methamphetamine). However, there are several studies that measured circadian rhythms in physiology and gene expression in animals exhibiting SCN-MASCO dissociation. The melatonin rhythm in rats aligns with the SCN activity rhythm, but not with the MASCO-driven rhythm.12 Extra-SCN brain areas, including the caudate putamen and parietal cortex, oscillate in phase with the MASCO-driven activity rhythm.12 These data indicate that the SCN and MASCO govern distinct physiological rhythms. We also recently discovered that Per1/2/3 triple knockout mice spontaneously express an ~20 h quasi-circadian rhythm every 20 days in DD (in normal conditions without methamphetamine).37 The period of MASCO in Per1/2/3 mice is ~20 h, which matches the period of this spontaneous rhythm. Other arousal stimuli, including running wheels and palatable meals, also reveal MASCO-like behavior rhythms in Per1/2/3 triple knockout mice.38 Thus, there is evidence to suggest that MASCO is continuously ticking with a circadian period even in normal conditions. We can confidently say that MASCO is an oscillator that can control physiological rhythms in the presence of arousing stimuli or drugs that increase dopamine signalling.\n\n\nProposed functional significance of MASCO\n\nThus far we have described the properties of MASCO revealed by treatment of rodents with stimulants. However, this is a very artificial situation that is rarely encountered under natural or physiological conditions. Thus, a critical question remains: what is the function of MASCO? First, we will review the experimental results that provide hints about MASCO function, and then we propose a working model of MASCO’s function and how it interacts with the circadian system.\n\nThe roles of the SCN are well-studied, so the approach to studying MASCO has been to investigate SCN-controlled functions in the presence of a robust MASCO oscillator (i.e., with methamphetamine in either SCN intact or SCN lesioned rodents). One major function of the SCN is to orchestrate the phase of peripheral circadian oscillators.39–41 The Menaker group showed that MASCO can at least partially substitute for this SCN function.34 They showed that the phases of peripheral tissues were coordinated with the phase of the MASCO-driven rhythm in SCN-lesioned mice treated with methamphetamine. This experiment shows that SCN and MASCO can share some functions, by acting at the top of the circadian hierarchy. On the other hand, there are several examples suggesting that the SCN and MASCO have distinct functions. Honma’s group showed that the peak of the melatonin rhythm in rats is always in phase with the SCN, even during SCN-MASCO dissociation, suggesting minimal influence of MASCO on the melatonin rhythm.12 They also showed that the phases of circadian gene expression rhythms in various brain regions coordinate with the phase of the MASCO-driven activity rhythm.12,15 They also examined circadian gene expression in different brain regions in rats during temporally restricted methamphetamine water availability.42 These data showed that gene expression in dopaminergic brain areas were in phase with MASCO.\n\nIn the 1970’s, Aschoff and Wever conducted studies in human subjects at the isolation facility in Andechs, Germany.43 When human subjects were isolated from natural and social environmental cues, their circadian rhythms free-ran with approximate 25-h periods. During long-term isolation, investigators often observed a phenomenon called internal desynchronization. When internal desynchronization occurs, the periods of core body temperature and melatonin rhythms become slightly shorter than before internal desynchronization. At the same time, the period of the sleep-wake cycle typically becomes extremely long (~30 h; but occasionally very short, ~17 h). The researchers concluded that there are two circadian oscillators in human, one that controls physiology (core body temperature and melatonin) with a period close to 24 h and another that controls the sleep-wake cycle with periods that significantly deviate from 24 h (either extremely longer or shorter than 24 h). This internal desynchronization in humans is very similar to SCN-MASCO dissociation observed in rodents.12,29 In addition, the rapid shifts in the period of the sleep-wake cycle to be either extremely short or long during internal desynchronization are similar to birhythmicity observed with MASCO in rodents.\n\nThe mechanisms directly controlling the human sleep-wake cycle (process S) are still under debate and may or may not require a self-sustained circadian oscillator.44 Researchers have theoretically shown that process S can be explained as an hourglass coupled with a circadian oscillator (process C). However, the observation that features of the sleep-wake cycle during internal desynchronization parallel MASCO studies in rodents support our working hypothesis that the functional significance of MASCO is to control the sleep-wake cycle. More support for a role of MASCO in controlling sleep-wake cycles comes from Honma’s group.45 They showed that a single meal can entrain the sleep-wake rhythm, but not core body temperature or melatonin rhythms in human subjects with internal desynchronization. This is similar to the observation in rodents that MASCO can entrain to restricted feeding. Rietveld and colleagues suggested that the MASCO-driven activity rhythm in SCN-lesioned rats can be simulated by the hourglass model and pointed out similarities between the MASCO-driven activity rhythm in rats and human sleep regulation (hourglass model).36 Regardless of whether MASCO is a self-sustained oscillator or an hourglass oscillator, it shares similarities with human sleep cycles.\n\n\nPossible roles for MASCO in human disorders\n\nNon-24-Hour Sleep-Wake Rhythm Disorder (N24SWD) is a human circadian disorder where sleep onset moves to a later hour each day. In rare cases, sleep onset moves earlier in persons with N24SWD.46 Recently, the period of the circadian rhythm in a person with N24SWD was measured in forced desynchrony and constant routine conditions. During forced desynchrony, the subject is forced to sleep with a period outside of the circadian range of entrainment (28 h is commonly used). This is used to estimate the period of the circadian pacemaker (presumably the SCN) by measuring the phase difference between melatonin onsets and the rectal temperature rhythm under constant conditions at the beginning and end of forced desynchrony. Czeisler and colleagues surprisingly found that the circadian pacemaker period in the individual with N24SWD was within the range of normal circadian periods (24.5 h).47 This individual exhibited ~25 h self-selected sleep cycles for a few weeks before and after forced desynchrony. This raises the possibility that N24SWD is internal desynchronization that occurs in the normal natural/social environment.\n\nMethylphenidate is a common treatment for people with attention-deficit/hyperactivity disorder (ADHD). Methylphenidate increases dopamine at synapses by blocking dopamine reuptake transporters and by increasing the expression of dopamine transporters in the brain. In rodents, methylphenidate treatment induces SCN-MASCO dissociation.19 It is estimated that 25–50% of people with ADHD experiences sleep problems48,49 and there is a positive correlation between the dose of methylphenidate and sleep problems in children with ADHD.50\n\n\nConclusions\n\nIt is now well established that disruption of circadian rhythms and impaired sleep increase the risk of human diseases. Sleep and circadian rhythms are impaired in several neurological disorders and in persons with drug addiction.51–53 However, we know little about the mechanisms of this sleep disruption. MASCO is an understudied circadian oscillator, but its link to dopaminergic signalling and rewarding stimuli is clear. We are learning more about how MASCO is altered in mutant mice, and we see parallels between sleep in human disorders and MASCO rhythms in rodents. Thus, increasing our knowledge of how MASCO regulates physiological and behavioral rhythms could help us understand how to manage circadian rhythm and sleep disruption in humans.\n\n\nData availability\n\nNo data are associated with this article.",
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Publisher Full Text\n\nAuger RR, et al.: Clinical Practice Guideline for the Treatment of Intrinsic Circadian Rhythm Sleep-Wake Disorders: Advanced Sleep-Wake Phase Disorder (ASWPD), Delayed Sleep-Wake Phase Disorder (DSWPD), Non-24-Hour Sleep-Wake Rhythm Disorder (N24SWD), and Irregular Sleep-Wake Rhythm Disorder (ISWRD). An Update for 2015: An American Academy of Sleep Medicine Clinical Practice Guideline. J. Clin. Sleep Med. 2015; 11(10): 1199–1236. PubMed Abstract | Publisher Full Text\n\nEmens JS, et al.: Behaviorally and environmentally induced non-24-hour sleep-wake rhythm disorder in sighted patients. J. Clin. Sleep Med. 2022; 18(2): 453–459. Publisher Full Text\n\nSung V, et al.: Sleep problems in children with attention-deficit/hyperactivity disorder: prevalence and the effect on the child and family. Arch. Pediatr. Adolesc. Med. 2008; 162(4): 336–342. 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}
|
[
{
"id": "150555",
"date": "20 Sep 2022",
"name": "Ralph Mistlberger",
"expertise": [
"Reviewer Expertise Chronobiology and sleep research"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well-organized and clearly written review of a fascinating phenomenon, whereby chronic ingestion of methamphetamine alters and/or induces circadian or quasi-circadian rest-activity rhythms in rodents. The article provides a good historical overview of studies on the phenomenon, and a cogent summary of the properties of these rhythms under different environmental conditions and in mouse lines with various clock gene mutations. I have a few suggestions for additional content:\nAbstract: “We discuss these fundamental properties of MASCO and synthesize studies of strain, sex, and circadian gene mutations on MASCO”. I suggest deleting the word ‘synthesize’, or replacing it with ‘integrate’ or some other word.\n\nAbstract: ‘Canonical’. Can we all stop using that word so much in reference to clock genes? Students often find it confusing, as if it refers to a particular type of gene.\n\nProposed functional significance of MASCO. “One major function of the SCN is to orchestrate the phase of peripheral circadian oscillators.39–41 The Menaker group showed that MASCO can at least partially substitute for this SCN function.” MASCO organizes rest-activity states, which determine when animals are awake to feed, which determines the daily rhythm of food intake. It would be worth noting that food intake may be the periodic stimulus that mediates synchrony of peripheral oscillators with rest-activity rhythms induced by methamphetamine intake. MASCO may be at the top of a hierarchy, but may in fact only control behaviour, and have no direct output to peripheral oscillators.\n\nProposed functional significance of MASCO. “The researchers concluded that there are two circadian oscillators in human, one that controls physiology (core body temperature and melatonin) with a period close to 24 h and another that controls the sleep-wake cycle with periods that significantly deviate from 24 h (either extremely longer or shorter than 24 h).” This phenomenon, in humans, has also been modelled as an artefact related to changes in time perception and to instructions not to nap. When naps did occur, they weren’t included in the actograms. When they were added to the actograms (Zulley and Campbell), the evidence for desynchrony disappeared (subjects slept at the temperature minimum most if not every cycle), at least in some of the published records for which nap data were available. Aschoff did not dispute this but did point out that there was a change in time perception, and meal timing etc. suggesting a prolonged biological day. The change in time perception could be independent of circadian timing, and related instead to an effect of temporal isolation.\n\nI’m surprised that the authors don’t discuss the possible relationship between MASCO and food-entrainable oscillators thought to drive food anticipatory activity rhythms in animals on daily feeding schedule. Both types of rhythms are SCN dependent, and seem robust to various clock gene knockouts, and may involve dopamine signalling pathways. I don’t believe that there is any compelling evidence ruling out the possibility that the two are manifestations of the same timing mechanism.\n\nPossible roles for MASCO in human disorders. I’m also surprised that the DUO model of bipolar disorder, proposed by Blum and Storch (citation 16) isn’t discussed here.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "8899",
"date": "17 Oct 2022",
"name": "Shin Yamazaki",
"role": "Author Response",
"response": "We thank the reviewer for the supportive and insightful comments. We replaced ‘synthesize’ with ‘integrate.’ In the abstract, we removed ‘canonical’ and simply said ‘circadian genes.’ We added this explanation as a possible mechanism by which MASCO coordinates the phases of peripheral oscillators. Thank you for bringing this to our attention. We were not aware of the possible artefact caused by instructions not to nap and the impact of changes in time perception. We reviewed this study and added the caveats to this paragraph. The reason we didn’t mention this is that we discuss this topic in our prior review articles. However, we agree this is important and therefore mentioned that the extra-SCN oscillators may utilize the same timekeeping mechanism and may be the same oscillator. Thank you for this suggestion. We have discussed that Blum and Storch proposed the DUO as a model of bipolar disorder."
}
]
},
{
"id": "149940",
"date": "06 Oct 2022",
"name": "Eric Zhang",
"expertise": [
"Reviewer Expertise circadian clock",
"sleep",
"mood disorders"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript summarizes the characteristic of MASCO which induced by methamphetamine in detail and clearly, points out the conditions under which MASCO should be investigated, and provides comprehensive overviews of phenomenon of MASCO in rodents, particularly, with kinds of chemical treatment and different genetic canonical circadian genes knockouts. This is a very well-written review containing detailed summaries and discussions which merit an imminent publication, and will surely promote research in related fields. However, several minor points need to be addressed and certain statements require further justification.\nPoints in details:\nProposed functional significance of MASCO. Considering the phenomenon that the period length is different in DD and LL condition with methamphetamine, but it is well-known that the locomotor activity rhythm to the light-dark cycle is entrained by SCN. Thus, it is necessary to explore the impact from external cues, such as light. By the way, we know that restricted feeding would like to induce dissociation of the MASCO and SCN activity rhythms during short-term methamphetamine treatment in 2014, it is perhaps also worth illustrating the relationship between food-entrainable oscillator and MASCO.\n\nPossible roles for MASCO in human disorders. The manuscript only discussed two human disorders which are N24SWD and ADHD, which is not enough, in my opinion, to cover all roles of MASCO in human disorders. My recommendation is to restructure this part to include more evidence and possibility (for example: the roles of methamphetamine in R6/2 and Q175 Huntington’s disease model mice).\n\nDiscovery of the extra-SCN pacemaker that is sensitive to methamphetamine. “There are also circadian pacemakers that control circadian rhythms of locomotor activity in rodents, but do not require the SCN or the canonical circadian molecular timekeeping mechanism. These extra-SCN circadian pacemakers are revealed by methamphetamine/amphetamine, restricted food availability (the food-entrainable oscillator or FEO), or other rewarding stimuli such as wheel-running activity and palatable meals”. These descriptions and “fig2” still cited author’s own review ” Extra-SCN Circadian Pacemakers” which published in 2017, it is in need of further discussion and modification.\n\nGenetic factors that influence the period of MASCO. “There are three possible reasons that methamphetamine has no apparent effect on activity rhythms in C3H mice.” More detailed arguments are needed here for the sensitivity of C3H mice to methamphetamine because MASCO is of short duration.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "8900",
"date": "17 Oct 2022",
"name": "Shin Yamazaki",
"role": "Author Response",
"response": "We thank the reviewer for the supportive comments and suggestions. Thank you for these suggestions. We added a sentence discussing the possibility that FEO and MASCO use the same timekeeping mechanism and are the same oscillator. Thank you for this suggestion. We added a discussion of the DUO as a possible model of bipolar disorder. Additionally, we added further discussion of schizophrenia. We added a sentence that FEO and MASCO may use the same mechanism to generate the rhythm. We added a sentence that the genetic factors causing a short MASCO period in C3H mice is unknown."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1018
|
https://f1000research.com/articles/11-1205/v1
|
21 Oct 22
|
{
"type": "Research Article",
"title": "A critical discourse analysis of the Quebec media’s portrayal of older adults in residences and long-term care homes pre- and peri-COVID-19",
"authors": [
"Olivia Archambault",
"Martine Lagacé",
"Sarah Anne Fraser",
"Olivia Archambault",
"Martine Lagacé"
],
"abstract": "Background: How we discuss older adults can influence our perceptions of aging and age-related policies, particularly during times of crisis. Ageist discourse in the media impacts how society views older adults and how older adults view themselves. Negative stereotypes have been associated with negative health outcomes and can exacerbate the adverse events faced by older adults during a pandemic. This study examined the Quebec media’s portrayal of older adults living in long-term care (LTC) homes before and during the first wave of COVID-19. Methods: The first confirmed COVID-19 case in Quebec was on 27 February 2020. The Factiva database was searched for newspaper articles that were published three months before (pre) and three months after (peri) the first confirmed case. Articles had to include the terms: older adults, LTC, and/or residence. Articles were excluded if they did not discuss direct or indirect impacts in the lives of people living in LTC (i.e., only discussed statistics of COVID-19 cases). After screening, 208 articles were retained, and critical discourse analysis was conducted. Results: The media discourse regarding older adults in LTC homes revealed a lack of resources (i.e., insufficient staff) and negative health outcomes for older adults (i.e., bed sores) in both the pre- and peri-COVID-19 articles. Negative and positive elements emerged from the peri-COVID-19 discourse, including increased social isolation of those in LTC, government action and advocacy (by health care practitioners and family) to support those in LTC homes. Conclusions: Existing systemic problems were exacerbated by the pandemic and this impacted older adults in LTC homes negatively. Despite this, the peri-COVID-19 discourse suggests meaningful change at the societal and policy levels to improve outcomes for future generations of older adults who reside in LTC homes.",
"keywords": [
"long term care homes",
"media discourse",
"residence",
"COVID-19",
"aging",
"older adult"
],
"content": "Introduction\n\nHeterogeneity in the aging population includes variability in social structure, genetics, and personality (Light et al., 1996; Ehni & Wahl, 2020). It may also reflect the outcome that some older adults will be independent while others will depend on support from their relatives, community services, or a residence or long-term care (LTC) home as they have higher care needs (Grigsby, 1996; Nguyen et al., 2021). In 2019, adults aged 65 and older in Quebec represented 19.2% of the population, making it the Canadian province with the highest proportion of older adults in its population (Statistics Canada, 2021; Institut de la statistique du Québec, 2019). It is estimated that for those older adults that do not live independently in the community, 85,000 live in private residences while 46,000 live in publicly funded LTC homes in Quebec (Bravo et al., 2014). Within this categorization, Quebec further differentiates its LTC homes into three types based on the level of care provided: (1) “centres d’hébergement de soins de longue durée” (CHSLD), (2) “résidences privée pour aînés” (RPA) and (3) “ressources intermédiaires” (RI) (Commissaire à la santé et au bien-être (CSBE), 2021). Older adults who need the highest level of care, in that they require help with daily tasks, are typically placed in CHSLDs (CSBE, 2021). In contrast RPAs are homes in which residents may require some care but the focus is more on providing a support system and a community (CSBE, 2021). The intermediate type of home is considered RI, where older adults need some assistance with their daily activities but not to the extent of older adults in CHSLDs (CSBE, 2021). It should also be noted that RIs are not limited to older adults but also include persons of all ages who have severe disabilities (CSBE, 2021). Currently in Quebec, there are 412 CHSLDs (private, private subsidized and public), 1791 RPAs and 1835 RIs (Lavoie, 2020).\n\nCOVID-19 is an infectious disease caused by a coronavirus, first discovered in Wuhan, China (World Health Organization, 2020). The first COVID-19 case in the province of Quebec was confirmed on 27 February 2020 (Olson, 2020). During the first wave, adults aged 60 years and above represented 36.8% of confirmed cases and 97.7% of deaths resulting from COVID-19 in the province (Gouvernement du Québec, 2020). During the crisis, Quebec became one of the top ten epicenters in the world largely due to the spread within the LTC homes (Bérubé, 2020). The pandemic served to highlight the already fragmented system serving LTC residents from years of understaffing and mismanagement of funds (le ministère de la Santé et des Services sociaux, 2021; CSBE, 2021). More than ever, people have been turning to the media to be informed of daily updates regarding the pandemic. In 2014, more than 57% of Quebecers said that they read print newspapers at least once a week (Siag, 2016). Adults over 50 years old make up the largest demographic of print newspaper readers in Quebec (Centre d’études sur les médias, 2019). The Journal de Montréal reported a 91% increase in readership compared to the year prior to the pandemic (Robitaille, 2020). As such, the media has been given a significantly larger role in public life, making its depiction of older adults during these unprecedented times not only more prominent but reaching a much larger audience. The degree of influence of the media on the perception of older adults during COVID-19 is therefore considerably higher.\n\nThe media has the power to influence the public’s opinion based on the ideas it presents as well as the many ideologies it supports (Happer & Philo, 2013). The media can act as a vector for the dissipation of stereotypical views that can make their way into societal perceptions (Happer & Philo, 2013). When the media creates and propagates stigma, the more neutralized the stereotypes become, thus making it easier to adopt these views into popular culture (Ross, 2019). Mainstream news media typically focuses on populations in power and often portrays institutional leaders, such as the government, positively (Ross, 2019). This consequently results in populations deemed less important and sometimes already marginalized, to receive less favorable and stereotypical portrayal (Ross, 2019).\n\nPositive and negative ideas of aging have been presented in the media, but many tend to reinforce ageist stereotypes (Fraser, Kenyon, Lagacé, Wittich & Southhall, 2015; Milner, Norman & Milner, 2012). Aging is often seen as a phenomenon that should be avoided, where older people create a burden on social and economic resources of the society (Milner et al., 2012). News and social media reinforce the ageist stereotypes where older adults are ultimately waiting to get sick and are helpless against illness (Ayalon et al., 2021; Bacsu et al., 2022; Fraser et al., 2020; Lagacé, Laplante & Nahon-Serfaty, 2013). Occasionally, aging is perceived positively by the media, but this is often in the form of an underlying anti-aging campaign (Milner et al., 2012).\n\nOne model that has attempted to explain why society, including the media, conveys stereotypes about older adults is the Stereotype Content Model (Fiske et al., 2002). This model identifies two categories in which groups may be stereotyped, according to: warmth and competence (Chasteen & Cary, 2015). Older adults may be described using this model, scoring high for warmth yet low for competence (Chasteen & Cary, 2015). Although scoring high for warmth may be perceived positively, it is typically paired with scores of low competency and this may contribute to the undermining of older adults in the society and consequently, to lowered self-esteem and decreased social participation (Chasteen & Cary, 2015). In fact, when older adults living in LTC are treated as able-minded and -bodied, positive health outcomes can be observed (Chasteen & Cary, 2015). Direct (e.g., old people are fragile) or indirect (e.g., walking canes are ugly) stereotypes can have a profound impact on the way not only society views a group of people but how the members of that group perceive themselves (Kang & Chasteen, 2009).\n\nOne way of critically examining, interpreting, and explaining how discourses create and reinforce social inequalities is critical discourse analysis (CDA) (Mullet, 2018). This method acknowledges the power of language on perception and social relations (Mullet, 2018). CDA also helps present a global context on what is happening in the society in terms of economic, historical, and governmental interactions in terms of the group of interest (Fraser et al., 2015). This method has been used before to examine differences and similarities in the ageism present in public discourse in a study related to the older population living in Ireland (Phelan, 2018). Semi-structured interviews were conducted with nurses who were asked their views on older adults. Many of the ageist stereotypes found within the oral discourse of the nurses were reaffirmed by older adults themselves when interviewed separately (Phelan, 2018). One older adult even said that living in her own home would be too dangerous, as older people are very vulnerable to violent break-ins and assault, as portrayed by the media (Phelan, 2018). Here, the older adult accepted and applied the stereotype of being vulnerable to her own life, demonstrating the power of language in public discourse (Phelan, 2018).\n\nSince one of the populations most affected by COVID-19 is older adults living in LTC homes, it is of interest to examine their portrayal in the media prior to and during the pandemic. This will allow for the exploration of existing issues of neglect in the care and quality of life outcomes of older adults in residences or LTC homes (Estabrooks, Squires, Carleton, Cummings, Norton, 2015; Katz, 2011), as well as their contribution to the poor health outcomes and mortality seen in the wake of COVID-19. Therefore, the goal of this study was to examine the Quebec mainstream print and online media material about older adults living in LTC homes pre- and peri-COVID-19 using critical discourse analysis.\n\n\nMethods\n\nSearch strategy: It is estimated that the Journal de Montréal and Journal de Québec reach 2.83 and 1.48 million readers per week respectively, making these the two newspapers the most dominant media platforms in Quebec, both in print and their online form (Québecor, 2019), and therefore these two newspapers were targeted in our search. In addition, with the goal of capturing media from as many regions and perspectives as possible, the following French-language news sources were included based on readership: Le Devoir, Le Soleil, La Presse.ca, La Tribune, Le Quotidien, and La Voix de L’ Est (Jacques, 2017). Using the Factiva database, these sources were searched on 13 May 2020, and the 6 previous months were examined. This allowed us to capture media texts from 3 months before the first confirmed COVID-19 case in Quebec to 3 months after. A preliminary database search was conducted using a list of basic search terms related to the research question (e.g., “aînés” [older adults] and “centres d’hébergement de soins de longue durée (CHSLD)” [long-term care homes]). This search was amended as it was found that several additional terms emerged that reflected the residences/care homes available in Quebec in a more concise manner. Each type of residence involved care services provided to older adults, but they varied in the number of hours of care and services provided. In addition to CHSLD, other search terms that related to LTC homes in Quebec were used, these included: “résidence pour aînés”, “résidence privée pour aînés” or RPA, and “ressource intermédiaire” or RI.\n\nInclusion/exclusion criteria: Selected articles had to include one of the type of residences in Quebec and health/quality of life outcomes of older adults. Any type of article (i.e., opinion, news, life, etc.) was eligible for inclusion and articles were coded according to type in order to better understand where in the newspaper the targeted discourse was emerging (i.e., front page news or life). Articles were excluded based on two criteria: (1) Unrelated and (2) Duplicates. Articles falling into criterion (1) did not include information pertaining to direct or indirect impact on the lives of older adults living in LTC homes. For example, the article was excluded if it only mentioned the word “CHSLD” without explaining the impact on the lives of older adults. Lastly, articles containing identical content with or without identical titles to previously included or excluded publications were considered duplicates.\n\nFrom 1413 generated articles, two authors determined that 316 fit the inclusion criteria for all search terms based on the immediate content surrounding the search term. The same authors screened the full texts of the 316 articles, discussed any conflicts and determined by consensus that an additional 108 articles be excluded. For the 208 included articles, a coding grid was created that included information about: (a) the newspaper (Journal de Montréal or Journal de Québec), (b) type of article (i.e., news, opinion, etc.), (c) author, (d) date of publication and (e) length of the article in words. The two authors then collaboratively coded 35 articles to discover common themes arising from the text. The coding of this subset was completed over a 2-week period, where discussion led to the formal definition of codes and a preliminary code book. Subsequently, the next 33 articles were coded with the code book and then discussed to make any final adjustments to the coding. All remaining articles were coded with the final code list (25 codes) by the first author. Codes were applied to different passages and the frequency of each code was quantified in Microsoft Excel.\n\nDuring the iterative coding process, OA and SF found that certain codes reflected emergent categories (or themes). For example, the codes: social isolation, neglect, abuse, and reduced autonomy (by others) were all found to reflect the category of mistreatment. The advocacy category emerged with respect to the codes: support and protection (from the public), family support, moral responsibility and justice system. After reviewing the data, seven conceptual categories emerged by author consensus. These categories were (i) mistreatment, (ii) positive care procedures, (iii) negative care procedures, (iv) communication, (v) stigma, (vi) government and (vii) advocacy. The minimum length of text coded was one sentence. Representative passages were selected and the first author, a bilingual researcher, translated the passages from French to English for reporting purposes. The code list, specific definitions and categories can be found in Figure 1. Once the sample (208 articles) was coded completely, thematic analysis was used to uncover themes from interacting codes. Thematic analysis helps identify themes from the text by the grouping of several categories that convey a similar meaning through the use of inductive analysis (Mogashoa, 2014). The recurring themes (or interactions between codes/categories) can help explain what is being said in the text in a more cohesive manner (Mogashoa, 2014).\n\n\nResults\n\nClose examination of the texts revealed that there were interactions between the different categories identified during coding, leading to two important themes emerging. The first theme, (1) Resources, health and government, represents the intersection between lack of resources, negative health outcomes and government action during the pandemic, encompassing categories (iii) and (vi). The second theme, (2) Social isolation and advocacy, represents the relationship between negative health outcomes and advocacy during the pandemic, encompassing categories (i), (ii) and (vii). The results of these two themes will be presented immediately after the reporting of the summary quantitative data comparing the code frequency in the pre- and peri-COVID-19 timeframes. These findings will be followed by additional results surrounding the discourse around the different types of residence and ageist language that are indirectly related to the research question.\n\nData collection yielded a total of 316 articles, of which 108 were excluded based on exclusion criteria, and the remaining 208 article contents were critically analyzed. A distribution of articles published per month during the selected time period can be found in Figure 2. Ninety-one percent of articles analyzed discussed the situation in LTC homes during the pandemic (peri-phase), the remaining 9% belonged to the pre-pandemic phase. The most common newspaper section reporting on older people in LTC homes was the news section, followed by opinion pieces. Most of the articles (87.5%) focused on CHSLDs while the remaining covered other types of residence, with private residences being the second most prevalent.\n\nBased on analyzed data, articles that fell within the pre-COVID-19 timeframe were most frequently coded for lack of resources in the care homes (i.e., insufficient staff) and negative health outcomes for older adults (i.e., bed sores). Similarly, these two codes were also the most frequently applied in the peri-COVID-19 phase. These codes emerged before the pandemic and seemed to be exacerbated by the effects of COVID-19 as the number of articles focused on these issues increased in the peri-COVID-19 phase. Furthermore, positive government action (i.e., improving policies, protecting older adults) played a significant role during the pandemic, whereas this code did not emerge in the data from before the pandemic. Additionally, social isolation (of older adults) and advocacy (toward older adults by health care practitioners (HCP) and family) were two codes that distinguished the two timeframes from one another, both of which were very largely present during the peri-COVID-19 phase.\n\nThe media representations highlighted that a lack of resources and negative health outcomes were a significant problem even before the pandemic, making up 36% of all codes that emerged and were applied during the pre-COVID-19 phase. The lack of resources code encompasses actions or language relating to the demand for space and services in LTC homes. Lack of resources additionally accounts for demands that LTC homes cannot meet due to lack of funding, staff, equipment, training, etc. Many of the factors contributing to a lack of resources can impact the physical wellbeing of older adults, such as is portrayed in the following pre-COVID example in which a family is advocating for their father. The son found his father badly injured after being left unsupervised during the night.\n\nThe family is now sending out a cry for help for improved training of those who care for people with Alzheimer’s. [The son said:] ‘The accident, it’s a lack of training …’\n\nDecember 2019; Amélie St-Yves; Journal de Montréal; section: news\n\nThe need for resources became more publicly apparent during the pandemic as the reporting of negative health outcomes among older adults began to increase, as evidenced in the following quote.\n\nThe number of COVID-19 cases in one of Montreal’s largest CHSLDs quadrupled in a few days, provoking anxiety to residents and employees.\n\n28 March 2020; Hugo Duchaine; Journal de Montréal; section: news\n\nThe testimonies of health care professionals and the residents themselves prompted the government to provide help during the crisis. One professional expressed her distress at the conditions faced by the residents and staff working in a LTC home with little support. Her voice and others reporting on the conditions in these homes helped bring about change.\n\n“I feel like I am abandoning ship, but it is them [the government] that are throwing me overboard,” exclaims Ms. XX, who believes she has post-traumatic stress disorder\n\n3 May 2020; Anne-Sophie Poiré; Journal de Montréal; section: news\n\nThe code for government action evolved during coding into two branches according to its impact on the lives of older adults (positive and negative). Positive government action focused primarily on protective actions taken regarding older adults living in LTC including reform (i.e., increasing funding). In contrast, negative government action was primarily concerned with institutional neglect (i.e., lack of inspections to ensure proper protocol was being followed). These two branches were coded with similar frequency during the peri-COVID-19 timeframe. At the beginning of the pandemic, the government put in place protective measures to limit the spread of the virus among the older population, urging older adults to stay at home. These measures were viewed by some older adults as restrictive and ageist. As seen below, Quebec Premier François Legault described his mother as being upset by the proposal that she stay at home.\n\n“I called my 91-year-old mother and told her: it would be better, in the next few weeks, to not leave the house. She was not happy. It’s not a pleasant thing to ask. But I’m asking everyone: call your parents, your grandparents that are over the age of 70 and tell them: it’s not a good idea to leave the house in the next few weeks,” Premier François Legault pleaded yesterday.\n\n15 March 2020; Charles Lecavalier; Journal de Montréal; section: news\n\nThere was also a link between reports of negative health outcomes, negative government action and lack of resources. As a result, many of the protective actions taken by the government during the pandemic were presented as an attempt to respond to previous institutional neglect. According to one journalist at the time, the residents living in LTC homes and the staff serving them had been neglected by the government for many years.\n\n[…] The deaths reflect the extreme political and spending negligence of which the residents and staff have been victims over the years.[…]\n\nThe CIUSSS1 network became a catastrophe like the SPCA [Society for the Protection of Cruelty to Animals] in the puppy mills. But where were the CIUSSS before?\n\nResult: for Montreal, the COVID-19 epicenter, the Premier made desperate calls for a helping hand: army, doctors, caregivers, civil servants, etc.\n\n21 April 2020; Josée Legault; Journal de Québec; section: opinions\n\nClearly, the government plays a major role in the distribution of resources to LTC, and this has a significant impact on the health of older adults. The following is another example demonstrating the interaction between government inaction and a lack of resources.\n\nThe shocking testimonials are multiplying: lack of staff, inadequate monitoring of facilities, obsolete infrastructure, dysfunctional care services, some private CHSLD owners have criminal records, etc.\n\n[…]\n\nNo less than four government terms have passed since the tabling of a report exposing the negligence that rules the management of housing facilities for older people with diminishing autonomy.\n\n23 April 2020; Nicolas Lachance; Journal de Montréal; section: news\n\nActions, dialogue, or language that led to the isolation or exclusion of older adults from social events and participation, is another aspect that seemed to be exacerbated by the protective measures put into place by the government. The data reveals that social isolation is tied to the poor mental and physical health of older adults and their family members, as demonstrated in the example below.\n\nAnother infected patient tries to leave the confinement zone, but I must tell him to return to his room. When he turns around, I notice that his gown is stained with blood. The patients confined to their little rooms do not have anything to do but to lie down, and many of them develop bed sores.\n\n14 April 2020; Félix Séguin; Journal de Montréal; section: news\n\nIn addition, although family members were not the focus of this study, some of the measures implemented, as well as communication practices (from the LTC home to the residents and family members), also had an impact on the mental health of the family members of the older adults living in LTC. One family member sought to explain the importance of physical distancing measures in place to her mother, who clearly wanted to maintain social contact.\n\nMy mother said, ‘You abandoned me.’ She cried and said, ‘I would rather die’. It eats away at us.\n\n20 April 2020; Kariane Bourassa; Journal de Québec; section: news\n\nOften, the absence of family support during the pandemic was also linked with negative health outcomes for older adults. Many of the quotes and passages coded under family support pertained to the pre-COVID-19 context as health guidelines placed restrictions on visits and regular caregiving provided by the family during the pandemic. However, once this informal care was stripped away, it became clear that family support played a large role in the continuity of care of older adults living in LTC centers. This is demonstrated in the following excerpt.\n\nShe would regularly receive visits from her family.\n\nExcept the health crisis put an end to the visits, destabilizing the woman, who started to lose her appetite, explains her granddaughter.\n\nBecause in addition to the shock of no longer being near her loved ones, the 90-year-old could no longer eat the traditional meals that they would prepare for her.\n\n“She wouldn’t stop asking where I was, why I wasn’t coming,” said Ms. Bour who, as an auxiliary nurse, knew how to care for her grandmother.\n\n10 May 2020; Michael Nguyen; Journal de Montréal; section: news\n\nAs the conditions of LTC homes deteriorated and were revealed to the public, public advocacy for older adults in LTC homes increased. This advocacy came in the form of additional aid or increased support from professionals, requests for additional funding and support, recognition of equity issues (e.g., importance of older adults in society), and acknowledgement of older adults’ rights and needs. Interestingly, not only were older adults advocated for but also their caregivers. While a select few residences were portrayed very negatively to the public, most reports on the residences and their staff were positive. Staff were praised for doing their best in the care of older adults during times of crisis. In the following example, a son makes a point to acknowledge the specific nurse who cared for his mother.\n\n“We’re currently seeing many horror stories. There are some, but there are also many wonderful stories and that cannot be forgotten,” said X, who wanted to thank Y [the nurse], but also all of her other colleagues and other ‘guardian angels’.\n\n11 May 2020; Hugo Duchaine; Journal de Montréal; section: news\n\nThe recognition of positive care procedures was facilitated by acts of advocacy and gave rise to a movement of solidarity among the public in view of the treatment of older adults. Social advocacy was demonstrated in two forms: direct and indirect acts. Direct acts of advocacy were seen in reports of individuals donating cooked meals to care facilities or providing remote entertainment to residents. Indirect acts came in the form of an emerging moral duty from the public regarding the treatment of older adults and their subsequent health consequences. The moral aspects of the situation are captured in the following excerpt.\n\nThe choice.\n\nThe terrible choice to decide to save a younger person at the expense of an older one because of a lack of ventilators or lack of resources of all kinds.\n\nThere is the greatest risk. It’s a collective sacrifice. To accept that we must put everything in place to not have to sacrifice those who contributed to build our society.\n\n8 April 2020; Jonathan Trudeau; Journal de Montréal; section: opinions\n\nThe emergence of this dialogue distinguishes a strong difference between the pre- and peri-COVID-19 phases. In the peri-COVID-19 phase, there was a rise in advocacy by the public once negative health outcomes were exposed by the media. Negative health outcomes were linked to restrictions on informal care provided by family members due to physical distancing and social isolation procedures. Confinement of older adults was the result of preventative measures put into place by the government; the goal was to protect but, in some cases, the resulting social isolation of older adults still fostered poor health. Therefore, the interactions between these codes are numerous and far from mutually exclusive. The interaction between lack of informal care, social isolation and subsequent health outcomes is demonstrated in the following example.\n\nWithout being an expert, he quickly realized that his mother appeared to be suffering more psychologically than from the virus.\n\n“It’s not hard to understand. There’s an important psychological component here,” he said. “But I am not pointing any fingers, they are overwhelmed.”\n\n[…When pandemic restrictions were lifted and family members could visit] Then, Ms. XX [the mother] almost instantly began to feel better. Her son helped feed her, she had mobility issues. He combed her hair and hummed her favorite songs.\n\n“It was night and day,” said Mr. XX [the son]. “The last time I saw her, she was talking and singing to Frank Sinatra.”\n\n3 May 2020; Jonathan Tremblay; Journal de Montréal; section: news\n\nAnalysis of the media texts revealed that very different language and terms emerged to describe the different types of residence included in the analysis. As mentioned previously, CHSLDs were the most prevalent type covered by the media. The two most common codes among CHSLDs were lack of resources and negative health outcomes. Similarly, the most common code among the other residences was negative health outcomes, but interestingly, the second most common code was distributed evenly between three codes: good care, positive psychological state among older adults, and lack of resources. In both CHSLDs and other residences, negative care procedures emerged as dominant over positive care procedures. However, among articles discussing CHSLDs, positive care procedures only made up 9% of total codes whereas for other residences, positive care procedures made up 20% of their codes. The latter can be explained by the fact that many of the other residences are privately funded and managed, therefore they may have more adequate staffing and resources (Bravo et al., 2014a,b). For example, as presented in the quote below, private residences often reported having proper equipment to protect not only employees but also the residents during the pandemic, whereas this was not the case for CHSLDs.\n\nThe patients were isolated, and the dining room was closed. The staff only had access to a limited number of zones. Gowns, masks and gloves were distributed to the staff at the end of March, in addition to the mandatory masks to all residents.\n\n20 May 2020; Anne-Sophie Poiré; Journal de Montréal; source: news\n\nMany differences arose among the types of residence regarding the level of organization and communication of information about COVID-19 procedures and the status of the older adults in the particular care setting. The types of residence diverged on the speaker chosen to represent the point of view of the older adult and the degree of ageist language. Poor communication was coded according to the following concepts: poor organization, procedures, and transmission of information within the LTC home and to caregivers. The latter included actions or language regarding the following of improper protocol in various LTC homes. This code was much more prevalent among CHSLDs than the other (mostly private) residences. For example, in many cases, the families of older adults reported not being updated on the health and well-being of their loved ones staying in LTC homes. This situation was much less common among the private residences in the selected texts. The following citation provides an example of the lack of information being shared with families during pandemic restrictions.\n\n[Article title] TWO WEEKS WITHOUT NEWS\n\n“Over the two weeks that followed, I tried to speak to someone to get news about my father and never heard back. Then the day that I made a complaint to the ministry, I got a call back,” explains Mr. Costa with irony.\n\n2 April 2020; Cédérick Caron; Journal de Montréal; section: news\n\nThe narration of the point of view of the older adults was another distinguishing factor between CHSLDs and the other residences. In the case of CHSLDs, the narrator was often a family member or a health professional whereas for RPAs and RIs, it was often the older adult themselves. For example, the caregivers working at the CHSLDs were often describing the psychological state of the older adults.\n\nThe solitude is starting to become draining. Separated from his wife that would visit him several times a week, one of the residents spent over a week crying in his room.\n\nAnother one [family member] could not see her mother. I heard her burst into tears on the phone when she heard her voice. Heartbreaking moments.\n\n9 May 2020; Marie-Christine Noël; Journal de Montréal; section: news\n\nThis may be attributed to the fact that many of the older adults living in CHSLDs require a greater level of care and may rely on the support of a family member as a proxy decision-maker in terms of their health care needs (Holroyd-Leduc et al., 2016). By comparison, residents in private care homes may hold a greater level of independence and mental capacity. Additionally, the principal issues concerning each type of LTC home varied as well. For CHSLDs, the main concerns were the family’s access to their loved one, as well as health care neglect. For the other types of residence, the main issues that arose were concerning the autonomy and freedom of the residents. For instance, even pre-COVID-19, residents living in private care homes reported feeling their autonomy infringed upon by their bus stop being displaced without consideration of their needs.\n\nThe construction of the tramway could bring serious consequences to the 330 residents of a residence for older persons in the Saint-Sacrement area. These older adults risk seeing their normal bus stop disappear and losing a part of their autonomy. That’s the worry [that] Director General Nathalie Arcand expressed.\n\nThe closest tramway station would be 300 meters from the residence.\n\nThis distance, that may seem trivial, will most likely be unattainable for persons with reduced mobility.\n\n5 December 2020; Taieb Moalla; Journal de Québec; section: news\n\nAgeist language was a common phenomenon in the texts discussing older adults and their LTC homes before and during the pandemic. Whether these terms were used in a compassionate or derogatory way, they were coded the same in contributing to stereotypical views of aging. Not only were terms directed toward older adults coded but also, terms referencing their place of residence. The use of language that feeds assumptions and fosters stereotypes and discrimination against older adults was much more prevalent in articles discussing CHSLDs. For example, a CHSLD was frequently described as a morgue or as a place to go to die.\n\n[Article title] CHSLDs TRANSFORMED INTO HOSPICES\n\n[…]\n\nMost Quebecers were not prepared to witness the horror scenes that occurred behind the walls of these places of suffering. People in end-of-life are vulnerable, anxious, and helpless.\n\nMany suffer from Alzheimer’s or have different cognitive problems. They are also abandoned by their family, as only 10% of residents are visited by their loved ones.\n\n17 April 2020; Denise Bombardier; Journal de Montréal; section: opinions\n\nThough the latter quote was taken from an opinion piece, stigmatizing words such as “vulnerable” were littered across the news section of many of the articles in our sample, painting a portrait of all older adults as vulnerable members of society. In many instances, the fragility of older adults depicted by the media was considered the prime cause of the accumulation of deaths in the LTC homes, instead of the possibility of intersecting external factors such as a lack of resources and neglect, as one reporter aptly states in the following quote:\n\nWe neglected the places where our society’s most vulnerable members live. […] Despite these warnings, the old are the main blind-spot in the current crisis.\n\n16 April 2020; Antoine Robitaille; Journal de Québec; section: news\n\n\nDiscussion\n\nThe goal of this study was to examine the Quebec media’s portrayal of older adults living in LTC before and during the first wave of COVID-19. The similarities and differences between the pre- and peri-COVID-19 phases highlight which aspects of LTC were problematic even before the pandemic and which aspects were exacerbated by the pandemic, resulting in poorer outcomes for older adults. The media presentation of the pandemic also fostered strong social advocacy for older adults living in LTC homes.\n\nFirstly, it is clear from the findings that there has been and still is a need for more resources in Quebec LTC homes. These resources can come in the form of staffing, training, equipment and most importantly, funds. From the data, a strong association between lack of resources in these homes and negative health outcomes for older adults was clear. A majority of older adults residing in CHSLDs require extensive amounts of care for daily living tasks (CSBE, 2021). Therefore, insufficient funds or staffing can have a profound impact on their quality of life and overall well-being. This was recognized by the Quebec government when preparing the 2018-2019 budget, as they allocated $378 million for services in all types of LTC homes, and specifically $96 million to improve the province’s CHSLDs (Gouvernement du Québec. 2018). However, despite the government’s budget plan, CHSLDs made up the largest proportion of deaths per living arrangement during the pandemic, largely because they were lacking resources (Gouvernement du Québec, 2020).\n\nThe findings highlighted that the relationship between lack of resources and negative health outcomes is further exacerbated by disasters (e.g., a pandemic) that limit access to informal care such as visits from family members, and can cause stressful conditions. Informal care provided by family members and non-professionals can facilitate a continuity of care as well as maximize the care (by providing additional assistance) and psychological support of the older adult (Triantafillou et al., 2010). The need for government reform was acknowledged more urgently during the peri-COVID-19 phase once the role of informal caregivers was finally recognized as an essential part of the continuity and quality of care among older adults. The reform calls for increased staffing and valuing the work of health care practitioners in LTC homes by increasing their salary and level of training. In May 2020, the Quebec government announced a plan to increase the staff working in CHSLDs by 10,000, increase the yearly salary of an orderly by 9,000 CAD and provide a 3-month training program for all new employees (Shingler, 2020). Although the need for distributive reform was addressed immediately during the pandemic, the lack of resources was evident before it. Perhaps the dependence of Quebec LTC homes on informal care was significant enough to mask the urgent need for government intervention prior to the pandemic. In comparison to the rest of the country, Quebec is not the only province that struggled with the effects of the pandemic on their LTC facilities (Holroyd-Leduc & Laupacis, 2020). Long-term care is a sector in Canada that has been historically overlooked, which contributed to the high mortality in these residences when faced with COVID-19 (Holroyd-Leduc & Laupacis, 2020). Many deaths in LTC homes across the nation were preventable if similar measures put into place in hospitals were implemented in care homes (Holroyd-Leduc & Laupacis, 2020). This pandemic has resulted in many provinces reevaluating the delivery of care in their LTC homes and planning for necessary reform (Holroyd-Leduc & Laupacis, 2020).\n\nThe pandemic highlighted and perhaps contributed to a rise in advocacy for older adults by those who value their lives and contributions. Advocates in Quebec society spoke out and defended those living in LTC. Other studies found that some older adults living in the community distanced themselves from those living in a CHSLD (Lagacé et al., 2021). As social isolation grew strong among the residents of various LTC homes and certain deleterious living conditions were exposed, some individuals demonstrated their advocacy directly, with deliberate acts of kindness, while others acted indirectly, challenging the underlying ageist views that are present in the public discourse. The extent of loneliness became more apparent not only in Quebec residences but in LTC homes across the world (Wu, 2020). Since the level of communication older adults maintained with their family during COVID-19 was a good predictor for their overall psychological wellbeing, a program that emphasizes communication would have a significant impact on the lives of older adults who are self-isolating. A Texas nursing home was popularized online for its pen-pal initiative (Henney, 2020). The latter provided older adults with a means of feeling connected to their society outside of their residential community. Social integration, exhibited by the pen-pal initiative, is a key factor to successful aging as a result of increasing life satisfaction, dissipating the extent of isolation older adults experience during a pandemic, and improving both physical and mental health (Vitman, Iecovich & Alfasi, 2014).\n\nMany Western societies view negative health consequences as resulting from an individual’s actions (Blanchard-Fields, Chen, Horhota & Wang, 2007). Furthermore, this cultural practice plays into the stereotype of aging, that individuals in better health are more valuable to the societies and those who are not considered burdens to social and economic systems (Milner et al., 2012). The discourse surrounding older adults often uses the words “burden” and “vulnerable”, creating negative attitudes towards aging that may promote the social exclusion of older adults, leading to negative health outcomes in this population (Vitman et al., 2014; Lagacé, Doucet, Dangoisse & Bergeron, 2021). Recognition of the latter in the media during COVID-19 raised public awareness over what was really happening in Quebec LTC and the years of neglect these institutions had endured. In this way, the media was a catalyst for a rise in social advocacy and people challenging stereotypical views of aging. This hopefully will promote a new culture that will facilitate social integration among older adults, thus creating an environment where all members of a society, regardless of age, feel a sense of belonging.\n\nDespite a growing number of advocates countering ageist views, the media continues to use language that undermines the status and self-image of older adults living in LTC. Though sometimes used in a compassionate or protective way, the use of ageist terms such as “vulnerable” reinforces a stereotypical view of aging, that all older adults must be vulnerable and taken care of (Fraser et al., 2015; Lagacé et al., 2013). In line with previous research in this area (Phelan, 2018), prejudicial speech can influence the way members of the stigmatized group perceive themselves. When confronted with stereotypes or consistently exposed to age-related stigma, older adults may use problem-focused or emotion-focused coping strategies (Chasteen & Cary, 2015). As age-related stereotypes are highly prevalent in our society, some older adults may not even recognize compassionate ageism having an impact on their self-esteem (Chasteen & Cary, 2015). This would, in turn, render problem-focused coping an imperfect strategy to reduce bias. Additionally, problem-focused coping may contribute to a stigmatized group being perceived as overly sensitive and reactive towards remarks made (Chasteen & Cary, 2015). Emotion-focused coping, however, enables older adults to recognize ageist remarks and dissociate them from their self-concepts (Chasteen & Cary, 2015). With this strategy, the stigmatized group can construct a barrier between prejudicial speech and how the group views themselves (Chasteen & Cary, 2015). Emotion-focused coping goes hand-in-hand with the increased mental adaptability that accompanies natural aging (Chasteen & Cary, 2015).\n\nUsing a technique such as critical discourse analysis (CDA), it was possible to unravel the specific social relations between the aging population and the media by looking at the language present in print newspapers (Mullet, 2018). Additionally, this CDA captures the modern context of the Quebec health, economic and governmental interactions in terms of older adults living in LTC facilities. Media outlets should consider that the majority of their readers are older adults (50 years and older; Centre d’études sur les médias, 2019) and may be significantly impacted by the language chosen to portray their age group (Chasteen & Cary, 2015).\n\n\nConclusion\n\nThe goal of this study was to examine the media discourse concerning older adults living in LTC homes prior to and during the COVID-19 pandemic. The findings support that COVID-19 served to exacerbate existing issues in LTC homes in Quebec while also attracting public attention and advocacy for older adults through the media reports. The findings highlight that there is a clear need for government reform regarding LTC residences and the resources attributed to them. With a larger audience reading media during the pandemic, the ideologies and language presented may have a wide impact, influencing the public, and older adults specifically. The dominant francophone newspapers in Quebec continue to use stigmatizing language when referring to older adults living in LTC, which can make its way into mainstream dialogue and further undermine the position of older adults in the Quebec population. It follows that it is imperative to counter these stereotypes using anti-stigma strategies to minimize the extent of the harm done to older adults in the province. It remains to be seen if the advocacy found for older adults in this discourse analysis has truly led to policy change to improve outcomes for older adults living in CHSLDs and residences.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
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PubMed Abstract | Publisher Full Text\n\nBravo G, Dubois MF, Dubuc N, et al.: Comparing the resident populations of private and public long-term care facilities over a 15-year period: A study from Quebec, Canada. Ageing Soc. 2014a; 35(10): 2039–2052. Publisher Full Text\n\nBravo G, Dubois MF, Demers L, et al.: Does regulating private long-term care facilities lead to better care? A study from Quebec, Canada. International Journal for Quality in Health Care: Journal of the International Society for Quality in Health Care. 2014b; 26(3): 330–336. PubMed Abstract | Publisher Full Text\n\nCentre d’études sur les médias: Presse quotidienne. Université Laval.2019.Reference Source\n\nChasteen AL, Cary LA: Age stereotypes and age stigma: Connections to research on subjective aging. Annu. Rev. Gerontol. Geriatr. 2015; 35(1): 99–119. Publisher Full Text\n\nCommissaire à la santé et au bien-être: Portrait: les milieux de vie pour aînés au Québec. Québec, QC:Gouvernement du Québec;2021a.Reference Source\n\nCommissaire à la santé et au bien-être: Rapport préliminaire: septembre 2021. Québec, QC:Gouvernement du Québec;2021b.Reference Source\n\nEhni HJ, Wahl HW: Six propositions against ageism in the COVID-19 pandemic. J. Aging Soc. Policy. 2020; 32(4-5): 515–525. PubMed Abstract | Publisher Full Text\n\nEstabrooks CA, Squires JE, Carleton HL, et al.: Who is looking after Mom and Dad? Unregulated workers in Canadian long-term care homes. Canadian Journal on Aging/La Revue Canadienne du Vieillissement. 2015; 34(1): 47–59. PubMed Abstract | Publisher Full Text\n\nFiske ST, Cuddy AJC, Glick P, et al.: A model of stereotype content as often mixed: Separate dimensions of competence and warmth respectively follow from status and competition. J. Pers. Soc. Psychol. 2002; 82(6): 878–902. PubMed Abstract\n\nFraser S, Lagacé M, Bongué B, et al.: Ageism and COVID-19: What does our society’s response say about us? Age Ageing. 2020; 49(5): 692–695. PubMed Abstract | Publisher Full Text\n\nFraser SA, Kenyon V, Lagacé M, et al.: Stereotypes associated with age-related conditions and assistive device use in Canadian media. Gerontologist. 2015; 56(6): 1023–1032. PubMed Abstract | Publisher Full Text\n\nGouvernement du Québec: Budget 2018-2019: Des services de santé accessibles et de qualité. Québec, QC.2018.Reference Source\n\nGouvernement du Québec: Date accessed: August 2020. Situation of the Coronavirus (COVID-19) in Québec.2020.Reference Source\n\nGrigsby JS: The meaning of heterogeneity: An introduction. Gerontologist. 1996; 36(2): 145–146. PubMed Abstract | Publisher Full Text\n\nHapper C, Philo G: The role of the media in the construction of public belief and social change. J. Soc. Polit. Psychol. 2013; 1(1): 321–336. Publisher Full Text\n\nHenney E: ‘It’s Just Incredible:’ Texas nursing home gets worldwide attention for pen pal initiative. ABC7 News.2020.Reference Source\n\nHolroyd-Leduc J, Laupacis A: Continuing care and COVID-19: A Canadian tragedy that must not be allowed to happen again. Can. Med. Assoc. J. 2020; 192(23): E632–E633. PubMed Abstract | Publisher Full Text\n\nHolroyd-Leduc J, Resin J, Ashley L, et al.: Giving voice to older adults living with frailty and their family caregivers: Engagement of older adults living with frailty in research, health care decision making, and in health policy. Res. Involv. Engagem. 2016; 2: 23. PubMed Abstract | Publisher Full Text\n\nInstitut de la statistique du Québec: Le bilan démographique du Québec: Édition 2019. Québec, QC:Gouvernement du Québec;2019.Reference Source\n\nJacques G: Quotidiens québécois: Le Journal de Montréal en tête, La Presse domine du côté numérique. Infopresse. 2017. Reference Source\n\nKang SK, Chasteen AL: Beyond the double-jeopardy hypothesis: Assessing emotion on the faces of multiply-categorizable targets of prejudice. J. Exp. Soc. Psychol. 2009; 45(6): 1281–1285. Publisher Full Text\n\nKatz PR: An international perspective on long term care: focus on nursing homes. J. Am. Med. Dir. Assoc. 2011; 12(7): 487–492.e1. PubMed Abstract | Publisher Full Text\n\nLagacé M, Laplante J, Nahon-Serfaty I: Canadian media’s discourse on older workers: reinforcing the dichotomy of “good” vs. “bad” old age? Int. J. Aging Soc. 2013; 2(4): 17–33. Publisher Full Text\n\nLagacé M, Doucet A, Dangoisse P, et al.: The “vulnerability” discourse in times of COVID-19: Between abandonment and protection of Canadian Francophone older adults. Front. Public Health. 2021; 9: 662231. PubMed Abstract | Publisher Full Text\n\nLavoie M: Privé, public, conventionné ou non: les différents types de foyers pour aînés.2020. Reference SourceReference Source\n\nLe ministère de la Santé et des Services sociaux: Des milieux de vie qui nous ressemblent: Politique d’hébergement et de soins et services de longue durée. Québec, QC:Gouvernement du Québec;2021.Reference Source\n\nLight JM, Grigsby JS, Bligh MC: Aging and heterogeneity: Genetics, social structure, and personality. Gerontologist. 1996; 36(2): 165–173.Publisher Full Text\n\nMilner C, Norman KV, Milner J:Chapter 4: The media’s portrayal of ageing.Beard J, Biggs S, Bloom D, et al., editors. Global Population Ageing: Peril or Promise? 2012; 25–28.Reference Source\n\nMogashoa T: Understanding critical discourse analysis in qualitative research. Int. J. Humanit. Soc. Sci. Edu. 2014; 1(7): 104–113.Reference Source\n\nMullet DR: A general critical discourse analysis framework for educational research. J. Adv. Acad. 2018; 29(2): 116–142. Publisher Full Text\n\nNguyen QD, Moodie EM, Forget MF, et al.: Health heterogeneity in older adults: Exploration in the Canadian longitudinal study on aging. J. Am. Geriatr. Soc. 2021; 69(3): 678–687. PubMed Abstract | Publisher Full Text\n\nOlson I: Québec’s first case of coronavirus confirmed by National Microbiology Lab. CBC News. 2020.Reference Source\n\nPhelan A:Researching ageism through discourse.Ayalon L, Tesch-Römer C, editors. Contemporary Perspectives on Ageism. International Perspectives on Aging. Cham:Springer International Publishing;2018; pp. 549–564. Publisher Full Text\n\nQuébecor: Avec près de 4 million de lecteurs, Le Journal de Montréal, Le Journal de Québec et le 24 Heures rejoignent plus de la moitié de la population du Québec!.2019.Reference Source\n\nRobitaille L: Merci à nos lecteurs en ces temps difficiles. Le Journal de Montréal. 2020.Reference Source\n\nRoss T:Media and stereotypes.Ratuva S, editor. The Palgrave Handbook of Ethnicity. Singapore:Springer;2019. (1–17). Publisher Full Text\n\nShingler B: After slashing immigration, Quebec turns to immigrants to fill shortage in long-term care homes. CBC News. 2020.Reference Source\n\nSiag J: Le nombre de lecteurs québécois en hausse. La Presse+. 2016.Reference Source\n\nStatistics Canada: Population estimates on 1 July, by age and sex.2022. Reference Source\n\nTriantafillou J, Naiditch M, Repkova K, et al.: Informal care in the long-term care system: European Overview Paper. ResearchGate. 2010.Reference Source\n\nVitman A, Iecovich E, Alfasi N: Ageism and social integration of older adults in their neighborhoods in Israel. Gerontologist. 2014; 54(54): 177–189. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization (WHO): Coronavirus Disease (COVID-19).2020.Reference Source\n\nWu B: Social isolation and loneliness among older adults in the context of COVID-19: a global challenge. Glob. Health Res. Policy. 2020; 5: 27. PubMed Abstract | Publisher Full Text\n\n\nFootnotes\n\n1 For reference, centre intégré universitaire de santé et de services sociaux (CIUSSS) is a branch of the provincial government that overlooks the quality, access and continuity of care among various health systems including CHSLDs (Gouvernment de Québec, n.d.)."
}
|
[
{
"id": "153922",
"date": "10 Nov 2022",
"name": "Mandy Stanley",
"expertise": [
"Reviewer Expertise Qualitative research methodologies",
"older people",
"well-being",
"dignity of risk"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this interesting paper. Examining how older people are represented within the media is a worthwhile research pursuit and the media around older people and Covid provides a good site of analysis.\n\nAbstract:\nRemember that the journal has an international audience so include the country as well as the city.\n\n'Peri-covid' is a term that I was not familiar with although I recognise that we can't really say 'post-covid' given its continued presence in our lives.\n\n\"Negative and positive elements\" is not very informative.\n\nIntroduction: There is a jump in the logic of the argument between the first two paragraphs, needs a transition sentence or phrase. The statistic provided for readers of print newspapers is quite old.\nMethods: The claim is made to a critical discourse analysis however I am struggling to see where the critical element comes in. It would be useful for the authors to position themselves in relation to the topic. The inclusion and exclusion criteria do not include Covid. Is that not an omission? Themes don't just arise, they come from the work that the researchers do in terms of interpreting the data. I expected to see some use of critical theory here. What authorities were drawn on to inform the analysis? In parts, there is quite a quantitative approach to the analysis. It reads very much like thematic analysis as there was nothing about examination of discursive elements or subject positioning.\nFindings: The chosen excerpts were interesting to read.\nDiscussion: What this study adds to knowledge is not coming through clearly. What was evident was the lack of preparedness for a pandemic. This study is quite specific to one area within Canada. Is there anything that has been learned that might have transferability to other geographical contexts?\nMy key critique is the claim to be a critical discourse analysis yet the paper reads as a descriptive piece rather than critical.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "153919",
"date": "25 Nov 2022",
"name": "Loredana Ivan",
"expertise": [
"Reviewer Expertise Communication",
"Aging & Communication Technologies"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article investigates the portrayals of older adults from the residence homes in the media prior (3 months before) and peri COVID-19 (three months after the announcement of the first case). The analysis was based on a corpus of news selected from a newspaper database.\nWhen discussing the way older adults are portrayed in the media, there are some relevant and recent works that could be useful and they are missed from the text:\nYlänne, V. (ed.). (2022). Ageing and the Media: International Perspectives1\n\nLoos, E., & Ivan, L. (2018). 'Visual ageism in the media'2\n\nLoos, E., Ivan, L., Fernández-Ardèvol, M., Sourbati M. et al. (2017). 'Ageing well? A cross-country analysis of the way older people are visually represented on websites of organizations for older people'3\nTogether with Eugene Loos, I have launched the concept of \"visual ageism\", a term which is used in the literature and describes exactly the stereotypical portrayals of older adults in the visual content. I believe the authors could have used the term. Both Eugene Loos and I have published recent works on this. Also, Virpi Ylänne is an important author when talking about portrayals of older people in the media. The authors of the manuscript should have included her work, in my opinion.\n\nThe research questions are not clearly stated in the text. Also, the results have to be presented in relation to the research questions.\nThe procedure of data selection is clear, but the method is not specified in the text. If the method is critical discourse analysis, then this should be clearly specified in the Method section.\nHowever, the analysis follows the procedure of a classic content analysis, by defining the main categories and then following those categories in the selected corpus. The Method section must be improved and the type of analysis should be according to the specification of the method.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1205
|
https://f1000research.com/articles/11-1204/v1
|
21 Oct 22
|
{
"type": "Clinical Practice Article",
"title": "Plasmodium knowlesi infection in East Kalimantan, Indonesia",
"authors": [
"Carta A. Gunawan",
"Loly R.D. Siagian",
"Edwin Prasetya",
"Carta A. Gunawan",
"Edwin Prasetya"
],
"abstract": "Plasmodium knowlesi is the fifth species of plasmodium infecting humans and the infection was first discovered in Southeast Asia in 2004. The incidence has been increasingly reported from almost all Southeast Asian countries, including Indonesia. Although the global incidence of malaria has decreased around 50% in the last decade, the increase of knowlesi malaria infection which can cause severe malaria is of concern. During the period of 2018 to 2021, there were seven newfound cases of knowlesi malaria infection in patients treated at hospital in Samarinda, East Kalimantan, Indonesia. The clinical manifestations and laboratory examinations of these patients are described here. All patients were male and worked in mining and palm oil plantations in the forest in several districts in East, North, and South Kalimantan. The diagnosis was based on microscopic examination of Giemsa-stained thin blood smear and confirmed by polymerase chain reaction (PCR) test. Antimalarial treatment was artemisinin-based combination therapy (ACT) / dihydroartemisinin-piperaquine (DHP) fixed-dose combination via oral administration for three days with the doses were based on body weight. All knowlesi malaria patients in this report were presented as uncomplicated cases with great response to ACT after 2-3 days of administration without any adverse effects. Besides fever, gastrointestinal symptoms were major symptoms. Anemia was rare, leukocyte count was normal, however thrombocytopenia was found in all patients. P. knowlesi infection has been discovered in East Kalimantan Province and recently the incidence might be higher than the reported cases, making it resemble an iceberg phenomenon. Therefore, we should build awareness of the rapid increasing of knowlesi malaria cases and its prevention.",
"keywords": [
"Plasmodium knowlesi",
"Malaria",
"East Kalimantan",
"Indonesia"
],
"content": "Introduction\n\nMalaria remains a public health problem in several Indonesia regions, including East Kalimantan Province. The majority of East Kalimantan land is covered by forest with some districts are still malaria endemic with either low, middle or high endemicity. National data showed there were 250,664 malaria cases in 2019 in Indonesia, which East Kalimantan having the fourth highest number of cases.1\n\nThe incidence of malaria worldwide has decreased in the last decade, with the incidence of malaria in Indonesia is decreasing significantly too.2 The majority of malaria cases in East Kalimantan were caused by Plasmodium falciparum and Plasmodium vivax. However, in 2018 we found a malaria case caused by Plasmodium knowlesi in East Kalimantan. Previously, knowlesi malaria cases had been reported from South Kalimantan and Central Kalimantan Province, the neighbouring provinces in the south and the west in 2013.3 Another region in Indonesia that had also reported P. knowlesi cases was Sumatera Island (North Sumatera and Aceh Province).4,5 In the period of 2008 to 2015, there were 418 cases of P. knowlesi infection reported from Indonesia.6 The first reported case was from our neighbouring state Sarawak, Malaysian Borneo in 2004 and since that time the incidence has been increasing rapidly.7 Until 2016, P. knowlesi infection in humans had been reported from South China, Myanmar, Thailand, Vietnam, Laos, Cambodia, the Philippines, Singapore, Peninsular Malaysia, Brunei, Indonesia and the highest incidence was reported from Malaysia (18,687 cases from 2010 to 2018).6 There were also increasing numbers of knowlesi malaria cases imported from Southeast Asia to Europe, Asia, America and Oceania.8 P. knowlesi vectors are member of the Anopheles leucosphyrus group that are found in Southeast Asia, associated with dense jungle and forest fringe, rest and feed outdoors (exophagic) typically after dusk.9\n\nPlasmodium knowlesi is known as the fifth Plasmodium species that can cause malaria in human beings, previously it was reported that it could infect the long-tailed macaque (Macaca fascicularis), and pig-tailed macaca (Macaca nemestrina, Macaca leonina).6,9,10 Plasmodium knowlesi infection can cause severe malaria like P. falciparum and P. vivax and recently its diagnosis should be confirmed by polymerase chain reaction (PCR) test since it is difficult to differentiate between P. knowlesi and P. Malariae morphoplogy by microscopic examination only. The ongoing increase of P. knowlesi cases poses a major challenge in malaria control and elimination program in Southeast Asia, including Indonesia.6\n\nWe would like to report the features of P. knowlesi infection cases in Samarinda, East Kalimantan Province, Indonesia from 2018 to 2021. This article was approved by The Ethical Committee for Health Research at Abdul Wahab Sjahranie General Hospital Samarinda, East Kalimantan (approval number 083/KEPK-AWS/V/2022).\n\n\nCase presentation\n\nThere were seven knowlesi malaria patients treated at hospital in Samarinda, East Kalimantan, Indonesia from 2018 to 2021. All patients were male and aged 34 to 56 years old (mean age 41.1 years). They worked in mining and palm oil plantations in the forest in several districts in East, North, and South Kalimantan (see Table 1). The patients’ locations were near to Sarawak, Malaysia, where P. knowlesi infection was initially discovered in Southeast Asia (see Figure 1). Four patients visited or worked at districts in East Kalimantan Province that were still malaria endemic areas. Two patients worked in South Kalimantan Province that had reported knowlesi malaria cases since 2013. One patient visited a district in North Kalimantan Province that was also a malaria endemic area. The patients presented to the hospital with three or four days of fever and chills. Besides fever, all patients had gastrointestinal symptoms such as nausea, vomiting, diarrhea, and abdominal pain. There was no patient who showed the clinical manifestations of severe malaria based on World Health Organization (WHO) criteria 2015.11 The patients had no concomitant conditions or a history of inherited or familial illnesses. Their physical examinations were normal, no abnormalities were found.\n\nThis figure has been reproduced from https://commons.wikimedia.org/wiki/File:Borneo2_map_english_names.PNG#filehistory. This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.\n\nDiagnosis of P. knowlesi infection was based on microscopic examination of Giemsa-stained thin blood smear and confirmed by PCR test performed at the National Institute of Health Research and Development, Ministry of Health, Indonesia. We used Olympus CX21 binocular microscope to identify the morphology. Blood smear tests of the patients showed erythrocytes with early trophozoite/ring form stage and band form trophozoite of P. knowlesi (see Figure 2 and Figure 3). All patients have been confirmed by PCR test and the results were P. knowlesi positive.\n\n(Giemsa staining with 1000× magnification).\n\n(Giemsa staining with 1000× magnification).\n\nAntimalarial treatment used was a fixed-dose combination of dihydroartemisinin-piperaquine (DHP) (40/320 mg) via oral administration once daily (3 tablets for body weight 41–60 kg, 4 tablets for body weight 61–80 kg, 5 tablets for body weight > 80 kg) for three days and primaquine 15 mg single dose on day one. Patients were treated at hospital for 3–5 days.\n\nParasite counts ranged from 3,194 parasites/μL blood to 12,981 parasites/μL blood with a mean of 6,538 parasites/μL blood. No one had the criteria of severe malaria with hyperparasitemia (parasite count > 20,000/μL blood) according to WHO criteria 2015.11 Two patients had co-infection with dengue virus confirmed by positive anti-dengue IgG. There was no difference in malaria treatment between patients with dengue co-infection and other patients who did not. Hemoglobin levels ranged from 9.8 g/dL to 16.1 g/dL (co-infection with dengue virus) with mean Hb level was 13.6 g/dL. There was only one patient who showed moderate anemia (9.8 g/dL). Leukocyte counts ranged from 5,300/μL to 8,900/μL with a mean of 7,010/μL. This meant all patients had normal leukocyte counts. Platelet counts ranged from 16,000/μL to 108,000/μL with a mean of 69,714/μL. This showed that all patients had moderate to severe thrombocytopenia. The lowest platelet count (16,000/μL) was found in a patient co-infected with dengue virus. Ureum levels ranged from 24.0 mg/dL to 47.9 mg/dL with mean ureum level was 32.8 mg/dL. Creatinine levels ranged from 0.8 mg/dL to 1.4 mg/dL with mean creatinine level was 1.0 mg/dL. No patients had renal dysfunction.\n\nAll patients showed great response to ACT given (dihydroartemisinin-piperaquine for three days) without any adverse effects occurred and free of fever on day 2 or 3 after treatment. The patients were discharged from the hospital after they were recovered.\n\n\nDiscussion\n\nSoutheast Asia and Southern China are regions with natural distribution of long-tail macaques and mosquitoes of the Anopheles leucosphyrus group. Anopheles balabacensis is known as the most efficient vector, capable of transmitting P. knowlesi from monkey-to-human, human-to-human, and human-to-monkey.9 In Sabah, Malaysian Borneo Anopheles balabacensis is the primary vector of P. knowlesi and found in village, forest and farming sites.12 Although human P. knowlesi is largely a zoonosis, human-to-human transmission could increase with time and parasite adaptation.9\n\nThe western and central parts of Indonesia (Sumatera, Java, Kalimantan/Borneo Islands) are included in the region where long–tail macaques and Anopheles leucosphyrus group are found. The first knowlesi malaria case in human being was reported from Sarawak, Malaysian Borneo in 2004 and the number of cases has been increasing rapidly.7 Epidemiology studies from Malaysia in the beginning of 2010 showed that 50–60% of malaria cases were caused by P. knowlesi.9 A hospital surveillance study from Sabah, Malaysian Borneo in 2015–2017 showed that of a total of 3,876 malaria cases recorded P. knowlesi accounted for 80%, 88%, 98% malaria cases in 2015, 2016, 2017, and the rest were caused by P. falciparum and P. vivax.10 This study also showed that the majority of P. knowlesi cases occurred in adults, while children < 13 years accounted for only 5.8% of cases.13 In 2016 WHO World Malaria Report documented substantial progress toward control and elimination of malaria, however the emergence of P. knowlesi as an important cause of human malaria in Southeast Asia should be considered as a major challenge in malaria control and elimination program in this region.3 Outside of Malaysia, P. knowlesi is frequently misdiagnosed by microscopic examination as P. falciparum or P. vivax, therefore P. knowlesi may be underdiagnosed and its true incidence is underestimated.3 There are five provinces in Kalimantan (part of Indonesia) and South Kalimantan province reported their first case in 2013, then followed by Central Kalimantan Province. First confirmed P. knowlesi case in East Kalimantan Province was found in 2018 in Samarinda, five years after the first confirmed case in our neigbouring province, South Kalimantan. It means that four of five provinces in Kalimantan Island have reported knowlesi malaria cases. It is possible that the cases occured in East Kalimantan Province long before the first confirmed case in 2018 caused by microscopic misdiagnosis as P. falciparum or P. vivax, the two major Plasmodium species found in this region. Data from the East Kalimantan Provincial Health Office from 2019 to 2021 showed that there were 191 suspected malaria knowlesi cases, while P. vivax and P. falciparum accounted for 55.2% and 38.1%, 50.2% and 45.8%, 50.5% and 48.1% of total malaria cases reported in 2019, 2020, 2021, respectively (unpublished). Nowadays, the true incidence of P. knowlesi cases in East Kalimantan Province may be much higher than the confirmed cases found.\n\nThe incubation period of P. knowlesi infection is 3–14 days (mostly > 8 days). Besides fever, other non-specific symptoms such as headache, muscle pain, joint pain, nausea, abdominal pain, lost of appetite are frequently found.10 Splenomegaly (40%) and hepatomegaly (15–33%) are also often found.10 Some studies in Borneo showed that thrombocytopenia was the most common laboratory abnormality in P. knowlesi infection, while anemia appeared to be mild.13 Our study in East Kalimantan Province also showed the similar findings where all patients had moderate to severe thrombocytopenia, but anemia was rare. Like P. falciparum and P. vivax, P. knowlesi also can cause severe malaria in humans. Plasmodium knowlesi multiplies as same as P. falciparum daily. Some frequent complications reported were hyperparasitemia, jaundice, acute respiratory distress syndrome (ARDS), hypotension, and acute kidney injury (AKI).13–15 A study by Barber et al. in Sabah, Malaysian Borneo showed that risk of severe malaria in adults caused by P. knowlesi appeared at least as high as that of P. Falciparum (severe malaria in patients with P. knowlesi 29%, in P. falciparum 11%, in P. vivax 16%).13 Plasmodium knowlesi has the shortest asexual replication cycle of all Plasmodium species leading to rapidly increased parasitemia levels.10 Plasmodium knowlesi has lower threshold of parasitemia (> 20,000 parasites/μL blood) than P. falciparum (> 500,000 parasites/μL blood) to be classified as severe malaria with hyperparasitemia.11 A hospital study in Sabah, Malaysia showed that the risk of severe knowlesi malaria increased 11-fold with parasitemia > 20,000/μL and 28-fold with parasitemia > 100,000/μL.13 A hospital surveillance study from Sabah, Malaysian Borneo from 2015–2017 showed that case fatality rate of P. knowlesi cases was 1.7 per 1,000 cases.14\n\nMicroscopic examination of thin blood smear can not differentiate P. knowlesi and P. malariae, therefore PCR test is used to confirm the species.16 However, a case report from Sarawak, Malaysian Borneo showed that rapid diagnostic test by OptiMAL and BinaxNOW could detect P. knowlesi infection (pan-malarial lactate dehydrogenase (LDH) and pan-malarial aldolase) although it was not specific and shoud be confirmed by PCR.17 Recently, P. knowlesi-specific rapid diagnostic tests (RDTs) have demonstrated low sensitivity.16 A systematic review of 40 studies showed that the sensitivities of RDTs in detecting Plasmodium knowlesi infections ranged from 2% to 48%.18\n\nAntimalarial used to treat uncomplicated knowlesi malaria case is artemisinin-based combination therapy. Currently, based on National Guidelines, we use a fixed-dose combination of dihydroartemisin-piperaquine (40/320 mg) for 3 days (3–5 tablets once daily based on body weight) and primaquine 15 mg single dose.19 A study in Malaysia using another ACT, a fixed-dose combination of artemether-lumefantrine showed parasite clearance time (PCT)90 was 13.7 hours and microscopy negative at 48 hours reached 100%.9 Artesunate intravenous injection is used in the management of severe knowlesi malaria like other severe malaria cases caused by P. falciparum or P. vivax. In Indonesia nowadays artemisinin derivatives remain show good efficacy in treating uncomplicated and severe malaria.\n\nOverall, the discovery of P.knowlesi infection cases in East Kalimantan, where cases had already been reported in the neighboring country, is particularly noteworthy for this study. However, there were not enough P. knowlesi instances to characterize in general due to the small number of reported cases would be the limitation of this study. The cause of the limitation was the difficulty to distinguish the morphology of P. knowlesi from the others by microscopic examination.\n\n\nConclusion\n\nPlasmodium knowlesi infection in human beings, previously reported from other regions of Kalimantan, Indonesia had also been found in East Kalimantan Province. All cases reported here were adult males working in mining and oil palm plantations in the forest and presented as uncomplicated malaria. Besides fever, gastrointestinal symptoms were major symptoms. Anemia was rare, leukocyte count was normal, but thrombocytopenia was found in all patients. All patients showed great response to ACT given (dihydroartemisinin-piperaquine for three days) without any adverse effects occurred and free of fever on day 2 or 3 after treatment. P. knowlesi infection that can cause severe malaria has been discovered in East Kalimantan Province and recently the incidence might be higher than the reported cases, making it resemble an iceberg phenomenon. Therefore, we should build awareness of the rapid increasing of knowlesi malaria case and its prevention.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patients.",
"appendix": "References\n\nMinistry of Health, Republic of Indonesia: Malaria Current Situation Factsheet 2020. Jakarta:Directorate General of Disease Control and Prevention of the Indonesian Ministry of Health;2020.\n\nWHO: World Malaria Report 2021. Geneva:World Health Organization;2021.\n\nBarber BE, Rajahram GS, Grigg MJ, et al.: World Malaria Report: time to acknowledge Plasmodium knowlesi malaria. Malar. J. 2017; 16: 135. PubMed Abstract | Publisher Full Text\n\nLubis IND, Wijaya H, Lubis M, et al.: Contribution of Plasmodium knowlesi to multispecies human malaria infections in North Sumatera, Indonesia. J. Infect. Dis. 2017; 215: 1148–1155. PubMed Abstract | Publisher Full Text\n\nHerdiana H, Irnawati I, Coutrier FN, et al.: Two clusters of Plasmodium knowlesi cases in a malaria elimination area, Sabang Municipality, Aceh, Indonesia. Malar. J. 2018; 17: 186. PubMed Abstract | Publisher Full Text\n\nJeyaprakasam NM, Liew JWK, Low VL, et al.: Plasmodium knowlesi infecting humans in Southeast Asia: what’s next? PLoS Negl. Trop. Dis. 2020; 14(12): e0008900. PubMed Abstract | Publisher Full Text\n\nSingh B, Sung LK, Matusop A, et al.: A large focus of naturally acquired of Plasmodium knowlesi infections in human beings. Lancet. 2004; 363: 1017–1024. PubMed Abstract | Publisher Full Text\n\nMuller M, Schlagenhaut P: Plasmodium knowlesi in travellers, update 2014. Int. J. Infect. Dis. 2014; 22: 55–64. PubMed Abstract | Publisher Full Text\n\nAbeyasinghe R: Outcome from the evidence review group on Plasmodium knowlesi. Geneva, Switzerland:WHO Malaria Policy Advisory Committee;22 March 2017.\n\nAntinori S, Galiberti L, Milazzo L, et al.: Plasmodium knowlesi: the emerging zoonotic malaria parasite. Acta Trop. 2013; 125(2): 191–201. Publisher Full Text\n\nWHO: Guidelines for The Treatment of Malaria. 3rd ed.Geneva:World Health Organization;2015.\n\nWong ML, Chua TH, Leong CS, et al.: Seasonal and spatial dynamics of the primary vector of Plasmodium knowlesi within a major transmission focus in Sabah, Malaysia. PLoS Negl. Trop. Dis. 2015; 9: e0004135. PubMed Abstract | Publisher Full Text\n\nBarber BE, William T, Grigg MJ, et al.: A prospective comparative study of knowlesi, falciparum and vivax malaria in Sabah, Malaysia: high proportion with severe disease from Plasmodium knowlesi and Plasmodium vivax but no mortality with early referal and artesunate therapy. Clin. Infect. Dis. 2013; 56(3): 383–397. PubMed Abstract\n\nCooper DJ, Rajahram GS, William T, et al.: Plasmodium knowlesi malaria in Sabah, Malaysia, 2015-2017: ongoing increase in incidence despite near-elimination of human-only Plasmodium species. Clin. Infect. Dis. 2020; 70: 361–367. PubMed Abstract | Publisher Full Text\n\nCox-Singh J, Hiu J, Lucas SB, et al.: Severe malaria – a case of fatal Plasmodium knowlesi infection with post-mortem findings: a case report. Malar. J. 2010; 9: 10. Publisher Full Text Reference Source\n\nSingh B, Daneshvar C: Human infection and detection of Plasmodium knowlesi. Clin. Microbiol. Rev. 2013; 26(2): 165–184. PubMed Abstract | Publisher Full Text\n\nHellemond JJ, Rutten M, Koelewijn R, et al.: Human Plasmodium knowlesi infection detected by rapid diagnostic tests for malaria. Emerg. Infect. Dis. 2009; 15(9): 1478–1480. Publisher Full Text\n\nYerlikaya S, Campillo A, Gonzalez IJ: A systematic review: performance of rapid diagnostic tests for detection of Plasmodium knowlesi, Plasmodium malariae, and Plasmodium ovale monoinfections in human blood. J. Infect. Dis. 2018; 218(2): 265–276. PubMed Abstract | Publisher Full Text\n\nMinistry of Health, Republic of Indonesia: Malaria Case Management Pocket Book. Jakarta:Directorate General of Disease Control and Prevention of the Indonesian Ministry of Health;2017."
}
|
[
{
"id": "165466",
"date": "30 Mar 2023",
"name": "Inke Nadia Diniyanti Lubis",
"expertise": [
"Reviewer Expertise malaria",
"infectious diseases",
"molecular diagnostics"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study provides important findings of Plasmodium knowlesi in humans in a region in Indonesia. However, there is still a very limited of information in the introduction. The authors should describe the ecological situation of the region, the burden of malaria specifically in the province, the availability of malaria diagnostics, the limitation of current diagnostic, the proportion of Pf, Pv and Pk in the areas, etc. The authors only provided sufficient information on the demographic data of patients, but did not include information on diagnostic methods, clinical manifestations, laboratory findings, hospitalisation status, and responses to treatment. Therefore, the above information should be included, or stated as the limitation of the study.\nWhile the authors mentioned there were 7 cases of P. knowlesi, it is still not clear whether the findings were confirmed by PCR as a single or mixed cases of Pk. The limitation of PCR diagnosis of Pk should also further be discussed if the current PCR methods used cross reacted with P. vivax, as many has previously been reported using the target of 18S rRNA. The authors should also focus on the diagnostic challenges as the major problem for Pk diagnosis in Indonesia. Further, there are still numerous grammatical and vocabulary errors, therefore the article can benefit from some copy editing.\nParagraph 2: The authors should state whether the previous case of Plasmodium knowlesi was confirmed by PCR.\n\nIntroduction should include by the current gaps in regards to Pk diagnosis or knowledge in Indonesia\n\nData on clinical manifestations, parasitological identification, laboratory findings should be presented in a table\n\nWere patients tested with RDTs? If they were, the authors should mention the brand used and the findings\n\nThe author should describe the protocol of blood smear, and how the calculation of parasite density. The protocol of PCR for Plasmodium confirmation should also be described.\n\nResponses to ACT should be more detailed, and present the proportion of patients that free of fever on days 2 or 3, and also include parasite free on the follow up blood smears.\n\nDiscussions can include the comparison of risk factors, clinical manifestations to the findings from the neighbouring Sarawak and Sabah.\n\nIs the background of the cases’ history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the conclusion balanced and justified on the basis of the findings? Partly",
"responses": []
},
{
"id": "324868",
"date": "30 Sep 2024",
"name": "Angelica F. Tan",
"expertise": [
"Reviewer Expertise Diagnostic methods of P. knowlesi malaria"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors presented seven cases of Plasmodium knowlesi malaria from Samarinda, East Kalimantan, Indonesia. Diagnoses were confirmed by microscopy and PCR, and patients were treated with DHA-PQP before discharge. Detailed symptoms and clinical data were provided, noting that two patients had concurrent dengue infections. There were several misspellings and capitalization errors for genus and species names. Treatment responses and outcomes need more precise descriptions; terms like “great response” are vague. Clarify “major symptoms” in terms of severity or frequency. The term “iceberg phenomenon” is unclear; specify whether it refers to the incidence of these cases locally or regionally. For demographic variables, median values are more appropriate than means. Clarify if the hemoglobin ranges pertain to all patients or only those with dengue co-infection. Specify parasite counts and platelet levels, and reference normal or abnormal ranges. In the results section, define recovery criteria more clearly, such as the proportion of patients clearing parasitemia by day 2 versus day 3. The first two paragraphs of the discussion should be moved to the introduction. Additional references are needed in the discussion, particularly for specific statements. The last paragraph of the discussion is unclear; specify if comparisons to other malaria species are unavailable. The discussion and conclusion sections need improvement. The conclusion should not replicate the abstract. Consider addressing whether P. knowlesi cases are increasing in number or severity, lessons learned, and the potential need for broader screening and alternative diagnoses and/or treatment plans.\n\nIs the background of the cases’ history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the conclusion balanced and justified on the basis of the findings? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1204
|
https://f1000research.com/articles/11-833/v1
|
26 Jul 22
|
{
"type": "Research Article",
"title": "Trends in authorship demographics for manuscripts published in endocrine journals - A 70-year analysis",
"authors": [
"Arpit Jain",
"Hritik Madan",
"Kamaldeep Singh",
"Yash Agarwal",
"Bharat Midha",
"Shreya Gulati",
"Priyanka Batra",
"Ankur Batra",
"Priyanshu Jain",
"Ipsa Arora",
"Madhav Prabhu",
"Shreyas Arya",
"Yashasvi Chugh",
"Shobhit Piplani",
"Arpit Jain",
"Hritik Madan",
"Kamaldeep Singh",
"Yash Agarwal",
"Bharat Midha",
"Shreya Gulati",
"Priyanka Batra",
"Ankur Batra",
"Priyanshu Jain",
"Ipsa Arora",
"Madhav Prabhu",
"Shreyas Arya",
"Yashasvi Chugh"
],
"abstract": "Background Over the previous few decades, demographics, gender, and the number of papers published have all changed considerably. One of the fields of medicine that has yet to be extensively investigated is endocrinology.\n\nMethods Journal of Endocrinology and General & Comparative Endocrinology are two landmark journals that publish articles from around the world. Each decade during the 70-year period from 1961 to 2021 has been examined in this study. Funding source, first author – last author gender, their demographics and proportion of papers with at least one female author were the parameters considered while studying each publication. It was predicted that the number of female authors per paper would increase with time, as would the range of degrees held by the authors, demographical variations in authorship, and the funding source. The aim was also to determine the distribution of female first authors and senior authors in endocrinology journals over a 70-year period, as well as to check the gender combinations using the Punnett square.\n\nResults Female initial authors rose from 7% to 29.6% (p<0.0006) between 1961 and 2021, whereas female senior authors rose from 15.6% to 22.2%. Despite women's small contributions to first and senior authors, female participation rose from 17.48% (25/143) to 70% (170/250) between 1961 and 2021. Male-Female and Female-Male combinations rose with Chi-Square = 124.6, (p<0.0001). Europe and the Americas had the most female academic medical contributors (p<0.0001) Regardless of author status, female participation rose from 17.48% in 1961 to 68% in 2021. Conclusion\n\nIn papers published in endocrinology journals, there was a rising trend in female contributions to academic medicine. Even with the large growth of female endocrinologists, there is still a disparity in why the increase in female authors is comparably fewer.",
"keywords": [
"endocrine",
"gender-gap",
"sex-ratio",
"demographics",
"bias",
"equity",
"medicine"
],
"content": "Abbreviations\n\nMM- Male-Male\n\nMF-Male-Female\n\nFM- Female-Male\n\nFF- Female-Female\n\nJOE-Journal of Endocrinology\n\nGCE- General & Comparative Endocrinology\n\n\nIntroduction\n\nWomen confront a variety of challenges, and most of us are aware of the discrimination they suffer on a daily basis, whether in society, the job, schools, or the scientific community1. Salaries and allowances are only a small part of the pay disparity2. Women have experienced more hurdles than their male counterparts in obtaining support in the field of medical research, including but not limited to assets, funding, assistance, and the peer-review process, to name a few3,4. In any type of study, motivation and the availability of resource reserves are crucial, and a lack of both might have a detrimental impact on the scientific advancement that the medical community is actively seeking5. Such difficulties are replicated when female writers seek funding for their projects and research, resulting in a \"gender pay gap\" that often goes unnoticed and discourages women from pursuing research2.\n\nWomen make up about half of the medical school students in the United States6. This is a significant rise from less than 10% in 19656,7. The proportion of female physicians in endocrinology is 44%8,9. The gender disparity is anticipated to narrow even more, as women made up three-quarters of endocrinology fellowship applicants in 20148,9.\n\nWomen remain underrepresented in senior academic positions including tenured faculty positions, though9. While female physicians filled 38% of faculty positions in US medical schools in 2014, only 22% of tenured professors were female4,10.\n\nWith numerous reforms and activism, the number of females active in delivering specialist healthcare in the field of endocrinology, or any other profession for that matter, has increased in recent decades11,12. A similar pattern has emerged among females active in indirect health care, such as females with backgrounds in basic sciences, epidemiologists, and others9. However, growth in the number of females working in these sectors does not always correspond to increased research possibilities10.\n\nA few papers in cardiology, gastroenterology, and pulmonology after analyzing the current literature were discovered by this study, however there was a noteworthy absence in endocrinology11,13,14. Therefore this study plans to fill this gap and analyze part of the reality by individually assessing articles published in two major endocrinology journals to evaluate whether there has been a proportionate change in the number of articles published by female authors, and whether the female authors were funded by government bodies, educational institutions, or organizations, or if they were solely self-funded. Additionally, demographic analysis was included to comment on how well specific geographical regions have performed in terms of fostering gender equality during the 70-year timeframe of our research.\n\n\nMethods\n\nTo find appropriate papers for this study, journal search engines such as PubMed, Scimago, Embase, OMICS, and Google Scholar were used15. The two journals had to have a comparable number of articles in each, data available from at least 1961, and an h-index over 100 to be eligible. One journal was chosen from a publisher in the United Kingdom, while the other was chosen from a publisher in the United States to reduce the bias and diversify the pool of authors who are submitting the manuscript and for better randomization. Bioscientifica's Journal of Endocrinology and General and Comparative Endocrinology were the two journals that met this study’s’ requirements. Any other journal that met the criteria but has already been examined in a similar study was ruled out16. Other important endocrinology journals, such as the Journal of Clinical Endocrinology & Metabolism and Thyroid, had already been utilized to track demographics and female authorship trends14.\n\nSelected publications were examined, and data for this research was gathered for the first year of each decade, beginning in 1961. In total, data from seven decades were examined: 1961, 1971, 1981, 1991, 2001, 2011, and 2021. The data was collected between January 1st and December 31st of the following year. A total of 2432 articles in both journals (JOE – 1162, GCE – 1270) were discovered. Book reviews, author indexes, animal indexes, subject indexes, inaccessible articles, or articles where the gender couldn't be determined were not included. Following the exclusion of articles, the total number of articles was estimated to be 2291(See Underlying data)17. (JOE- 1115, GCE -1176).\n\nIn the manuscript, data was gathered for both the first and last authors, and the categories assigned were further documented. A total of 'n' papers from both journals were independently evaluated. If they were book reviews, author indexes, or cumulative indexes, a 'm' number of articles had to be eliminated due to a lack of reasonable evidence on the gender, demography, or funding of the paper. As a result, (n-m) papers in this research were included (Table 1). Using the aforementioned methodology, each item was immediately assessed in order to analyze the following variables:\n\nThe following approaches were used to collect data, in order of preference based on availability: To gather information from University/Organization/LinkedIn pages, I) Google was used to search for writers by their names and departments. II) Assuming gender based on nomenclature conventions (e.g., John being the name of a male author; Christy being a female author).\n\nIII) The biological genders of some authors who were registered on Scopus and Google Scholar were used to assign genders. In addition, in the event of a snag, https://gender-api.com was used to resolve the issue.\n\nThe following approaches were used to collect data, in order of preference based on availability: I) Data from University/Organization/LinkedIn/ORCiD pages; II) Author affiliations specified in the article; III) data from University/Organization/LinkedIn/ORCiD pages; IV) Based on regional nomenclature conventions and trends (e.g., Asian names being Raja Gopalchandra, Li-Hu Wang, BK Gupta, Chandragouda Patil, etc.). Author affiliation was one of the variables used to assign demographics to the authors, therefore a lot of focus was placed on where they were affiliated.\n\nTo include all other authors engaged in the study, the presence of at least one female author was determined using the same methods to determine the biological gender of the first and last authors.\n\nBecause all qualifications overlap, authors were divided into broad categories. MBBS/MD/DM/DO was included in Category 1. Ph.D./MSc/MPH were placed in category 2, and other paramedical areas were placed in category 3. To prevent prejudice while reporting, authors were divided into groups that classified qualifications according to international criteria.\n\nUNESCO's international standard classification of education was also used in this study18.\n\nData on funding was gathered by skimming through articles and looking for keywords such as 'grant, \"support,' 'fund,' 'acknowledgement,' 'thank,' and so on19.\n\nThe articles were divided into major groups such as government, university or organization, industry, self, other, and not stated. The majority of the available data came from the government, university, organization, or industry, with the exception of a few articles where funding was a problem, in which case the category ‘others’ was used, and for articles where funding was not available, the category ‘not mentioned’ was used. In research with several funding sources, government-based sources were given priority over other sources.\n\nCompanies/Industry/commercial sources were given preference over organizational or university financing in other multi-source sponsored studies without any government backing.\n\nData was incorporated in Microsoft Excel Sheet and further data was analyzed using GraphPad Prism Version 9.3.1., data was reported in tabular form. Unpaired t test (non-parametric, Kolmogorov-Smirnov test) was used to compare the outcomes with two variables, one way ANOVA (Kruskal Wallis Test) was used for comparison in places with three or more variables. Chi-Square was used for categorical variables.\n\n\nResults\n\nThere was an increase in female first authors from 1961 to 2021. The contribution of females as first authors increased from 7% (10/143) in 1961 to 29.6% (74/250) in 2021 (p=0.0006). An unpaired, non-parametric t-test was employed to determine significance. Not only first authors, but participation from female senior authors grew as well, however, the rise in senior authors occurred between 1971 and 2021, whereas the rise in female first authors occurred between 1961 and 2021. The unpaired, non-parametric t-test was performed to correlate significance, in senior female authors rise was seen from 12.5 % (43/344) in 1971 to 22.2 % (48/245) in 2021 (p=0.0006). (Figure 1) Surprisingly, the senior female contribution was 15.6 % in 1961 (14/90) a bit more than expected. When the data was stratified by region, it was discovered that Europe was the leading contributor in terms of female involvement in research for both first and senior authors, followed by the Americas. Additionally, initial writers and senior authors were viewed as having similar levels of involvement. The African and Australian continents made the least contribution. (Figure 2) Remarkably, a growing trend in which female engagement was included as a variable was noticed. All the writers in the paper were thoroughly assessed, and even if one of the authors was a woman, it was marked as yes and placed in a different category.\n\nAlthough female involvement, with respect to all authorship orders, rose from 17.48% (25/143) in 1961 to 68% (170/250) in 2021, females continue to publish fewer manuscripts as first (29.6%) and senior (22.2%) authors.\n\nCategories of first writers and senior authors were created using a new representation in which a mix of male and female authors were used to report the four possible results. The categories Male-Male, Male-Female, Female-Male, and Female-Female were used. Data evaluation resulted in Chi-Square = 124.6 with p<0.0001. (Figure 3)\n\nCalculations were made to examine the distribution of funding sources for submissions with female first authors, as well as the qualifications possessed by the writers at the time. This section contains related data as well as observations made for the core goals of this study (Table 2).\n\n\nDiscussion\n\nThis study focused on the articles published from 1961 to 2021 (Seven-decades), in two major endocrinology journals i.e. Bioscientifica's Journal of Endocrinology and General and Comparative Endocrinology, though there are more landmark journals in the field of endocrinology they were excluded because they were already used in the study by El Hakimi et al. showing authorship trends in major endocrinology journals14. Although El Hakimi et al. analyzed four prominent endocrinology journals (Thyroid, Journal of Clinical Endocrinology & Metabolism, Journal of Bone and Mineral Research, and Diabetes Care), each journal's purpose and scope were distinct, resulting in a bias when comparing them14. El Hakimi et al. found that the overall percentage age of female authors increased from 23.3 % in 1991 to 39.2 % in 2015, but in this study, female contributions as first author increased from 7% (10/143) in 1961 to 29.6 % (74/250) in 2021. Female qualification was one of the key reasons for limited female involvement from 1961 to 2021, as discovered in this study, making it one of the most significant factors to keep in mind as the increasing trend in female contribution is observed. This has to do with the fact that the number of females involved is proportional to their qualifications.\n\nDespite the fact that, according to the American Association of Medical Colleges, there were 51.3 % female endocrinologists compared to 48.3 % males in the United States in 2019, there is still a mystery as to why there are still so few female authors in scientific literature20. Female first authors made up 3.0 % of all publications in 1958, compared to 23 % in 2016, according to Amankwah et al.21 In other specialties, such as cardiology, female first authors made up 3.0 % of all publications in 1958, compared to 23 % in 201621. Similarly, in 1958, female last authors accounted for 5.2 % of all publications, compared to 20% in 2016. There was also a rise in the number of articles from Europe and Asia compared to this study where an increase in articles from Americas and Europe was observed.\n\nDespite the overwhelming positive findings, the studies also point to several potential areas of concern. Although the percentage age of female authors has increased over time, the data show that there was a lack of momentum among both first and senior authors between 1981 and 1991. Expanding and combining ideas from various articles published in major journals such as Endocrinology, Cardiology, and Gastroenterology, additional factors such as qualifications, funding source and further stratified, and female involvement as any co-author were considered.\n\nSeveral studies have looked into gender inequalities in medicine, such as Sidhu et al. work in the United Kingdom, or Mehran et al. works in Cardiology where Data from randomized controlled trials was investigated to assess gender gap. However, there was still a need to look into a way to assess the outcomes over a longer period of time. Because, in order to see the change, a long-term strategy must be implemented across several years to obtain more precise findings. The aim was to assess the same in this study by including 70 years of data, resulting in a more skewed conclusion. Researchers have incorporated data indicating trends over 20 or 30 years in the past or recently, but this is the first research of such kind, with articles gathered over 70 years.\n\nSeveral combinations of male-female First and Senior Authors were employed, resulting in four possible scenarios of MM, MF, FM, FF, where a decline in MM combination of authors and an increase in MF or FM from 1961 to 2021 was noticed (Figure 3)\n\nThis was unique because, whereas other authors identified patterns in sole females, this study viewed this as a fact that needed to be addressed. In a cross-sectional study published by Gayet-Ageron et al., a similar combination was employed, although the major focus was on author contribution rather than gender inequality.\n\nThis study employed methods to determine the gender of first and senior contributors that were similar to those previously reported in studies on gender and authorship. As a result, the findings of this study provide a more accurate and comprehensive picture of change over time than a sample consisting exclusively of original research articles published in the included journals in a single year per decade, for example. Qualification, continent, and female participation in all the authors present were also factored in this study.\n\n\nConclusion\n\nThis research found a statistically significant rise in the number of female authors participating in endocrinology research, both as first and senior authors. Despite the increase in female engagement, it was discovered that it still falls short of male participation. Female involvement had previously increased sharply, but it plateaued in the 2000s, remaining significantly below 50% and consequently less than male participation. Female contribution increased initially in the Americas and then on the European continent. Female authors from Europe contributed the most, followed by those from the American continent, both of which are high-income regions of the world. The rise in female contributions was not restricted to affluent countries; the Asian continent, which still contains many low-income regions, had a similar upward trend. Despite a large rise in female participation, changes for females and gender equality are still needed to boost female empowerment and the scientific community.\n\n\nData availability\n\nDryad: Trends in authorship demographics for manuscripts published in endocrine journals - A 70-year analysis\n\nhttps://doi.org/10.5061/dryad.rjdfn2zdh17\n\nThis project contains the following underlying data:\n\nData-Sheet.csv. (Data were collected from two major journals and analyzed for individual parameters as mentioned in the first row of the excel sheet. The first row describes all the numeric coding used to allot different categories to the study parameters.)\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Universal (CC0 1.0) Public domain dedication).",
"appendix": "Author contributions\n\nArpit Jain: Methodology, Data curation, Writing- original draft\n\nHritik Madan: Data curation, Writing- review & editing\n\nKamaldeep Singh: Methodology, Project administration, Writing- original draft\n\nYash Aggarwal: Data curation, Writing- review & editing\n\nBharat Midha: Data curation, Writing- review & editing\n\nShreya Gulati: Methodology, Project administration, Writing- review & editing\n\nPriyanka Batra: Project administration, Supervision, Writing- review & editing\n\nAnkur Batra: Conceptualization, Project administration, Supervision\n\nPriyanshu Jain: Supervision, Visualization, Writing- review & editing\n\nIpsa Arora: Conceptualization, Supervision, Validation\n\nMadhav Prabhu: Supervision, Visualization\n\nShreyas Arya: Formal Analysis, Supervision, Validation\n\nYashasvi Chugh: Formal Analysis, Validation\n\nShobhit Piplani: Conceptualization, Data curation, Formal Analysis, Methodology, Writing- original draft\n\n\nReferences\n\nSteelFisher GK, Findling MG, Bleich SN, et al.: Gender discrimination in the United States: Experiences of women. Health Serv Res. 2019; 54 Suppl 2(Suppl 2): 1442–1453. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoff T, Lee DR: The gender pay gap in medicine: A systematic review. Health Care Manage Rev. 2021. PubMed Abstract | Publisher Full Text\n\nWaisbren SE, Bowles H, Hasan T, et al.: Gender Differences in Research Grant Applications and Funding Outcomes for Medical School Faculty. J Womens Health (Larchmt). 2008; 17(2): 207–214. PubMed Abstract | Publisher Full Text\n\nMakarova E, Aeschlimann B, Herzog W: The Gender Gap in STEM Fields: The Impact of the Gender Stereotype of Math and Science on Secondary Students’ Career Aspirations. Front Educ. 2019; 4: 60. Publisher Full Text\n\nAzad AD, Charles AG, Ding Q, et al.: The gender gap and healthcare: associations between gender roles and factors affecting healthcare access in Central Malawi, June-August 2017. Arch Public Health. 2020; 78(1): 119. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeiss J, Balasuriya L, Cramer LD, et al.: Medical Students’ Demographic Characteristics and Their Perceptions of Faculty Role Modeling of Respect for Diversity. JAMA Netw Open. 2021; 4(6): e2112795. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJefferson L, Bloor K, Maynard A: Women in medicine: historical perspectives and recent trends. Br Med Bull. 2015; 114(1): 5–15. PubMed Abstract | Publisher Full Text\n\nThomas CC, Zeytinoglu M: Primary Care Endocrinology in the Adult Woman. Obstet Gynecol Clin North Am. 2016; 43(2): 325–346. PubMed Abstract | Publisher Full Text\n\nPelley E, Danoff A, Cooper DS, et al.: Female Physicians and the Future of Endocrinology. J Clin Endocrinol Metab. 2016; 101(1): 16–22. PubMed Abstract | Publisher Full Text\n\nOnumah C, Wikstrom S, Valencia V, et al.: What Women Need: a Study of Institutional Factors and Women Faculty’s Intent to Remain in Academic Medicine. J Gen Intern Med. 2021; 36(7): 2039–2047. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJagsi R, Guancial EA, Worobey CC, et al.: The “Gender Gap” in Authorship of Academic Medical Literature — A 35-Year Perspective. N Engl J Med. 2006; 355(3): 281–287. PubMed Abstract | Publisher Full Text\n\nOuyang D, Sing D, Shah S, et al.: Sex Disparities in Authorship Order of Cardiology Scientific Publications. Circ Cardiovasc Qual Outcomes. 2018; 11(12): e005040. PubMed Abstract | Publisher Full Text\n\nAmankwah N, Park M, Gu A, et al.: Trends in Authorship Demographics for Manuscripts Published in The American Journal of Cardiology. Am J Cardiol. 2018; 122(7): 1255–1259. PubMed Abstract | Publisher Full Text\n\nElhakimi W, Al Othman A, El Yahia M, et al.: Female authorship in major endocrinology journals: a 25-year progression. Journal of Endocrinology, Metabolism and Diabetes of South Africa. 2018; 23(3): 76–79. Publisher Full Text\n\nFalagas ME, Pitsouni EI, Malietzis GA, et al.: Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses. FASEB J. 2008; 22(2): 338–342. PubMed Abstract | Publisher Full Text\n\nRison RA, Shepphird JK, Kidd MR: How to choose the best journal for your case report. J Med Case Rep. 2017; 11(1): 198. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJain A: Trends in authorship demographics for manuscripts published in Endocrine journals: A 70-year analysis. Dryad, [Data], 2022. http://www.doi.org/10.5061/dryad.rjdfn2zdh\n\nInternational Standard Classification of education ISCED 2011. Reference Source\n\nPowell K: Searching by grant number: comparison of funding acknowledgments in NIH RePORTER, PubMed, and Web of Science. J Med Libr Assoc. 2019; 107(2): 172–178. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNumber of People per Active Physician by Specialty. 2019. Reference Source\n\nAmankwah N, Park M, Gu A, et al.: Trends in Authorship Demographics for Manuscripts Published in The American Journal of Cardiology. Am J Cardiol. 2018; 122(7): 1255–1259. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "145850",
"date": "12 Sep 2022",
"name": "Kunal Mahajan",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have done a good quality analysis of the gender trends along with inclusion of other variables but a few vague terms in the manuscript make it difficult for a reader to comprehend the true meaning of the sentence as intended by the authors. I recommend rectification of the following points:\nResult sections in ‘Abstract’ & in complete ‘Results’: The use of words ‘initial authors’ provides an ambiguous meaning to the reader. Please clarify whether initial authors is the first author or the first few authors, etc.\n\n‘Background’ section of ‘Abstract’: It would be nice to paraphrase this section of the abstract as it provides an unclear meaning and warrants a further reading to decipher the purpose of this article.\n\n‘Methods’ section of the ‘Abstract’: The authors have mentioned the use of Punnett square for depiction of gender combinations, but such an illustration has not been included in their paper. Authors are encouraged to provide a 2x2 table as it will further enhance their results by including number and gender distribution trends of lone authors i.e. papers having a single author.\nRectification of these minor inconsistencies will allow a reader to better comprehend the article and further enhance this much needed article in the field of Endocrinology and in a world where gender equality should matter.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8764",
"date": "20 Oct 2022",
"name": "Shobhit Piplani",
"role": "Author Response",
"response": "Thank you for your valuable response and review of our article. In the revised version of our paper, we have included a Punnett Square (Figure 4) depiction of our trends to facilitate the visualization of gender combinations as well as the inclusion of solitary authors. Additionally, the abstract has been rewritten to eliminate any ambiguity that may have arisen from differing viewpoints. While describing authors, the word 'initial' has been replaced with 'first', which defines the order of authorship more precisely."
}
]
}
] | 1
|
https://f1000research.com/articles/11-833
|
https://f1000research.com/articles/11-751/v1
|
06 Jul 22
|
{
"type": "Research Article",
"title": "Returning to work at school during the COVID -19 pandemic, is it stressful for schoolteachers? Assessment of immediate psychological effects: a cross sectional study",
"authors": [
"Sowmini Padmanabh Kamath",
"Prasanna Mithra",
"Jayashree K",
"Vaman Kulkarni",
"Jayateertha Joshi",
"Padmanabh Kamath",
"Bhaskaran Unnikrishnan",
"Keshava Pai",
"Prasanna Mithra",
"Jayashree K",
"Vaman Kulkarni",
"Jayateertha Joshi",
"Padmanabh Kamath",
"Bhaskaran Unnikrishnan",
"Keshava Pai"
],
"abstract": "Background: The adoption of remote classes for students has been in vogue since the onset of the pandemic. Schools reopened in a phased manner after the second wave of coronavirus disease 2019 (COVID-19) in India. Reverting to the regular face-to-face teaching for students became a challenge to the teachers and students, especially at times when there was an impending third wave on the way. The study aimed to assess the presence of symptoms of depression, anxiety, and stress in teachers who attended reopened schools in the scenario of face-to-face classes. In addition, we studied the association of psychological symptoms with teachers' age groups, gender, school boards, and school institution type. Methods: A cross-sectional study was conducted between October to December 2021 after schools had reopened. Data was collected using Google Form questionnaires in 124 schoolteachers. The Depression, Anxiety, and Stress Scale - 21 Items (DASS-21) questionnaire assessed the psychological symptoms. Results: Of 124 schoolteachers, 108(87.1%) were female, 112 (90.3%) were from private institutions, and 70(56.5%) were from Central Board of Secondary Education (CBSE) school boards. The prevalence of depression, anxiety, and stress in teachers was 30.6%, 45.2%, and 20.2%, respectively. Nearly 80% of the female teachers expressed depression, anxiety, and stress symptoms. Amongst all the age groups, symptoms were higher in 40-49 group. We found anxiety to be statistically significant when compared with gender (p-0.042). We found no statistically significant differences concerning age groups, school boards, or school institutions with any psychological symptoms. Conclusions: The prevalence of psychological symptoms was high among schoolteachers after schools reopened for regular face-to-face teaching. Gender was associated with anxiety in teachers. We agree that identifying teachers' symptoms and providing adequate psychological counseling/support would improve their mental health status and thereby the quality of teaching to students.",
"keywords": [
"Anxiety",
"counseling",
"COVID -19",
"depression",
"pandemics",
"schools",
"prevalence",
"school teachers"
],
"content": "Introduction\n\nThe coronavirus disease 2019 (COVID-19) pandemic has influenced significant economic, health, psychological, social, and educational changes across the globe (World Health Organization (WHO)). With the onset of a pandemic, social distancing as a strategic measure was adopted worldwide to curtail the spread of COVID-19 infection. Schools and educational institutes had gone for closures and lockdowns in various countries (Centers for Disease Control (CDC)). As per The United Nations Educational, Scientific and Cultural Organization (UNESCO), school closures as a social distancing measure varied in different countries (UNESCO).\n\nWith school closures, the regular face-to-face teaching had to be stopped abruptly with a rapid shift to an online mode of education; this was unlike planned online learning.1 Online learning used to prevail among higher classes and university students even during pre-COVID times. Moving to completely remote teaching across all age groups of children impacted the teachers, children, and their families as well (EDUCASE). UNESCO reported stress and confusion among teachers in all parts of the world (UNESCO).\n\nIn addition, teachers had to adjust rapidly to the remote teaching from regular face-to-face teaching to meet the expectations of students’ parents and school management. There was inadequate training for using digital resources and the insufficient provision of necessary equipment for online classes.2 The instructional planning involved in transferring the teaching material into an online environment with maintaining its relevance was a challenge for the teachers (The Brookings Institution). Along with the hectic professional life they led, they had increased family responsibilities during the pandemic. Earlier studies during the pandemic have shown that teachers have increased psychological symptoms with varying prevalence of anxiety,3–7 stress,7,8 and depression.3,7,9\n\nAnother study showed that more than half of the teachers experience burnout; risk factors for burnout included skill development in distance teaching, increased workload on distance education,10 and a new need for communication with parents because of increased involvement in remote teaching.11 In addition, they experienced conflicts at work and within family, and there was lesser social support because of confinement.10\n\nEven before the pandemic, teachers have expressed that they experience psychological symptoms related to stress.12–14 Teachers are always of prime importance since they are role models who influence students’ academic success and overall development. The teaching profession is otherwise also stressful, especially during pandemic times. Since the pandemic, the stress and anxiety levels have risen for reasons such as fear of getting infected, fear of the future, the health of oneself, their families,15 economic crises, and uncertainties daily.\n\nWe presumed that going back to face-to-face teaching after reopening schools will reduce their psychological symptoms. However, teachers continued to have challenges when reverting because of the day-to-day uncertainties with the pandemic,16 impending possibilities of upcoming waves (India Today), children yet to receive vaccination (Ministry of Health and Family Welfare), and extra responsibilities of teachers to maintain COVID appropriate behaviors among students (Ministry of Education). A single study conducted in Spain on teachers found higher anxiety, stress, and depression levels with face-to-face teaching after school reopening.7 However, there is minimal literature on anxiety, stress, and depression levels among Indian teachers returning to work at reopened schools in the time of the COVID-19 pandemic.\n\nTeachers’ mental health monitoring becomes essential considering significant changes in teachers’ professional and personal lives. Therefore, the present study assessed the prevalence of anxiety, stress, and depression among teachers who attended reopened schools during the COVID-19 pandemic. Further, we studied associations of age, gender, type of school institutions, and school boards with anxiety, stress, and depression symptoms.\n\n\nMethods\n\nA cross-sectional study was conducted among teachers at selected schools of Dakshina Kannada District, located in the coastal south Indian state of Karnataka. We collected the data by convenience sampling when the schools reopened following the second wave of COVID-19 infection (between October and December 2021).\n\nThis study follows ‘The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement guidelines.17 A completed STROBE checklist can be found in the Reporting guidelines.18 The study flow as per STROBE guidelines is depicted in the Figure 1.\n\nWe calculated a minimum sample size of 115, considering 80% power, 95% confidence level, relative precision of 10%, 20% non-response error, and an anticipated anxiety level in teachers to be 49.4%.7\n\nThe institutional ethical committee of Kasturba Medical College, Mangalore, approved the study (ethics committee approval number: IEC KMC MLR - 06/2020/184 dated 24/06/2020). We visited schools on a pre-informed date and took permission from the educational school authorities after explaining the purpose of the study. Teachers were provided the participant information sheet and informed consent was collected via an online platform (Consent form provided as Extended data).18\n\nTeachers who were willing to participate in the study were included. Teachers who could not join the school because of their chronic medical conditions or lack of access to internet facilities were excluded.\n\nWe obtained the list of all the schools within our district from the office of the Block Education Officer (BEO). The sample size was divided equally among the public and private schools. In the ascending order of number of teachers, the schools were listed. Using a lottery technique, schools were then selected until we achieved the required sample size.\n\nWe obtained permission from the BEO and the respective school authorities, after explaining the details of the study. Data were collected using the online platform Google Forms to create the questionnaire as an infection control measure.\n\nThe link of the questionnaire with the participant information sheet containing details of study, the permission letter from the BEO and the IEC certificate were sent to the head teacher/principal of the selected school via WhatsApp and school email. The principal circulated the link in their respective schoolteachers’ WhatsApp group. A reminder message by the investigator with request to participate in the study was sent once after two weeks to the head teacher/principal. Informed consent was collected through the questionnaire link.\n\nThe questionnaire (provided as Extended data)18 had two sections: section 1 for demographic data and section 2 included the questions from the standard questionnaire of Depression, Anxiety and Stress Scale - 21 Items (DASS-21) questionnaires (available from ePROVIDE). DASS-21 questionnaire was used to assess depression, anxiety, and stress levels. All the questions were compulsory. Participants could scroll down to the next question after answering the question in hand.\n\nDASS-21 (English version) of the questionnaire was employed. It is a self-report questionnaire and is mapped out to ascertain the psychological states of anxiety, stress, and depression. The scale consists of 21 items with each statement having four response options (score 0-did did not apply to me at all; score 1-applied to me to some degree or some of the time; score 2-applied to me to a considerable degree or a good part of the time; and score 3-applied to me very much or most of the time). The responses specify how much the statement pertains to them over the last week. The questions are grouped for three scales, namely depression, anxiety, and stress, with seven items in each domain. The scores were summed up for pertinent items of each domain and multiplied by two to arrive at the final score. Based on the final scores for each domain, we classified the severity of symptoms as per cut-off scores into i) no symptoms, ii) mild, iii) moderate, iv) severe, and v) extremely severe symptoms.\n\nPublic schools include schools that are managed/aided by the Government. The Council for the Indian School Certificate Examinations (a private board of secondary education in India) conducts the Indian Certificate of Secondary Education (ICSE) examination. The Government of India manages the national level education board named “The Central Board of Secondary Education (CBSE)” for Indian public and private schools. The Karnataka state government operates the State Education Examination Board (State board). We grouped school boards as (CBSE+ICSE) versus state boards, and the type of schools was grouped as public versus private schools for comparison with anxiety, stress, and depression levels among teachers.\n\nIBM SPSS Statistics for Windows, Version 25.0. Armonk, NY: IBM Corp. was used to analyze the collected data. We expressed our results as proportions using appropriate tables. We analyzed the groups for their association with psychological symptoms by Chi-square test. A p-value of <0.05 was considered statistically significant.\n\n\nResults\n\nA total of 180 teachers were contacted, of which 12418 responded to the questionnaire with a response rate of (68.89%). Of 124 teachers, 108 (87.1%) were female, 112 (90.3%) were from private institutions, and 70 (56.5%) were from CBSE school boards (Table 1). The frequency and symptom severity of depression, anxiety, and stress as per the DASS 21 scale is depicted in Table 2.\n\nOf the sample, 45.2% of teachers indicated anxiety features, with 7.3% reporting features of extremely severe anxiety and 3.2% with severe anxiety. About 20.2% of teachers reported stress; 2.4% had extremely severe stress, and 5.6% had severe stress. Around 30.6% of teachers suffered from symptoms suggestive of depression, and extremely severe and severe symptoms were reported in 1.6%, and in 3.2% respectively. Symptoms of depression, anxiety and stress were seen in 78.95%, 80.36%, and 80% of female teachers, respectively. Similarly, symptoms of depression (52.63%), anxiety (50%), and stress (60%) were seen predominantly in teachers aged between 40-49 years.\n\nFurthermore, we grouped the symptoms as presence or absence of symptoms, namely as “No anxiety” and “anxiety present”; “No stress and stress present”; and “No depression and depression present” (Table 3). We compared the gender, age groups, school boards, and school type with groups categorized with the presence or absence of symptoms for depression, anxiety, and stress. We found anxiety to be statistically significant when compared with gender (p-0.042). However, we found no statistically significant differences when we compared age groups, school boards, and school institutions with the psychological symptoms in teachers (Table 4).\n\n* p value significant at < 0.05 level.\n\n\nDiscussion\n\nIn our study, among the schoolteachers’ anxiety, stress, and depression symptoms were 45.2%, 20.2%, and 30.6%, respectively. These symptoms were in the context of face-to-face teaching after schools had reopened following the second wave of COVID-19 in India. Similar higher prevalence of anxiety (49.4%), stress (50.6%), and depression (32.2%) were present among teachers who had face-to-face teaching after schools reopened in Spain.7\n\nOne significant change in the education system worldwide was adopting remote learning (e-learning) across all age groups. The higher stress levels during the COVID-19 pandemic could be because teachers had to adjust to the online teaching mode.19 Home teaching had increased their workload, and there was a concomitant increase in anxiety, depression, and disturbances in sleep. With school closures, the teachers experienced stress and confusion because of the uncertainties regarding the duration of school closures and the unprecedented option of distance/online learning (UNESCO).\n\nA recent study found that some challenges and factors influence the use and receipt of online learning as a tool for higher education teaching. Among the challenges, the highest barriers were unstable or insufficient internet connectivity, lack of computers/laptops, and other technical issues.20 Teachers’ perceptions on e-learning in India documented moderate and severe anxiety (each 5% by Hamilton rating scale for anxiety), with 37% of teachers reporting that the major drawback of online classes was a lack of face-to-face communication with students.5 However, our study did not assess the teachers’ perceptions of e-learning.\n\nA study that assessed the effect of online homeschooling on children, teachers, and 1-9 grades through the COVID-19 pandemic in China found that 17.6% of students (by parent-rated Strengths and Difficulties Questionnaire (SDQ)) had emotional or behavioral problems with more vulnerability in low-grade students. Elevated anxiety levels (by self-rating anxiety scale (SAS)) were seen in 17.2% of teachers and 9.6% of parents.6 Their teacher’s anxiety levels were less than that reported in our study.\n\nOn similar grounds of returning to teaching at school in pandemic times, a survey assessed the differences in anxiety levels from the first day of joining to the end of one-month education. More than half (56.2%) of teachers did not show a change in the anxiety, 38.9% had decreased levels, and 4.9% of teachers had increased anxiety levels. The survey found communication within the school, the stress in teachers, and teaching instructions by virtual modes to be significant predictors of an increase in teachers’ anxiety.21\n\nContrary to our study, university employees reported stress in 13% of participants, depression in 15.9%, anxiety in high to moderate levels in 13% (by DASS), and 43% reported high exhaustion at work. More than half of them (58.3%) had opined of having worsened overall well-being concerning COVID-19 work/life changes.9\n\nIn the early part of the pandemic, an extensive survey conducted in China showed 58.1% of teachers being ‘very worried’ about the COVID-19 situation.22 Our study had teachers’ anxiety levels more than three times that found in teachers in China (13.67% by the Generalized Anxiety Disorder tool (GAD-7)).4 Gender, age, educational status, type of teachers, school location, worry, or fear level of teachers were associated with anxiety in a study done in China.4 Unlike our findings, university teachers in Jordan,8 reported severe distress in 31.4% of participants to mild to moderate distress in 38.2% (Kessler Distress scale-K10).\n\nA systematic review and meta-analysis documented anxiety, depression, and stress in teachers as 17%, 19%, and 30%, respectively.23 In yet another similar systematic review in teachers, the stress levels varied from 12.6% to 50.6%, anxiety levels between 10% and 49.4%, and depression levels between 15.9% and 28.9%.24 In our study and a survey conducted among Spanish teachers,7 the prevalence of stress, anxiety, and depression in teachers was higher. Daily uncertainties of the COVID situation, getting exposed to more contacts while commuting to school, and interacting with students were reasons for higher stress and anxiety.25 In addition, the need to be more vigilant in maintaining the appropriate COVID behaviors for face-to-face classes with increased responsibilities to monitor students (Ministry of Education; Learning Policy Institute), can affect their psychological symptoms to a large extent. Further, we had conducted the study when the schools had reopened after the second wave of COVID-19 infection, which had a devastating impact on Indians.\n\nA study assessment of mental health status when the people returned to work in China noted that 10.8% had the criteria to fulfill post-traumatic stress disorder (PTSD), anxiety levels in 3.8%, stress in 1.5%, depression in 3.7%, and insomnia in 2.3%.26 Their prevalence of psychological symptoms was lesser and contrasts our study and the Spanish study,7 probably because of the faith induced by adopting preventive and social distancing measures before they started working.26\n\nA study in Poland found a negative relationship between social/marital/close links and coping of stress, anxiety, and depression among teachers; their psychological symptoms progressively worsened from the first to the second wave in Poland.27 Another study assessed the teachers’ anxiety-related factors towards COVID-19 infection and education in school when they started having face-to-face classes; six reasons for infection-related and four factors for educational-related anxiety were found to be significant. Factors such as their anxiety regarding their safety/families (infection-related), anxiety about students’ home situations, and delay in students’ education (education-related) were strongly associated with anxiety.28\n\nThe psychological symptoms were higher in schoolteachers3,5,6 compared to university teachers4,8,9 Our study mainly focused on schoolteachers. The higher prevalence among schoolteachers could be because more minor children need more supervision and monitoring of appropriate COVID behaviors than young adults in university.\n\nIt is a known fact that the most schoolteachers are female. Our study also had more participation from female teachers (87.1%) with higher levels of symptomatology in them. Similarly, earlier studies have shown female teachers to have higher psychological symptoms through COVID-19 pandemic,23,24 and this is true even in the pre-COVID times.12,13 The present study showed a significant association between differences in gender with anxiety in teachers; such similar results were seen in previous studies.4,7,29\n\nThe new mode of online teaching to conduct classes with a heavy workload at school, homeschooling and attending family duties, extra responsibilities of parenting, child-care, and multitasking to meet the family demands30 may be reasons for the female teachers to be more symptomatic. Professional and personal commitments increase stress levels. Our study did not assess these factors separately.\n\nThe present study showed psychological symptoms to be predominant in the teachers between 40-49 years. Similar findings of older teachers (>47 years) having more significant anxiety and younger teachers having higher stress scores were seen among Spanish teachers.13 However, age groups did not show a significant association with any of the symptoms in our study. With age, there is probably a building of resilience with frequent exposures to various stressors over time, molding them to have stabler emotional management and lower psychological symptoms.31\n\nIn the present study, teachers working in CBSE+ICSE school boards and private institutions had higher symptoms than state boards and Government aided schools, probably because of more response rates from the former. There was no significant association of school boards and type of school institution (Government aided versus private) with psychological symptoms with limited literature available until date.\n\nThe study’s limitations include a small sample size and lesser participation of teachers from public/government-aided institutions. In addition, results may not reflect the teachers’ opinions from other areas of the state/country, and we did not ascertain the casualty in factors related to psychological symptoms. The study’s strengths were that we used a standard questionnaire to assess the prevalence of symptoms of anxiety, stress, and depression (DASS 21) in teachers. We compared the symptom prevalence with school boards and public versus private school institutions, which has not been assessed in previous studies.\n\n\nConclusion\n\nAfter schools reopened, teachers had a higher prevalence of psychological symptoms when reverting to face-to-face classes. Gender was significantly associated with anxiety. Teachers’ role in shaping children stands beyond the mundane syllabus, courses, and exams. They are considered torchbearers of hope for a bright future for young children, and if they are affected by psychological symptoms, it will influence the quality of teaching. Thus, it is essential to identify the psychological symptoms teachers face during the COVID-19 pandemic crisis and encourage them to seek the professional help of counselors to adapt smoothly during current so-called new-normal situations. Further creating an encouraging/positive working atmosphere that will help teachers get connected and aid them in sharing matters that concern them would help them.\n\n\nData availability\n\nOpen Scientific Framework: Returning to work at school during COVID -19 pandemic, is it stressful for schoolteachers: Assessment of immediate psychological effects. https://doi.org/10.17605/OSF.IO/8VHJ323\n\nThis dataset contains the following underlying data:\n\n• Excel data F1000 research.xlsx\n\n• Data Key.docx\n\nOpen Scientific Framework: Returning to work at school during COVID -19 pandemic, is it stressful for schoolteachers: Assessment of immediate psychological effects. https://doi.org/10.17605/OSF.IO/8VHJ323\n\nThis dataset contains the following underlying extended data:\n\n• DASS-21 PDF.pdf\n\n• Participant Information Sheet and Informed Consent-F1000 research.docx\n\n• Questionnaire-F1000 research.docx\n\n• Study-flow-figure-F1000-research.jpg\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReporting guidelines\n\nOpen Scientific Framework: STROBE checklist for “Returning to work at school during COVID -19 pandemic, is it stressful for schoolteachers: Assessment of immediate psychological effects.” https://doi.org/10.17605/OSF.IO/8VHJ3\n\n\nCompeting interests\n\nNo competing interests were disclosed.\n\n\nGrant information\n\nThe author(s) declared that no grants were involved in supporting this work.",
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Dev. 2021; 12: 204–208.\n\nZhao Y, Guo Y, Xiao Y, et al.: The Effects of Online Homeschooling on Children, Parents, and Teachers of Grades 1-9 During the COVID-19 Pandemic. Med. Sci. Monit. 2020; 26: e925591. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOzamiz-Etxebarria N, Berasategi Santxo N, Idoiaga Mondragon N, et al.: The psychological state of teachers during the COVID-19 crisis: The challenge of returning to face-to-face teaching. Front. Psychol. 2021; 11: 620718. PubMed Abstract | Publisher Full Text\n\nAkour A, Al-Tammemi AB, Barakat M, et al.: The Impact of the COVID-19 Pandemic and Emergency Distance Teaching on the Psychological Status of University Teachers: A Cross-Sectional Study in Jordan. Am. J. Trop. Med. Hyg. 2020; 103: 2391–2399. PubMed Abstract | Publisher Full Text\n\nEvanoff BA, Strickland JR, Dale AM, et al.: Work-Related and Personal Factors Associated With Mental Well-Being During the COVID-19 Response: Survey of Health Care and Other Workers. J. Med. Internet Res. 2020; 22(8): e21366. PubMed Abstract | Publisher Full Text\n\nAmri A, Abidli Z, Elhamzaoui M, et al.: Assessment of burnout among primary teachers in confinement during the COVID-19 period in Morocco: case of the Kenitra. Pan Afr. Med. J. 2020 Jun 25; 35(Suppl 2): 92. Publisher Full Text\n\nPressley T: Factors contributing to teacher burnout during COVID-19. Educ. Res. 2021; 50: 325–327. Publisher Full Text\n\nParasher M, Ellawadi D, Singh M, et al.: Level of stress among school teachers of a school in South Delhi. Chismed J. Health Res. 2019; 6: 150–155.\n\nDawn S, Talukdar P, Bhattacharjee S, et al.: A study on job related stress among school teachers in different schools of West Bengal, India. East J. Psychiatry. 2016; 19: 12–17.\n\nChaly PE, Anand SP, Reddy VCS, et al.: Evaluation of occupational stress among software professionals and school teachers in Trivandrum. Int. J. Med. Dent. Sci. 2014; 3: 440–450. Publisher Full Text\n\nCori L, Curzio O, Adorni F, et al.: Fear of COVID-19 for Individuals and Family Members: Indications from the National Cross-Sectional Study of the EPICOVID19 Web-Based Survey. Int. J. Environ. Res. Public Health. 2021; 18(6): 3248. Publisher Full Text\n\nMaison D, Jaworska D, Adamczyk D, et al.: The challenges arising from the COVID-19 pandemic and the way people deal with them. A qualitative longitudinal study. PLoS One. 2021 Oct 11; 16(10): e0258133. PubMed Abstract | Publisher Full Text\n\nvon Elm E , Altman DG, Egger M, et al.: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. Lancet. 2007 Oct 20; 370(9596): 1453–1457. Publisher Full Text\n\nKamath SP, Mithra P, Kulkarni KJ, et al.: Returning to work at school during COVID -19 pandemic, is it stressful for school teachers:Assessment of immediate psychological effects.2022. Publisher Full Text\n\nBesser A, Lotem S, Zeigler-Hill V: Psychological Stress and Vocal Symptoms Among University Professors in Israel: Implications of the Shift to Online Synchronous Teaching During the COVID-19 Pandemic. J. Voice. 2020 Jun 5; 36(20): 291.e9–291.e16. PubMed Abstract | Publisher Full Text\n\nZalat MM, Hamed MS, Bolbol SA: The experiences, challenges, and acceptance of e-learning as a tool for teaching during the COVID-19 pandemic among university medical staff. PLoS One. 2021; 16: e0248758. PubMed Abstract | Publisher Full Text\n\nPressley T, Ha C, Learn E: Teacher stress and anxiety during COVID-19: An empirical study. Sch. Psychol. 2021; 36: 367–376. Publisher Full Text\n\nWang C, Pan R, Wan X, et al.: Immediate Psychological Responses and Associated Factors during the Initial Stage of the 2019 Coronavirus Disease (COVID-19) Epidemic among the General Population in China. Int. J. Environ. Res. Public Health. 2020; 17: 1729. PubMed Abstract | Publisher Full Text\n\nOzamiz-Etxebarria N, Idoiaga Mondragon N, Bueno-Notivol J, et al.: Prevalence of Anxiety, Depression, and Stress among Teachers during the COVID-19 Pandemic: A Rapid Systematic Review with Meta-Analysis. Brain Sci. 2021; 11: 1172. PubMed Abstract | Publisher Full Text Reference Source\n\nSilva DFO, Cobucci RN, Lima SCVC, et al.: Prevalence of anxiety, depression, and stress among teachers during the COVID-19 pandemic: A PRISMA-compliant systematic review. Medicine (Baltimore). 2021; 100: e27684. PubMed Abstract | Publisher Full Text\n\nZiauddeen N, Woods-Townsend K, Saxena S, et al.: Schools and COVID-19: Reopening Pandora’s box?. Public Health Pract. (Oxf). 2020; 1: 100039. PubMed Abstract | Publisher Full Text Reference Source\n\nTan W, Hao F, McIntyre RS, et al.: Is returning to work during the COVID-19 pandemic stressful? A study on immediate mental health status and psychoneuroimmunity prevention measures of Chinese workforce. Brain Behav. Immun. 2020; 87: 84–92. PubMed Abstract | Publisher Full Text\n\nJakubowski TD, Sitko-Dominik MM: Teachers’ mental health during the first two waves of the COVID-19 pandemic in Poland. PLoS One. 2021; 16: e0257252. PubMed Abstract | Publisher Full Text\n\nWakui N, Abe S, Shirozu S, et al.: Causes of anxiety among teachers giving face-to-face lessons after the reopening of schools during the COVID-19 pandemic: a cross-sectional study. BMC Public Health. 2021 Jun 2; 21(1): 1050. PubMed Abstract | Publisher Full Text\n\nStachteas P, Stachteas C: The psychological impact of the COVID-19 pandemic on secondary school teachers. Psychiatriki. 2020; 31: 293–301. Publisher Full Text\n\nHupkau C, Petrongolo B: Work, Care and Gender during the COVID-19 Crisis. Fisc. Stud. 2020; 41: 623–651. PubMed Abstract | Publisher Full Text\n\nSolomou I, Constantinidou F: Prevalence and Predictors of Anxiety and Depression Symptoms during the COVID-19 Pandemic and Compliance with Precautionary Measures: Age and Sex Matter. Int. J. Environ. Res. Public Health. 2020; 17: 4924. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "145634",
"date": "05 Aug 2022",
"name": "Ajay Risal",
"expertise": [
"Reviewer Expertise MD Psychiatry",
"Ph.D. Clinical Medicine"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is a very good study that assessed the psychological symptoms, mainly anxiety, depression, and stress, among the school teachers of Karnataka State in India while the schools became open for physical classes in the post-COVID phase.\nIt has used a valid instrument DASS for assessing the psychology of the teachers. However, the following two concerns need clarification and explanation before this research can be considered acceptable for indexing:\nWhich version of DASS-21 was used for the assessment? It is not clear. Is it acceptable to use the English version (if it was the case) for all the participants whose mother tongue is supposedly not English for assessing their psychological issues? Will this procedure be socio-culturally accepted or valid? Is this methodology culture-sensitive? I think this concern needs good clarification and explanation.\n\nDASS-21 was able to assess the individual depression (D), anxiety (A), and stress (S) symptoms independently as per the results you have shown, but it is not clear how many participants had combined D+A or D+S, A+D, or D+A+S symptoms. Was this result not important? Does not D symptoms affect A or S symptoms or vice versa? How were those effects analyzed? Were not D symptoms confounder for A or S symptoms; or A confounder to D and S; or S confounder to D or A? How were these possible confounding issues handled? I think this should also be the finding. These issues must get space in the Methodology and Results or at least in the Discussion as a possible limitation.\n\nOtherwise, it is a good study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8904",
"date": "21 Oct 2022",
"name": "Sowmini Padmanabh Kamath",
"role": "Author Response",
"response": "1. Which version of DASS-21 was used for the assessment? It is not clear. Is it acceptable to use the English version (if it was the case) for all the participants whose mother tongue is supposedly not English for assessing their psychological issues? Will this procedure be socio-culturally accepted or valid? Is this methodology culture-sensitive? I think this concern needs good clarification and explanation. Thank you for the suggestion. We have addressed the query with an explanation in the introduction section (para 7 and 8) and in the methodology section (DASS 21 questionnaire). 2. DASS-21 was able to assess the individual depression (D), anxiety (A), and stress (S) symptoms independently as per the results you have shown, but it is not clear how many participants had combined D+A or D+S, A+D, or D+A+S symptoms. Was this result not important? Does not D symptoms affect A or S symptoms or vice versa? How were those effects analyzed? Were not D symptoms confounder for A or S symptoms; or A confounder to D and S; or S confounder to D or A? How were these possible confounding issues handled? I think this should also be the finding. These issues must get space in the Methodology and Results or at least in the Discussion as a possible limitation. Thank you for the suggestion. We have now included the number of school teachers with combined psychological symptoms in the results section (para 3). Yes, the symptoms affect each other to some extent and vice versa. The symptoms can be a confounder with each other. To evaluate the link between the domains of stress, anxiety, and depression, we employed a partial correlation test and correlation coefficients were generated. These issues have been incorporated in the statistical analysis section of the methodology and in the results section (para 4) with correlation coefficients. In the discussion section, it has been included as a limitation."
}
]
},
{
"id": "148222",
"date": "05 Sep 2022",
"name": "Rajesh Mithur",
"expertise": [
"Reviewer Expertise Neuropsychiatry",
"Adult psychiatry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nA good study indeed done in COVID times. Kindly provide the following clarifications and address the corrections:\n\"India today\" reference may not be appropriate for a scientific journal.\n\n\"Returning to work at school during the COVID -19 pandemic, Is it stressful for school teachers?\" - the title gives an impression that the teachers faced stress due to schools reopening after the COVID pandemic. Kindly specify in the study that the stress teachers are facing is due to the COVID-19 pandemic and not due to school reopening per se. The causality of the stress was not established in the study. The psychological symptoms are seen in these teachers mostly due to the COVID pandemic.\n\nThe overview of the DASS 21 scale quotes, “The DASS is based on a dimensional rather than a categorical conception of psychological disorder. The assumption on which the DASS development was based is that the differences between the depression, anxiety, and stress experienced by normal subjects and the clinically disturbed, are essential differences in degree. The DASS, therefore, has no direct implications for the allocation of patients to discrete diagnostic categories postulated in classificatory systems such as the DSM and ICD.”1 - The overview quotes that depression, anxiety, and stress are taken as a single dimension in the scale and not as separate unique entities, hence, percentage depictions of individual entities have to be clarified. There will be a significant overlap of stress, depression, and anxiety among patients which has to be specified.\n\nPage 9: casualty term has to be corrected. Causality is not established is a main drawback of the study.\n\nLimitation: COVID-related socioeconomic issues themselves may be a significant contributor to stress and cause of depression and anxiety which was not investigated.\n\nReferences: 6, 7, 18, 22, 23, 24, 25, 27, 28, 31 has to be in proper reference style.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8905",
"date": "21 Oct 2022",
"name": "Sowmini Padmanabh Kamath",
"role": "Author Response",
"response": "1. \"India today\" reference may not be appropriate for a scientific journal. Thank you for the suggestion. We have changed the reference as advised (in the sixth paragraph of the introduction). 2. \"Returning to work at school during the COVID -19 pandemic, Is it stressful for school teachers?\" - the title gives an impression that the teachers faced stress due to schools reopening after the COVID pandemic. Kindly specify in the study that the stress teachers are facing is due to the COVID-19 pandemic and not due to school reopening per se. The causality of the stress was not established in the study. The psychological symptoms are seen in these teachers mostly due to the COVID pandemic Thank you. We have described this in the limitation section of the discussion. We agree that the causality of stress was not established and conjecture that it was a combination of reopening after a hiatus, challenges of practicing and enforcing new behaviors and fear of unpredictable resurgence of infection. 3.The overview of the DASS 21 scale quotes, “The DASS is based on a dimensional rather than a categorical conception of psychological disorder. The assumption on which the DASS development was based is that the differences between the depression, anxiety, and stress experienced by normal subjects and the clinically disturbed, are essential differences in degree. The DASS, therefore, has no direct implications for the allocation of patients to discrete diagnostic categories postulated in classificatory systems such as the DSM and ICD.”1 - The overview quotes that depression, anxiety, and stress are taken as a single dimension in the scale and not as separate unique entities, hence, percentage depictions of individual entities have to be clarified. There will be a significant overlap of stress, depression, and anxiety among patients, which has to be specified. Thank you for the suggestion. Depictions of individual entities and overlap of psychological symptoms have been included in the results section (third paragraph). 4. Page 9: casualty term has to be corrected. Causality is not established is a main drawback of the study. Thank you for the suggestion. The spelling is corrected and changes made are in the limitation section of the discussion. 5. Limitation: COVID-related socioeconomic issues themselves may be a significant contributor to stress and cause of depression and anxiety, which was not investigated. Thank you for the suggestion. I have added this point in the limitation section of the discussion. 6. References: 6, 7, 18, 22, 23, 24, 25, 27, 28, 31 has to be in proper reference style. Thank you. Vancouver reference style has been adopted."
}
]
}
] | 1
|
https://f1000research.com/articles/11-751
|
https://f1000research.com/articles/11-1201/v1
|
20 Oct 22
|
{
"type": "Research Article",
"title": "Mulberroside A could serve as a pan inhibitor for the tyrosine kinase domains of the HER family",
"authors": [
"Jaafar Wadi",
"Othman Sagheer",
"Othman Sagheer"
],
"abstract": "Numerous medicines were authorized for their targeting of the tyrosine kinase domain (TKD) of human epidermal receptors (HER). However, it has been demonstrated that these TKDs exhibit persistent resistance, necessitating the development of additional inhibitors with different modes of action. A single pharmacophore can be manipulated to create a pan-inhibitor where the binding site of these receptors has been highly conserved. The development of anti-cancer agents and the introduction of synergistic action to increase the efficacy of current medications have both recently benefited from the use of medicinal plants and herbal extracts as a reliable source. The binding affinity to the TKDs was predicted by molecular docking, followed by molecular dynamic simulation to examine the changes in the motion of the enzymes, with a focus on the components responsible for catalytic activity (C α-helix), activation (activation loop), and autophosphorylation (C-terminal loop). According to the ∆G value provided by Autodock Vina (-40.54, -40.12, -37.20, -37.62 kJ/mol for HER1, HER2, HER3, and HER4, respectively) and MM/PBSA, which indicates a strong affinity for the TKDs, the outcomes are undeniably positive. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and the principal component analysis (PCA) detected significant dynamic changes in the TKDs, particularly in the C α-helix and the activation loop for all TKDs, suggesting that mulberroside A may alter the function of these enzymes. This study will expand our understanding of the dynamics of the TKDs and shed light on the anticancer potential of the polyphenolic compounds.",
"keywords": [
"Polyphenols",
"mulberroside A",
"molecular docking",
"cancer",
"molecular dynamic simulation",
"protein kinase inhibitors."
],
"content": "1. Introduction\n\nHuman epidermal receptors (HERs) have been shown to play a crucial role in a variety of cancer forms, including non-small cell lung cancer (NSCL), which kills more people than prostate cancer, breast, colorectal combined and around 20% of breast cancers, which are characterized by overexpression of human HER2 protein and associated gene (Majeed et al., 2021).\n\nThere are four HER receptors: HER1, also known as EGFR, HER2, HER3, and HER4. The members of the HER family are transmembrane receptor tyrosine kinases, which are enzymes that catalyze tyrosine phosphorylation, specifically the transfer of adenosine triphosphate (ATP) to tyrosine residues on protein substrates and the subsequent recruitment and activation of downstream signaling proteins. This results in the activation of downstream signaling pathways that promote cell proliferation, differentiation, migration, survival, adhesion, and angiogenesis. Numerous malignancies have been associated with a mutation that enables some tyrosine kinases to be constitutively active and/or occasionally act improperly.\n\nThe extracellular domain (ECD), a transmembrane segment, and an intracellular portion all comprise the structure of HER receptors. The intracellular region consists of a juxtamembrane segment and a functional protein kinase domain (with the exception of HER3, which lacks tyrosine kinase activity and must be activated in conjunction with another family member). The catalytic domain or the tyrosine kinase domain (Figure 1) contains the conserved ATP binding groove, which is required for ATP binding (Jura et al., 2009). The tyrosine kinase domain (TKD) is made up of an activation loop, a C-lobe, and an N-lobe, which contains a C α-helix. The activation loop, which is a polypeptide region outside the binding site cleft that, upon phosphorylation, induces kinase activation and C α-helix must adopt a particular, “active” configuration in order for a TKD to function (Wintheiser & Silberstein, 2021; Adams, 2003).\n\nThere are two lobes (C-lobe and N-lobe) that are spanned by a loop-like structure called the activation loop (purple in color). The N-lobe contains the C α-helix (purple in color) which is essential for the catalytic activity of the enzymes. The sequence alignment reveals the residues that are primarily responsible for forming the binding site (green-shaded) and that are predicted to interact with mulberroside A, along with their RMSD values, which show the deviation from each other.\n\nThe development of acquired resistance to chemotherapy is one of the most perplexing concerns confronting oncologists. Although cancer cells initially respond to chemotherapy, later as treatment progresses, mutations and epigenetic alterations may occur, resulting in a high degree of plasticity of these cells that leads to the emergence of resistance. Due to receptor mutations, anti-HER resistance has risen over the years, necessitating an ongoing search for new inhibitors.\n\nNumerous studies on the antioxidative, anti-inflammatory, and anticarcinogenic properties of dietary polyphenolic substances have been carried out extensively. In this regard, dietary polyphenols have been shown in preclinical models to display chemo-preventive and therapeutic benefits against a variety of malignancies. However, available medications have a high level of unspecific cytotoxicity, which has a detrimental effect on normal cells as well. As a result, the search for anticancer agents derived from natural medicinal plants has progressively increased throughout the years (Mechchate et al., 2021). Phenolic compounds are one of the most abundant and diverse classes of plant metabolites, with over 8,000 compounds described. Stilbenes, benzoquinones, acetophenones, flavonoids, anthocyanins, phenolic acids, catechins/epicatechins, ellagitannins, and proanthocyanidins are the various polyphenolic classes. The most extensively studied of these are (-)-epigallocatechin-3-gallate, resveratrol (found in grape skin), and curcumin (found in turmeric) (Pandey et al., 2009). In this context, certain polyphenols have been shown to act as chemosensitizers, enhancing the efficacy of chemotherapeutic agents when used in combination. For instance, it has been demonstrated that the flavonoid silibinin considerably showed activity against the resistant lung cancer cells to the tyrosine kinase inhibitor (TKI) erlotinib which led to a suggestion of using silibinin in combination with TKIs as a treatment regimen (Verdura et al., 2021). Curcumin is another polyphenol which, when combined with 5-fluorouracil, demonstrated antimetastatic activity (colon carcinoma) (Yang et al., 2017). Additionally, it has been reported that resveratrol enhances the anticancer effects of gemcitabine by reducing the emergence of resistance in pancreatic cancer cells and sensitizing glioma stem cells to radiation (Zhou, et al., 2019). Stilbenes are a non-flavonoid polyphenolic phytochemical with a 1,2-diphenylethylene nucleus. They hold exceptional promise for the prevention and treatment of cancer, due to their antioxidant, cell death activation, and anti-inflammatory properties, all of which are associated with low toxicity in vivo (Sirerol et al., 2016). Numerous methoxy and hydroxy derivatives of trans-stilbene have been shown to inhibit the growth of varied human cancer cells by causing cell apoptosis (Parida et al., 2018). Mulberroside A is a stilbenoid found in Morus alba (the white mulberry) and a diglucoside of oxyresveratrol. Due to its successful docking results, mulberroside A will be the focus of this study, and its effect on the dynamics of the proteins will be investigated further.\n\n\n2. Methodology\n\nThe crystal structures of the TKD of the HERs were obtained from the protein data bank. 3POZ (chain A), 3RCD (chain A), 6OP9 (chain A), and 3BBT (chain B) are the PDB codes for HER1 (sequence 701-1017), HER2 (sequence 710-1022), HER3 (sequence 680-960), and HER4 (sequence 683-973), respectively. The missing residues were added by Salilab modeler (Pieper et al., 2006) and they were for HER1 748-754, 734-737, 868-874, 1004-1009 segments, for HER2 757-760, 867-883, 992-999, 1013-1015 segments, for HER3 847-851 segment, and for HER4 844-858 segment. The evaluation of the modeled missing parts was carried out by normalized Discrete Optimized Protein Energy (zDOPE), an atomic distance-dependent statistical score (Shen & Sali, 2006). The residues of the proteins were renumbered as a requirement of the modeler starting from number one (HER1; 1-317, HER2; 1-312, HER3; 1-280, HER4; 1-290). The binding sites have been chosen based on the coexisted inhibitors that occupy an orthosteric site, which is the active one.\n\nPrior to docking, all water molecules, ions, and ligands were eliminated from the enzymes. These enzymes were then prepared for docking by adding hydrogen atoms and charges (Charges were modeled by AMBER ff14SB for the residues) using Dockprep's UCSF chimera-building feature (Pettersen et al., 2004). Afterward, the ligand was obtained from PubChem and prepared for docking by adding hydrogen atoms and charges. Charges were modeled by AM1-BCC (Austin model with bond and charge correction) for the ligand (Maier et al., 2015; Jakalian et al., 2002). The ligand structure was minimized and optimized by MM2 force field that built in chemoffice software (Hocquet & Langgård, 1998).\n\nThe docking process and the estimated free binding energy were handled by the AutoDock Vina (Trott & Olson, 2010). Up to 10 poses were produced for the ligand within the binding site of the enzymes, and the selection was for the pose that was characterized by a high binding energy. The docking process was validated (Figure 2) by redocking the native crystallized ligands (HER1; TAK285, HER2; TAK285, HER3; bosutinib, HER4; lapatininb), and the webserver DockRMSD was used to calculate the RMSD between the redocked and crystallized ligands (Bell & Zhang, 2019). The box grid dimensions were determined based on the production of the best proximity to the conformation of the inhibitors from the original x-ray crystal structure. The dimensions were as follows: HER1 (Center |18.544|34.556|4.399, size|37.219|19.332|32.395), HER2 (Center |8.879|1.626|24.569, Size |39.994|37.149|22.890), HER3 (Center|-46.127| 19.229 |21.339, Size |26.413|19.229|21.339), HER4 (center|-39.845|49.482|21.561, Size|39.904|33.612|32.051).\n\nThe RMSD values indicating the difference between crystallized and redocked ligands for HER1, HER2, HER3, and HER4 are 1.125, 2.036, 2.515, and 1.341, respectively. The redocked native ligands have docking scores of -44.35, -41, -35, and -43.5 kJ/mol for TAK285 (HER1 and HER2) bosutinib (HER3), and lapatininb (HER4), respectively.\n\nThe MD simulation process was carried out for the ligand-protein complexes that had given the best-free binding energy scores. The GROMACS 2018.2 package (Abraham et al., 2015) was used along with Charmm27 to parametrize the residues (Brooks et al., 2009). The system was solvated by applying the TIP3P water model (Jorgensen et al., 1983). Swissparm server (http://www.swissparam.ch) were employed to generate the topology and parameters of mulberroside A. A triclinic periodic box (periodic boundary condition) was generated, and the distance between the edge of the box and the complex of protein-ligand was set to 1.0 nm (Fletcher & Powell, 1963). Chloride and sodium ions were added at a concentration of 0.15 M to achieve a neutral system. Energy minimization was run using the steepest descent (Jaidhan et al., 2014) to make the system's potential energy reach -7×105, -5×105, -6×105, and -6×105 kJ/mol for HER1, HER2, HER3, and HER4, respectively. The energy step size was set to 0.01 nm, and a maximum of 50,000 steps was introduced. The temperature represented by the isochoric-isothermal (NVT) ensemble was equilibrated to 310.15 K. The time of equilibration was fixed to 1 ns with a time step of 2 fs. Afterward, isothermal-isobaric (NPT) equilibration was processed for 1 ns with a time step of 2 fs. Further settings of the NPT ensemble were 0.1 nm for both van der waals (VDW) and electrostatic interactions. The modified Berendsen thermostat for temperature coupling (310.15 K), the particle mesh ewald (PME) for calculating the long-range electrostatics, and the Parrinello-Rahman method as a barostat for pressure coupling were also used (Parrinello & Rahman, 1981). The MD simulations were performed for 200 ns with the same settings mentioned for NPT. The free binding energy, VDW interactions, electrostatic interactions, SASA, and the polar solvation energy were carried by the MM/PBSA method (Genheden & Ryde, 2015). RMSD, RMSF, Rg, and the PCA tools that are built-in gromacs software were used to monitor the conformations of the proteins. (Fuglebakk et al., 2012; Lobanov et al., 2008; Balsera et al., 1996). For additional information on the MD simulation parameter, a link is provided in the section of data availability.\n\n\n3. Results and discussion\n\nConcerning the modeling of the missing parts of the receptor kinases, the zDOPE scores for HER1, HER2, HER3, and HER4 are -1.84, -1.94, -1.87, and -1.58, respectively; negative values indicate superior models. Upon docking mulberroside A into these domains, all displayed a high binding affinity; however, HER1 and HER2 displayed the highest affinity, with scores of -40.54 and -40.12 kJ/mol, respectively (Table 1). Compared to the docking scores of the co-crystallized native ligands (mentioned in the caption of Figure 2), the binding energy of mulberroside is very close.\n\nAs shown in Figure 4, five H-bonds were formed between the residues Ser20, Leu77, Met93, Asp155, and Phe156 of HER1 and the ligand. The bonds that were established with Met93 and Phe156 were the strongest of the five, and these bonds remained within the range of H-bond length (which is 2.5-3.5 Å) throughout the entirety of the simulation. HER2 formed four H-bonds by the residues Ser74, Leu76, Leu87, and Asp154. The H-bond formed by Leu87 is the most stable of the four because it did not exceed the length threshold for a strong H-bond while the simulation was being run. The ligand was unsuccessful to build strong H-bonds with HER3; upon docking, the two H-bonds were perfectly with good length (2.57 Å with Leu92 and 2.39 Å with Ser96) but unfortunately, did not survive the MD simulation. The five H-bonds that were recognized within the binding site of HER4 upon the binding of the ligand were with Thr89, Glu99, Arg140, and Asp154 residues. The strongest were the bonds with Asp154 and Glu99, which remained stable during the simulation.\n\nMolecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) calculation was performed for the last 100 frames (the last 1 ns) and the results revealed some relevant outcomes to the docking score except for the interaction with HER2, which was scored -52.16 kJ/mol, the lowest due to low electrostatic interaction (energy) and a high wasting of binding energy in polar solvation energy (Table 2). The binding energy with HER1 is -119.1 kJ/mol, and it is based on strong electrostatic and VDW forces. Even though binding to HER4 required a high polar solvation energy, there was a noticeable offset from the energy gained from VDW, electrostatic, and SASA interactions.\n\nFigure 3 depicts the binding poses of mulberroside A within the four kinases. In the case of HER1, mulberroside A was close enough to interact with both the activation loop (via VDW interaction with Thr154 and two H-bonds with Asp155 and Phe156) and the C α-helix (via VDW interaction with Met65). In HER2, the ligand has successfully interacted through VDW with Met65 of the C α-helix while no direct interaction with the activation loop was observed. In HER3, the ligand was unable to successfully establish direct interaction with the C α-helix; however, Val157 of the activation loop was close enough to the ligand to engage in direct VDW interaction. Concerning HER4, no interaction was found between the activation loop and the ligand. On the other hand, VDW interaction was found with the C α-helix, which was mediated by the residue Met65.\n\nThere were roughly 10 H-bond donors and 11 H-bond acceptor spots in the binding pocket of HER1. 10 donors and 8 acceptors made up HER2. There were 10 donors and 12 acceptors for HER3. 8 donors and 10 acceptors comprise HER4. This led us to deduce that an increase in acceptors within the binding site would have an impact on the binding affinity of mulberroside A. By modifying the responsible moieties, the binding affinity of the ligand could be increased by avoiding clashes (acceptor-acceptor clashes) with Lys44 and Leu87 in the HER3 binding site and with Cys96 and Met92 in the HER4 binding site.\n\nFor MD simulation, the RMSD plot (Figure 5a) over the duration of the simulation showed that the conformation of the TKDs had undergone a very slight shift. When the ligand bound to the TKD of HER1, the protein became more rigid, resulting in less conformational variation than when the enzyme was in its apo state. This conformational variability is caused by one of the terminals in the apo form fluctuating more, as demonstrated by the region 1—10 in the RMSF plot (Figure 5b). Whereas in holo TKD of HER2, region 150—200 was the most variable segment, representing a portion of the binding site and extending into the activation loop. Both the apo and holo TKD of HER2 exhibited behavior that is, to some extent, comparable. Both of them fluctuated more at the beginning of the simulation, but by 90 ns, they had reached a point of convergence. The region 40—60, which included the binding site and a portion of the C -helix, shared the same overtones as the region 150—200. When compared to HER1 and HER2, the TKD of HER3 appeared to have a greater degree of instability in regard to regions 40—60 (C α-helix region) and 150—200 (activation loop region). The apo form and the holo form had the same tone for region 150—200, but the apo form has a different tone for region 40—60 due to the fact that the apo form was more flexible. The last few nanoseconds of simulation could reveal that holo-HER3 became more stable and less prone to conformational variations than apo-HER3. The high RMSD records were the direct result of the extreme fluctuation that occurs at one of the terminals in the TKD of HER4. In the apo form, the fluctuation began at 50 ns, whereas in the holo form, it began at 170 ns. In general, the apo form is very dynamically active in the region of the terminal and the region 150—200, whereas the holo form is characterized by a calm motion to some extent, in contrast to the apo form.\n\nAll of the TKD receptors showed more compactness in unoccupied form rather than occupied form as shown in the radius of gyration plot (Figure 5c), the most noticeable being HER4 which upon binding of the ligand led to a decrease in the compactness by 2 Å which was the largest. The solvent accessible surface area calculation (Figure 5d) showed an expansion (unfolding) in the structures of HER1 and HER4 in the presence of the ligand comparable of its absence, without any remarkable change in HER2 and HER3.\n\nIn all plots, the red and black lines represent holo-HER1 and apo-HER1, respectively. In all plots, the blue and green lines represent holo-HER2 and apo-HER2, respectively. In all plots, the brown and yellow lines represent holo-HER3 and apo-HER3, respectively. In all plots, the purple and grey lines represent holo-HER4 and apo-HER4, respectively.\n\nPCA for the backbone of the receptors was performed and the first three eigenvectors were calculated and evaluated; the first two eigenvectors were taken for consideration as the most dynamical conformations present (Figure 6; Figure 8). Calculation and identification of the essential dynamic (PCA) is a method to monitor the motion of the protein to recognize its biological function. Also, PCA can help in making the trajectories shorter to spot the protein configurational spaces with irregular rhythm. To put it another way, PCA demonstrates, that a relatively small number of modes are sufficient to account for the majority of the fluctuations (Balsera et al., 1996). Fifty frames structures were isolated from each vector (one and two particularly) to facilitate spotting the change in the proteins structure (Figure 8). In terms of HER1, the PCA for the apo-protein showed that the region 164—180 contained the most observable irregular motion, and this region was duplicated in fluctuations caused by the binding of the ligand. Additionally, a portion of the 1—32 region was more pliable in the holo form (Figure 7). In contrast, the RMSF plot of vector one uncovered the fact that a portion of the region 199—232 was more flexible in its apo form than in its holo form. According to the results of the PCA plane analysis for the TKD of HER1, the apo form traveled through more configurational spaces than the holo form did. Whilst the PCA plane for the TKD of HER2 (Figure 6) postulated that both the holo and apo form visited different spaces at most, the significant difference in the dynamics was related to the region around residue 166, as revealed by the RMSF for the vector one, whereas the vector two had not shown any change in its behavior. Mulberroside A did not exert a significant influence on TKD of HER3 due to the fact that the principal plane demonstrated a stability and occupation almost for the same configurational spaces regarding holo and apo-form (Figure 6). As can be seen in the RMSFs of both vector one and vector two, the small change in the conformation that occurred as a result of the ligand's occupancy was primarily attributable to a reduction in the flexibility of the multiple parts that make up region 1—100. According to the principal plane of the apo form, which completely visited different spaces with a very wide transition in the conformation in comparison to the holo-form, TKD of HER4 dramatically changed its conformations upon interaction with the ligand. The change was primarily represented by the C-terminal and the portion between 160 and 180. When these receptors are activated, their C-terminal regions undergo autophosphorylation and act as a binding site for signaling proteins that transfer the signal downstream (Kovacs et al., 2015; Monsey et al., 2010).\n\nConcerning HER4, the fifty frames of vector one for both the apo (blue) and holo (khaki) forms were matched to better visualize the major conformational difference between them. These changes appear to originate from the highly fluctuated region 160—180 and the C-terminus.\n\nThe holo proteins are shown in red, while the apo proteins are shown in black. The docked and undocked HER1 is shown in the upper left square, the docked and undocked HER2 is shown in the upper right square, the docked and undocked HER3 is shown in the lower right square, and the docked and undocked HER4 is shown in the lower left square.\n\nThe C -helix and the activation loop are colored purple, as should be noted. As illustrated by the aligned frames, the degree and pattern of the activation loop's fluctuation differ slightly between the holo and apo forms of HER1, as does the orientation of the C α-helix. Upon the binding of the ligand to HER2, the decrease in HER2's flexibility is readily apparent. The flexibility of HER3's activation loop and neighboring regions appears to be greater than that of other proteins, both in the occupied and unoccupied state. Regarding HER4, the degree and pattern of fluctuation for the C -helix and the activation loop did not change significantly, with the exception of the regions shown in Figure 6.\n\n\n4. Conclusion\n\nThe dearth of chemotherapeutic agents that are still effective against cancers through the tyrosine kinase receptors due to pervasive resistance is a significant issue for the scientific community. Mulberroside A a natural polyphenolic compound has been approved for its capability to bind tightly to these receptors leading to significant changes in the dynamic of the vital parts of their structures. RMSD, RMSF, Rg, and SASA calculations have revealed a change in the conformation, compactness, and the folding pattern of the TKDs upon the binding of mulberroside A. These findings were also supported by the PCA, which elucidated a variation in the dynamic of the backbone of the proteins. Due to the polar properties of the binding site of the human epidermal receptors, the polyphenolic compound mulberroside A perfectly interacted with them. The C α-helix changed in behavior upon the binding of the ligand to the TKD in HER1, HER2, and HER3, which may lead to a change in the catalytic activity of the enzyme. The activation loop is affected as well in HER1, HER2, and HER3 and could lead to a prediction of changing the activation level of these enzymes. Regarding HER4, the region that was affected by the ligand is different and may affect the autophosphorylation process. Broadly speaking, mulberroside A is a promising tyrosine kinase domain inhibitor, and the HERs overexpressed cell-based assay is recommended for further investigation of its in-vitro activity.\n\n\nData availability statement\n\nProtein sequences and structures are taken from Protein Data Bank:\n\n- Accession number: Protein Data Bank, PD3POZ\n\n- Root URL: https://identifiers.org/pdb\n\n- Accession number URL: https://identifiers.org/pdb:3POZ\n\n- Accession number: Protein Data Bank, PD3RCD\n\n- Root URL: https://identifiers.org/pdb\n\n- Accession number URL: https://identifiers.org/pdb:3RCD\n\n- Accession number: Protein Data Bank, PD6OP9\n\n- Root URL: https://identifiers.org/pdb\n\n- Accession number URL: https://identifiers.org/pdb:6OP9\n\n- Accession number: Protein Data Bank, PD3BBT\n\n- Root URL: https://identifiers.org/pdb\n\n- Accession number URL: https://identifiers.org/pdb:3BBT\n\nThe following link contains all molecular dynamic parameter (mdp) files:\n\nhttps://drive.google.com/drive/folders/1zdkRAnzupDKNjmojd7n-vR3EkdZiq5Rd?usp=sharing\n\n\nEthical approval\n\nThe scientific committee of Al-Rafidain University College has approved the publication of this study, which employs only computational aspects and does not involve any human or animal subjects.",
"appendix": "References\n\nAbraham MJ, Murtola T, Schulz R, et al.: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015; 1-2: 19–25. Publisher Full Text\n\nAdams JA: Activation loop phosphorylation and catalysis in protein kinases: is there functional evidence for the autoinhibitor model? Biochemistry. 2003; 42(3): 601–607. PubMed Abstract | Publisher Full Text\n\nBalsera MA, Wriggers W, Oono Y, et al.: Principal component analysis and longtime protein dynamics. J. Phys. Chem. 1996; 100(7): 2567–2572. Publisher Full Text\n\nBell EW, Zhang Y: DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. J. Cheminformatics. 2019; 11(1): 40–49. PubMed Abstract | Publisher Full Text\n\nBrooks BR, Brooks CL III, Mackerell AD Jr, et al.: CHARMM: the biomolecular simulation program. J. Comput. Chem. 2009; 30(10): 1545–1614. PubMed Abstract | Publisher Full Text\n\nFletcher R, Powell MJ: A rapidly convergent descent method for minimization. Comput. J. 1963; 6(2): 163–168. Publisher Full Text\n\nFuglebakk E, Echave J, Reuter N: Measuring and comparing structural fluctuation patterns in large protein datasets. Bioinformatics. 2012; 28(19): 2431–2440. Publisher Full Text\n\nGenheden S, Ryde U: The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin. Drug Discovery. 2015; 10(5): 449–461. PubMed Abstract | Publisher Full Text\n\nHocquet A, Langgård M: An evaluation of the MM+ force field. Molecular Modeling Annual. 1998; 4(3): 94–112. Publisher Full Text\n\nJaidhan BJ, Rao PS, Apparao A: Energy minimization and conformation analysis of molecules using steepest descent method. Int. J. Comput. Sci. Inf. Technol. 2014; 5(3): 3525–3528.\n\nJakalian A, Jack DB, Bayly CI: Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 2002; 23(16): 1623–1641. PubMed Abstract | Publisher Full Text\n\nJorgensen WL, Chandrasekhar J, Madura JD, et al.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983; 79(2): 926–935. Publisher Full Text\n\nJura N, Endres NF, Engel K, et al.: Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell. 2009; 137(7): 1293–1307. PubMed Abstract | Publisher Full Text\n\nKovacs E, Das R, Wang Q, et al.: Analysis of the role of the C-terminal tail in the regulation of the epidermal growth factor receptor. Mol. Cell. Biol. 2015; 35(17): 3083–3102. PubMed Abstract | Publisher Full Text\n\nLobanov MY, Bogatyreva NS, Galzitskaya OV: Radius of gyration as an indicator of protein structure compactness. Mol. Biol. 2008; 42(4): 623–628. Publisher Full Text\n\nMajeed U, Manochakian R, Zhao Y, et al.: Targeted therapy in advanced non-small cell lung cancer: current advances and future trends. J. Hematol. Oncol. 2021; 14(1): 1–20. Publisher Full Text\n\nMaier JA, Martinez C, Kasavajhala K, et al.: ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 2015; 11(8): 3696–3713. PubMed Abstract | Publisher Full Text\n\nMark P, Nilsson L: Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. Chem. A Eur. J. 2001; 105(43): 9954–9960. Publisher Full Text\n\nMechchate H, Costa de Oliveira R, Es-Safi I, et al.: Antileukemic activity and molecular docking study of a polyphenolic extract from coriander seeds. Pharmaceuticals. 2021; 14(8): 770. PubMed Abstract | Publisher Full Text\n\nMonsey J, Shen W, Schlesinger P, et al.: Her4 and Her2/neu tyrosine kinase domains dimerize and activate in a reconstituted in-vitro system. J. Biol. Chem. 2010; 285(10): 7035–7044. Publisher Full Text\n\nPandey KB, Rizvi SI: Plant polyphenols as dietary antioxidants in human health and disease. Oxidative Med. Cell. Longev. 2009; 2(5): 270–278. PubMed Abstract | Publisher Full Text\n\nParida PK, Mahata B, Santra A, et al.: Inhibition of cancer progression by a novel trans-stilbene derivative through disruption of microtubule dynamics, driving G2/M arrest, and p53-dependent apoptosis. Cell Death Dis. 2018; 9(5): 1–18. Publisher Full Text\n\nParrinello M, Rahman A: Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 1981; 52(12): 7182–7190. Publisher Full Text\n\nPettersen EF, Goddard TD, Huang CC, et al.: UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 2004; 25(13): 1605–1612. Publisher Full Text\n\nPieper U, Eswar N, Davis FP, et al.: MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2006; 34(suppl_1): D291–D295. PubMed Abstract | Publisher Full Text\n\nShen MY, Sali A: Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006; 15(11): 2507–2524. PubMed Abstract | Publisher Full Text\n\nSirerol JA, Rodríguez ML, Mena S, et al.: Role of natural stilbenes in the prevention of cancer. Oxidative Med. Cell. Longev. 2016; 2016: 1–15. PubMed Abstract | Publisher Full Text\n\nTrott O, Olson AJ: AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010; 31(2): 455–461. PubMed Abstract | Publisher Full Text\n\nVerdura S, Cuyàs E, Ruiz-Torres V, et al.: Lung cancer management with silibinin: a historical and translational perspective. Pharmaceuticals. 2021; 14(6): 559. PubMed Abstract | Publisher Full Text\n\nWintheiser GA, Silberstein P: Physiology, Tyrosine Kinase Receptors - StatPearls - NCBI Bookshelf. Physiology, Tyrosine Kinase Receptors - StatPearls - NCBI Bookshelf.2021, October 1.Reference SourceReference Source\n\nYang H, Huang S, Wei Y, et al.: Curcumin enhances the anticancer effect of 5-fluorouracil against gastric cancer through down-regulation of COX-2 and NF-κB signaling pathways. J. Cancer. 2017; 8(18): 3697–3706. PubMed Abstract | Publisher Full Text\n\nZhou C, Qian W, Ma J, et al.: Resveratrol enhances the chemotherapeutic response and reverses the stemness induced by gemcitabine in pancreatic cancer cells via targeting SREBP 1. Cell Prolif. 2019; 52(1): e12514. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "153765",
"date": "10 Nov 2022",
"name": "Tahir Ali Chohan",
"expertise": [
"Reviewer Expertise computatinal chemistry",
"Molecular docking",
"MD simulation",
"free energy calculation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPresent manuscript reports Mulberroside A as a pan inhibitor for the tyrosine kinase domains of the HER. In this manuscript the hypothesis is supported by molecular docking and MD simulations. Overall, the work is good and interesting. However, there are multiple things that should be addressed and/or added before publication. I suggest a major revision of manuscript before publication.\nOverall, the writing of the manuscript is good, but some sentences are too long and difficult to understand.\n\nAuthor has performed Molecular docking in which same compound is docked into different isoforms of HER. Despite huge structural similarity in HER-isoforms, the same ligand is showing drastically different interaction pattern. The rational of this difference must be explained.\n\nIn the docking section, only docking-scores and H-bond interactions are discussed. Please also discuss the impact of other non-bonding interactions with nearby residues.\n\nIn MD simulations Figure 5A, RMSD of Apo-HER4 and Holo-HER4 is too high, but no explanation of this fluctuation has been provided.\n\nIn the manuscript, the author has used 100 frames from last 1 ns, but in Figure 5A, RMSD shows unstable MD trajectories during stated duration. Which means the MMGBSA results for HER4 are not acceptable.\n\nAuthor has performed MD simulations for 200ns, but used only 100 frames from last 1 ns which is surprising. Author should use at least 10 ns for MMGBSA analysis.\n\nLast but not the least, author has reported the docking and MD simulation of Mulberroside A against different isoforms but didn’t compare with any benchmark inhibitor of corresponding targets.\nKeeping in view above issues I suggest major revision before indexing of this manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "305229",
"date": "06 Sep 2024",
"name": "Uchechukwu Chibuzo Ogbodo",
"expertise": [
"Reviewer Expertise Cancer research",
"genomics and drug discovery",
"bioinformatics",
"molecular docking and dynamics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have investigated the potential of Mulberroside A as an agent against isoforms of HER binding on the TKD for its inhibitory action through the use of molecular docking and MD analysis and by so doing have done a commendable job. The manuscript is generally well written with promising insights about the potential role of Mulberroside A in cancer treatment. However, a few corrections have been highlighted for the authors to apply to make the manuscript more scientifically sound.\n\n1. The manuscript was well written with excellent grammatical and technical terms used to describe the methods and explain the results. The authors should ensure correct spellings and punctuations where applicable and state full meaning of abbreviated words before using them.\n2. The authors should provide, in context, explanation why they performed MM/PBSA calculation on the last 100 frames in the last 1 ns.\n3. Most of the variations in the MDS of the compound to the HER isoforms are not explained out properly. For example, the decrease in radiation of gyration by 2A in HER4 may be due to some factors, which the authors have not suggested.\n4. The discussion of the results is poorly cited/backed up with references to support their findings.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1201
|
https://f1000research.com/articles/11-1200/v1
|
20 Oct 22
|
{
"type": "Research Article",
"title": "Green campus universities: case studies on problems and prospects",
"authors": [
"Junainah Mahdee",
"Normazalila Abu Bakar",
"Vincent Oh Kim Seng",
"Normazalila Abu Bakar",
"Vincent Oh Kim Seng"
],
"abstract": "Background: Sustainability is a crucial social issue. In recent years, many scholars have suggested that the issue should be tackled at universities because they act as leaders in education, research and innovation. Universities are in a good position to foster progressive action towards global issues within current and future generations. As universities seek to create sustainable campuses, the green campus approach can create opportunities for a cultural paradigm shift, where universities become global leaders in sustainability. There have been various studies related to sustainability issues that include how universities can seek to create sustainable campuses. However, there are some gaps in the research on the “green campus approach” as a way to create sustainable campuses. This paper intends to examine the problems and prospects of creating a green campus university.\n\nMethods: Data collection was conducted using the qualitative method. Structured interviews and observations were conducted via visits to the selected case-study universities as well as panels and discussions with experts in respective ministry and government agencies. All collected data were transcribed before being analysed using the NVivo software and thematic coding. Results: Most universities in Malaysia have plans toward sustainability and the green campus approach. The awareness of going green and creating sustainability on university campuses has gradually increased. A strategic framework is needed as a guideline for creating green campuses in the higher education setting of Malaysia. Conclusions: This study offers new insights into creating green campus universities in Malaysia as a means to create sustainability in higher education settings. The study involved three of the oldest universities in Malaysia. Future research may expand into other universities in Malaysia or internationally.",
"keywords": [
"Green campus",
"Sustainability",
"University",
"Problems",
"Prospects"
],
"content": "Introduction\n\nSustainability is an ultimate goal to many individuals, organisations, industries, and nations in creating a better world. Sustainability can be created in various ways. In most cases, it is driven towards the selected goals of energy saving and reducing emissions. For instance, in the higher education setting, there are many elements that support sustainability such as education, research, infrastructure, technology, finance and campus management system. These elements can be optimised to create a lasting impact.\n\nMany scholars have suggested that the sustainability issue must be challenged at universities. Universities act as leaders in education, research and innovation. This places universities in a good position to foster progressive action and address any global issues within current and future generations. Nevertheless, many scholars have also argued that “becoming and being a sustainable university is not a singular ‘before and after’ event, rather it is a journey or process of transformation that takes place over time”.1\n\nA sustainable campus can be defined as: “[…] a higher education institution […] that addresses, involves and promotes […] the minimisation of environmental, economics, societal and health negative effects in the use of their resources [in] its main functions of teaching, research, outreach and partnership, and stewardship […] to [help] society make the transition to sustainable lifestyles.”2 In a similar vein, a green campus is a campus that combines education and environmental-friendly practices, with the aim to promote eco-friendly practices and sustainability.3\n\nAs universities seek to create sustainable campuses, the green campus approach appears to be an ideal one.\n\nVarious studies have been done related to the sustainability issues including how universities seek to create sustainable campuses. However, there are some gaps in the studies related to the ‘green campus approach’ as a means to create sustainable campuses. The green campus approach leads to opportunities to initiate a cultural paradigm shift, where universities become global leaders in sustainability. This paper intends to examine the problems and prospects of creating a green campus university.\n\nThis research intends to achieve the following objectives:\n\n1. To examine the current state of the green campus approach among Malaysian universities.\n\n2. To assess how effective the green campus approach is.\n\n3. To investigate problems in implementing the green campus practices.\n\n4. To investigate prospects for the future development of green campus practices.\n\nRecently, many scholars have debated on topics such as green campuses and sustainable universities.4,5 The main discussion seems to focus on a single initiative by universities across the world. However, many of these studies are unreliable as they do not have a solid theoretical foundation.6,7 Therefore, the generalisation of results can be difficult as the insights obtained are beyond the limitations of the specific case. However, despite the limitation and challenges towards sustainability such as resource scarcity, green campus projects were still initiated. Politecnico di Bari at Italian public technical university became a reference for many universities.\n\nQuantifiable evidence of sustainable universities has also been reported.5,8 Velazquez et al. (2006)2 propose a model of sustainable universities which are built based on the best practices9–18 from several universities around the world: literature reviews and simultaneous adoption of surveys. The model has evolved into a top-down approach: “a shift from defining the university’s own vision on sustainability and developing a consistent mission so as to lay a foundation for future actions and philosophies that underlie them.”19\n\nAs for promoting the initiatives, universities are urged to leverage from internal drivers and focus on pressures coming from external stakeholders. This includes employee wellbeing, incentives and trainings for professional development. The need to achieve high performance from key people of the organization has also increased, mainly on sustainability issues. Alshuwaikhat and Abubakar (2008) identify three streams of an integrated approach for universities working towards sustainability: “(i) sustainability teaching and research; (ii) implementation of an environmental management system that encompasses both infrastructures (what is called green campus) and day-by-day operations, such as energy efficiency, waste management, and pollution prevention; (iii) public participation and social responsibility, in terms of establishment of partnerships with stakeholders to promote various initiatives that range from spreading knowledge on sustainability to overcoming people’s disparities and discriminations”.20 De Castro and Jabbour (2013) apply this framework to test an Indian university’s sustainability.21 Shi and Lai (2013) suggest another approach to rank and assess higher education institutions’ sustainability,22 applying a model by Velazquez et al. (2006).2\n\nToday, a significant number of higher education institutions (HEIs) and universities have set their goals to the fundamentals of sustainability. This applies to universities’ role in bringing transformation toward sustainability which is also attested to in both the practitioner and scholarly literature.23,24 Typically, their initiatives consist of operational and wider stakeholder outreach activities, as well as academic activities,25,26 such as work on: the re-design of curricula27,28; greening campuses29,30; and building networks in local, regional and international areas to influence behaviour.31,32 Universities have also been expanding and experiencing the means to integrate sustainable thinking. Attempts include activities such as: developing institutional guidelines and frameworks; examining sustainability through campus life experience (e.g., campus as a living lab); and, maintaining programmes of sustainability audits by using, for example, the Auditing Instrument for Sustainability in Higher Education.4,28,33–35\n\nIn spite of such activity, there has been criticism on performance mainly in regards to it being technologically opportunistic and lacking coordinated leadership and coherence,23,36,37 which created debate and unaddressed questions on sustainability, such as the social dimension38 and a lack of enduring effects.39\n\n\nMethods\n\nThe study uses the OECD (2015) Policy Coherence and Green Growth as shown in Figure 1. The notion is that the selected mechanisms and policy interaction in place will give way to lasting impact, as coherence.\n\nThis research was conducted using a qualitative method. Data collection involved semi-structured interviews and observations via visits to the selected universities that promote green campus practices, namely Universiti Putra Malaysia (UPM), Universiti Kebangsaan Malaysia (UKM) and Universiti Malaya (UM). These universities were selected because they were among the earliest universities established in Malaysia. Participants were selected based on their position and seniority in their sustainability roles or within environmental facilities in the universities. They were contacted via email to set an appointment for an interview at their office. The interviews were conducted on a semi-structured basis to allow rich data collection. This enabled the researcher to understand the root cause of problems. Observations made via the campus tour during the visit to the campus included a composting centre and energy saving stickers pasted on all light switches. Interview appointments have also been arranged with panels and discussions with experts in respective ministry and government agencies including the Ministry of Agriculture & Food Industries (MAFI) and Solid Waste Management and Public Cleansing Corporation (SWCorp) for the second phase of the study.\n\nAll collected data were transcribed- before being analysed using the NVivo version 11 software using a free 14-day trial (download available here). Data analysis was conducted by focusing on the problems and prospects of going green in Malaysian universities. Interview transcripts and patterns were identified across different interviews by researchers Normazalila and Vincent. These are summarised in the findings. All transcripts were deidentified during data processing.\n\nEthics and consent\n\nEthical approval was obtained from Universiti Kebangsaan Malaysia (UKM), Universiti Malaya (UM) and Universiti Putra Malaysia (UPM) (ethical approval number: EA1162021). All participants were informed of the objectives and design of the study and a written consent form40 was received from the participants for interviews. Participants were informed they could leave at any time if they wish.\n\n\nResults\n\nThe findings show that most universities in Malaysia have plans towards creating a sustainable approach if not the green campus approach. The awareness of going green and creating sustainability on university campuses has gradually increased across universities between 2016 and 2021. The full transcripts can be found under Underlying data.40\n\nThe main challenges (see Table 1) arising from this came from maintenance, financial/resources, rapid change of technology, mindset/culture, space/logistic/infrastructure, and lack of support from municipal council or expertise.\n\nPromising areas were found to be the commitment from universities, strategies, waste management (recycling, composting), cost saving, awareness, and the generation of income and sustainability. For instance, it is evident that these universities create strategies for sustainable green approaches in the university’s key performance indicators (KPIs).\n\nIn this study, most of the interviewees were males (87%) aged 35-60 years old who had worked for more than 10 years. Based on the qualitative analysis, other than problems and prospects, there were five main themes that emerged from the transcribed data, namely: “energy saving,” “greenery view”, “3Rs (Reduce, Reuse, Recycle)”, “waste management” and “change”. These themes were considered important factors in creating a green campus as they were found in all case study universities’ transcripts. The themes and the frequency they appeared in the transcripts are presented in Table 2.\n\n\nDiscussion\n\nIt is best to discuss further the problems and prospects in this section. Firstly, maintenance is an issue due to some initiatives for going green requiring experts. For example, one of the case-study universities had to hire a special arborist to monitor dying trees surrounding the campus area.\n\nOne of the interviewees said:\n\n“Some of our trees are dying. They aged more than 60 years. We had to hire an arborist to maintain them and that costs us money.”40\n\nJust like many other research projects, funding is a common issue that poses challenges to the green campus initiative. Ironically, rapid changes in technology require these initiatives to keep up to date. This becomes an obstacle to universities as they may have limited funds. Some initiatives such as a composting centre may require a proper infrastructure, space and logistics. The resources, including people to organise and execute the green approach on the campus must be properly identified. If executed poorly, this will result in other failures. Similarly, knowledge management has to be in place in order to encourage knowledge sharing. Lack of awareness, littering, vandalism were other problems caused by a culture of low civic-mindedness. More importantly, despite all these efforts, strong support from all stakeholders must always be present. There were cases at one of the case-study universities where their green initiatives did not receive full support from the local authority (Municipal Council).\n\nOne of the interviewees said:\n\n“It is hard when you didn’t get the support you need. It is even harder when that involves the Municipal Council.”40\n\nWhile the vast majority of people are becoming aware of how important the green campus initiative is to their campuses, there were still incidents of change refusal.\n\nOne of the interviewees said:\n\n“Some people just want to stay in their comfort zone, forever.”40\n\nHowever, there were still some good prospects found in the study. For instance, there were many committed personnels with good leadership in the universities that have utilised their capabilities to filter down the information on green initiatives via a top-down structure. This comes with planning and strategising, steering committee set up as well as sponsorship from industries. The involvement from industries such as Coca-Cola in sponsoring a recycling facility at one of the case-study universities has inspired many other companies to do the same. So far, waste management, recycling activities and composting are the most popular initiatives achieved by these case-study universities. In fact, some of these activities are generating income to the universities to become self-sustaining.\n\nOne of the interviewees said:\n\n“A sustainable university also means self-sustaining - that it is able to maintain itself by independent effort.”40\n\nIn addition to that, there were also many cost saving activities: energy saving, and low CO2 emission campaigns conducted across campuses. In general, the awareness toward green initiatives has gradually increased. Universities have become a reference point for societies and agencies in various events such as seminars, talks and campaigns. The case-study universities have also won some international awards for their greening activities. Hence, it attracts many collaborators to approach them to collaborate further. The achievement awards have brought these universities to a higher level and have enabled further collaborations in the green campus approach.\n\n\nConclusion\n\nCreating green campus facilities is viewed as a means of improving the effectiveness and quality of sustainable development initiatives in higher education. Some key points have been identified that can help campuses to achieve this result effectively, starting with awareness of environmental sustainability, the promotion of the well-being concept among campus communities and engaging them in all its components in order to participate in the change. The green campus initiatives by the case study universities such as waste management, energy saving, reducing pollution and green planting correspond with what was found in the literature reviews as to creating sustainable campus. It is clear that all themes identified in the study play an important role in its success. These themes are common and found in all case study universities. Thus, it suggests that their roles are crucial.\n\nFurthermore, it is a duty of academia to promote societal development, to make use of the campus as a “test field” to implement any innovative methods to be sustainable. The green campus approach must lead to a wider spectrum of sustainability and not limit its focus. The findings from this study are beneficial to any organisation mainly in the higher education sector.\n\nThis study has involved only three case study universities in Malaysia and these are public universities, hence further research could consider involvement from private universities. Comparison can then be made between public and private universities in lining up their priorities toward creating a green campus.\n\n\nData availability\n\nDANS: Green Campus Universities: Problems and Prospects. https://doi.org/10.17026/dans-xrf-82dc.40\n\nThis project contains the following underlying data:\n\n- Green Campus_Case Uni 1.pdf [interview transcript]\n\n- Green Campus_Case Uni 2.pdf [interview transcript]\n\n- Green Campus_Case Uni 3.pdf [interview transcript]\n\n- Green Campus-Findings Report.pdf [list of findings]\n\nThis project contains the following extended data:\n\n- Consent Form_Green Campus.pdf [consent form to be completed by interviewees before interview session]\n\n- Green Campus_demographic data.pdf\n\n- Info Sheet_Green Campus.pdf [brief information on the study and the researcher’s contact details]\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe acknowledge the support from the Multimedia University (MMU) for providing opportunity to publish this article.\n\n\nReferences\n\nMohrman SA, Worley CG: The organizational sustainability journey: Introduction to the special issue. Organ. Dyn. 2010; 39(4): 289–294. Publisher Full Text\n\nVelazquez L, Munguia N, Platt A, et al.: Sustainable university: what can be the matter? J. Clean. Prod. 2006; 14(9): 810–819. Publisher Full Text\n\nToo L, Bajracharya B: Sustainable campus: engaging the community in sustainability. Int. J. Sustain. High. Educ. 2015; 16: 57–71. Publisher Full Text\n\nLozano R, Lukman R, Lozano FJ, et al.: Declarations for sustainability in higher education: becoming better leaders, through addressing the university system. J. Clean. Prod. 2013; 48: 10–19. Publisher Full Text\n\nAmaral LP, Martins N, Gouveia JB: Quest for a sustainable university: a review. Int. J. Sustain. High. Educ. 2015; 16: 155–172. Publisher Full Text\n\nAdomssent M, Godemann J, Michelsen G: Transferability of approaches to sustainabledevelopment at universities as a challenge. Int. J. Sustain. High. Educ. 2007; 8(4): 385–402. Publisher Full Text\n\nKaratzoglou B: An in-depth literature review of the evolving roles and contributions of universities to education for sustainable development. J. Clean. Prod. 2013; 49: 44–53. Publisher Full Text\n\nLozano R, Lukman R, Lozano FJ, et al.: Declarations for sustainability in higher education: becoming better leaders, through addressing the university system. J. Clean. Prod. 2013; 48: 10–19. Publisher Full Text\n\nSharp L: Green campuses: the road from little victories to systemic transformation. Int. J. Sustain. High. Educ. 2002; 3(2): 128–145. Publisher Full Text\n\nUhl C:Process and practice: creating the sustainable university.Barlett PF, Chase GW, editors. Sustainability on campus. Cambridge:The MIT Press;2004.\n\nBrennan J, King R, Lebeau Y: The role of universities in the transformation of societies. Association of commonwealth universities and the Open University;2004. Accessed 20 June 2021.Reference Source\n\nKoester RJ, Eflin J, Vann J: Greening of the campus: a whole-systems approach. J. Clean. Prod. 2006; 14(9–11): 769–779. Publisher Full Text\n\nParker A: Creating a Green campus. Bioscience. 2007; 57(4): 321–321. Publisher Full Text\n\nKrasny ME, Delia J: Natural area stewardship as part of campus sustainability. J. Clean. Prod. 2014; 106: 87–96.Publisher Full Text\n\nMüller-Christ G, Sterling S, van Dam-Mieras R , et al.: The role of campus, curriculum, and community in higher education for sustainabledevelopment — a conference report. J. Clean. Prod. 2014; 62: 134–137. Publisher Full Text\n\nSimpson J: A shared vision for sustainable development in higher education, Higher education funding council for England (HEFCE).2010. Accessed 20 May 2021.Reference Source\n\nYuan X, Zuo J, Huisingh D: Green universities in China — What matters? J. Clean. Prod. 2013; 61: 36–45. Publisher Full Text\n\nWals AEJ: Sustainability in higher education in the context of the UN DESD: a review of learning and institutionalization processes. J. Clean. Prod. 2014; 62: 8–15. Publisher Full Text\n\nBellantuono N, Pontrandolfo P, Scozzi B, et al.:Assessing Resources and Dynamic Capabilities to Implement the “Green Campus” Project. The Contribution of Social Sciences to Sustainable Development at Universities. Cham:Springer;2016; (pp. 213–227).\n\nAlshuwaikhat HM, Abubakar I: An integrated approach to achieving campus sustainability: Assessment of the current campus environmental management practices. J. Clean. Prod. 2008; 16(16): 1777–1785. Publisher Full Text\n\nDe Castro R, Jabbour CJC: Evaluating sustainability of an Indian University. J. Clean. Prod. 2013; 61: 54–58. Publisher Full Text\n\nShi H, Lai E: An alternative university sustainability rating framework with a structuredcriteria tree. J. Clean. Prod. 2013; 61: 59–69. Publisher Full Text\n\nTrencher G, Bai X, Evans J, et al.: University partnerships for codesigning and co-producing urban sustainability. Glob. Environ. Chang. 2014; 28: 153–165. Publisher Full Text\n\nRamos TB, Caeiro S, van Hoof B , et al.: Experiences from the implementation of sustainable development in higher education institutions: Environmental Management for Sustainable Universities. J. Clean. Prod. 2015; 106: 3–10. Publisher Full Text\n\nLuna H, Maxey L: Towards a green academy.Sterling S, Maxey L, Luna H, editors. The sustainable university: Progress and prospects. Oxon:Earthscan from Routledge;2013; pp. 281–303.\n\nShiel C, Filho WL, do Paço A , et al.: Evaluating the engagement of universities in capacity building for sustainable development in local communities. Eval. Program Plann. 2016; 54: 123–134. Publisher Full Text\n\nBeusch P: Towards sustainable capitalism in the development of higher education business school curricula and management. Int. J. Educ. Manag. 2014; 28(5): 523–545. Publisher Full Text\n\nMcCoshan A, Martin S: From strategy to implementation: the second evaluation of the Green Academy programme. The Higher Education Academy;2013. Accessed May 2021.Reference Source\n\nBrinkhurst M, Rose P, Maurice G, et al.: Achieving campus sustainability: topdown, bottom-up, or neither? Int. J. Sustain. High. Educ. 2011; 12(4): 338–354. Publisher Full Text\n\nISCN Secretariat: Best Practice in Campus Sustainability – Latest Examples from ISCN and GULF Schools. Boston, MA:International Sustainable Campus Network (ISCN);2014.\n\nArbo P, Benneworth P: Understanding the regional contribution of higher education institutions: Understanding the regional contribution of higher education institutions: A literature review. OECD/IMHE;2007.\n\nBansal P, Bertels S, Ewart T, et al.: Bridging the Research–Practice Gap. Acad. Manag. Perspect. 2012; 26(1): 73–92. Publisher Full Text\n\nShriberg M: Institutional assessment tools for sustainability in higher education: strengths, weaknesses, and implications for practice and theory. Int. J. Sustain. High. Educ. 2002; 3(3): 254–270. Publisher Full Text\n\nWright TS: Developing research priorities with a cohort of higher education for sustainability experts. Int. J. Sustain. High. Educ. 2007; 8(1): 34–43. Publisher Full Text\n\nMarans RW, Callewaert J, Shriberg M: Enhancing and monitoring sustainability culture at the University of Michigan, Transformative Approaches to Sustainable Development at Universities. Springer;2015; 165–179.\n\nButt L, More E, Avery GC: The myth of the ‘green student’: student involvement in Australian university sustainability programmes. Stud. High. Educ. 2014; 39(5): 786–804. Publisher Full Text\n\nMartin J: Organizational Culture, Wiley Encyclopedia of Management. John Wiley & Sons, Ltd;2015.\n\nBone E, Agombar J: First-year attitudes towards, and skills in, sustainable development. Higher Education Academy/National Union of Students;2011.\n\nCotton DRE, Alcock I: Commitment to environmental sustainability in the UK student population. Stud. High. Educ. 2013; 38(10): 1457–1471. Publisher Full Text\n\nMahdee J: Green Campus Universities: Problems and Prospects. DANS. [Dataset].2021. Publisher Full Text"
}
|
[
{
"id": "197991",
"date": "08 Sep 2023",
"name": "Enrique Orduna-Malea",
"expertise": [
"Reviewer Expertise Enrique Orduna-Malea is an expert in institutional research and higher education",
"together with experience in Bibliometrics",
"research evaluation and university rankings. Núria Bautista is an expert in Sustainability in higher education",
"and Bibliometrics."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe “Green Campus Universities: Case Studies on Problems and Prospects” study investigates the problems and prospects of creating a green campus university using qualitative methods (interviews, panels, and discussions).\nThe topic covered is of interest, the methodology is adequate (however it needs to be more detailed), and there is an overall relation to the scope of publication in the F1000 journal (to the best of our knowledge no other paper has addressed this issue).\nHowever, we find some major issues that should be addressed, which are detailed below:\na) The research gap is not clearly defined. There are other studies that have explored green campuses in the Malaysian context, even with a larger sample (e.g. Anthony Jnr, 2021) and an in-depth analysis (e.g. Najad, Ahmad, and Zen, 2018), even including a barrier analysis in a Malaysian campus (e.g. in Universiti Teknologi Malaysia; Gholami et al., 2020; Hooi, Hassan and Mat, 2012). Therefore, the authors should highlight (and justify) the main novelty and contribution of this paper.\nb) The methodology should be improved and better explained (e.g. reader is not aware of the interviewees). The results are scarce (e.g. are the authors defining a strategic framework? What are the prospects for the future?), and the Discussion section seems more like a continuation of the results, instead of describing the significance of the findings in relation to what was already known about the research problem.\nWe will go slightly more into detail with them in the position-specific comments below.\nAbstract The research gap is not clear enough (Background section). The authors mention that ‘there have been various studies related to sustainability issues that include how universities can seek to create campuses’ (are these studies more theoretical? or descriptive?) but, in the following sentence, the meaning of ‘green campus approach’ is not clear (do authors means operationalization?). Is the purpose to create a framework for creating green campuses? It needs clarification to better guide the readers.\nMoreover, the sample (three universities in Malaysia) should be specified in the Methods section.\nThe Conclusion section is not a real conclusion, but a brief summary.\nKeywords Please, avoid general keywords (e.g. problems, prospects) and be more specific. Maybe 'sustainability barriers' or 'sustainability challenges' (instead of ‘problems and prospects’) could be more appropriate.\nIntroduction and Literature Review It is recommended that the authors contextualize the paper strongly, putting it firmly grounded in the literature. It seems that the authors have carried out this task to a very limited extent. As an example, what does mean ‘the green campus approach appears to be an ideal one’? Is it a model? or a conceptualization?\nMoreover, the author mixes sustainability in general at higher education institutions with green campuses. We suggest better introducing the topic. As an example, mentioning the different system elements in which sustainability is embedded would be more appropriate (e.g. teaching, research, community outreach, assessment and reporting, and campus operations). We do recommend checking the following references:\nLozano, R., Ceulemans, K., Alonso-Almeida, M., Huisingh, D., Lozano, F. J., Waas, T., ... & Hugé, J. (2015). A review of commitment and implementation of sustainable development in higher education: results from a worldwide survey. Journal of cleaner production, 108, 1-18.\nCortese, A. D. (2003). The critical role of higher education in creating a sustainable future. Planning for higher education, 31(3), 15-22.\nConsequently, the paper would benefit from having a paragraph on the different definitions of green campus (e.g., there are different terms like sustainability offices, green offices, green campus, etc.) and how green campuses are evaluated: indicators, rankings (e.g. Greenmetrics ranking that evaluates different indicators), reports (e.g. with directives like GRI), etc.\nLastly, the text requires a better contextualization of the Malaysian region, as there are studies that have already explored similar topics (green campus barriers, different universities from Malaysia, etc.). We do recommend reading the following references:\nAnthony Jnr, B. (2021). Green campus paradigms for sustainability attainment in higher education institutions–a comparative study. Journal of Science and Technology Policy Management, 12(1), 117-148.\nGholami, H., Bachok, M. F., Saman, M. Z. M., Streimikiene, D., Sharif, S., & Zakuan, N. (2020). An ISM approach for the barrier analysis in implementing green campus operations: Towards higher education sustainability. Sustainability, 12(1), 363.\nHooi, K. K., Hassan, F., & Mat, M. C. (2012). An exploratory study of readiness and development of green university framework in Malaysia. Procedia-Social and Behavioral Sciences, 50, 525-536.\nNajad, P. G., Ahmad, A., & Zen, I. S. (2018). Approach to environmental sustainability and green campus at Universiti Teknologi Malaysia: A Review. Environment and Ecology Research, 6(3), 203-209.\nOtherwise, certain statements lack references (e.g. di Bari at an Italian public technical university became a reference for many universities.). In addition, when the authors mention ‘Universities have also been expanding and experiencing the means to integrate sustainable thinking’, are they referring to competencies/pedagogical approaches?\nOther references of interest (not mentioned by the authors):\nTan, H., Chen, S., Shi, Q., & Wang, L. (2014). Development of green campus in China. Journal of Cleaner Production, 64, 646-653.\nResearch objectives We suggest the authors to rethink the research objectives of this study. As the sample is composed of three universities, we believe it could not be generalized to ‘the current state of the green campus among Malaysian universities’, especially when the authors indicate in the literature section, referring to previous literature, that ‘the generalisation of results can be difficult as the insights obtained are beyond the limitations of the specific case’. Moreover, ‘to investigate problems’ or ‘investigate prospects’ seem too ambiguous and unclear research objectives.\nSimilarly, how authors evaluate ‘how effective’ is not properly addressed in this study.\nMethods This section needs to be better explained, as it will benefit the interpretation of the results.\nThe use of the OECD (2015) Policy Coherence and Green Growth (i.e. policies, in Fig. 1) is not clearly justified, and results cannot be directly related to this scheme.\nMore information should be provided on the sample of the three Malaysian universities considered in this study, as the reader should not be aware of the university size, number of students, etc.). In addition to this, why did the authors decide to select those universities? The authors mention in the text that these universities are the older universities in the country, why is this fact relevant in this study?\nRegarding the methods used, more details should be provided about the interviewees. The authors stated they conducted semi-structured interviews. In this sense:\nHow many interviewees did the authors interview? 1, 2, or 3 by university?\n\nWhat is their sustainable-related role?\n\nWhat are their features (e.g. gender, age, etc.)? Few descriptions are provided in the Results, but there is no way to understand the characteristics of the sample.\n\nWhat was the duration of these interviews?\nSimilarly, no details are provided on the experts of Ministry and Government agencies. Having this information is fundamental. Moreover, the authors have two sides: the view of the university professionals and the view of the policymakers. As a suggestion, this could be differentiated or highlighted in the results section.\nA brief description of how the questionnaire was designed would benefit the reader (apart from the transcriptions, already included as a link to the dataset). While some of this information is included in the dataset, it should be distilled and included in the full-text.\nIt is not necessary to mention that the NVivo version was a 14-day trial.\nResults There is a lack of clarity about the origin of the respondents (i.e. whether they were university staff from the three universities or policymakers). It seems the view might be completely different depending on this issue.\nWe believe the challenges (which are more barriers in fact) are a relevant finding of this study. However, it is not clear whether it is common among the three universities. On the other hand, the main themes, which may be the prospects or challenges, are not clear. As an example: change (of what?); mindset change (from whom?), ‘Greenery view’ (what does it mean?), resistance to change (why?).\nRegarding the 3Rs, we do recommend using the more common and advanced Rs (4Rs,... to 9Rs). As regards the challenges pointed out in Table 1, would be of interest to include some kind of quantification, as some challenges would have been mentioned more intensively or frequently than others. However, all topics do appear as equally important.\nAs mentioned before, this section would benefit from knowing the differences between the three institutions (maybe the involvement of industries is only conducted in one university) as well as the different levels.\nDiscussion Please, remove the following sentence, as it is not necessary. You can describe the structure of the paper in advance at the end of the introduction if needed:\n‘It is best to discuss further the problems and prospects in this section’\nThis section seems a continuation of the results and not a discussion actually. As an example. The authors mention ‘lack of funding’, ‘lack of awareness’, and ‘vandalism’... Why are those elements not considered barriers? (See table 1).\nAre these results from the panel/discussion or the semi-structured interviews?\nA limitations section should be included, including potential shortcomings of the method followed, potential generalization of findings, comparison with similar studies carried out in other countries, etc.\nThe few textual mentions from interviewees seem to be cherry-picked, but other comments with different or divergent opinions are not shown (at least, there is no mention of the absence of disparity). The method needs to reinforce objectivity when collecting information from people interviewed.\nConclusions We do recommend the authors answer the four main research questions stated at the beginning of the article.\nResearch objective 1 cannot be answered with the methodology followed; research question 2 has not been actually responded to (and the sample analyzed could not be representative enough), and conclusions from research questions 3 and 4 are too general, needing more distilled discussion.\nWhat really implies the views gathered from the interviewees and the effects of the ‘key points to improve’ on the universities (staff, budget, facilities) should be explored to improve the final sections of the article.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "208790",
"date": "09 Oct 2023",
"name": "Hilma Tamiami Fachrudin",
"expertise": [
"Reviewer Expertise Hilma Tamiami Fachrudin is an expert on architecture",
"urban design",
"green building/campus/city and urban planning"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The research phenomenon is not clear, please add supporting research so that this research is suitable to be carried out\nIn text:\n\"Many scholars have suggested that the sustainability issue must be challenged at universities. Universities act as leaders in education, research and innovation\"\nIt is not explained what the issues in sustainability are, especially at universities. It would be better to add an explanation based on previous studies so that the research phenomenon is clearer\n2. The references used should be able to support the research and be confirmed by the results of the analysis\nThe results of the analysis should be confirmed with the theory explained in the literature review section for example:\n\"In addition to that, there were also many cost saving activities: energy saving, and low CO2 emission campaigns conducted across campuses. In general, the awareness toward green initiatives has gradually increased. Universities have become a reference point for societies and agencies in various events such as seminars, talks and campaigns. The case study universities have also won several international awards for their greening activities. Hence, it attracts many to approach them to collaborate further. The achievement awards have brought these universities to a higher level and have enabled further collaborations in the green campus approach\"\nThis explanation can be confirmed whether or not it is in accordance with previous research which states that activities or campaigns regarding university sustainability must be carried out\n3. In the method section, it does not explain how samples were taken and what approaches or words were used for analysis\nParticipants were selected based on their position and seniority in their sustainability roles or within environmental facilities in the universities\nThis research should explain the level of position or seniority, for example as head of the sustainability university program at UPM, UM or UKM, etc. It should also explain how many people were sampled at each university and what sampling method was used?\n4. The results of the analysis do not answer the research questions in detail\nResearch objectives\nTo examine the current state of the green campus approach among Malaysian universities.\n\nTo assess how effective the green campus approach is.\n\nTo investigate problems in implementing the green campus practices.\n\nTo investigate prospects for the future development of green campus practices\nEach research objective prepared based on the research question should be explained in the conclusion section. For example: how effective is the green campus approach? It should be explained that from the analysis results it was found that the green campus approach is............. and so on for other research objective\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1200
|
https://f1000research.com/articles/11-1199/v1
|
20 Oct 22
|
{
"type": "Research Article",
"title": "Isolation and identification of fluoride sensitive and fluoride resistant Streptococcus mutans strains from dental carries of diabetic patients using conventional methods in Sudan.",
"authors": [
"Nuha M. Elhage",
"S.M. El Sanousi",
"Rami Y Hassab Elrasul",
"Wafa I.Elhag",
"S.M. El Sanousi",
"Rami Y Hassab Elrasul",
"Wafa I.Elhag"
],
"abstract": "Background Dental caries also known as cavities are the most predominant disease today. Streptococcus mutans can form a biofilm on the tooth surface, produce high levels of lactic acid following fermentation of dietary sugars, and are resistant to the adverse effects of low pH, properties which are essential for oral micro biota. The aim of this study was to isolate S. mutans and characterize their antimicrobial properties against sodium fluoride. Fresh dental caries samples were collected from diabetic patients. The isolates were identified based on their acidogenic, biochemical test, and antimicrobial properties. Methods The socio-demographic data collected through a structure designated questionnaire and the biological data collected through sterile cotton swabs. For analysis of data, Statistical Package for Social Sciences software, version 23.0 (IBM SPSS Inc., Chicago, IL) was used. Results\nOnly 32 of the 80 samples (40%) gave a positive growth for S. mutans on MSBA (mitis salivarius bacitracin agar). The sensitivity of the isolates against sodium fluoride was tested by preparing NaF of four different concentrations (80, 125, 250, and 500) mg\\L. Fifty percent of isolates were found to be resistant to NaF at a concentration of 80 mg/L, while 28% were resistant to 125 mg/L NaF, 16%\n\nto 250 mg/L and 3% to 500mg/L NaF. The majority of the participants were aged between 51–60 years (33%), were female (54%), had type II diabetes mellitus (64%), and the duration of their diabetes was less than five years (35%). Conclusions By using the information in this study, we were able to discover strains of S. mutans that are resistant to fluoride. This study can be used as an essential key to study the genetic mutation that occurred.",
"keywords": [
"Streptococcus mutans",
"fluoride resistant",
"dental carries",
"diabetics."
],
"content": "Introduction\n\nBacteria have the ability to form biofilms on the surface of teeth and produce high levels of lactic acid, leading to the emergence of dental caries, which is the most prevalent dental disease today.1 Fluoride (F−) is an inorganic, monatomic anion, which was discovered in 1931. Fluoride-based salts and minerals are important industrial chemicals as fluoride has been widely used in dental products to prevent caries by inhibiting demineralization and increasing remineralization. Furthermore, it affects bacterial growth by directly inhibiting metabolic activity through inhibition of enolase and ATPase enzymes, leading to a reduction in sugar uptake and glycolysis.2 When the PH is 7, fluoride is in an ionic state, it cannot enter the bacterial cell membrane. Cariogenic bacteria ferments carbohydrates, leading to the formation of an acidic PH. Fluoride then binds to a hydrogen atom to form a HF (hydrogen fluoride) compound which can enter the bacterial cell membrane and interfere with the ability of the bacterium to tolerate acid. Consequently, the antimicrobial action of fluoride is known to be pH-dependent.3\n\nOne of the risks of prolonged use of fluoride is the occurrence of bacterial resistance. Fluoride resistant strains have been discovered in many studies, for example Streptococcus mutans can gain fluoride resistance either by acquiring resistance genes or through developing phenotypically, altering their physical appearance on the culture media containing flouride.4 When comparing the resistant strains with the wild type, S. mutans UA130 and S. mutans U159, they were found to be less cariogenic. It has been discovered in many clinical studies that fluoride resistant strains are created in the laboratory by subculturing colonies many times the presence of 400–600 mg/L fluoride.4 Microbes are excellent at adapting to stressful situations which is why antibiotic resistance is such a significant problem today.\n\nDiabetes mellitus (DM) is a metabolic disorder characterized by chronic hyperglycemia and disturbances in the metabolism of carbohydrates, fats, and proteins.5 Poorly controlled DM has been associated with an increased susceptibility to oral infections including periodontal disease.6 The hypothesis of this research is that S. mutans develop fluoride resistance among Sudanese diabetic patients with dental caries.\n\nThe objective of this study is to isolate and identify S. mutans and characterize its antimicrobial properties against different concentrations of sodium fluoride and to estimate the prevalence of S. mutans among diabetic patients with dental caries in Sudan.\n\n\nMethods\n\nThis was a descriptive, cross-sectional study involving 80 diabetic patients aged from 19 to 80 years old which was conducted in Khartoum-Sudan from patients attending diabetics center in Bahari and Army dental clinic, between September 2019–June 2022. The patients were 46% male and 54% female.\n\nThe samples collected from dental caries by using sterile cotton swap which was well rotated in the teeth cavity after mouth wash, from patients in the dental clinic and the diabetic’s center. The sample was inoculated onto mitis salivarius bacitracin agar containing 0.2 units of bacitracin and 20% of sucrose, as a selective media for S. mutans and onto chocolate agar. To detect alpha (partial) hemolysis of streptococcus mutans, they were incubated in a candle jar (10% CO2) at 37°C from 24–48 hours. The purified isolates were then sub-cultured on appropriate slopes prepared from brain heart infusion agar medium for 24 hours at 37°C and stored in a refrigerator at 4°C for further identification. All isolates were Gram stained according to gram stain protocol7 and examined by microscopy using an 100× magnification oil immersion lens to study their staining properties and their shape and arrangements were recorded.\n\nThe isolates were identified based on their biochemical production of catalase enzyme by using 3% hydrogen peroxide (H2O2).8 A sterile wooden stick was used to transfer a small amount of a colony to the surface of a clean and dry glass slide. A drop of 3% H2O2 was placed onto the colony. Evolution bubbles were not observed. The acidogenic sugar fermentation (glucose, sucrose, mannitol, and lactose)9 solutions were prepared by dissolving 2 g peptone powder in one liter of distilled water, and then sterilized by autoclaving at 121°C for 15 minutes. Twenty-five mL of sterile 0.2% bromocresol purple solution was added to 950 mL of peptone water. Sugar solutions were prepared by dissolving 10 g of each sugar in 100 mL of distilled water and sterilized by autoclaving at 100oC for 10 minutes. Twenty-five mL of sugar solution was then added to peptone water indicator solution and poured into a sterile test tube. A few colonies from a pure culture of the test organism were transferred to the test tube containing the sugar solution and peptone water using a sterile transfer lobe, the sets of inoculated test tubes were incubated in an aerobic incubator for 24 hours at 37oC. The antimicrobial properties against optochin, using a disc impregnated with 5 μg of optochin were applied to 5% sheep blood ager plate, streaked with the organism being tested. After overnight incubation at 37°C in a 10% CO2 atmosphere, isolates either displayed a zone of inhibition or did not. The method used to detect optochin sensitivity was the Kirby-Bauer disc diffusion method.10\n\nData was collected using a structured questionnaire for socio-demographic data, while the samples were collected using sterile cotton swabs. Data was analyzed using Statistical Package for Social Sciences software, version 23.0 (IBM SPSSInc., Chicago, IL, SPSS (RRID:SCR_002865)). Initially, all information was gathered via questionnaires then coded into variables. Both descriptive and inferential statistics involving Fishers’ exact test and binary logistic regression were used to present the results. A p-value of less than 0.05 was considered statistically significant.\n\n\nResults and discussion\n\nFrom the 80 participants caries samples were collected from, 37 were male (46%) and 43 were female (54%), the majority were aged over 50, and 51 participants (64%) had type II DM while 29 (36%) had type I DM. Thirty-four patients (43%) had good control of their diabetes according to their HbA1C levels. Seventy-one (89%) patients do not regularly follow up with the doctor for 6 months or more and 34 (43%) reported cleaning their teeth once per day and 75 (94%) use toothpaste. Sixty-nine (86%) of the patients do not have a history of heart disease, 64 (80%) show the invasion of tooth caries, and 60 (75%) have not used antibiotics for 6 months before the sample was collected. The sample was cultured and 68 (85%) had a positive growth while only 12 (15%) had a negative growth. S. mutans grew on MSA medium containing bacitracin inoculated with samples from 32 (40%) patients and 48 (60%) patients had samples which showed growth for organisms other than S. mutans.\n\nTo assess the sensitivity of the isolates to sodium fluoride, the technique stated by Ying et al. (2018)4 was used to prepare four different concentration of sodium fluoride (80, 125, 250, and 500 mg/L). Half of the isolates were found to be resistant to 80 mg/L NaF, as displayed in Figure 1.\n\n* p value < 0.05, thus considered statistically significant.\n\nPatients who had suffered with DM for longer time, were more likely to have a S. mutans infection AOR (adjustment odds ratio): 2.233 (CI 95%; 1.272–3.920) times statistically significant with a p value of 0.005<0.05.\n\nPatients with previous antibiotic use were more likely to have S. mutans infections, with AOR: 3.413 (CI95%; 1.048–11.117), which is statistically significant with a p value of 0.042 which is <0.05. All other predictors contributed to the prediction of an S. mutans infection but had statistically insignificant p values of >0.05.\n\nFluoride concentrations in oral hygiene products vary from 250 to 1500 ppm the fluoride concentration remaining in dental biofilms after the application of these products was reported to be only between 1.14 and 5.7 ppm.11 The biofilm fluoride level may induce resistance in oral bacteria when the pH of the environment remains low for an extended period of time.12 In the present study, we used fluoride salt to investigate its antimicrobial activities against isolated S. mutans.\n\n\nConclusion\n\nIt can be concluded that 40% of the 80 samples collected showed the isolation of Streptococcus mutans. There was a significant correlation between having an S. mutans infection and patients suffering from diabetes mellitus disease for more than 20 years and with previous antibiotic use. Fifty percent of isolated S. mutans were found to be resistant to 80 ppm sodium fluoride, while 28% were resistant to 125 ppm NaF, 16% to 250 ppm and 3% to 500 ppm NaF.\n\nIt’s necessary to create a protocol for a superior examination of study results, which can improve the identification of fluoride-resistant strains. Further studying fluoride resistant S. mutans may highlight novel molecular methods to study the prevalence of fluoride resistance in the oral bacterial community. The role and importance of these mutations on gene regulation in the presence or absence of fluoride will be the subjects of follow-up studies.\n\n\nEthical approval\n\nEthical approval was obtained from ministry of health – Khartoum state general administration of strategic and information innovation, developments and scientific research. Serial number: KMOH-REC-018.2-2022\n\n\nConsent\n\nWritten informed consent for publication of the patients’ data was obtained from the participants.\n\n\nData availability\n\nDryad: Isolation and Identification of Fluoride Sensitive and Fluoride Resistant Streptococcus mutans Strain from Diabetics Dental Carries raw data, https://doi.org/10.5061/dryad.g1jwstqtq.13\n\nThe project contains the following underlying data:\n\n- README_datadrnuha.sav (sav, raw data).\n\n- the antimicrobial effect of fluoride against streptococcus mutans (figure.docx)\n\n- README_raw_data.xlsx (excel sheet, raw data).\n\nDryad: STROBE checklist for Isolation and Identification of Fluoride Sensitive and Fluoride Resistant Streptococcus mutans Strain from Diabetics Dental Carries raw data, https://doi.org/10.5061/dryad.g1jwstqtq.13\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgments\n\nAll thanks, appreciation, and gratitude to all those who helped me to complete this research A great thanks to Miss Temaz Tag Alsir, Manasik and Haggier for their standing throughout this research. A great thanks to everyone in the microbiology department of medical laboratory science at the University of Medical Science and Technology and Alneelain University.\n\n\nReferences\n\nSilk H: Diseases of the mouth. Prim. Care. March 2014; 41(1): 75–90. PubMed Abstract | Publisher Full Text\n\nJohn D, Featherstone B: Restorative Dentistry, Box 0758, University of California at San Francisco, 707 Parnassus Avenue, San Francisco.14 February 2007. Publisher Full Text\n\nHoelscher GL, Hudson MC: Department of Biology, University of North Carolina at Charlotte, Charlotte, NC 28223, USA Characterization of an Unusual Fluoride-Resistant Streptococcus mutans isolate.Publisher Full Text\n\nLiao Y, Yang J, Brandt BW, et al.: Genetic Loci Associated With Fluoride Resistance in Streptococcus mutans. Front. Microbiol. 2018; 9: 3093. PubMed Abstract | Publisher Full Text\n\nAlberti KG, Zimmet PZ: Definition, diagnosis and classification of diabetes mellitus and its complications. Part 1: diagnosis and classification of diabetes mellitus provisional report of a WHO consultation. Diabet. Med. 1998; 15: 539–553. PubMed Abstract | Publisher Full Text\n\nLim LP, Tay FB, Sum CF, et al.: Relationship between markers of metabolic control and inflammation on severity of periodontal disease in patients with diabetes mellitus. J. Clin. Periodontol. 2007 Feb; 34(2): 118–123. PubMed Abstract | Publisher Full Text\n\nCoico R: Gram staining. Curr. Protoc. Microbiol. 2006 Feb; (1): A-3C. Publisher Full Text\n\nReiner K: Catalase test protocol. American Society for Microbiology. 2010 Nov 11; 1–6.\n\nReiner K: Carbohydrate fermentation protocol. Energy. 2012; 11: 12.\n\nHudzicki J: Kirby-Bauer disk diffusion susceptibility test protocol. American Society for Microbiology. 2009 Dec 8; 15: 55–63.\n\nDuckworth RM, Morgan SN, Murray AM: Fluoride in saliva and plaque following use of fluoride-containing mouthwashes. J. Dent. Res. 1987; 66: 1730–1734. PubMed Abstract | Publisher Full Text\n\nCai Y, Liao Y, Brandt BW, et al.: The fitness cost of fluoride resistance for different streptococcus mutans strains in biofilms. Front. Microbiol. 2017; 8: 1630. PubMed Abstract | Publisher Full Text\n\nElhage N, Mohamed S, Sanousi E, et al.: raw,excel file, Dryad, Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "205028",
"date": "21 Sep 2023",
"name": "Essie Octiara",
"expertise": [
"Reviewer Expertise Pediatric dentistry",
"early childhood caries",
"cariology",
"S. mutans",
"fluoride"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: it is not explained about the type of data analysis that being used.\nResearch methods:\nThe minimum sample is not explained because from the 80 patients only 85% (68 people) were research subjects (S. mutans that could be isolated).\n\nInclusion criteria: are there only diabetic patients for this study without any specific criteria so there are no exclusion criteria?\n\nThe research method needs to be added to the explanation that each isolation of S. mutans from each patient was tested with various concentrations of NaF (80 ppm, 125 ppm, 250 ppm, 500 ppm). A brief explanation of the research results should be transferred to the research method.\nResearch results and discussion:\nThe results of the study only compared S. mutans isolation with demographic characteristics. If you can add an analysis of S. mutans resistance to fluoride by type of diabetes, duration of diabetes, use of antibiotics or other demographic factors that may influence resistance to fluoride (based on literature).\n\nThe discussion needs to be deepened because it is very minimal in writing and references need to be added to deepen the discussion better\nBibliography\nNeed to add to the bibliography.\n\n61% of the bibliography is over 10 years old, please replace more with those under 10 years old.\nJournal criteria: ordinary Recommendation: needs to be changed majorly if it is to be indexed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1199
|
https://f1000research.com/articles/11-512/v1
|
12 May 22
|
{
"type": "Research Article",
"title": "Effectiveness of forest honey (Apis dorsata) as therapy for ovarian failure causing malnutrition",
"authors": [
"Erma Safitri",
"Hery Purnobasuki",
"Muhammad Thohawi Elziyad Purnama",
"Shekhar Chhetri",
"Hery Purnobasuki",
"Muhammad Thohawi Elziyad Purnama",
"Shekhar Chhetri"
],
"abstract": "Background: Malnutrition is a crucial issue that contributes to approximately 45% of deaths among children under 5 years old and even >50% of deaths when accompanied by diarrhea. Several studies have stated that the use of honey can overcome cases of infertility due to malnutrition. Methods: An infertile female rat model with a degenerative ovary was induced with malnutrition through a 5-day food fasting but still had drinking water. The administration of (T1) 30% (v/v) and (T2) 50% (v/v) forest honey (Apis dorsata) were performed for ten consecutive days, whereas the (T+) group was fasted and not administered forest honey and the (T−) group has not fasted and not administered forest honey. Superoxide dismutase, malondialdehyde, IL-13 and TNF-α cytokine expressions, and ovarian tissue regeneration were analyzed. Results: Antioxidant activity (SOD) was significantly different (p<0.05) in T1 (65.24±7.53), T2 (74.16±12.3), and T− (65.09±6.56) compared with T+ (41.76±8.51). Oxidative stress (MDA) was significantly different (p<0.05) in T1 (9.71±1.53), T2 (9.23±0.96), and T− (9.83±1.46) compared with T+ (15.28±1.61). Anti-inflammatory cytokine (IL-13) expression was significantly different (p<0.05) in T1 (5.30±2.31), T2 (9.80±2.53), and T− (0.30±0.48) compared with T+ (2.70±1.57). Pro-inflammatory cytokine (TNF-α) expression was significantly different (p<0.05) in T1 (4.40±3.02), T2 (2.50±1.65), and T− (0.30±0.48) compared with T+ (9.50±1.78). Ovarian tissue regeneration was significantly different (p<0.05) in T− (8.6±0.69) and T2 (5.10±0.99) compared with T1 (0.7±0.95) and T+ (0.3±0.67). Conclusion: The 10-day administration of 50% (v/v) forest honey can be an effective therapy for ovarian failure that caused malnutrition in the female rat model.",
"keywords": [
"forest honey",
"ovarian failure",
"malnutrition",
"oxidative stress",
"inflammation"
],
"content": "Introduction\n\nMalnutrition in the form of protein–energy malnutrition (PEM) is a challenge in developing countries, including Indonesia. 1 Malnutrition is the imbalance between intake and nutritional needs, resulting in a decrease in body weight, composition, and physical function. 2 Furthermore, malnutrition contributes to approximately 45% of deaths among children under 5 years old. 3 PEM accompanied by diarrhea has been reported to contribute >50% of deaths among children. 4 In experimental animals, PEM causes infertility due to intestinal 5 and liver degeneration, 6 which may progress to testicular 7 – 9 and ovarian degeneration. 10\n\nMalnutrition is closely related to oxidative stress, which is an increase in reactive oxygen species (ROS) that causes damage to cellular components, such as DNA, proteins, and lipids. 11 The binding between ROS and lipids can lead to increased levels of malondialdehyde (MDA), a biomarker of increased lipid peroxidation. 12 The increased ROS in malnutrition conditions can cause a decrease in the amount of antioxidants in the body. One of the antioxidants that play a significant role in protection from ROS reactions is superoxide dismutase (SOD). 13 SOD is an essential enzyme (scavenger) that plays a role in preventing the oxidation process. Decreased antioxidant protection, such as SOD, can lead to various disorders in the form of an immunological response, such as an excessive inflammatory process.\n\nInflammation is one of the responses of the body’s immune system in recognizing and eliminating harmful components, thereby promoting the healing process. The inflammatory process involves communication between various components in the body. Several components involved in the inflammatory process include tumor necrosis factor alpha (TNF-α) and interleukin 13 (IL-13). TNF-α and IL-13 are cytokines that are formed in response to inflammatory reactions. The two cytokines act antagonistically. TNF-α is a pro-inflammatory cytokine that plays a role in systemic inflammation and one of the cytokines that complete the acute phase reaction, 14 whereas IL-13 is an anti-inflammatory cytokine. TNF-α is primarily produced by activated macrophages although can be produced by other cells. The anti-inflammatory response is controlled mainly by IL-13, which is a multifunctional cytokine. 15\n\nAccording to several previous studies, PEM can be overcome by monofloral honey administration. 7 – 9 , 16 Honey has various benefits both as a food source and for medicinal purposes, including antibacterial, anti-inflammatory, anti-apoptotic, and antioxidant properties. 17 Honey consists of various compounds, which are divided into major and minor compounds. The major compounds are carbohydrates in the form of monosaccharides (fructose and glucose), disaccharides (sucrose, maltose), and oligosaccharides; whereas the minor compounds are amino acids, enzymes, vitamins, minerals, and polyphenols. 17 , 18 Honey is grouped into two types: monofloral (derived from one type of flower) and polyfloral (more than one type of flower). 19\n\nForest honey from Apis dorsata bees is one example of polyfloral honey that can be found in Indonesia. The phenolic and flavonoid content of forest honey (A. dorsata) is a strong combination as an antioxidant. 20 The antioxidants possessed by forest honey (A. dorsata) have a higher value than those of monofloral honey.\n\nSome studies have been performed regarding the administration of honey. 5 , 16 , 21 , 22 Homing and differentiation of stem cells were expected in the honey administration in the animal model with ovarian failure. 5 Stem cells are derived and differentiated by culture originating from the body itself, facilitating follicle regeneration in the ovary. Ovarian regeneration can be proven by molecular and microscopic studies. 23 , 24 The microscopic histological appearance will reveal ovarian tissue regeneration at the molecular level, wherein several expressions, such as cluster of differentiation like CD45+ and CD34+ from biomarker of hematopoietic stem cells, 5 , 25 expression of transforming growth factor-β, 21 growth differentiation factor-9, 26 , 27 vascular endothelial growth factor, and granulocyte colony-stimulating factor of the ovary, were evident. 21 , 26 , 27\n\nHoney has properties that promote wound healing from several antibacterial agents, stimulate the growth of wound tissue, and facilitate an anti-inflammatory response, which rapidly reduces pain, edema, and exudate production. 28 Therefore, it is necessary to know about the effect of forest honey (A. dorsata) on SOD and MDA levels, TNF-α and IL-13 expressions, and ovarian tissue regeneration in female white rats (Rattus norvegicus) experiencing PEM.\n\n\nMethods\n\nThis study was approved by the ethical committee through the Ethical Clearance institution (Komisi Etik Penelitian), Animal Care and Use Committee, Faculty of Veterinary Medicine, University of Airlangga, Surabaya, Indonesia (Number 065-KE).\n\nOvarian tissue degeneration was achieved by performing a study using a female rat model. Very healthy female Wistar rats (R. norvegicus) with a body weight of 250–300 g each, 8–10 weeks old, were used in this case study. The female rats went without food for 5 days, although they were provided with water. 5 , 10 The rats were placed in individual plastic cages in the Experimental Animal Laboratory at the Veterinary Medicine Faculty, Universitas Airlangga. Experimental animal laboratories were designed with adequate air circulation, humidity and temperature regulation. In addition, the use of litter and counterflow replacement was performed to ensure eligibility during the study.\n\nA total of 40 rats were divided into four groups as follows: normal rats, without honey (T−); infertile rats, without honey (T+); infertile rats administered 30% (v/v) honey for 10 days (T1); and infertile rats administered 50% (v/v) honey for 10 days (T2).\n\nForest honey (A. dorsata) from the forest in Batu Malang East Java, Indonesia, was used in this study. MDA and SOD levels, TNF-α and IL-13 expressions, and subsequent folliculogenesis and ovarian tissue regeneration were analyzed. The analysis of MDA and SOD levels was performed using the ELISA method. 29 , 30 Pro-inflammatory and anti-inflammatory properties of TNF-α 14 and IL-13 15 expressions were analyzed using the immunohistochemical (IHC) method in the ovarian tissue. 5 , 10 Folliculogenesis was indicated by an increase in the follicle De Graaf expression 31 and ovarian tissue regeneration using routine hematoxylin and eosin (H&E) staining. 10\n\nThe analysis of MDA and SOD levels in serum was performed using the double-antibody sandwich ELISA kit. 29 , 30 The working principle of this kit is identified by precoated capture antibody (anti-rat MDA monoclonal antibody/anti-rat SOD monoclonal antibody) and detection antibody (biotinylated polyclonal antibody) simultaneously. Furthermore, staining was performed using a substrate of 3,3′,5,5′-tetramethylbenzidine (TMB). TMB reacts through peroxidase activity to form a blue color, and the addition of a stop solution causes a yellow color change. Color intensity has a positive correlation with the target analyte quantity being analyzed.\n\nSerum sample preparation was performed by cooling the extracted blood at 4°C for one night. The serum from the blood sample that has been coagulated and contained in the top layer was then separated and centrifuged for 10 min at a speed of 1,000–3,000 rpm. The supernatant formed can be directly used in ELISA testing or stored (lasts for 1–3 months if stored at a temperature of −20°C to −80°C).\n\nThe ELISA test was performed by preparing wells from the ELISA plate of serum samples, standards, and blanks. Initially, 100 μL of serum and blank samples were added to each well and incubated at 37°C for 90 min, and the ELISA plate was subsequently washed two times using a 350-μL wash buffer in each well. After, the liquid was removed by placing the blotting paper on the ELISA plate to remove the liquid. Then, a 100-μL biotinylated polyclonal antibody was added to each well and incubated at 37°C for 30 min. The ELISA plate was then washed five times and dried using the abovementioned method. Next, 100 μL of TMB was added to each well and incubated at 37°C until a color gradient was formed with a maximum time of 30 min. Then, 100 μL of stop solution was added, and the ELISA plate was subsequently read at 450 nm optical density. ELISA plate readings were immediately performed.\n\nIHC analysis was performed to determine the expressions of TNF-α 14 and IL-13. 15 First, an incision was made through the ovarian tissues transversely from paraffin blocks. IHC techniques were performed using monoclonal antibodies anti-TNF-α and IL-13. TNF-α and IL-13 expression analyses were performed using a light microscope with a magnification of 400×. TNF-α and IL-13 expressions were indicated by the number of cells with brownish discoloration due to DAB-chromogen in each incision. 32 The five fields of view were assessed for each slide through a scoring system. The following IHC scoring system was used: IHC score=A×B, wherein A denotes the wide percentage of expressions and B is the intensity of the chromogen color (Table 1). 33\n\nThe identification of follicle De Graaf and ovarian tissue regeneration was performed using light microscopy examination. 31 Histological preparations were performed, including fixing the rat ovary in 10% buffer formalin; dehydrating using a series of alcohol, that is, 70%, 80%, 90%, and 96% (absolute); and clearing of the rat ovary in xylene solution. The tissues were infiltrated with liquid paraffin, which is an embedding agent. Sectioning was performed with a microtome that could be set with a distance of 4–6 μm, and the sections were placed on a slide. The embedding process must be reversed to get the paraffin wax out of the tissue and allow water-soluble dyes to penetrate the sections. Therefore, before any staining can be performed, the slides are “deparaffinized” by running them through xylenes to alcohols to water. Routine H&E staining was used. The stained section was subsequently mounted with Canada balsam, and a coverslip was placed. Analyses and identifications of follicle De Graaf and ovarian regenerations are based on the histological measures of the normal tissue. 5\n\nThe MDA concentration and SOD activity, TNF-α and IL-13 expressions, and growing follicle count were statistically analyzed using SPSS 15 (SCR_016479) for Windows XP with the level of significance set at 0.05 (p=0.05) and the confidence level at 99% (α=0.01). Steps of comparative hypothesis tests are as follows: test data normality with the Kolmogorov–Smirnov test, homogeneity of variance test, analysis of variance factorial, and post hoc test (least significant difference test) using the Tukey HSD 5%.\n\n\nResults\n\nThe effectiveness of forest honey (A. dorsata) as a therapy for ovarian failure that caused malnutrition was based on the following: increased antioxidant enzyme activity, such as SOD, and decreased oxidative stress concentration, such as MDA; increased anti-inflammatory cytokine expression, such as IL-13, and decreased pro-inflammatory cytokine expression, such as TNF-α; and ovarian tissue regeneration with increased growing follicle count.\n\nThe antioxidant activity was analyzed using the ELISA double-antibody sandwich method and was based on increased SOD and decreased MDA concentration as oxidative stress. The SOD analysis showed a significant difference (p<0.05) in T1 (65.24±7.53), T2 (74.16±12.3), and T− (65.09±6.56) compared with T+ (41.76±8.51) (Table 2). The MDA analysis showed a significant difference (p<0.05) in T1 (9.71±1.53), T2 (9.23±0.96), and T− (9.83±1.46) compared with T+ (15.28±1.61) (Table 2).\n\nThe anti-inflammatory expression was analyzed using the IHC method and was based on increased IL-13 cytokine expression and decreased TNF-α pro-inflammatory cytokine expression. The IL-3 analysis showed a significant difference (p<0.05) in T1 (5.30±2.31), T2 (9.80±2.53), and T− (0.30±0.48) compared with T+ (2.70±1.57) (Table 2, Figure 1). The TNF-α analysis showed a significant difference (p<0.05) in T1 (4.40±3.02), T2 (2.50±1.65), and T− (0.30±0.48) compared with T+ (9.50±1.78) (Table 2, Figure 2).\n\nIHC = immunohistochemical.\n\nIHC = immunohistochemical.\n\nOvarian tissue regeneration was analyzed using the H&E method and was based on the increased growing follicle count. The growing follicle count analysis showed a significant difference (p<0.05) in T− (8.6±0.69) and T2 (5.10±0.99) compared with T1 (0.7±0.95) and T+ (0.3±0.67) (Table 2, Figure 3).\n\nA. Fertile female, negative control group (T−): shows growing follicle (); B. Infertile female, positive control group (T+): congestion of the ovary () and widely hemorrhagic (), also visible hemosiderin () due to blood cell hemolysis (brownish-yellow color) with fibrin deposition (), indicating that chronic congestive has occurred; C. Infertile female with 30% honey v/v group (T1): ovary does not regenerate, congestion appears along the hemosiderin expression and remains widely hemorrhagic; D. Infertile female with 50% honey v/v group (T2): ovaries begin to regenerate, making it appear intact; hemorrhage and congestion still appears in some areas with growing follicles.\n\n\nDiscussion\n\nThe increased antioxidant activity and decreased oxidative stress were analyzed using the ELISA double-antibody sandwich method. The increased anti-inflammatory and decreased pro-inflammatory expressions were analyzed using the IHC method, and ovarian tissue regeneration was analyzed using the H&E staining method.\n\nThe increased antioxidant activity, such as SOD in T2, can reduce oxidative stress, which allows the MDA concentration to decrease (Table 2). SOD is a type of essential enzyme that functions as a scavenger against oxidative stress that occurs in the body. Various factors can affect the level and activity of antioxidants in dealing with oxidative stress. Physiological conditions, as well as environmental and genetic conditions, can affect the composition and amount of antioxidants. 34 Some researchers say that administering food supplements can also increase the amount of antioxidants in the body. The antioxidants derived from exogenous sources, such as those from food, also have an important role in increasing the endogenous antioxidant activity and neutralizing oxidative stress. 35\n\nDecreased antioxidant activity is a sign of oxidative stress conditions. These results are in agreement with the results of another study, which states that nutritional deficiencies can affect the defense system of several scavenger enzymes, such as SOD, glutathione peroxidase, and catalase, in the form of a decreased activity in overcoming oxidative stress. 36 Similar results were also found, which stated that antioxidant levels can be significantly decreased (p<0.05) under certain conditions, such as malnutrition. 37\n\nBased on the results of this study (Table 2), significant differences were observed in the T+ group test compared with T1 and T2. The group of infertile rats without forest honey (T+) had a lower activity value and was significantly different (p < 0.05) than the group of infertile rats treated with forest honey (T1 and T2). The significantly higher SOD activity values in the T1 and T2 groups indicated that forest honey therapy could increase the SOD activity in infertile female white rats due to malnutrition. The results of this study are consistent with those of another study conducted in 2003, wherein the results can prove that the application of natural ingredients of honey can increase the antioxidant activity in the recipient’s blood plasma. 38\n\nMDA is a marker of oxidative stress. An increase in MDA indicates an increase in oxidative stress. Malnutrition is one of the causes of oxidative stress. The results of this study are consistent with those of other studies, which state that a lack of nutritional intake can be the cause of oxidative stress, 7 which ultimately leads to an increase in MDA concentrations. 39\n\nBased on the statistical analysis of the results of this study (Table 2), a significant difference was noted in the MDA concentration (p<0.05) in T+ compared with T1 and T2. The group of infertile rats without forest honey (T+) had a higher and significantly different MDA concentration than the group of infertile female rats treated with forest honey (T1 and T2), indicating a decrease in oxidative stress conditions in rats administered with forest honey. The results of this study are supported by the results of other studies, stating that honey has an antioxidant property, through a significant decrease in the MDA concentration compared with controls without honey. 40 , 41\n\nFurthermore, regarding the immune response based on the anti-inflammatory cytokine IL-13 expression, the highest IL-13 expression was found in the T2 treatment group (infertile rats administered with forest honey with a 50% concentration) and the lowest expression was found in the T+ and T− groups. IL-13 is an anti-inflammatory cytokine produced by innate or adaptive immune cells. 42 The IL-13 expression that appears indicates that the addition of honey in malnourished rats can reduce the occurrence of inflammatory conditions in the ovarian tissue of experimental white rats. This is supported by a study conducted in 2016, which states that the administration of honey to malnourished female rats regenerates ovarian tissues. 5\n\nAnother study in 2016 stated that rats that were not fed for 5 days would experience damage to various organs, including reproductive organs. 10 ROS is strongly suspected to be one of the factors that cause organ damage due to malnutrition. Not being fed for a long time and in a row experienced by white rats as experimental animals in this study can cause an imbalance between the ROS produced and the defense or the presence of antioxidants in the body. This imbalance can ultimately lead to oxidative stress that results in the occurrence of lipid peroxidation in cell membranes, which in turn leads to cell membrane and lipoprotein damage. 43\n\nDamage to the cell membrane triggers the release of cellular components that will eventually cause cell death. The emergence of an active immune response occurs as a result of cellular damage. Immune system activation rapidly elicits an acute inflammatory response, which begins with the secretion of various cytokines and chemokines to recruit immune cells to the site of the defect. 44\n\nThe inflammatory process occurs in response to injury or damage to organs. 45 IL-13 is a cytokine that plays a significant role in the anti-inflammatory response. 15 In this study, the IL-13 expression appeared in the T1 and T2 treatment groups, wherein the rats received honey therapy. In the negative control group (T−), wherein the condition of the rats was healthy, it could be inferred that IL-13 was not expressed (Table 2), which was due to the absence of injury in healthy rats. However, in the positive group (T+), wherein the rats were injured and without forest honey, the IL-13 expression was also low.\n\nForest honey has the highest antioxidant content than other types of honey; therefore, it has an optimal effect on wound healing and inflammation. 46 Phenolic compounds are contained in honey and are factors that have a major influence on antioxidant and anti-inflammatory activities. 17 IL-13 exerts its anti-inflammatory function through the deactivation of monocytes and macrophages and plays a major role in reducing the pro-inflammatory cytokine production. 47 Moreover, IL-13 inhibits potentially damaging inflammatory responses and plays a role in blocking antigen presentation by dendritic cells as well as blocking the activation and infiltration of macrophages to the site of the defect. 48\n\nIn this study, the increased IL-13 expression proves that forest honey acts as an anti-inflammatory agent. Another anti-inflammatory activity of honey is the decrease in the production of pro-inflammatory cytokines or inflammatory transcription factors, such as NF-κB and MAPK. 49 The increased IL-13 expression indicates that the body’s response, through the addition of forest honey, toward tissue damage can be improved. The increase in IL-13 expression in the T1 and T2 forest honey therapy groups showed that the inhibitory reaction to inflammation that occurred was also influenced by the presence of honey therapy.\n\nThe next observation is the effectiveness of honey therapy based on a decrease in pro-inflammatory cytokines. Based on the results of this study, the lowest TNF-α expression was in the T2 group, which received the highest forest honey therapy (50% v/v), whereas the highest TNF-α expression was found in the infertile rat group without honey (T+). This indicates that the greatest inflammatory reaction occurred in the malnourished condition in the positive control group (T+) rats. TNF-α is an inflammatory cytokine produced by macrophages or monocytes during acute inflammatory events. TNF-α further contributes to a wide range of cell signaling, causing cell death, such as necrosis or apoptosis. 50 TNF-α is mainly secreted by macrophages to stimulate the induction of systemic inflammation. 51\n\nProlonged starvation conditions that cause malnutrition in rats cause damage to various organs, including the ovaries, due to an imbalance between ROS production and the rat body’s antioxidant defenses. In a study conducted in 2016, it was stated that there was severe damage to cells from the ovarian tissue of rats that were not fed for five consecutive days. 10 Excessive amounts of ROS in cells can cause damage to cell components, including cell membranes, lipids, proteins, nucleic acids, and other organelles. 52 ROS at high concentrations is damaging to cells because ROS can oxidize proteins and lipid cellular components and injure DNA in the cell nucleus. 44 The body responds to damage or defects in tissues with the appearance of an inflammatory reaction. 45 Inflammation itself is an important part of innate immunity and is regulated by several mechanisms, one of which is through the cytokine mechanism. One of the cytokines that play an important role in the inflammatory response is TNF-α. TNF-α is a pro-inflammatory cytokine that is rapidly released during trauma or infection and is an early mediator in inflamed tissues. 53 Inflammation has the aim of eliminating irritant agents and accelerating tissue regeneration. TNF-α signals through two membrane receptors, namely TNFR1 and TNFR2. 54 Signaling via TNFR1 and TNFR2 that activates NF-κB and MAPK induces inflammation, tissue regeneration, cell survival, and proliferation, and regulates immune defense against pathogens. 55 TNF-α increases the synthesis of anti-inflammatory factors, such as IL-13, corticosteroids, or prostanoids, which can regulate TNF-α expression. 54 That if anti-inflammatory factors cannot balance TNF-α, excessive inflammation occurs. In this study, the decrease in TNF-α expression observed in rats administered with forest honey, both at concentrations of 30% v/v and 50% v/v showed that the decrease in inflammatory reactions that occurred was also influenced by forest honey therapy.\n\nIn this study, ovarian tissue regeneration, which is shown as an intact ovarian tissue with growing follicles, is the third determinant of the effectiveness of forest honey administration. Ovarian regeneration can be observed microscopically using H&E staining. 56 , 57 Microscopic examination showed that 50% v/v forest honey therapy (T2), which leads to ovarian tissue repair. Improvements are identified based on the regeneration of the ovary with growing follicles. Overview of these improvements can be compared with the negative control group (T−), which did not suffer from ovarian failure and remained in normal condition with growing follicles (Figure 3). The abnormal feature of the damaged ovary can be compared with the positive control group of rats (T+) with ovarian failure (degenerative). The microscopic examination showed congested, and severe hemosiderosis (yellow-brown color) was observed owing to the hemolysis of red blood cells with fibrin deposition and then hemorrhage, indicating that chronic congestion has occurred (Figure 3).\n\n\nConclusions\n\nTherapy of 50% v/v forest honey for ten consecutive days in female rats with ovarian failure reveals the following findings: increased antioxidant enzyme activity, such as SOD, and decreased oxidative stress concentration, such as MDA; increased anti-inflammatory cytokine expression, such as IL-13, and decreased pro-inflammatory cytokine expression, such as TNF-α; and ovarian tissue regeneration with increased growing follicle count.\n\n\nData availability\n\nFigshare: Raw data of growing follicle, MDA concentration, TNF-alfa, IL-13 and SOD activity.\n\nhttps://doi.org/10.6084/m9.figshare.19173857.v3. 58\n\nThis project contains the following underlying data:\n\n• anova_growing follicle.xlsx\n\n• anova_MDA concentration.xlsx\n\n• anova_TNF-alfa.xlsx\n\n• anova_IL-13 expression.xlsx\n\n• anova_SOD Activity.xlsx\n\nFigshare: Immunohistochemical reaction figures on TNF-alpha.\n\nhttps://doi.org/10.6084/m9.figshare.19397636.v2. 59\n\nThis project contains the following underlying data:\n\n• Fig. 1 TNF A.jpeg\n\n• Fig. 2 TNF A.jpeg\n\n• Fig. 3 TNF A.jpeg\n\n• Fig. 4 TNF A.jpeg\n\nFigshare: Histopathological figure: Ovary.\n\nhttps://doi.org/10.6084/m9.figshare.19397630.v2. 60\n\nThis project contains the following underlying data:\n\n• Fig. 1 HE.jpeg\n\n• Fig. 2 HE.jpeg\n\n• Fig. 3 HE.jpeg\n\n• Fig. 4 HE.jpeg\n\n\nReporting guidelines\n\nFigshare: ARRIVE checklist for ‘Effectiveness of forest honey (Apis dorsata) as therapy for ovarian failure that caused malnutrition’, https://doi.org/10.6084/m9.figshare.19642266.v1. 61\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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Biochim. Biophys. Acta. 2016; 1863(12): 2977–2992. Publisher Full Text\n\nParameswaran N, Patial S: Tumor Necrosis Factor-α Signalling in Macrophag. Crit. Rev. Eukaryot. Gene Expr. 2010; 20(2): 87–103. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZelova H, Hosek J: TNF-α in Signalling and Inflammation: Interaction Between Old Acquaintances. Inflamm. Res. 2013; 62(7): 641–651. PubMed Abstract | Publisher Full Text\n\nKalliolias GD, Ivashkiv LB: TNF biology, pathogenic mechanism and emerging theraupetic strategies. Nat. Rev. Reumathol. 2016; 12(1): 49–62. Publisher Full Text\n\nDong J, Albertini DF, Nishimori K, et al.: Growth differentiation factor-9 is required during early ovarian folliculogenesis. Nature. 1996; 383(6600): 531–535. PubMed Abstract | Publisher Full Text\n\nDan S, Haibo L, Hong L: Review: Pathogenesis and stem cell therapy for premature ovarian failure. OA Stem Cells. 2014; 2(1): 1–8.\n\nSafitri E, Purnobasuki H, Purnama MTE, et al.: Raw data of growing follicle, MDA concentration, TNF-alfa, IL-13 and SOD activity. figshare. Dataset. 2022. Publisher Full Text\n\nSafitri E, Purnobasuki H, Purnama MTE, et al.: Immunohistochemical reaction figures on TNF-alpha. figshare. Figure. 2022. Publisher Full Text\n\nSafitri E, Purnobasuki H, Purnama MTE, et al.: Histopathological figure: Ovary. figshare. Figure. 2022. Publisher Full Text\n\nSafitri E, Purnobasuki H, Purnama MTE, Chhetri S: ARRIVE Checklist: Effectiveness of forest honey (Apis dorsata) as therapy for ovarian failure that caused malnutrition. figshare.2022. Online resource. Publisher Full Text"
}
|
[
{
"id": "149430",
"date": "15 Sep 2022",
"name": "Ujjwal Layek",
"expertise": [
"Reviewer Expertise Plant-pollinator interactions",
"Honeybee biology",
"stingless bee biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors determine the effect of honey feeding on the fertility of rats. They measured superoxide dismutase (SOD) and malondialdehyde (MDA) levels and observed ovarian tissue regeneration in different treatments. I think the work has a significant impact on medical science. However, the manuscript needs to improve by focusing on the following:\n\nAbstract\nBackground: needs to focus on the effect of malnutrition on fertility.\n\nResults: SOD, MDA; I think full forms will be better for readers.\nIntroduction\nInflammation due to malnutrition is needs to be illustrate.\n\n\"monofloral\" delete it.\n\n\"medical purposes ......... antioxidant properties\".---- use more references.\n\n\"Monofloral (derived ...) and polyfloral.... ).\" --- The honey sample in which one pollen type is predominant (>45%) is called unifloral/monofloral. In contrast, absence of predominant pollen type within a honey sample is treated as multiflral/polyfloral.\nVonder Ohe et al. 2004. Apidologie 35: S18-S25. doi: 10.1051/apido:2004050 Layek and Karmakar 2018. Grana 57(4): 298-310. doi: 10.1080/00173134.2017.1390604\n\nApis dorsata ----- add author citation Fabricius\n\n\"Forest honey ...... in Indonesia.\" --- why polyfloral? Monofloral and polyfloral depend on surrounding vegetation. Mention plants and add references.\nMethods\nMDA and SOD ....\n100-uL---- correct\n\nFigure ligands: need to be concise\nConclusion\nadd text about the importance of the work\nReferences\nseveral errors are there and do not maintain the journal's style\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8879",
"date": "20 Oct 2022",
"name": "Muhammad Thohawi Elziyad Purnama",
"role": "Author Response",
"response": "Dear Reviewer, Thanks for your valuable comments and suggestions on the manuscript entitled: Effectiveness of forest honey (Apis dorsata) as therapy for ovarian failure causing malnutrition We welcome feedback. We have made modifications to the manuscript according to the following: Abstract Background: needs to focus on the effect of malnutrition on fertility. Answer: We have revised with the focus research contribution. Results: SOD, MDA; I think full forms will be better for readers. Answer: We have revised with the full form of SOD and MDA. Introduction Inflammation due to malnutrition is needs to be illustrate. Answer: We have revised. \"monofloral\" delete it. Answer: We have revised. \"medical purposes ......... antioxidant properties\".---- use more references. Answer: We have added a reference. \"Monofloral (derived ...) and polyfloral.... ).\" --- The honey sample in which one pollen type is predominant (>45%) is called unifloral/monofloral. In contrast, absence of predominant pollen type within a honey sample is treated as multiflral/polyfloral. Vonder Ohe et al. 2004. Apidologie 35: S18-S25. doi: 10.1051/apido:2004050 Layek and Karmakar 2018. Grana 57(4): 298-310. doi: 10.1080/00173134.2017.1390604 Answer: We have added this two reference. Apis dorsata ----- add author citation Fabricius Answer: We have revised. \"Forest honey ...... in Indonesia.\" --- why polyfloral? Monofloral and polyfloral depend on surrounding vegetation. Mention plants and add references. Answer: We have revised. Methods MDA and SOD .... 100-uL---- correct Answer: We have revised. Figure ligands: need to be concise Answer: We have revised. Conclusion add text about the importance of the work Answer: We have added the brief conclusion regarding these finding. References several errors are there and do not maintain the journal's style Answer: We have revised all references according to journal's style."
}
]
},
{
"id": "143797",
"date": "15 Sep 2022",
"name": "Aulanni’am Aulanni'am",
"expertise": [
"Reviewer Expertise Molecular Biochemistry: the molecular mechanism of carbohydrate",
"protein and lipid metabolism",
"molecular pharmacology: mechanism or drugs",
"herbal or natural resources",
"animal model: a design for some animal models such as diabetes",
"cancers",
"infertility",
"malnutrition"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Title: will be better if showed the object (Rat)\nThe dose of Honey, will be stronger for conclusion if you have 3 doses, so we will know the trends.\nThis is good research. however, I had some questions :\nIn this study you used IHC (immunohistochemistry) for measuring TNFa as an inflammatory mediator rather than ELISA because by ELISA we will know the level of TNFa directly.\n\nThis study also only used 2 doses of forest honey. because pharmacologically at least 3 doses are needed to know the trends and dose-response curve.\n\nThere is such a jumping discussion about tissue damage. I thought tissue damage was the end point of this research, and several variables (MDA, SOD, TNFa and IL-13) is an intermediate variables that explained the endpoint.\nOverall, this is a good experiment with good results\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8880",
"date": "20 Oct 2022",
"name": "Muhammad Thohawi Elziyad Purnama",
"role": "Author Response",
"response": "Dear Reviewer, Thanks for your valuable comments and suggestions on the manuscript entitled: Effectiveness of forest honey (Apis dorsata) as therapy for ovarian failure causing malnutrition We welcome feedback. We have made modifications to the manuscript according the track comment."
}
]
}
] | 1
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https://f1000research.com/articles/11-512
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https://f1000research.com/articles/11-1198/v1
|
20 Oct 22
|
{
"type": "Data Note",
"title": "SPME-GC-HRTOF-MS dataset of fermented maize flour volatilome",
"authors": [
"Oluwafemi Ayodeji Adebo",
"Sefater Gbashi",
"Yusuf Olamide Kewuyemi",
"Sunday Samuel Sobowale",
"Adedola Sulaiman Adeboye",
"Patrick Berka Njobeh",
"Samson Adeoye Oyeyinka",
"Jonathan D. Wilkin",
"Chiemela Enyinnaya Chinma",
"Sefater Gbashi",
"Yusuf Olamide Kewuyemi",
"Sunday Samuel Sobowale",
"Adedola Sulaiman Adeboye",
"Patrick Berka Njobeh",
"Samson Adeoye Oyeyinka",
"Jonathan D. Wilkin"
],
"abstract": "Background: The volatilome of fermented food products are essential metabolites that significantly contribute to such foods’ overall composition and sensorial quality. The dataset presented herein represents the volatilome of raw and fermented maize flour samples. Methods: Maize grains were milled and naturally fermented at 35°C into sourdough at different periods (24, 48 and 72 h) and, at each point, the profile of the volatiles was investigated. Samples at the different fermentation periods were analyzed using solid phase microextraction coupled with a gas chromatography-high resolution time of flight-mass spectrometry (SPME-GC-HRTOF-MS). Results: Data obtained were classified into different compound groups such as alcohols, aldehydes, aromatic compounds, esters, organic acids, terpenes, ketones, among others and their characteristics such as the retention time, observed mass, molecular formular, mean peak areas and mass spectra also presented. Conclusion: These datasets of fermented maize volatilome can be used as biomarkers for maize fermentation.",
"keywords": [
"Volatiles",
"SPME-GC-HRTOF-MS",
"whole maize grain",
"Sourdough",
"Fermentation",
"gas chromatography"
],
"content": "Introduction\n\nMaize (Zea mays L.) is an edible staple grain and one of the most sought-after cereals for human consumption in sub-Saharan Africa (Erenstein et al., 2022). The recent production statistics suggested that maize is the most globally produced cereal, followed by rice (paddy) and wheat (http://www.fao.org/faostat/en/#data/QCL). South Africa is among the top ten largest producers of maize, with over 15 million tonnes in 2020. A whole maize grain comprises macro and micro phytochemicals of nutritional and health significance. Simple processing means for maize grain use include food fermentation, a biological process that produces sourdough and other intermediate fermented products. Such products represent a critical product developmental phase, are sensorially distinct and typically contain appreciable levels of bioactive components for improving human wellness (Achi & Asamudo, 2019; Pswarayi & Gänzle, 2022).\n\nThe volatilome of fermented food products are essential metabolites that significantly contribute to such foods’ acceptance in terms of aroma and taste (Annan et al., 2003; Saa et al., 2019; Adebo et al., 2021). Important dough fermentation conditions, including time-dependent changes, can significantly define the volatilome profile of the resulting fermented dough, with implications for its use in further product development (Lee et al., 2016; Huang et al., 2022). The previous study on aroma volatiles in fermented maize dough (72 hours) identified 64 volatile compounds using gas chromatography-mass spectrometry (GC-MS), and the injected extracts were prepared through the Likens-Nickerson simultaneous distillation and extraction method (Annan et al., 2003). In this present work, a solvent-free extraction procedure, solid-phase micro-extraction (SPME) and gas chromatography-high resolution time of flight-mass spectrometry (GC-HRTOF-MS) were employed to provide a robust dataset detailing volatilome changes in maize flour and resulting sourdough with varying fermentation time. Thus, the data in this study represents a profile of volatiles in fermented maize (sourdough) and unfermented maize, which could indicate the compounds that contribute to the aroma of these products.\n\n\nMethods\n\nMaize (Zea mays) grains were obtained from the Agricultural Research Council (ARC Grain Crops), Potchefstroom, South Africa (26°43′31.0″S 27°04′53.8″E). The grains were milled (Perten Laboratory Mill 3310, Perten Instruments AB, Helsinki, Finland) and the resulting maize flour was mixed with sterile distilled water (1:1, v/w) and spontaneously fermented at 35 oC (Incotherm, Labotec, Johannesburg, South Africa) for 24, 48 and 72 h. Each fermentation process was done in triplicate.\n\nThe volatilome analysis was carried out at the University of Johannesburg (Doornfontein Campus), Johannesburg, South Africa (26o11′32.6″S 28o03′28.9″E). Five grams (5 g) of the respective sample was loaded into amber headspace vials (Restek, Bellefonte, USA). The vial was heated and incubated at 40 oC for 20 min with intermittent agitation on and off for 10 and 1 seconds (s), respectively, at 250 rpm. Subsequently, sampling was done by exposing the 50/30 μm SPME fiber coated with divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) (Supelco, Inc., Bellefonte, USA) at 54 mm injection penetration vial depth for 20 min. The extracted volatiles were analyzed on a GC-HRTOF-MS system (Agilent 7890A gas chromatograph, Agilent Technologies, Inc., Wilmington, DE, USA and LECO Corporation, St. Josheph, MI, USA), equipped with a Gerstel MPS multipurpose sampler (Gerstel Inc. Mülheim an der Ruhr, Germany) and Rxi®-5 ms column (30 m × 0.25 mm ID × 0.25 μm) (Restek, Bellefonte, USA). The extracts were injected in a spitless mode and desorped for 60 s, with helium as the carrier gas. Inlet and transfer line temperatures were set at 250 and 225 oC, respectively, and the ion source temperature was 250 oC. The oven temperature cycle used was: initial temperature of 30 oC for 0.5 min; then an increase of 10 oC/min to 220 oC held for 0.5 min; then ramped to 270 oC for the fiber at 43 mm penetration to ‘bake-out’ for 5 min pre-and post-bake out times. Experiments for blanks were also conducted to observe possible impurities and contamination. To identify the metabolites, spectra were matched with the National Institute of Standards and Technology (NIST), Mainlib and Feihn reference library databases, and their identities were determined. To process raw data, parameters such as signal-to-noise ratio of 100, similarity match above 70% and the occurrence of metabolites at least two times out of the triplicate data were strictly adopted (Achi & Asamudo, 2019). The raw and processed data (Adebo et al., 2022a, 2022b) provides information on the volatilome of maize and derived fermented products at different fermentation periods (24, 48 and 72 h). The retention time, observed mass, average peak area and volatilome class of each compound are presented in Table 1. The compounds were also classified and the percentage distribution is shown in Figure 1.\n\n\nData availability\n\nMendeley Data: Raw SPME-GC-HRTOF-MS data and spectra of maize and sourdough volatilome. https://data.mendeley.com/datasets/kytshjccrc/2 (Adebo et al., 2022a).\n\nThis project contains the following underlying data:\n\n- Maize and Fermented Maize Volatilome SPME-GC-HRTOF-MS Spectra Data.pdf (Mass spectra of compounds from maize and fermented maize volatilome, obtained using solid phase microextraction coupled with a gas chromatography-high resolution time of flight-mass spectrometry (SPME-GC-HRTOF-MS))\n\n- Processed Maize and Fermented Maize Volatilome SPME-GC-HRTOF-MS data.xlsx (The processed dataset of compounds from maize and fermented maize volatilome, obtained using SPME-GC-HRTOF-MS). Raw (unfermented maize); 24 h – sourdough fermented for 24 h; 48 h – sourdough fermented for 48 h and 72 h – sourdough fermented for 72 h\n\n- Raw SPME-GC-HRTOF-MS data set.zip (The raw dataset (.csv) of compounds from maize and fermented maize volatilome, obtained using SPME-GC-HRTOF-MS). WM0H (unfermented maize); WM24H – sourdough fermented for 24 h; WM48H – sourdough fermented for 48 h and WM72H – sourdough fermented for 72 h\n\n- Table 1 - Compounds in the volatilome of maize and fermented maize sourdoughs.xlsx (The processed and tabulated compounds from maize and fermented maize volatilome, obtained using SPME-GC-HRTOF-MS). Raw (unfermented maize); 24 h – sourdough fermented for 24 h; 48 h – sourdough fermented for 48 h and 72 h – sourdough fermented for 72 h\n\nUniversity of Johannesburg’s Open Access Data Repository: UJ Research Data. https://doi.org/10.25415/ujhb.20223447.v1 (Adebo et al., 2022b).\n\nThis project contains the following underlying data:\n\n- (SPME-GC-HRTOF-MS dataset of fermented maize flour volatilome) (The raw dataset (.MZML) of compounds from maize and fermented maize volatilome, obtained using SPME-GC-HRTOF-MS). WM0H (unfermented maize); WM24H – sourdough fermented for 24 h; WM48H – sourdough fermented for 48 h and WM72H – sourdough fermented for 72 h\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe support of the Food Innovation Research Group members is acknowledged.\n\n\nReferences\n\nAchi OK, Asamudo NU: Cereal-based fermented foods of Africa as functional foods. Bioactive Molecules in Food. Mérillon JM, Ramawat KG, editors.Cham. Switzerland:Springer;2019; pp. 1527–1558.\n\nAdebiyi JA, Njobeh PB, Kayitesi E, et al.: GC-HRTOF-MS dataset of metabolites extracted from sorghum and ting (a fermented product) produced using two strains of Lactobacillus fermentum (singly and in combination). Data Brief. 2021; 36: 107102. PubMed Abstract | Publisher Full Text\n\nAdebo OA, Oyeyinka SA, Adebiyi JA, et al.: Application of gas chromatography–mass spectrometry (GC-MS)-based metabolomics for the study of fermented cereal and legume foods: A review. Int. J. Food Sci. Technol. 2021; 56: 1514–1534. Publisher Full Text\n\nAdebo OA, Gbashi S, Kewuyemi YO, et al.: Raw SPME-GC-HRTOF-MS data and spectra of maize and sourdough volatilome. Mendeley Data. 2022a; V2.\n\nAdebo OA, Gbashi S, Kewuyemi YO, et al.: SPME-GC-HRTOF-MS dataset of fermented maize flour volatilome. University of Johannesburg. Dataset.2022b.\n\nAnnan NT, Poll L, Sefa-Dedeh S, et al.: Volatile compounds produced by Lactobacillus fermentum, Saccharomyces cerevisiae and Candida krusei in single starter culture fermentations of Ghanaian maize dough. J. Appl. Microbiol. 2003; 94: 462–474. PubMed Abstract | Publisher Full Text\n\nErenstein O, Jaleta M, Sonder K, et al.: Global maize production, consumption and trade: trends and R&D implications. Food Security. 2022; 14: 1295–1319. Accessed date 11th September 2022. Publisher Full Text\n\nHuang Y, Wan J, Wang Z, et al.: Variation of volatile compounds and corresponding aroma profiles in Chinese steamed bread by various yeast species fermented at different times. J. Agric. Food Chem. 2022; 70: 3795–3806. PubMed Abstract | Publisher Full Text\n\nLee SM, Oh J, Hurh BS, et al.: Volatile compounds produced by Lactobacillus paracasei during oat fermentation. J. Food Sci. 2016; 81: C2915–C2922. PubMed Abstract | Publisher Full Text\n\nPswarayi F, Gänzle M: African cereal fermentations: A review on fermentation processes and microbial composition of non-alcoholic fermented cereal foods and beverages. Int. J. Food Microbiol. 2022; 378: 109815. PubMed Abstract | Publisher Full Text\n\nSaa DLT, Nissen L, Gianotti A: Metabolomic approach to study the impact of flour type and fermentation process on volatile profile of bakery products. Food Res. Int. 2019; 119: 510–516. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "188199",
"date": "07 Aug 2023",
"name": "Dody Dwi Handoko",
"expertise": [
"Reviewer Expertise Flavor analysis",
"sensory evaluation",
"and rice grain quality"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article presented data on the effect of the natural fermentation of maize flour on volatile compounds.\n\nThe authors used tentative identification, using only the library database to identify the volatile compounds of the maize and fermented maize sourdoughs.\n\nTable 1 well presented the volatile compounds of the maize and fermented maize sourdoughs. However, the label in Figure 1 is not readable.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1198
|
https://f1000research.com/articles/10-232/v1
|
24 Mar 21
|
{
"type": "Systematic Review",
"title": "SARS-CoV-2 and the role of airborne transmission: a systematic review",
"authors": [
"Carl J. Heneghan",
"Elizabeth A. Spencer",
"Jon Brassey",
"Annette Plüddemann",
"Igho J. Onakpoya",
"David H. Evans",
"John M. Conly",
"Tom Jefferson",
"Elizabeth A. Spencer",
"Jon Brassey",
"Annette Plüddemann",
"Igho J. Onakpoya",
"David H. Evans",
"John M. Conly",
"Tom Jefferson"
],
"abstract": "Background: Airborne transmission is the spread of an infectious agent caused by the dissemination of droplet nuclei (aerosols) that remain infectious when suspended in the air. We carried out a systematic review to identify, appraise and summarise the evidence from studies of the role of airborne transmission of SARS-CoV-2. Methods: We searched LitCovid, MedRxiv, Google Scholar and the WHO Covid-19 database from 1 February to 20 December 2020 and included studies on airborne transmission. Data were dual extracted and we assessed quality using a modified QUADAS 2 risk of bias tool. Results: We included 67 primary studies and 22 reviews on airborne SARS-CoV-2. Of the 67 primary studies, 53 (79%) reported data on RT-PCR air samples, 12 report cycle threshold values and 18 copies per sample volume. All primary studies were observational and of low quality. The research often lacked standard methods, standard sampling sizes and reporting items. We found 36 descriptions of different air samplers deployed. Of the 42 studies conducted in-hospital that reported binary RT-PCR tests, 24 (57%) reported positive results for SARs-CoV-2 (142 positives out of 1,403 samples: average 10.1%, range 0% to 100%). There was no pattern between the type of hospital setting (ICU versus non-ICU) and RT-PCR positivity. Seventeen studies reported potential air transmission in the outdoors or in the community. Seven performed RT-PCR sampling, of which two studies report weak positive RNA samples for 2 or more genes (5 of 125 samples positive: average 4.0%). Ten studies attempted viral culture with no serial passage for viral culture. Conclusion: SARS-CoV-2 RNA is detected intermittently in the air in various settings. Standardized guidelines for conducting and reporting research on airborne transmission are needed. The lack of recoverable viral culture samples of SARS-CoV-2 prevents firm conclusions over airborne transmission.",
"keywords": [
"SARs-CoV-2",
"transmission",
"COVID",
"Airborne"
],
"content": "Introduction\n\nAirborne transmission is defined as the spread of an infectious agent caused by the dissemination of droplet nuclei (aerosols) that remain infectious when suspended in air over long distances and time1. A collection of particles (liquid or solid) ranging in size from 0.001 μm to over 100 mm suspended in a gas defines an aerosol2. Droplet nuclei are airborne residue (with or without embedded pathogens) of a respiratory droplet containing non-volatile solutes, from which water has evaporated to the point of equilibrium with the ambient relative humidity defines3.\n\nAirborne transmission via droplets and aerosols enables some viruses to spread efficiently among humans, causing outbreaks that are difficult to control. Many studies, however, often report inconclusive findings as many outbreaks are studied retrospectively and evidence to inform transmission from controlled experiments is often not available4,5. Among case clusters for which airborne transmission is hypothesised, published detailed investigations cannot rule out that droplet and fomite transmission could also explain human-to-human transmission6. Therefore, we aimed to systematically review the airborne transmission evidence for SARS-CoV-2.\n\n\nMethods\n\nWe are undertaking a series of living systematic reviews investigating factors and circumstances that impact the transmission of SARS-CoV-2, based on our published protocol last updated on 1 December 2020 (archived protocol: Extended data: Appendix 17) Briefly, this review aims to identify, appraise, and summarize the evidence (from studies peer-reviewed or awaiting peer review) relating to the role of airborne transmission of SARS-CoV-2 and the factors influencing transmissibility.\n\nWe searched four main databases: LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database for COVID-19 using the terms Airborne: aerosol OR airborne OR airbourne OR inhalation OR air OR droplet) from 1 February 2020 up to 20 December 2020 (see Extended data: Appendix 2 for the search strategies7). Searches were updated every two weeks. We aimed to include sampling for the detection of SARs-CoV-2 in the population or the environment on airborne transmission. Studies can be observational including case series, ecological, or prospective; or interventional including randomised trials and clinical reports, outbreak reports, case-control studies, experimental studies, non-predictive modelling. Studies should include sampling for the detection of SARs-CoV-2. Studies on factors influencing transmission are included, such as location settings, meteorological or immunological factors. Studies incorporating models to describe observed data were eligible. Studies reporting solely predictive modelling were excluded. For relevant articles citation tracking was undertaken. We searched the included studies of all retrieved reviews and included them in the results section for reference.\n\nWe included field studies that included airborne sampling for SARs-CoV-2 in the population or the environment. JB performed the searches, TJ and ES performed the first screen and CH checked these initial screening of studies. One reviewer (ES) extracted data for each study, and a second reviewer (CH) checked and edited the extraction. We extracted information on the study characteristics, the study population, setting and methods, and the main results from included studies. We also extracted data on the type of study, setting, sample source and methods, RT-PCR positive samples for SARS-CoV-2 RNA including cycle threshold (Ct) and copies per m3, viral culture methods and results, size of air particles (when reported) and proportion in the sample. We tabulated the data and summarised the data narratively by type of sample. Because of substantial heterogeneity across the included studies, we did not perform a meta-analysis. We assessed quality using a modified QUADAS 2 risk of bias tool,8. We simplified the tool as the included studies were not designed as primary diagnostic accuracy studies and the quality of transmission studies is known to be low9. We gave particular importance to the description of methods for air sampling and the reporting of sufficient detail to replicate. We summarise data narratively and report the outcomes as stated in the paper, including quantitative estimates when reported and the detection of culture of SARS-CoV-2.\n\n\nResults\n\nWe identified 89 studies (see Figure 1; 19 full-text studies were excluded because they were not reviews or there was no SARs-CoV-2 airborne transmission outcome studied and we excluded four laboratory studies: see Extended data: Appendix 3 for a list of excluded studies7). We included 67 primary studies and 22 systematic reviews (see Extended data: Appendix 3 for references to included studies and Table 1 and Table 2 for the characteristics of the included studies7).\n\nWe found 22 reviews on SARS-CoV-2: 16 reviews [Anderson EL 2020, Agarwal 2020, Bahl P 2020, Birgand G 2020, Carducci A 2020, Chen PZ 2020, Comber L 2020, Ekram W 2020, Ji B 2020, Mehraeen E 2020, Niazi S 2020, Noorimotlagh Z 2020, Rahmani 2020, Ren Y 2020, Singhal S 2020, and Wilson NM 2020] were about airborne transmission and prevention; three reviews on airborne transmission and procedures [Hussain A 2020, Kay JK 2020, and Schünemann HJ] and three on ventilation, air conditioning filtration and recirculation [Mousavi EH 2020, Chirico F 2020, and Correia G 2020] (see Table 2). The final search date of these reviews varied from April up to 27 October 2020. Only five reviews met systematic review methods criteria that include systematically searching for all available evidence, appraising the quality of the included studies, and synthesising the evidence into a usable form10.\n\nAll included primary studies were observational (some with experimental components) and low quality (see Table 3). We could not identify a published protocol for any of the studies. Most studies were based on convenience sampling. While the description of methods provided sufficient detail to replicate 91% of studies (see Figure 2), the research often lacked standard methods, standard sampling sizes and reporting. In 69% of the studies, the sample sources were clear, however, outcomes that aimed to demonstrate the detection of viable, replicable viruses were lacking. Limitations of the sampling methods and the poor-quality reporting make it difficult to discriminate between airborne or droplet nuclei transmission. Interpretation is further limited by the variability in reporting of patient distance from the sampler, use of protective or oxygen masks by patients, patient activities (coughing and sneezing during sampling time), air movement, air conditioning sampler type, sampling, storage and transfer conditions.\n\nWe included 67 primary studies, of which 53 (79%) reported binary data on RT-PCR air samples (see Table 1). All were descriptive observational and none were comparative. Twelve studies reported Ct values and 18 report copies per sample volume (see Table 4). Two studies reported a Ct value < 25: Razzini K 2020 et al. reports in the intensive care unit the mean Ct was 22.6, and Guo ZD 2020 et al. report a Ct of 12.5 near the doctor's office area. Ten studies report Ct values > 35; two [Guo ZD 2020, Lei H 2020] report Ct > 40, and three studies [Dumont-Leblond 2020, Kenarkoohi 2020, Nissen 2020] report the detection of single genes.\n\nTable 5 shows eight studies reporting the size of detectable particles containing RNA [Binder 2020, Chia PY 2020, Chirizzi D 2020, Feng B 2020, Hernández JL 2020, Liu Y & Ning Z 2020, McGain F 2020, and Santarpia 2020a]. Overall the reporting was heterogeneous. SARS-CoV-2 RNA was detectable in a range of air sample sizes from <1 μm through to >18 µm. Seven studies detected particles below <4 μm, and Chirizzi D 2020 et al. reported on coarse particles up to diameter > 18 µm. In one study, different samplers detected different size particles: McGain F 2020 et al. reported that the APS detected larger aerosols (> 0.37 µm) and MiniWRAS smaller particles (0.01–0.35 µm) (see Figure 3).\n\nWe found 36 different descriptions of air samplers deployed: the two most used samplers were the MD8 sampler, Sartorius, Goettingen, Germany (n=7 studies) and the National Institute for Occupational Safety and Health (NIOSH) BC 251 Aerosol sampler (n=6 studies) (see Extended data: Appendix 47). One study used four different methods [Ding Z 2020], and in seven studies the sampler used was unclear [Hernández JL 2020, Horve PF 2020, Kang M 2020, Kwon KS 2020, Seyyed Mahdi SM 2020, Tan L 2020 and Zhang D 2020].\n\nHospital. There were 50 studies conducted in healthcare settings: 45 studies included binary RT-PCR air samples (42 hospitals, 2 outdoors and 1 student healthcare centre).\n\nOf the 42 studies that reported air sampling RT-PCR data within a hospital environment, 24 (57%) reported positive samples (142 positives out of 1,403 samples: average 10.1%). Samples taken per study varied from 2 to 135. In two studies [Ahn 2020 and Santarpia JL 2020b] the denominator was unclear. There was no pattern observed in terms of the type of hospital setting (ICU versus non-ICU) and RT-PCR positivity. Three studies involving ICUs reported 0% of samples were positive [Ma J, Song Z, Wu S] (see Figure 4).\n\nRed bars indicate studies sampling ICUs.\n\nTwo studies conducted in hospitals also sampled other spaces. Liu Y & Ning Z et al. reported 4/13 public areas were RT-PCR positive; Ma J et al. reported 1 positive sample from an unventilated quarantine hotel toilet room out of 26 samples taken. Zhang D et al. sampled the outdoor environment of three hospitals and reported 3/16 samples were RT-PCR positive. Lednicky JA 2020b sampled in a respiratory infection evaluation area of a student health care center and reported one positive sample with a CT of 39 (virus genome equivalent of 0.87 virus genomes L–1 air).\n\nTwo studies reported on Exhaled Breath Condensate (EBC). Ma J et al. reported 14/52 EBC samples as RT-PCR positive and Feng B et al. reported 2/8 positive EBC samples. Five studies conducted in hospitals did not attempt RT-PCR air sampling [Bays D 2020; McGain F 2020; Mponponsuo K 2020 Ogawa Y 2020 and Wong SCY 2020] In Lei H et al., it was not possible to separate air from surface sample results.\n\nOutdoors and community. Seventeen studies reported on the outdoors and in the community (see Figure 1). These settings were buses (four studies: two in china [Luo K 2020 and Shen Y 2020]; one in Italy [Di Carlo P 2020] and one from Spain that included subway trains [Moreno T 2020]); two studies each for the outdoors; restaurant; choir practice & block of flats, and one study each for a meat processing plant; home residence; quarantine hotel; quarantined household and a care home.\n\nSeven of these studies undertook RT-PCR sampling [Di Carlo P 2020: inside a bus; Dohla M 2020: quarantined households; Kang M 2020: a block of flats; Kwon KS 2020: the community; Moreno T 2020; buses and subway trains; Setti L 2020: outdoor sampling; and Wong JCC 2020: in the home residence], and one Chirizzi D 2020 sampled atmospheric concentrations.\n\nOf the eight studies, two reported positive RT-PCR samples (5 of 125 samples positive for 2 or more genes, average 4.0%), and one Chirizzi 2020 et al. found outdoor atmospheric concentrations of SARS-CoV-2 RNA at low levels <0.8 copies m3. Moreno 2020 et al. sampled on buses and subway trains in Barcelona, and reported samples were mainly positivity for only 1 of the 3 RNA targets, and Setti et al., in a study of outdoor sampling, reported 20/34 (59%) Particulate Matter (PM) samples were RNA positive for one gene, and 4/34 (11.8%) were positive for two genes (see Table 1). Five studies found no positive samples [Di Carlo P 2020: Dohla M 2020; Kang M 2020, Kwon KS 2020 and Wong JCC 2020].\n\nThree studies reported on two choir practices and potential air transmission. Charlotte N et al. followed-up a choir practice in France with 27 participants who attended a choir practice on 12 March 2020. Two separate publications [Hamner L 2020 and Miller SL 2020] published on the same Choir Practice Skagit County, Washington, USA. In total, 78 members attended two practices: 87% of choir members subsequently became ill (32 confirmed cases and 20 probable secondary cases).\n\nViral culture. Ten studies attempted viral culture [Binder 2020, Dohla M 2020, Dumont-Leblond N 2020, Hu J 2020, Lednicky JA 2020a, Lednicky JA 2020b, Nissen K 2020, Santarpia JL 2020a, Santarpia JL 2020b, Zhou J 2020]. In seven of the ten studies, the infectious virus could not be isolated and cytopathic effects could not be observed [Binder 2020, Dohla M 2020, Dumont-Leblond N 2020, Hu J 2020, Nissen K 2020, Santarpia JL 2020b and Zhou J 2020] (see Table 6).\n\nOf the remaining three studies, Lednicky JA 2020b reported that general virus-induced cytopathic effects were observed within two days post-inoculation. The amount of virus present in 390 L of sampled air was low (approximately 340 virus genome equivalents). RT-PCR for SARS-CoV-2 RNA from the cell culture were negative, and three other respiratory viruses were identified: Influenza A H1N1, Influenza A H3N2, and human coronavirus OC43.\n\nLednicky JA 2020a observed presumed virus-induced CPE for 4/4 RNA-positive hospital air samples. The authors report that plaque assays could not be performed due to a nationwide non-availability of some critical media components in the USA. They also report that it took 6 to 11 days post-inoculation before rounding of the cells was observed with material collected by the air sampler and there is no report of a serial subculture of the positive air samples to demonstrate propagation of a complete replicating virus.\n\nSantarpia JL 2020a reported 3/39 aerosol samples (particle size <1 μm) that cell culture resulted in increased viral RNA at very low levels. An intact virus was observed via transmission electron microscopy in the submicron sample from one room. This study was published as a preprint (checked 5 March 2021) and is subject to methodological criticisms. Serial RT-PCR of cell culture supernatant was unclear and incongruent with the statement that some increase in viral RNA may have occurred. No size-fractionation techniques were used to determine the size range of SARS-CoV-2 droplets and particles. (Table 7 sets out several methodological issues relating to viral culture).\n\n\nDiscussion\n\nWe identified 67 primary studies, all were observational and low quality. The results show that RT-PCR RNA can be detected sporadically in airborne samples in a variety of settings. About half the studies did not detect RNA positivity. Some of the reasons for this may be methodological weaknesses in the study design, the lack of validated methods and the location and variable distance of the sampling. There was no clear relationship between the type of setting and positivity of sampling or detectable viral RNA concentrations. The reporting of viral RNA concentrations was heterogeneous as were the sampling methods.\n\nPast attempts to detect infectious particles have proved difficult: aerosols are dilute and culturing fine particles is problematic. In a NEJM editorial, Roy et al., report ‘the only clear proof that any communicable disease is transmitted by aerosol came from the famous experiment by Wells, Riley, and Mills in the 1950s, which required years of continual exposure of a large colony of guinea pigs to a clinical ward filled with patients who had active tuberculosis11.’ A 2019 review reported that viral RNA or DNA, depending on the virus, could be found in the air near patients with influenza, respiratory syncytial virus, adenovirus, rhinovirus, and other coronaviruses but rarely reported viable viruses12. For coronaviruses, previous evidence supporting the airborne route of transmission is weak13.\n\nSeveral studies included in our systematic review and reported in the tables, do not support the airborne transmission hypothesis. An included US study performed active case finding from two index patients and 421 exposed HCWs [Bays D 2020]. Eight secondary infections in HCWs were reported, but despite multiple aerosol-generating procedures, there was no evidence of airborne transmission. No transmission events were found in multiple high-risk exposures from five symptomatic COVID-19 health care workers [Mponponsuo K 2020]; Wong SCY et al. reported none of 120 contacts of a patient with initially undetected Covid-19 subsequently became infectious, and Kim UJ et al. reported that all 52 air samples were negative for SARS-CoV-2 RNA.\n\nThere is a current lack of well-conducted studies addressing airborne transmission: only nine studies identified during the search period reported air sampling outdoors and, in the environment, outside of hospitals. The findings of our review are limited by the low-quality included studies that lack standardised methods, reporting and outcomes. The small sample sizes, the absence of study protocols and the lack of replication further undermine the findings. Sporadic isolation of viral RNA may be due to problems with sampling techniques. Lack of quality is noted across several of the airborne reviews. Furthermore, while our search was comprehensive, it is likely there are studies that we have missed. Our continual updating and scoping of the literature mean we intend to update this review as more studies and evidence become available.\n\nEvidence from the referenced systematic reviews noted the need to improve the quality of evidence. Anderson et al. reported the need for further data collection under differing conditions of temperature and humidity14. Carducci et al. considered no studies had sufficient confirmatory evidence, and only a hypothesis supports airborne transmission15, Schünemann et al. noted direct studies in COVID-19 are limited and poorly reported16, and Mousavi et al. noted the need for rigorous and feasible lines of research in the area of air filtration and recirculation in healthcare facilities17.\n\nFuture studies are warranted to verify findings (particularly including viral culture) before conclusions can be reached about a mode of transmission and important knowledge such as infectious dose. Because of the heterogeneity of the settings, the case-mix limitations, the sampling techniques used clear descriptions and variable study protocols, it is difficult to make meaningful comparisons of air sampling positivity or viral concentrations between settings. Many factors including relative humidity, temperature, aerosolization medium, exposure period, the chemical composition of the air, seasonality, sampling methods, and ultraviolet light exposure can affect the potential infectivity of airborne viruses. While sampling techniques have improved greatly over time, the lack of standardization requires addressing as it limits the development of general recommendations for the sampling of airborne viruses18.\n\nOne essential question is whether observed epidemiologic associations are causal19,20. Establishing transmission modes requires integrated epidemiological and mechanistic approaches to narrow uncertainty21. Transmission evidence should be context-specific to particular settings (i.e., indoor or outdoor), environment-specific (i.e., the presence of UV light. ventilation etc.) and ensure that exposure an infectious agent has taken place. Identifying those circumstances that promote transmission using all types of relevant evidence that are more likely to promote viral transmission, and therefore, more amenable to intervention.\n\nMethodological issues of the culture methods used, as well as knowledge of the infectiousness of the patient hinder interpretation and suggest that the results should be interpreted with caution. The detection of SARS-CoV-2 RNA in the air cannot presume transmission, since only viable virions can cause disease. No airborne study to date definitively demonstrates SARS-CoV-2 is of an infectious nature, which offers the most robust evidence of transmissibility22. CPE alone cannot be relied upon to establish SARS-CoV-2 replication and additional methods are required, including demonstration of viral growth on permissive cell lines, immunofluorescence staining, and confirmed the exclusion of other pathogens or contaminants with sequence confirmation. General virus-induced cytopathic effects were observed in one study, however, RT-PCR tests for SARS-CoV-2 were negative while three other respiratory viruses were identified23.\n\n\nConclusion\n\nSARS-COV-2 RNA can be detected intermittently by RT-PCR in the air in a variety of settings. A number of studies that looked for viral RNA in air samples found none, even in settings where surfaces were found to be contaminated with SARS-CoV-2 RNA. The lack of recoverable viral culture samples of SARS-CoV-2 prevents firm conclusions to be drawn about airborne transmission. The current evidence is low quality, and there is an urgent need to standardise methods and improve reporting.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: SARS-CoV-2 and the Role of Airborne Transmission: Systematic review, https://doi.org/10.6084/m9.figshare.14248055.v27.\n\nThis project contains the following extended data:\n\n- Appendix 1: Updated protocol\n\n- Appendix 2: Search strategy\n\n- Appendix 3: References of included studies\n\n- Appendix 4: Sampling methods\n\nFigshare: PRISMA checklist for ‘SARS-CoV-2 and the role of airborne transmission: a systematic review’, https://doi.org/10.6084/m9.figshare.14248055.v27.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThis work was commissioned and paid for by the World Health Organization (WHO). Copyright on the original work on which this article is based belongs to WHO. The authors have been given permission to publish this article. The author(s) alone is/are responsible for the views expressed in the publication. They do not necessarily represent views, decisions, or policies of the World Health Organization.\n\n\nReferences\n\nWHO: Transmission of SARS-CoV-2: implications for infection prevention precautions. Scientific Brief. Reference Source\n\nHinds WCJ: Aerosol Technology. John Wiley and Sons. 1982; 424. Reference Source\n\nWells WF: ON AIR-borne infection: study II. Droplets and droplet nuclei. Am J Epidemiol. 1934; 20: 611–618. Publisher Full Text\n\nKutter JS, Spronken MI, Fraaij PL, et al.: Transmission routes of respiratory viruses among humans. Curr Opin Virol. 2018; 28: 142–151. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTellier R, Li Y, Cowling BJ, et al.: Recognition of aerosol transmission of infectious agents: A commentary. BMC Infect Dis. 2019; 19(1): 101. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTransmission of SARS-CoV-2: implications for infection prevention precautions. Reference Source\n\nHeneghan C, Spencer E, Plüddemann A, et al.: SARS-CoV-2 and the Role of Airborne Transmission: Systematic review. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14248055.v2\n\nWhiting PF, Rutjes AW, Westwood ME, et al.: QUADAS-2 Group. QUADAS-2: a revised tool for the quality assessment of diagnostic accuracy studies. Ann Intern Med. 2011; 155(8): 529–36. PubMed Abstract | Publisher Full Text\n\nSavvides C, Siegel R: Asymptomatic and presymptomatic transmission of SARS-CoV-2: A systematic review. medRxiv. 2020; 2020.06.11.20129072. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahtani KR, Jefferson T, Heneghan C, et al.: What is a ‘complex systematic review’? Criteria, definition, and examples. BMJ Evid Based Med. 2018; 23(4): 127–130. PubMed Abstract | Publisher Full Text\n\nRoy CJ, Milton DK: Airborne transmission of communicable infection—the elusive pathway. N Engl J Med. 2004; 350(17): 1710–1712. PubMed Abstract | Publisher Full Text\n\nShiu EYC, Leung NHL, Cowling BJ: Controversy around airborne versus droplet transmission of respiratory viruses: implication for infection prevention. Curr Opin Infect Dis. 2019; 32(4): 372–379. PubMed Abstract | Publisher Full Text\n\nHerfst S, Böhringer M, Karo B, et al.: Drivers of airborne human-to-human pathogen transmission. Curr Opin Virol. 2017; 22: 22–29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnderson EL, Turnham P, Griffin JR, et al.: Consideration of the Aerosol Transmission for COVID-19 and Public Health. Risk Anal. 2020; 40(5): 902–07. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCarducci A, Federigi I, Verani M: Covid-19 Airborne Transmission and Its Prevention: Waiting for Evidence or Applying the Precautionary Principle? Atmosphere. 2020; 11(7): 710. Publisher Full Text\n\nSchünemann HJ, Khabsa J, Solo K, et al.: Ventilation techniques and risk for transmission of coronavirus disease, including COVID-19: a living systematic review of multiple streams of evidence. Ann Intern Med. 2020; 173(3): 204–216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMousavi EH, Kananizadeh N, Martinello RA, et al.: COVID-19 Outbreak and Hospital Air Quality: A Systematic Review of Evidence on Air Filtration and Recirculation. Environ Sci Technol. 2020; acs.est.0c03247. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerreault D, Moineau S, Caroline D: Methods for sampling of airborne viruses. Microbiol Mol Biol Rev. 2008; 72(3): 413–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHowick J, Glasziou P, Fau - Aronson JK, et al.: The evolution of evidence hierarchies: what can Bradford Hill's 'guidelines for causation' contribute? J R Soc Med. 2009; 102(5): 186–94. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHill AB: The Environment and Disease: Association or Causation? Proc R Soc Med. 1965; 58(5): 295–300. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTellier R, Li Y, Cowling BJ, et al.: Recognition of aerosol transmission of infectious agents: a commentary. BMC Infect Dis. 2019; 19(1): 101. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJefferson T, Spencer EA, Brassey J, et al.: Viral cultures for COVID-19 infectious potential assessment - a systematic review. Clin Infect Dis. 2020; ciaa1764. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLednicky JA, Shankar SN, Elbadry MA, et al.: Collection of SARS-CoV-2 Virus from the Air of a Clinic within a University Student Health Care Center and Analyses of the Viral Genomic Sequence. Aerosol Air Qual Res. 2020; 20(6): 1167–1171. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "82591",
"date": "16 Apr 2021",
"name": "David R. Tomlinson",
"expertise": [
"Reviewer Expertise My regular daytime job since 2009 has been as Consultant Cardiologist and Electrophysiologist - perhaps an unlikely job title for anyone reviewing this manuscript. However",
"as MedRxiv Affiliate since June 2019",
"I have been exposed to and performing 'release review' of a constant stream of early published works on SARS-CoV-2 - something which has catalysed my interest in this field. I am also experienced in assessing the validity of experimental methods chosen (please see my recent peer reviewed publications and/or preprints) and believe my background allows me to approach this topic without risk of anchoring bias towards one or other mode of respiratory viral transmission. My interest in this area can be further affirmed by evidence of my 'peer review' of the WHO SARS-CoV-2 IPC Scientific Briefing July 2020",
"assessing the validity of the chosen references *against* airborne transmission of SARS-CoV-2 (my pinned tweet @DRTomlinsonEP). I mention this to illustrate the breadth and depth of my reading and background on this subject",
"which may otherwise be assumed to be insufficient for someone in my professional role. I hope this is acceptable and that you are able to consider my comments constructively - since this is my intention. Thank you."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Professor Heneghan and team,\nI would firstly like to congratulate you for publishing this systematic review on an open access site and for inviting comments. I am grateful for being given the opportunity to respond and to provide peer review. I hope you will consider the points I raise to be in the spirit of the best principles of scientific discourse - i.e., having a focus on methodology and without bias. I also hope that you and your team are open to performing major revisions to your manuscript, after consideration of all comments I provide below, and the other forms of feedback received through open access disclosure of this manuscript. Thank you.\n1. Page 4: ‘A collection of particles (liquid or solid) ranging in size from 0.001 μm to over 100 mm suspended in a gas defines an aerosol.’\nYou have made a typographical error here (easily done!), since aerosols – ‘suspensions in air (or a gas) of solid or liquid particles small enough that they will remain airborne for a prolonged period of time because of their low settling velocity’ (Tellier R, 20091) – are typically stated as being <100µm diameter, not mm. In addition, the definition of an aerosol typically includes reference to the time over which such particles may remain suspended in the air: would you consider adding this to the definition used in this present manuscript, please? For example, your methods document uses this wording, which is rather more complete in this respect: ‘Respiratory droplets <5μm in diameter are referred to as droplet nuclei or aerosols. Airborne transmission is the spread of an infectious agent caused by the dissemination of aerosols that remain infectious when suspended in air over long distances and time.’ Thank you.\n2. Paragraph 2 of your introduction contains two sentences with 55% match to the abstract of Kutter et al. (2018) - your reference 4.\nThis is evidence of presumably accidental plagiarism. The wording should be modified to remedy this please. Thank you.\n3. Appendix 7 outlines chosen methodology for excluding studies. Phrases including words such as 'adequately', 'sufficient' and 'clearly defined' are used yet without objective definition provided, introducing the possibility of selection bias.\nI would be grateful if you could provide such methodological points in objectively definable terms, please, thereby permitting a more appropriate description as to why each of these studies was ineligible for inclusion. Thank you.\n4. Thank you for providing a link to the ‘Protocol for a living evidence review (Version 3: 1 December 2020)’. Under ‘Study inclusion and exclusion’ is stated: ‘Eligible studies should include sampling for the detection of SARs-CoV-2 in the population or the environment on any potential mode of transmission, including droplet, airborne, fomite, orofecal, bloodborne, vertical or other. Studies can be observational including case series, ecological, or prospective; or interventional including randomised trials and clinical reports, outbreak reports, case-control studies, experimental studies, non-predictive modelling. Studies should include sampling for the detection of SARs-CoV-2.’\nGiven this description of your intended methods, I am surprised that the methods for the present manuscript state: ‘We included field studies that included airborne sampling for SARs-CoV-2 in the population or the environment.’Ironically, table 3 of Kutter et al. (your ref 4) is highly relevant to this important methodological point, since these authors describe the pros and cons of various methods to determine respiratory virus transmission. The cons of air sampling are noted: technical difficulty and possibly only circumstantial level evidence. However, these authors provide a list of further methods usefully employed including virus stability, outbreak (household or hospital) reports, aircraft outbreaks, non-pharmaceutical intervention, experimental infection, air tracer studies and computational modelling / simulation. Each method has its pros and cons, but it is my contention that restricting your present analyses to studies which ‘included airborne sampling’ excludes a large body of data which has been the foundation of investigations towards establishing routes of transmission of respiratory viruses amongst humans. Indeed, if your present methods were applied to measles, one would have to conclude that measles is not transmitted via the airborne route since live virus has never been successfully cultured from air samples. Therefore, and in line with this accepted and referenced practice within the field of infectious diseases, it is my contention that your present manuscript should include data from all suitably rigorous* experimental resources and outbreak reports listed here and as described by Kutter et al. Thank you. [*Please forgive my use of a subjective term here: wording would be usefully informed by your response to point (3) I raise, above.]\nIn case this suggestion seems rather ‘obtuse’, I would like to draw upon two examples of excluding studies purely on the basis of their laboratory setting and the impact this may have on the validity of any such transmission review.\nFirstly, the experiments of van Doremalen et al. (2020)2, in my opinion, represent a particularly valuable contribution towards understanding the possibility of airborne transmission of SARS-CoV-2.\nVan Doremalen outline methods: 'Virus stability in aerosols was determined as described previously at 65% relative humidity (RH) and 21-23°C (Fischer et al., 2016). In short, aerosols (<5 μm) containing HCoV-19 (105.25 TCID50/mL) or SARS-CoV-1 (106.75-7 TCID50/mL) were generated using a 3-jet Collison nebulizer and fed into a Goldberg drum to create an aerosolized environment. Aerosols were maintained in the Goldberg drum and samples were collected at 0, 30, 60, 120 and 180 minutes post-aerosolization on a 47mm gelatin filter (Sartorius). Filters were dissolved in 10 mL of DMEM containing 10% FBS. Three replicate experiments were performed.'\n\n'Viable virus in all surface and aerosol samples was quantified by end-point titration on Vero E6 cells as described previously (van Doremalen et al., 2013).'\nResults (extract): 'SARS-CoV-2 remained viable in aerosols throughout the duration of our experiment (3 hours), with a reduction in infectious titer from 103.5 to 102.7TCID50 per liter of air. This reduction was similar to that observed with SARS-CoV-1, from 104.3 to 103.5TCID50 per milliliter.'\nConclusions (extract): 'Our results indicate that aerosol and fomite transmission of SARS-CoV-2 is plausible, since the virus can remain viable and infectious in aerosols for hours and on surfaces up to days (depending on the inoculum shed). These findings echo those with SARS-CoV-1, in which these forms of transmission were associated with nosocomial spread and super-spreading events, and they provide information for pandemic mitigation efforts.'\nThat this study was excluded from your review on the basis of its laboratory setting can only imply that you believe different physical laws might be in operation in a Goldberg drum compared to 'normal air'. However, it is clearly inconceivable that the air within a Goldberg drum using the methods described has unique virus lifespan-enhancing properties. Furthermore, it is biologically implausible that SARS-CoV-2 only ever achieves aerosol viability when these same aerosols are created using a Collison nebuliser. Indeed, if the converse was true, you must have reason to believe that physiological aerosol creation during breathing, speech, singing, coughing and/or sneezing uniquely results in immediate (presumably mechanical?) viricidal action. No evidence is presented for this hypothesis, and on the basis of universally applicable physical laws, it is impossible.\nExtending this thought process, since WHO IPC Scientific Brief (July 2020) authors (including, I note, co-author TJ on this present manuscript) consider SARS-CoV-2 to be transmitted via close-range respiratory droplets, following the logic presented above, for aerosols released from COVID-19 patients to be non-infectious, the only mechanism by which SARS-CoV-2 released on respiratory droplets (>5-10µm diameter as per WHO criteria) to be infectious, is for SARS-CoV-2 visions to be possessed with the ability to simultaneously measure and move between liberated respiratory particles to ensure that only those >5-10µm diameter contain live SARS-CoV-2. Clearly, this is fantasy, since it also [logically] implies that SARS-CoV-2 is sentient and is aware of the current WHO convention for dichotomising respiratory particle size.\nSecondly, excluding animal models of transmission not only goes against methods used by Wells and Riley towards the original proof that TB transmission occurs via the airborne route, but suggests that methods employing animal models of infection within strictly controlled environmental conditions are of no use towards understanding human-to-human transmission. It is my contention that – for example – the experiments of Kutter et al. (2021) using ferrets represent a very important contribution to our understanding, providing ‘experimental evidence of robust transmission of SARS-CoV-2 via the air' 3.\nI hope you are able to appreciate the important possible harms in excluding such lines of research towards 'understanding the objective nature of reality', and that you are able to provide major revisions to this present manuscript to include all relevant data, as described. Thank you.\n5. From this same review article (your ref 4), table 2 states the known transmission routes of SARS-CoV (Coronaviridae) as contact, droplet & aerosol.\nAs I am sure you are aware, the WHO Ebola 2014 IPC guideline states 'scientists are unaware of any virus that has dramatically changed its mode of transmission'. So, in light of what is already known about human-to-human Coronaviridae transmission and the potential harms in failing to adequately mitigate every transmission route of SARS-CoV-2, I am curious as to why any infectious disease specialist or team of scientists investigating viral transmission would seek to ‘second-guess’ the inevitability of its [SARS-CoV-2] airborne transmission? This requires explanation please. Thank you.\n6. Following the logic of point (3), your table 3 cannot be interpreted since objectively defined descriptions of ‘Quality of included studies’ is not provided.\nI would be grateful if this analysis of study ‘quality’ could be updated in line with my suggestion of adopting objective ‘quality definitions’ above, please. Thank you.\nFinally, I do not think it would be appropriate – and I don’t want to risk wasting your time in reading yet further comments – for me to undertake any further point-by-point discussion/review of the conclusions which you have drawn from your chosen methods, since it is my contention that your chosen methods are so importantly flawed that the present manuscript should be completely re-written using methods with greater scientific validity, and including the whole range of available data towards SARS-CoV-2 transmission, as described. I hope this seems reasonable.\nMany thanks again for providing me with the opportunity to provide peer review. This is a hugely important topic and I sincerely hope you can use comments raised during this process to improve the quality of this manuscript.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No",
"responses": [
{
"c_id": "7079",
"date": "06 Sep 2021",
"name": "Carl Carl",
"role": "Author Response",
"response": "Peer reviewers’ comments Authors’ responses Peer Reviewer #1 Dear Professor Heneghan and team, I would firstly like to congratulate you for publishing this systematic review on an open access site and for inviting comments. I am grateful for being given the opportunity to respond and to provide peer review. I hope you will consider the points I raise to be in the spirit of the best principles of scientific discourse - i.e., having a focus on methodology and without bias. I also hope that you and your team are open to performing major revisions to your manuscript, after consideration of all comments I provide below, and the other forms of feedback received through open access disclosure of this manuscript. Thank you. Response: Thank you. 1. Page 4: ‘A collection of particles (liquid or solid) ranging in size from 0.001 μm to over 100 mm suspended in a gas defines an aerosol.’ You have made a typographical error here (easily done!), since aerosols – ‘suspensions in air (or a gas) of solid or liquid particles small enough that they will remain airborne for a prolonged period of time because of their low settling velocity’ (Tellier R, 20091) – are typically stated as being <100µm diameter, not mm. In addition, the definition of an aerosol typically includes reference to the time over which such particles may remain suspended in the air: would you consider adding this to the definition used in this present manuscript, please? For example, your methods document uses this wording, which is rather more complete in this respect: ‘Respiratory droplets <5μm in diameter are referred to as droplet nuclei or aerosols. Airborne transmission is the spread of an infectious agent caused by the dissemination of aerosols that remain infectious when suspended in air over long distances and time.’ Thank you. Response: We have revised the definition. “There are varied definitions of aerosols in the published literature. An aerosol is defined as a collection of particles (liquid or solid) with varying aerodynamic diameters, suspended in the air (gas) for a prolonged period of time. The size of the particles and the distance they may travel is highly variable and depends on many factors,(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2843947/; https://apps.who.int/iris/bitstream/handle/10665/112656/9789241507134_eng.pdf;jsessionid=41AA684FB64571CE8D8A453C4F2B2096?sequence=1)”Consider to add this reference Xie X, Li Y, Chwang AT, Ho PL, Seto WH. How far droplets can move in indoor environments--revisiting the Wells evaporation-falling curve. Indoor Air. 2007 Jun;17(3):211-25. doi: 10.1111/j.1600-0668.2007.00469.x. PMID: 17542834 2. Paragraph 2 of your introduction contains two sentences with 55% match to the abstract of Kutter et al. (2018) - your reference 4. This is evidence of presumably accidental plagiarism. The wording should be modified to remedy this please. Thank you. Response: We have revised the wording. “Transmission via droplets and aerosols in specific settings or situations may potentiate the spread of some viruses in humans, resulting in disease outbreaks that are difficult to manage. The results of several studies investigating human-to-human virus transmission have been largely inconclusive, and the evidence to inform such transmission in experimental studies is often not available.” 3. Appendix 7 outlines chosen methodology for excluding studies. Phrases including words such as 'adequately', 'sufficient' and 'clearly defined' are used yet without objective definition provided, introducing the possibility of selection bias. I would be grateful if you could provide such methodological points in objectively definable terms, please, thereby permitting a more appropriate description as to why each of these studies was ineligible for inclusion. Thank you. Response: There is no Appendix 7 in the submission. However, see the response to comment 6 below where we expand on the methods used to assess reporting quality. 4. Thank you for providing a link to the ‘Protocol for a living evidence review (Version 3: 1 December 2020)’. Under ‘Study inclusion and exclusion’ is stated: ‘Eligible studies should include sampling for the detection of SARs-CoV-2 in the population or the environment on any potential mode of transmission, including droplet, airborne, fomite, orofecal, bloodborne, vertical or other. Studies can be observational including case series, ecological, or prospective; or interventional including randomised trials and clinical reports, outbreak reports, case-control studies, experimental studies, non-predictive modelling. Studies should include sampling for the detection of SARs-CoV-2.’ Given this description of your intended methods, I am surprised that the methods for the present manuscript state: ‘We included field studies that included airborne sampling for SARs-CoV-2 in the population or the environment.’Ironically, table 3 of Kutter et al. (your ref 4) is highly relevant to this important methodological point, since these authors describe the pros and cons of various methods to determine respiratory virus transmission. The cons of air sampling are noted: technical difficulty and possibly only circumstantial level evidence. However, these authors provide a list of further methods usefully employed including virus stability, outbreak (household or hospital) reports, aircraft outbreaks, non-pharmaceutical intervention, experimental infection, air tracer studies and computational modelling / simulation. Each method has its pros and cons, but it is my contention that restricting your present analyses to studies which ‘included airborne sampling’ excludes a large body of data which has been the foundation of investigations towards establishing routes of transmission of respiratory viruses amongst humans. Indeed, if your present methods were applied to measles, one would have to conclude that measles is not transmitted via the airborne route since live virus has never been successfully cultured from air samples. Therefore, and in line with this accepted and referenced practice within the field of infectious diseases, it is my contention that your present manuscript should include data from all suitably rigorous* experimental resources and outbreak reports listed here and as described by Kutter et al. Thank you. [*Please forgive my use of a subjective term here: wording would be usefully informed by your response to point (3) I raise, above.] In case this suggestion seems rather ‘obtuse’, I would like to draw upon two examples of excluding studies purely on the basis of their laboratory setting and the impact this may have on the validity of any such transmission review. Firstly, the experiments of van Doremalen et al. (2020)2, in my opinion, represent a particularly valuable contribution towards understanding the possibility of airborne transmission of SARS-CoV-2. Van Doremalen outline methods: 'Virus stability in aerosols was determined as described previously at 65% relative humidity (RH) and 21-23°C (Fischer et al., 2016). In short, aerosols (<5 μm) containing HCoV-19 (105.25 TCID50/mL) or SARS-CoV-1 (106.75-7 TCID50/mL) were generated using a 3-jet Collison nebulizer and fed into a Goldberg drum to create an aerosolized environment. Aerosols were maintained in the Goldberg drum and samples were collected at 0, 30, 60, 120 and 180 minutes post-aerosolization on a 47mm gelatin filter (Sartorius). Filters were dissolved in 10 mL of DMEM containing 10% FBS. Three replicate experiments were performed.' \"Viable virus in all surface and aerosol samples was quantified by end-point titration on Vero E6 cells as described previously (van Doremalen et al., 2013).' Results (extract): 'SARS-CoV-2 remained viable in aerosols throughout the duration of our experiment (3 hours), with a reduction in infectious titer from 103.5 to 102.7TCID50 per liter of air. This reduction was similar to that observed with SARS-CoV-1, from 104.3 to 103.5TCID50 per milliliter.' Conclusions (extract): 'Our results indicate that aerosol and fomite transmission of SARS-CoV-2 is plausible, since the virus can remain viable and infectious in aerosols for hours and on surfaces up to days (depending on the inoculum shed). These findings echo those with SARS-CoV-1, in which these forms of transmission were associated with nosocomial spread and super-spreading events, and they provide information for pandemic mitigation efforts.' That this study was excluded from your review on the basis of its laboratory setting can only imply that you believe different physical laws might be in operation in a Goldberg drum compared to 'normal air'. However, it is clearly inconceivable that the air within a Goldberg drum using the methods described has unique virus lifespan-enhancing properties. Furthermore, it is biologically implausible that SARS-CoV-2 only ever achieves aerosol viability when these same aerosols are created using a Collison nebuliser. Indeed, if the converse was true, you must have reason to believe that physiological aerosol creation during breathing, speech, singing, coughing and/or sneezing uniquely results in immediate (presumably mechanical?) viricidal action. No evidence is presented for this hypothesis, and on the basis of universally applicable physical laws, it is impossible. Extending this thought process, since WHO IPC Scientific Brief (July 2020) authors (including, I note, co-author TJ on this present manuscript) consider SARS-CoV-2 to be transmitted via close-range respiratory droplets, following the logic presented above, for aerosols released from COVID-19 patients to be non-infectious, the only mechanism by which SARS-CoV-2 released on respiratory droplets (>5-10µm diameter as per WHO criteria) to be infectious, is for SARS-CoV-2 visions to be possessed with the ability to simultaneously measure and move between liberated respiratory particles to ensure that only those >5-10µm diameter contain live SARS-CoV-2. Clearly, this is fantasy, since it also [logically] implies that SARS-CoV-2 is sentient and is aware of the current WHO convention for dichotomising respiratory particle size. Secondly, excluding animal models of transmission not only goes against methods used by Wells and Riley towards the original proof that TB transmission occurs via the airborne route, but suggests that methods employing animal models of infection within strictly controlled environmental conditions are of no use towards understanding human-to-human transmission. It is my contention that – for example – the experiments of Kutter et al. (2021) using ferrets represent a very important contribution to our understanding, providing ‘experimental evidence of robust transmission of SARS-CoV-2 via the air' 3. I hope you are able to appreciate the important possible harms in excluding such lines of research towards 'understanding the objective nature of reality', and that you are able to provide major revisions to this present manuscript to include all relevant data, as described. Thank you. Response: We understand the reviewer’s point involving the use of other methods to determine respiratory virus transmission. However, in our pre-specified “a priori” protocol, we planned to include sampling in the population or the environment. We do not discount the suggestion that SARS-CoV-2 can be sampled via other methods as the reviewer suggests. We have included this as a limitation of the study. “We excluded study designs/settings that attempted to detect SARS-CoV-2 via other methods apart from air sampling, e.g., virus stability, outbreak reports, aircraft outbreaks, non-pharmaceutical intervention, experimental infection, air tracer studies and computational modelling/simulation” Laboratory studies such as the one quoted provide insights into the stability of the virus in airborne suspensions but provide no insights into whether there exist ordinary biological mechanisms capable of generating such high-titer aerosols in the first place. The fact that one can put humans into orbit, doesn’t mean it is an easily achieved or common task. It simply says humans can survive in orbit. The inclusion of laboratory studies was not a part of our protocol but could be included as a part of a separate review but is outside the scope of our study. The suggestion to include animal models or laboratory-based studies, in general, would not be appropriate. An animal review would be a separate review with a specific methodology. The Collaborative Approach to Meta-Analysis and Review of Animal Experimental Studies (CAMARADES) research group aims to address the gap in systematic review and meta-analysis in this area. See: CAMARADES | The University of Edinburgh. We would like to point the classic 1964 Nature paper Survival of Measles Virus in Air | Nature (DE JONG, J., WINKLER, K. Survival of Measles Virus in Air. Nature 201, 1054–1055 (1964). https://doi.org/10.1038/2011054a0). 5. From this same review article (your ref 4), table 2 states the known transmission routes of SARS-CoV (Coronaviridae) as contact, droplet & aerosol. As I am sure you are aware, the WHO Ebola 2014 IPC guideline states 'scientists are unaware of any virus that has dramatically changed its mode of transmission'. So, in light of what is already known about human-to-human Coronaviridae transmission and the potential harms in failing to adequately mitigate every transmission route of SARS-CoV-2, I am curious as to why any infectious disease specialist or team of scientists investigating viral transmission would seek to ‘second-guess’ the inevitability of its [SARS-CoV-2] airborne transmission? This requires explanation please. Thank you. Response: We do consider a peer review seriously and do not seek to second-guess any conclusion but prefer to examine the evidence base in a rigorous manner. We have published over a hundred (100) systematic reviews and synthesize the evidence objectively in both this and a previous pandemic (see as an example: Neuraminidase inhibitors for preventing and treating influenza in adults and children Version published: 10 April 2014 Version history https://doi.org/10.1002/14651858.CD008965.pub4). We analysed as in our previous work the published evidence to the date specified. We set out to determine whether SARS-CoV-2 could be detected in air samples. We have stated in our conclusion that the lack of positive samples does not rule-out airborne transmission and have tried to be as objective and open as possible but maintaining a rigorous evidence based approach. The citation “WHO Ebola 2014 IPC guideline” may have been quoted out of context. Coronaviruses exhibit a variety of infection modes (respiratory, enteric, systemic), but if one looks beyond humans the disease is most commonly enteric in nature [see Saif (2004) Rev. sci. tech. Off. int. Epiz., 23 (2), 643-660]. The human respiratory strain OC-43 may have originated as a bovine enteric coronavirus. This is the reason why there has been so much interest in trying to detect and retrieve the SARS-CoV-2 from fecal specimens. 6. Following the logic of point (3), your table 3 cannot be interpreted since objectively defined descriptions of ‘Quality of included studies’ is not provided. I would be grateful if this analysis of study ‘quality’ could be updated in line with my suggestion of adopting objective ‘quality definitions’ above, please. Thank you. Response: Thank you. We have expanded the section on the methods used to assess the quality of reporting. “We assessed quality using a modified QUADAS 2 risk of bias tool,8. We simplified the tool as the included studies were not designed as primary diagnostic accuracy studies and the quality of transmission studies is known to be low9. We gave particular importance to the description of methods for air sampling and the reporting of sufficient detail to enable replication of the study. We examined the following domains: (i) Source population – did the study authors adequately describe the source population? E.g. setting, severity of SARS-CoV-2, baseline demographics including concurrent respiratory infections or other comorbidities, distance between study subjects; (ii) Methods – did the study authors sufficiently describe the methods used to enable replication of the study? E.g. methods used for diagnosing SARS-CoV-2 in patients, procedure used for air sampling, time-point for sampling, number of samples per site, cycle thresholds, culture methods, airflow/ventilation settings, humidity; (iii) Sample sources – did the authors clearly describe the sources for the air samples? What was the volume of air in each sample? Was the period of sampling similar across various sites? (iv) Outcome reporting – was the reporting of the results consistent with the study outcomes? Was the analysis of the results appropriate – e.g., interval and time-point for testing study participants for potential transmission; (v) Follow-up – was the pattern and number of air samples sufficient to demonstrate airborne transmission - e.g. repeat sampling, serial sampling?” The risk of bias for each domain was rated “low”, “moderate” or “high” depending on the adequacy of reporting. One reviewer (CJH) assessed the risk of bias while a second author (EAS) independently verified the risk of bias. Any disagreements were resolved through discussion. Where a consensus could not be reached, a third reviewer (IJO) arbitrated.” Finally, I do not think it would be appropriate – and I don’t want to risk wasting your time in reading yet further comments – for me to undertake any further point-by-point discussion/review of the conclusions which you have drawn from your chosen methods, since it is my contention that your chosen methods are so importantly flawed that the present manuscript should be completely re-written using methods with greater scientific validity, and including the whole range of available data towards SARS-CoV-2 transmission, as described. I hope this seems reasonable. Response: We already have a published protocol that has been used to conduct our series of systematic reviews of studies investigating transmission dynamics of COVID-19. However, our research is ongoing, the quality of the evidence and methods have changed over time and we make necessary adjustments to improve the robustness of the evidence as more studies (and evidence) become available (and examined). We are in contact with several original authors to clarify and update the methods. Many thanks again for providing me with the opportunity to provide peer review. This is a hugely important topic and I sincerely hope you can use comments raised during this process to improve the quality of this manuscript. Response: Thanks. We have made several revisions to improve the quality of the manuscript."
}
]
},
{
"id": "82064",
"date": "22 Apr 2021",
"name": "Nancy H. L. Leung",
"expertise": [
"Reviewer Expertise Infectious disease epidemiology",
"aerosol transmission",
"modes of transmission",
"respiratory viruses",
"air sampling studies",
"field studies"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this systematic review, Heneghan et al. attempted to summarise the literature on the role of airborne transmission for SARS-CoV-2, with a focus of air sampling studies or epidemiologic studies that may evaluate the aerosol mode of transmission. They described that all primary research studies selected were low quality, probably attributing to the lack of standard methods, sampling sizes and reporting items. They concluded that SARS-CoV-2 was intermittently detected in the air, but the lack of recoverable viral culture samples prevents conclusions over airborne transmission.\nI applaud the authors' attempt in summarising the current literature. I also agree the results of the selected studies are heterogeneous, and that currently there is very minimal number of studies that demonstrated infectious virus recovered in the air. This review would have been very useful as an evidence base for future discussion on the importance of aerosol transmission; however, the lack of objective and systematic evaluation of the methodology used in the selected studies precludes such usefulness. My major concern is that the review set out with the assumption that \"the quality of transmission studies is known to be low\" (reference #9 was also irrelevantly cited as described further below), although one of the main purposes of this review would be to evaluate the quality of evidence of each study. The benchmarks used to evaluate whether \"Analysis & reporting outcomes (are) appropriate\" (Table 3) were not described, but which were critical to evaluate the quality of each study. The assumption of air sampling studies were of poor quality in general can be felt along the manuscript, especially in Table 6 with a very large paragraph of criticism on Santarpia 2020, but personally I think a lot of evaluation on this particular study was misguided due to insufficient understanding of the methodology used (as described further below). In some instances, studies were being described as poorly done without explanation of why the authors think so. I think including authors who have working knowledge in the field of air sampling studies and/or epidemiologic transmission studies would help to improve this review greatly.\nThere are also quite a number of missing information in the Tables, truncated sentences and typos, which requires a thorough re-read and check.\nPlease also find my specific comments below:\nIntroduction Airborne transmission is defined as the spread of an infectious agent caused by the dissemination of droplet nuclei (aerosols) that remain infectious when suspended in air over long distances and time\nFor this definition of airborne (aerosol) transmission, emerging discussion has suggested aerosol transmission occurs in both short- and long-range (see my review1).\nA collection of particles (liquid or solid) ranging in size from 0.001 μm to over 100 mm suspended in a gas defines an aerosol.\nThis is the classic definition of aerosols from the discipline of occupational hygiene, but other disciplines with a specific focus on bioaerosols with the origin of infectious pathogens may differ based on different aspects of transmission1.\nMethod Studies can be observational including case series, ecological, or prospective; or interventional including randomised trials and clinical reports, outbreak reports, case-control studies, experimental studies, non-predictive modelling. Studies should include sampling for the detection of SARs-CoV-2. Studies on factors influencing transmission are included, such as location settings, meteorological or immunological factors. Studies incorporating models to describe observed data were eligible. Studies reporting solely predictive modelling were excluded.\nThese classification of study design are ambiguous; for example, what was the intervention being studied in interventional studies? Shouldn't clinical reports, outbreak reports and case-control studies be classified as observational studies? Were retrospective observational studies included, and on the other hand randomised trials would always be prospective? Overall, if these study designs are merely summaries of studies identified from systematic search based on well-defined search terms and are not being used for inclusion/ exclusion of studies, I would suggest to move these descriptions to the Results section instead, and only keep those that are relevant to study selection in the Method section (e.g. \"Studies should include sampling for the detection of SARs-CoV-2.\")\nStudies should include sampling for the detection of SARs-CoV-2.\n\nDo you mean \"air sampling for the detection of SARS-CoV-2\"?\nWe also extracted data on the type of study, setting, sample source and methods, RT-PCR positive samples for SARS-CoV-2 RNA including cycle threshold (Ct) and copies per m3, viral culture methods and results, size of air particles (when reported) and proportion in the sample.\nFor \"copies per m3\", do you mean \"copies per m3 air sampled\"? For \"proportion in the sample\", what is the numerator and the denominator - e.g., NIOSH sampler is commonly used in air sampling study, and for each time of collection the same volume of air are segregated into 3 size-fractions, would this be counted as 1 or 3 air samples? Alternatively, some studies will use multiple samplers in the same collection (e.g. being placed at different locations in the patient room), would this be considered as multiple samples or one sample (run)? A clear definition is needed to allow comparison between studies, and should also be clearly described in Table 1.\nWe assessed quality using a modified QUADAS 2 risk of bias tool,8. We simplified the tool as the included studies were not designed as primary diagnostic accuracy studies and the quality of transmission studies is known to be low9.\n\nAs listed in Table 3, one of the criteria was \"Analysis & reporting outcomes appropriate\". What were the benchmarks that were being used to be evaluated against about whether the analysis or the reporting outcomes are appropriate or not? The use of reference #9 here is inappropriate as it refers to transmission during the symptomatic or asymptomatic phase, with no mention of any modes of transmission. Truncated sentence (\"after tool,\").\nResults Limitations of the sampling methods and the poor-quality reporting make it difficult to discriminate between airborne or droplet nuclei transmission.\nIs \"airborne\" a typo here?\nWe included 67 primary studies, of which 53 (79%) reported binary data on RT-PCR air samples (see Table 1). All were descriptive observational and none were comparative.\nComparative refers to comparison between what?\nOverall the reporting was heterogeneous.\nDo you mean the methods or the results in the reported studies were heterogeneous?\nHospital. There were 50 studies conducted in healthcare settings: 45 studies included binary RT-PCR air samples (42 hospitals, 2 outdoors and 1 student healthcare centre).\n\nShould \"outdoors\" be considered as healthcare settings? Similarly in the paragraphs follow about outdoors and community, actually I would think the distinction lies in outdoors vs. indoors, and within indoor higher-risk (e.g. healthcare settings/ households with confirmed cases) vs lower-risk (restaurants/ public transport etc)\n(142 positives out of 1,403 samples: average 10.1%).\n\nPlease refer to my above comments on the numerator/ denominator for the proportion of samples - can the proportions from different studies (which may refer to different things) be combined? What does this 10.1% represent/ how to interpret?\nThree studies reported on two choir practices and potential air transmission. Charlotte N et al. followed-up a choir practice in France with 27 participants who attended a choir practice on 12 March 2020. Two separate publications [Hamner L 2020 and Miller SL 2020] published on the same Choir Practice Skagit County, Washington, USA. In total, 78 members attended two practices: 87% of choir members subsequently became ill (32 confirmed cases and 20 probable secondary cases).\n\nI suggest to move this paragraph to a new section, as these evidence refers to whether a transmission event has occurred (i.e. whether someone is infected), which is a different outcome measure from recovering virus in the air.\nDiscussion Some of the reasons for this may be methodological weaknesses in the study design, the lack of validated methods and the location and variable distance of the sampling.\nPlease elaborate what (1) the weaknesses and (2) the lack of validated methods are referring to\nPast attempts to detect infectious particles have proved difficult: aerosols are dilute and culturing fine particles is problematic.\nWhy is culturing fine particles (as opposed to coarse particles?) problematic, apart from being diluted?\nIn a NEJM editorial, Roy et al., report ‘the only clear proof that any communicable disease is transmitted by aerosol came from the famous experiment by Wells, Riley, and Mills in the 1950s, which required years of continual exposure of a large colony of guinea pigs to a clinical ward filled with patients who had active tuberculosis11.’\nThere was clear evidence in terms of observed transmission event via the aerosol route for measles, chickenpox and rhinovirus1.\nFor coronaviruses, previous evidence supporting the airborne route of transmission is weak13.\n\nPlease clarify that this review was published before the COVID-19 pandemic.\n\nThere is a current lack of well-conducted studies addressing airborne transmission: only nine studies identified during the search period reported air sampling outdoors and, in the environment, outside of hospitals.\n\nHow do air sampling studies conducted outdoors (as opposed to indoors), or the lack thereof, suggest the studies are not well-conducted - should the studies be evaluated based on methodological robustness instead (e.g. sampling duration, attempt to recover infectious virus, etc.)?\nTransmission evidence should be context specific to particular settings (i.e., indoor or outdoor), environment- specific (i.e., the presence of UV light. ventilation etc.) and ensure that exposure an infectious agent has taken place.\nexposure to an infectious agent?\nNo airborne study to date definitively demonstrates SARS-CoV-2 is of an infectious nature, which offers the most robust evidence of transmissibility22.\nDo you mean \"SARS-CoV-2 _recovered in the air_\"? Do you mean \"evidence of aerosol transmission\" instead of \"transmissibility\" (please note the difference between \"transmissibility\" and \"modes of transmission\"1)? I'm not sure whether identifying infectious virus in the air is the most robust evidence of aerosol route, as whether aerosol transmission can take place also depends on the susceptibility of the infected person to the aerosol route, and I would think a demonstration of transmission event takes place via the aerosol route would be a stronger evidence.\nTable 1\nBinder 2020: which decreases t\\o approximately 40% efficiency for aerosols ~80 μm in diameter ---> typo. Charlotte N 2020: please describe the lack of ventilation as described in Charlotte et al. Horve PF 2020: 14/56 s ---> typo. Li & Qian 2020: missing notes. Lu J 2020: please describe the study scenarios/ findings that were relevant to why the study was selected (e.g. airflow consistent with transmission). Mponponsuo 2020: why was this study selected? the type of high-risk behaviour/ procedure has not been described in the study? Bahl P 2020: please be aware of plagiarism and rephrase. Ji B 2020: Missing main results. Singhai S 2020: Missing main results and key conclusions. Hussain A 2020: Missing key conclusions. Correia G 2020: Missing main results.\nFigure 1\nFull-text articles excluded because no transmission outcome studied ---> What does 'transmission outcome' refer to here? From my understanding, 'transmission outcome' refers to whether an infection is initiated in an exposed person; but most of the air sampling studies included in this review did not demonstrate such 'transmission outcome'\nFigure 2\nFor \"Was follow up sufficient\", referring to Table 2, shouldn't the 83.6% mostly be \"Not Applicable\" instead of \"No/Unclear\"?\nTable 4\nplease check to see the use of unit symbol is consistent in the Table (uM vs. um; copies/L vs. /L, copies/m3 vs. copies m3, m2 vs. m3, m3 vs. m3). Chirizz D 2020: please kindly indicate which size ranges were reported. Horve PF 2020: truncated sentence. Liu Y & Ning Z 2020: typo (\"rang-\"). Zhou J 2020: 101 copies per how much air?\nTable 5\nFeng B 2020: truncated sentence.\nFigure 4\nSimilar to my comments about numerator/ denominator above, were the proportions reported between studies directly comparable?\nTable 6\nBinder 2020: a Ct of <20 would be considered as high viral load that may be sufficient to be culturable? Hu J: missing publication year.\nLednicky 2020a:\n\nit is not clear why plaque assays could not be performed due to a nationwide non-availability of some critical media components in the US. ---> I think Lednicky et al. meant that due to lack of components which make up the culture media (for cultivating the cells to be infected), plaque assay (which involves the use of cells to be infected) cannot be performed.\nSantarpia JL 2020a:\nFor Santapria 2020 (a) we could only find a preprint publication. ---> it is now published in Scientific Reports.\n\nIncreased viral RNA presence is a surrogate and subject to many interpretations and should not be considered equal to the cultivation of replication and infection competent virus on cell culture which was not identified. ---> Please elaborate on this statement - how to explain the increased viral RNA presence if it is not because of viral replication?\n\nWestern blot assay was not done in cell supernatant samples with non-statistically significant evidence of replication, which would have acted as a control to ensure the findings were not spurious. Western blots are very weak, with no positive control or size markers and the signal doesn’t necessarily come from a replicating virus, there’s no “before culture” analysis. ---> In contrast to this statement, referring to Figure 2 in Santarpia JL 2020a, mock (negative control) samples have already been included. Anti-SARS nucleocapsid protein (SARS-CoV N) antibody were used in Western blot which is specific to SARS-CoV-2 virions. A significant test has been done for viral load between day 1 vs. day 5/6, and significant increase in viral load would be suggestive of viral replication between these days.\n\nNo size-fractionation techniques were used to determine the size range of SARS-CoV-2 droplets and particles, raising major issues with the statement the data suggests that viral aerosol particles are produced by individuals that have the COVID-19. ---> The NIOSH samplers (commonly used in air sampling studies) were used in this study, which size-fractionated the sampled air.\n\nNo plaques were reported to have been detected and no serial passage on subculture was reported. ---> Plaque assay nor serial passage was attempted in the study.\n\nStatistical inferences are very difficult to interpret in Figure 1 based on the error bars. ---> Student's t test was done to compare viral load between day 1 vs. day 5/6.\n\nThe broad sweeping conclusions that SARS-CoV-2 RNA exists in respired aerosols less than 5 μm in diameter; that aerosols containing SARS-CoV-2 RNA exist in particle modes that are produced during respiration is difficult to justify based on the findings presented. ---> Refers to above comment on the use of NIOSH samplers in this study.\n\nIt is likely an equation as used to calculate the concentration of the virus, however, it is more robust to measure the virus directly than use an equation. ---> Virus in the sample was being measured directly to obtain Ct values, which was then translated to viral load based on standard curve (i. e. a serial dilution of virus of different concentration) from a known quantity of SARS-CoV-2 virus.\n\nEM also does not confirm live virus and does not indicate active viral replication as the authors suggest – where are the comparisons control EM photomicrographs. ---> The significant increase in viral RNA from day 1 to day 5/6 would be suggestive of viral replication.\nTable 7\nSantarpia JL 2020b: Partial evidence of virus replication from one air sample. ---> typo.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "7081",
"date": "06 Sep 2021",
"name": "Carl Carl",
"role": "Author Response",
"response": "Peer reviewer 2 1. In this systematic review, Heneghan et al. attempted to summarise the literature on the role of airborne transmission for SARS-CoV-2, with a focus of air sampling studies or epidemiologic studies that may evaluate the aerosol mode of transmission. They described that all primary research studies selected were low quality, probably attributing to the lack of standard methods, sampling sizes and reporting items. They concluded that SARS-CoV-2 was intermittently detected in the air, but the lack of recoverable viral culture samples prevents conclusions over airborne transmission. Response: Thank you. Our team includes an expert virologist, a vaccinologist and an infectious disease specialist and epidemiologists. We have expanded our methods section to show how we assessed the quality of included studies (see response above). 2. I applaud the authors' attempt in summarising the current literature. I also agree the results of the selected studies are heterogeneous, and that currently there is very minimal number of studies that demonstrated infectious virus recovered in the air. This review would have been very useful as an evidence base for future discussion on the importance of aerosol transmission; however, the lack of objective and systematic evaluation of the methodology used in the selected studies precludes such usefulness. My major concern is that the review set out with the assumption that \"the quality of transmission studies is known to be low\" (reference #9 was also irrelevantly cited as described further below), although one of the main purposes of this review would be to evaluate the quality of evidence of each study. The benchmarks used to evaluate whether \"Analysis & reporting outcomes (are) appropriate\" (Table 3) were not described, but which were critical to evaluate the quality of each study. The assumption of air sampling studies were of poor quality in general can be felt along the manuscript, especially in Table 6 with a very large paragraph of criticism on Santarpia 2020, but personally I think a lot of evaluation on this particular study was misguided due to insufficient understanding of the methodology used (as described further below). In some instances, studies were being described as poorly done without explanation of why the authors think so. I think including authors who have working knowledge in the field of air sampling studies and/or epidemiologic transmission studies would help to improve this review greatly. Response: Thanks for your observations. We have made some revisions. We have revised the statement regarding reference #9. “We simplified the tool because the included studies were not designed as primary diagnostic accuracy studies, and there is a lack of high-quality data in published transmission studies” We have expanded the process used to assess the reporting quality in the methods section. Our team includes viral transmission experts, epidemiologists, clinicians and systematic review experts. This review set out to assess whether published studies demonstrated evidence of SARS-CoV-2 transmissibility. The included studies where the culture of viable virus was attempted were analysed in-depth given their importance and the potential for bias. We have considerable expertise in transmission studies. Across nine reviews we have assessed over 500 studies to date. CH and TJ are contact editors in the Cochrane Acute Respiratory Group and as a group, we have over 3 decades of experience in systematic reviews and infections. We, therefore, dispute this reviewer's assertion. We have clarified the methods as per the previous reviewer's response. 3. There are also quite a number of missing information in the Tables, truncated sentences and typos, which requires a thorough re-read and check. Response: We have re-read the manuscript to check for any grammatical errors and typos. 4. Introduction Airborne transmission is defined as the spread of an infectious agent caused by the dissemination of droplet nuclei (aerosols) that remain infectious when suspended in air over long distances and time For this definition of airborne (aerosol) transmission, emerging discussion has suggested aerosol transmission occurs in both short- and long-range (see my review). Response: Our definition was based on current WHO guidance. However, we have added a statement to reflect this view: “Airborne transmission is defined as the spread of an infectious agent caused by the dissemination of droplet nuclei (aerosols) that remain infectious when suspended in air over long distances and time.1 However, some authors have defined aerosol transmission as occurring over both short and long distances (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7982882/).” 5. A collection of particles (liquid or solid) ranging in size from 0.001 μm to over 100 mm suspended in a gas defines an aerosol. Response: We have revised our definition of aerosol (see response to peer reviewer 1 above). 6. Method Studies can be observational including case series, ecological, or prospective; or interventional including randomised trials and clinical reports, outbreak reports, case-control studies, experimental studies, non-predictive modelling. Studies should include sampling for the detection of SARs-CoV-2. Studies on factors influencing transmission are included, such as location settings, meteorological or immunological factors. Studies incorporating models to describe observed data were eligible. Studies reporting solely predictive modelling were excluded. Response: We have revised the paragraph. “We primarily included studies that reported sampling for the detection of SARS-CoV-2. However, we also included observational and randomised studies that investigated airborne transmission of SARS-CoV-2.” Non-predictive and experimental studies were also considered for inclusion.” 7. Studies should include sampling for the detection of SARs-CoV-2. Do you mean \"air sampling for the detection of SARS-CoV-2\"? Response: Thank you. Revised. “air sampling for the detection of SARS-CoV-2” 8. We also extracted data on the type of study, setting, sample source and methods, RT-PCR positive samples for SARS-CoV-2 RNA including cycle threshold (Ct) and copies per m3, viral culture methods and results, size of air particles (when reported) and proportion in the sample. Response: Revised to “copies per m3 of sampled air”. The included studies reported the total number of air samples as well as proportion of positive samples (if any). We presented the results as reported by the authors. We have added the following footnote to table 1: “For positive air sample proportions, the denominator refers to the total number of air samples as reported by the study authors irrespective of the method used for sampling.” 9. Results Limitations of the sampling methods and the poor-quality reporting make it difficult to discriminate between airborne or droplet nuclei transmission. Is \"airborne\" a typo here? Response: Thanks. Revised. “The variation in sample methods coupled with flaws in the reporting make it difficult to distinguish between aerosol and droplet nuclei transmission.” 10. We included 67 primary studies, of which 53 (79%) reported binary data on RT-PCR air samples (see Table 1). All were descriptive observational and none were comparative. Response: Revised. Deleted “and none were comparative”. “All the studies were observational.” 11. Overall the reporting was heterogeneous. Do you mean the methods or the results in the reported studies were heterogeneous? Response: Thanks. We have revised the sentence. “Overall, there was heterogeneity in the methods used for air sampling across the studies.” 12. Hospital. There were 50 studies conducted in healthcare settings: 45 studies included binary RT-PCR air samples (42 hospitals, 2 outdoors and 1 student healthcare centre). Response: The outdoors here refers to hospital outdoor environments. We have revised the statements. “Hospital. There were 50 studies conducted in healthcare settings: 45 studies included binary RT-PCR air samples: 42 hospitals, 1 hospital outdoor environment, 1 hospital indoor and outdoor environment and 1 student healthcare centre).” (revise figure 1). “Of the studies conducted in the community, 15 were conducted in indoor settings: choir practice (2), care home (1), inside a bus (3), quarantine households (1), meat processing plant (1), block of flats (2), restaurant (3), buses and subway trains (1), and home residence (1); three studies were conducted in outdoor settings: public places (1), industrial outdoor (1) and outdoor of a working/residential area (1).” 13. (142 positives out of 1,403 samples: average 10.1%). Response: We have described the denominator above (total number of air samples irrespective of sampling method). 14. Three studies reported on two choir practices and potential air transmission. Charlotte N et al. followed-up a choir practice in France with 27 participants who attended a choir practice on 12 March 2020. Two separate publications [Hamner L 2020 and Miller SL 2020] published on the same Choir Practice Skagit County, Washington, USA. In total, 78 members attended two practices: 87% of choir members subsequently became ill (32 confirmed cases and 20 probable secondary cases). Response: Revised. Added a new sub-title. “Indoors.” 15. Discussion Some of the reasons for this may be methodological weaknesses in the study design, the lack of validated methods and the location and variable distance of the sampling. Response: We have emphasized the need for a framework to assess studies of transmissibility and included a reference. 16. Past attempts to detect infectious particles have proved difficult: aerosols are dilute and culturing fine particles is problematic. Why is culturing fine particles (as opposed to coarse particles?) problematic, apart from being diluted? Response: Thank you for raising this point. We have several references below which address this point. The reference by Verreault is one of the most comprehensive on this subject. Verreault D, Moineau S, Duchaine C. Methods for sampling of airborne viruses. Microbiol Mol Biol Rev. 2008;72(3):413-444. doi:10.1128/MMBR.00002-08 Aaron J. Prussin, II, Linsey C. Marr, Kyle J. Bibby, Challenges of studying viral aerosol metagenomics and communities in comparison with bacterial and fungal aerosols, FEMS Microbiology Letters, Volume 357, Issue 1, August 2014, Pages 1–9, see also Lednicky Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients https://www.ijidonline.com/article/S1201-9712(20)30739-6/fulltext#. ‘The amount of airborne virus detected per liter of air was small, and future studies should address (a) whether this is typical for COVID-19, (b) if this represented virus production relative to the phase of infection in the patient, (c) if this was a consequence of active air flow related to air exchanges within the room, (d) or if the low number of virus was due to technical difficulties in removing small airborne particles from the air.’ See also Collection, particle sizing and detection of airborne viruses Pan A, Lednicky JA, Wu C.-Y. International Journal of Infectious Diseases. 100 (2020) 476–482 We have referenced Verreault D and Pan M as new references. 17. In a NEJM editorial, Roy et al., report ‘the only clear proof that any communicable disease is transmitted by aerosol came from the famous experiment by Wells, Riley, and Mills in the 1950s, which required years of continual exposure of a large colony of guinea pigs to a clinical ward filled with patients who had active tuberculosis.’ Response: We quote what Roy et al. reported in the New England Journal of Medicine who also states there is a “need for a better understanding of aerosol-acquired disease.’ 18 For coronaviruses, previous evidence supporting the airborne route of transmission is weak13. Please clarify that this review was published before the COVID-19 pandemic. Response: Clarified: “For coronaviruses, previous review evidence supporting the airborne route of transmission is weak13; however, it should be noted that this review was published before the COVID-19 pandemic.” 19. There is a current lack of well-conducted studies addressing airborne transmission: only nine studies identified during the search period reported air sampling outdoors and, in the environment, outside of hospitals. Response: We have deleted this statement within the manuscript. 20. Transmission evidence should be context specific to particular settings (i.e., indoor or outdoor), environment- specific (i.e., the presence of UV light. ventilation etc.) and ensure that exposure an infectious agent has taken place. Response: Revised: “… ensure that there is evidence of exposure to a transmissible agent” 21. No airborne study to date definitively demonstrates SARS-CoV-2 is of an infectious nature, which offers the most robust evidence of transmissibility22. Response: We have revised the statement. “None of the included studies definitively demonstrated that SARS-CoV-2 can be recovered in the air.” 22. Table 1 Response: Thank you for pointing out the typographical errors and missing notes. We have made revisions to Table 1 ≥80 µm in diameter The choir rehearsal room was not ventilated. 14 out of 56 samples Analysed outbreak using computer models and experiments based on airflow dynamics Air-conditioned, 5-floor building without windows It satisfied our inclusion criteria - observational studies of RCT that investigated airborne transmission Revised; used quotation marks where necessary Results added Added Added Added 24. Figure 1 Response: For instance, several modelling studies did not ‘study’ a transmission outcome and were therefore excluded. This is different to whether studies ‘demonstrate’ an effect or not as both would be included irrespective of the result. Otherwise, we would introduce publication bias. 25. Figure 2 Response: We have revised what we mean by follow-up. See methods section. 26. Table 4 Response: Thanks. Revised. We have presented the units as reported by the study authors (D < 0.056 µm) up to coarse particles (D > 18 µm); as reported by the study authors No truncation. Sentence extends into next page Corrected Corrected 27. Table 5 Response: No truncation; statement extends into the next page. 28. Figure 4 Response: We have addressed this comment earlier. 29. Table 6 Response: “A Ct of <20 would be considered positive…” Corrected: Hu J 2020 30 Lednicky 2020a: Response: Revised: “The authors reported that plaque assays could not be performed due non-availability of the components which make up the culture media in the USA.” 31. Santarpia JL 2020a: Response: As far as we are aware, Santarpia 2020(a) is still only available as a preprint. The Scientific Reports citation is the journal publication for Santarpia 2020(b) See the following reference. The reported changes in RNA were very small and may not be truly reflective of active replicating virus. Jefferson T, Spencer EA, Brassey J, Heneghan C. Viral cultures for COVID-19 infectious potential assessment - a systematic review [published online ahead of print, 2020 Dec 3]. Clin Infect Dis. 2020;ciaa1764. doi:10.1093/cid/ciaa1764 ‘Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with a high cycle threshold are unlikely to have infectious potential.’ Thanks. We have deleted the statement changed text to: \"Neither plaque assay nor serial passage was attempted in the study.\""
}
]
},
{
"id": "82052",
"date": "05 May 2021",
"name": "Maosheng Yao",
"expertise": [
"Reviewer Expertise I obtained a PhD in conducting bioaerosol related studies from Rutgers University",
"and did postdoc training at Yale in the same field. I am currently a Professor from Peking University",
"and has been working in bioaerosol field for about 20 years. My expertise ranges from bioaerosol sampling and detection to air pollution health effects and particulate matter toxicity."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReview for Heneghan et al. (2021), SARS-CoV-2 and the role of airborne transmission: a systematic review, F1000Research 2021, 10:232 .\nFirst, I have to declare that this review is provided solely based on scientific evidence and reasoning without any discipline preferences or conflicting interests. Despite not being exhaustive, I have to greatly applaud the efforts of all the authors for developing this review, especially the compiling of relevant COVID-19 aerosol related articles. However, to me this review serves as a perfect piece for evidence compiled for probable airborne transmission of COVID-19 if the biased discussion and preferences of content inclusion are eliminated/avoided. Thus, I feel this review, if to be indexed, needs to completely change the tone, and better suited for an article with a title like: Evidences for probable aerosol transmission of COVID-19: a systematic review. For its current form, there are many problematic issues with this review, and the discussion is also biased.\nMajor comments are listed below:\n1. This review is commissioned and supported by the WHO (World Health Organization) which has clearly stated in March 2020 that COVID-19 is not airborne. An effort supported by the WHO is hardly believed to use to overturn its own statements or harm its authority. Thus, the authors should provide documents that can demonstrate such potential conflicting interests can be sufficiently cleared. Otherwise, I can only say that this review just serves as a proxy of the WHO for its statements with a biased science provided.\n2. The aerosol definition was not effectively or properly communicated. For example, in the Introduction, they state that “aerosol particle ranges from 0.001 μm to over 100 mm”. Are they sure that there are 10 cm (100 mm) aerosol particles in the air? In case they mistyped the unit, e.g., 100 μm should be used. Experimental data in many studies (they did not cite) show that major fraction of exhaled particles during breathing or speaking in controlled and real world scenarios are smaller than 5 μm, and sometimes they peak at 1 μm. Most recently, US CDC states that surface contact transmission of COVID-19 is minimal (the authors should certainly update the review). Therefore, how do the authors explain the COVID-19 transmission between people? They might attribute the droplet transmission. But, airborne droplet is an aerosol by definition. The review did not provide any data for droplet transmission. Instead, they have provided a lot of studies that have detected SARS-CoV-2 in aerosol particles.\n3. This review lacks a significant amount of discussion of aerosol physics (very important) in terms with aerosol transmission of COVID-19. For example, a lot of studies they provided used a filter to sample air, and it is known that filtration itself can cause desiccation which affects the integrity of biological cells/particles over a prolonged time period. Accordingly, it partially attributed to low recovery of viable SARS-CoV-2 virus. For impaction or liquid based studies, the sampling velocity could also damage the integrity of the viruses, e.g., the BioSampler has an impact velocity of up to 300 m/s by calculation, which would somehow damage the virus. Besides, when the viruses are released into the air, they would be rapidly diluted and transported away given any ventilation of either natural or mechanical nature is present. Thus, the airborne viral concentration level is time, ventilation, and space dependent. The aging of the virus in the air also affect its viability. In addition, the in vitro viability tests with cells can not be directly translated back to the infection of human cells inside the body where the overall physiological environment is different, and more favorable for viral replication. So far, no studies have demonstrated that those in vitro tested non-infectious viruses cannot infect humans. Human inhalation takes place at a rate of about 12 L/min, which is relatively gentle in terms of sampling stress on the virus. Therefore, their argument that lack of recovery of viable virus prevents a firm conclusion of airborne transmission of COVID-19 is not supported by their reasoning and existing data. Instead, many outbreaks or infections are difficult to explain without referring to airborne/aerosol transmission.\n4. In their review, I do not know how they could define a low quality study. They stated that all 67 primary studies are of low quality. However, these studies are published by peer-reviewed journals including those premier ones. If they are of low quality, how they could pass the rigorous screening of these journals? On the other hand, this review did not state which are high quality studies and they did not provide them either. I think they should at least provide high quality data to support their conclusion. It seems they used “low quality data” to produce “high quality” conclusions.\n5. For bioaerosol studies, there are no unified or standardized methods or procedures. Different studies have different purposes, different circumstances, different set of sampling tools (the efficiencies could vary greatly; in terms of sampling biological agents higher physical efficiency usually results in higher damage). So, different sampling tools have very different efficiencies. Because viral level is greatly diluted in the air, higher volume or longer sampling time is required to enrich enough viral particles for detection. Most of the studies they complied used RT-PCR for quantification. Depending on the detection kit used, the efficiencies could also vary greatly. Generally, the detection limits of RT-PCR are higher, and accordingly those samples with low viral level would be tested negative. If a more sensitive method such as digital PCR (1 copy per uL) was used, higher percentage of positive samples would be reported.\n6. Clearly the review did not discuss how any ventilation would affect the airborne viral levels. Air is constantly moving in not enclosed environments. Thus, air sampling is very time sensitive. Besides, emission of viral particles by the patients might not be continuous. Airborne detection of SARS-CoV-2 is highly time dependent in ventilated environments.\n7. For airborne transmission, increasing physical distance significantly reduces the viral levels depending on the indoor building ceiling height and ventilation status. Human inhalation of the airborne virus is a comparably gentle sampling (causing less damage), and the respiratory tract provides a better incubation environment for SARS-CoV-2. Thus, mechanical air sampling together with in vitro viability tests cannot confirm the true non-infectiveness of airborne SARS-CoV-2 given the results are negative. In addition to shared space, shared time in an indoor space might be also important for airborne transmission to occur. Shared time would allow the virus not to age for too long in the air before inhaled. All of this should be discussed in the review.\n8. The tables take up most of the review, however high quality discussion is lacking. It is often observed that the statements in the review lack references.\nMinor comments\n1. Technical presentation of the data are not good. To me, all the tables prepared are like a laundry list of items without in-depth discussion or elaboration. Often, some important information present in certain studies they cited are not included in the table or in the discussion. For example, Ma et al. (2020)1 found COVID-19 patients emit millions of SARS-CoV-2 during just breathing, implying great potential of aerosol transmission of the diseases. Breathing produces fine aerosol particles. However, they did not elaborate on this. Nonetheless, viable SARS-CoV-2 was indeed recovered from hospital air. But, the review did not provide direct data against the airborne transmission.\n2. There are many grammar mistakes throughout the manuscript as pointed out by other reviewers.\n3. The debate or discrepancy might primarily arise from different understanding and definition of aerosol, droplet or airborne transmission from different communities. Aerosol concentration is higher in close ranges, while it is substantially diluted with increasing physical distance, like injecting a drop of ink into a sea. The dose and viability of the virus also play important roles in terms of causing an infection. This should be discussed in a more neutral tone in the review.\nI strongly encourage the authors to include aerosol scientists to provide a comprehensive and correct guidance/review that the WHO can use to save millions of lives. Time and resources for certain regions are running out & actions need to be taken immediately.\nI have provided some references for the authors to further read the details of relevant topics I have discussed in the report:\nGreenhalgh, Trisha, Jose L. Jimenez, Kimberly A. Prather, Zeynep Tufekci, David Fisman, and Robert Schooley. Ten scientific reasons in support of airborne transmission of SARS-CoV-2. The Lancet 397, no. 10285 (2021): 1603-1605.\nMorawska, Lidia, Julian W. Tang, William Bahnfleth, Philomena M. Bluyssen, Atze Boerstra, Giorgio Buonanno, Junji Cao et al. How can airborne transmission of COVID-19 indoors be minimised?. Environment international 142 (2020): 105832.\nYao, Maosheng, Lu Zhang, Jianxin Ma, and Lian Zhou. On airborne transmission and control of SARS-Cov-2. Science of The Total Environment 731 (2020): 139178.\nWilson, Nick, Stephen Corbett, and Euan Tovey. Airborne transmission of covid-19. BMJ 370 (2020).\nMorawska, Lidia, and Donald K. Milton. It is time to address airborne transmission of coronavirus disease 2019 (COVID-19). Clinical Infectious Diseases 71, no. 9 (2020): 2311-2313.\nPrather, Kimberly A., Linsey C. Marr, Robert T. Schooley, Melissa A. McDiarmid, Mary E. Wilson, and Donald K. Milton. Airborne transmission of SARS-CoV-2. Science 370, no. 6514 (2020): 303-304.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? No",
"responses": [
{
"c_id": "7080",
"date": "06 Sep 2021",
"name": "Carl Carl",
"role": "Author Response",
"response": "Peer Reviewer #3 First, I have to declare that this review is provided solely based on scientific evidence and reasoning without any discipline preferences or conflicting interests. Despite not being exhaustive, I have to greatly applaud the efforts of all the authors for developing this review, especially the compiling of relevant COVID-19 aerosol related articles. However, to me this review serves as a perfect piece for evidence compiled for probable airborne transmission of COVID-19 if the biased discussion and preferences of content inclusion are eliminated/avoided. Thus, I feel this review, if to be indexed, needs to completely change the tone, and better suited for an article with a title like: Evidences for probable aerosol transmission of COVID-19: a systematic review. For its current form, there are many problematic issues with this review, and the discussion is also biased. Revised: Thanks. We have made several revisions to the original submission and we believe the quality of the manuscript is much improved. We do not agree with the reviewer that the title must be changed based on our rigorous review of the evidence presented within the papers we assessed. Major comments are listed below: 1. This review is commissioned and supported by the WHO (World Health Organization) which has clearly stated in March 2020 that COVID-19 is not airborne. An effort supported by the WHO is hardly believed to use to overturn its own statements or harm its authority. Thus, the authors should provide documents that can demonstrate such potential conflicting interests can be sufficiently cleared. Otherwise, I can only say that this review just serves as a proxy of the WHO for its statements with a biased science provided. Response: The guidance by the WHO on modes of transmission of SARS-COV-2 is constantly evolving and has done so since March 2020. The reviewer has made assumptions which are simply untrue and inaccurate. Such documents do not exist as WHO had no influence in any of our reviews, the process included for the reviews or the interpretation of the results. This standard of proof is not required by editors for submitted manuscripts (CH has been an Editor-in-Chief of a BMJ journal, IJO has been a research editor and JMC has also been an Editor-in-Chief of a Journal). A peer reviewer who has submitted previous research would know the requirements for submission according to the ICMJE criteria. The insinuation of overt bias by this reviewer is unfounded and the statement should be retracted. 2. The aerosol definition was not effectively or properly communicated. For example, in the Introduction, they state that “aerosol particle ranges from 0.001 μm to over 100 mm”. Are they sure that there are 10 cm (100 mm) aerosol particles in the air? In case they mistyped the unit, e.g., 100 μm should be used. Experimental data in many studies (they did not cite) show that major fraction of exhaled particles during breathing or speaking in controlled and real world scenarios are smaller than 5 μm, and sometimes they peak at 1 μm. Most recently, US CDC states that surface contact transmission of COVID-19 is minimal (the authors should certainly update the review). Therefore, how do the authors explain the COVID-19 transmission between people? They might attribute the droplet transmission. But, airborne droplet is an aerosol by definition. The review did not provide any data for droplet transmission. Instead, they have provided a lot of studies that have detected SARS-CoV-2 in aerosol particles. Response: We have redefined aerosol (see the response to peer reviewer #1 above). 3. This review lacks a significant amount of discussion of aerosol physics (very important) in terms with aerosol transmission of COVID-19. For example, a lot of studies they provided used a filter to sample air, and it is known that filtration itself can cause desiccation which affects the integrity of biological cells/particles over a prolonged time period. Accordingly, it partially attributed to low recovery of viable SARS-CoV-2 virus. For impaction or liquid based studies, the sampling velocity could also damage the integrity of the viruses, e.g., the BioSampler has an impact velocity of up to 300 m/s by calculation, which would somehow damage the virus. Besides, when the viruses are released into the air, they would be rapidly diluted and transported away given any ventilation of either natural or mechanical nature is present. Thus, the airborne viral concentration level is time, ventilation, and space dependent. The aging of the virus in the air also affect its viability. In addition, the in vitro viability tests with cells can not be directly translated back to the infection of human cells inside the body where the overall physiological environment is different, and more favorable for viral replication. So far, no studies have demonstrated that those in vitro tested non-infectious viruses cannot infect humans. Human inhalation takes place at a rate of about 12 L/min, which is relatively gentle in terms of sampling stress on the virus. Therefore, their argument that lack of recovery of viable virus prevents a firm conclusion of airborne transmission of COVID-19 is not supported by their reasoning and existing data. Instead, many outbreaks or infections are difficult to explain without referring to airborne/aerosol transmission. Response: We have shown the bewildering array of samplers used in the studies. The reviewer raises a good point, but it is a subject matter beyond the scope of our systematic review and our protocol. We might suggest the reviewer and others in the field could contribute to establish an international standard for air capture and hope that all primary studies conform to that standard which we will be quite happy to report in future reviews. The review by Verreault and colleagues (Methods for sampling of airborne viruses. Microbiol Mol Biol Rev. 2008;72(3):413-444. doi:10.1128/MMBR.00002-08) sets out some of the basic principles in improving the methods in this area and has been included as a reference in the revised manuscript. ‘Many types of samplers have been used over the years, including liquid impingers, solid impactors, filters, electrostatic precipitators, and many others. The efficiencies of these samplers depend on a variety of environmental and methodological factors that can affect the integrity of the virus structure. The aerodynamic size distribution of the aerosol also has a direct effect on sampler efficiency. Viral aerosols can be studied under controlled laboratory conditions, using biological or nonbiological tracers and surrogate viruses, which are also discussed in this review. Lastly, general recommendations are made regarding future studies on the sampling of airborne viruses.’ 4. In their review, I do not know how they could define a low quality study. They stated that all 67 primary studies are of low quality. However, these studies are published by peer-reviewed journals including those premier ones. If they are of low quality, how they could pass the rigorous screening of these journals? On the other hand, this review did not state which are high quality studies and they did not provide them either. I think they should at least provide high quality data to support their conclusion. It seems they used “low quality data” to produce “high quality” conclusions. Response: We have expanded the methods section describing how we assessed study quality (see the response to peer reviewer #1 above). 5. For bioaerosol studies, there are no unified or standardized methods or procedures. Different studies have different purposes, different circumstances, different set of sampling tools (the efficiencies could vary greatly; in terms of sampling biological agents higher physical efficiency usually results in higher damage). So, different sampling tools have very different efficiencies. Because viral level is greatly diluted in the air, higher volume or longer sampling time is required to enrich enough viral particles for detection. Most of the studies they complied used RT-PCR for quantification. Depending on the detection kit used, the efficiencies could also vary greatly. Generally, the detection limits of RT-PCR are higher, and accordingly those samples with low viral level would be tested negative. If a more sensitive method such as digital PCR (1 copy per uL) was used, higher percentage of positive samples would be reported. See response to comment 3. Response: We agree that the methods can be improved and made more sensitive. This should be the focus of future work but is not an area that we are able to address. 6. Clearly the review did not discuss how any ventilation would affect the airborne viral levels. Air is constantly moving in not enclosed environments. Thus, air sampling is very time sensitive. Besides, emission of viral particles by the patients might not be continuous. Airborne detection of SARS-CoV-2 is highly time dependent in ventilated environments. Response: We agree and ventilation issues were considered to be beyond the scope of work outlined for this systematic review. It would be a very interesting topic for a future systematic review. 7. For airborne transmission, increasing physical distance significantly reduces the viral levels depending on the indoor building ceiling height and ventilation status. Human inhalation of the airborne virus is a comparably gentle sampling (causing less damage), and the respiratory tract provides a better incubation environment for SARS-CoV-2. Thus, mechanical air sampling together with in vitro viability tests cannot confirm the true non-infectiveness of airborne SARS-CoV-2 given the results are negative. In addition to shared space, shared time in an indoor space might be also important for airborne transmission to occur. Shared time would allow the virus not to age for too long in the air before inhaled. All of this should be discussed in the review. Response: Thanks for the comments. We appreciate the points raised but these mechanistic hypotheses are beyond the scope and intent of our systematic review. A separate review of mechanistic modes of transmission would be of value in the future. 8. The tables take up most of the review, however high quality discussion is lacking. It is often observed that the statements in the review lack references. Response: The tables report the evidence, we can comment but it’s up to the readers to consider our conclusions. Minor comments 1. Technical presentation of the data are not good. To me, all the tables prepared are like a laundry list of items without in-depth discussion or elaboration. Often, some important information present in certain studies they cited are not included in the table or in the discussion. For example, Ma et al. (2020)1 found COVID-19 patients emit millions of SARS-CoV-2 during just breathing, implying great potential of aerosol transmission of the diseases. Breathing produces fine aerosol particles. However, they did not elaborate on this. Nonetheless, viable SARS-CoV-2 was indeed recovered from hospital air. But, the review did not provide direct data against the airborne transmission. Response: We have attempted to lay out the information in the tables in line with previous reviews. We have also revisited the information to ensure the information presented is relevant. Ma and colleagues suggested COVID-19 patients recruited in Beijing exhaled millions of SARS-CoV-2 RNA copies into the air per hour and that exhaled breath emission may play an important role in the COVID-19 transmission. The Ct values of the breath and air samples, respectively (35.54±3.14 and 38.40) are extremely high and not compatible with infectious virus based on other studies that have correlated infectious virus and Ct values (Jefferson T, Spencer EA, Brassey J, Heneghan C. Viral cultures for COVID-19 infectious potential assessment - a systematic review. Clin Infect Dis. 2020 Dec 3:ciaa1764. doi: 10.1093/cid/ciaa1764. Epub ahead of print. PMID: 33270107; PMCID: PMC779932). The mere presence of RNA copies based on PCR sampling does not imply infectiousness and the reviewer comments suggesting millions of SARS-CoV-2 intact viruses are emitted during breathing and capable of causing infection does not have evidence to support the statement from what we have been able to find. Response: Meaningful inference can only be drawn from solid evidence. 2. There are many grammar mistakes throughout the manuscript as pointed out by other reviewers. Response: Thanks. We have checked for grammatical errors and typos. 3. The debate or discrepancy might primarily arise from different understanding and definition of aerosol, droplet or airborne transmission from different communities. Aerosol concentration is higher in close ranges, while it is substantially diluted with increasing physical distance, like injecting a drop of ink into a sea. The dose and viability of the virus also play important roles in terms of causing an infection. This should be discussed in a more neutral tone in the review. Response: We have already commented on the confusing nature of the definitions of aerosol, droplet and airborne transmission. I strongly encourage the authors to include aerosol scientists to provide a comprehensive and correct guidance/review that the WHO can use to save millions of lives. Time and resources for certain regions are running out & actions need to be taken immediately. Response: We have substantial expertise and experience within our team (see the response to peer reviewer #2 above. Of note, in undertaking peer review the ICMJE states: ‘Reviewers should declare their relationships and activities that might bias their evaluation of a manuscript and recuse themselves from the peer-review process if a conflict exists.’ Intellectual conflicts would introduce such bias to peer review assessments. And according to COPE’s Ethical Guidelines for Peer Reviewers, COPE also highlights that the professional responsibility underpinning the peer review requires the necessary expertise to assess the manuscript and can provide an unbiased assessment. We do not engage in emotive statements regarding the reviewers' opinions. We ensure our comments are evidence-based, unbiased and reflect the best available evidence. The reviewer should note that we do not speak for WHO and two co-authors of this review are currently collaborating with aerosol scientists to look for high-quality evidence relating to the mechanism(s) of transmission."
}
]
}
] | 1
|
https://f1000research.com/articles/10-232
|
https://f1000research.com/articles/11-1195/v1
|
19 Oct 22
|
{
"type": "Research Article",
"title": "Effects of the COVID-19 pandemic on university-based research conduct and training: Exploring university-based researchers’ perspectives and experiences",
"authors": [
"Marcia G. Ory",
"Shinduk Lee",
"Tiffany A. Radcliff",
"Sagar Jani",
"Allison Rice-Ficht",
"Amy L. Waer",
"Shinduk Lee",
"Tiffany A. Radcliff",
"Sagar Jani",
"Allison Rice-Ficht",
"Amy L. Waer"
],
"abstract": "Background: The academic environment is critical for advancing knowledge through research and training of students who will serve as researchers, advocates, and leaders in the future, yet there is limited data on how the higher institution-based research enterprise is being impacted by the coronavirus disease 2019 (COVID-19) pandemic. The current study examines the perceived and expected impact of COVID-19 on engaging in a higher education institution setting, particularly focusing on student engagement in research and conduct of human subject research (HSR). Method: The authors collected an online survey with faculty and staff in a large US university system focused on education, research, and service (6/8/2020-7/10/2020; N=709). The authors performed bivariate and multivariable logistic regression models to examine the differences in research impact by HSR. Results: The majority of survey respondents (i.e., faculty and staff from a large US university system) perceived and expected at least some impact of COVID-19 on research and reported the impact to be negative. Researchers reported increased challenges in recruiting students for research activities and providing research-related learning opportunities for students. While COVID-19 impacted both HSR and non-HSR, HSR investigators have been disproportionately impacted by the pandemic. Conclusions: Efforts are needed to further understand and overcome research challenges so that the university-based research environment can flourish for all researchers across disciplines and overcome the potentially lost learning opportunities for students. Lessons learned will help address future challenges to academic research activities and providing student research training.",
"keywords": [
"COVID-19",
"pandemic",
"academic research",
"research training",
"human subject research"
],
"content": "Introduction\n\nThe coronavirus disease 2019 (COVID-19) global pandemic has impacted most aspects of daily life. As of the time of the writing (June 2020), there were over 182 million confirmed COVID-19 cases and nearly four million mortality cases involving COVID-19 from around the globe (CSSE, 2021). Alone in the United States, there were over 33.7 million confirmed COVID-19 cases and over 600,000 mortality cases involving COVID-19 (CSSE, 2021). Mortality is only a part of the larger impact COVID-19 exerts on the social and political environment of people worldwide. The safety measures, such as social distancing, face coverings, travel restrictions, business closures, testing and quarantine, have impacted the daily activities and social norms and created a new normal of social and business interactions (Bartik et al., 2020; Carel et al., 2020; Donthu and Gustafsson, 2020; Haleem and Mohd, 2020; UN, 2020). These changes are not only limited to the individuals but have also impacted whether and how organizations and institutions function (Donthu and Gustafsson, 2020; Krishnamurthy, 2020; Soto-Acosta, 2020). Primarily led by a group of health science researchers, this study will focus on the impact of the pandemic on the university-based research enterprise.\n\nGiven COVID-19 related health risks, higher education institutions have adopted additional safety protocols in response to the pandemic, with particular attention to social distancing, cleaning and disinfecting, and face covering (ACHA, 2020; CDC, 2020). Similar to other disaster epochs, conducting human subject research amid the COVID-19 pandemic raises questions about ‘ethics’ (Packenham et al., 2020; WHO, 2020). As such, some major higher education institutions in the United States have adopted regulations for academic researchers to get permission to conduct their research and others were required to enforce local government or state-wide restrictions, such as stay-at-home orders that prevented on-premise research altogether for a prescribed timeframe. These new guidelines are likely to impact the research environment in both intended and unintended ways. For example, mandated preventive measures, such as social distancing and wearing of protective equipment designed to provide safety to both investigators and study participants are also likely to impact how researchers operate a lab or implement interventions and experiments. In addition, researchers in academic hospital settings may face greater challenges due to greater health concerns, safety risks, and increased volume of vulnerable patients.\n\nWhile the COVID-19 pandemic might offer opportunities for new research questions, new research approaches, and additional funding for some researchers, challenges in carrying out research have been reported from diverse health science fields (Omary et al., 2020; Rhodus et al., 2020; Weiner et al., 2020; Yanow and Good, 2020). For example, Yanow and Good (2020) discussed potential challenges in conducting ‘non-essential’ research and potential harm of neglecting research that are related to diseases other than COVID-19. Nicol et al. (2020) and Weiner et al. (2020) discussed potential challenges and solutions in conducting geriatric research and pediatric research, respectively. Difficulty in conducting health science research can restrict medical and health science students’ research training and associated competency, which is critical for their research development, as well as their ability to review scientific evidence and ability to make evidence-based clinical decisions. Despite the foreseeable impact of COVID-19 on research entities, there has been limited data on the topic. The National Institutes of Health survey on COVID-19 was one of the few data-based discussion of the topic, and its preliminary findings showed increases in non-research burden, changes in productivity, and increases in research expenses (Bernard and Lauer, 2020). Another gap in understanding of COVID-19 impact on academic research is COVID-19 impacts on training of future researchers and professionals. For example, medical and health science students’ research competency is critical for their research development, as well as, their ability to review scientific evidence and make evidence-based clinical decisions.\n\nThis paper attempts to address this gap by exploring researchers’ perspectives and early experiences of COVID-19 impact on their ability to conduct research. Given how diverse the research fields and methods are, each research entity can be uniquely impacted by COVID-19 (Yanow and Good, 2020; Myers et al., 2020). As a primary objective, this study focuses on the differential experiences and expectation of researchers based on whether they engage in human subject research (HSR) or not. HSR refers to research involving a living individual about whom data are obtained through interaction or intervention or identifiable, private information are obtained or generated (NIH, 2020). While COVID-19 has impacted both researchers working with and without human subjects, researchers working with human subjects are hypothesized to face unique challenges in recruiting and interacting with human subjects, as well as in providing needed research training and learning opportunities for students. This exploratory study adds to the current literature by examining the COVID-19 impact on human subject research versus non-human subject research and the research training of students. This timely cross-sectional study can provide valuable insights regarding the immediate pandemic impact perceived by the researchers in an academic setting and can better inform the future pandemic preparation.\n\n\nMethods\n\nThe study was reviewed and approved by the Texas A&M Institutional Review Board (IRB2020-0622M). All included study participants provided electronic informed consent by reviewing the study information and checking “I agree to participate in this study.”.\n\nA cross-sectional online survey was collected (June 2020 – July 2020) from 872 individuals in a large Research 1 university system focused on public state-wide educational, research, and service in the United States designated as a member of the American Association of Universities. Faculty and staff of the university system were sent recruitment emails through the university system email lists. Since multiple email lists were used, some individuals received multiple recruitment emails. The recruitment email contained a brief description of the study and a link to the online survey, and the survey began with detailed study information and consent section. 872 opened the online survey, and 863 (99.0%) provided informed consent to participate in the study. Among those who consented, 709 (82.2%) were eligible to participate in the study. A person was eligible to complete the survey if he/she was a current faculty or staff in the university system and engaged in any research activities. The final sample included in this study was 642 respondents who reported whether they engaged in HSR or not. Of 642 respondents included in this study, 238 self-reported engaging in HSR. Given the limited data availability, approximate response rate was calculated for a sub-group (principal investigators at the main campus location). This sub-group (n = 248) constituted over 82% of the respondents from the main campus location and 48% of the overall respondents who reported their principal investigator status. The sub-group had about 11% response rates (248 out of ~2300). As a recruitment incentive, at the end of the survey, respondents were invited to participate in a drawing for a chance to win $100 gift cards, and five of eligible researchers were randomly selected and awarded from the drawing. A copy of the survey can be found in the Extended data (Ory, 2022).\n\nThis study used an online survey that was developed by the researchers and was sent to a number of university system researchers from various disciplines via email to evaluate its face validity. The questions used in this study was presented in Table 1. Main outcomes were specified to capture several possible aspects of COVID-19 impact on research: (1) overall impact on their research; (2) impact on specific research activities; (3) impact on student engagement; and (4) direct COVID-19 related changes (example: social distancing and wearing of personal protective equipment). Aspects of overall impact included: perceived severity of the impact, directionality of the impact, expected severity of the impact, and changes in research focus. Specific research activities included: data collection, data analyses, and dissemination of the study findings. Particularly for HSR, this study also examined participant recruitment, participant retention, and participant interaction. Because engaging students in research is considered an important aspect of research activities in large university systems, three different areas of student engagement in research were included: student recruitment, student financial support, and research-related learning opportunities for students. The direct changes in research due to COVID-19 included specific concerns and safety measures (e.g., social distancing and wearing of protective equipment) in relation to impacts on research activities. The questions that used 5-Likert point scale ranging from ‘very negative’ to ‘very positive,’ were dichotomized into ‘negative’ and ‘neither or positive.’ Dichotomization was performed because there were too few respondents reporting positive impacts. For example, for the question, ‘Taken all together, what has the impact of COVID-19 outbreak been on your research?,’ there were 4 (0.7%) respondents reporting ‘very positive’ and 18 (3.3%) reporting ‘somewhat positive.’\n\nN = total number of valid responses;\n\na Originally 5 categories – merged because of skewed response distribution (i.e., only a small number of respondents responding ‘somewhat positive’ or ‘very positive’);\n\nb Respondents could respond ‘Not sure’ or ‘Not Applicable’ to these questions, and such responses were excluded from N and the rest of the analyses.\n\nThe primary independent variable was a dichotomous indicator, reflecting whether researchers engaged in HSR or not. This was determined based on respondents’ self-reported research types that they engaged in. Assessed covariates included principal investigator status (response categories: yes/no), number of years engaging in research, and use of experimentation or interventions. At the end of the survey, respondents reported their primary affiliation school/college, faculty status (response categories: faculty/staff/others) and sociodemographic characteristics (age, sex, race, and ethnicity). Primary affiliation was coded into multiple binary variables representing each school/college.\n\nSociodemographic characteristics of researchers and their research roles and experiences were described using frequency and percentage or mean and standard deviation and were compared based on engagement in HSR (e.g., Chi-square test for categorical variables and independent group t-test for interval variables). Each outcome variable was described using frequency and percentage, and bivariate analyses (i.e., bivariate logistic regression) were performed to examine the association between the outcome variables and engagement in HSR. For each outcome variable, multivariable logistic regression models were performed by adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions. All statistical analyses were performed using SAS 9.4 (SAS Institute Inc., Cary, North Carolina).\n\n\nResults\n\nThe majority of respondents were ages 35–64 years old (n = 362, 78.8%), male (n = 269, 56.6%), white (n = 394, 90.8%), not Hispanic (n = 424, 91.0%), faculty (n = 415, 78.3%), and currently serving as a principal investigator (n = 420, 81.6%). The respondents were from various fields of study including agriculture and life sciences (n = 78, 15.2%), health sciences (n = 60, 11.7%), liberal arts (n = 56, 10.9%), engineering (n = 55, 10.7%), sciences (biology, chemistry, mathematics, physics & astronomy, and statistics) (n = 51, 9.9%), education and human development (n = 46, 8.9%), and other fields (n = 168, 32.7%). On average, the respondents have engaged in research for over 19 years.\n\nCompared to the respondents who did not engage in HSR, those who engaged in HSR were significantly more likely to be females (n = 106, 61.3% vs. n = 100, 33.1%, p < .001) and faculty (n = 163, 84.9% vs. n = 252, 74.6%, p = .02). Compared to those who did not engage in HSR, a greater percentage of respondents engaging in HSR were in education and human development (n = 44, 24.0% vs. n = 2, 0.6%, p < .001) and less percentage in agriculture and life sciences (n = 17, 9.3% vs. n = 61, 18.4%, p = .006), engineering (n = 6, 3.3% vs. n = 49, 14.8%, p < .001), or science (n = 4, 2.2% vs. n = 47, 14.2%, p < .001). While a greater percentage of respondents engaging in HSR were in health sciences (n = 28, 15.3% vs. n = 32, 9.7%), the statistical significance was marginal (p = 0.06). The respondents who engaged in HSR were also less likely to report using experimentation or interventions (n = 122, 51.3% vs. n = 252, 63.8%, p = .002) and had fewer years of experience engaged in research (16.0 vs. 20.8 years, p < .001).\n\nThe majority perceived (n = 504, 92.1%) and expected (n = 494, 96.1%) at least some impact of COVID-19 on research, reported the impact to be negative (n = 430, 78.8%), and made changes in their research focus because of COVID-19 (n = 245, 45.5% somewhat and n = 64, 11.9% a lot) (Table 2). Compared to the respondents not engaging in HSR, the respondents engaging in HSR had significantly higher odds of perceiving (Odds Ratio (OR) = 2.25, 95% Confidence Interval (CI) = [1.07, 4.74], p = .03) and expecting (OR = 4.86, 95% CI = [1.50, 15.79], p = .009) severe impacts of COVID-19 on research. Compared to the respondents not engaging in HSR, the respondents engaging in HSR were 2.28 times more likely to make some changes to their research focus and 3.73 times more likely to make a lot of changes to their research focus because of COVID-19. Adjusted associations between the perceived and expected impacts and engagement in HSR were comparable to the observed bivariate associations.\n\n* p < 0.05;\n\n** p < 0.001.\n\na Multivariable model after adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions.\n\nThe majority of the study respondents reported negative impact of COVID-19 on data collection (n = 387, 76.5%), and over 41% reported negative impact on data analyses (n = 209) and dissemination of the study findings (n = 206) (Table 3). Compared to the respondents who did not engage in HSR, those who engaged in HSR were significantly more likely to report negative impact of COVID-19 on data collection (OR = 2.16, 95% CI = [1.36, 3.45], p = .001). There was not any statistically significant association observed between engagement in HSR and impact of COVID-19 on data analyses (OR = 0.94, 95% CI = [0.65, 1.36], p = .74) or dissemination (OR = 1.35, 95% CI = [0.93, 1.95], p = .11). After adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions, the odds of the respondents who engaged in HSR to report negative impact on data collection remained higher than the odds of the respondents who did not engage in HSR (Adjusted Odds Ratio (aOR) = 2.74, 95% CI = [1.63, 4.62], p < .001). The associations between engagement in HSR and impact of COVID-19 on data analyses (aOR = 0.92, 95% CI = [0.61, 1.37], p = .67) and dissemination (aOR = 1.28, 95% CI = [0.86, 1.92], p = .23) remained statistically insignificant after adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions.\n\n* p < 0.05;\n\n** p < 0.001.\n\na Multivariable model after adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions.\n\nThe majority of the study respondents reported negative impact of COVID-19 on recruiting students for research activities (n = 327, 70.3%) and providing research-related learning opportunities for students (n = 328, 69.2%), and 43.1% (n = 192) reported negative impact on providing financial support for students. There was not any statistically significant difference observed in impact of COVID-19 on recruiting students for research activities (OR = 1.13, 95% CI = [0.75, 1.71], p = .56), providing financial support for students (OR = 0.98, 95% CI = [0.66, 1.45], p = .93), and providing research-related learning opportunities for students (OR = 0.999, 95% CI = [0.67, 1.50], p = .997) based on engagement in HSR. The association between engagement in HSR and impact of COVID-19 on student engagements remained statistically insignificant after adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions.\n\nThe majority reported at least some impact of the needs for social distancing (n = 465, 87.9%) or the needs for wearing personal protective equipment (n = 368, 70.9%) on conducting research (Table 4). Compared to the respondents who did not engage in HSR, those who engaged in HSR were significantly more likely to experience a lot of impact of the needs for social distancing (OR = 1.83, 95% CI = [1.02, 3.31], p = .045) or personal protective equipment (OR = 2.37, 95% CI = [1.42, 3.94], p < .001) on their research. After adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions, the respondents who engaged in HSR remained significantly more likely to experience a lot of impact from the needs for social distancing (aOR = 2.82, 95% CI = [1.46, 5.45], p = .002) or personal protective equipment (aOR = 2.98, 95% CI = [1.69, 5.24], p < .001) than those who did not engage in HSR.\n\n* p < 0.05;\n\n** p < 0.001.\n\na Multivariable model after adjusting for principal investigator status, number of years engaging in research, and use of experimentation or interventions.\n\n\nDiscussion and conclusions\n\nThis study examined the university-based researchers’ perceived and expected impact of COVID-19 on conducting HSR and non-HSR. Consistent with other studies (Omary et al., 2020; Rhodus et al., 2020; Weiner et al., 2020; Yanow and Good, 2020), the current study found that both researchers engaging in HSR and non-HSR perceived that their research was impacted negatively by COVID-19. As predicted, the perceived and expected impact tend to be more severe for HSR than in non-HSR. This study showed greater likelihoods of changing research focus, experiencing negative impacts on data collection, and experiencing negative impacts from the needs for social distancing or wearing of personal protective equipment among the researchers conducting HSR versus those not conducting HSR.\n\nBoth researchers engaging and not engaging in HSR reported increased challenges in recruiting students for research activities and providing research-related learning opportunities for students. This finding can be particularly relevant for health science students who were pulled from direct patient contact in their clinical clerkships in mid-March 2020. The students returning to their clerkship rotations are likely to face unprecedented learning and training environments (Weiner, 2020). Our medical students in particular where allowed to return to direct patient contact in June 2020 with the exception of limited access to COVID-19 positive patients or patients under investigation for COVID-19. This alone created the need for complex algorithms as it pertains to different medical specialties (e.g. Intensive Care Units) and required significant faculty and student instruction/education to navigate. This observation aligns with Yanow and Good (2020)’s discussion of the uncertainty in day-to-day operation and productivity students and trainees are faced. According to the National Opinion Research Center (NORC)’s January 2021 report on the COVID-19 impact on graduate school, only 24% of institutions agreed consistent graduate advising was received by students during the pandemic (Stewart et al., 2021).\n\nIn the short-term, the limited ability to recruit and engage students in research activities can result in an inadequate workforce to meet current research needs. This can also reduce the opportunities for students to learn about the cutting-edge knowledge in the field and gain applicable research skills. In the long-term, this can potentially impact the quantity and quality of the future research workforce. This finding implies the importance of dedicated efforts to enable higher education institutions to continue to engage students in research activities and to provide quality research-related learning opportunities in the context of the pandemic. While the NORC report provides valuable insights regarding the innovations emerged in graduate schools during the pandemic (Stewart et al., 2021), the report did not discuss about the research training for students. Monitoring of future research pipeline and especially impact on academic medicine should be an area for future research.\n\nCompared to the researchers not engaging in HSR, those engaging in HSR can potentially face greater challenges in maintaining their research focus and data collection because of the short- and long-term changes generated by COVID-19 on individual attitudes, behaviors, lifestyle, and social norms (Bartik et al., 2020; Carel et al., 2020; UN, 2020). Some HSR investigators could be influenced directly by COVID-19 and inevitably need to adapt their research as illustrated in the following examples. Research focusing on efficacy of diabetes education programs in community or clinical settings might inevitably be put on a hold until the appropriate safety measures were built into its research protocol. A major revision might include shift to an online education platform. While such shift to digital tools can create an opportunity for some researchers, the opportunity may not be appreciated by all researchers in the field and the changes can directly impact any ongoing research projects. For instance, in an evaluation research focusing on opioid overdose and naloxone administration training for health science students shifted the program delivery from in-person format to an online format. Shift to the online course format could limit the comprehensiveness of naloxone administration training. Furthermore, shift to the digital tools can restrict diversity of the training and research program reach. Another example is the delays or pause of clinical trials due to the government restrictions on travel to administer the proposed intervention. While executive orders restricting travel are perceived as a necessary or inevitable safety measures, such safety initiative negatively influences the progress of research and limits the opportunity to train students, who are likely to have limited time in a school, in research conduct.\n\nHSR could also be indirectly influenced. Previous studies showed that demographic characteristics and appearance of researchers and social interaction between human subjects and researchers can influence the data collected from the human subjects (Campbell et al., 2019; Bittmann, 2020). The needs for social distancing and wearing of personal protective equipment could influence both appearance of researchers and social interaction with human subjects. For example, a medical student commented about facial masks impeding verbal communication with her patients (Weiner, 2020). In addition, COVID-19 can directly impact human subjects’ experiences with interpersonal interaction (Carel et al., 2020; Ghosh et al., 2020), as well as their safety concern about participating in a research study. Depending on their locations, medical and health science students returning to their clerkship rotations might need to work with a greater volume of patients with lower health care capacity.\n\nThe long- and short-term impacts of COVID-19 on both University budgets and household financial situations can also affect the provision of and meaning of research stipends to human subjects. Furthermore, the comparability of the study findings before, during, and after COVID-19 presents challenges for HSR, especially if the outcome variable of interest is impacted independently of any intervention efforts (e.g., lifestyle behaviors such as physical activity or substance abuse behaviors).\n\nThe current study findings are based on self-reported perceptions rather than objective measures, such as research productivity. While the questionnaires used in this study was face-validated by researchers from various disciplines, the questionnaires did not go through a vigorous validation and reliability assessments. Further limitations of the current study include the sample representativeness and study generalizability. While the overall response rate could not be estimated, the response rates among the principal investigators at the main campus location was about 11%. In terms of demographics, the faculty respondents consisted of a higher proportion of White (85%) and a smaller proportion of female (43%), as observed in the institutional and national faculty demographics. The latest institutional diversity data available showed 63% non-Hispanic White and 36% female (Office of Diversity, 2021). Nationwide full-time faculty in degree-granting postsecondary institutions data showed less than 70% White and 44% female (NCES, 2018). There were some over-representation of White faculty members in this study, which may be related to the selection bias or related to the differences in the target population (i.e., faculty engaging in research or teaching vs. faculty engaging in research and teaching).\n\nThis study utilized the data collected from a large public Research 1 university system at a single point in time, and hence the study finding may not be generalizable to other types of universities or settings. However, given the common themes in COVID-19 associated changes (examples: social distancing, sanitation, and personal protective equipment), it can be assumed that the observed impact of COVID-19 on research is comparable in academic medicine and other settings and will continue to be a challenge as the pandemic timeline is uncertain. More studies from diverse research settings could help illuminate the impact of pandemics and other prolonged global emergencies on the research enterprise. Another limitation is that the sample had incomplete representation of researchers from diverse fields. While the study team attempted to make the survey relevant to all existing research fields by consulting about the survey questions and wording with researchers from various backgrounds, not all fields use common language and research methods. The study team received some questions from the respondents about the survey language (e.g., ‘secondary data’) and post-survey comments regarding relevancy of some questions (e.g., a question about participant interaction) in the survey to their fields. Therefore, this study focused on the general questions that were likely to be relevant in most fields. In addition, the survey questions are shared (Table 1) for the readers’ information.\n\nSeveral brief reports and perspectives have anecdotally discussed the impact of COVID-19 on research and scientists (Omary et al., 2020; Yanow and Good, 2020; Wigginton et al., 2020). Despite the limitations, this study adds to the growing body of research based on primary data collected from researchers. First, this study provides important insights regarding the potentially lost learning opportunities for students to be addressed in higher education institutions, with specific focus on research training. Bridging from the lessons learned from the current pandemic, higher education institutions should develop the emergency standards of operation for faculty, staff, and students to enable continued learning and training opportunities. Further qualitative or mixed-methods evaluation of phenomenon can benefit the development of such emergency standards of operation. Lessons learned from this process will make us better equipped to deal with future challenges and the potential negative consequences to our ongoing academic research activities.\n\nSecond, the empirical findings in this study showed that researchers engaging in HSR have been disproportionately impacted by COVID-19 and that efforts are needed to further understand and overcome their challenges. For example, the needs for social distancing and wearing personal protective equipment generated additional hurdles for researchers engaging in HSR. Potential solutions might be to consider pandemic or emergency preparation budget as a part of the grant budget or higher education institutions develop emergency fund for research in academic settings.\n\nWhile such efforts may already be underway in response to the swiftly changing circumstances, a natural progression of the current work would be to identify and examine the existing efforts and provide insights into ways that researchers, research institutions, and sponsoring agencies can adapt their research. These findings have strong implications for the academic medicine community, whether primarily lab-based studies or involving clinical or community-based research involving human subjects.\n\nNext steps include continuing to analyze the ongoing impact of COVID-19, as well as its vaccine deployment, on both our HSR and non-HSR throughout our institution and utilizing our findings to try and find creative ways to mitigate the negative effects of the pandemic we are currently still facing or other challenges that we will face in the future. It is critical to move beyond a simplistic view of negative research impacts to a better understanding of how academic research and associated training can be enriched by meeting challenges of the past year.\n\n\nData availability\n\nThe data supporting the findings of the study are not made publicly available due to the data use restrictions stated in the informed consent form (approved by TAMU IRB) and considerations that their containing information that could compromise the privacy of research participants. Given that the data were collected from staff and faculty from a university system there are concerns that a combination of several key demographic characteristics, research fields, and research types can potentially identify an individual. For researchers with specific research/study questions relating to the data, the anonymized data can be available on request from the lead author [MO]. Upon reasonable request, with TAMU IRB approval, we can share whether participants engaged in any human subject research (yes/no) and key outcome data (i.e., COVID-19 impact on research) without any demographic characteristics, research fields, and research type data that can potentially identify an individual.\n\nTexas Data Repository: Effects of the COVID-19 pandemic on university-based research conduct and training. https://doi.org/10.18738/T8/W6IGCE (Ory, 2022).\n\nThis project contains the following extended data:\n\n- COV19Res_Online Survey_TDR_220411.pdf (A copy of the online questionnaire)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nWe thank Jason Moats, PhD, Texas A&M Engineering Extension Service and core member of the Texas Emergency Management Advisory Group for his helpful insights on research impacts. Also, the authors wish to thank all respondents who volunteered to participate in this study and our colleagues who supported the study by providing insight and expertise and assisting with recruitment.\n\n\nReferences\n\nAmerican College Health Association (ACHA): ACHA guidelines preparing for COVID-19.2020. June 30, 2021.Reference Source\n\nBartik AW, Bertrand M, Cullen Z, et al.: The impact of COVID-19 on small business outcomes and expectations. Proc. Natl. Acad. Sci. U. S. A. 2020; 117(30): 17656–17666. PubMed Abstract | Publisher Full Text\n\nBernard MA, Lauer M: COVID-19 Survey of NIH and extramural staff – Preliminary findings.2020. March 19, 2021.Reference Source\n\nBittmann F: The more similar, the better? How (mis) match between interviewers and respondents in survey situations affects item nonresponse and data quality. Survey Research Methods. 2020; 14(3): 301–323. Publisher Full Text\n\nCampbell JI, Musiimenta A, Burns B, et al.: The importance of how research participants think they are perceived: Results from an electronic monitoring study of antiretroviral therapy in Uganda. AIDS Care. 2019; 31(6): 761–766. PubMed Abstract | Publisher Full Text\n\nCarel H, Ratcliffe M, Froese T: Reflecting on experiences of social distancing. Lancet. 2020; 396(10244): 87–88. PubMed Abstract | Publisher Full Text\n\nCenters for Disease Control and Prevention (CDC): Considerations for Institutions of Higher Education.2020. November 27, 2020.Reference Source\n\nDonthu N, Gustafsson A: Effects of COVID-19 on business and research. J. Bus. Res. 2020; 117: 284–289. PubMed Abstract | Publisher Full Text\n\nGhosh A, Sharma K, Choudhury S: COVID-19 and physician-patient relationship: potential effects of ‘masking’, ‘distancing’ and ‘others.’. Fam. Pract. 2020; 38(2): 193–194. PubMed Abstract | Publisher Full Text\n\nHaleem A, Mohd J: Effects of COVID-29 pandemic in daily life. Current Medicine Research and Practice. 2020; 10(2): 78–79. PubMed Abstract | Publisher Full Text\n\nJohns Hopkins University Center for Systems Science and Engineering (CSSE): COVID-19 dashboard.2021. June 30, 2021.Reference Source\n\nKrishnamurthy S: The future of business education: A commentary in the shadow of the COVID-19 pandemic. J. Bus. Res. 2020; 117: 1–5. PubMed Abstract | Publisher Full Text\n\nMyers KR, Tham WY, Yin Y, et al.: Unequal effects of the COVID-19 pandemic on scientists. Nat. Hum. Behav. 2020; 4(9): 880–883. PubMed Abstract | Publisher Full Text\n\nNational Center for Education Statistics (NCES): Table 315.20. Full-time faculty in degree-granting postsecondary institutions, by race/ethnicity, sex, and academic rank: Fall 2015, fall 2016, and fall 2017.2018. March 19, 2021.Reference Source\n\nNational Institutes of Health (NIH): Human Subjects Research.2020. October 29, 2020.Reference Source\n\nNicol GE, Piccirillo JF, Mulsant BH, et al.: Action at a distance: Geriatric research during a pandemic. J. Am. Geriatr. Soc. 2020; 68(5): 922–925. PubMed Abstract | Publisher Full Text\n\nOffice for Diversity: Data: Faculty. nd. 2021 March 19.Reference Source\n\nOmary MB, Eswaraka J, Kimball SD, et al.: The COVID-19 pandemic and research shutdown: Staying safe and productive. J. Clin. Investig. 2020; 130(6): 2745–2748. PubMed Abstract | Publisher Full Text\n\nOry MG: Online Survey (6/8/2020-7/10/2020).2022. Texas Data Repository, [dataset], V1. Publisher Full Text\n\nPackenham JP, Rosselli RT, Ramsey SK, et al.: Conducting science in disasters: Recommendations from the NIEHS working group for special IRB considerations in the review of disaster related research. Environ. Health Perspect. 2020; 125(9): 094503. PubMed Abstract | Publisher Full Text\n\nRhodus EK, Bardach SH, Abner EL, et al.: COVID-19 and geriatric clinical trials research. Aging Clin. Exp. Res. 2020; 32: 2169–2172. PubMed Abstract | Publisher Full Text\n\nSoto-Acosta P: COVID-19 pandemic: Shifting digital transformation to a high-speed gear. Inf. Syst. Manag. 2020; 37(4): 260–266. Publisher Full Text\n\nStewart DW, Davoren AK, Neumeister JR, et al.: Graduate schools respond to COVID-19: Promising pathways to innovation and sustainability in stem education.2021. June 30, 2021.Reference Source\n\nUnited Nations (UN): Everyone Included: Social Impact of COVID-19.2020. November 27, 2020.Reference Source\n\nWeiner DL, Balasubramaniam V, Shah SI, et al.: COVID-19 impact on research, lessons learned from COVID-19 research, implications for pediatric research. Pediatr. Res. 2020; 88: 148–150. PubMed Abstract | Publisher Full Text\n\nWeiner S: Excited, scared, ready: Medical students head back to clerkships. AAMC. 2020 June 2. June 30, 2021.Reference Source\n\nWigginton NS, Cunningham RM, Katz RH, et al.: Moving academic research forward during COVID-19. Science. 2020; 368(6496): 1190–1192. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization (WHO): Ethical standards for research during public health emergencies: Distilling existing guidance to support COVID-19 R&D.2020. June 30, 2021.Reference Source\n\nYanow SK, Good MF: Nonessential research in the new normal: The impact of COVID-19. Am. J. Trop. Med. Hyg. 2020; 102(6): 1164–1165. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "225226",
"date": "30 Nov 2023",
"name": "Daniel Hermawan",
"expertise": [
"Reviewer Expertise Marketing",
"communication",
"innovation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. This paper give an overview of university-based researchers’ perspectives and experiences, focusing on student engagement in research and conduct of human subject research (HSR), however \"experiences\" in this context is not yet clearly defined and quite few discuss in this paper.\n2. Several parts of this paper still lack of references.\n3. Elaborate human subject research (HSR) from a large US university system's overview in Introduction.\n4. Several Table, i.e. Table 1. need to discuss more, since quite unclear.\n5. Explain the reason to choose bivariate and multivariable logistic regression models in this research.\n6. Title can be revised to be more concise.\n7. Give implication of this research if Covid-19 situation or similar occur again in the future.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1195
|
https://f1000research.com/articles/10-803/v1
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13 Aug 21
|
{
"type": "Research Article",
"title": "Interplay between COVID-19 vaccines and social measures for ending the SARS-CoV-2 pandemic",
"authors": [
"Glenn Young",
"Pengcheng Xiao",
"Ken Newcomb",
"Edwin Michael",
"Pengcheng Xiao",
"Ken Newcomb",
"Edwin Michael"
],
"abstract": "Background: The development and authorization of COVID-19 vaccines has provided the clearest path forward to eliminate community spread and thus end the ongoing SARS-CoV-2 pandemic. However, the limited pace at which the vaccine can be administered motivates the question, to what extent must we continue to adhere to social intervention measures such as mask wearing and social distancing? Methods: We develop a mathematical model of COVID-19 spread incorporating both vaccine dynamics and socio-epidemiological parameters. We use this model to study two important measures of disease control and eradication, the effective reproductive number Rt and the peak intensive care unit (ICU) caseload, over three key parameters: social measure adherence, vaccination rate, and vaccination coverage. Results: Our results suggest that, due to the slow pace of vaccine administration, social measures must be maintained by a large proportion of the population until a sufficient proportion of the population becomes vaccinated for the pandemic to be eradicated. By contrast, with reduced adherence to social measures, hospital ICU cases will greatly exceed capacity, resulting in increased avoidable loss of life. We then investigate the threat of localized outbreaks in low-vaccinated populations that have removed all social intervention mandates, and show that such populations could remain highly susceptible to major outbreaks particularly in the face of more easily transmissible variants. Conclusions: These findings highlight the complex interplay involved between vaccination and social protective measures, and indicate the practical importance of continuing with extant social measures while vaccines are scaled up to allow the development of the herd immunity needed to end or control SARS-CoV-2 sustainably.",
"keywords": [
"COVID-19",
"SARS-CoV-2",
"mathematical modeling",
"vaccination",
"non-pharmaceutical intervention",
"epidemiology",
"differential equations",
"boundary value problems"
],
"content": "Introduction\n\nThe advent of COVID-19 vaccines and mass vaccinations of populations have led to widespread public expectation that we may be able to end the ongoing SARS-CoV-2 pandemic in some economically advanced countries by as early as the of beginning 20221. While the pace at which these vaccines have been developed and authorized by governments for population-wide usage has been unprecedented2 reflecting the desire to fast track the ending or control of the pandemic given the socio-economic costs of protracted non-pharmaceutical interventions (NPIs), such as cyclical lockdowns and social distancing measures3, it is also clear that several features of the current vaccines and vaccination strategies for achieving this goal remain unresolved4,5.\n\nFirst, it is important to consider that vaccines serve two major purposes: to protect the individual from contracting the disease and to stop the transmission of community infection. While the initial vaccine trial data for the three major vaccines approved for use thus far in developed world settings, viz. Pfizer-BioNTech, Moderna, and Oxford-AstraZeneca, indicate that these could induce very high levels of protection (70–90%) against symptomatic disease6, more recent data with regard to the AstraZeneca vaccine suggests that vaccination may also reduce community transmission of the virus significantly7. These data suggest that both disease outcomes and transmission could be significantly reduced in communities as a result of mass deployments of these vaccines. A key factor, however, is that in both cases current vaccines are not 100% protective. Second, it is apparent that the number of vaccines initially available and the logistical challenges connected with their delivery will hamper the rapid vaccination of populations, which will prolong the time to eradicate the disease through vaccination in populations8. An added challenge is the reduced effectiveness of these vaccines as currently formulated against newly emerging virus variants9.\n\nA third important factor is to consider the epidemiological and social contexts in which vaccinations will take place. This is important because many populations undergoing vaccinations will have already experienced one or more waves of COVID-19, as a result of which some level of natural immunity to SARS-CoV-2 will likely to be in operation in these communities. Such pre-existing immunity could indicate that the vaccine coverage to end the pandemic (reduce the prevailing effective reproduction number, Rt to below 1 sustainably) need not be too high even if vaccine effectiveness is not perfect10, increasing the prognosis of using the current vaccines to end the pandemic. On the other hand, these populations are also currently experiencing various levels of NPIs3. Such social mitigation or containment measures, while protecting the susceptible fraction from infection will act also to depress the development of natural immunity in the population. These outcomes suggest that there may be complex interactions between the two interventions, a better understanding of which will be crucial in determining how best to optimally deploy these tools for controlling or ending the pandemic. Further, investigating such interactions will also be important in fully understanding the implications of relaxing these NPIs as vaccinations roll out10,11.\n\nHere, we extend our existing data-driven socio-epidemiological SEIR-based COVID-19 mathematical model12 by incorporating imperfect vaccination dynamics in order to undertake a theoretical investigation of this topic. To enhance realism we use the basic model calibrated to infection data on the course of the pandemic in the Tampa Bay region, and use the resulting model to investigate the interplay between vaccination and social protective measures for effective control or elimination of the pandemic. In particular, we explore the dynamical implications of imperfect vaccine effectiveness, vaccine rollout rates, and coverage of vaccination and social measures on the eradication of the disease in the community, and the effects these will have for virus transmission and critical care requirements. We also inspect the effect that the current vaccination roll out will have on the extent to which a population may relax social measures to return to normalcy, and the threat of future outbreaks in communities with low vaccination rates.\n\n\nMethods\n\nHere we develop an extended SEIR model to assess population-level disease dynamics of COVID transmission. We consider a population of fixed size that we divide into eleven interacting sub-populations: susceptible without access to a vaccine (S), vaccinated susceptible (V), unvaccinated susceptible (with access to a vaccine) (X), exposed but not infectious (E), asymptomatic infected (Ia), pre-symptomatic infected (Ip), mildly symptomatic infected (Im), hospitalized infected (Ih), critical care infected (Ic), recovered (R), and died (D). Since the population size is fixed, we can impose the condition that S + X + V + E + Ia + Ip + Im + Ih + Ic + R + D = 1, and each population can therefore be interpreted as a proportion of the total population.\n\nOur model is visualized as a diagram in Figure 1. Importantly, we assume that asymptomatic, pre-symptomatic, and mildly symptomatic individuals transmit the disease at the same rate β, and that these are the only sources of transmission. The transmission rate is reduced due to social measures (face masks, social distancing, self quarantine, etc) by a factor of 1 – ac among all infectious individuals, where c is the efficacy of social measures and a is the proportion of the population adhering to social measures.\n\nThe vaccine becomes available to the population at rate µ, and individuals can choose whether or not to get the vaccine. Specifically, proportion ϕ of the susceptible population S enters the vaccinated population V at rate µ, while proportion 1 – ϕ of the susceptible population enters the unvaccinated class X at the same rate. This parameter ϕ allows us to analyze the effects of vaccine coverage, specifically as a consequence of individuals who are unwilling to receive the vaccine13. Vaccinated individuals are infected at a rate reduced by 1 – ξ, where ξ is the efficacy of the vaccine, while the unvaccinated class X has the same dynamics as the susceptible without access to a vaccination class S.\n\nWith these assumptions, our model is given by the following system of eleven ordinary differential equations:\n\nThe state variables and parameters are defined in Table 1 and Table 2, respectively. The parameters are estimated by the methods described below.\n\nEach variable should be interpreted as a proportion of the total population.\n\nThe value for each parameter is used throughout this work unless stated otherwise. All rate parameters are measured in units of (day)−1.\n\nWe used a Monte Carlo based Bayesian Melding approach to parameterize the base model using case notification, death, and mobility data reported for the Tampa Bay region for the period between March 10th and August 24th 2020. (details of methods provided in 12). Briefly, all social and epidemiological model parameters that could not be fixed at initiation were sequentially updated using 10-day blocks or segments of data between the above estimated period from their initial prior values using this procedure, and the final model thus estimated was used for the simulations carried out in this paper. Confirmed case data for the four counties comprising Tampa Bay, viz. Hillsborough, Pasco, Pinelles and Polk, were obtained from the Johns Hopkins University Coronavirus Resource Center14. Mobility data serve as an estimate for population mixing and the fraction of the population under restricted movement in the counties concerned were obtained from the location data firm, Unacast. Our consolidated parameter data can be accessed in 15.\n\nThe effective reproductive number Rt quantifies the average number of secondary infections caused by each new infection. We can calculate Rt using the next generation matrix method developed in 16. The next-generation matrices for system (1) are:\n\nand\n\nwhere\n\nis the force of infection.\n\nThen the effective reproduction number Rt is exactly the spectral radius of FV−1:\n\nWe use this formula to assess the viability of vaccination programs on disease eradication in the following sections.\n\nHere we use our model 1 to establish two boundary value problems (BVPs). The first allows us to determine the time necessarily to drive Rt < 1, and thereby control the spread of the disease, under varied vaccination rates. Solution of the second determines the peak ICU case load over the same vaccination rate.\n\nFor both BVPs, we consider system (1) extended to include an auxiliary variable τ:\n\nThis new variable provides an additional degree of freedom allowing us to solve the system as a BVP with a terminal, parameter-dependent boundary condition (BC).\n\nTo determine the time until Rt < 1, we solve system (3) with BCs\n\nwhere Rt(t) is defined in equation (7). The variable tau within solutions of this BVP represents the time at which Rt(t) = 1. Since Rt(t) is strictly decreasing over time, Rt(t) < 1 for all t > τ, and τ is therefore the time at which the disease is eradicated.\n\nTo determine peak ICU cases, we consider system (3) with BCs\n\nThe third boundary condition is equivalent to Ic′(τ) = 0 and therefore requires Ic to be at a local maximum at time τ. The variable τ is therefore the time at which Ic reaches its maximum17. Evaluating Ic at t = τ for any solution of BVP (3)–(5) provides the peak ICU cases for the fixed parameter set.\n\nUsing XPPAUT (Version 8.0)18, we can numerically continue solutions to system (3) with BCs (4) or (5) over any system parameter; in particular, we use this method to evaluate the influence of ϕ and µ in the following section.\n\nAll model simulation and numerical analysis was performed using XPPAUT (Version 8.0). Our code can be accessed at15. Data from XPPAUT was exported to MATLAB (Version R2019a) to create Figure 2–Figure 6. Julia (Version 1.6.2) is an open-source software that could alternatively be used to the same effect.\n\nThe vaccination rate and efficacy are µ = 0.02 and ξ = 0.94, respectively. The right panel shows the same blue and green curves from the left panel, but zoomed in.\n\nEach curve defines Rt = 1 over varied parameters with ξ = 0.94. (Left) Rt = 1 plotted over vaccine coverage ϕ and social measure compliance a. The region above each curve represents parameter pairs for which Rt < 1. (Right) Rt = 1 plotted over vaccine coverage ϕ and remaining susceptible population Sr with no, medium, and high proportions of social measure compliance. The region below each curve represents parameter pairs for which Rt < 1.\n\n(Left) Time until Rt < 1 over ϕ. (Right) Peak ICU cases over ϕ (log scale). In both panels, µ = 0.02, and the red curve corresponds to no social measures (a = 0), the blue curve corresponds to moderate social measure compliance (a = 0.5), and and the black curve corresponds to high compliance (a = 0.8). The curves in this figure were created by solving boundary value problem (3) with boundary conditions (4) and (5) in the left and right panels, respectively.\n\n(Left) Time until Rt < 1 over µ. (Right) Peak ICU cases over µ (log scale). In both panels, ϕ = 0.6, and the red curve corresponds to no social measures (a = 0), the blue curve corresponds to moderate social measure compliance (a = 0.5), and and the black curve corresponds to high compliance (a = 0.8). The curves in this figure were created by solving boundary value problem (3) with boundary conditions (4) and (5) in the left and right panels, respectively.\n\nThe top row (A and B) visualizes outbreak scenarios with baseline transmission rate β = 0.76. The bottom row (C and D) visualizes outbreak scenarios with 1.5× baseline transmission rate β = 1.14. The left column (A and C) shows peak ICU cases; the right column (B and D) shows total active cases when Ic is at its peak. In each panel, the colored curves correspond to varied remaining susceptible population sizes: fully susceptible (red curves), 80% susceptible (blue curves), and 60% susceptible (black curves). In each curve, ϕ = 0.6, µ = 0.02, a = 0, and the simulations were all initialized with E(0) = 0.001.\n\n\nResults\n\nWe begin by determining the extent to which a population can relax social measures once a vaccine becomes available and still control the virus. Here, we use simulations of the number of individuals requiring intensive care as a measure of control, and thus consequently, we consider the relationship between vaccine coverage ϕ and social measure compliance a on ICU hospitalization to address this question. Figure 2 shows ICU hospitalizations over time under various vaccine coverages and social measures. The red curve shows ICU cases without any vaccine or social measures, serving as a baseline for comparison. The black curve shows these cases with some vaccination and no social measures; the green curve shows ICU cases with strong social measures and no vaccine; the blue curve shows ICU cases with both vaccine coverage and social measures. Of course, greater vaccine coverage and stronger social measures result in fewer cases; however, social measures reduce the incidence of cases requiring intensive care much more than vaccine coverage. This is due to the slow vaccination rate µ, as we show in Time to eradication, below.\n\nWe use the effective reproduction number Rt to study strategies by which the virus can be eradicated. Importantly, Rt = Rt(t) is a function of time due to its dependence on S, X, and V: as the susceptible populations decrease, so does Rt. We consider the temporal dynamics of Rt in the following section. Here, we consider the idealized case in which proportion ϕ of the population is instantaneously vaccinated, V = ϕSr and X = (1 – ϕ)Sr, where Sr is a new parameter representing the remaining susceptible proportion of the population at the time the vaccine is administered (that is, 1 – Sr is the proportion of the population who are currently infected, recovered, or deceased). In this case, λ can be written\n\nand so\n\nThe ideal goal in eradicating the disease is to permanently reduce the effective reproductive number below the threshold Rt = 1. Figure 3 shows curves in parameter space satisfying Rt = 1 with ξ = 0.94. On the left, curves are plotted over vaccine coverage ϕ and social measure compliance a and remaining susceptible population Sr = 1 (red curve) and Sr = 0.8 (blue curve). In order to achieve Rt < 1, (ϕ, a) pairs must lie above the curve. Note that disease eradication without social measures (a = 0) would require more than 80% of the population to receive a vaccine that is 94% effective in a naive population (Sr = 1); a population in which 20% have already been exposed would require approximately 75% to receive a vaccine in order to eradicate the disease without social measures. On the right, we show curves defined by Rt = 1 over vaccine coverage ϕ and remaining susceptible population Sr for varied social measures. For each fixed value of a, (ϕ, Sr) pairs must be below the curve to drive Rt < 1. Without social measures in place (red curve), approximately 75% of the population would have to be exposed to the virus before the disease is eradicated without a vaccine. In general, the larger the remaining susceptible population, the higher the vaccination coverage required to eradicate the disease. Importantly, the vaccine coverage threshold necessary to drive Rt < 1 decreases with increased social measures.\n\nVaccine rollout will not be instantaneous; it will likely take months to vaccinate a majority of the population. We therefore must consider the simultaneous effects of infection dynamics and slow vaccination rates on disease eradication, which requires considering the effective reproduction number as a function of time:\n\nAs the three susceptible populations S, X, and V change over time via infection and vaccination dynamics, Rt(t) strictly decreases. We denote the time at which Rt(t) decreases below 1 by th; that is, Rt(th) = 1. Time th marks the beginning of the end of community spread, and we therefore refer to th as the time to eradication. The left panel of Figure 4 shows th as a function of vaccination coverage ϕ for varied social measure compliance a with vaccination rate µ = 0.02. The time to eradication remains nearly constant over all ϕ for low social measure compliance (a = 0, 0.5; red and blue curves): this is due to the slow vaccination rate µ, and the comparably fast infection rate due to low social measure compliance. That is, for sufficiently small a, the virus spreads quickly through the population, infecting the susceptible population S much more quickly than the susceptibles become vaccinated. Thus, eradication is achieved primarily through infection, rather than through vaccination. For high social measure compliance (a = 0.8; black curve), th is large for small ϕ. This is because, for large a, the infection dynamics are slowed down, but because ϕ is small, the vaccination rate is also slow. The two mechanisms by which eradication is achieved (infection and vaccination) are therefore both slow, and so th is large. As ϕ increases, however, th decreases dramatically. The effective reproduction number Rt decreases as a increases, and thus achieving Rt = 1 requires less vaccination and infection for large a. Thus, despite the slow vaccination rate µ, there is a critical ϕ value past which the susceptible population becomes vaccination quickly enough so that Rt decreases below 1 due primarily to vaccine administration. In other words, the vaccination timescale overtakes the infection rate timescale for sufficiently large ϕ.\n\nThe right panel of Figure 4 shows the maximum ICU case load (that is, the peaks of the curves in Figure 2) as a function of vaccination coverage for varied a. Unsurprisingly, as ϕ increases, the maximum ICU load decreases for each a. However, the peak ICU load remains comparatively high for a = 0 and a = 0.5 (red and blue curves, respectively) compared with a = 0.8 (black curve). For this latter case, the peak ICU load decreases dramatically from ϕ = 0 until around ϕ = 0.4, then remains low for all larger ϕ. ICU capacity in most states is between 10−4 and 3 × 10−4: peak ICU cases only remain below this threshold for high social measure compliance and vaccination coverage.\n\nFigure 4 suggests that sustained social measures help to eradicate the disease more efficiently than vaccination programs. This at least in part due to a relatively slow vaccination rate: µ = 0.02. We now investigate the influence of vaccination rate µ on the time to eradication and on peak ICU cases. The left panel of Figure 5 shows the time until the disease is eradicated, th, as a function of vaccination rate, µ, with ϕ = 0.6. Without or with sufficiently low social measure compliance (a = 0 and a = 0.5; red and blue curves), the time until eradication increases with µ. For both cases, vaccination coverage ϕ is too low to to eradicate the disease in a completely susceptible population (Figure 3), and consequently a non-negligible percentage of the population must become infected before Rt < 1. As µ increases, the infection dynamics slow down, causing the time it takes for Rt to drop below 1 to increase. For high social measure compliance (a = 0.8; black curve), the time to eradication decreases with µ. When a is sufficiently large, ϕ = 0.6 is large enough to eradicate the disease through vaccination alone (Figure 3), and increasing the vaccination rate therefore reduces the time to eradication. Thus, rapid eradication of the virus is only achievable with sustained, widely obeyed social measures.\n\nThe right panel of Figure 5 shows the peak ICU load over µ. Naturally, the faster the vaccine is administered to the population, the lower the peak ICU case load will be. However, peak ICU load only remains below typical ICU capacity (1–3×10−4) for small µ when social measure compliance is high (black curve). This again suggests that social measures must remain in place throughout the vaccination program in order to avoid hospital strain and associated loss of life.\n\nHere we consider the potential for localized outbreaks within low-vaccinated populations in which social measures are no longer observed (a = 0). We focus on two important quantities: the proportion of the population that have already received the vaccination at the onset of the outbreak, V(0), and the proportion of the population that are still susceptible at the onset, Sr. The quantity Sr is interpreted as the proportion of the population that has not contracted and recovered from COVID-19, and consequently 1 – Sr is the proportion that has contracted the virus and is no longer susceptible. Figure 6 visualizes peak ICU cases (Ic; Figures 6A and C) and total active cases (Ia + Ip + Im + Ih + Ic) at the time when ICU cases are at their peak (Figures 6B and D) as a function of V(0). In the upper two figures (A and, the transmission rate is the baseline value we have used throughout this work (β = 0.76). We assess the risk that a fast-spreading variant poses in the lower two figures (C and D) by increasing the transmission rate by 50% relative to baseline (β = 1.14). In each curve, the model is initialized with E(0) = 0.001. The colored curves correspond to varied values of Sr: Sr = 1 is shown in red, Sr = 0.8 in blue, and Sr = 0.6 in black. Naturally, outbreaks are reduced in magnitude for smaller Sr. Similarly, each curve decreases as V(0) increases. Both of these observations provide an obvious but important conclusion: the smaller the proportion of fully-susceptible individuals, the smaller the outbreak will be. Moreover, for each curve, there is a critical V(0) value after which the total number of cases is constant. This is the V(0) value for which R1 = 1 given the corresponding value of Sr. For all V(0) larger than this critical value, Rt < 1, and the only active cases are those that develop among the initially exposed individuals.\n\n\nDiscussion and conclusion\n\nWe introduce an extended SEIR socio-epidemiological model incorporating vaccination dynamics to evaluate the interactions between vaccination and social measures for controlling or ending the spread of COVID-19. Following standard analytical techniques16, we derived an explicit form for the effective reproduction number Rt. This value is of central concern to controlling the pandemic: through a combination of natural infection, social measures, and vaccination administration, we must drive Rt < 1 in order to eradicate the disease. Our analysis therefore focused on the influence of social measures and vaccination rates on the time until the disease is eradicated, but also considered hospital demand as a function of these interventions. Importantly, we show that while eliminating social measures entirely might help eradicate the disease faster, the hospital demand, and therefore death toll, are reduced dramatically with even partial adherence to social intervention strategies.\n\nOur analysis focused on three parameters: the proportion of the population willing to receive a vaccine ϕ, the proportion of the population willing to adhere to social measures a, and the rate at which vaccines are administered to the population µ. Figure 3–Figure 5 summarize the major results arising from these interactions, and suggest that, with low vaccination rate µ, sustained social measures become increasingly important to keep the hospitalization rates low, even if a large proportion of the population are willing to receive the vaccine (that is; even if ϕ is large). This finding is consistent with previous studies under varied assumptions10,19,20.\n\nThe interplay between social measures and vaccine administration is perhaps most complicated when considering the time until eradication. When the proportion of the population who adhere to social measures is small, the time to eradication is relatively fast (Figure 4 and Figure 5, left panels). This is because, without social measures, the virus spreads quickly, thereby increasing the number of individuals with infection-conferred immunity (or who die due to the disease). On the other hand, when social measure adherence is high, the time to eradication is large for low vaccination coverage and rate, but decreases with both parameters. For low vaccination coverage or rate, population-level immunity is primarily being conferred via infection, and infection rates are low due to high levels of social measures. As vaccination coverage or rate increases, however, the rate at which individuals become vaccinated begins to outpace the rate at which individuals become infected, and the time until eradication becomes small. Importantly, only in the case of high social measure compliance and high vaccination rate or coverage do the number of ICU cases remain manageable (Figure 4 and Figure 5, right panels).\n\nWe further use our model to predict the magnitude of future outbreaks in partially-vaccinated communities. Naturally, if a sufficiently high proportion of the population is vaccinated or has infection-derived immunity, then the Rt value within that community is less than unity, and any new infections are not expected to cause an outbreak (Figure 6). However, if too few individuals are vaccinated, outbreaks remain a significant threat, particularly in light of new, highly contagious variants21.\n\nWe developed our model under a set of assumptions that captured important features of COVID-19 transmission. However, we omitted one or more realities of COVID-19 dynamics that could quantitatively influence our results. First, we did not include any age structure to our model. It is well known that mortality rates due to COVID-19 are disproportionately high among elderly populations. By including age structure, one can study targeted vaccination programs in which the elderly are given earlier access to the vaccine. Second, we include only a single vaccine in our model, while many with varying efficacies are likely to enter the market before the pandemic is over22–24. While incorporating these features into our model would surely result in quantitative differences, the qualitative predictions of our current model would likely remain unchanged; that is, social measures must remain in place throughout the vaccination campaign in order to mitigate hospital and mortality rates. An important consideration for future work is the degree to which variants of the SARS-CoV-2 will increase community spread21, which can be incorporated into our model as a second set of infected classes.\n\nNotwithstanding these limitations, this work highlights several major implications for the use of vaccination for either controlling or eradicating the current pandemic. The first is that slow vaccination roll out rates mean that continuing with currently applied social measures is imperative to containing the clinical outcomes (demand for ICU care and deaths) of the pandemic for a population. Only a ramped-up vaccination rate will allow easing of these social measures. The second important finding arising from the present results is that while social measures under the current slow rate of vaccinations will be crucial to prevent hospitalizations and the death toll from the virus, this intervention will also delay the development of herd immunity in the population. However, two critical results here are that at high levels of social measures, the numbers of individuals that are required to be vaccinated to achieve Rt < 1 can be significantly small, and that there might be a vaccination coverage level past which this can be achieved. We term this as “herd immunity due to social measures”, which will be much lower than the corresponding herd immunity in the absence of social measures. Note, however, that the imposition of social measures will keep a large fraction of the population continuing to be susceptible, and while achieving the lower level of herd immunity through vaccination under these measures will allow interruption of transmission, any relaxation of the latter in the presence of infected individuals, or if infected individuals were to arrive into an area lifting such restrictions, would seed resurgences of infection. This conclusion suggests that only by ramping up vaccinations to achieve natural herd immunity (i.e. the higher level of herd immunity that will be required to prevent transmission in the absence of any social containment measures) will the pandemic be fully suppressed over the longer-term.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nSoftware availability\n\nGithub: COVID-Vaccination-Paper. https://github.com/EdwinMichaelLab/COVID-Vaccination-Paper.\n\nThis project contains the following parameter data and code:\n\n• ParameterSets (Parameter values found using the methods described in Parameter estimation)\n\n• IC_BVP_ac.ode (XPPAUT code used to find the peak ICU cases over varied parameters, shown in the right panels of Figures 4 and 5 in the paper)\n\n• Rt_BVP_ac.ode (XPPAUT code used to track the time to Rt = 1 across parameters, shown in the left panels of Figures 4 and 5)\n\n• model_Vax_ac.ode (XPPAUT code used to run model simulations)\n\nAll code and parameter data available at http://doi.org/10.5281/zenodo.513833215\n\nMIT License.",
"appendix": "References\n\nRandall T: When will life return to normal? in 7 years at today’s vaccine rates. 2021. Reference Source\n\nLurie N, Saville M, Hatchett R, et al.: Developing covid-19 vaccines at pandemic speed. N Engl J Med. 2020; 382(21): 1969–1973. PubMed Abstract | Publisher Full Text\n\nEbrahim SH, Ahmed QA, Gozzer E, et al.: Covid-19 and community mitigation strategies in a pandemic. BMJ. 2020; 368: m1066. PubMed Abstract | Publisher Full Text\n\nBuckner JH, Chowell G, Springborn MR: Dynamic prioritization of covid-19 vaccines when social distancing is limited for essential workers. medRxiv. 2020. Publisher Full Text\n\nLipsitch M, Dean NE: Understanding covid-19 vaccine efficacy. Science. 2020; 370(6518): 763–765. PubMed Abstract | Publisher Full Text\n\nTerry M: Updated comparing covid-19 vaccines: Timelines, types and prices. 2021. Reference Source\n\nWise J: Covid-19: New data on oxford astrazeneca vaccine backs 12 week dosing interval. BMJ. 2021; 372: n326. PubMed Abstract | Publisher Full Text\n\nRitchie H, Ortiz-Ospina E, Beltekian D, et al.: Coronavirus (covid-19) vaccinations - statistics and research. 2021. Reference Source\n\nDavies NG, Barnard RC, Jarvis CI, et al.: Estimated transmissibility and severity of novel sars-cov-2 variant of concern 202012/01 in england. medRxiv. 2020. Reference Source\n\nIboi EA, Ngonghala CN, Gumel AB: Will an imperfect vaccine curtail the covid-19 pandemic in the us? Infect Dis Model. 2020; 5: 510–524. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJentsch P, Anand M, Bauch CT: Prioritising covid-19 vaccination in changing social and epidemiological landscapes. medRxiv. 2020. Publisher Full Text\n\nNewcomb K, Smith ME, Donohue RE, et al.: Iterative near-term forecasting of the transmission and management of sars-cov-2/covid-19 using social interventions at the county-level in the united states. 2020. Publisher Full Text\n\nYoung G, Shim E, Ermentrout GB: Qualitative effects of monovalent vaccination against rotavirus: A comparison of north america and south america. Bull Math Biol. 2015; 77(10): 1854–1885. PubMed Abstract | Publisher Full Text\n\nDong E, Du H, Gardner L: An interactive web-based dashboard to track covid-19 in real time. Lancet Infect Dis. 2020; 20(5): 533–534. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYoung G, Xiao P, Newcomb K, et al.: Interplay between COVID-19 vaccines and social measures for ending the SARS-CoV-2 pandemic. 2021. Reference Source\n\nvan den Driessche P, Watmough J: Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. Math Biosci. 2002; 180(1–2): 29–48. PubMed Abstract | Publisher Full Text\n\nYoung G, Ermentrout B, Rubin JE: A boundary value approach to optimization with an application to salmonella competition. Bull Math Biol. 2015; 77(7): 1327–1348. PubMed Abstract | Publisher Full Text\n\nErmentrout B: Simulating, analyzing, and animating dynamical systems: a guide to XPPAUT for researchers and students. SIAM. 2002. Publisher Full Text\n\nBrett TS, Rohani P: Transmission dynamics reveal the impracticality of covid-19 herd immunity strategies. Proc Natl Acad Sci U S A. 2020; 117(41): 25897–25903. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChoi W, Shim E: Optimal strategies for vaccination and social distancing in a game-theoretic epidemiologic model. J Theor Biol. 2020; 505: 110422. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahase E: Covid-19: What new variants are emerging and how are they being investigated? BMJ. 2021; 372: n158. PubMed Abstract | Publisher Full Text\n\nOliver SE, Gargano JW, Marin M, et al.: The Advisory Committee on Immunization Practices' Interim Recommendation for Use of Pfizer-BioNTech COVID-19 Vaccine - United States, December 2020. MMWR Morb Mortal Wkly Rep. 2020; 69(50): 1922–1924. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOliver SE: The advisory committee on immunization practices’ interim recommendation for use of moderna covid-19 vaccine—united states, december 2020. MMWR Morb Mortal Wkly Rep. 2021; 69(5152): 1653–1656. PubMed Abstract | Publisher Full Text\n\nKaur SP, Gupta V: Covid-19 vaccine: A comprehensive status report. Virus Res. 2020; 288: 198114. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "124239",
"date": "11 Mar 2022",
"name": "Sam Moore",
"expertise": [
"Reviewer Expertise Epidemiological modelling"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a compartmental model fitted to COVID-19 metrics observed in the Tampa Bay region of the US during part of 2020. The model is extended to include simple vaccination and NPI (non-pharmaceutical intervention) dynamics which are explored to provide an assessment of the levels of each necessary to reduce the effective reproductive number below the critical threshold. The paper is clearly written and the presented results mathematically consistent. However, the scope of the model lacks many of the features required for the results to be meaningful in the context of the current pandemic.\nThe model firstly assumes a homogeneous population. While all modelling necessitates a certain degree of approximation, a detailed spatial structure may be intractable and of limited benefit, some stratification by age and/or vulnerability is arguably essential in the study of COVID-19 dynamics given the highly uneven level of risk, especially given results in the paper are principally presented in terms of severe disease outcomes. Due to the highly contagious nature of the disease and damaging socio-economic consequences of prolonged NPIs, most countries around the world have aimed to use vaccination principally to reduce the worst disease effects by targeting the vulnerable rather than aiming for epidemic turnover as concentrated on in this study.\nThe vaccine dynamics included in the model are also overly simplistic. While in the introduction the authors do make some discussion about the multiple benefits of vaccination, in terms of reducing severe disease outcomes and symptom prevalence as well as infection and transmission, their model makes no attempt to incorporate this. Many of the vaccines used have proved highly effective in reducing severe disease outcomes (as much as ~98% effective in preventing mortality) which would have significant consequences for the projected hospital/ICU numbers presented.\nResults throughout the study are framed with a view to disease eradication, assumingly achieved by reducing the effective reproduction below 1. There are several issues with this measure in the context however; firstly, waning immunity and rapidly emerging viral variants both mean that the herd immunity threshold is by no means fixed, and secondly the study frames presents the threshold as a function of a fixed NPI level, while in reality no country is likely to leave control measures in place in perpetuity and these should rather be explored as a temporary dynamic and not to effect a final threshold.\nFinally, the model is fitted to provide a single a static set of parameters. However, a broad parameter set can clearly match the same data. Due to the sensitivity of the results to the fitting, it would be greatly beneficial to see this explored to some extent, to provide some sort of prediction intervals. Due to significant changes in both viral characteristics and available treatment over time, many of these parameters are also not constant as presented—for instance one assumes the parameters are chosen to match the characteristics of variants in circulation at one particular time, but this is a rapidly changing situation. The control parameter presented is also entirely abstract, and one feels it would be greatly more informative if it had some grounding in reality—what range has actually been observed in practice?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8860",
"date": "18 Oct 2022",
"name": "Glenn Young",
"role": "Author Response",
"response": "We thank the reviewer for his useful suggestions for improving our paper. We have addressed all comments below. 1. The model firstly assumes a homogeneous population. While all modelling necessitates a certain degree of approximation, a detailed spatial structure may be intractable and of limited benefit, some stratification by age and/or vulnerability is arguably essential in the study of COVID-19 dynamics given the highly uneven level of risk, especially given results in the paper are principally presented in terms of severe disease outcomes. Due to the highly contagious nature of the disease and damaging socio-economic consequences of prolonged NPIs, most countries around the world have aimed to use vaccination principally to reduce the worst disease effects by targeting the vulnerable rather than aiming for epidemic turnover as concentrated on in this study. Thank you for your feedback. We understand that considering a homogeneous population limits our model’s predictive scope, as we mention in our manuscript’s discussion. However, the stated goal of the work in this manuscript is to qualitatively understand how pharmaceutical and non-pharmaceutical interventions influence the spread of COVID-19, particularly by focusing on the incidence of severe cases requiring intensive care. These theoretical results are most effectively found through the rigorous analytical methods we employ here, methods that would not be available to us with an age-structured model. Our assumption of a homogeneous population is therefore appropriate because homogeneity simplifies the required analysis and parameterization, and our results are robust to parameter perturbations. We have added text to the discussion elaborating on the necessity of our model’s simplicity. 2. The vaccine dynamics included in the model are also overly simplistic. While in the introduction the authors do make some discussion about the multiple benefits of vaccination, in terms of reducing severe disease outcomes and symptom prevalence as well as infection and transmission, their model makes no attempt to incorporate this. Many of the vaccines used have proved highly effective in reducing severe disease outcomes (as much as 98% effective in preventing mortality) which would have significant consequences for the projected hospital/ICU numbers presented. We agree that many of the vaccines have proven highly effective in reducing severe disease outcomes. In fact, when we submitted this manuscript, initial data on the widely administered MRNA vaccines (Pfizer, Moderna) reduced all COVID-19 cases by ∼ 95%, not just severe [1]. This is reflected in our assumption that vaccinated individuals’ risk of infection is reduced by a factor of ξ = 0.94. We further emphasize that this assumption, that vaccination reduces only the risk of infection and does not subsequently reduce the risk of severe outcomes, was based on data available at the time, and that limitations on available data would have made any assumption on the vaccine’s downstream effects impossible to parameterize in any meaningful way. Further: in our model, hospitalization is being driven primarily by the unvaccinated, and consequently differentiating the rates at which vaccinated versus unvaccinated individuals develop severe symptoms has no qualitative effect on our results. We include here a visualization of ICU cases with total ICU cases (solid curves) and ICU cases among unvaccinated individuals (dotted curves) visualized separately. For both zero (green curves) and high (blue curves) NPI adherence, the unvaccinated population comprises over 97% of ICU cases at their peak. These results suggest that even if we assume that vaccinated individuals cannot develop severe symptoms, our results remain qualitatively unchanged. We have added text and Figure 5 in the manuscript clarifying this important point. 3. Results throughout the study are framed with a view to disease eradication, assumingly achieved by reducing the effective reproduction below 1. There are several issues with this measure in the context however; firstly, waning immunity and rapidly emerging viral variants both mean that the herd immunity threshold is by no means fixed, and secondly the study frames presents the threshold as a function of a fixed NPI level, while in reality no country is likely to leave control measures in place in perpetuity and these should rather be explored as a temporary dynamic and not to effect a final threshold. We again ask the reviewer to understand that this work was submitted in August 2021, shortly before evidence of waning immunity began to emerge [2] (note that the cited article was first published on medRxiv on Au- gust 31, 2021). Before this evidence was released, many considered herd immunity through a combination of vaccination and infection to be an achievable goal [3]. Moreover, while we do present conditions such that the effective reproductive number is reduced below unity, we also consider the impact of subsequent outbreaks in on communities with low vaccination rates and relaxed social measures in Figure 6. This consideration was aimed to address the reality that the virus might never be eradicated. We have added text regarding waning immunity to the discussion. However, we do agree that terms like “eradication” overstate what was ever considered feasible. We have modified the language throughout the manuscript to focus on control, rather than eradication. 4. Finally, the model is fitted to provide a single a static set of parameters. However, a broad parameter set can clearly match the same data. Due to the sensitivity of the results to the fitting, it would be greatly beneficial to see this explored to some extent, to provide some sort of prediction intervals. Due to significant changes in both viral characteristics and available treatment over time, many of these parameters are also not constant as presented for instance one assumes the parameters are chosen to match the characteristics of variants in circulation at one particular time, but this is a rapidly changing situation. The control parameter presented is also entirely abstract, and one feels it would be greatly more informative if it had some grounding in reality what range has actually been observed in practice? Thank you for the comment; we agree that many of the parameters in our model can and will change over time. As stated above, the goal of our work is to assess the influence of intervention strategies on the incidence of severe covid cases, and while changing parameters affects the quantitative results of our model, the qualitative results remain unchanged. We illustrate this by the addition of two new figures, both in Fig 3 in the manuscript. Since we do not know for certain how parameters will change over time, we allow every parameter in our model except φ (vaccine coverage), ξ (vaccine efficacy), μ (vaccination rate), and a (proportion of population adhering to NPIs) to randomly vary by up to 20% above or below its baseline value. We then simulate our model and collect data to make the figures, as described below. The left figure shows the region in which 80% of simulations fall as we vary parameters as described above over 5000 iterations. The solid curve shows the ICU caseload over time with φ = 0.6 and a = 0 (the same curve shown in black in Figure 4 in our manuscript) and 80% of simulations fall within the two dashed curves. The right figure shows peak ICU caseloads over φ. The solid middle curve shows the peak ICU caseload for our baseline parameters with φ = 0.6 and a = 0 (same curve shown in red in Figure 7 in our manuscript). We then vary φ from 0 and 1 in 0.2-unit steps and simulate our model 5000 times for each value of φ with parameters randomly selected as described above. 80% of peak ICU caseloads fall within the dash-dotted curves above and below the central curve. These results suggest that our model’s results are qualitatively robust; that is, we expect disease eradication or control to require a combination of vaccination and NPI strategies even as these characteristic parameters change over time. [1] Polack, Fernando P., et al. “Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine.” New England Journal of Medicine (2020). [2] Goldberg, Yair, et al. “Waning immunity after the BNT162b2 vaccine in Israel.” New England Journal of Medicine 385.24 (2021): e85. [3] Randolph, Haley E., and Luis B. Barreiro. “Herd immunity: understanding COVID-19.” Immunity 52.5 (2020): 737- 741."
}
]
},
{
"id": "143358",
"date": "30 Aug 2022",
"name": "Matthew Adewole",
"expertise": [
"Reviewer Expertise Mathematical Biology",
"Numerics of PDEs"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis work is relevant in this present world as it discusses an ongoing issue. Authors of this work have put in good efforts to get this work done. The presentation is quite good however, it is not without flaws:\nAuthors assumed a closed population where there is no demographic data. This kind of scenario can only be true when the time-duration is small enough. However, Figure 2 shows a time series plot over a period of about 400 days. Saying there is no demographic process within this period is far from reality. I suggest that the authors include demographic data.\n\nIt was said that S represents “susceptible without access to vaccine”. How come individuals in S compartments are vaccinated at a rate μ? I think something is wrong with the nomenclature.\n\nThe first term on the right side of Equation 1c should by μϕS.\n\nA significant part of this work is the parameter estimation. Authors should make this more explanatory. Authors should display graphs showing data and fitted curves. Authors should differentiate between estimated parameter values and the parameter values taken from literature.\n\nThe data used for parameter estimation are quite outdated. Therefore the estimated parameter values and, consequently, the results of this work may not represent the present-day reality.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8862",
"date": "18 Oct 2022",
"name": "Glenn Young",
"role": "Author Response",
"response": "We thank the reviewer for his useful suggestions for improving our paper. We have addressed all comments below. 1. Authors assumed a closed population where there is no demographic data. This kind of scenario can only be true when the time-duration is small enough. However, Figure 2 shows a time series plot over a period of about 400 days. Saying there is no demographic process within this period is far from reality. I suggest that the authors include demographic data. While Figure 3 displays data out through 365 days, the most important dynamics (namely time to peak ICU caseload) occur within 100 days of outbreak. Similarly, the caseload reduces to 20% of its maximum within about half a year. These are a short enough timespans relative to the dynamics of the model that the demographics within the population should not change enough to influence the course of the outbreak. For this reason we do not suspect that the addition of demographic processes will influence our results in any qualitative way. 2. It was said that S represents “susceptible without access to vaccine”. How come individuals in S compartments are vaccinated at a rate μ? I think something is wrong with the nomenclature. The S population is the proportion of individuals who have not yet had the opportunity to receive a vaccination. We agree that our description within the manuscript is unclear and confusing. We have changed the description of S from “susceptible without access to vaccine” to “susceptible population prior to vaccine access. 3. The first term on the right side of Equation 1c should be μφS. •\\ You are correct. Thanks for catching this mistake. 4. A significant part of this work is the parameter estimation. Authors should make this more explanatory. Authors should display graphs showing data and fitted curves. Authors should differentiate between estimated parameter values and the parameter values taken from literature. The primary goal of this work is to investigate the tradeoffs between pharmaceutical and non-pharmaceutical interventions for controlling the spread of COVID, not on parameter estimation. The parameter estimation work was done in another paper by co-authors Newcomb and Michael [1], and we consequently leave the details of the method out of the present manuscript. However, we agree that additional detail regarding the method could benefit readers, and so we have added a new figure (now Figure 2) showing a fitted curve of COVID case data and include a slightly longer, though still brief, description of the method used to fit parameters. 5. The data used for parameter estimation are quite outdated. Therefore the estimated parameter values and, consequently, the results of this work may not represent the present-day reality. This is true and is of course a limitation of any covid modeling work that is not continuously updated with new data. However, the goal of this work is not to inform real-time decisions, but to understand the qualitative effects of coupled pharmaceutical and non-pharmaceutical interventions on the spread of the virus. In an effort to understand how robust our results are to changes in parameters, we have included a sensitivity analysis in our revised manuscript. Please see our response to Reviewer #1 comment 4. [1] Newcomb, Ken, et al. “Iterative data-driven forecasting of the transmission and management of SARS-CoV-2/COVID- 19 using social interventions at the county-level.” Scientific Reports 12, no. 1 (2022): 1-19."
}
]
}
] | 1
|
https://f1000research.com/articles/10-803
|
https://f1000research.com/articles/11-1190/v1
|
18 Oct 22
|
{
"type": "Research Article",
"title": "Detection of sleep apnea using polysomnographic signals",
"authors": [
"Ch. Usha Kumari",
"Swaraja K",
"Meenakshi K",
"Padma T",
"Swaraja K",
"Meenakshi K",
"Padma T"
],
"abstract": "Introduction: Sleep is important in humans, and it is affected by lifestyle changes. Improper sleep leads to serious physiological problems and disorders that occurs in human brain/scalp. These physiological changes and electrical activity of the human brain are recorded as electroencephalogram (EEG) signals. This paper describes the detection of a major sleep disorder \\textit{i.e.}, sleep apnea (SA). Methods: In this paper, sleep apnea is measured using various artifacts taken from the subjects. The discrete wavelet transform (DWT) is used to extract characteristics from an electroencephalogram (EEG) signal and to detect sleep. This is used to determine whether a person has obstructive sleep apnea (OSA) or central sleep apnea (CSA). The wavelet technique is used to split the EEG signal into five frequency bands: delta, theta, alpha, beta, and gamma. Results: For these five frequency bands, the mean, standard deviation, variance, maximum, minimum, and energy are computed. Discussion: A sleep problem is detected based on these characteristics.",
"keywords": [
"Polysomnographic signals",
"OSA",
"CSA",
"Mixed Apnea and Discrete Wavelet Transform"
],
"content": "Introduction\n\nSleep disorders are most commonly seen in humans due to life style changes. Sleep is interrupted based on the person’s behaviour during sleep and due to changes in physiological signals, i.e., electrical rhythms in human brain or scalp. These electrical rhythms are recorded as electroencephalogram (EEG) signals. Sleep is defined as quiescent sleep or non-rapid-eye-movement (NREM) sleep or rapid-eye-movement (REM) sleep based on the subject’s physiological behaviour and the EEG.1,2 The study of normal sleep and sleep disorders is critical because these are the most frequently encountered difficulties in people. Sleep apnea (SA) is a common sleep disorder defined by intermittent breathing during sleep phases. It is a partial lack of airflow for more than 10 seconds in patients.3,4\n\nIf the amplitude of the breathing signal falls below 75% of the normal respirative signal level for a period 10 seconds or more, then SA is considered to be significant. SA is of three types: obstructive sleep apnea (OSA), central sleep apnea (CSA) and mixed sleep apnea (MSA). OSA is caused due to blockage of airway flow, this event occurs during sleep where the soft tissue in throat may be collapsed which then closes. In CSA, the blockage of airflow does not occur but the brain stops giving signals to the muscles to breathe.5,6\n\nOSA is the most common type of SA, accounting for approximately 84% of all patients diagnosed. As illustrated in Figure 1, this syndrome is defined by complete or partial obstruction of the airways, which prevents oxygen from reaching the lungs. OSA is seen in loud snoring people because of blockage of upper airways in the respiratory system. A blockage can be resulted due to various physiological behaviours, that is genetically and progresses over time. The blockage is more common in obese individuals or those with a bigger neck with more surrounding fat and tissue. SA can be difficult to identify since the signs and symptoms are sometimes generalised and misconstrued as signs and symptoms of less serious conditions. OSA patients are frequently unaware they have the illness; rather, it is diagnosed by a partner or spouse due to the loud snoring and repetitive gasping while sleeping.7,8\n\nCSA is generalized by continuous cessation of oxygen intake throughout the duration of sleep, whereas OSA is the cessation event occuring due to reduced ventilatory drive for obese subjects.9,10 CSA-related disorder is seen when cessation in breath occurs for a period greater than 10 seconds and less than 30 seconds.11,12 When a patient has more than five central apneas per hour of sleep, as well as the concomitant symptoms of frequent awakenings and/or daytime sleepiness, CSA syndrome is diagnosed. Because central apneas can occur in people who have obstructive apneas, 50 to 80% of apneic events must be central rather than obstructive in order to determine CSA. Cheyne–Stokes respiration (CSR), which is common in patients with heart failure, neurovascular disorders, and dementia, is strongly linked to CSA. Doctors struggle to make a diagnosis of CSA syndrome, and OSA requires full-night polysomnography to determine the frequency and pattern of central apnea.13\n\nComplex or mixed sleep apnea syndrome (CompSAS) illustrates the characteristics of sleep-disordered breathing. In this, repetitive central apneas (≥5 per hour) can continue or appear when such obstructive events are eliminated through positive airway pressure (PAP). CompSAS is very dangerous combination consists of both OSA and CSA.14 The subjects suffering from both experience blockage of uppper airway and brain stops giving signals to muscles to breathe. This is inability of feedback mechanism which controls the brain. When the central-apnea-index (CAI) exceeds 5 events per hour, it becomes a major and disruptive event.15\n\n\nRelated works\n\nCurrently, various methods have been published in establishing sleep apnea from biomedical signals. With reference to,16 OSA along with CSA events can be separated with wavelet packet analysis of electrocardiogram signals. With reference to,17 SVM classifier gained a precision of 91.08%. A new approach was developed to categorize and evaluate the electroencephalogram (EEG) and identify the EEG features for detection of SA stages with the DWT techniques and ANN classifier.18\n\nThe feature extraction and optimization techniques for OSA, CSA and MSA is investigated. Based on decomposition stages along with bivariate methods was used to examine the features of EEG signals via a Hilbert–Huang transform. Once an apnea has happened then there will be an energy waveform in low frequencies, which is related to the delta power and it represents the body autonomous system and homeostasis regulation. Another sleep apnea review, the result of transient, apnea-induced hypoxemia on electrocortical activity, five patients having adverse obstructive sleep apnea syndrome (OSAS) were analysed during nocturnal sleep. While non rapid eye movement (NREM) apneas, amplitude of the delta band rises, the abnormality of sleep in adverse OSAS may form such a tendency for slow-wave sleep that stages pass too much rapid than in normal persons.\n\nThe co-efficients are used as inputs to the classifiers. The novel classfication method uses features as inputs for apnea stages identification. The primary goal of sleep apnea study is to develop an algorithm for sleep stage recognition, which is done by analysing the electrooculography (EOG) signals. The secondary goal is to use sleep quality features to categorize and screen sleep apnea–hypopnoea syndrome (SAHS) patients and periodic limb movements of sleep (PLMS) patients, as different from healthy control subjects. Brain condition can be measured by EEG, which records the electrical state of the scalp. Electroencephalogram (EEG is more convenient tool for knowing the typical actions of the scalp. The goal of this paper is to visualize the abnormalities in the EEG signal.\n\n\nProposed work\n\nThe proposed work describes the raw electroencephalogram (EEG) data obtained from the MIT-BIH database (physionet data base). The obtained EEG dataset is in the form of .mat and it is loaded in to the matrix laboratory (MATLAB) workspace and generates the EEG signal. The resulting EEG signal is segmented using the Daubechies wavelet transform, which yields all of the electroencephalogram signal’s fundamental frequency components. The segmented bars correspond to various brain states. Energy, standard deviation, mean, maximum, minimum, and variance are all computed (extracted) from EEG bands and can be used to detect sleep apnea. The flowchart depicting the diagnosis and classification of sleep apnea is illustrated in Figure 2. Five steps comprise the process flow. The first stage involves acquiring the signal from the MIT-BIH data base, the second stage involves segmenting the EEG signal, the third stage involves extracting features from the segmented signal, the fourth stage involves detecting the severity of apnea, and the fifth stage involves classifying the abnormality as OSA, CSA, or CompSAS.\n\nThe signals are extracted from polysomnographic data taken from the MIT-BIH Polysomnographic Database. The monitoring of patient overnight in a sleep laboratory is called polysomnography (PSG). In general, PSG is the common test for identification of OSAS. PSG is also used to evaluate irregularities of sleep and different physiologic disorders which influence the health. One-night PSG is enough to determine if OSA is present.9,10 A PSG test constitutes concurrent recording of several physiologic parameters which belong to sleep and wakefulness. Electrical signals are transmitted by using specialized sensors or electrodes which are applied to the various body parts. The translation of these signals into records is done by specialized amplifiers and filters which are present in recording instrument.13,14\n\nThere are many signals that are acquired. These include:\n\n1. Electroencephalogram (EEG) signal\n\n2. Electrocardiogram (ECG) signal\n\n3. Airflow signal\n\n4. Thoracic+abdomen positional sum signal\n\n5. Electroculogram (EOG) signal\n\n6. Electromyogram (EMG) signal\n\n7. Oxyhemoglobin saturation signal (SpO2)\n\nElectrical activity of the brain can be recorded from the scalp and which is quite small, measured in microvolts. The EEG waveform can be decomposed into five frequency bands, namely delta, theta, alpha, beta and gamma. These bands can give important information for observing, diagnosing and managing neurological features and disorders11,12\n\nFeature extraction is the technique of extracting specific information from the electroencephalogram (EEG) as recorded by neuronal activity in the brain. A feature extraction methodology is an ideal way for dissecting the input EEG signal into a set of characteristics and differentiating samples with distinct patterns. With the purpose of minimising the loss of vital information, patterns are represented by features. Feature extraction is the process of identifying a characteristic or characteristic vector from a pattern vector.\n\nThe discrete wavelet transform method is used to extract features in this article. Wavelet transform (WT) provides the general approaches, which can be used to a wide variety of signal processing jobs. Wavelets can be used to analyse abrupt, short-duration signal changes. The primary application is to calculate and regulate data that has been reduced to a few parameters, referred to as features. As a result, the time-varying biological signal contains a large number of data points that can be condensed via WT to a few parameters. These parameters describe the behaviour of a time-varying biological signal. The time-varying biomedical signal is represented by a smaller number of parameters, which are particularly important for recognition and diagnostic purposes. Statistical features are computed for each sub bands which are mean, energy, standard deviation, maximum, minimum and variance. Signal energy characterizes the power at all instances of time interval. Standard deviation (SD) is easy to calculate the changeability of a data set. Variance parameter gives the distance between values in the data set from mean.\n\n\nResults\n\nThe analysis was performed on EEG signal and features are extracted from the each frequency band of the EEG signal by using wavelet transform.\n\nThe EEG signal acquisition for one subject is shown in Figure 3; it is the normal EEG signal without any abnormality. Various physiologic signals sampled at 250 Hz frequency and plotted for 60 seconds for the subject slp32m is shown in Figure 4. These physiologic signals are ECG, BP (blood pressure), Resp nasal (respiration at nasal) and SpO2 (oxygen saturation). In Figure 5 the area between two lines indicated the sleep apnea event has occured. This clearly shows the abnormality in the ECG, EEG, Nasal, EOG and EMG. It is characterized by reduction in breathing. These changes in signals is compared to the normal PSG.\n\nThe EEG signal is divided into subbands such as gamma, beta, theta, alpha, and delta using the wavelet technique as illustrated in Figure 6 DWT is used to extract features from the EEG signals during the feature extraction stage. Table 1 summarises the computed properties, such as standard deviation, variance, and energy, for each frequency band that can be utilised to depict the EEG signals’ characteristics.\n\n\nConclusions\n\nIn this paper the physiologic signals ECG, BP, EEG, respiratory signal at nasal, oxygen saturation (SpO2) for normal subject and abnormal subject is analyzed. The EEG signal is segmented into delta, theta, alpha, beta, gamma for both normal and abnormal subjects. Various features like standard deviation, variance and energy, mean, maximum and minimum are extracted from both normal and abnormal subjects. Using DWT Daubechies order 2, the detailed and approximate coefficients are extracted. These inputs are given to the classifier for detection of sleep disorder stages.\n\n\nAuthor contributions\n\nCh. Usha Kumari, K. Swaraja: Conception and design of study. Ch. Usha Kumari, K. Meenakshi: Acquisition, analysis and/or interpretation of data. Ch. Usha Kumari, T Padma: Drafting the manuscript and revising the manuscript critically for important intellectual content.\n\n\nData availability\n\nUnderlying data Raw polysomnographic data were from taken from the MIT-BIH database (https://physionet.org/content/slpdb/1.0.0/).\n\nFigshare: Underlying data for “Detection of sleep apnea using polysomnographic signals” https://figshare.com/s/08009ff4301370a5f58d\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nCvetkovic D, Übeyli ED, Cosic I: Wavelet transform feature extraction from human ppg, ecg, and eeg signal responses to elf pemf exposures: A pilot study. Digit. Signal Process. 2008; 18(5): 861–874. Publisher Full Text\n\nShriram R, Sundhararajan M, Shete S, et al.: Statistical features-based comparison of analysis and synthesis of normal and epileptic electroencephalograms for various wavelets. Turk. J. Electr. Eng. Comput. Sci. 2017; 25(3): 1795–1806. Publisher Full Text\n\nLeong WY: Feature extraction and optimisation for sleep apnea. 2014 IEEE International Symposium on Robotics and Manufacturing Automation (ROMA). IEEE;2014; pp. 200–205.\n\nPhinyomark A, Nuidod A, Phukpattaranont P, et al.: Feature extraction and reduction of wavelet transform coefficients for emg pattern classification. Elektronika ir Elektrotechnika. 2012; 122(6): 27–32. Publisher Full Text\n\nMane AR, Biradar SD, Shastri RK: Review paper on feature extraction methods for eeg signal analysis. Int. J. Emerg. Trend Eng. Basic Sci. 2015; 2(1): 545–552.\n\nAl-Fahoum AS, Al-Fraihat AA: Methods of eeg signal features extraction using linear analysis in frequency and time-frequency domains. Int. Sch. Res. Notices. 2014; 2014: 1–7. Publisher Full Text\n\nKalaivani M, Kalaivani V, Anusuya V, et al.: Analysis of eeg signal for the detection of brain abnormalities. at International Journal of Computer Applications® year. 2014.\n\nKavya Devarajan E, Jyostna KJ, Balasampath V: Eeg-based epilepsy detection and prediction. Int. J. Eng. Technol. 2014; 6(3): 212–216. Publisher Full Text\n\nGubbi J, Khandoker A, Palaniswami M: Classification of obstructive and central sleep apnea using wavelet packet analysis of ecg signals. 2009 36th Annual Computers in Cardiology Conference (CinC). IEEE;2009; pp. 733–736.\n\nLin R, Lee R-G, Tseng C-L, et al.: A new approach for identifying sleep apnea syndrome using wavelet transform and neural networks. Biomed. Eng.: Appl. Basis Commun. 2006; 18(03): 138–143. Publisher Full Text\n\nKumari U, Panigrahy AK, Vignesh NA, et al.:Sleep bruxism disorder detection and feature extraction using discrete wavelet transform. Proceedings of ICETIT 2019. Springer;2020; pp. 833–840. Publisher Full Text\n\nKumari U, Padmavathi Kora K, Meenakshi KS, et al.: Feature extraction and detection of obstructive sleep apnea from raw eeg signal. International Conference on Innovative Computing and Communications. Springer;2020; pp. 425–433. Publisher Full Text\n\nPadma T, Usha C, Kumari: Deep learning based chest x-ray image as a diagnostic tool for covid-19. 2020 international conference on smart electronics and communication (ICOSEC). IEEE;2020; pp. 589–592.\n\nKumari CU: Investigation: Life-time and stability period in wireless sensor network. 2018 3rd International Conference for Convergence in Technology (I2CT). IEEE;2018; pp. 1–5.\n\nKumari CU, Krishna MR: High performance wireless communication channel using leach protocols. Pak. J. Biotechnol. 2016; 13: 52–56.\n\nDouglas Bradley T, Floras JS: Sleep apnea and heart failure: Part ii: central sleep apnea. Circulation. 2003; 107(13): 1822–1826. Publisher Full Text\n\nSubasi A: Eeg signal classification using wavelet feature extraction and a mixture of expert model. Expert Syst. Appl. 2007; 32(4): 1084–1093. Publisher Full Text\n\nJahankhani P, Kodogiannis V, Revett K: Eeg signal classification using wavelet feature extraction and neural networks. IEEE John Vincent Atanasoff 2006 International Symposium on Modern Computing (JVA’06). IEEE;2006; pp. 120–124."
}
|
[
{
"id": "153861",
"date": "25 Oct 2022",
"name": "Xavier N. Fernando",
"expertise": [
"Reviewer Expertise Signal processing",
"Machine Learning",
"Wireless Communications"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this paper the EEG signal is segmented into delta, theta, alpha, beta, gamma for both normal and abnormal subjects. Various features like standard deviation, variance and energy, mean, maximum and minimum are extracted from both normal and abnormal subjects. In my opinion this work is superficial and inconclusive. What are the benefits obtained from the obtained paramaters (mean, standard deviation etc.)?\nThe article does not describe how the classifier is performing and how accurately it detects abnormal patients. Please see the given reference to see how classification can be done in a better way (Magtibay et al., 20221).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1190
|
https://f1000research.com/articles/11-219/v1
|
23 Feb 22
|
{
"type": "Review",
"title": "Reconsidering the ethics of compulsive treatment under the light of clinical psychiatry",
"authors": [
"Luis Duarte Madeira",
"Jorge Costa Santos",
"Jorge Costa Santos"
],
"abstract": "The ethics of compulsive treatment (CT) is a medical, social and legal discussion that reemerged after the ratification by 181 countries of the 2007 United Nations Convention on the Rights of Persons with Disabilities (UN-CRPD). The optional protocol of the UN-CRPD was ratified by 86 countries aiming to promote, protect and ensure the full and equal enjoyment of all human rights. It also determined the need to review mental health laws as under this light treatment of persons with disabilities, particularly those with mental disorders, cannot accept the use of CT. This selective review of literature aims to clarify inputs from clinical psychiatry adding evidence to the multi-disciplinary discussion. It focuses on how patients experience CT and its impact on their mental health and treatment programs, the reasons for the use of CT versus voluntary treatment and what efforts have been made to reduce, replace and refine the presence of CT in psychiatry.",
"keywords": [
"involuntary treatment",
"ethics",
"CRPD",
"human rights"
],
"content": "Introduction\n\nCompulsive treatment1 of people with psychosocial disabilities, particularly when these disabilities result from mental disorders, is a problem of a medical, social, and legal nature. Under the umbrella of Public Health and Health Policies there has been intensive research for legal solutions aiming to settle on the one hand, the need for coercive treatment of people with disabilities who, for various reasons, do not recognize the disorder that affects them (or refuse therapeutic interventions) with the protection of their rights, freedoms and guarantees. Table 1 clarifies some of the historical developments on paternalism and autonomy in the last 50 years.\n\nThe Council of Europe (CE) and its Bioethics Committee, the European Court of Human Rights (ECHR) promoted several reviews of the mental health legislations. First, the European Convention on Human Rights and Biomedicine (ECHRB), also known as the Oviedo Convention, in 1997 aimed to protect persons that failed to show capacity for consent to treatment (article 6), particularly those with mental disorders (article 8) by considering that all medical interventions that could benefit health could be performed under legal provisions in emergency situations (article 8). Second, a new international human rights treaty was drafted in December 2006 and opened for signatures in March 2007 (Nations 2007) the United Nations Convention on the rights of Persons with Disabilities, UN-CRPD. It represents the first comprehensive human rights treaty of the twenty-first century, in force since 2008, and is ratified by 181 countries. Subsequently, several other documents were developed focused on the protection of autonomy, agency and dignity of persons with psychosocial disabilities of which Annual report of the United Nations High Commissioner on Human Rights A/HRC/34/32 is recent example.\n\nThe UN-CRPD aims to “promote, protect and ensure the full and equal enjoyment of all human rights and fundamental freedoms by all persons with disabilities” (Nations 2007, p. 4) and therefore provides an opportunity to discuss and review the ethical foundations of the treatment of persons with mental disorders. Table 2 highlights significant articles from the UN-CRPD.\n\nAll these provisions are especially important as they imply that disabilities shall in no case justify the deprivation of liberty and that competence should be considered at all times – third parties only supporting organization and communication of their will. A literal interpretation of these ideals would determine the immediate interruption of the use of coercive measures in the field of psychiatry, particularly compulsive treatment (CT), for they would consist in a violation of the rights of patients (forcing treatment, discriminating, and marginalizing them). Yet there are several clinical situations that show that providing full autonomy to patients with mental disorders would be devastating – e.g., patients with dementia (unable to manage themselves or their property), with depressive episodes (with suicidal ideation and risk) and psychotic episodes (refusing to feed themselves because they believe they are being poisoned). Indeed, the coercion of persons who can choose (disrespecting autonomy) should be measured against the obligation to make a choice when unable to do so (disrespecting vulnerability). Arguments are raised considering the necessary changes in the restrictions of rights of patients with mental disorders and when it would be ethically and clinically reasonable to objectively limit their autonomy. A powerful/convincing argument against the CRPD effectiveness refers to the fact that its predictions focus on autonomy and are silent on how to effectively determine the duty to protect persons with disabilities and on how to provide adequate health care for those with a severe mental disorder. The general worries about the CRPD are included in Table 3.\n\nThe use of the CRPD should avoid two extreme positions on CT for mental disorders: (1) continuing with the coercive measures acting while considering the “best interest of the patient” and sustaining the proportionality due to “adverse consequences” or the risk of “serious and imminent damage” or (2) determining the immediate abolition of all forms of coercive treatment as its radical reduction is insufficient.\n\nThis is a review of literature which provides inputs from psychiatric practice that could clarify how CT is used and felt in the life of patients and health professionals. Particularly, empirical evidence on the uses (and eventual abuses) of CT, of the negative (and possible positive) experience of coercion and of the present ways to reduce and refine CT.\n\n\nThe use of CT in daily practice\n\nDecisions on coercive measures and on compulsive treatment (CT) appear in the reviewed literature supported by four main reasons: risk, diagnosis, lack of capacity and the effectiveness of the measures. Risk reduction is such a critical factor in the context of compulsive treatment (both in the beginning and interruption) that the measure is perceived as a risk control mechanism (Hsieh et al. 2017). Risk in psychiatry has several dimensions and is subject to qualitative and quantitative assessment - risk of harm to oneself, harm to other persons, of greater social adversity, of suffering more or of compromising a treatment plan (Light et al. 2015).\n\nRisk and diagnosis are fundamental in the decision of CT, as evidence suggests that persons with severe mental disorder can attack and harm others, including health professionals (Steinert and Traub 2016). Even after CT 25% of patients admitted to an adult psychiatry unit could be at risk of committing an act of violence (Iozzino et al. 2015). Yet while individual risk factors appeared for violent behaviors and CT decisions (Menculini et al. 2018) – e.g. male, diagnosis of schizophrenia, substance abuse and previous history of violence – their predictive value for violent behavior was not found. Of all the reasons the risk of occurrence or recurrence of violence seems the most liable to abuse (due to the subjective nature of risk in psychiatry) and perhaps the target of the CRPD worries and predicaments – that a measure aimed at the treatment of persons with mental disorders becomes a control mechanism for social risk situations. Indeed, some argue that it overlaid the true reason of CT need for treatment (Rotvold and Wynn 2015a, 2015b, 2016).\n\nPsychotic episodes and behavioral disturbances in patients under previous psychiatric care are most often associated with CT and the symptom profile includes activation, resistance to treatment and “positive” symptoms (Mosele et al. 2018), risk of suicide and low insight (Braitman et al. 2014, Masood et al. 2017). Evidence for the clinical rational for CT is detailed in Table 4.\n\nYet for each country there are legal requirements which might not be under use – more than 40% patients failed to provide them in their records (Godet and Niveau 2018). These clinical findings are worrying from an ethical and legal point of view where risk/hazard criteria could lead to dismissal of the need for a diagnosis or for treatment (Carabellese et al. 2017) and also increase prejudice and negative social representations of CT (Curley et al. 2016). The excess of coercive measures in non-Caucasian patients (Henderson et al. 2015) or gender disparities (Curley et al. 2016) furthers the need to explore the motivations for CT. Particularly the risk of coercion (Rotvold and Wynn 2015b) from other health professionals, from family or the police (Sjostrand et al. 2015) and organizational (Sjostrand et al. 2015) and financial issues (Green-Hennessy and Hennessy 2015).\n\nThe role of decision making for CT is challenging, as psychiatrists must distinguish between signs and symptoms of psychiatric disorders (which would determine the use of CT) and those representing behavioral disturbances resulting from a medical condition (no ground for CT). Disregarding such differences might increase the stigma of mental disorders and awareness of them improves the moral weight and reduces random interpretations of clinical practice (Fistein et al. 2016). If CT is to be considered for both then perhaps segregating their legal features is valuable (1) Medical Incapacity Hold (MIH) to those who are considered unable to decide and have a psychiatric illness, and (2) Involuntary Psychiatry Hold (IPH) for patients with psychiatric disease without insight and in need of treatment (Heldt et al. 2018). This would allow health professionals to Drug and addiction disorders have other ethical challenges and while they are clear disturbances of behavior they do not fit into key features of mental disorders and also don’t apply to “medical” incapacities (Williams 2015).\n\nCT for public health issues, such as tuberculosis, is of particular complexity and represents perhaps the clearest violation of the rights to liberty and privacy in persons whose competence might be unspoiled. Arguments which forward it stand upon both the inviolability of human life (e.g., supporting the coercive use of helmets or forced recycling) and the principle of reciprocity (social obligation as an individual if a group is exposed to detrimental effects on their health resulting from spreading of diseases) which supports the standards of vaccination. Yet CT for public health reasons has had several censures (McLaren et al. 2016) and other strategies have been proposed (Karumbi and Garner 2015). First, promotion of health education, increased access to services and settling socioeconomic and organizational determinants are effective for these situations (Mburu et al. 2016). Second, there is contradicting evidence of its effectiveness (Nagata et al. 2014) and it is rarely used even when there is legislation toward it (Villalbi et al. 2016).\n\nThe impact of CT in the treatment process should also be measured. Eating disorders (ED) are a good example of the complexity of CT considering clinical severity, capacity to decide, overall risk and effectiveness of the measure. First ED patients don’t seem to have lost the capacity to decide and decision stands upon risk of death (Westmoreland et al. 2017), severity, comorbidities, previous admissions, the incidence of self- injurious behavior (Clausen and Jones 2014) and yet it might damage therapeutic alliance (Douzenis and Michopoulos 2015) and lead to early drop-out from other programs (Schreyer et al. 2016). Postmodern ethics suggest that forms of power and control (and the need to regulate them) are not only external to the subject but can rise from within. In such case, the patient would need external help in managing, building, and applying decision making or else suffer internal coercion. Internal forms of coercion would then be mediated in the clinical relation in which directivity and surrogate decision making might be helpful. Table 5 shows other contradicting evidence on the effects of CT.\n\nExperiences of coercion and CT are not one and the same – the first occur in 15% of patients under CT but 20% of patients under voluntary treatment also report coercion (Edlinger et al. 2018). Emotional and cognitive features of the coercive events rather than the number of events appear responsible for its negative impact (Rusch et al. 2014). Such reactions are reduced when patients are allowed to exercise their autonomy, when they experience satisfaction and in the context of a good therapeutic alliance and increased if they endure trauma and humiliation (Danzer and Wilkus-Stone 2015). Forms of physical coercion appear linked with greater dissatisfaction (Smith et al. 2014, Mielau et al. 2016) and therefore medication should be preferred to physical restraint (Guzman-Parra et al. 2018). Yet the evidence isn’t definitive as one study points to involuntary drug administration as the most censored measure (McLaughlin et al. 2016). Moreover, the coercive experience of being under CT might even be linked with dynamic process of recovery – several patients admit that CT was a necessary measure in the end of the treatment (Gowda et al. 2017). Table 6 presents evidence of the negative impact of CT, Table 7 shows evidence on how to reduce these effects (Opsal et al. 2016).\n\nA range of measures have aimed to reduce the use of coercion and CT (Kelly et al. 2018) either by quantitatively reducing it, by replacing harsher measures or by modifying the experience of coercion. Table 8 indicates these three sorts of changes.\n\nAll these interventions have not received full empirical support due to several contradictory studies. There is paradoxical evidence, such as negative effect of social support (Hengartner et al. 2016) or positive impact of assertive treatments (Schottle et al. 2014, 2018). Moreover, CTO have shown to reduce mortality (9%) and the risk of self-inflicted damage (32%) and provide a modest improvement in the quality of life (Segal et al. 2017) while also requiring large and continued engagement to avoid worse consequences (Kisely and Campbell 2014, Riley et al. 2014). Another paradox is the fact that CT in inpatient settings appears to be better regulated as other team members and patients can supervise what is happening to the patient (Riley et al. 2014).\n\n\nConclusion\n\nThe CRPD addressed the issue of autonomy and decision making by patients with mental disorders determining that alternative solutions to CT must be considered when patients can’t perform responsible decisions. Yet health is a fundamental right and CT offers a protection from hazard which dissolution does not seem to solve – affirming autonomy by conventional ethical models or simplistic clinical approaches (Kendall 2014) might damage other rights and dignity of persons with mental disorders (Kelly 2014). Ultimately there is empirical evidence that clinical psychiatry has aimed to clarify the uses and possible abuses of CT, to determine experiences and consequences of its use and developed strategies to reduce, refine and replace it. While there is need for the interruption of forms of CT the measures taken cannot risk the misinterpretation of concepts and ignoring the complexity of clinical practice and the systemic changes involved. The stakeholders at nationwide discussions and decisions at a macro level (and possible mental health policies reformations) would benefit from acknowledging these efforts and evidence rising from the settings where CT takes place.\n\n\nData availability\n\nNo data are associated with this article.",
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(Psychiatric Rehabilitation Journal 34 2010). PubMed Abstract | Publisher Full Text\n\nReitan T: Commitment without confinement. Outpatient compulsory care for substance abuse, and severe mental disorder in Sweden. Int. J. Law Psychiatry. 2016; 45: 60–69. PubMed Abstract | Publisher Full Text\n\nRiley H, Hoyer G, Lorem GF: ‘When coercion moves into your home’--a qualitative study of patient experiences with outpatient commitment in Norway. Health Soc. Care Community. 2014; 22(5): 506–514. Publisher Full Text\n\nRotvold K, Wynn R: Involuntary psychiatric admission: The referring general practitioners’ assessment of patients’ dangerousness and need for psychiatric hospital treatment. Nord. J. Psychiatry. 2015a; 69(8): 637–642. PubMed Abstract | Publisher Full Text\n\nRotvold K, Wynn R: Involuntary psychiatric admission: Characteristics of the referring doctors and the doctors’ experiences of being pressured. Nord. J. Psychiatry. 2015b; 69(5): 373–379. PubMed Abstract | Publisher Full Text\n\nRotvold K, Wynn R: Involuntary psychiatric admission: how the patients are detected and the general practitioners’ expectations for hospitalization. An interview-based study. Int. J. Ment. Heal. Syst. 2016; 10: 20. PubMed Abstract | Publisher Full Text\n\nRusch N, Muller M, Lay B, et al.: Emotional reactions to involuntary psychiatric hospitalization and stigma-related stress among people with mental illness. Eur. Arch. Psychiatry Clin. Neurosci. 2014; 264(1): 35–43. PubMed Abstract | Publisher Full Text\n\nSantillanes G, Kearl YL, Lam CN, et al.: Involuntary Psychiatric Holds in Preadolescent Children. West. J. Emerg. Med. 2017; 18(6): 1159–1165. PubMed Abstract | Publisher Full Text\n\nSchottle D, Schimmelmann BG, Karow A, et al.: Effectiveness of integrated care including therapeutic assertive community treatment in severe schizophrenia spectrum and bipolar I disorders: the 24-month follow-up ACCESS II study. J. Clin. Psychiatry. 2014; 75(12): 1371–1379. PubMed Abstract | Publisher Full Text\n\nSchottle D, Schimmelmann BG, Ruppelt F, et al.: Effectiveness of integrated care including therapeutic assertive community treatment in severe schizophrenia-spectrum and bipolar I disorders: Four-year follow-up of the ACCESS II study. PLoS One. 2018; 13(2): e0192929. PubMed Abstract | Publisher Full Text\n\nSchreyer CC, Coughlin JW, Makhzoumi SH, et al.: Perceived coercion in inpatients with Anorexia nervosa: Associations with illness severity and hospital course. Int. J. Eat. Disord. 2016; 49(4): 407–412. PubMed Abstract | Publisher Full Text\n\nSegal SP, Hayes SL, Rimes L: The Utility of Outpatient Commitment: I. A Need for Treatment and a Least Restrictive Alternative to Psychiatric Hospitalization. Psychiatr. Serv. 2017; 68(12): 1247–1254. PubMed Abstract | Publisher Full Text\n\nSjostrand M, Sandman L, Karlsson P, et al.: Ethical deliberations about involuntary treatment: interviews with Swedish psychiatrists. BMC Med. Ethics. 2015; 16(1): 37. PubMed Abstract | Publisher Full Text\n\nSmith D, Roche E, O’Loughlin K, et al.: Satisfaction with services following voluntary and involuntary admission. J. Ment. Health (Abingdon, England). 2014; 23(1): 38–45. PubMed Abstract | Publisher Full Text\n\nSteinert T: Ethics of Coercive Treatment and Misuse of Psychiatry. Psychiatr. Serv. 2017; 68(3): 291–294. PubMed Abstract | Publisher Full Text\n\nSteinert T, Traub H-J: Violence by and against people with mental illnesses. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2016; 59(1): 98–104. PubMed Abstract | Publisher Full Text\n\nVillalbi JR, Rodriguez-Campos M, Orcau A, et al.: Hospital detention in tuberculosis control. Gac. Sanit. 2016; 30(2): 144–147. PubMed Abstract | Publisher Full Text\n\nWestmoreland P, Johnson C, Stafford M, et al.: Involuntary Treatment of Patients With Life-Threatening Anorexia Nervosa. J. Am. Acad. Psychiatry Law. 2017; 45(4): 419–425. PubMed Abstract\n\nWilliams JB: Adjusting Treatment for an Inmate-Patient Receiving Medication Involuntarily. J. Am. Acad. Psychiatry Law. 2015; 43(2): 223–229. PubMed Abstract\n\nWullschleger A, Berg J, Bermpohl F, et al.: Can ‘Model Projects of Need-Adapted Care’ Reduce Involuntary Hospital Treatment and the Use of Coercive Measures?. Front. Psych. 2018; 9: 168. PubMed Abstract | Publisher Full Text\n\n\nFootnotes\n\n1 Scientific literature uses the words “involuntary” (more frequently) or “compulsory” to qualify for hospitalization and/or psychiatric treatment (s) without the informed consent of the mentally ill patient. S/He is considered unable to express autonomously either because s/he refuses to adopt such measures restricting her/his freedom of action, or because s/he does not recognize the disease by which s/he is affected and, consequently, the need for treatment. In this review we chose to favor the term “compulsive”, not only because this is what appears in the relevant legal texts, but also because it is the one that facilitates the communication between the various actors in the process (jurists, doctors, law enforcement and family members). (translated from Lei n.° 36/98, de 24 de Julho (Lei de Saúde Mental), accessible in https://www.pgdlisboa.pt/leis/lei_mostra_articulado.php?nid=276&tabela=leis&so_miolo= ou em CEJ: Internamento Compulsivo. Lisboa, Coleção Formação Inicial, 2016, acessível em http://www.cej.mj.pt/cej/recursos/ebooks/civil/eb_Internamento_Compulsivo.pdf."
}
|
[
{
"id": "142241",
"date": "11 Jul 2022",
"name": "Mohammadreza Shalbafan",
"expertise": [
"Reviewer Expertise Psychiatry",
"Mental Health",
"Stigma",
"COVID-19",
"OCD",
"Psychopharmacology",
"Depression"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript discusses an important topic and it`s well-written, by and large. I have some additional comments in order to improve the manuscript:\nType of the paper should be added to the title.\n\nMain findings of the paper should be emphasized in the abstract.\n\n'CRPD' should be replaced with an appropriate key-word from MeSH.\n\n'(article 6)' and some others are not clear enough and should be mentioned more clearly.\n\nDescription of the columns should be added to the tables.\n\nThe manuscript needs proof-reading, particularly for capitals.\n\nWhat`s 'CTO'?\n\nCultural and trans-cultural aspects of the topic should be discussed briefly.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "8507",
"date": "19 Jul 2022",
"name": "Luis Madeira",
"role": "Author Response",
"response": "Answer to the reviewer, We thank the reviewer for going through our paper and provide a critical appraisal of its content which we believe greatly improve its quality. We answer below individually to the changes requested. The manuscript discusses an important topic and it`s well-written, by and large. I have some additional comments to improve the manuscript: Type of the paper should be added to the title. Answer: We thank the reviewer for considering this add on to the paper. It now reads “Reconsidering the ethics of compulsive treatment in light of clinical psychiatry: A selective review of literature”. We also agree that it clarifies the purpose of the paper. Main findings of the paper should be emphasized in the abstract. Answer: We agree with the suggestion of the reviewer. We’ve now edited the abstract though due to limitations in the number of words we’ve greatly abbreviated the main findings of the paper. It now reads “The ethics of compulsive treatment (CT) is a medical, social and legal discussion that reemerged after the ratification by 181 countries of the 2007 United Nations Convention on the Rights of Persons with Disabilities (UN-CRPD). The optional protocol of the UN-CRPD was ratified by 86 countries aiming to promote, protect and ensure the full and equal enjoyment of all human rights. It also determined the need to review mental health laws as under this light treatment of persons with disabilities, particularly those with mental disorders, cannot accept the use of CT. This selective review of literature aims to clarify inputs from clinical psychiatry adding evidence to the multi-disciplinary discussion. It provides contradictory evidence on how patients experience CT and its impact on their mental health and treatment programs, also which are main reasons for the use of CT and what efforts in psychiatry have been made to reduce, replace and refine it.” 'CRPD' should be replaced with an appropriate key-word from MeSH. Answer: We agree with the reviewer that the word should be replaced, and we suggest that it Persons with Mental Disabilities which is the closest mesh term. '(article 6)' and some others are not clear enough and should be mentioned more clearly. Answer: We’ve now added extra density to the article 6 which reads “aimed to protect persons that failed to show capacity for consent to treatment (including minors and adults with diminished capacity without representatives) (article 6)” Description of the columns should be added to the tables. Answer: We thank the reviewer for pointing this idea as we have now edited the tables and added the description of columns to all tables with 2 or more columns. We believe that single column tables are described by the descriptor above them. The manuscript needs proof-reading, particularly for capitals. Answer: Our manuscript was proof-readed by a paid English-speaking professional translator. Yet we’ve now asked two native English speakers to go through the manuscript again. What`s 'CTO'? Answer: We replaced CTO for Community Treatment Orders – a specific form of compulsive ambulatory treatment. The explanation was in the table but fits better in the text itself as the reader might be unable to reach understand CTO abbreviation. Cultural and trans-cultural aspects of the topic should be discussed briefly. Answer: This is a very interesting and relevant topic in the field of compulsive treatment. Considering the limitations in the number of words we have included the following paragraph “We must bear in mind that culture and other social factors are also determinants in the application of CT and countries legislations frequently express the cultural milieu and possible constitutional rights (which differ significantly from western to eastern countries as well as from southern to northern Europe).”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-219
|
https://f1000research.com/articles/11-1188/v1
|
17 Oct 22
|
{
"type": "Data Note",
"title": "Cross-sectional data on stablecoin characteristics",
"authors": [
"Katarzyna Włosik",
"Blanka Łęt",
"Konrad Sobański",
"Wojciech Świder",
"Blanka Łęt",
"Konrad Sobański",
"Wojciech Świder"
],
"abstract": "The article presents a dataset on the characteristics of stablecoins. Stablecoins represent a relatively young but increasingly important branch of the cryptocurrency market. Although they all share the same goal of maintaining a stable value in the digital market, they form a highly heterogeneous group. They differ in terms of collateral and stabilization mechanism, peg, availability of the technical documentation, presence on crypto exchanges or age. The dataset is cross-sectional and was created based on internet research. Individual information was collected from websites of the stablecoin projects and a crypto-data aggregator, and to a lesser extent from other auxiliary sources (websites related to finance and cryptocurrencies). The dataset is unique as there are no publicly available databases encompassing the features of stablecoins. It can be used in all stablecoin-related analyses to characterise the examined coins and to investigate the relationship between cryptocurrency market developments and stablecoin features.",
"keywords": [
"Stablecoin",
"cryptocurrency",
"whitepaper",
"exchanges",
"market cap",
"collateral type"
],
"content": "Introduction\n\nStablecoins can be defined as digital units of value that, through special stabilisation mechanisms, are supposed to maintain a stable value in relation to a selected benchmark – one or more traditional currencies or other types of assets, including crypto assets.1 Stablecoins are drawing the attention of policymakers due to their dynamic growth, the increasing number of use cases and the risks they may pose to financial stability.1 The stablecoin market is also appealing to investors and researchers. Nevertheless, very few papers explore the importance of stablecoin features. The work of García et al.,2 who consider stablecoin features when developing a framework for risk assessment, is among the exceptions. Jarno and Kołodziejczyk3 analyse the volatility of stablecoins with respect to the type of these digital assets. It is worth noting that while all stablecoins aim to maintain a stable value, they differ in many aspects. This fact creates research opportunities.\n\nThe dataset presented in this Data Note combines multiple data sources on individual stablecoins to form a unique database on the stablecoin market (on features of stablecoins). It can be useful for researchers and practitioners interested in the functioning and development of the cryptocurrency market. The dataset might be used for cross-sectional comparative studies on the stablecoin market. This branch of the cryptocurrency market is relatively young and there are no publicly available databases encompassing the features of these digital assets. The dataset can be applied in all stablecoin-related analyses to characterise the examined coins and investigate the relationship between cryptocurrency market developments and stablecoin features without the need to dedicate efforts to time-consuming studies of individual stablecoins.\n\n\nMethods\n\nThe data was collected via internet research. The list of stablecoins was compiled from information available on the website of CoinMarketCap – the aggregator of cryptocurrency data which is frequently used in research (see for example Refs. 4–7). Then, data on these stablecoins was collected from various sources – websites of the stablecoin projects, CoinMarketCap, and, to a limited extent, other websites.\n\nOut of the group of 98 stablecoins that were listed by CoinMarketCap (as of 8 May 2022) the data was collected for 30 of them. A coin was excluded from the analysis if:\n\n• it was launched after 1 July 2021,\n\n• there was virtually no information on this stablecoin and the project’s website was not working when the study took place (e.g. Xaurum.org),\n\n• it was misclassified as a stablecoin – such cases were determined based on the price charts provided by CoinMarketCap and also the analysis of the projects’ websites (e.g. Reserve Rights – RSR, was classified as a stablecoin when the study took place, however the price chart showed great variability8 and the website of the project informed that RSR was a governance token supporting the functioning of a stablecoin developed within the same protocol9,10),\n\n• its operation has been suspended (e.g. DigixDAO11).\n\nThe information used to create the database came from several sources:\n\n• the CoinMarketCap.com website (list of stablecoins, tickers, approximated start date, market capitalisation, number of crypto exchanges listing a particular stablecoin, number of trading pairs in which a particular stablecoin is included),\n\n• websites of the analysed stablecoin projects (type of stablecoin, availability of whitepaper/documentation, peg),\n\n• other websites (other relevant information, e.g. link to any crypto exchange).\n\nDue to the large number of websites, their addresses are provided in the dataset file. Each data point is accompanied there by a source.\n\n\nData description\n\nThe dataset (see Underlying data 12) includes 30 stablecoins: Tether, USD Coin, Binance USD, Terra USD, Dai, True USD, Pax Dollar, Neutrino USD, Frax, HUSD, Origin Dollar, Gemini Dollar, Stasis Euro, sUSD, Celo Dollar, Qcash, Vai, Steem Dollars, mStable USD, USDK, Rupiah Token, EOSDT, CryptoFranc, NuBits, Italian Lira, Fei, Liquity USD, XSGD, TerraKRW, Basis Cash.\n\nThe database contains 14 features characterising each of the above-mentioned stablecoins. The features were selected to show different aspects of stablecoins, including their technical properties, connections to different trading venues and properties that may affect their attractiveness, credibility and availability for market participants. The description of these characteristics is provided in Table 1.\n\n\nData availability\n\nMendeley Data: Cross-sectional data on stablecoin characteristics. https://doi.org/10.17632/v4pgsyn6dr.1.12\n\nThis project contains the following underlying data:\n\n- Dataset.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAdachi M, Pereira Da Silva PB, Born A, et al.: Stablecoins’ role in crypto and beyond: functions, risks and policy.European Central Bank;2022. (accessed 14 September 2022).Reference Source\n\nGarcía A, Lands B, Yanchus D: Stablecoin assessment framework.Bank of Canada Staff Discussion Paper, 2021, No. 2021-6, Bank of Canada, Ottawa.\n\nJarno K, Kołodziejczyk H: Does the Design of Stablecoins Impact Their Volatility? J. Risk Fin. Manag. 2021; 14(42). Publisher Full Text\n\nKristoufek L: Tethered, or Untethered? On the interplay between stablecoins and major cryptoassets. Financ. Res. Lett. 2021; 43: 101991. Publisher Full Text\n\nAssaf A, Bhandari A, Charif H, et al.: Multivariate long memory structure in the cryptocurrency market: The impact of COVID-19. Int. Rev. Financ. Anal. 2022; 82: 102132. Publisher Full Text\n\nLong H, Zaremba A, Demir E, et al.: Seasonality in the Cross-Section of Cryptocurrency Returns. Financ. Res. Lett. 2020; 35: 101566. Publisher Full Text\n\nMeyer A, Ante L: Effects of initial coin offering characteristics on cross-listing returns. Digital Finance. 2020; 2: 259–283. Publisher Full Text\n\nCoinMarketCap: Reserve Rights.2022. (accessed 8 May 2022).Reference Source\n\nReserve: Introduction to the Reserve protocol.(accessed 8 May 2022).Reference Source\n\nReserve Rights (RSR): Introduction to the Reserve protocol.(accessed 8 May 2022).Reference Source\n\nDigix: Customer Notice.(accessed 8 May 2022).Reference Source\n\nWłosik K, Łęt B, Sobański K, et al.: Cross-sectional data on stablecoin characteristics, Mendeley Data, V1, 2022. [Dataset].Reference Source\n\nRosa G, Pareschi R: Tether: A Study on Bubble-Networks. Front. Blockchain. 2021; 4: 686484. Publisher Full Text\n\nPaxos: Pax Dollar (USDP): White Paper.2021. (accessed 8 July 2022).Reference Source\n\nHuobi Global: The Safe and Secure Stablecoin. Frequently Asked Questions. Who is the issuer of HUSD?2022. (accessed 8 July 2022).Reference Source\n\nCentre: Introducing USD COIN: A stablecoin brought to you by Circle and Coinbase.2022. (accessed 8 July 2022).Reference Source\n\nPaxos: Binance USD (BUSD).2022. (accessed 8 July 2022).Reference Source\n\nKwon D: Announcing TerraUSD (UST) – the Interchain Stablecoin.2020. (accessed 8 July 2022).Reference Source\n\nPerryman E: What is the USDK stablecoin?2019. (accessed 8 July 2022).Reference Source\n\nGemini: Gemini dollar.2022. (accessed 8 July 2022).Reference Source\n\nNeutrino: Decentralized Forex. Trade national currencies on a decentralized exchange.2022. (accessed 8 July 2022).Reference Source\n\nNeutrino: USDN.2022. (accessed 8 July 2022).Reference Source\n\nKwenta: FAQ.2022. (accessed 8 July 2022).Reference Source\n\nGemini: What Are Stablecoins?2022. (accessed 8 July 2022).Reference Source\n\nMoin A, Sekniqi K, Sirer EG:SoK: A Classification Framework for Stablecoin Designs.Bonneau J, Heninger N, editors. Financial Cryptography and Data Security. FC 2020. Lecture Notes in Computer Science. Cham:Springer;2020; 12059.\n\nAlexander C, Dakos M: A critical investigation of cryptocurrency data and analysis. Quant. Finance. 2020; 20(2): 173–188. Publisher Full Text"
}
|
[
{
"id": "156525",
"date": "05 Dec 2022",
"name": "Sergio Luis Náñez Alonso",
"expertise": [
"Reviewer Expertise Digital Economy",
"Decentralised Finance",
"Central Bank digital Currency"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe data note under review presents a brief introduction to the characterization of digital currencies called Stablecoins. This has allowed the authors to build up a novel database on stablecoins, mainly by searching the Internet. It is therefore a brief scientific review of the current state of the art on stablecoins, proposing a database that can be used by other researchers in their studies. It is in this last point that the value of the study lies.\nAfter reviewing the data note, it can be qualified as highly original, given that there are no other cross-sectional databases available for consultation by potential cryptocurrency researchers. This means that the contribution to scholarship is also high. Regarding the structure, the data note under evaluation is of the short-paper type, so the introduction is sufficient.\n\nThere are a few issues that should be improved by the authors:\nIn the methodology section, the authors should refer to previous database generation studies with their limitations.\nIn the data description section, the authors should indicate a valid reason why only 30 Stablecoins were selected. In other words, originality in the attempt to construct this database is appreciated. The methodology details the criteria for selecting the sample of 30 stablecoins based on the information that appears in CoinMarketCap, the websites of the stablecoins themselves and other websites (at this point, they could mention some, perhaps including references). I understand that of the 98 listed on CoinMarketCap as of May 2022, many were excluded (down to 30) for the reasons stated. I don't know if Terra USD is no longer classified as a stablecoin after the crash that month (it dropped 40% in value). Do you guys consider keeping it in the sample? If so, I would like you to explain.\nI find table 1 very interesting as it raises 14 characteristics (a sufficient number) and a description of these. It is a research note that adds value to academic research on this topic. I recommend, however, to expand the references, either in the text or in Table 1, as there are many publications on stablecoins, in order to characterize stablecoins with previous studies and authors.\nFinally, I thank you for inviting me to review this data note. I found it relevant and interesting.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
},
{
"id": "154508",
"date": "03 Feb 2023",
"name": "Rekha Pillai",
"expertise": [
"Reviewer Expertise Corporate governance",
"cryptocurrency",
"firm performance",
"behavioral finance"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is novel. The rationale for creating the aforesaid data set is clearly outlined. The authors have collected Individual information from websites of the stablecoin projects and a crypto-data aggregator and they have clearly mentioned about the limited availability of stablecoin related information available on the public domain. It can be considered as an exploratory study as it unearths the stable coin dimensions, a less researched topic but one of high significance.\n\nFuture studies can build on the same and this is the main contribution of the paper. The data set is clearly presented in a useable and accessible format. It is clearly evident that no other cross- sectional studies of a similar nature has been conducted till date. However, as a suggestion, you may also justify the rationale behind why only 30 stable coins were selected, although the attempt is highly appreciated. You have clearly highlighted the rationale in excluding certain stable coins but you may elaborate on the total available, ones included and those excluded for providing a comprehensive picture.\n\nAs a recommendation to improve the paper, a brief literature review in a tabular form which only contains author names, year and key findings can add value. The paper may include a concluding paragraph, wrapping up the study with some future research/practical implications. Limitations of the study can be highlighted and suggest potential use of aforesaid data collected as recommendations for future research.\n\nFinally thank you for giving this opportunity to review the paper and I hope the comments will be taken positively.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1188
|
https://f1000research.com/articles/11-1187/v1
|
17 Oct 22
|
{
"type": "Research Article",
"title": "Knowledge and attitude of the people in San Juan de Miraflores towards the disposal of medicines",
"authors": [
"Ambrocio Teodoro Esteves Pairazaman",
"Juan Manuel Parren̈o Tipian",
"Antonio Guillermo Ramos Jaco",
"Taylor Anthony Lujȧn Orbegȯn",
"Noemi Eva Manami Manami",
"Ramiro Ismael Trujillo Roman",
"Manuel Jaime Caballero Garcia",
"Juan Carlos Salazar Lopez",
"Ana Lourdes Huarcaya Laura",
"Juan Manuel Parren̈o Tipian",
"Antonio Guillermo Ramos Jaco",
"Taylor Anthony Lujȧn Orbegȯn",
"Noemi Eva Manami Manami",
"Ramiro Ismael Trujillo Roman",
"Manuel Jaime Caballero Garcia",
"Juan Carlos Salazar Lopez",
"Ana Lourdes Huarcaya Laura"
],
"abstract": "Background: Medicines that are expired or deteriorated within a household must be disposed of in an effective and environmentally friendly manner, to the point that they do not end up being a risk to the community and the environment. To do this, the members of Peruvian households must have the knowledge and the appropriate attitude, together with the necessary tools for the effective disposal of these drugs. For this reason, the research objective is as follows: to evaluates the relationship between the level of knowledge and attitudes on how to dispose of medicines in households in the district of San Juan de Miraflores. Methods: Hypothetical-deductive, quantitative approach, applied type and non-experimental, observational design, for which 385 households in the district of San Juan de Miraflores were surveyed. Results: 48.3% of the respondents have an average level of knowledge of how to dispose of medicines. 93.2% of the respondents have a positive attitude towards the disposal of medicines, and there is a relationship between the level of knowledge and attitude towards the disposal of medicines (P-value = 0.000). Conclusions: Increased knowledge is associated with a better attitude to the disposal of medicines.",
"keywords": [
"Disposal",
"medicines",
"attitude",
"knowledge",
"medicine waste"
],
"content": "Introduction\n\nOne of the problems that people currently face is how to dispose of expired, deteriorated and unusable medicines in their homes, as there is no system for returning medicines, which is why people inappropriately dispose of medicines, contributing to environmental pollution and public health problems. The cause of this problem is due to the lack of advice to the population and also the absence of regulations and laws on the part of the authorities that allow the disposal of waste medicines at home, as happens in many countries in the world.1\n\nGlobally, the consumption of medicines is on the rise. In the last five years, it has increased by 4-5% according to a report detailed by the Institute of Human Data Science (IQVIA) in 2019. According to Olivar, Berenguer and Rodilla, when a patient is undergoing pharmacological treatment, he or she does not fully or correctly consume his or her medicines due to various factors, causing them to accumulate at home. It is estimated that billions of medicines are wasted worldwide.2 Per the Food and Drug Administration (FDA), unusable and expired medicines that are not consumed in households should be disposed of as soon as possible to reduce the likelihood of others accidentally taking or misusing the medicine, as well as to reduce the number of medicines in the environment.\n\nCurrently, there are developed countries and some regions in Latin America that have the support of their national government in presenting initiatives to solve the disposal of unwanted medicines from the home. One of these initiatives is to collect medicines in authorized pharmacies, where people can deposit their medicines properly in special bins, raising awareness among people about the correct disposal of medicines and protecting the environment.3,4\n\nIn 2015, the Ibero-American Network of Medicines Post-consumption Programs (RIPPM) was created, and is an organization formed with the aim of exchanging experiences that contribute to identifying the advantages and disadvantages of the different medicines’ post-consumption programs in the following countries: Spain, where there is an organization known as the Integrated System for the Management and Collection of Packaging (SIGRE); Mexico, where there is the organization Sistema Nacional de Gestión de Residuos de Envases y Medicamentos (SINGREM); Portugal, with the organization Valormed Sociedade Gestora de Resíduos de Embalagens e Medicamentos, Lda. (VALORMED); and in Colombia, with the Punto Azul Corporation.\n\nIn Peru there is Law N° 27314: “General Law on Solid Waste” which ensures the management and handling of solid waste. In addition, there is the Technical Health Standard (NTS) N°144-MINSA/2018/DIGESA which sets out the management and handling of solid waste in health facilities, medical support services and research centers, but does not specify the disposal of unusable and expired medicines in households. According to the National Centro Nacional de Documentación e Información de Medicamentos (CENADIM), the 2012 bulletin “Disposal of medicine waste in the home” contains certain recommendations provided by international institutions for the proper disposal of medicines in households.\n\nOn 18 December 2019, the Ministerio de Salud (MINSA), in Perú, launched a national campaign called ‘Collection points for expired and unusable medicines from the home’, implemented in each district of Lima and various regions nationwide. The collection points are red containers where people can dispose of their expired and unused medicines, as this waste puts people's health at risk, contaminates the environment and promotes illegal trade. This campaign was in turn promoted by the Dirección General de Medicamentos Insumos y Drogas (DIGEMID) and the Colegio Químico Farmacéutico del Perú who provided information on the collection points and promoted awareness of waste disposal.\n\nFor all of the above reasons, and taking into account the negative impact on public health and the increase in environmental pollution caused by medicines, unused and expired medicines should be disposed of correctly in order to avoid possible consequences. It is essential to know how much the population knows about how to dispose of medicines and also to investigate whether there is any relationship between the knowledge of the population and their attitude towards medicine waste management.\n\nThe purpose of the study is to provide up-to-date information on the disposal of expired and unusable medicines since it is of interest to compare the level of knowledge and attitudes regarding the disposal of medicines with what is reported in households in the district of San Juan de Miraflores and in other towns. This information will help to find out how the current campaign established by MINSA to comply with the regulations on solid waste management is being implemented. This will serve to solve a collective problem, proposing activities such as: educational talks, pharmaceutical counselling by pharmaceutical chemists and health professionals through pharmacies and health centers; as well as the reinforcement of information to the population about the campaigns in force by the competent authorities.\n\n\nMethods\n\nThe research carried out did not harm the ethics and morals of the people. When visiting homes in the district of San Juan de Miraflores, the people living in each home were informed of the purpose of the survey and were asked to sign a voluntary informed consent form before the survey was carried out.\n\nParticipants were assured that their data would be anonymous and confidential, and that the information was for academic purposes.\n\nThe research was approved by Resolution No. 042-2022-DFFB/UPNW issued January 14, 2022, by the Dean of the Faculty of Pharmacy and Biochemistry of the Norbert Wiener Private University.\n\nThe research method was hypothetico-deductive, with a quantitative approach, applied and non-experimental, observational design.5,6\n\nThe population consisted of 7589 households in the Pamplona Alta and Pamplona Baja areas.\n\nIt should be noted that for each household only one person will be interviewed who meets the inclusion and exclusion criteria.\n\nInclusion criteria:\n\n• Male or female persons, who is over 18 years of age and who lives in the Pamplona Alta and Pamplona Baja areas.\n\nExclusion criteria:\n\n• Children, youth or adolescent minors (under 18 years of age).\n\n• Persons with any mental disability.\n\nThe sample was made up of 385 households in the districts of Pamplona Alta and Pamplona Baja, San Juan de Miraflores.\n\nThe sample consisted of 385 households in the neighborhoods of Pamplona Alta and Pamplona Baja, San Juan de Miraflores.\n\nNone of the 385 people refused to participate in the study. Each person was surveyed at the door of their respective homes, they read and filled out the questionnaire given voluntarily and personally, the researchers only observed and did not intervene in the answers given by each respondent.\n\nData collection took place between March and April 2022.\n\nThe technique used was the survey and the instrument used was a questionnaire, applied to the study sample and divided into three sections. The first section was focused on providing information on the socio-demographic factors of the sample and comprised of questions one to five. The second part is focused on measuring the level of knowledge of the inhabitants on how to dispose of medicines in household, measured on a three-level scale (low level of knowledge, medium level of knowledge and high level of knowledge) evaluated by means of single responses within the questionnaire and comprised of a single dimension called “Knowledge of how to dispose of medicines” where nine evaluation indicators are comprised. Finally, the third part of the questionnaire is focused on measuring the attitude of the population on how to dispose of medicines in households; this was measured on a two-level scale (negative attitude and positive attitude) made up of a dimension called “Attitude towards how to dispose of medicines”, with response alternatives: Strongly disagree,1 Disagree,2 Neither disagree nor agree,3 Agree4 and Strongly agree.5\n\nLevel of knowledge:\n\n• High knowledge = 6 to 9 points.\n\n• Medium knowledge = 2 to 5 points.\n\n• Low knowledge = 0 to 1 point.\n\nType to attitude:\n\n• Positive attitude: 19 to 30 points\n\n• Negative attitude: 6 to 18 points.\n\nThe instrument was validated through the judgement of four experts and reliability was obtained through a pilot test of 30 people. The questions with dichotomous answers were evaluated with the Kuder Richardson test (Kr-20>0.5) and the questions with polytomous answers were evaluated with Cronbach's Alpha test (α>0.7), in both tests the instrument obtained a value of Kr-20>0.676 and α>0.784 positive reliability results.\n\nThe data were processed using the statistical program IBM SPPS Statistics version 26.\n\nTo analyze the results, descriptive statistics were used and cross tables were drawn up. Inferential statistics, for which tables and graphs were drawn up, were used to show the results. Finally, the correlation was analysed with Spearman's Rho coefficient.\n\n\nResults\n\nOut of a total of 385 households, 41.56% indicated that they correctly dispose of unused, expired, or damaged pills at home, 37.66% of ointments, 30.39% for syrups and 39.22% indicated that they dispose of inhalers by depositing them at the drug disposal collection point. Others in the sample indicated that they disposed of medicines such as tablets (58.44%), ointments (62.34%), syrups (69.61%) and inhalers (60.78%) by throwing them in the bin, flushing them down the toilet or simply kept them at home without knowing what to do with them (see Table 1 and Table 2).\n\nFigure 1 shows the level of knowledge about how to dispose of expired, deteriorated and unused medicines in households, where people were asked whether they knew how to dispose of certain medicines and the negative environmental and community impact that these could cause if certain criteria for correct disposal were not taken into account. Of the sample studied, 19.74% (76 households) had a low level of knowledge about how to dispose of pharmaceuticals, 48.31% (186 households) had a medium level and 31.95% (123 households) had a high level of knowledge about the topic under study.\n\nFigure 2 shows the attitudes of family members in households in the district of San Juan de Miraflores regarding the disposal of medicines, evaluating the care, opinions and actions that people take regarding the disposal of medicines in their place of residence. Of the sample studied, 93.25% (359 households) had positive attitudes towards the disposal of medicines and 6.75% (26 households) had negative attitudes towards the subject studied.\n\nHo: There is no relationship between the level of knowledge and attitude towards the disposal of medicines in households in the district of San Juan de Miraflores.\n\nHi: There is a relationship between the level of knowledge and attitude towards the disposal of medicines in households in the district of San Juan de Miraflores.\n\nIn Table 3, Spearman's Rho correlation test (Sig.>0.05) found that the p-value of the statistical test was 0.000 with a low positive correlation (Rho = 0.345), approving the alternative hypothesis (Hi), indicating that there is a relationship between the level of knowledge and attitude towards the disposal of medicines. This indicates that the greater the knowledge and increase in the level of knowledge, the greater the attitude towards the correct disposal of medicines that are expired, deteriorated and unusable in the households of San Juan de Miraflores.\n\n\nDiscussion and conclusion\n\nAlthough there are several studies on the subject, our study is important because it is one of the few studies in the area. In addition, it allows us to understand and get closer to the local reality about knowledge and attitudes towards medicine disposal.\n\nOne of the main limitations of the study is that the data represent only one district of Lima, therefore the data could not be generalized to the whole department. The objective of the study was to identify medicine disposal practices, so data such as the quantity of medicines discarded and the cost of disposal have not been quantified. In other words, the results are general ideas for future studies to highlight the extent of medicine disposal problems and to investigate the environmental impact in depth.\n\nAs can be seen, more than 50% of the population disposes of medicines by throwing them in the trash or flushing them down the toilet, or does not know what to do with them, while fewer dispose of expired and unused medicines from the household at designated collection points.\n\nOne study analyzed the environmental impact of different methods of medicine disposal, such as incineration, dumping and landfilling, and found that medicines entering the environment through different disposal methods cause air pollution and can harm children, adults, animals, and the environment through improper disposal.7\n\nRegarding the level of knowledge of how to dispose of medicines in the households of the study site, it was found that 48.31% had a medium level of knowledge and 31.95% had a high level of knowledge. These indicators are positive in the study, due to the clear evidence that the locals have some knowledge of how to dispose of medicines and have also learned about what they should do to get rid of medicines that will no longer be used by family members in the household or that have simply expired. This differs from the findings of Rodríguez and Vargas,8 who conclude that the level of knowledge of the population of San Borja and Puente Piedra is low, with 76.2% and 97.0%, respectively, not knowing how to dispose of medicines,9 whose study population was in Gujarat (India), found that 61% did not know the methods and places to dispose of their medicines, implying a low level of knowledge, due to a lack of education on safe medicine disposal methods on the part of patients.\n\nAbout the attitude towards the disposal of medicines in households in the district of the study site, it was found that 93.25% had a positive attitude, a positive indicator that shows that people have a good attitude towards the disposal of medicines that are no longer available for consumption in their homes. This is similar to what was found by Kahsay, et al.,10 who concluded that the population of the cities of Adrigat and Tigray (Ethiopia) had a positive attitude of 82.2% in the disposal of medicines, as did Zuñiga11 who showed similar results, concluding that the population of the district of Los Olivos had a positive attitude of 96.3% in the disposal of medicines in their homes.\n\nFinally, about the relationship between the level of knowledge and attitude on how to dispose of medicines, a significant relationship was found between the two variables using Spearman's correlation test (P-value = 0.000), similar to the study by Zuñiga,11 which showed a significant relationship (P-value 0.015) between attitude and level of knowledge, using the same correlation test. Therefore, health professionals should be trained and knowledgeable about the correct and safe disposal of medicines and provide this information to patients when they visit them, and pharmacy specialists have an important role to play in providing adequate information about the safe disposal of medicines to develop positive disposal practices.12\n\nIn conclusion, the level of knowledge and attitude of household residents in the San Juan de Miraflores district regarding the disposal of expired, damaged and/or unusable medicines is positively correlated, showing that if they know about the measures and are aware of the forms and methods to be considered when disposing of medicines, they will dispose of them correctly. This highlights the importance of developing environmental policies through public policies that are not only publicized, but also educate through awareness programs for the safe and proper disposal of expired, unwanted, or unused medicines.\n\n\nData availability\n\nZenodo: Knowledge and attitude of the people in San Juan de Miraflores towards the disposal of medicines, https://doi.org/10.5281/zenodo.6991474.13\n\nThis project contains the following underlying data:\n\n- DATA.csv\n\n- DATA.sav\n\nZenodo: Knowledge and attitude of the people in San Juan de Miraflores towards the disposal of medicines, https://zenodo.org/record/7109117#.Yy9xnnbMLIU.13\n\nThis project contains the following extended data:\n\n- DATA KEY Knowledge and attitude.txt\n\n- English questionnaire.docx\n\n- Spanish questionnaire.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nFernandez MR, Figueiredo RC, Silva LG, et al.: Storage and disposal of expired medicines in home pharmacies: emerging public health problems. Einstein (São Paulo). 2020; 18: 1. Publisher Full Text Reference Source\n\nAfriyie A, Drewry J, Ampratwum F: What happens to unused, expired and unwanted medications? A survey of a community-based medication disposal practices. Int. J. Dev. Sustain. 2014; 3(12): 2175–2185.Reference Source\n\nBettington E, Spinks J, Kelly F, et al.: Returning unwanted medicines to pharmacies: prescribing to reduce waste. Aust. Prescr. 2018; 41(3): 78–81. PubMed Abstract | Publisher Full Text Reference Source\n\nKumar L, Logeshwaran S, Vanitha N, et al.: Assessment of Knowledge and Awareness on the Disposal of Expired and Unused Medicines among Medication Consumers. J. Young Pharm. 2019; 11(4): 410–416. Publisher Full Text Reference Source\n\nÑaupas H, Valdivia M, Palacios J, et al.: Metodología de la investigación cuantitativa – cualitativa y redacción de tesis. 5ta ed.Colombia:Ediciones de la U;2018.\n\nHernández-Sampieri R, y Mendoza C: Metodología de la investigación. Las rutas cuantitativa, cualitativa y mixta. México:Grupo editorial Mc Graw Hill Education;2018.\n\nTong AYC, Peake BM, Braund R: Disposal practices for unused medications around the world. Environ. Int. 2011; 37(1): 292–298. PubMed Abstract | Publisher Full Text\n\nRodríguez M, Vargas I:2019; Nivel de conocimiento de la forma de eliminar los medicamentos en hogares de los distritos de San Borja y Puente Piedra en mayo 2018. [Tesis para optar el grado de licenciado en Farmacia y Bioquímica]. Lima:Universidad Privada Norbert Wiener;Reference Source\n\nSonowal S, Desai C, Kapadia JD, et al.: A Survey of Knowledge, Attitude, and Practice of Consumers at a Tertiary Care Hospital Regarding the Disposal of Unused Medicines. Rev. J. Basic Clin. Pharm. 2016; 8(1): 4–7. Publisher Full Text Reference Source\n\nKahsay H, et al.: Assessment of Knowledge, Attitude, and Disposal Practice of Unused and Expired Pharmaceuticals in Community of Adigrat City, Northern Ethiopia. J. Environ. Public Health. 2020; (1): 1–11. PubMed Abstract | Publisher Full Text Reference Source\n\nZuñiga CH: Nivel de conocimiento y actitud sobre la forma de eliminar los medicamentos de los usuarios externos en oficinas farmacéuticas independientes del distrito de Los Olivos, año 2020 [Tesis para optar el grado de bachiller en Farmacia y Bioquímica]. Lima:Universidad Privada Roosevelt;2021.Reference Source\n\nAlAzmi A, AlHamdan H, Abualezz R, et al.: Patients' knowledge and attitude toward the disposal of medications. J. Pharm. 2017; 2017(2): 1–179. Publisher Full Text Reference Source\n\nPairazaman E, Teodoro A, Tipian P, et al.: Knowledge and attitude of the people in San Juan de Miraflores towards the disposal of medicines. [Dataset]. Zenodo.2022. Publisher Full Text"
}
|
[
{
"id": "153506",
"date": "22 Nov 2022",
"name": "Carlos Seas",
"expertise": [
"Reviewer Expertise Infectious Diseases"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study that reports the level of knowledge and attitudes of people living in a district in Lima. While the study is well conducted, this reviewer has several observations\nThe study was conducted in a single district in Lima, Peru and the results can not be extrapolated to the whole capital of Peru. What is the value of evaluating a single district not been selected randomly?\n\nThe Spearman correlation coefficient was extremely low to conclude that an association between the level of knowledge and attitudes does exist\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "9093",
"date": "05 Dec 2022",
"name": "AMBROCIO TEODORO ESTEVES PAIRAZAMAN",
"role": "Author Response",
"response": "The value of evaluating a single district is because the district of \"San Juan de Miraflores\" deserved a study, because after a tour of the different districts of Lima, it was decided to choose one of them. A previous tour was made in the district of SJM on its knowledge and attitude of drug disposal, which merits a study in the district. The sample was obtained by convenience. The results could be extrapolated to the entire capital of Peru (Lima), but maps of all the districts would be needed to know the different population sectors, blocks, and lots, and this would imply asking each municipality of each district to apply the methodology to all the districts. In a correlation test it is the p-value (the statistical significance or bilateral Sig. < 0.05) that rules. Although the value of the coefficient may be low, if the p_value is significant then the association is accepted in the study. In other studies for other districts these results may vary."
}
]
},
{
"id": "170124",
"date": "27 Apr 2023",
"name": "Bruce Sunderland",
"expertise": [
"Reviewer Expertise Pharmacy Practice"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis short paper considers the relationship of knowledge and attitude towards the disposal of medicines. Overall the paper considers most factors. Although the sampling frame is provided, no power calculation is provided for the final sample. No information is provided on how the sample was selected. The results section provides the demographics of the sample participants but it is unknown if they are reflective of those of the sampling frame or the population of Lima. Notably 45.% had higher technical or university qualifications. The contrast between knowledge level and depositing expired medicines at designated collection points is evident. Knowledge is 80.63% whereas correct deposition was 30 to 40%. Is this because not all had any medicines for disposal? Some regression statistics would have provided further insight into the data. The Ho and Hi definitions could be removed. The limitations could be further enhanced by providing comparative population data the the district and city.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1187
|
https://f1000research.com/articles/11-702/v1
|
27 Jun 22
|
{
"type": "Research Article",
"title": "Phytochemical study of the plant species Bidens pilosa L. (Asteraceae) and Croton floccosus (Euphorbiaceae)",
"authors": [
"Enrique Ruiz-Reyes",
"Mayte Ariana Mendoza-Cevallos",
"Ana Patricia Polanco-Moreira",
"Diego Germán Segovia-Cedeño",
"Ulbio Eduardo Alcivar-Cedeño",
"Alex Dueñas-Rivadeneira",
"Mayte Ariana Mendoza-Cevallos",
"Ana Patricia Polanco-Moreira",
"Diego Germán Segovia-Cedeño",
"Ulbio Eduardo Alcivar-Cedeño",
"Alex Dueñas-Rivadeneira"
],
"abstract": "Background: Given the chemical richness of medicinal plants (Bidens pilosa L. and Croton floccosus) in Ecuador, they are considered the natural source of numerous medicines. Methods: The leaves were dried at 40°C and 50°C and the extracts were characterized by means of phytochemical screening, verifying the presence of secondary metabolites such as alkaloids, reducing sugars, phenols, flavonoids, tannins and saponins. Three extraction processes were carried out, with two solvents of different polarities: hexane and ethanol. The extraction methods that were applied to the leaves of the plants were Soxhlet, ultrasonic bath and maceration, the latter two at room temperature and Soxhlet at the boiling temperature of the solvent. Determination of the total content of phenols and flavonoids is carried out using the Follin-Ciocalteau colorimetric reaction, Quercetin standard, Aluminum Chloride solution measured with a UV-Vis spectrophotometer. The antioxidant activity was performed with the DPPH radical and measured with the same equipment. Results: The highest content of total phenols obtained by employing the Soxhlet method for extraction when the material was dried at 50°C was 48.609 ± 0.370 mg GAE/g of dry sample for Bidens pilosa L. while in the case of Croton floccosus it was 128.212 ± 0.601 mg GAE/g of dry sample obtained from the extraction by means of maceration. Finally, the antioxidant activity against the 1.1-diphenyl-2-picryl-hydrazyl radical was determined, and it was found that the Bidens pilosa L. species performed better and responded better to the test, with an IC50 value of 239.33 µg/mL, than Croton floccosus (IC50 of 644.125 µg/mL). Conclusions: The following preliminary phytochemical study of the Bidens pilosa L. and Croton floccosus plants provided important information on the content of secondary metabolites and response to the DPPH radical reported for the first time in Ecuador, which may be future use for medicinal application.",
"keywords": [
"extraction",
"phytochemical study",
"phenols",
"flavonoids",
"Bidens pilosa L",
"Croton floccosus",
"Asteraceae",
"Euphorbiaceae"
],
"content": "Introduction\n\nThe biodiversity of Ecuador ranks sixth worldwide for the number of species.1 Many species comprise the Croton genus in this country, and 39 have been recognized.2 Of these, 13 are considered native,3 and the others have been documented in the last 15 years.4,5 Many species of this genus have been used in traditional medicine by the country’s indigenous population. Antimicrobial,6 antioxidant,7 anti-inflammatory8 and anticancer9,10 biological activity studies have been carried out on them in America, Asia and Africa.\n\nBrian A. Smith found a new species of Croton (Euphorbiaceae) on the western slopes of the Ecuadorian Andes in 2006, Croton floccosus.11 This is described as a medium-sized tree with grayish external and internal bark with a reddish exudate, along with simple leaves (4–15 × 2.5–8 cm) and alternate elliptic-oval unisexual flowers and tricoco-type fruits with persistent styles. This plant is commonly found next to streams and disturbed sites in the provinces of Pichincha and Imbabura in Ecuador.\n\nSome 230 to 240 species of Bidens have been described,12,13 including Bidens pilosa, which was identified in 1753 by Carl Linnaeus. This is a representative perennial herb, distributed globally in temperate and tropical regions, which has traditionally been used in food and medicine without having any obvious adverse effects. About 116 publications on this species have documented its medical use,14 and phytochemical studies show that it contains a high number of flavonoids and polyines, which have anticancer,15 anti-inflammatory,16 antibacterial17 biological activity, as well as antifungal,18 antimalarial,19 and antioxidant20,21 properties.\n\nBidens pilosa is an erect, strongly branched plant with a strong aromatic odor. It has opposite leaves and a long petiole, whose limbs are generally deeply divided into 3 to 5 segments giving it the appearance of a compound leaf. It also has white ray flowers and numerous yellow tubular flowers.13\n\nAlthough this species has been studied to a greater extent than Croton floccosus, we have not found phytochemical studies of these plants in Ecuador, which is why it has important research potential that may allow us to transform traditional knowledge into scientific knowledge.\n\nIn the following work, a preliminary phytochemical study of the leaves of the species Bidens pilosa and Croton floccosus was carried out using the Tukey test,22 which is employed in ANOVA in order to compare the means of the values obtained. This study joins the recently published work by Ruiz-Reyes et al. on Melampodium divaricatum and Zanthoxylum sprucei plants,23 in an attempt to discover which active compounds are present and if they have the potential to be used as medicinal plants.\n\n\nMethods\n\nThe fresh leaves of the Bidens pilosa L. and Croton floccosus species were collected in January 2021 from the Botanical Garden at the Technical University of Manabí (UTM), Portoviejo, in the Manabí province in western Ecuador. The botanical identification was carried out by the botanists in charge of the herbarium in the botanical garden at the UTM. The vouchers of the specimens were deposited with the following codes Bidens pilosa L. (Asteraceae) and Croton floccosus (Euphorbiaceae).\n\nThe chemicals and reagents employed in this study were: Folin-Ciocalteu reagent, 1.1-diphenyl-2-picryl-hydrazyl (DPPH), sodium nitrite, aluminum chloride, sodium hydroxide, sodium carbonate, catechin, quercetin, trolox, methanol, and ethanol. All the reagents and solvents were supplied by Sigma-Aldrich and are of an appropriate analytical grade for study.\n\nThe plant material was dried in a tray dryer (universal oven UF110, Memmert) at temperatures of 40°C and 50°C. A reference weight was taken every two hours until it remained constant. The material was then allowed to finish drying, after which it was pulverized. The extracts of the crude plants were obtained using the ultrasonic bath, maceration and Soxhlet extraction methods. In the case of Soxhlet extraction, 10 g of plant material were used and placed in the equipment extractor cartridge with 250 mL of ethanol. Between 8 and 10 extractions were performed at the boiling temperature of the solvent, and the solvent was eventually evaporated in order to obtain the extracts. With regard to ultrasonic bath extraction, 10 g of finely divided plant material was placed in a 250 mL beaker containing 100 mL of ethanol. The mixture was sonicated at 50 W for 1 h in an ultrasonic bath and subsequently filtered. The solvent was then evaporated in a vacuum to obtain the corresponding extracts for analysis. In the case of extraction with maceration, 10 g of finely divided plant material was placed in a 250 mL beaker with 100 mL of ethanol. The mixture was macerated for 72 hours and stirred from time to time. It was subsequently filtered and the solvent was evaporated in a vacuum to obtain the corresponding extracts for analysis.\n\nThe crude extracts were evaluated phytochemically to determine the presence of chemical constituents using standard procedures, following the same methodology described by Ruiz-Reyes23,24 for the determination of metabolites: Alkaloids: Each extract (10 mg) was dissolved in 2 mL of 5% hydrochloric acid and, after mixing and filtering, three aliquots were taken. Drops of Wagner, Mayer, Bouchardat, and Dragendorff reagents were added to each one. A red-brown precipitate (Wagner), a yellowish white precipitate (Mayer), a brown precipitate (Bouchardat), and an orange-red precipitate (Dragendorff) indicated the presence of these metabolites. Flavonoids (Shinoda test): 1 ml of absolute ethanol and three drops of concentrated hydrochloric acid were added to 10 drops of the extract diluted in isopropyl alcohol. The formation of a red color indicated the presence of aurones and chalcones while the formation of an orange, red, or magenta color formation indicated the presence of isoflavones, flavonols, and flavonoids, respectively. Saponins (with sodium bicarbonate): 1 mL of distilled water and one drop of saturated sodium bicarbonate solution were added to five drops of the extract dissolved in isopropyl alcohol (20 mg/mL) in a test tube and shaken vigorously for three minutes. The formation of honeycomb shaped foam indicated the presence of saponins, and tannins: 10 mg of each extract was dissolved in 1 mL of ethanol and extract with 3 mL of boiling distilled water for 15 minutes. Once it had been allowed to stand at room temperature, 0.2 mL of 10% sodium chloride solution was added to the mixture and filtered. In addition, four drops of 10% ferric chloride solution were added. The precipitation observed was indicative of the presence of tannins. For reducing sugars, 200 μL of the extract were dissolved in a tube, Benedict’s reagent was added until the extract turned bluish, it was then heated in a water bath at a temperature of 60°C. It was considered positive if it turned reddish brown.25\n\nDetermination of the total content of phenols in the extracts was carried out using the Follin-Ciocalteau reaction and by employing gallic acid as the reference phenolic compound. The gallic acid calibration curve was prepared by weighing 2 mg of gallic acid and making it up to a volume of 10 mL with distilled water, which is the stock solution at a concentration of 0.2 mg/mL. Aliquots of 50 μL were subsequently taken, after which 200 μL of Follin-Ciocalteau reagent and 2 mL of 7% Na2CO3 were added, and the solution was made up to 5 mL. After the absence of light for 30 minutes and at room temperature, we measured the absorbance at 725 nm using the prepared solution as a blank without the analyte. Total flavonoid content was determined using quercetin as standard. For the preparation of the Quercetin standard, 2 mg of the Quercetin standard was weighed and dissolved with 70% methanol in a 10 mL volumetric flask, which is considered the mother solution with a concentration of 0.2 mg/mL. The aluminum chloride solution was subsequently prepared by weighing 500 mg of AlCl3 and dissolving it with a solution of 25 mL 5% Acetic Acid in methanol, which led to a solution with a concentration of 20 mg/mL and aluminum chloride. In order to perform the calibration curve with the Quercetin standard, aliquots of 5, 10, 15, 20, 25, 30, 35, 40 μL of the standard solution were taken, and made up to 1 mL with methanol (70%), after which 1 mL of the AlCl3 solution was added. The same solution was used as a blank without adding the standard compound. After waiting 15 min for the reaction, the absorbance of the solution was measured at a wavelength of 430 nm in the UV-Vis spectrophotometer. The preparation of the extracts was carried out by taking 5 mg of the sample, which was dissolved in 5 mL of 70% aqueous methanol. The determination procedure for total flavonoids was carried out by taking 200 μL aliquots of different extracts of the sample in triplicate and making them up with 1 mL of methanol (70%), after which 1 mL of the AlCl3 solution was added. After waiting 15 min, the absorbance of the solution was measured at a wavelength of 430 nm in the UV-Vis spectrophotometer. Both methodologies were described by Ruiz-Reyes.23,26–28\n\nThe antioxidant activity was determined using a spectrophotometer and the DPPH molecule as a reagent to generate the free radical following the methodology described by the author himself and other authors.23,29 DPPH reagent preparation: 0.02 g of the DPPH reagent was weighed out and made up to volume with 100 mL of methanol in a flask. This was then homogenized and left to react for 24 hours in an amber bottle in the dark.\n\n• Wavelength determination\n\n2.5 mL of the prepared DPPH reagent was taken and 15 mL ethanol added. A scan was carried out in the spectrophotometer. A maximum absorbance of 0.750 ± 0.05 should appear at a wavelength of 517 nm.\n\n• Blank preparation\n\nMethanol (15 mL) was added and a scan was performed in the spectrophotometer to verify that it did not have absorbance in the working wavelength range in which the maximum of the sample is found.\n\n• Sample preparation\n\nWe took 3.0 mL of the DPPH reagent and 100, 200, 300, 400, 500 μL of the extract added. Once the sample and the blank were prepared, the absorbance reading was performed in the Thermo Scientific Genesys 180 (UV-Visible) spectrophotometer at 517 nM every 10 minutes.\n\n\nResults and discussion\n\nA multifactorial statistical analysis of variance (ANOVA) was carried out for the different species studied, with a maximum order of interaction of 2 for the yield values. This made it possible to determine which of the extraction factors evaluated had a statistically significant effect on the yield. Table 1 presents a summary of the multifactorial arrangement used for the processes of obtaining extracts from Bidens pilosa L. and Croton floccosus at drying temperatures of 40 and 50°C.\n\nTable 2 shows the analysis of variance for the extraction performance in the case of Bidens pilosa L., for which it was determined that there is a statistically significant difference in the treatments. The contribution of each factor was measured by eliminating the effects of the other factors. The P-values test the statistical significance of each of the factors. Since the P-value of factor C (solvent) is less than 0.05, this factor has a statistically significant effect on performance at a confidence level of 95.0%.\n\nFigure 1 shows the influence of the factors of the experimental design with respect to the extraction yield for the extracts obtained from Bidens pilosa L. A notable decrease in yields is observed when the extraction process is carried out using hexane. Although it is not statistically significant, it is necessary to mention that there was a better yield in the extraction processes in which leaves dried at 50°C were used. The process that obtained the best yields was the Soxhlet extraction.\n\nFor each significant factor, multiple range tests provide information regarding which means were significantly different from others. Tukey’s honestly significant difference (HSD) method was selected for this test because it allows the comparison of individual means from an analysis of variance of several samples subjected to different treatments, thus widening the intervals in order to allow multiple comparisons between all pairs of means.\n\nThis test showed that there was no significant difference between the means for the drying temperatures of the leaves of Bidens pilosa L., as is noted in Figure 2. It is necessary to mention that although there was no statistically significant difference between the temperatures used for drying, the extraction processes during which 50°C was used led to higher yield values.\n\nThe multiple range test carried out for Bidens pilosa L. also showed that there was no difference between the extraction process methods evaluated, as is noted in Figure 3. It is, however, necessary to mention that the extraction with an ultrasonic bath and Soxhlet led to higher yields than the maceration process, despite the fact that they are not statistically different.\n\nFurthermore, Table 3 shows the analysis of variance for the extraction performance of Croton floccosus, which determined that there is a statistically significant difference in the treatments. The contribution of each factor is measured by eliminating the effects of the other factors. The P-values test the statistical significance of each of the factors. Since the P-value of factor C (solvent) is less than 0.05, this factor has a statistically significant effect on the extraction yield for Croton floccosus at a confidence level of 95.0%. It is also necessary to highlight that the interaction between factor B (extraction process) and C (solvent) has a significant effect on the extraction process.\n\nFigure 4 shows the influence of the factors of the experimental design on the extraction yield. A notable decrease in yields is observed when hexane is used in the extraction process. It will also be observed that there is a difference with respect to the yields obtained as regards the interaction between the extraction method and the solvent (B and C), showing that the highest yields are obtained with the Soxhlet extraction processes with ethanol at both drying temperatures.\n\nAs described above for the temperatures selected in order to dry Bidens pilosa L., there is no significant difference between the means obtained for the drying temperatures of Croton floccosus leaves (Figure 5). However, it is necessary to mention that, although there is no statistically significant difference, the extraction processes during which the drying temperature of the material was 50°C obtained better extraction yields, as occurred with the Bidens pilosa L.\n\nIt was also noted that the multiple range test carried out for Croton floccosus made it possible to identify that there was a difference between the Soxhlet and maceration process extraction methods (Figure 6). The Soxhlet extraction process method obtains higher yields than the maceration and ultrasonic bath extraction methods.\n\nFinally, in the case of both plants, the multiple range test showed that there was a difference between the solvents used in the extraction (Figure 7). The processes in which hexane was used obtained a low yield when compared to extractions with ethanol.\n\nTable 4 details the qualitative results of the phytochemical tests performed on the ethanolic extracts of Bidens pilosa L. (Asteraceae) and Croton floccosus (Euphorbiaceae), obtained with Soxhlet extraction. There is a low presence of flavonoids and saponins, and a relatively abundant presence of phenols and tannins for both species. In addition, a relatively abundant presence of alkaloids is detected for the species Croton floccosus and no reducing sugars are detected, while a low presence of reducing sugars is detected for the species Bidens pilosa L.\n\nThe equivalent mg of gallic acid corresponding to each gram of dry sample of Bidens pilosa L. were obtained, as shown in (Table 5). As will be noted, Tukey’s HSD test for the phenolic content of the different samples made it possible to determine that there are significant differences among them (p<0.05). Samples that share the same letter are homogeneous.\n\nAs can be seen in Figure 8, the phenolic content for the extracts has values of 27–49 mg GAE/g of dry sample for the different processes employed to obtain ethanolic extracts of Bidens pilosa L. with leaves dried at 40°C and 50°C. Those with the lowest value correspond to the extracts obtained using the maceration method and those with the highest value correspond to the Soxhlet extraction process, with a value of 48.609 ± 0.370 mg GAE/g of dry sample of the extract obtained from the material dried at 50°C. In their research, Singh et al.31 obtained methanolic extracts from leaves of Bidens pilosa L. dried at 30°C with a total phenolic content corresponding to 72 mg GAE/g of dry extract. This value is approximately 32% higher than that obtained in the present investigation, but it is necessary to mention that the extraction carried out by Singh et al. was carried out using an extraction process involving broken evaporation at a reduced pressure. In their investigation, meanwhile, Falowo et al.32 obtained phenolic content for the extracts of B. pilosa corresponding to 75.9 mg GAE/g of dry extract when an exhaustive maceration was carried out with an ethanol-water solution (7:3) with shaking at room temperature for two days.\n\nThe equivalent mg of gallic acid corresponding to each gram of dry Croton floccosus sample were obtained in the same way. These values are presented in Table 6. It was noted that Tukey’s HSD test for the phenolic content of the different samples determined that there is a significant difference among them (p <0.05) Samples that shared the same letter are homogeneous.\n\nA range of 42–129 mg GAE/g of dry sample were obtained from the different processes employed to obtain ethanolic extracts of Croton floccosus, as can be seen in Figure 9. Those with the lowest value correspond to the extracts obtained using the ultrasonic bath method, and those with the highest value correspond to the extraction process carried out using maceration, with a value of 128.212 ± 0.601 mg GAE/g of dry sample of the extract obtained from the material dried at 50°C. This contrasts strongly with the values obtained for Bidens pilosa L., since the extracts obtained by means of maceration had the lowest total phenolic content. Taking into account that this species is considered endemic to Ecuador, Pazmiño,33 in his research, obtained ethanolic extracts from the freeze-dried “latex” of Croton floccosus, which had a total phenolic content corresponding to 271.212 ± 3.1728 mg GAE/g of dry extract. This value is approximately 53% higher than that obtained in the present investigation, and it is necessary to mention that the values presented by this author correspond to those of an extract obtained from the “latex” of this species.\n\nThe equivalent mg of quercetin corresponding to each gram of dry sample of Bidens pilosa L. were obtained, as shown in Table 7. Tukey’s HSD test for the flavonoid content of the different samples determined that there is a significant difference among them (p<0.05). Samples that shared the same letter are homogeneous.\n\nA range of 12–18 mg QE/g of dry sample were obtained from the different processes employed to obtain ethanolic extracts of Bidens pilosa L., as can be seen in Figure 10. Those with the lowest value correspond to the extracts obtained using the maceration method, and those with the highest value correspond to the extraction process carried out with Soxhlet and the ultrasonic bath. There is statistical homogeneity between the values obtained for both processes, with a value of 17.795 ± 0.0644 and 17.665 ± 0.0042a mg QE/g of dry sample of the extract obtained from the corresponding material dried at 40°C. In their study, Cortes-Rojas et al.34 determined the flavonoid content of Bidens pilosa L. extracts by employing dynamic maceration, Soxhlet, ultrasound and microwave, obtaining corresponding values of 21.988 ± 0.127; 19.623 ± 0.100; 16.482 ± 0.180 and 11.590 ± 0.042 mg QE/g dry sample. These values coincide with those obtained in the present study, with the exception of those for dynamic maceration and microwave.\n\nThe equivalent mg of quercetin corresponding to each gram of dry Croton floccosus sample were obtained in the same way, as shown in Table 8. Tukey’s HSD test for the flavonoid content of the different samples determined that there is a significant difference among them (p <0.05). Samples that shared the same letter are homogeneous.\n\nThe established range of total flavonoids comprises values between 7–35 mg QE/g of dry samples for the different processes used to obtain ethanolic extracts of Croton floccosus (Figure 11). As can be seen, there is a great difference between the different treatments. That with the highest flavonoid content corresponds to the Soxhlet extraction process of the material dried at 40°C, with a value of 34.139 ± 0.06224 mg QE/g, while that with the lowest value corresponds to the extracts obtained by employing the ultrasonic bath method at the same temperature, with a value of 7.284 ± 0.15096 mg QE/g of dry sample.\n\nThe in vitro antioxidant activity was performed by employing the 2.2-diphenyl-1-picryl-hydracil radical scavenging method (DPPH assay). All the antioxidant activity values for the ethanolic extracts of both species were obtained from the Trolox equivalent calibration curve (TEAC). The established range for the Trolox equivalent antioxidant activity (TEAC) for Bidens pilosa L. is 74–78 μmol Trolox equivalent (TE)/g of dry samples for the different processes used to obtain ethanolic extracts with leaves dried at 40°C and 50°C (Figure 12). The means of the values were compared using the Tukey test, which showed that there is no marked difference among the processes studied with regard to the TEAC. It was, therefore, established that the drying temperatures do not directly influence the TEAC values for the maceration, ultrasonic bath and Soxhlet extraction processes.\n\nConsidering that there was no marked difference among the processes, we then proceeded to establish the mean radical inhibition coefficient (IC50) of the process that attained the highest antioxidant activity value equivalent to Trolox, Soxhlet extraction of the material dried at 50°C. Table 9 shows the inhibition coefficient (IC50) determined by the DPPH method performed on the extract of Bidens pilosa L. and Trolox (standard). The difference between the extract and the standard used in the previous determinations is compared.\n\nThe values reported in the present study are lower than those reported by Cortés-Rojas et al.,34 who obtained an IC50 for the DPPH radical of 35.35 μg/mL for Bidens pilosa L. extracts from flowers and leaves collected in Brazil using dynamic maceration at 45°C and with 200 rpm of agitation. Furthermore, Singh et al.31 obtained an IC50 value of 80.45 μg/mL for extracts from the leaves of the same species collected in India using maceration with methanol for 48 h. We are, therefore, of the opinion that the differences between our IC50 values and those reported are related to the time of year and the country in which the plant was collected, along with the conditions under which the plant material was prepared and the method used to obtain the extract of secondary metabolites.\n\nThe established range for the Trolox equivalent antioxidant activity (TEAC) for Croton floccosus is 22–27 μmol TE/g of dry samples for the different processes used to obtain ethanolic extracts with leaves dried at 40°C and 50°C (Figure 13). The means of the values were compared using the Tukey test. No marked difference among the processes studied was found for the TEAC, and there was statistical homogeneity among them. It was, therefore, established that, as with Bidens pilosa L., there is no marked difference in the antioxidant activity values obtained using the different extraction processes carried out in the present research.\n\nAs with the previous process, there is no marked difference among the methods, and we, therefore, proceeded to establish the mean radical inhibition coefficient (IC50) of the process that obtained the highest value of antioxidant activity equivalent to Trolox, which was the ultrasound of the material dried at 40°C.\n\nTable 10 shows the inhibition coefficient (IC50) determined by the DPPH method performed on the extract of Croton floccosus and Trolox (standard). The difference between the extract and the standard used in the previous determinations is compared.\n\nIt is necessary to mention that, since Croton floccosus is a species that is endemic to Ecuador, there are only a few studies referring to this species. In his study, M.E. Flores35 obtained IC50 values of 91.16 μg/mL for extracts obtained from the leaves of Croton floccosus collected during the flowering period of this species using a maceration process in which ethanol was employed as a solvent. This, therefore, made it possible to establish what is described by Altamirano36 in his research work on Croton species, which states that the collection carried out to obtain extracts must take place at the beginning of flowering because it is the moment at which these plants contain the greatest amount of active substances. This may, therefore, have influenced the properties of the extract, as may the conditions under which the material was prepared, the extraction and the storage of the extracts.\n\n\nConclusions\n\nThe use of phytochemical tests to identify metabolites, along with their qualitative characterization show that the plants studied have a great variety of chemical compounds, which contain flavonoids, phenols, reducing sugars, saponins and tannins in the case of Bidens pilosa L., and alkaloids, phenols, flavonoids, tannins and saponins in that of Croton floccosus. It has been shown that the content of total phenols for Bidens pilosa L. had the highest yield of phenolic compounds when the Soxhlet extraction method was used with the plant material dried at 50°C, with a value corresponding to 48.609 ± 0.370 mg GAE/g of dry sample. With regard to the content of flavonoids, a maximum value of 17.795 ± 0.0644 mg QE/g of dry sample was obtained, corresponding to the Soxhlet extraction process method at 40°C. In the case of Croton floccosus, the maximum reported value of total phenols corresponds to the maceration extraction process when the material had been dried at 50°C, with a value of 128.212 ± 0.601 mg GAE/g of dry sample. With regard to the content of total flavonoids, the best results corresponded to the extraction process carried out using Soxhlet extraction with the plant material dried at 40°C, with a value of 34.139 ± 0.06224 mg QE/g dry sample. Finally, both plant species showed antioxidant potential, although it is necessary to establish that the Bidens pilosa L. species responded better to the test established, with an IC50 of 239.33 μg/mL when compared to Croton floccosus, which attained an IC50 of 644.125 μg/mL.\n\n\nData availability\n\nOpen Science Framework: Underlying data for ‘Phytochemical study of the plant species Bidens pilosa L. (Asteraceae) and Croton floccosus (Euphorbiaceae)’, https://doi.org/10.17605/OSF.IO/VNPMJ.30\n\nThis project contains the following underlying data:\n\n• Data file: Antioxidant activity DPPH.xlsx\n\n• Data file: Flavonoids.xlsx\n\n• Data file: Phenols.xlsx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe authors acknowledge the support of the Universidad Técnica de Manabí (UTM) in the Convocation Project approved in 2018 with the “Tamizaje fitoquímico y determinación de la actividad antioxidante y antibacterial de 8 familias de plantas medicinales que se encuentran en la provincia de Manabí”.\n\n\nReferences\n\nMittermeier RA: Primate diversity and the tropical forest. Washington, DC Washington, DC:National Academy Press;1988.\n\nJørgensen PMlLo-YnSMBG: Catalogue of the vascular plants of Ecuador = Catologo de las plantas vasculares del Ecuador. St. Louis, Mo:Missouri Botanical Garden Press;1999.\n\nRiina R, Vigo MA, Ceron CE: Croton condorensis: an enigmatic new species of Euphorbiaceae from southern Ecuador. Phytotaxa. 2014; 164(2): 154–158. Publisher Full Text\n\nRiina R, Cumbicus N, Feio AC, et al.: A new species of dragon’s blood Croton (Euphorbiaceae) from South America with singular inflorescences. Webbia. 2015; 70(1): 187–192. Publisher Full Text\n\nRiina R, Berry PE:Two new South American species of Croton (Euphorbiaceae) and their phylogenetic affinities. Anales del Jardín Botánico de Madrid. Consejo Superior de Investigaciones Científicas;2010; 67(1): 23–27.\n\nObey JK, von Wright A , Orjala J, et al.: Antimicrobial activity of Croton macrostachyus stem bark extracts against several human pathogenic bacteria. J. Pathog. 2016: 1–5. Publisher Full Text\n\nNath R, Roy S, De B, et al.: Anticancer and antioxidant activity of croton: a review. Int. J. Pharm. Pharm. Sci. 2013; 5(2): 63–70.\n\nSuárez AI, Blanco Z, Compagnone RS, et al.: Anti-inflammatory activity of Croton cuneatus aqueous extract. J. Ethnopharmacol. 2006; 105(1–2): 99–101. PubMed Abstract | Publisher Full Text\n\nSavietto JP, et al.: Antiproliferative activity of methanol extracts of four species of Croton on different human cell lines. Rev. Bras. 2013; 23: 662–667. 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Publisher Full Text\n\nHoriuchi M, Seyama Y: Antiinflammatory and Antiallergic Activity of Bidens pilosa L. var. radiata SCHERFF. J. Health Sci. 2006; 52(6): 711–717. Publisher Full Text\n\nDeba F, Xuan TD, Yasuda M, et al.: Chemical composition and antioxidant, antibacterial and antifungal ac-tivities of the essential oils from Bidens pilosa Linn. var. Radiata. Food Control. 2008; 19(4): 346–352. Publisher Full Text\n\nDeba F, Xuan TD, Yasuda M, et al.: Herbicidal and fungicidal activities and identification of potential phyto-toxins from Bidens pilosa L. var. radiata Scherff. Weed Biology and Management. 2007; 7(2): 77–83. Publisher Full Text\n\nUchôa VT, de Paula RC , Krettli LG, et al.: Antimalarial activity of compounds and mixed fractions of Cecropia pachystachya. Drug Dev. Res. 2010; 71(1): 82–91.\n\nBartolome AP, Villaseñor IM, Yang WC: Bidens pilosa L. (Asteraceae): Botanical properties, traditional uses, phytochemistry, and pharmacology. Evidence-based Complementary and Alternative Medicine, Review. 2013; vol. 2013. Art. no. 340215.\n\nJayasundera M, Florentine S, Tennakoon KU, et al.: Medicinal value of three agricultural weed species of the asteraceae family: A review. Pharmacognosy Journal, Review. 2021; 13(1): 264–277. Publisher Full Text\n\nAbdi H, Williams LJ: Tukey’s honestly significant difference (HSD) test. Encyclopedia of research design. 2010; 3(1): 1–5.\n\nRuiz-Reyes E, Moreira-Castro JM, Pin-Molina JM, et al.: PHYTOCHEMICAL STUDY OF THE PLANT SPECIES ZANTHOX-YLUM SPRUCEI (RUTACEAE) AND MELAMPODIUM DIVARICATUM (ASTERACEAE). Pharmacol. Ther. 2021; 1: 322–335.\n\nRondón M, García I, Cornejo X, et al.: Phytochemical screening and antioxidant activity of seven me-dicinal plants species from Ecuador. Pharmacol. Ther. 2015; 3: 19–28.\n\nSólis P, De Solis N, Gattuso S, et al.: Manual de caracterización y análisis de drogas vegetales y productos fitoterapéuticos. Proyecto de desarrolllo y tecnología de cultivo de plantas medicinales y producción de fitoterápicos.2003.\n\nTomás-Barberán FA, Gil MI, Cremin P, et al.: HPLC− DAD− ESIMS analysis of phenolic compounds in nectarines, peaches, and plums. J. Agric. Food Chem. 2001; 49(10): 4748–4760. PubMed Abstract | Publisher Full Text\n\nYucailla A: Composición química y actividad antioxidante de extractos obtenida de las hojas de Mansoa alliacea. SANTA CLARA:UNIVERSIDAD CENTRAL “MARTA ABREU” DE LAS VILLAS;2018.\n\nCamacho O, Melgarejo S: Actividad antioxidante del extracto etanólico e hidroalcohólico y determinación quí-mica de los componentes mayoritarios del fruto de Eugenia jambolana (Uva venezolana). Tesis Pregrado Programa de Farmacia.2017.\n\nDeng J, Cheng W, Yang G: A novel antioxidant activity index (AAU) for natural products using the DPPH assay. Food Chem. 2011; 125(4): 1430–1435. Publisher Full Text\n\nRuiz-Reyes E, Mendoza-Cevallos MA, Polanco-Moreira AP, et al.: PHYTOCHEMICAL STUDY OF THE PLANT SPECIES BIDENS PILOSA L. (ASTERACEAE) AND CROTON FLOCCOSUS (EUPHORBIACEAE). Open Science Framework. Dataset. 2022, May 30. Publisher Full Text\n\nSingh G, et al.: Pharmacological potential of Bidens pilosa L. and determination of bioactive compounds using UHPLC-QqQLIT-MS/MS and GC/MS. BMC Complement. Altern. Med. 2017; Article vol. 17(no. 1): Art. no. 492. Publisher Full Text PubMed Abstract |\n\nFalowo A, Muchenje V, Hugo C, et al.: In vitro antimicrobial activities of Bidens pilosa and Moringa oleifera leaf extracts and their effects on ground beef quality during cold storage. Cyta-J. Food. 2016; 14(4): 541–546. Publisher Full Text\n\nPazmiño Chancusi DA: Estudio farmacognósico de los productos naturales procesados de uso medicinal a base de sangre de drago y del látex en su forma natural. Quito:UCE;2021.\n\nCortés-Rojas DF, Chagas-Paula DA, Da Costa FB, et al.: Bioactive compounds in Bidens pilosa L. populations: A key step in the standardization of phytopharmaceutical preparations. Revista Brasileira de Farmacognosia, Article. 2013; 23(1): 28–35. Publisher Full Text\n\nFlores Herrera ME: Evaluación de la actividad antimicrobiana del extracto de corteza y hojas de Sangre de drago. Quito:UCE;2021.\n\nAltamirano Pérez IV: Evaluación de la actividad antioxidante de cuatro especies del género Croton. Quito:UCE;2015."
}
|
[
{
"id": "142422",
"date": "19 Jul 2022",
"name": "Pawel Konieczynski",
"expertise": [
"Reviewer Expertise Analytical chemistry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the work entitled: Phytochemical study of the plant species Bidens pilosa L. (Asteraceae) and Croton floccosus (Euphorbiaceae). The strengths of the manuscript can be listed below:\nThe Authors have thoroughly studied two important folk medicine plants originating from two botanical species growing in Ecuador. They investigated total content of phenols and flavonoids as well as the antioxidant activity using DPPH method for comparison of two plants.\n\nThe choice of materials and methods were appropriate, not counting my minor comments given below.\n\nThe statistics applied for interpretation of the experimental data is correct.\n\nThe conclusions drawn by the Authors are justified by their results.\nMinor comments\nPage 3: in Methods (Vegetal material) - please write whether the fresh leaves of the studied plant species were collected only from one plant or from several plants, and then mixed to create the sample for analysis?\n\nPage 3: in Extraction - please add more details on how the sample was pulverized (for example what type of sample mill was used, how long it lasted)?\n\nI also think that it would be helpful to add a map showing the collection places in Portoviejo Botanical Garden.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8551",
"date": "17 Oct 2022",
"name": "Enrique Ruiz Reyes",
"role": "Author Response",
"response": "1 - Referee's first comment: The leaves that present better conservation in their structure are chosen to clean them of dust and branches, then the petiole of the leaf blade is extracted. The studied leaves were collected from various plants and then mixed to create the sample for analysis. 2 - Referee's second comment: The sample was pulverized using a blade mill (grinder) with a sieve so that a more uniform size of the material can be obtained, in order to fractionate the plant tissue and produce a better extraction. The time used for grinding was 5 minutes. 3 - Referee's third comment: It is shown in the following map of the botanical garden. The collection points of the studied species. For croton floccosus it was two points while for bidens pilosa it was three points. The coordinates of the studied species are placed on the map, which is linked here."
}
]
},
{
"id": "151932",
"date": "04 Oct 2022",
"name": "Yailet Albernas Carvajal",
"expertise": [
"Reviewer Expertise Chemical Engineering"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article entitled \"Phytochemical study of the plant species Bidens pilosa L. (Asteraceae) and Croton floccosus (Euphorbiaceae)\" is very interesting because it performs a preliminary phytochemical study of the plants Bidens pilosa L. and Croton floccosus. Important information was determined related to the content of secondary metabolites and the response to the DPPH radical reported for the first time in Ecuador, a relevant aspect, which may be of future use for its application in the field of medicine. They show that both plants studied have antioxidant potential, although they state that it is necessary to establish that the species Bidens pilosa L. responded better to the established test, with an IC50 of 239.33 μg/mL compared to Croton floccosus, which reached an IC50 of 644.125 μg/mL.\nThe methods employed are very well supported with adequate techniques, using modern analytical equipment and techniques. It presents a correct description as to be replicable should any reader need it with any other species.\nMinor point:\nIncorporate other references from the last three years.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8865",
"date": "17 Oct 2022",
"name": "Enrique Ruiz Reyes",
"role": "Author Response",
"response": "I agree with the evaluation issued by the reviewer and, following their suggestion, references 24, 25 and 26 were replaced by others that correspond to the last 3 years."
}
]
}
] | 1
|
https://f1000research.com/articles/11-702
|
https://f1000research.com/articles/11-1185/v1
|
17 Oct 22
|
{
"type": "Research Article",
"title": "Antifungal activity of propolis extract against Candida albicans in patients with vulvovaginal candidiasis",
"authors": [
"Ambrocio Teodoro Esteves Pairazaman",
"Jesus Daniel Collanque Pinto",
"Britt Alvarado Chávez",
"Gabriel Leon Apac",
"Consuelo Berta Horna Sandoval",
"Federico Martin Malpartida Quispe",
"Vadir Ali Jesús Collanque Meza",
"Walter Gregorio Ibarra Fretell",
"Gina Andrea Rodríguez Loyola",
"Jesus Daniel Collanque Pinto",
"Britt Alvarado Chávez",
"Gabriel Leon Apac",
"Consuelo Berta Horna Sandoval",
"Federico Martin Malpartida Quispe",
"Vadir Ali Jesús Collanque Meza",
"Walter Gregorio Ibarra Fretell",
"Gina Andrea Rodríguez Loyola"
],
"abstract": "Background: The aim was to evaluate the antifungal activity of propolis extract against Candida albicans (or C. albicans) in patients with vulvovaginal candidiasis. Methods: The research presents a quantitative approach with an experimental design, with a population of C. albicans strains isolated from patients diagnosed with vulvovaginal candidiasis who were admitted to the Gynecology Service of the Maria del Socorro Clinic, district of Ate, Lima; a sample of 34 strains was chosen in total, considering three repetitions per strain, obtaining 102 experimental units. The antifungal susceptibility test was carried out by the disc diffusion plate method using a single concentration of propolis extract, with fluconazole as a positive control. Results: Propolis extract was shown to inhibit all strains of C. albicans, as was fluconazole, with the effect of the latter being significantly greater than that of the product under investigation. Conclusions: The conclusion is that propolis extract does show antifungal activity against C. albicans in patients with vulvovaginal candidiasis.",
"keywords": [
"Propolis extract",
"Candida Albicans",
"Antifungal activity",
"Vulvovaginal candidiasis"
],
"content": "Introduction\n\nCandidiasis affects approximately 138 million women worldwide each year, and is the second most common type of vaginal infection.1,2 Studies show that approximately 6000 women from different countries have a 9% prevalence of recurrent vulvovaginal candidiasis (VVC) and the likelihood of progression is high3; about 75% of women experience an episode of VVC during their childbearing years; about 40-50% experience a second VVC infection, and 5-8% of adult women have four or more episodes per year.4,5\n\nThe World Health Organization (WHO) considers C. albicans as one of the most recurrent causes of vaginal infections, because it is responsible for 80 to 92% of the cases of VVC.6 It is known that in the regions of Europe and Latin America, infection rates are 20 to 25%, of which 75% of adult women have contracted C. albicans at least once7; a study carried out in a Tertiary Care Hospital in India showed that out of 180 patients who underwent microbiological tests, 76-89% of the population studied had C. albicans as the most frequent pathology-causing species.8 In regions of the Americas, such as Mexico, a study of CVV was conducted on 412 people and found that 25% of them were positive. In the United States, 65% of hospitalised patients had fungal infections, and 78% of them are known to reach mortality depending on the risk factors presented by the patient.9 It is worth noting that C. albicans is considered to be the second most common cause of vaginal infections.10\n\nIn Peru, the most frequent species causing VVC is C. albicans, with a prevalence of 40-60% in adult patients.11 An obstetrician-gynecologist from the Instituto Especializado Materno Perinatal in Peru, after conducting a study, mentioned that, of all the cases found, 50% had vaginal discharge due to VVC and the vast majority were due to self-medication and overdose.12 In addition, the prevalence of VVC was found in 24% of pregnant women in the areas of Monsefu (Chiclayo) and 29.8% in Inkawasi (Ferreñafe), C. albicans always stood out as the aetiological agent for all these cases.11 In the Arzobispo Loayza National Hospital in Lima, of the total population investigated, 42.2% had a prevalence of vaginal infections.13\n\nCurrent VVC treatment regimens have lost relevance in the face of antifungal resistance challenges,14 because the treatment of fungal infections such as VVC lacks specific drugs, unlike bacterial infections. These shortcomings require the production of a vaginal drug delivery system (VDDS) capable of attenuating, treating, and eliminating CVV clinically and effectively, thus avoiding the risk of disease recurrence and prolongation.15\n\nCurrently, amphotericin B and fluconazole are readily available azoles frequently used to treat candidiasis; amphotericin B is considered to be an excellent antifungal, but its level of toxicity is very high. However, their efficacy is poor due to the development of natural resistance by strains of C. albicans and non-albicans.16\n\nAntifungal resistance is considered a consequence of inappropriate drug use, inadequate dosage, and incomplete treatment, as resistance to antifungal drugs has been increasing by up to 40% in recent years.16,17 These data are alarming in addition to the symptoms, recurrent misuse of medications, self-medication,18 short medication cycles or incomplete treatment of antifungal drugs19; these affect women who suffer from VVC as they have a poor quality of life that is unfavorable to their health.18 Therefore, the aim is to provide a solution to this common problem in women by considering the use of alternatives from natural products.\n\nThe aim of this study was to evaluate the antifungal activity of propolis extract against strains of Candida albicans isolated from patients diagnosed with acute and recurrent VVC, and to compare the antifungal activity of propolis extract and fluconazole.\n\n\nMethods\n\nThe research was hypothetico-deductive, with a quantitative approach. The type of research was basic, and the design was experimental.20–22\n\nThe population consisted of Candida albicans strains isolated from patients diagnosed with VVC who were admitted to the gynaecology department of the María del Socorro Clinic in the district of Ate in Lima.\n\nThe sample size was 34 strains, a figure derived from the interaction between 17 strains of C. albicans (nine from acute VVC and eight from recurrent VVC) and two treatments (propolis extract and fluconazole), considering three replicates per strain, a total of 102 experimental units were obtained.23\n\nIt was suggested that there may be a significant difference between the antifungal activity of propolis extract and fluconazole against C. albicans strain types, this being the study hypothesis which will be tested by analysis of variance (ANOVA).\n\nIn the present investigation, to measure antifungal activity, the manual for susceptibility testing indicated by the Clinical and Laboratory Standards Institute (CLSI) in document M44 - A was used. Inocula of clinical strains of C. albicans were prepared and adjusted to the turbidity of the scale at 0.5 McFarland. Following the standardised susceptibility protocol established by Bauer et al.,24 the technique used was direct observation of the susceptibility of C. albicans strains.\n\nThe technique used was direct observation of inhibition halos and the instrument used was a data collection sheet to record the information obtained.\n\nPrior to data processing and analysis, the following was applied:\n\nPropolis extract\n\nThe propolis extract was collected with the support of beekeepers in the Oxapampa district, Cerro de Pasco region, Peru. Once the sample was obtained, we began with the separation of some components that were not part of the analysis, such as dust, wood chips, wood remains, among others that may alter the composition of the extract.25\n\nPreparation of the extract\n\nThe characterization and preparation of the propolis at 50% concentration were done under aseptic conditions in a laminar flow cabinet at room temperature where impurities were discarded; then the sample was chopped and pulverized with the aid of a pestle and mortar.\n\nThe extract was prepared using 50 g of propolis in 100 mL of 70% ethanol, then the mixture was subjected to maceration for eight days at 37°C without contact with light. Subsequently, the sample was filtered with the help of Whatman No. 60 filter paper and then taken to a rotary evaporator at 60°C for the ethanol to be evaporated. The total extracts were transferred to the rotary evaporator until the solvent was eliminated and the solid obtained was placed in an oven for two hours at 70°C.\n\nFinally, the ethanolic dry extract of propolis was obtained using the dilution and filtration technique to obtain propolis at a concentration of 50%. The selected propolis was visually identified according to its organoleptic characteristics, being predominantly brown in colour and lacking a defined aroma, to ensure its quality and purity.18\n\nMethod for obtaining clinical strains of Candida albicans\n\nPermission was requested from the gynaecology service of the Clínica María del Socorro in the district of Ate in Lima to work with volunteer patients, who were previously informed of the study and agreed to sign the informed consent form.\n\nOnce authorization was obtained, samples of vaginal exudate were collected from the patients and taken by the doctor in charge of the area, who used a sterile dry vaginal swab to obtain the sample from the bottom of the vaginal sac, identifying the patients who presented acute and recurrent VVC; then, the samples were labelled with the corresponding type of infection and transported in sterile containers in a vertical position, in a cool environment and protected from light, to the laboratory of the aforementioned clinic. For isolation of the strains, the technique of depletion-streaking was used in Petri dishes with Sabouraud Dextrose Agar (SDA), and then incubated in an oven at 37°C.11\n\nCandida albicans identification tests\n\nAfter incubation, growth was observed on the surface of SDA, then a colony was taken for seeding on Chromogenic Candida agar to differentiate C. albicans from other Candida species, and microscopic observation was performed (see Figure 1 and Figure 2).\n\nNote. a and b) Isolation on chromogenic agar.\n\nIn addition, for confirmation purposes, the growth of Candida sp. was validated with the germ tube test and then tested with the API 20 C AUX Candida test.10\n\na) Germ tube testing:\n\nThe germ tube test is highly useful in differentiating C. albicans and non-albicans Candida species. The procedure was performed with 0.5 mL of fresh human serum using the culture loop, inoculated with the strain under study and incubated at 37 °C. After three hours, a wet mount was prepared to observe under the light microscope, with 40× objective; the presence of the germ tube consisted of the filamentous extension of the yeast, where both C. albicans and C. dubliniensis formed a small extension similar to a “hand mirror” (Reynolds - Braude phenomenon). For this reason, the API 20 C AUX Candida test was used for confirmation.15\n\nb) API 20 C AUX Candida test\n\nThe API 20 C AUX Candida test is an accurate yeast identification system consisting of 20 microtubes containing dehydrated substrates. These microtubes are inoculated into a minimal medium of API C medium and grow only yeasts capable of utilizing these substrates.\n\nWith 2 mL of saline and a young yeast culture, a suspension was made to a turbidity of McFarland scale 2.0. Then 100 uL of this suspension was added to the ampoule with API C Medium to proceed to fill the domes, always avoiding the formation of bubbles. The suspension was then kept in a humid chamber and incubated for 48-72 hours at 37°C.14\n\nFinally, once the incubation time was over, the results were read and interpreted, observing growth by turbidity and with the help of the manufacturer's own numerical profile and the Apiweb identification program, the exact identification of the yeasts was carried out.\n\nPreparation of culture environment\n\nTo measure antifungal activity, Müller Hinton Agar medium was used, which is validated for susceptibility testing as indicated by the Clinical and Laboratory Standards Institute (CLSI) M44 - A. Inocula of C. albicans clinical strains were prepared and adjusted to scale turbidity at 0.5 McFarland. The wavelength was 610 mm in the spectrophotometer for measuring the turbidity of the inoculum of the strains; it was then inoculated onto the agar surface with the help of a swab by streaking in three directions, allowed to dry for about 10 minutes and placed on fluconazole discs (positive control) and distilled water (negative control).9\n\nPreparation of control groups\n\n• Positive control: Fluconazole (25 mg/100 mL distilled water).\n\n• Negative control: Distilled water (100 mL).\n\nQuality control of the growth of C. albicans strains\n\nOne litre of Müller Hinton Agar was prepared according to the recommendation of the DIFCO manual26 by adding 20 g of glucose and 100 μL of stock solution of methylene blue. The latter solution is prepared by adding 0.1 g of methylene blue to 20 mL of distilled water (obtaining 5 μ/mL concentration). It was then autoclaved for 15 minutes at a temperature of 121°C and 15 lbs of pressure; following this, we let the temperature drop to about 50°C and poured 27 mL per Petri dish to reach 4 mm thickness, in 90 mm diameter plates. Two plates were considered for sterility control at 35°C for 24 hours.\n\nNext, the previously grown C. albicans ATCC 90028 strain was taken to be seeded on agar. As described above, susceptibility testing was performed by adjusting the strain inoculum to 0.5 turbidity on the McFarland scale, seeding in three directions and placing a 25 μg disc of fluconazole for reading after 24 hours. To ensure quality control of strain growth, inhibition halos were observed.27\n\nOnce the C. albicans strains were obtained, the disc diffusion plate method was used, for which filter paper discs containing 200 μL of propolis extract and the respective controls were used, placing each embedded disc on a Petri dish with Müller Hinton agar and incubated for 24 hours at 37°C.10\n\nAfter the incubation period, the antifungal growth inhibition halos were analyzed; the results were expressed by measuring the halos formed in the Petri dish, where the diameter of each zone was measured in millimeters, following the standardized susceptibility protocol established by Bauer, et al.24\n\nOnce the experimental procedure was completed, the data obtained were processed and a flow chart was elaborated for general data processing and analysis of the C. albicans strains.\n\nThe data collection process was carried out during September, October and November 2021, using a data collection sheet, and then tabulating the information in Microsoft Office Excel v. 2019 software, in which the information was recorded in a dataset.\n\nThe project was approved by Resolution N°1561-2022 by the president of the Institutional Research Ethics Committee of the Norbert Wiener Private University.\n\nAt the same time, written authorization was obtained from the Clinic María del Socorro to obtain samples and information through official letter N°017-2021-GMO-CMS.\n\nThe data collection instrument was applied at the time of measuring the growth inhibition halos of C. albicans strains by the effect of the antifungal activity of propolis extract and fluconazole, as well as recording the type of vvc and whether the causative agent was C. Albicans.\n\nFor the statistical analysis of the data, SPSS version 23.0 statistical software was used, in which analysis of variance (ANOVA) was used in order to establish whether the antifungal activity of propolis extract and fluconazole was equal in all studied strains; this was complemented with the Tukey significance test (α = 0.05) to define the differences in antifungal activity according to the types of C. albicans strains and the treatments used.\n\nParticipants were informed about the aim of the study, and those who agreed to participate signed an informed consent form, where they gave their approval for the use of the strains to be processed for the purpose of the study. All patients, carriers of the strain, were informed that their personal data would remain anonymous according to Law No. 29733 “Law on the protection of personal data”.28\n\n\nResults\n\nTable 1 describes the antifungal activity of propolis extract and fluconazole against C. albicans strains isolated from patients with vulvovaginal candidiasis (VVC), showing mean inhibition halos of 15.2 mm for propolis extract and 18.0 mm for fluconazole.\n\nTable 2 shows the existence of a statistically significant difference between the types of C. albicans strains that were inhibited by propolis extract and fluconazole. Thus, C. albicans strains isolated from acute VVC showed inhibition halos of a larger size on average than those from recurrent infection.\n\nTable 3 shows the existence of a statistically significant difference between the antifungal activity of propolis and fluconazole, the latter showing the largest average size of inhibition halos on C. albicans strains compared to propolis extract.\n\nH0-1: There is a significant difference between the antifungal activity of propolis extract and fluconazole against C. albicans strain types.\n\nH0-2: There is no significant difference between the antifungal activity of propolis extract and fluconazole against C. albicans strain types.\n\nIn Table 4, the observed p-value was <0.0001, which is less than 0.05; therefore, we rejected the null hypothesis and affirm that there is a significant difference between the antifungal activity of propolis extract and fluconazole against the types of Candida albicans strains.\n\n\nDiscussion and conclusions\n\nThe antifungal activity of propolis extract was evaluated against Candida albicans strains isolated from patients diagnosed with VVC; in the present investigation it was determined that propolis extract at a concentration of 50% showed antifungal activity on C. albicans strains. Studies by De La Cruz,13 and Joya et al.,3 who used ethanolic extracts of propolis against strains of the fungal species in question, differed from the present study in that they did consider using higher and lower concentrations of the product. The above suggests that a key factor in the sensitivity of C. albicans is its chemical composition, which is represented by proteins and polysaccharides. In addition, these microorganisms are known to have a cell wall, which is mainly composed of polysaccharides such as glucan and chitin. In addition, these species have a cytoplasmic membrane, where the antifungal agents carry out their function. In addition, the cytoplasmic membrane is composed of large amounts of carbohydrates and proteins in smaller proportions, which allow the entry and exit of substances such as secondary metabolites e.g., flavonoids, tannins, terpenes, and alkaloids.11,29\n\nRegarding the specific objective of evaluating the antifungal activity of propolis extract against C. albicans strains isolated from patients diagnosed with acute and recurrent VVC, it was found that propolis extract showed inhibition of C. albicans strains isolated from acute and recurrent VVC. This finding is related to that reported by Adjapong et al.30 who compared the susceptibility of C. albicans strains isolated from acute and recurrent VVC, where the former showed greater sensitivity to fluconazole compared to those with recurrent infection, applying three doses of the antifungal agent.30 In the case of propolis, precise studies comparing its effect on both types of strains could not be found; however, it can be suggested that, in recurrent candidiasis, C. albicans expresses resistance to antifungal agents such as azoles, and therefore also to metabolites that induce their inhibition.31\n\nAdditionally, to compare the antifungal activity of C. albicans strains isolated from patients diagnosed with acute and recurrent VVC, it was found that C. albicans strains isolated from acute VVC showed a higher average inhibition halo than those from recurrent infection when exposed to propolis extract and fluconazole, and this difference was statistically significant. This finding is very similar to that reported by Adjapong et al.30 who compared the susceptibility of C. albicans strains isolated from acute VVC and recurrent VVC, where the former showed greater sensitivity to fluconazole compared to those with recurrent infection, applying three doses of the antifungal (2 μg/mL, 4 μg/mL and 8 μg/mL).30 In the case of propolis, precise studies comparing its effect on both types of strains could not be found; however, it can be suggested that, in recurrent candidiasis, C. albicans expresses resistance to antifungal agents such as azoles and, therefore, to the metabolites present in propolis extract that induce their inhibition as well.32\n\nFinally, taking into account the specific objective of comparing the antifungal activity of propolis extract and fluconazole against strains of C. albicans isolated from patients diagnosed with VVC, it was possible to establish significant differences between the antifungal activity of propolis extract and fluconazole, the latter showing the highest average inhibition halo; this finding was very similar to that found by Capoci et al.7 who used propolis and fluconazole as a positive control for the inhibition of biofilms caused by C. albicans, the latter showing the greatest inhibitory effect against the strains of the microorganism in question.7 This suggests that, although the metabolites of the product studied may be involved in the growth and development of the infectious agent, antifungal agents have been shown to be more effective, as they not only affect the external component of the fungi, but also the cellular interior, causing a greater and faster inhibition. It should be noted that the metabolites described above, in most cases, stimulate the inhibition of biofilm formation, however, the antifungal agents par excellence, such as fluconazole, can pass through the cytoplasmic membrane of the fungus and affect cellular respiration and therefore cause its death more rapidly.32,33\n\nIt was concluded that:\n\n• Propolis extract showed antifungal activity against strains of C. albicans isolated from patients diagnosed with both water-borne and recurrent vulvovaginal candidiasis.\n\n• There was a significant difference between the antifungal activity of propolis extract and fluconazole against C. albicans strains isolated from patients diagnosed with vulvovaginal candidiasis.\n\n• There was a significant difference between the inhibition halos of C. albicans strains isolated from patients diagnosed with acute and recurrent vulvovaginal candidiasis.\n\n\nData availability\n\nZenodo: Antifungal activity of propolis extract against Candida albicans in patients with vulvovaginal candidiasis, https://doi.org/10.5281/zenodo.6981744.34\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nMaureira N, Viera P, Fernandez A, et al.: Susceptibilidad de Cepas de Candida Oral a Extracto Etanólico del Propóleo Chileno de Olmué. Int J Odontostomatol. 2017; 11(3): 295–303. Publisher Full Text\n\nParker M, Vaginitis SC, Vulvovaginitis, et al.: Textbook of Natural Medicine. 5° Edición.Missouri, Estados Unidos:Elsevier;2021; pp. 1840–1849. Publisher Full Text\n\nJoya M, Gil M, Bastidas-Pacheco G: Actividad fungistática y fungicida de extractos etanólicos de propóleos sobre el crecimiento in vitro de cepas del género Candida. Tecnol en Marcha. 2017; 30(3): 3–11. Publisher Full Text\n\nTulikangas PK, Schimpf MO:Genital and urinary tract infections. General Gynecology. 1° Edición.Philadelphia, Estados Unidos:Elsevier Inc.;2007; pp. 523–542. Publisher Full Text\n\nPrieto-Granada C, Lobo A, Minhm M:Skin Infections. Diagnostic Pathology of Infectious Disease. 2° Edición.Philadelphia, Estados Unidos:Elsevier Inc.;2018; pp. 542–647. Publisher Full Text\n\nGavanji S, Larki B: Comparative effect of propolis of honey bee and some herbal extracts on Candida Albicans. Chin J Integr Med. 2015; 23(3): 201–207. PubMed Abstract | Publisher Full Text\n\nCapoci IRG, Bonfim-Mendonça PDS, Arita GS, et al.: Propolis is an efficient fungicide and inhibitor of biofilm production by vaginal Candida Albicans. Evidence-based Complement Altern Med. 2015; 2015(1): 1–9. PubMed Abstract | Publisher Full Text\n\nMendoza E: Estudio comparativo del efecto antifúngico del extracto etánolico de propóleos de la sierra y costa liberteña sobre cepas de Candida Albicans ATCC 10231, Trujillo - 2018. Tesis para Optar el Grado de Bachiller en Medicina, Universidad Católica los Ángeles de Chimbote.2019.Reference Source\n\nHuaytalla RM, Gálvez CM, Carhuapoma-Yance M, et al.: Efecto inhibidor in vitro del extracto etanólico de propóleo al 15% y 30% frente a cepas de Lactobacillus acidophilus. Rev Estomatológica Hered. 2018; 28(1): 36–43. Publisher Full Text\n\nSobel J: Vulvovaginal candidosis. Lancet. 2007; 369(1): 1961–1971. Publisher Full Text\n\nCalla K, Quispe D: Evaluación del efecto antimicrobiano in vitro del propolis “Propóleos” de Tres Regiones del Sur del Perú sobre el crecimiento de Candida Albicans, Escherichia coli, Staphylococcus aureus y Pseudomona aeruginosa. Tesis Para optar el Título Profesional de Químico Farmacéutico, Universidad Católica de Santa María.2016.Reference Source\n\nLeón G, Sacsaquispe S, Zurita S: Efecto antifúngico in vitro sobre el crecimiento en Candida Albicans ATCC 90028, Candida glabrata ATCC 90030 y Candida krusei ATCC 6258 expuestas al propóleos de Oxapampa a las 24, 48 y 120 horas. Rev Investig la Univ Norbert Wiener. 2014; 3(1): 23–29. Publisher Full Text Reference Source\n\nDe la Cruz M: Actividad Antimicotica Del Extracto Etanólico De Propóleo Sobre El Crecimiento in vitro De Candida Albicans. Tesis para Optar el Grado Académico de Bachiller en Estomatología, Universidad Nacional de Trujillo.2013.Reference Source\n\nFirdaus S, Hassan N, Aamir M, et al.: FbD directed fabrication and investigation of luliconazole based SLN gel for the amelioration of candidal vulvovaginitis: a 2 T (thermosensitive & transvaginal) approach. Saudi J Biol Sci. 2021; 28(1): 317–326. PubMed Abstract | Publisher Full Text\n\nDovnik A, Golle A, Novak D, et al.: Treatment of vulvovaginal candidiasis: a review of the literature. Acta Dermatovenerologica. 2015; 24(9): 5–7. Publisher Full Text\n\nFaustino C, Pinheiro L: Lipid systems for the delivery of amphotericin B in antifungal therapy. Pharmaceutics. 2020; 12(1): 1–47. PubMed Abstract | Publisher Full Text\n\nHuang K, Zhang B, Shen ZY, et al.: Enhanced amphotericin B production by genetically engineered Streptomyces nodosus. Microbiol Res. 2021; 242(1): 126623–126636. PubMed Abstract | Publisher Full Text\n\nLírio J, Giraldo PC, Amaral RL, et al.: Antifungal (oral and vaginal) therapy for recurrent vulvovaginal candidiasis: A systematic review protocol. BMJ Open. 2019; 9(5): 1–6. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization (WHO): Candida auris, un patógeno emergente. Acciones y prevención en Colombia. WHO;2021 [citado el 14 de noviembre de 2021].Reference Source\n\nCabezas E, Andrade D, Torres J: Introducción a la Metodología de la investigación científica com.ed. F.F.A.A. ESPE;. Ecuador.2018 [citado 21 noviembre 2021]. Prim. Edic.Reference Source\n\nÑaupas H, Valdivia M, Palacios J, et al.: Metodología de la investigación cuantitativa – cualitativa y redacción de tesis. 5ta ed.Colombia:Ediciones de la U;2018.\n\nHernández-Sampieri R, y Mendoza C: Metodología de la investigación. Las rutas cuantitativa, cualitativa y mixta. México:Grupo editorial Mc Graw Hill Education;2018.\n\nBerndt AE: Sampling Methods. J Hum Lact. 2020; 36(2): 224–226. Publisher Full Text\n\nBauer A, Kirby WM, Sherris J, et al.: Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol. 1966; 45(4): 493–496. PubMed Abstract | Publisher Full Text\n\nAnjum SI, Ullah A, Khan KA, et al.: Composition and functional properties of propolis (bee glue): A review. Saudi J Biol Sci. 2019; 26(7): 1695–1703. PubMed Abstract | Publisher Full Text\n\nDIFCO: The Difco Manual. 11° Edició ed.Maryland, Estados Unidos:Difco Laboratories;1998; 157.Reference Source\n\nZurita S, Ausejo F: Manual De Procedimientos Técnicos Para El Diagnóstico Micológico. 1° Edición ed.Lima, Perú:Repositorio Institucional - INS;2017; 139.Reference Source\n\nDiario El Peruano: Ley de protección de datos personales – Ley N° 29733. Lima:Diario El Peruano;2011.Reference Source\n\nBoisard S, Le Ray AM, Gatto J, et al.: Chemical composition, antioxidant and anti-AGEs activities of a French poplar type propolis. J Agric Food Chem. 2014; 62(6): 1344–1351. PubMed Abstract | Publisher Full Text\n\nAdjapong G, Hale M, Garrill A: A comparative investigation of azole susceptibility in Candida isolates from vulvovaginal candidiasis and recurrent vulvovaginal candidiasis patients in Ghana. Med Mycol. 2017; 55(1): 686–689. PubMed Abstract | Publisher Full Text\n\nSobel JD: Recurrent vulvovaginal candidiasis. Am J Obstet Gynecol. 2016; 214(1): 15–21. Publisher Full Text\n\nVademecum: Fluconazol.2013 [citado el 29 de noviembre de 2021].Reference Source\n\nSeleem D, Pardi V, Murata RM: Review of flavonoids: A diverse group of natural compounds with anti-Candida Albicans activity in vitro. Arch Oral Biol. 2017; 76(1): 76–83. PubMed Abstract | Publisher Full Text\n\nPairazaman E, Ambrocio CP, Daniel J, et al.: Antifungal activity of propolis extract against Candida albicans in patients with vulvovaginal candidiasis [Data set]. Zenodo.2022. Publisher Full Text"
}
|
[
{
"id": "262081",
"date": "25 May 2024",
"name": "Manuela Gómez-Gaviria",
"expertise": [
"Reviewer Expertise Taking into account the area of study in which I am currently working",
"which is microbiology",
"immunology and molecular biology",
"I consider that this article does not meet the microbiological aspects necessary to be published. First",
"the method they use to determine susceptibility and resistance is obsolete. Currently there are new tools such as microplates to do this type of experiments. Second",
"the figures are not of good quality",
"nor are they appropriate for an original article. And finally",
"the methodology is confusing and not written properly."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI consider that the article is very incomplete, the methodology used is not the best, in addition, details need to be reviewed in the introduction, as well as in the results and discussion. It is necessary to organize some spelling errors and clarify some things within the text. I consider that there is a lot of information on this topic, and taking this into account, the bibliography used in this article is very little.\nIntroduction:\n\nParagraph 1: I consider it necessary to add more information about Candidiasis Paragraph 4 y 5: These paragraphs could be together Paragraph 6: I consider that in this paragraph should be included more information about new natural therapies Check the spelling of scientific names.\nMethodology:\nReliability pg 4: The choice of the technique of direct observation of inhibition halos to evaluate resistance and susceptibility can generate some controversy. I consider that it is better to use the microplate technique, since it has more precise control of the experimental conditions and the possibility of quantifying the results in a more objective and reproducible way. Preparation of the extract pg 4: Can the solvent used for the extract affect the interaction with the fungus? Figure 1 pg 5: This photo is not clear, if they are identifying C. albicans, why do they put C. tropical is in the petri plate? Figure 2 pg 5: The caption has nothing to do with what is seen in the photo. Quality control of the growth of C. albicans strains pg 6: “obtaining 5 µ/ml” Check concentration Antifungal susceptibility testing pg 6: I consider it necessary to use different extract concentrations Bauer et al.,: that reference is very old\nResults Check the spelling of scientific names.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1185
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https://f1000research.com/articles/11-1182/v1
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17 Oct 22
|
{
"type": "Software Tool Article",
"title": "abmAnimalMovement: An R package for simulating animal movement using an agent-based model",
"authors": [
"Benjamin Michael Marshall",
"Alexander Bradley Duthie"
],
"abstract": "Animal movement datasets are growing in number and depth, and researchers require a growing number of analytical approaches to adequately answer questions using movement datasets. As the complexity of questions and analyses increase, deciding on the best approach both in terms of study design and analysis can become more difficult. A potential solution is to simulate an array of synthetic datasets under varying study designs and simulation parametrisations to gain insight into the impact of analysis choice(s) in different contexts. The abmAnimalMovement R package provides the means of simulating animal movement for this purpose. The abmAnimalMovement simulations use a discrete time agent-based model and does not require previous movement data as an input. The simulations include a number of key internal and external movement influences, as well as parameters for navigation and mobility capacity of the animal. Internal influences include three predefined behavioural states (e.g., rest, explore, forage) and any number of activity cycles (e.g., diel, seasonal). External influences are implemented via matrices describing landscape characteristics (e.g., shelter quality, foraging resources, movement ease), and predefined points describing shelter sites and points the animal aims to avoid. Navigation capacity is defined by the range the animal can dynamically choose a foraging location to which it is subsequently attracted. Mobility capacity is implemented by user defined distributions, from which step length and turn angles are draw at each time step, governing the possible subsequent locations of the animal. Critically, the navigation capacity (the choice of destination) operates on a different time scale to the mobility capacity, allowing the internal state of the animal to differ from the observed movements. When combined with other emergent properties, such as site fidelity generated via repeated shelter site use, the simulations offer opportunities to test whether movement analyses can accurately recover hidden mechanisms, states, and drivers.",
"keywords": [
"Movement ecology",
"agent-based",
"individual-based",
"simulation",
"behavioural states",
"spatial ecology"
],
"content": "1. Introduction\n\nAs the biodiversity crisis deepens, we are in constant need of new refined methods of mitigating human impacts on animals. Developing mitigation strategies is aided by a strong understanding of animals lives and needs. How animals move offers a window into their decisions making process,1,2 as well as how they prioritise resources,3–5 avoid threats,6 and react to anthropogenic modification of the environment.7–9 Examinations of animal movement are frequently integrated into conservation plans10 because of the insights they provide on habitat and space requirements, but also because they offer avenues to explore fundamental questions about ecology. For example, space use has been tied directly to body size connected via the energy requirements for animals,11 and movement has provided incredible insights into behaviour.12\n\nThe information gathered from animal movement studies is only as robust as the methods and analysis applied. In the past decade, the volume of animal data has exploded,13,14 and the infrastructure for collating these data has improved drastically.15 There are stand out examples of novel methods,16 and exceptionally detailed insights into animal behaviour using new bio-logging technology (e.g., Ref. 12). However, on the whole, analysis approaches to maximise the information extracted have arguably lagged behind the technological and data improvements.13 The bodily cost of attaching bio-telemetry devices (with examples from reptiles17; mammals18; and birds19), as well as the possible conservation sensitivity of study animals, means researchers have an ethical duty to maximise the value/impact of the data collected.\n\nMaximising the value of data should include ensuring that results gained are robust and replicable. Meta-analyses have revealed that several textbook examples in ecology are not as universally replicable as once thought.20–23 Whereas lab studies can more feasibly be repeated (although such replications are far from cheap), movement studies conducted on free-ranging wild animals are difficult to repeat while satisfactorily meeting the conditions of the true replication.24 It is hard to justify placing bio-telemetry devices on more animals to repeat a study, especially when they are of conservation concern. Studies tend to focus on larger, less vulnerable species,25,26 but as the benefits of detailed movement data grow, we can expect greater demand for tracking species of conservation concern.10 With the limited scope for repeating wild movement studies, and the desire to maximise study-to-benefit ratio for sensitive species, it is imperative that we maximise the quality of the initial studies.\n\nExpanding pre-study planning and developing better approaches to guide study design may provide a partial solution.27 Study scenarios where researchers have control over the environment, randomisation, and controls can satisfy the assumptions of many statistical approaches.28 Movement studies conducted in the wild are fraught with uncontrollable confounding variables and often further restricted by sample sizes limited by ethics, capture rates, and cost of bio-telemetry equipment. As the complexity of the research environment increases, so must the analytical approach to account for the uncontrollable –but potentially extraneous to the question– variables. Testing these analysis approaches, and their limitations therefore becomes more difficult to asses a priori.\n\nA potential solution is virtual ecology: where synthetic data are simulated to cover a range of possible scenarios allowing researchers to explore different study approaches/designs with the aim of identifying the best for a given question.29 Exploration of analysis methods using simulations can yield useful insights even for broadly understood techniques (e.g., Generalised linear mixed model30). Such an approach has the potential to adequately recreate the complex emergent properties that could hamper analyses.30 The suite of tools for simulating aspects of ecological systems (e.g., landscapes,31 genetics,32 conservation choices,29 ecological community comparisons,33 resource selection34) is growing, and some are explicitly focusing on aiding study design. There are also examples of simulation approaches being directly tied to applied issues like human-wildlife conflict (e.g., snakes,35 tigers36).\n\nPopulation monitoring studies offer a great example of a mature relationship between simulated data, study design, and applied research, implemented in a complex study environment.37 There are examples of simulated datasets being used to validate field protocols (e.g., camera trap effort 38,39) and analyses (e.g., accounting for species interactions,40 or difficult to account for variation in populations41). More recently, explicitly simulating animal movement processes rather than the population distribution has helped validate spatially-explicit capture recapture methods (SECR), while also prompting deeper questions concerning the findings generalisably to drastically different movement processes.37 Once validated with real-world data, simulated explorations of study design presents opportunities to understand the trade-offs between effort and precision.39 But similarly, disagreements on the implementation of surveying methods have led to further explorations of how we conceptualise and simulate animal processes.42\n\nAs illustrated by the SECR example, different simulation approaches and different analyses accounting for different additional complexities offer different suggestions on the optimal study design. There are a number of approaches for simulating animal movement including (but not limited to):\n\n1. continuous movement processes, best exemplified by the R package ctmm43 and worked examples such as Ref. 44 and Ref. 37. These methods rely on a mathematically defined movement process (such as Ornstein–Uhlenbeck foraging process 45). A key aspect of animal movement they simulate is correlated speeds and central tendency (i.e., home range).\n\n2. hidden markov models, exemplified by the simData function from the R package moveHMM.46 Their biggest contribution to simulating animal movement is the inclusion of state switching (i.e., different behaviours). They are best used in conjunction with existing movement data for parametric bootstrapping to explore estimator uncertainty.46\n\n3. agent-based approach, is a bottom-up approach where simulations of an agent (e.g., an animal) are based upon a number of rules,47 and through repeatedly following those rules a complex output emerges. In the model we present here, this output represents the movement pathways in a landscape. Previous examples of agent-based movement models have targeted specific key components of animal movements such as movement heavily constrained by landscape features,48 simulating memory/home range,49 or migratory behaviour.50\n\nHere we present an agent-based approach to supplement those existing simulations, which provides a unique combination of features. The agent-based approach is suited to explore a combination of the complexities of animal movement, and the emergent properties. Our model does not require fitting to prior movement data, allows for multiple predefined points of attraction/avoidance, multiple-levels of activity cycling, three behavioural states, and multiple spatial environmental covariates. A new independently developed approach to simulating animal movement will provide a additional routes to test the robustness of movement analyses.\n\n\n2. Methods\n\nThe abmAnimalMovement package provides the functionality to simulate animal movements via an agent-based model. We wrote the model using C++ via the Rcpp v.1.0.8.3 package51–53 to ensure it runs efficiently while allowing for easier manipulation of model inputs and outputs via R (R is the most used analysis tool in movement ecology with numerous supporting packages13,54).\n\nThe model simulates animal locations over a given period of time at discrete time steps. At each time step, the agent (i.e., simulated animal) is presented with a range of movement options in the form of new locations [Figure 2], and will choose from amongst these (i.e., sum-based model as opposed to facing a series of sequential binary decisions, see Ref. 2 for an example of the latter). The possible movement options, and how the new location is selected, are influenced by several factors: behavioural state of the animal, environmental quality, and proximity to points of attraction/avoidance. By simulating these drivers of animal movement, we hope to capture aspects of the internal state (i.e., motivation to move via behaviour); motion capacity (i.e., the individual’s varying ability to move); navigation capacity (i.e., ability to plan ahead beyond the immediate movement distance); and external factors (i.e., the landscape that steers and limits movement), all of which are defined as key components of animal movement.47,55\n\nThe animal has three behavioural states, broadly defined here as state 0 - sheltering (or resting), state 1 - exploring, and state 2 - foraging. Each behavioural state modifies the movement characteristics of the animal; for example, exploring comprises of more random movements with longer distances between subsequent chosen locations, whereas resting behaviour is largely defined by stationary or very low discrete movements after returning to a shelter site. The movement characteristics are defined by two distributions: a Gamma distribution that step lengths are drawn from, and a Von-Mises that turn angles are drawn from. The resulting step length, combined with a turn angle describes the change in animal location between each time step (as selected from a given number of options). We will largely define these based on the movement capacity of the animal over a minute.\n\nAs the simulation will be running with three behavioural states, we need to define how likely an animal is to switch between the behaviours. We achieved this by creating a transition matrix that describes the probability at each time step of the animal changing to another behaviour [Figure 1], where each value describes the probability of the animal transitioning from the current behaviour (row: b0, b1, b2), to the behaviour for the next time step (columns: b0, b1, b2). The diagonal describes the probability of the animal remaining in the same behavioural state. These probabilities can be kept very high to introduce autocorrelation in the behavioural state; a high autocorrelation is required if we are modelling time steps as one minute.\n\nRemain values indicate the probabilities of the animal remaining in the same behavioural state. Values correspond directly to those in the transition matrix used as a simulation input.\n\nAnimals behaviour is frequently expressed via cycles, such as day/night or diel cycles56; therefore, we want the transition matrix to vary over time. We describe a number of cycles (or waves) that can be applied to the core transition matrix impacting the probability of entering resting behaviour. For example, a diel cycle can be expressed via a Sine wave with a frequency of 12 hours and an amplitude of 0.1. At each time step we draw a value from the wave, and by added that weighting (from -0.05 to 0.05) to the transition probability of entering resting state (row 1, column 1 of the matrix); therefore, the probability of resting will increase and decrease following the Sine wave approximately a 12 hour activity pattern. We can define as many cycles as needed, and they impact the resting probability additively.\n\nWhen entering the resting state the animal will seek out a shelter site. In the abmAnimalMovement package, we can supply a number of shelter sites to simulate this need and create site fidelity. As these shelter sites act as points of attraction for the animal for each rest, the animal occupies a consistent area, or something approximating a home range. Home ranges are meant to represent areas in which the animal can source all resources required for a given life stage.44 The predefined and steady state of these shelter sites provides the stability we look for in a home range, as well as a means of predefining a level of site fidelity. As the abmAnimalMovement model can have multiple attraction (rest) sites supplied, we can simulate home ranges with unequal and behaviourally influenced space use.\n\nIn addition to the predefined attraction to shelter sites, the abmAnimalMovement package allows for a more dynamic attraction to areas of high resource quality. Movements cannot be directly translated to animal preference; for example, habitat preference may miss key movement corridors57; or the habitat decisions may occur at scales different to observed movement.1 Therefore, the simulation required a mechanism that somewhat detaches the preference/choice for observed movements. When entering foraging mode, the animal randomly selects foraging destinations as a point of attraction (but weighted towards areas of higher quality) [Figure 2]. This attraction impacts the movement choices made at each time step, with the animal more likely to choose (and therefore move to) options closer to the foraging destination. Therefore, foraging destination choice operates on a different time frame to the movement and allows movements through low-quality foraging areas. This presents a critical benefit of the simulation approach, as we define the internal state decision making process of the animal. The two time frames also allow exploration of assumptions connecting observed movement choices to choices grounded in resource use, and whether downstream analyses can accurately recover a hidden decision making process.\n\nA - the time frame of the destination choice, B - the time frame of movements at each time step.\n\nAt all times, the subsequent locations of the animal are impacted by a movement resistance matrix. Differing values represent different environmental conditions that could change how easily/likely an animal is to use that area to move towards a destination. For example, rivers or hard barriers within a landscape could present very high movement resistance and an animal would aim to avoid traversing them. Alternatively areas of lower movement resistance could aid movement, and potentially form movement corridors. The movement matrix has values that describe the weighting of movement probability (lower values indicating a lower probability of entering a cell). Whereas the resource environmental layer and shelter locations interact with destination/goal decisions, the movement resistance affects the step-by-step movement decisions.\n\nThe interplay between shelter sites, foraging quality, and movement resistance simulates the site fidelity required for home ranges, while allowing the environment to help shape the size and diffusion of that home range. Simulating a more dynamic and messy array of movements can help test how far assumptions of uniform circular animal movement are practical.\n\nTo demonstrate the variation that movement ecology methods needs to wrangle, as well as the scope of movements the agent-based model can recreate, we provide three example species. The examples cover a range of movement capacities, site fidelity, and resting/sheltering patterns. Unlike alternative methods that are built to fit and simulate movements from existing data, our examples are loosely based on summary statistics from previous published results (cited below in each example species’ section). The choice of using species specific examples is intended to provide some biological context while demonstrating a range of simulation parametrisations. Therefore, we are only interested in whether the simulated data returns the intended traits we are attempting to simulate for each example species (e.g., avoidance, site fidelity, expected step lengths). We show one example via a more detailed walk-through (badger), and the other example parametrisations are included as uses cases at the end of the manuscript (vulture, king cobra).\n\n2.3.1 Ecology and objectives - badger\n\nOur primary example is based on a badger. Badgers occupy setts, in our example a two home/shelter sites, to where they routinely return.58,59 When not at the sett, the badger forages, and the foraging distances are impacted by resource position and movement capacity of the badger (i.e., how far can a badger feasibly travel for food from the sett). The badger therefore expresses very high site fidelity, a range dictated by the spatial positioning of resources, and is subject to the movement resistance of the terrestrial environment.\n\nWe can draw on studies such as Refs. 58 and 60 to roughly gauge the speed of badgers (i.e., step length per minute). How this speed differs between behaviours is more difficult to estimate from existing literature, but we can use Ref. 58 reported maximum speed to guide more direct movements (e.g., state 0 - sheltering and state 1 - exploring). In particular Ref. 58 mentioned the heightened speeds moving from and to the setts. We also want to allow the exploratory (state 1) movements to be great enough to occasionally exceed the normal home range or territory.61 We can draw on statements regarding maximum distance travelled in a night from papers such as, Refs. 58, 60 and 62 to approximate how distance foraging locations could be from a sett, While also confirming the nocturnal activity cycle for the badger. For the example, we will consider badgers as fully nocturnal, and with active periods lasting for around 8 hours each night.60,63 The 8 hour active periods are not consistent throughout the year. Badger occupying temperate areas are impacted by seasonal shifts that modify daylight hours and available resources.60,63 Badger movements are also impacted by their territoriality, avoiding areas occupied by other badger groups, but also displaying occasional extra-territorial movements.59,61 This suggests a general, but not complete avoidance of areas occupied by other badger groups.\n\nWe can broadly summarise the badger ecology we want to parametrise as follows:\n\n1. Exhibits site fidelity via the use of two shelter sites58,59\n\n2. Movement speed approximated by summary statistics from previous studies,58,60,62 while constrained by terrestrial environment and territoriality59,61\n\n3. An 8-12 hour activity cycle, that shifts over the year60,63\n\nThe abmAnimalMovement package requires links to the Rcpp (>= 1.0.8.3)51–53 and BH (>= 1.78.0.0) packages,64 and therefore requires a version of R >=3.5.065 (available from www.r-project.org). Currently the abmAnimalMovement package can be installed from Github using install_github provided by the devtools package.66\n\nA submission to the Comprehensive R Archive Network (CRAN) is under way, which will streamline installation and ensure compatibly with a wide range of platforms.\n\nWhile only the abmAnimalMovement package is required for running core simulations (abm_simulate function), to generate, organise, and review the inputs and outputs of simulations, we make use of a number of R packages. An alternative simpler implementation with no dependencies is provided as a package vignette.\n\nWe used R v.4.2.165 via RStudio v.2022.2.2.485,67 and used rmarkdown v.2.14,68–70 bookdown v.0.26,71,72 tinytex v.0.39,73,74 and knitr v.1.3975–77 packages to generate type-set outputs. We used the here v.1.0.1 package78 to help with relative file path definition. We used the dplyr v.1.0.9 and reshape2 v.1.4.4 packages for data manipulation.79,80 We used ggplot2 v.3.3.6 for creating figures,81,82 with the expansions: ggridges v.0.5.3,83 ggtext v.0.1.1,84 ggforce v.0.3.3,85 and patchwork v.1.1.1.86 We used the raster v.3.5.21,87 sp v.1.4.7,88–90 and NLMR v.1.191,92 for generating environmental matrices.\n\n2.5.1 Generating environmental matrices\n\nTo ensure that the simulation completed during this example is repeatable, we set a seed. For the sake of simplicity, the year the examples was written (2022) is used.\n\nBefore starting to simulate animal movement, we need to generate a landscape. The landscapes in this case will take the form of matrices, where each cell is describing the quality of foraging, shelter, and movement ease. The highest quality locations/cells are coded as 1, with quality decreasing as the values range down to 0. The 1 to 0 quality values in each cell are later used to help the animal to choose how and where it moves throughout the landscape. Depending on the behavioural state, the weighing of which matrix/layer used will change (e.g., when in a resting behavioural state the shelter site quality layer is used).\n\nFor most applications, a landscape would be known a priori, but for this demonstration and testing of methods we will use a selection of random generated landscape matrices [Figure 3], using the NLMR package (neutral landscape models).\n\nWe used a Gaussian field with an autocorrelation range of 40, a magnitude of variation across the landscape of 5, a magnitude of variation in the scale of autocorrelation range of 0.2, and a mean of 0.5. For foraging, we build on the Gaussian field already produced, allocating all values lower than 0.4 as 0 (i.e., no value for foraging), then normalising the remaining values between 0 and 1.\n\nFor a baseline movement resistance layer, we take the original Gaussian field and increase areas greater than 0.6 by 0.5 to allow areas of high resource quality to be easily accessible. We also greatly increase the movement ease in “edge” habitat (+1), where values fall between 0.6 and 0.3. Again we normalise between 0 and 1, where 1 are areas easily traversed. The resulting environment is one with easily traversable edge areas, surrounding better quality foraging locations than can be moved into easily.\n\nShelter quality is intermediate; we increased weighting by +1 in areas where cell values were greater than 0.5 and lower than 0.7. Thereby shelter sites are more likely to occur in the areas of higher foraging quality, but not in the core (i.e., >0.7), nor in the edge areas (<0.5). This provides some balance between accessibility and proximity to resources. The three matrices described provide a baseline for our examples, but can easily be modified for different scenarios [Figure 3]. To aid balancing, we keep values between 0 and 1; any numeric value can be used, but the simulation will interpret the values as relative weights when the animal is making decisions (Note: The current implementation of cpp_get_values that extracts values from the matrices during the simulation returns -99.9 weighting when presented with NA values; therefore, -99.9 serves as a lower limit to the matrix weighting values).\n\nOnce generated will supply the core simulation function (abm_simulate) with each of these layers via the shelteringMatrix, foragingMatrix, and movementMatrix arguments.\n\n2.5.2 Animal parameters\n\nWe predefine a suite of parameters describing the movement and behaviour characteristics of the animal (e.g., badger) loosely based on summary statistics and general statements from previous research (e.g., Refs. 58–63). We store the parameters as objects we can later input into the abm_simulate function. We complete this process for three species; the badger values are displayed below, whereas the values for vulture and king cobra examples are provided at the end of the manuscript.\n\nWe parametrise shelter information in the following ways. For the sett, we draw a two sets of coordinates from the shelter quality layer. During the simulation the badger will randomly select a sett to return to each time it enters the resting behavioural state. The choice of which sett to return to is weighted by the values supplied via the shelter quality environmental layer [Figure 3]. The coordinate data frame is provided to the core simulation function’s shelterLocations argument.\n\nThe shelterSize argument describes the radius around the shelter locations within which the animal exhibits near stationary behaviour. We specify the shelter size to be 8 m, meaning that when within 8 m of the selected shelter site the animal’s possible step lengths are decreased 100-fold. The shelter site size of 8 m allows for small movements near/within the sett during resting behaviour.\n\nBadger movement is set via the definition of three pairs of Gamma and Von Misses distributions. Each behavioural state is provided with a Gamma distribution to describe the step lengths between locations, and a Von Mises to describe the turn angles. When combined these two distributions provide the animal with a number of locations to choose from at each time step [Figure 2]. As we have three behavioural states, each movement parameter takes the form of a vector of length three. The step lengths require predefined shape (k) and scale (θ) parameters to describe the Gamma distributions, and we provide these to the simulate function via the k_step and s_step arguments. For the turn angles we require the mean (μ) and concentration (κ) to defined the Von Mises distributions, and provide these via the mu_angle and k_angle arguments.\n\nThe perceptual range, in other words, where the badger decides to forage is set in a similar fashion. Where destinationRange provides the shape (k) and scale (θ) for the Gamma distribution describing distance of possible foraging locations, and destinationDirection provides the mean (μ) and concentration (κ) the Von Mises distribution describing the angle which those locations can fall [Figure 4].\n\nThe distribution displayed is generated from the same shape and scale parameters that will be input into the simulation function for the badger simulation. The lower plot shows the distribution used to generate potential foraging desintations.\n\nWe can also alter the strength of attraction to the foraging destinations. At each time step, the animal is offered a number of location options to move to next time step. The simulation calculates the distance between all options and the destination (i.e., a foraging location or shelter site), then normalises the distances between 0 and 1. The normalises values serve as weighting to increase the chances the animal will move towards its destination. We modify the weighting with the destinationTransformation and destinationModifier arguments. The destinationTransformation allows for weightings to be transformed (where 0 = no transformation, 1 = weights are square-rooted, 2 = weights are squared). Values supplied destinationModifier applies a linear multiplicative effect to all the weightings. When these weightings increase in value the animal will exhibit a stronger attraction and choose more direct movements to its current destination.\n\nWe also store a value ready for the rescale_step2cell argument. The rescale value is a simple means of adjusting the environment layers to fit with the scale/unit in which the step lengths are provided. In this case, we treat each cell as 5m by 5m, thereby ensuring that our 2000x2000 matrix is sufficient for the badger to traverse without leaving. The rescale value therefore allows high resolution movements on lower resolution environments, offering a crucial memory saving optimisation.\n\nThe territoriality is not simulated directly via other individuals, instead we approximate it by supplying a number of point locations the badger will avoid. An alternative way of simulating this behaviour would be to create areas of high movement resistance to prevent the badger from entering. We provide a set of x, y coordinates of locations to be avoided. Alongside the locations, we need to define how strongly the badger will avoid them using avoidTransformation (distance to point is weighting squared) and avoidModifier (distance to point is weighting multiplied by 4). Both avoidTransformation and avoidModifier operate in the same way as the destination attraction arguments, but inverted; therefore, the avoidance behaviour will directly counteract the attraction to destination behaviour.\n\nWe implement two cycles to capture the daily and seasonal cycles the badger experiences. Both cycles are created by describing a Sine wave defined by its amplitude, midline, offset (ϕ) and frequency (τ; via the cycle_draw function). The abm_simulate function has two arguments for wave parameters: rest_Cycle is a mandatory input to describe diel activity cycling, and additional_Cycles to define any number of additive additional cycles. For rest_Cycle we will store a vector of length 4, with values defining the amplitude, midline, offset, and frequency in that order (Frequency is supplied in hours, i.e., 60 times the time step). We set the amplitude to 0.12 and midline as 0, meaning the probability of resting will be modified by values ranging from -0.06 to 0.06 depending on the location in the wave. Our badger example requires a 24 hour cycle where the probability of resting will peak and nadir, hence offset and frequency are set to 24 hours. When combined with the base transition probability to rest, the above parametrisation creates a scenario of approximately 8 hour periods of activity every 24 hours.\n\nTo add a seasonal cycle we will use additional_Cycles. We predefine a data frame where each row contains four elements describing the amplitude, midline, offset, and frequency. Whereas our diel activity is defined by a 24 hour cycle, a seasonal cycle is 365 days and we shift the peak half a year (offset = 365/2). The seasonal wave will increase the probability of resting behaviour during a portion of the year, while not also overwhelming a relatively stable diel cycle (i.e., badger will sleep longer during one part of the year) as we have set a lower amplitude for the seasonal cycle (0.075). A more extreme implementation of the second cycle could introduce hibernation behaviour.\n\nWe also pull forward the behaviour transition matrix we showed during the overview, and rename it so all simulation input objects have the BADGER_ prefix.\n\n2.5.3 Running the simulation\n\nWe need to initially define a start location for our animal. To introduce some more individual variation, we can randomly vary this starting location, but we will restrict the start locations to be proximal to the centre of the environment. For the simulation, we need a vector of length 2, where the first value is the x location, the second is y.\n\nWe finally have some parameters that describe the scope and intensity of the simulation. The length of the simulation is provided via the timesteps argument; in our examples we are operating under the assumption that one time step is equal to one minute. Equally timesteps can be thought as the number of movement choices simulated. We also need to specify how many options will be drawn and considered by the animal at each time step. The options argument is where this is input. Similarly des_options is where we specify the number of dynamically selected foraging attraction/destinations to choose from when it enters the foraging behaviour mode (state 1).\n\nWe can then call all our settings describing badger behaviour and movement settings we stored as objects previously, and run the simulation using abm_simulate.\n\n\n3. Results\n\nThe simulation function (abm_simulate) outputs a list containing: (1) a dataframe of realised movements, (2) a dataframe of options the animal had available, and (3) a list of the inputs used to simulate the movement. The realised movement dataframe (locations) describes all realised locations the animal occupied, step length information, behavioural state, and current point of attraction, where each row is equal to a time step. Note the simulation is scale agnostic, so each row can represent a different time step to the example. Other than the lack of timestamps and location error, the format largely mirrors a typical movement dataset. Our example is minute by minute; changing the time step would require a reparametrisation of step length and behavioural transition probabilities. The options dataframe describes all the options available to the animal over the entire simulation duration, where each row is equal to an option repeated for each time step.\n\nOnce simulated, we can review the movement characteristics of the three species. The simplest to examine is the movement speeds or step lengths. During the simulation parametrisation we provided rescale values for the size of the cells describing environmental information (see rescale_step2cell argument). The simulated movement will return the scaled values, so to plot something comparable to the input values, we must rescale the simulated step lengths.\n\nWe can compare the simulation’s inputs displayed in Figure 4 to the simulated/observed outputs displayed in Figure 5 and see that they largely agree as expected. The turn angles are more variable, as the destination decisions and attraction to locations heavily influence the distribution overriding the initial parametrisation of the Von Mises distribution. Figure 10 and Figure 12 in the uses cases section show the outputs for vulture and king cobra simulations.\n\nStep lengths are scaled to the input units. Inset pie chart show the number of step lengths that were below the shelter site size; the sub-shelter site step lengths are excluded from the density plot. Note that x axis is not consistent between the three plots.\n\nWe can review how the movements appear in space. With the badger example, the impact of the avoidance points is clearly visible [Figure 6A, Figure 7A], whereas the lack of or weaker avoidance in vulture [Figure 6B] and king cobra [Figure 6C] makes the avoidance less influential. The vulture’s movements and chosen foraging locations are largely to the east [Figure 7B], demonstrating the impact of the underlying foraging quality environmental layer. The king cobra plot shows the impact of a near impermeable barrier truncating the southward movements [Figure 7C].\n\nBlack points show the observed location at each time step. The orange squares show the dynamically selected foraging destinations. Circles with an interior S show the shelter site locations, and cricles with an interior A show the avoidance points. Note that the size represented by each unit on the x and y axis differs depending on the species.\n\nGrey path shows the overall movement during that month, overlaid points indicate where the animal was in a given behavioural mode. Circles with an interior S show the shelter site locations, and cricles with an interior A show the avoidance points, black squares show the dynamically selected foraging destinations. Note that the size represented by each unit on the x and y axis differs depending on the species.\n\nThe activity cycles and the timing of behavioural shifts is a key component in the simulations. We can examine that the predefined cycles result in expected patterns. A year of data makes observing all but the broadest cycles difficult, so in Figure 8 we can look at several months of data as well as the daily cycle. Badger and vulture daily cycles are largely the same [Figure 8A & B], with a consistent daily activity cycle differing only slightly in the time spent active and balance between shifts from sheltering to foraging and exploring. Some of the differences are a result of the different behavioural transition matrix provided to simulated the two species, where both had different baseline probabilities of shifting between behavioural states. By contrast, the king cobra example demonstrates the interaction between the daily and weekly cycles [Figure 8]. We can see intermittently extended sheltering periods, punctuated by short exploratory or foraging bouts.\n\nPoint colour and position describe the behavioural state at each simulated time step, whereas the purple waves indicated the input values. Note that the input waves acting on the simulated animal in conjunction with the beahvioural transition matrix.\n\nAt the daily and monthly scale, we cannot see the impact of the broad scale seasonal cycles. Instead we can look at the percentage of time steps per day the animal was in sheltering behaviour [Figure 9]. Again the Badger and Vulture sheltering rates are similar, differing in intensity, but with both demonstrating a seasonal decrease in the middle of the simulation. The king cobra cycles reveal decrease in the number of days spent entirely sheltering and an overall impression that the seasonal cycle is less influential (as it is only one of three activity cycles).\n\n\n4. Discussion\n\nAnimal movement datasets are complex and require a suite of analytical approaches to tackle satisfactorily. Efforts to develop new, and test existing, analyses would be aided by access to a range of diverse datasets. While ideal simulations often accompany new analysis methods and provide superb validation for the method in question, reaffirming the method’s robustness and pushing them to new limits with a messier, more stochastic, simulation approach could greatly strengthen our confidence in results. The abmAnimalMovement package provides an independent route to test new methods that covers a range of interacting movement features, not necessarily directly tied to a single analytical method.\n\nBy including a range of features linked to movement and behaviour, the abmAnimalMovement package can be implemented to investigate a suite of questions commonly asked of movement data –from habitat selection, to behaviour detection (for examples of common themes see Ref. 13). While some of the features can appear simplistic, there remains ample flexibility to simulate a wide range of useful scenarios. For example, we conceptualise the three movement states as sheltering, exploring, and foraging. However, only several aspects are immutable: one state exhibits site fidelity (state 0), one state is free from all attraction (state 1), and one state is driven by an underlying environmental layer (state 2).\n\nThe abmAnimalMovement package has an advantage over data-driven simulation methods in scenarios where data are scarce, as much of the animal world is untracked.13,25 For the untracked animals, we may be limited to basic information of speed, activity, and resources, or such information may even need to be inferred from ecologically similar species. In such data starved situations, the abmAnimalMovement package’s low computational cost and minimal data requirements allows for a large number of alternative parametrisations to be explored. Via the explorations of different parametrisations researchers can help build a picture of the study and analysis methods best suited for their questions, with the opportunity to test those analyses on synthetic simulated data.\n\nIn cases where data cannot be shared (e.g. due to concerns over species sensitivity), using a synthetic dataset could allow researchers to provide peer reviewers a dataset to test and error-check analysis code.93 Providing data is a key component to ensuring computational reproducibility,94 and synthetic datasets provide an avenue to limit the reproducibility loss from data sharing restrictions. Additionally, such synthetic datasets could be integrated into preregistration as a means of demonstrating the validity of an analysis plan prior to undertaking a study.\n\nProducing a range of simulated datasets that cover alternate scenarios may present researchers opportunities to test real data against a null model. For example, researchers looking to investigate whether an animal was avoiding a certain landscape feature could calibrate a number of simulations covering a range of differing avoidance strengths. The simulated results could then be compared to the real data to gauge how different the real data was from simulations exhibiting zero avoidance (i.e., a null model scenario). This approach could complement current analysis methods, akin to sensitivity analysis.\n\nThe abmAnimalMovement package provides adequate functionality to simulate a range of scenarios and movements. However, there are several aspects that will bear updating in future versions.\n\n1. Dynamic state 0. While state 0 and the steady state of the attraction locations is key to simulating range stability (i.e., home range), there maybe scenarios where this stability is not desired. For example, simulating dispersal behaviour of juvenile or sub-adult animals there may be a desire to have shelter site dynamically chosen for a time. Currently such behaviour could be simulated, but it would require the dispersal to occur immediately, and the dispersal destination to be predefined (i.e., the sites for state 0 attraction). Therefore, in the current state the package may be limited in its ability to help predict possible dispersal destination, but potentially capable of informing dispersal routes.\n\n2. Autocorrelated speed. We may need to improve the autocorrelation of the animal’s speed. Currently the speeds are non-independent based on the behavioural mode of the animal. The need to implement a more aggressive movement momentum/autocorrelative structure may be felt more acutely at different time frames, and for animals with a great variation in step lengths (i.e., a larger θ for the Gamma distribution). Explorations of simulated data using methods that measure autocorrelation in animal speed will reveal how much of a priority this should be.\n\n3. Dynamic environment. All the environmental matrices are static; currently there is no system to update values during the simulation. This prevents shifts in the landscape such as seasonal variation in resources, or the development of trails. Currently, the closest solution is to run multiple simulations where the end location of simulation1 is the start location for simulation2, where simulation2 is provided with a new season-appropriate resource layer. This solution would be inadequate for trail development, as trail development would require a system within the simulation to update previously used cells for the animal at each time step.\n\nThis section provides alternative parametrisations for the secondary examples to better demonstrate the range of movement types and scenarios the abmAnimalMovement package can replicate. We provide example implementations of vulture and king cobra-like movement.\n\nUnlike badgers and other terrestrially moving animals, vultures can move great distances with minimal obstruction [Figure 11]. Vultures can also move greater distances more rapidly,95 resulting in a more variable and distribution of step lengths96–98 [Figure 10].\n\nThe distribution displayed is generated from the same shape and scale parameters that will be input into the simulation function for the vulture simulation. The lower plot shows the distribution used to generate potential foraging desintations.\n\nSimilar to badgers vultures exhibit significant site fidelity, re-using roosting and nesting sites.99 Such shelter sites could be predefined; for example, if shelter sites were known a priori discovered via the capture and tagging of animals, which in the case of birds is more likely.\n\nVultures also offer an opportunity to demonstrate how the underlying resource availability impact the movements of animals. In the case of vultures, their moments have been seen to follow carcass, creating starkly contrasting areas where vultures will and will not travel9 [Figure 11].\n\nVultures have a very similar cycle pattern to the badgers (just inverted), one defined by a standard 12 hours of activity during the day, and 12 hours of increased resting behaviour during the night. The importance of simulating such cycles is made clear by vultures studies demonstrating that day-night cycles can impact rates of location collection.100 How the the animals’ activity cycle and the probability of collected data interact could be key consideration for some research questions. Again similar to badgers we would expect seasonal shifts in the form of an increase and decrease in activity depending on the time of year.95–97,101\n\nWe can broadly summarise the vulture ecology we want to parametrise as follows:\n\n1. Medium site fidelity via the use of multiple roosting/resting sites99\n\n2. Movement speed approximated by summary statistics from previous studies,95–98 with minimal landscape derived resistance\n\n3. A 8-12 hour activity cycle,100 that shifts over the year95,96,101\n\n4.2.2 Ecology and objectives - king cobra\n\nWhereas the previous two species have a very limited or single shelter sites, king cobras make use of a wider range of shelter sites distributed more widely over their home ranges.102,103 These sites can also be larger, comprising burrow systems or rock complexes.\n\nWhat more dramatically sets king cobras, and other snakes, apart is a vastly differing rest-forage cycle. While snakes still exhibit a diel cycle, the intermittent depredation of large prey items and the time required sheltering to digest large meals results in a second broader activity cycle operating over a more widely observed diel cycle.103–106 We can conceptualise this pattern as two additive cycles, one that will describe the daily activity cycle, and a second that describes the foraging and digestion cycle. Seasonality also impacts king cobra activity. As king cobras occupy tropical regions, the seasonality they experience is not as pronounced as the badger or vulture examples. Overall king cobras have three activity cycles acting on three different scales.\n\nIn this example we can also demonstrate the movement resistance dramatically impacting movement possibilities. King cobra movement can be limited by roads,107,108 where unless provided with crossing structures king cobras are vulnerable to vehicle hits [Figure 13]. In addition to roads presenting linear barriers across the landscape, king cobras face persecution when near or in human settlements.108,109 Despite the risks, avoidance of such areas appears weak.\n\nFinally, king cobra movement characteristics will be dramatically reduced compared to the vulture’s, but with similar shape to the badger with greater variability [Figure 12] as king cobras are known to range over large areas.102,103,110\n\nThe distribution displayed is generated from the same shape and scale parameters that will be input into the simulation function for the king cobra simulation. The lower plot shows the distribution used to generate potential foraging desintations.\n\nWe can broadly summarise the king cobra ecology we want to parametrise as follows:\n\n1. Lower site fidelity via the use of many shelter sites102,103\n\n2. Movement speed approximated by summary statistics from previous studies,102,103,110 with examples of very high landscape derived resistance107,108\n\n3. A 8-12 hour activity cycle, with a approximately weekly forage-digest cycle, and weak seasonality103–106\n\n4.2.3 Simulation inputs\n\nVulture Inputs Largely the vulture parametrisation matches the badger. We specified a number of predefined resting/shelter sites, assuming that bird bio-tagging is more likely to occur at known site (i.e., nests or roosts). The shelter site size is smaller than the badger sett, so is only 5 m. Step length parameters are all larger and more variable, along with destination ranges [Figure 10]. We set a larger rescale value also to ensure the vulture has a larger landscape to operate across. The rest cycle is broadly similar, with a 12 hour diel cycle and gentle seasonality. We make two small modifications to the transition matrix allows for more frequent switches between foraging and exploring. We also alter two of the environmental matrices. We maximise movement ease across the entire landscape, while also lowering the foraging quality for an area to the West reflecting lower resources in that area [Figure 11]. Finally, we specify that the vulture will not be avoiding any locations; we still require inputs for the simulation, but we can provide zeroes to negate the effect.\n\nKing Cobra Inputs Compared to the vulture, the king cobra movements are smaller, but king cobras can still occupy large areas [Figure 12]. We provide a rescale value of 10 m to provide a large enough landscape to capture a potentially large range. The activity cycle provides an opportunity to demonstrate three additive cycles. The diel cycle is largely similar to the other examples, but we also define an approximately weekly cycle to cover the forage-digestion cycle as well as weak seasonal cycle. Combined the three cycles create an activity pattern quite different from either the badger or vulture. To balance the three cycles and their influence on the behaviour transitions, we make some minor adjustments to the underlying behavioural transition matrix. As mentioned in the ecology and justifications, we want to simulate a barrier limiting movement. We construct this by altering the values in the environmental matrices, minimising the weighting in cells following two perpendicular lines [Figure 13]. We also provide a set of avoidance locations and a relatively weak avoidance weighting coefficient. Finally, we can set the shelter sites. We draw 12 sites randomly based on shelter site quality, and limit the area that they can be draw from to ensure they are not on the far side of the barrier. We use a larger shelter site size, as king cobras are known to occupy large rock complexes at times.\n\nMovement ease is blocked by bars of -99 weighting.\n\n4.2.4 Simulation outputs\n\nFigures 10 and 12 describe the inputs for the vulture and king cobra example respectively, and can be compared to Figures 14 and 15 that display the realised movements. Figures 14, and 15 also provide information on the rates of stationary behaviour, defined in the plot as step lengths less than the shelter site size. The king cobra example in particular highlights the prolonged near weekly resting periods.\n\nStep lengths are scaled back to the input units. Inset pie chart show the number of step lengths that were below the shelter site size; the sub-shelter site step lengths are excluded from the density plot. Note that x axis is not consistent between the three plots.\n\nStep lengths are scaled back to the input units. Inset pie chart show the number of step lengths that were below the shelter site size; the sub-shelter site step lengths are excluded from the density plot. Note that x axis is not consistent between the three plots.\n\n\nData availability\n\nThe parameters used to generate the examples (based on Refs. 58–63 for the badger example; Refs. 95–101 for the vulture example; and Refs. 102–110 for the king cobra example) presented in this study are included in the GitHub and Zenodo repositories in the file ‘notebook/manuscript/Agent-based_model_walkthrough.Rmd’.\n\nZenodo: Simulated data from abmAnimalMovement: An R package for simulating animal movement using an agent-based model, https://doi.org/10.5281/zenodo.6992495.111\n\nThis project contains the following underlying data:\n\n• eg_simdata_BADGER_locations.csv (A csv file that contains the realised locations of the example badger simulation, where each row is equal to a timestep. Columns include: timestep, the timestep as a integer; x, the x coordinate of the animal; y, the y coordinate of the animal; sl, the step length between locations used during the simulation; sl_rescale the rescale factor required to return step lengths back to the input scale; ta, turning angle between locations in degrees; behave, the behavioural mode the animal was in at a given timestep; chosen, the location chosen out of the number of options available; destination_x and destination_y the point the animal was attracted to at that time (note exploratory behaviour is not subject attraction)).\n\n• eg_simdata_BADGER_options.csv (A csv file that contains the options available to the example badger simulation over the entire simulation duration, where each row is equal to an option repeated for each timestep. Columns include: timestep, the timestep as an integer; oall_x, and oall_y show the x and y coordinates of all the options available to an animal at a timestep; oall_steplengths are the step lengths from the current location compared to all the options).\n\n• eg_simdata_completelist.RDS (This RDS file contains a list object of length three, where the full simulation outputs from each three example is stored. Each species slot contains the “locations” dataframe (see description of locations.csv), the “options” dataframe (see description of options.csv), and a nested list containing all the “inputs” used to generate the simulated results (split into subsections: inputs_basic that contains inputs linked to simulation duration and intensity, inputs_destination that contains inputs linked to destination and attraction aspects, inputs_movement that contains inputs linked to movement capacity and behavioural switching, inputs_cycle that contains inputs linked to activity cycling, inputs_layerSeed that contains the environmental matrices and seed). A fourth object is return called “others” that captures all other outputs, mainly used internally for debugging and checking).\n\n• eg_simdata_KINGCOBRA_locations.csv (A csv file that contains the realised locations of the example king cobra simulation, where each row is equal to a timestep. The file structure follows the same as the BADGER_options.csv file).\n\n• eg_simdata_KINGCOBRA_options.csv (A csv file that contains the options available to the example king cobra simulation over the entire simulation duration, where each row is equal to an option repeated for each timestep. The file structure follows the same as the BADGER_options.csv file).\n\n• eg_simdata_VULTURE_locations.csv (A csv file that contains the realised locations of the example vulture simulation, where each row is equal to a timestep. The file structure follows the same as the BADGER_locations.csv file).\n\n• eg_simdata_VULTURE_options.csv (A csv file that contains the options available to the example vulture simulation over the entire simulation duration, where each row is equal to an option repeated for each timestep. The file structure follows the same as the BADGER_locations.csv file).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nSoftware availability\n\nSource code available from: https://github.com/BenMMarshall/abmAnimalMovement/tree/v.0.1.3.0000\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.6951938112\n\nLicense: GPL-3.0-only",
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Stat. 2018; 72(1): 28–36. Publisher Full Text\n\nJoo R, Boone ME, Clay TA, et al.: Navigating through the r packages for movement. Börger L, editor. J. Anim. Ecol. 2020 Jan [cited 2021 Aug 29]; 89(1): 248–267. Publisher Full Text\n\nNathan R, Getz WM, Revilla E, et al.: A movement ecology paradigm for unifying organismal movement research. Proc. Natl. Acad. Sci. 2008; 105(49): 19052–19059. PubMed Abstract | Publisher Full Text Reference Source\n\nRivera K, Fidino M, Farris ZJ, et al.: Rethinking habitat occupancy modeling and the role of diel activity in an anthropogenic world. Am. Nat. 2022 May [cited 2022 May 6]; 200: 556–570. PubMed Abstract | Publisher Full Text\n\nScharf AK, Belant JL, Beyer DE, et al.: Habitat suitability does not capture the essence of animal-defined corridors. Mov. Ecol. 2018; 6(1): 18. PubMed Abstract | Publisher Full Text\n\nKowalczyk R, Zalewski A, Bogumiła J: Daily movement and territory use by badgers Meles meles in Białowieża Primeval Forest, Poland. Wildl. Biol. 2006 Dec [cited 2022 May 26]; 12(4): 385–391. Publisher Full Text\n\nFeore S, Montgomery WI: Habitat effects on the spatial ecology of the European badger (Meles meles). J. Zool. 1999 Apr [cited 2022 May 26]; 247(4): 537–549. Publisher Full Text\n\nRosalino LM, Macdonald DW, Santos-Reis M: Activity rhythms, movements and patterns of sett use by badgers, Meles meles, in a Mediterranean woodland. Mammalia. 2005 Jan [cited 2022 May 26]; 69(3-4): 395–408. Publisher Full Text\n\nKelly DJ, Gaughran A, Mullen E, et al.: Extra Territorial Excursions by European badgers are not limited by age, sex or season. Sci. Rep. 2020 Dec [cited 2022 May 25]; 10(1): 9665. PubMed Abstract | Publisher Full Text Reference Source\n\nLoureiro F, Rosalino LM, Macdonald DW, et al.: Path tortuosity of Eurasian badgers (Meles meles) in a heterogeneous Mediterranean landscape. Ecol. Res. 2007 Aug [cited 2022 May 26]; 22(5): 837–844. Publisher Full Text\n\nMagowan EA, Maguire IE, Smith S, et al.: Dead-reckoning elucidates fine-scale habitat use by European badgers Meles meles. Animal Biotelemetry. 2022 Dec [cited 2022 May 26]; 10(1): 10. Publisher Full Text\n\nEddelbuettel D, Emerson JW, Kane MJ: BH: Boost c++ header files.2021.Reference Source\n\nR Core Team. R: A language and environment for statistical computing. Vienna, Austria:R Foundation for Statistical Computing;2021.Reference Source\n\nWickham H, Hester J, Chang W, et al.: Devtools: Tools to make developing r packages easier.2021.Reference Source\n\nRStudio Team: RStudio: Integrated development environment for r. Boston, MA:RStudio, PBC;2021.Reference Source\n\nAllaire J, Xie Y, McPherson J, et al.: Rmarkdown: Dynamic documents for r.2022.Reference Source\n\nXie Y, Allaire JJ, Grolemund G: R markdown: The definitive guide. Boca Raton, Florida:Chapman; Hall/CRC;2018.Reference Source\n\nXie Y, Dervieux C, Riederer E: R markdown cookbook. Boca Raton, Florida:Chapman; Hall/CRC;2020.Reference Source\n\nXie Y: Bookdown: Authoring books and technical documents with R markdown. Boca Raton, Florida:Chapman; Hall/CRC;2016.Reference Source\n\nXie Y:Bookdown: Authoring books and technical documents with r markdown.2022.Reference Source\n\nXie Y: TinyTeX: A lightweight, cross-platform, and easy-to-maintain LaTeX distribution based on TeX live. TUGboat. 2019; 1: 30–32.Reference Source\n\nXie Y: Tinytex: Helper functions to install and maintain TeX live, and compile LaTeX documents.2022.Reference Source\n\nXie Y: Dynamic documents with R and knitr. 2nd ed.Boca Raton, Florida:Chapman; Hall/CRC;2015.Reference Source\n\nKnitr XY:A comprehensive tool for reproducible research in R.Stodden V, Leisch F, Peng RD, editors. Implementing reproducible computational research. Chapman:Hall/CRC;2014.Reference Source\n\nXie Y: Knitr: A general-purpose package for dynamic report generation in r.2022.Reference Source\n\nMüller K: Here: A simpler way to find your files.2020.Reference Source\n\nWickham H, François R, Henry L, et al.: Dplyr: A grammar of data manipulation.2022.Reference Source\n\nWickham H: Reshaping data with the reshape package. J. Stat. Softw. 2007; 21(12): 1–20. Publisher Full Text Reference Source\n\nWickham H, Chang W, Henry L, et al.: ggplot2: Create elegant data visualisations using the grammar of graphics.2022.Reference Source\n\nWickham H: ggplot2: Elegant graphics for data analysis. New York:Springer-Verlag;2016.Reference Source\n\nWilke CO: Ggridges: Ridgeline plots in ggplot2.2021.Reference Source\n\nWilke CO: Ggtext: Improved text rendering support for ggplot2.2020.Reference Source\n\nPedersen TLG: gforce: Accelerating ggplot2.2021.Reference Source\n\nPedersen TL: Patchwork: The composer of plots.2020.Reference Source\n\nHijmans RJ: Raster: Geographic data analysis and modeling.2022.Reference Source\n\nBivand RS, Pebesma E, Gomez-Rubio V: Applied spatial data analysis with R. 2nd ed.NY:Springer;2013.Reference Source\n\nPebesma EJ, Bivand RS: Classes and methods for spatial data in R. R News. 2005; 5(2): 9–13.Reference Source\n\nPebesma E, Bivand R: Sp: Classes and methods for spatial data.2022.Reference Source\n\nSciaini M, Fritsch M, Scherer C, et al.: NLMR and landscapetools: An integrated environment for simulating and modifying neutral landscape models in r. Methods Ecol. Evol. 2018; 1–9. Publisher Full Text\n\nSciaini M, Fritsch M, Hesselbarth M, et al.: NLMR: Simulating neutral landscape models.2021.Reference Source\n\nQuintana DS: A synthetic dataset primer for the biobehavioural sciences to promote reproducibility and hypothesis generation. Zaidi M, Büchel C, Bishop DVM, editors. elife. 2020 Mar; 9: e53275. PubMed Abstract | Publisher Full Text\n\nGerstner K, Moreno-Mateos D, Gurevitch J, et al.: Will your paper be used in a meta-analysis? Make the reach of your research broader and longer lasting. Methods Ecol. Evol. 2017; 8(6): 777–784. Publisher Full Text\n\nHribsek I, Plecas M, Skoric S, et al.: First description of movement and ranging behavior of the Griffon vulture (Gyps fulvus) from Serbia using GPS satellite tracking. Arch. Biol. Sci. 2021 [cited 2022 May 25]; 73(2): 185–195. Publisher Full Text Reference Source\n\nGarcía-Jiménez R, Pérez-García JM, Margalida A: Drivers of daily movement patterns affecting an endangered vulture flight activity. BMC Ecol. 2018 Dec [cited 2022 May 25]; 18(1): 39. PubMed Abstract | Publisher Full Text\n\nMargalida A, Pérez-García JM, Afonso I, et al.: Spatial and temporal movements in Pyrenean bearded vultures (Gypaetus barbatus): Integrating movement ecology into conservation practice. Sci. Rep. 2016 Dec [cited 2022 May 25]; 6(1): 35746. PubMed Abstract | Publisher Full Text Reference Source\n\nSubedi TR, Pérez-García JM, Sah SAM, et al.: Spatial and temporal movement of the Bearded Vulture using GPS telemetry in the Himalayas of Nepal. Ibis. 2020 Apr [cited 2022 May 25]; 162(2): 563–571. Publisher Full Text\n\nBracis C, Bildstein KL, Mueller T: Revisitation analysis uncovers spatio-temporal patterns in animal movement data. Ecography. 2018; 41: 1801–1811. Publisher Full Text\n\nSilva R, Afán I, Gil JA, et al.: Seasonal and circadian biases in bird tracking with solar GPS-tags. Margalida A, editor. PLoS One. 2017 Oct [cited 2022 May 25]; 12(10): e0185344. PubMed Abstract | Publisher Full Text\n\nPeshev H, Grozdanov A, Kmetova-Biro E, et al.: New insight into spatial ecology of Griffon Vulture (Gyps fulvus) on the Balkans provides opportunity for focusing conservation actions for a threatened social scavenger. Biodivers. Data J. 2021 Aug [cited 2022 May 25]; 9: e71100. PubMed Abstract | Publisher Full Text Reference Source\n\nMarshall BM, Strine CT, Jones MD, et al.: Space fit for a king: Spatial ecology of king cobras (Ophiophagus hannah) in Sakaerat Biosphere Reserve, Northeastern Thailand. Amphibia-Reptilia. 2019 Mar; 40(2): 163–178. Publisher Full Text\n\nMarshall BM, Crane M, Silva I, et al.: No room to roam: King Cobras reduce movement in agriculture. Movement. Ecology. 2020 Dec [cited 2020 Aug 4]; 8(1): 33. PubMed Abstract | Publisher Full Text\n\nD’souza A, Gale GA, Marshall BM, et al.: Space use and activity of Boiga cyanea – A major songbird nest predator in a seasonal tropical forest in Thailand. Glob. Ecol. Conserv. 2021 Dec [cited 2021 Oct 27]; 32: e01875. Publisher Full Text Reference Source\n\nSmith SN, Jones MD, Marshall BM, et al.: Native Burmese pythons exhibit site fidelity and preference for aquatic habitats in an agricultural mosaic. Sci. Rep. 2021 Dec [cited 2021 Mar 29]; 11(1): 7014. PubMed Abstract | Publisher Full Text Reference Source\n\nSiers SR, Yackel Adams AA, Reed RN: Behavioral differences following ingestion of large meals and consequences for management of a harmful invasive snake: A field experiment. Ecol. Evol. 2018 Oct; 8(20): 10075–10093. PubMed Abstract | Publisher Full Text\n\nJones MD, Marshall BM, Smith SN, et al.: How do King Cobras move across a major highway? Unintentional wildlife crossing structures may facilitate movement. Ecol. Evol. 2022 Mar [cited 2022 Mar 21]; 12(3): e8691. PubMed Abstract | Publisher Full Text\n\nMarshall BM, Strine CT, Jones MD, et al.: Hits Close to Home: Repeated Persecution of King Cobras (Ophiophagus hannah) in Northeastern Thailand. Tropical Conservation Science. 2018 Jan; 11: 194008291881840. Publisher Full Text\n\nShankar PG, Ganesh SR, Whitaker R, et al.: King Cobra Ophiophagus hannah (Cantor, 1836) encounters in human-modified rainforests of the Western Ghats, India. Hamadryad. 2013; 36(2): 62–68.\n\nSilva I, Crane M, Suwanwaree P, et al.: Using dynamic Brownian Bridge Movement Models to identify home range size and movement patterns in king cobras. Munderloh UG, editor. PLoS One. 2018 Sep; 13(9): e0203449. PubMed Abstract | Publisher Full Text\n\nMarshall BM, Duthie AB: Simulated data from abmAnimalMovement: An R package for simulating animal movement using an agent-based model (v.0.1.3.0000). [Data set]. Zenodo.Publisher Full Text\n\nMarshall BM: BenMMarshall/abmAnimalMovement: v.0.1.3.000 Initial pre-print submission version (v.0.1.3.0000). Zenodo. [Software].Publisher Full Text"
}
|
[
{
"id": "164972",
"date": "24 Apr 2023",
"name": "Rocío Joo",
"expertise": [
"Reviewer Expertise Statistical ecology",
"movement ecology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors developed an R package to simulate movement using an agent-based approach. It allows accounting for three predefined behavioral states and motion characteristics in each state, activity cycles at different scales and external influences. The purpose is to offer opportunities to test whether movement analyses can accurately recover hidden mechanisms, states, and drivers.\nThe package certainly presents opportunities to simulate movement, but I do not know how useful it is for ecologists. The authors present three case studies of simulated tracks of badger, vulture and king cobra. They explain their rationality for the parameterization. However, it is not easy to see if these would be realistic movements. They come from the parameters defined by the authors and based on the literature, but it is not so clear still. This could be better done by consulting experts (e.g. movement ecologists with fieldwork and tracking data expertise for each of those species) and showing their expert validation, and editing figures of observed tracks vs. simulated tracks side by side for easy comparison. I also think that there is a lack of insight into how those simulated movements could contribute to the movement ecology of the animals. The manuscript shows that the package can be used to simulate movement with certain parameterization, but it would be better to also show and discuss the usefulness of those simulations for the case studies (specifically for badger ecologists, vulture ecologists and king cobra ecologists, respectively). What questions could those simulations allow answering? I would not expect the authors to answer those questions, but at least discuss them when presenting the case studies.\nThe presentation of the code could improve as well. First, I would encourage the authors to show examples in the manuscript that can be run on their own, which is not the case in the current version of the manuscript. The abm_simulate examples are extremely long because of all the comments describing the arguments of the function. I would suggest creating tables in the manuscript listing the main functions of the package and describing the arguments of those functions (and default values) so that the example would take less space and can be read easily. Also, some arguments were named in the examples and some others were not. There should be more consistency.\nOther comments:\nThe abstract refers to navigation capacity as \"the range the animal can dynamically choose a foraging location\", but navigation is not only for foraging.\n\nThe agent acts at regular time steps, but do they actually choose from among a range of movement options at regular time steps (e.g. every minute as it seems to be in the case studies)? Does it make sense? And how sensitive is the simulation to the choice of time step? I would like the authors to discuss this.\n\nThe simulation requires animals to have three internal states. Is there a workaround for cases with fewer or more states? This seems to be related to point one in future directions but could be more explicit.\n\nNLMR is one of the packages used for the examples and it has been removed from CRAN. I would suggest adding a line to say how to install it (if necessary).\n\nThe definitions of destination range and destination direction should be clearly stated.\n\nThe x-axes in Fig. 5 should be the same for the three plots.\n\nSince movement is being simulated, I would suggest showing plots of individual trajectories (with the three states) and not just plots of points of several overlapping tracks.\n\nFig. 8: I might have missed it (and I apologize if that's the case), but I did not understand where the observed data comes from, and what \"rest prob. modifier\" is.\n\n\"The abmAnimalMovement package provides an independent route to test new methods (...)\" Which methods? Could the authors provide some examples?\n\nInstead of presenting the Use cases at the end, I would suggest presenting them at the same time as the badger case, perhaps in a shorter version and presenting more details in a supplementary form. A table comparing and summarizing the parameters in the three case studies would be helpful too.\n\nOverall, I think the idea behind the manuscript and the package is good, and I commend the authors for their work. I would suggest making clearer the usefulness of the package for research questions and its usability by using tables to present the details of the functions and examples of code that can be run directly.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
},
{
"id": "180404",
"date": "16 Aug 2023",
"name": "Andrea Contina",
"expertise": [
"Reviewer Expertise Movement Ecology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript describes a new R package called abmAnimalMovement that ecologists can use to build agent-based movement models. The core of the movement simulations is based on three behavioral states (rest, explore, and forage) and activity cycles. Thus, abmAnimalMovement provides an open-source platform to explore movement parameters and mechanisms underlying animal behavior. Overall, the manuscript is straightforward and generally well-written. Importantly, this new R package facilitates the exploration of complex animal behaviors relevant to movement ecology.\nWith that being said, I have a few concerns about the clarity of the manuscript as well as the rationale used to develop the examples and figures. The authors offer three examples that describe movement simulations in three species (badger, vulture, and king cobra) but it is hard to tell if these simulations are meaningful. In particular, I am confused by the generation and use of the simulated environmental layers. These raster layers have a significant impact on the movement patterns. However, a mix of approaches is presented; the movement parameters (e.g., speed, home range, etc.) are imported from the literature and the environmental conditions are drawn at random. What are the benefits of this approach? Why not using real environmental raster layers?\nEven within the realm of simulated scenarios, which do not always need to be realistic and allow for a mix of observed and alternative/simplified parameters and conditions, there must be a strong rationale that justifies this approach. What did we learn about this R package after running the simulations and comparing these three species? Is there a specific question or hypothesis to test? I understand that the aim of the manuscript is not to investigate ecological questions, but why using three species as opposed to a clear single example? It would be helpful to openly address these questions in the Introduction and Methods.\nAlso, by looking at the figures, it seems that the movements of the snake are pretty extensive compared to the vulture. This result is counterintuitive. Is this a meaningful movement pattern truly representative of the behavioral differences between the two species?\nIn my opinion, the presentation of the R package would be much stronger and easy to read if the authors shift their focus on the badger example (already presented as the primary example) and explain how different parameters and environmental layers could change the movement outcome in this species. The other two examples could be moved to the suppl. material to streamline the narrative. Ideally, a small set of badger movement simulations with substantially different environmental scenarios (e.g., 3 scenarios) and/or different behaviors could be added to create a comparative framework helpful to show 1) how sensitive the model is to different transition probabilities and 2) how strongly/easily the parameters and input data (raster) can affect the results. Perhaps the authors already attempted to show different outcomes across parameters and taxa, but I find it confusing because I don’t think that these results are comparable. Alternatively, if the authors decide to maintain the existing framework based on these three species, several clarifications (see my comments/questions above) and thorough justifications of the analytical rationale are needed.\nFinally, I encourage the authors to simplify the R code presented in the “grey boxes” embedded in the main text. The R code is certainly helpful and necessary but there are too may annotations and it is hard to read. One way to address this problem is to reduce the length of the # annotated comments to just a few key words and move them along the same code line whenever possible.\nFor example: # vulture has zero avoidance of the place holder point VULTURE_avoidTransformation <- 0\nCould be presented in a single line as: VULTURE_avoidTransformation <- 0 # zero avoidance of the place holder point\nOther comments\n“In the past decade, the volume of animal data has exploded…” I would not use the term “exploded”.\n\nThis work should be cited in the introduction: Gochanour et al. 20231.\n\n“(e.g., Ref. 12)” I would simply include the reference after “technology” and delete “e.g., Ref.”\n\nIn the third paragraph of the Methods, what is the difference between exploring and foraging?\n\nIn the Methods, the authors introduce the transition matrix but it is hard to determine how these probabilities are calculated: “We achieved this by creating a transition matrix that describes the probability at each time step of the animal changing to another behaviour [Figure 1], where each value describes the probability of the animal transitioning from the current behaviour (row: b0, b1, b2), to the behaviour for the next time step (columns: b0, b1, b2)”. Yet, it is not clear how the behavior is being translated into a matrix of values.\n\nIn the next paragraph, the authors describe cycles (or waves) “that can be applied to the core transition matrix impacting the probability of entering resting behaviour”. This is fine but it does not clearly address the issue that I mentioned above (i.e., how to calculate the transition probabilities). Moreover, there are several cases in which animal movements are not described by daily cycles, for example migration and dispersal. Is abmAnimalMovement suitable to study long-distance movements related to seasonal cycles? This aspect should be further clarified in the Discussion.\n\nIn Figure 3, what are the units on the axes? There are two “S” in the first panel but no mention of what they represent. Importantly, these landscape layers need “to be fed into the simulation”, but I wonder if the sequence matters. Is there a difference in the output if “foraging resources” is being added before “shelter quality”? It would be helpful to clarify this point.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1182
|
https://f1000research.com/articles/11-258/v1
|
02 Mar 22
|
{
"type": "Study Protocol",
"title": "Feasibility of an intervention for increasing moderate-to-vigorous intensity physical activity (MVPA) in primary school physical education: a study protocol",
"authors": [
"Lan Sum WONG",
"Fiona Muirhead",
"Emma Powell",
"Lorayne A Woodfield",
"Cameron Stewart",
"John J Reilly",
"Fiona Muirhead",
"Emma Powell",
"Lorayne A Woodfield",
"Cameron Stewart",
"John J Reilly"
],
"abstract": "Background: Most primary school Physical Education (PE) has relatively little health-enhancing moderate-to-vigorous physical activity (MVPA). - A promising theory and evidence-based intervention, the ‘SHARP Principles’ model, has been effective in making PE lessons more active in one area of England. This protocol paper explains the rationale for use of the SHARP intervention, and the methods used to examine the feasibility and acceptability of a version of SHARP translated for use in Scotland (SHARP Scotland). Methods: The feasibility of SHARP Scotland will be evaluated by key areas of focus for feasibility studies: Acceptability, Implementation, Integration, Limited Efficacy Testing. A combination of process measures, including observations, session delivery records, accelerometry-data collection, questionnaires, and semi-structured qualitative focus groups with teachers and pupils will be used. The feasibility and suitability of the SHARP Scotland intervention for a future Randomised Control Trial (RCT) will be assessed. The study will involve children from 8-11 years old (Primary 4 to 6) in two schools, one large urban school, and one smaller school; four classes will be randomly assigned to the intervention group, and four classes randomly assigned to the usual-care (standard curriculum) control group. Within the 8-week intervention, MVPA in the intervention group will be targeted by encouraging class teachers to deliver their PE classes in more active ways, following SHARP Principles. A maximum of 64 PE lessons delivered in a SHARP way will be conducted to assess the effectiveness of the intervention. Discussion: The outcome of this study will be an assessment of whether applying the SHARP intervention is feasible in Scottish schools. Identification of any modifications to the intervention or evaluation which are required will provide insight for a fully powered effectiveness trial in the future, if appropriate.",
"keywords": [
"Moderate-to-vigorous physical activity",
"Intervention",
"Primary school",
"Children",
"Physical education",
"Health",
"Accelerometry-measured",
"Feasibility."
],
"content": "List of abbreviations\n\nMRC: Medical Research Council\n\nMVPA: Moderate-to-vigorous physical activity\n\nPA: Physical activity\n\nPE: Physical education\n\nRCT: Randomised Control Trial\n\nSHARP: Stretching whilst moving, High repetition of skills, Accessibility, Reducing sitting and standing, and Promotion of physical activity\n\nUK: United Kingdom\n\nUSA: United States of America\n\nWHO: World Health Organisation\n\n\nIntroduction\n\nModerate-to-vigorous intensity physical activity (MVPA) is very important to the health and well-being of children as it provides both immediate and long-term health and non-health benefits.1–4 Despite these positive impacts, it is estimated that approximately only 20% of children and adolescents globally meet the previous WHO recommendation of 60 minutes of MVPA per day every day.5 As a result, children’s current and future health is at risk.6 As there is good evidence that physical activity generally declines by age 6–7 years in the UK and globally,7 future interventions to promote MVPA should start before adolescence.8\n\nThere is high potential for school time to help pupils meet the WHO MVPA recommendation.9 Schools are an important setting for promoting children’s daily physical activity (PA) as pupils from all socio-economic and cultural backgrounds spend around half of their days per year at school.10 Schools can therefore play a vital role in keeping young people active through all activity opportunities,11 such as morning and lunch breaks, recess, active travel, afterschool activities, play and sports,12 but most importantly in physical education (PE) lessons.\n\nThe United States Centers for Disease Control and Prevention (CDC, USA)13 recommends that MVPA levels during primary school PE lessons should reach 50% of lesson time. The UK Association for Physical Education (AfPE, UK)14 recommends that children be actively moving for 50-80% of the available PE learning time. In its health position paper, AfPE also outlines that active learning time is about developing children’s physical skills by providing them with the opportunity to practise those skills during lessons in a fun and purposeful learning environment, as PE involves ‘learning to move’ and ‘moving to learn’,14 so PE lessons can enhance MVPA beyond just class time. Nevertheless, most primary school PE lessons globally do not meet recommendations for the MVPA content of class time,15 so there is a need to find more effective and sustainable good practices to increase children’s MVPA levels during school time and in PE lessons.16\n\nIn Scotland, there is a great public health need for population-wide interventions to increase Scottish children’s physical activity as few children reach the recommended minimum of 60 minutes of MVPA per day.5,17 Scotland faces a crisis arising from unhealthy lifestyles which begin in early childhood: poor diet and low physical activity or exercise create a massive burden of later heart disease and stroke, diabetes, obesity, and cancers.18 Hence the Scottish Government is keen to improve children’s health and wellbeing as guidelines stated in the national “Curriculum for Excellence19 that “Learning in health and wellbeing ensures that children and young people develop the knowledge and understanding, skills, capabilities, and attributes which they need for mental, emotional, social and physical wellbeing now and in the future”.\n\nTo find interventions that could increase the MVPA content of school PE, a systematic review was undertaken by the author in 2019.20 A literature search of global evidence (within the past decade) on effective interventions to increase MVPA during PE classes in children (8 to 11 years) was conducted. The systematic review identified five eligible intervention studies.21–25\n\nOne study from our recent systematic review20 was identified as the most promising for translation to Scotland among the five eligible studies, the ‘SHARP Principles’ model (SHARP), an intervention developed in one part of England.21 This intervention, with a few modifications, now forms the basis of the present feasibility study. The SHARP intervention was chosen for future intervention development and evaluation, starting with the proposed feasibility study, as it:\n\n1. had clear evidence of efficacy in increasing MVPA content of PE in children in our target age range. Indeed, there was evidence that the SHARP lessons had a much higher MVPA content than standard (control) PE lessons in the original evaluation studies. SHARP had been tested twice across multiple schools in the West Midlands, England it increased children’s MVPA during PE lessons by 30% and 27% respectively.21,26\n\n2. had a theoretical basis - the intervention was grounded in a combination of theoretical frameworks namely the Self-Determination Theory (SDT),27 the Socio-Ecological Model,28 and key components (e.g., barrier identification, action planning, and providing instruction) from Behaviour Change Taxonomy.29 In the original development of SHARP, SDT was applied to connect the roles of the Head Teachers, PE subject leader, and the individual teachers. The components of SDT were implemented through a supportive autonomous role (autonomy) along with developing teachers’ social networks (relatedness) and knowledge (competency). Implementation of the SHARP Principles in Scotland is underpinned through the original SHARP Principles model. It is intended that when the intervention is translated to Scotland teachers have relatedness through the shared aims of PE within the school and their connection with each other as professional practitioners working towards this shared aim, along with the support of their PE subject leader and school leadership team. Moreover, since SHARP is applied to teachers’ existing planning, it ensures that they can retain autonomy, so it is also faithful to SDT.\n\n3. could be applied at little cost, as it could be potentially applied to any PE lessons with no additional equipment or other resources.\n\n4. appeared applicable for the Scottish context, in part due to the close cultural and social contexts between England and Scotland. SHARP involves teaching existing PE lessons but in a more physically active way and does not require curriculum changes or extensive re-learning by teachers.\n\n5. had readily accessible online resources available. The SHARP teaching resource cards and videos were available online for teachers’ use.30 The SHARP Principles can be learned by both generalist class teachers and specialist teachers of primary PE in a workshop with the support of these materials.\n\nThe present study aims to describe how we will test the feasibility of the SHARP intervention in Scotland. We propose this study as the foundation of future research which tests whether the SHARP-Scotland intervention works or not, and how it might be implemented across various parts of Scotland to increase MVPA during PE (two lessons of PE per week are timetabled in Scottish primary schools), and in turn increase overall MVPA. Hence, to assess the issue of ‘can the SHARP Scotland intervention work?’, the current study is planned to assess some key areas of focus for feasibility studies as proposed by Bowen et al.,31 particularly Acceptability, Implementation, Integration, and Limited Efficacy Testing (Table 1).\n\n\nMethods\n\nChildren from 8-11 years old (Primary 4 to 6) will be involved from two local authority primary schools in the Glasgow area, characterised for socio-economic status using the Scottish Index of Multiple Deprivation (SIMD).32 All class teachers from 18 classes will be invited to take part and we intend to recruit a total of eight classes/class teachers which will then be randomly allocated to four intervention classes and four control classes (standard curriculum, offered the SHARP intervention training after the eight-week intervention, i.e., a wait-list control) by a member of staff from the Mathematics and Statistics Department in our university who is not connected to the study. A total maximum of around 240 children will be involved in this study (the typical class size in Scottish primary schools is 30 pupils).\n\nWe have not yet registered this trial because the local authority will only give agreement in principle until the schools are operating normally post-COVID. We also cannot apply for ethics approval until schools are operating normally post-COVID. When schools will be operating normally is unclear, and the restrictions which might apply to PE classes, or to our research (e.g., access to schools) are unknown at present. Once confirmed, this study will seek ethical approval from the University of Strathclyde’s School of Psychological Sciences and Health Ethics Committee. Any amendment to the study protocol will be submitted for ethical approval before implementation. Consent will be obtained from all participating children via parental consent forms. All pupils attending the relevant PE classes will be considered as suitable for inclusion, with no exclusions, though if children have health reasons which might impair their ability to take part in PE this will be noted. Teachers will be required to provide informed written consent. Verbal assent will be sought from children before enrolment in the study, and their parents will be required to provide informed written consent.\n\nThe intervention will be delivered by generalist class teachers and the SHARP Principles (more active approach) will be adopted when they are teaching PE lessons. Teachers of intervention classes will be trained in the SHARP approach (via a workshop) before intervention commencement. They will then be asked to apply the principles in their PE lessons over one school term (eight weeks). The workshop will be delivered by the originator of the SHARP (EP) and the PE specialist (CS) involved in translating SHARP Scotland. Existing SHARP resources and training materials are available online30 and will be used by the teachers involved. Group planning sessions (30 minutes), as required will be used to help teachers deliver the intervention and intended also to motivate teachers to use the SHARP Principles in their planning and teaching. Training content will be flexible and would depend on what is needed to modify the SHARP Principles according to the curriculum and environment of Scotland. To provide additional motivation for teachers to take part, the training will count towards continuous professional development hours.\n\n(A summary of the intervention description (trial process) is outlined in Figure 1).\n\nThe SHARP intervention is based on five teaching principles named ‘SHARP Principles’ (Stretching whilst moving, High repetition of skills, Accessibility, Reducing sitting and standing, and Promotion of physical activity21,26). SHARP Principles are designed specifically to help teachers deliver their existing PE classes but to do so in ways that involve more children in the class moving for much more of the class time, to increase MVPA during the lesson. The authors of the present study consist of the original developers of the SHARP intervention in England, a PE specialist teacher from Scotland, and the researchers responsible for evaluation. We consider that SHARP can be adapted to the Scottish context relatively easily, in part because it does not seek to change what is taught in the class but focuses on how it is taught (in a more active way).\n\nIn brief, the SHARP Principles are as follows30:\n\nStretching whilst moving - During the warm-up section of a SHARP PE lesson, activities are to include dynamic movements (such as movements that engage the lower and upper body), and stretches (e.g., side shuffles, jump and twist, high knees, and skipping).\n\nHigh repetition of motor skills - SHARP increases active learning time by reducing queueing. SHARP can also increase the amount of existing equipment used in each class or increase the number of learning stations.\n\nAccessibility through differentiation - SHARP focuses on setting tasks appropriate to children’s physical, cognitive and social development, which will enable them to engage in more active learning time. Teachers can use the ‘STEP framework’ (space, task, equipment, and people) for more effective differentiation of activities in class.21,26\n\nReducing sitting and standing - SHARP increases teachers' awareness of the amount of time children are sitting and standing during the lesson with knowledge transfer, teacher feedback, and improved organisation of equipment. In a SHARP lesson, teachers should engage children in activity as soon as possible at the start of a lesson, they should not stop the whole class from moving while instructions are being given, they should encourage children to stay active (e.g., by continuing to practice skills) while receiving instructions, and they should organize equipment to minimize queueing.\n\nPromoting in-class physical activity - This principle is based on teachers’ encouragement of greater children's in-class physical activity through positive praise such as ‘Great teamwork, keep moving and looking for space’.\n\nThe Bowen et al. Framework31 (Acceptability, Implementation, Integration, Limited Efficacy Testing) will be used to assess the feasibility of the SHARP intervention and evaluation in Scotland (Table 1).\n\nAcceptability assessment is an attempt to answer the question framed by Bowen et al. but applied to the present study of ‘Can SHARP work in Scotland?’31 Qualitative methods will be used to assess the willingness of school staff to deliver the programme, (e.g., willingness to be allocated randomly to intervention or control groups, willingness to deliver lessons using the SHARP Principles), and willingness of children to participate. Acceptability of the methods used for measuring the intervention effect in a future evaluation (e.g., whether children find using the accelerometer acceptable) will also be assessed. All qualitative data will be collected via questionnaires and semi-structured focus groups with teachers and pupils on completion of the intervention.\n\nImplementation is an assessment of the extent to which the intervention was delivered as planned31 - can it be implemented as planned/what refinements are needed? The process evaluation will be supported by the Medical Research Council (MRC) guidance on process evaluation of complex interventions.33 Quantitative methods will be used to assess recruitment and participant attrition rates (class level and individual level), and intervention fidelity. The researcher’s observations of the delivery, relevant documentation, and records (such as teachers’ logs - teachers will be asked to log each PE lesson delivered and whether they used SHARP Principles and which ones, using a checklist) will enable the researcher to reflect on the appropriate use of and application of behaviour change tools utilised. Qualitative semi-structured focus groups with the class teachers will be used to identify any refinements to the delivery of the SHARP Scotland intervention which might be required from teachers’ perspective.\n\nIntegration, as defined by Bowen et al.31 and applied to the present study, is an assessment of the extent to which changes to the school were necessary to integrate SHARP PE lessons (e.g., any changes to timetabling, equipment, unintended teacher impacts such as increased workload). This type of assessment, as framed by Bowen et al.,31 is necessary to assess whether the intervention is feasible beyond the counting of the number of sessions delivered. The integration will be assessed by qualitative methods. Semi-structured focus groups with class teachers will be used to identify the changes to the school which was necessary and to identify any unintended consequences if integrating SHARP lessons.\n\nTo some extent, the issue of integration of SHARP Principles into the Scottish primary school system has been addressed by co-production work34 involving the study authors (researchers, original SHARP development team in England, plus primary school PE specialist from Scotland) before the feasibility study. The main outcome of this co-production was a modified version of the original SHARP Principles intervention (‘SHARP Scotland’). Table 2 outlines the differences between the original SHARP intervention and the translated version of the SHARP Scotland intervention which will be tested for feasibility.\n\n\n\n• Support by head teachers at the organisational/policy levels, PE coordinators, and other staff members in the use of the SHARP Principles during PE lessons\n\n• Joint planning sessions (30 minutes)\n\n\n\n• Four teachers provided with a “3-hour workshop”. Aimed to get teachers on board, motivate them with initiate peer group support among trained teachers, and empower them with the knowledge and skills to deliver the SHARP.\n\n• Arranged with ongoing support plus online communication to provide instant feedback if required.\n\n• Group planning sessions (30 minutes).\n\n\n\n• Pedagogical guidelines for teachers to consider during the planning and delivery stage of their PE lessons\n\n• Provide the SHARP Principles instruction and resources cards\n\n\n\n• Pedagogical dialogue on what and how to modify the SHARP Principles Model according to the curriculum and environment of Scotland.\n\n• Provide the SHARP Principles instruction and resources cards and an overview video resource & SHARP PE lessons – for example, video resource.\n\n• Online communication to provide instant feedback if required.\n\n\n\n• A minimum of two different activity areas of the primary PE National Curriculum (e.g., dance, gymnastics, games, athletics, and adventure activities), joint planning\n\n• Content aligned with the National Curriculum for England.\n\n\n\n• Co-production approach to the translation of SHARP to Scotland (input of PE coordinator and relevant class teachers will be needed via online if necessary) has already taken place.\n\n• Minimal modifications made to original SHARP intervention content and training materials as it was felt that SHARP Principles can be applied to existing PE lessons. Teachers will be using their normal PE curriculum but delivering the lesson in a SHARP (more active) way.\n\n• Contents align with the Curriculum for Excellence in Scotland as based on existing PE classes.\n\n\n\n• A quasi-experimental, non-equivalent group design intervention\n\n\n\n• A feasibility study\n\n\n\n• Self Determination Theory\n\n• Behaviour Change Taxonomy\n\n• Social-Ecological Components\n\n• (Specifically directed at teachers)\n\n\n\n• Self Determination Theory – (Teachers’ competence relatedness and autonomy)\n\n• Behaviour Change Taxonomy\n\n• Social-Ecological Components (Teachers’ individual level, interpersonal level, organisational level)\n\n\n\n• SOFIT, (pre-and post-direct observation, training provided to observers)\n\n• Semi-structured teachers interview during the post-intervention\n\n\n\n• Accelerometer/activity monitor used during PE lessons and whole school day\n\n• Quantitative evaluation of SHARP PE lesson delivery\n\n• Semi-structured teachers/pupils focus groups\n\n\n\n• Pre-school visit/observation.\n\n• Talk to school health staff, if appropriate.\n\n• City Council meeting.\n\nBowen et al.31 recommend limited efficacy testing in feasibility studies. Only preliminary evidence of efficacy will be obtained in the present study, and the extent to which the primary outcome of a future evaluation (MVPA content of PE lessons in both the intervention and control groups using accelerometer) can be measured feasibly will be assessed by quantitative methods. We will measure MVPA during PE lessons and the whole school day in all children with hip-worn Actigraphs. Children will be asked to wear the Actigraph during school time for five days from the beginning to the end of the intervention.\n\nWhole-school day MVPA data will be collected to provide useful contextual information on the amount of MVPA being accumulated during the school day, and because in previous studies we have found that it is more practical to collect accelerometry data during specific periods of the school day (e.g., PE class, recess) if children simply put the Actigraph on at the start of the school day and return it to class teachers at the end of the school day. The feasibility of accelerometry will be assessed as the number of school days with at least 75% of wear time as a percentage of the total number of school days in which children were asked to wear the accelerometers. The teachers in the classes will be shown how to help children put the monitors on/check that they are being worn and worn properly and asked to ensure that the monitors will be put on the consenting participants at the start of the school day and remove just before school finishing. This process of accelerometry data collection also minimizes disruption and delay to PE classes (by avoiding the need to distribute accelerometers during the PE class). Teachers will also be asked to record children’s PE classes (PE date, day start time, and finish time) in a class diary.\n\nAnalyses of between-group differences in the MVPA content of PE (the percentage of time in PE class spent in MVPA), will be preliminary, as the feasibility study is not powered to test for intervention effects. As this is a feasibility study, one of the main objectives is to collect appropriate data to inform a power calculation for a future Randomised Control Trial (RCT). Therefore, no sample size calculation was undertaken for this feasibility study, but the samples will be sufficient to measure important feasibility parameters, notably accelerometer loss, accelerometer data loss, and our ability to identify and extract accelerometer data from PE classes. The analyses will inform a future full-scale trial if feasibility is high.\n\nFindings of the study will be disseminated via publications in peer-reviewed journals, conference presentations, and lay summary reports/presentations which will be given to parents and primary school teachers who participate in the study.\n\nPaper-format documents (e.g., field notes) will be kept locked in filing cabinets. All electronic data will be stored in the University of Strathclyde’s centralised secure data storage system. Only the immediate research team will have access to raw data and will be kept for five years before being destroyed. Participants’ information will also be given codes and will not be referred to by name in published documents. Only the researchers will have access to the codes and their relating participant names. Consent forms will be stored separately from participant data. Teachers’ and pupils’ questionnaires will be kept by the researchers after completion. After the transcription, data from interviews will be deleted immediately from voice recorders, with pseudonyms used in all reports in place of participants’ names. All data collection and storage procedures will be general data protection regulation compliant.\n\nEvery primary school has its health and safety policies, which the SHARP Scotland feasibility study will not breach. In the event of an accident occurring as a direct consequence of participation in the study (no high-risk activities were identified by risk assessment during ethics application) primary school teachers will report this to the research team and appropriate measures will be taken according to existing policies. The researchers will adhere to any Covid-19 safety requirements in place at the time of the study.\n\nA descriptive analysis will summarise the findings of the feasibility and acceptability parameters of interest such as the proportion of children measured at baseline and follow-up to calculate recruitment and attrition rates. Accelerometer data (primary outcome MVPA during PE lessons) will be used to estimate differences in the MVPA content of school PE between intervention and control groups and it is useful for planning future trials. Qualitative interviews/focus groups will be audio-recorded, transcribed verbatim, and thematically analysed. Due to the small sample size, anticipate these analyses will be exploratory and will be used to inform a future trial rather than to draw definitive conclusions regarding the effectiveness of the intervention.\n\nTeacher training in the intervention is currently scheduled for summer 2022 (at the end of the 2021-2022 school year in Scotland) and the feasibility study itself is intended to begin later in 2022, ideally towards the start of the school year in 2022-2023 (August-October, 2022), but with the precise timing depending on how the COVID-19 pandemic is affecting schools in Scotland at the time.\n\n\nDiscussion\n\nWhile concerns about insufficient MVPA in childhood have focused on the impact on their physical and mental health, low MVPA also impairs cognitive function and academic attainment in children.1,35 Only a small proportion of Scottish children are achieving the recommended minimum of 60 minutes of MVPA daily36,37 and so a simple school-based intervention could provide an effective measure in childhood for increasing MVPA. Therefore, it is hoped that the outcome of this study will be a demonstration that applying the SHARP Principles intervention is feasible in Scottish schools. An intervention that is translated so that it fits the Scottish context well could produce much more active PE lessons and consequently help large numbers of children achieve the MVPA recommendations.\n\nThis paper describes the protocol for the SHARP Scotland intervention feasibility study. As noted above, the original SHARP Principles intervention studies21,26 were successful in improving MVPA significantly in school PE lessons in the Midlands of England. Adapting successful interventions for use in other settings should be more efficient than developing entirely new interventions. Using existing interventions means that intervention evaluation does not need to start at the beginning of the process described by the UK MRC.33 To translate an existing intervention from one setting to the other, context-specific modifications might need to be made to ensure the intervention can function as intended while still meeting its desired aims. The study outlined in this protocol aims to test whether the SHARP Scotland intervention is both feasible and acceptable in the Scottish primary schools while it follows along with the intervention development and evaluation pathway described by the UK MRC Framework.33\n\nThere are some strengths to this study. First, it is a translation of a previously successful intervention (SHARP Principles Model) to be used in another setting (SHARP Scotland) and the feasibility testing is a low-cost, culturally relevant school-based intervention with great public health potential.21,26 Furthermore, both quantitative (accelerometry data; process evaluation logs; recruitment data) and qualitative (interviews/focus groups) approaches are utilised to test feasibility in the present study, so the data are complementary and can be triangulated. Lastly, information on the feasibility of the SHARP intervention and SHARP evaluation in Scotland will be useful to provide insight for a fully powered effectiveness trial in the future.\n\nHowever, there are also limitations to the study. Firstly, in this study, we are only dealing with one part of the school day, PE lessons. However, PE lessons are an important part of school day MVPA since they can both increase MVPA directly (MVPA during PE time, 2 lessons per week in Scotland), and indirectly (e.g., by enhancing motor competence, physical fitness, and/or physical literacy). The MVPA accumulated in the whole school day is crucial, but it is the result of a complex system made up of many other elements e.g., influences on what children do during recess, lunchtime, and whether they have active breaks at other times. A whole school day MVPA intervention will probably be required to achieve desired population levels of MVPA but is beyond the scope of the present study. This study will be focused on one element of the whole-school complex system, but future studies will have to build on it and address the other parts of the school system. The present study is restricted to the issue of enhancing existing PE lessons through teaching strategies designed to increase physical activity above routine practice.38 Secondly, as a small-scale pilot and feasibility study, the generalisability of this study may be limited due to its short duration and small sample size. However, the feasibility study is required to develop and evaluate the intervention on a larger scale in the future - it is a foundation for future evaluation research. Thirdly, since the feasibility study may be carried out during the COVID-19 pandemic in 2022, an unstable education environment might cause research delays and modifications may be required to the proposed intervention or feasibility evaluation.",
"appendix": "References\n\nCenters for Disease Control and Prevention: Physical Activity Guidelines Advisory Committee. Scientific Report 2018. Accessed Oct 2020. Reference Source\n\nInchley J, et al., editors: Growing up unequal: gender and socioeconomic differences in young people’s health and well-being. Health Behaviour in School-aged Children (HBSC) study: international report from the 2013/2014 survey. Copenhagen: WHO Regional Office for Europe; 2016. (Health Policy for Children and Adolescents, No. 7).\n\nOwens S, Galloway R, Gutin B: The case for vigorous physical activity in youth. Am. J. Lifestyle Med. 2016; 11(2): 96–115. PubMed Abstract | Publisher Full Text\n\nCarson V, Rinaldi RL, Torrance B, et al.: Vigorous physical activity and longitudinal associations with cardiometabolic risk factors in youth. Int. J. Obes. 2014; 38(1): 16–21. PubMed Abstract | Publisher Full Text\n\nWHO: Physical Inactivity: A Global Public Health Problem. Geneva: World Health Organization; 2014. Accessed Jan 20, 2021. Reference Source\n\nGuthold R, Stevens GA, Riley LM, et al.: Global trends in insufficient physical activity among adolescents: a pooled analysis of 298 population-based surveys with 1.6 million participants. Lancet Region Health. 2019; 4: 23–35. Publisher Full Text\n\nFarooq MA, Parkinson KN, Adamson AJ, et al.: Timing of the decline in physical activity in childhood and adolescence. Br. J. Sports Med. 2018; 48: 265–270.\n\nFarooq A, Martin A, Janssen X, et al.: Longitudinal changes in moderate-to-vigorous-intensity physical activity in children and adolescents: a systematic review and meta-analysis. Obes. Rev. 2020; 21: e12953. Accessed Oct 2020. Publisher Full Text\n\nSallis JF, McKenzie TL, Beets MW, et al.: Physical education’s role in public health: steps forward and backward over 20 years and HOPE for the future. Res. Q. Exerc. Sport. 2012; 83(2): 125–135. PubMed Abstract | Publisher Full Text\n\nLangford R, Bonell CP, Jones HE, et al.: The WHO health promoting school framework for improving the health and well-being of students and their academic achievement. Cochrane Database Syst. Rev. 2014; 4: CD008958. Publisher Full Text\n\nUK Chief Medical Officers' Physical Activity Guidelines 7 September 2019: UK Chief Medical Officers' Physical Activity Guidelines. Accessed Feb 19, 2021. Reference Source\n\nPulling Kuhn A, Stoepker P, Dauenhauer B, et al.: A Systematic Review of Multi-Component Comprehensive School Physical Activity Program (CSPAP) Interventions. Am. J. Health Promot. May 2021; 35: 1129–1149. Publisher Full Text\n\nCenters for Disease Control and Prevention: The association between school-based physical activity, including physical education, and academic performance. Accessed Jan 20, 2021. Reference Source\n\nAssociation for Physical Education (AfPE), Health Position Paper. Loughborough, UK: Loughborough University; 2020. Accessed Jan 20, 2021. Reference Source\n\nHollis JL, Williams AJ, Sutherland R, et al.: A systematic review and meta-analysis of moderate-to-vigorous physical activity levels in elementary school physical education lessons. Prev. Med. 2015; 86: 34–54.\n\nLonsdale C, Rosenkranz RR, Peralta LR, et al.: A systematic review and meta-analysis of interventions designed to increase moderate-to-vigorous physical activity in school physical education lessons. Prev. Med. 2013; 56(2): 152–161. PubMed Abstract | Publisher Full Text\n\nHughes AR, et al.: Results from Scotland’s 2018 Report Card on Physical Activity for Children and Youth. J. Phys. Act. Health. 2018; 15S2: S402–S403. Accessed March 8, 2021. Reference Source\n\nPublic Health Information Scotland: The Scottish Burden of Disease Study, 2015, Overview report. NHS Health Scotland; 2017. Accessed March 8, 2021. Reference Source\n\nEducation Scotland: Curriculum for excellence: health and wellbeing across learning: responsibilities of all experiences and outcomes. Accessed Dec 11, 2020. Reference Source\n\nWong LS, Gibson AM, Farooq A, et al.: Interventions to Increase Moderate-to-Vigorous Physical Activity in Elementary School Physical Education Lessons: Systematic Review. J. Sch. Health. 2021; 91(10): 836–845. PubMed Abstract | Publisher Full Text\n\nPowell E, Woodfield LA, Nevill AM: Increasing physical activity levels in primary school physical education: the SHARP principles model. Prev. Med. Rep. 2016; 3: 7–13. PubMed Abstract | Publisher Full Text\n\nBoulley GE, Tessier D, Ntoumanis N, et al.: Need-supportive professional development in elementary school physical education: effects of a cluster-randomized control trial on teachers’ motivating style and student physical activity. Sport Exerc. Perform. Psychol. 2017; 7(2): 218–234.\n\nFairclough SJ, McGrane B, Sanders G, et al.: A non-equivalent group pilot trial of a school-based physical activity and fitness intervention for 10-11 year old English children: born to move. BMC Public Health. 2016; 16: 861. PubMed Abstract | Publisher Full Text\n\nSmith L, Harvey S, Savory L, et al.: Physical activity levels and motivational responses of boys and girls: a comparison of direct instruction and tactical games models of games teaching in physical education. Eur. Phys. Educ. Rev. 2015; 21(1): 93–113. Publisher Full Text\n\nTelford RM, Olive LS, Cochrane T, et al.: Outcomes of a four-year specialist-taught physical education program on physical activity: a cluster randomized controlled trial, the LOOK study. Int. J. Behav. Nutr. Phys. Act. 2016; 13: 64. PubMed Abstract | Publisher Full Text\n\nPowell E, Woodfield LA, Powell AJ, et al.: Assessing the wider implementation of the SHARP principles: increasing physical activity in primary physical education. Sports. 2020; 8(1): 6. PubMed Abstract | Publisher Full Text\n\nRyan RM, Deci EL: Self-determination theory and the facilitation of intrinsic motivation, social development, and well-being. Am. Psychol. 2000; 55(1): 68–78. PubMed Abstract | Publisher Full Text\n\nMcLeroy KR, Bibeau D, Steckler A, et al.: An ecological perspective on health promotion programs. Health Educ. Q. 1988; 15: 351–377. Publisher Full Text\n\nMichie S, Ashford S, Sniehotta FF, et al.: A refined taxonomy of behaviour change techniques to help people change their physical activity and healthy eating behaviours: the CALO-RE taxonomy. Psychol. Health. 2011; 26(11): 1479–1498. PubMed Abstract | Publisher Full Text\n\nPowell E, Woodfield LA, Powell AJ, et al.: Active Learning Time in Physical Education: The SHARP Principles – Teaching Resources. Birmingham: Newman University; 2020. Accessed Dec 1, 2020. Reference Source\n\nBowen DJ, Kreuter M, Spring B, et al.: How we design feasibility studies. Am. J. Prev. Med. 2009; 36(5): 452–457. PubMed Abstract | Publisher Full Text\n\nScottish Government: Scottish Index of Multiple Deprivation (SIMD).2020. Accessed Dec 6, 2020. Reference Source\n\nCraig P, Dieppe P, Macintyre S, et al.: Research methods & reporting, developing, and evaluating complex interventions: the new medical research council guidance. BMJ. 2008; 337: a1655. Publisher Full Text\n\nLoeffler E, Power G, Bovaird T, et al.: Co-production of health and wellbeing in Scotland: Governance International.2013.\n\nBooth JN, Leary SD, Joinson C, et al.: Associations between objectively measured physical activity and academic attainment. Br. J. Sports Med. 2014; 48: 265–270. PubMed Abstract | Publisher Full Text\n\nBrooks FM, Magnusson J, Klemera E, et al.: HBSC England National Report: Health Behaviour in School-aged Children (HBSC): World Health Organization Collaborative Cross National Study. University of Hertfordshire; 2015; 113.\n\nMcCrorie P, Mitchell R, Ellaway A: Comparison of two methods to assess physical activity prevalence in children: an observational study using a nationally representative sample of Scottish children aged 10–11 years. BMJ Open. 2018; 8: e018369. PubMed Abstract | Publisher Full Text\n\nBeets MW, Okely A, Weaver RG, et al.: The theory of expanded, extended, and enhanced opportunities for youth physical activity promotion. Int. J. Behav. Nutr. Phys. Act. 2016; 13: 120. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "138839",
"date": "25 Jul 2022",
"name": "Freya MacMillan",
"expertise": [
"Reviewer Expertise Lifestyle behaviour intervention development",
"implementation and evaluation"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper reports on the protocol for a PE based intervention that will be feasibility tested in Scotland. The intervention being tested is novel as it has been adapted to the Scottish setting from an evidence-based approach previously used in England. This is an important study to show that the intervention can be tailored to other countries - important for translational capacity of the SHARP intervention. The design is rigorous and considers implementation measures to guide feasibility as well as indicators of initial efficacy (which the authors correctly state is not a powered analysis). Overall this is a very well written paper that includes the necessary details to replicate the study.\nI have some minor suggestions to improve this paper:\nThe abstract describes the study as a RCT (randomised control trial). The methods section describes the RCT as being of wait list design. Please add 'wait list' to the abstract so it is consistent. It would be good to concisely mention in the abstract too that the teachers delivering the intervention are not the same teachers taking the control classes (there is a worry over potential contamination if they were - eg once trained up in SHARP, how easy would it be to revert back to a usual care style).\n\nNon-health benefits is a clunky term. Instead can you provide an example of the types of benefits outside of health (eg additional benefits such as academic performance).\n\nWhy the 'previous' WHO recommendation and not the 'current?'\n\n2nd sentence of the 'limited efficacy testing' section should read 'accelerometery' or 'accelerometers'.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-258
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https://f1000research.com/articles/11-1176/v1
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17 Oct 22
|
{
"type": "Research Article",
"title": "Polypharmacological drug design opportunities against Parkinson's disease",
"authors": [
"Ezra Michelet Garcia-Romero",
"Edgar López-López",
"Catalina Soriano-Correa",
"José L. Medina-Franco",
"Carolina Barrientos-Salcedo",
"Ezra Michelet Garcia-Romero",
"Edgar López-López",
"Catalina Soriano-Correa",
"José L. Medina-Franco"
],
"abstract": "Background: Parkinson's disease is an attractive disease model to extend research towards a better understanding of the interrelationship between genes and the environment (exposome) therefore is an ideal model for a polypharmacological approach due to its clinical heterogeneity. Methods: In this paper, we present a series of polypharmacological chemical scaffolds extracted from ChEMBL 30 Database, with two or more targets of PD-related proteins obtained through chemoinformatics methods. This way, we describe the first adaptation of the Dual Activity Difference (DAD) map that allows the direct identification of \"dual activity cliffs\". Results: We identified 25 antiparkinson small molecules whose pharmacological targets are directed to dopaminergic and muscarinic acetyl choline M1-M5 receptors; 2 small molecules with three pharmacological targets with norepinephrine transporter, dopaminergic D1-D2 and muscarinic acetyl choline M1-M5 receptors; 6 with both targets norepinephrine transporter and muscarinic acetyl choline M1-M5 receptors; 2 small molecules with norepinephrine transporter and muscarinic acetyl choline M1-M5 receptors and 1 with both adenosine A2a and Dopamine D1-D5 receptors. Conclusion: Chemoinformatics methods identified 36 polypharmacological chemical scaffolds related to Parkinson's disease. Demonstrating that the design of polypharmacological drugs is an opportunity in PD.",
"keywords": [
"Parkinson drugs",
"Activity Cliffs",
"Chemoinformatics",
"Dual Activity Cliffs",
"Polypharmacology",
"Structure-Activity Relationships."
],
"content": "Introduction\n\nParkinson’s disease (PD) is a complex and multifactorial neurodegenerative disease (Ontology: DOID:14330; OMIM: 168600).1 The underlying aspects of the neurodegenerative process have been unraveled and are becoming known, while treatments that can modify this process are still in the experimental stage. Currently, PD has a symptomatic treatment derived from the gradual loss of neurons in the substantia nigra, which contributes to motor and non-motor symptoms. At the onset of the disease, motor symptoms respond predominantly to levodopa treatment. However, the symptoms of chronic PD tend not to respond satisfactorily to levodopa treatment, which is partly explained by the fact that PD is considered a complex disease combining genetic and environmental factors, in which genes can either generate the disease on their own or be part of the risk factors. Parkinson Disease are associated with five targets, one of this is an immuno-relevant target. In Figure 1 shows the protein targets that have been associated with various stages of PD. It should be noted that in the Synuclein Alpha (SNCA) pathway siRNAs have been described as negative regulators. Likewise, some small molecules such as Nilotibib are immunoregulators.2\n\nThe PD patients have an insidious quality of life, which is stressful due to treatments based solely on symptomatic features. As the world’s population continues to age, the prevalence of PD is expected to double in some age groups, placing a considerable burden on healthcare systems. Fortunately, the rise of rational polypharmacological approaches is increasing, in particular for the treatment of multifactorial and complex diseases, such as neurodegenerative diseases. PD is an ideal model for a polypharmacological approach due to its clinical heterogeneity. Indeed, the search for specific targets has been the basis of pharmacology for many years. With the advent of systems pharmacology, a quantitative area based on computational methods it has become possible to develop compounds directed to more than one target. In this sense, it has been possible to take data from fields such as clinical neurophysiology and neuropharmacology, and organize them with high-throughput screening methods, such as ligand-based virtual screening, or structure-based virtual screening. Thus, PD compounds represent a promising approach to shed light on the etiology and treatment of complex neurodegenerative diseases such as PD. There are few candidate polypharmacological compounds targeting dopaminergic neurons,3–5 although none of them are in clinical development yet. For this reason, we are interested in contributing to show polypharmacological opportunities in PD.\n\nChemoinformatics allows systematic studies of chemical structure discernment and comparison of chemical structures present in compound databases. The relationships that can be established through informatics strategies reveal pharmacological or polypharmacological compounds with PD-related endpoints as a common factor. Polypharmacology is the binding of drugs to multiple targets, the main one being the search for lead structures that interact with several biological targets related to a specific pathological entity; not others that may produce unwanted adverse effects.6 Therefore, the goal of this paper is to identify compounds with over one receptor target related to PD.\n\n\nMethods\n\nThe compound dataset was constructed in three steps: (1) An initial dataset with 15,119 compounds, tested against different human (Homo sapiens), rat (Rattus norvergicus), and mouse (Mus musculus) endpoints. In the same way, datasets related to the development of PD (reported in the ChEMBL V.30 database7), (2) Then, duplicated structures were removed, yielding a dataset with 5,992 unique compounds (see Table S1 in the Supplementary Material). In the case of duplicated compounds, those with the highest reported activity (< IC50) were retained. For this analysis, compounds with dose-response values equal to or lower than 10 μM were considered “active”, and compounds with higher values were considered “inactive”. It should be noted that a value of 10 μM has been used as a general threshold to define active/inactive molecules in other large-scale studies8; (3) 1,562 compounds were considered active for almost one set of the data (see Table S2 in the Supplementary Material). All compounds have been associated with the IC50 values indicated for each data set. SMILES representation of structures and the pIC50 (-log IC50) values are summarized in Table S1 of the Supplementary Materials. In general, the range of activity values for each set is similar, which facilitates cross-comparisons of the activity landscape (vide infra).9\n\nActivity cliffs (AC) represent pairs of compounds with high structural similarity but with an unexpected change in their biological activity. The Structural Activity Landscape Index (SALI) value has been commonly used in the systematic identification of AC.9\n\nAC has been optimized by identifying chemical shifts related to enhanced biological activity against two data sets simultaneously (Dual activity cliffs and D-AC). Here, the dual activity difference (DAD) map is a tool for structure-activity relationship (SAR) analysis of data sets of compounds tested against two molecular targets. DAD maps are based on the activity landscape concept and are suitable for the fast identification of “selective switches”, defined as compounds with structural changes, that completely reverse the selectivity towards two different biological targets.10 DAD maps are based on systematic pairwise comparisons of compounds in a dataset, comparing similarity (using the extended connectivity fingerprint of radius 4 - ECFP4 - fingerprint, and the Tanimoto coefficient), and differences in activity (pIC50) against two targets (simultaneously) for each compound pair.\n\nThis work describes an extension of the DAD map that allows the rapid identification of D-ACs. The newly proposed 3D Dual map includes a Z-axis that represents the Dual Structural Activity Landscape Index (D-SALI). which Is calculated with the equation:\n\nA1 = Values of activity against the first target.\n\nA2 = Values of activity against the second target.\n\ni = The first compound on the pair analyzed.\n\nj = The second compound on the pair analyzed.\n\n\nResults\n\nIn our study we selected 1,562 active compounds (IC50 equal to or lower than 10 μM) reported against almost one target related to PD, shown in Figure 2. It is relevant that 36 of the compounds have a polypharmacological activity against over two different target families (Table S1). Of these multi-target compounds, only two exhibit activities against different target families related to PD (e.g., muscarinic acetylcholine receptors, norepinephrine transporter, and dopamine receptors). Additionally, strategic search reveals promising chemical dual-entities. For example, a compound with activity against adenosine A2a and dopamine D1 receptors, six compounds with activity against norepinephrine transporter and dopamine receptors (D1-D5), and two compounds with dual activity against norepinephrine transporter and muscarinic acetylcholine receptors (M1-M5). Interestingly, 25 compounds with dual activity against dopamine receptors and muscarinic acetylcholine receptors has been identified. The chemical structures and activity profile of representative polypharmacological compounds were shown in Figures 3 and 4.\n\nA) Representative Poly-active compounds. B) Dual compounds related with dopamine and muscarinic acetylcholine receptors.\n\nExamples of the most studied targets related to PD, are the dopamine and muscarinic acetylcholine receptors. These targets are associated with multiple biological functions in the CNS (e.g., dopaminergic denervation) and diseases (e.g., Huntington’s disease, Alzheimer’s disease, PD, etc.) For this reason, the pharmacological irruption of these targets is one of the most important topics in drug discovery and design. Particularly, in PD, the dual inhibitions (dopamine and muscarinic acetylcholine receptors) have been associated with their symptom improvement,20 which suggests that is a promising strategic the explicit design of compounds with dual activity. According to this idea, Figure 4 shows an overview of the most potent active compounds (reported on ChEMBL V.30) against dopamine (D1-D5) and muscarinic acetylcholine (M1-M5) receptors.\n\nAs been illustrated in Figure 4, the scaffold N-(4-(4-(benzo [d]isothiazol-3-yl)piperazin-1-yl)butyl) acetamide is a representative structure of the most potent dual inhibitors (dopamine and muscarinic receptors). This scaffold is present in six of the ten most potent dual compounds (2,4,5,6,9 and 10). The associated activity of this scaffold is only surpassed by compound 1 (CHEMBL4128926) which has higher activity against both targets (especially, is more potent against muscarinic receptors). Additionally, CHEMBL4128926 has been associated with other CNS targets (e.g., GABA-gated chloride channel, 6 and 2 serotonin receptors, Mu and Kappa opioid receptors, and neurokinin receptors 3).21 Interestingly, their pharmacokinetic profile reveals that have a desirable oral bioavailability, distribution volume, and half-life on in vivo (Rattus norvergicus) models.22,23 In contrast, compound 2 (CHEMBL343838), which contains the representative scaffold N-(4-(4-(benzo [d]isothiazol-3-yl)piperazin-1-yl)butyl) acetamide, has been associated with the inhibition of the serotonin 1a and 2 receptors, and it has an acceptable ADMET profile.24\n\nThe identification of AC is a crucial step in the complete understanding of Structure–Multiple Activity Relationships (SMARt).25 For compound datasets with measured experimental activity. Small changes in the chirality, chemical substituents, and scaffold are the common reason to generate cases of AC. Figure 5 shows four representative dual AC cases against dopamine and muscarinic acetylcholine receptors.\n\nExample (1) refers to the pair of compounds CHEMBL545546 against CHEMBL544375 (see Figure 5) with a chirality change on the carbon bonding with the -OH group on the structures. This chiral change reduces the activity against both targets in ~1 logarithmic unit. This observation suggests that dopamine and muscarinic acetylcholine receptors could be stereoselective. Besides, the example (2) refers that the elongation of the structure is another key factor in the design of new dual active compounds. For example, CHEMBL134527 (larger) in contrast to CHEMBL342267 (shorter) increases the activity against both targets in ~1 logarithmic unit.\n\nIn contrast with pair of compounds 1 and 2, the example (3) (CHEMBL72292 and CHEMBL310712) illustrates an example of an isomeric change that increases the activity against dopamine receptors in ~2 logarithmic units but decreases the activity against muscarinic acetylcholine receptors in ~2 logarithmic unit. Finally, study case (4) exhibits a bidirectional activity profile from the substitution of nitrogen by oxygen on the scaffold (i.e., the isomeric change decreases the activity against dopamine receptors in ~2 logarithmic units but increases the activity against muscarinic acetylcholine receptors in ~2 logarithmic units).\n\nThe examples described in Figure 4 are multi-target compounds with improved IC50s against dopaminergic and muscarinic receptors. In fact, cases (1) and (2) show that is possible to identify chemical changes associated with the activity improvement against multiple endpoints, but that also is possible to regulate the selectivity of these compounds without loss of potency against a specific endpoint (as shown in the case (3) and (4)).\n\nInterestingly, there are compounds with large activity differences (around 3 logarithmic units) with the dopamine and muscarinic acetylcholine receptors. Figure 6 shows examples of selective compounds. For example, we highlight the selectivity of CHEMBL54 (haloperidol), CHEMBL4085780, and CHEMBL831 against the dopamine receptors.\n\n\nDiscussion\n\nAs discussed in the Introduction section, multi-target therapy offers new perspectives that could resolve different issues in relationship with single-target drug design. At same time, polypharmacology therapy offers the possibility to generate novel and refined approaches to address to complex diseases such as neurological diseases. In this context, the generation and optimization of polypharmacological agents, represents a new challenge in drug design.\n\nThis study is an overview of multitarget compounds reported in the literature with potential application against PD. The data was obtained from ChEMBL V.30 (the most recent version, at the time or writing). These data do not represent all the compounds reported in the public domain against the different related targets on PD. For example, there are other primary resources with reported activity data such as PubChem or Binding DB, as well as those of private companies,26 that have not been included in this study. For example, a recent case remarks the not exhaustive data exploration on the literature (related with PD), is the case of 9-deazaxanthine derivatives, that has been dual against A2A (antagonists) and MAO-B (inhibitors), reported with nanomolar activity.27 Furthermore, this study is limited by the targets selected (Figure 2) to explore. This is a key point in the design and optimization of new chemical entities against PD.\n\nThis study uncovers the possibility of optimizing the tested compounds (e.g., shown in Figures 3-6) to identify new chemical structures and features related to a polypharmacological or selective profile against different PD targets. This offers a possibility to identify compounds that act on different molecular levels (i.e., changing the signaling, gene expression, or physiological effects) on PD. In fact, the parallel modulation of different endpoints could contribute to reducing the necessary doses to generate a therapeutic effect, that at the same time contributes to reducing the associated side effects on in vivo models.\n\nCurrently, there are 15 original and 3 repurposing compounds that have been approved for clinical use and other 19 compounds continue to be tested in clinical trials phase 3 with a single drug target.28,29 This data remarks a key opportunity to change the paradigm of “one compound one target” in drug discovery, and that the “promiscuity” concept should not be associated (directly) with serious side effects.\n\nThis new drug design approach has been guided by computational methods that have contributed to reducing the gap in information related to the development of new poly-active compounds. For example, now machine and deep learning techniques contribute to predicting and identifying optimized compounds against two or more endpoints.30 However, this model has been constructed using classification, clustering, or regression models that have not been possible to identify small chemical changes related to unexpected activity changes (i.e., activity cliff, AC). Accordingly, Figure 5 shows a new “proof of concept” to explore and use the reported dual-activity data to identify D-AC, and using D-SALI values to identify the most prominent selective and dual compounds on a data set. In fact, a perspective is an adaptation of the D-SALI value to identify triple (or quadruple, quintuple, etc.) activity cliffs.\n\nThis study has illustrated the potent (<10 μM) poly-active compounds against different targets related to PD existence. However, same compounds have been associated with promiscuity against other central nervous system (CNS) targets. For example, CHEMBL461571 and CHEMBL115280 (Figure 3-A). They have also been associated with opioid and adrenergic receptor and dopamine transporter uptake, to name a few of these targets.11,12 CHEMBL250699 (Figure 3-B) has been associated with the irruption of serotonin receptors,13,14 CHEMBL257991 are other examples with associated activity against adrenergic receptors and sirtuins (epigenetic targets),15,16 and CHEMBL1949930 with activity against serotonin receptor and dopamine transporter.17 Interestingly, these results reveal the promiscuity of some compounds interacting with different targets in the CNS.\n\nDespite the high CHEMBL115280 and CHEMBL250699 promiscuity, these compoundshave been associated with a promising bioavailability profile on in vivo models.18 Another excellent case, reflecting these compounds potential, is CHEMBL1949930, which exhibits low toxicity, brain permeability, and a good bioavailability profile.19 These examples show that not in all cases poly-activity is associated with toxicological or bioavailability issues.\n\nIn the last decade, techniques and tools have emerged to design dual compounds; this facilitates the design of multi-target polyactive drug candidates. It is now possible to optimize compounds for two end-targets at the same time, provided the data exist to process them. In the next section, we present a study case of 25 compounds, with dual activity against dopamine receptors (D1-D5) and muscarinic acetylcholine receptors (M1-M5), illustrated In Figure 3.\n\n\nConclusions\n\nIn this paper, identified 36 polypharmacological chemical scaffolds related to Parkinson’s disease. In this manner we demonstrate that design of polypharmacological drugs is an opportunity in Parkinson’s Disease treatment.\n\nIn recent years, the old concept that drug selectivity meant having a single drug target has been left behind. Mainly, in multifactorial diseases, which involve interactions between molecular, cellular, and physiological pathways. Thus, in neurodegenerative disorders, including PD, the polypharmacological design approach is a fertile field for the development of new therapeutic strategies.\n\n\nData availability\n\nFigshare. Supplementary material, DOI: https://doi.org/10.6084/m9.figshare.21096919.v1.31\n\nThis project contains the following data:\n\n‐ Table S1. Datasets related to the development of PD reported in the ChEMBL V.30 Database.\n\n‐ Table S2. Compounds considered active for at least one data set.",
"appendix": "Acknowledgments\n\nE.M-G.R. and E.L-L. thanks the Consejo Nacional de Ciencia y Tecnología (CONACyT), Mexico, for the scholarships No. CVU:666583, and No. CVU: 894234, respectively.\n\n\nReferences\n\nWorld Health Organization: International statistical classification of diseases and related health problems (ICD-11).Accessed May 2022.Reference Source\n\nSimuni T, Fiske B, Merchant K, et al.: Efficacy of nilotinib in patients with moderately advanced Parkinson disease: A randomized clinical trial. JAMA Neurol. 2021; 78(3): 312–320. Publisher Full Text\n\nKampen S, Duy Vo D, Zhang X, et al.: Structure-guided design of G-protein-coupled receptor polypharmacology. Angew. Chem. Int. Ed. Engl. 2021; 60(33): 18022–18030. Publisher Full Text\n\nButini S, Nikolic K, Kassel S, et al.: Polypharmacology of dopamine receptor ligands. Prog. Neurobiol. 2016; 142: 68–103. PubMed Abstract | Publisher Full Text\n\nOyinloye BE, Iwaloye O, Ajiboye BO: Polypharmacology of Gongronema latifolium leaf secondary metabolites against protein kinases implicated in Parkinson’s disease and Alzheimer’s disease. Scientific African. 2021; 12(e00826): e00826. Publisher Full Text\n\nMedina-Franco JL, Giulianotti MA, Welmaker GS, et al.: Shifting from the single to the multitarget paradigm in drug discovery. Drug Discov. Today. 2013; 18(9–10): 495–501. PubMed Abstract | Publisher Full Text\n\nMendez D, Gaulton A, Bento AP, et al.: ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Res. 2019; 47(D1): D930–D940. Publisher Full Text\n\nYongye AB, Byler K, Santos R, et al.: Consensus models of activity landscapes with multiple chemical, conformer, and property representations. J. Chem. Inf. Model. 2011; 51(6): 1259–1270. PubMed Abstract | Publisher Full Text\n\nPérez-Villanueva J, Santos R, Hernández-Campos A, et al.: Structure–activity relationships of benzimidazole derivatives as antiparasitic agents: Dual activity-difference (DAD) maps. Medchemcomm. 2011; 2(1): 44–49. Publisher Full Text\n\nDebenham SD, Chan A, Lau FW, et al.: Highly functionalized 7-azaindoles as selective PPAR gamma modulators. Bioorg. Med. Chem. Lett. 2008; 18(17): 4798–4801. Publisher Full Text\n\nPoulain R, Horvath D, Bonnet B, et al.: From hit to lead. Analyzing structure-profile relationships. J. Med. Chem. 2001; 44(21): 3391–3401. Publisher Full Text\n\nJarvis MF, Honore P, Shieh CC, et al.: A-803467, a potent and selective Nav1.8 sodium channel blocker, attenuates neuropathic and inflammatory pain in the rat. Proc. Natl. Acad. Sci. U. S. A. 2007; 104(20): 8520–8525. PubMed Abstract | Publisher Full Text\n\nTripathy R, McHugh RJ, Bacon ER, et al.: Discovery of 7-arylsulfonyl-1,2,3,4, 4a,9a-hexahydro-benzo[4,5]furo[2,3-c]pyridines: identification of a potent and selective 5-HT6 receptor antagonist showing activity in rat social recognition test. Bioorg. Med. Chem. Lett. 2012; 22(3): 1421–1426. Publisher Full Text\n\nVu CB, Bemis JE, Disch JS, et al.: Discovery of imidazo[1,2-b] thiazole derivatives as novel SIRT1 activators. J. Med. Chem. 2009; 52(5): 1275–1283. PubMed Abstract | Publisher Full Text\n\nYang L, Ma X, Yuan C, et al.: Discovery of 2-((4,6-dimethylpyrimidin-2-yl)thio)-N-phenylacetamide derivatives as new potent and selective human sirtuin 2 inhibitors. Eur. J. Med. Chem. 2017; 134: 230–241. Publisher Full Text\n\nChiken S, Takada M, Nambu A: Altered dynamic information flow through the Cortico-basal ganglia pathways mediates Parkinson’s disease symptoms. Cereb. Cortex. 2021; 31(12): 5363–5380. Publisher Full Text\n\nMurakami H, Shiraishi T, Umehara T, et al.: Recent advances in drug therapy for Parkinson’s disease. Intern. Med. 2022; (8940-21). PubMed Abstract | Publisher Full Text\n\nKorczyn AD: Drug treatment of Parkinson’s disease. Dialogues Clin. Neurosci. 2004; 6(3): 315–322. Publisher Full Text\n\nRamprasad C, Douglas JY, Moshiree B: Parkinson’s disease and current treatments for its gastrointestinal neurogastromotility effects. Curr. Treat. Options Gastroenterol. 2018; 16(4): 489–510. PubMed Abstract | Publisher Full Text\n\nStoker TB, Barker RA: Recent developments in the treatment of Parkinson’s disease. F1000Res. 2020; 9: 862. PubMed Abstract | Publisher Full Text\n\nIarkov A, Barreto GE, Grizzell JA, et al.: Strategies for the treatment of Parkinson’s disease: Beyond dopamine. Front. Aging Neurosci. 2020; 12: 4. Publisher Full Text\n\nKonnova EA, Swanberg M, et al.:Animal models of Parkinson’s disease. Parkinson’s Disease: Pathogenesis and Clinical Aspects. Codon Publications; 2018; 83–106.\n\nCrans RAJ, Wouters E, Valle-León M, et al.: Striatal dopamine D2-muscarinic acetylcholine M1 receptor-receptor interaction in a model of movement disorders. Front. Pharmacol. 2020; 11: 194. PubMed Abstract | Publisher Full Text\n\nPrieto-Martínez FD, López-López E, Juárez-Mercado K, et al.:Computational drug design methods—current and future perspectives. In Silico Drug Design. Elsevier; 2019; 19–44.\n\nSaldívar-González FI, Naveja JJ, Palomino-Hernández O, et al.: Getting SMARt in drug discovery: chemoinformatics approaches for mining structure–multiple activity relationships. RSC Adv. 2017; 7: 632–641. Publisher Full Text\n\nRivara S, Piersanti G, Bartoccini F, et al.: Synthesis of (E)-8-(3-chlorostyryl) caffeine analogues leading to 9-deazaxanthine derivatives as dual A(2A) antagonists/MAO-B inhibitors. J. Med. Chem. 2013; 56(3): 1247–1261. Publisher Full Text\n\nGilson MK, Liu T, Baitaluk M, et al.: BindingDB in 2015: A public database for medicinal chemistry, computational Chemistry and systems pharmacology. Nucleic Acids Res. 2016; 44(D1): D1045–D1053. Publisher Full Text\n\nAmerican Parkinson Disease Association: Medications approved for the treatment in the Parkinson’s disease in the USA.Published June 2018. Accessed May 2022.Reference Source\n\nMcFarthing K, Rafaloff G, Baptista MAS, et al.: Parkinson’s disease drug therapies in the clinical trial pipeline: 2021 update. J. Parkinsons Dis. 2021; 11(3): 891–903. PubMed Abstract | Publisher Full Text\n\nFeldmann C, Philipps M, Bajorath J: Explainable machine learning predictions of dual-target compounds reveal characteristic structural features. Sci. Rep. 2021; 11(1): 21594. PubMed Abstract | Publisher Full Text\n\nLópez-López E: Supplementary Material. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "153474",
"date": "03 Nov 2022",
"name": "Giulio Rastelli",
"expertise": [
"Reviewer Expertise Drug design and discovery"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article by Garcia-Romero et al. reports an interesting chemoinformatics analysis in search of multi-target scaffolds potentially useful against PD. The analyses of the activity cliffs in relation to the multi-target profiles of the ChEMBL examples shown in this paper are also very informative. The results are expected to be useful in the discovery and optimization of multi-target compounds directed against PD.\nI would suggest consideration of the following points:\nIn the Methods section, a clearer definition of human, rat, and mouse \"endpoints\" would be beneficial. Are these the PD targets reported in Figure 2?\n\nI would rather use the terminology \"multi-target\" instead of poly-target, or poly-active.\n\nSynuclein alpha should be alpha Synuclein.\n\nThe last sentence of the Introduction is not well formulated.\n\nReference 18 is too dated. The sentence reported in the Discussion section should be re-formulated according to novel findings.\n\nThe last sentence of the Discussion, \"In the next section...Figure 3\" is not in the appropriate location.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "247838",
"date": "29 Feb 2024",
"name": "Yassir Boulaamane",
"expertise": [
"Reviewer Expertise Cheminformatics",
"Parkinson's disease",
"natural products",
"molecular modelling"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors propose a novel cheminformatics approach to extract chemical scaffolds with biological activity against multiple protein targets in a polypharmacological context, which is relevant to neurological disorders such as Parkinson’s disease. In their methodology, they adapted the Dual Activity Difference (DAD) map to identify \"dual activity cliffs,\" allowing direct insights into compound activity relationships. Through their investigation, the authors identified 36 multi-target chemical scaffolds associated with PD, emphasizing the potential for polypharmacological drug design as a promising strategy for PD treatment. Regarding concerns:\nDuplicate compounds with multiple reported activities should be averaged by calculating a mean value, which could provide a more representative compound activity. While 10 μM is commonly used as a threshold for defining activity or inactivity in large-scale studies, authors might consider experimenting with lower thresholds. Since 10 μM also serves as the threshold for inactive compounds, I suggest starting with 1 μM for active compounds to establish distinct classes more clearly. This lower threshold could help differentiate between compounds with varying degrees of activity and enhance the resolution of the analysis. Provide additional insights into the potential benefits of targeting dopamine transporters and muscarinic acetylcholine receptors. It would be beneficial to elaborate further on the therapeutic implications and rationale behind focusing on these specific targets. Regarding Figure 5, it seems that the same compound (4) is depicted with a minor variation in the nitrogen position within the ring structure. There doesn't seem to be a substitution of nitrogen with oxygen as stated. Authors should verify if these are indeed the intended compounds intended to be highlighted for comparison. I recommend that the authors include a comprehensive list of tools and software utilized throughout the study in the methods section or supplementary materials. This would enhance the transparency and reproducibility of the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1176
|
https://f1000research.com/articles/11-546/v1
|
19 May 22
|
{
"type": "Case Report",
"title": "Case Report: Vertebro-vertebral arteriovenous fistula showing symptoms mimicking ALS: Diagnostic imaging supports accurate differentiation between ALS and mimicking conditions",
"authors": [
"Hinako Kirikae",
"Ryuhei Harada",
"Tatsuhiko Hosaka",
"Tatsuro Misu",
"Daisuke Ando",
"Hitoshi Warita",
"Toshiki Endo",
"Shinya Sonobe",
"Kuniyasu Niizuma",
"Masashi Aoki",
"Hinako Kirikae",
"Tatsuhiko Hosaka",
"Tatsuro Misu",
"Daisuke Ando",
"Hitoshi Warita",
"Toshiki Endo",
"Shinya Sonobe",
"Kuniyasu Niizuma",
"Masashi Aoki"
],
"abstract": "We report a rare case of a vertebro-vertebral arteriovenous fistula (VVAVF) manifesting as amyotrophic lateral sclerosis (ALS). A 76-year-old female patient presented with progressive weakness, muscle atrophy, fasciculation, and preserved deep tendon reflexes in the right upper limb. Electrophysiological testing showed lower motor neuron dysfunction. The patient was suspected to have ALS, but cervical magnetic resonance imaging (MRI) revealed enlarged blood vessels in the spinal canal, which compressed the cervical spinal cord and nerve roots. Angiography showed a shunt from the right vertebral artery to the right intervertebral vein and the vertebral venous plexus; therefore, the patient was diagnosed with VVAVF. Transarterial embolization was performed to obliterate the shunt, and weakness in the patient’s right upper limb subsequently improved. It is worth considering VVAVF as a differential diagnosis of ALS-like diseases.",
"keywords": [
"vertebro-vertebral arteriovenous fistula",
"amyotrophic lateral sclerosis",
"ALS mimics",
"angiography",
"diagnostic imaging"
],
"content": "Introduction\n\nAmyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that affects upper motor neurons (UMNs) and lower motor neurons (LMNs), causing muscle weakness and atrophy and, eventually, death.1 Published criteria for diagnosing ALS include the assessment of clinical or electrophysiological signs of UMN and LMN dysfunction, as well as the exclusion of ALS-mimicking diseases.2\n\nVertebro-vertebral arteriovenous fistula (VVAVF) is a rare vascular malformation defined as a direct shunt from the vertebral artery (VA) to the surrounding venous plexus.3 Although the most frequent symptom of this disorder is bruit, some patients present with neurological symptoms such as muscle weakness, numbness, and pain.3,4 VVAVF diagnosis is made via magnetic resonance angiography (MRA), computed tomography angiography (CTA) and/or digital subtraction angiography.5 In many cases, subsequent endovascular or surgical treatment results in symptom improvement.3,5\n\nHere we describe a case of a patient with VVAVF presenting symptoms mimicking ALS.\n\n\nCase report\n\nA 76-year-old unemployed Japanese woman presented to our hospital with a complaint of weakness in the right upper limb that had developed progressively over a period of more than eight months. The patient had a history of schizophrenia with onset at the age of 19, which included seizures and insomnia, and she was treated with oral medications of clotiazepam (20 mg three times a day every day), quetiapine (320 mg four times a day every day), sertraline (25 mg once a day every day), levetiracetam (500 mg twice a day every day), brotizolam (0.25 mg once a day every day), and suvorexant (15 mg once a day every day). She had no history of trauma or surgery. Her mother suffered from a mental illness of unknown details, and there is no other apparent family history. Neurological examination revealed moderate muscle atrophy and weakness in the right upper limbs with preserved reflexes, and fasciculation in the right first dorsal interosseous muscle.\n\nElectromyography showed active and chronic denervation in the right biceps brachii and first dorsal interosseous muscle. Nerve-conduction studies showed repeater F-waves and decreased F-wave persistence in the bilateral median and ulnar nerves. These results suggested the presence of LMN dysfunction in the cervical region. Therefore, the patient appeared to meet the criteria for “possible ALS” according to the revised El Escorial criteria.6\n\nHowever, cervical magnetic resonance imaging (MRI) demonstrated a dilated internal vertebral venous plexus in the right side of the spinal canal from the C1 to C6/7 levels (Figure 1A); this imaging showed compression of the spinal cord and spinal nerve roots at the same level, most severely at the C6/7 level (Figure 1B). Axial T2-weighted imaging showed high signal intensity around the right anterior horn (AH) at that level (Figure 1B). MRA and CTA revealed an arteriovenous fistula from the right VA to the right vertebral vein at the C6/7 level and showed dilation of the right intervertebral vein and the vertebral venous plexus (Figure 1C-E). Right vertebral angiography revealed right VVAVF with reflux to the anterior internal vertebral venous plexus via the right intervertebral vein (Figure 2A and B). Left vertebral angiography showed retrograde filling of the right VA distal to the arteriovenous fistula and running into the draining vein (Figure 2C).\n\n(A) Sagittal T2-weighted imaging of the cervical spine showed the dilated internal vertebral venous plexus in the right side of the spinal canal from the C1 to C6/7 levels (arrowheads). (B) (the cross-section image of A at the yellow line) Axial T2-weighted imaging of the cervical spine showed the dilated right intervertebral vein (asterisk) at the C6/7 level compressing the spinal cord, and high signal intensity around the right AH at the same level.\n\n(C) Three-dimensional reconstruction of contrast-enhanced computed tomography revealed a dilated intervertebral vein and anterior internal vertebral venous plexus (blue, arrowheads). Arteriovenous fistula at the C7 level (purple) was also shown.\n\n(D) Oblique view of maximum-intensity projection cervical MRA showed a dilated right intervertebral vein and anterior internal vertebral venous plexus. The yellow line indicates the cross-sectional position of (E).\n\n(E) Axial image of time-of-flight cervical MRA showed an arteriovenous fistula at the C7 level (arrow). AH, anterior horn; MRA, magnetic resonance angiography.\n\n(A, B) Right vertebral angiography revealed the right vertebro-vertebral arteriovenous fistula with reflux to the anterior internal vertebral venous plexus via the right intervertebral vein.\n\n(C) Left vertebral angiography showed retrograde filling of the right vertebral artery distal to the arteriovenous fistula and running into the draining vein (arrowheads).\n\nTransarterial embolization of the fistula was performed using coil and n-butyl cyanoacrylate with no adverse events. There were no significant problems with intervention adherence and tolerability. Postprocedural angiography demonstrated a significant reduction of the shunt blood flow (Figure 3A and B). Three months after treatment, a follow-up angiography was performed and revealed complete disappearance of the shunt blood flow (Figure 3C). Furthermore, the presenting weakness in the patient’s right upper proximal limb slightly improved without the occurrence of any new neurological abnormalities.\n\n(A) Anteroposterior and (B) lateral right vertebral angiography showed remarkable reduction of the shunt flow.\n\n(C) Three months post-fistula embolization, anteroposterior right vertebral angiography demonstrated complete disappearance of the shunt flow.\n\n\nDiscussion\n\nVVAVF is a rare vascular malformation, and, to our knowledge, a total of 293 cases have been reported from 1990 to 2018, of which 280 cases were well-documented. Of these 280 cases and the present case, 136 cases (49%) were spontaneous, 76 (27%) were traumatic, and 68 (24%) were iatrogenic.3 The male/female ratios of spontaneous, traumatic, and iatrogenic VVAVF were 1:2, 2:1 and 1:1, respectively.3 Although the etiology of VVAVF was not identified in the present case, spontaneous VVAVF would be associated with connective tissue disorders including Ehlers-Danlos syndrome, neurofibromatosis type 1, and fibromuscular dysplasia.3 Among the variety of presenting symptoms and clinical observations in VVAVF, bruit is the most common clinical manifestation.3 Other frequently observed symptoms include weakness and numbness, pain, and headache.3 On fewer occasions, tinnitus, subarachnoid hemorrhage, and congestive heart failure have also been reported.3,4 Radiculopathy has been rarely reported as a manifestation of VVAVF.4\n\nSymptoms in the present case were likely caused by compression of the spinal cord and the ventral nerve root, as the patient’s symptoms were localized to the right upper limb without sensory involvement and partially improved following shunt-vessel embolization. The dilated blood vessels compressed the spinal cord from the C1 to C7 levels—most severely at the C6/7 level—and a high signal intensity around the right AH at that level was revealed via T2-weighted imaging, whereas no signal change was observed in the spinal cord at other affected levels. This suggests that the AH cells at the C6/7 level were more severely affected than in the other regions, leading to the patient’s partial posttreatment improvement. Furthermore, it is likely that the AH and the ventral nerve root were selectively damaged by spinal-cord compression, resulting in ALS-like symptoms brought on by damage to the affected UMNs and LMNs.\n\nIn the present case, the patient’s initial presenting symptoms were progressive UMN and LMN signs in the right upper limb, which are classified by current diagnostic criteria as possible ALS. According to criteria for diagnosis of ALS—including revised El Escorial, Awaji, and recently proposed Gold Coast criteria—the clinical or electrophysiological signs of UMN and LMN dysfunction, and exclusion of other possible diagnoses, are necessary for accurate ALS diagnosis.2,6,7\n\nCertain medical conditions that can be described as “ALS mimics” show motor neuron dysfunctions similar to those of ALS. ALS mimics tend to present atypical initial symptoms, namely the absence of LMN signs via electromyography and the absence of isolated UMN or LMN signs in the physical examination.8 Other atypical signs suggesting ALS mimics include patient age younger than 50 years, slow or no progression of symptoms, and involvement of sensory symptoms.9 A recent retrospective study conducted at an ALS clinic in Argentina found that 11.7% of patients with motor neuron disease symptomatology were later diagnosed as having ALS mimics.8 Furthermore, even after being diagnosed as ALS, fully 3.9–9.7% of cases later turned out to be ALS mimics.8,9 The alterative diagnoses of those patients include spinal cord pathology, hereditary spastic paraparesis, neuropathy, inclusion body myositis, multiple sclerosis, and paraneoplastic syndrome.8–10 Accurate diagnosis of ALS mimics—even following an initial incorrect diagnosis of ALS—can lead to improved treatment options and higher quality of life.\n\nVascular malformations including epidural AVF, dural AVF, and perimedullary AVF may present symptoms mimicking ALS11,12 and may lead to spinal-cord compression that can be treated by endovascular or surgical treatment.4,11,12 To our knowledge, this is the first case report of VVAVF with symptoms mimicking ALS.\n\nWhen diagnosing a patient with an ALS-like clinical presentation, it is critical to consider all the other possible diagnoses. More precisely, diagnostic imaging such as computerized tomography (CT), CTA, MRI, and/or MRA should be performed to differentiate from alternative diagnoses, including VVAVF.\n\n\nConclusions\n\nWe report a case of VVAVF presenting motor neuron symptoms mimicking ALS. VVAVF is treatable and is worth considering as a differential diagnosis despite its clinical rarity, and diagnostic imaging should be performed when a patient presents with motor neuron dysfunctions resembling those of ALS.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.",
"appendix": "Acknowledgements\n\nThe authors would like to thank Enago for the English language review.\n\n\nReferences\n\nOskarsson B, Gendron TF, Staff NP: Amyotrophic Lateral Sclerosis: An Update for 2018. Mayo Clin. Proc. 2018; 93(11): 1617–1628. PubMed Abstract | Publisher Full Text\n\nCosta J, Swash M, de Carvalho M : Awaji criteria for the diagnosis of amyotrophic lateral sclerosis: a systematic review. Arch. Neurol. 2012; 69(11): 1410–1416. PubMed Abstract | Publisher Full Text\n\nAljobeh A, Sorenson TJ, Bortolotti C, et al.: Vertebral Arteriovenous Fistula: A Review Article. World Neurosurg. 2019; 122: e1388–e1397. Publisher Full Text\n\nLarson AS, Rinaldo L, Arnold Fiebelkorn CE, et al.: Spontaneous Vertebral Arteriovenous Fistula Mimicking Brachial Radiculoplexopathy. World Neurosurg. 2020; 138: 309–312. PubMed Abstract | Publisher Full Text\n\nBrinjikji W, Yin R, Nasr DM, et al.: Spinal epidural arteriovenous fistulas. J. Neurointerv. Surg. 2016; 8(12): 1305–1310. Publisher Full Text\n\nBrooks BR, Miller RG, Swash M, et al.: World Federation of Neurology Reserch Group on Motor Neuron Diseases. El Escorial revisited: revised criteria for the diagnosis of amyotrophic lateral sclerosis. Amyotroph. Lateral Scler. Other Motor Neuron Disord. 2000; 1: 293–299. PubMed Abstract | Publisher Full Text\n\nShefner JM, Al-Chalabi A, Baker MR, et al.: A proposal for new diagnostic criteria for ALS. Clin. Neurophysiol. 2020; 131(8): 1975–1978. PubMed Abstract | Publisher Full Text\n\nQuarracino C, Segamarchi MC, Rodríguez GE: Predictors of amyotrophic lateral sclerosis mimic syndrome. Acta Neurol. Belg. 2019; 119(2): 253–256. PubMed Abstract | Publisher Full Text\n\nJacobson RD, Goutman SA, Callaghan BC: Pearls & Oy-sters: The importance of atypical features and tracking progression in patients misdiagnosed with ALS. Neurology. 2016; 86(13): e136–e139. PubMed Abstract | Publisher Full Text\n\nHannaford A, Pavey N, van den Bos M , et al.: Diagnostic Utility of Gold Coast Criteria in Amyotrophic Lateral Sclerosis. Ann. Neurol. 2021; 89(5): 979–986. PubMed Abstract | Publisher Full Text\n\nSato K, Endo T, Niizuma K, et al.: Concurrent dural and perimedullary arteriovenous fistulas at the craniocervical junction: case series with special reference to angioarchitecture. J. Neurosurg. 2013; 118(2): 451–459. PubMed Abstract | Publisher Full Text\n\nBrinjikji W, Colombo E, Lanzino G: Clinical and angioarchitectural characteristics of spinal vascular malformations of the cervical spine. J. Neurosurg. Spine. 2020; 32: 755–762. Publisher Full Text"
}
|
[
{
"id": "142017",
"date": "12 Jul 2022",
"name": "Masafumi Hiramatsu",
"expertise": [
"Reviewer Expertise \"dural arteriovenous fistula\"",
"\"spinal arteriovenous fistula\"",
"\"neuroendovascular therapy\""
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors report a case of VVAVF (Vertebro-vertebral arteriovenous fistula) with ALS-like symptoms. The present case is a typical case of VVAVF and the authors suggest that novelty exists only because ALS was required for differential diagnosis.\nWhen there are few abnormal findings in imaging studies, it may be challenging to differentiate the case from ALS. On the other hand, in the present case, the abnormalities are evident in imaging studies, and it is questionable whether ALS should be listed as a differential diagnosis. In the setting of progressive paralysis and muscle atrophy in the upper extremities, imaging studies of cervical spine lesions are often performed before suspecting ALS.\nThe presence or absence of trauma or findings suspicious of connective tissue disorder should be noted.\n\nThe presence or absence of bruit or findings suspicious of radiculopathy, such as pain and numbness, should be noted.\n\nThe authors should state whether the findings described in the case report are upper or lower motor neuron dysfunction.\n\nThe CTA shows red coiling vessels suggesting intradural reflux of shunt flow. Is there reflux on angiography? Intradural reflux may cause progressive congestive myelopathy. How about the presence of myelopathy on MR imaging and clinical examination?\n\nRight vertebral angiography shows the steal phenomenon, but is there any symptom of stealing, such as vertebra-basilar ischemia?\n\nOn treatment, the coil mass appears to protrude into the VA; if the coil protrudes into the VA, there is a risk of thrombosis and stroke. It would be better to reconstruct the VA with a stent or occlude the VA completely.\n\nWhat do the authors believe is causing the hyperintensity signal in the anterior horn at the C6/7 level, spinal cord compression, or myelopathy due to intradural reflux of abnormal shunt flow?\n\nThe authors state that the damaged anterior horn leads to partial posttreatment improvement, but I think the mass effect of the coil is the cause of the limitation of the symptom improvement.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "8580",
"date": "04 Aug 2022",
"name": "Ryuhei Harada",
"role": "Author Response",
"response": "Dear Dr. Hiramatsu, Thank you very much for the thoughtful and constructive feedback. We are thankful for the time and energy you expended. Our responses to your comments are as follow: Q1: \"The authors report a case of VVAVF (Vertebro-vertebral arteriovenous fistula) with ALS-like symptoms. The present case is a typical case of VVAVF and the authors suggest that novelty exists only because ALS was required for differential diagnosis. When there are few abnormal findings in imaging studies, it may be challenging to differentiate the case from ALS. On the other hand, in the present case, the abnormalities are evident in imaging studies, and it is questionable whether ALS should be listed as a differential diagnosis. In the setting of progressive paralysis and muscle atrophy in the upper extremities, imaging studies of cervical spine lesions are often performed before suspecting ALS.\" A1：Thank you for raising an important point. We agree that the diagnosis of VVAVF was clear from the imaging findings. However, in the progressive course, upper motor neuron signs and lower motor neuron signs were observed, especially muscle atrophy, weakness, and fasciculation, and the clinical findings were mimicking ALS. On the other hand, VVAVF is rare, and the present patient had no past medical history that may be involved in the development of VVAVF (more detailed description in Q2). From this point of view, we considered it to be an instructive case. Q2: \"The presence or absence of trauma or findings suspicious of connective tissue disorder should be noted.\" A2：Thank you for this suggestion. The patient had no history of trauma other than a history of a fracture of the left upper arm at the age of 68. The patient had no findings suggesting connective tissue diseases (e.g., tissue fragility, hyperextensibility of skin or joints, neurofibroma, elevated inflammatory markers, or collagen disease-related autoantibodies). We have reflected this comment by lines 8-11 from the top of the “Case report” section. Q3: \"The presence or absence of bruit or findings suspicious of radiculopathy, such as pain and numbness, should be noted.\" A3：Thank you for this suggestion. After reviewing the imaging findings, a careful review of the physical examination revealed a bruit in the right neck and a slight tingling sensation in the radial side of the right forearm. Symptoms of pain were not present. We have reflected this comment by lines 29-31 from the top of the “Case report” section. Q4: \"The authors should state whether the findings described in the case report are upper or lower motor neuron dysfunction.\" A4：Thank you for this suggestion. Preserved reflexes in the right upper extremity with muscle atrophy reflect upper motor neuron dysfunction. Muscle atrophy and fasciculation in the right upper extremity reflect lower motor neuron dysfunction. We have reflected this comment by lines 13-15 from the top of the “Case report” section. Q5: \"The CTA shows red coiling vessels suggesting intradural reflux of shunt flow. Is there reflux on angiography? Intradural reflux may cause progressive congestive myelopathy. How about the presence of myelopathy on MR imaging and clinical examination?\" A5：Thank you for providing these discussions. The red coiling vessels of figure 1C represent anterior and posterior spinal arteries. Angiography did not reveal reflux into them, and their involvement in the arteriovenous shunt was not apparent. We have not observed clinical or imaging findings suggestive of congestive myelopathy. We have reflected this comment by figure legend 1C and lines 36-37 from the top of the “Case report” section. Q6: \"Right vertebral angiography shows the steal phenomenon, but is there any symptom of stealing, such as vertebra-basilar ischemia?\" A6：Thank you for this suggestion. The patient had no symptoms suggestive of vertebra-basilar ischemia (e.g., vertigo, dizziness, loss of vision, nausea, vomiting, and dysarthria). We have reflected this comment by lines 34-36 from the top of the “Case report” section. Q7: \"On treatment, the coil mass appears to protrude into the VA; if the coil protrudes into the VA, there is a risk of thrombosis and stroke. It would be better to reconstruct the VA with a stent or occlude the VA completely.\" A7：Thank you for the important advice. Follow-up angiography after 3 months of treatment showed residual protrusion of the coil mass into the VA, although the blood flow in the VA main trunk was maintained. Therefore, we agree that careful follow-up is needed. Q8: \"What do the authors believe is causing the hyperintensity signal in the anterior horn at the C6/7 level, spinal cord compression, or myelopathy due to intradural reflux of abnormal shunt flow?\" A8：Thank you for this suggestion. You have raised an important question. We consider the hyperintensity signal in the anterior horn at the C6/7 level to be caused primarily by spinal cord compression by dilated blood vessels. The level of intramedullary hyperintensity signal coincidences with the site of the most intense spinal cord compression. It is a finding that supports the mechanism of spinal cord compression. On the other hand, the intramedullary lesion appears too localized to be considered congestive myelopathy. As noted above, there is also no apparent reflux of the anterior and posterior spinal arteries, nor is there apparent regurgitation in the spinal canal. Please see lines 13-23 from the top of the “Discussion” section. Q9: \"The authors state that the damaged anterior horn leads to partial posttreatment improvement, but I think the mass effect of the coil is the cause of the limitation of the symptom improvement.\" A9: Thank you for providing these insights. Indeed, I agree with the point that the mass effect of the coils may offset the improvement in spinal cord compression due to the reduction of dilated vessels. However, we have observed improvement in clinical symptoms and imaging findings of spinal cord compression after endovascular treatment. Again, thank you for giving us the opportunity to strengthen our manuscript with your valuable comments and queries. We have worked hard to incorporate your feedback and hope that these revisions persuade you to accept our submission. Sincerely, Ryuhei Harada Department of Neurology, Tohoku University Graduate School of Medicine"
}
]
}
] | 1
|
https://f1000research.com/articles/11-546
|
https://f1000research.com/articles/10-477/v1
|
16 Jun 21
|
{
"type": "Research Article",
"title": "Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers",
"authors": [
"Andy R. Eugene"
],
"abstract": "Background. Recent in vitro studies have shown fluoxetine inhibits the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen, including variants B.1.1.7 and B.1.351, SARS-CoV-2 spike mutations (E484K, K417N, N501Y), and one retrospective clinical study reported fluoxetine exposure at a median dose of 20 mg in patients with the SARS-CoV-2 coronavirus disease 2019 (COVID-19) had a significantly lower risk of intubation and death. The aim of this study is to conduct in silico population pharmacokinetic dosing simulations to quantify the percentage of patients achieving a trough level for the effective concentration resulting in 90% inhibition (EC90) of SARS-CoV-2 as reported in Calu-3 human lung cells. Methods. Population pharmacokinetic parameter estimates for a structural one-compartment model with first-order absorption were used to simulate fluoxetine pharmacokinetic data. A population of 1,000 individuals were simulated at standard fluoxetine doses (20 mg/day, 40 mg/day, and 60 mg/day) to estimate the percentage of the patients achieving a trough plasma level for the EC90 SARS-CoV-2 inhibitory concentration for a 10 day treatment period. All analyses were conducted via statistical programming in R. Results. Standard fluoxetine antidepressant doses resulted in a range of 81% to 97% of the patient population achieving a trough target plasma concentration of 23.2 ng/ml at day 10 and translates to a lung-tissue distribution coefficient of 60-times higher (EC90 of 4.02 mM). At a dose of 40 mg per day, at least 87% of patients will reach the trough target EC90 concentration within three days.\n\nConclusion. Overall, the findings of this population pharmacokinetic dosing study corroborates in vitro and observational clinical studies reporting the first selective serotonin reuptake inhibitor fluoxetine inhibits the SARS-CoV-2 pathogen at commonly treated doses in the practice of psychiatry.",
"keywords": [
"Prozac",
"Sarafem",
"SARS- COV- 2",
"COVID-19",
"antidepressant",
"pharmacokinetics",
"dose",
"lungs"
],
"content": "Introduction\n\nThe selective serotonin reuptake inhibitor (SSRI) fluoxetine is a racemic mixture of two stereoisomers, R-fluoxetine and S-fluoxetine, and maintains regulatory approvals for a wide-array of clinical indications in the practice of psychiatry. Two recent in vitro studies showed fluoxetine inhibits replication of the Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) pathogen (Schloer et al., 2020; Zimniak et al., 2020, 2021). Specifically, Zimniak et al. reported that following a three-day incubation period of fluoxetine in Vero cells, inoculated at a multiplicity of infection (MOI) of 0.5, resulted in the median maximal effective concentration (EC50) of 387 ng/ml (1.1 μM) and further found a concentration of 800 ng/ml (2.3 μM) significantly inhibited SARS-CoV-2 replication (Zimniak et al., 2020, 2021). Similarly, Schloer et al. found that fluoxetine significantly decreases SARS-Cov-2 titers, after a 48-hour incubation period, in both African green monkey kidney epithelial Vero E6 cells (EC50 = 0.69 μM and 90% maximal effective concentration [EC90] = 1.81 μM, MOI = 0.01) and human-lung Calu-3 cells (EC50 = 0.82 μM and EC90 = 4.02 μM, MOI = 0.1) (Schloer et al., 2020). Taken together these in vitro studies prove in a dose-dependent manner that the SSRI fluoxetine inhibits the SARS-CoV-2 pathogen known to cause the worldwide pandemic, the novel coronavirus disease 2019 (COVID-19).\n\nConsidering the COVID-19 clinical symptoms affecting the lungs, fluoxetine lung concentrations would be an important factor to consider when interpreting any study results. Johnson et al. reported human-tissue concentrations of fluoxetine in airline pilots in whole-blood ranged from 0.021–1.4 μg/ml and lung concentrations ranged from 1.56 μg/ml to 51.9 μg/ml, leading to a fluoxetine distribution coefficient of 60 (Johnson, Lewis & Angier, 2007). Clinically, the fluoxetine SARS-CoV-2 in vitro findings were corroborated by Hoertel et al. who showed in a multicenter observational retrospective cohort study of patients who were treated with fluoxetine and diagnosed with COVID-19, experienced a lower risk of intubation and death (hazard ratio = 0.32; 95% confidence interval, 0.14–0.73, p = 0.007) at a median fluoxetine dose of 20 mg (standard deviation [SD] = 4.82) (Hoertel et al., 2020). In this context, the aim of this study is to conduct in silico population pharmacokinetic dosing simulations to quantify the percentage of patients expected to achieve the trough effective concentration resulting in 90% inhibition of SARS-CoV-2.\n\n\nMethods\n\nPharmacometric model estimates for differential equation parameters and respective variances for a structural one-compartment pharmacokinetic model with first-order absorption were used to simulate fluoxetine concentration-time data. Model estimates were derived from drug plasma concentrations in 25 females taking a mean dose of 29.4 mg (7.5–80 mg/day) when fluoxetine plasma levels were at steady-state due to being collected for analysis at a minimum median time of fluoxetine treatment of greater than 40 days (Tanoshima et al., 2014). The following parameters were used: volume of distribution (Vd) value of 20.5 liters (variance [ω], 1.24), clearance rate (CL) value of 13.3 liters/hour (ω = 0.052), and absorption rate (Ka) of 0.016 (1/hour) (ω = 0.231) (Tanoshima et al., 2014).\n\nThe molecular weight of fluoxetine hydrochloride is 345.8 g/mol and the reported EC50 (0.82 μM) and EC90 (4.02 μM) values from the Schloer et al. study are equivalent to EC50 = 283.6 ng/ml and EC90 = 1390.1 ng/ml, respectively. The fraction of fluoxetine bound in human plasma is 94%, which leaves only 6% of the compound being unbound in human plasma (Sommi, Crismon & Bowden, 1987). Despite fluoxetine being highly protein bound, a study by Mantinieks et al. reported in paired fluoxetine concentrations of antemortem and postmortem cases (n = 18), fluoxetine has a human whole-blood to plasma ratio of 0.8-1.0, meaning that the whole-blood concentration is actually less than plasma or has up to a 1:1 ratio (Mantinieks et al., 2020). Further, Mantinieks et al. found the postmortem (range: 0.031–1.4 mg/L) to antemortem (range: 0.018–0.51 mg/L) fluoxetine drug concentration ratio as 1.8, but was not statistically significant as the p-value >0.05 and thus the 1.8 ratio is not applicable to this study (Mantinieks et al., 2020). Therefore, this study will directly translate the simulated plasma concentrations and apply the tissue distribution coefficients from the Johnson et al. study and the original preprint version of the manuscript is updated to account for the findings from Mantinieks et al. (Johnson, Lewis & Angier, 2007; Eugene, 2020; Mantinieks et al., 2020). Lastly, for all calculations, the trough target plasma concentration is referenced from the Schloer et al. study who reported after a 48-hour incubation period in Calu-3 lung cells the 90% maximal effective concentration is 4.02 μM (Schloer et al., 2020), which is significantly higher than the EC90 in Vero E6 cells (1.81 μM) and EC50 results from Zimniak et al. and the Schloer et al. studies (Schloer et al., 2020; Zimniak et al., 2020, 2021).\n\nTo estimate the percentage of patients from a population of one thousand simulated patients who would achieve the trough target EC90 concentration, pharmacokinetic dosing of fluoxetine consisted of three dosing trials of fluoxetine: 20 mg/day, 40 mg/day, and lastly 60 mg/day.\n\nAll pharmacokinetic dosing simulations are conducted with a population of 1,000 patients using mrgsolve and pharmacokinetic parameter estimates using PKNCA in R version 3.6.3 (R Core Team, 2015). The overall R script has been adapted from a study published in Clinical Pharmacology and Therapeutics using hydroxychloroquine (Al-Kofahi et al., 2020; Eugene, 2021). Statistical results providing percentage estimates are calculated from trough concentrations of patients achieving the effective concentrations and is referenced from the Schloer et al. study reporting the EC90 value in human-lung Calu-3 cells (Schloer et al., 2020).\n\n\nResults\n\nThe EC90 target fluoxetine lung concentration is 1390.1 ng/ml [4.02 μM] and 1/60 of this concentration is the new EC90-plasma concentration of 23.2 ng/ml [0.067 μM]. The percentage of the 1,000 simulated patients are illustrated in Figure 1 (20 mg/day), Figure 2 (40 mg/day), and Figure 3 (60 mg/day) with a horizontal dashed-line throughout the pharmacokinetic dosing figures showing the required trough EC90-plasma level of 23.2 ng/ml that translates to the EC90 level of 1390.1 ng/ml [4.02 μM] in the lungs.\n\nThe shaded regions illustrate the 10th (lower) and 90th (upper) percentiles with the solid line within the shaded region representing the median fluoxetine concentration. The dashed horizontal line depicts the effective concentration resulting in 90% inhibition (EC90) of SARS-Cov-2 that will result in 60-times higher level in the lungs.\n\nThe shaded regions illustrate the 10th (lower) and 90th (upper) percentiles with the solid line within the shaded region representing the median fluoxetine concentration. The dashed horizontal line depicts the effective concentration resulting in 90% inhibition (EC90) of SARS-Cov-2 that will result in 60-times higher level in the lungs.\n\nThe shaded regions illustrate the 10th (lower) and 90th (upper) percentiles with the solid line within the shaded region representing the median fluoxetine concentration. The dashed horizontal line depicts the effective concentration resulting in 90% inhibition (EC90) of SARS-Cov-2 that will result in 60-times higher level in the lungs.\n\nFigure 1 shows the concentration-time data for a fluoxetine dose of 20 mg per day and results in the maximum plasma concentration (Cmax) with a geometric mean (geometric coefficient of variation, CV%) of 65.8 ng/mL (CV=70.2%), median time at maximum concentration (Tmax) of 220 hours (range, 49–220), area under the concentration-time curve (AUC0➔Last) of geometric mean from baseline to 10 days of 10,200 ng•hour/ml, and a half-life (t ½) – expressed as arithmetic mean (standard deviation, SD) – of 84.7 hours (SD = 181). These aforementioned pharmacokinetic results translate to 24% of the population reaching the target concentration at the end of day one and 81% of the population achieving the target trough EC90 concentration by end of day 10. Figure 2 shows at a dose of 40 mg per day, the Cmax is 132 ng/mL (CV = 68%), Tmax of 220 hours (range, 49–220), AUC0➔Last is 20,500 ng•hour/ml, and population t ½ is 81.4 (SD = 113), which is interpreted as 59% of the population achieving the EC90 trough target at day one and 93% by day 10. Moreover, Figure 3 shows a patient population treated with fluoxetine at 60 mg daily results in a Cmax of 191 ng/mL (CV = 71%), 220 hours (range, 49–232), AUC0➔Last 29,700 ng•hour/ml, and t ½ of 85.4 (SD = 209) allowing 74% of the population to reach the target trough concentration threshold on day one and 97% by day 10 of fluoxetine treatment. Table 1 provides an overview of the pharmacokinetics and pharmacodynamics with blood levels (ng/ml and μM) in plasma as well as calculated organ concentrations (whole-blood, lung, brain, heart, liver, spleen, and kidney) as well as the percent of the population achieving trough EC90 target during a treatment period of 10 days. All underlying fluoxetine pharmacokinetic study data in an.xlsx format, the one-compartment population pharmacokinetic model file in C++ format, and the R programming script are available (Eugene, 2021).\n\n\nDiscussion\n\nAccording to the United States Food and Drug Administration (FDA) Adverse Events Reporting System (FAERS) during the window period of 1982 to June 30, 2020, fluoxetine was reported to have a total of 79,929 cases, 62,948 serious cases, and 10,043 end of life cases (https://www.fda.gov/drugs/questions-and-answers-fdas-adverse-event-reporting-system-faers/fda-adverse-event-reporting-system-faers-public-dashboard). Females represented 58% of the adverse drug reactions (ADRs), males represented 27% of the ADRs, and 15% of the ADRs did not specify a gender. The most common adverse drug event reported for fluoxetine is Drug Interaction and amounts to 3,798 cases (4.75% of total). Given this information, drug interactions associated with fluoxetine are due to inhibition of the cytochrome P450 (CYP) system. Specifically, CYP2C19 and CYP2D6 may have interactions such as in patients taking tamoxifen for breast cancer by inhibiting conversion to the active endoxifen metabolite via CYP2D6 or in cases of clopidogrel in cardiology by inhibiting the conversion of clopidogrel to the active 2-oxo-clopidogrel metabolite (Spina, Trifirò & Caraci, 2012; Eugene, 2019).\n\nExtrapolating from in vitro to in vivo concentrations are dependent on intracellular versus extracellular concentrations, as well as the methodology of quantifying either whole blood versus plasma concentrations in human pharmacokinetic studies. The EC50 and EC90 target concentrations represent the extracellular fluoxetine concentrations in the SARS-CoV-2 cell culture media. As COVID-19 is known to affect the brain during active infection and in post-COVID-19 states, adequate brain concentrations would be clinically important in patients who may experience depression. Bolo et al. reported fluoxetine brain concentrations, at steady-state, using fluorine magnetic spectroscopy and showed fluoxetine concentrations were 10-times higher in the brain than in human plasma (Bolo et al., 2000). Specifically, Bolo et al. found in study participants taking oral doses (10mg, n = 1; 20 mg, n = 1; 40 mg, n = 2) with a treatment period ranging from three months to 12-months that fluoxetine human brain concentrations were 13 μM (SD = 7) versus 1.73 μM (SD = 1.00) in human plasma fluoxetine (Bolo et al., 2000). In comparison, Johnson et al. found the coefficients for tissue distribution of fluoxetine relative to whole blood was: 60 for lung, 15 for brain, 10 for heart, 38 for liver, 20 for spleen, and 9 for kidneys (Johnson, Lewis & Angier, 2007).\n\nAs patients recover from the acute COVID-19 symptoms, long-term sequelae are being documented and in one of the post-SARS-Cov-2 infection studies in young patients, 92% were found to have ongoing cardiorespiratory symptoms with organ dysfunction and impairment in the lungs (33%), heart (32%), kidneys (12%) (Dennis et al., 2020). In another post-COVID-19 syndrome study, 96% of the patients were female and experienced statistically significant exercise intolerance, dyspnea, and chest pain when compared to those not diagnosed with COVID-19 (Walsh-Messinger et al., 2020). Moreover, Walsh-Messinger et al. found patients with post-COVID-19 syndrome had higher ratings of depression subscale markers of altered sleep and thinking, but depression severity was not significantly different with patients not diagnosed with COVID-19 (Walsh-Messinger et al., 2020).\n\nDirect clinical translation of this current pharmacokinetic study corroborates with a retrospective multicenter observational study by Hoertel et al., who found a median fluoxetine dose of 20mg/day resulted in a significantly lower risk of intubation and death in a population composed of 63% women and 37% men (Hoertel et al., 2020). Comparing the Hoertel et al. and Zimniak et al. publications, Hoertel et al. found that in addition to fluoxetine, venlafaxine (median dose of 75mg/day) and escitalopram (median dose of 10mg) were also associated with a lower risk of intubation and death, however, Zimniak et al. showed that neither escitalopram nor paroxetine inhibited SARS-CoV-2 in vitro (Hoertel et al., 2020; Zimniak et al., 2020, 2021). Of note, as shown in Table 1, a 40 mg or 60 mg daily fluoxetine dose results in 90% inhibition of the SARS-CoV-2 infection due to surpassing the EC90 value of 4.02 μM as found in Calu-3 cells and the EC90 value of 1.81 μM in Vero E6 cells (Schloer et al., 2020).\n\nAntiviral properties of fluoxetine are well reported in the literature. Carpinteiro et al. reported that fluoxetine inhibits acid sphingomyelinase preventing infection of both cultured cells and human nasal epithelial cells in SARS-CoV-2, as well as in vesicular stomatitis virus pseudoviral particles presenting the SARS-CoV-2 spike protein (Carpinteiro et al., 2020). A study by Zuo et al. showed fluoxetine resulted in potent inhibition of the coxsackievirus by reducing both synthesis of viral RNA and protein (EC50 of 2.3 μM) exhibiting peak antiviral properties at 6.25 μM (Zuo et al., 2012). Bauer et al. showed, in a broad-spectrum manner, fluoxetine inhibited enterovirus (picornaviridae family) replication with the S-fluoxetine enantiomer exhibiting a 5-fold lower EC50 than the racemic mixture of R- and S-fluoxetine (Bauer et al., 2019). Further, Bauer et al. found the following fluoxetine EC50 values for the following pathogens: coxsackievirus B3 (racemate-EC50 = 2.02 μM, S-fluoxetine-EC50 = 0.42 μM), enterovirus EV-D68 (racemate-EC50 = 1.85 μM, S-fluoxetine-EC50 = 0.67 μM), and S-fluoxetine values alone for rhinovirus HRV-A2 (EC50 = 7.95 μM) and HRV-B14 (EC50 = 6.34 μM) (Bauer et al., 2019). Notably, Zimniak et al. found that individual stereoisomers, R-fluoxetine and S-fluoxetine, inhibited the SARS-CoV-2 viral load; however, in contrast, fluoxetine could not inhibit gene expression of the herpes simplex-1 virus, human herpes virus-8, rabies virus, nor the respiratory syncytial virus (Zimniak et al., 2020, 2021). Lastly, as shown in Table 1, standard fluoxetine doses are capable of achieving the aforementioned EC50s for all of the aforementioned microbes.\n\nA limitation of this study is associated with the previously validated fluoxetine pharmacometric model being in women and did not include men (Tanoshima et al., 2014). However, as shown from the aforementioned FAERS data, women represented 58% of all ADR cases overall from 1982 to 2020. A significant study strength is that a study from the University of Helsinki reported fluoxetine inhibits SARS-CoV-2 variants (B.1.1.7 and B.1.351) and the spike mutations (E484K, K417N, N501Y) (Fred et al., 2021). Overall, from a drug-safety perspective, prior to administering fluoxetine, a careful review of all patient medications and clinical status by a clinical pharmacologist physician would be recommended to avoid drug interactions due to fluoxetine’s ability to strongly inhibit CYP2C19 and CYP2D6 (Hefner, 2018). Compounds that are sensitive and moderate CYP2C19 substrates (e.g. omeprazole, diazepam, lansoprazole, rabeprazole, voriconazole) and CYP2D6 substrates (e.g. dextromethorphan, eliglustat, nebivolol, tolterodine, encainide, metoprolol, propranolol, tramadol) will have an increased total area under the concentration-time curve of ≥ 5-fold drug exposure when treated with fluoxetine (https://www.fda.gov/drugs/drug-interactions-labeling/drug-development-and-drug-interactions-table-substrates-inhibitors-and-inducers). Lastly, patients who have a pharmacogenomic profile of being a CYP2D6 Poor Metabolizer or CYP2D6 Intermediate Metabolizer should be closely monitored for potential fluoxetine side-effects; but they may also have a higher rate of achieving the target trough EC90 concentration at a 20 mg daily fluoxetine dose relative to CYP2D6 Normal (Extensive) Metabolizers.\n\n\nConclusions\n\nThis study investigated fluoxetine pharmacokinetics and human organ tissue distribution which confirmed that previously published median effective concentrations and specifically the EC90 fluoxetine value inhibiting SARS-CoV-2 in Calu-3 human lung cells are achievable using standard fluoxetine doses (20mg/day, 40mg/day, and 60mg/day) and also corroborates findings from a retrospective clinical study showing fluoxetine exposure was associated with reduced risk of intubation and death. Overall, assuming patients are not treated with medications that result in drug-drug interactions with fluoxetine, a dose of 40 mg per day of fluoxetine will likely be most effective with inhibiting the SARS-CoV-2 viral titers with 59% of the population achieving the trough EC90 target on day one, 92% by day seven, and 93% of patient population achieving the trough target EC90 concentration to inhibit the SARS-CoV-2 within 10 days.\n\n\nData availability\n\nOpen Science Framework: Underlying data for ‘Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers’, https://doi.org/10.17605/OSF.IO/R7ND6 (Eugene, 2021).\n\nThis project contains the following underlying data:\n\n• Data File 1: fluoxetine_20mg_PO_QAM.xlsx\n\n• Data File 2: fluoxetine_40mg_PO_QAM.xlsx\n\n• Data File 3: fluoxetine_60mg_PO_QAM.xlsx\n\nOpen Science Framework: Software for ‘Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers’, https://doi.org/10.17605/OSF.IO/R7ND6 (Eugene, 2021).\n\nThis project contains the following software:\n\n• poppk_fluoxetine_sars_cov2_inhibition.cpp\n\n• Fluoxetine_pharmacokinetic_sars_cov2_simulation_script.R\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThis author acknowledges the researchers who conducted the in vitro studies, as well as the retrospective clinical study that encouraged this population pharmacokinetic dosing study with fluoxetine to be realized.\n\n\nReferences\n\nAl-Kofahi M, Jacobson P, Boulware DR, et al.: Finding the Dose for Hydroxychloroquine Prophylaxis for COVID-19: The Desperate Search for Effectiveness. Clin Pharmacol Ther. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBauer L, Manganaro R, Zonsics B, et al.: Fluoxetine Inhibits Enterovirus Replication by Targeting the Viral 2C Protein in a Stereospecific Manner. ACS Infect Dis. 2019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBolo NR, Hodé Y, Nédélec JF, et al.: Brain pharmacokinetics and tissue distribution in vivo of fluvoxamine and fluoxetine by fluorine magnetic resonance spectroscopy. Neuropsychopharmacology. 2000. PubMed Abstract | Publisher Full Text\n\nCarpinteiro A, Edwards MJ, Hoffmann M, et al.: Pharmacological inhibition of acid sphingomyelinase prevents uptake of SARS-CoV-2 by epithelial cells. Cell Rep Med. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDennis A, Wamil M, Kapur S, et al.: Multi-organ impairment in low-risk individuals with long COVID. medRxiv :2020.10.14.20212555. 2020. Publisher Full Text\n\nEugene AR: Optimizing drug selection in psychopharmacology based on 40 significant CYP2C19- And CYP2D6-biased adverse drug reactions of selective serotonin reuptake inhibitors. PeerJ . 2019; 2019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEugene AR: Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers. medRxiv. 2020. Publisher Full Text\n\nEugene AR: Data for Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers. Open Science Framework. 2021. Publisher Full Text\n\nFred SM, Kuivanen S, Ugurlu H, et al.: Antidepressant and antipsychotic drugs reduce viral infection by SARS-CoV-2 and fluoxetine show antiviral activity against the novel variants in vitro. bioRxiv:2021.03.22.436379. 2021. Publisher Full Text\n\nHefner G: Consensus guidelines for therapeutic drug monitoring in neuropsychopharmacology: Update 2017. Psychopharmakotherapie. 2018. PubMed Abstract | Publisher Full Text\n\nHoertel N, Sanchez Rico M, Vernet R, et al.: Association between SSRI Antidepressant Use and Reduced Risk of Intubation or Death in Hospitalized Patients with Coronavirus Disease 2019: a Multicenter Retrospective Observational Study. medRxiv . 2020. Publisher Full Text\n\nJohnson RD, Lewis RJ, Angier MK: The distribution of fluoxetine in human fluids and tissues. J Anal Toxicol. 2007. PubMed Abstract | Publisher Full Text\n\nMantinieks D, Gerostamoulos D, Glowacki L, et al.: Postmortem Drug Redistribution: A Compilation of Postmortem/Antemortem Drug Concentration Ratios. J Anal Toxicol. 2020. PubMed Abstract | Publisher Full Text\n\nR Core Team: R: A Language and Environment for Statistical Computing.2015.\n\nSchloer S, Brunotte L, Goretzko J, et al.: Targeting the endolysosomal host-SARS-CoV-2 interface by clinically licensed functional inhibitors of acid sphingomyelinase (FIASMA) including the antidepressant fluoxetine. Emerg Microbes Infect. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSommi RW, Crismon ML, Bowden CL: Fluoxetine: A Serotonin-specific, Second-generation Antidepressant. Pharmacotherapy: J Human Pharmacol Drug Therapy. 1987. PubMed Abstract | Publisher Full Text\n\nSpina E, Trifirò G, Caraci F: Clinically significant drug interactions with newer antidepressants. CNS Drugs. 2012. PubMed Abstract | Publisher Full Text\n\nTanoshima R, Bournissen FGA, Tanigawara Y, et al.: Population PK modelling and simulation based on fluoxetine and norfluoxetine concentrations in milk: a milk concentration-based prediction model. Br J Clin Pharmacol. 2014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalsh-Messinger J, Manis H, Vrabec A, et al.: The Kids Are Not Alright: A Preliminary Report of Post-COVID Syndrome in University Students. medRxiv:2020.11.24.20238261. 2020. Publisher Full Text\n\nZimniak M, Kirschner L, Hilpert H, et al.: The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2 in human lung tissue. Sci Rep. 2021; 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZimniak M, Kirschner L, Hilpert H, et al.: The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2. bioRxiv. 2020. Publisher Full Text\n\nZuo J, Quinn KK, Kye S, et al.: Fluoxetine is a potent inhibitor of coxsackievirus replication. Antimicrob Agents Chemother. 2012. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "87881",
"date": "21 Jun 2021",
"name": "Nicolas Hoertel",
"expertise": [
"Reviewer Expertise Psychiatry",
"antidepressants",
"methodology",
"biostatistics",
"epidemiology",
"sphingomyelinase",
"COVID-19."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a review of the manuscript \"Fluoxetine pharmacokinetics and tissue distribution suggest a possible role in reducing SARS-CoV-2 titers\" submitted for publication in F1000Research. This is a very interesting and important study, which addresses a timely and important question – in a context of a growing number of preclinical and clinical studies showing a potential efficacy of certain antidepressants, and particularly fluoxetine, in COVID-19, what dose of fluoxetine should be optimally prescribed in clinical trials to ensure a maximum of patients achieve the effective concentration resulting in 90% inhibition (EC90) of SARS-CoV-2 as reported in Calu-3 human lung cells. On a more general, and potentially more innovative front, it is one of a small (but quickly increasing) number of studies contributing to this topic and the first study to the reviewer’s knowledge addressing this specific pharmacokinetic issue, which is an important area of inquiry with major implications in this context of pandemic. There is much to like about this manuscript. The results are presented clearly, the methods are sound, the discussion follows well from it, and the manuscript is very well written. Below are several points that would strengthen the submission:\n\nTitle:\nA minor suggestion would be a modification of the title to increase the interest to this important study, such as “Fluoxetine pharmacokinetics and tissue distribution suggest a possible therapeutic role in COVID-19 at usual antidepressant dose”.\n\nIntroduction:\nThe introduction section should be updated and include a description of results from recent studies focused on the association between antidepressant use and the course of COVID-19, which would be very helpful to readers to understand the clinical context of this study and why this study (and its results) are important. In addition to the medRxiv one, the reference to the published article of Hoertel N et al. should be cited (Hoertel N et al. (20211)). This association/potential effect of certain antidepressants in COVID-19 has been confirmed in several other observational studies (Diez-Quevedo et al. (20212), Hoertel et al. (20213), Hoertel et al. (20214)), two clinical trials (1 RCT and 1 open-label study) with the antidepressant fluvoxamine (which is, like fluoxetine, a functional inhibitor of sphingomyelinase acid and a S1R agonist) (Lenze et al. (20205), Seftel & Boulware (20216)), and other preclinical studies (Dechaumes et al. (20217), Fred et al. (20218)). Results from all those studies, increasing the interest in the present submission, should be recognized and briefly summarized in the Introduction.\n\nAs evoked in the discussion, potential underlying mechanisms include antiviral effect of certain antidepressants, and particularly fluoxetine, through the inhibition of the acid sphingomyelinase/ceramide system, which may play a central role in COVID-19, as suggested by preclinical studies (Carpinteiro et al. (20209), and Carpinteiro et al. (202110)) and observational studies (Hoertel N et al. (20213), Darquennes G et al. (202111), Hoertel et al. (20214)), as well as anti-inflammatory properties through sigma-1-receptor agonist effect of certain antidepressants, and particularly fluoxetine and fluvoxamine (Köhler CA et al. (201812), Rosen D et al. (201913), Sukhatme VP et al. (202114), Roumestan C et al. (200715)). Moreover, a recent study (Marín-Corral et al. (202116)) showed that ceramide plasma concentration is associated with inflammatory markers and clinical outcomes in COVID-19 patients. I think that results from all those studies should also be recognized and shortly summarized in the Introduction.\n\nThe abstract might include some of these points listed above.\n\nResults:\nImportantly, results from that study can help guide the choice of the right dose to use in COVID-19 clinical trials. I would strongly recommend the author to present in the result section as well as in the abstract (for main findings) for each following dose: 20 mg/d, 30mg/d (which is also interesting for clinical tolerability purpose), 40 mg/d and 60 mg/d the percentage of patients reaching a) EC90 and b) EC50 at (i) 1 day, (ii) 2 days, and (ii) 3 days. In addition, given that 40 mg/d might lead to increased risk of mild side effects among older adults and that at the same time reaching the efficient dose as fast as possible is desirable given the potential antiviral properties of fluoxetine, would a loading dose of 30 mg or 40 mg the first or two first days, followed by a dose of 20 mg/day, perform better than only taking 20 mg/d?\n\nFinally, is there a way to ensure that at no point of the 10 day treatment course, no patient (typically older adults) will reach a toxic plasma dose with the different scenarios, as I think 40 mg/d is the maximum recommended dose in the elderly population? Even if the reviewer recognizes that it may represent a substantial additional amount of work, these detailed results will certainly be of great help to clinicians to balance the risks associated for each dose and the potential benefits, and help them design ideal clinical trial.\n\nWith the different scenarios, at the end of the 10-day treatment, how long would it take to have a substantial decrease in the fluoxetine plasma concentration (and its metabolite norfluoxetine)? This information would give an idea of the duration of potential protection of the treatment against SARS-CoV-2 once stopped and of the required duration of medical follow-up.\n\nConclusion:\nFinally, with these different dose scenarios, what recommendation(s) of dose would do the author for a clinical trial including fluoxetine for COVID-19? Would it be desirable to do a loading dose then decrease to the standard 20 mg/d dose which is known to be very well tolerated in older adults? Or keeping 30 mg/d or 40 mg/d throughout the trial would be the best choice?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "87690",
"date": "23 Jun 2021",
"name": "Eero Castren",
"expertise": [
"Reviewer Expertise Neuropharmacology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAndy Eugene has written an interesting paper on a very timely topic. Preclinical as well as limited clinical data support the idea that some antidepressants and related compounds may protect cells from SARS-CoV2 infection, but it has been unclear whether concentrations that are found in cell culture studies to be inhibitory are really achieved in clinical treatments. It is unfortunate that there is only limited amount of high-quality data on the tissue concentrations and distribution of fluoxetine in human tissues, but Eugene has taken advantage of the data that is available to model fluoxetine pharmacokinetics in human lung tissue. His results suggest that sufficiently high lung tissue concentrations are achieved within a 10 day treatment period in majority of patients with a standard 20 mg/day dosing, and with higher doses, the trough concentration is achieved within the first days of treatment. The simulations appear properly conducted and the manuscript is well written. I have a few issues that might improve the manuscript further.\n\nThe conclusions about how fast trough concentrations are achieved is based on the assumption that fluoxetine immediately distributes to lung tissue at the estimated 60 fold concentration compared to plasma levels. However, there is some (although clearly incomplete) information that fluoxetine may accumulate into tissues over time. Rasenick and colleagues have found that certain antidepressants accumulate in lipid rafts in vitro over several days of exposure (Erb et al. 20161) For human brain, Karson et al. have found that, using spectroscopy, fluoxetine/norfluoxetine is not detectable in human brain at about 1 week, but at about 2-3 weeks of treatment, concentrations of several micromolar can be assayed (Karson et al. (19932)) indicating that fluoxetine accumulates in brain over time. If the same is true for lung tissue, the 60-fold concentrations may not be reached in lung tissues as quickly as estimated here. Although paucity of information prevents any proper estimations, I think it would be important to discuss this issue in the discussion section.\n\nThe author should be complemented for indicating in many places in the manuscript fluoxetine concentrations in both ng/ml and in molar units, however, this is not done systematically. It would be very helpful to, wherever possible, indicate both units. In the figures, it may not be feasible to have double set of units in the Y-axis, I would prefer molar units, but if the author prefers ng/ml, that is not a major problem.\n\nThe author may want to mention that a clinical phase 3 trial evaluating the effect of fluvoxamine vs. placebo is ongoing and should be completed by September this year.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-477
|
https://f1000research.com/articles/8-1587/v1
|
04 Sep 19
|
{
"type": "Software Tool Article",
"title": "Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads",
"authors": [
"Andrian Yang",
"Joshua Y. S. Tang",
"Michael Troup",
"Joshua W. K. Ho",
"Andrian Yang",
"Joshua Y. S. Tang",
"Michael Troup"
],
"abstract": "Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads. We showed that Scavenger could recover unaligned reads in a range of simulated and real RNA-seq datasets, including single-cell RNA-seq data. We found that recovered reads tend to contain more genetic variants with respect to the reference genome compared to previously aligned reads, indicating that divergence between personal and reference genomes plays a role in the false-negative non-alignment problem. Even when the number of recovered reads is relatively small compared to the total number of reads, the addition of these recovered reads can impact downstream analyses, especially in terms of estimating the expression and differential expression of lowly expressed genes, such as pseudogenes.",
"keywords": [
"RNA-seq",
"Read alignment",
"Unaligned read",
"Read recovery"
],
"content": "Introduction\n\nRead alignment is the process of mapping high-throughput sequencing reads against a reference genome or transcriptome to identify the locations from which the reads originate. This step is typically one of the first steps in the analysis of RNA sequencing (RNA-seq) data prior to downstream analyses such as variant calling and gene expression analysis. There have been a number of published tools which have been developed to perform RNA-seq alignment, such as HISAT21, STAR2 Subread3, CRAC4, MapSplice25 and GSNAP6. More recently, new alignment-free tools have been developed specifically for gene expression analysis which skips the alignment of reads to the reference and instead performs pseudoalignment. However, these alignment-free tools are only applicable to specific types of analyses and have limitations compared to traditional alignment methods7. The correctness of alignment programs are crucial to the accuracy of the downstream analyses. Unfortunately, previous studies have shown that while these tools have low false positive rates, they do not necessarily have low false negative rates8,9. This means that while many of the reads were likely to be correctly aligned, there are still many incorrectly unaligned reads which should have been aligned. These incorrectly unaligned reads, or false negative non-alignments, adversely affect the accuracy of the alignment produced and can also affect the result of downstream analyses, such as variant calling, indel (insertion-deletion) detection and gene fusion detection9.\n\nThere are a number of factors which contribute to the false negative non-alignment problem. One such factor is the type of algorithm utilised in the alignment tool. In order to efficiently perform alignment against a typically large reference genome in an acceptable amount of time, and to account for splicing events inherent in RNA-sequencing data, many alignment tools use heuristic-based matching of seed sequences generated from read sequences. Due to the typically short length of a seed sequence and the existence of repetitive regions within the genome, there may be multiple locations assigned to a given read which results in the alignment tool excluding the read due to ambiguity – a problem known as multi-mapping reads. Another factor which causes false negative non-alignment problems is the divergence between the reference genome and the personal genome of the organism being sequenced. The reference genome is typically constructed from a small number of samples and thus will only represent a limited degree of the organism’s diversity. Alignment of reads to the reference genome will thus be imperfect due to natural variation present in an individual organism. While alignment tools do take into account the variability between the reference genome and an individual’s genome by allowing for mismatches, insertions and deletions during alignment, they are unable to handle a substantial degree of genetic variation, such as hyper-edited sites, gene fusion and trans-splicing.\n\nCorrecting for a false negative non-alignment problem is much more difficult compared to correcting false positive reads. For false positive reads, there are a number of strategies which can be employed to help filter these type of reads, such as by removing lower quality alignments, removing reads with multiple alignment locations and re-aligning reads with a more specific alignment tool. Recovering false negative reads, on the other hand, is not as straightforward as it is not possible to identify their putative alignment region in the genome. One possible strategy for solving the false negative non-alignment problem is to tune the parameters used for alignment in order to maximise the amount of reads aligned, such as by increasing the threshold for multi-mapping reads and/or increasing the number of mismatches allowed. However, this approach is limited as there is no ground truth in real data to help with optimisation, and increasing the number of reads aligned will also result in an increase in the number of false positive reads. Another strategy for solving the false-negative non-alignment problem is by incorporating variation information during alignment, in the form of utilising alternate loci sequences within the reference genome10 or integration of a single nucleotide polymorphism database to the reference1, to help minimise the effect of divergence of the personal genome compared to the reference genome. This approach is also limited as it requires existing variation information, which may not be available in non-model organisms.\n\nWe have recently applied the idea of Metamorphic Testing – a software testing technique designed for the situation where there is an absence of an oracle (a method to verify the correctness of any input) – for performing software testing on the STAR sequence aligner11. Metamorphic testing involves multiple executions of the program to be tested with differing inputs, constructed based on a set of relationships (Metamorphic relations - MR), and checking that the outputs produced satisfy the relationships12,13. In our previous study11, we developed an MR to test the realignability of previously aligned reads in the presence of irrelevant ’control’ chromosomes constructed from previously unaligned reads. We discovered that a non-trivial amount of reads that were previously aligned to the reference genome were now aligned to the control chromosomes consisting of reads which were unable to be aligned to the reference. Further investigation indicated that some of the unaligned reads have high similarity to the aligned reads, indicating the possibility of these reads being false negative non-alignments.\n\nIn this paper, we aim to tackle the problem of false-negative non-alignments by taking inspiration from our previous work on metamorphic testing. We have developed Scavenger, a pipeline designed to recover incorrectly unaligned reads by exploiting information from reads which are successfully aligned. We applied the Scavenger pipeline on a number of simulated and actual RNA-seq datasets, including both bulk (normal) and single-cell RNA-seq datasets, and demonstrated the ability of Scavenger in recovering unaligned reads from these datasets. We then analysed the impact of adding these recovered reads on downstream analyses, in particular gene expression analysis, and discovered that lowly expressed genes, in particular genes of the pseudogenes category, are more affected by the false-negative non-alignment problem. We also verified that the divergence between the personal genome and the reference genome is a contributing factor to the false-negative non-alignment problem and showed that Scavenger is able to recover reads which are unaligned due to higher degree of variability within the reads sequence.\n\n\nMethods\n\nScavenger is a python-based pipeline designed to recover unaligned reads by utilising information from aligned reads. The pipeline takes in sequencing reads in FASTQ format as the input, along with a reference genome sequence in FASTA format and a corresponding index for the alignment tool built using the reference genome. There are 4 main steps in the Scavenger pipeline - source execution of alignment tool, follow-up execution using aligned reads as input and unaligned reads as index, consensus filtering of follow-up execution result to obtain putative alignment location, and re-alignment of unaligned reads to the reference genome (Figure 1). The unaligned reads which are able to be successfully re-aligned back to the genome are then re-written back to the alignment result from the source execution.\n\nScavenger first aligns sequencing reads against the reference genome using the STAR alignment tool in the source execution step. Scavenger then extracts both the aligned and unaligned reads from the source alignment result and creates a sequencing reads file based on the aligned reads and an artificial genome file containing chromosomes built using sequences of unaligned reads. The sequences of aligned reads are then aligned to the artificial genomes using the same alignment tool from the source execution (STAR) in the follow-up execution steps to find aligned reads which have similar sequences to unaligned reads. Next, consensus filtering is performed to select putative sites for re-aligment based on where the majority of aligned reads originate from in the reference genome. Finally, re-alignment is performed for unaligned reads which pass consensus filtering and the source alignment result is updated based on the result of re-alignment.\n\nThe first step of the Scavenger pipeline is the source execution where sequencing reads are aligned to the reference genome using a sequence alignment program. The alignment program used must satisfy the three properties which are required to validate the metamorphic relation underlying the read recovery pipeline - deterministic alignment, realignability of mapped reads, and non-realignability of unmapped reads. Currently, STAR is utilised for aligning RNA sequencing reads in the Scavenger pipeline as it has been previously evaluated as being a reliable general-purpose RNA-seq aligner, with good default performance8, as well as satisfying the three properties above11. The source execution step can be skipped if the user has previously performed alignment of sequencing reads by passing in the alignment file produced in either SAM or BAM format as input to the Scavenger pipeline.\n\nIn the follow-up execution step, both aligned and unaligned reads are first extracted from the alignment file produced during source execution. For reads which have been successfully and uniquely aligned, a sequencing reads file (in FASTQ format) is created using the reads’ sequence and qualities retrieved from the alignment records. In the case of reads which did not align to the reference genome, reads with identical sequences are first grouped together in order to minimise computational complexity and to reduce the potential location for alignment. The unique unaligned sequences are then extended with spacer sequences (sequence of N nucleotides) in order to form sequence bins of equal length and to ensure that aligned reads do not align between two unaligned sequences. These sequence bins are concatenated into artificial chromosomes and stored into a new temporary genome file. Depending on the alignment program utilised, a new index will then need to be created based on the temporary genome containing the artificial chromosomes prior to alignment. Finally, sequencing reads of previously aligned reads are aligned to the temporary genome containing unaligned read sequences using the alignment tool used in source execution. In the current Scavenger pipeline, STAR is again utilised in the follow-up execution with a number of extra parameters in order to disable spliced alignment to ensure that input reads only align to one unaligned read sequence and to remove the restriction of the number of locations (i.e. unaligned read sequence) that the input reads can align to in the temporary genome.\n\nThe next step of the Scavenger pipeline is consensus filtering. Reads which align during the follow-up execution step are extracted from the alignment file produced from the previous step to obtain information regarding similarity between reads aligned during source execution and reads which did not align during source execution. Each unaligned sequence may have alignments to multiple aligned reads from the source execution. As these aligned reads may be aligned to different regions in the reference genome, consensus filtering is performed to select putative sites for re-alignment. For each unaligned sequence, intervals are created based on the reference genome location of previously aligned reads that align to the unaligned sequence. Overlapping intervals are then merged to form longer intervals to both reduce the number of putative sites and to increase the support for the interval to be selected as a putative site. An interval is considered as being a putative site if there is more than one read within the interval and the level of support for the interval (i.e. the number of aligned reads that fall within the interval) is greater than the consensus threshold, which is set to 60% of the number of previously aligned reads that align to the unaligned sequence by default. During this step, there is also an optional filtering criteria that can be utilised to remove unaligned sequences which likely originate from a low complexity region or tandem repeat region. The filtering method is based on the tandem repeat detection step used in the ROP tool14, which uses MegaBLAST15 to align reads against a repeat sequence database, such as RepBase16.\n\nThe final step is the re-alignment step where unaligned sequences which pass the filtering steps are re-aligned to the reference genome using the putative location obtained from reads aligned during source execution as a guide. For each unaligned sequence, the reference genome sequence around the putative location (extended 100 base pairs at both the start and the end of the putative location) is extracted and stored as the new genome for aligning the unaligned sequence. Alignment of the unaligned sequence is then performed against the new genome using either MegaBLAST or STAR depending on whether the putative location of the unaligned sequence originated from unspliced alignment or from spliced alignment during the source execution, respectively. MegaBLAST is utilised for unspliced alignment due to its high sensitivity, though a strict parameter of 64% overlap and 85% query identity (which replicates the result of STAR alignment) is also utilised to reduce the false positive recovery of sequences. Unaligned sequences which are successfully and uniquely aligned back to the reference genome are then added back to the alignment file of the source execution by modifying the alignment records of previously unaligned reads whose sequence matches the recovered unaligned sequence.\n\nBoth the consensus and re-alignment steps of the Scavenger pipeline are computationally expensive due to the potentially large number of unaligned reads to be processed. However, the processing of the inputs are independent to each other thus allowing for parallelisation of processing unaligned reads in order to reduce the overall runtime of the pipeline. Scavenger takes advantage of Python’s built-in multiprocessing library in order to parallelise the consensus and re-alignment steps across the available CPU cores of the machine.\n\nTo enhance the scalability of Scavenger, a framework has been provided to enable parallel computation of a read recovery session on cloud computing resources. Cloud computing enables convenient, on-demand network access to a shared pool of configurable computing resources17. Central to the model of cloud computing is the virtualisation of computing resources to enable sharing of pooled resources. These resources can be commissioned and decommissioned as the user requires. Scavenger has a framework that employs the resources offered by the cloud provider Amazon Web Services (AWS). The cloud provider enables the user, using their own account credentials, to create a number of computing \"instances\", which are the virtual machines upon which the user can perform their computational workload. In the case of AWS, such resources are termed \"EC2 instances\". An instance typically can be provisioned within minutes of the user request, and the user is charged by the hour. Some cloud providers, such as AWS, offer reduced price \"spot\" instances at a greatly reduced price, such that the user places a \"bid\" for a spot instance on the proviso that the instance will be terminated should the current market price for the instance exceed the initial bid price. To minimise the cost for users, Scavenger utilises AWS spot instances. The cloud computing feature of Scavenger, after initial configuration on the user’s controlling computing resource, uses the AWS EC2 cloud instances to perform the various steps of read recovery, and also uses AWS cloud storage (S3) to store test data and results. The Scavenger cloud processing feature co-ordinates all interactions with the cloud resources, with logging information stored both locally and on the cloud. The user can elect to have a large job to be spread among a number of cloud instances, with Scavenger creating the instances and distributing the work load evenly amongst the instances. The cloud computing feature of Scavenger is optional, and the user can elect to use their own computing resources if desired.\n\nScavenger is written in Python 3 and is designed primarily as a command line program for Linux operating system. The runtime and memory requirement of Scavenger depends on the size of the sequencing reads input and the aligner used, with 30GB being the minimum amount of RAM required for alignment and recovery of reads from human dataset using STAR aligner. The Scavenger pipeline is available from Scavenger GitHub repository (https://github.com/VCCRI/Scavenger), with archived source code available from Zenodo18.\n\nThree different types of RNA-seq datasets – simulated, normal (bulk) and single-cell – were utilised to evaluate the Scavenger pipeline. The simulated datasets were obtained from a previous study8 which generated 3 sets of simulated RNA-seq datasets from the hg19 reference genome using BEERS simulator19 with varying parameters to emulate different level of dataset complexity. As the simulated datasets were formatted in FASTA format, high quality scores were added to each of the simulated reads to produce corresponding FASTQ files. These files were then input into Scavenger for both source alignment and read recovery with either STAR v2.5.3a or Subread v1.6.0 as the alignment tool. The GRCh37.p13 reference genome was obtained from GENCODE20 and modified to contain reference chromosomes only, and used to create the indexes for each alignment tool. For STAR specifically, the annotation file was extracted from a previous study8 and utilised in index creation to help increase the accuracy for alignment across splice junctions. In the evaluation of alignment results for simulated datasets, we used the analysis script that was used in the previous study8 to analyse the correctness of the alignment results.\n\nThe normal and single-cell RNA-seq datasets were obtained from publicly available human and mouse datasets which were deposited to the NCBI Sequence Read Archive21 (Table 1). Pre-processing of the datasets was performed using Trimmomatic v0.36 to remove low quality sequence and short reads. The pre-processed datasets were then analysed by Scavenger using STAR v2.5.3a as the alignment tool in the source execution and for realignment of spliced reads, together with BLAST v2.6.0 for re-alignment of unspliced reads. Indexes used for aligning of both human and mouse datasets were generated from GRCh38 and GRCm38 reference genomes respectively, which were obtained from GENCODE together with the corresponding annotation files (version 27 for human and version 15 for mouse). As before, annotation was used to augment the index to increase accuracy for alignment. The Repbase database16 was also utilised to remove low complexity reads and reads from repetitive regions. For human datasets, the simple, humrep and humsub sequence files from Repbase were concatenated and used to create a BLAST database. Reads that passed consensus were aligned to this database and the aligned reads that have a minimum of 90% sequence identity and 80% sequence coverage were removed for further processing in Scavenger. A similar approach was used for the mouse datasets, but the simple and mousub sequence files were used instead.\n\nThe datasets are divided into three sections: 1. Datasets from selected non-reference mouse strain, 2. Normal (bulk) RNA-seq dataset from either human or mouse, and 3. Single-cell RNA-seq dataset from mouse.\n\nFor mouse strain analysis, strain-specific VCF files for non-reference mouse strains containing SNPs derived against the reference C57BL/6J mouse genome were downloaded from the Mouse Genome Project (MGP)22. The calculation of the number of SNPs found within aligned reads was performed using the intersect tool from Bedtools v2.27.123, while statistical analysis were performed using the independent t-test function from SciPy library v1.2.1 (Python v3.6.4).\n\nFor running the alignment using STAR, the following command is used: STAR –runThreadN <threads> <aligner_extra_args> –genomeDir <genome_index> –readFilesIn <read_files> –outFileNamePrefix <output_prefix>. As for running the alignment using subread, the following command is used: subread-align -T <threads> -t 0 <aligner_extra_args> -i <genome_index> <read_files> -o <output_file> <bam_option>. And lastly, for running the alignment using BLAST, the follow command is used: blastn -query unmapped_read -subject target_genome -task megablast -perc_identity <identity> -qcov_hsp_perc <coverage> -outfmt \"17 SQ SR\" -out <sam_output> -parse_deflines. During follow-up alignment using STAR, the following parameters are additionally used: –outFilterMultimapNmax <num_reads> –alignIntronMax 1 –seedSearchStartLmax 30.\n\n\nResults\n\nTo evaluate the ability of the Scavenger pipeline to recover false-negative non-aligned reads, we first tested Scavenger using previously published human simulated data. The varying level of complexity of the simulated datasets represents the degree of divergence between the sequencing reads generated compared to the reference genome, ranging from low polymorphism and error rate (T1), moderate polymorphism and error rate (T2) and high polymorphism and error rate (T3). The results of the source execution of STAR with default parameters are consistent with the previously published result, with >99% of reads being aligned in both T1 and T2 and >90% of reads being aligned in T3 (Table 2). After running the Scavenger pipeline, we were able to recover between 4-30% of the previously unaligned reads in the three datasets, resulting in an increase of aligned reads ranging from ~1,500 to ~160,000. The majority of reads recovered by Scavenger are aligned in the correct position, with 79.4% of reads being correctly recovered in T1 and >98% of reads being correctly recovered in T2 and T3.\n\nThe result shown is an average from 3 samples.\n\nThe difference in the number of aligned reads between the three datasets can be explained by the degree of divergence between the sequencing reads and the reference genome; and the limitation of the alignment tool in aligning reads which display a high degree of polymorphism. The simulated sequencing reads in both T1 and T2 have high homology to the reference genome due to the lower degree of polymorphism and error rate introduced meaning that the majority of these reads will be accurately mapped to the reference genome with a very small number of mismatches during alignment. In contrast, the sequencing reads in T3 – with the higher polymorphism and error rate – have a much higher degree of divergence compared to the reference genome thus resulting in more mismatches during alignment and therefore causing it to fail to be aligned. The Scavenger pipeline is able to recover more reads in T2 and T3 compared to T1 due to the greater number of aligned reads that contain mutations within the sequence. During follow up execution, Scavenger exploits the fact that these aligned reads will have closer similarity to the unaligned reads, which will also contains mutations, therefore resulting in the alignment of the aligned reads to the unaligned reads to obtain the putative location for the unaligned reads for recovery.\n\nAnother method to solve the false-negative non-alignment problem is to adjust the parameters of the alignment tool utilised in order to allow alignment of reads with a higher degree of polymorphism. As has been shown previously, alignment of the simulated datasets using STAR with optimised parameters results in >99.2% of the reads being aligned, with T1 and T2 reaching nearly 99.9% of reads being aligned (Table 3). The Scavenger pipeline is unable to obtain the high degree of alignment achieved with parameter optimisation due to limitations in Scavenger’s approach to recover reads. Since Scavenger utilises information from aligned reads to find the putative location of unaligned reads for recovery, it is not possible to recover any unaligned reads from regions which have no read alignments. As such, the reads that the Scavenger pipeline is able to recover are reads from regions which already have alignment. This is unlike parameter optimisation, which allows for alignment with a higher threshold of mismatches in any region irrespective of whether there was alignment in the region. This observation can be seen in the high degree of overlap (>96.5%) of the reads recovered by the Scavenger pipeline compared to the reads recovered by optimised parameters. The Scavenger pipeline is still able to recover some reads which are unaligned with optimised parameters, particularly in T3 where Scavenger recovered ~9.75% of previously unaligned reads. Unlike Scavenger recovery with default parameters, the majority of recovered reads after alignment with optimised parameters are incorrectly aligned in both the T1 and T2 datasets. Given the very high degree of alignment in these lower complexity datasets, it is likely that the unaligned reads are reads which can align to many locations in the genome and thus correctly recovering these reads is very difficult and error prone. These results indicate that parameter optimisation provides a solution to the false-negative non-alignment problem, performing better than Scavenger. However, given that performing parameter optimisation is not trivial due to lack of ground truth in real datasets, these results also show that Scavenger can be utilised as an alternative to help recover false-negative non-aligned reads.\n\nThe result shown is an average from 3 samples.\n\nWe also performed a comparison of the Scavenger pipeline against a recently published tool, Read Origin Protocol (ROP) v1.0.8, which is primarily designed to identify the origin of unaligned reads14. The ROP tool consists of 6 steps, with each step designed to identify different causes for unaligned reads: reads with low quality, lost human reads, reads from repeat sequences, non-colinear RNA reads, reads from V(D)J recombination and reads belonging to microbial communities. The result of running ROP on the simulated dataset shows that ROP is able to identify an average of ~29,000 reads in the T1 and T2 datasets, and ~58,500 reads in T3 dataset (Table 4). In particular, the majority of reads in the T1 and T2 dataset are correctly identified as lost human reads, while the majority of reads in T3 dataset are incorrectly identified as immune reads. Checking the correctness of ROP identified reads is not straightforward given that most steps within ROP does not produce alignment information. Thus, correctness testing was performed only on the genome-based alignment information produced during the lost reads steps. The result of the correctness testing shows that >92.6% of the reads identified by ROP are incorrectly aligned (Table 5).\n\nThe result shown is an average from 3 samples.\n\nThe result shown is an average from 3 samples.\n\nOne factor which may affect the false-negative non-alignment problem is the divergence of sequences between the reference genome and personal genome which results in alignment tools being unable to properly align the reads due to the higher number of mismatches. To evaluate the ability of Scavenger in recovering these false-negative non-aligned reads which arise due to divergence of the personal genome, an experiment was devised where reads from non-reference inbred laboratory mouse strains were aligned to the reference C57BL/6J mouse genome to imitate alignment of reads from the personal genome against the reference genome. Multiple nonreference mouse strains – 129S1/SvImJ, A/J, CAST/EiJ, DBA/2J and NOD/ShiLtJ – were utilised as the genomes of these strains have previously been characterised by the Mouse Genome Project (MGP), with variations from each strain identified relative to the reference mouse genome. We collected 80 publicly available RNA-seq samples from the selected mouse strains, with each strain having a minimum of 13 samples from at least 3 different projects with varying characteristics, and performed alignment of these samples against the reference genome using STAR with default parameters. The result of the source alignments shows that there is generally a high degree of mappability of the reads, ranging from 82.2% up to 98.1%. After recovery with Scavenger, we were able to re-align ~4.75% of unaligned reads in the source execution, corresponding to an increase in the number of aligned reads ranging from 17,000 to 396,000 reads (Table 6).\n\nThe result shown is an average of all samples per accession ID.\n\nFurther analysis was performed to evaluate the hypothesis that reads recovered by Scavenger have a higher degree of polymorphism due to the divergence between the ’personal’ non-reference mouse strain genome against the reference genome. We randomly selected 1,000 unspliced reads which are aligned in the source execution and 1,000 unspliced reads recovered by Scavenger from each sample, and then calculated the number of single nucleotide polymorphisms (SNP) found within the location of the aligned reads from the list of strain-specific SNPs published by MGP against the reference mouse genome. The same analysis was then repeated a further 9 times, for a total of 10 iterations, to allow for significance testing. The majority of the reads which are either successfully aligned or recovered did not contain any known SNPs. However, the number of reads which contain SNPs is significantly higher (by t-test, p-value < 10−27) in the reads recovered by Scavenger compared to the reads aligned in the source execution for 4 of the 5 strains analysed (Figure 2A). Furthermore, the number of reads with a high number of SNPs (> 5) are also significantly higher (by t-test, p-value < 10−21) in the reads recovered by Scavenger for all of the strains analysed indicating that Scavenger is able to recover reads which are more polymorphic compared to the reads aligned during the source execution (Figure 3 and Figure 2B). These results validate the hypothesis that reads recovered by Scavenger have a higher degree of polymorphism as a result of the divergence between the personal genome and the reference genome and further demonstrates the ability of Scavenger in dealing with the false-negative non-alignment problem.\n\nA. The number of reads with ≥ 1 SNPs found within reads. B. The number of reads with high number of SNPs (> 5) found within reads.\n\nA. The number of reads with ≥ 1 SNPs found within reads. B. The number of reads with high number of SNPs (> 5) found within reads.\n\nWhile alignment of reads is an important step in RNA-seq analysis, further downstream analyses are required in order to interpret the data into meaningful results. As one of the most common applications of RNA-seq analysis is gene expression analysis, we focused on identifying the effect of adding reads recovered by Scavenger on the expression of genes. The dataset utilised for testing consisted of 23 publicly available RNA-seq samples selected from 3 separate projects of varying characteristics, with 11 samples originating from two human projects and 12 samples originating from a single mouse project. The result of source execution using STAR with default parameters shows a high degree of mappability in all datasets, ranging from ~95.9% in human datasets and ~92.9% in the mouse dataset (Table 6). After recovery of reads with Scavenger, we were able to recover ~3.1% of unaligned reads on average across the three datasets, corresponding to an increase ranging from 7,000 reads up to 102,000 reads. While the number of reads recovered are quite low relative to the number of previously aligned reads, the addition of tens and hundred of thousands of reads is still likely to affect the expression of the genes.\n\nGene quantification of aligned reads is performed using featureCounts24 to produce read counts per gene, which is then normalised to reads per million (RPM). In the source alignment, the number of genes expressed, defined as having non-zero read counts, in the human datasets average to 26,000 genes, while the number of genes expressed in the mouse dataset is 25,800 genes. In Scavenger recovered alignment, we see an increase of up to 3 expressed genes per sample, indicating the ability of Scavenger to recover genes which are falsely considered as non-expressed in the source alignment (Figure 5A). The recovery of reads in previously non-expressed genes is likely due to the extension of putative alignment locations, which may introduce regions which have no alignment in the source execution. Further investigation into the reads recovered by Scavenger shows that the reads are not distributed evenly across all the expressed genes – with only ~2150 and ~5900 genes receiving an increase in read counts in human and mouse datasets, respectively. The majority of genes with increased read counts do not see much change in gene expression, with only ~14 genes having more than 1 fold-change difference between source expression and recovered expression. Interestingly, genes which have substantial difference after recovery are generally genes with low expression in the source execution (log2(RPM) < 5), potentially indicating that some lowly expressed genes may actually have higher true expression than what is reported due to the alignment tool being unable to pick up these reads (Figure 4). This also has implications in further downstream analyses as lowly expressed genes are typically excluded from analysis, when instead it should not have been excluded as their true expression is actually higher.\n\nColoured points indicates genes with expression difference of greater than 1 fold change.\n\nA. The number of genes whose reads are recovered by Scavenger, categorised based on the fold change in normalised expression (RPM) between source alignment and after Scavenger recovery. B. The number of genes with more than 1 fold change in normalised expression categorised based on their gene types.\n\nWe then performed further investigations into the genes with more than 1 fold-change difference after recovery to study the types of genes affected by the false-negative non-alignment problem. The majority of genes with recovered expression in the human and mouse dataset are classified as pseudogenes (>60%), with the second most frequent type being protein coding genes (22% and 9% for human and mouse dataset, respectively) (Figure 5B). Moreover, most recovered genes with very low expression in the source alignment (log2(RPM+1) < 5) are in the pseudogenes category implying that many pseudogenes expression are likely to be under-reported due to reads originating from pseudogenes not being picked up by the alignment tool (Figure 4). Frequency analysis of the recovered genes also shows that some genes are consistently recovered across at least half of the samples in human and mouse datasets respectively, potentially indicating that these genes are harder to be picked up by the alignment tool due to its sequence being highly polymorphic. The finding that expression of pseudogenes are particularly affected by the false-negative non-alignment problem is significant as recent studies have shown that pseudogenes are incorrectly assumed to be non-functioning and actually have a role in regulating biological processes, particularly in diseases such as cancer25,26. The reason that pseudogenes are more affected by Scavenger recovery is likely due to a number of factors, including the large number of mutations accumulated which results in divergence between pseudogene sequences and personal genomes; and the typically low expression of pseudogenes which is therefore more affected by increase an in reads as a result of recovery by Scavenger (Figure 6).\n\nIn general, most reads are located in a region without a feature or within a protein coding gene. However, a high percentage of reads in human bulk RNA-seq datasets are located in other gene types, more specifically mitochondrial genes, due to the high source expression of these genes.\n\nSingle cell RNA-sequencing (scRNA-seq) is fast becoming a mainstream method for transcriptomics analysis due its ability to elucidate transcriptional heterogeneity of individual cells. However, there are a number of challenges when dealing with scRNA-seq datasets due to systematically low read counts, as a result of the small amount of transcripts which are captured during library preparation, and a high degree of technical noise27. Given Scavenger’s ability in recovering false-negative non-recovered reads in normal bulk RNA-seq datasets and the effect it has on downstream analyses, we hypothesise that recovery of unaligned reads in scRNA-seq datasets with Scavenger will likely have a greater impact on downstream analysis due to limited amount of reads available, while also helping with reducing technical noise. To test this hypothesis, 80 randomly selected samples were collected from a mouse brain scRNA-seq dataset and which are then aligned with STAR, followed by recovery of reads with Scavenger. The scRNA-seq samples have an average read depth of ~2.3 million reads (after pre-processing), with ~57.3% of the reads able to be aligned in the source execution (Table 6). Scavenger was only able to recover 0.6% of the unaligned reads, corresponding to an increase of ~5,400 reads. The low number of reads which are able to be successfully recovered by the Scavenger pipeline is likely due to the low number of aligned in reads in source alignment, which provides less information that Scavenger can utilise during the follow-up execution.\n\nAs per the norm for scRNA-seq datasets, the number of genes with non-zero read counts is much lower compared to the number of non-expressed genes in bulk RNA-seq datasets, averaging 5,800. Of these expressed genes, only 12% of the genes (~700) have an increase in read counts, with the majority of these genes having little difference in expression and ~12 genes having a fold-change difference greater than 1 (Figure 7A). Unlike in bulk RNA-seq datasets, genes with substantial difference after recovery range from lowly expressed genes up to highly expressed genes, though genes with the greatest difference in expression are still those with low expression in the source alignment (Figure 4). Furthermore, a different pattern was also observed in the types of genes which have substantial difference in scRNA-seq datasets, with the protein coding category being the majority, followed by the pseudogene category (Figure 7B). The difference in pattern is likely due to comparatively higher abundance of protein coding genes and the low capture efficiency of scRNA-seq methods, meaning that reads from pseudogenes are less likely to be captured and therefore rescued. This can be seen from the much lower number of pseudogenes expressed in scRNA-seq dataset (~150) compared to bulk RNA-seq datasets (~3,500).\n\nA. The number of genes whose reads are recovered by Scavenger, categorised based on the fold change in normalised expression (RPM) between source alignment and after Scavenger recovery. B. The number of genes with more than 1 fold change in normalised expression categorised based on their gene types.\n\n\nDiscussion\n\nThe false-negative non-alignment problem is a prevalent problem in many of the published RNA-seq alignment tools, resulting in loss of information from incorrectly unaligned reads. To help solve the false-negative non-alignment problem, we have developed Scavenger – a pipeline for recovery of unaligned reads using a novel mechanism based on sequence similarity between unaligned and aligned reads. Scavenger utilises the follow-up execution concept adapted from our previous work on metamorphic testing to find aligned reads from the source execution which have similar sequences to the unaligned reads by aligning the aligned reads against unaligned reads. The location of the aligned reads are then used as a guide to re-align the unaligned reads back to the reference genome using either BLAST or the original alignment tool depending on if the putative location originates from unspliced or spliced alignment, respectively, to ensure that splicing information is retained in recovered reads.\n\nWe have applied Scavenger on simulated datasets with varying degrees of complexity and showed that Scavenger is able to recover unaligned reads across all complexity levels with a reasonably high degree of accuracy. In particular, Scavenger is able to recover the most amount of reads in datasets that exhibit a high degree of complexity where read sequence is more divergent compared to the reference genome. We further show that although alignment of reads with optimised parameters are able produce a higher number of aligned reads compared to after recovery with Scavenger, the reads recovered by Scavenger have high degree of overlap to reads recovered with parameter optimisation. The lower number of reads recovered by after Scavenger is a result of Scavenger using information from aligned reads to find putative locations for unaligned reads, meaning that Scavenger is unable to recover reads from region with no alignment – unlike parameter optimisation which does not have the same limitation. Given the non-trivial difficulty of performing parameter optimisation on real datasets, we recommend the use of Scavenger as an alternative to help with recovering incorrectly unaligned reads.\n\nThere are a number of possible factors which may contribute to the false-negative non-alignment problem. One such factor is the divergence between the reference genome and the personal genome, leading to higher mismatches during alignment of sequenced reads against the reference genome. In order to validate that divergence of genomic sequences result in incorrectly unaligned reads, we devised an experiment whereby RNA-seq datasets from non-reference mouse strains were aligned against the reference mouse strain. We then analysed the reads which were aligned in the source execution against those recovered by Scavenger and showed that Scavenger is able to significantly recover more reads which have a higher number of reported strain-specific SNPs. This result both confirms that divergence of sequences between the reference genome and the personal genome does affect the false-negative non-alignment problems and that Scavenger is able to recover reads which are incorrectly unaligned due to a higher degree of sequence divergence.\n\nAs alignment of reads is only the first step in an RNA-seq data analysis, we also investigated the effect of the false-negative non-alignment problem on downstream analyses, in particular on gene expression analysis. After recovery of reads with Scavenger, we show that ~14 genes have more than 1 fold change in expression compared to the source alignment and that these genes are typically genes with low expression. Interestingly, the majority of genes with >1 expression difference belong to the pseudogenes category, indicating that the expression of pseudogenes are likely to be under-reported due to reads from pseudogenes being incorrectly unaligned by the alignment tool. Given the ability of Scavenger to recover gene expression in normal (bulk) RNA-seq datasets, we then investigated the ability of Scavenger in recovering reads from scRNA-seq dataset as scRNA-seq datasets have the characteristics of having low reads counts and high degree of technical noise. Scavenger recovery affected the expression of 12% of the expressed genes, with ~12 genes having more than 1 fold change in expression. Unlike the bulk RNA-seq dataset, the genes with >1 change in expression range from lowly expressed genes up to highly expressed genes, with the genes belonging primarily to the protein coding category.\n\nThe current version of Scavenger supports STAR as the alignment tool for source execution and re-alignment of spliced reads. However, the user can choose to modify the alignment tool utilised by Scavenger with the alignment tool of their choice. Ideally the tool should satisfy the three properties underlying the read recovery pipeline – deterministic alignment, realignability of mapped reads, and non-realignability of unmapped reads – to ensure that the recovered reads are deterministic. To show the extensibility of Scavenger, we have tested Subread, another RNA-seq alignment tool, as a replacement for STAR within the Scavenger pipeline and demonstrated that Scavenger is still able to recover incorrectly unaligned reads with similar performance to STAR (Table 7 and Table 8). It should be noted that the recovery performance of Subread is different compared to STAR due to the different algorithm employed by Subread for alignment and, potentially, due to Subread violating the deterministic alignment property.\n\nThe result shown is an average from 3 samples.\n\nThe result shown is an average from 3 samples.\n\n\nData availability\n\nSimulated datasets used in this study were obtained from Baruzzo et al.8\n\nThe datasets are publically available from: http://bioinf.itmat.upenn.edu/BEERS/bp1/datasets.php\n\n\nSoftware availability\n\nProject name: Scavenger\n\nProject home page: https://github.com/VCCRI/Scavenger\n\nArchived source code: https://doi.org/10.5281/zenodo.335899518\n\nOperating system(s): Linux\n\nProgramming language: Python 3 and Shell\n\nOther requirements:STAR and Subread\n\nLicense:MIT",
"appendix": "References\n\nKim D, Langmead B, Salzberg SL: HISAT: a fast spliced aligner with low memory requirements. Nat methods. 2015; 12(4): 357–60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDobin A, Davis CA, Schlesinger F, et al.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29(1): 15–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiao Y, Smyth GK, Shi W: The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013; 41(10): e108. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPhilippe N, Salson M, Commes T, et al.: CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biol. 2013; 14(3): R30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang K, Singh D, Zeng Z, et al.: MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 2010; 38(18): e178. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu TD, Reeder J, Lawrence M, et al.: GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality. Methods Mol Biol. 2016; 1418: 283–334. PubMed Abstract | Publisher Full Text\n\nHayer KE, Pizarro A, Lahens NF, et al.: Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics. 2015; 31(24): 3938–3945. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaruzzo G, Hayer KE, Kim EJ, et al.: Simulation-based comprehensive benchmarking of RNA-seq aligners. Nat Methods. 2017; 14(2): 135–139. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAudoux J, Salson M, Grosset CF, et al.: SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. BMC Bioinformatics. 2017; 18(1): 428. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee W, Plant K, Humburg P, et al.: AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes. Bioinformatics. 2018; 34(14): 2401–2408. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTang JYS, Yang A, Chen TY, et al.: Harnessing Multiple Source Test Cases in Metamorphic Testing: A Case Study in Bioinformatics. In 2017 IEEE/ACM 2nd International Workshop on Metamorphic Testing (MET). IEEE. 2017; 10–13. Publisher Full Text\n\nChen TY, Ho JW, Liu H, et al.: An innovative approach for testing bioinformatics programs using metamorphic testing. BMC Bioinformatics. 2009; 10(1): 24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen TY, Cheung SC, Yiu SM: Metamorphic testing: a new approach for generating next test cases. 1998. Reference Source\n\nMangul S, Yang HT, Strauli N, et al.: ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol. 2018; 19(1): 36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCamacho C, Coulouris G, Avagyan V, et al.: BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10(1): 421. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBao W, Kojima KK, Kohany O: Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015; 6(1): 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMell P, Grance T: The NIST definition of cloud computing. NIST Special Publication. 2011; 145(12): 7. Reference Source\n\nAndrian: Vccri/scavenger: Scavenger v1.0. 2019. http://www.doi.org/10.5281/zenodo.3358995\n\nGrant GR, Farkas MH, Pizarro AD, et al.: Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011; 27(18): 2518–2528. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarrow J, Frankish A, Gonzalez JM, et al.: GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012; 22(9): 1760–1774. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeinonen R, Sugawara H, Shumway M: The sequence read archive. Nucleic Acids Res. 2011; 39(Database issue): D19–D21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKeane TM, Goodstadt L, Danecek P, et al.: Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 2011; 477(7364): 289–294. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6): 841–842. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiao Y, Smyth GK, Shi W: featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014; 30(7): 923–930. PubMed Abstract | Publisher Full Text\n\nKalyana-Sundaram S, Kumar-Sinha C, Shankar S, et al.: Expressed pseudogenes in the transcriptional landscape of human cancers. Cell. 2012; 149(7): 1622–1634. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShi X, Nie F, Wang Z, et al.: Pseudogene-expressed RNAs: a new frontier in cancers. Tumour Biol. 2016; 37(2): 1471–8. PubMed Abstract | Publisher Full Text\n\nKolodziejczyk AA, Kim JK, Svensson V, et al.: The technology and biology of single-cell RNA sequencing. Mol Cell. 2015; 58(4): 610–620. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "53438",
"date": "21 Oct 2019",
"name": "Quan Nguyen",
"expertise": [
"Reviewer Expertise Transcriptomics",
"genomics",
"machine-learning",
"single-cell"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present Scavenger, a pipeline to recover false unaligned reads by remapping or BLAST-search unmapped reads that are similar to aligned reads. The false unaligned reads commonly arise from two sources: the actual sequence variation to the shared reference genome and the mapping to multiple regions. These reads are usually discarded in a standard analysis pipeline.\n\nThe software can be useful to rescue unmapped reads in a quantifiable way, which can be important in many sequencing data analysis scenarios. Example usage cases are to study the expression of frequently mutated genes in diseased samples and in the mapping cases where a genome reference is not complete or high divergence to the reference exists.\nThe authors comprehensively tested Scavenger using three simulation settings, 80 RNA-seq datasets from non-reference inbred laboratory mouse strains, 11 human and 12 mouse datasets and 80 single-cell datasets. They performed analyses on the effects of recovering falsely unaligned reads to downstream analyses and show that pseudogenes affect expression measurements. Scanvenger input files are FASTQ files, or mapped BAM/SAM files, and the software has functionalities for parallelisation on CPUs and AWS cloud processing.\n\nI suggest some minor revisions below:\n\nFASTQ read statistics like length and quality should be described. What preprocessing steps are required, for example trimming of N bases, filtering of low-quality reads? While multiple mapping and divergence in genome sequence are two primary sources of false unaligned reads, another common source can be from sequencing base calling error. The authors may add discussion on how quality scores affect read recovery.\n\nThe tests for difference in the level of polymorphism between unligned and aligned reads are interesting and can lead to important conclusions. These tests can be improved. The sample size from a random sampling of reads (1000 reads) is small relative to the total mapped reads (< 0.1%), and t-test for results from 10 iterations is not suitable to test for testing the enrichment of SNPs in aligned vs unaligned reads. The authors may consider the permutation test or others. The authors may also consider known regions of the genome where more mutations are expected.\n\nThe recovery of un-detected genes and effects on fold-change are interesting. The author may consider adding information or a panel in figure 5 to show expression levels of these affected genes before and after read recovery.\n\nPage 4: clarify \"qualities\" as mapping or sequencing qualities.\n\nPage 4: clarify \"to reduce potential location for alignment\". Can be useful to output total reads that can not be rescued due to multiple mapping.\n\nTables 2 and 3, the unaligned category on the third column should be a part of the source execution.\n\nAdd discussion on when Scavenger should be used as an alternative for parameter optimisation approach in STAR alignner. For example, on Pages 8 and 15, the authors dicuss \"performing parameter optimisation is not trivial due to lack of ground truth\", how does Scavenger perform better in the absence of ground truth? Would it be due to speed, accuracy and quantitativeness?\n\nFigure 3, add label A) and B), and description for panel titles and graph axis titles.\n\nPage 12, what single-cell sequencing platforms were used for the selected datasets. Variation in recovery efficient may occur in, for example, 3'-sequencing and full-length sequencing data.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "8591",
"date": "03 Aug 2022",
"name": "Andrian Yang",
"role": "Author Response",
"response": "We thank the reviewer for their overall positive assessment of our work, as well as their constructive comments. Please find below our point-by-point response to the reviewer's comments: FASTQ read statistics like length and quality should be described. What preprocessing steps are required, for example trimming of N bases, filtering of low-quality reads? While multiple mapping and divergence in genome sequence are two primary sources of false unaligned reads, another common source can be from sequencing base calling error. The authors may add discussion on how quality scores affect read recovery. We would like to highlight Table 6 to the reviewer which contains the read length statistics for each sample. Unfortunately, the read quality information is not readily available so we are not able to provide the statistics in the manuscript. With regards to read pre-processing, we performed basic pre-processing of sequencing reads using Trimmomatic to remove low quality sequence and short reads, though recent studies have shown that read pre-processing may not be required for RNA-seq alignment as demonstrated in Liao and Shi 2020 (https://academic.oup.com/nargab/article/2/3/lqaa068/5901066). We agree with the reviewer that low quality reads likely contribute to false unaligned reads by aligner due to increased mismatches/indel in read sequence as previously described by Dobin and Gingeras 2015 (https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1114s51). However, since the recovery process largely re-utilise the aligner used in the initial alignment (source execution), the recovery rate of low quality sequences are likely to be low as the recovery process imposes the same minimum sequence requirement for recovery. The tests for difference in the level of polymorphism between unligned and aligned reads are interesting and can lead to important conclusions. These tests can be improved. The sample size from a random sampling of reads (1000 reads) is small relative to the total mapped reads (< 0.1%), and t-test for results from 10 iterations is not suitable to test for testing the enrichment of SNPs in aligned vs unaligned reads. The authors may consider the permutation test or others. The authors may also consider known regions of the genome where more mutations are expected. We thank the reviewer for their feedback regarding the experiment where we evaluated the degree of polymorphism between source aligned and scavenger recovered reads. We will endeavour to perform more rigorous experiments as suggested by the reviewer in future studies. The recovery of un-detected genes and effects on fold-change are interesting. The author may consider adding information or a panel in figure 5 to show expression levels of these affected genes before and after read recovery. We would like to highlight Figure 4 to the reviewer, which provide a summary of the gene expression before and after read recovery for the three different type of datasets. Page 4: clarify \"qualities\" as mapping or sequencing qualities. Page 4: clarify \"to reduce potential location for alignment\". Can be useful to output total reads that can not be rescued due to multiple mapping. Tables 2 and 3, the unaligned category on the third column should be a part of the source execution. We have added clarifications to the sections that the reviewer highlighted and fixed the table layout. Add discussion on when Scavenger should be used as an alternative for parameter optimisation approach in STAR alignner. For example, on Pages 8 and 15, the authors dicuss \"performing parameter optimisation is not trivial due to lack of ground truth\", how does Scavenger perform better in the absence of ground truth? Would it be due to speed, accuracy and quantitativeness? A typical alignment optimisation approach, especially in the absence of ground truth, is to minimise the amount of unaligned reads by increasing the edit distance threshold during alignment at the risk of increasing the number of incorrectly aligned read. While it is possible to find an optimised parameter which maximise the number of aligned reads while minimising the number of incorrectly aligned reads through varying different parameter values, this is not entirely possible to do in the absence of ground truth and will likely take a lot of time and effort to test all possible permutation of alignment parameters. Scavenger has been shown to be able to recover reads with reasonably high degree of accuracy without the need for extensive parameter optimisation, with the reads recovered having very degree of overlap to reads recovered with parameter optimisation, and as such, would be a good method to utilise after minimal or no parameter optimisation. We have added extra discussion in the manuscript. Figure 3, add label A) and B), and description for panel titles and graph axis titles. We have now revised the caption for Figure 3 and added graph axis titles to the figure. Page 12, what single-cell sequencing platforms were used for the selected datasets. Variation in recovery efficient may occur in, for example, 3'-sequencing and full-length sequencing data. The single-cell sequencing platform utilised for generating the mouse brain scRNA-seq dataset by Zeisel et al. is the Fluidigm C1 system with a custom protocol using 5’ capture and tagging of RNA modules as described in Islam et al. 2013 (https://www.nature.com/articles/nmeth.2772)."
}
]
},
{
"id": "68338",
"date": "27 Aug 2020",
"name": "Marco Previtali",
"expertise": [
"Reviewer Expertise algorthmic bioinformatics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nYang et al. present Scavenger, a tool for rescuing unaligned RNA-Seq reads by exploiting information from reads which are successfully aligned. Scavenger is split into four main steps and can be easily run on cloud-based computing platforms.\nWe think that the problem tackled in this paper is interesting and that the tool proposed may improve the overall accuracy of any downstream RNA-Seq analysis. Indeed, many studies have shown that unaligned reads carry important information that is usually discarded from RNA-Seq analysis pipelines, thus recovering such reads will improve their results and shed more light on the dataset under analysis.\nOverall the paper is easy to read and the authors clearly state the problem they are tackling. The method is well described and a big part of the paper is devoted to an extensive evaluation of the tool using real data.\nMajor remarks: We have a single main remark for the authors. Although we appreciate the extensive experimental evaluation, it is not easily reproducible. We suggest the authors publish the commands used to run all the experiments in a supplementary repository or document, ideally in the form of a Snakemake or Nextflow pipeline. Moreover, in Section “Dataset” the authors report the commands used to run STAR, subread-align, and blastn. We think that it is not useful to report them in the manuscript and we suggest to remove them for better readability.\nMinor remarks and typos:\nPage 4: \"(i.e. the number of aligned reads that fall within the interval)\" -> which aligned reads? the unaligned realigned or the aligned?\n\nPage 4: please describe (intuitively) what “realignability of mapped reads” and “non-realignability of unmapped reads” means.\n\nPage 6: \"mousub\" > “mouse”?\n\nPage 6-7: command lines are ugly (maybe due to two columns page format).\n\nSection “Results”: it would be useful to describe the running times and the RAM requirements of Scavenger in the various experimental analysis to better understand whether it can be run on low-end and mid-range servers.\n\nTable 6 reports the results of different experiments described in the manuscript. The last sentence on page 9 might be confusing since it states that the minimum number of rescued reads is 17,000 whereas the table includes two smaller values (12,347 and 5,368). We suppose that these two lines refer to the results on Mouse scRNA reads. We suggest the authors to better specify the experiment on each line (or split the table in two).\n\nTable 6 reports the results for all the samples considered in the evaluation (human and mouse). We believe that the authors should specify the organism for each accession ID.\n\nPage 10: We concur with the other reviewer and we think that the sample size for random sampling of reads is too small relative to the total mapped reads. The authors should improve this part of the manuscript.\n\nPage 10: \"11 samples originating from two human projects\" -> there is no table. I would like to see it (as done for the mouse samples).\n\nFigure 3: the caption is wrong. There is no B subfigure. Moreover, the axes have no labels making the charts harder to understand.\n\nPage 12: “and the typically low expression of pseudo- genes which is therefore more affected by increase an in reads as a result of recovery by Scavenger” -> please rephrase this sentence since it’s not completely clear to us.\n\nPage 15: \"are able produce\" -> \"are able to produce\"\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "8592",
"date": "13 Oct 2022",
"name": "Andrian Yang",
"role": "Author Response",
"response": "We thank the reviewer for their overall positive assessment of our work, as well as their constructive comments. Please find below our point-by-point response to the reviewer's comments: Major remarks: We have a single main remark for the authors. Although we appreciate the extensive experimental evaluation, it is not easily reproducible. We suggest the authors publish the commands used to run all the experiments in a supplementary repository or document, ideally in the form of a Snakemake or Nextflow pipeline. We thank the reviewer for the suggestion and will be happy to share commands used with viewers upon request. We will endeavour to make all code available upon publication in future studies. Moreover, in Section “Dataset” the authors report the commands used to run STAR, subread-align, and blastn. We think that it is not useful to report them in the manuscript and we suggest to remove them for better readability. While we thank the reviewer for the suggestion, we believe the inclusion of the commands used are helpful for the viewer to understand the alignment parameter used in each of the program as the result of the alignment may differ depending on the alignment parameters used. Minor remarks and typos: Page 4: \"(i.e. the number of aligned reads that fall within the interval)\" -> which aligned reads? the unaligned realigned or the aligned? We have added a clarification in the section highlighted by the reviewer. Page 4: please describe (intuitively) what “realignability of mapped reads” and “non-realignability of unmapped reads” means. The requirement of realignability of mapped reads is for reads which are mapped in one run of the alignment to also be mapped in other runs of the alignment if no other alignment parameters are modified. Similarly the definition of non-realignability of unmapped reads is for reads which are unmapped in one run of the alignment to also still be unmapped other runs of the alignment if no other alignment parameters are modified. These requirements differs from the deterministic alignment property, as some (multi) mapped reads may be assigned to different mapping location in different runs of the alignment even with identical alignment parameters. Page 6: \"mousub\" > “mouse”? The mousub term used here refers to the name of the sequence file provided by Repbase for mouse organism. We have added extra clarification in the manuscript. Page 6-7: command lines are ugly (maybe due to two columns page format). Section “Results”: it would be useful to describe the running times and the RAM requirements of Scavenger in the various experimental analysis to better understand whether it can be run on low-end and mid-range servers. We unfortunately did not record the running times for scavenger across the experimental analysis so we are not able to include this information within the manuscript. The RAM requirement of Scavenger is largely dictated by the RAM requirement for the alignment tool used (~30GB for human genome to run STAR), though it may also scale depending on the number of reads processed. Table 6 reports the results of different experiments described in the manuscript. The last sentence on page 9 might be confusing since it states that the minimum number of rescued reads is 17,000 whereas the table includes two smaller values (12,347 and 5,368). We suppose that these two lines refer to the results on Mouse scRNA reads. We suggest the authors to better specify the experiment on each line (or split the table in two). The amount of reads recovered as alluded to in the last sentence on page 9 refers to the first section of the table, which give statistics for the datasets from selected non-reference mouse strain. We have added extra clarification in the figure caption. Table 6 reports the results for all the samples considered in the evaluation (human and mouse). We believe that the authors should specify the organism for each accession ID. We have added extra clarification in the figure caption. Page 10: We concur with the other reviewer and we think that the sample size for random sampling of reads is too small relative to the total mapped reads. The authors should improve this part of the manuscript. We thank the reviewer for their feedback regarding the experiment where we evaluated the degree of polymorphism between source aligned and scavenger recovered reads. We will endeavour to perform more rigorous experiment as suggested by the reviewer in future studies. Page 10: \"11 samples originating from two human projects\" -> there is no table. I would like to see it (as done for the mouse samples). The details of the human samples used in this study is included in Table 1. Figure 3: the caption is wrong. There is no B subfigure. Moreover, the axes have no labels making the charts harder to understand. Page 12: “and the typically low expression of pseudo- genes which is therefore more affected by increase an in reads as a result of recovery by Scavenger” -> please rephrase this sentence since it’s not completely clear to us. Page 15: \"are able produce\" -> \"are able to produce\" We have now fixed the sections highlighted by the reviewers following the reviewers’ suggestions."
}
]
}
] | 1
|
https://f1000research.com/articles/8-1587
|
https://f1000research.com/articles/11-1168/v1
|
12 Oct 22
|
{
"type": "Research Article",
"title": "Prevalence of depression among medical students in River Nile State Universities 2021",
"authors": [
"Tarteel Musa",
"Alwathig Yahia",
"Alwathig Yahia"
],
"abstract": "Studying medicine is uphill and tiring requiring long hours of study and, continuous dealing with patients and death. A medical student in River Nile state suffers from a high rate of depression due to academic stress, expectations of parents, and comparisons with peers. Medical education is stressful and exhausting for mental health and has a negative impact on academic, health, and social performance. It also affects the student’s future as a doctor and patient care. The aim of this study knowledge prevalence of depression and its relation to socio-demographic variables among medical students in River Nile State Universities. This cross-sectional study in River Nile State describes the prevalence of depression. We used random samples of students from the first to fifth years, including 335 questionnaires, the Hospital Anxiety, and Depression Scale (HADS) data tool, and an additional question regarding the demographic variable. We found a high prevalence of depression .77.9%(depression 38.8 and borderline depression 39.1%). There was no significant association between college and depression (p= 0.67) and no significant in depression scores among different academic year (p= 0.21), gender (p= 0.23), notionally (p=0.7), smoking (p=0.79), and showed associated drugs (p=0.5). There are some risk factors other than university and smoking that lead to depression The rate of depression is high among medical students. Students must be identified and assisted and taken seriously.",
"keywords": [
"depression",
"prevalence",
"River Nile State",
"medical students."
],
"content": "Introduction\n\nDepressed mood is more pervasive, more likely to be experienced as unusual or atypical, associated with negative ideas (e.g. hopelessness, helplessness, pessimism about the future), and may influence behavior. its low self-esteem and low self-confidence with low mood. As experienced by most people, it generally lasts only minutes to days in non-clinical situations.1 Depression is characterized by sorrow, pessimism, guilt, loss of passion, enjoyment and concentration, difficulty sleeping, appetite disturbance, and a sense of uselessness in your life. If depression lasts for a long time or it repeats, it significantly affects the person's practical, scientific and daily life. its intense depression can lead to suicide. Depressive disorder is divided into two main categories: major depressive disorder/its symptom include a sad mood, loss of enjoyment, fatigue, and the lethargy, depending on the number and severity of a depressive episode may be classified as gentle, moderate, or severe; and the other categories are Dysthymia depression, a persistent or chronic kind of gentle depression; the symptom of clinical depression or almost like a depressive episode, however tend to be less intense and last longer.2 The population affected by depression are estimated to be more than 322 million globally suffer from depression or 4.4% from world population.2 Many studies have showed that medical students have high level of distress compare to another. Medical school teachers need to understand that, and know the occurrence and causes of distress in their students because of its impact on the personality, well-being, and health of their students.3 One of the reasons that can lead to depression is not completing the course before the exam, not knowing how to face the exam, or because there are less than a month for most exams, as well as students burdening themselves with expectations, the expectations of parents and comparisons with colleagues.4 The other reasons for stress on students: are the short period of the study compared to the enormity of the curriculum, the change in the method of reading, the acceleration in medical science update, lack of proper guidance for communication/failing in exams, inadequate time for clinical phase, insufficient bedside teaching, social stress: relationship with peer groups, residence friends, leaving home pressure from classmates and change in the way of education, physical stress: unsuitable residence facilities, poor residence food, etc.5\n\nMedical education is generally considered stressful, and high rates of mental illness have been reported in medical students, ranging from stress and personal problems to suicidal ideas.6 About one-third of the medical students worldwide suffer from depression or depressive symptoms.7 It is serious to determine the prevalence of depression among medical due to increased rates of mental illness affecting their careers.8 Depression increases physician suicide rates. At the same time, student sorrow negatively affects the academic level and professional development, which leads to a lack of academic integrity and drug abuse. Dent stress has been associated with a variety of negative outcomes, including general affect of health life. Strain impairs the quality of life of medical students, and the doctor-patient relationship also affects patient care and attention.5\n\n\nMethods\n\nDescriptive Cross-sectional study design.\n\nStudy area: The area is in the state of the Nile River, one of the states of Sudan. In the faculty of medicine at Elsheikh Abdalla Elbadri University in Barbar city, the faculty of Medicine of the Nile Valley University in Atabara city, and the Faculty of Medicine of the University of Shendi in Shendi city.\n\nMedical students at Elsheikh Abdallah Elbadri University, Nile Valley University, and Shendi University.\n\nInclusion criteria: Medical student.\n\nExclusion criteria\n\n1. student previously leave depression.\n\n2. students with other medical conditions (malaria, typhoid, encephalitis).\n\nSample technique: Voluntarily sampling. The questionnaire was prepared in Google format, then the format was distributed to medical students' social media groups, volunteer participants conducted the format and complete it then submit also through google format.\n\nThe Equation used\n\nP = expected prevalence = 0.5 q = 1-p\n\nD = random sample error = 0.05\n\n> sample size = 335\n\nPart one of the questionnaire contained the background questions, also the Questionnaire contain closed questions prepared based on the HADS scale (Zigmond & Snaith 1983), the questionnaire contained 14 questions seven of them related to assessing depression and the another is for anxiety. The assessment has three catalogers first is normal and the degree lies from 0 to 7, the second is borderline which is lie from 8 to 10, and the final category is abnormal or cases (depression or anxiety or bipolar) and the score is 11 to 21.\n\nThe data was entered into the STATA program version13 (statistic program for analysis of data). The figure pie chart was used to present the prevalence of depression and anxiety and the table was used to describe the data, also we used chi squire, P-value value is considered to be significant if it is less the 0.05.\n\nEthical approval was conducted by ElSheikh Abdulla Elbadri University. Ethical principles and informed consent were considered before filling out a questionnaire.\n\n\nResults\n\n\n\n\nDiscussion\n\nThe current study aimed to measure the prevalence of depression among medical students in River Nile state there about half of students from Elsheikh Abdullah Elbadri university, and one third from Nile Valley university and the rest from Shendi university. there students from first year represent more than half of participants. Most of students who participate in the study were female. Around eight percent of participants were smoker, and not more than two percent of students were using substance abuse. Prevalence of depression is about forty percent, and same percentage for those in borderline depression. In this study found there was no significant association between college and depression, also there is no statistical significance in depression scores and school years, as was found in studies done in Khartoum university.5 and Sudan international university.9 While found significance in New Delhi10 and Egypt.11 The prevalence of depression was high among second and third years as compared to other; It may be due to pressure in studying due to taking the Intermediate Exam Universities in the second and third years. The decline in the fourth and fifth years due to adaptation to the environment and getting used to the pressure of study. In our study we found that gender was not significant, as was found in studies done in Sudan international university9 and New Delhi.10 while found significance in Egypt.11 previous study According to a the prevalence of depression in China ranged from 13. 1 to 76.21% with mean 32.74%and in Egypt about 36% it is similar to this study.11,12 the prevalence of depression in Sudan international university(67.%) which is very high compare to our result.9\n\n\nConclusion\n\nMeasures such as early detection and prevention programs must play a role in verifying psychological support must be strengthened in the college through the dissemination of psychological knowledge and the provision of courses and lectures related to mental health, the establishment of an office for psychological counseling within the college. Limitations:Age and residence were asked in the questionnaire and then their association with depression was not determined.\n\n\nData availability\n\nDryad. Prevalence of depression among medical students in River Nile State Universities 2021. DOI: https://doi.org/10.5061/dryad.r4xgxd2gf",
"appendix": "References\n\nMichael G, Nancy C, Juan J, et al.:Mood disorders. New Oxford textbook of psychiatry. (2nd edn).Oxford University Press;2009.\n\nEstimates GH: Depression, and Other Common Mental Disorders Global Health Estimates.\n\nKumar S, Kumar A: Assessment of the depression, anxiety and stress levels among the medical undergraduate students using DASS.2020; 3(11): 206–212.\n\nInfo A: Depression, anxiety and stress among first-year undergraduate medical students.2015.\n\nDafaalla M, Farah A, Bashir S, et al.: Depression, Anxiety, and Stress in Sudanese Medical Students: A Cross-Sectional Study on Role of Quality of Life and Social Support. Am J Educ Res. 2016; 4(13): 937–942.Reference Source\n\nTaneja N, Sachdeva SDN: Assessment of Depression, Anxiety, and Stress among Medical Students Enrolled in a Medical College of New Delhi, India. Indian J Soc Psychiatry. 2018; 34: 285–288.Reference Source\n\nAdhikari A, Dutta A, Sapkota S, et al.: Prevalence of poor mental health among medical students in Nepal: a cross-sectional study.2017; 1–7.\n\nAbdallah AR, Gabr HM: Depression, anxiety, and stress among first-year medical students in an Egyptian public university.2014; 2(February): 11–19.\n\nEiman A, Blgees G, Ebtehag B, et al.: Prevalence of Depression Among Medical Students in Sudan International University in May 2017.2475-529X.\n\nSidana S, Kishore J, Ghosh V, et al.: Prevalence of depression in students of a medical college in New Delhi: A cross-sectional study. Australas Med J. 2012; 5: 247–250. PubMed Abstract | Publisher Full Text\n\nFawzy M, Hamed SA: Prevalence of psychological stress, depression, and anxiety among medical students in Egypt. Psychiatry Res. 2017; 255: 186–194. PubMed Abstract | Publisher Full Text\n\nYing M, Ning Z, Jinlin L, et al.: A systematic review of depression and anxiety in medical students in China. Mao BMC Medi Educ. 2019; 19: 327. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "153218",
"date": "03 Nov 2022",
"name": "Hanaa E bayomy",
"expertise": [
"Reviewer Expertise Public health & Community Medicine"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this manuscript is not qualified for indexing. The language of the manuscript is poor which makes it difficult to follow. The components of the research are not represented appropriately, as regards to the methods, results and discussion, and conclusion. So, I would reject it for indexing.\nTopic & title: the topic and title of the study are good. Depression in medical students is an important problem that needs more attention and care for students, and the title is describing the objective of the study.\nAbstract: All items of an abstract are there, but it is written in poor language.\nIntroduction: The topic of the study was defined and analyzed leading to the rationale of the study. However, the language is poor.\nMethods: study design, setting, inclusion, and exclusion criteria were defined. However, the sampling technique is not clear. The equation for sample size needs more explanation and reference.\nResults: Add comments on the results. Add a title for the figure (below it). In tables, write the Chi-square and p-values in separate columns.\nDiscussion: It is too short, and needs more explanation and discussion of the results. Add the advantages, limitations, and implications of the study, and recommendations for future research.\nConclusion: The conclusion should be based on the results of the study.\nReferences: Write the references in a systematic and consistent way. For electronic citations, write the URL and date of access. The authors missed the name of journals of references 3, 7, 8, and 9.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "193156",
"date": "08 Aug 2023",
"name": "Daniele Cavaleri",
"expertise": [
"Reviewer Expertise Mood disorders"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very simple and straightforward study about prevalence of depression among medical students in River Nile State Universities in 2021. Although the topic is surely relevant in view of the importance of mental health in university students, this manuscript has critical issues that need to be addressed with major revisions.\nIn general, structure and language are severely deficient, often impairing the understandability of the paper. It requires a complete restoration in its structure as well as extensive language revisions, editing, and correction of typos (e.g., \"chi squire\" is \"chi-square\").\nMore specifically:\nThe Introduction section should end with declaring the purposes and the hypothesis of the study.\n\nI strongly advise the Authors to follow (and cite) the STROBE statement (https://www.strobe-statement.org) for reporting observational research.\n\nInclusion criteria should be outlined better. For instance, was any age limit applied? This should be declared.\n\nWas the Declaration of Helsinki for studies involving human beings followed?\n\nThe manuscript lacks a proper Results section, which is limited to tables without any text.\n\nOn the other hand, the Discussion section is a results repetition and stops at a merely descriptive level, with no speculations and implications in both clinical practice and future research.\n\nIn their Conclusion section, the Authors highlight the importance of detection and prevention as well as of support and psychological counseling. These concepts should be moved to the Discussion section and surely broadened implemented. For example, it is well known that the delivery of relevant interventions is often complicated by the reluctance of students to access university counselling and supporting services, mainly because of barriers such as stigma or lack of adequate information (Ennis et al., 20191). Moreover, how can digital mental health interventions, a strategy that has been shown to be effective in promoting the mental health and well-being of university students, help in these situations? Please refer to and cite this recent and important review by Riboldi et al., 20222.\n\nThe statement about limitations of the study (to be moved to the Discussion section anyways) is quite reductive. Among limitations, the Authors should acknowledge: (i) the fact that the sampling of participants was done by convenience, possibly producing artifact high rates of depressive symptom prevalence; (ii) the limited external value of the findings.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1168
|
https://f1000research.com/articles/11-1167/v1
|
12 Oct 22
|
{
"type": "Research Article",
"title": "Feasibility of contextualizing the Informed Health Choices learning resources in Italy: A pilot study in a primary school in Florence",
"authors": [
"Camilla Alderighi",
"Raffaele Rasoini",
"Giulio Formoso",
"Maria Grazia Celani",
"Sarah E. Rosenbaum",
"Camilla Alderighi",
"Raffaele Rasoini",
"Giulio Formoso",
"Maria Grazia Celani"
],
"abstract": "Background The Informed Health Choices (IHC) project team developed learning resources for primary school children to teach critical thinking about treatments claims and health choices and evaluated their effect in a randomized controlled trial of 120 schools in Uganda. Children taught with these resources showed a better ability to think critically about treatments claims and health choices than children not taught with these resources. Teams in multiple countries are contextualising the IHC resources for use in other languages and settings; in this pilot we describe contextualization for use in Italian primary school.\n\nMethods\nAfter translating the IHC resources to Italian and holding an introductory workshop with participating schoolteachers, we piloted the resources with two classes of a primary school in Florence over nine lessons. Our aims were: 1) to assess the feasibility of introducing the IHC curriculum in Italian primary school; 2) to evaluate students’ ability to assess health claims and make informed health choices; to explore 3) students’ and 4) teachers’ experiences with the IHC learning resources; 5) to identify barriers and facilitators to implementation of IHC learning resources in Italian primary school. To assess these objectives, we used qualitative and quantitative methods.\nResults\nBoth qualitative and quantitative analyses consistently showed that the IHC learning resources had a positive impact on the objectives examined. The resources integrated well into the Italian primary school curriculum. Both students and teachers considered these resources comprehensible, appealing in design and content, and stimulating for the development of a critical attitude. The only barrier teachers and students expressed was using the resources in a remote learning context.\n\nConclusions Findings from our contextualisation of IHC learning resources in Italian primary school indicate that these resources are well-suited for Italian teachers and students in a primary school context and compatible with the Italian primary school curriculum.",
"keywords": [
"Critical thinking",
"evidence-based medicine",
"informed health choices",
"critical health literacy",
"health literacy",
"public health"
],
"content": "Introduction\n\nPeople’s desire and demand to be involved in health decisions have increased progressively in the last few decades.1 In a systematic review of 115 studies on patients’ decision role preferences for treatment and screening, most patients preferred sharing decisions with physicians in 63% of the studies. This represents a shift from an earlier model, where doctors make most of the decisions about patients’ health, to a shared decision model where patients participate more actively.\n\nA first step for a person who wants to participate in their own health decisions is to be able to access reliable information about the treatment effects of options that are relevant to them. There is no lack of information about treatments - claims about “what works” come from a wide variety of sources, such as healthcare professionals, acquaintances, relatives, blogs, TV, social media, scientific magazines, and the lay press. Despite this abundance of information, most claims about health interventions that people hear or read about every day are far from reliable.2,3 Easily accessible claims published on the internet, on TV or in the lay press are often not based on sound scientific evidence; even if they are, they can be reported in incomplete or misleading ways.4\n\nPhysicians and scientists are not exempt from making unreliable health claims. For example, physicians often underestimate the risks and overestimate the benefits of diagnostic and therapeutic interventions.5 This biased perspective can lead to unbalanced conversations with patients and tend to favour interventions’ advantages over disadvantages.6 It is challenging for people to make good health choices when they are subjected to an overabundance of unreliable or unbalanced information, and they need skills to be able to navigate this landscape.\n\nHealth literacy is the degree to which individuals can find, understand, and use information and services to make informed health decisions for themselves and others.7 But health literacy skills are lacking, both in Europe and more specifically in Italy. In a European survey, 47% of the adult population had problematic or inadequate self-perceived health literacy; for the Italian adult population this number increased to 54%.8\n\nIn response to the importance of this problem and the widespread lack of skills to address it, a group of physicians, teachers, public health experts, epidemiologists, designers, and journalists developed the Informed Health Choices (IHC) project in 2012. Their objective was to improve people’s ability to think critically about health choices, starting with primary school children.9\n\nWhereas learning new concepts in adulthood can be hindered by prejudices, misconceptions, and entrenched personal narratives, children have a more open and flexible approach towards learning. Moreover, children have been found to be able to learn the bases of critical thinking since primary school.10 Teaching critical thinking to primary school children can prepare them for making informed and unbiased choices as adults.\n\nUsing a human-centred design approach,11 the IHC group developed learning resources that aimed at teaching primary school children how to evaluate health claims and make informed health choices. Their first step was to develop a group of Key Concepts that established what students needed to learn to develop these skills. These concepts also provide a map to orient people towards critical thinking both in medicine and other knowledge areas.12 The full set of IHC Key Concepts (reviewed and updated yearly since 2012 and published at thatsaclaim.org) are classified into three thematic areas: claims, evidence, and choices: how to assess the reliability of health claims about treatment effects; what characterises reliable evidence from health research; and how to make informed health choices using the information that is available to you.\n\nAmong the 49 Key Concepts, 12 were selected by the IHC group to be the basis for the resources for primary school children, age 10-12 years (Table 1). The main resources for teaching are the Health Choices Book, Teachers’ Guide, Exercise Book13,14 (Figures 1-3).\n\nAfter being taught with the Key Concepts, students are requested to fill in a final test—questions from the “Claim Evaluation Tool”. This is a flexible battery of multiple-choice questions designed to assess understanding and use of the Key Concepts, iteratively developed and validated for use by children and adults across high- and low-income settings.15,16\n\nThe IHC project team evaluated the impact of the school resources in a cluster randomized trial involving 120 primary schools in Uganda.17 The trial—published in 2017—found that 10- to 12-year-old children who were taught lessons from the Health Choices Book that covered 12 Key Concepts, developed a better critical and decisional attitude about health claims and treatments than those who did not use these learning resources. Moreover, a follow-up of this trial found that children retain the ability to assess health claims for at least one year after the end of the lesson cycle,18 and a process evaluation showed that the resources were highly valued by both teachers and students.19\n\nThe core IHC group also developed contextualization guidance, to support subsequent translation and adaptation of learning resources to contexts that differ from where they were developed and tested in East Africa.20–22 Several research teams around the world have since engaged in contextualisation activities, with the aim of assessing the feasibility of resource application in different contexts.\n\nIn 2019, two authors of this article (CA and RR) started the Italian translation of the IHC learning resources and initiated a pilot study at a public primary school (Matteotti Primary School, Poliziano Institute) in Florence, Italy, in 2020. This study was designed to explore this contextualization of the IHC learning resources in Italy.\n\nOur primary study objective was to assess the feasibility of introducing the IHC curriculum in Italian primary schools. Our secondary objectives were to evaluate the ability of students in the pilot to assess health claims and make informed health choices, to explore students’ and teachers’ experiences of the learning resources, and to identify barriers and facilitators to implementation of the IHC curriculum in Italian primary schools.\n\n\nMethods\n\nWe carried out two main contextualisation activities: translation of the IHC learning resources to Italian and piloting of these translated resources in an Italian primary school.\n\nThe objective of the translation activities was to ensure that the language used in the IHC learning resources was suitable for use in Italian primary schools. We translated the learning resources from English into Italian from February to November 2019, following guidance from the IHC group,20,22 guidance for cultural adaptation23 and for translating and adapting tests.24 CA and RR independently translated the Health Choices Book and Exercise Book. We then reviewed and collated these into a single draft, making further adjustments after comparing it to the French and Spanish translations, based on linguistic analogies with Italian language. We collected feedback in two rounds, described under ‘Data collection’.\n\nFor the pilot, we had five objectives: 1) to assess the feasibility of introducing the IHC curriculum in Italian primary school, 2) to evaluate pilot students’ ability to assess health claims and make informed health choices, to explore 3) students’ and 4) teachers’ experiences of the IHC learning resources 5) to identify barriers and facilitators to implementation of the IHC learning resources in Italian primary schools.\n\nWe carried out the pilot during the second half of the 2019 to 2020 school year in two fifth-grade classes at Matteotti Primary School. We used the Guide for piloting the Informed Health Choices learning resources21 as methodological reference. The pilot study tasks are reported in Table 2, and a Gantt chart is presented in Table 3.\n\nSchool selection\n\nMatteotti Primary School (part of Istituto Comprensivo Poliziano) is a public school in Florence that is open to external projects and settled in a mixed socio-economic context. This school was selected by convenience sampling. In June 2019, CA and RR presented the project in person to the school principal and then to the collegial school bodies. After being approved by all the bodies, the project was introduced among the external projects for the 2019 to 2020 school year. Ten hours for each participating class were allocated to this project.\n\nClass selection\n\nThe school principal selected two fifth-grade classes to participate. These two classes were selected by exclusion: classes with either a reduced course load or that were delayed in teaching school curriculum subjects were excluded.\n\nParticipants\n\nA total of 46 children (aged 10–11 years) from two fifth-grade classes, four of their teachers, and two physicians (CA and RR) participated the piloting. CA and RR led the lessons. The four participating teachers were regularly in charge of the two selected classes. They performed the role of outside observers but also had a supporting role during the lessons (semi-participant observation).\n\nEthics approval and informed consent\n\nWe obtained an approval exemption for the study protocol from the Paediatric Ethics Committee of the Meyer Hospital in Florence, as no patients, biological specimen or clinical data were involved in the project. We obtained informed consent (extended data - S1 File)42 for piloting from the schoolteachers and children’s families prior to the onset of the pilot.\n\nThe pilot intervention\n\nThe intervention included the following activities:\n\n• Meeting with the schoolteachers before the beginning of the lessons\n\n• Pre-lesson assessment using Claim Evaluation Tool\n\n• Teaching nine lessons\n\n• Post-lesson assessment using Claim Evaluation Tool\n\nMeeting with the teachers\n\nBefore the lessons we met with the teachers to introduce them to the IHC learning resources and schedule the lessons. We gave each teacher a copy of the Health Choices Book, Italian translated version.25\n\nOne week before starting the lessons, CA and RR delivered 46 paper copies of the Claim Evaluation Tool (Italian translation) to the teachers. The teachers administered the Claim Evaluation Tool to the children and explained to them that it was a preliminary questionnaire before the project started. From the second half of January 2020 to the first half of June 2020, CA and RR taught nine lessons to each of the two classes. Lessons were scheduled to finish in mid-April, but were interrupted in March after Lesson 7, because of the national lockdown due to the SARS-CoV-2 pandemic. We restarted lessons in May and taught Lessons 8 and 9 remotely through Google Meet.\n\nBefore the start of the lessons, CA and RR gave each child a copy of the Health Choices Book (Italian translated version). Every lesson was focused on a chapter of the Health Choices Book. We performed a further online meeting with the children during which we conducted individual oral interviews with each child. During each lesson, at least one schoolteacher was present, both to observe and support interactions with the children.\n\nCA and RR taught the lessons according to the Teachers’ Guide. During the first 5 minutes of each lesson, we reviewed the previous lesson through a questions and answers session. During this time, we also addressed the most frequent mistakes that we had detected while correcting Exercise Books from the previous lesson, by explaining the topic again and using additional examples as needed.\n\nDuring the next 10 minutes of the lesson, we explained the keywords that are at the beginning of each chapter of the Health Choices Book. Then, we introduced the lesson’s topics in two ways: by asking questions to the children and by using real-world examples. For example, before Lesson 5 (“Comparisons of Treatments”), we asked the children how, in their opinion, health researchers could build a good basis for a health claim. After a brief discussion, some children in both classes suggested that a comparison was needed to form a good basis. After this phase, we used the story of James Lind and scurvy26 as vivid example of why we need to make comparisons to determine the effectiveness of treatments. In other lessons, we provided examples not found in the Health Choices Book, such as the case of hormone replacement therapy27 to help explain why people included in a treatment comparison should not decide which treatment they got, the ORBITA trial28 to delve into the placebo effect, and sham procedures. Since the story of James Lind attracted children’s attention, we ran other examples from real clinical trials and narrated these examples to the children as stories.\n\nIn Lessons 8 and 9 (taught remotely), we used the theme of COVID-19 to explain how study groups that are too small or studies without a proper control group can provide unreliable results. We discussed the case of hydroxychloroquine in COVID-19.29\n\nFollowing this introduction phase, we read a chapter from the Health Choices Book for 15 minutes, where CA was the voice of female characters and RR that of male characters. Then we facilitated class discussion by asking questions and exploring real-life examples.\n\nIn the next 15 minutes, we guided the class through group activities related to each chapter. Then the children filled in exercises in the Exercise Books and returned them to us for correction before the next lesson.\n\nWe used the last 15 minutes of each lesson for questions, comments, and feedback through focused conversations30 with the children. After each lesson, CA and RR noted comments and observations from the schoolteachers and filled in observation forms (extended data - S7 File).42\n\nAt the end of the lesson cycle, right before the upcoming school year ended, we gave students access to the Claim Evaluation Tool through the online school platform, with instructions to fill in the questionnaire alone and send it by email to CA. We sent email reminders to students during the following weeks.\n\nTranslation feedback\n\nThe Italian translation finalized draft of the Health Choices Book was subjected to two rounds of feedback. In the first round, two teachers not involved in the project (a former humanities teacher in secondary school and a primary school teacher) provided feedback. CA and RR selected the teachers by sampling convenience and based on these teachers’ wide experience in school projects and as teacher trainers. We gave the teachers a copy of the draft and asked them to respond to a 6 items questionnaire (extended data - S2 File)42 in addition to writing a comment about their general impressions of the translated IHC resources (extended data - S3 File).42\n\nIn the second round, we collected feedback from 10 children, ages 10 to 11 years, who attended the fifth grade in Matteotti Primary School, and who were not scheduled to participate in the upcoming lessons of the IHC project. One of the fifth-grade classes was randomly selected by the vice-principal and the class teacher selected 10 children based on a progressive gradient of reading and comprehension skills. We sent a letter to the selected children and their parents asking each child to read one chapter of the latest version of the Health Choices Book (Italian translation) and to answer three questions about the text (extended data - S4 File).42\n\nPilot data collection\n\nTo analyse the five pilot objectives, we used seven different methods of data collection (for an overview of what data informed which objective, see Table 4):\n\n1. Teachers’ semi-participatory observations after each lesson. At least one schoolteacher attended each lesson. After each lesson CA or RR had a brief meeting with the teachers and conducted semi-structured interviews with them, based on three open questions: 1) Do you have any observation about the lesson you have attended? 2) How do you think the children dealt with the Key Concepts? 3) Do you have any suggestion for improvement? CA or RR made written notes from the teachers’ answers after the meeting.\n\n2. Feedback at the end of each lesson by CA and RR. After leading each lesson, CA and RR filled in the observation form, which is provided in the “Guide for Piloting the Informed Health Choices Learning Resources”21 (extended data - S7 File and S8 File).42\n\n3. Children’s focused conversations after each lesson. CA or RR moderated these focused conversations that included four categories of questions, referred as ORID set of questions31: Objective (to collect information about the context): “What was this lesson about?”; Reflective (to identify feelings associated with information): “Was there anything less easy to understand? What did you like most? What did you dislike?”; Interpretive (what it means to you): “Have you got any insights or comments about the lesson concepts?”; Decisional (what are the next steps): “What would you improve or change in the lesson or in the textbook?” We spoke to the children as a class. CA or RR (whoever was not moderating the conversation) collected data through written notes during the session (see extended data - S10 File).42\n\n4. Children’s answers to exercises in the Exercise Book for Lessons 1 to 7 (not feasible for Lessons 8 and 9 which were taught remotely). After each lesson, each student filled in the corresponding exercises in their Exercise Book and handed them in to CA and RR. We corrected and returned them to the children at the beginning of the next lesson. Exercises included true/false statements, requests to define terms (e.g. “What is a claim?”), and detection activities (e.g., identify the basis of a provided health claim).\n\n5. Individual children’s interviews after the end of the lesson cycle. After the lessons’ cycle, CA or RR interviewed children individually, asking one question to each child. These questions were designed to assess knowledge of the Key Concepts and ability to apply this knowledge to real or hypothetical situations. Each child answered one different question that we chose randomly (extended data - S13 File),42 and we made written notes of their answers.\n\n6. Teachers’ evaluation of the IHC learning resources at the end of the lessons cycle. After the end of the lessons’ cycle, we explored the teachers’ experience of the IHC learning resources. We emailed them an evaluation questionnaire (see extended data - S11 File and S12 File).42 Each teacher filled in the questionnaire and emailed it back to us.\n\n7. Children’s answers to the Claim Evaluation Tool questionnaire, both before and after the lessons’ cycle. The objective was to address the ability of the students to assess health claims about treatments and make informed health choices. After the end of the lessons, the Claim Evaluation Tool was uploaded to the online school platform. The questionnaire included 24 questions (15 multiple-choice questions and 9 true/false statements). The students were asked to fill in the questionnaire alone and send it via email. We collected and anonymized the data.\n\nTranslation feedback: qualitative analysis\n\nWe analyzed the data using a thematic analysis approach.32 After familiarizing ourselves with the translation feedback, CA and RR categorized the feedback through six thematic labels already used for the evaluation of teachers’ feedback about the IHC resources20: errors in the text; expressions or concepts not understood; expressions or concepts that can improve their understanding; additional text suggestions to improve understanding; general comments to improve resources; and errors in the edition. We coded all the answers from the teachers’ 6 items questionnaire (extended data - S2 File)42 according to these themes, except for the final comment, attributed these data to the six thematic labels and made a summary report. Then, we analyzed the teachers’ final comments through a deductive thematic analysis based on categories teams have previously employed when exploring user experience of the IHC learning resources19–21: understandability, desirability, suitability, and usefulness.\n\nWe independently assigned each data to a user experience category and resolved disagreements through a reassessment of the attributions until a final agreement was reached. Then, we generated a final narrative summary (extended data - S3 File).42\n\nWe coded the children’s answers to the interview questions using three thematic labels based on categories teams have previously employed exploring children’s user experience of IHC learning resources20: what children liked about the text, what children did not like about the text, difficult words that were highlighted and generated a narrative summary of this feedback (extended data - S5 File).42\n\nThe pilot intervention: quantitative analysis\n\nFor the children’s answers in the Exercise Books, we assessed the mean proportion of correct answers for each chapter, the mean proportion of correct answers in chapters 2, 3 and 4 (content focused on bad bases of health claims) and in chapters 5, 6 and 7 (content focused on comparisons of treatments). For each question in the Exercise Book, we also assessed the proportion of answers with less than 70% correct rate.\n\nTo analyse the Claim Evaluation Tool answers, both pre- and post-intervention, we assessed the mean score and standard deviation (SD) of the proportion of correct answers at the individual level; the proportion of the students with a passing score (≥13 right answers out of 24); and the proportion of the students with a mastery score (≥20 right answers out of 24). These cut-off scores for passing (having at least a borderline ability to apply the concepts) and mastery (having mastered the concepts) were determined in a previous study, using judgments made by researchers and teachers in a combination of established methods to reach consensus.33\n\nThe pilot intervention: qualitative analysis\n\nThe following qualitative data were collected: (1) Teachers’ semi-participatory observations after each lesson; (2) Feedback at the end of each lesson by CA and RR; (3) Children’s focused conversations with CA and RR after each lesson; (4) Individual children’s interviews after the end of the lessons; (5) Teachers’ evaluation of the IHC learning resources at the end of the nine lessons cycle.\n\nWe conducted a deductive thematic analysis32 of the collected data based on the categories previously employed in IHC project pilots19–21: user experience (understandability, desirability, suitability, and usefulness), seriousness of these experiences for the user, teaching method, barriers and facilitators, proposals, and comments. CA and RR organized transcribed interviews of children and teachers in two files. Then we independently coded the data according to categories. For each category, we discussed attributions, and dealt with disagreements through extended discussion. Data that we could not place into prespecified categories were coded as “Comments”. Finally, we created a narrative summary of the data for each category and explored the range and nature of the phenomenon, as well as some possible explanations for the results.\n\nRegarding the final individual children interview, we evaluated children’s answers based on three categories related to learning the IHC Key Concepts: assessing the reliability of health claims about treatments’ effects; assessing if a comparison between treatments is fair; knowing how to make an informed health choice. We defined the first and second objective as ‘Knowledge’ and the third objective as ‘Orientation’.34 Moreover, we evaluated students’ learning of each objective based on four descriptive grades of evaluation in accordance with those indicated by the Italian Ministry of Education for the learning evaluation in primary schools: advanced, intermediate, basic, in the process of first acquisition (extended data - S9 File).42\n\n\nResults\n\nNo major difficulties or issues were encountered with the Italian translation of the learning resources. However, we made several choices that are explained below:\n\n• The title “The Health Choices Book” has been translated into the Italian equivalent of “Health Decisions Book”. Choice and decision are not true synonyms in Italian: from an etymological perspective, both terms refer to the concept of “selection” (ex-legere and de-caedere in Latin), but from a semantic perspective, their meaning is different. “Choice” refers to the power or capability to choose, whereas “decision” refers to determination that is achieved after examining the available information. As the objective of the IHC project is to teach how to make health decisions that are informed by an adequate evaluation of the available evidence and how this evidence matches with an individual’s values and preferences, we opted to use the term “decision” instead of “choice —in line with the Spanish and French translations.\n\n• The first names of professors “Connie Compare” and “Francis Fair” were omitted, and only their translated surnames were used, such as in the Spanish translation. Moreover, in Italian, there is no alliteration between names and surnames, which is present in English. The names have, therefore, been translated as “Professoressa Confronto” (English translation: Professor Compare) and “Professor Giusto” (English translation: Professor Fair).\n\n• In the original text, some keywords are provided in Kiswahili, the state language of Uganda, to aid understanding. We substituted with these with English terms in the Italian translation. As English language is a curricular subject in Italian primary schools, this provided children with an extra opportunity for language learning.\n\n• Feedback from teachers and children about the draft translation of the Health Choices Book are presented in S2 File, S3 File and in S5 File (see extended data).42 Teachers found no errors or comprehensibility issues over the text. They both found the text well written, the story compelling and age appropriate for the children. They made suggestions about how to convey some contents of the text to the children. One teacher stressed the need to explain to the primary school children a broader meaning of “personal experience”: in the Health Choices Book personal experience is presented as an incorrect basis for a claim about a health treatment’s effect. However, in other areas, personal experience can be a vehicle for identity and growth because it informs on the personal impact with a life event. Another teacher pointed out that, while learning the Key Concepts, children should be considered as individuals within a specific context (both the class and the family context). “The family, in particular, should be involved through various initiatives”.\n\nAll children rated the text as interesting and fun and did not raise any major issue. Challenging terms that children understood less well are “mislead”, “herbalist”, “malaria”.\n\nCA and RR made minor changes to the draft after according to teachers’ and children’s feedback, and a final version was completed in the autumn of 2019.\n\nIn December 2019, an Italian publisher—Il Pensiero Scientifico Editore—printed 100 copies of a limited edition of the Health Choices Book25 and 60 copies of the Exercise Book for free.\n\nQuantitative analysis\n\nThe main results of quantitative analysis are summarized in Table 5, Table 6, and Figure 4.\n\nExercise book answers\n\nA total of 46 students attended the lessons (two classes with 24 and 22 children, respectively) and participated to either CET-1 or CET-2. Twenty-eight (60.9%) were female. All children were 10 to 11 years old. 91.3% of the students completed the exercises included in the Exercise Book, except for Lessons 8 and 9 that took place remotely.\n\nFor Lessons 2 to 4, which focused on the need to assess inadequate bases of health claims, the mean proportion of correct answers was 88.3% (DS 4.6). For Lessons 5 to 7, which focused on comparisons of treatments, the mean proportion of correct answers was 83.2% (DS 7.8) (Table 5 and Table 6).\n\nThe lesson showing the least proportion of correct answers (72.2%) was Lesson 6, which was about fair treatment comparisons.\n\nWe also analysed the proportion of correct answers for each question, with the following questions resulting in less than 70% of the children with correct answers:\n\n- 35.0%: “Should the people in the comparison choose who gets the vaccine? Why?” (Lesson 6, page 34, question 1)\n\n- 47.5%: “In a fair comparison, the treatment is the only important difference between groups” (Lesson 6, page 32, true/false statement 3)\n\n- 58.1%: “This book tells you what treatments to use” (Lesson 1, page 7, true/false statement 2 of exercise 2)\n\n- 62.5%: “Should the professor choose who gets the vaccine? Why?” (Lesson 6, page 33, exercise 2, question 2)\n\n- 69%: “The basis for the claim is more important than who is making the claim” (Lesson 4, page 20, exercise 1, true/false statement 4)\n\nSee also extended data - S14 File.42\n\nClaim evaluation tool\n\nOut of 46 children, 45 (97.8%) completed CET-1 and 40 (87.0%) completed CET-2. The mean proportion of right answers for all children was 56.3% (SD 16,6) for CET-1 and 89.2% (SD 9.4) for CET-2.\n\nThe proportion of students who achieved a passing score (≥13 correct answers out of 24) was 71.1% (32/45) for CET-1 and 100% (40/40) for CET-2. The proportion of students who achieved a mastery score (≥20 correct answers out of 24) was 2.2% (1/45) for CET-1 and 82.5% (33/40) for CET-2 (Table 5).\n\nThirty-nine students completed both CET-1 and CET-2. Among these students, the mean difference in the proportion of correct answers between CET-1 and CET-2 was 30.1% (95% CI 25,5%-34,8%; p< 0.00001). The mean difference in the proportion of those achieving a passing score was 23.1% (95% CI 9.2%-36.9%), while the mean difference in the proportion of those achieving a mastery score was 79.5% (95% CI 66.2%-92.7%). Thirty-seven students out of 39 (94.9%) improved their score from CET-1 to CET-2, while 2 students out of 39 reached the same score in the two tests. No student worsened between CET-1 and CET-2 (Figure 4).\n\nSee also extended data - S15 File.42\n\nThe results of the qualitative analysis are summarized with more detail in S6 File (see extended data).42\n\nSeriousness for the users\n\nNeither the students nor the schoolteachers reported any major or minor issues during the lessons. The teachers pointed out that the Health Choices Book is written with an adequate language for these students’ age and that drawings and dialogues among characters further help comprehension and positively attract students’ attention. Moreover, the teachers underlined positively how the book’s topics are dealt with according to a gradient of difficulty.\n\nThe students unanimously observed that the comic makes it easier and enjoyable to learn concepts and that most examples made were consistent with their everyday lives.\n\nThe schoolteachers underlined the relevance of the first chapter, which lays the foundation for many concepts that are addressed over the subsequent chapters. One teacher suggested splitting the first chapter into two lessons to facilitate learning.\n\nUnderstandability and desirability\n\nBoth the students and the schoolteachers found the understandability of the IHC learning resources to be good. They highlighted how the subdivision of episodes helped the children isolate each topic and understand it better. Moreover, the teachers observed that the questions in the Exercise Book offered the children a moment of self-assessment and that group activities promoted a consolidation of what had been learnt. RR and CA noted that the main difficulties were about learning language children are not used to. For example, the distinction between claim, basis, treatment, and effect can be difficult at first, but the structure of the book with repeated examples and activities helped children to increasingly master these concepts.\n\nSome students observed that the keywords at the beginning of each chapter were not always easy to understand at first (such as “chance” or “claim”), but they were subsequently fully clarified by examples provided in the Health Choices Book.\n\nRegarding desirability, the students and schoolteachers valued it as excellent. They did appreciate the comic, characters, and dialogues. Most of the students appreciated learning about the bad bases of treatment claims. From the beginning, the students were very interested in the Key Concepts and enthusiastic about the lessons. This positively affected their motivation to learn.\n\nSuitability\n\nWe also found suitability to be high. Concepts explained in the Health Choices Book elicited examples from the students’ daily lives. For example, the “new is better” concept inspired a discussion among the children about the differences between branded and non-branded products. Moreover, they discussed the widespread claim that carrots are good for sight while learning the concept that “widely used treatments or those that have been used for decades are not necessarily beneficial or safe”.\n\nNone of the children raised issues about the location of the Health Choices Book (the book story takes place in Africa, and the main characters are two students at a local school). On the contrary, as a schoolteacher pointed out, the different setting and unusual sound of some African names constituted an added value for the children’s interest and curiosity. Furthermore, the teachers also observed that although the book is set in a context that differs in some ways from the children’s own, the situations, dialogues, and concepts in the book are universal and independent from the context.\n\nUsefulness\n\nRegarding the usefulness of the Key Concepts, the schoolteachers used these concepts to integrate the core curriculum of the students with new competencies, such as a project about the critical appraisal of advertisements. Moreover, the children were enthusiastic about transposing the learned concepts to drawings and to examples from their daily lives (e.g. the concept of personal experience as a bad basis for a treatment claim) (Figure 5).\n\nFacilitators and barriers\n\nValue of the IHC learning resources\n\nBoth the students and the schoolteachers highlighted the value of the IHC learning resources. The students appreciated the comic and realistic examples and found the activities proposed in the Exercise Book to be very entertaining.\n\nThe schoolteachers underlined the value of the IHC learning resources in terms of the ability of these resources to teach critical thinking. The kind of comic, way of teaching the lessons, and group activities were considered facilitators of the learning of the Key Concepts.\n\nFinally, the schoolteachers attending the lessons underlined how class participation was widespread and did not involve only the most enterprising students.\n\nCompatibility with the Italian school curriculum and with the teaching style of teachers\n\nThe development of critical thinking is deemed a cross-cutting competence between the various topics of the individual school curriculum. Importantly, we discovered that teachers used the Key Concepts in parallel projects in other subjects. For example, building on the concepts about the bad bases for health claims, one teacher started a project about taking a critical approach to advertisements. The teacher selected some advertisements making claims about food and about oral supplements. The students, organized in small groups, had to analyze both the design and the content of each advertisement, and identify the sender and receiver of the message, the claim of the advertisement and the basis of the claim. Then a representative from each group reported the responses to the class and the children discussed the reliability of the advertising message.\n\nAnother teacher upgraded the science topic \"human body\" through the exploration of treatments’ effects about illnesses of organs or systems. This teacher asked CA and RR to correlate some of the “human body” topics to some Key Concepts of the IHC lessons. For example, we used the topic of the musculoskeletal system to explain to children the concepts of placebo effect and shame procedures regarding meniscus degeneration treatments and described how this was investigated in clinical trials.\n\nFinally, another teacher asked the children to transfer the learned Key Concepts into drawings. The transposition of the concepts into images helped the children focus on what they had learned (Figure 5), and it also helped us discover which students did not completely understand a given concept.\n\nMoreover, teachers pointed to additional potential areas of projects parallel to the IHC curriculum: e.g., in mathematics, civic education, and technology (extended data - S6 File).42\n\nThe teachers observed that the resources were compatible with their usual teaching method. They valued interactivity of the lessons and the employment of practical examples.\n\nIncentives and disincentives\n\nThe teachers underlined that support from the school principal and the possibility of connecting the IHC learning resources to the school curriculum were incentives for the project implementation. They also cited the school’s openness to external projects and the possibility of using the interactive whiteboard to visualize the learning resources as incentives for project realization.\n\nThe only disincentive that was highlighted by both the students and the schoolteachers was remote learning in the later lessons. The teachers pointed out that remote learning hindered interaction with and within students, with a negative impact on lessons participation: teachers observed that lessons’ engagement was mostly reduced in children with lower school performance.\n\nChildren’s attendance was also lower for the online lessons. CA and RR observed that technical issues during online lessons (e.g., internet connection, microphone malfunctioning) often hindered interaction with the students and within the students.\n\nTransfer to real life experience\n\nAll the teachers observed that learning about the Key Concepts raised their awareness about how unreliable health claims have the power to mislead health choices and how it is crucial to become able to recognize the correct basis of a health claim. Teachers were impressed by the concept that expert opinions are not a good basis for a health claim if these opinions are not grounded on fair comparisons.\n\nThey also pointed out that, after attending the IHC lessons, they felt more confident in asking their physicians questions about the potential adverse effects of treatments and about the option of not using a treatment at all during an illness.\n\nDuring the lessons, the students mentioned and reconsidered many claims that they had been exposed to (e.g., through advertisements or through friends’ and relatives’ claims), even outside health science. For example, one child described making a comparison between a set of branded and expensive crayons with a cheaper and not-branded set: she coloured two drawings with these two crayons sets and didn’t observe any major difference in the final effect.\n\nFinal oral interview with children\n\nA qualitative evaluation of the final oral interview with children is reported in S9 File (see extended data).42\n\nWe found that 30 out of 44 students (68.2%) had an advanced knowledge of the Key Concepts and 30 out of 44 (68.2%) had an advanced orientation. These results confirmed that most students acquired a good knowledge and a good orientation about the Key Concepts presented in these resources and skills to begin think critically about health claims.\n\n\nDiscussion\n\nFindings from this first study about the contextualization of the IHC learning resources in Italian primary school indicate that these resources are compatible with the Italian primary school context and with the Italian primary school curriculum. Results of the quantitative and the qualitative analyses consistently showed positive experiences with the IHC learning resources in both children and teachers.\n\nThese findings are consistent with those reported in other contextualization studies of the IHC learning resources in different countries.35 Like other IHC pilot experiences in Europe, the unfamiliar African village setting of the story in the Health Choices Book was not an obstacle to the children’s interest. Instead, it appeared to add value, as the story set in a different place from children’s usual life context seemed to stimulate children’s curiosity. Furthermore, although the Health Choices Book sometimes refers to common practices that are unusual for the Italian cultural context (e.g., putting cow dung on burns), some of these are comparable to Italian local practices (e.g., putting oil of olive on burns), and therefore did not constitute a barrier for text comprehension.\n\nA novel result of this study was the suitability of the Key Concepts to be applied to other knowledge areas in primary school: for example, in parallel with the IHC lessons, the schoolteachers started projects about taking a critical approach to advertisements and creating figurative representations of the Key Concepts. Although, to our knowledge, this finding has not been reported yet in other IHC pilot experiences in primary schools, the IHC Key Concepts have been transposed to fields outside health science, such as education and environmental policies,12 and can therefore provide a common conceptual map for thinking critically about effect claims across subjects.\n\nThis study has important limitations. First, it involved a small number of children belonging to a single primary school, which weakens the generalizability of the results. Second, unlike the Ugandan trial, two physicians (CA and RR) taught the lessons to the children, rather than the schoolteachers. CA and RR also gathered the data and were part of the research group that analysed them. It is uncertain to what extent this involvement could have influenced the lesson’s delivery, as well as the data collection and analysis. However, the Ugandan randomized trial found that the use of these learning resources improved children’s ability to assess health claims, even when taught by teachers with no medical background.17 Therefore, we can hypothesize that having teachers with medical background lead the lessons did not constitute the key element for this piloting’s results.\n\nThird, the very positive results from the Claim Evaluation Tool may not be reliable. In this study, not only all the students involved in the IHC lessons obtained a passing score on the Claim Evaluation Tool final questionnaire, but 80% of them obtained a mastery score, i.e., they mastered the Key Concepts. However, there was no control group for the assessment of CET results, and the CET was administered to the children both before and after the lessons. The before-after test administration could have given an advantage to the children and be ultimately responsible for an overestimation of the final scores.\n\nHowever, the primary objective of this piloting was not to demonstrate the ability of the IHC learning resources to improve critical thinking about health claims in primary school children —an objective already met in a large randomized controlled trial— but to evaluate to what extent these resources could be integrated into the Italian school curriculum. The dramatic difference in Key Concepts learning we found before and after the lessons is an indirect indication that these contextualized resources are understandable and suitable for teaching Italian primary school children.\n\nAn important strength is the consistency of the feedback received from different sources and gathered through heterogeneous methods. The results of both the qualitative and quantitative analyses converge, underscoring the feasibility of implementing contextualized IHC learning resources in Italian primary school.\n\nThe mean percentage of correct answers from the Exercise Book was more than 80%. However, some concepts were found to be more difficult to understand for the children. For example, a few questions about chapters 4 and 6 had the highest rate of errors. In these chapters, the concepts of blinding participants and blinding personnel within a fair comparison was particularly difficult to understand for children. Whether confirmed in future pilot studies, these findings could be useful for teachers to be aware of.\n\nAll teachers reported remote learning as the only barrier detected for the implementation of the IHC learning resources. In March 2020, Italy was the first country in Europe to have a national lockdown and the resulting closure of all grade schools led to a shift to remote learning. Although remote learning has been an opportunity to carry on the school programs and to maintain contact between teachers, children and families, research has pointed out also its downsides. In a survey, which was carried out between October and November 2020 in eight countries, more than 2,500 teachers were asked about the effectiveness of online schooling. Overall teachers gave remote learning an average effectiveness of five out of ten. Moreover, they observed some students had a learning delay of around three months and that those from poorer backgrounds were falling further behind. These observations are consistent with our experience: during our piloting, both we and the teachers observed that the interaction between students and teachers was reduced during the remote lessons. Teachers also observed that this phenomenon occurred to a greater extent in students with lower school performances. Moreover, during the online lessons we were unable to carry out activities at the end of the lesson precisely because the online mode would have greatly limited the interaction necessary for these activities. Although we have replaced the activities with oral questions, we have lost a tool that allowed the children to consolidate the Key Concepts they learned while having fun. Consistently, some studies indicate that active-learning results in better learning outcomes than passive learning or instructor-centered approach, both in-person and online.36–39\n\n\nConclusions\n\nHealth literacy is a conditio sine qua non for making good health choices. The SARS-CoV-2 pandemic has further underlined the desperate need for widespread health literacy in the whole population.40 Education and health have common interests in developing students’ ability to think critically about the information they encounter. Acquiring a critical attitude toward health claims starting in primary school can lay the foundations of thinking carefully about health choices later in life, with the potential to impact health outcomes across a wide population group.\n\nIn Italy, objectives of the scientific curriculum for primary school entail “detecting phenomena, asking questions, constructing hypotheses; observe, experiment and collect data; formulate conclusive hypotheses and verify them” in order to “raise the logical and critical thinking”. The IHC learning resources satisfy all these objectives and may therefore represent an engaging foothold towards science since they concern health, that is a highly relevant and universal topic. Children can learn the bases of critical thinking about health treatments in primary school and refine these skills as they grow up. That way, as adults, they will be able to make better health decisions for themselves and to successfully participate to an informed public debate.\n\nThis pilot study represents a first step for broader contextualization activities aimed at consolidating our results and at fostering the inclusion of IHC concepts in the scientific curriculum of Italian primary schools.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and its supporting information figures and tables.\n\nZenodo: Feasibility of contextualizing the Informed Health Choices learning resources in Italy: A pilot study in a primary school in Florence. Supporting information, DOI: https://doi.org/10.5281/zenodo.6581224.42\n\nThis project contains the following extended data:\n\n- S1 File. Informed Consent for children’s parents and teachers\n\n- S2 File. Teacher’s feedback about the Italian translation of the IHC resources\n\n- S3 File. Qualitative analysis of teachers’ final comments about the Italian translation of the Health Choices Book\n\n- S4 File. Feedback collection from children about the translation of the Health Choices Book\n\n- S5 File. Children’s feedback about the Italian translation of the Health Choices Book\n\n- S6 File. Thematic analysis of qualitative data (extended version)\n\n- S7 File. Lesson Observation Form IHC\n\n- S8 File. Lesson Observation Form IHC Results\n\n- S9 File. Results of the final individual interview with the children\n\n- S10 File. Focused Conversation with the students\n\n- S11 File. Evaluation Questionnaire for Schoolteachers after the end of the 10-lessons’ cycle\n\n- S12 File. Teachers’ answers to the evaluation questionnaire of the IHC learning resources at the end of the lessons’ cycle\n\n- S13 File. Final individual interview with each child\n\n- S14 File. Exercise Book results\n\n- S15 File. Claim Evaluation Tool results\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: COREQ (COnsolidated criteria for REporting Qualitative research) Checklist. Feasibility of contextualizing the Informed Health Choices learning resources in Italy: A pilot study in a primary school in Florence, DOI: https://doi.org/10.5281/zenodo.6581224.43\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthor contributions\n\nCA made the draft of the article. RR and SR reviewed the draft. All authors have reviewed the draft. CA and RR codified the categories of the qualitative thematic analysis, and all authors evaluated the attributions to each label. CA, RR and GF performed the quantitative analysis. CA, RR and SR reviewed the final quantitative analysis. CA and SR reviewed the final qualitative analysis. CA and SR revised the final version of the tables and figures.",
"appendix": "Acknowledgements\n\nWe thank Luca De Fiore and Il Pensiero Scientifico Editore for having published a limited edition of the Italian translation of the “Health Choices Book” free of charge, therefore allowing us to pilot the resources in Florence.\n\nThis article is dedicated to Alessandro Liberati, who was a pioneer in advocating the need for health research to be patient-oriented and for people to participate in their own health decisions in an informed and critical way. 41\n\n\nReferences\n\nChewning B, Bylund C, Shah B, et al.: Patient preferences for shared decisions: A systematic review. Patient Educ. Couns. 2012 January; 86(1): 9–18. PubMed Abstract | Publisher Full Text\n\nMoynihan R, Bero L, Ross-Degnan D, et al.: Coverage by the news media of the benefits and risks of medications. N. Engl. J. Med. Overseas Ed. 2000; 342: 1645–1650. 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PubMed Abstract | Publisher Full Text\n\nNsangi A, Semakula D, Oxman AD, et al.: Effects of the Informed Health Choices primary school intervention on the ability of children in Uganda to assess the reliability of claims about treatment effects: a cluster-randomised controlled trial. Lancet. 2017; 390(10092): 374–388. PubMed Abstract | Publisher Full Text\n\nNsangi A, Semakula D, Oxman AD, et al.: Effects of the Informed Health Choices primary school intervention on the ability of children in Uganda to assess the reliability of claims about treatment effects, 1-year follow-up: a cluster-randomised trial. Trials. 2020; 21: 27. PubMed Abstract | Publisher Full Text\n\nNsangi A, Semakula D, Glenton C, et al.: Informed health choices intervention to teach primary school children in low-income countries to assess claims about treatment effects: process evaluation. BMJ Open. 2019; 9: e030787. PubMed Abstract | Publisher Full Text\n\nThe Informed Health Choices group: Guide for translating the Informed Health Choices school resources. Informed Health Choices Working Paper, Norwegian Institute of Public Health. 2019. ISBN (digital): 978-82-8082-994-8.\n\nThe Informed Health Choices group: Guide for piloting the Informed Health Choices (IHC) school resources. Informed Health Choices Working Paper, Norwegian Institute of Public Health. 2017. ISBN 978-82-8082-895-8 (updated February 2018).\n\nThe Informed Health Choices group: Resource production guide for translating and adapting Informed Health Choices learning resources. Informed Health Choices Working Paper, Norwegian Institute of Public Health. 2019. ISBN (digital): 978-82-8082-994-8.\n\nTranslation is not enough: Cultural adaptation of health communications materials, a report commissioned by the European Centre for Disease Prevention and Control (ECDC) Stockholm.April 2016. Publisher Full Text .\n\nITC Guidelines for Translating and Adapting Tests (Second Edition). Int. J. Test. 18(2): 101–134.\n\nGruppo Informed Health Choices: Il Libro delle Decisioni sulla Salute: Imparare a riflettere sui trattamenti. Un libro di scienza della salute per i bambini della scuola primaria. Roma: Il Pensiero Scientifico Editore, 2019 (Titolo originale: The Health Choices Book: Learning to think carefully about treatments. A health science book for primary school children). Olso:Norwegian Institute of Public Health;2016.978-88-490-0671-1.\n\nMilne I, Chalmers I: Documenting the evidence: the case of scurvy. Bull. World Health Organ. October 2004; 82: 10.\n\nWassertheil-Smoller S, Hendrix S, Limacher M, et al.: Effect of Estrogen Plus Progestin on Stroke in Postmenopausal Women: The Women's Health Initiative: A Randomized Trial. JAMA. 2003; 289(20): 2673–2684. PubMed Abstract | Publisher Full Text\n\nAl-Lamee R, Thompson D, Dehbi HM, et al.: ORBITA investigators. Percutaneous coronary intervention in stable angina (ORBITA): a double-blind, randomised controlled trial. Lancet. 2018 Jan 6; 391(10115): 31–40. Epub 2017 Nov 2. Erratum in: Lancet. 2018 Jan 6;391(10115): 30. PubMed Abstract | Publisher Full Text\n\nAxfors C, Schmitt AM, Janiaud P, et al.: Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials. Nat. Commun. 2021; 12: 2349. PubMed Abstract | Publisher Full Text\n\nFritzen-Pedicini C, Bleasdale SC, Brosseau LM, et al.: Utilizing the focused conversation method in qualitative public health research: a team-based approach. BMC Health Serv. Res. 2019; 19: 306. PubMed Abstract | Publisher Full Text\n\nAslam H, Naumchev A, Bruel J-M, et al.: Examining Requirements Documentation through the Focused Conversation Method. 29th International Conference on Information Systems Development (ISD 2021). Sep 2021. València, Spain. ⟨hal-03435282⟩\n\nNowell LS, Norris JM, White DE, et al.: Thematic Analysis: Striving to Meet the Trustworthiness Criteria. Int. J. Qual. Methods. 2017; 16(1): 160940691773384–160940691773313. Publisher Full Text\n\nDavies A, Gerrity M, Nordheim LV, et al.: Measuring ability to assess claims about treatment effects: establishment of a standard for passing and mastery. IHC Working Paper. 2017. 978-82-8082-802-6.\n\nJoughin G: A short guide to oral assessment. Leeds Met Press in association with University of Wollongong.2010. 978-1-907240-09-6.\n\nNsangi A, Semakula D, Rosenbaum SE, et al.: Development of the informed health choices resources in four countries to teach primary school children to assess claims about treatment effects: a qualitative study employing a user-centred approach. Pilot Feasibility Stud. 2020; 6: 18. PubMed Abstract | Publisher Full Text\n\nKids learn better in class than when studying from home, finds teacher survey.Last access Sept 14, 2022.Reference Source\n\nFreeman S, Eddy SL, McDonough M, et al.: Active learning increases student performance in science, engineering, and mathematics. Proc. Natl. Acad. Sci. 2014; 111: 8410–8415. PubMed Abstract | Publisher Full Text\n\nChen B, Bastedo K, Howard W: Exploring best practices for online STEM courses: active learning, interaction & assessment design. Online Learn. 2018; 22: 59–75. Publisher Full Text\n\nDavis D, Chen G, Hauff C, et al.: Activating learning at scale: a review of innovations in online learning strategies. Comput. Educ. 2018; 125: 327–344. Publisher Full Text\n\nRoozenbeek J, Schneider CR, Dryhurst S, et al.: Susceptibility to misinformation about Covid-19 around the world. R. Soc. Open Sci. 2020; 7(10): 201199. [published Online First: 2020/11/19]. PubMed Abstract | Publisher Full Text\n\nLiberati A: Need to realign patient-oriented and commercial and academic research. Lancet. 2011 Nov 19; 378(9805): 1777–1778. PubMed Abstract | Publisher Full Text\n\nAlderighi C, Rasoini R, Formoso G, et al.: [Dataset] Feasibility of contextualizing the Informed Health Choices learning resources in Italy: A pilot study in a primary school in Florence.2022. Publisher Full Text\n\nAlderighi C, Rasoini R, Formoso G, et al.: Feasibility of Contextualizing the Informed Health Choices Learning Resources in Italy: A pilot study in a primary school in Florence. 2022. Publisher Full Text"
}
|
[
{
"id": "153255",
"date": "28 Oct 2022",
"name": "Emanuela Guarcello",
"expertise": [
"Reviewer Expertise General Pedagogy"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary\nThe article addresses the topic of the promotion of critical thinking about treatments claims and health choices in primary school. Within the frame of this topic, the authors focused on the hypothesis that the improvement of a child's ability to think critically about health choices, starting with primary school, could positively affect their capacity to make good health choices when they will be adults, navigating the overabundance of unreliable or unbalanced information and sharing in a founded way, their health decisions with Physicians.\nThe authors found support for this hypothesis in a previous study realized starting from 2012 within the Informed Health Choices (IHC) project, through a randomized controlled trial of 120 schools in Uganda. On the basis of the results obtained in this research, the authors worked to a contextualization of the IHC resources for using them in other languages and settings. In particular, the article describes the contextualization for using them in Italian primary school, with specific regard to assessing the feasibility of introducing the IHC curriculum in Italian primary schools, to evaluate the ability of students in the pilot to assess health claims and make informed health choices, to explore students’ and teachers’ experiences of the learning resources, and to identify barriers and facilitators to the implementation of the IHC curriculum.\nGeneral comments\nThe manuscript is well written, comprehensive and clearly presented, and interesting both for the health and teaching fields. The logic of the submission is cogent, and the presented elements fit well together. In particular, the objectives are clearly and specifically articulated, the theoretical frame is clear, and the literature is indicated and appropriate. The research methods employed, and the data analysis techniques used are appropriate and clear. The sources are clearly defined and well-articulated. The results and the findings are clear, and the final data support the conclusion and the implications that the author states. The findings contribute to advancing our knowledge and understanding with particular regard to the strategies of promotion of critical thinking in primary school, with a special focus on health choices.\nSpecific comments\nAmong the main advantages of the presented research, it is possible to identify:\nThe well-founded background on which the presented article is placed (randomized controlled trial of 120 schools in Uganda).\n\nThe structure and contents of the resources for teaching, elaborated and tested by the research group.\n\nThe well-articulated methods of data collection and analysis.\n\nThe general research vision, aimed at structuring a systematic curriculum for primary schools in Italy on the promotion of critical thinking (with respect to the topic of Informed Health Choices). This is a point of innovation in the scientific panorama and in current scholastic practices.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "153254",
"date": "28 Oct 2022",
"name": "Biesty Linda",
"expertise": [
"Reviewer Expertise Evidence synthesis",
"qualitative research",
"midwifery and maternity care",
"public engagement in research"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper was an absolute pleasure to read. The background section and the links to other activity within the IHC Group programme of research are clearly identified. The rational for methods used in this study are offered, the different methods are reported clearly and in a manner that contributes to the rigour of the work. Findings are presented clearly and supplemented with links to allow the read a more in-depth exploration of the audit trail and data that contribute to the findings. Interesting conclusions drawn that are grounded in the strengths and acknowledged limitations of this work, this will be useful across the community for researchers, teachers and the public interested in this space.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1167
|
https://f1000research.com/articles/11-1165/v1
|
11 Oct 22
|
{
"type": "Research Article",
"title": "Family size desires and intentions in the lowest fertility region in Vietnam",
"authors": [
"Vinh Duc Nguyen",
"Thuy Thi Nghiem",
"Thuy Thi Nghiem"
],
"abstract": "Background: Vietnam's total fertility rate has been relatively stable around the replacement level since 2005. Meanwhile, fertility in the Southeast of Vietnam has always been far below the replacement level. As reproductive desires and intentions are important determinants of fertility, the article estimates family size desires and intentions in the Southeast and analyse related sociodemographic factors, contributing insights to the low fertility in this region. Methods: Based on data from a survey of people aged 18-45 in the Southeast in 2020, bivariate analysis and multinomial logistic regressions were applied to examine family size desires and intentions in this region. Results: Most respondents want two (57.3%) or more (33.1%) children, and only 8.4% of them want to have fewer than two children. There are wide gaps within reproductive desires and intentions and the actual fertility. The mean intended family size is nearly 2.1, lower than the mean desired family size but much higher than the total fertility rate in 2020. Young people and unmarried females are more likely to have desires and intentions of fewer than two children. The most frequent reason for no intention of attaining desired family sizes is the fear of not having enough financial resources to raise their children as their expectations. Discussion and Conclusion: The low fertility in the Southeast of Vietnam is not due to a substantial decline in the value of children, but mainly because socioeconomic conditions are not favourable for having two or more children. In the current context in the Southeast, when most people of reproductive age still want and intend to have at least two children, support policies to reduce difficulties and obstacles to having would be much more effective in increasing the fertility rate than later when the desire of fewer than two children become more popular.",
"keywords": [
"Family size desire",
"family size intention",
"low fertility",
"determinants of fertility",
"Southeast Vietnam"
],
"content": "Introduction\n\nSoutheast is the region with the most developed economy in Vietnam. According to Vietnam Population Census in 2019,1 the Southeast has nearly 17.83 million people, accounting for 18.5 percent of the country's population. In the past nearly two decades, while Vietnam’s fertility has been relatively stable around the replacement level (2.1), fertility in the Southeast has been always remarkably lower. In particular, the total fertility rate (TFR) in this region decreased from 1.85 in 1999 to only 1.46 in 2016 and then increased slightly to 1.62 in 2020. Meanwhile, the TFR in the Red River Delta, the second highest income region in Vietnam with Hanoi capital centred, was 2.34 in 2020 and has never been below 2.0 (GSO, 2022). Low fertility rates have been observed in many countries during the process of modernization and economic development (Jones et al., 2008; Timæus and Moultrie, 2020). However, low fertility in the Southeast is certainly a distinct phenomenon among regions in Vietnam that needs to be examined to identify and evaluate the key socioeconomic determinants. This became even more important as the government of Vietnam recently launched a new population strategy, with a sustainable development orientation and the goal of firmly maintaining the replacement fertility rate, through an ambitious plan to reduce fertility in provinces with a TFR higher than 2.1 and to increase fertility in provinces with a TFR lower than 1.8 (Government, 2019, 2020). But the new population strategy has not been fully legislated into laws, as the Ordinance on Population issued by the National Assembly in 2003, revised in 2008 with a provision stipulating that each couple has only one or two children, is still in effect.2 Perhaps due to the lack of scientific evidence, there are both concerns that Vietnam's fertility will fall far below the replacement level as in the Southeast region and that fertility will increase sharply if the one-or-two-child policy is officially removed.\n\nNevertheless, there is very little research on fertility desires and intentions in Vietnam, particularly after its total fertility rate declined to the replacement level in 2005. The most recent national survey in Vietnam collecting information on desired and intended family sizes was the Demographic and Health Survey in 2002 that interviewed only married women (CPFC and ORC Macro, 2003). An analysis using data from Vietnam Inter-Censal Demographic Survey in 2014 and the analytical framework of Bongaarts (2001) found two main direct factors determining the low total fertility rate in the Southeast, including the high rate of unmarried women and the postponement of childbearing among married women (Nguyen, 2017). However, this analysis had to rely on the assumption that the mean desired family size in the Southeast was approximately two children. So far, understandings on the reasons of low fertility in the Southeast are still limited. This article investigates family size desires and intentions in the Southeast and their determinants, aiming to answer the question whether low fertility in this region is mainly caused by changes in social norm on values of children or other factors.\n\n\nTheoretical background\n\nDesired family size is conceptualized as the need for children, or the number of children parents would have if there were no subjective or economic obstructs involved in childbearing. Intended family size is the number of children parents planned to have after considering their desires and actual involved conditions (McClelland, 1983; Thomson, 2015). There have been many studies worldwide indicating that desired and intended family sizes are important determinants of actual number of children as well as fertility (Bongaarts, 2001; Duvander et al., 2020; Schoen et al., 1999; Tan and Tey, 1994; Thomson, 1997; Westoff, 1990, 2010), although there are always certain gaps between these factors (Toulemon and Testa, 2005; Philipov, 2009; Vitali et al., 2009; Miller, 2011; Dommermuth et al., 2015; Mencarini et al., 2015; Casterline and Han, 2017; Trinitapoli and Yeatman, 2018). Desired family size is often reported inconsistently at the individual level but very reliably at the aggregate level. In comparison to intentions, family size desires often reflect less closely future fertility but may be a useful indicator of social norms in examining fertility (Bankole and Westoff, 1998; Trinitapoli and Yeatman, 2018; Westoff, 2010). Studies often show good overall consistencies between ideal and actual family sizes over an entire lifetime, but the relationship between fertility intentions and actual fertility behaviour is relatively weak, as it depends on many other factors (Toulemon and Testa, 2005). Related research has led to a conclusion that “fertility intentions remain the central concept for understanding contemporary fertility trends and differences” (Hagewen and Morgan, 2005: 524).\n\nBongaarts (2001) proposed a widely applied framework on the relationship between fertility and desired family size, in which fertility is the result of the “desired number of children” after the combined effects of three factors that increase fertility (unwanted fertility, replacement of deceased offspring, and sex preference) and three other factors that decrease fertility (high reproductive age, involuntary infertility, and competitive preferences). Intended family size is an intermediate variable in this process. Low fertility is often caused by strong effects of competitive preferences or unfavoured socio-economic and demographic conditions that hamper couples from achieving their desired family size, but can also be attributable to changes in social norms on the value of children, or all of them. In many societies, if people want to have less than two children on average, it is likely that the total fertility rate will fall below the replacement level and cannot easily recover. On the other hand, if most people want to have two children, then mitigating the reducing fertility factors can help to obtain and maintain replacement fertility. Therefore, desired and intended family sizes are useful indicators for predicting fertility as well as proposing policy implications.\n\nExisting research has paid much attention to examining socioeconomic and cultural factors that influence desired and intended family sizes as well as childbearing intentions. According to the theory of planned behaviours (TPB) proposed by Icek Ajzen (1985, 1991), attitude, subjective norms, and perceived behavioural control are three key components forming behavioural intentions. This psychological theory has been widely employed in developing analytical frameworks of fertility desires and intentions. For example, Miller and Jones (2009) proposed a model of the relationship between fertility desires and intentions, in which preconception childbearing desires (of woman and partners) predict both childbearing intentions and pregnancy desires. Research on childless men and women in Australia found that, unlike fertility intentions, childbearing desires were hardly affected by changing life circumstances, but were often adjusted if people recognized that their desires were not likely to be achieved (Gray et al., 2013). Besides, previous theoretical and empirical findings indicate the link between gender inequality and fertility intention as well as fertility behaviour (Yoon, 2016). Very low fertility may be attributable to the situation of high levels of gender equity in society but low levels of gender equity in families (McDonald, 2000).\n\nIn summary, the main factors affecting both family size desires and intentions include personal and family demographic characteristics (age, gender, marital status, ethnicity, religion), education, employment, economic conditions, children's value, etc. In addition, family size intentions are determined by family size desires and many other factors, such as child-rearing costs, gender equality, gender role attitude, division of domestic work, and fertility and family support policies (Hashemzadeh et al., 2021; Preis et al., 2020). Recent research suggests that the patterns of childbearing intentions and behaviours observed in high-fertility societies may not be necessarily applicable in low-fertility settings (Chen et al., 2022). As results from existing research indicate very complex and varying determinants of family size desires and intentions across societies, more research is promising to provide more insights into this topic.\n\n\nMethods\n\nThe Scientific Ethics Committee of the Institute of Sociology, Vietnam Academy of Social Sciences, granted formal approval to the research protocol (No: 16/2019/XHH-HĐKH) on 14th May 2021. Written informed consent was obtained from all participants.\n\nThe research conducted a survey in Ho Chi Minh City and Dong Nai, the two largest provinces in the Southeast. The populations of these two provinces in 2020 were 9.23 and 3.18 million respectively, accounting for more than two-thirds of the Southeast population. A multistage sampling method was applied with a designed sample size of 800 individuals of the main reproductive age, corresponding to the 95% confidence level, the 4.9% margin of error, and the estimated design effect of 2.0. In the first stage, seven communes, including one urban commune and one rural commune in Dong Nai and four urban communes and one rural commune in Ho Chi Minh City, were selected by using the PPS (probability proportional to size) method. The numbers of selected communes relatively reflect the levels of urbanization in each province. In the second stage, with an estimated non-response rate of 25%, about 533 households from two communes in Dong Nai and 533 households from five communes in Ho Chi Minh City were randomly selected for the target of 400 completed interviews in each province. Finally, an unmarried person or married woman aged from 18 to 45 years was randomly selected from each household to obtain her/his consent before interviewing. Married men were not selected as information on their family size desires and sociodemographic characteristics were collected via interviewing their spouses.\n\nThe CAPI (computer-assisted personal interviewing) was applied with a structured questionnaire installed on smartphones via CSPro software version 7.3 to collect data about fertility desires and intentions, socio-demographic characteristics, attitudes on marriage and value of children, and perception of factors affecting childbearing and childrearing. The main questions to identify family size preferences of the respondents include “How many children would you like to have if there are no economic or health constraints?”, “How many children do you currently have?”, and “How many more children do you plan to have?” for unmarried people or “How many more children do you and your spouse plan to have?” for married women. Family size intentions are measured as the sum of the number of existing children and the number of additional planned children. A copy of the full questionnaire can be found in the Extended data (Nguyen, 2022a).\n\nAfter a pre-test in March 2020, the main survey was carried out in May 2020, completing interviews with 808 individuals, including 382 cases from Dong Nai and 426 cases from Ho Chi Minh City, or 273 unmarried persons and 535 married women. In addition, family size desires and socio-demographic characteristics of 535 married men were asked when interviewing their spouses. As such, the survey collected information on the family size desires of 1,343 individuals. The analyses were performed using SPSS version 26, in which the dataset was weighted as individuals were not selected with equal probability. Bivariate analysis with chi-square test, independent samples t tests and one-way analysis of variance (ANOVA) were performed to describe family size desires and intentions in and their differentials across groups. Then multinomial logistic regressions were applied to identify the determinants of desired and intended family sizes. For a dependent variable with three choices, the multiple logistic regression estimates the parameters for the following two equations (Long, 1997:154)\n\n\nResults\n\nThe results show that more than half (57.3%) of the respondents want to have two children and about one-third (33.1%) want more than two children, while only 8,4% of them want fewer than two children (Table 1). That means the desire for medium or large family size (two or more children) remains very popular in society. Indeed, the mean desired family size is nearly 2.4 (Table 2), approximately the mean ideal number of children from the national survey of married women in Vietnam in 2002 (Westoff, 2010: 4), but remarkably higher than the current TFR in the Southeast region of Vietnam.\n\n* p < 0.05,\n\n** p < 0.01,\n\n*** p < 0.001;\n\nT-test or ANOVA:\n\n+ p < 0.05,\n\n++ p < 0.01,\n\n+++ p < 0.001\n\nData: Survey in the Southeast Vietnam in 2000.\n\nThe differences in desired family size by socio-demographic characteristics are presented in Table 2. In general, the mean desired family sizes are not significantly different between the two provinces, between rural and urban areas, and within levels of economic status, but vary slightly across categories of other socio-demographic factors. The groups with mean desired family sizes over 2.5 children include people aged 35 or older, married men, people with under secondary education, at least seven years of staying in the commune, working for self or family, and below average economic status. The figures suggest that some characteristics of a traditional society seem to be still significant factors affecting the desire for large family sizes. Meanwhile, the mean desired family sizes are higher than 2.0 in all groups presented in Table 2, and particularly lowest in unmarried women (2.02 children), in the group aged 18-24 years (2.12 children), and students or not-working people (2.13 children).\n\nIn the context of the government's new policy to encourage the universal two-child family model, the proportion of people with the desire for two children is an important indicator. Results from the survey in the Southeast reveal that the proportion of two-child family desire is 58% in the whole sample (excluding a few individuals with no answer) but only less than 45% in the group aged 40 years or older (44.4%) and married men (44.5%), and on the other hand, quite high in the youngest age group (68.6%), unmarried men (71.8%), and those who still have no children (69.1%). The proportion of desire for three or more children is often highest in the groups with low percentages of wanting two children. The proportion of people who want to have fewer than two children is only 8.6%, but significantly higher in Ho Chi Minh City (10.3%) and urban areas (10.1%) than in Dong Nai province (3.8%) and rural areas (5%). The figures are highest in the group aged under 25 years (11.1%), unmarried women (16.2%), people having one child (14.1%), non-Kinh ethnic groups (17.1%), students or not working people (12.4%), above-average standard of living (12.1%).\n\nThe finding that more than 90% of people want to have two or more children is surprising if compared to the low fertility rate in the Southeast. The fertility of this region is lower than the replacement level despite of high value of children in people's perception, indicating that actual socio-economic and health conditions are unsuitable, not only for large family sizes but also for the two-child family model. The proportion of desire for fewer than two children is not high, but more concentrated among young women and in urban areas, indicating that this rate will increase with the process of urbanization and generational transition in the Southeast.\n\nResults from the multi-logistic regression indicate that some of the socio-economic characteristics are significantly predictive of changes in family size desires (Table 3). In comparison to living in Ho Chi Minh City, living in Dong Nai province is associated with a lower likelihood to desire one or no child but not statistically significant for desire for three or more children. Unmarried men are related to a higher possibility of desire to have two children than married men. Higher education is associated with a lower likelihood to desire a two-child family. Religion does not significantly affect the desire for a one-or-no-child family but increases the probability of desire to have more than two children. People who work for themself or for their families are associated with a higher likelihood for desire of three or more children than students or people who do not work or work in the public sector. On the other hand, age, urban-rural area, ethnicity, and respondents' self-perception of their living standard are not found to be related to changes in the desired family size.\n\n* p < 0.05,\n\n** p < 0.01,\n\n*** p < 0.001\n\nThe figures in Table 4 show that 70% of the respondents intend to have two children, but only about 17.4% of them intend to have more than two children and 11.9% intend to have fewer than two children. The mean intended family size is 2.07, very close to the replacement level of fertility and remarkably lower than the mean desired family size, but still higher than the TFR in 2020 in the Southeast of Vietnam. This pattern of fertility preference has been observed in a number of studies in developing and developed countries (Bongaarts, 2001; Westoff, 2010).\n\nThe differences in family size intentions by sociodemographic characteristics are presented in Table 5. It is not surprising that people in more developed areas (Ho Chi Minh City, urban areas) intend to have smaller family sizes. Similar to the desired family sizes, the mean intended family sizes are low in unmarried women (1.84 children), the group aged 18-24 years (1.91), the non-Kinh ethnic groups (1.93), Catholic and other religions (1.93), and people with one child (1.84). Correspondingly, the percentages of intention to have fewer than two children in those groups are significantly higher than 12% (from 17.4% to 23.3%).\n\n* p < 0.05,\n\n** p < 0.01,\n\n*** p < 0.001; T-test or ANOVA:\n\n+ p < 0.05,\n\n++ p < 0.01,\n\n+++ p < 0.001\n\nThe intended family size is found to be significantly lower than the desired family size, but there is undoubtedly a strong association between the two variables, especially between the two-child desire and the two-child intention. Indeed, nearly 88% of people who want a two-child family intend to realize this desire. The corresponding figures are 64.6% for the intention of one-or-no child and only 44.5% for the intention of three-or-more children. On the other hand, nearly 30% of people who want fewer than two children and more than half (51.1%) of people who want more than two children plan to have two children. The results suggest the existence of factors that hinder people from realizing their desired number of children. In the present social, cultural and policy context of the Southeast, the desire for a two-child family seems to be the easiest to accept and receive more encouragement. Therefore, many people want to have fewer or more than two children but intend to have two children like most other couples in society. Most of the gap between family size desires and intentions is generated by the shift from the desires of three-or-more children and one-or-no child to the intention to have two children. Among those people who want a two-child family, only 12.1% of them intend to have more or fewer than two children.\n\nResults from the multi-logistic regression reveal several socioeconomic characteristics, that are significantly predictive of the variation in family size intentions (Table 6). In comparison to the two-child intention, living in Ho Chi Minh City, in the age from 30 to 34 years, being an unmarried woman, working in the public sector, and having an average living standard are the factors associated with a lower likelihood of the intention to have three or more children. On the other hand, being unmarried females, younger than 25 years of age, non-Kinh ethnic groups, and being Catholic or other non-Buddhism religions are related to a higher possibility of intention to have fewer than two children.\n\n* p < 0.05,\n\n** p < 0.01,\n\n*** p <0.001\n\nIn the context of low fertility in the Southeast, the survey also interviewed the respondents about their awareness of challenges they would face if having one more child (Table 7). It is reasonable that the challenges perceived by the respondents will be a significant barrier to their determination to realize their family size intentions. The results show that all three most commonly perceived challenges are related to the financial aspect. High proportions of respondents informed that they were worried about how to have enough money to raise children (65%), for children's education (56%), and for children’s medical care (51.3%). These proportions are highest among married females, as more than 90% of them already have at least one child and have experienced these financial challenges, but lowest among married females, who might feel less responsible than unmarried men in being the breadwinners in their future family. The next challenges are less frequently reported and may be considered as indicators of competitive preferences in the framework proposed by Bongaarts (2001). About 38% of the respondents were concerned that “It takes much time and effort to take care of children”, and unmarried males are more likely to think about this challenge (40.5%) than unmarried females (35.6%). The proportion of concern that one more birth would badly affect women's health and appearance is nearly 29% among unmarried women and 24.1% among married women, but only 17.1% among unmarried men. More than 21% of female respondents but only 11.4% of unmarried men were afraid of many hardships and risks during pregnancy and childbirth, possibly including infertility and miscarriage. Similarly, nearly 24% of unmarried women but only 11.6% of unmarried men worried about losing their job opportunities and promotions. Only 6.4% of respondents were concerned of housing problems if they have one more child.\n\n\nDiscussion and conclusion\n\nThe analysis of survey data in the Southeast reveals that most people want two or more children, and only a small proportion of them want to have a childless or one-child family. As a result, the mean desired family size is nearly 2.4, indicating the persistence of a relatively high value of children in the Southeast social norms, though the primary value of children might have transited from economic assistance to psychological and social merits to their parents during an impressive process of economic development and modernization of this region over the past several decades. In other words, the low fertility in the Southeast of Vietnam is not due to a substantial decline in the value of children, but mainly because current socioeconomic conditions are not favourable for having and raising two or more children with current standards. Indeed, the analysis found wide gaps within reproductive desires and intentions and the actual fertility. The mean intended family size is approximately 2.0 children, significantly lower than the mean desired family size but much higher than the total fertility rate in 2020. The results indicate the existence of socioeconomic factors that hinder people from attaining their desired family size.\n\nThere is a strong association between family size desires and intentions, especially between the two-child desire and the two-child intention. Most people who want a two-child family intend to realize this desire. Moreover, nearly 30% of people wanting fewer than two children and more than half of people wanting three or more children plan to have a two-child family. The intention for a two-child family seems to be more easily accepted and encouraged in the current socio-political and cultural context in the Southeast as well as in Vietnam. Therefore, many people want to have fewer or more than two children but intend to have two children like most other couples in society. In contrast, among those people who want two children, only about one-eights of them intend to have a larger or smaller family. Nevertheless, the difference between family size desires and intentions in the Southeast seems to be positive for the government’s policy of firmly maintaining the replacement fertility rate and promoting a universal two-child family model in Vietnam. Most of this difference is generated by the shift from the desires of three-or-more children or one-or-no child to the intention to have a two-child family. The findings indicate that not family size intentions but the factors affecting the realisation of those intentions have been the key determinants of the below-replacement fertility in the Southeast.\n\nThe analysis reveals the existence of some socioeconomic factors affecting family size desires and intentions. Young people and unmarried females are more likely to have desires and intentions of fewer than two children, suggesting possibly even smaller family size and lower fertility in the next generation. Being non-Kinh ethnic groups, non-Buddhism religions and some indicators involved in modernization, such as living in urban areas or in big cities, are the factors associated with a lower likelihood of the intention to have one or no child. The process of economic development and modernization has significantly improved the income and living conditions in the Southeast, but also brought about new social contexts, with many factors discouraging childbearing, even just one or two children. Young people, especially women, need to devote much time and effort for education and employment, and have many other preferences that compete with having children. Indeed, the survey in the Southeast found considerable proportions of people of reproductive age were afraid that having an additional child would require too much time and effort to take care, badly effect women’s health and appearance, or diminish their job opportunities, promotions. However, the most common challenge perceived by both married and unmarried people in the survey the Southeast is the costs of raising children according to current standards and expectations, supposing they have one more child. That is certainly one of the main factors of the gaps between the relatively high desired family size and the medium intended family size and the low fertility rate in the Southeast. Moreover, the concern about unaffordable costs of raising children may help to explain for the delay of childbearing, one of two major determinants of low fertility in the Southeast as found in previous research (Nguyen 2017). From the theoretical aspect, the factor of competing preferences in the framework of Bongaarts (2001) should be understood as including both competing preferences and obstacles in the current context of Vietnam.\n\nIn regard to Vietnam’s new population strategy aiming to firmly maintain the replacement fertility rate, the two-child family model can be promoted but unlikely to be universal as childbearing depends on various objective and subjective factors. In the current context in the Southeast, when most people of reproductive age still want and intend to have at least two children, support policies to reduce difficulties and obstacles to childbearing and childrearing would be much more effective in increasing the fertility rate than later when the desire of fewer than two children become more popular.\n\nThere are two major limitations in this study that could be addressed in future research. The first limitation is that information on family size desires and intentions of married men was derived through interviewing their wives, and this may lead to a certain bias. The second limitation is related to the gender equality factor, an important determinant of fertility intentions in existing literature, but was not included in the analysis.\n\n\nData availability\n\nHarvard Dataverse: Survey on fertility preference in the Southeast of Vietnam in 2020. https://doi.org/10.7910/DVN/XXOEWV (Nguyen 2022a)\n\nThis project contains the following underlying data:\n\n• SEVNFS2020.SAV (SPSS format; all datasets have been de-identified in accordance with the Safe Harbor method.)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nHarvard Dataverse: Questionnaire for Survey on fertility preference in the Southeast of Vietnam in 2020.\n\nhttps://doi.org/10.7910/DVN/3G7FW9 (Nguyen, 2022b)\n\nThis project contains the following extended data:\n\n• Questionnaire for Survey on fertility preference in the Southeast of Vietnam in 2020\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThis research was performed at the Institute of Sociology, Vietnam Academy of Social Sciences. The authors would like to thank all staff at the Institute of Sociology for supporting this research.\n\n\nReferences\n\nAjzen I: From Intentions to Actions: A Theory of Planned Behavior. Action Control: From Cognition to Behavior. Kuhl J, Beckmann J, editors. Berlin Heidelberg:Springer;1985; pp. 11–39. Publisher Full Text\n\nAjzen I: The Theory of Planned Behavior. Organ. Behav. Hum. Decis. Process. 1991; 50(2): 179–211. Publisher Full Text\n\nBankole A, Westoff CF: The Consistency and Validity of Reproductive Attitudes: Evidence from Morocco. J. Biosoc. Sci. 1998; 30(4): 439–455. PubMed Abstract | Publisher Full Text\n\nBongaarts J: Fertility and Reproductive Preferences in Post-Transitional Societies. Popul. Dev. Rev. 2001; 27(Supplement: Global Fertility Transition): 260–281.\n\nCasterline JB, Han S: Unrealized Fertility: Fertility Desires at the End of the Reproductive Career. Demogr. Res. 2017; 36(1): 427–454. Publisher Full Text\n\nChen R, Baochang G, Chen R, et al.: Childbearing Intention and Childbearing Behavior in Low Fertility Society: Evidence from Shanghai. China Popul. Dev. Stud. 2022; 6: 115–126. Publisher Full Text\n\nCPFC and ORC Macro: Vietnam Demographic and Health Survey 2002. Calverton, Maryland, USA:National Committee for Population, Family and Children [Vietnam] & ORC Macro;2003.\n\nDommermuth L, Klobas J, Lappegård T: Realization of Fertility Intentions by Different Time Frames. Adv. Life Course Res. 2015; 24: 34–46. PubMed Abstract | Publisher Full Text\n\nDuvander AZ, Fahlén S, Brandén M, et al.: Who Makes the Decision to Have Children? Couples’ Childbearing Intentions and Actual Childbearing. Adv. Life Course Res. 2020; 43: 100286. Publisher Full Text\n\nGovernment: Vietnam Population Strategy to 2030. Decision No 1679/QD-TTg, November 22, 2019.2019.\n\nGovernment: Program to Adjust Fertility Levels to Suit Regions and Subjects by 2030. Decision No 588/QĐ-TTg, April 28, 2020.2020.\n\nGray E, Evans A, Reimondos A: Childbearing Desires of Childless Men and Women: When Are Goals Adjusted?. Adv. Life Course Res. 2013; 18(2): 141–149. PubMed Abstract | Publisher Full Text\n\nGSO (General Statistics Office of Vietnam):2022. Statistical Data: Total Fertility Rate by Province.Reference Source\n\nHagewen K, Morgan P: Intended and Ideal Family Size in the United States, 1970-2002. Popul. Dev. Rev. 2005; 31(3): 507–527. PubMed Abstract | Publisher Full Text\n\nHashemzadeh M, Shariati M, Nazari AM, et al.: Childbearing Intention and Its Associated Factors: A Systematic Review. Nurs. Open. 2021; 8(5): 2354–2368. PubMed Abstract | Publisher Full Text\n\nJones GW, Straughan PT, Chan A (eds): Ultra-Low Fertility in Pacific Asia: Trends, Causes and Policy Issues. Routledge;2012.\n\nLong JS: Regression Models for Categorical and Limited Dependent Variables. Sage Publications;1997.\n\nMcClelland GHFamily-Size Desires as Measures of Demand. Determinants of Fertility in Developing Countries. Volume 1: Supply and Demand for Children. Bulata RA, Lee RD, editors.New York:Academic Press;1983.\n\nMcDonald P: Gender Equity in Theories of Fertility Transition. Popul. Dev. Rev. 2000; 26(3): 427–439. Publisher Full Text\n\nMencarini L, Vignoli D, Gottard A: Fertility Intentions and Outcomes: Implementing the Theory of Planned Behavior with Graphical Models. Adv. Life Course Res. 2015; 23: 14–28. Publisher Full Text\n\nMiller BW: Differences between Fertility Desires and Intentions: Implications for Theory, Research and Policy. Vienna Yearbook of Population Research. 2011; 9: 75–98. Publisher Full Text\n\nMiller WB, Jones J: The Effects of Preconception Desires and Intentions on Pregnancy Wantedness. J. Popul. Res. 2009; 26(4): 327–357. Publisher Full Text\n\nNguyen V: Survey on fertility preference in the Southeast of Vietnam in 2020.2022a. Harvard Dataverse, V1. [dataset]. SEVNFS2020.tab [fileName], UNF:6:NbwsrhTuEp5FDXAFPEwJXA== [fileUNF]. Publisher Full Text ,\n\nNguyen V: Questionnaire for Survey on fertility preference in the Southeast of Vietnam in 2020.2022b. Harvard Dataverse,V1 [Dataset]. Publisher Full Text\n\nNguyen DV: Determinants of Low Fertility in the Southeast Region and Implications for Population Policy in Vietnam. Tạp Chí Xã Hội Học (Sociology). 2017; 1: 42–54. (in Vietnamese).\n\nPhilipov D: Fertility Intentions and Outcomes: The Role of Policies to Close the Gap. Eur. J. Popul. 2009; 25(4): 355–361. Publisher Full Text\n\nPreis H, Tovim S, Mor P, et al.: Fertility Intentions and the Way They Change Following Birth: A Prospective Longitudinal Study. BMC Pregnancy Childbirth. 2020; 20(1): 1–11. Publisher Full Text\n\nSchoen R, Astone NM, Kim YJ, et al.: Do Fertility Intentions Affect Fertility Behavior? J. Marriage Fam. 1999; 61(3): 790. Publisher Full Text\n\nTan PC, Tey NP: Do Fertility Intentions Predict Subsequent Behavior? Evidence from Peninsular Malaysia. Stud. Fam. Plan. 1994; 25(4): 222–231. PubMed Abstract | Publisher Full Text\n\nThomson E: Couple Childbearing Desires, Intentions, and Births. Demography. 1997; 34(3): 343–354. Publisher Full Text\n\nThomson E: Family Size Preferences. International Encyclopedia of the Social & Behavioral Sciences. Wright DJ, editor.Elsevier;2015; pp. 805–808.\n\nTimæus IM, Moultrie TA: Pathways to Low Fertility: 50 Years of Limitation, Curtailment, and Postponement of Childbearing. Demography. 2020; 57: 267–296. Publisher Full Text\n\nToulemon L, Testa M-R: Fertility Intentions and Actual Fertility: A Complex Relationship. Popul. Soc. 2005; 415(4): 1–4.\n\nTrinitapoli J, Yeatman S: The Flexibility of Fertility Preferences in a Context of Uncertainty. Popul. Dev. Rev. 2018; 44(1): 87–116. PubMed Abstract | Publisher Full Text\n\nVitali A, Billari FC, Prskawetz A, et al.: Preference Theory and Low Fertility: A Comparative Perspective. Eur. J. Population. 2009; 25(4): 413–438. Publisher Full Text\n\nWestoff CF: Reproductive Intentions and Fertility Rates. Int. Fam. Plan. Perspect. 1990; 16(3): 84–89. Publisher Full Text\n\nWestoff C: Desired Number of Children: 2000-2008. Maryland:ICF Macro;2010.\n\nYoon SY: Is Gender Inequality a Barrier to Realizing Fertility Intentions? Fertility Aspirations and Realizations in South Korea. Asian Popul. Stud. 2016; 12(2): 203–219. Publisher Full Text\n\n\nFootnotes\n\n1 https://www.gso.gov.vn/wp-content/uploads/2019/12/Ket-qua-toan-bo-Tong-dieu-tra-dan-so-va-nha-o-2019.pdf\n\n2 https://vbpl.vn/boyte/Pages/vbpq-toanvan.aspx?ItemID=12661"
}
|
[
{
"id": "153179",
"date": "26 Jan 2023",
"name": "Youngtae Cho",
"expertise": [
"Reviewer Expertise Population Studies"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe purpose of this study is to examine the ideal number of children for women in southern Vietnam with very low total fertility rates, and to determine whether the ideal number of children is due to changes in social norms about their children's values or to other factors. Currently, Vietnam's fertility rate is very stable nationwide, but as the authors pointed out, the fertility rate in the southern region is very low at 1.5.\nThis study was conducted to investigate the cause of the low birth rate in the southern part of Vietnam using social survey data conducted only in the southern part of Vietnam.\nIt is clear that this study makes an important academic contribution to the recent status of Vietnam's fertility. Nevertheless, if the following matters can be considered, the academic and policy value of the paper will be further enhanced.\n1. This study was analyzed by combining men and women. But since women and men have different social roles, it is necessary to divide the analysis between men and women. Although the sample size may become smaller and statistically sound results may not be obtained in multiple regression analysis, it is still worthwhile to analyze men and women separately.\n2. The TFR is around 1.5 in the South, but most of the samples included in this study showed their desired and intended number of children at 2 or higher. As the authors reviewed that the numbers of desired and intended children have positive relationship with the actual number of children, the major research question should be “why does the desire or intention not be translated into actual level of fertility” rather than “has the social norm for two children been deteriorated in the Southern part of Vietnam.” Therefore, I do not doubt that the results of this study have ample academic contribution, but it is not easy to say that policy utilization of this study is equivalent.\nThe authors suggested that socioeconomic conditions, not changes in values, created a lower number of intended children than the desired. The proposal is not wrong, but it is hard to say that it is a new discovery in policy. It's too general a suggestion.\nIf socioeconomic conditions in the course of economic development have weakened people's willingness to give birth, economic development has not only been in HCMC and Dong Nai, but also in northern Vietnam, where fertility rates have not been lowered.\n3. The question might be useful is why many people actually have about 1.5 children even though the desire for two children is so high in the South. Unfortunately, the results of this study do not explain this. If you asked the actual number of children in the survey, you could put the difference between the actual number of children and the number of intended children as a dependent variable, and see what factors make the difference. Then, the cause of the low birth rate can be identified more directly, and policy implications can be stronger.\n4. Since this study used data collected only in HCMC and Dong Nai, it is fundamentally impossible to compare with northern Vietnam, where the total fertility rate is relatively high. Therefore, it is impossible for this study to explain why the fertility rate in southern Vietnam is low. Nevertheless, in order to increase the academic and policy contributions of this study, it is necessary for the authors to discover similar studies conducted in the northern region and compare them with the results of this study. If literature is not enough to achieve the purpose of the study, it may be good to exercise some educated and trained guess as demographers.\n5. Typo at the bottom of page 9: one-eights à one-eighth\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "161617",
"date": "08 Feb 2023",
"name": "Heather Booth",
"expertise": [
"Reviewer Expertise Demography",
"quantitative analysis"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper makes a useful contribution to the understanding of fertility in Vietnam in the context of social and economic change. The analysis is both important and timely as Vietnam is considering revising its population policy to maintain replacement level in all regions.\nThis paper seeks to understand why fertility in the Southeast region of Vietnam is lower than the policy (replacement) level of 2.1 children per woman. It uses 2000 survey data for two provinces in Southeast, including urban and rural settings, to examine ‘whether low fertility in this region is mainly caused by changes in social norm on values of children or other factors’. This aim (as stated) is problematic and should be revised: the data do not permit a causal analysis, nor analysis of changes in social norms.\nMultinomial regression models identify the factors predicting desired and intended number of children. The analysis appears technically competent, but it should be explained why ordinal logistic regression was not used. The two measures are not independent, as is acknowledged; it would be helpful to cross-tabulate them. The analysis (Table 6) takes no account of the dependency. Given methodological inconsistencies (below) it is impossible to compare Tables 3 and 6.\nA weakness is the inclusion of married men via proxy reporting by their wives (of desired number of children and socio-economic variables), introducing a lack of independence between their responses (most couples would share many characteristics). Further, married males’ intended number of children would appear to be taken as the same as their wives’ (given that the sample size is the same). This is inadequately explained. How has this dependence been taken into account in the analysis (if at all), and how does it affect the results (you briefly mention bias)?\nIndividual points by page/para/line:\n3/1/last 3 This sentence is misleading. Removing the current policy of 1 or 2 children would not logically lead to lower fertility; it could only lead to higher fertility, though this seems unlikely to occur based on existing scientific evidence.\nPolicy is ‘…each couple has only one or two children’: clarify whether childlessness is a matter for current policy… or perhaps rephrase to ‘…each couple has no more than two children’.\n5/3/3 ‘Economic status’ is not a listed variable; religion is not mentioned. Others are said to ‘vary slightly’ - but they are very highly significant. Chi2 is ignored: why is it there? Why are the very highly significant number and sex of existing children ignored? Sex of children data seem to be contrary to son preference! Is this something the authors could explore (perhaps in another paper)?\n7/2/4- The statement for education is problematic (also, is the table labelled correctly?). Religion is presented as causal.\nTerminology The multinomial logistic regressions are mislabelled ‘multi-logistics’ regression in tables etc. The model is of log odds, but the interpretation is in terms of ‘possibility’ and ‘likelihood’.\nTables Inconsistent labelling of variables; inconsistent listing of variables; inconsistent or non-ordinal listing of categories within variables. Inconsistent choice of reference category in the two multinomial regressions. Numbers should be right-aligned\nTable 2: Gender and marital status … lists unmarried female twice\nTable 3: Why is ‘married male’ (based on proxy reporting) used as the reference? Please justify this choice (is it an error?)\nTables 2 and 5 headings Tables do not show ‘differences’, but simply ‘family size’. Check text also.\nTables 3 and 6 Why are number and sex of existing children not included in the regression? Also ‘area’ is non-significant but it remains in both models. Explain the rationale for inclusion and exclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1165
|
https://f1000research.com/articles/11-1158/v1
|
10 Oct 22
|
{
"type": "Research Article",
"title": "Predictive value of 18F-fluorodeoxyglucose accumulation in visceral fat activity to detect colorectal cancer metastases (prospective observational cohort study)",
"authors": [
"Amil Suleimanov",
"Aigul Saduakassova",
"Denis Vinnikov",
"Vadim Pokrovsky",
"Saltanat Mamyrbekova",
"Anara Daniyarova",
"Lyaila Kozhabek",
"Aigul Saduakassova",
"Denis Vinnikov",
"Vadim Pokrovsky",
"Saltanat Mamyrbekova",
"Anara Daniyarova",
"Lyaila Kozhabek"
],
"abstract": "Background: To evaluate functional visceral adipose tissue (VAT) activity assessed by 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography/computed tomography (PET/CT) as a predictive factor of metastases in colorectal cancer (CRC) patients. Methods: We reviewed study protocols and PET/CT data of 534 CRC patients; 474 patients were subsequently excluded for various reasons. The remaining 60 patients with histologically confirmed adenocarcinoma were then prospectively assessed and were exposed to 18F-FDG PET/CT after a surgical treatment and chemoradiotherapy. Age, histology, stage, and tumor grade data were recorded. Functional VAT activity was verified with maximum standardized uptake value (SUVmax) using 18F-FDG PET/CT and tested as a predictive factor of later metastases in eight subdomains of abdominal regions (RE – epigastric region, RLH – left hypochondriac region, RRL – right lumbar region, RU – umbilical region, RLL – left lumbar region, RRI – right inguinal region, RP – hypogastric (pubic) region, RLI – left inguinal region) and pelvic cavity (P) in the adjusted regression models. In addition, we studied the best areas under the curve (AUC) for SUVmax with the corresponding sensitivity (Se) and specificity (Sp). Results: In both adjusted for age regression models and receiver operating characteristic (ROC) curve analysis, 18F-FDG accumulation in RLH (cut-off SUVmax 0.74; Se 75%; Sp 61%; AUC 0.668; p=0.049), RU (cut-off SUVmax 0.78; Se 69%; Sp 61%; AUC 0.679; p=0.035), RRL (cut-off SUVmax 1.05; Se 69%; Sp 77%; AUC 0.682; p=0.032) and RRI (cut-off SUVmax 0.85; Se 63%; Sp 61%; AUC 0.672; p=0.043) could predict later metastases in CRC patients, as opposed to age, sex, primary tumor location, tumor grade and histology. Conclusions: Functional VAT activity was importantly related to later metastases in CRC patients and can be used as their predictive factor.",
"keywords": [
"18F-FDG",
"PET/CT",
"Colorectal cancer",
"Predictive value"
],
"content": "Introduction\n\nColorectal cancer (CRC) is one of the main causes of high worldwide oncological mortality, and its metastasis to the lymph nodes (LN) is an important prognostic factor.1 Globally, CRC is the third most commonly diagnosed cancer, with an estimated 1.9 million (10%) new cases and 935,173 (9.4%) deaths.2 Furthermore, CRC is the second leading cause of cancer mortalities in 2020, according to the WHO GLOBOCAN database.3 In South-Central Asia, 102,987 (63%) new cases of CRC and 59,206 (36%) mortality incidences were registered in 2020.2,4\n\nPositron-emission tomography/computed tomography (PET/CT) is a hybrid diagnostic method that shows the value of metabolic processes of the tissue at the molecular level in the tomographic mode. The advantage of PET/CT is to visualize viable tumor tissue and assess its biological activity by the degree of radiopharmaceutical agent accumulation in tissues and can be used to measure the hypermetabolic focus of visceral adipose tissue (VAT) activity. 18F-Fluorodeoxyglucose (18F-FDG) is now extensively used to assess functional VAT activity during PET/CT; therefore, it can identify accumulation loci and further detect metastases.5\n\nAlthough the predictive role of 18F-FDG PET/CT in detecting metastases has been poorly studied, the studies on the reported prognostic value for various cancer locations have yielded inconsistent findings.6–11 Thus, VAT has been shown to increase the CRC risk, but the relationship between VAT and the predictive outcome in CRC is ambivalent. VAT is closely associated with dysregulated visceral fat activity increasing adipokines related to systemic inflammation, and can play a role in oncogenesis and metastatic lesion.1,12 The increased inflammatory condition of VAT activity might influence the status of LN in CRC patients.13–17\n\nByung Wook Choi et al. were among the few to retrospectively show the predictive value of metabolic parameters on 18F-FDG PET/CT in classical rectal adenocarcinoma.12 Another study by Sung Hoon Kim et al. retrospectively showed the prognostic factor of 18F-FDG PET/CT for LN metastasis in rectal cancer,18 whereas Kisoo Pahk et al. retrospectively showed the predictive value of functional VAT activity measured by preoperative 18F-FDG PET/CT for regional LN or distant metastasis in CRC patients.1\n\nGiven that the findings of these studies have been inconsistent in showing the exact maximum standardized uptake value (SUVmax) readings indicative of a higher risk of metastases, more data is needed to verify whether PET/CT can assist in early metastases identification in CRC patients. Therefore, the objective of this study was to quantitatively define functional VAT activity via 18F-FDG PET/CT in patients with CRC and its predictive potential for early LN metastases detection.\n\n\nMethods\n\nApproval was obtained from Local Bioethics Commission of the Medical Centre Hospital of President’s Affairs Administration of the Republic of Kazakhstan (approval #17/2020 on 24 January 2020) and Local Ethical Commission of the Al-Farabi Kazakh National University (approval #102 IRB – A102 on 28 May 2020). All patients routinely provided written informed consent for all medical tests and examinations and written informed consent was obtained for participation in the current study. We minimized selection bias by enrolling all patients for whom data were available in the database and of sufficient quality. When calculating the sample size, we allowed the maximum standard deviation. The significance level (α) was 0.05, and the study power was 80%, with a confidence probability of 95% (t=1.96). This study follows the TREND guidelines.19\n\nWe enrolled 534 patients with CRC, among which 60 patients had no metastases, 175 patients had metastases, 98 patients had a postoperative relapse with high metabolic activity, and 201 patients had a primary cancer disease progression. Patients who had metastases, postoperative relapse with high metabolic activity and primary cancer disease progression were excluded from the study. In total, we have prospectively evaluated 60 patients with a histologically confirmed diagnosis of adenocarcinoma who underwent 18F-FDG PET/CT in the Nuclear Medicine Unit of the Diagnostic Center of the Medical Centre Hospital of President’s Affairs Administration of the Republic of Kazakhstan (Nur-Sultan) during the period time between November 2015 and June 2021.\n\nThe study included 60 patients (age 39–81; median 60 (interquartile range (IQR) 55–68) years; 46 women) after a surgical treatment and courses of Folfiri and Folfox chemoradiotherapy according to the regimen. During the initial screening for eligibility, patients with histologically unverified colon cancer or with metastases confirmed at the baseline examination were excluded from the study. We also excluded patients with concurrent cancers. Tumor, lymph nodes, and metastasis (TNM) staging system along with American Joint Committee on Cancer (AJCC) stages of recruited patients are shown in Table 1. As Table 1 presents, there were no patients with AJCC stage IV, whereas adenocarcinoma was identified in 100% of patients. Of note, patients were classified into AJCC stages at their baseline examination, after which they were subjected to treatment and then underwent baseline PET/CT. By the time enrolled patients underwent baseline PET/CT, they had completed their treatment, had no signs of cancer or metastases, and this baseline PET/CT was considered as day 0 of the research.\n\nPatients underwent 18F-FDG PET/CT at the initial enrollment and then again at a follow-up medical examination scheduled six months or more (median 12, IQR 6–40) after the baseline examination. All images were reconstructed using dedicated workstations and software (image evaluation system Wizard). Patients’ data were anonymized and de-identified before studies.\n\n18F-FDG was produced at the Republican Diagnostic Center (Nur-Sultan, Kazakhstan) and was used on the day of the study due to the ultra-short shelf life (109 minutes). The whole-body 18F-FDG PET/CT images were completed using PET/CT scanner (Biograph TruePoint PET·CT, Siemens Medical Solutions USA Inc., USA) and carried out in conformity with the accepted clinical protocol of 18F-FDG PET/CT examination.20 Prior to PET/CT procedure and the corresponding 18F-FDG injection, patients fasted for at least 6 hours, and the glucose serum level in all patients was <11 mmol/l. The average activity dose of the injected 18F-FDG was 252.55 MBk, ranging from 132.5 to 465.3 MBk. The average effective radiation dose was 8.75 mSv, with a range from 6.8 to 17.1 mSv. CT scans were obtained following PET emission scanning. PET/CT study protocol included a topogram, a low dose CT to eliminate signal attenuation and anatomical correlation, and the collection of PET data. Duration of PET data collection depended on the patient’s height and weight, but usually completed within 25–40 minutes. Once PET data were obtained, CT and PET images were reconstructed and stored in the transaxial, coronal, and sagittal slices.\n\nImage analysis was performed using the extended Siemens workspace (Biograph TruePoint PET·CT operating manual) in a region of interest (ROI). We calculated the standardized uptake value accumulation (SUV) in VAT automatically with the software using the formula:\n\nVAT areas were identified by using predefined Hounsfield units (HU), ranging from [-70] to [-110] from background CT images. To measure the VAT activity, ROI (1.00 mm for each measured point) was divided into regions according to the topographic structure, including eight subdomains of abdominal regions (RE – epigastric region, RLH – left hypochondriac region, RRL – right lumbar region, RU – umbilical region, RLL – left lumbar region, RRI – right inguinal region, RP – hypogastric (pubic) region, RLI – left inguinal region) and pelvic cavity (P). They were located on three consecutive sections of the abdominal cavity to exclude the kidneys’ extra physiological absorption of 18F-FDG. We measured SUVmax in the axial plane for each area, and the average SUVmax of each area was calculated separately. All images were reconstructed in transaxial, sagittal and coronal multiplanar planes and read visually. With these functional parameters, the analysis was carried out by the status of metastatic LN lesions.\n\nThe primary end-point of this analysis was SUVmax of selected nine locations at baseline and follow-up. Image analysis was performed by determining the maximum standardized uptake value (SUVmax) VAT accumulation in each abdominal and pelvic cavity point. Each measured point was 1.00 mm and varied depending on the volume of VAT of the measured area. VAT areas were identified from background CT images, and SUVmax was defined on PET images, including a hypermetabolic focus on 18F-FDG PET/CT. We report SUVmax values for nine locations of the VAT, whereas the SUVmax at baseline and follow-up was a mean of several loci for each area with a 1-mm shift.\n\nWe first tested all variables for normality using the Kolmogorov-Smirnov test. Quantitative variables following the normal distribution pattern are presented as means (M) with the corresponding standard deviation (SD); alternatively, we reported medians with the corresponding IQR. SUVmax values for different locations and at different time periods (baseline or follow-up) were then compared with nonparametric tests, such as the Mann-Whitney U-test or Wilcoxon test. Because, in total, we selected nine locations to report SUVmax values, we tested SUVmax values for each location in the univariate analyses with regard to sex, primary tumor location, and other variables, using either Mann-Whitney U-test (for two groups) or Kruskall-Wallis test (for three or more groups). We also used a similar approach to compare groups depending on metastases status, including positive (pLM) patients in whom metastases were detected at a follow-up visit and negative (nLM) who showed no metastases. In such an analysis, we compared baseline SUVmax as a predictor. In addition, we tested age and sex as predictors of showing pLM at follow-up. Locations with significant differences between groups with regard to SUVmax and other tested predictors (age, sex) showing significant associations with LM status, were then tested in a logistic regression analysis, first crude, and then adjusted for other significant predictors, where we report the odds ratios (OR) of developing metastases at follow-up with the corresponding 95% confidence intervals (CI).\n\nFinally, we applied receiver operating characteristic (ROC) curve analysis to assess the diagnostic performance of quantitative variables when predicting a categorical outcome. The optimal cut-off value of the quantitative variable was estimated using the Youden’s J statistic. All statistical analyses were performed using StatTech v. 2.7.1 (StatTech LLC, Russia).\n\n\nResults\n\nThere were more women in the studied group (n=46). The most prevalent primary tumor location (PTL) was the rectum (n=21), n=20 patients had the PTL in the colon, including n=6 as ascending, n=6 as descending and n=8 as transverse, whereas n=19 patients had tumor in the sigmoid, as presented in Table 2. With regard to tumor AJCC classification, most patients were classified as stage II (n=31) and III (n=27), with no patients having stage IV. At the baseline examination, the overall mean SUVmax was 0.80, with a significant difference in a nine-group comparison (p=0.016), whereas the highest accumulation level was found in RP (0.89) and the lowest in RLI (0.68). Sex affected the SUVmax in RLH (p=0.043) and RLL (p=0.048) locations, yielding higher readings in women compared to men. We also found differences in baseline SUVmax for colon, sigmoid and rectum in RRL (p=0.006), RU (p=0.016) and RLL (p=0.004), but not for a histological grade, TNM or AJCC stage (Table 2).21\n\nAt the follow-up examination of the 60 patients recruited initially, metastases developed in 16 (27%) patients, and these were classified as positive lymphatic metastasis (pLM), whereas the remaining 44 (73%) patients were classified as negative lymphatic metastasis (nLM). Such metastases location included LN of the neck, mediastinum, chest, peritoneum, retroperitoneum, and pelvis. We tested whether baseline SUVmax was different in those who developed metastases compared to those who did not. We found that such differences were statistically significant but not for all locations, only for RRL (1.29 vs. 0.82, p=0.032) and RU (1.00 vs. 0.74, p=0.041) (Table 3), indicative of some predictive potential of SUVmax in these two locations for metastasis at follow-up.\n\nThe median SUVmax of all locations increased from 0.8 at baseline to 0.94 at follow-up (p<0.001). We did not find a statistically significant SUVmax increase when considered separately in out of nine locations (Table 3), mostly because the sample size of each location was only 1/9 of the overall sample. We found the trend of SUVmax increase overall when stratified nLM to pLM, but it was insignificant. In addition, follow-up SUVmax for colon nLM equaled 0.93, with no difference compared to pLM (1.12; p=0.72). Similarly, we failed to confirm statistically significant differences of SUVmax when comparing nLM (0.93) with pLM (0.98) for sigmoid (p=0.62) and rectum (0.92 for nLM and 1.05 for pLM) (p=0.68).\n\nIn the univariate analysis, age and sex were not associated with metastases at follow-up (median age in nLM 59 vs. 63 years in pLM, p=0.12). We then tested whether baseline SUVmax of the selected two locations found to be significantly associated with metastases at follow-up, including RRL and RU, could predict metastases in the unadjusted and adjusted for age regression models. In the model adjusted for age, the OR for positive metastases at follow-up for RRL was non-significant and equaled 2.88 (95% CI 0.79; 10.70), and this model accounted for only 8% variability, whereas the OR for RU in a similar model adjusted for age was significant and equaled 5.42 (95% CI 1.20; 24.50), with an even greater R2 (0.13).\n\nOf the nine locations in which we tested SUVmax as a predictor of metastasis on the follow-up visit, the highest areas under the curve (AUC) were found for RLH, RRL, RU and RRI. For RLH, SUVmax of 0.74 yielded the greatest AUC (0.668; 95% CI 0.505 – 0.831) with quite high sensitivity (75%) and specificity (61%). Although this model was statistically significant (p=0.049) (Figure 1), we failed to identify SUVmax corresponding to high sensitivity (80% or above) with acceptable specificity. When a high sensitivity of 80% was reached, we observed a dramatic fall in specificity. The corresponding SUVmax value with the highest AUC (0.682; 95% CI 0.520 – 0.843) for RRL was 1.05, for which sensitivity reached 69% and specificity was as high as 77%. This model was also statistically significant (p=0.032) (Figure 2). SUVmax value with the highest AUC (0.672; 95% CI 0.509 – 0.835) for RU was 0.85, for which sensitivity equaled 63% with almost similar specificity (61%). This model was also statistically significant (p=0.043), and Figure 3 illustrates AUC for this location. Finally, SUVmax with the highest AUC (0.679; 95% CI 0.517 – 0.841) for RRI was 0.78, for which sensitivity reached 69%, but specificity was only 61%, but statistically significant (p=0.035). Figure 4 reflects AUC for this analysis. Finally, PTL, tumor stage system, tumor grade and staging on LM did not affect SUVmax.\n\n\nDiscussion\n\nThe current prospective observational cohort study is one of very few to identify the location of greater 18F-FDG accumulation by functional VAT activity as early markers of later metastases indicative of the metastatic status of CRC patients. In a cohort of 60 patients in adjusted regression models and ROC analysis we showed that 18F-FDG accumulation in RLH, RU and RRL and RRI were predictors of later metastases in CRC patients with moderate, but statistically significant sensitivity and specificity values. The threshold value of SUVmax 0.74 for RLH resulted in 75% sensitivity and 61% specificity, whereas the corresponding SUVmax for RRI was 0.78 with a sensitivity of 69% and a specificity of 61%. We also found that a threshold value of SUVmax 1.050 resulted in 69% sensitivity and 77% specificity for accumulation in RRL, whereas the SUVmax value of 0.85 warranted 63% sensitivity and 61% specificity for RU. In our analysis, 18F-FDG accumulation in the remaining tested five locations was not associated with later metastases risk.\n\nThe predictive value of 18F-FDG PET/CT for CRC has been reported in a number of preceding studies, reporting different SUVmax values. Byung Wook Choi et al. retrospectively emphasized the predictive value of metabolic parameters on 18F-FDG PET/CT in classical rectal adenocarcinoma in 149 patients on two models (AUC 0.778 and 0.762, p=0.04; 0.814 and 0.779, p=0.83).12 One more study by Sung Hoon Kim et al. retrospectively showed the prognostic value of 18F-FDG PET/CT for LN metastasis in rectal cancer in 166 patients, nodal SUVmax 2.356, AUC 0.698 (p=0.04), 0.720 (0.033), 0.806 (p=0.04).18 Finally, Kisoo Pahk et al. retrospectively showed the prognostic role of functional VAT activity evaluated by preoperative 18F-FDG PET/CT for regional or distant LN metastasis in 131 CRC patients; however, the ratio of visceral to subcutaneous fat activity (VAT/SAT) was evaluated, while the ratio of SUVmax 1.88, AUC 0.862, sensitivity 84.6%, specificity 78.8%, p<0.001.1 Emir Sokolović et al. showed the predictive metabolic value of SUVmax with metastatic CRC patients, and concluded that SUVmax could be used as a novel predictive factor of disease progression among metastatic CRC patients. Average ±SD progression-free survival with a SUVmax above 4.1 was 11.3±9.37 months, and a SUVmax below 4.1 was 19.6±12.05 months (p=0.001).22 Esra Arslan et al. showed the predictive potential of 18F-FDG PET/CT and KRAS mutation in CRC, where the mean SUVmax with primary tumor was estimated to be 21.1±9.1 (range= 6.0–47.5) and tumor mean SUVmax with a KRAS mutation (24.0±9.0) was found to be significantly higher than those without a KRAS mutation (17.7±8.2) (p=0.001).23\n\nA number of prior reports ascertained the relationship between visceral adiposity and the prediction of CRC.24 Nevertheless, the outcomes were versatile and did not reach consent. These analyses used CT to measure VAT volume as a surrogate marker of VAT activity. But, VAT volume is reportedly unrelated to the visceral fat inflammatory process,25 whereas the identification of VAT volume by CT may not be satisfactory in affecting the current functional VAT activity.5 Therefore, a functional imaging modality like 18F-FDG PET/CT could be more suitable for evaluation of functional VAT activity than CT.\n\nPrevious research on functional VAT activity and 18F-FDG PET/CT concentrated on systemic inflammatory diseases, such as atherosclerosis or chronic obstructive pulmonary disease.5 Liang-qian Tong et al. illustrated the association between pulmonary 18F-FDG metabolism and smoking history in 347 healthy adults with chronic obstructive pulmonary disease where differences in the pulmonary SUVmax according to smoking status were analyzed. The mean SUVmax of current smokers was higher than that of ex-smokers with a medium (1.03±0.14 vs 0.88±0.16) or larger tobacco burden (1.08±0.15 vs 0.89±0.11) (p=0.012, p<0.001, respectively). However, there were no differences between the mean SUVmax of ex-smokers (0.91±0.13) and current smokers (0.91±0.16) with a smaller tobacco burden (p=0.888). The mean SUVmax of ex-smokers and current smokers with less tobacco burden were both significantly higher than that of non-smokers (0.78±0.13) (p<0.001, p<0.001, respectively).26\n\nThis research used 18F-FDG PET/CT to demonstrate the practical application of functional VAT activity for cancer disease, which can provide molecular data about inflammatory processes in CRC LM.\n\nThe current analysis has some limitations. Firstly, despite its prospective design, the study sample was limited, although patients were consecutively recruited for several years. Secondly, we could only enroll patients from a single nuclear medicine unit and only in the country’s capital. However, PET/CT is not yet widely available elsewhere in the country; therefore, the current sample is comprised of patients who were forced to travel to the capital for the examination, thus, representing a population from almost the entire country. Thirdly, predictive value was evaluated for SUVmax only, and other crucial factors such as grade, and location of the primary tumor could not be analyzed. Further prospective research data with larger populations will be necessary to verify our outcomes.\n\nFinally, functional VAT activity evaluated by 18F-FDG PET/CT is substantially associated with LM. Furthermore, it is a useful factor for the prediction of LM. Implementing the results into practical medicine will help practitioners choose tactics and control CRC patients.\n\n\nConsent\n\nAll patients provided written informed consent for the study and participation.\n\n\nData availability\n\nOpen Science Framework: ‘Raw Underlying Data Colorectal Cancer for Predictive Value’. https://doi.org/10.17605/OSF.IO/NSZFK.21\n\nThis project contains the following underlying data:\n\n• Raw Underlying Data CRC for PV.xlsx (Demographic and preparation accumulation data in the studied cohort)\n\nOpen Science Framework: TREND checklist for ‘Predictive value CRC’ https://doi.org/10.17605/OSF.IO/PRM95.19\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nPahk K, Rhee S, Kim S, et al.: Predictive Role of Functional Visceral Fat Activity Assessed by Preoperative F-18 FDG PET/CT for Regional Lymph Node or Distant Metastasis in Patients with Colorectal Cancer. PLoS One. 2016 Feb 10; 11(2): e0148776. Publisher Full Text\n\nXi Y, Xu P: Global colorectal cancer burden in 2020 and projections to 2040. Transl. Oncol. 2021 Jul 6; 14(10): 101174. PubMed Abstract | Publisher Full Text\n\nBray F, Ferlay J, Soerjomataram I, et al.: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 2018 Nov; 68(6): 394–424. PubMed Abstract | Publisher Full Text\n\nSung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 2021; 71(3): 209–249. PubMed Abstract | Publisher Full Text\n\nBucerius J, Vijgen GHEJ, Brans B, et al.: Impact of Bariatric Surgery on Carotid Artery Inflammation and the Metabolic Activity in Different Adipose Tissues. Medicine (Baltimore). 2015 May 22; 94(20): e725. PubMed Abstract | Publisher Full Text\n\nOzis SE, Soydal C, Akyol C, et al.: The role of 18F-fluorodeoxyglucose positron emission tomography/computed tomography in the primary staging of rectal cancer. World J. Surg. Oncol. 2014 Feb 1; 12(1): 26. PubMed Abstract | Publisher Full Text\n\nSuzuki Y, Okabayashi K, Hasegawa H, et al.: Metabolic Tumor Volume and Total Lesion Glycolysis in PET/CT Correlate With the Pathological Findings of Colorectal Cancer and Allow Its Accurate Staging. Clin. Nucl. Med. 2016 Oct; 41(10): 761–765. PubMed Abstract | Publisher Full Text\n\nHong JH, Kim HH, Han EJ, et al.: Total Lesion Glycolysis Using 18F-FDG PET/CT as a Prognostic Factor for Locally Advanced Esophageal Cancer. J. Korean Med. Sci. 2016 Jan; 31(1): 39–46. PubMed Abstract | Publisher Full Text\n\nBang JI, Ha S, Kang SB, et al.: Prediction of neoadjuvant radiation chemotherapy response and survival using pretreatment [18F] FDG PET/CT scans in locally advanced rectal cancer. Eur. J. Nucl. Med. Mol. Imaging. 2016 Mar 1; 43(3): 422–431.\n\nOgawa S, Itabashi M, Kondo C, et al.: Prognostic Value of Total Lesion Glycolysis Measured by 18F-FDG-PET/CT in Patients with Colorectal Cancer. Anticancer Res. 2015 Jun; 35(6): 3495–3500.\n\nShi D, Cai G, Peng J, et al.: The preoperative SUVmax for 18F-FDG uptake predicts survival in patients with colorectal cancer. BMC Cancer. 2015 Dec 21; 15(1): 991.\n\nChoi BW, Kang S, Bae SU, et al.: Prognostic value of metabolic parameters on 18F-fluorodeoxyglucose positron tomography/computed tomography in classical rectal adenocarcinoma. Sci. Rep. 2021 Jun 21; 11(1): 12947. PubMed Abstract | Publisher Full Text\n\nDeantonio L, Caroli A, Puta E, et al.: Does baseline [18F] FDG-PET/CT correlate with tumor staging, response after neoadjuvant chemoradiotherapy, and prognosis in patients with rectal cancer? Radiat. Oncol. 2018 Oct 25; 13(1): 211. PubMed Abstract | Publisher Full Text\n\nPark JS, Huh JW, Park YA, et al.: Prognostic Comparison Between Mucinous and Nonmucinous Adenocarcinoma in Colorectal Cancer. Medicine (Baltimore). 2015 Apr 17; 94(15): e658. PubMed Abstract | Publisher Full Text\n\nBoellaard R, Delgado-Bolton R, Oyen WJG, et al.: FDG PET/CT: EANM procedure guidelines for tumour imaging: version 2.0. Eur. J. Nucl. Med. Mol. Imaging. 2015; 42(2): 328–354. PubMed Abstract | Publisher Full Text\n\nMilardovic R, Beslic N, Sadija A, et al.: Role of 18F-FDG PET/CT in the Follow-up of Colorectal Cancer. Acta Inform. Medica. 2020 Jun; 28(2): 119–123.\n\nNiccoli Asabella A, Simone M, Ballini A, et al.: Predictive value of 18F-FDG PET/CT on survival in locally advanced rectal cancer after neoadjuvant chemoradiation. Eur. Rev. Med. Pharmacol. Sci. 2018 Dec; 22(23): 8227–8236. PubMed Abstract | Publisher Full Text\n\nKim SH, Song BI, Kim BW, et al.: Predictive Value of [18F] FDG PET/CT for Lymph Node Metastasis in Rectal Cancer. Sci. Rep. 2019 Mar 21; 9: 4979. PubMed Abstract | Publisher Full Text\n\nSuleimanov A, Saduakassova A, Vinnikov D, et al.: TREND Checklist - Predictive Value CRC.2022 Aug 1 [cited 2022 Sep 15].Reference Source\n\nBoellaard R, Delgado-Bolton R, Oyen WJG, et al.: FDG PET/CT: EANM procedure guidelines for tumour imaging: version 2.0. Eur. J. Nucl. Med. Mol. Imaging. 2015 Feb; 42(2): 328–354. PubMed Abstract | Publisher Full Text\n\nSuleimanov A, Saduakassova A, Vinnikov D, et al.: Raw Underlying Data Colorectal Cancer for Predictive Value.2022 Jul 22 [cited 2022 Sep 15].Reference Source\n\nSokolović E, Cerić T, Cerić Š, et al.: The Prognostic Value of SUVmax of 18F-FDG PET/CT in Patients with Metastatic Colorectal Cancer. Acta Medica Acad. 2020 Apr; 49(1): 1–8. PubMed Abstract | Publisher Full Text\n\nArslan E, Aksoy T, Gürsu RU, et al.: The Prognostic Value of 18F-FDG PET/CT and KRAS Mutation in Colorectal Cancers. Mol. Imaging Radionucl. Ther. 2020 Feb; 29(1): 17–24. PubMed Abstract | Publisher Full Text\n\nRickles AS, Iannuzzi JC, Mironov O, et al.: Visceral Obesity and Colorectal Cancer: Are We Missing the Boat with BMI? J. Gastrointest. Surg. 2013 Jan 1; 17(1): 133–143. PubMed Abstract | Publisher Full Text\n\nChristen T, Sheikine Y, Rocha VZ, et al.: Increased glucose uptake in visceral versus subcutaneous adipose tissue revealed by PET imaging. JACC Cardiovasc. Imaging. 2010 Aug; 3(8): 843–851. PubMed Abstract | Publisher Full Text\n\nQian TL, Fang SY, Nan JS, et al.: The Association Between Lung Fluorodeoxyglucose Metabolism and Smoking History in 347 Healthy Adults. J. Asthma Allergy. 2021 Mar 31; 14: 301–308. Publisher Full Text"
}
|
[
{
"id": "156188",
"date": "08 Dec 2022",
"name": "Jandos Amankulov",
"expertise": [
"Reviewer Expertise Radiology and Nuclear Medicine in Cancer Diagnosis"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article addresses the relationship between 18F-fluorodeoxyglucose uptake level in visceral adipose tissue (VAT) and the development of metastasis in colorectal cancer (CRC) patients. It addresses an important topic as early predictor markers of metastasis can improve the prognosis of the disease. Despite the rather small sample size noted by the authors, this study will be the beginning of further research on large samples.\nHowever, there are a number of issues that need to be clarified/corrected:\nPlease use MBq as the unit of measurement instead of MBk.\n\nPlease use mmol/L as the unit of measurement instead of mmol/l, as a broader group more easily recognizes the capitalized version.\n\nMany studies have extensively analyzed the effect of blood glucose levels and other confounding factors on 18F-FDG uptake in normal tissue and tumor. In your research, have you corrected the VAT SUVmax measurements based on the participant’s blood glucose levels in normoglycemia?\n\nThe study results do not support the statement that implementation of VAT 18F-FDG uptake measurement will improve CRC patients’ management. The clinical utility/usefulness of this biomarker was not assessed within this study. This hypothesis would need to be validated in other non-inferiority trials. So use “would/might help” instead of \"will help\" in the sentence \"Implementing the results into practical medicine will help practitioners choose tactics and control CRC patients\", or remove this sentence.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "175503",
"date": "13 Jun 2023",
"name": "Marianie Musarudin",
"expertise": [
"Reviewer Expertise Nuclear Medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study highlights the potential for early LN metastases detection, by quantitatively measures the functional VAT activity using 18F-FDG PET/CT. Eight subdomains of abdominal regions and pelvic cavity was included in the assessment. The study utilised ROC analysis as the statistical method.\nSome clarifications needed:\n\"The average activity dose of the injected 18F-FDG was 252.55 MBk, ranging from 132.5 to 465.3 MBk.\" ----> Use SI unit, MBq.\n\nThe VAT areas were identified by using predefined HU, ranging from -70 to -110. Justify this selection with citation.\n\nYou have calculated the sample size. Is the sample size of 60 actually less than the estimated sample number? If yes, according to the sample size calculation, how much sample is actually needed? Some authors use a flow chart to show the study design and present the sample size and excluded sample number (with the causes).\n\nSome studies considered total adipose tissue SUV (SUVTAT) or relative SUV (SUVVAT normalized to the SUVTAT) for their analysis. Add a sentence explaining why SUVMAX was used in this study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1158
|
https://f1000research.com/articles/11-665/v1
|
16 Jun 22
|
{
"type": "Research Article",
"title": "Perception of health care students towards lectures as a teaching and learning method in the COVID era - A multicentric cross-sectional study from India",
"authors": [
"Vijay Pratap Singh",
"Anand Ramakrishna",
"Neloy Sinha",
"Bidita Khandelwal",
"Nitin Joseph",
"Purnima Barua",
"Anand Ramakrishna",
"Neloy Sinha",
"Bidita Khandelwal",
"Nitin Joseph",
"Purnima Barua"
],
"abstract": "The sudden precipitation of the pandemic forced undergraduates to take refuge at home, deserting the campus. Consequently, the age-old classroom in person teaching-learning (T-L) method shifted and lessons had to be conducted online. In previous decades, archetypical classroom lectures survived a lot of criticism in the face of the quasi-passive nature of T-L methodology. There are very few studies that reflect undergraduate students' perceptions of lectures. This study aimed to evaluate undergraduate students’ perceptions of lectures using an online questionnaire with 13 items, which was circulated to undergraduate students of medical, physiotherapy, and nursing courses in three settings at different locations of private and public health schools. There was a total of 877 responses. The surveyed students were in favor of lectures and considered them indispensable for undergraduate learning. They preferred it as a kind of organized learning through the teacher’s own experiences. Our study suggests that it is not the ‘lecture’ that requires mending but possibly teachers require better training, application of effective audio-visual aids, and innovative techniques to sustain students' interest in the class.",
"keywords": [
"classroom lectures",
"COVID era",
"perception",
"students",
"health profession"
],
"content": "Introduction\n\nThe lecture was an integral part of the revered teaching-learning method since the time of Gurukul.1 It might have morphed internally to tackle the ever-increasing demands of modern educational policies and pressures but it cannot be completely replaced in the name of innovative teaching methods.2\n\nWithout being prejudiced against the tech-savvy tribe, we must revisit the basics. Is India a technology-supported country at the grassroots level? Do we have adequate broadband strength in remote villages, hilly areas, and in low economic setups?\n\nIn India broadband strength is a concern for many residents in hilly areas and in low economic setups. Despite knowing the answers to the above questions, in this “COVID-19 lockdown” phase, the media highlighted the poor access of rural students and their inability toward 100% participation in the online teaching-learning opportunities.3 A sudden move toward digital technology will undermine the underprivileged section while working in favor of the urban learning fraternity.4,5\n\nNone of the methods are good or bad but should be evaluated from the perspective of the situational fulcrum. A search of literature revealed a scarcity of methodical in-depth studies that showed students’ perceptions of lectures from a global perspective. While earlier authors emphasized the rebuilding of a new curriculum in health/medical education, which could be created through digital and internet media, they also undermined the effectiveness of classroom lectures.6 We take this opportunity to find out students’ perception toward lectures, a method that is time tested but had to undergo and withstand strong criticisms from the penmanship and propaganda of educationists of the past who wanted to devote their time in publication at the cost of classroom teaching.6,7 They considered classroom teaching as sacrificial and were in favor of emerging technologies.7,8 Most studies that criticized lectures were either viewpoints of teachers or policymakers to stress their side of the story.9,10 There is scarcity of data about the viewpoints of the students and what they think about lectures. The COVID-19 era is the right time to explore students’ perceptions of lectures, due to the rapid shift away from this technique, and we aim to do this through a structured set of questionnaires. This study operationally defines lectures as traditional classroom ones, which are large group teaching methods, face-to-face, and in accordance with the publications by Brown2 and Harden.11 Brown and Manogue2 focused on the importance of a lecture that cannot be replaced by any other teaching-learning method, its limitations, different methods, how learning happens through lectures, and skills required for a good interactive one. Harden and Crosby11 explained how a lecturer should emulate the role of a teacher, and the authors mentioned 12 roles of a teacher that cannot be seen in a different canvas; rather, it overlaps with the lecturer model. A lecturer is a teacher and his interaction with students is not just an hourly lecture but a holistic role to be part of their learning and making their learning environment safe.2,10 The sudden shift of policy makers’ attention to research pushed lectures to a somewhat lower pedestal and the time dedicated to lecturing and mentoring got diverted to research. Students’ views were hardly included, and everything was left in the name of self-directed learning.12,13 It is a major method of teaching and learning for post-graduates, but its applicability in undergraduate and preclinical days should be evaluated with caution. If students are not sensitized primarily to an entirely new topic, self-directed learning can prove ineffective.14 There is no roadmap provided to them. In such cases, lectures are of great use, these can give a blueprint for learning a topic through the experiences of the lecturer and students can build upon it by self-directed learning as per their ability and interest in line with the competencies required.15\n\nTo address some of the concerns mentioned in this section, this study aims to evaluate students’ perceptions of lectures in different settings, courses, and among private and state-supported health care institutions.\n\n\nMethods\n\nThe study was approved by the institutional ethics committee of Kasturba Medical College, Mangalore registration number ECR/541/Inst/KA/2014/RR-20 and reference code IECKMCMLR-08/2020/223. The study was carried out in accordance with relevant guidelines and regulations in ethics approval. All participants were asked for written informed consent for both collection of their data and for publication of this data, those who did not give this consent were not included in this study. Participants were students from the first to final year enrolled in medical, nursing, or physiotherapy courses from the Sikkim Manipal Institute of Medical Sciences (SMIMS), Gangtok; Kasturba Medical College (KMC), Mangalore; and Jorhat Medical College (JMC), Assam. It was a cross-sectional, exploratory, online survey that was implemented online through a questionnaire. We aimed for complete enumeration, blinded, and voluntary, without asking the identity of the students. This was to avoid bias.\n\nThis questionnaire based study was done during the first wave of COVID-19. We conducted the study in two phases. In phase I, we developed and validated the questionnaire, and in phase II, we measured the students’ perceptions of lectures during the COVID-19 period when most teaching happened through the online mode.\n\nTo the best of our knowledge we could not retrieve a questionnaire which measured students perception after sudden shift from classroom teaching-learning to internet based online teaching. Therefore, there was a challenge to develop a questionnaire which can measure the intended objective of this study. We used the keywords “lectures”, “class room lectures”, “large group teaching”, “Students perception”, “student experiences” and combined it with the BOOLEAN operator “AND.” We searched the following databases: PubMed (MEDLINE, RRID:SCR_002185), Cochrane (Cochrane Library, RRID:SCR_013000), Web of Science (Clarivate Analytics, RRID:SCR_017657) for articles published till August 2020 and retrieved 52 studies. After screening the articles, we included some studies and experts’ opinion to develop items for the questionnaire.\n\nThe initial questionnaire had 20 items. Initial items for the study were generated by our team of ten teaching faculties from medical education unit with three rounds of brainstorming meetings and consensus-building. Initial questionnaire was preliminary and was based upon faculties experiences, literature search and informal discussions. Then an initial item pool was created and the items were tested with 30 students from medical, physiotherapy, and nursing courses to reach a consensus. These students were class representatives in academic or co-curricular committees. These students were selected because they have maximum interaction with students and are seen as representatives for what students thought about sudden shift of on-campus lecture hall classes to online mode. The questionnaire was sent to these students as a Google Form (Google, Google Forms) but meetings were held through online video modes to derive final set of questions.34 In pilot testing students were asked to rate each question on a Likert scale ranging from 1 to 5 (where 1=not at all relevant and 5=extremely relevant). Open feedback was also taken on any items not included, wording and clarity of the questions. For item validation responses were also categorized into dichotomy as agree, if respondent scored 3 or more. Item-content validity index (I-CVI) and scale-content validity index (S-CVI) were calculated for the item pool. The I-CVI was calculated by dividing the number of agreed participants by the total number of participants’ responses according to the dichotomous response scale.16 The S-CVI was calculated by taking the average I-CVI and dividing it by the total number of items. The acceptable agreement for I-CVI was 0.78 or higher, and the acceptable agreement for S-CVI was 0.80 or higher. The research team used I-CVI and any open responses in the survey to guide them in modifying, removing, or replacing the items.\n\nA final set of questions with 13 items was chosen, as shown in Table 1. The reliability of the data collection tool was calculated using Cronbach’s alpha value and was found to be 0.72 indicating good internal consistency.17\n\nFor the final questionnaire a Google form (Google, California) was created, and the link was sent to students to their email IDs. All students eligible were included in this initial round of emails. A participant information sheet and consent form were embedded on the first page, while names and email IDs were not asked to maintain anonymity. Data were analyzed in SPSS (IBM SPSS Statistic® version 25) (RRID:SCR_016479). The analyses included descriptive statistics and chi-square tests. Statistical significance was set at p<0.05.\n\n\nResults\n\nWe coded options on a Likert scale from 5 to 1 as SA (strongly agree-5), A (Agree-4), N (Neutral-3), D (Disagree-2), and SD (strongly disagree-1). Further, we divided the semesters into years to ensure uniformity and homogeneity, as shown in Table 2. There were a total of 1,545 students across all three institutions who received the questionnaire from students’ section. The link was sent to all students’ email. From JMC we received 300 respondents out of which 93 were males and 207 were females. From KMC we received respondents 677 out of which 380 were males and 297 were females. And from SMIMS we received 568 respondents out of which 171 were males and 397 were females. There were a total of 877 responses including responses from all three institutions and descriptive data is shown in Table 3. There were more female respondents than male (474 and 403 respectively). Responses from each year were comparable, and there was no significant difference, as shown in Table 3.34\n\nIn medical, there are 9 semesters over 4 and half years, therefore, we grouped 3,4, and 5 semesters as year 2 because the same subjects are learned in this period of one and half years.\n\nTable 4 shows question wise responses of students on the Likert scale. Question 1 (Q1) was about missing lectures for which 58.7% of the students agreed (or strongly agreed) they had, which is very large compared to disagree(10.9%) and strongly disagree(6.6%). Around 60% of students agreed (or strongly agreed) to genuinely missing lectures, as a response to Q 2. However, 65.6% of the students agreed that they were happy that online teaching was available. Despite this, answers to Q4 77.9% reinforced that the online mode of the lecture could not replace usual classroom lectures. In Q5, 87.6% students agreed (or strongly agreed) and expressed that the quality of the teacher, makes a good classroom lecture. Around 48.9% of students disliked a lecture where the teacher was either reproducing the book or confused about their teaching methods; 55.2% of students believed that it is better to shift to technology-based lectures only when the teacher is not capable of delivering a good lecture. This means that students find online mode as an alternate when teaching quality in the classroom is not good. Also, 81.3% of students eagerly wait for some lectures because of the teacher’s ability, this may show students seeing a role model in teachers. Only 23.2% of students thought that the online mode was sufficient and could be a replacement for classroom teaching. Further, 59.2% of students felt that classroom teaching is the best method of teaching-learning and it gives great impetus to strengthening lectures. In Q11, 87.8% of students agreed that lectures are nothing but the teacher’s ability to deliver, and its success depends on the quality of the teacher. Next, 83% of students felt that technology such as video streaming is just an adjunct to make lectures better, but it cannot suffice and replace the role of the teacher in the lecture. Also, 71.4% of students looked for role models in their teachers during lectures, which is a big factor to be analyzed.\n\nTable 5 shows that KMC Mangalore students had a statistically significant better perception of onsite lectures compared to other institutions (p=0.007). There was no significant association between the gender of students and choices for the lecture; both genders felt that lectures were important (p=0.715). All the students had a good perception in favor of lectures, and they felt that a large group of teachers is indispensable as per the items of the questionnaire (p=0.445). Across disciplines, there was no significant difference (p=0.635), and all healthcare students in medical, nursing, and physiotherapy had a good perception of classroom lectures.\n\nThe questionnaire was a Likert scale and for ease of study, scores were divided into two. Strongly disagree, disagree, and neutral was combined to be called ‘poor perception in favour of lectures’, and strongly agree and agree were combined to get one score and to be called ‘good perception favour of lectures’. This was done to get a clear distinction between the perception of students to have or not to have lectures.\n\n\nDiscussion\n\nOur study showed that students value lectures as a preferred teaching-learning method and do not see it as replaceable through online lectures or any other form of learning. There were 13 questions that tested students’ perceptions in different ways, such as asking whether it was just their fear or anxiety of having moved out of campus overnight and detached from the usual form of learning on campus; the majority students still rated lectures as indispensable (59.2%) of students responding to question 10.\n\nA question we considered when completing this study was is it human nature to underestimate something that is easily available? Students by default attend lectures and the COVID-19 era was an unwarranted blow that shifted them from campus life to the home set up. In this dire state, we believe they could introspect the superior method and the importance of regular lectures better, especially when it was no longer feasible. Lectures are not mere delivery of content, but students can see a dynamic teacher in the classroom. It illuminates soft skills, aspects of delivery styles, and often looks for a role model in one of the teachers,2 which is not possible when lectures are arranged online. The shift to online lecture was not a choice; rather a hard decision and better than nothing in the face of COVID-19 and social distancing protocols. However, the COVID-19 era could be seen as a blessing in disguise to have brought introspection about the method of face-to-face classroom lectures and its utility.\n\nOur results suggest that self-directed, web-based, and video-based learning can be an adjunct to in person lectures but not a direct replacement; they must be engraved in the curriculum with caution, and teachership should not lose its essence. The teacher is the director of learning and changing roles in the new era and increasing workload or a teacher gaining multiple roles could be solved by bringing more teachers on board rather than replacing lectures.18\n\nA previous landmark study identified 12 roles of teachers derived from three models and six broad areas underneath. It is not a lecture per se, which is disliked but the poor quality of lecturing.2,10 Our results suggest that, if the lecture is just a reproduction of text material, large coverage with no take-home message, amorphous talking, unorganized content, lack of audio-visual aids, poor voice quality, and inaudible, a large amount of students seem to avoid it. The few available literature note suggest that lectures are the best in presenting information, explaining, provoking new thoughts, adapting a problem-solving approach, improving inquisitiveness, critical and rational thinking, and deductive reasoning in limited time to a large group and all from the experiences of a good lecturer, which cannot be found in any other method.19–22\n\nLectures can be improved by structuring and sustaining the interest of students with a clear learning objective during the session and a high engagement process.23 The key messages can be summarized at the end, and students may take notes or handouts may be provided. There are various skills of lecturing, including planning, set induction, effective narration, questioning, and effective use of audio-visual aid making them interactive to improve learning.23,24 This also takes away the notion that lecturing is an inborn quality; rather it can be learned.10,25 An effective method is to obtain feedback from students and peers with a positive intent. Lectures need not be replaced; they should be improved by new digital innovations.2,11 The purpose of two published studies26,27 was to determine the lecturers’ or students’ perceptions and their achievement between two learning cultures, the traditional and the flipped classroom. Changing from traditional to flipped has reportedly had a positive impact on students’ perception and achievement. The cost to achieve this will include greater effort and time in the development of resources, planning, and implementation of in-class activities. The authors10,11 stated that a new learning environment helped lecturers achieve their learning outcomes and made the teaching-learning process more engaging, active, and student-centered. These are innovative methods that can be used as adjuncts and not replace lectures, such as flipping.\n\nAnother study28 examined student perceptions of lecture videos used as a means to increase the available time for in-class problem-solving in a teaching and learning context. A portion of the face-to-face lecture were replaced with pre-recorded lecture videos, which were assigned as homework. The freed lecture period was used for additional in-class problem-solving development without sacrificing the theory and fundamental background. To assess the effectiveness of the format change, student perceptions were assessed through an anonymous online survey. It was administered after completion of the course. Student perception of the lecture video was used to increase the time for an in-class course on ‘problem-solving applications. 70% of respondents in this study approved video lectures but they did not compare to the efficacy of classsroom lectures rather they informed that they can see video lectures at their ease, faster way of covering the syllabus and escaping from question-answer interaction of classrooms.\n\nAnother study29 related to higher education, stressed students’ ratings to evaluate and improve the quality of courses and professors’ instructional skills. It is concerned with the psychometric properties of the instructional skills questionnaire (ISQ), a new theory-based student-rating-of-teaching questionnaire with specific questions concerning lecturing skills. The ISQ was developed by authors of this study and was administered after a single lecture in this study. It serves as a formative feedback instrument for university professors during courses to assist, improve, and re-evaluate their skills as deemed necessary. The ISQ contains seven dimensions of the professor’s instructional skills and three student-specific (self-perceived) learning outcomes. In this study,13 Dutch students from an array of 75 courses rated three 90-minute lectures (T1, T2, and T3) and their respective professors using this ISQ. In aggregate, 14,298 ISQ forms were used to rate 225 lectures. The form is about a set of questions that were developed for the students’ post-lecture feedback, while the lecturers were instructed to conduct interactive classes. We reiterate that lecture classes were assumed to be taken as interactive and interesting to sustain students’ focus on improving learning.\n\nAnother study30 used web-based learning support, augmented by multimedia theory, comprising interactive quizzes, glossaries with audio, short narrative PowerPoint presentations (Microsoft, US), animations, and digitized video clips. Here, 81 % of the students valued interactive multimedia learning only as an adjunct but were not yet ready to abandon the traditional face-to-face mode of lectures. This finding contributes to an understanding of how web-based resources can be supplementary, but not a substitute for face-to-face lectures. Similar findings were shown in our study, where students felt web-based learning only as a support medium for lectures.\n\nOnline learning is not a new concept. However, until a decade ago, these were mainly print-based and postal department-dependent. In India and the so-called third world nations on the threshold of emerging as developed ones, the technical aspect and resource limitations side-tracked us from web-based learning, in preference to traditional lectures.31 Despite its immense potential, online teaching was not intended to be used exclusively, this was changed due to the spread of the pandemic, which opened the flood gate.\n\nThe authors reinforce that to ensure quality to be retained during online learning, the principles that had been identified during traditional classroom teaching should be incorporated into the online milieu. When we accessed old literature/journals, they mentioned that technology-based learning was not a replacement for the lecture because the very principles of web-based learning were configured in traditional classrooms.32,33\n\nLectures are at least as effective as other teaching methods for imparting information and explanations. Intention, transmission, and output are the basis for model lecturing. The key skills of preparing lectures, explaining, and varying student activities may be derived from the models proposed in the published literature.2\n\n\nConclusions\n\nClassroom teaching has evolved through experiments of the past. There is still scope for improvement in different aspects, but it should not be discarded in favor of online teaching. This small but sincere study again strongly reasserts its position and acceptance among contemporary students.\n\nThis study has limitations, and its generalizability will depend on context. This study has been done when students were suddenly shifted from On-campus education to online learning amidst COVID pandemic. Students might be having many questions about reopening of the colleges, impact of pandemic etc. which might influence their responses.\n\nThis study has a unique strength that it tried to find importance of classroom lectures and large group teaching amidst the crisis whereas most of the studies published in this era focused on Online learning.\n\n\nData availability\n\nOSF: Perception of Health care students towards lectures as a Teaching-learning method in COVID era - A multicentric study from India. DOI: https://doi.org/10.17605/OSF.IO/FUEW434\n\nThis project contains the following underlying data:\n\n- All in One.xlsx (raw Likert scale data and key)\n\nOSF: Perception of Health care students towards lectures as a Teaching-learning method in COVID era - A multicentric study from India. DOI: https://doi.org/10.17605/OSF.IO/FUEW434\n\nThis project contains the following extended data:\n\n- Data analysis final.doc (Data used in analysis).\n\n- INITIAL QUESTIONNAIRE.docx (A word document containing the full set of questions used in the final questionnaire)\n\nOSF: Perception of Health care students towards lectures as a Teaching-learning method in COVID era- A multicentric study from India. DOI: https://doi.org/10.17605/OSF.IO/FUEW434\n\nThis project contains the following reporting guidelines:\n\n- STROBE for lecture stody.docx",
"appendix": "References\n\nKak V: Neurosciences Education: From “Gurukul” to e-Learning. Neurol. India. 2015; 63(3): 298–299. Publisher Full Text\n\nBrown G, Manogue M: AMEE Medical Education Guide No. 22: Refreshing lecturing: a guide for lecturers. Med. Teach. 2001 May; 23(3): 231–244. PubMed Abstract | Publisher Full Text\n\nMuthuprasad T, Aiswarya S, Aditya KS, et al.: Students’ perception and preference for online education in India during COVID -19 pandemic. Soc. Sci. Humanit Open. 2021; 3(1): 100101. Publisher Full Text Reference Source\n\nO’Doherty D, Dromey M, Lougheed J, et al.: Barriers and solutions to online learning in medical education – an integrative review. BMC Med. Educ. 2018; 18(1): 130. Publisher Full Text\n\nRajab MH, Gazal AM, Alkattan K: Challenges to Online Medical Education During the COVID-19 Pandemic. Cureus. 2020 Jul 2; 12(7): e8966–e8966. Publisher Full Text Reference Source\n\nRockwood K, Patterson CJ, Hogan DB: Nodding and napping in medical lectures: an instructive systematic review. C. Can. Med. Assoc. J. = J. l’Association Medicale Can. 2005 Dec; 173(12): 1502–1503. Publisher Full Text\n\nAliukonis V, Poškutė M, Gefenas E: Perish or Publish Dilemma: Challenges to Responsible Authorship. Medicina (Kaunas). 2020 Mar; 56(3) Publisher Full Text\n\nLadouceur R: Publish or perish. Vol. 65, Canadian family physician Medecin de famille canadien.2019; p. 86.\n\nLectures aren’t just boring, they’re Ineffective, too, study finds|Science|AAAS.[cited 2021 Feb 4]. Reference Source\n\nCrosby Joy RMH: AMEE Guide No 20: The good teacher is more than a lecturer - the twelve roles of the teacher. Med. Teach. 2000 Jan 1; 22(4): 334–347. Publisher Full Text\n\nHarden RM, Crosby JR, Davis MH, et al.: AMEE Guide No. 14: Outcome-based education: Part 5-From competency to meta-competency: a model for the specification of learning outcomes. Med. Teach. 1999; 21(6): 546–552. Publisher Full Text\n\nCamargo CP, Tempski PZ, Busnardo FF, et al.: Online learning and COVID-19: a meta-synthesis analysis. Clinics (Sao Paulo). 2020; 75: e2286. PubMed Abstract | Publisher Full Text\n\nDaniel SJ: Education and the COVID-19 pandemic. Prospects. 2020 Apr; 49: 91–96. Publisher Full Text\n\nTowle A, Cottrell D: Self directed learning. Arch. Dis. Child. 1996 Apr; 74(4): 357–359. Publisher Full Text\n\nBhandari B, Chopra D, Singh K: Self-directed learning: assessment of students’ abilities and their perspective. Adv. Physiol. Educ. 2020 Sep; 44(3): 383–386. PubMed Abstract | Publisher Full Text\n\nZamanzadeh V, Ghahramanian A, Rassouli M, et al.: Design and Implementation Content Validity Study: Development of an instrument for measuring Patient-Centered Communication. J. Caring Sci. 2015 Jun 1; 4(2): 165–178. PubMed Abstract | Publisher Full Text\n\nGottems LBD, De Carvalho EMP , Guilhem D, et al.: Good practices in normal childbirth: reliability analysis of an instrument by Cronbach’s Alpha. Rev. Lat. Am. Enfermagem. 2018/05/17. 2018; 26: e3000–e3000. Publisher Full Text Reference Source\n\nRose S: Medical Student Education in the Time of COVID-19. JAMA. 2020 Jun 2; 323(21): 2131–2132. Publisher Full Text\n\nGe L, Chen Y, Yan C, et al.: Effectiveness of flipped classroom vs traditional lectures in radiology education: A meta-analysis. Medicine (Baltimore). 2020 Oct; 99(40): e22430. PubMed Abstract | Publisher Full Text\n\nLuscombe C, Montgomery J: Exploring medical student learning in the large group teaching environment: examining current practice to inform curricular development. BMC Med. Educ. 2016 Jul; 16: 184. PubMed Abstract | Publisher Full Text\n\nMüller T, Montano D, Poinstingl H, et al.: Evaluation of large-group lectures in medicine - development of the SETMED-L (Student Evaluation of Teaching in MEDical Lectures) questionnaire. BMC Med. Educ. 2017 Aug; 17(1): 137. PubMed Abstract | Publisher Full Text\n\nOikarainen A, Mikkonen K, Kenny A, et al.: Educational interventions designed to develop nurses’ cultural competence: A systematic review. Int. J. Nurs. Stud. 2019 Oct; 98: 75–86. PubMed Abstract | Publisher Full Text\n\nUnteregger F, Mayer P: Medical lectures upgraded: 11 hacks from comedy. GMS. J. Med. Educ. 2019; 36(3): Doc23.\n\nTuma F: The use of educational technology for interactive teaching in lectures. Ann. Med. Surg. 2021 Feb; 62: 231–235. PubMed Abstract | Publisher Full Text\n\nBhattarai B, Gupta S, Dahal S, et al.: Perception of Online Lectures among Students of a Medical College in Kathmandu: A Descriptive Cross-sectional Study. JNMA J. Nepal Med. Assoc. 2021 Mar; 59(235): 234–238. PubMed Abstract | Publisher Full Text\n\nGoh CF, Ong ET: Flipped classroom as an effective approach in enhancing student learning of a pharmacy course with a historically low student pass rate. Curr. Pharm. Teach. Learn. 2019 Jun; 11(6): 621–629. PubMed Abstract | Publisher Full Text\n\nKohli S, Sukumar AK, Zhen CT, et al.: Dental education: Lecture versus flipped and spaced learning. Dent. Res. J. (Isfahan). 2019; 16(5): 289–297. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDolan DSL, Prodanov VI, Taufik T: Student Perception of Lecture Video Use as a Means to Increase Time for in Class Problem Solving Applications. Vancouver, BC: ASEE Conferences.Reference Source\n\nKnol MH, Dolan CV, Mellenbergh GJ, et al.: Measuring the Quality of University Lectures: Development and Validation of the Instructional Skills Questionnaire (ISQ). PLoS One. 2016; 11(2): e0149163. PubMed Abstract | Publisher Full Text\n\nKoch J, Andrew S, Salamonson Y, et al.: Nursing students’ perception of a Web-based intervention to support learning. Nurse Educ. Today. 2010 Aug; 30(6): 584–590. PubMed Abstract | Publisher Full Text\n\nVyas R, Anshu D, Hemlata, et al.: Application of classroom good teaching practices to an online faculty development programme in India. Southeast Asian J. Med. Educ. 2010 Jan 1; 4(2): 14–17.\n\nClark RE: Media will never influence learning. Educ. Technol. Res. Dev. 1994; 42(2): 21–29. Publisher Full Text\n\nClark RE: Reconsidering Research on Learning from Media. Rev. Educ. Res. 1983 Dec 1; 53(4): 445–459. Publisher Full Text\n\nSingh VP; R, AKhandelwal B, Joseph N: Perception of health care students towards lectures as a teaching and learning method in the COVID era - A multicentric cross-sectional study from India. [Dataset].2022, May 10. Publisher Full Text"
}
|
[
{
"id": "142261",
"date": "01 Aug 2022",
"name": "Jyotsna Rimal",
"expertise": [
"Reviewer Expertise Oral health",
"assessment",
"teaching learning",
"curriculum",
"quality assurance",
"problem based learning",
"faculty development programs"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript brings one of the most debated topic of large group physical lecturing Vs online teaching to its highlight. This work is important and brings richness of data through its multicentric design. However there are few minor corrections needed to bring it to indexed form. Please see the attached pdf for further comments.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8874",
"date": "10 Oct 2022",
"name": "VIJAY PRATAP SINGH",
"role": "Author Response",
"response": "Reviewer’s comments Changes made Inference drawn in the introduction itself. The facts followed by evidence based inference would be better Response: removed and reframed No method is good or bad however..... Response: No method is good or bad however any method should be evaluated from the perspective of the situational fulcrum. took this opportunity Response: We took this opportunity to find out students’ perception toward lectures….. In order to avoid bias, the research design was aimed at complete enumeration, blinding and voluntary nature. Response: done This and the subsequent sentence not needed. Response: done should be strongly disagree not otherwise Response: done typographic error Response: done shows not needed Response: done This is an important table. This table's result should be inferred and discussed in the discussion section. For eg: what could be the inference from the first question? Response: done shows not needed Response: done The column heading is missing Response: done just the way question number 10 is addressed...other questions need to be discussed and inferred Response: done how did the study show 'self directed learning could be an adjunct? Response: This is an extrapolation based on the fact that how some Institutions want to replace Lectures by these methods. Kindly accept Since, the study findings support lectures, 'at least' seem inappropriate here Response: done should have been ' which might have influenced.....' Response: done The conclusion is to recommend lectures so the last part of the sentence seem irrelevant (Whereas most of the studies......on online learning) Response: done"
}
]
},
{
"id": "151525",
"date": "29 Sep 2022",
"name": "Tapasya Karemore",
"expertise": [
"Reviewer Expertise Education",
"Medical education",
"Oral Medicine and Radiology",
"Dental Education Technology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is a very novel study. COVID brought many questions to the thought of health educationists. During COVID platform of education got shifted to Online. But what about Lectures? Whether students are really satisfied with online. Pertaining to this issue many educationists published papers which were more of narrative and hardly inquired about the perception of students.\nBiggest positive point of this study is taking three different health profession students, medical, nursing and physiotherapy across three geography, three reputed institutions in India, and explored students' perception through a survey using a questionnaire. The questionnaire was validated well, as per standard guidelines. Data was collected with confidentiality and then most appropriate statistical tools were used. Data is well presented. Sample size is very good. Discussion is well written. Authors are reputed and related to education. Conclusion is well drawn. This study is well at time and requires early publication before it gets its impact among readers and policy makers. Lectures and Large group teaching can not be replaced by anything, it can be made better using innovative ways to sustain students attention. This point is well written by authors.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-665
|
https://f1000research.com/articles/11-1157/v1
|
10 Oct 22
|
{
"type": "Study Protocol",
"title": "Increase in colonic PRopionate as a method of prEVENTing weight gain in adults aged 20–40 years (iPREVENT): protocol of a multi-centre, double-blind, randomised, parallel-group trial to investigate the efficacy of inulin-propionate ester versus inulin (control) in the prevention of weight gain over 12 months",
"authors": [
"Jennifer E Pugh",
"Aisha Anjum",
"Katerina Petropoulou",
"George Thom",
"Louise Mccombie",
"Martina Tashkova",
"Sumayya Alaraj-Alshehhi",
"Daphne Babalis",
"Christina Prechtl",
"Mike J Lean",
"A. Toby Prevost",
"Joana C. Vasconcelos",
"Tom Preston",
"Douglas Morrison",
"Gary Frost",
"Jennifer E Pugh",
"Aisha Anjum",
"Katerina Petropoulou",
"George Thom",
"Louise Mccombie",
"Martina Tashkova",
"Sumayya Alaraj-Alshehhi",
"Daphne Babalis",
"Christina Prechtl",
"Mike J Lean",
"A. Toby Prevost",
"Joana C. Vasconcelos",
"Tom Preston"
],
"abstract": "Introduction: Overweight and obesity affects over 70% of the UK population and is a major risk factor for the development of co-morbidities, including type 2 diabetes and cardiovascular disease. There now exists a considerable evidence base for the management of obesity. However, this is not the case for the prevention of obesity. Preventing weight gain in periods of life where there is an elevated risk of fat mass expansion could be beneficial to preventing associated diseases in later life. This protocol investigates the impact of novel food ingredient inulin propionate ester (IPE) in the prevention of weight gain. This trial aims to investigate the primary hypothesis that IPE has a superior effect on preventing body weight gain, compared with inulin, in young (<40 years old) adults over 12 months, whilst also investigating several complementary mechanisms that may explain the prevention of weight gain and improved long-term energy balance from consuming IPE.\n\nMethods: In this multi-centre, double-blind, randomised, parallel-group study, eligible participants will be randomly assigned to consume 10g IPE or 10g inulin (control) daily for 12 months. Study visits will be conducted at baseline, two-month, six-month and 12-month time points. The primary outcome is weight gain from baseline to 12 months. Secondary outcomes will examine changes in metabolic and cardiovascular health biomarkers, body composition and appetite. A mechanistic sub-group will explore causal mechanisms around energy balance, body composition, appetite regulation and the gut microbiota. Based on the power calculation, the sample size required is 270 participants or 135 per study group. Ethics and dissemination: The trial protocol and participant-facing documents have been reviewed and approved, by the London Hampstead Ethics Committee (REC Reference 19/LO/0095, 29th January 2019). Upon completion, the trial results will be published in peer-reviewed journals and presented at scientific conferences. Trial registration number: ISRCTN16299902, 1st March 2018.",
"keywords": [
"obesity",
"prevention",
"short-chain fatty acids",
"propionate",
"gut microbiota"
],
"content": "Trial Registration\n\nISRCTN: 16299902, 1st March 2018, https://doi.org/10.1186/ISRCTN16299902\n\n\nREC reference\n\n19/LO/0095\n\n\nProtocol version\n\nV5.0, 15th February 2021\n\n\nIntroduction\n\nOverweight and obesity affect over 68.2% of men, and 60.4% of women in the UK and drive the prevalence of several common co-morbidities, including type 2 diabetes, cardiovascular disease and cancer. Although significant advances have been achieved in the management of obesity, there has not been the same level of research activity in obesity prevention. Once an individual becomes obese the probability of returning to normal body weight is extremely low (1 in 210 for men and 1 in 124 for women).1\n\nWeight gain occurs commonly throughout adulthood and younger adults are at the greatest risk of substantial gains in body weight, according to a National Health and Examination Survey (NHANES) of adults aged 25–74. Major weight gain over 10 years is categorised as a gain in Body Mass Index (BMI) ≥5 kg/m2, this weight gain was highest in those aged 25–35 years.2 Whilst a relatively modest weight gain of 1 kg over a single year would present a very low risk to health in young adults, the accumulated weight gain over a decade or longer leads to a clear deterioration of cardiovascular and diabetes risk factors. For example, the 10-year Coronary Artery Risk Development in Young Adults (CARDIA) study demonstrated that weight gain during early adulthood produced measurable adverse changes in blood lipids, fasting insulin, and blood pressure, irrespective of race or gender.3\n\nEpidemiological and experimental studies have demonstrated an inverse association between dietary fibre intake and body weight gain.4,5 Current fibre intake is approximately 17–20g/d,6 well below the 30g recommendation.7 The daily intake of dietary fibre in the UK has not increased for 10 years.6 Although the mechanisms surrounding how elevated dietary fibre intake affects energy balance are not fully understood there is evidence that the fermentation of dietary fibre in the colon by the microbiota produces short chain fatty acids (SCFA) that stimulate the release of anorectic gastrointestinal hormones PYY and GLP-1.8,9 In previous research, a methodology for delivering the SCFA propionate to the colon was developed by esterifying it to a non-digestible fructooligosaccharide. It has been demonstrated that this novel food ingredient, inulin propionate ester (IPE), stimulated the release of PYY and GLP-1 and lowered energy intake.10 The proof of principle study demonstrated that over six months, the consumption of 10 g of IPE daily significantly prevented weight gain.10\n\nThe current study aims to investigate the impact of IPE on the prevention of weight gain in young adults aged 20 to 40 years over a period of 12 months.\n\n\nProtocol\n\nThis clinical trial is a randomised, placebo-controlled, double-blind trial to investigate the efficacy and safety of inulin propionate ester (IPE) versus the inulin (fermentable oligosaccharide) control upon weight gain prevention. Participants will be randomised to either IPE or inulin for 12 months. This trial will be performed at two UK sites: Imperial Clinical Research Facility (CRF) in London - Imperial College Healthcare NHS Trust and Glasgow CRF - NHS Research Scotland. This trial was registered with International Standard Randomised Controlled Trial Number (ISRCTN) registry (ISRCTN16299902) on 1st March 2018 (https://doi.org/10.1186/ISRCTN16299902), before recruitment commenced. Participants will be invited to attend a screening, baseline/randomisation and all subsequent trial visits at two, six and 12 months will be conducted at the CRF of each participating site. See participant timeline, Figure 1. Participants recruited at Imperial will also be invited to participate in a mechanistic sub-study and if they agree these assessments will take place at baseline and 12 months at the Imperial CRF.\n\nInclusion criteria\n\n• Males and females aged 20–40 years\n\n• Body Mass Index (BMI) of 24.0–27.0 kg/m2 if of South-Asian ethnicity or 25.0–30.0 kg/m2 if non-South-Asian\n\n• At least one of the following:\n\n○ A self-reported weight gain of 2 kg or more over the last 12 months\n\n○ Low self-reported physical activity (‘low’ activity as per International Physical Activity Questionnaire)\n\n○ <2 servings of fruit and vegetables consumed per day\n\n○ >1 serving of sugar-sweetened beverages per day\n\n• On same medication for >3 months at point of screening\n\n• Written informed consent\n\nExclusion criteria\n\n• Diagnosed chronic disease Type 1 and 2 diabetes, cancer, renal failure, heart disease, organic acidaemia (propionic acidaemia, methylmalonic acidaemia)\n\n• Diagnosed gastrointestinal condition (coeliac disease, inflammatory bowel disease and irritable bowel syndrome)\n\n• Previous bowel reconstruction surgery\n\n• Pregnancy or lactation\n\n• Use of antibiotics in the past three months\n\n• Vitamin B12 deficiency (<160 ng/L)\n\n• Taking part in a weight loss program or consuming a weight loss product\n\n• Have lost 3 kg or more in the last three months\n\n• Gastrointestinal upset in the last two weeks\n\nA wide variety of recruitment methods were used for this clinical trial, including recruitment via GP practices and within NHS trusts, newspaper adverts, pop-up events and posters, amongst other methods. Recruitment was completed in October 2021 (Figure 2).\n\nRandomisation will be undertaken using minimisation with a random element to balance the arms by research centre, sex, and BMI within ethnicity (South Asians: 24.00–25.49 kg/m2 and 25.50–27.00 kg/m2/non-South Asians: 25.00–27.49 kg/m2 and 27.50–30.00 kg/m2) and whether they take part in the mechanistic sub-study. Minimisation will be conducted by researchers using sealed envelope software (Open-source software, www.sealedenvelope.com).\n\nParticipants will receive blinded and identical-looking trial intervention of either IPE or inulin control. Both IPE and inulin present as white powders and will be delivered in pre-packed plain foil-backed sachets. Participants will be identified with a unique trial identifier and each IPE or control sachet will be identified with a unique treatment code linked to the allocation and trial identification (ID). The treatment code will not be broken except in medical emergencies or if expedited reporting to the Research Ethics Committee (REC) of an unexpected and related Serious Adverse Event (SAE) is required.\n\nAt each trial visit, trial researchers will conduct all necessary measurements and sample collections as described in Tables 1 and 2. In the main study, written informed consent is given at the screening visit, blood samples are taken (excluding two-month visits), blood pressure, body weight, body composition and compliance are measured and occurrence of Adverse Events (AEs) and SAEs are documented at all study visits. In the sub-study breath, stool, urine and blood samples are taken and breath hydrogen, energy expenditure, subjective appetite and energy intake are measured.\n\nPrimary outcome\n\nThe primary outcome is weight gain from baseline to 12 months.\n\nSecondary outcomes\n\n• Occurrence of AEs and SAEs\n\n• Changes in fasting biochemistry:\n\n- Glucose\n\n- Insulin\n\n- Triglycerides\n\n- Total cholesterol\n\n- Low-Density Lipoprotein (LDL) cholesterol\n\n- High-Density Lipoprotein (HDL) cholesterol\n\n• Changes in blood pressure\n\n• Changes in body weight\n\n• Changes in waist/hip/BMI/body composition measurements\n\n• Changes in compliance\n\nMechanistic outcomes\n\n• Gut microbiota: 16S rRNA profiles from stool samples\n\n• Impact on neuroendocrine cell number: Proliferation in intestinal organoids using the level of SCFA and other metabolites identified from nuclear magnetic resonance spectroscopic analyses of stool\n\n• Appetite regulation: Measured by visual analogue scales (VAS), food diaries, ad libitum intake, and appetite-regulating gut hormones PYY, GLP-1, Gastrin and CCK\n\n• Energy expenditure: Open-loop indirect calorimetry\n\n• Hepatic lipid metabolism: Stable isotope tracers of fat oxidation (13C palmitate) and De Novo Lipogenesis (DNL)\n\n• Total body water through dilution analysis of 2H2O as already applied.\n\nProposed amendments to the protocol and aforementioned documents will be submitted to the REC for approval as instructed by the Sponsor. Amendments requiring REC approval may be implemented only after a copy of the REC’s approval letter has been obtained. The regulatory authorities and REC will be sent annual progress reports and informed about the end of the trial, within the required timelines. Table 3 details the amendments that have been submitted/approved by the REC so far.\n\nThe following amendments have been submitted/approved by the REC so far.\n\n\n\n• Revised protocol (admin changes, updated sampling details, NHS digital follow-up details, updated packaging company details).\n\n• PIS/CF changes to reflect the above.\n\n• Study templates include newspaper advertisements, participant diaries, questionnaires and instructions.\n\n\n\n• Age in inclusion criteria extended from '20-35 years' to '20-40 years'.\n\n• PIS/CF changes to reflect the above.\n\n• Updated advertising details including template text message for GPs and study webpage.\n\n• Study templates including poster ad and updated pre-screening questionnaire.\n\n\n\n• Notification of pause in recruitment due to initial COVID-19 lockdown.\n\n• Guideline document created for remote follow-up visits/changes to the trial during this period.\n\n\n\n• The title of the project was amended as requested by NIHR, following the previous change in inclusion criteria (age).\n\n• Clarification of recruitment strategies being used.\n\n• Addition of PIC site.\n\n• Script and topic guide drafted for animation video and information videos to be created, for social media.\n\n\n\n• Study clinic visits resuming at all sites, following the pause in March 2020 due to COVID-19 restrictions.\n\n• Additional data collection was required as remote visits did not capture accurate primary outcome data, and blood samples (for secondary outcomes) were missed.\n\n• Wider visit windows for flexibility.\n\n• Additional NHS boards were added for Scotland, for a wider search of research volunteers via the SHARE database.\n\n• Addition of the PIC site.\n\n\n\n• Removal of ECG from screening procedures.\n\n• Exclusion criteria for the main study were amended from 'vitamin B12 deficiency' to 'untreated vitamin B12 deficiency.\n\n• ‘Anaemia’ specified as an exclusion for sub-study only (previously for main study too).\n\n• Joint screening/randomisation visit for those not taking part in the sub-study and addition of remote consent as a 7-day food diary required to be completed before the joint visit.\n\n• PIS/CF changes to reflect all the above.\n\n\n\n• Costed extension from NIHR - new grant end date.\n\nParticipants may discontinue trial intervention for the following reasons:\n\n• At the request of the participant\n\n• Due to an Adverse Event/Serious Adverse Event\n\n• If the investigator considers that a participant's health will be compromised due to AEs or concomitant illnesses that develop after entering the trial.\n\nIf a participant permanently discontinues the trial intervention, they will be invited to continue to attend trial visits, if possible, to allow for the collection of key outcome and safety data.\n\nDiscontinuation of trial intervention and procedures can occur for the following reasons:\n\n• Participant decision (withdrawal of consent)\n\n• Loss to follow-up\n\nIf a participant withdraws from trial procedures, an attempt will be made to obtain self-reported body weight (primary endpoint) at the point of withdrawal and at the final study visit time point. If the participant does not agree for data and samples collected to be retained, the samples must be destroyed and data excluded from the analyses.\n\nIf the participant withdraws consent to further be contacted at all for the study purposes, no attempts to obtain a self-reported body weight for the primary endpoint will be made.\n\nAll serious and non-serious AEs will be reported on the trial database, from the point of screening until the end of the study, except for elective medical procedures. All SAEs will be reviewed by both the local investigator and chief investigator or a designated medically qualified representative to confirm ‘expectedness’ and ‘causality’. SAEs are assessed on whether they are possibly, probably or definitely related to the trial protocol/intervention. An unexpected event would be a type of event that is not listed in the trial protocol or document associated with the intervention, as an expected occurrence. Expected AEs for this trial are gastrointestinal effects. If the investigator becomes aware of safety information that appears to be related to the trial, this should be reported to the trial coordination centre and sponsor.\n\nPPI panels were held during the design and management and recruitment phases of this clinical trial.\n\nRecruitment for this study was completed in October, the study is currently in follow-up phase and 12-month visits will be completed by the end of October 2022.\n\nSample size calculations\n\nIn the randomised proof of concept trial, the difference between arms in the change in body weight over 24 weeks was 1.4 kg (95% CI: -0.3 to 3.1), p = 0.099. Using a Bayesian method recommended for preliminary trials in which evidence in the 95% CI is translated into probabilities,11 there was a 95% posterior probability of an underlying positive between-arm difference favouring the intervention. The posterior probability of intervention-favouring differences greater than 1 kg, 1.5 kg, and 2 kg were respectively 69%, 47% and 25% based on 24-week intervention. The difference increased in magnitude through successive eight-week, 16-week, and 24-week time points. By 24 weeks there were significant reductions in the proportion of intervention participants gaining 3%, and 5% of body weight from a mean baseline of 90 kg. A 2 kg between-arm 12-month effect size was therefore chosen. This agreed with a weight gain prevention trial over nine months in young adults12 which aimed to detect a 2 kg effect and achieved 4.3 kg, with a pooled standard deviation (SD) for body weight change of 4.35 kg, and 81% retention.\n\nOn this basis a sample size of 270 randomised participants (135 per arm) was chosen to provide 90% power to detect a 2 kg difference between arms in mean body weight change over 12 months using a two-sided 5% level significance test, assuming a 4.35 kg SD and with 25% dropout allowance (68 participants). The sample size was calculated using R Project for Statistical Computing (RRID: SCR_001905).\n\nFor the mechanistic study, 34 volunteers (17 per group) would provide sufficient statistical power to detect a 15 pmol/L effect size in PYY and GLP-1 concentrations between groups, with 90% power, 5% significance level, SD 13 pmol/L. These differences are based on previously published findings that report enhanced gut hormone release following IPE supplementation.9,13 A subsample of 52 volunteers (26 per group), was chosen, to allow a 70% retention rate.\n\nData analysis plan\n\nThis trial has both a pragmatic element, to answer the question of whether the policy of prescribing and uptake of inulin propionate ester as specified in the trial will reduce further weight gain compared with control, and an explanatory element to understand the mechanisms of the causal pathway of such body weight change and any limitations from compliance. Therefore, analyses will be primarily on an ‘Intention to Treat’ basis. Secondarily, analyses will incorporate mechanistic sub-study data, and use this to understand the ‘Intention to Treat’ effect estimated in the trial.\n\nStatistical methods for the analysis of the study endpoints are described below. IBM SPSS Statistics (RRID: SCR_019096), version 28.0.1, will be used for all statistical analyses. A separate detailed Statistical Analysis Plan (SAP) has been prepared and approved by the Trial Steering Committee.14 This contains the rationale for the methods chosen and the assessment of their assumptions. It includes pre-specifying the handling of covariates and missing data, compliance analyses, and the primary estimand. Changes to the plan can be revised and re-approved by trial oversight committees prior to database lock.\n\nAny deviations from the SAP during analysis after the data lock will be documented and signed off by the statisticians and CI and filed in the statistics section of the Trial Master File (TMF) which will be merged with the main TMF at the end of the study. The final approved SAP, being in accordance with the protocol, takes precedence for undertaking the analysis of the main trial paper.\n\nPrimary endpoint analysis\n\nThe analysis of the primary endpoint will incorporate the earlier correlated interim measurements of body weight in a linear mixed effects model and will adjust for baseline continuous body weight and other categorical randomisation stratifiers with further specification of the role of timepoint, and correlation structure, detailed in the SAP. The implicit ‘missing at random’ assumption will be challenged through a set of sensitivity analyses.15 As these involve all randomised participants, this is therefore an Intention to Treat Strategy.16\n\nSecondary endpoints analysis\n\nWhere possible, continuous secondary endpoints will be adjusted for their baseline to improve the precision of estimated intervention effects. Repeated measures will be analysed using linear mixed-effects models adjusting also for randomisation stratifiers. Comparisons between arms for binary outcomes will be summarised as differences in proportions. Confidence intervals of 95% will be used to make inferences from estimated effect sizes.\n\nEthical and safety considerations\n\nThe investigator(s) will ensure that this trial is conducted in full conformity with the 7th revision of the 1964 Declaration of Helsinki. The trial will be conducted following the guidelines laid down by the International Conference on Harmonisation for Good Clinical Practice (ICH GCP E6 guidelines and Addendum ICH GCP E6 (R2)). The trial protocol and participant-facing documents have been reviewed and approved by the London Hampstead REC Reference 14/LO/2004). Clinical trial authorisation from the Medicines and Healthcare products Regulatory Agency (MHRA) is not required as the study intervention is a dietary supplement.\n\nData management\n\nAll personal identifiable data, including screened patients, will be kept securely in the local site files and will not be uploaded to the main trial database. The InForm™ trial database will be used for all visits data entries. All data recorded in the eCRFs will be signed off by the site investigator. The central coordinating site will visit local recruiting sites to ensure compliance with the protocol, good clinical practice and local regulatory compliance.\n\nDissemination policy\n\nAll publications and presentations relating to the study will be authorised by the Trial Management Group. Authorship will be determined according to the internationally agreed criteria for authorship (www.icmje.org). Authorship of parallel studies initiated outside of the Trial Management Group will be according to the individuals involved in the project but must acknowledge the contribution of the Trial Management Group and the Study Coordination Centre.\n\nTrial organisation and committees\n\nA fully independent Data Monitoring and Ethics Committee (DMEC) has been set up to monitor progress, participant safety and any ethical issues involved in this trial. They review trial progress, recruitment rates and safety data. Meetings are approximately six-monthly. Furthermore, a Study Advisory Group consisting of public representatives was also set up. The committees were set up and coordinated in accordance with the funder guidelines. Upon completion, the trial results will be published in peer-reviewed journals and presented at national and international scientific meetings. A Trial Steering Committee (TSC) has been convened to provide overall supervision of trial conduct and progress. The TSC meet approximately six-monthly throughout the trial. DMEC reports include details of recruitment, randomisation balance and stratification effectiveness, baseline characteristics, unblinding, withdrawals, compliance, concomitant medications, efficacy, mediators, and Aes.\n\n\nDiscussion\n\nTo date, few randomised controlled trials focus on the prevention of obesity, especially in those most at risk of weight gain.2 High intakes of dietary fibre are associated with lower body weight.13 Evidence suggests that this is due to the generation of SCFA from colonic fermentation of dietary fibre by the gut microbiota.8 Furthermore, there is prior evidence to suggest that IPE could have a substantial impact on lowering individuals’ weight gain trajectory leading to a lowering of their long-term risk of obesity-related co-morbidities.9,12 This trial will explore all aspects of the novel food ingredient IPE; assessing efficacy via the primary endpoint of weight change, whilst attempting to identify potential mechanisms via the sub-study and accounting for compliance, tolerability and safety. The latter is an aspect that often goes unreported in similar trials; however, it is required to build a multifaceted evaluation of any intervention. This study methodology is not without limitations, primarily, narrowing the age range of the study sample may mean that results cannot be translated to the wider population. Additionally, the aforementioned scarcity of studies exploring the effects of SCFA on human populations meant that researchers had few studies to refer to when calculating population sample size, which may lead to a difference in predicted versus actual study power. However, it should be acknowledged that the study duration and sample size are greater than similar previously conducted studies.9,17–20 This randomised controlled trial aims to build upon previous literature to support evidence for the delivery of propionate to the colon for the prevention of weight gain.21\n\n\nConclusions\n\nObesity research has limited emphasis on prevention. Therefore, this randomised controlled double-blinded trial was designed to investigate whether inulin-propionate ester prevents further weight gain in adults most at risk of substantial increases in their BMI. Furthermore, the study adopts novel approaches to determine the underlying mechanisms influencing these beneficial effects.\n\n\nData availability\n\nNo data are associated with this article.\n\nMendeley Data: Extended data for ‘Increase in colonic Propionate as a method of prEVENTing weight gain in adults aged 20-40 years (iPREVENT): A multi-centre, double-blind, randomised, parallel-group study to investigate the efficacy of inulin-propionate ester versus inulin (control) in the prevention of weight gain over 12 months’ statistical analysis plan’.\n\n• Data file 1: iPREVENT Statistical Analysis Plan. pdf. https://doi.org/10.17632/n33kky5dww.214\n\n• Data file 2: iPREVENT Protocol v5.0 15Feb2021.pdf. https://doi.org/10.17632/5n7h4xfz2n.1.21\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)",
"appendix": "Acknowledgements\n\nInfrastructure support for this research was provided by the NIHR Imperial Biomedical Research Centre (BRC) and the NIHR Imperial Clinical Research Facility.\n\n\nReferences\n\nFildes A, Charlton J, Rudisill C, et al.: Probability of an Obese Person Attaining Normal Body Weight: Cohort Study Using Electronic Health Records. Am. J. Public Health. 2015 Sep; 105(9): e54–e59. PubMed Abstract | Publisher Full Text\n\nWilliamson DF, Kahn HS, Remington PL, et al.: The 10-year incidence of overweight and major weight gain in US adults. Arch. Intern. Med. 1990 Mar; 150(3): 665–672. PubMed Abstract | Publisher Full Text\n\nNorman JE, Bild D, Lewis CE, et al.: The impact of weight change on cardiovascular disease risk factors in young black and white adults: the CARDIA study. Int. J. Obes. Relat. Metab. Disord. 2003 Mar; 27(3): 369–376. PubMed Abstract | Publisher Full Text\n\nLudwig DS, Pereira MA, Kroenke CH, et al.: Dietary fiber, weight gain, and cardiovascular disease risk factors in young adults. JAMA. 1999 Oct 27; 282(16): 1539–1546. PubMed Abstract | Publisher Full Text\n\nDu H, van der AD, Boshuizen HC, et al.: Dietary fiber and subsequent changes in body weight and waist circumference in European men and women. Am. J. Clin. Nutr. 2010 Feb; 91(2): 329–336. PubMed Abstract | Publisher Full Text\n\nWhitton C, Nicholson SK, Roberts C, et al.: National Diet and Nutrition Survey: UK food consumption and nutrient intakes from the first year of the rolling programme and comparisons with previous surveys. Br. J. Nutr. 2011 Dec; 106(12): 1899–1914. PubMed Abstract | Publisher Full Text\n\nEaton SB: The ancestral human diet: what was it and should it be a paradigm for contemporary nutrition? Proc. Nutr. Soc. 2006 Feb; 65(1): 1–6. Publisher Full Text\n\nCummings JH, Pomare EW, Branch WJ, et al.: Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut. 1987 Oct; 28(10): 1221–1227. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChambers ES, Viardot A, Psichas A, et al.: Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut. 2015 Nov; 64(11): 1744–1754. PubMed Abstract | Publisher Full Text\n\nBurton PR, Gurrin LC, Campbell MJ: Clinical significance not statistical significance: a simple Bayesian alternative to p values. J. Epidemiol. Community Health. 1998 May; 52(5): 318–323. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAllman-Farinelli M, Partridge SR, McGeechan K, et al.: A Mobile Health Lifestyle Program for Prevention of Weight Gain in Young Adults (TXT2BFiT): Nine-Month Outcomes of a Randomized Controlled Trial. JMIR Mhealth Uhealth. 2016 Jun 22; 4(2): e78. PubMed Abstract | Publisher Full Text\n\nPolyviou T, MacDougall K, Chambers ES, et al.: Randomised clinical study: inulin short-chain fatty acid esters for targeted delivery of short-chain fatty acids to the human colon. Aliment. Pharmacol. Ther. 2016 Oct; 44(7): 662–672. PubMed Abstract | Publisher Full Text | Free Full Text\n\nReynolds A, Mann J, Cummings J, et al.: Carbohydrate quality and human health: a series of systematic reviews and meta-analyses. Lancet. 2019 Feb 2; 393(10170): 434–434, 445. PubMed Abstract | Publisher Full Text\n\nVasconcelos J, Toby P, Morrison D, et al.: Increase in colonic PRopionate as a method of prEVENTing weight gain in young adults: IPREVENT Clinical Trial Statistical Analysis Plan. Mendeley Data, V2, [Dataset]. 2022. Publisher Full Text\n\nSivaprasad S, Prevost AT, Vasconcelos JC, et al.: Clinical efficacy of intravitreal aflibercept versus panretinal photocoagulation for best corrected visual acuity in patients with proliferative diabetic retinopathy at 52 weeks (CLARITY): a multicentre, single-blinded, randomised, controlled, phase 2b, non-inferiority trial. Lancet. 2017 Jun; 389(10095): 2193–2203.\n\nWhite IR, Carpenter J, Horton NJ: Including all individuals is not enough: lessons for intention-to-treat analysis. Clin. Trials. 2012; 9(4): 396–407. PubMed Abstract | Publisher Full Text\n\nChambers ES, Byrne CS, Rugyendo A, et al.: The effects of dietary supplementation with inulin and inulin-propionate ester on hepatic steatosis in adults with non-alcoholic fatty liver disease. Diabetes Obes Metab. 2019 Feb; 21(2): 372–376. PubMed Abstract | Publisher Full Text\n\nChambers ES, Byrne CS, Morrison DJ, et al.: Dietary supplementation with inulin-propionate ester or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised cross-over trial. Gut. 2019 Aug 1; 68(8): 1430–1438. Publisher Full Text\n\nByrne CS, Chambers ES, Preston T, et al.: Effects of Inulin Propionate Ester Incorporated into Palatable Food Products on Appetite and Resting Energy Expenditure: A Randomised Crossover Study. Nutrients. 2019 Apr 16; 11(4): E861. Publisher Full Text\n\nPolyviou T, MacDougall K, Chambers ES, et al.: Randomised clinical study: inulin short-chain fatty acid esters for targeted delivery of short-chain fatty acids to the human colon. Aliment. Pharmacol. Ther. 2016 Oct; 44(7): 662–672. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFrost G, Morrison D, Anjum A, et al.: “Protocol for the IPREVENT Trial”, Mendeley Data, V1, [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "264288",
"date": "06 May 2024",
"name": "Hoi Leong Xavier Wong",
"expertise": [
"Reviewer Expertise Metabolic disorder",
"Microbiome",
"Metalloproteinase"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper provides a study protocol for investigating the efficacy of inulin-propionate ester in the prevention of weight gain over 12 months. The protocol design is scientifically sound and feasible. Please see the comments below:\n\nMajor point: (1) For the primary outcome, the changes in BMI instead of weight gain may be a better measurement. (2) The study protocol for the sample collection should be provided. (3) What is the strategy of reducing the dropout rate in the proposed study?\n\nMinor point: (1) The ratio of male and female participants should be provided.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1157
|
https://f1000research.com/articles/11-1156/v1
|
10 Oct 22
|
{
"type": "Study Protocol",
"title": "(Re)conceptualizing vulnerability in health under the syndemics perspective: protocol for a scoping review",
"authors": [
"Yisel Hernández",
"Dennis Pérez",
"Yosiel Molina",
"Koen Peeters Grietens",
"Claudia Nieto-Sánchez",
"Dennis Pérez",
"Yosiel Molina",
"Koen Peeters Grietens"
],
"abstract": "The concept of vulnerability has been widely used in global health research to assess susceptibility to diseases and disasters in individuals and groups. This perspective has proven to be useful for policy making by bringing attention to the unequal distribution of risks and impacts in specific populations and contexts. However, it is often insufficient to explain interactions between environmental, zoonotic, and social realms involved in the experience of health and disease. Theoretical developments proposed under the syndemics approach have intended to explore this gap by studying the underlying political, economic, and social dynamics affecting the occurrence of overlapping health issues. During the coronavirus disease 2019 (COVID-19) pandemic, the term syndemics has been used to refer to underlying conditions and social factors impacting disease outcomes. This scoping review aims to explore the contributions of the syndemics perspective to the (re)conceptualization of vulnerability during the COVID-19 pandemic. We intend to do so by identifying social and environmental arrangements so far described in original research, opinion pieces or reviews published since December 2019. Variations in the explanations provided about the role played by socio-environmental dynamics in the observed interactions in populations, settings, and interacting conditions will be subsequently examined. Finally, we will track the contributions and limitations of the syndemics perspective to the study of vulnerability in health in light of the evidence produced around COVID-19.",
"keywords": [
"Vulnerability",
"syndemics",
"COVID-19",
"syndemic vulnerability",
"interactions"
],
"content": "Introduction\n\nIn the last decades, the concept of vulnerability has been widely used in global health research to assess susceptibility to diseases and disasters in individuals and groups. Along with its increasing use, its polysemous character and scope have become more evident. Patterns and variations of this concept within the health field are articulated around historical contexts, conjunctural circumstances, lifetime trajectories, individual risk factors, and conditions of exposure to specific pathogenic agents (Wardrop et al., 2021). Although vulnerability is now recognized as a dynamic trait compounded by biomedical, social, and environmental dynamics, sanitary perspectives —particularly focused on individual vulnerability to disease-specific risk factors—have substantially informed research on this area (Hufschmidt, 2011; Osborne et al., 2021). While adding a vulnerability angle has proven to be useful to bring attention to the unequal distribution of the risks to and consequences of diseases and disasters (Faas, 2016), this perspective is often insufficient to explain interactions between environmental, zoonotic, and social dynamics in the generation of health and disease (Jeleff et al., 2022). Moreover, labeling specific groups and vast geographical areas under the category of ‘vulnerable’ seems to have been more blurring than illuminating in terms of the actual capacity of this concept to explain the realities of those covered by it, acknowledge their responses generated under unfavorable conditions, and counter the dynamics of marginalization and exclusion originating such vulnerability in the first place (Marino & Faas, 2020).\n\nTheoretical arguments developed around the concepts of structural vulnerability (Holmes, 2011), structural violence (Farmer, 1996), and syndemics (Singer, 2009), have explored these underlying factors and interactions. The concept of ‘syndemics’, in particular, seems to have special traction. This perspective intends to explore how synergistic interactions between two or more diseases under specific social conditions can negatively affect the mutual course of each disease trajectory, and, consequently, enhance vulnerability and health inequities (Brazil, 2022; Sharma, 2017; Singer et al., 2017). Core to this concept is the identification of a bio-social interface, understood as the intersection in which social and environmental arrangements structurally linked to the overlap of diseases can cause or exacerbate their occurrence (Singer et al., 2020).\n\nSince its first inception, the concept of vulnerability was constitutive of this approach, as social factors have been usually presented as generators or instigators of heightened vulnerability in particular social groups and contexts (Mendenhall et al., 2017; Singer, 2009; Singer et al., 2020; Sharma, 2017). The idea of ‘syndemic vulnerability’, specifically, links both concepts by alluding to the integration of “epidemiological and experiential levels of analysis of multiple, overlapping social and health problems that increase morbidity and mortality as a result of syndemic clustering of social and health conditions within a certain context” (Singer et al., 2017). This specific variation has been used to bring forward issues of power-sustaining inequities involved in the clustering of diseases and risk factors (Singer & Rylko-Bauer, 2021).\n\nWhat seems to be the most important contribution of the syndemics perspective to public health practice, i.e., applying a systemic perspective to understand health and disease (Hossain et al., 2022; Mendenhall et al., 2022; Newfield, 2022), has come into question in the last years. Recent critiques to syndemics’ research have alerted of the danger of generating diffuse predictions based on the assumption of mutually reinforcing factors for which interactions cannot be clearly described (Tsai, 2018), as well as the persistent practice of applying biomedical lenses to describe specific contexts in terms of risks (Weaver & Kaiser, 2022), while ignoring other layers of complexity also emerging from said contexts (Slagboom et al., 2022). Similarly, researchers have claimed that there is still much to learn about the specific ways in which environmental, economic, cultural, and social factors interact to create high-risk contexts for overlapping health conditions (Mendenhall et al., 2017; Willen et al., 2017). In 2020, a scoping review found that most articles on syndemic interactions published between 2015 and 2019 described the influence of social determinants such as poverty, inequity, and racism on the clustering of diseases or disease outcomes (Singer et al., 2020). The same review, however, recognized that the articulation of those factors in relation to disease trajectories just starts to be understood (Nichter, 2016; Singer et al., 2020).\n\nThis scoping review acknowledges the potential to continue improving the scientific literature on syndemics, particularly about the systemic nature of vulnerability in health. One of the reasons to consider the current relevance of this approach is the extensive use of the syndemics perspective in the study of the overlapping biomedical and socio-economic conditions exacerbating the impacts of the coronavirus disease 2019 (COVID-19) pandemic around the world (McMahon, 2021). The interactions of the infection with pre-existing chronic diseases, their articulation with environmental factors (Yadav et al., 2020), and the early impacts of COVID-19 in marginalized or socially excluded groups (Gravlee, 2020; Lund, 2020; Selden & Berdahl, 2020) have brought a new impetus to syndemics’ research (Poteat et al., 2020; Singer & Rylko-Bauer, 2021), which we are interested in further exploring.\n\nWith this review, we intend to systematically explore the contributions of the syndemics perspective to conceptualizations of vulnerability articulated during the COVID-19 pandemic. We intend to do so by identifying social and environmental arrangements so far described in syndemic research published since December 2019 and their associations with the idea of vulnerability. In first place, interactions among diseases and health conditions, species, social factors; and environmental dynamics so far described in the literature will be examined. Subsequently, we will focus on bio-social interactions and will capture variations in the explanations provided about the role played by those socio-environmental dynamics in the observed interactions in relation to populations, settings, and interacting conditions. Finally, we will track the contributions and limitations of the syndemics perspective to the study of vulnerability in health in light of the evidence produced around COVID-19.\n\nThree questions will guide this review:\n\na. Which social and environmental arrangements (determinants, factors, dynamics, and aspects) have been described in syndemics’ research around COVID-19?\n\nb. How have those social arrangements been conceptualized and studied (methodological approaches)?\n\nc. What are the main contributions and limitations of the syndemics perspective to the study of vulnerability in health in the context of the current pandemic?\n\n\nMethods\n\nIn the first phase of data extraction, records will be included if they meet all the following criteria:\n\n• Original research, opinion pieces, or reviews\n\n• Include the words syndemics, vulnerability, and COVID-19 in the title, abstract, or keywords\n\n• Elaborate on issues of vulnerability in the body of the text\n\n• Published since December 2019\n\nNo restrictions of language, studied conditions, or geographical location will be applied.\n\nAt the stage of full-text screening, publications will be excluded if they are focused only on the bio-bio interface of the interaction, do not sufficiently explain the social aspects of the syndemic, or if they do not sufficiently elaborate on the concepts of syndemics and/or vulnerability.\n\nThe primary source of records will be PubMed with no restriction of language. We expect to screen the reference lists of the records included (especially review papers) and contact some experts in the field to ask for other potentially relevant records that we do not identify through the search strategy.\n\nThe search strategy is based on the combination of three categories: COVID-19, syndemics, and vulnerability. The Boolean operators “AND” and “OR” will be used to combine search terms. Table 1 summarizes the proposed search syntax for PubMed. In the secondary sources of research records, the same strategy will be used.\n\nAll retrieved records from the primary and secondary sources of the search will be imported to COVIDENCE. Duplicate records will be identified and excluded using COVIDENCE and Mendeley. Title, abstract, and keyword screening will be conducted by two members of the research team, who will select those articles that will be included in the full-text review. Discrepancies will be discussed and solved by the review team. The review of articles’ reference lists will be conducted at this stage. Two reviewers will extract data into the COVIDENCE database according to the categories previously defined (Table 2). A preliminary data extraction form will be tested with at least 10 of the selected records. The results of the pilot test will be used to refine the first draft of the data extraction form. Data extraction and analysis will be based only on the content of the published records. Thematic analysis based on the categories included in the data extraction form will be conducted for each research question. Given its intersection with the syndemics perspective, we will use the dimensions proposed by Ribera and Hausmann-Muela (2011)—structural, agent driven, and conjunctural—for the analysis of the vulnerability.\n\nResults will be presented as narrative synthesis, following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist as a guideline. In addition, tables and figures will be created to show the findings related to the categories included in the final data extraction form.\n\nThe protocol has been prepared according to the Prisma Extension for Scoping Reviews (PRISMA-ScR).\n\nTable 3 summarizes the time frame planned to conduct the review.\n\nFormal review will not start before the publication of the protocol; however, some preliminary searches were conducted to explore the scope of available records about the research topic.\n\nFindings will be disseminated through scientific publications in peer review journals and academic spaces in which the authors participate, including conferences, courses, and seminars.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "References\n\nBrazil N: The multidimensional clustering of health and its ecological risk factors. Soc. Sci. Med. 2022; 295: 113772. PubMed Abstract | Publisher Full Text\n\nFaas AJ: Disaster vulnerability in anthropological perspective. Ann. Anthropol. Pract. 2016; 40(1): 14–27. Publisher Full Text\n\nFarmer P: On Suffering and Structural Violence: A View from Below. Daedalus. 1996; 125(1): 261–283. Retrieved September 10, 2022.Reference Source\n\nGravlee CC: Systemic racism, chronic health inequities, and COVID-19: A syndemic in the making? Am. J. Hum. Biol. 2020; 32: e23482. PubMed Abstract | Publisher Full Text\n\nHolmes SM: Structural vulnerability and hierarchies of ethnicity and citizenship on the farm. Med. Anthropol. 2011; 30(4): 425–449. PubMed Abstract | Publisher Full Text\n\nHossain M, Saha N, Rodela TT, et al.: Global research on syndemics: a meta-knowledge analysis (2001-2020). MedRxiv. 2022; 11. Publisher Full Text\n\nHufschmidt G: A comparative analysis of several vulnerability concepts. Nat. Hazards. 2011; 58(2): 621–643. Publisher Full Text\n\nJeleff M, Lehner L, Giles-Vernick T, et al.: Vulnerability and One Health assessment approaches for infectious threats from a social science perspective: a systematic scoping review. Lancet Planet. Health. 2022; 6(8): e682–e693. PubMed Abstract | Publisher Full Text\n\nLai J, Mary Oommen A, Narayan Yadav U, et al.: A Syndemic Perspective on the Management of Non-communicable Diseases Amid the COVID-19 Pandemic in Low- and Middle-Income Countries. Front. Public Health. 2020; 8: 508. PubMed Abstract | Publisher Full Text\n\nLund EM: Even more to handle: Additional sources of stress and trauma for clients from marginalized racial and ethnic groups in the United States during the COVID-19 pandemic. Couns. Psychol. Q. 2020; 34(3-4): 321–330. Publisher Full Text\n\nMarino EK, Faas AJ: Is Vulnerability an Outdated Concept? After Subjects and Spaces. Ann. Anthropol. Pract. 2020; 44(1): 33–46. Publisher Full Text\n\nMcMahon NE: Understanding COVID-19 through the lens of ‘syndemic vulnerability’: possibilities and challenges. Int. J. Health Promot. Educ. 2021; 59(2): 67–69. Publisher Full Text\n\nMendenhall E, Kohrt BA, Norris SA, et al.: Non-communicable disease syndemics: poverty, depression, and diabetes among low-income populations. Lancet. 2017; 389(10072): 951–963. PubMed Abstract | Publisher Full Text\n\nMendenhall E, Newfield T, Tsai AC: Syndemic theory, methods, and data. Soc. Sci. Med. 2022; 295: 114656. PubMed Abstract | Publisher Full Text\n\nNewfield TP: Syndemics and the history of disease: Towards a new engagement. Soc. Sci. Med. 2022; 295: 114454. PubMed Abstract | Publisher Full Text\n\nNichter M: Comorbidity: Reconsidering the Unit of Analysis. Med. Anthropol. Q. 2016; 30(4): 536–544. Publisher Full Text\n\nOsborne J, Paget J, Giles-Vernick T, et al.: Community engagement and vulnerability in infectious diseases: A systematic review and qualitative analysis of the literature. Soc. Sci. Med. 2021; 284: 114246. PubMed Abstract | Publisher Full Text\n\nPoteat T, Millett GA, Nelson LRE, et al.: Understanding COVID-19 risks and vulnerabilities among black communities in America: the lethal force of syndemics. Ann. Epidemiol. 2020; 47: 1–3. PubMed Abstract | Publisher Full Text\n\nRibera JM, Hausmann-Muela S: The Straw That Breaks the Camel's Back Redirecting Health-Seeking Behavior Studies on Malaria and Vulnerability. Med. Anthropol. Q. 2011; 25(1): 103–121. PubMed Abstract | Publisher Full Text\n\nSelden TM, Berdahl TA: COVID-19 and racial/ethnic disparities in health risk, employment, and household composition. Health Aff. 2020; 39(9): 1624–1632. PubMed Abstract | Publisher Full Text\n\nSharma A: Syndemics: health in context. Lancet. 2017; 389: 881. Publisher Full Text\n\nSinger M: Introduction to Syndemics: A Critical Systems Approach to Public and community health. San Francisco:John Wiley & Sons, Inc.;2009. 978-0-470-47203-3. Merrill Singer - Google Libros.Reference Source\n\nSinger M, Bulled N, Ostrach B: Whither syndemics?: Trends in syndemics research, a review 2015–2019. Glob. Public Health. 2020; 15(7): 943–955. PubMed Abstract | Publisher Full Text\n\nSinger M, Bulled N, Ostrach B, et al.: Syndemics and the biosocial conception of health. Lancet. 2017; 389(10072): 941–950. PubMed Abstract | Publisher Full Text\n\nSinger M, Rylko-Bauer B: The Syndemics and Structural Violence of the COVID Pandemic: Anthropological Insights on a Crisis. Open Anthropol. Res. 2021; 1(1): 7–32. Publisher Full Text\n\nSlagboom MN, Crone MR, Reis R: Exploring syndemic vulnerability across generations: A case study of a former fishing village in the Netherlands. Soc. Sci. Med. 2022; 295: 113122. PubMed Abstract | Publisher Full Text\n\nTsai AC: Syndemics: A theory in search of data or data in search of a theory? Soc. Sci. Med. 2018; 206: 117–122. Publisher Full Text\n\nWardrop R, Crilly J, Ranse J, et al.: Vulnerability: A concept synthesis and its application to the Emergency Department. Int. Emerg. Nurs. 2021; 54: 100936. PubMed Abstract | Publisher Full Text\n\nWeaver LJ, Kaiser BN: Syndemics theory must take local context seriously: An example of measures for poverty, mental health, and food insecurity. Soc. Sci. Med. 2022; 295: 113304. PubMed Abstract | Publisher Full Text\n\nWillen SS, Knipper M, Abadía-Barrero CE, et al.: Syndemic vulnerability and the right to health. Lancet. 2017; 389(10072): 964–977. PubMed Abstract | Publisher Full Text\n\nYadav UN, Rayamajhee B, Mistry SK, et al.: A syndemic perspective on the management of non-communicable diseases amid the COVID-19 pandemic in low-and middle-income countries. Front. Public Health. 2020; 8: 508. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "157627",
"date": "09 Jan 2023",
"name": "Merrill Singer",
"expertise": [
"Reviewer Expertise Health and inequality",
"infectious diseases",
"syndemics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper lays out the strategy be used in a Scoping Review of the recent literature on vulnerability to COVID-19 syndemics. In light of the attraction of COVID researchers to the syndemics approach and the potential benefits of gaining insights on this issue, this is a very timely review.\n\nOne notable limitation of the proposed methodology is restriction to PubMed as the search focus as it will eliminate non-medical journals not tracked by PubMed that have published highly relevant syndemics articles. The proposal to supplement Pub Med by contacting some experts in the field to ask for other potentially relevant records that the authors do not identify through their primary search strategy is vague and hardly insures that all relevant literature is included.\nMoreover, research may address vulnerability without using that term specifically and instead use cognate terms (eg, risk, susceptibility).\nAdditionally how will disagreements among literature reviewers be resolved is not specified.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
},
{
"id": "251513",
"date": "25 May 2024",
"name": "Morten Hulvej Rod",
"expertise": [
"Reviewer Expertise Social inequalities of health",
"public health intervention research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this protocol. The topic of the proposed scoping review is clearly relevant and I would personally be very interested in reading the results. The introduction section is excellent and provides a good overview of the field and a clear rationale. Considering that the suggested timeframe for the review is 2022, I hope that my comments can still be used to improve the search strategy where I have a few comments and concerns:\n\nI agree with the previous reviewer that PubMed might provide too narrow a basis for identifying relevant literature. It is stated as an eligibility criteria that the words syndemics, vulnerability, and COVID-19 occur in the title, abstract, or keywords. However, in the search strategy it is proposed to use both “AND” and “OR” as operators. This appears to be inconsistent. It might be problematic if the intention is to only include papers that use the concept of vulnerability in the title, abstract, or keywords. As the authors state in their introduction, the use of this concept is a topic of debate and quite a few relevant studies may have been conducted that adopt a syndemics perspective in relation to COVID-19 while for good reasons avoiding the term “vulnerability” It is suggested to exclude papers that “do not sufficiently elaborate on the concept of syndemics and/or vulnerability”. I would imagine that it is difficult to assess in a consistent manner what constitutes a sufficient elaboration. Finally, the authors intend to use Ribera & Hausmann-Muela’s dimensions in the analysis of vulnerability. It would have been helpful to include a brief explanation of this work (e.g. in the introduction) to provide a clearer rationale for this choice of analytical framework.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
},
{
"id": "271357",
"date": "30 May 2024",
"name": "Lianne Tripp",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe proposed scoping review on the syndemics approach to conceptualizing the vulnerability associated with COIVD-19 will make an important contribution of the medical literature and will also make a contribution to the medical anthropology. Despite the merits of the protocol, I have some reservations.\nCOVID-19 should be included in the title.\nI understand the importance of the concept of vulnerability in disease to assess susceptibility in diseases, however there is too much emphasis on this concept and not enough on syndemics. In fact, I think the proposal would benefit from starting with the concept of syndemics and how it is a better approach for addressing risk, vulnerability etc.\nThere is also a lack of information of general background information on COVID-19, which would set the stage for explaining the vulnerability of those with COVID-19 to other infections or health issues.\nThere also needs to be more explicit rationale for why the authors think it is important to reconceptualize COVID-19 as a syndemic, one reason is given, but it is vague (“overlapping biomedical and socio-economic conditions exacerbating the impacts of the coronavirus disease 2019”). Should mention that disease and health conditions interactions have been observed (as this is fundamental to a syndemic). In other words, in the introduction there should be more specific as to what is known about the syndemic interaction of COVID-19 with other diseases and/or health conditions.\nThe authors mentioned that “Interaction among diseases and health conditions….” will be examined, but none of the review questions appear to identify these diseases/health conditions involved, the focus seems to be on the social and environmental conditions.\nI am not sure the word vulnerability is needed in the search to find studies on syndemics of COVID-19.\nOne way to explore the limitations in the literature of syndemics with respect to COVID-19 is to include words such as’ COVID-19 interaction/susceptibility’ to specific diseases, this way you can find literature that that discussed a syndemics of COVID without explicitly using the concept and thus you can identify studies that are unaware of the concept.\nI’m in agreement with reviewer 1, a PubMed search will not be sufficient to discover all the literature on syndemics of COVID-19. Other search engines should be used to ensure that the literature that may not be included in strictly medical journals (it is important to note that the concept of syndemics comes from the field of anthropology, in particular the subfield of medical anthropology) is included in the study.\n\nIs the rationale for, and objectives of, the study clearly described? No\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1156
|
https://f1000research.com/articles/11-1152/v1
|
10 Oct 22
|
{
"type": "Case Report",
"title": "Case Report: Effectiveness of tocilizumab in obese patient for treatment of severe COVID-19 pneumonia",
"authors": [
"Oshna Pandey",
"Samish Adhikari",
"Tsewang Yangzom Ghising",
"Purnima Shakya",
"Samish Adhikari",
"Tsewang Yangzom Ghising",
"Purnima Shakya"
],
"abstract": "The purpose of this case report was to demonstrate the efficacy of Tocilizumab in the treatment of severe coronavirus disease 2019 (COVID-19) in obese patients who presented with a week's history of fever and one day of shortness of breath (SOB). It is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). COVID-19 has rapidly spread throughout the world, resulting in a global pandemic. Severe COVID-19 causes proinflammatory cytokine release and is associated with a high morbidity and mortality rate. Furthermore, obesity is an independent risk factor for developing severe COVID-19 complications with a high mortality. Stopping this cascade early in the disease's progression has resulted in a significant improvement in outcome. Tocilizumab in conjunction with systemic corticosteroids as part of the standard of care for halting pro-inflammatory cytokine cascades in early disease courses and prone positioning has been shown to improve respiratory parameters while also reducing the need for mechanical ventilation and Intensive Care Unit (ICU) stay (14 days as in our case).",
"keywords": [
"IL-6",
"Severe COVID-19",
"Tocilizumab"
],
"content": "Introduction\n\nThe COVID-19 outbreak caused by SARS-Cov-2 is the leading cause of mortality and morbidity due to ARDS, pneumonia, hypercoagulability, and septic shock.1 Furthermore, obesity is an independent risk factor for developing severe COVID-19 complications with a high mortality. Pro-inflammatory cytokine markers such as IL-6 are discovered to play an important role in the systemic inflammatory status of severe COVID-19 patients. Inhibiting IL-6 has shown promising results in terms of cytokine storm reduction.2\n\nTocilizumab is a monoclonal antibody that inhibits IL-62 production. It is now one of the therapeutic options for cytokine release syndrome management. We present a case of a 32-year-old obese patient who has severe COVID-19 pneumonia. With the addition of Tocilizumab to standard care, the patient experienced rapid clinical improvement.\n\n\nCase study\n\nA 32-year-old male from the Bhaktapur area of Nepal who was otherwise healthy was admitted to the COVID Ward with a week’s history of fever and one day of shortness of breath (SOB). He had no previous medical history other than a few virus illnesses in the past. Ten days prior, his wife tested positive for COVID. With a body mass index of 39.21 kg/m2, he qualified as obese. His total weight was 120 kg. He worked as a businessman. He worked at a desk most of the day and led a sedentary lifestyle. His peripheral oxygen saturation (SPO2) was 88% in room air, and his respiratory rate was 28 beats per minute. It increased to 94% when using a 10 L/min face mask.\n\nOn admission, a nasal swab confirmed SARS-CoV2 infection. Inflammatory markers such as ferritin, CRP, D-dimer, and IL-6 were significantly elevated at 94.5 (normal 7 pg/ml).\n\nDespite O2 supplementation via non-rebreather mask @15 l/min, his SPO2 dropped from 94% to 80% several hours after admission, so he was kept on High Flow Nasal Cannula (HFNC) with a flow rate of 60L/min and FiO2 of 100%. The patient was given TOCILIZUMAB 800 mg in 100 ml of 0.9% normal saline intravenously over 1 hour due to increasing O2 demands and impending respiratory distress. Despite all precautions, the patient developed severe ARDS. Following tocilizumab administration, the patient’s ABG revealed PH-7.48, PO2-34, PCO2-38, HCO3-: 28, PO2/FiO2-87, and he was intubated in the ICU the same day. At the same time, the patient was given standard empirical antibiotics (piperacillin, tazobactam, and azithromycin), steroids (Dexamethasone 20 mg iv od for 5 days, followed by 10 mg iv od for another 5 days), subcutaneous low molecular weight heparin, and vitamin supplements such as Tab Vitamin C, Zinc, and Vitamin D. The patient was also kept in a prone position for 16–18 hours per day (Figure 1).\n\nThe patient began to improve clinically 48 hours after receiving tocilizumab. All of the inflammatory markers, including IL-6, that were elevated two days ago began to return to normal (Table 1). The patient’s condition significantly improved on the 12th day of admission, meeting extubation criteria, and he was thus extubated. He was transferred to the medical ward on the 14th day and discharged home on the 23rd.\n\n\nDiscussion\n\nSARS-Cov-2 causes COVID-19. The leading causes of death in severe COVID-19 are ARDS and pneumonia, both of which are caused by uncontrolled inflammatory processes and multi-organ failure. This process primarily involves the release of pro-inflammatory cytokines (IL-2, IL-6, IL-7, tumor necrosis factor alpha).3 Tocilizumab is critical in preventing cytokine storms and associated ARDS. It is a monoclonal antibody against IL-6 receptors that has been humanized.2 A retrospective cohort study in Ohio, USA,1 discovered that using tocilizumab shortens the time to clinical improvement and the duration of invasive ventilation.\n\nIn our case, the IL-6 level was extremely high (94.5 pg/ml), which could have coincided with the occurrence of a cytokine storm. This stage is associated with increased levels of other inflammatory mediators such as ferritin, LDH, CRP, and D-dimer. During this course, specific and timely intervention may result in better outcomes. On the same day, our patient received tocilizumab and was placed on mechanical ventilation. There was a significant improvement in the patient’s respiratory parameters after receiving tocilizumab and other standard care; Pao2/FiO2 ratio improved from 87 to 373 and FiO2 gradually tapered from 100% to 40%; PEEP from 15 cm of H2O to 5 cm of H2O, respectively, which is comparable with the case reports by Gentile et al.4\n\nInitial signs of an unfavourable prognosis include the severity of lung damage, clinical deterioration, and the need for mechanical ventilation. However, with an effective treatment protocol, the patient recovered completely.\n\nThe findings of our case report, like any other case report, cannot be generalized, so well-designed research with a large sample size is needed to validate the efficacy of tocilizumab in COVID-19 patients.\n\n\nConclusion\n\nOur findings show that using Tocilizumab in conjunction with systemic corticosteroids as part of the standard of care for halting pro-inflammatory cytokine cascades in early disease courses and prone positioning improves the outcome of mechanically ventilated patients with high risk of complications, while also shortening ICU stay. With the use of Tocilizumab in conjunction with other standard care, we saw a regression in radiological changes and a rapid clinical improvement.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nFigshare. CARE guidelines. DOI: https://doi.org/10.6084/m9.figshare.20690110.5\n\n\nConsent for publication\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient.",
"appendix": "References\n\nKewana T, Covuta F, Al-Jaghbeer MJ, et al.: Tocilizumab for treatment of patients with severe COVID-19. EClinicalMedicine THE LANCET. 2020 june 20; 24: 100418. Publisher Full Text Reference Source\n\nCampochiaroa C, Della-Torrea E, Cavallia G, et al.: Efficacy and safety of Tocilizumab in severe COVID19 patients. Eur. J. Intern. Med. 2020 May22; 76: 43–49. PubMed Abstract | Publisher Full Text Reference Source\n\nSoin AS, Kumar K, Choudhary NS, et al.: Tocilizumab plus standard care versus standard care in patients in India with moderate to severe COVID-19- associated cytokine release syndrome (COVINTOC). Lancet. 2021 March 4; 9(5): 511–521. Publisher Full Text Reference Source\n\nGentile G, Davies R, Manfreda VM, et al.: Successful treatment of severe COVID-19 pneumonia and hyperinflammatory syndrome with tocilizumab. BMJ. 2021 January 8; 14(1): 1–3. Publisher Full Text Reference Source\n\nPandey O, Adhikari S, Ghising TY, Shakya P: Effectiveness of tocilizumab in obese patient for treatment of severe COVID-19 pneumonian. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "217441",
"date": "02 Nov 2023",
"name": "Md Jahidul Hasan",
"expertise": [
"Reviewer Expertise Immunology and pharmacology",
"due to time limitation",
"I can't go through this manuscript further."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n\"a few virus illness\"- what are the infections, hospitalized or not, recovery status, are these within the last 3 month? Please response to these question.\n\nWhat were the early signs of the disease 10 days back?\n\nPlease add initial X-ray (if have) and the compare with the post-treatment X-ray for clear understanding radiological improvement.\n\nWhy abroad-spectrum antibiotic (Pip-Taz) was used with Azith.; is there any other concomitant infection or any microbiological investigation?\n\nIs there any side effects shown with the use of tocilizumab at this dose?\n\nPlease discuss the case with other similar treatment cases with references.\n\nPlease write abbreviations in full sentences first.\n\nWas the patient monitored at post-tocilizumab therapy (like next 2-3 weeks) for any post-treatment complication?\n\nPlease make improvements in your language and sentence makings to meet the journal's standards.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1152
|
https://f1000research.com/articles/11-1151/v1
|
10 Oct 22
|
{
"type": "Case Report",
"title": "Case Report: Localized Ewing’s sarcoma of the scapula in an adult",
"authors": [
"Rafik Elafram",
"Majdi Ben Romdhane",
"Nayssem Khassairi",
"Sarrah Ben Rjeb",
"Saiffallah Toumi",
"Majdi Sghaier",
"Majdi Ben Romdhane",
"Nayssem Khassairi",
"Sarrah Ben Rjeb",
"Saiffallah Toumi",
"Majdi Sghaier"
],
"abstract": "Background: Ewing’s sarcoma (ES) of the scapula is a rare entity. It is often discovered late at the metastatic stage of the disease because of its deep location. This neoplasm is common in children and adolescents. We present the first reported case of a localized Ewing’s sarcoma of the scapula in an adult over 40 years-old. Case presentation: A 48-year-old man presented with left shoulder pain evolving for one year. Physical examination showed a painful, ill-defined swelling of the left shoulder measuring 5 x 3 cm. Magnetic resonance imaging (MRI) was performed showing a mass of the left scapula invading the soft tissues of the shoulder suggestive of a sarcoma. The patient underwent a surgical biopsy finding an ES of the scapula with no secondary localization on the computerized tomography (CT) scan nor on the bone scintigraphy. Neo-adjuvant multiagent chemotherapy was started obtaining a total response. Therefore, the patient underwent a total left scapulectomy. Histopathological examination confirmed the diagnosis of ES with a complete response to chemotherapy. Adjuvant chemotherapy was then indicated. After 3 years of follow-up, no local or distant recurrence was found. Discussion: ES is a high-grade aggressive lesion that most commonly originates in bone. The ES may affect any bone but is frequent in femur, tibia and ilium, the tumors arising from the scapula comprise fewer than 4% of all ES. No cases of localized Ewing’s sarcoma in adults have been reported to our knowledge. The diagnosis is confirmed by immunohistochemical examination and cytogenic. A multimodal treatment approach including a combination of chemotherapy, surgery, and radiation can modestly improve local tumor outcomes. Metastatic tumors still have poor diagnosis. Conclusions: ES occurs rarely in adults greater than 20 years-old, and tumors localized in the scapula are even rarer. Histopathology differentiates it from other primary bone/soft tissues tumors.",
"keywords": [
"Ewing’s sarcoma",
"Scapula",
"Tumors"
],
"content": "Introduction\n\nEwing’s sarcoma (ES) is an aggressive primary osseous neoplasm and those arising from the scapula comprise fewer than 4% of all ES.1 ES of the scapula are often asymptomatic and grow quite large before being diagnosed due to their deep location, thus these tumors are discovered late and usually at the metastatic stage of the disease.2,3 This neoplasm is the second most common malignant bone tumor of children and young adults, but it’s incidence declines rapidly as age increases beyond 20 years and is extremely rare in adults over 40 years of age.4 Our literature review showed only two reported cases of Ewing’s sarcoma of the scapula in adults over 40 years old which were discovered at the metastatic stage3,14 (cases with insufficient data information were excluded). Here, we present the first case reported to our knowledge of a localized ES of the scapula in an adult over 40 years of age.\n\nThis case report has been reported in line with the SCARE Criteria.5\n\n\nCase presentation\n\nA 48-year-old male Caucasian police officer presented with a painful swelling of the left shoulder evolving for one year. The patient had no medical or surgical history nor allergies. There was no history of systemic symptoms such as fever, anorexia, or recent subjective weight loss. The increase in size of the swollen shoulder brought him to seek medical attention without taking any medication so far. Physical examination showed a hard, painful, and ill-defined bony mass of the left scapular region measuring 5 × 3 cm without adjacent cutaneous lesions.26 The mobility of the upper limb was preserved. Cardiovascular, respiratory, and abdominal examinations were unremarkable. An X-ray of the left shoulder showed a bony mass with osteolytic lesions suggestive of a primary bone tumor. Magnetic resonance imaging (MRI) was performed showing a necrotic mass invading the scapula and the soft tissues of the left shoulder suggesting a sarcoma (Figure 1). A full body computerized tomography (CT) scan and bone scintigraphy didn’t show any other localization of the tumor. The patient underwent a surgical biopsy of the mass. The intervention was performed by a group of senior orthopedic surgeons in an orthopedic surgery department of a university hospital in Tunisia (Figure 2). Histopathological examination found a malignant tumoral proliferation with large areas of necrosis. The tumor was made of small round cells which have a poorly distributed cytoplasm with ill-defined borders and a vacuolated aspect rich in periodic acid Shiff (PAS) positive glycogen. Immunohistochemically these cells were cluster designation (CD20) negative, Desmine and Myogenine negative, cytoKeratine (CK) and CD56 negative, and were positive for CD99 with a heavy membranous marking. The immunohistochemical results also demonstrated a diffuse nuclear positivity for the NKX2.2. The Ki67 proliferative index was 70% (Figures 3, 4, 5). Thus, the diagnosis of Ewing’s sarcoma of the left scapula was confirmed. After a multidisciplinary meeting, the patient had six cycles of neo-adjuvant vincristine, Ifosfamide, doxorubicin, etoposide (VIDE) chemotherapy. This involved Vincristine 1.5 mg/m2 (max 2 mg) intravenous IV Day 1 Doxorubicin 20 mg/m2 IV Days 1, 2 and 3 of cycle Etoposide 150 mg/m2 IV Days 1, 2 and 3 of cycle Ifosfamide 3 g/m2 IV Days 1, 2 and 3 of cycle. The protocol is repeated every 21 days 06 cycles.\n\nAn intermediate MRI showed a total response to the treatment. He then underwent an en-bloc total left scapulectomy carrying the scapula, the infraspinatus muscle, the supraspinatus muscle, and the upper part of the deltoid muscle. No postoperative problems were noticed. Histopathological examination confirmed the diagnosis of ES, with no residual viable tumor cells Grade IV according to Huvos’ criteria and wide resection margins. The patient continued the protocol with an adjuvant VIDE chemotherapy. After 3 years of clinical and radiological follow-up, an MRI was performed showing the absence of local recurrency. Clinically, the patient has a preserved mobility of the upper limb, arm flexion is possible, and he is capable of doing the hand to mouth movement.\n\n\nDiscussion\n\nEwing’s Sarcoma (ES) was first described by James Ewing in 1925.6 ES is a primary osseous neoplasm. It is also part of the Ewing sarcoma tumor family, which includes primitive neuroectodermal tumor, Ewing soft tissue sarcoma, and Askins tumor.6,7 It accounts for 8% of all malignancies and 2% of all primary bone tumors.2,8 ES is a high-grade aggressive lesion, most commonly of bony origin, with large soft-tissue masses and frequent metastases. 15–30% of patients have distant metastases at diagnosis.8,9 The sites of metastasis are mainly lung (85%), bone (69%), pleura (46%), but also lymph nodes (40%) and central nervous system (12%). 4110,11;. ES is the second most common malignant bone tumor in children and young adults. It occurs primarily in the first decade of life (mean age 14 years) and has a slight preference for males. Incidence declines rapidly with increasing age after age 20.4 The average age at diagnosis he is 15 years.2,12 ES is diagnosed in Caucasian Caucasians <25 years of age with an incidence of 0.3/100,000 per year, but is very rare in African and Asian populations.4,13 The ES may affect any bone but is frequent in femur, tibia and ilium and the tumors arising from the scapula comprise fewer than 4% of all ES.1,3 Patients with ES of the scapula are slightly older at time of diagnosis, since these tumors are often asymptomatic and grow quite large before being diagnosed.12 Thus, these tumors are usually discovered late, in the metastatic stage of the disease. No cases of localized ES in adults have been reported to our knowledge. The reported cases of metastatic ES of the scapula in adults over 40 years of age are summarized in Table 1.\n\nClinically, ES commonly presents as a dull to severe persistent shoulder pain that gradually increases in size. Although the etiology of the ES remains unknown, it has been confirmed that majority of cases had a cytogenetic translocation consisting of Rearrangements of the EWS gene and a member of the ETS gene family (FLI1) on chromosome 22q12. These translocations define the Ewing sarcoma tumor family (ESFT) and provide valuable tools for accurate and unambiguous diagnosis.15 Radiologically, ES presents as an ill-defined osteolytic lesion, Permeable or worm-eaten bone destruction, often associated with an onion slit-type multi-layered periosteal reaction. On the MRI, the lesion is classically described as a prominent mass that contains areas of necrosis or hemorrhage.3,12,16–18 Histopathologically, typical ES is made of uniform small round blue cells with a clear cytoplasm and distant cellular borders, has a uniform small oval blue nucleus. The principal differential diagnosis with ES are small cell osteosarcoma, mesenchymal chondrosarcoma, lymphoma and metastatic neuroblastoma.7,13,19 The diagnosis is confirmed by immunohistochemical examination showing a diffuse strong cytoplasmic membrane positivity for CD99 combined with NKX2.2 positivity and cytogenic examination showing the t (11;22) (q24;q12) translocation.2,20–22 Neither the NKX2.2 nor CD99 alone are entirely specific for the Ewing’s family tumors, but when combined the diagnostic specificity is high. NKX2.2 is positive in 91.5% of the tumors, and CD99 is positive in 99% Before the advent of modern chemotherapy. Fewer than 10% of her ES patients survived more than 5 years after diagnosis when treated with surgery or radiotherapy alone, but it increases to 60–70% in localized tumors when neo-adjuvant and adjuvant chemotherapy are used in conjunction with surgery/radiotherapy.2,13 Currently, the treatment of the Ewing’s sarcoma Coordinated through cooperative groups. Although multimodality treatment approaches involving a combination of chemotherapy, surgery, and radiation have resulted in modest improvements in localized tumor outcomes. Prognosis remains poor for patients with metastatic disease.3,4,13 The most common surgical approach of the malignant tumors of the scapula was the forequarter amputation until 1970, after that the Tikhoff-Linberg procedure was used.14,23,24 The most used protocol for ES is an intense multiagent neoadjuvant chemotherapy, followed by en bloc excision of the tumor mass and radiotherapy postoperatively if doubt of tumor residue which was achieved with our patient. Adjuvant chemotherapy for consolidation is decided according to the response of the tumor to chemotherapy (Huvos tumor necrosis grading system).3,10,12 Prognostic factors may define subgroups requiring different treatment intensities, the most common are age of the patient, tumor size and location, metastatic pattern, and histologic response to chemotherapy. For the patients with ES of the scapula, those who have metastatic disease, marginal resection, or a chemotherapy response of <80% (Grade I and II of Huvos’ criteria) have the worst prognosis.1,3,25\n\n\nConclusion\n\nThe ES is common in children and adolescent’s long bones and pelvis, but ES of the scapula in adults is a very rare entity. It is often discovered after a diffuse local progression and distant metastases. Diagnosis is confirmed histologically and immunohistochemically. Neo-adjuvant chemotherapy combined with surgery is the most common treatment for localized tumors.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.\n\n\nData availability\n\nElafram, rafik; romdhane, majdi ben (2022): Ewing’s Sarcoma of the Scapula.docx. figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.20508903.v3.26\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nCotterill SJ, Ahrens S, Paulussen M, et al.: Prognostic factors in Ewing’s tumor of bone: analysis of 975 patients from the European Intergroup Cooperative Ewing’s Sarcoma Study Group. J. Clin. Oncol. Off. J. Am. Soc. Clin. Oncol. 2000; 18: 3108–3114. Publisher Full Text\n\nMoore DD, Haydon RC: Ewing’s sarcoma of bone. Cancer Treat. Res. 2014; 162: 93–115. Publisher Full Text\n\nMalik SS, Tahir M, Ahmed U, et al.: Outcome of Ewing’s sarcoma of the scapula-a long-term follow-up study. Orthop. Traumatol. Surg. Res. OTSR. 2020; 106: 25–30. PubMed Abstract | Publisher Full Text\n\nEsiashvili N, Goodman M, Marcus RB: Changes in incidence and survival of Ewing sarcoma patients over the past 3 decades: Surveillance Epidemiology and End Results data. J. Pediatr. Hematol. Oncol. 2008; 30: 425–430. PubMed Abstract | Publisher Full Text\n\nHajdu SI: The Enigma of Ewing’s Sarcoma. Ann. Clin. Lab. Sci. 2006; 36: 108–110. PubMed Abstract\n\nUnni KK, Inwards CY: Dahlin’s Bone Tumors: General Aspects and Data on 10,165 Cases. Lippincott Williams & Wilkins;2010.\n\nNiu X, Xu H, Inwards CY, et al.: Primary Bone Tumors: Epidemiologic Comparison of 9200 Patients Treated at Beijing Ji Shui Tan Hospital, Beijing, China, With 10 165 Patients at Mayo Clinic, Rochester, Minnesota. Arch. Pathol. Lab. Med. 2015; 139: 1149–1155. Publisher Full Text\n\nEwing J: The Classic: Diffuse endothelioma of bone. Proceedings of the New York Pathological Society. 1921;12:17. Clin. Orthop. 2006; 450: 25–27. PubMed Abstract | Publisher Full Text\n\nRalapanawa DMPUK, Jayawickreme KP, Ekanayake EMM, et al.: Spinal intradural metastasis from scapular Ewing sarcoma. BMC. Res. Notes. 2015; 8: 298. Publisher Full Text\n\nAsif N, Khan AQ, Siddiqui YS, et al.: Metastasis from scapular Ewing’s sarcoma presenting as sutural diastasis: An unusual presentation. Int J Shoulder Surg. 2010; 4: 18–21. PubMed Abstract | Publisher Full Text\n\nYeung CM, Kaiser CL, Peleteiro-Pensado M, et al.: Characteristics and oncologic outcomes of patients with Ewing sarcoma of the scapula. Surg. Oncol. 2021; 38: 101619. PubMed Abstract | Publisher Full Text\n\nESMO/European Sarcoma Network Working Group. Bone sarcomas: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann. Oncol. Off. J. Eur. Soc. Med. Oncol. 2014; 25: iii113–iii123. Publisher Full Text\n\nMavrogenis AF, Mastorakos DP, Triantafyllopoulos G, et al.: Total scapulectomy and constrained reverse total shoulder reconstruction for a Ewing’s sarcoma. J. Surg. Oncol. 2009; 100: 611–615. PubMed Abstract | Publisher Full Text\n\nBurchill SA: Molecular abnormalities in Ewing’s sarcoma. Expert. Rev. Anticancer. Ther. 2008; 8: 1675–1687. Publisher Full Text\n\nMarquezy RA; Christol null: Ewing’s tumor of the scapula in a 13-year-old girl; pulmonary metastases with relapsing pneumothorax; cerebral metastasis. Arch. Fr. Pediatr. 1950; 7: 282–288. PubMed Abstract\n\nJinkala SR, Basu D, Mathath D, et al.: A rare case of congenital Ewing sarcoma/PNET of the scapula. J. Pediatr. Hematol. Oncol. 2014; 36: e134–e135. PubMed Abstract | Publisher Full Text\n\nShahid M, Varshney M, Maheshwari V, et al.: Ewing’s sarcoma of scapula: a rare entity. Case Rep. 2011; 2011: bcr0220113810. PubMed Abstract | Publisher Full Text\n\nOzdemirli M, Fanburg-Smith JC, Hartmann D-P, et al.: Differentiating Lymphoblastic Lymphoma and Ewing’s Sarcoma: Lymphocyte Markers and Gene Rearrangement. Mod. Pathol. 2001; 14: 1175–1182. PubMed Abstract | Publisher Full Text\n\nOn the histogenesis of Ewing’s sarcoma: An ultrastructural, immunohistochemical, and cytochemical study - Navas-Palacios - 1984 - Cancer - Wiley Online Library:n.d. (accessed March 14, 2022). Publisher Full Text\n\nKavalar R, Pohar Marinsek Z, Jereb B, et al.: Prognostic value of immunohistochemistry in the Ewing’s sarcoma family of tumors. Med. Sci. Monit. Int. Med. J. Exp. Clin. Res. 2009; 15: CR442–CR452.\n\nMachado I, Yoshida A, López-Guerrero JA, et al.: Immunohistochemical analysis of NKX2.2, ETV4, and BCOR in a large series of genetically confirmed Ewing sarcoma family of tumors. Pathol. Res. Pract. 2017; 213: 1048–1053. PubMed Abstract | Publisher Full Text\n\nDi XY, Jin MS, Xin YP: Radical resection of the shoulder girdle for a malignant tumor: four case reports. Orthopedics. 1989; 12: 1017–1022. PubMed Abstract | Publisher Full Text\n\nPuchner SE, Panotopoulos J, Puchner R, et al.: Primary malignant tumours of the scapula—a review of 29 cases. Int. Orthop. 2014; 38: 2155–2162. PubMed Abstract | Publisher Full Text\n\nRodríguez-Galindo C, Liu T, Krasin MJ, et al.: Analysis of prognostic factors in ewing sarcoma family of tumors: review of St. Jude Children’s Research Hospital studies. Cancer. 2007 Jul 15;110(2): 375–84. Analysis of prognostic factors in ewing sarcoma family of tumors: review of St. Jude Children’s Research Hospital studies - PubMed n.d. (accessed March 14, 2022). Publisher Full Text Reference Source\n\nElafram R, Romdhane MB: Ewing’s Sarcoma of the Scapula.docx. figshare. Journal contribution. [Dataset]. 2022. Publisher Full Text"
}
|
[
{
"id": "267318",
"date": "15 May 2024",
"name": "Iyad Sultan",
"expertise": [
"Reviewer Expertise Pediatric Oncology",
"sarcomas",
"solid tumors",
"cancer epidemiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report documents a rare instance of localized Ewing's sarcoma in the scapula of a 48-year-old man, which seldom seen in adults at this location. Successful treatment included neo-adjuvant chemotherapy, complete surgical removal of the affected scapula, and subsequent adjuvant chemotherapy. Three years post-treatment, there was no recurrence.\nComments: 1- Introduction vs. Abstract Contradiction: The abstract states this is the \"first reported case of a localized Ewing’s sarcoma of the scapula in an adult over 40 years-old,\" whereas the introduction mentions that there are two reported cases of Ewing’s sarcoma of the scapula in adults over 40 years old, discovered at the metastatic stage. This could confuse readers about whether it is truly the first case or not, especially since those earlier cases were not localized. Clarification is needed to differentiate this case clearly from previous ones.\n2-Discussion on Prognosis and Outcomes: Expand the discussion to include more about the prognosis of Ewing's sarcoma arising from the scapula specifically. This could also include a discussion of how age and tumor location affect outcomes based on current literature.\n3- The manuscript should be carefully proofread to correct typographical errors.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1151
|
https://f1000research.com/articles/11-37/v1
|
12 Jan 22
|
{
"type": "Method Article",
"title": "Paradigm shift in medical education due to the COVID-19 pandemic: guidelines for developing a blended learning curriculum in medical education",
"authors": [
"Aisha Rafi",
"Muhammad Idrees Anwar",
"Ayesha Younas",
"Shamaila Manzoor",
"Muhammad Idrees Anwar",
"Ayesha Younas",
"Shamaila Manzoor"
],
"abstract": "Background: The coronavirus disease 2019 (COVID-19) pandemic has transformed the world’s economy, health and education in a blink of an eye. Almost 1 billion learners have been affected across the globe. This has resulted in a paradigm shift to blended learning. Therefore, it was felt necessary to provide practical guidelines for the development of blended curriculum in medical education. It would help to overcome the challenges faced due to unprecedented transformation of medical education on account of pandemic. Methods: Guidelines based on personal experience of the authors and literature search were developed using the complex adapted blended learning system (CALBS) framework. Seven experts developed these guidelines using the nominal group technique. The consent form and literature for CABLS framework was shared with experts. The experts developed the guidelines independently during phase one of the technique. After a given time, phase 2 started with moderator mediated discussion about the individual guidelines developed by the experts. After discussion and mutual consensus four types of guideline ideas were developed. During the third phase the experts ranked the guideline ideas on a scale of 1 to 5. The guideline idea that ranked highest was selected as a final guideline for developing a blended learning curriculum. Results: The group consensus resulted in developing seven guidelines for a blended course or curriculum in medical education. These guidelines are based on a conceptual framework supplemented by expert’s own personal experience and current evidence from literature. Conclusions: These guidelines would provide a comprehensive and systematic approach to develop a blended learning curriculum in medical education.",
"keywords": [
"Blended learning",
"curriculum",
"guidelines",
"paradigm shift",
"Covid-19",
"Nominal group technique"
],
"content": "Introduction\n\nBlended learning can be classified as an integrated learning approach where two or more teaching and learning strategies are blended to achieve the learning outcome. Combining modes of web-based technology, pedagogical approaches, instructional technologies with tasks concerned with face-to-face teaching and learning constitute all forms of blended learning.1\n\nBlended learning strategies have been studied in the past with studies concluding that they facilitated an improvement in students’ academic performance, motivation, and attitude along with convenient and flexible learning.2\n\nThe coronavirus disease 2019 (COVID-19) pandemic has transformed the world in a blink of an eye in the context of the economy, health and education at all levels.3 Educational landscapes across the globe have seen rapid improvisations at all levels due to partial or complete lock down and other protective strategies to minimize the spread of the virus.4 Almost 1.5 billion learners have been affected worldwide due to pandemic, which5 has resulted in varied responses to education, from complete cessation of all educational activities to a holistic shift to online learning. This has instigated a paradigm shift from traditional face to face or physical classrooms setting to virtual classrooms, which has been challenging for faculty, students and the institutions alike.6 Education in the health professions was not spared this paradigm shift. Realistically speaking, virtual environments traditionally do not cater to the needs of medical education because medical skills can never be achieved exclusively online.7 The pandemic has caused moderate to extreme level of anxiety particularly among the university students.8\n\nAt the same time, the COVID-19 pandemic has helped to develop technologically smart medical teachers and students to meet the challenges of digital world. Digital technology and artificial intelligence are the future of medical science and healthcare. This calls for a change in the learning outcomes, expected competencies and entrustable professional activities (EPA) in medical education.9 Virtual reality teaching is a new norm and calls for unprecedented transformation of medical education and the health care system as a whole. One day it will likely become a standard and the term blended will not be used anymore. Very soon blended learning will be a default model.10\n\nBlended learning programs can use different models and frameworks that best match their outcomes. Planning and implementing a blended learning course entails that we should first understand the related hypotheses and the theoretical underpinnings of the blended learning concept. In medical education the most successful model of blended learning is the rotational model.11 To aid medical educators involved in developing blended learning courses, we developed a set of guidelines utilizing the theoretical framework, complex adaptive blended learning system (CABLS). The main framework is organized around the learner support, the teacher, the content and technology and the institution (Figure 1). The salient features of the framework are that the learner’s role changes from a passive to an active learner. The learner support including self-regulation, collaborative skills and technical skills etc., to achieve the learning outcome. The teacher must adopt the pedagogical approaches that engage the learners in a blended classroom. The content should be delivered in a blended learning strategy.\n\nThe leadership support includes technology, infrastructure, budget, resources, addressing the barriers etc.\n\n\nMethods\n\nThe present study was conducted in March 2021. The present study was based on personal experiences of the experts of the study supplemented by the literature review, therefore it did not require ethical approval from ethical review board. The CABLS framework for blended learning was used for developing the guidelines proposed in our study.\n\nWe utilized an iterative process of nominal group technique (NGT), because it is a suitable technique for developing guidelines besides being cost effective and less time consuming.12 For our study, participants were selected by purposive sampling technique. At least seven participants are recommended for NGT.13 The NGT was modified according to prevailing circumstances due to COVID-19. The online meetings were scheduled for NGT. Medical experts were invited specifically from those universities where blended learning curricula are being implemented in true letter and spirit in lieu of pandemic. Ten proposed experts who fulfilled the inclusion criteria were contacted initially via email. The criteria for selection of the participants were based on their expertise, academic and community practice. The demographic details of experts are given in Table 1. Apart from this it was also ensured that participants were actively involved in developing undergraduate medical and dental curricula and consented to take part in all rounds of NGT. Those who did not consented for full round of NGT were excluded. Faculty members who were not actively involved in curriculum development were also excluded.\n\nThe details of the proposed study were sent via e-mail along with a consent forms and instructions for the nominal group technique to all the experts. The link for Pertinent literature about the CABLS framework and literature on blended learning was also sent in instructions. The due date for submission of draft was also mentioned. Participants were requested to confirm their availability for all four rounds of the study to ensure reliability of the process. Only six experts acknowledged and consented to be a part of the whole study. The seventh expert was approached face to face in our own institution. As per instructions during silent or phase one of the nominal group technique the experts prepared the initial draft based on the CABLS framework in private. They were instructed to submit the draft via postal address to the principal author within a due date mentioned in instructions. The experts submitted their ideas for guidelines to the principal author after two weeks.\n\nThe phase-II was scheduled online on Zoom. The meeting was moderated by the principal author. All the guidelines submitted previously to the principal author was shared on zoom one after the other anonymously. The name of the expert was not shared to control bias. All the experts went through all the guidelines. Before discussion the guidelines that overlap in meaning were combined to develop a new guideline that best conveys the intention of all the combined guidelines.\n\nThe moderator presented the guidelines again developed after deleting the duplication and after combining the similar guidelines. This was the longest and crucial stage for developing guidelines. The experts discussed in detail the inclusion of tip or idea for a blended learning course with reference to Covid-19. Some of the experts were of the view that Harden’s14 ten points for developing the curriculum fit in every situation, others did not agree. One of the experts advocated the guidelines given by Kern15 for developing the curriculum. The discussion lasted for two hours. The feasibility was also addressed. After the consensus of the experts four sets of guidelines were developed for the third phase. The two sets of guidelines given by Harden and Kern consisting of consisting of ten steps approach and six steps approach respectively were kept as such. Whereas the other two sets with six and seven guidelines were developed after discussion among the experts. There were ten, seven, six and six guidelines in sets number one (Harden), two, three and four (Kern) respectively (Table 2). The experts award scores ranging from 1 to 5 to each guideline in the given sets. The moderator add the total points for each guideline (Table 2). The whole session was recorded. The four sets of guidelines were emailed to the experts for further evaluation. During phase-III the sets of guidelines were ranked from 1 to 5 by the experts. The Zoom meeting was scheduled for the third phase after confirming the availability of the experts. During this phase the four sets of guidelines were ranked from 1 to 5. Number 1 being strongly disagree and number 5 being strongly agreed. Rank 2,3, 4 is interpreted as disagree, neutral and agree respectively (Table 3). The moderator facilitated the session by sharing the sets of guidelines on the screen and awarding the scores written in the chat box by the experts. The ranked score were added. The set no 2 was ranked highest (Table 3). Set number 2 consisted of 7 tips or guidelines for developing a blended learning course in medical education. Set number 2 was selected unanimously by all the experts for developing the guidelines (Table 3). The threat to reliability and validity were controlled during data collection and analysis by anonymity, multiple rounds and controlled feedback. It decreased the social and cognitive biases.\n\n* Low score.\n\n\nResults\n\nThe guidelines were developed after thorough discussion during phase II of nominal group technique. All the experts were qualified medical educationists belonging to clinical and basic medical sciences. These guidelines for blended learning curriculum were organized around CABLS framework. Almost all the experts developed guidelines outlining the four basic components of curriculum i.e. outcomes, teaching and learning strategies, assessment and evaluation. Only twenty percent experts wanted to include Mission and vision of the curriculum. The guidelines regarding the mission and vision scored least (Table 2) because most of the experts were agreed that in context of covid-19 the vision and mission of the curriculum would be same all around the globe. Similarly, the student support and facilities, an important component of CABLS framework was included in guideline for resources. The guideline for educational strategy also scored less (Table 2). It was discussed that SPICES model given by Harden14 as an educational strategy is for exclusive for on campus delivery of curriculum in medicine. It cannot be applied to blended learning because the social and emotional component in blended learning is not same as in full on-campus curriculum in medicine. The problem identification and general needs assessment guideline given by Kern scored lowest because it was merged into need assessment. Usually the curriculum development began with the goals, aims and objectives, The separate guideline for goals, aims and objectives scored low (Table 2). The experts had consensus in merging the aims and objectives in the guideline for developing the content for blended learning because they opined that content should always align with the aims and objectives of the curriculum so it should be placed in the same guideline. One of the greatest drawbacks pointed out by all the experts was lack of teaching psychomotor skills online. They were of the opinion that simulations cannot be substituted for real world learning. All the experts stressed upon a face to face component of blended learning in medicine ensuring all the standard operating procedures (SOP).\n\nThe set 2 of guidelines scored highest among all the sets of guidelines (Table 2). It was also ranked highest among the four sets of guidelines (Table 3). The guidelines given in set 2 are described below:\n\nNeeds assessment is a process that seeks need for change to cope with meeting the demands of society at large.16 Qualitative and comparative methods should be used to determine priorities for the most effective use of resources for the blended learning.16\n\nThe simplest method of needs assessment is that teachers, clinicians, educationists and students should have several meetings for selecting the course content and mode for blended learning sessions. Blended learning does not mean that the course content should be compromised in any way. The teaching and learning activities should be according to mode of blended learning environment. The effective course design always begins with the needs assessment about the level and type of students who will benefit the program. Assess the learning style of students and their knowledge about the use of digital technology. All the activities, materials, and assignments should support student learning to gain specific outcomes. Assess the faculty needs by what do they want students be able to do and whether they are able to use digital media effectively. The questions to ask are: What is the standard of online sessions? How can students be engaged and assessed online? Can the outcomes be achieved successfully?\n\nThe convergence of two archetypal learning environments calls for systematic integration and alignment between the components in a meaningful way both pedagogically and didactically.17 The content should be chosen wisely so that it is best for each mode of delivery but the two learning environments should be connected in a way to provide a sense of class cohesion and community.18\n\nThere should be more learner independence and autonomy in blended learning course design because learner autonomy and self-direction are essential to successful blended courses. The students’ diverse abilities and learning styles should be acknowledged for a successful design.19\n\nThe appropriate adjustments should be made according to learner needs and situations i.e. the level of instruction and time allocation to online and face to face learning. Flexibility of the schedule, role of the teacher and student in online and face to face teaching and learning are other components to consider in student support.\n\nA course outline should be developed regarding time allocation, activities, assignments and assessments. Alignment between the components of curriculum helps to determine when, where, and how the outcomes will be achieved. Frequent weekly meetings are required among all the stake holders to decide the dimensions of the program. The frequency of meeting times should be defined by the course structure.20 Every precaution should be observed so that online components should not turn into extended homework in a blended course design.18 Integrate the components in such a way so the students are more motivated to participate and take onus of their learning.\n\nLike in any other course the needs assessment should be transformed into well written measurable objectives. The identified learning needs are linked to formulation of learning outcomes defining the three domains of knowledge, skills, and attitude.21 Great care should be taken in segregating the objectives for different modes of teaching and learning in a blended learning approach.\n\nThe curriculum planners should sit together and divide the objectives suitable for online and face to face teaching based on its inherent need, effectiveness, and suitability. This is the key step for blended teaching. The planner must be aware that not all objectives can be achieved either by online and face to face teaching alone. Predominantly the cognitive objectives can suitably be adjusted for online sessions but for attitude and psychomotor skills, one has to be more pragmatic. The psychomotor domain presents a challenging task of replicating the hands-on clinical skills in a synchronous environment. However, simple psychomotor skills, for example, examination of nerve and muscle injury can be taught online with equally comparable results.22 Medicine is a practice-based profession and special care must be taken while developing a table of specification (TOS) for practical skills.23 The complex practical skills which need hand eye co-ordination and hands-on practice must be delivered within a classroom setting, with immediate feedback. This is essential for making safe practitioners. The attitude domain can be taught both with face-to-face interaction and online.24 Many soft skills like communication skills involving counseling a patient can be successfully taught in online sessions. However, one must keep this in mind that internalization of attitude requires patient student interaction.25\n\nInteractive online communication and discussion has resulted in improvement in the quality of e-learning among students.26 The technology should be suitable for planning the methodology and content for flexible and effective delivery of concept. The mastery level of students, resource materials and type of content should be kept in mind while selecting an online teaching and learning tool.27 The teaching and learning strategies should align with the learning objectives. All efforts should be exercised to engage the learner with the learning material. The learner can be engaged during online sessions by providing opportunities for online discussion, empowering students for making their own decisions in the activity based learning, promoting joint ownership and decision making among students and teachers.28\n\nBoth synchronous and asynchronous strategies should be used. Some of the most frequently used tools are e-lecture (video podcast),29 case studies & flipped classroom,30 online problem based learning (PBL),26 webinar and video-based instructions.32 Google classroom should be used as asynchronous mode of teaching.33\n\nThe flipped classroom strategy has been used in many places even before COVID-19. This strategy is liked by educationists and students alike. In a flipped classroom session, the activity involves the mixing up of the short presentations, questions and answers, zoom polls, clickers to reinforce and summarize the content previously asynchronously on Google classroom.\n\nThe learner should be engaged with the learning material with a constructive approach. The online constructivist classroom sessions should be based on activity. Use break out rooms or zoom polls to divide class into small groups. This online tool provides collaborative learning via peer interaction and engagement with the task. The facilitator should use the main room periodically to monitor the progress. The task should be highly structured with appropriate length for meaningful engagement with the learning task.34\n\nThe discussion boards are another important tool for an interactive classroom. It helps to address the learner’s issues in real time within the supportive environment. The immediate feedback to the learner would help in solving the problem.\n\nPre-recorded videos have been used for teaching soft skills.35 Videos can either passively present content to learners or actively engage them by asking them to perform in a live online session.\n\nTailor the learning environment according to different learning needs and contexts. An online academic debate and panel discussion by experts can be a good addition to revision and reinforcement sessions. It gives a good platform for case-based discussions, case study or problem. This is particularly effective for clinical clerkship sessions.36\n\nThe effective use of social platforms should be encouraged in developing a sense of classroom community among the students and the teacher. Adding a Twitter badge to the homepage of the course and using hashtags to post relevant information can generate discussion on this important social platform. Similarly, Facebook features can be used for collaborative learning and communication.37\n\nMany studies claim that online and face to face teaching ensures the same outcomes but one has to be skeptical.38,39 The psychomotor and affective domain can only be learned best in the real-life scenarios. The psychomotor skills are taught, acquired, performed, and lastly learned in the face-to-face real settings.40 Similarly, the knowledge component for attitude change, can be acquired online but performance and experience can only be acquired face to face.41\n\nStudents must have adequate exposure of patients to acquire clinical competencies by becoming active participants of the health care team, and also have periods of independent learning in outpatient and inpatient settings.42 Only when students are involved actively with patient care and have the chance to perform, demonstrate, communicate, and empathize will they be able to fully internalize the professional attitude and will therefore be safe to practice.43\n\nAll objectives that require face-to-face interaction should be tabulated with specifications along with instructional strategies. Maximum patient encounter and interaction should be used to consolidate online learning sessions.\n\nTeachers also have to be technologically smart and aware of modern pedagogical approaches. The institute has to ensure a robust faculty development program to make teachers up to date with new advances especially with IT skills and software use. The faculty should devise the activities for effective delivery of content online. The information transfer, resource exploration and collaborative knowledge-creation can be achieved by developing study resources using the mass media. Help the learners via digital simulations for experimental laboratory work. Develop enquiry-based activities like problem-based learning in a blended environment. Prepare hyperlinked documents, audio files, narrated slide shows, interactive image maps and simple interactive games for asynchronous classroom activity.43\n\nThe course materials have to be modified in a suitable format like pdf and posted on learning management system (LMS), Moodle etc. Use digital technology to develop a one stop shop solution to all students’ queries and issues.44 Access to state-of-the-art research laboratories, databases, and libraries may be required for perusing advanced studies and research base projects.45\n\nIn blended teaching it is imperative that assessment is provided to check the depth of students’ learning. Many techniques that are used in face to face can also be used in blended teaching. Online assessment strategies in blended programs include quizzes and tests, assignments, individual and group projects, participation in discussions, and proctored face-to-face midterm and final exams. All methods have strengths and limitations while preparing and administering the courses. Therefore, online and traditional assessment methods are used complementarily to overcome their respective weaknesses. Assessment techniques have to be developed using the same blueprint outline as in conventional teachings. This assessment grid includes objective, domain assessment tools, weightage, number of items and type of assessment (Table 4).\n\nSome studies have shown that the use of e-assessment raised efficiency and quality of assessments especially in clinical settings. The face-to-face assessment is more reliable, valid and free from cheating and intellectual dishonesty. The cheating during assessment can be controlled via an online proctoring system where the student is monitored by the invigilator online; however, this requires faculty training.8\n\nThe goals, standards and criteria should be set and communicated to stakeholders for the online and face to face component of blended learning. Rubrics and criteria for awarding marks and pass/fail should be communicated. Develop a program of assessment for collecting maximum data points for a pass/fail judgment. In case of unstable internet connection the arrangement for remedial sessions of those students who missed the online session should be made and communicated effectively to the students.8\n\nThe continuous assessment can be achieved by recognizing the student’s accomplishment in achieving the competency or performance throughout the session.\n\nUse multiple methods of assessment both for online and face to face tests. The formative assessment should be done using Padlet, Socrative etc.\n\nBlended teaching is more student-centered. The students are responsible for their learning due to the flexible nature of the curriculum as well as the use of technology. The teachers’ relations with students change as students have more control and teachers adopt more facilitative roles.28 A central body, such as a curriculum committee should be responsible for communication of content and mode of delivery. The communication to staff and students should be the responsibility of the working group. There should be proper planning for the material to be communicated to the staff and students. The students should be communicated timetables, study guides, case scenarios for online problem based learning (ePBL), guidelines for e-practical lab sessions as well as for online discussion forums, well ahead of time. The faculty should provide resource materials and associated links well in advance to students. Similarly, instructions and guidelines for online assessment should be communicated in time.\n\nThe time for online and on campus classes should be communicated for smooth execution of the program. The students should also be provided with the contact details of the faculty.\n\nFeedback has been regarded as the best tool for evaluating the ongoing progress of a program. It is ideal to take feedback after every session from both the students and faculty, as this would help in improving the course to achieve the desired objectives. One of the simplest tools for feedback is an online survey. The survey should be developed on the questions meant for evaluation such as students’ interaction and satisfaction, type of e-learning tool and its impact on learning, challenges faced during implementation and suggestions for improvements.\n\nPre and post-test exercises are another effective tool to assess the progress of a course and achievement of objectives. The course should be evaluated during and after the session. Make necessary changes after consulting all the stakeholders. The results of evaluations should be used for developing an improved contingency plan for emergency situations encountered in the future.\n\n\nDiscussion\n\nThe COVID-19 pandemic had compelled medical educationists around the globe to design new methods for teaching and learning. Seminars have become webinars and video calls, with web conferencing systems like Zoom and Microsoft teams becoming the exclusive mode of communication during this pandemic.46 Online learning in medical education may not guarantee the same level of quality of education as on campus study but despite this fact, education needs to be continued. Blended courses have been developed for a number of specialties other than medicine and dentistry. It was an immediate challenge to implement blended learning on account of lockdown restrictions. A challenge bigger than this was to develop a blended curriculum for undergraduate medical curriculum.\n\nThis study was conducted to address the challenge of developing a blended curriculum in undergraduate medical education. For this purpose, a consensus developing technique (nominal group technique) was adapted for designing guidelines for a blended learning curriculum in medical education. In this democratic method all participants have an equal voice in the process and all the responses are bias free due to feedback and discussion. The process can be adapted according to need and focus of study as well as the constraints of study.47 NGT has been used in a wide range of research studies. NGT allows for adaptation and modification without compromising the basic tenets of the process.47 In this study NGT was modified for online development of the guidelines. Adopting the NGT online allows participation from all over the country. It results in generating a rich dataset from diverse faculty members who are involved in developing different types of curricula. Besides providing innovative ideas an online NGT would also help faculty from underdeveloped countries to learn from international faculty with a minimal resource requirement. This can be shown by this study in which there is a plethora of advice from a learned community of experts.\n\nThe goals, aims and objectives of the curriculum are almost similar across the globe due to the suspension of on campus face-to-face activity during the COVID-19 pandemic. Countries have come up with different options and solutions depending upon the resources and the burden of disease. They had prioritized and adjusted accordingly. The aims and objectives define the content to be taught so they are included in the guidelines for the course outline in this study. The objectives of the course were part of the content in another study for developing the curriculum.48 The goal of curriculum development during pandemic is to facilitate the designing and implementation of the curriculum to the emerging education challenges during and after the pandemic.49\n\nIt has also been stated in one study that needs assessment stage for curriculum development also took into account the aims, goals and objectives of the curriculum in relation to the problem addressed.50 Needs assessment has been prioritized as the first guideline for developing the blended curriculum in this study. It identifies the actual barriers and problems related to planning a curriculum. The needs assessment not only defines the aims and goals but it also delved into resources required for the curriculum implementation.51\n\nGuideline number two and three about blended learning content and teaching and learning strategies is a must for any type of curriculum. All the experts stress upon the careful selection of content and alignment of learning outcomes with teaching and learning strategies. The blended learning environment should be planned in a pedagogically sound manner for face-to-face and online teaching, representing the best attributes of both learning environments.52 The teaching and learning activities should fit in well with the students characteristics, technology quality, online tools and face to face environment.53\n\nThe guideline for developing the effective resources called for overcoming the barriers in terms of cost and training of faculty and students in technology enhanced blended learning environment.9 In this study all the parameters integrating technology in a blended environment for medical education were discussed. The experts had consensus on faculty training and students training for using the digital technology for teaching and learning. Instead of developing the teaching and learning resources from scratch the medical institutions should invest in already available digital learning resources.54 It is advisable that same platforms, tools and setting should be used for training the students and faculty.9\n\nWhile developing the guideline for assessment blue print all the experts were aware of the basic principle that the learning objectives, and teaching and learning strategies should align with formative and summative assessment.9 The experts of this study stressed the effective use of technology by the students and faculty. All the basic principles for making a valid and reliable assessment be ensured as well, they added.\n\nThe guideline for implementation called for addressing the challenges and their emerging responses for curriculum success. Every effort should be exercised to deliver the curriculum in a safe environment. The barrier for successful implementation of blended curriculum lies with the technology for information and communication, simulation modeling technology, faculty readiness and acceptance by the students.55\n\nThe last guideline for curriculum evaluation mandated that curriculum should be evaluated during and after the course for formative and summative evaluation.23 Apart from this, blended curriculum should be holistically evaluated including the satisfaction of students and faculty. It should include the feedback from all the stakeholders9,39\n\nThe strength of this study is generating a wide range of ideas on a single problem, prioritizing and final selection of ideas through an anonymous democratic method. All the participants of this study had acknowledged that their opinions and suggestions were given importance in developing the guidelines. There had been an equal opportunity to participate. The non-hierarchical participation reduces influential bias and helped in collecting a rich data. Another strength was that all the participants were working from home due to pandemic, so they were available at a flexible time period.\n\nWeaknesses of the nominal group method is that it addresses a single problem., and the small sample size can affect the validity of results as one random vote can alter the overall ranking of the guidelines.47\n\nThis study promotes sharing experiences and experimenting with new pedagogies which may assist in adopting the digital technology. This study would also provide the useful guidance for transforming the curriculum for such emergency situations in the future.\n\n\nConclusion\n\nThe shifting of on campus medical education to online owing to the COVID-19 pandemic posed a great challenge to institutions and stakeholders in medical education. It requires a comprehensive and systematic approach to address this challenge. Blended learning in medical education is not an ideal strategy to follow but will preserve the academic sessions of students. The practical sessions can be conducted by strict compliance with standard operating procedures on campus. All stakeholders of the system are required to follow the guidelines in true essence to achieve the desired outcomes.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: Paradigm shift in medical education due to the COVID-19 pandemic: guidelines for developing a blended learning curriculum in medical education. https://doi.org/10.5281/zenodo.5802622.56\n\nThis project contains the following extended data:\n\n• CONSENT___Instructions_to_experts_.docx\n\n• Draft_Guidelines_prepared_by_experts.docx\n\n• README_file.docx\n\n• Scores_and_ranking_of_guidelines.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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}
|
[
{
"id": "126341",
"date": "06 Apr 2022",
"name": "Naushaba Sadiq",
"expertise": [
"Reviewer Expertise Educational research ."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is written to address the global issue of the closure of medical schools resulting from the COVID-19 pandemic. The guideline will be helpful in establishing a blended learning program.\nSummary of Article; As a result of the challenges faced, the author has conducted this study to develop a guideline with the help of seven experts and nominal group technique. In phase one experts worked independently and developed guidelines. In phase 2, after discussion among the experts in the presence of a moderator, 2 sets of guidelines were developed and 2 pre-existing sets of guidelines for curriculum development available in the literature were considered for the next phase of this study.\n\nDuring the third phase, the set of guidelines that ranked highest on a scale of 1-5 was selected as a final guideline for developing a blended learning curriculum. This guideline has 7 items/tips for developing a blended curriculum.\n\nReview report;\nIs the rationale for developing the new method (or application) clearly explained? Response; Partly Are sufficient details provided to allow replication of the method development and its use by others Response; Partly\n\nJustification of the above two points;\nIn methodology, some terminologies are used interchangeably which can cause confusion in the mind of the reader. for example guideline ideas, guidelines, set of guidelines, and in the end seven guidelines. The statement \"There were ten, seven, six and six guidelines in sets number one (Harden), two, three and four (Kern) respectively (Table 2)\" is not clearly understood.\nIt is suggested that in phase one guidelines were developed by experts independently. In phase two, two sets of guidelines were developed and 2 sets were adopted from literature. In phase three, 4 sets of guidelines were considered. The terminology of \" Number of items or tips \" in each set of guidelines can be used to give the details of each guideline.\n\nAs mentioned above, amendment is required in the statement mentioning \" After the consensus of the experts four sets of guidelines were developed for the third phase\" Two sets of guidelines (Harden and Kern)were included in the study from the literature. Please give reference to the statement mentioned in the result section \"It was discussed that SPICES model given by Harden14 as an educational strategy is for exclusive for on campus delivery of curriculum in medicine. It cannot be applied to blended learning because the social and emotional component in blended learning is not same as in full on-campus curriculum in medicine.\"\nIt is stated that \"we developed a set of guidelines utilizing the theoretical framework, complex adaptive blended learning system (CABLS). The main framework is organized around the learner support, the teacher, the content and technology and the institution (Figure 1).\" The actual CABLS has six elements that are not overlapping, in this study five elements are used with repetition of items i.e. Assessment.\n\nIn the section of Develop a course outline \"Alignment between the components of curriculum helps to determine when, where, and how the outcomes will be achieved.\" In the final guideline, the tip/item on outcome is not included. In my experience, it is a very important point that must be included in any guideline.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Partly\n\nAre sufficient details provided to allow replication of the method development and its use by others? Partly\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
},
{
"id": "144319",
"date": "16 Aug 2022",
"name": "Noor Akmal Shareela Ismail",
"expertise": [
"Reviewer Expertise Medical Education"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for sharing your write-up regarding the guideline for a blended medical curriculum. I think this manuscript has highlighted the conduct of developing a guideline with several medical educationists to assist other lecturers/administration with a novice experience in medical education.\n\nSince I have a medical education background, I am judging the guideline based on my experience. However, the write-up is a formal narrative of what other people have done elsewhere and the novelty is not something the authors can sell. Almost every institution in the world is adapting to a blended curriculum and all have agreed to test the psychomotor (and affective) skills is difficult as compared to cognitive. But, teachers, as well as learners, do adapt. The practicality is much depending on the resources, strengths, and weaknesses of one's institution.\n\nTherefore, I would agree this write-up can assist other institutions to embark on a fully blended medical curriculum. Apart from the typo in Fig 1, I have no issue with the narrative throughout the text, except there was a repetition in one of the earlier paragraphs. I would strongly suggest the authors summarize the methodology in a figure so a non-medical education background can digest the wordings better.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Partly\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-37
|
https://f1000research.com/articles/11-1148/v1
|
07 Oct 22
|
{
"type": "Research Article",
"title": "Aspergillus oryzae attenuates quorum sensing -associated virulence factors and biofilm formation in Klebsiella pneumoniae extended-spectrum beta-lactamases",
"authors": [
"Lailia Nur Rachma",
"Loeki Enggar Fitri",
"Sumarno Reto Prawiro",
"Tri Yudani Mardining Raras",
"Lailia Nur Rachma",
"Loeki Enggar Fitri",
"Sumarno Reto Prawiro"
],
"abstract": "Background: Klebsiella pneumoniae communicate between and among species using quorum sensing (QS). Biofilm formation and virulence factors are regulated by QS. This QS is indirectly responsible for K. pneumoniae pathogenicity. Inhibiting QS is a novel and highly effective method for controlling K. pneumoniae extended-spectrum beta-lactamases (KP-ESBL) infections. This study aimed to investigate how Aspergillus oryzae extracellular protein (AOEP) affected QS and KP-ESBL virulence factors. Methods: Methods used included minimal inhibitory concentration (MIC) through the microdilution method, biofilms with crystal violet staining, extracellular polysaccharides using the Congo Red assay, quantifying the expression of genes coding for capsular polysaccharide (wzI gene) and adhesion (mrkA gene) through quantitative reverse-transcription polymerase chain reaction (RT-qPCR), siderophore level measurement using Chrome Azurol sulphonate assay (CAS assay), biofilm morphology using a scanning electron microscope (SEM), and confirmation using the life span killing assay method on Caenorhabditis elegans (C. elegans). Results: In vitro studies revealed that AOEP inhibited biofilms and exopolysaccharides (EPS) in KP-ESBL at the sub-MIC level. In addition, AOEP inhibited the expression of the mrkA gene, which is involved in the adhesion process. Furthermore, an in vivo study revealed that AOEP levels of 75 and 150 µg/mL respectively increased C. elegans survival rates by 72.67% and 80.76% against K. pneumoniae infection. Conclusions: Our findings suggest that the extracellular protein of A. oryzae may be an effective QS inhibitor and a novel anti-virulence agent to control bacterial pathogens.",
"keywords": [
"A. oryzae",
"QS",
"Virulence factors",
"Biofilm",
"KP-ESBL."
],
"content": "Introduction\n\nThe severity of infectious diseases caused by bacterial strains that are resistant to treatment has made their advent a global problem today, including Klebsiella pneumoniae extended-spectrum beta-lactamases (KP-ESBL).1 KP-ESBL can hydrolyze beta-lactam antibiotics in addition to producing biofilms that hinder medications from penetrating cells.2 Biofilms comprise an extracellular matrix (polysaccharides, proteins, and extracellular doxyribonucleic acid [DNA]) that acts as a strong barrier for bacteria and makes them more resilient to environmental stress than planktonic cells.3 Additionally, biofilms aid KP-ESBL in spreading the infection and provide an environment that fosters the development of antibiotic resistance.4–6 Finding novel compounds that can suppress KP-ESBL virulence factors and biofilms is therefore urged in order to assist in fighting these bacteria.\n\nQuorum sensing (QS) molecules, adhesion molecules, iron, and exopolysaccharides (EPS) can affect the formation of biofilms.7–9 Because QS is a regulator for the expression of capsule polysaccharides, the development of this biofilm is inversely related to the polysaccharide capsule's virulence factor.10 It is now crucial to find antibiofilm and antivirulence chemicals, especially those derived from natural sources. Biofilms have been shown to be inhibited by bioactive substances obtained from nature.11–14\n\nAspergillus sp., a filamentous fungus, is well known for its potent antibacterial properties.15–17 Inhibition of virulence factors and direct harm to the K. pneumoniae are known antibacterial mechanisms of Aspergillus sp. However, little is known about Aspergillus sp ability's to combat KP-ESBL biofilms. Our preliminary research proves Aspergillus crude protein which has the greatest biofilm inhibition is Aspergillus oryzae extracellular crude protein (AOEP). The aim of this study was to evaluate any potential antibiofilm properties of Aspergillus oryzae extracellular protein against KP-ESBL.\n\n\nMethods\n\nKP-ESBL (ID.100029) were obtained from the Laboratory of Microbiology, Faculty of Medicine, Brawijaya University, Malang, Indonesia. Luria Broth (LB) medium was used to cultivate the KP-ESBL strain, which was then incubated at 37°C for 16–18 hours. Sterile saline was diluted 100 times after being equalized with the Mc. Farland standard to produce a concentration of 106 CFU/mL. This bacterial suspension was then ready for testing. The fungal strain Aspergillus oryzae was provided by the Indonesian Culture Collection (Ina-CC). Preparation of Aspergillus oryzae begins with sub-culture and preservation of previously isolated Aspergillus oryzae. Sub-cultures were carried out from cryo to Luria Bertani solid medium. The culture was then treated in the form of H2O2 and without glucose, then stored at 37°C in an incubator. The nematode Caenorhabditis elegans was maintained on agar medium for nematode growth media (NGM) fed with Eschericia coli OP50. Gravid C. elegans were treated with hypochlorite to synchronize C. elegans culture at the first larval stage. Before being employed for infection, the C. elegans were then reared at 25°C until they reached the young adult stage.\n\n100 mL of potato dextrose broth (PDB) medium were inoculated with 8-mm (diameter) Aspergillus oryzae mycelium and placed in a 250 mL Erlenmeyer flask containing 2% glucose. The flask was incubated for 72 hours at 27°C in a shaker incubator under static conditions (OD600 = 1.2). The culture was filtered using 0.22-micron filter paper after incubation (Whatman, Sigma Aldrich). As a source of extracellular protein, the supernatant was centrifuged at 12.000 rpm for 15 minutes at 4°C. Ammonium sulfate was used to precipitate extracellular proteins at saturation values of 80%. After one hour of stirring in the ice bath, ammonium sulfate was added to the supernatant. The crude protein extract was centrifuged at 4°C for 15 minutes at 12,000 rpm the next day after being maintained at 4°C overnight. After that, the complete protein precipitate underwent a twenty four hour-dialysis in a 0.01 M phosphate buffer at pH 7 using a 10×-sample volume. After that, the Aspergillus oryzae extracellular protein (AOEP) was prepared for the assay.\n\nA growth inhibition test was conducted using microdilution broth. Briefly, fresh cultures were inoculated on LB medium at turbidity equivalent to 0.5 McFarland standard, 500 μL of each bacterial culture were added to a 96-well polystyrene flat-bed microtiter plate. The samples were added to the bacterial suspension in each well at final concentrations ranging from 0 to 150 g/mL. The growth control wells only contained bacteria on LB media and kanamycin as positive control. Double serial dilution of the Aspergillus oryzae extracellular protein (AOEP) tested sample was made starting from the first well by adding 50 μL of the tested sample, dissolved at 150 μg/mL. After incubation at 37°C for 24 hours, the absorbance was measured at 600 nm. The lowest absorbance value of the sample that could reduce more than 90% of the absorbance of the negative control was recorded as the MIC value. All experiments were performed in triplicate. Minimum bacterial concentration (MBC) for each sample was calculated by coating the contents of the first three wells, which showed no visible bacterial growth on the LB plate, and incubated for 24 hours.\n\nThe test well on a 96-well microplate received a total of 100 μL of Aspergillus oryzae extracellular protein (AOEP) at various concentrations (18.75, 37.5, 75, and 150 μg/mL). The negative control wells received 200 μL of mixed LB media and 1% glucose, while the positive control wells received 64 μg/ml of kanamycin. Each well was then filled with 100 μL of the KP-ESBL suspension. For 24 hours, the microplate was wrapped and kept at 37°C in an incubator. The microplate's contents were taken out the following day, thoroughly cleaned with sterile distilled water three times, and then dried. 200 μL of 0.1 % crystal violet dye was added to each well once the microplate had dried, and it was air dried at room temperature for 15–20 minutes. The microplate's contents were then cleaned with sterile distilled water and dried. After 15 minutes of incubation at room temperature, 200 μL of a 96% ethanol solution were added to each well, and the results were measured at 570 nm with a microplate reader.\n\nBiofilm growth inhibition was calculated using the following formula:\n\n(OD Control = Optical density control negative. OD Test = Optical density test)\n\nVisual evaluation of AOEP's impact on KP-ESBL morphology was conducted using a scanning electron microscope (SEM, model Zeiss 224 EVO 50 VP, Germany). KP-ESBL bacteria were cultivated in LB broth and incubated for 24 hours in an aerobic environment at 37°C. A 1-mL volume of the bacterial suspension was obtained and treated with AOEP for two hours once it reached around 1×108 CFU/ml. Another 1 mL sample was taken from the culture and left untreated. These two bacterial samples were centrifuged after two hours for three minutes at 1400 rpm, and the pellets were then cleaned twice with 0.1 M phosphate buffer saline (PBS). KP-ESBL cells were exposed to 2.5% glutaraldehyde for two hours at 4°C for the SEM analysis. Samples were exposed to each concentration after fixation for one to two minutes in order to dehydrate them. The samples were then centrifuged at 1400 rpm for 10 min, after which the pellets were re-dispersed in 100% ethanol and air dried. The samples were coated with gold and palladium in an 80:20 ratio prior to examination under SEM at 20 kV. The working magnification was kept at less than 10 mm for better focusing.\n\nCultures of bacterial isolates left overnight were inoculated to 9.5 mL of LB broth along with 0.5 mL of cell lysate and incubated at 30°C for 24 hours. The late-log phase cells attached to the test tube walls were harvested by centrifugation at 8500 rpm for 30 min at 2°C. The filtered supernatant was added with three volumes of cold ethanol and incubated overnight at 2°C to precipitate the released EPS. The precipitated EPS were then collected by centrifugation at 5000×g for 30 min and dissolved in 1 mL of deionized water. Enzyme-free media culture added with PBS served as a control. The bacterial cells were removed, resuspended in sterile PBS, and read at 600 nm. The collected EPS was quantified using the phenol-sulfuric acid method.\n\nSimilar to the anti-infection screen, the liquid-based survival test was carried out with a few minor adjustments. A total of 30 young adult C. elegans were used in place of the N2 young adults that received treatment. As a result, the C. elegans were kept at 16°C to create gravid C. elegans, and they were given a hypochlorite treatment to develop eggs. In order to conduct an infection assay, eggs were sown on NGM agar and developed into sterile young adults of C. elegans at 25 °C. Every four hours following infection, both alive and dead C. elegans were counted. Each extract was examined in three wells, each representing about 100 C. elegans. In control wells, dimethyl sulfoxide (DMSO) was used in place of the extract, and Escherichia coli OP50 were fed. To examine the impact of AOEP on KP-ESBL pathogenicity to C. elegans, we performed a slow-killing survival experiment. On a 48-well microplate, KP-ESBL were first cultured for an overnight period at 37°C in the presence of AOEP (18.75, 37.5, 75, and 150 μg/mL). When 100 sterile young adult C. elegans were put into the well, the infection began. KP-ESBL was given DMSO treatment as a negative control in place of AOEP. After 48 hours, the C. elegans that were still alive were counted under microscope with a magnification of 100×.\n\nThe hot phenol method was used to extract total ribonucleic acid (RNA), where the DNA was removed using TURBO DNA-free (Ambion, Inc.), and the RNA quality was determined using a NanoDrop (ND-1000; Thermo Scientific) and an Agilent 2100 bioanalyzer with a Picochip (Agilent Technologies). After 35 qPCR cycles, the absence of contaminating DNA was determined by the absence of amplification products. A 1 μg of RNA, random hexamer primers (0.2 μg/L), and M-MulV-RT (20 U/L, Moloney murine leukemia virus reverse transcriptase; Thermo Fisher Scientific) were used to synthesize cDNA. Specific primers for mrkA 5′-CGGTAAAGTTACCGACGTATCTTGTACTG-3′, and wzI 5′-GCTTAYGCRGCYGGGTTAGTRGT-3′ designed with the Primer3Plus software (Primer3Plus is an open alternative). A master mix of the following components was prepared for light cycler reactions: 3.0 mL PCR-quality water, 1.0 μL (10 M), 10 μL 2× SYBR Green I Master Mix, 10 μL reverse primer, and 5.0 μL cDNA (50–100 ng). A multi-well plate was sealed with sealing foil, centrifuged for two minutes at 1500 g, and loaded into the LightCycler 480 instrument (Roche). For each sample examined, amplification was carried out in triplicate wells. All reactions had control reactions with no template (water) and minus-reverse transcriptase (RNA). Cycling conditions were as follows: denaturation (95°C for 10 minutes); amplification and quantification repeated for 45 cycles (95°C for 10 seconds, 57°C for 20 seconds, 72°C for 30 seconds with a single fluorescence measurement); melting curve (95°C for 10 seconds, 65°C for one minute with continuous fluorescence measurement at 97°C); and finally, a cooling step at 40°C for 10 seconds. After each run, a melting curve analysis was performed to confirm the specificity of the primers. For normalization, 16S rRNA was used as a reference gene, and relative gene expression was calculated using the 2Ct method.\n\n\nResults\n\nThe antimicrobial activity of AOEP was quantitatively assessed by measuring the turbidity at a wavelength of 600 nm. The results in Figure 1 represent crude proteins’ MIC and MBC values in various concentrations with kanamycin as positive control. The concentration of AOEP, which could inhibit > 90% of the bacterial population, represented MIC and was 300 μg/mL. The concentration used in the growth inhibition test of antibiofilm activity was sub-MIC, namely at 1/8 and 1/16 × MIC. This study used a 64-μg/mL dose of kanamycin as a positive control.\n\nMIC at a concentration of 300 μg/mL was 92.74% (bold). Kanamycin as a positive control, was only able to inhibit KP-ESBL 78.51%. The negative control of KP-ESBL without AOEP exposure was 0%. Bars indicate the standard error, and the sign (*) above the bars indicates a significant difference (p < 0.05).\n\nThe highest concentration used for the AOEP inhibition test against KP-ESBL biofilms was 150 μg/mL, which was the MIC (p-value < 0.05). The Tukey Post Hoc test showed that there were significant differences between the overall treatment group and the negative control. The linear regression test results showed a R-value of 0.797, reflecting that AOEP could inhibit the growth of KP-ESBL in a dose-dependent manner. Furthermore, measurement of the inhibitory ability of biofilms and virulence factors used sub-MIC concentrations of 1/8 and 1/16 MIC, there were 18.75, 37.5, 75, and 150 μg/mL.\n\nThe microdilution method was used to test the inhibitory activity of the AOEP biofilm against KP-ESBL. Figure 2 displays the AOEP biofilm's inhibitory efficacy against KP-ESBL.\n\nInhibitory effect of AOEP on biofilms after co-incubation for 24 h with different concentrations of AOEP. The concentration of AOEP is given relative to MIC KP-ESBL. The AOEP biofilm inhibition concentrations of 18.75, 37.5, 75, and 150 μg/mL were 32.94%, 39.17%, 68.14%, and 72.18%, respectively. Bars indicate the standard error, and the sign (*) above the bars indicates a significant difference (p < 0.05).\n\nInhibitory effect of AOEP on cell-free exopolysaccharide KP-ESBL after being incubated together for 24 hours with different concentrations: 18.75, 37.5, 75, and 150 g/mL. Bars indicate the standard error and the sign (*) above the bars indicates a significant difference (p < 0.05). KP-ESBL\n\nAOEP was administered relative to the MIC. The MIC value of the K. pneumoniae strain was 300 μg/mL, so the highest concentrations for the anti-biofilm test were 1/8, 1/16 MIC. The biofilm inhibition value [100-(sample ABS/control ABS × 100)] for each AOEP concentration can be seen in Figure 2. In the crystal violet staining assay, KP-ESBL biofilms were significantly inhibited at concentrations of 1/4 × MIC (75 μg/mL) and 1/2 × MIC (150 μg/mL) (p < 0.05). Interestingly, AOEP inhibited biofilm formation at concentrations below the MIC. The ability of AOEP to inhibit biofilm formation in KP-ESBL exceeded the ability of the kanamycin (69.46 μg/mL and 37.9 μg/mL). The positive control had a biofilm inhibitory value of 37%, which was lower than the AOEP biofilm inhibitory level of 150 and 75 μg/mL. The negative control (KP-ESBL bacteria without AOEP exposure) showed the lowest biofilm inhibition value (0), which indicated that biofilm production was not inhibited at all. When administering the four concentrations of AOEP, the resulting OD value decreased significantly as the dose increased when compared with the OD of the negative control. This indicates AOEP inhibition of the KP-ESBL biofilm. Tukey test results indicated that there were significant differences between the overall treatment group against the negative control. The linear regression test results show that the R-value (0.957) that represented AOEP could inhibit the growth of KP-ESBL biofilm in a dose-dependent manner.\n\nThe assay was performed to test the ability of AOEP to reduce cell-free exopolysaccharide KP-ESBL.\n\nKP-ESBL treated with AOEP 150 μg/mL could reduce the bond matrix with Congo Red dye by as much as 49% after staining and assessment with a spectrophotometer. As the dose of AOEP was reduced (75 μg/mL, 37.5 μg/mL, 18.75 μg/mL), its inhibition ability decreased (42%, 38%, 37%). Cell-free EPS might be reduced by 19% using AOEP 150 μg/mL and it surpassed the kanamycin (30 %). There was a significant difference, according to the one way ANOVA test (p-value < 0.05). The results of the Tukey Post Hoc test revealed that the overall treatment group and the unfavorable control group differed significantly. The findings of the linear regression test indicated that AOEP might inhibit the cell-free EPS KP-ESBL in a dose-dependent manner, and the R-value for this test was 0.896.\n\nThe delta-delta Ct method (2 DDCt) was used to quantify RT-qPCR results. Results are represented as “Target/adh3 fold change.” The results of gene expression analysis via RT-qPCR (Figure 4) showthat AOEP downregulated the gene expression for fimbriae mrkA, which acts as an adhesion molecule. Meanwhile, capsular EPS as measured by the wzI gene expression was increased.\n\nThe expression of these two genes was measured in response to AOEP: mrkA (type 3 fimbrial shaft) and wzI (surface assembly of capsule). The expression of the adh3 house-keeping gene was used as an internal control for each sample. The concentration of AOEP treatment was 150 μg/mL, while the control group was KP-ESBL without AOEP exposure.\n\nThe impact of AOEP on cellular alterations was examined using SEM analysis. To supplement the information of the quantity of the biofilm, observation of the architecture of the biofilm mass using SEM was conducted. The impact of AOEP on the KP-ESBL biofilm structure was demonstrated by SEM data (Figure 5).\n\nK. pneumoniae biofilms grew after incubation for 24 hours. AOEP was added with different concentrations: 150 μg/mL (B), 75 μg/mL (C), 37.5 μg/mL (D), 18, 75 μg/Ml (E) Positive control with the addition of the Kanamycin (F).\n\nThe negative control group showed bacterial colonies along with thick biofilms evenly distributed on the adhesion surface (Figure 5A). This was different from when the bacteria were treated with the 150 μg/mL AOEP (Figure 5B), the cells failed to aggregate, and there was a highly significant decrease in biofilm mass. In this group, the bacterial colonies were separated and became planktonic bacteria, and the adhesion surface was free of bacterial biofilms. Biofilm mass was also decreased in the AOEP 75 μg/mL (C) group, while the positive control group (Kanamycin, F) showed partial inhibition of the KP-ESBL biofilm. It can be seen that the biofilm structure of KP-ESBL was impaired due to the addition of AOEP when compared to the control. The control group was KP-ESBL which was not exposed to AOEP, as shown in Figure 5A. When bacteria stick together, the attachment of bacteria is more clearly facilitated by a thick mass of biofilm surrounding the bacterial colony. In this group, the biofilm appeared to cover all bacterial colonies on the surface of the adhesion medium. This appearance differed significantly from the group treated with 150 μg/mL of AOEP (Figure 5B) provides a clearer picture of the dispersal in the bacterial colonies treated with AOEP reflecting the impair the biofilm. The inhibition of biofilm mass formation in the group exposed to AOEP at a dose of 75 μg/mL (Figure 5C) also shows that the bacterial colony dispersed. However, the number of bacteria was higher than for a concentration of 150 μg/mL. At an AOEP dose of 37.5 μg/mL (Figure 5D), it was seen that some bacteria were separated, and some bacteria were attached (left). At 10000× magnification, a biofilm mass began to surround the bacteria and facilitated adhesion between bacteria and the adhesion medium.\n\nMeanwhile, at the lowest concentration of AOEP, a dose of 18.75 μg/mL (Figure 5E), the presence of a thick biofilm was seen that matched the negative control. Interestingly, the sub-MIC ability of AOEP to reduce biofilm mass formation produced stronger effect than the kanamycin (Figure 5F). Overall, SEM results showed the highest reduction in biofilm mass formation occurred with a treatment of AOEP 150 μg/mL, which had a stronger effect than the kanamycin. These results indicate that AOEP can be used as a candidate antibiofilm agent at concentrations lower than MIC, especially against biofilm formation by KP-ESBL.\n\n\nAOEP increased survival rates of C. elegans when challenged against KP-ESBL\n\nTo observe the effect of AOEP on the infection caused by KP-ESBL, an in vivo study was conducted on C. elegans.\n\nFigure 6 shows the percentage of C. elegans survival after 48 hours of exposure to KP-ESBL. Only about 4% of C. elegans infected with KP-ESBL survived up to 48 hours, while C. elegans exposed to E. coli OP50 88% survived until the end of the test. Surprisingly, the C. elegans that were exposed to AOEP and KP-ESBL (18.75, 37.5, 75, and 150 μg/mL) had significantly increased survival rates (17 – 68%) compared to the group of C. elegans that were only infected with KP-ESBL. The highest survival was in the 150 μg/mL group (68.25 ± SD 4.6). the one-way ANOVA test showed that there was a significant difference between negative control and treated groups (p-value < 0.05). The linear regression test results showed the R-value was 0.958. The analysis showed that AOEP could reduce the ability of KP-ESBL to infect C. elegans in a dose-dependent manner. Figure 7A shows the propidium iodide fluorescence micrograph of C. elegans (10× magnification) and infected with KP-ESBL. The C. elegans showed negative PI fluorescence when cultured under standard conditions with OP50 as a food source. There was an increase in the fluorescence intensity of propidium iodide when the C. elegans were infected with KP-ESBL and treated with AOEP (Figure 7B). The results of the in vivo survival assay showed that AOEP was able to reduce the virulence of KP-, which could be observed from the increased survival of C. elegans that were infected with KP-ESBL.\n\nThe graph shows the percentage survival rates when the test was carried out without exposure to AOEP with four different concentrations. KP-ESBL without AOEP was a negative control, while KP-ESBL with Escherichia coli OP50 (non-pathogenic) was a positive control. Results are expressed as mean ± SD.\n\n(A) C. elegans infected with KP-ESBL without AOEP administration. (B) C. elegans infected with KP-ESBL with AOEP administration. Propidium iodide fluorescence micrograph of C. elegans (100× magnification). C. elegans infected with KP-ESBL without AOEP died and showed positive red fluorescence when cultured (increased fluorescence intensity of propidium iodide indicated the death of the nematode parasiteof C. elegans).\n\nA liquid chromatography-mass spectrometry LC-MS/MS study against AOEP was carried out in order to identify the A. oryzae molecule that contributes to KP-ESBL virulence and biofilm suppression. The results were displayed as a chromatogram, which showed the peak height and molecular weight of the sample substance. Figure 8 and Table 3 show the outcomes of the LC-MS/MS study.\n\nIn order (from top to bottom), 3-oxo-C6-HSL, 3-OH-C6-HSL, C10-HSL, NHQ, NQNO, 3-OH-C12-HSL.\n\nThe chromatograms showed a number of substances with various peaks and molecular weights. Six compounds had prominent and high peaks (Figure 8). Based on the precursor ion (m/z), ion product (m/z), cone voltage, and impact energy, the six peaks were identified. The six peaks contained substances with properties resembling those of the QS substance K. pneumoniae. The six substances were NHQ, NQNO, 3-OH-C12-HSL, 3-oxo-C6-HSL, and C10-HSL. The six compounds were found to match the typical precursor parameters 3-oxo-C6-HSL, 3-OH-C6-HSL, C10-HSL, NHQ, NQNO, and 3-OH-C12-HSL (see Table 1).\n\n* The inhibitory effect of AOEP on cell-free EPS of KP-ESBL after incubation for 24 hours with different concentrations of AOEP exhibited inhibitory effect on cell-free EPS of KP-ESBL after incubation for 24 hours. The reduction of cell-free EPS by AOEP at concentrations of 18.75, 37.5, 75, and 150 μg/mL was 31.93%, 34.53%, 40.11%, and 48.08%, respectively. The kanamycin was only able to reduce 19.38% of cell-free EPS, while the negative control of KP-ESBL without AOEP exposure was 0%. The inhibition value of cell-free EPS by AOEP was better than that by kanamycin (48.08% versus 19.38%).\n\n* p < 0.001 showed a significant difference in the percentage of survival rates among C. elegans not exposed to AOEP and those exposed to AOEP 150 μg/mL.\n\nQSSM: quorum sensing-like molecule.\n\n\nDiscussion\n\nThe antibacterial ability of antibiofilm derived from natural sources can come from the production of enzymes, the formation of secondary metabolites or compounds that inhibit QS signals.18 QS inhibition can be mediated by receptor antagonists or quorum quenching enzymes.19 In this study, we searched for QS inhibitor compounds derived from the fungus A. oryzae. A. oryzae was harvested at a stationary phase in order to obtain the dominant secondary metabolite.20 A. oryzae produces secondary metabolites, such as asperfuranon, aspyridone, penicillin, isocoumarin, aspercryptin, and indole diterpene.21 However, from the LC-MS/MS analysis, we did not find any secondary metabolites or quorum quenching enzyme compounds from A. oryzae. This result is different from the LC-MS analysis from extract of A. meleus that produce AHL acylase, which can inhibit P. aeruginosa biofilms.22 In another study, A. niger produced cellobiose dehydrogenase which reduced the biofilm of Gram-negative bacteria.23\n\nWe discovered three new substances that are similar to the QS molecules of Gram-negative bacteria, which is interesting because we did not uncover secondary metabolites or quorum quenching enzymes. We propose those molecules, i.e., C10-HSL, 3-oxo-C6-HSL, 3-OH-C6-HSL and suggest them as QS molecules because, despite the fact that the three chemicals resemble the QS molecules found in Gram-negative bacteria, their activity is inversely related. We believe that A. oryzae’s QS molecules function as a competitive adversary. When it comes to attaching to AHL binding sites in LuxR, QS molecules compete with native AHL. One of the genes regulated by QS, the biofilm-encoding gene, is downregulated as a result of QS molecules binding to LuxR. According to this investigation, AOEP significantly reduced the KP-ESBL bacterial biofilm (74.24%). Aside from preventing the growth of biofilms, AOEP has also been demonstrated to lower EPS levels. EPS make up a robust biofilm matrix.3,22,24 The decrease in EPS synthesis was consistent with the structure of the KP-ESBL biofilm as determined by SEM. In the presence of AOEP, the bacterium cells were unable to aggregate. The matrix that holds bacteria together was also obviously thinner. Therefore, the absence of QS barriers may be the cause of the decline in biofilms. QS inhibitors (QSI) function by obstructing the binding sites for autoinducers. It also interferes with the formation of pili types 1 and 3 and cyclic diguanylate mono phosphate (c-di-GMP).25 As a result, QSI's inhibition will cause the expression of pili types 1 and 3 to be suppressed. Our findings are consistent with this notion. After exposure to AOEP, the expression of the pili type 3 gene (mrkA) was significantly reduced. This suggests that AOEP include QSI, which lowers mrkA expression. Sadly, there is no research to support our findings.\n\nThe expression of the wzI gene was assessed in order to support the mechanism through which AOEP inhibits KP-ESBL QS. Because QS controls the formation of capsular polysaccharides (CPS)10,26,27, inhibiting QS will impair its regulator role and cause the CPS to continue to be produced.26 The administration of AOEP in this investigation had no effect on the excretion of CPS by KP-ESBL. Through QS inhibition, it was discovered in this work that AOEP has antibacterial and antibiofilm activities against KP-ESBL. Because it synergistically reduces the expression of numerous virulence factors controlled by QS, QS inhibition in KP-ESBL is particularly helpful in the management of pneumonia.19\n\nWe chose C. elegans as a model because it is ideal for assessing QS inhibitors in order to further examine the therapeutic potency of AOEP on the infection caused by KP-ESBL. AOEP showed antibacterial and anti-QS action against KP-ESBL in in vitro experiments. The protective effect of AOEP against K. pneumoniae infection on C. elegans lends weight to these findings. The survival of infected C. elegans was generally increased by AOEP. We verified the anti-QS activity of AOEP in our investigation. Results from the C. elegans pneumoniae infection model demonstrate how AOEP can successfully reduce virulence by obstructing KP-QS ESBL's activity in in vitro investigations. It is possible to create new medicines for infectious diseases using K. pneumoniae QS inhibitors.\n\n\nConclusions\n\nThis study showed that the extracellular protein of A. oryzae posseses antimicrobial and antibiofilm activity against KP-ESBL. QSI is an AOEP compound that inhibits QS and degrade biofilms, EPS, and mrkA (type 3 pili). AOEP could protect C. elegans from KP-ESBL infection. AOEP is a potential source of natural antibiofilm agents against KP-ESBL.\n\n\nData availability\n\nFigshare: Aspergillus oryzae attenuates quorum sensing -associated virulence factors and biofilm formation in Klebsiella pneumoniae extended-spectrum beta-lactamases raw data, https://doi.org/10.6084/m9.figshare.20290929.28\n\nThis project contains the following underlying data:\n\n- Biofilm inhibition.xlsx\n\n- c. elegans survival rates.xlsx\n\n- Exopolysaccharide.xlsx\n\n- Minimum Inhibitory concentration.xlsx\n\n- qRT-PCR.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe thank the Central Laboratory of Biomedik, Brawijaya University particularly to Suci Megasari for technical assistance.\n\n\nReferences\n\nPaczosa MK, Mecsas J: Klebsiella pneumoniae: Going on the Offense with a Strong Defense. Microbiol. Mol. Biol. Rev. 2016; 80(3): 629–661. PubMed Abstract | Publisher Full Text\n\nHaghighifar E, Norouzi F, Kamali DR: Molecular detection of Extended-Spectrum β-lactamases (ESBLs) and biofilm formation in uropathogen Klebsiella pneumoniae in Iran. Med. J. Islam Repub. Iran. 2021; 35. PubMed Abstract | Publisher Full Text\n\nYin W, Wang Y, Liu L, et al.: Biofilms: The Microbial “Protective Clothing” in Extreme Environments. Int. J. Mol. Sci. 2019; 20(14): 3423. PubMed Abstract | Publisher Full Text\n\nOleksy-Wawrzyniak M, Junka A, Brożyna M, et al.: The in vitro Ability of Klebsiella pneumoniae to Form Biofilm and the Potential of Various Compounds to Eradicate It from Urinary Catheters. Pathogens. 2021; 11(1): 42. PubMed Abstract | Publisher Full Text\n\nPapenfort K, Bassler BL: Quorum sensing signal–response systems in Gram-negative bacteria. Nat. Rev. Microbiol. 2016; 14(9): 576–588. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchroll C, Barken KB, Krogfelt KA, et al.: Reosealrechoartficlteype 1 and type 3 fimbriae in Klebsiella pneumoniae biofilm formation.2010; 10.\n\nHolden VI, Bachman MA: Diverging roles of bacterial siderophores during infection. Metallomics. 2015; 7(6): 986–995. PubMed Abstract | Publisher Full Text\n\nVuotto C, Longo F, Pascolini C, et al.: Biofilm formation and antibiotic resistance in Klebsiella pneumoniae urinary strains. J. Appl. Microbiol. 2017; 123(4): 1003–1018. PubMed Abstract | Publisher Full Text\n\nWu C-C, Lin C-T, Cheng W-Y, et al.: Fur-dependent MrkHI regulation of type 3 fimbriae in Klebsiella pneumoniae CG43. Microbiology. 2012; 158(Pt_4): 1045–1056. PubMed Abstract | Publisher Full Text\n\nBrimacombe CA, Stevens A, Jun D, et al.: Quorum-sensing regulation of a capsular polysaccharide receptor for the Rhodobacter capsulatus gene transfer agent (RcGTA): R. capsulatus gene transfer agent receptor. Mol. Microbiol. 2013; 87(4): 802–817. PubMed Abstract | Publisher Full Text\n\nLeonard CA, Brown SD, Hayman JR: Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity. International Journal of Microbiology. 2013; 2013: 1–5. Publisher Full Text\n\nGoutam J, Kharwar RN, Tiwari VK, Singh R, Sharma D: Efficient Production of the Potent Antimicrobial Metabolite “Terrein” From the Fungus Aspergillus terreus. Nat. Prod. Commun. 2020; 15(3): 1934578X2091286. Publisher Full Text\n\nMishra R, Panda AK, De Mandal S, et al.: Natural Anti-biofilm Agents: Strategies to Control Biofilm-Forming Pathogens. Front. Microbiol. 2020; 11: 566325. PubMed Abstract | Publisher Full Text\n\nSrinivasan R, Santhakumari S, Poonguzhali P, et al.: Bacterial Biofilm Inhibition: A Focused Review on Recent Therapeutic Strategies for Combating the Biofilm Mediated Infections. Front. Microbiol. 2021; 12: 676458. PubMed Abstract | Publisher Full Text\n\nAl-Fakih AA, Almaqtri WQA: Overview on antibacterial metabolites from terrestrial Aspergillus spp. Mycology. 2019; 10(4): 191–209. PubMed Abstract | Publisher Full Text\n\nHouda SN, Rachid B, Julio G, et al.: In Vitro Antimicrobial, Antiviral and Cytotoxicity Activities of Aspergillus oryzae Isolated From El-Baida Marsh in Algeria. Journal of Drug Delivery and Therapeutics. 2020; 10(4): 191–195. Publisher Full Text\n\nNacef HS, Belhattab R, Larous L: Chemical Composition, Antimicrobial Study Against Human and Plant Pathogenic Microorganisms and Optimization of Bioactive Metabolites Produced by the New Strain Aspergillus oryzae 18HG80 Isolated from Saline Soil (El-Baida Marsh, Algeria). Journal of Microbiology Research. 2020; 11.\n\nLaSarre B, Federle MJ: Exploiting Quorum Sensing To Confuse Bacterial Pathogens. Microbiol. Mol. Biol. Rev. 2013; 77(1): 73–111. PubMed Abstract | Publisher Full Text\n\nChen G, Swem LR, Swem DL, et al.: A Strategy for Antagonizing Quorum Sensing. Mol. Cell. 2011; 42(2): 199–209. PubMed Abstract | Publisher Full Text\n\nCalvo AM, Wilson RA, Bok JW, et al.: Relationship between Secondary Metabolism and Fungal Development. Microbiol. Mol. Biol. Rev. 2002; 66(3): 447–459. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFlipphi M, Sun J, Robellet X, et al.: Biodiversity and evolution of primary carbon metabolism in Aspergillus nidulans and other Aspergillus spp. Fungal Genet. Biol. 2009; 46(1): S19–S44. PubMed Abstract | Publisher Full Text\n\nIvanova K, Fernandes MM, Francesko A, et al.: Quorum-Quenching and Matrix-Degrading Enzymes in Multilayer Coatings Synergistically Prevent Bacterial Biofilm Formation on Urinary Catheters. ACS Appl. Mater. Interfaces. 2015; 7(49): 27066–27077. PubMed Abstract | Publisher Full Text\n\nRasouli R, Navidinia M, Shams GM, et al.: Antibiofilm Activity of Cellobiose Dehydrogenase Enzyme (CDH) Isolated from Aspergillus niger on Biofilm of Clinical Staphylococcus epidermidis and Pseudomonas aeruginosa Isolates. Archives of Clinical Infectious Diseases. 2020; 15(1). Publisher Full Text\n\nRollefson JB, Stephen CS, Tien M, et al.: Bond Identification of an Extracellular Polysaccharide Network Essential for Cytochrome Anchoring and Biofilm Formation in Geobacter sulfurreducens. J. Bacteriol. 2011; 193(5): 1023–1033. PubMed Abstract | Publisher Full Text\n\nWilksch JJ, Yang J, Clements A, et al.: MrkH, a Novel c-di-GMP-Dependent Transcriptional Activator, Controls Klebsiella pneumoniae Biofilm Formation by Regulating Type 3 Fimbriae Expression. PLoS Pathog. 2011; 7(8): e1002204. PubMed Abstract | Publisher Full Text\n\nLee K-J, Kim J-A, Hwang W, et al.: Role of capsular polysaccharide (CPS) in biofilm formation and regulation of CPS production by quorum-sensing in Vibrio vulnificus: Quorum-sensing represses CPS production and biofilm. Mol. Microbiol. 2013; 90(4): 841–857. PubMed Abstract | Publisher Full Text\n\nXie Z, Meng K, Yang X, et al.: Identification of a Quorum Sensing System Regulating Capsule Polysaccharide Production and Biofilm Formation in Streptococcus zooepidemicus. Front. Cell. Infect. Microbiol. 2019; 9: 121. PubMed Abstract | Publisher Full Text\n\nRaras TYM, Rachma LN, Fitri LE, et al.: Aspergillus oryzae attenuates quorum sensing -associated virulence factors and biofilm formation in Klebsiella pneumoniae extended-spectrum beta-lactamases raw data. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "307666",
"date": "21 Aug 2024",
"name": "Lokender Kumar",
"expertise": [
"Reviewer Expertise Quorum sensing",
"Biofilm",
"Pseudomonas aeruginosa",
"Antibiotic Resistance",
"Bacteriophages",
"Microbiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The introduction is too brief and should provide more details on the clinical significance and global impact of KP-ESBL, quorum sensing signaling, and its role in biofilm formation. Additionally, some background on fungal proteins and their role in biofilm inhibition is needed. 2. Provide a stronger rationale for why Aspergillus oryzae was chosen for this study. Mention any relevant previous studies on Aspergillus sp. that support its potential as an antibiofilm agent. 3. The shift from discussing general biofilm inhibition to focusing on Aspergillus oryzae is abrupt. Introduce the relevance of Aspergillus sp. more smoothly. 5. The authors have used ammonium sulfate precipitation to isolate extracellular proteins, but the number of proteins present in this preparation is unclear. Details are missing. 6. The authors must provide SDS-PAGE analysis of the AOEP and mention the molecular weight of the proteins. The total yield of the protein and the concentration of the protein used in each experiment should be carefully mentioned. 7. The authors must cite the papers if they are following a method, for example, a biofilm assay or SEM. 8. Statistical analysis is not performed in various results; many bar charts do not show statistical significance. In Figure 6, the * symbols are not placed on top of the bars. 9. The C. elegans morphology under the microscope is not satisfactory. Are these adult worms or larval stages? The C. elegans images should be replaced with better images. Panel B in Figure 7 is completely dark. The authors should also show merged images to justify the experiments. 10. Ion-extracted liquid chromatography-mass spectrometry results are shown in Figure 8. The authors need to provide details of these signaling molecules and their presence (with citations) in KP-ESBL. Also, mention their role in quorum sensing pathways. 11. The authors are trying to show that the fungus produces molecules similar to the signal molecules of KP-ESBL, thereby potentially causing competitive inhibition of quorum sensing. However, this is confusing, as the study focused on the extracellular proteins of KP-ESBL. 12. Why was an ESBL-producing strain used in the study without performing antibiotic susceptibility testing? The authors should include more strains in the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1148
|
https://f1000research.com/articles/11-1147/v1
|
07 Oct 22
|
{
"type": "Method Article",
"title": "Viewing the global health system as a complex adaptive system – implications for research and practice",
"authors": [
"Josephine Borghi",
"Sharif Ismail",
"James Hollway",
"Rakhyun E. Kim",
"Joachim Sturmberg",
"Garrett Brown",
"Reinhard Mechler",
"Heinrich Volmink",
"Neil Spicer",
"Zaid Chalabi",
"Rachel Cassidy",
"Jeff Johnson",
"Anna Foss",
"Augustina Koduah",
"Christa Searle",
"Nadejda Komendantova",
"Agnes Semwanga",
"Suerie Moon",
"Sharif Ismail",
"James Hollway",
"Rakhyun E. Kim",
"Joachim Sturmberg",
"Garrett Brown",
"Reinhard Mechler",
"Heinrich Volmink",
"Neil Spicer",
"Zaid Chalabi",
"Rachel Cassidy",
"Jeff Johnson",
"Anna Foss",
"Augustina Koduah",
"Christa Searle",
"Nadejda Komendantova",
"Agnes Semwanga",
"Suerie Moon"
],
"abstract": "The global health system (GHS) is ill-equipped to deal with the increasing number of transnational challenges. The GHS needs reform to enhance global resilience to future risks to health. In this article we argue that the starting point for any reform must be conceptualizing and studying the GHS as a complex adaptive system (CAS) with a large and escalating number of interconnected global health actors that learn and adapt their behaviours in response to each other and changes in their environment. The GHS can be viewed as a multi-scalar, nested health system comprising all national health systems together with the global health architecture, in which behaviours are influenced by cross-scale interactions. However, current methods cannot adequately capture the dynamism or complexity of the GHS or quantify the effects of challenges or potential reform options. We provide an overview of a selection of systems thinking and complexity science methods available to researchers and highlight the numerous policy insights their application could yield.\n\nWe also discuss the challenges for researchers of applying these methods and for policy makers of digesting and acting upon them. We encourage application of a CAS approach to GHS research and policy making to help bolster resilience to future risks that transcend national boundaries and system scales.",
"keywords": [
"complex adaptive system",
"global health system",
"health system"
],
"content": "Introduction\n\nGlobalisation has increased interconnections across sectors and countries globally, intensifying transnational challenges that threaten global health, such as climate change, financial crises, anti-microbial resistance, and COVID-19.1 However, the global health system (GHS), which has been defined as the transnational actors aiming to improve health and the governance, financing, and delivery systems within which they operate,2 is ill-equipped to tackle these issues. In relation to COVID-19, for example, there remain profound inequities in the distribution of and access to vaccines, resulting from vaccine nationalism, inadequate global legal, pricing, procurement, allocation and delivery systems3,4\n\nThere are renewed calls to re-imagine the GHS5 to enhance global resilience to future transnational health risks. We argue that a key step towards this is improving the way we conceptualise and study the GHS. Health systems are recognised to be complex adaptive systems (CAS) and there is growing application of systems thinking and complexity science methods to help understand health system functionining6,7 and to theorise, design and evaluate public health interventions to enhance health system performance at the national and sub-national levels.8,9 The importance of a complexity lens to understanding and responding to the COVID-19 pandemic has also been highlighted,10 together with the need for a paradigm shift away from a component-based view of the system towards a more dynamic view of how systems actually behave.11 However, a CAS perspective has not typically been applied to the GHS within empirical research. In March 2021, a transdisciplinary group of public health, economics, health systems, global health governance, environmental science, systemic risk and resilience, mathematics, computer science, and engineering researchers with an interest in complex systems met to reflect on what we could learn from viewing the GHS as a CAS. This article draws on the workshop discussions and the participants’ research applying systems thinking and complexity science methods to national health systems and global systems outside of health (such as trade and environment) and policy engagement.\n\nWe begin by defining the features of a CAS, why the GHS can be considered a CAS and the limitations of current approaches to studying the GHS. We highlight how, by viewing it as a CAS, the GHS can be considered a multilevel system of systems, and show how four methods from systems thinking and complexity science could contribute to improving our understanding of the GHS and reforming it towards more effective global health outcomes.\n\n\nWhat is a complex adaptive system?\n\nA system comprises of elements, interconnections (the way elements feed into and relate to each other), and a purpose.12 A defining feature of a CAS is the focus on interconnections between system elements and in particular, the adaptability of those elements in response to changing conditions.11 A CAS is self-organising and the properties of elements and the relationships between them can give rise to wholly new system behaviour, a property known as emergence. CASs are dynamic: constituent elements learn, adapt and evolve over time, shaped by interactions, past behaviours, and the external environment.\n\nThe GHS is a complex system13 due to the large and escalating number of global health actors,2 the varying and extensive networks linking them,14 and the interconnections between health and other sectors, such as food, trade and the environment.15 GHS behaviour demonstrates non-linear characteristics: small actions or inactions by specific actors can have large global level effects: vaccine hoarding by individual countries contributing to low vaccination availability in others. The GHS is also adaptive, responding to exogenous changes (the formation of the Access to COVID-19 Tools (ACT)-Accelerator Partnership in 2020 in response to COVID-19) or to changing characteristics of system elements (Germany increasing investment in the World Health Organization following United States threats of withdrawal). Furthermore, in hierarchical multi-level systems, both higher and lower levels, demonstrate layer dependent CAS properties.16\n\n\nLimitations of current research and practice\n\nCurrent research fails to consider the GHS as a CAS, which limits its potential to inform a reconfiguration of the GHS. Analysis of the GHS often focuses on specific system elements such as medicines,17 or particular health actors18; with less attention to the interactions and interconnections between elements/actors. Equally, there is fairly limited research on how the GHS influences national health systems,19 the interconnections between national health systems, such as cross-border health systems20 or regional health systems21 despite their importance for pandemic threats, and the interconnections between health and other systems.22\n\nEpidemiological and economic studies grounded in game theory frameworks (the mathematical modeling of strategic interactions) have examined global solutions to transnational problems, such as cooperation on vaccine coverage for disease eradication.23–25 Evolutionary game theory was recently used to analyze the factors influencing active cooperative governance and proposed a series of recommendations for promoting international cooperation in relation to COVID-19.26 However, such models often assume actors are rational utility maximisers and the global system is in equilibrium, overlooking the evolving and dynamic nature of the GHS. Political economy approaches can provide insight into power dynamics, values, economic and political interests shaping global health institutions and policy27 together with historical factors underpinning these, but have difficulty quantifying their effects or modelling the consequences of potential reform options.\n\nThe effects of framing GHS behaviour without reference to complex adaptive behaviour can be seen in COVID-19 policy responses which have tended to overlook ways in which interventions would interact with existing health system structures. For example, calls for a Global Health Threats Fund28 have not considered the administrative costs (and relative efficiency) of creating and running a new global fund, nor how the fund would interact with an already highly fragmented global financing landscape and the consequences for domestic financing arrangements. Equally, efforts to estimate the costs of pandemic preparedness at the global, regional and national levels and to identify mechanisms to finance these, often ignore the interconnections between global, regional and national systems, and how investments at one level will affect costs and resource needs at other levels.29\n\n\nThe value of a complex adaptive systems approach\n\nA CAS approach can be used to study the supra-national actors and systems that support global health consistent with the definition of the GHS provided earlier.2 Through a CAS lens, the GHS can also be conceptualised as a multi-level health system, a continuum of health systems from local to global, comprising all the national systems globally together with the supranational global ‘health system’ architecture, as illustrated in the simplified configuration in Figure 1. Taking a multilevel systems view of the GHS is helpful when a system goal is influenced by actions across system levels, as is the case for COVID-19 vaccination equity. For example, resolving vaccine production and allocation constraints requires global level actions30 (e.g. patent and pricing regulations, contract manufacturing arrangements), while affordability and deployment constraints require actions at the national (e.g. funding/budgetary allocations, transport, storage, logistics) and local levels (overcoming vaccine hesitancy to enable population uptake31).\n\nNote: System behaviour responds to bottom up and top-down influences, with higher level entities (global actors (pharmaceutical companies) and initiatives (COVAX)) influencing COVID-19 vaccine production, affordability and deployment options of lower-level agents; and actions of lower level agents (e.g. patients uptake or not of vaccines) influencing global responses.35\n\nA CAS lens further recognizes the interconnections between national health systems which may be relevant to understanding how, for example, allocation of COVID-19 vaccines is affected by inter-country transfers of vaccines,32 or how in-country deployment is shaped by policies to enhance supply chains and vaccination uptake in neighboring countries.\n\nThe importance of taking a multi-scale approach to health is only slowly starting to be recognised in relation to COVID-19,29 while multi-level governance systems and the study of cross-scale interactions have long been the subject of climate research.30\n\nBeyond an alternate conceptualization of the GHS, as we set out below, a CAS approach can help to visualize and understand system structure and dynamics, quantify the effect of a problem, and predict system behaviour in response to exogenous shocks or policy reforms. Importantly such an approach considers how system structure and the interaction and behaviour of elements within the system can result in the emergence of internal vulnerabilities rather than assuming that system failures are solely due to events outside the system.11 This helps move towards an ex-ante approach of understanding and reducing risk.33 By conceptualizing interconnections and offering tools enabling their study, a CAS lens could potentially offer new insights on global and local system constraints, emergent systemic risks, and feasible and effective reform strategies for policy and practice.\n\n\nOperationalising a complex adaptive systems approach for the global health system\n\nIn this section we illustrate the potential of a series of systems thinking and complexity science approaches to improve understanding of the GHS by offering new and complementary insights relative to existing methods. Rather than attempting to model the GHS in its entirety, these sense-making tools instead focus on establishing what contributes to a particular system behaviour (or outcome) of interest, and how.\n\nA critical first step to operationalizing a CAS approach is determining the boundaries of the system of interest – i.e. to consider what is relevant to the behaviour of interest and its spatial and temporal scope, while acknowledging what is external to the system but may nevertheless influence system functioning. System boundaries depend on the goal of the system34 (or the problem within the system one is trying to address) and are ultimately arbitrary. If drawn too narrowly, important feedback loops may be missed; if drawn too broadly the analysis becomes meaningless as to the problem addressed.35 Thus boundaries can be determined through stakeholder discussion using methods such as group model building,36 which develop a shared understanding of the system, or use of a conceptual frame.37 The “critical systems” tradition in systems thinking, and more specifically critical systems heuristics, provides a framework to problematise researcher and stakeholder assumptions about system boundaries (and system goals), and encourage critical reflection on what these imply.38 The goal and the level of the system to which it applies will determine who to engage in boundary setting (typically those influencing the goal and those affected by it). Existing frameworks can facilitate researcher and policy reflection about goals and system boundaries for the GHS.1,2,39\n\nWe now focus on four approaches that have been applied to the study of health systems at the national and sub-national levels and have been used to study global systems in other sectors: causal loop diagrams, system dynamic modelling, agent based modelling and network analysis. We also introduce the concept of global system science as an approach to studying the interaction between global systems.\n\nMapping techniques derived from systems thinking such as causal loop diagrams (CLDs), can be used by researchers or policy makers to identify and visually represent causal relationships between elements within the GHS and determine how these influence system behaviour and thereby its ability to achieve desired outcomes. CLDs illustrate feedback loops, such as a reinforcing loop (R), where a relationship shows an amplified effect over time, or a balancing loop (B), reflecting stabilizing behaviour. By identifying feedback loops reinforcing problem behaviours, and critical elements that underpin system functioning,40 CLDs can be used to determine leverage points, where interventions should be focused to enhance system performance and thereby inform policy development and prioritization. Figure 2 provides a simplified illustratation of a causal loop representation showing how early on, high income country (HIC) pursuit of bilateral deals undermined COVAX as HICs were unwilling to procure vaccines through COVAX. This reduced the funds available to COVAX and its purchasing power, limiting the ability of COVAX to procure COVID-19 vaccines, reinforcing the pursuit of bilateral deals by HICs (R1). The impetus to bilateral deals by HICs was in theory constrained by rising HIC vaccine stock (B1) but in the early phases of the global vaccine rollout, this feedback loop was in reality weak. It did eventually strengthen, helping to trigger an increase in HIC investment in COVAX.\n\nNote to Figure:\n\n1. Principles of balancing and reinforcing feedback loops: “+” indicates a change in the same direction, “-”in the opposite direction to the change in the variable at the start of an arrow. A reinforcing (R) loop has an even number, a balancing (B) loop an uneven number of “-”relationships. “//” indicates a delay.\n\n2. The principle context of COVAX has been omitted for simplicity reasons, and only the impact of making bilateral agreements has been illustrated.\n\nThere is growing use of CLDs to study national health systems and their response to policy reforms40,41 and exogenous shocks42 to identify factors shaping vaccine demand, supply and trust.43,44 CLDs have great potential to address GHS issues by apriori examining the implication of planned policy shifts.\n\nAdding data and functional relationships to the structure generated through CLDs creates system dynamics models (SDM) which use stocks and flows to simulate aggregate system behaviours over time and quantify the relationship and dynamic interactions between system elements and how changes in the stock of one element, such as financing, would affect other elements, such as the stock of vaccines. In this way, SDM can quantify the effect of an exogenous shock, such as COVID-19, or the impact of a mitigating strategy or policy intervenention on an outcome of interest.45\n\nA network consists of a set of nodes and links connecting them. Network analysis techniques can map, measure, and model the network structure or topology of the GHS and its evolution over time. They can be used to determine whether the structure is polycentric or fragmented, as has been done in relation to global environmental governance,46 or understand how that structure came to be formed in the first place. Network analysis can also be used to determine systemic risk and explore how reshaping the system’s network topology might enhance its resilience. Quantifying the interdependencies between system nodes, and the relative contribution of these to overall systemic risk allows identification of nodes whose failure due to their size or interconnectedness could trigger ripple and cascading system effects.33,47\n\nFigure 3 provides a simple network schematic highlighting how the failure of a single node may lead to very different systemic outcomes depending on its position in the network. Let us assume that the central node in red is COVAX and the other nodes are national COVID-19 vaccination procurement systems. The left panel illustrates the situation where COVAX fails, as it did early on in vaccine deployment when the limited stock of vaccines held by COVAX contributed to limited allocation of vaccines to LMICs. The right panel illustrates the more limited consequences when it is a more peripheral node that fails, such as when allocation problems chiefly arose at the country-level, due to weak health systems and demand constraints, but without necessarily affecting other countries’ access. This highlights some of the advantages and disadvantages of a reasonably centralized topology.\n\nThe network on the right remains intact whereas the network on the left disintegrates into four fragments.\n\nNetwork analysis is increasingly used to study national and local health systems,48 including the performance of facility networks and provider networks within health facilities. Its application at the global level has been less frequent, but includes the study of the global spread of COVID-19 vaccine misinformation49 or vaccine patents which pinpointed constraints to technology transfer.50 There is thus further potential to apply these methods to other aspects of the GHS and governance as has been done within the European Union.51\n\nWith agent-based models (ABM), the system is modelled as a collection of automous and heterogenous agents that interact and make decisions based on their attributes and a set of rules governing their behaviour.52 ABM provides an exploration of the dynamic behaviour of the system resulting from the interactions between agents within the GHS (such as non-governmental organizations, corporations, governments, multilaterals, health facilities, or individuals) and with their external environment. Agents can learn and evolve, allowing for unanticipated effects to emerge from the agents’ characteristics and behaviours within a system. There is growing application of ABM to study national health systems, for example, identifying design features within a provider payment mechanism to achieve maximum financial and quality outcomes.53 ABM has been used to study global systems outside of health, examining constraints to global governance and opportunities for greater coordination between nation states54 and could be potentially used to support more effective global health governance. For example, ABM could be used to identify which incentive structure would be most effective in getting high income countries’ vaccine production, allocation, and deployment to align with the interests of the global South.\n\nWhile these methods can be used in isolation, they can also be used jointly, with potential to build hybrid SDM and ABM models,7 using SDM as an input to ABM and vice versa; and linking network analysis and ABM.55,56\n\nMoving beyond the GHS to study interactions and interdependencies with other global systems, global system science examines system behaviour at the global scale, involving complexity science, informatics, policy implementation and public engagement57 and could be extended to global health, for example, examining the effect of trade, environment and communication systems on the GHS.1\n\n\nChallenges\n\nDespite the advantages, there are a number of challenges in applying a CAS lens to the GHS. When mapping or modelling any system, it can be a struggle to get the right balance between capturing enough detail to convey the complexity of the system without obfuscating major patterns. Given the scale of the global system and potential for cross-scale influences, containing complexity to enable meaningful insights is not without challenge. However, CAS studies of other global systems provide reassurance this can be achieved for the GHS.14,46\n\nIn addition, models typically rely on data that may be inaccessible, incomplete or inconsistent across geographies, requiring assumptions and reliance on researcher values with the inherent risk of bias. Engagement with a diverse set of stakeholders is critical in defining the problem/s to be addressed and making boundary judgements, building a qualitative understanding of the system through a visual map, before iteratively building, parameterising, and validating quantitative models, and thereby increasing their acceptability and validity. However, stakeholders may differ in their understanding of the system and in its perceived goals, which can create challenges in building a unified model of the system.\n\nFurthermore, there are limits to the methods reviewed. For example, SDM have not, to date, been used extensively to consider power dynamics, nor the economic consequences of reforms, and would need to be complemented and informed by political economy and policy analysis to assess the political acceptability of potential reform options, and economic models, to determine their financial and macro-economic implications. Studying the GHS as a CAS will require an interdisciplinary research effort to integrate knowledge on global health governance and policy, health systems, social science, mathematics and engineering, requiring collaboration across research departments and institutions, and the development of a shared lexicon and understanding of related concepts and methods.\n\nFrom a policy perspective, increased awareness and understanding of systems and complexity thinking58 will be needed to encourage the use of complexity science models among policy makers and the uptake of resulting research.59 Evidence of growing policy engagement with systems thinking approaches as evidenced by guidance documents produced by government and intergovernmental organisations is encouraging.60,61 Furthermore, the political interests of actors and power imbalances within the GHS could limit the global community's willingness to implement reform recommendations resulting from CAS research on the GHS. However, COVID-19 has created recognition of the need for reform and resulted in initiatives to enhance global health solidarity, which provides an avenue to which systems thinking and complexity science could contribute.5,62,63\n\n\nConclusions\n\nWe have shown that the GHS embodies the properties of a nested multi-scale CAS and that greater researcher and policy engagement with CAS tools could offer new insights into system constraints and potential leverage points to better achieve GHS goals. We encourage application of system dynamics, agent based modelling, network analysis and other systems and complexity science methods to inform the effective design of global systems that promote global public goods for health to tackle future transnational challenges such as pandemics and climate change. Arising proposals will need to be complemented by political economy studies of the feasibility and potential acceptability of reform options, and economic studies of their financial implications. Recognizing the complexity of the GHS and being able to analyze and predict the performance of the GHS is an essential precondition for reforming and strengthening it in an impactful way.\n\n\nData availability\n\nNo data are associated with this article.",
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PubMed Abstract | Publisher Full Text\n\nJamal Z, Alameddine M, Diaconu K, et al.: Health system resilience in the face of crisis: analysing the challenges, strategies and capacities for UNRWA in Syria. Health Policy Plan. Feb 1 2020; 35(1): 26–35. Publisher Full Text\n\nRwashana AS, Williams DW, Neema S: System dynamics approach to immunization healthcare issues in developing countries: a case study of Uganda. Health Informatics J. Jun 2009; 15(2): 95–107. PubMed Abstract | Publisher Full Text\n\nOzawa S, Paina L, Qiu M: Exploring pathways for building trust in vaccination and strengthening health system resilience. BMC Health Serv. Res. Nov 15 2016; 16(Suppl 7): 639. PubMed Abstract | Publisher Full Text\n\nSemwanga AR, Nakubulwa S, Adam T: Applying a system dynamics modelling approach to explore policy options for improving neonatal health in Uganda. Health Res. Policy Syst. May 4 2016; 14(1): 35. Publisher Full Text\n\nKim RE: Is Global Governance Fragmented, Polycentric, or Complex? The State of the Art of the Network Approach. Int. Stud. Rev. 2020; 22(4): 903–931. Publisher Full Text\n\nRoukny T, Bersini H, Pirotte H, et al.: Default cascades in complex networks: topology and systemic risk. Sci. Rep. 2013; 3(2759): 1–8.\n\nBrunson JC, Laubenbacher RC: Applications of network analysis to routinely collected health care data: a systematic review. J. Am. Med. Inform. Assoc. Feb 1 2018; 25(2): 210–221. PubMed Abstract | Publisher Full Text\n\nMelton C, Olusanya OA, Shaban-Nejad A: Network Analysis of COVID-19 Vaccine Misinformation on Social Media. Stud. Health Technol. Inform. Nov 18 2021; 287: 165–166. PubMed Abstract | Publisher Full Text\n\nGaviria M, Kilic B: A network analysis of COVID-19 mRNA vaccine patents. Nat. Biotechnol. 2021; 39: 546–548. Publisher Full Text\n\nMartinsen DS, Schrama R: Networked Health Care Governance in the European Union. J. Health Polit. 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}
|
[
{
"id": "166534",
"date": "18 Apr 2023",
"name": "Alastair Ager",
"expertise": [
"Reviewer Expertise Health systems resilience",
"Global health policy",
"Evaluation of humanitarian action."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper articulates the argument that institutions and actors active in the field of global health be conceived as part of a global health system that operates as a form of ‘complex adaptive system’ (CAS). The authors go on to outline a number of analytic approaches associated with the ‘systems thinking’ of value in understanding the behavior of CAS - including causal loop modelling, system dynamic analysis, network analysis and agent-based modelling - and to consider both the value of and challenges associated with each in their application if the field of global health.\nThe authors particularly draw upon the experience of the COVID-19 pandemic – and responses such as the COVAX vaccine initiative – to illustrate the value of seeing the behavior of actors and institutions within the global health system as interdependent. The paper usefully draws attention to complexity being associated with both the multi-scalar nature of analysis required in any context (e.g. from communities through to national Ministries) and the reality of globalization that sees national and international actors connected though a wide variety of multilateral, bilateral and commercial relationships. By illustration, the authors clearly illustrate interdependence and systems effects, although the claim that a complex adaptive system approach can “predict system behavior in response to exogenous shocks or policy reforms” is perhaps best understood as an aspiration at this stage.\nThe brief introductions to systems methods are effective in illustrating the character and potential of each, again with appropriate illustration provided. The paper thus serves as a useful ‘reader’ compiling examples of recent applications of these methods in addressing health systems challenges. While the simplified examples are warranted – supporting a clear, concise narrative for the paper – they fall some way short of fulfilling the vision established at the start of the paper for anticipating adaptations such as emergence and non-linear characteristics in a manner that would inform health sector policy and practice.\nThe challenges with which the paper closes – the balance of detail and comprehensibility in analyses, data availability, measurement of influential but ‘hard-to-operationalize variables such as power and trust, policymaker openness to complexity – are, in my view, indeed the key challenges in advancing such forms of analysis at this time. However, they are addressable, and the paper serves as a useful call for greater engagement with this burgeoning field of work in informing – in increasingly concrete and evidence-informed ways – the formulation of global health policy and strategy.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Partly\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
},
{
"id": "173947",
"date": "16 Aug 2023",
"name": "Corinna Elsenbroich",
"expertise": [
"Reviewer Expertise Complexity Social Science"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a really good statement piece about systems methods and how they can help to improve the Global Health System. The authors describe the methods in sufficient detail and with enough motivation to let the reader understand the importance of a new approach. My one suggestion is to maybe extend the problem of data and evidence a bit more in the Challenges section. Whilst the authors talk about that data can be inconsistent across countries or not collected to date, there are even worse problems with some data not being available in principle (some things that are modelled in complex systems models might not be quantifiable). On evidence, in particular in health there is a strong focus on \"gold standard evidence\" and CSM will not provide this kind of evidence.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? No\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1147
|
https://f1000research.com/articles/11-883/v1
|
02 Aug 22
|
{
"type": "Case Report",
"title": "Case Report: Interstitial-intralesional laser therapy and laser-assisted new attachment procedure for the treatment of an aggressive pyogenic granuloma",
"authors": [
"Anon Akkarapatum",
"Poramaporn Klanrit",
"Sajee Sattayut",
"Anon Akkarapatum",
"Poramaporn Klanrit"
],
"abstract": "Background: A pyogenic granuloma (PG) is a common benign vascular lesion found in the oral cavity. The gold standard treatment of this lesion, comprising surgical excision and the elimination of etiological factors, cannot avoid tooth loss in the case of an aggressive pyogenic granuloma. Because of the prominent properties of 980 nm and 635 nm diode lasers in photocoagulation and photobiomodulation, we applied these wavelengths in the treatment of a large pyogenic granuloma with alveolar bone loss. Case presentation: Our objective was to use a combination of interstitial-intralesional laser therapy, photocoagulation and laser-assisted new attachment procedure (LANAP) to preserve the teeth and periodontal tissue in a case of an aggressive pyogenic granuloma. Results: The patient was a 13-year-old Thai male with a pyogenic granuloma involving the interdental papilla and lingual gingiva of the lower left first and second molars. The teeth were also displaced by the lesion. After treatment with three sessions of photocoagulation, three sessions of interstitial-intralesional laser therapy and two sessions of LANAP, the lesion was completely resolved. The periodontal status of the teeth was improved at the six-month follow-up. Conclusion: The combination of interstitial-intralesional laser therapy, photocoagulation and LANAP was able to treat an aggressive pyogenic granuloma with tooth preservation.",
"keywords": [
"pyogenic granuloma",
"interstitial-intralesional laser therapy",
"photocoagulation",
"LANAP",
"diode laser",
"tooth preservation"
],
"content": "Introduction\n\nA pyogenic granuloma is a lobulated exophytic lesion with a painless red erythematous papule. This lesion presents either as a pedunculated mass or with a sessile base. Pathogenic factors include chronic low-grade local irritation, hormonal factors and certain medications.1 As this lesion is composed of a vascular component, blade excision leads to considerable bleeding and demands hemostatic intervention.\n\nNear-infrared and red diode lasers provide favorable photocoagulation and photobiomodulation. These diode lasers are able to stimulate the formation of blood clots and promote healing after surgery.2 Therefore, these wavelengths are widely used for the treatment of vascular lesions in the oral cavity via surface photocoagulation and interstitial-intralesional laser therapy.3\n\nRegarding periodontal disease treatment, laser-assisted new attachment procedure (LANAP) is able to stimulate the formation of new attachments. This technique also has advantages in hemostasis, granulation tissue removal and the reduction of periodontal disease pathogens.4\n\nHence, we introduce an interstitial-intralesional laser technique for the treatment of aggressive pyogenic granulomas, aiming to treat lesions with minor gingival excision and preservation of periodontal tissue. Periodontal tissue recovery was achieved by LANAP. This case report presents a typical pyogenic granuloma with aggressive characteristics treated through the use of interstitial-intralesional laser therapy, photocoagulation and LANAP.\n\n\nCase report\n\nThis case report was authorized by the ethics committee in human research, Khon Kaen University, reference number HE632040. The informed consent in Thai language from the patient and his parent was submitted to the ethics committee. The patient was a 13-year-old Thai male patient with a chief complaint of a rapidly swelling mass of the lower-left molar gingivae without pain for 10 days. There was no history of medical and psychological disorders of the patient and family. There was no systemic disease based on physical examination and laboratory investigation. The oral examination found an approximately 2×2 cm erythematous pedunculated mass with ulceration in the area of the interdental papilla and on the lingual gingiva of tooth no. 36 and tooth no. 37. The mass was soft consistency with no bleeding and no pus (Figure 1A). Tooth no. 37 exhibited buccal displacement, as shown in Figure 1B. Tooth no. 36 and tooth no. 37 exhibited second-degree and third-degree mobility, respectively.\n\nA. The erythematous pedunculated mass at tooth no. 36 and tooth no. 37.\n\nB. Tooth no. 37 was displaced from the normal position.\n\nThe periapical radiograph showed distinct periapical bone destruction of tooth no. 36 and tooth no. 37 (Figure 2).\n\nThe periapical radiograph demonstrating alveolar bone loss at tooth no. 36 and tooth no. 37.\n\nA sample obtained with an incisional biopsy using a 980 nm diode laser at 4 W continuous-wave with a 320-micron optical fiber confirmed the diagnosis of a pyogenic granuloma with histopathological features presenting endothelial cell proliferation, fibroblasts, neutrophils and chronic inflammatory cells in the connective tissue stroma (Figure 3A and B).\n\nHistopathology section showing endothelial cell proliferation and distribution throughout the lesion, which are the characteristics of a pyogenic granuloma.\n\nA. At ×10 magnification and B. At ×40 magnification.\n\nThe lesion was firstly treated by interstitial-intralesional laser therapy under local anesthesia using a 980 nm diode laser at 3 W continuous-wave with a 200-micron optical fiber, as shown in Figure 4A and B. After the insertion of the optical fiber tangentially to the tooth and root surface into the lesion, the laser was irradiated for five seconds. The lesion became pale and harder, indicating that coagulation was achieved.\n\nA. The optical fiber was inserted into the lesion, beginning at the base of the lesion and then progressing to the top. The optical fiber was placed tangentially to the tooth and root surface.\n\nB. After a single treatment with interstitial-intralesional laser therapy on four areas.\n\nThis treatment was then immediately followed by treatment with using a 635 nm diode laser at 100 mW, continuous wave and 4 J/cm2 to achieve photocoagulation and photobiomodulation effects (Figure 5).\n\nThe patient was invited to have appointments for interstitial-intralesional laser therapy as previously described every two to three weeks. The remission of the pyogenic granuloma was observed, as shown in Figure 6A, B and C.\n\nA. 2 weeks after the first therapy.\n\nB. 2 weeks after the second therapy.\n\nC. 3 weeks after the third therapy.\n\nAfter two months of follow-up, the pyogenic granuloma involving soft tissue lesion was completely resolved. Tooth no. 37 returned to the normal position. The degrees of mobility of tooth no. 36 and tooth no. 37 were reduced to first-degree and second-degree mobility, respectively. The periodontal pocket was approximately 4 to 6 mm. The patient was treated with LANAP under local anesthesia to preserve the teeth.\n\nThe LANAP procedure consisted of three steps4 as follows:\n\nStep 1: After supragingival scaling with an ultrasonic scaler, a 980 nm diode laser at 0.7 W and continuous wave was delivered via a 200-micron optical fiber into the gingival sulcus (Figure 7A). Then, it was followed by scaling and root planning (Figure 7B).\n\nA. The 980 nm diode laser was used for dilating the gingival sulcus.\n\nB. Scaling and root planning with hand instruments.\n\nC. The 980 nm diode laser was used for ablating the long junctional epithelium and granulation tissue in the gingival sulcus.\n\nD. Toluidine blue was injected as a photosensitizer into the gingival sulcus.\n\nE. The gingival sulcus was irradiated with a 635 nm diode laser via a 200-micron flexible tip to initiate photosensitizer.\n\nStep 2: The epithelium and granulation tissue in the gingival sulcus was photoablated with a CW 980 nm diode laser at 2 W and continuous wave via a 200-micron optical fiber (Figure 7C).\n\nStep 3: Photodynamic therapy was administered using 0.1% toluidine blue as a photosensitizer and a 635 nm diode laser at 200 mW and CW for 15 sec via a 200-micron flexible optical fiber as a light source (Figure 7D and E).\n\nAfter one month of LANAP, tooth no. 37 showed only first-degree mobility. No recurrence of the pyogenic granuloma was observed. The periodontal pocket depth was reduced, and no gingival recession of tooth no. 36 and tooth no. 37 was observed. The periapical radiograph showed improvement through the indication of bone formation at the periapical areas of tooth no. 36 and tooth no. 37, as shown in Figure 8. The second LANAP was conducted to maintain the periodontal status. There was no adverse and unanticipated event in overall treatments and outcomes.\n\nA, B and C. Intraoral features after LANAP showing the normal appearance of the gingivae of the lower left molars and the repositioning of the teeth to their previous location and occlusion.\n\nD. Periapical radiograph of tooth no. 36 and tooth no. 37 showing an increase in periapical radiopaque characteristics in the previous defect.\n\nDue to the limitation of travelling from the COVID-19 pandemic, the patient was followed up by the dentist at his local health services. We followed the patient for another two sessions every three months for a- 6- month. There had been still no sign of recurrent of the lesion.\n\nThe patient and his parent were satisfied with the less invasion procedures and remission of the lesion with tooth preservation. Therefore, they allowed the authors as a team of surgeons to present and report this treatment for this may benefit the others who have the same condition.\n\n\nDiscussion\n\nThe selection of laser wavelengths for biopsy and therapy is an important choice. An infrared diode laser was chosen in this case because of its hemoglobin absorption ability. This resulted in ablation with hemostasis.2\n\nFor the photocoagulation technique, in this case, using a 635 nm diode laser at a power less than 0.5 W not only promoted clot formation but also resulted in photobiomodulation, which allowed a positive response to the healing process, such as an increase in microcirculation, the stimulation of cell growth, and a reduction in inflammatory substances.5\n\nThe treatment of the pyogenic granuloma in this report preserved the teeth and surrounding periodontal tissue. This outcome was different from that of a previous report in which the treatment of a pyogenic granuloma at tooth no. 11 in an 11-year-old female patient by total excision of the lesion resulted in gingival defects. The patient had to undergo free connective tissue graft.6 Our technique with combined laser therapy showed no gingival defect after the resolution of the lesion.\n\nIn addition, there was a case report with a similar lesion: an aggressive pyogenic granuloma near the area of tooth no. 46 and no. tooth no. 47 in an 11-year-old female patient. With the use of surgical excision, tooth no. 46 near the lesion had to be extracted.7 While in our patient, who was treated by a combination of interstitial-intralesional laser therapy, photocoagulation and LANAP, we were able to preserve the teeth and eliminate the lesion.\n\n\nConclusions\n\nFrom this report, a pyogenic granuloma with extensive periapical bone loss in a 13-year-old Thai male patient was treated with 980 nm and 635 nm interstitial-intralesional laser therapy, photocoagulation and LANAP. After six months of follow-up, there was no recurrence of the lesion and no complication of gingival recession. The periodontal status was improved. Therefore, we propose a combination of interstitial-intralesional laser therapy, photocoagulation and LANAP for the treatment of aggressive pyogenic granulomas to preserve the teeth involved in the lesions.\n\n\nAuthor contributions\n\nAK: Data Curation, Investigation, Methodology, Visualization, Writing – Original Draft Preparation\n\nPK: Data Curation, Investigation, Visualization, Writing – Original Draft Preparation\n\nSS: Conceptualization, Methodology, Project Administration, Supervision, Writing – Review & Editing\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nFigshare. CARE flowchart. DOI: https://doi.org/10.6084/m9.figshare.20367705",
"appendix": "References\n\nJafarzadeh H, Sanatkhani M, Mohtasham N: Oral pyogenic granuloma: a review. J. Oral Sci. 2006; 48(4): 167–175. Publisher Full Text\n\nBlack JF, Wade N, Barton JK: Mechanistic comparison of blood undergoing laser photocoagulation at 532 and 1,064 nm. Lasers Surg. Med. 2005; 36(2): 155–165. PubMed Abstract | Publisher Full Text\n\nAzma E, Razaghi M: Laser treatment of oral and maxillofacial hemangioma. J. Lasers Med. Sci. 2018; 9(4): 228–232. PubMed Abstract | Publisher Full Text\n\nDe Angelis N, Hanna R, Signore A, et al.: Effectiveness of dual-wavelength (Diodes 980 Nm and 635 Nm) laser approach as a non-surgical modality in the management of periodontally diseased root surface: a pilot study. Biotechnol. Biotechnol. Equip. 2018; 32(6): 1575–1582. Publisher Full Text\n\nKaroussis IK, Kyriakidou K, Psarros C, et al.: Effects and Action Mechanism of Low Level Laser Therapy (LLLT): Applications in Periodontology. Dentistry. 2018; 08(09): 4–10. Publisher Full Text\n\nJoda T: Esthetic management of mucogingival defects after total excision in a case of pyogenic granuloma. Eur. J. Esthet. Dent. 2012; 7(2): 110–119. PubMed Abstract\n\nKumar D, Agarwal T: A Case Report: Aggressive Pyogenic Granuloma. Dent. J. Adv. Stud. 2019; 07(01): 046–050. Publisher Full Text"
}
|
[
{
"id": "146326",
"date": "17 Aug 2022",
"name": "Kenneth Luk",
"expertise": [
"Reviewer Expertise Lasers in Dentistry"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this case report, the treatment protocol with wavelengths were well thought out. Laser parameters and techniques were well documented. Patient management was comprehensive.\nPulsed Nd:YAG (1064nm) laser for LANAP protocol was cleared by the FDA in 2004.1 Yukna demonstrated LANAP protocol with Nd:YAG laser can produce new cementum-mediated connective tissue attachment.2 Recently, LANAP seem to be broadened to include near-infra-red diode wavelengths.3\nIn this report, 980nm diode laser was used for LANAP protocol in step 1 and 2. Photodynamic therapy (PDT) with 635nm red laser was used in step 3. The initial LANAP protocol uses only Nd:YAG laser and no PDT was required. It would be more appropriate to describe the LANAP protocol in this case report as a modified LANAP protocol.\nAlternative lasers for this case: Like 980nm, 810nm, 940nm and 970nm are also well absorbed by haemoglobin and melanin. They can also be used for ablation, coagulation and photobiomodulation.\nInstead of PDT, photothermal therapy can be considered using Indocyanine green as a photosensitiser with 810nm diode laser.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "8688",
"date": "30 Aug 2022",
"name": "Sajee Sattayut",
"role": "Author Response",
"response": "Many thanks for your comment on expanding the details of LANAP in terms of the development of techniques. We will add these to the manuscript."
},
{
"c_id": "8726",
"date": "06 Sep 2022",
"name": "Sajee Sattayut",
"role": "Author Response",
"response": "Reviewer: Ken Luk In this case report, the treatment protocol with wavelengths were well thought out. Laser parameters and techniques were well documented. Patient management was comprehensive. Response: Many thanks for your kind consideration. Pulsed Nd:YAG (1064nm) laser for LANAP protocol was cleared by the FDA in 2004.1 Yukna demonstrated LANAP protocol with Nd:YAG laser can produce new cementum-mediated connective tissue attachment.2 Recently, LANAP seem to be broadened to include near-infra-red diode wavelengths.3 In this report, 980nm diode laser was used for LANAP protocol in step 1 and 2. Photodynamic therapy (PDT) with 635nm red laser was used in step 3. The initial LANAP protocol uses only Nd:YAG laser and no PDT was required. It would be more appropriate to describe the LANAP protocol in this case report as a modified LANAP protocol. Alternative lasers for this case: Like 980nm, 810nm, 940nm and 970nm are also well absorbed by haemoglobin and melanin. They can also be used for ablation, coagulation and photobiomodulation. Instead of PDT, photothermal therapy can be considered using Indocyanine green as a photosensitiser with 810nm diode laser. Response: Your suggestion on emphasizing the modification of LANPP technique used for this case report was added in a discussion. Regarding the LANAP used in this case report, it was based on the techniques of De Angelis el al 4 which combined photoablation and photodynamic therapy. This differed from other LANAP techniques by using only either Nd;YAG laser8 or diode laser9 for ablating epithelium and granulation tissue in the gingival pocket and root resurface. Owing to this being a case report, we would like to reserve other types of lasers or photosensitizers to be claimed that these would be applied as similar results have been proved in this study. References 1. Gregg II R. H: The LANAP Protocol: laser-assisted new attachment procedure. International Journal of Periodontics and Restorative Dentistry. 2007. 87 2. Yukna RA, Carr RL, Evans GH: Histologic evaluation of an Nd:YAG laser-assisted new attachment procedure in humans.Int J Periodontics Restorative Dent. 2007; 27 (6): 577-87 PubMed Abstract 3. Shetty A, Ramachandra V. K, Shubhashini N. S, Anjali K, et al.: Diode laser assisted management of endo-perio lesion in maxillary incisor using LANAP: A Case Report. International Dentistry South Africa. 2010. 38-43 Response: We could not find your suggested references in the Pubmed database. The references in the Pubmed database that supported the same ideas as you suggested were included. Jha A, Gupta V, Adinarayan R: LANAP, Periodontics and Beyond: A Review. J Lasers Med Sci. 2018;9(2):76-81. Chandra S, Shashikumar P: Diode Laser - A Novel Therapeutic Approach in the Treatment of Chronic Periodontitis in Type 2 Diabetes Mellitus Patients: A Prospective Randomized Controlled Clinical Trial. J Lasers Med Sci. 2019;10(1):56-63."
}
]
},
{
"id": "146327",
"date": "22 Aug 2022",
"name": "Samir Namour",
"expertise": [
"Reviewer Expertise Oral surgery",
"laser dentistry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nVery interesting paper. Authors treated with success the problem of severe bone resorption and tooth mobility that can result in teeth loss by preserving the proximal part of the tumor to avoid food retention and pocket complication in case of total excision of the proximal part at the tumor at the first step of surgery. This way offers a new and original way to treat this kind of risk. The paper is very interesting and an excellent and smart procedure to avoid future pocket complications and the loss of mobile teeth. Congratulations. To resume, this case report is bringing a new procedure and a new clinical management for the treatment of this kind of sensitive clinical cases. I highly recommend the indexing of this paper.\nHowever, we advise authors to do some adaptations to the manuscript:\nAdaptation of the title to the content of the manuscript:\nActually, the title is : Case Report: Interstitial-intralesional laser therapy and laserassisted new attachment procedure for the treatment of an aggressive pyogenic granuloma. My proposition is to make it as follow: “Interstitial-intralesional laser therapy and laser-assisted new attachment procedure for the treatment of alveolar bone loss provoked by an aggressive pyogenic granuloma. Case Report”.\nIn the case report description:\nSecond paragraph: the sentence is: “The periapical radiograph showed distinct periapical bone destruction of tooth no. 36 and tooth no. 37” . We propose to add the words: and proximal in the sentence. The sentence becomes as follow: “ The periapical radiograph showed distinct periapical and proximal bone destruction of tooth no. 36 and tooth no. 37 “\n\nIn the description of the photobiomodulation (PBM) paragraph: Authors have to add, despite the description in the photo 5 showing the way of application, a descriptive text mentioning: sites of application of PBM and the way of application, contact or non-contact, more details despite the photo. They have to also mention the total irradiation time per session, diameter of the fiber, etc.\n\nIn the same paragraph of PBM, authors have to erase the word “photocoagulation”. Because the photobiomodulation can not deliver enough energy to heat tissue and to provoke any coagulate. It is a contradiction with the aim of the Photobiomodulation except if they omit to indicate the power used to induce a coagulation. The Diode (980 nm) can induce a coagulation under some irradiation conditions. The sentence becomes : “ …continuous wave. and 4 J/cm2 to achieve photocoagulation and photobiomodulation effects (Figure 5)”.\n\nAuthors have to add a paragraph with the Indication of the chronology of different treatments. Three procedures were used for the complete treatment: The interstitial-intralesional laser therapy, Photobiomodulation and LANAP were used in the treatment. Authors have to indicate clearly the chronology details. All of the 3 procedures were used in the same session or separately. We understand that Covid pandemic delayed some sessions, but authors should resume and indicate, in a separate paragraph the exact and advised chronology of 3 procedures per each session, the optimal timing for the different sessions and the chronology of the 3 procedures. Did they use the 3 procedures one after another in the same session or in separate sessions? What is the time between sessions? Their precise details and their news protocol has to allow other practitioners to perform similar procedures in order to obtain similar results.\n\nIn the discussion authors wrote :\nFirst paragraph: “ An infrared diode laser was chosen in this case because of its hemoglobin absorption ability. This resulted in ablation with hemostasis”. We advise authors to adapt their sentence similar to this way: “ An infrared diode laser was chosen in this case because of its low absorption ability by water of soft tissue and its capacity to generate deeper and more heat. This resulted in ablation with hemostasis”.\n\nIn fact, the diode laser ( 980 nm) has low absorption by hemoglobin. But because of its low absorption by water and by consequence this low absorption by water allows this wavelength to have a deeper penetration in tissue resulting in an important heat generation allowing coagulation.\n\nSecond paragraph, the sentence: “For the photocoagulation technique, in this case, using a 635 nm diode laser at a power less than 0.5 W not only promoted clot formation but also resulted in photobiomodulation, …” We advise authors to reformulate or to erase their paragraph because the Diode laser 635 nm (red light) at 0.1 W (energy delivered in the case report) cannot coagulate. This wavelength at 0.1 W can only induce a Photobiomodulation. To induce a coagulation, the delivered energy has to be used at high output power. We advise authors to erase the word: “photocoagulate” from their paragraph and replace it by “Photobiomodulation”.\n\nAgain, congratulations to the authors for this new and very interesting clinical procedure. They are bringing to the lecturer a new way to treat this kind of disease avoiding the loss of teeth.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "8689",
"date": "30 Aug 2022",
"name": "Sajee Sattayut",
"role": "Author Response",
"response": "We are very grateful to your kind and smart advices. Those provide this manuscript more meaningful. We will modify the manuscript as suggested and will back to reply to you."
},
{
"c_id": "8727",
"date": "06 Sep 2022",
"name": "Sajee Sattayut",
"role": "Author Response",
"response": "Reviewer: Samir Nammour Very interesting paper. Authors treated with success the problem of severe bone resorption and tooth mobility that can result in teeth loss by preserving the proximal part of the tumor to avoid food retention and pocket complication in case of total excision of the proximal part at the tumor at the first step of surgery. This way offers a new and original way to treat this kind of risk. The paper is very interesting and an excellent and smart procedure to avoid future pocket complications and the loss of mobile teeth. Congratulations. To resume, this case report is bringing a new procedure and a new clinical management for the treatment of this kind of sensitive clinical cases. I highly recommend the indexing of this paper. However, we advise authors to do some adaptations to the manuscript: Adaptation of the title to the content of the manuscript: Actually, the title is : Case Report: Interstitial-intralesional laser therapy and laser-assisted new attachment procedure for the treatment of an aggressive pyogenic granuloma. My proposition is to make it as follow: “Interstitial-intralesional laser therapy and laser-assisted new attachment procedure for the treatment of alveolar bone loss provoked by an aggressive pyogenic granuloma. Case Report”. Response: The title was modified as your good suggestion. In the case report description: Second paragraph: the sentence is: “The periapical radiograph showed distinct periapical bone destruction of tooth no. 36 and tooth no. 37” . We propose to add the words: and proximal in the sentence. The sentence becomes as follow: “The periapical radiograph showed distinct periapical and proximal bone destruction of tooth no. 36 and tooth no. 37“ Response: More description of radiographic examination was wrote as you suggested. In the description of the photobiomodulation (PBM) paragraph: Authors have to add, despite the description in the photo 5 showing the way of application, a descriptive text mentioning: sites of application of PBM and the way of application, contact or non-contact, more details despite the photo. They have to also mention the total irradiation time per session, diameter of the fiber, etc. In the same paragraph of PBM, authors have to erase the word “photocoagulation”. Because the photobiomodulation can not deliver enough energy to heat tissue and to provoke any coagulate. It is a contradiction with the aim of the Photobiomodulation except if they omit to indicate the power used to induce a coagulation. The Diode (980 nm) can induce a coagulation under some irradiation conditions. The sentence becomes : “ …continuous wave. and 4 J/cm2 to achieve photocoagulation and photobiomodulation effects (Figure 5)”. Response: More details of laser irradiation and application were added as indicated in red. It was noted that we applied this photobiomodulation to achieve hemostasis effect of the lesion. Therefore, the alteration was as below:- This treatment was then immediately followed by treatment with using a 635 nm diode laser via an 8 mm optical fiber at 100 mW, continuous wave and 4 J/cm 2 with non-contact mode to the lesion at the buccal and lingual sites for 1 session per area to achieve photocoagulation and photobiomodulation and hemostasis effects (Figure 5). Authors have to add a paragraph with the Indication of the chronology of different treatments. Three procedures were used for the complete treatment: The interstitial-intralesional laser therapy, Photobiomodulation and LANAP were used in the treatment. Authors have to indicate clearly the chronology details. All of the 3 procedures were used in the same session or separately. We understand that Covid pandemic delayed some sessions, but authors should resume and indicate, in a separate paragraph the exact and advised chronology of 3 procedures per each session, the optimal timing for the different sessions and the chronology of the 3 procedures. Did they use the 3 procedures one after another in the same session or in separate sessions? What is the time between sessions? Their precise details and their news protocol has to allow other practitioners to perform similar procedures in order to obtain similar results. Response: The treatment procedures were defined in chronologically in the part of the case report. The chronology of the treatment regime for this patient as follows:- interstitial-intralesional laser therapy with photobiomodulation repeating treatments of interstitial-intralesional laser therapy for 2 sessions every two to three weeks the LANAP at a two-month after the third session of the interstitial-intralesional laser therapy and repeating the final LANAP a month after the first LANAP. First paragraph: “ An infrared diode laser was chosen in this case because of its hemoglobin absorption ability. This resulted in ablation with hemostasis”. We advise authors to adapt their sentence similar to this way: “ An infrared diode laser was chosen in this case because of its low absorption ability by water of soft tissue and its capacity to generate deeper and more heat. This resulted in ablation with hemostasis”. In fact, the diode laser ( 980 nm) has low absorption by hemoglobin. But because of its low absorption by water and by consequence this low absorption by water allows this wavelength to have a deeper penetration in tissue resulting in an important heat generation allowing coagulation. Response: We accepted your advice by altering the sentence as your suggestion. An infrared diode laser was chosen in this case because of its low absorption by water of soft tissue and its capacity to generate more heat producing a deeper coagulative zone. This resulted in ablation with hemostasis.2 Second paragraph, the sentence: “For the photocoagulation technique, in this case, using a 635 nm diode laser at a power less than 0.5 W not only promoted clot formation but also resulted in photobiomodulation, …” We advise authors to reformulate or to erase their paragraph because the Diode laser 635 nm (red light) at 0.1 W (energy delivered in the case report) cannot coagulate. This wavelength at 0.1 W can only induce a Photobiomodulation. To induce a coagulation, the delivered energy has to be used at high output power. We advise authors to erase the word: “photocoagulate” from their paragraph and replace it by “Photobiomodulation”. Response: We do appreciate your advice to reserve photocoagulation to be a phenomenon from photothermal reaction only besides explaining the real clinical outcome of hemostasis effect. Therefore, we modified the sentences as below: In this case, using a 635 nm diode laser at a power less than 0.5 W not only initiated clot formation but also resulted in photobiomodulation, which allowed a positive response to the healing process, such as an increase in microcirculation, the stimulation of cell growth, and a reduction in inflammatory substances. 5 Again, congratulations to the authors for this new and very interesting clinical procedure. They are bringing to the lecturer a new way to treat this kind of disease avoiding the loss of teeth. Response: We deeply appreciated your kind consideration and suggestion."
}
]
}
] | 1
|
https://f1000research.com/articles/11-883
|
https://f1000research.com/articles/11-1089/v1
|
22 Sep 22
|
{
"type": "Research Article",
"title": "Mental health problems of asymptomatic or mildly symptomatic COVID-19 patients in hospitel in Thailand: A cross-sectional study",
"authors": [
"Nitchawan Kerdcharoen",
"Pantri Kirdchok",
"Chayut Wonglertwisawakorn",
"Yingrat Naviganuntana",
"Nongnuch Polruamngern",
"Chotiman Chinvararak",
"Nitchawan Kerdcharoen",
"Pantri Kirdchok",
"Chayut Wonglertwisawakorn",
"Yingrat Naviganuntana",
"Nongnuch Polruamngern"
],
"abstract": "Background There is evidence that patients with COVID-19 have a higher prevalence of mental health problems than the normal population. This study aimed to investigate the prevalence of mental health problems and their associated factors in patients with asymptomatic or mildly symptomatic in the hospitel in Thailand. Methods Mental health problems were evaluated using the Depression, Anxiety, and Stress Scale - 21 items, and Patient Health Questionnaire-9. The prevalence of mental health problems was presented by frequency and percentage. McNemar's test was used to compare the prevalence of mental health problems between day 1 and day 7. Binary logistic regression was used to identify potential predictors of mental health problems. Results A total of 186 participants (68.3% female; mean age = 37.21 years (SD 13.66) were recruited. The depression, anxiety, and stress rate on day 1 of admission was 26.9%, 32.3% and 25.8%, respectively. Having mild COVID-19 symptoms was a significantly associated factor with anxiety (OR=2.69, 95%CI: 1.05-6.89) and stress (OR=4.53, 95%CI: 1.32-15.55). Conclusions There was a high rate of mental health problems in COVID-19 patients. Detecting and managing mental health problems should be considered standard care for COVID-19 patients.",
"keywords": [
"Mental health problems",
"COVID-19",
"Hospitel",
"Thailand"
],
"content": "Introduction\n\nSince the World Health Organization announced the emergency statement regarding the pandemic of novel coronavirus disease 2019 (COVID-19) on 30 January 2020, Thailand, like other countries, has to face the rise of new cases of COVID-19. The number of positive COVID-19 cases exceeded the health system's capacity. However, at the beginning of the pandemic, Thailand did not have a home isolation policy and stated that all patients would be under the medical team's care. Therefore, the Thai government set up the “hospitel”, a new type of health care facility.1\n\nThe term “hospitel” is the compound noun from the “hospital” and “hotel”. It is a new type of health care facility specialised for COVID-19 patients who are asymptomatic or have only mild symptoms. A hospitel is organised and run by the hotel and medical staffs from an affiliated public hospital. The team includes general practitioners, nurses and paramedics. Patients in hospitel are monitored regularly and are quarantined for seven days or until they have negative COVID-19 test results.1 Hence, hospitels also aim to prevent the spread of COVID-19 in the community.1\n\nAlthough patients are regularly monitored for physical complications, mental health problems, especially stress adjustment, may be under-recognised. The meta-analysis study by Liu et al., 2021 found that anxiety symptoms and depression rates in COVID-19 patients were 32% and 27.6%, respectively.2 Moreover, insomnia was found to have a prevalence of 30.30%. While the study in Thailand by Lerthattasilp et al., 2020 showed that the prevalence of depression was found to be 22.5%, whilst the anxiety rate was 30%, and the stress rate was 20%.3 The study by Lerthattasilp et al. was conducted in a field hospital that has a similar concept of caring to “hospitel”.3 This data demonstrated that patients with COVID-19 are more likely to suffer mental health problems than the normal population. In addition, early studies revealed that the female gender, physical symptoms related to COVID-19, duration of hospitalisation, and a history of psychiatric disorders were associated factors to mental health problems.3–7\n\nThe objective of the present study was to investigate the prevalence of mental health problems, including depression, anxiety and stress, as well as their associated factors in patients with asymptomatic or mildly symptomatic in the hospitel in Thailand, which is under the supervision of the Faculty of Medicine Vajira Hospital. We hypothesise that the prevalence of mental health problems is likely to be high on day 1 at admission and will decline after 7 days. However, despite to the new outbreak of COVID-19 globally, there are still limited studies on mental health problems. Recognising this concern is essential to the Thai public health sector in order to implement appropriate measures to tackle mental health problems related to COVID-19 infection.\n\n\nMethods\n\nWe obtained approval from the Ethical Committee of the Institutional Review Board of the Faculty of Medicine Vajira Hospital on July 2nd, 2021 (COA no. 120/64E). Before starting the survey, all participants were informed of the study's objectives, method, and provided written informed consent.\n\nWe employed a cross-sectional descriptive study based on STROBE guidelines.8 The sample size was calculated following the Cochrane formula.9 As the number of COVID-19 patients (N) admitted to the hospitel between July and September 2021 was 250, the sample size was estimated by p = 0.198 according to the study by Jeong et al., 2019.7 Using alpha at 0.05 and error (d) at 0.05, the required sample size was 124. 186 asymptomatic or mildly symptomatic COVID-19 patients, according to COVID-19 treatment guidelines by the National Institutes of Health (NIH), aged 18 years and older were recruited by purposive sampling in-person when the participant was initially admitted to the hospitel under the supervision of the Faculty of Medicine Vajira Hospital from July to September 2021. Patients who could not use the internet were excluded from this study.\n\nThe study instruments consisted of four questionnaires: 1) demographic characteristics including sex, age, education level, employment status, financial status, and living status; 2) clinical characteristics including severity of COVID-19, duration of COVID-19 infection, duration admitted in the hospitel, referring status, admission status, history of medical and mental disorders and perceived psychological support while in the hospitel; 3) the Depression, Anxiety, and Stress Scale - 21 items (DASS-21); and 4) Patient Health Questionnaire-9 (PHQ-9) would performed if participants had moderate to severe severity from DASS-21 score in any domains. In addition, we collected participants' data on day 1 and day 7 of admission by Google form.\n\nDASS-21 consists of three domains; each domain comprises seven items, and the depression, anxiety, and stress scores are calculated by summing. Then, the severity of each part is categorised into normal, mild, moderate, severe and extremely severe. The Cronbach's alpha coefficient of the DASS-21 Thai version is 0.75 reflecting good internal consistency.10,11\n\nPHQ-9 Thai version has a total of 9 depressive questions. The total score of PHQ-9 is classified into normal (0–6), mild (7–12), moderate (13–18), and severe (≥19). The sensitivity and specificity of PHQ-9 are 84% and 77%, respectively, to detect depression.12,13\n\nData were analysed using SPSS software (version 28.0; IBM, Chicago, IL, USA). The prevalence of mental health problems was presented by frequency and percentage. McNemar's test was used to compare the prevalence of mental health problems between day 1 and day 7. In addition, binary logistic regression (odds ratio [OR] and 95% confidence interval [CI]) was used to identify potential predictors of depression, anxiety and stress. P<0.05 was considered statistically significant.\n\n\nResults\n\nOf 186 participants recruited in this study, they had a mean age of 37.21 years old (SD 13.66). The majority of participants were female (68.3%), single (54.8%), had an undergraduate degree (44.1%), employed (49.5%), and were living with family (59.7%) (Table 1).\n\nTable 2 demonstrates the clinical characteristics of the patients. Approximately 16% of participants had at least one underlying medical illness. Only 1.1% of participants had an underlying mental disorder. In addition, around 80% of participants had mild COVID-19 symptoms, and the symptoms lasted at least 7 days. The median duration of hospitel admission was 12 days (IQR 10-13). Most participants were admitted alone (86.6%), and eventually, they could be discharged from the hospitel after 7 days of admission. Interestingly, around 90% of participants perceived that they were provided psychological support while in the hospitel.\n\nRegarding the prevalence of mental health problems (Table 3), the depression, anxiety, and stress rates were 26.9%, 32.3% and 25.8%, respectively, on day 1 of hospitel admission. The most common level of depression measured by PHQ-9 was mild severity. However, after 7 days of admission, the depression, anxiety, and stress rates decreased to 18.3%, 17.2% and 12.9%, respectively. This difference in the proportion of mental health problems between day 1 and day 7 was statistically significant (P<0.05) (Figure 1).\n\na McNemar's test.\n\n* P<0.05.\n\n** P<0.01.\n\nThe results of binary logistic regression analysis revealed that having mild COVID-19 symptoms was a significantly associated factor with anxiety (OR=2.69, 95%CI: 1.05-6.89) and stress (OR=4.53, 95%CI: 1.32-15.55). In contrast, other factors were not associated with depression, anxiety and stress (P>0.05) (Table 4).\n\n* P<0.0.\n\n\nDiscussion\n\nTo the best of our knowledge, this is the first study to explore the prevalence of mental health problems among patients with COVID-19 in the hospitel in Thailand. The prevalence of depression was 26.9%, anxiety was 32.3%, and stress was 25.8% in patients with asymptomatic or mild COVID-19 symptoms at day 1 of their stay at the hospitel under the Faculty of Medicine Vajira Hospital supervision. Compared to the meta-analysis study from multinational countries, including China, the United States, Japan, India, and Turkey, the depression and anxiety rates had a similar trend (27.6 % vs 26.9 for depression and 32.6% vs 32.3% for anxiety).2 On the contrary, the stress rate in this study was relatively lower than in the study at the Thammasat University field hospital (30% vs 25.8%).3 Although we also used the DASS-21, the same questionnaire, the prevalence of stress in this study might have been lower since the study at the Thammasat University field hospital had more moderate to severe COVID-19 cases.3\n\nThe mental health problems rate declined significantly on day 7 of admission (P<0.05). The potential explanation may be that most patients can adjust to acute stress over time and with perceived psychological support.14,15 Moreover, the medical team at the hospitel always provide basic psychoeducation via a leaflet and video clip about coping with stress.16 The high-risk cases of mental disorders would then be referred to psychologists or psychiatrists.\n\nIn this study, mild COVID-19 symptoms was the only factor associated with anxiety and stress. This could be a helpful predictor of psychological screening problems in patients admitted to hospitel. However, unlike prior studies, we could not find the association between the female gender, duration of hospitalisation, and a history of psychiatric disorders and mental health problems. This could be because there were few patients with psychiatric disorders in this study. Additionally, we did not collect data on the detail of the physical symptoms of COVID-19.\n\nWe are aware of some limitations of the present study. First, we can only indicate associated factors, not causal relationships, due to the descriptive design. Secondly, we included only asymptomatic and mild symptoms, which may not represent all COVID-19 patients. Finally, the mental health problems in this study were assessed by online self-reporting questionnaires, which could demonstrate only symptoms, not disorders and patients who could not use the internet were excluded. Thus, patients with high-risk mental disorders should be further evaluated by psychiatrists or clinical psychologists.\n\nFuture research should investigate the prevalence of posttraumatic stress disorder (PTSD), which could be occurred following COVID-19 as a traumatic stressor.17 In addition, psychological intervention to prevent stress-related illnesses or psychological distress18 should be performed.\n\n\nConclusions\n\nThe prevalence of mental health problems in COVID-19 patients was common, especially on the first day of admission. However, it declined on the 7th day after admission. In addition, having mild symptomatic COVID-19 infection was an associated factor with anxiety and stress. Therefore, detecting and managing mental health problems should be considered standard care for COVID-19 patients.\n\n\nData availability\n\nfigshare: Mental health problems of asymptomatic or mildly symptomatic COVID-19 patients in hospitel in Thailand: A Cross-Sectional Study, https://doi.org/10.6084/m9.figshare.21108790.v1.19\n\nThis project contains the following extended data:\n\n• Hospitel Data.sav (anonymised responses in spss)\n\nfigshare: Mental health problems of asymptomatic or mildly symptomatic COVID-19 patients in hospitel in Thailand: A Cross-Sectional Study, https://doi.org/10.6084/m9.figshare.21108790.v1.19\n\nThis project contains the following extended data:\n\n• Demographic data record-Hospitel.docx (blank English copy of the demographic and clinical characteristics questionnaire used in this study)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe authors acknowledge all study participants and would like to thank Mr Anucha Kamson for his assistance in the statistical analysis.\n\n\nReferences\n\nTangcharoensathien V, Sachdev S, Viriyathorn S, et al.: Universal access to comprehensive COVID-19 services for everyone in Thailand. BMJ Glob. Health. 2022; 7(6): e009281. PubMed Abstract | Publisher Full Text\n\nLiu X, Zhu M, Zhang R, et al.: Public mental health problems during COVID-19 pandemic: a large-scale meta-analysis of the evidence. Transl. Psychiatry. 2021; 11(1): 384. PubMed Abstract | Publisher Full Text\n\nLerthattasilp T, Kosulwit K, Phanasathit M, et al.: Psychological impacts on patients with COVID-19 in a Thai field hospital. Arch. Clin. Psychiatry. 2020; 47(6): 215–217. Publisher Full Text\n\nLi J, Yang Z, Zhang J, et al.: The psychological symptoms of patients with mild symptoms of coronavirus disease (2019) in China: A cross-sectional study. J. Adv. Nurs. 2021; 77(4): 1813–1824. PubMed Abstract | Publisher Full Text\n\nIsmael F, Bizario J, Battagin T, et al.: Post-infection depressive, anxiety and posttraumatic stress symptoms: A prospective cohort study in patients with mild COVID-19. Prog. Neuro-Psychopharmacol. Biol. Psychiatry. 2021; 111: 110341. PubMed Abstract | Publisher Full Text\n\nLeung T, Chan A, Chan EW, et al.: Short- and potential long-term adverse health outcomes of COVID-19: a rapid review. Emerg. Microbes Infect. 2020; 9(1): 2190–2199. PubMed Abstract | Publisher Full Text\n\nJeong SJ, Chung WS, Sohn Y, et al.: Clinical characteristics and online mental health care of asymptomatic or mildly symptomatic patients with coronavirus disease 2019. PLoS One. 2020; 15(11): e0242130. PubMed Abstract | Publisher Full Text\n\nvon Elm E , Altman DG, Egger M, et al.: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. J. Clin. Epidemiol. 2008; 61(4): 344–349. Publisher Full Text\n\nWayne WD: Biostatistics: a foundation for analysis in the health sciences. 6th ed.New York:Wiley & Sons;1995.\n\nLovibond SH, Lovibond PF: Manual for the Depression Anxiety Stress Scales. 2nd. ed.Sydney:Psychology Foundation;1995.\n\nOei TP, Sawang S, Goh YW, et al.: Using the Depression Anxiety Stress Scale 21 (DASS-21) across cultures. Int. J. Psychol. 2013; 48(6): 1018–1029. PubMed Abstract | Publisher Full Text\n\nKroenke K, Spitzer RL, Williams JB: The PHQ-9: validity of a brief depression severity measure. J. Gen. Intern. Med. 2001; 16(9): 606–613. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLotrakul M, Sumrithe S, Saipanish R: Reliability and validity of the Thai version of the PHQ-9. BMC Psychiatry. 2008; 8: 46. PubMed Abstract | Publisher Full Text\n\nBabić R, Babić M, Rastović P, et al.: Resilience in Health and Illness. Psychiatr. Danub. 2020; 32(Suppl 2): 226–232. PubMed Abstract\n\nLakey B, Orehek E, Hain KL, et al.: Enacted support's links to negative affect and perceived support are more consistent with theory when social influences are isolated from trait influences. Personal. Soc. Psychol. Bull. 2010; 36(1): 132–142. PubMed Abstract | Publisher Full Text\n\nBrooks SK, Webster RK, Smith LE, et al.: The psychological impact of quarantine and how to reduce it: rapid review of the evidence. Lancet (London, England). 2020; 395(10227): 912–920. PubMed Abstract | Publisher Full Text\n\nYuan K, Gong YM, Liu L, et al.: Prevalence of posttraumatic stress disorder after infectious disease pandemics in the twenty-first century, including COVID-19: a meta-analysis and systematic review. Mol. Psychiatry. 2021; 26(9): 4982–4998. PubMed Abstract | Publisher Full Text\n\nLife event, stress and illness: The psychological impact of quarantine and how to reduce it: rapid review of the evidence. Lancet. 395(10227): 912–920. PubMed Abstract | Publisher Full Text\n\nChinvararak C: Demegraphic data record-Hospitel.docx. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "151293",
"date": "26 Sep 2022",
"name": "Sorawit Wainipitapong",
"expertise": [
"Reviewer Expertise Psychiatry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this article. The report was well written and organized.\nHereby, please find my suggestion for this work to become better suitable for indexing:\nSome general profiles of study location, Vajira Hospital, should be stated. For example, is it located in the metropolitan, urbanized, or regional area? Readers would gain benefit for generalizability regarding mental health-related profiles and conditions.\n\nAre previous mental disorders enrolled in the exclusion criteria?\n\nHow did the authors measure ‘perceived psychological support while in the hospitel’? Please clarify.\n\nPlease kindly check the psychometric properties of PHQ-9 Thai version. Because the categorized severity of depression and the cut-off score of two cited references are not similar, the authors are suggested to carefully use the interpretation of this screening tool and specify the cut-off score used in the study.\n\nTable 1 – Does ‘income’ refer to ‘income per month’?\n\nTable 2 – Should ‘asymptomatic’ in the ‘Duration with COVID-19’ section be placed in the proper position?\n\nFigure 1 – P-value could also be shown in the figure for it was mentioned in the text.\n\nTable 4 – Please check the indent used in the table (i.e. Widow/Divorced/Separated and Educational level).\n\nTable 4 – Please check the spelling ‘P<0.0.’ in the end of the table.\n\nCompared to the finding from another Thai field hospital, the authors might provide additional discussions regarding the location or uniqueness of the hospital besides the severity of COVID-19.\n\nCongratulations to all authors. They have done great work and I enjoyed reading this manuscript a lot.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8824",
"date": "21 Oct 2022",
"name": "Chotiman Chinvararak",
"role": "Author Response",
"response": "Thank you very much for your review. We will try to address all your comments and improve them in version 2 of this paper. 1. Vajira hospital is located in Bangkok and is responsible for caring for COVID-19 patients, especially those from the Thonburi district. 2. We did not exclude participants with previous mental disorders. There were 2 participants with preexisting mental disorders (shown in Table 2). 3. We used close-ended question (yes or no) to measure perceived psychological support while in the hospitel. We will update this information in version 2 of this paper. 4. We used the classification of depression (PHQ-9 Thai version) following reference number 13. 5. Yes, it refers to income per month. We will add this detail in version 2 of this paper. 6. We will change the position of \"asymptomatic\" in version 2 of this paper. 7. We will demonstrate P-value in Figure 1. 8. We will check the indent used in Table 1. 9. We will correct this mistake. The phrase is P<0.05. 10. We will discuss this issue (location of the hospitel) in version 2 of this paper."
}
]
}
] | 1
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https://f1000research.com/articles/11-1089
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https://f1000research.com/articles/11-117/v1
|
28 Jan 22
|
{
"type": "Research Article",
"title": "Research Software vs. Research Data II: Protocols for Research Data dissemination and evaluation in the Open Science context",
"authors": [
"Teresa Gomez-Diaz",
"Tomas Recio"
],
"abstract": "Background: Open Science seeks to render research outputs visible, accessible and reusable. In this context, Research Data and Research Software sharing and dissemination issues provide real challenges to the scientific community, as consequence of recent progress in political, legal and funding requirements. Methods: We take advantage from the approach we have developed in a precedent publication, in which we have highlighted the similarities between the Research Data and Research Software definitions. Results: The similarities between Research Data and Research Software definitions can be extended to propose protocols for Research Data dissemination and evaluation derived from those already proposed for Research Software dissemination and evaluation. We also analyze FAIR principles for these outputs. Conclusions: Our proposals here provide concrete instructions for Research Data and Research Software producers to make them more findable and accessible, as well as arguments to choose suitable dissemination platforms to complete the FAIR framework. Future work could analyze the potential extension of this parallelism to other kinds of research outputs that are disseminated under similar conditions to those of Research Data and Research Software, that is, without widely accepted publication procedures involving editors or other external actors and where the dissemination is usually restricted through the hands of the production team.",
"keywords": [
"Research Data",
"Research Software",
"Open Science",
"Research outputs’ dissemination",
"Research Evaluation",
"FAIR principles."
],
"content": "1. Introduction\n\nResearchers produce many different outputs in their work in order to obtain the results that will be published in scientific journals, in articles that are still the main exchanging information mechanism in the scientific conversation. Among others, researchers produce Research Data (RD) and Research Software (RS), but yet again, both outputs have not currently a publication procedure as widely accepted as the one existing for articles, which constitutes one of the main drawbacks for their acceptance as first class citizens in the scientific ecosystem. This is one of the goals of the FAIR guiding principles 1:\n\n…is for scholarly digital objects of all kinds to become ‘first class citizens’ in the scientific publication ecosystem, where the quality of the publication – and more importantly, the impact of the publication – is a function of its ability to be accurately and appropriately found, reused, and cited over time, by all stakeholders, both human and mechanical.\n\n[…] we do not pay our valuable digital objects the careful attention they deserve when we create and preserve them.\n\nOn the other hand, the following definition sets up Open Science goals related to research outputs 2:\n\nOpen Science is the political and legal framework where research outputs are shared and disseminated in order to be rendered visible, accessible and reusable.\n\nIn this context, as reported in 3, the necessary skills to reach out these goals are complex:\n\nThe skills needed for Open Science cover a broad span from data management to legal aspects, and include also more technical skills, such as data stewardship, data protection, scholarly communication and dissemination (including creating metadata)…\n\nand still require to be engineered 4 (see also section 5 of 5):\n\nAn acceptable workflow needs to be created. However, most researchers, while experts in their own fields, have little awareness of metadata standards for data publication and information science in general, leading to cognitive and skill barriers that prevent them from undertaking routine best-practice data management.\n\nAnother drawback of this missing publication procedure for RD and RS is the possible loss of the expert knowledge that has been acquired along the research process 6:\n\nIf not traditional papers and volumes, what, then, should researchers be publishing? Whilst the digital exchange of data is straightforward, the digital exchange and transfer of scientific knowledge in collaborative environments has proven to be a non-trivial task, requiring tacit, and rapidly changing expert knowledge – much of which is lost in traditional methods of publication and information exchange. We believe that there is a need for mechanisms that support the production of self-contained units of knowledge and that facilitate the publication, sharing and reuse of such entities.\n\nExamples of this lost knowledge include the report of failure cases, which are rarely published; or the description of the modifications that have been included in the final implemented algorithms, and that are the result of a long trial and error process to improve the initially conceived algorithm or to avoid computational errors.\n\nAlthough the current trend in the scientific publication ecosystem is to place RS and RD into a better position, many researchers are still at a loss when facing RS and RD dissemination, and do not possess the needed skills, support or assistance for their disclosure in the right conditions. Moreover, they consider that much work and effort would be necessary to accomplish this goal, while having little or no positive effect in their curriculum 4:\n\nPut crudely, the large amount of effort involved in preparing data for publication release, coupled with the negligible current incentives and rewards, prevents many researchers from doing so.\n\nOn the other hand, research funders, like the European Commission, are currently laying out Open Science policies in their calls, in which it is required open access to the generated RD of the funded projects (although there may be exceptions), and where it is recommended to provide open access to research outputs in all generality, beyond publications and data, e.g. software tools 30. Notice that in the dissemination of these research outputs it is necessary to provide significant information in order to facilitate their visibility, accessibility and their reuse 7:\n\nDetailed provenance includes facets such as how the resource was generated, why it was generated, by whom, under what conditions, using what starting-data or source-resource, using what funding/resources, who owns the data, who should be given credit, and any filters or cleansing processes that have been applied post-generation.\n\nBearing in mind the above described landscape, the goal of our work here is to contribute to the improvement of the scientific endeavor with protocols that could help researchers, and the community at large, in the dissemination of their produced RD and RS, while contributing to the accomplishment of Open Science goals.\n\nWe concentrate here in practical matters, that is, in the how to: how to disseminate RD and RS to make them first class citizens so that they become visible, accessible, reusable. But dissemination procedures are not enough. With the aim to motivate researchers to deal with better dissemination tasks, most of the times considered by the members of the scientific community as an additional, useless burden, we should also take into consideration pathways that yield improved research evaluation practices, so relevant for researchers. That is, pathways that contribute to evaluate correctly the disseminated outputs with protocols that help both the researchers – to know what will be evaluated and how – as well as the evaluators – into setting the evaluation process.\n\nOur proposal is grounded on our knowledge and experience concerning RS 8-12. This translation of knowledge from RS to RD has been already successfully applied 13 to propose a RD definition and to tackle some of the Borgman’s conundrum challenges 14. In the present paper we attempt to extend this approach to the case of RD dissemination and evaluation practices.\n\nThe plan of this work is as follows. The next section is devoted to revisit the corresponding points related to RS: definition, dissemination, evaluation and consideration of the role of FAIR principles in this context. Section 3 focus then in RD topics, reviewing the proposed RD definition 13 and to present the main contribution: some comprehensive RD dissemination and evaluation procedures. Conclusions will end this work.\n\n\n2. Research Software\n\nThree are the main components of this section: the RS definition coming from 11,12, the RS dissemination procedure coming from 8, the CDUR RS evaluation protocol from 11. Some comments on FAIR principles for RS will complete this section.\n\nIn this work we consider the following definition of RS 11,12:\n\nResearch software is a well identified set of code that has been written by a (again, well identified) research team. It is software that has been built and used to produce a result published or disseminated in some article or scientific contribution. Each research software encloses a set (of files) that contains the source code and the compiled code. It can also include other elements as the documentation, specifications, use cases, a test suite, examples of input data and corresponding output data, and even preparatory material.\n\nWe observe, following the above definition, that RS has three main characteristics:\n\n• the goal of the RS development is to do research,\n\n• it has been written by a research team,\n\n• the RS is involved in the obtention of the results presented in scientific articles (as the most important means for scientific exchange are still articles published in scientific journals).\n\nNote that documentation, licenses, examples, data, tests, software management plans and other related information and materials can also be part of the set of files that constitutes a specific RS.\n\nMoreover, a RS development team may not just use software produced by other teams, but also include external software as a component inside the ongoing development, something which is facilitated by the Free/Open Source Software (FLOSS)1 licenses. This potential external component will qualify here as RS if it complies with the three characteristics given in the above definition 13. Moreover, the responsible team of the resulting work should clearly identify the included external components and their licenses, as well as highlight, by means of recommended citation practices 8,11,15, the external components that qualify as RS.\n\nGeneral aspects of FLOSS issues can be consulted, for example, in 16. Let us remark that good practices for software development management ask for updating regularly the RS related information, like, for example, project’s funding, publications or involved teams and contributors. A Software Management Plan (SMP) can be a powerful tool to help and to handle this information, see for example 10.\n\nLet us recall that RS reference and citation recommendations have been considered in section 2.5 of 11 where we propose easy to adopt methods to improve RS citation practices.\n\nLet us begin by recalling that, as stated in 30:\n\nDissemination means the public disclosure of the results by appropriate means (other than resulting from protecting or exploiting the results), including by scientific publications in any medium.\n\nThe following RS dissemination procedure has been proposed in 8 and was first published2 in the PLUME project3 (2006-2013) 11,17. The French initial version includes a close analysis of legal issues (French author rights, licensing) in order to produce FLOSS RS. It is slightly updated and completed in the following. More information on the legal issues can be found in 9.\n\nAs a general recommendation, it is best practice to consider licensing issues and to keep them in a SMP from the very first stages of the RS development. The RS license establishes its sharing conditions: it gives rights for access, copy, modification, redistribution of the RS, and it can establish reciprocity clauses that should be respected by the potential RS users. Licenses should be put well into place before releasing the RS.\n\nHere we present the proposed RS dissemination procedure. Steps marked with (*) are to be revisited regularly for each version release.\n\n• Choose a name or title to identify the RS, avoid trademarks and other proprietary names, you can associate date, version number, and target platform. Consider best practices in file names4.\n\n• (*) Establish the list of authors and affiliations (this is the so called research team step). An associated percentage of participation, completed with minor contributors can be useful. If the list is too long, keep updated information in a web page or another document like a SMP, for example, where you can mention the different contributor roles. This is the step in which the intellectual property producer’s rights are established. Producers include the RS authors and rightholders. This is then the step in which RS legal issues related to copyright information are dealt with.\n\n• (*) Establish the list of included software and data components, indicate their licenses (or other documents like the component’s documentation) giving the rights to access, copying, modification and redistribution for each component. In the case of software and data that fall in the category of RS or RD, please take into consideration best citation practices 11,15.\n\n• Choose a software license, with the agreement of all the rightholders and authors, and establish a signed agreement if possible. The licenses of the software components that have been included and/or modified to produce the RS can have impact in your license decision, see for example 8,16,18. Software licenses and licensing information can be found at the Free Software Foundation (FSF)5, the Open Source Initiative (OSI)6, and the Software Package Data Exchange (SPDX)7. Consider using FLOSS licenses to give the rights of use, copy, modification, and/or redistribution. This is then the step in which legal issues related to the RS sharing conditions are to be taken into consideration. Indicate the license in the RS files, its documentation, and the project web pages. Give licenses, like GNU FDL8, Creative Commons (CC)9, LAL10, to documentation and to web sites.\n\n• Choose a web site, forge, or deposit to distribute your product; licensing and/or conditions of use, copy, modification, and/or redistribution should be clearly stated, as well as the best way to cite your work. Good metadata and respect of open standards are always important when giving away new components to a large community: it helps others to reuse your work and increases its longevity. Use Persistent Identifiers (PIDs)11 if possible.\n\n• (*) This step deals with the utility of the RS and how it has been used for your research (this is the research work step). Establish the list of main functionalities, and archive a tar.gz or similar for the main RS versions in safe place. Keep a list of the associated research work, including published articles. Update your documentation, SMP, web site, etc. with the new information in each main RS version.\n\n• Inform your laboratories and head institutions about this RS dissemination (if this has not be done in the license step).\n\n• Create and indicate clearly an address of contact.\n\n• Release the RS.\n\n• Inform the community (e.g via mailing lists), consider the publication of a software paper, see for example the list of Journals where you can publish articles focusing on software12.\n\nThis proposed procedure is flexible and can be adapted to many different situations.\n\nWe include in this section the summarized version of the CDUR protocol that can be found in 11 (section 4.1). This reference gives a detailed description and analysis of the protocol as well as a complete list of references related to this work. This procedure for RS evaluation contains four steps to be applied in the following chronological order: Citation, Dissemination, Use and Research. For example, as we have seen in the Section 2.2, the first steps in the RS dissemination procedure correspond to the correct RS identification, and in order to be correctly cited, the RS reference should be clearly indicated. Let us introduce a resumed version of these four steps.\n\n(C) Citation. This step measures to what extent the evaluated RS is well identified as a research output. It is also the step where RS authors are correctly identified as well as their affiliations.\n\nSection 2.5 of 11 proposes three different ways to establish a RS reference, in order to facilitate its citation. Moreover, a more evolved RS identification level could be provided in the form of a metadata set. Reference and metadata include, among other informations, the list of the RS authors and their affiliations (11, section 2.2).\n\n(D) Dissemination. This step measures the quality of the RS dissemination plan involving actions such as:\n\n• Choosing a license, with the agreement of all the rights’ holders and authors. Consider, preferably, using FLOSS licenses.\n\n• Choosing a web site, forge, or deposit to distribute the product; stating clearly licensing and conditions of use, copy, modification, and/or redistribution.\n\n• Creating and indicating a contact address.\n\nThis step deals with legal issues involving the authors and rightholders (as established in the Citation step) deciding and installing the license(s) for the RS dissemination. This is also the step concerning Open Science, as the RS license expresses its sharing conditions; and where policy makers should establish the Open Science policies that will be applied in the evaluation process.\n\nFinally, let us recall that the inclusion of the list of related publications, data sets and other related works in the dissemination procedure helps to prepare the reproducible science issues that are to be taken into account in the Use step.\n\n(U) Use. This step is devoted to the evaluation of the technical software aspects. In particular, this step measures the quality of the RS usage, considering that a performing RS is one that is both correct and usable by the target scientific community.\n\nThe RS usability does not only refer to the quality of the scientific output but also can deal with other matters, such as the provided documentation, tutorials and examples (including both inputs and outputs), an easy and intuitive manipulation, testing and version management, etc.\n\nThis is the reproducible science step, where it is measured how the published results obtained with the RS can be replicated and reproduced.\n\n(R) Research. This step measures the impact of the scientific research that has required in an essential way the RS under consideration.\n\nThe evaluation of this item should follow whatever standards for scientific research quality in the concerned community.\n\nThis is the step where the RS related publications (as described in the RS definition in Section 2.1) come into play, and where the evaluation should consider the difficulty of the addressed scientific problems, the quality of the obtained results, the efficiency of the proposed algorithms and data structures, etc. The RS impact can also be assessed through the research impact of the related publications, and through its inclusion (or use) as software component in other RS.\n\nEach of these four steps can reach different levels of qualification and the corresponding scale is to be set up by the policy makers considering a particular evaluation event. Thus, the CDUR protocol can be easily adapted to different circumstances: career evolution, recruitment, funding, RS peer review or other procedures to be applied by universities and other research performing institutions, research funders, or scientific journals, and it can also be adapted to different evaluation situations arising in different scientific areas.\n\nAlthough the FAIR principles have been first designed for data, they apply as well to other digital objects 1:\n\n…it is our intent that the principles apply not only to ‘data’ in the conventional sense, but also to the algorithms, tools, and workflows that led to that data. All scholarly digital research objects – from data to analytical pipelines – benefit from application of these principles, since all components of the research process must be available to ensure transparency, reproducibility, and reusability.\n\nIn the case of RS, FAIR principles have been considered in several conferences and publications, although some adaptations seem to be necessary 19-21.\n\nIn this section we highlight two points regarding these principles that appear in our RS dissemination procedure (see Section 2.2) and the CDUR evaluation protocol (see Section 2.3), namely those referring to Persistent Identifiers (PIDs) and metadata, as remarked in 5:\n\nCentral to the realization of FAIR are FAIR Digital Objects. These objects could represent data, software, protocols or other research resources. They need to be accompanied by Persistent Identifiers (PIDs) and metadata rich enough to enable them to be reliably found, used and cited.\n\nNote that these two points are included in the basic “minimum standar” of 5 (p. 13). In particular we would like to observe the following points regarding PIDs:\n\n• we recommend to use PIDs associated to authors, like ORCID13,\n\n• we recommend to associate PIDs to the disseminated RS; as a RS can have several versions, do consider a different PID for each main release,\n\n• as PIDs can be provided by the chosen deposit, PID provision should be one of the arguments favoring the selection of a deposit like, for example, Zenodo14,\n\n• articles associated to the RS should have their own PID, furnishing in this way the RS with other possible citation forms 11 (section 2.5), i.e. with complementary means to reliably finding the RS, facilitating thus its use and citation by other researchers,\n\n• if the included data and software components or other external components that are necessary to run the disseminated RS have associated their own PIDs, it is convenient to refer to them in order to contribute to their own access and visibility.\n\nOn the other hand, concerning the role of metadata sets in our RS dissemination and evaluation proposals, let us observe that metadata is a very flexible concept, going from a simple reference or citation form to a very complete and precise RS description. In any case, our protocols consider that they are an important tool to set attribution to the RS and to facilitate credit. One possibility we would like to suggest is the metadata format proposed in the PRESOFT SMP template 10, that has a manageable size and has also the advantage that it is based in the RS index card elaborated in the PLUME project (2006-2013). See, for example, the index card corresponding to OpenMVG15, a RS developed at the Laboratoire d’informatique Gaspard-Monge. A different, more complex metadata set can be generated, for example, with COdeMeta16.\n\nFinally, we consider the implementation and adoption of FAIR principles 1,5,7,22 and other standards as arguments favoring the choice of a deposit for the RS. A tool to help taking such decision could be the FAIRsharing platform17, that provides a large amount of community-developed standards, as well as indicators (among others) necessary to monitor their adoption, and to follow data policies established by funders, editorials and other organizations. See, for example, the information that appears in the FAIRsharing platform associated to the FAIR Principles18.\n\n\n3. Research Data\n\nThis section translates to RD the previously addressed RS issues: definition, dissemination and evaluation, ending with some RD FAIR considerations.\n\nIn coherence with the declared parallelism between RS and RD, we consider here the RD definition proposed in 13.\n\nResearch Data is a well identified set of data that has been produced (collected, processed, analyzed, shared and disseminated) by a (again, well identified) research team. The data has been collected, processed and analyzed to produce a result published or disseminated in some article or scientific contribution. Each research data encloses a set (of files) that contains the dataset maybe organized as a database, and it can also include other elements as the documentation, specifications, use cases, and any other useful material as provenance information, instrument information, etc. It can include the research software that has been developed to manipulate the dataset (from short scripts to research software of larger size) or give the references to the software that is necessary to manipulate the data (developed or not in an academic context).\n\nThus, RD has three main characteristics:\n\n• the goal of the collection and analysis is to do research, that is, to answer a scientific question,\n\n• it has been produced by a research team,\n\n• the RD is involved in the obtention of the results presented in scientific articles (as the most important means for scientific exchange are still articles published in scientific journals).\n\nThe identified set of data constitute a database in the case the data are arranged in a systematic or methodical way and is individually accessible by electronic or other means 23-27. The sui generis database rights primarily protects the producer of the database and may prohibit the extraction and/or reuse of all or a substantial part of its content for example 23.\n\nRemark that it is becoming a general practice for research funders to ask for a Data Management Plan (DMP) concerning the data generated in a funded project19 28-30. See for example the DMPonline platform of the Digital Curation Center (DCC) as a helpful tool to create, review, and share DMPs that meet institutional and funder requirements20. In particular, French research projects can benefit from DMP OPIDoR21.\n\nThe following procedure has been adapted to RD from the RS dissemination procedure proposed in Section 2.2. Similarly, steps marked with (*) are to be revisited regularly in each version release, if necessary.\n\nAgain, as a general recommendation, it is best practice to consider licensing issues and to keep a DMP from the very first stages of the RD development. The RD license establishes the sharing conditions: it gives rights for access, copy, modification, redistribution of the RD, and it can establish reciprocity clauses that should be respected by the potential RD users. It should be put well into place before releasing the RD.\n\n• Choose a name or title to identify the RD, avoid trademarks and other proprietary names, you can associate date, version number… Consider best practices in file names22.\n\n• (*) Establish the list of the persons that have participate to the RD production, that is, the persons who have collected, processed, analyzed, shared and disseminated the RD; as well as their affiliations (this is the so called research team step). If the list is too long, keep updated information in a web page or another document like a DMP, for example, where you can mention the different contributor roles. This is the step in which the producer’s rights are established, if any. Producers include the RD authors (in the case there are intellectual property rights associated to the RD) and the corresponding rightholders. This is then the step in which legal issues related to copyright and ownership information are dealt with 25,26,31,32.\n\n• Data can have associated other legal (or ethical) contexts 13,27,32,33, they can be intimately related to the ongoing research work, consider them with the help of legal experts if necessary.\n\n• (*) Establish the list of included software and data components, indicate their licenses (or other documents like the component’s documentation) giving rights to access, copying, modification and redistribution for the component. In the case of software and data that fall in the category of RS or RD, please take into consideration best citation practices 34-37.\n\n• Choose a data license, with the agreement of all the producers and rightholders, and establish a signed agreement if possible. The licenses of data components that have been included and/or modified to produce the RD can have impact in your license decision 27. Consider using licenses like the Creative Common licenses (V4.0)23 or the Open Data Commons Licenses24, for example. Other data licenses can be found at SPDX25. This is then the step in which legal issues related to the RD sharing conditions are to be taken into consideration. Indicate the license in the RD files, its documentation, the project web pages, etc. Give licenses, like GNU FDL26, Creative Commons (CC)27, LAL28, to documentation and to web sites.\n\n• Choose a web site, forge, or deposit to distribute your product; licensing and conditions of use, copy, modification, and/or redistribution should be clearly stated, as well as the best way to cite your work. Good metadata and respect of open standards are always important when giving away new components to a large community: it helps others to reuse your work and increases its longevity. Use Persistent Identifiers (PIDs)29 if possible.\n\n• (*) This step deals with the utility of the RD and how it has been used for your research (it is then the research work step). Establish the list of the main RD research issues that appear in your work and that can facilitate its reuse. Archive a tar.gz or similar for the main RD versions in safe place. Keep a list of the associated research work, including published articles. Update your documentation, DMP, web site… with the new information in each main release.\n\n• Inform your laboratories and head institutions about this RD dissemination (if this has not be done in the license step).\n\n• Create and indicate clearly an address of contact.\n\n• Release the RD.\n\n• Inform the community (e.g. via mailing lists), consider the publication of a data paper.\n\nThis proposed procedure is also flexible and can be adapted to many different situations.\n\nA much more complete and complex vision of data sharing can be found, for example, in 5.\n\nSimilarly to the RS CDUR evaluation protocol proposed in Section 2.3, the CDUR protocol for RD evaluation that we propose out in here contains four steps to be carried out in the following chronological order: Citation, Dissemination, Use and Research. The RS CDUR protocol translates to RD evaluation in a straightforward way:\n\n(C) Citation. This step measures to what extent the evaluated RD is well identified as a research output. It is also the step where RD producers are correctly identified as well.\n\nAs seen in the dissemination procedure (Section 3.2), a reference to cite the work should be well established. If required in a evaluation process, a complete set of RD metadata should be provided.\n\n(D) Dissemination. This step measures the quality of the RD dissemination plan, as seen in the previous Section 3.2.\n\nThis is also the step dealing with legal (and ethical) issues 13,27,32,33 related to the producers and rightholders (as established in the Citation step) deciding and installing the license(s) for the RD dissemination. It can also take into consideration further legal issues related to the objects under study represented in the RD and their legal contexts (13, section 3).\n\nThis is also the step concerning Open Science, as the RD license expresses its sharing conditions; and the step where policy makers should establish the Open Science policies that will be applied in the evaluation process.\n\nFinally, let us recall that the inclusion of the list of related publications, software and data sets and other works mentioned in the dissemination procedure helps to prepare the reproducible science issues that are to be taken into account in the Use step.\n\n(U) Use. This step is devoted to the evaluation of the technical data aspects. In particular, this step measures the quality of the RD. The RD usability does not only refer to the quality of the scientific output but also can deal with other matters, such as the provided documentation, tutorials and examples of use for easy and intuitive manipulation, etc.\n\nThis is the reproducible science step, where it is measured how the published results obtained with the RD can be replicated and reproduced.\n\n(R) Research. This step measures the impact of the scientific research that has required in an essential way the RD under consideration.\n\nThe evaluation of this item should follow whatever standards for scientific research quality in the concerned community.\n\nThis is the step where the RD related publications (as described in Section 3.1) come into play, and where the evaluation should consider the difficulty of the addressed scientific problems, the quality of the obtained results, the efficiency of the proposed algorithms and data structures, etc. The RD impact can also be assessed through the research impact of the related publications, and through its inclusion (or use) as a data component in other RD.\n\nTo end this section, let us remark that similar considerations for the flexibility of the application of the CDUR RS evaluation protocol do apply for RD.\n\nRemark that, as stated in Section 2.4, FAIR principles have been initially designed for data, so there is no need for a more detailed description here. Indeed, there is a lot of recent work on FAIR data issues, see for example 1,5,7,22,38 and the references mentioned there.\n\nAs we have seen all along in Section 3, what we have proposed for RS translates directly to RD: definition, dissemination, evaluation. Therefore, we think that the same applies for the points studied in the Section 2.4, namely PIDs and metadata: they find as well a direct translation to RD, so we think that there is no real need to develop them in here again.\n\nFinally, to complete our considerations on FAIR issues, we would like to mention some FAIR assessement tools currently under development, such as the automatic FAIR evaluator (DIGITAL.CSIC) of the EOSC-Synergy project30 or the data sharing evaluation project31.\n\n\n4. Conclusion\n\nDesigning and following best practices for research output dissemination are important steps toward accomplishing the Open Science goals, to render research visible, accessible and reusable 2. We also consider that the current evolution in research evaluation practices will enable the adoption of Open Science methods 39,11, as well as they will facilitate their integration in every day research activities.\n\nAs we have already detailed in our work, RS and RD present many similarities concerning dissemination and evaluation issues. For example, we have included in Section 3.1 a RD definition that has been proposed in 13 and that it is clearly based on a RS definition (see 11,12 and Section 2.1). Following the same scheme, in Section 3 we have proposed and argued in detail RD dissemination and evaluation procedures grounded in the RS proposed dissemination (Section 2.2 and 8) and evaluation (Section 2.3 and 11) procedures.\n\nIt is pending work for the future to analyse the potential extension of this parallelism to other kinds of research outputs that are disseminated under similar conditions as RD and RS, that is, without widely accepted publication procedures involving editors or other external actors and where the dissemination is usually restricted through the hands of the production team (eventually including platforms or repositories).\n\nSections 2.4 and 3.4 on FAIR RS and RD issues study the role of PIDs and metadata in the proposed dissemination and evaluation protocols. Yet, we can notice that the FAIR principles do not provide precise dissemination and evaluation provisions but general guidelines 1,7. We consider that our dissemination and evaluation (CDUR) proposals, if followed correctly, may clearly contribute towards a more sound implementation of FAIR principles.\n\nIn fact, our proposals here provide concrete instructions for RD and RS producers to make them more findable and accessible, as well as arguments to choose suitable dissemination platforms to complete the FAIR framework. Moreover, interoperability and reusability could be also fostered with best documentation practices, such as it is proposed in our dissemination procedure; practices that can be evaluated with our CDUR protocol. Furthermore, we consider that our dissemination and evaluation mechanims contribute towards open access outputs as we highlight precisely the steps that deal with licensing issues.\n\nOn another note, we consider that one of the advantages of the CDUR protocols for RS and RD described here is that they separate the evaluation of research aspects from those related to much more technical issues concerning software or data, as these different contexts may involve evaluators with disparate levels of expertise in the corresponding areas.\n\nAs remarked in Sections 2.3 and 3.3, the first two steps of the CDUR protocols correspond to best dissemination practices. A research output that is to be disseminated should be identified correctly to increase the visibility of the output, as well as the visibility of its producer team and their research work, in order to make it accessible and reutilizable. We have already highlighted in 11 that one of the roles of the evaluation stages is to improve best dissemination practices, such as best credit, attribution and citation, practices that are still to be widely adopted:\n\n… we consider that it is in the interest of the research communities and institutions to adopt clear and transparent procedures for the evaluation of research software. Procedures like the proposed CDUR protocol facilitate RS evaluation and will, as a consequence, improve RS sharing and dissemination, RS citation practices and, thus, RS impact assessment.\n\nFinally, we would like to emphasize the dissemination/evaluation loop: first, the CDUR protocol points out to the research community the need to correctly disseminate outputs, as only well disseminated outputs are potential subject of evaluation; secondly, the CDUR protocol also implies that outputs are to be disseminated following the adopted evaluation policies.\n\nIn this imbricated context, it is the intention of this work to contribute towards improving dissemination and evaluation procedures, and thus, to enhance best Open Science every day practices.\n\n\nData availability\n\nData underlying the arguments presented in this article can be found in the references and footnotes.",
"appendix": "References\n\nWilkinson M, Dumontier M, Aalbersberg I, et al.: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016; 3: 160018. PubMed Abstract | Publisher Full Text\n\nGomez-Diaz T, Recio T: Towards an Open Science definition as a political and legal framework: on the sharing and dissemination of research outputs. POLIS N. 2020; 19. Last Version dated 28/02/2021 is available on Zenodo. Publisher Full Text Reference Source (Last Version)\n\nEuropean Commission: Directorate-General for Research and Innovation, Open Science Skills Working Group Report: Providing researchers with the skills and competencies they need to practise Open Science.2017. Reference Source\n\nTask Group on Data Citation Standards and Practices, C.-I: Out of Cite, Out of Mind: The Current State of Practice, Policy, and Technology for the Citation of Data. Data Sci J. 2013; 12: CIDCR1–CIDCR7. Publisher Full Text\n\nEuropean Commission: Directorate-General for Research and Innovation. European Commission Expert Group on FAIR Data (2018) Turning FAIR into reality. Final Report and Action Plan from the European Commission Expert Group on FAIR Data.2018. Reference Source\n\nBechhofer S, De Roure D, Gamble M, et al.: Research objects: Towards exchange and reuse of digital knowledge. Nature Proceedings 2010. 2010. Publisher Full Text\n\nJacobsen A, de Miranda AR , Juty N, et al.: FAIR Principles: Interpretations and Implementation Considerations. Data Intell. 2020; 2(1-2): 10–29. Publisher Full Text\n\nGomez-Diaz T: Free software, Open source software, licenses. A short presentation including a procedure for research software and data dissemination.2014. Presented at the Workshop on open licenses: Data licencing and policies, EGI Conference 2015, Lisbon, May 2015. Spanish version: Software libre, software de código abierto, licencias. Donde se propone un procedimiento de distribución de software y datos de investigación, Septembre 2015. Reference SourceReference SourceReference Source\n\nGomez-Diaz T: Article vs. Logiciel: questions juridiques et de politique scientifique dans la production de logiciels. 1024 - Bulletin de la société informatique de France.2015; 5. First version initially published in the platform of the PLUME project, October 2011. Reference SourcePublisher Full TextReference Source\n\nGomez-Diaz T, Romier G: Research Software management Plan Template V3.2. Projet PRESOFT, Bilingual document (FR/EN).2018. Reference Source\n\nGomez-Diaz T, Recio T: On the evaluation of research software: the CDUR procedure [version 2; peer review: 2 approved]. F1000Res. 2019; 8: 1353. First published: 05 Aug 2019. PubMed Abstract | Publisher Full Text\n\nGomez-Diaz T, Recio T: Open comments on the Task Force SIRS report: Scholarly Infrastructures for Research Software (EOSC Executive Board, EOSCArchitecture). Research Ideas and Outcomes. 7: e63872. Publisher Full Text\n\nGomez-Diaz T, Recio T: Research Software vs. Research Data I: Towards a Research Data definition in the Open Science context.2021. F1000Res.\n\nBorgman CL: The conundrum of sharing research data. J Am Soc Inf Sci Tec. 2012. 63: 1059–1078. Publisher Full Text\n\nSmith AM, Katz DS, Niemeyer KE, et al.: Software citation principles. Peer J Comput Sci. 2016; 2: e86. Publisher Full Text\n\nFogel K: Producing Open Source Software: How to Run a Successful Free Software Project.2005. Reference Source\n\nGomez-Diaz T: Le Projet PLUME et le paysage actuel des logiciels de la recherche dans la science ouverte. Zenodo preprint. 2019. Reference Source\n\nAimé T: A Practical Guide to Using Free Software in the Public Sector.Reference SourceReference Source\n\nLamprecht AL, Garcia L, Kuzak M, et al.: Towards FAIR Principles For Research Software. Data Science. 2020; 3(1): 37–59. Publisher Full Text\n\nHasselbring W, Carr L, Hettrick S, et al.: From FAIR research data toward FAIR and open research software. Information Technology. 2020; 62(1): 39–47. Publisher Full Text\n\nKatz DS, Gruenpeter M, Honeyman T: Taking a fresh look at FAIR for research software. Patterns. March 12, 2021; 2(3): 100222. PubMed Abstract | Publisher Full Text Reference Source\n\nAnsone SA, McQuilton P, Rocca-Serra P, et al.: FAIRsharing as a community approach to standards, repositories and policies. Nature Biotechnology. 2019; 37: 358–367. PubMed Abstract | Publisher Full Text\n\nEuropean Parliament and the Council: Directive 96/9/EC of 11 March 1996 on the 1248 legal protection of databases.Reference Source\n\nJournal officiel de la République française: Lois et décrets: Code de la propriété intellectuelle, Version en vigueur au 23 juin 2021.Reference Source\n\nGuibault L, Wiebe A: Safe to Be Open: Study on the Protection of Research Data and Recommendations for Access and Usage. Universitätsverlag Göttingen; 2014. Publisher Full Text Reference Source\n\nde Cock BM , van Dinther B , Jeppersende Boer CG, et al.: The Legal Status of Research Data in the Knowledge Exchange Partner Countries. Knowledge Exchange Report. 2011. Reference Source\n\nLabastida I, Margoni T: Licensing FAIR Data for Reuse. Data Intelligence. 2020; 2(1-2): 199–207. Publisher Full Text\n\nEuropean Commission: Commission Recommendation (EU) 2018/790 of 25 April 2018 on access to and preservation of scientific information C/2018/2375.Reference Source\n\nScience Europe: Presenting a framework for discipline-specific research data management. Science Europe Guidance Document D/2018/13.324/1. 2018. Reference Source\n\nEuropean Commission: Horizon Europe Programme Guide.2021. Reference Source\n\nMaurel L: La réutilisation des données de la recherche aprés la loi pour une République numérique. La diffusion numérique des données en SHS - Guide de bonnes pratiques éthiques et juridiques. Presses Universitaires de Provence. 2018. Reference Source\n\nBoistel R, Bordignon F, Maurel F: Aspects juridiques de la gestion et du partage Des données. Journées Nationales de la Science Ouverte. 2019. Paris, France. Reference Source\n\nStérin AL: Diffuser des données de la recherche dans le respect du droit et de l'éthique: Comment faire lorsqu'on n'est pas juriste ? Guide de bonnes pratiques éthiques et juridiques. Presses Universitaires de Provence. 2018. Reference Source\n\nCallaghan S: Preserving the integrity of the scientific record: data citation and linking. Learned Publishing. 2014; 27: S15–S24. Publisher Full Text\n\nData Citation Synthesis Group: Joint Declaration of Data Citation Principles.Martone M, editor. San Diego CA: FORCE11; 2014. Reference Source\n\nKatz DS, Niemeyer KE, Smith AM, et al.: Software vs. data in the context of citation. Peer J Preprints. 2016; 4: e2630v1. Publisher Full Text\n\nDaTaCite Metadata Working Group: DataCite Metadata Schema Documentation for the Publication and Citation of Research Data. Version 4.3. DataCite e.V. 2019. Reference Source\n\nFAIR Data Maturity Model Working Group: FAIR Data Maturity Model. Specification and Guidelines (1.0).2020. Reference Source\n\nGuédon JC, Jubb M, Kramer B, et al.: Future of Scholarly Publishing and Scholarly Communication. Report of the Expert Group to the European Commission. 2019. Publisher Full Text\n\n\nFootnotes\n\n1 https://en.wikipedia.org/wiki/Free_and_open-source_software\n\n2 Diffuser un logiciel de laboratoire: recommandations juridiques et administratives, 2010, https://projet-plume.org/fr/ressource/diffuser-logiciel-recomm-juridiques-admin. In French.\n\n3 https://projet-plume.org/, https://projet-plume.org/en\n\n4 See for example https://libguides.princeton.edu/c.php?g=102546&p=930626, https://doranum.fr/stockage-archivage/comment-nommer-fichiers/\n\n5 https://www.fsf.org/licensing/\n\n6 https://opensource.org/licenses\n\n7 https://spdx.org/licenses/\n\n8 http://www.gnu.org/copyleft/fdl.html\n\n9 https://creativecommons.org/choose/\n\n10 http://artlibre.org/licence/lal/en/\n\n11 http://en.wikipedia.org/wiki/Persistent_identifier\n\n12 This list is mantained by Neil Chue Hong in the Software Sustainability Institute web page https://www.software.ac.uk/which-journals-should-i-publish-my-software\n\n13 https://orcid.org/\n\n14 https://zenodo.org\n\n15 https://projet-plume.org/en/relier/openmvg\n\n16 https://codemeta.github.io/codemeta-generator/\n\n17 https://fairsharing.org/\n\n18 https://fairsharing.org/FAIRsharing.WWI10U\n\n19 https://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-data-management/data-management_en.htm\n\n20 https://dmponline.dcc.ac.uk/\n\n21 https://opidor.fr/planifier/\n\n22 See for example https://libguides.princeton.edu/c.php?g=102546&p=930626, https://doranum.fr/stockage-archivage/comment-nommer-fichiers/\n\n23 https://creativecommons.org/choose/\n\n24 https://opendatacommons.org/licenses/\n\n25 https://spdx.org/licenses/\n\n26 http://www.gnu.org/copyleft/fdl.html\n\n27 https://creativecommons.org/choose/\n\n28 http://artlibre.org/licence/lal/en/LAL\n\n29 http://en.wikipedia.org/wiki/Persistent_identifier\n\n30 https://github.com/EOSC-synergy/FAIR_eva\n\n31 https://hal.archives-ouvertes.fr/hal-01943521"
}
|
[
{
"id": "121544",
"date": "07 Feb 2022",
"name": "Charles Romain",
"expertise": [
"Reviewer Expertise FAIR data",
"workflows for data publication",
"chemistry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript aims to highlight similarities between research software (RS) and research data (RD) in the context of Open Science. The authors propose protocols and procedures for the dissemination and its evaluation for both RS and RD. The introduction provides a clear overview of the context by citing relevant sources. The manuscript then discusses definition, dissemination procedures and evaluation protocols for both RS and RD.\nThe comparison of RS and RD in the context of dissemination (and its evaluation) is interesting and highlights some similarities in the bottlenecks and challenges that need to be addressed.\nHowever, our main general concern is the high heterogeneity of RD compared to RS (maybe a naïve vision) which makes these general procedures and protocols not always applicable or too vague to be practically useful as they don’t provide practical solutions.\nHowever, they have the merit to draw the attention to the importance of following good practices (e.g. protocols, procedures) to disseminate RD and RS, and provide general guidance which can help to identify what could be some potential practical solutions. We recommend this article to be indexed as a good basis for further discussions.\nBelow we provide some detailed comments and suggestions on specific points discussed in the manuscript that could be included in future version of the article.\nProposed definitions:\nThe proposed definitions used in this article are based on another article currently awaiting peer review1. The authors should update these definitions after comments from the reviewers and approval of the other manuscript.\n\nWe generally agree with the proposed definitions. However, regarding the definition of RD we would add that following protocols and standards established in the field are important. For example, “the data has been collected, processed and analysed following protocols, procedures and standards established in the field to produce a results…..”\nDissemination and evaluation procedures:\nThe dissemination procedure and the CDUR protocol for RS have previously been reported and reviewed, we don’t have further comments on these.\n\nOne important aspect and challenge for RD dissemination that should be mentioned is to make data “machine-readable” to facilitate collection and enable re-use, and thus contribute to new data-driven discoveries (e.g. using machine-based tool). In some fields, RD are mainly shared as “human-readable” format only, usually in a monolithic supporting information document along with a scientific publication (e.g. PDF format). RS in contrast has well developed repositories which to a certain extent are machine actionable, as well as being closely integrated into the publication processes (such as Github via https://github.com/openjournals and https://joss.theoj.org). Overall, we think this article should have a paragraph where the state of play might be on machine-readable or even machine-actionable RD and RS and perhaps comparing how this is evolving for both of them.\n\nIn general, it would be good to further emphasise that many aspects discussed in these procedures and protocols can easily be addressed with relevant metadata which are keys to address the FAIR principles. In terms of metadata, this plays a key role in ensuring Findability/Discovery of the object, using the metadata registry MDS (metadata store). It would be good for this article to perhaps illustrate the role of registered metadata in finding both RD and RS, and perhaps to explore the granularity of the metadata for both. Is it good enough to use metadata purely to discover the functionality of a RS code, or might it be necessary to explore in more details the functions and libraries in RS?\n\nIt is maybe a naïve vision, but research data features a much broader heterogeneity than RS, so many different types of data can be generated that it makes these procedures difficult to apply or generalise to RD in general (As mentioned in the report of reviewer 1 for RS2).\n\nIn general, more specific examples are provided for RS than for RD. More examples or references for RD would be useful for the readers.\nDissemination steps:\nContrary to RS, versioning is rare or can be difficult to achieve with RD. Complementary data can be generated to support new conclusions but does not necessarily feature new versions of the previous ones, thus “revisiting version release” as mentioned doesn’t necessarily make sense, but each time new data are generated would be more appropriate.\n\nA single name or title for RD is not necessarily as straightforward as it is with RS, as RD usually are made available along with scientific articles (as mentioned in the three main characteristics), the name of the dataset can be related to the title of the narrative it accompany though.\n\n\"Choose a web site, forge…\" Data repository should be explicitly mentioned. In addition, selecting data repository which generate relevant metadata for the discipline (if available) should be considered (rather than generic data repository).\n\nThe address of contact can easily be addressed via PID associated with the authors (i.e. ORCiD).\nEvaluation steps:\nWe would encourage the author to discuss how the different C, D, U, R steps of the protocol help to meet the FAIR criteria. To some extent, the Citation step help to address the Findability, the Use step deals with the interoperability, etc…\nData citation:\nThese can easily be evaluated via the attribution of DOI, and PID for the researchers (OrCiD). The data citation can follow some guideline previously defined by various organisation (see joint declaration for data citation - FORCE11) and should be given as examples.\nThe choice of file format (e.g. non-proprietary, open format, machine-readable) to enable re-use is important and something that should be evaluated in the protocol.\nThe replicability and reuse steps are highly challenging for RD, even if RD are “well-disseminated”. We would emphasize the importance of the context and how the RD have been generated, to maximize reuse and reproducibility.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8746",
"date": "08 Sep 2022",
"name": "Teresa Gomez-Diaz",
"role": "Author Response",
"response": "Dear Charles Romain and Henry S. Rzepa, Many thanks for all your comments that have helped us a lot to improve our work. Here are some answers while we are preparing a new version. - [high heterogeneity of RD compared to RS] We will include some explanations. Indeed, heterogeneity appears obviously between software and data, yes. But if we keep these aspects aside and focus on the similarities, we can learn a lot from the common features that appear in the production context of RD and RS. This is a general procedure that can be adapted to several situations. Even when the differences are too important, and maybe the proposed dissemination and evaluation procedures are not directly applicable as such in both settings, they could help to suggest hints to address the diverse issues appearing in each environment. - [to draw the attention to the importance of following good practices] Many thanks! - [Proposed definitions, article currently awaiting peer review] We are preparing Version 2 of [Reference 13] bearing in mind Referees’ comments. - [Proposed definitions, would add following protocols and standards] We agree with you, but we do not think that is necessary to change the formulation of our definition. Yet, in the new version of [Reference 13], we have detailed and emphasized the relevance, in order to characterize the RD concept, of the research team decisions in the scientific production framework, which includes the protocols, procedures and standards to be followed in order to consider some given data as true RD. See, for example, our reference to the STRENDA standards developed for investigations on enzyme activities. Some of your comments to the present paper have helped us to improve the new version of [Reference 13], as they are related to the conceptual framework. For this reason, the new version of the present paper does not reflect them in here. - [Dissemination and evaluation procedures, machine-readable...] Yes, there are many relevant issues that are not detailed in our definition and proposed protocols, as we aim to address the subject from a more conceptual perspective. This point of view has been clarified in the new version of [Reference 13]. The decision of considering such broad point of view has required us to include in the new version of [Reference 13] comments reacting to some Referee questions that asked us, like you do, the consideration of different specific issues that they considered we had forgotten. - [Dissemination and evaluation procedures, a paragraph where the state of play might be on machine-readable or even machine-actionable RD and RS...] Again, out of our scope/goals, we agree that machine actionable is an important issue, but we do not enter in this kind of very concrete aspects. Some of your comments to the present paper have helped us to improve the new version of [Reference 13], as they are related to the conceptual framework. For this reason, the new version of the present paper does not reflect them in here. - [Dissemination and evaluation procedures, FAIR principles....] We deal with FAIR issues Sections 2.4 and 3.4, and as remarked there, we do remain in a conceptual level that does not enter in many challenging issues like the ones you mention. - [Dissemination and evaluation procedures, research data features a much broader heterogeneity than RS] See our comment above about heterogeneity issues. - [Dissemination and evaluation procedures, more specific examples are provided for RS than for RD] It seems to us that the targeted research audience is used to handle RS and/or RD as part of their everyday research practices, so they do not require further examples. Anyway, we have made references to different aspects of linguistic, environmental and geographical data in Section 3 of [Reference 13]. Moreover, further examples can be found easily in the literature, as can be seen in the bibliography included at the end of both works (the present article and [Reference 13]) . - [Dissemination steps, RD versioning is rare] References 49 and 50 of [Reference 13] do mention data versioning as the standard term. Indeed there are cases where versioning could be a difficult issue. But we consider that the RD production team can select the data that is to be released, and maybe provide several versions of the same RD object, thus, “version” seems to be the correct term. The inclusion of the sentence “each time new data are generated” could generate confusion: are we are referring to the same RD object or not? This is similar to what happens to new versions or main releases of software. - [Dissemination steps, single name or title for RD is not necessarily as straightforward] When we speak about the publications associated to RS or RD this means the place where the obtained results are published. Several articles or other scientific contributions (e.g. conferences, books…) can present the scientific results obtained with the RS and/or the RD. These objects (articles, RS, RD) can have different names. See for example the list of publications related to SageMath-Combinat [https://www.sagemath.org/library-publications-combinat.html] or the RD entitled “Vital Statistics data” associated to the publication [Recio Alcaide A, Pérez López C, Bolúmar F. Influence of sociodemographic factors in birth seasonality in Spain. Am J Hum Biol. 2022 Aug 8:e23788. doi: 10.1002/ajhb.23788]. It is usually difficult to foresee if some lines of code, or some collected data will become few months later more organized RS or RD. The fact of giving a name to this initial object is the first step to identify it as a research output. - [Dissemination steps, Data repository should be explicitly mentioned] Yes, you are right. This point has been studied in the Conclusions of [Reference 13], that is the Where? question of the RD Borgman’s conundrum challenges. We will modify in the new version of the present article the RD dissemination procedure to include your suggestion. - [Dissemination steps, The address of contact can easily be addressed via PID associated with the authors (i.e. ORCiD).] Well, we do not fully agree with this optimistic view, as ORCID usually refers to one researcher, while a mail address can refer to a (evolving) team, which is a much more generic solution. In our opinion, the identification issue can still be a quite challenging issue, mainly for software or data that have been developed for many years collectively. Thus, we do prefer to keep the current formulation in Sections 2.2 and 3.2 of the present article. - [Evaluation steps, how the different C, D, U, R steps of the protocol help to meet the FAIR criteria] Yes, you are right, and many thanks for this interesting suggestion, that have addressed in sections 2.4 and 3.4 of the new version. - [Data citation, can easily be evaluated via the attribution of DOI..] Citation examples are already available in the cited works, see for example References 4,34,35,37, and we will add this one: Altman M, Crosas M. The evolution of data citation: From principles to implementation . IASSIST Quarterly. 2013;37]. See also our comments above concerning ORCID issues. - [choice of file format] Yes, but we think that this issue is already addressed – perhaps not in such level of detail as you mention, as this level does not correspond to the more conceptual approach of our work – , as indicated in the dissemination protocols, in Sections 2.2 and 2.3: Good metadata and respect of open standards are always important when giving away new components to a large community: it helps others to reuse your work and increases its longevity. And this is to be evaluated in the CDUR protocol in the Dissemination step, as the use of open formats corresponds to Open Science issues. Other technical issues can be evaluated in the Use step, see the description of this step in section 4.2 of [Reference 11]. - [The replicability and reuse steps are highly challenging for RD, even if RD are “well-disseminated”. We would emphasize the importance of the context and how the RD have been generated, to maximize reuse and reproducibility.] Yes, see [Reference 13] where the importance of the context, that is intimately related to the data and RD concepts, is examined thoroughly in Section 3 (OECD Glossary of Statistical Terms and Reference 18 indicated in [Reference 13]. Following your suggestion, this point has been highlighted now in the new version in preparation, see the CDUR protocols proposed for RD (Section 3.3). Teresa Gomez-Diaz, Tomas Recio"
}
]
},
{
"id": "125654",
"date": "26 Apr 2022",
"name": "Mark Leggott",
"expertise": [
"Reviewer Expertise Research data management",
"research software",
"digital research infrastructure."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general I found the intent of the article (to propose a common rubric for making data and SW adhere to Open Science and FAIR Principles) to be a reasonable goal, but I'm not sure the article clearly achieves that goal. The authors state that \"Bearing in mind the above described landscape, the goal of our work here is to contribute to the improvement of the scientific endeavor with protocols that could help researchers, and the community at large, in the dissemination of their produced RD and RS, while contributing to the accomplishment of Open Science goals.\" I don't feel that the proposed protocols (CDUR) provide sufficiently detailed recommendations to support this goal.\nPart of the challenge I have in saying this is that work of initiatives like FAIR4RS would be very informative in this article, but they are not mentioned. Also, the FAIR4RS Principles have direct intersections with some of the CDUR approaches, which seems overly simplified in view of this FAIR4RS rubric. I find it unusual that the paper does not even mention the work of the FAIR4RS Working Group, which has articulated a number of the concepts and approaches highlighted in this article. The work of the RDA-FORCE11 Software Source Code Identification Working Group is also of direct relevance to the PID discussion in 2.4, so should be highlighted.\nA table comparing the CDUR recommendations against data and SW might be useful, as it would extract the key elements of the proposed approach and make it easier for the reader to make the connections.\nThe authors could mention the value of a Software Bill of Materials (SBOMs) in section 2.1, para 4 (Moreover...) Mentioning how a SMP can be integrated with a DMP, reinforcing the idea that the data and SW can be considered in a common rubric, would also be beneficial. There has been some work by the Software Sustainability Institute to develop a SMP meant to be integrated with standard DMP tools.\nI find the idea of drawing connections between the practices needed to support similar Open Science/FAIR concepts with data and SW is very desirable, and the authors do provide one of the few attempts to articulate this. If they were able to achieve a better integration of additional and specific resources and best practices with their CDUR approach, it would benefit the article substantially.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8747",
"date": "08 Sep 2022",
"name": "Teresa Gomez-Diaz",
"role": "Author Response",
"response": "Dear Mark Leggott, Many thanks for all your comments that have helped us a lot to improve our work. Here are some answers while we are preparing a new version. - [intent of the article] - [proposed protocols (CDUR) provide sufficiently detailed recommendations] Of course, it is our opinion that the article achieves that goal to a sufficient extent as to merit its approval by the Referees. - [initiatives like FAIR4RS...] Perhaps you have not noticed that in the original version of this paper there were specific references to FAIR RS in References 19,20,21. In the new version we have added more recent ones following your suggestion. We will also include Research Data Alliance/FORCE11 Software Source Code Identification WG, Allen, Alice, Bandrowski, Anita, et al. (2020). Software Source Code Identification Use cases and identifier schemes for persistent software source code identification (1.1). https://doi.org/10.15497/RDA00053. Many thanks for this suggestion. - [table table comparing the CDUR recommendations against data and SW] Thanks for your suggestion, but we do not think a comparison table is necessary, as CDUR for RS and for RD find pretty similar formulation, only a new item for RD dissemination (item 3 in Section 3.2) has been added to the RS dissemination protocol to highlight the potential difficulties concerning RD legal (and ethical) issues. - [Software Bill of Materials (SBOMs)] Many thanks for your suggestion, but we consider that software security issues, the main topic of, for example, the report https://linuxfoundation.org/wp-content/uploads/LFResearch_SBOM_Report_020422.pdf, are not part of our conceptual approach of Section 2.1. As already mentioned to other Referees, we do not enter in several concrete and technical issues. The point of software security issues, as well as many other ones, could be considered by the evaluation committees in the Use step of the CDUR protocol, which can be easily adapted by the committees to consider such technical points. Indeed, there are many relevant issues that are not detailed in our definition and proposed protocols, as we aim to address the subject from a more conceptual perspective. This point of view has been clarified in the new version of [Reference 13]. The decision of considering such broad point of view has required us to include in the new version of [Reference 13] comments reacting to some Referee questions that asked us, like you do, the consideration of different specific issues that they considered we had forgotten. - [how a SMP can be integrated with a DMP] Thanks again for your suggestion. This could be the subject of future extension of our work, but it is out of the scope of the present article. - [I find the idea of drawing connections between the practices needed to support similar Open Science/FAIR concepts with data and SW is very desirable, and the authors do provide one of the few attempts to articulate this.] Thank you so much for this very positive comment, that in some sense supports our perception that this article already provides enough contributions to merit its publication as it is, although, there is always room for improvements in future work. - [achieve a better integration of additional and specific resources and best practices] Following your suggestion we provide a new version of sections 2.4 and 3.4 regarding additional reflections on the relationships between FAIR and CDUR issues. For more detailed information on the CDUR protocol the appropriate reference is [Reference 11], while in the present paper we have included only a short description to explain that CDUR can be applied in a similar way for RS and for RD. Teresa Gomez-Diaz, Tomas Recio"
}
]
}
] | 1
|
https://f1000research.com/articles/11-117
|
https://f1000research.com/articles/10-114/v1
|
15 Feb 21
|
{
"type": "Research Article",
"title": "Associated predictor covariates of cervical cancer and impact on survival at Khartoum oncology hospital, Sudan",
"authors": [
"Amanda Elgoraish",
"Ahmed Alnory",
"Ahmed Alnory"
],
"abstract": "Background: Cervical cancer can be invasive and advanced at diagnosis causing devastating suffering and premature death. Cancer stage at presentation is related to survival evaluation and several factors determine stage. The aim of the study was to examine predictors covariates associated with cervical cancer stage and its impact on patient prognosis and survival. Methods: This retrospective cross-sectional study was carried out at Khartoum oncology hospital, Sudan. Participants were 239 cervical cancer patients diagnosed and treated between 2011-2015. Patients’ pathological and socio-demographic data were extracted from their medical files and survival times calculated from follow-up. Chi-square, Kaplan-Meier, Log-rank test and Cox regression model were used to examine relationships between demographic and clinical variables and survival outcome. Results: The mean age of the participants was 56.91 years and the majority were ≥45 years. Cancer survival analysis showed that stage at diagnosis had limited association with socio-demographic factors, with the exception of where patients residing. Multivariate regression using the Cox proportional hazard model confirmed strongly that stage (p=0.035, chemotherapy (p=0.000) and radiotherapy (p=0.001) were the most likely predictor covariates of patient prognosis and survival time. Conclusions: The results of this study suggest cancer stage at diagnosis and certain treatments are the most important factors impacting prognosis and survival of patients with cervical cancer. Early detection and vaccination of women against HPV infection provide enormous opportunities for early diagnosis, more effective treatment and better chances of survival.",
"keywords": [
"Cervical cancer",
"survival",
"stage",
"Cox model",
"Sudan"
],
"content": "Introduction\n\nCancer is a global public health problem, particularly in low- and middle-income countries, due to aging populations as well as broader social and environmental factors such as infectious diseases, education and ethnicity1. There are observed disparities in global cancer prognosis as mortality is higher among developing countries due to a lack of comprehensive early detection and effective medical care2. Cancer is a leading cause of death among women in both developing and developed countries and increasing3. Women in developing countries develop the disease during their prime reproductive period and face more suffering from the disease complications and risk of death4. The most common cancers afflicting women are those of the breast and cervix. These cancers are closely related to sexual and reproductive behaviour in Woman4.\n\nCervical cancer is a considerable cause of death among women in developing countries despite the fact that it is preventable. It is, also, potentially curable if detected early and treated effectively. It is the second most commonly diagnosed cancer in women in developing countries4. In these countries, cancer mortality exceeds that of diseases related to death in pregnancy. However, there is clear diversity of trends among world regions, within regions and individual countries, in the incidence and mortality of cervical cancer. In Africa, there is a wide variation due to different exposure and disease susceptibility1. In Sub-Saharan Africa, the incidence is low but mortality rates are high due to advanced stage at presentation5. In the Sudan, cervical cancer represents more than 16% of all cancer in women and 85% of cases are diagnosed at an advanced stage6,7. Cervical cancer is closely related to human papillomavirus (HPV) 16/18 infection and 78% of cases in the Sudan are diagnosed as invasive Lesions8. Moreover, the incidence and mortality rates of this invasive cervical cancer have increased during the last decade, especially among relatively young women3. This increase can be attributed to major changes in demography, economic and social factors, other disease risk factors and disease awareness9.\n\nCancer burden and disparity among countries and people can be explained by prevalence, incidence and mortality, but the most direct measure of disease severity can only be provided by survival rates10. Early detection and prevention are the most effective ways to reduce premature death from cervical cancer; however, from a short-term perspective, immediate and effective treatment is the optimal solution11.\n\nAnalysing cancer survival rates is an important way of discovering potential measures to be taken to improve the chances of better prognosis and survival. Cancer survival varies widely among different countries of the world due to differences in early detection and treatment modalities. By examining cancer survival from preventative measures and early detection, one can assess factors that have the greatest impact on cancer patient survival. Several studies have attempted to explain the relationships between patient survival and stage at diagnosis. These studies came to different conclusions about the strength and shape of these relationships and their impact. Researchers have a found significant association between stage of cancer at diagnosis and survival. Socio-demographic attributes such as age, education, gender and ethnicity have also been shown to have some effects12. On other hand, differences in the type of treatment and quality of medical services might have an important effect on survival outcome11.\n\nPrevious literature has shown the complexity of determining the drivers of international differences in the incidence and mortality of cervical cancer. It is most likely that each step in a patient’s journey to seek treatment contributes to some extent to these variations12. Many factors have been suggested to explain these variations; however, there is no complete agreement on potential predictor covariates that give overall explanations. Nevertheless, stage at diagnosis, tumor features and effective treatment have been postulated as the most widely accepted predictor covariates explaining degree and extent of their impact on prognosis and survival. For variations in cancer severity and survival, stage at diagnosis remains the strongest predictor of cancer survival13. One can conclude that stage at diagnosis is related to survival evaluation and assessment. Several factors determine stage at diagnosis, including age, education, occupation, location, tumor features, availability and accessibility of adequate diagnostic and treatment facilities11. Stage at diagnosis is crucial to disease treatment as treatment plans are usually based on stage of the disease14. The aim of this study was to examine predictor covariates associated with cervical cancer stage at diagnosis and its impact on cancer patient prognosis and survival.\n\n\nMethods\n\nThis was a retrospective cross-sectional hospital-based study. It was carried out at Khartoum oncology hospital, Sudan, which is the only medical institution providing complete diagnostic and cancer treatment services, where more than 80% of all Sudan cancer patients are registered15. Available patient information was collected from the hospital’s medical records during the study period of 2011-2015.\n\nThe target population of the study was patients with cervical cancer at Khartoum oncology hospital. To be included in the study, patients had to be between 18-79 years, be registered at the hospital, have complete medical records, have histopathologically confirmed cervical cancer and had received available treatment. Patients with incomplete medical records, unclear diagnosis and not treated at the hospital were excluded from the analysis. Written consent was obtained from the hospital to use participants’ data. No direct contact was made with patients during this data collection level. However, consent was obtained from participants during the active follow-up period.\n\nThe total number of patients at the hospital during the study period who met inclusion criteria, and were included in the analysis, was 239. This sample size of randomly selected participants was calculated from the number of cervical cancer patients among all cancer patients at this hospital as follows:\n\nThe formula n = 3.84 p(1-p)/(precision)2\n\nProportion = 0.044 (report of Federal Ministry of Health 2015), precision=0.026 with 95% CI\n\nn = 3.84*0.044(1-0.044)/(0.026)2 = 239\n\nThe study data collected from Khartoum oncology hospital patients’ medical files were checked and rechecked for accuracy, duplication, completeness and consistency by the researcher with continuous assistance from the hospital medical staff. Active follow-up was carried out during the year 2016 by the researcher through contacting patients or next of kin to ensure collection of needed information concerning patients survival status data(dead or alive). Moreover, a checklist was prepared by the researcher from the literature of cancer patients’ survival concerning socio-demographic and clinical factors affecting survival to assist in needed data collection16,33. Data collected were tabulated and coded according to the American Joint Committee on Cancer (AJCC) and the Union for International Cancer Control (UICC) TNM staging system for analysis17.\n\nData collected concerning socio-demographic characteristics and clinical status of patients included age at diagnosis, level of education, occupation, marital status, urban/rural residential area, tribe, menopausal status, cancer stage at diagnosis, tumor grade, tumor cell differentiation, histological subtype, treatment modalities, residence state and close family relation with previous disease experience. Dates of birth, death, loss to follow-up, diagnosis and survival times were checked by using other information provided by hospital medical and statistical staff. This information was clearly defined in medical terms concerning certificate of death, confirmation of diagnosis and calculation of survival time.\n\nThe statistical analysis is divided into two parts, descriptive statistics and regression analysis, using Stata version 11 (StataCorp, College Station, Texas) software. In the descriptive analysis, visual presentation of data in tables and figures given, provides socio-demographic and clinical data in numbers, percentage, chi2 and p-values and figures as clear indication of study population data distribution, relationships and associations. Then, important statistical conclusions were drawn. Statistical methods such as chi2, Kaplan-Meier, log-rank test and Cox regression were used to find out most prognostic factors associated with cancer disease. Socio-demographic variables and stage at diagnosis were tested by chi2. Stage, treatment, age and menopausal status were tested by log-rank test for equality. Socio-demographic variables, stage and treatment were tested by Cox regression. Stage was tested by Kaplan-Meier for survival rate between early and advanced levels. The analysis focuses on stage at diagnosis as the most crucial prognostic predictor of cervical cancer patient survival.\n\n\nResults\n\nThe total number of patients included in the analysis was 239 (Table 1)32. The median age of participants was 56.91 years (SE=0.88, at 95%CI=55.17-85.65) with the majority 82.9% ≥45 years old. In total, 94.6% of participants were married, 92.5% were unemployed, and 97.9% were illiterate and/or had no formal education. Most participants resided in western, Khartoum and eastern states of Sudan.\n\n* P-value<0.05 statistically significant association.\n\nThe distribution frequency of cervical cancer cases, according to the tumor, node and metastasis (TNM) staging classification system demonstrated that the majority 64.9% of participants were of advanced stage (III & IV), invasive squamous cell carcinoma 98.0%, with a high probability of spreading to distant organs (Table 2). Most of these patients’ tumors were of high grade and moderately to poorly differentiated cells. Furthermore, most of these patients had first-degree relations with previous disease history. Regarding treatment, 76.6% of these patients received radiotherapy, 57.3% chemotherapy, 10.5% hormone therapy and 6.3% surgery, alone or in combination with other therapies.\n\na % of invasive squamous cells carcinoma (98.0%), moderately to poorly differentiated cell (75.0%).\n\nThere was no significant correlation between age group of participants and stage (p-value>0.05), though the most frequent group among advanced stage was ≥45 years group. There was no significant correlation between cancer stage at diagnosis and other socio-demographic variables except state of residence (chi2=11.23, df=5, p=0.047). This could be explained by the fact that Khartoum and nearby states have diagnostic and treatment facilities.\n\nThe overall mean survival time after 60 months follow-up from time of diagnosis to the end of the study period was 32.0 months (95% CI=26.92 to 37.12). The lowest mean survival time according to stage levels was recorded at 13.1 months for stage IV(95% CI=6.55 to 19.62) (Table 2). Moreover, the log-rank test when performed to compare and explain survival distribution clearly showed highly statistically significant differences between various levels of the stage at diagnosis (chi2=33.49, df=3, p=0.000). Furthermore, the survival curve (Figure 1) gives a visual description of these differences in survival times of different stage levels. The Kaplan-Meier and log-rank tests were performed according to early and advanced stages and indicated clear differences in survival time means between the two groups. A low mean survival time of 23.77 months at the advanced stage was observed compared to 40.49 months at the early stage. The chi2 was 7.91, df=1 with p=0.004 (Table 2). The graph of the two survival functions curves were statistically equivalent of the two groups. The lowest probability of 30% was recorded at the advanced stage (Figure 1).\n\nThe Kaplan-Meier method and log-rank test were performed on the main four treatment therapies and only chemotherapy showed a highly statistically significant impact of chemotherapy on survival time. The chi2 was 19.12, df=1 with p=0.000. As for age groups and survival times, the analysis revealed there was a clear difference in the age group ≥ 75 years. The log-rank test equals 10.13, df=4 and p=0.038. However, when the comparison was made according to their menopausal status, the results showed the difference was not statistically significant (Table 2).\n\nThe Cox proportional hazards model was performed in four phases18. In the first univariate model, single predictor covariates; stage, treatment modality (chemotherapy) and age were statistically significantly associated with survival time (Table 3) while other factors were not. The hazard ratio of advanced stage at diagnosis was more than twice that at an earlier stage (HR=2.18 at 95% CI=1.24 to 3.83, p=0.007). This large difference was highly statistically significant with P-value <0.05. In the second multivariate (adjusted) model, all predictor covariates were included simultaneously which showed that advanced stage at diagnosis, treatment (chemotherapy and radiotherapy), state (eastern and western) and urban status were the only predictor covariates of survival time. Then, in the third model, all non-significant predictors, except age and surgery, were dropped from the model. The third model showed that stage and treatment (chemotherapy and radiotherapy) were statistically significant predictor covariates. The hazard ratio which measures the risk of dying from cervical cancer was nearly two times at the advanced stage compared to the early one (HR=1.84, at 95% CI=1.05 to 3.26, p=0.035). Other covariates were not statistically significant. However, the final multivariate model confirmed strongly stage, chemotherapy and radiotherapy, after age and surgery were dropped from the model, were the most likely predictor covariates of survival times and cervical cancer patient prognosis and survival outcome (Table 4).\n\n* P-value<0.05 statistically significant association.\n\n** P-value<0.001 highly statistically significant association.\n\n* P-value<0.05 statistically significant association.\n\n** P-value<0.001 highly statistically significant association.\n\na age, surgery and hormonal were dropped from the model.\n\nFinally, one of the main assumptions of the non-parametric Cox proportional hazard model is proportionality upon which the Cox model and log-rank test procedure are based. This assumption is based on the requirement of the hazard ratios being constant overtime or that the hazard for one individual is proportional to the hazard for any other individual. This proportionality constancy is independent of time. The test of proportionality showed clearly that the dependent covariate was statistically non-significant as the global test chi2 was 1.23, df=4 and p=0.873, an indication of the constancy of hazard overtime. This result indicated that the model did not violate the proportionality assumption. So, the appropriateness of the use of the model in the analysis was confirmed. Moreover, interaction in the model analysis showed that these interaction terms had no significant effects on the performance of the model.\n\n\nDiscussion\n\nA range of factors contribute to global and regional differences in cervical cancer incidence and mortality. Determining the drivers of these variations is complicated and there have been no comprehensive studies looking at this to date. However, stage, clinical features and quality of treatment are the most likely accepted explanations for this international differences12. Cervical cancer survival mainly depends on early detection and effective treatment modalities. Thus, by examining this survival through the eyes of prevention and control of the disease at diagnosis, one can assess and evaluate potential covariates with the most impact on patient survival. This study focused on cancer stage at diagnosis as the most important potential predictor covariate of survival. The result showed that these patients were relatively old, married, unemployed, illiterate, urban and belonged to non-Arab descent African groups. Cervical cancer, in the Sudan, is described as advanced at presentation and grade, aggressive and invasive squamous cell carcinoma and moderately to poorly differentiated cells leading to poor survival. Several previous studies reached to the conclusion of the disease as being invasive and advanced at presentation12,19-21. The stage at diagnosis is much related to survival and cancer survival analysis measures this relationship and the effectiveness of the health care system.\n\nThis study showed clearly that advanced cancer stage presentation at diagnosis had a significantly negative impact on survival outcome compared to the early stage. This conclusion is in agreement with previous studies in different developed and developing countries14,16,19,21-24. Cancer survival is measured as a proportion of cancer patients who remained alive after a specific period, usually 5-years. However, this cancer survival measure is fundamentally influenced by stage, age, treatment therapy and if it is preventable and curable. Cervical cancer is preventable and relatively curable if detected at an early stage though most cancer cases are diagnosed at a late stage in low- and medium-income countries and Sudan as shown in this study6,25-27. Late stage diagnosis has been found to be correlated with low survival rates, as well as complicated treatment, poor prognosis and survival outcome28-30.\n\nThis study demonstrated not only that late stage cancer diagnosis influences survival negatively but, also, how each predictor covariate affects the slope of the survival curve using Cox regression analysis. In a four step elimination process of confounding factors, the results confirmed strongly that stage, chemotherapy and radiotherapy were the most likely predictor covariates of survival times. This result was in agreement with a recent study in Saudia Arabia31. Though the late cancer stage at diagnosis has proven to be closely related to poor survival, there are other factors associated with low survival rates such as socio-demographic, cultural, and economic characteristics of the patient, and histopathological features of the tumor12.\n\nAside from the impacted survival rate, diagnosis of cervical cancer at an advanced stage has been explained by delays in diagnosis at presentation and initiation of treatment12. For cervical cancer, effective control measures are generally available and affordable. This disease can be, to a large extent, prevented by vaccination against HPV infection and by screening and treating pre-cancerous lesions. Other than this, early detection of cervical cancer is imperative to improve treatment outcomes. Assessment of the study conclusion should be interpreted with caution since the study was based on retrospectively routinely collected data from one referral hospital with the largest registration of cancer patients in the country. It does not include all data of cervical cancer patients in the country and is limited by the type of available data. Due to the huge differences in settings, it is prudent not to extrapolate from one experience in developed countries to others in developing countries.\n\n\nConclusion and recommendations\n\nThe results of this study suggest that cervical cancer stage at diagnosis and certain treatments are the most important factors impacting patient prognosis and survival outcome. The evidence presented has shown the complexity of determining what drives most variations in cancer outcomes between nations. It is most likely all steps the cancer patient takes when seeking medical care contribute to some degree to the differences in cervical cancer survival rates.\n\nCancer survival analysis can help in the diagnosis and treatment of cervical cancer and provide important information about where more effort should be directed. Early detection of cancer and vaccination of women against HPV infection provide tremendous opportunities for prevention, early diagnosis, more effective treatment and a higher probability of better survival and outcomes.\n\nGovernment intervention to reduce the suffering of cervical cancer treatment is of vital importance by providing diagnostic and oncological services in all general public hospitals and the introduction of oncology units in all state capital’s public hospitals. Early detection of cervical cancer should be the core of a proposed female cancer strategy through providing intensive and comprehensive vaccination, cervical cancer screening, and raising disease awareness among patients. This strategy needs to be closely linked to primary, secondary and tertiary care services.\n\n\nData availability\n\nZenodo: Elgoraish A. and Alnory A. cervical cancer dataset. http://doi.org/10.5281/zenodo.439944132\n\nThis project contains the following underlying data:\n\n- Cervical cancer dataset\n\nZenodo: Elgoraish A. Cervical cancer form. https://doi.org/10.5281/zenodo.446965433\n\nThis project contains the following extended data:\n\n- checklist.pdf\n\n- consent form.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nCompeting interests\n\nThe authors declare that they have no competing interests.",
"appendix": "Acknowledgements\n\nWe are thankful to all people who participated in the study. We thank the medical and statistical staff of Khartoum oncology hospital for their help in collecting personal and clinical data of cancer patients.\n\n\nEthical approval\n\nThis study received ethical approval from the Sudan Federal Ministry of Health (number:3-10-2015, dated: 15/12/2015). The health ministry asked the participating hospital to provide the researchers with existing data of cervical cancer patients in accordance with the protection of the patients’ personal information from improper use as required by law. The ethics board provided a waiver of consent for collecting participant’s medical records before follow-up. When participants were called for follow-up, they or their next of kin were informed about the study and oral informed consent was obtained.\n\n\nReferences\n\nParkin DM, Bray F, Ferlay J, et al.: Cancer in africa 2012. Cancer Epidemiol Biomarkers Prev 2014. PubMed Abstract | Publisher Full Text\n\nTorre LA, Siegel RL, Ward EM, et al.: Global cancer incidence and mortality rates and trends—an update. Cancer Epidemiol Biomarkers Prev 2015; 25Suppl: 16-27. PubMed Abstract | Publisher Full Text\n\nAmericanCancerSociety:Global Cancer: Facts and Figures. In: 2nd (Ed.), edition Altanta: American Cancer Society; 2012.\n\nTsu VD, Jeronimo J, Anderson BO: Why the time is right to tackle breast and cervical cancer in low-resource settings. Bull World Health Organ 2013; 91: 683-690. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRani R, Singh U, Trivedi V, et al.: Determinants of Survival of Cervical Cancer: A Hospital Based Study. Gynecol Obstet 2017; 7Suppl 5: 437. Publisher Full Text\n\nIbrahim A, Rasch V, Pukkala E, et al.: Predictors of cervical cancer being at an advanced stage at diagnosis in Sudan. Int J Womens Health 2011; 3: 385. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDenny LA, Anorlu R: Cervical cancer in Africa. Cancer Epidemiol Biomarkers Prev 2012; 21: 1434-1438. PubMed Abstract | Publisher Full Text\n\nICO/IARC:Human Papillomavirus and Related Diseases in Sudan: Information Centre on HPV and Cancer.2019Reference Source Accessed 15 oct 2019.\n\nBerraho M, Obtel M, Bendahhou K, et al.: Sociodemographic factors and delay in the diagnosis of cervical cancer in Morocco. Pan Afr Med J 2012; 12(1). PubMed Abstract | Free Full Text\n\nAlvi RA: Breast, cervical and colorectal cancer survival rates for northern Saskatchewan residents and First Nations (Master dissertation, University of Saskatchewan).1999Reference Source\n\nIAEA:Inequity in Cancer Care: A Global Perspective Vienna.International Atomic Energy Agency; 2011.\n\nFoot C, Harrison T: How to improve cancer survival Explaining England’s relatively poor rates. The King’s Fund.2011Reference Source Accessed 20 Feb 2019.\n\nAmericanCancerSociety:Global Cancer: Facts and Figures. In: 3rd (Ed.), edition Altanta: American Cancer Society; 2015.\n\nSankaranarayanan R, Swaminathan R, Brenner H, et al.: Cancer survival in Africa, Asia, and Central America: a population-based study. Lancet Oncol 2010; 11(2): 165-173. PubMed Abstract | Publisher Full Text\n\nSaeed MEM, Cao J, Fadul B, et al.: A five-year survey of cancer prevalence in Sudan. Anticancer Res 2016; 36Suppl 1: 279-286. PubMed Abstract\n\nNelima KE: Estimating the survival of patients with cancer of the cervix at Kenyatta National Hospital in Nairobi, Kenya. Afr J Health Sci 2013; 25: 92-103.\n\nGreene FL, Sobin LH: A worldwide approach to the TNM staging system: collaborative efforts of the AJCC and UICC. J Surg Oncol 2009 Apr 1; 99(5): 269-272. PubMed Abstract | Publisher Full Text\n\nKleinbaum DG, Klein M: Survival Analysis: A Self-Learning Text, Third Edition. Statistics for Biology and Health New York: Springer; 2005.\n\nColeman MP, Forman D, Bryant H, et al.: Cancer survival in Australia, Canada, Denmark, Norway, Sweden, and the UK, 1995-2007 (the International Cancer Benchmarking Partnership): an analysis of population-based cancer registry data. Lancet 2011; 377(Suppl 9760): 127-138. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSugarman JR, Dennis LK, White E: Cancer survival among american indians in western Washington state (United states). Cancer Causes Control 1994; 5Suppl 5: 440-448. PubMed Abstract | Publisher Full Text\n\nYan DD, Tang Q, Chen JH, et al.: Prognostic value of the 2018 FIGO staging system for cervical cancer patients with surgical risk factors. Cancer Manag Res 2019; 11: 5473-5480. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHalpern MT, Ward EM, Pavluck AL, et al.: Association of insurance status and ethnicity with cancer stage at diagnosis for 12 cancer sites: a retrospective analysis. Lancet Oncol 2008; 9Suppl 3: 222-231. PubMed Abstract | Free Full Text\n\nCarmo CC, Luiz RR: Survival of a cohort of women with cervical cancer diagnosed in a Brazilian cancer center. Rev Saude Publica 2011; 45Suppl 4: 661-667. PubMed Abstract | Publisher Full Text\n\nMadli F, Leong E, Ong SK, et al.: Predictive factors associated with survival rate of cervical cancer patients in Brunei Darussalam. Brunei International Medical Journal 2019; 15: 125-132.\n\nBouzouaia KA: Cancer Control in Tunisia 2006-2010,in WHO cancer control: Knowledge into active: WHO guide for effective programme, module 3, early detection.Geneva: World Health Organization; 2007Reference Source Accessed 2 Jun 2019.\n\nMwaka AD, Garimoi CO, Were EM, et al.: Social, demographic and healthcare factors associated with stage at diagnosis of cervical cancer: cross-sectional study in a tertiary hospital in Northern Uganda. BMJ open 2016; 6Suppl 1: e007690. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeverakonda A, Gupta N: Diagnosis and Treatment of Cervical Cancer: Research & Reviews. J Nurs Health Sci 2016; 2Suppl 3.\n\nVinh-Hung V, Bourgain C, Vlastos G, et al.: Prognostic value of histopathology and trends in cervical cancer: a SEER population study. BMC cancer 2007; 7Suppl 1: 164. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThomson CS, Forman D: Cancer survival in England and the influence of early diagnosis: what can we learn from recent EUROCARE results? Br J Cancer 2009; 101Suppl 2: S102-S109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWassie M, Argaw Z, Tsige Y, et al.: Survival status and associated factors of death among cervical cancer patients attending at Tikur Anbesa Specialized Hospital, Addis Ababa, Ethiopia: a retrospective cohort study. BMC cancer 2019; 19(Suppl 1): 1221. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnfinan N, Sait K: Indicators of survival and prognostic factors in women treated for cervical cancer at a tertiary care center in Saudi Arabia. Ann Saudi Med 2020; 40(Suppl 1): 25-35. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElgoraish A, Alnory A: cervical cancer dataset [dataset].Zenodo; 2020. Publisher Full Text\n\nElgoraish A: cervical cancer form.Zenodo; 2021. Publisher Full Text"
}
|
[
{
"id": "84246",
"date": "24 May 2021",
"name": "Nazik Hammad",
"expertise": [],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, the work is presented well. Some minor details that could be addressed:\nThe introduction is too long and has number of repetitions. It needs to be shortened and made succinct.\nI recommend replacing developing and developed countries with the more current terms: low-and-middle-income countries (LMIC) and high-income countries (HIC).\nIt is best to situate this article in the context of the WHO cervical cancer elimination strategy launched 2020; the 90-70-90 targets for 2030 especially in the recommendation section where Sudan should strive to achieve the WHO cervical cancer elimination targets by 2030. These are measurable targets for the Ministry of Health in Sudan and various stakeholders.\nThe last sentence in the discussion about the prudence of “not extrapolating from one experience in developed countries”, while correct, does not have relevance to the paragraph. I would suggest removing it.\nThe study design is appropriate. Outcome research is desperately needed in LMIC to inform policy and measure that need to be taken to improve access to cancer care across the continuum.\nI have reviewed the methodology, the consent form and the follow-up and they have sufficient details. However, it would be of added benefit if the following could be addressed:\nIs there a different intake form that has the employment status and other sociodemographic variables?\n\nThe authors may wish to explain what is the category “other tribes” that are neither non Arab descent Africans or Arab descent Africans mean. This constitutes 11% of the cohort.\n\nIt would add to the value of the research if a sentence can be added about how consent was obtained from women who cannot read and write?\nThe statistical analysis is very well done; however, I have the following questions:\nHas the chemotherapy and radiotherapy use been defined by stage? e.g., how many patients with advanced stage received chemotherapy versus those with early stage?\n\nThe data shows that 57% of patients received chemotherapy. Was there any correlation between receiving chemotherapy and residing in Khartoum versus peripheral areas, between receiving chemotherapy and education or ethnic origin?\nThe data supports that access to early diagnosis and treatment is needed to improve survival. As such the conclusion is supported by the results. While this is not surprising, it is important for future planning of health services to document this in Sudan.\nThe authors’ use of employment data as an indicator of socioeconomic status (SE) should be listed as a limitation as not all unemployed women in Sudan are of similar SE status especially in this cohort of older women. Household income and area of residence are likely to be indicative of socioeconomic status which may influence access to care. This data might have been difficult to collect but this should also be acknowledged.\nThe data does not provide indications as to the reasons for lack of access to chemotherapy. Lack of treatment details such as completion of a full course or radiotherapy and chemotherapy is also a limitation.\nHealth equity and cancer disparities should be highlighted. The data revealed that these patients are 62.2% non Arab descent African. Is this reflective of the general population in the area or is there more prevalence of cervical cancer among non Arab descent Africans? This is of relevance when planning prevention (vaccination), screening, treatment interventions by targeting the most vulnerable population.\nThe conclusion could be strengthened by calling further research looking into barriers to access to treatment. For example, this current cohort could be further interrogated in the future by investigating details of initiation and completion of treatment including chemotherapy and radiotherapy\nOverall excellent effort in a much needed area of health services research. I believe the paper has academic merit, but I ask for a number of small changes to the article and response to some queries.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6859",
"date": "30 Jun 2021",
"name": "Amanda Elgoraish",
"role": "Author Response",
"response": "Your comments concerning length of introduction, using LIMC instead of developing and developed countries and the last sentence of limitation paragraph have been taken notice of and appreciated. The suggestion of outcome research is commended but it is beyond the purpose of this study. However, implementation research is more urgent to assess efficacy and effectiveness of intervention and early detection programmes. Consent and follow-up was conducted by phone to collect vital status data (dead or alive) after explaining purpose of the interview and having verbal consent. Missing socio-demographic data were also, obtained during the interview to complete already collected data from patients medical files and diagnosis profiles. Other tribes indicate to participants who were Sudanese but did not belong to any of the known Sudanese tribes. They are most likely belong to non-Sudanese foreign ethnic groups. Participant were classified as early or advanced stages at diagnosis and majority of them were at the advanced stage. Thus, most of participants who received chemo and radio therapies are most likely belong to this advanced stage. The study focus was on stage at diagnosis as the major determinant of survival. Other socio-demographic factors, residence state and rural/urban centres were considered insignificant confounding variables. Household income and area of residence are proxy of socio-economic status and may influence access to care but the final conclusion of data analysis after removal of confounding variables and interaction terms affirmed that only stage at diagnosis and chemo and radio therapies are the effectors of cervical patient survival and outcome. The majority of participants of cervical cancer disease were from the non-Arab decent African tribes is an indication which can be of great help in planning vaccination and screening programmes. Suggested future research on barriers to treatment is commended but barriers to early detection is more urgent and appropriate in the short term future perspective. Sufficient details of methods and analysis and source data are available and adequate for further reproducibility by looking into data availability section of the article. Amanda Elgoraish Corresponding author"
}
]
},
{
"id": "147507",
"date": "06 Sep 2022",
"name": "Elvynna Leong",
"expertise": [
"Reviewer Expertise Statistics",
"Public Health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper is very meaningful, especially for Sudan, as there are currently not many studies published from the Africa region or Sudan on cervical cancer survival. However, there are a few key components that require further clarification or analysis from the researchers.\nTitle\nThe researchers aimed to examine predictors associated with cervical cancer stage at diagnosis and its impact on cancer patient prognosis and survival. However, the title of the paper does not state the word “stage”.\nMethods Data collection and sources\nThe authors stated a study period of 2011-2015 in the study design and follow-up in 2016. What is the earliest year of diagnosis? Were the participants recruited diagnosed during the 2011-2015 period only? Also, please give more details on the follow-up period. How long was the follow-up period? Is it up to December 2016?\nStatistical analysis\nThe statement “Statistical methods such as chi2, Kaplan-Meier, log-rank test and Cox regression were used to find out most prognostic factors associated with cancer disease” is not entirely correct. This needs to be revised. Explain why you used chi2, Kaplan-Meier, log-rank test and Cox PH regression separately.\n\n\"Log-rank test for equality.\" We suggest adding more detail on ‘equality’.\n\nResults Presentation of results needs to be improved, such as\nParagraph 1 in Descriptive statistics: removing at in \"(SE=0.88, at 95%CI=55.17-85.65)\".\n\nParagraph 1 in Descriptive statistics: rewriting “majority 82.9% ≥45 years old”.\n\nTable 2: It is very important to keep the statistics consistent in tables, such as p-values of the log-rank test should be kept to 3 decimal places.\n\nTable 2: We suggest replacing 0.000 with <0.001, which is more commonly used in literature.\n\nTable 2: For Treatment, each p-value from the log-rank test is compared with no treatment?\n\nTable 2: On mean of survival time, to label months in the table.\n\nRegression analysis: \"(chi2=33.49, df=3, p=0.000)\". Is chi2 =33.49 or 31.27, as indicated in Table 2?\n\nRegression analysis: \"The chi2 was 7.91, df=1 with p=0.004 (Table 2).\" p-value is 0.005 (rounded up to 3 d.p).\n\nRegression analysis: “The graph of the two survival functions curves were statistically equivalent of the two groups”. The p-value of 0.005 did not indicate statistical equivalence.\nTable 1\nThere were indications that geographical locations were significantly associated with stage of diagnosis, further discussion on this could be helpful.\nFor the survival analysis, was there a breakdown by 1-year or 3-years and 5-years survival rates? Was there any comparison or benchmarking of the findings or survival rates with other similar studies? It would also help to have some discussion on the potential explanations for these findings and to suggest for further studies. The researchers could identify the limitations of the study e.g. duration of treatment or any delay in treatment was not analyzed in the study.\nSome grammar problems should also be paid attention.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8863",
"date": "07 Oct 2022",
"name": "Amanda Elgoraish",
"role": "Author Response",
"response": "Some of your comments and suggestions have been taken care of in the text while others are clarified as below: The study period is called 5-years survival, 2011-2015, starting from 1st Jan 2011 till 31st Dec 2015. The follow-up was passively collected from participants' medical records and active follow-up during the year 2016 by contacting lost-to-follow-up participants to confirm their life status (dead or alive). The log-rank test for equality was intended to compare between different groups of covariates and to confirm their statistical significance differences. The survival tools of analysis were used to explain data analysis to suit descriptive and analytical sections and meet the requirement of each tool of analysis. Table 2: all p-values of the log rank test are kept to 3 decimal places. Table 2: for treatment each p-value of the log rank test basically is treatment and no treatment. Table 1: the location result (east and west) included p-values which were insignificant in the univariate model, but significant in multivariate model. It was also insignificant in the final regression model. The study was intended to examine cases in a referral hospital in Khartoum State. So it is difficult to make final conclusion on a very small dataset of participants outside Khartoum State which was beyond the scope of the study objectives. The study focused on 5-years survival (standard period for cancer survival analysis) and comparison with other short periods was not within the scope of the study. The study discussed other explanations for survival of cervical cancer patients in developing countries despite the paucity of similar studies. It refers to most recent published studies. Delay was mentioned as one of the most plausible explanations for cervical cancer patients' stage at diagnosis. We are in the final stage of presenting our new article on associated predictor covariates at diagnosis focusing on the delay as the most important factor. The study explained clearly its limitation based on availability and quality of data collected from participants' medical files and other sources."
}
]
}
] | 1
|
https://f1000research.com/articles/10-114
|
https://f1000research.com/articles/11-1143/v1
|
06 Oct 22
|
{
"type": "Research Article",
"title": "Risk factors for the incomplete immunization of children of health workers at a tertiary referral hospital in Surabaya, Indonesia",
"authors": [
"Yunita Puspitasari",
"Dominicus Husada",
"Budi Utomo",
"Anang Endaryanto",
"Risky Vitria Prasetyo",
"Santi Martini",
"Yunita Puspitasari",
"Budi Utomo",
"Anang Endaryanto",
"Risky Vitria Prasetyo",
"Santi Martini"
],
"abstract": "Background: Health workers as role models play a key role in increasing immunization coverage. The coverage of complete basic immunization in the city of Surabaya is 98.1%, a figure not similar to the incidences of infectious diseases that can be prevented by immunization. This study aims to determine the risk factors for incomplete immunization of the children of health workers. Methods: A case-control questionnaire study comparing incompletely immunized children (case group) and completely immunized children (control group) was done. Participants were children of health workers at a tertiary referral hospital in Surabaya. We conducted interviews and distributed and collected questionnaires from December 2021 to April 2022. Bivariate and multivariate analyses were conducted using the Pearson chi-square test and binary logistic regression. Results: Overall, 148 questionnaires were distributed, 33 of which were excluded due to incomplete data. Therefore, 115 health workers’ children were eligible participants. 62 participants (53.9%) made up the case group, while the control group consisted of 53 participants (46.1%). The average age of the children was 12.5 months, 51.3% were boys and 48.7% were girls. The parental age, parental knowledge, mother's education, and the presence of the coronavirus disease 2019 (COVID-19) pandemic has a significant association with the children’s immunization status with p-values of 0.043, 0.005, 0.002, and p < 0.001, respectively. The children of health workers with a low level of knowledge are 4.8 times more likely to be incompletely immunized (OR 4.887, 95% CI 1.346–35.152). In addition, the possibility of the incomplete immunization of a child is eight times higher for a low-income family (OR 8.679; 95% CI 1.429–52.701). Conclusions: Low levels of parental knowledge and income are associated with the occurrence of incomplete immunization among the children of health workers at a tertiary referral hospital in Surabaya.",
"keywords": [
"Incomplete immunization",
"Risk factors",
"Children",
"Health workers"
],
"content": "Introduction\n\nA health worker is a person who devotes themselves to the health sector and has the knowledge and skills from education in the health sector which, for certain roles, require(s) the authority to carry out health efforts. The health efforts of health workers can provide the example of the complete basic immunization status of their children to the wider population. The criteria for complete immunization in Indonesia followed the Ministry of Health Regulation No. 12 of 2017 concerning the administration of immunization: Every infant (aged 0–11 months) is required to receive complete basic immunization consisting of one dose of Hepatitis B, one dose of Bacillus Calmette–Guérin (BCG), three doses of diphtheria/pertussis/tetanus (DPT), hepatitis B (HB), Haemophilus influenza type B (HiB), four doses of polio drops, and one dose of measles-rubella (MR).1 Research suggests that health workers play a key role in maintaining and increasing immunization coverage.2,3 However, a systematic review found that health workers who have good knowledge still have negative attitudes toward immunization, such as less belief in the benefits and safety of immunization,3,4 so they are less likely to have their children receive immunizations and recommend them to the public.3–7\n\nIn 2019, in the East Java province, complete basic immunization coverage was at 95.5%.7 Meanwhile, in the city of Surabaya, complete basic immunization coverage was 98.1%. The Universal Child Immunization (UCI) indicator shows villages or sub-districts that have received complete child immunizations. UCI data shows that in 2019, out of 8501 villages, 7686 (90.4%) had implemented village UCI, a figure that had risen from the previous year's 85.4%.8 However, these figures are not comparable with the incidences of infectious diseases that can be prevented by immunization. In Indonesia, diphtheria is a re-emerging disease, especially in East Java. In 2019 alone, there were 358 cases of diphtheria in East Java.8\n\nIndonesian society is still influenced by community leaders, professionals, and/or environmental leaders who can serve as role models in certain matters and situations. Therefore, health workers as role models play a key role in increasing immunization coverage. Research has found that the determinants of immunization status are immunization goals, the readiness of health facilities, and community access.9 Educational, economic, and health access factors play an important role in increasing immunization coverage, so much so that mothers who give birth in health facilities have a higher immunization awareness.10 The community's motivation for immunization reflects the health workers’ motivation for immunization, including the respective risk factors and beliefs about immunization.11 Dr. Soetomo Academic Hospital in Surabaya is a referral hospital for eastern Indonesia with 1714 beds and 3332 health workers. Many studies show that people's motivation for immunization is the same as those of health workers.11 Health workers as role models play an important role in increasing immunization coverage. This study aims to determine the risk factors for incomplete immunization among the children of health workers at Dr. Soetomo Hospital.\n\n\nMethods\n\nA cross-sectional questionnaire-based study was conducted at the Dr. Soetomo Hospital in Surabaya, Indonesia, from December 2021 to April 2022. This study compared incompletely immunized children (case group) with completely immunized children (control group). In this study, interviews were conducted for 30 minutes. The notes taken during the interview used only for research interest. A questionnaire was used to collect demographic data from the participants including the age of the children, parental age, place of birth, sex, ethnicity, place of immunization, father's education, mother's education, parental income, religion, and history of child immunization. In addition, the questionnaire contained 10 questions on basic immunization knowledge to assess the parent’s level of knowledge about their child's immunization status. The questions included immunization targets, types of immunization, immunization schedules, immunization goals, and immunization contraindications. Before the start of the study, we conducted a pilot study with 20 participants to check the validity and reliability of the questionnaire. The participants were recruited from the general public in the community health post (near the hospital) randomly. Participants who scored 0–70% on the 10 questions were considered to be in the low level of knowledge category, while participants who scored above 70% were considered to be in the high level of knowledge category. Based on the result of this pilot study, the questionnaire can be used without further modification. The questionnaire can be found as Extended data.28\n\nThe inclusion criteria for health workers were doctors, nurses, midwives, pharmacists, nutritionists, physiotherapists, and medical record administration staff. The criteria for complete immunization followed Ministry of Health Regulation No. 12 of 2017 concerning the administration of immunization: Every infant (aged 0–11 months) is required to receive complete basic immunization consisting of one dose of Hepatitis B, one dose of Bacillus Calmette–Guérin (BCG), three doses of diphtheria/pertussis/tetanus (DPT), hepatitis B (HB), Haemophilus influenza type B (HiB), four doses of polio drops, and one dose of measles-rubella (MR).12\n\nThe inclusion criteria for the case group participants in this study were parents who worked as hospital health workers and had children aged less than 24 months with incomplete immunization records. Meanwhile, the inclusion criteria for the control group were parents who worked as hospital health workers and had children aged less than 24 months with complete immunization records. The exclusion criteria in this study included participants who did not have an immunization control book, could not speak the Indonesian language and had a history of incomplete immunization data. The sample was taken using the random sampling method and with the formula for two populations, a 95% confidence interval, a statistical power of 80%, p1 0.9, and p2 0.7. We assumed 10% drop out from this subject. The minimal sample size requirement was 148.\n\nThis research was approved by and received ethical clearance from the Health Research Ethical Committee of Dr. Soetomo Hospital (number 0244/KEPK/VIII/2021). Confidentiality of the research participants was well maintained by not mentioning particular names; instead, initials were used. The results of this study are for research purposes only.\n\nThe data were analyzed using Microsoft Excel version Windows 11 and IBM Statistic SPSS Version 25. The dependent variables in this study were the immunization statuses of the children. The completely immunized children were the control group, while the incompletely immunized children were the case group. The independent variables in this study were parental knowledge, parental education, religion, parental income, parental age, type of health workers, place of birth, child's birth order, ethnicity, and the coronavirus disease 2019 (COVID-19) pandemic (the pandemic made people afraid to bring their children for the immunization services). Univariate analysis was conducted to determine the characteristics of completely and incompletely immunized children, as well as to describe the independent and dependent variables. We also determined the significance value between the independent and dependent variables using the Pearson chi-square and/or Fisher’s exact test to identify the odds ratio (OR) with a 95% confidence interval (CI). A p-value below 0.05 was considered significant. Multivariate analysis was conducted to determine the most influential risk factors for the incomplete immunization of the children of health workers.\n\n\nResults\n\nA total of 148 questionnaires were distributed to participants who met the inclusion and exclusion criteria: 31 refused to fill out the questionnaire and two provided incomplete data, so a total of 115 participants were obtained.27 Of the 115 participants, 62 participants (53.9%) were included in the case group, which comprised health workers with incompletely immunized children, and 53 participants (46.1%) were included in the control group, which comprised health workers with completely immunized children (Figure 1). The average age of the health worker participants was 31.8 years. The health workers were divided into two types: medical personnel (13.9%) and non-medical personnel (86.1%). The characteristics of the participants are presented in Table 1. Table 2 shows that the incomplete immunization of the children is 48.4% due to the COVID-19 pandemic, 29% due to illness, and 22.6% due to no time.\n\nTable 3 shows the analysis of the bivariate test between several factors and the immunization status of the health workers’ children. Factors that had significant differences included parental age, parental knowledge, mother's education, and the presence of a pandemic with p-values of 0.043, 0.005, 0.002, and <0.001, respectively. Parental age had a 3.250 times greater risk of influencing incomplete child immunization. The older the parents, the greater risk for incomplete child immunization. For the mother's education factor, an OR of 3.221 was obtained, which means that the mother's low level of education had a 3.221 times greater risk of influencing incomplete child immunization. There were no significant differences between religion, occupation, father's education, parental income, birth order, history of the place of birth, and ethnicity in the immunization status of the children of health workers working at a tertiary referral hospital.\n\n* A p-value below 0.05 means the variable is statistically significant. OR: odds ratio, CI: confidence interval, COVID-19: coronavirus disease 2019.\n\nThe results of the multivariate analysis on parental knowledge and income had a significant effect on the completeness of children's immunization, with a p-value of 0.017, 0.019; OR 4.887, 8.679; 95% CI 1.333–17.917, 1,429–52,701, respectively (Table 4). Table 4 shows that low parental knowledge has a 4.8 times greater risk of influencing the incomplete immunization of children. In addition, parents with low incomes of around 1–3 million Indonesian Rupiah (IDR) (USD 67-201) have an eight times greater risk of incompletely immunizing their children. This suggests that the knowledge and income of parents may have an effect on the immunization status of the children of health workers at the tertiary referral hospital.\n\n* A p-value below 0.05 means the variable is statistically significant. OR: odds ratio, CI: confidence interval, COVID-19: coronavirus disease 2019.\n\n\nDiscussion\n\nThis study investigated the completeness of the immunization of children of health workers from the age of 0–to 24 months. To determine the immunization status of the children, the participants were required to have data records in their immunization books and/or cards. The knowledge of the participants in this study had a significant difference, with a p-value of 0.005 and an OR of 0.236, which means that the parents' knowledge has a 0.236 times greater risk of determining the incomplete immunization of children. In line with these results, research in Finland showed that the majority of Finnish health workers have high confidence in the benefits and safety of immunization and show confidence in other health professionals. However, low immunization confidence is found among a non-negligible proportion of health workers.3 This study found that there were still health workers with low levels of knowledge, which led to the incomplete immunization status of their children. A systematic review stated that health workers who have good knowledge still have negative attitudes toward immunization: they have less belief in the benefits and safety of vaccination, so they are less likely to have their children receive immunizations and recommend it to the community.3,5,13,14\n\nOur research found that 101 (87.8%) of the participants were mothers. A study in Eritrea, with a sample of 1323 mothers with children aged 0–59 months, found that the children of educated mothers had complete basic immunization compared to the children of mothers who were not educated.15 Research in Georgia found that incomplete immunization is associated with a lack of maternal knowledge about immunization.16 The findings of our study agree with those of Verulava et al.’s: maternal education plays an important role and is related to the completeness of the child's immunization (p = 0.002). A study in China found that parental education is an important variable that influences parents' decisions on immunization. Parents with a bachelor's degree and above were more likely to immunize their children in the hope of effectiveness, but parents with a low level of education were less likely to have their children receive immunizations for this reason. Few highly educated parents refused immunization because of the risk of immunization, while less educated parents significantly declined immunization for that reason.17\n\nParental age was also found to have a significant relationship with determining the immunization status of children. Previous research found that mothers and parents aged 20–39 years have doubts about immunization, especially in terms of its safety and effectiveness.18,19 Meanwhile, according to Adokiya (2017), the increase in maternal age corresponds to an increase in the child's immunization status since mothers who are older have more knowledge of and exposure to previous immunizations than younger mothers.20 In Indonesia, women under the age of 16 are less likely to use health services than older women. Young mothers are often unable to make decisions on their own and tend to discuss decisions with family members.10 In addition to parental age, the family income also has a significant influence on the immunization status of children. In Indonesia, based on law number 12 of 2017 concerning the administration of immunization, Article 30 states that the administration of complete basic immunization is provided free of charge according to a predetermined schedule.1 Although the implementation of immunization in Indonesia is free, incompletely immunized children are not uncommon. By providing complete immunizations, family welfare is one of the preventive health measures for children.10,21\n\nThis study found that many parents (41.9%) with incompletely immunized children stated that their reason for delaying immunization was due to the COVID-19 pandemic. The bivariate analysis of the difference between the COVID-19 pandemic incident factor and the immunization status of the children of health workers had a significant difference, with a p-value of <0.001. According to research by Olusanya et al. (2021), the background of the COVID-19 pandemic is an obstacle to vaccine non-compliance or rejection.22 Immunization service providers facilitate standard health protocols that must be applied in immunization services. To combat the health issue during this pandemic, telemedicine video conferencing, outdoor/curbside/drive-through vaccine administration, minimization of the number of onsite patient visits at one time, and providing special, well-ventilated vaccine visits should be introduced to address the health crisis.23 The catch-up vaccine protocol issued by the Centers for Disease Control and Prevention to facilitate immunization coverage for children who missed their vaccine schedule during the pandemic should be implemented.24\n\nHealth workers have knowledge in the field of health, an important aspect to consider when investigating the attitudes of health workers towards immunization compared to the general population. Health workers are expected to have obtained evidence-based information about immunization. Such knowledge can also be obtained through experience gained both formally and informally. This knowledge includes the definition of immunization, immunization schedule, type of immunization, immunization goals, how to administer immunizations, and the effects of immunization. This knowledge shapes the health worker’s perception of whether or not their children should receive immunizations. Communities consider this knowledge to be the most crucial factor for locating immunization information. Low immunization confidence is found among a non-negligible proportion of health workers.3\n\nAlthough the participants in this study were health workers with the good, formal education necessary for a health worker, a low level of knowledge regarding immunization was still present, which indicates that the low level of knowledge factor would have a four times greater risk of influencing the incomplete immunization of the children of health workers at the tertiary referral hospital in Surabaya. In this study, family welfare was seen from parental income; low parental income signifies that the possibility of children being incompletely immunized is eight times higher than in the case of high parental income. This is supported by data on the characteristics of immunization facilities that are widely used by health workers, namely in hospitals, as many as 40%. The advantages of this research are that the data used were the immunization data records in the immunization books and/or cards of the participants’ children. A better source of data for tracking immunization status is medical records such as the Health Card or Maternal and Child Health books.25,26 This study was conducted retrospectively; therefore, recall bias may have occurred, which is the limitation of our study. Recall bias may have occurred in regard to the parents’ reasons for the incomplete immunization of their children since all the data pertaining to that were based on the parents’ memory. However, this was unavoidable as we cannot track events that are not recorded objectively.\n\n\nConclusion\n\nLow levels of parental knowledge and income are correlated with the immunization of the children of health workers at the tertiary referral hospital in Surabaya. More than half of the children of the health workers are incompletely immunized. This is a major concern, but many factors were not found to be related to the situation other than parental knowledge and income. However, another important factor that requires significant attention is the motivation of parents to get the best health-related quality of life for their children. People were reluctant to bring their children for immunization services due to the COVID-19 outbreak. Moreover, parental adherence to childhood immunization need to be investigated further to identify the parental motivations for providing the best quality of life for children. The role of the work environment also needs to be investigated further as it is related to the low level of knowledge of the participants with a complete immunization state.\n\n\nData availability\n\nFigshare: Raw data of Incomplete Immunization of Health Workers' Children at a Tertiary Referral Hospital in Surabaya, https://doi.org/10.6084/m9.figshare.21097213.v1.27\n\nFigshare: Online resource the questionnaire immunization form, https://doi.org/10.6084/m9.figshare.21021715.v2.28",
"appendix": "Acknowledgments\n\nThe authors would like to thank the Head of the Department of Child Health at the hospital for permitting us to carry out this study. We appreciate the help of the Education Coordination Committee for their support and provision of access to reach health worker participants in hospitals.\n\n\nReferences\n\nIndonesia Ministry of Health: Permenkes Nomor 12 Tahun 2017 Tentang Penyelenggaraan Imunisasi (Ministry of Health Regulation Number 12 of 2017 concerning the Implementation of Immunization).2017.\n\nEsposito S, Principi N, Cornaglia G: Barriers to the vaccination of children and adolescents and possible solutions. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. 2014 May; 20: 25–31. eng. PubMed Abstract | Publisher Full Text\n\nKarlsson LC, Lewandowsky S, Antfolk J, et al.: The association between vaccination confidence, vaccination behavior, and willingness to recommend vaccines among Finnish healthcare workers. PLoS One. 2019; 14(10): e0224330. Epub 2019/11/02. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCollange F, Verger P, Launay O, et al.: Knowledge, attitudes, beliefs and behaviors of general practitioners/family physicians toward their own vaccination: A systematic review. Hum. Vaccin. Immunother. 2016 May 3; 12(5): 1282–1292. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNapolitano F, Bianco A, D'Alessandro A, et al.: Healthcare workers' knowledge, beliefs, and coverage regarding vaccinations in critical care units in Italy. Vaccine. 2019 Oct 31; 37(46): 6900–6906. eng. PubMed Abstract | Publisher Full Text\n\nPaterson P, Meurice F, Stanberry LR, et al.: Vaccine hesitancy and healthcare providers. Vaccine. 2016 Dec 20; 34(52): 6700–6706. eng. PubMed Abstract | Publisher Full Text\n\nIndonesia Ministry of Health: Data dan Informasi Profil Kesehatan Indonesia 2019 (Indonesia Health Profile Data and Information.2019.Reference Source\n\nIndonesia Ministry of Health: Profil Kesehatan provinsi jawa timur tahun 2019 (Health Profile of East Java Province in 2019). Dinas Kesehatan Profinsi Jawa Timur.2020.\n\nPhillips DE, Dieleman JL, Lim SS, et al.: Determinants of effective vaccine coverage in low and middle-income countries: a systematic review and interpretive synthesis. BMC Health Serv. Res. 2017 Sep 26; 17(1): 681. PUBLICATION: Not applicable COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER’S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Epub 2017/09/28. eng. Publisher Full Text | PubMed Abstract | Free Full Text\n\nHolipah MA, Maharani A, Kuroda Y: Determinants of immunization status among 12- to 23-month-old children in Indonesia (2008-2013): a multilevel analysis. BMC Public Health. 2018 Feb 27; 18(1): 288. Epub 2018/02/28. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrewer NT, Chapman GB, Rothman AJ, et al.: Increasing Vaccination: Putting Psychological Science Into Action. Psychological Science in the Public Interest: A Journal of the American Psychological Society. 2017 Dec; 18(3): 149–207. eng. PubMed Abstract | Publisher Full Text\n\nIndonesia Ministry of Health: Kementerian Kesehatan, Penyelenggaraan Imunisasi (Immunization Administration). 12. Indonesia.2017.Reference Source\n\nCallaghan T, Motta M, Sylvester S, et al.: Parent psychology and the decision to delay childhood vaccination. Soc. Sci. Med. 2019 Oct; 238: 112407. Epub 2019/08/02. eng. PubMed Abstract | Publisher Full Text\n\nLarson HJ, de Figueiredo A , Xiahong Z, et al.: The State of Vaccine Confidence 2016: Global Insights Through a 67-Country Survey. EBioMedicine. 2016 Oct; 12: 295–301. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKibreab F, Lewycka S, Tewelde A: Impact of mother's education on full immunization of children aged 12-23 months in Eritrea: population and health survey 2010 data analysis. BMC Public Health. 2020 Feb 22; 20(1): 267. Epub 2020/02/24. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerulava T, Jaiani M, Lordkipanidze A, et al.: Mothers’ Knowledge and attitudes towards child immunization in georgia. Open Public Health J. 2019; 12(1): 232–237. Publisher Full Text\n\nZhao M, Liu H, Qu S, et al.: Factors associated with parental acceptance of influenza vaccination for their children: the evidence from four cities of China. Hum. Vaccin. Immunother. 2021 Feb 1; 17(2): 457–464. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMohd Azizi FS, Kew Y, Moy FM: Vaccine hesitancy among parents in a multi-ethnic country, Malaysia. Vaccine. 2017 May 19; 35(22): 2955–2961. eng. PubMed Abstract | Publisher Full Text\n\nYufika A, Wagner AL, Nawawi Y, et al.: Parents' hesitancy towards vaccination in Indonesia: A cross-sectional study in Indonesia. Vaccine. 2020 Mar 4; 38(11): 2592–2599. eng. PubMed Abstract | Publisher Full Text\n\nAdokiya MN, Baguune B, Ndago JA: Evaluation of immunization coverage and its associated factors among children 12-23 months of age in Techiman Municipality, Ghana, 2016. Archives of public health = Archives belges de sante publique. 2017; 75: 28. Epub 2017/06/28. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsif AM, Akbar M, Tahir MR, et al.: Role of Maternal Education and Vaccination Coverage: Evidence From Pakistan Demographic and Health Survey. Asia Pac. J. Public Health. 2019 Nov; 31(8): 679–688. eng. PubMed Abstract | Publisher Full Text\n\nOlusanya OA, Bednarczyk RA, Davis RL, et al.: Addressing Parental Vaccine Hesitancy and Other Barriers to Childhood/Adolescent Vaccination Uptake During the Coronavirus (COVID-19) Pandemic. Front. Immunol. 2021; 12: 663074. Epub 2021/04/06. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBramer CA, Kimmins LM, Swanson R, et al.: Decline in child vaccination coverage during the COVID-19 pandemic - Michigan Care Improvement Registry, May 2016-May 2020. American journal of transplantation: official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2020 Jul; 20(7): 1930–1931. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAdvisory Committee on Immunization Practices: ACIP meeting information. Atlanta, GA:US Department of Health and Human Services, CDC;2020; vol. 2020. .\n\nHughes GJ, Mikhail AF, Husada D, et al.: Seroprevalence and Determinants of Immunity to Diphtheria for Children Living in Two Districts of Contrasting Incidence During an Outbreak in East Java, Indonesia. Pediatr. Infect. Dis. J. 2015 Nov; 34(11): 1152–1156. eng. PubMed Abstract | Publisher Full Text\n\nNanthavong N, Black AP, Nouanthong P, et al.: Diphtheria in Lao PDR: Insufficient Coverage or Ineffective Vaccine? PLoS One. 2015; 10(4): e0121749. Epub 2015/04/25. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPuspitasari Y, Husada D: Dataset of Incomplete Immunization Status of Health Workers' Children at a Tertiary Referral Hospital in Surabaya. figshare. [Dataset].2022. Publisher Full Text\n\nPuspitasari Y, Husada D: The questionnaire immunization form.docx. figshare. Online resource. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "152621",
"date": "22 Nov 2022",
"name": "Astri Ferdiana",
"expertise": [
"Reviewer Expertise Public health",
"epidemiology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comment: English proofreading is necessary to improve readability.\nAbstract\nRecommend to rewritten to be more concise.\n\nAdd recommendation in the Conclusion.\nIntroduction\nParagraph 2: Need some more contextual information about the East Java Province.\n\nParagraph 3: Not sure what's the correlation between the 1st and 2nd sentences. The argument of why community motivation reflects health worker's motivation is not very clear. Information on the study setting should be in the \"Setting\" under Methods section.\n\nI don't think we can identify risk factors with this study design, better use \"predictors\".\nMethods\nIn the Abstract it is mentioned \"case control\" as study design, but it is mentioned as \"cross sectional\" in the Study Design section. I think this is a cross sectional study and not a case control study. All variables were measured at the same time.\n\nIt should be made more clear how \"incomplete\" and \"complete\" immunization status was defined. How about late immunization?\n\nThere should be section on \"Variables and Instruments\".\n\nTable 4: why you used the term eligibility test? And how did you choose the covariates to be entered in the model? Please explain in more detail in the Methods section.\n\nIt was not clear how the random sampling was done.\n\nIt was not explained whether written informed consent was obtained and how.\n\nIt wasn't very clear how the multivariate analysis done. Was logistic regression used? I don't think multivariable regression analysis is appropriate given the sample size.\n\nResults\nSex should be male-female instead of boy-girl.\n\nI think it is better to separate the tables into \"characteristics of respondents\" and \"knowledge\" etc.\n\nWith such a study design, we cannot say that an A predictor has greater risk/lower risk of having the outcome. We can only say that the predictor is associated with the outcome.\n\nAvoid writing \"tertiary referral hospital\" too often. It should be mentioned only once.\nDiscussion\nPlease do not repeat the figures from the Results section in the Discussion.\n\nStart with main findings, and organize the findings based on the research question. Compare with the previous literature, and implications to policy, research and or practice.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "163845",
"date": "03 Apr 2023",
"name": "Eleni Vergadi",
"expertise": [
"Reviewer Expertise Infectious diseases",
"vaccines",
"immunology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study from Yunita Puspitasar et al., addresses the reasons of incomplete immunization of children of healthcare workers in a tertiary hospital in Indonesia. Interesting study, although the main limitation is that is single center study of the low sample size.\nSome comments:\nTitle\nPlease change the phrase 'risk factors' in the whole manuscript. The word 'determinants' may be more appropriate.\nAbstract\nThe introduction needs to be rewritten to be more concise and to the point.\n\nChange the phrase 'case control' to 'cross sectional study'.\nIntroduction\nPlease avoid the phrase 'risk factors'.\n\nAvoid mentioning the name of the hospital in the whole manuscript.\n\nAs the vaccination coverage is reported high 98%, the rationale of the study is unclear. Please clarify.\n\nHepat B dosing is referred to twice.\nMethods\nWhat do you mean as 'incomplete status'? Please define better - how many vaccines were missing in these children?\n\nHow was random sampling done?\nResults\nSex should be 'male – female' and not 'mother – father'.\n\nWhere there siblings among participants (e.g., from same family)? Please clarify.\nDiscussion\nPlease amend the limitations by discussing the low sample size and as well as the fact that the data are derived of a single center and may not represent other populations of health care workers.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1143
|
https://f1000research.com/articles/11-1139/v1
|
05 Oct 22
|
{
"type": "Research Article",
"title": "Characterization of lactic acid bacteria isolated from budu, a West Sumatra fish fermentation product, and their ability to produce exopolysaccharides",
"authors": [
"Yusra Yusra",
"Hafrijal Syandri",
"Yempita Efendi",
"Nurul Huda",
"Hafrijal Syandri",
"Yempita Efendi",
"Nurul Huda"
],
"abstract": "Background: Probiotics are instrumental in maintaining the equilibrium of the gut microbiota and improving the health of the human body. This study examined the presence and physiological features, including the ability to produce exopolysaccharides, of lactic acid bacteria from fermented Tenggiri (Scomberomorus guttatus) and Talang (Chorinemus spp.) fish, also known as budu fish. Methods: Lactic acid bacteria were isolated from budu fish. These bacteria were characterized to determine tolerance to gastric pH values, growth curve, inhibitory ability against pathogenic bacteria, and ability to produce exopolysaccharides and to perform a molecular identification. Results: Twenty-nine lactic acid bacteria isolates from budu fish were determined to be of the Pediococcus species. Assessment of the physiological characteristics showed that Pediococcus sp. had a high acidifying activity and could grow at a pH between 2 and 11; the pH of the supernatant after 36 hours of incubation was 4.49. In terms of inhibitory activity against pathogenic bacteria, Pediococcus sp. demonstrated an inhibitory diameter of 20.5 mm against Escherichia coli, 23.0 mm against Staphylococcus aureus, and 21.0 mm against Salmonella thypi. The Pediococcus sp. strain produced exopolysaccharides ranging from 870 to 1910 mg/l and had 100% similarity with Pediococcus pentosaceus strain 4942. Conclusions: This study confirmed the presence of Pediococcus pentosaceus strain 4942 in budu fish, which can be used as a new probiotic based on its capabilities to kill pathogenic bacteria and produce exopolysaccharide compounds.",
"keywords": [
"characterization",
"budu",
"Pediococcus",
"antimicrobial",
"exopolysaccharide"
],
"content": "Introduction\n\nWest Sumatra has many foods that are processed through a natural fermentation process with or without the addition of microbes or a microbial inoculum. Foods derived from fermented fish are locally known as budu, tukai, and pado fish.1,2 Budu is processed through spontaneous fermentation of large pelagic fish such as Tenggiri (Scomberomorus guttatus) and Talang (Chorinemus spp.) because their flesh is white.3 Lactic acid bacteria found in budu fish can be used as probiotics and biopreservatives. One of the potential bacteria obtained from budu fish is Bacillus cereus strain HVR22, which possesses antimicrobial properties against Escherichia coli, Salmonella thypi, and Listeria monocytogenes bacteria.4,5 A bacteriocin produced by the bacterium B. cereus strain HVR22 can be used to preserve tuna fillets.6 Lactic acid bacteria that have been isolated from budu fish can produce gamma-aminobutyric acid (GABA) and exert antistress activity in broilers.7 Lactobacillus sp. has also been isolated from budu fish and can produce glutamic acid.8 Furthermore, Saccharomyces sp. strains SC 11, SC 12, and SC 21 have been isolated from budu and can be used as potential probiotics.9\n\nProbiotics are microbes that benefit health only if used appropriately.10,11 It has been proven that probiotics can help with metabolism, the immune system, protein absorption, and inflammation reduction.12 Commercially, strains of lactic acid bacteria (LAB) are widely available in utilitarian meals as probiotics.13 LAB have the following features: a coccus shape, thick cell walls, are non-spore-forming, and are capable of fermenting carbohydrates.14 For probiotic bacteria to survive in the intestine and have a constructive effect on the body, they must have the fundamental property of being tolerant to the acidic pH of the gut and intestines.15 Digestive fluid is comprised of HCl(aq), which gives the bowels a pH value between 2.5-3.5.16 As a result, it is critical to characterize the probiotic candidate bacteria for their ability to pass through the acidic gastric surroundings and reach the jejunum.\n\nOther essential criteria for selecting probiotic organisms are their antimicrobial properties, such as their ability to produce bacteriocins, oxidizers, and organic acids. These properties are vital for their ability to inhibit the pathogenic bacteria commonly present in the intestine.17 LAB have been identified in a variety of fermented foods that can be used as probiotics and are beneficial for human and animal health.18 Several LAB groups are known to produce secondary metabolites, namely, exopolysaccharides (EPSs) or extracellular polysaccharides. EPS is a polymer that is secreted by bacteria under unfavorable conditions. Conditions of environmental stress induce the bacterial cells to secrete exopolysaccharides as a form of self-protection. In addition, EPS also protects bacterial cells against bacteriophages, phagocytosis, and osmotic pressure. This polymer improves product texture, can act as an emulsifier, gelling agent, or stabilizer, and can provide viscosity and taste.19 EPS can organize the microbial cycle, participate in some symbiotic processes by increasing bacterial colonization through its presence between cells, and protect against dangerous substances such as poisonous materials and pathogenic bacteria.20\n\nMany studies on the ability of LAB to produce exopolysaccharides have been carried out.21–28 Nevertheless, little is known about the potential of exopolysaccharides produced by LAB from budu fish. Therefore, this research is vital to determine the presence of LAB in budu fish, the physiological characteristics of the isolated LAB and the potential of these LAB to produce exopolysaccharides.\n\n\nMethods\n\nThe study was carried out at the Integrated Research Lab, Faculty of Fisheries and Marine Sciences, the University of Bung Hatta, West Sumatra, Indonesia, from January 2021 to August 2021.\n\nSamples of budu fish were purchased from traditional processors in the Sungai Sirah and Gasan areas, Padang Pariaman and Sasak districts, Pasaman districts, West Sumatra Province. A total of three samples of budu fish were purchased from three traditional processors from the Sungai Sirah and Gasan areas, Padang Pariaman and Sasak districts, Pasaman districts, West Sumatra Province. Budu was produced from Tenggiri (Scomberomorus guttatus) and Talang fish (Chorinemus spp.), as shown in Figure 1. Samples were collected using sterile plastic for microbiological examination. Before sample analysis, our samples were stored in a refrigerator at 4 °C.\n\nIsolation of the samples was carried out with serial dilutions of up to 10-5 using 9 ml of sterile sodium chloride solution in a beaker, which were then homogenized using a vortex shaker. From three dilutions (10–3 to 10–5), 1 ml of each was used to inoculate a pour plate containing de Man Rogosa Sharpe (MRS) agar medium supplemented with 1% CaCO3 (w/v). These inoculations were incubated at 37 °C for 24 to 72 hours.29 The isolates that produced a clear zone were then purified to obtain the pure isolates. Purification was carried out using a four-quadrant streak plate technique. Isolates were identified based on their physiological characteristics, such as the gram-staining reaction, morphology, CO2 production from glucose, motility, oxidase activity, nitrate reduction, and patterns of sugar agitation.30\n\nLAB resistance to gastric pH\n\nThe test was carried out using two test tubes containing MRS broth. One test tube served as a control, and in the other test tube, we added 37% HCl to obtain a pH of 2.5. After that, 0.5 ml of the bacterial culture containing approximately 109 CFU/ml was added to 5 ml of MRS HCl broth, followed by incubation for 36 hours at 37 °C. The absorbance was measured based on optical density (OD) using a spectrophotometer at a wavelength of 600 nm. Resistance to gastric pH values was ascertained as a percentage based on the standards.31 The pH of the culture after incubation at 37 °C was used to specify the acidulation gauge of LAB at 6, 12, 24, and 36 hours using the pH indicator PT-10 (Sartorius AG, Gottingen, Germany).32\n\nLAB growth curve\n\nA total of one dose of bacterial culture was inoculated into 10 ml of aseptic de Man Rogosa Sharpe Broth (MRSB) medium and incubated for 24 hours at 37 °C. The bacteria were then injected into 90 ml of aseptic MRSB medium and grown in an incubator shaker at 37°C. For the growth curve, the optical density of the culture was determined from four to 48 hours using the turbidity method with the aid of a spectrophotometer at a wavelength of 600 nm.33\n\nInhibitory ability of LAB against pathogenic bacteria\n\nPaper discs were immersed in a 20 L LAB supernatant solution and then removed and attached to nutrient agar (NA) solid media containing the test bacteria (E. coli, S. thypi, and S. aureus). Then, the culture plate was incubated at 37°C for 24 to 72 hours. The width of the inhibitory area generated was determined using a caliper.34\n\nProduction of exopolysaccharides from LAB\n\nUsing MRS broth as the culture medium, exopolysaccharides were isolated and purified. LAB were cultivated for 24 hours in an incubator shaker in one litre of MRS broth with saccharose. The LAB culture was then heated at 100 °C for 10 minutes and centrifuged at 12,000 × g for 15 minutes to pellet the cells. Cold ethanol was added to the supernatant at twice the volume of the supernatant produced, and then this mixture was centrifuged at 5,000 g for 30 minutes at 4 °C. In a 50 °C oven, the pellets were dried to a consistent weight, and the EPS samples were then stored at -20 °C until they were assessed.35,36\n\nMolecular identification of LAB\n\nLactic acid bacteria isolates were cultured in MRS broth at 37°C for 24 hours. Genomic DNA isolation was carried out using a Promega KIT (USA) following the manufacturer’s instructions. To break down the bacteria cell wall we used lysozyme at a concentration of 20 mg/ml to improve protein or nucleic acid extraction efficiency.37 Genomic DNA of LAB was used for amplification of 16S rRNA gene. Amplification was done using forward primer 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and primer 1492R (5′-GGTTACCTTGTTACGACTT-3′) for reverse. The reaction was carried out in a volume of 50 μl. The PCR mixture contained 22 μl of MQ, 25 μl DreamTaq Green DNA Polymerase (Thermo Fisher Scientific, USA), 1 μl of each forward and reverse primer (10 μM each, IDT synthesized) and 1 μl template. Amplification conditions were 5 minutes of preheating at 95°C, 30 seconds denaturation at 95°C, 30 seconds primer annealing at 58°C, one minute extension step at 72°C and post cycling extension of five minutes at 72°C for 35 cycles. The reactions were carried out in a thermal cycler (Biometra’s T-Personal Thermal Cycler, USA). PCR products were stored at 4°C for further examination using 1% (w/v) agarose electrophoresis in 1× TAE, 100 V for 30 minutes. The DNA bands formed from the electrophoresis process were visualized using a UV transluminator. The marker used was 1 Kb Plus DNA ladder (ThermoFisher Scientific). Sequencing of the 16S rRNA gene was performed at the Laboratory of Microbiology, Biological Research Center, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia. The products of the sequencing cycle were purified again with the ethanol purification method. Analysis of the nitrogen base sequence readings was performed using an automated DNA sequencer (ABI PRISM 2130 Genetic Analyzer) (Applied Biosystems). The BioEdit version 7.2.5 tool (RRID:SCR_007361) was then used to trim and combine the sequence data in its raw form. The assembled sequence data were then used in a BLAST search against genomic data registered with the NCBI to determine the microbe strain with the greatest similarity and other close relatives.\n\n\nResults\n\nFrom three samples of budu fish, 56 LAB were identified. LAB isolation was conducted using MRSA CaCO3 medium (Figure 2). Twenty-nine of the LAB species identified were suspected to be Pediococcus sp. This is based on the identified physiological characteristics (Table 1), which matched the information in Cowan and Steel (1975).38 To further confirm the strain of LAB, subsequent characterization was carried out.\n\nAfter incubation for 0 to 36 hours, the pH of the supernatant decreased incrementally to 6.10, 5.08, 4.52, 4.50, and 4.49. The results obtained after incubation for three and six hours showed that LAB isolates could survive at pH 2.5. LAB generated from budu fish had a minimum resistance of 50%, indicating that they can be utilized as probiotics. The results of the LAB isolate cultures at various pH values using MRS broth showed that the isolates could grow at pH 2, 3, 4, 5, 6, 7, 8, 9, 10, and 11. The bacterial culture that was initially clear became cloudy as a sign of bacterial growth. From this research, it is clear that Pediococcus sp. from budu fish had a good acidification ability. The pH of the supernatant produced after incubation for 24 hours decreased for up to 36 hours.\n\nThe growth curve of Pediococcus sp. incubated on MRS broth medium for 36 hours is presented in Figure 3. The four stages of the growth phase of Pediococcus sp. namely the lag, exponential, stationary, and death phases.\n\nPediococcus sp. also showed a high antimicrobial activity, with inhibition zones reaching 20.5 mm against E. coli, 23.0 millimeters against S. aureus, and 21.0 millimeters against S. thypi (Figure 4).\n\nPediococcus sp. produced exopolysaccharides at concentrations ranging from 870–1910 mg/l. The average EPS production was 2,700 mg in wet conditions and 400 mg/l in dry conditions (Figure 5). The bacteria Pediococcus sp. isolated from budu fish was able to produce a large amount of EPS on MRS agar modified with the addition of 20% saccharose.\n\nTo determine the strain of the bacterium Pediococcus sp., identification was carried out based on the 16S rRNA gene. Based on the BLAST results, Pediococcus sp. isolated from budu fish had a 16S rDNA gene that was 1514 bp in length, which showed the highest percentage of similarity (100%) with the Pediococcus pentosaceous strain 4942. The sequence homology results of Pediococcus sp. using BLAST in NCBI can be seen in Table 2, and the phylogenetic tree can be seen in Figure 6.\n\n\nDiscussion\n\nMRSA medium is a selective medium for detecting lactic acid bacteria. CaCO3 was added to the MRSA medium that was used. The addition of CaCO3 was used as an indicator of bacterial colonies capable of producing acid by showing the growth of colonies that formed a clear zone (Figure 2). From the MRS agar medium to which CaCO3 was added, the colonies obtained were characterized by a clear zone around them.39 Pediococcus is a lactic acid bacterium that is often found in fermented foods, including budu fish. The Pediococcus pentosaceus strain has been isolated from kombucha, fermented fish products, “idli”, a traditional food from South India, the Korean liquor “omegisool”, and “dadih”, a fermented buffalo milk.40–45 Furthermore, Weissella, Pediococcus, and Lactobacillus bacteria are prevalent LAB during the food fermentation process based on their habitus.46 Similar claims by other researchers have also reported that P. pentosaceus LBM 18 was prevalent during the corn silage fermentation process and had antibacterial and antifungal properties.47 Recently, Pediococcus activity was demonstrated, which was shown to have properties that can make this bacterium useful in food preparation.48 P. pentosaceus microbes can be used as food additives because of their abilities to improve taste, food nutrition, and preservation of animal products and to exert antibacterial and probiotic activities (anti-inflammatory, cancer-fighting, oxidation-inhibiting, hypolipidemic, and detoxifying activities).49\n\nFor the use of LAB strains as cultures to produce some fermented foods, it is important to determine the bacterial features such as acidifying activity, exopolysaccharide synthesis ability, and pathogen-killing bactericidal activity.50 Furthermore, acidulation activity is also a significant factor in characterizing bacteria, especially as a potential starter culture. These findings support research in which it was shown that LAB isolated from fermented food products in Ethiopia had a survival rate of 90.13% at pH 2.5 with an incubation of two hours.51 The resistance of LAB isolates from budu fish had a value of 60.15% with a three-hour incubation period and reached 60.68% after six hours, a small decrease of only 0.53%. This indicates that LAB from budu fish had a high survival rate, as seen from the increased resistance from three to six hours of incubation. Probiotics have a high survival and growth rate. At pH 2.5, L. brevis, L. plantarum, and P. ethanolidurans isolated from conventional pickles had viability ranging from 33–64%, 35–85%, and 40–76%, respectively.31 Furthermore, L. fermentum bacteria isolated from fermented milled flour had a survival rate of approximately 80% and a pH of 2.5 after a four-hour incubation period.52\n\nFor Pediococcus sp., the lag stage lasts from one to four hours. The exponential phase occurs from the fifth to the twentieth hour. This is because the nutrient content of the medium is frequently used as a source of power for growth of the cells. The stationary phase occurs from the twenty-first to the forty-eighth hour, and in this phase, there is no increase in the number of bacterial cells because the number of growing cells is equal to the number of dying cells. The final phase is the death phase, during which the number of bacterial cells begins to decline as the nutrients in the media begin to be depleted. Primary metabolites are also formed by this time, which accumulate in this medium and inhibit bacterial development. This phase occurs after the bacteria have been incubated for 72 hours. The results of this study were in accordance with the optimization of the growth of the P. pentosaceus 2397 strain, in which the exponential phase occurs at 12–48 hours and begins to decrease at 72 hours of incubation.53 Likewise, research on the bacterium P. pentosaceous ATCC 43200 found an exponential phase starting at four to 10 hours, after which the bacteria entered a stationary phase until 48 hours.54 The bacteria P. pentosaceus 63, P. pentosaceus 145, and P. pentosaceus 146, isolated from cheese made in Minas, Brazil, reached a stationary phase at 15 hours.55 The bacteria L. lactis PFC77 and P. acidilactici PFC69, isolated from fermented milk, a fermented soup originating from Anatolia, were able to inhibit the enlargement of S. aureus ATCC 29213 and B. cereus ATCC 11778 because they could produce bacteriocins and could be used as food preservatives.56 Optimal bacterial growth depends on the medium used.\n\nLAB’s antibacterial activity against harmful bacteria has been extensively researched in food.57,58 The broad antibacterial range is associated with the LAB’s capability to generate antibacterial agents, i.e., acetic acids, H2O2, and antimicrobial compounds, that can inhibit the growth of other dangerous organisms.59 P. pentosaceus bacteria are lactic acid-producing bacteria that can create antibacterial compounds, hydrogen peroxide, and bacteriocins that are effective against S. enteritidis and E. casseliflavus and have the highest inhibitory activity compared to other LAB isolates.60 Several species of Pediococcus sp. have been reported to produce bacteriocins capable of inhibiting the growth of infectious agents.61,62 Pediococcus sp. can cause a decrease in the pH matrix of fermented foods, which leads to inhibition of the growth of unwanted bacteria.59 The acidifying activity of Pediococcus sp. strains has been observed, which causes a decrease in the pH matrix of food preservation and pathogenic microorganisms.63 Pediococcus spp., which were isolated from a fermented kombucha drink, were able to inhibit all test bacteria, namely, L. monocytogenes, S. enterica, B cereus, P hauseri, and L. ivanovii.48 Pediococcus acidilactici BK01 bacteria isolated from tamarind showed inhibition against S. aureus and E. coli during storage for a month at various temperatures.64 Furthermore, P. acidilactici M76 bacteria isolated from a black raspberry fermented drink showed antimicrobial activity against the pathogenic bacteria S. aureus, S. epidermidis, S. xylosus, P. aeruginosa, P. putida, B. cereus, B. subtilis, B. vallismortis, E. coli, and P. acnes.65\n\nThe ability of LAB to produce EPS is an important consideration when choosing an LAB culture to be utilized in dairy manufacture because these compounds function as texturizers and stabilizers, which are needed to create a smooth and creamy product.66 Furthermore, when utilized as a supplementary culture to speed up food fermentation time, the synthesis of a large amount of EPS by Pediococcus strains is regarded as a benefit for LAB from other varieties. Exopolysaccharides are usually secreted by microbes to the outside of cells and are generally found outside of the bacterial cellular structure. EPS is connected to the cell in the form of a capsule or mucus that is present on the cell surface. Lactic acid bacteria have been identified in Nigerian fermented food products (ogi, gari, and fufu) that are capable of producing exopolysaccharides and can be used as starter cultures to make functional foods.32 Furthermore, it was also found that the bacterium P. acidilactici M76 isolated from a fermented black raspberry drink could produce EPS and be used as a functional probiotic.65 L. plantarum JLAU103, isolated from hurood, a Chinese soured food, produced 75 mg/l exopolysaccharide after incubation for 24 hours.67 L. fermentum MC3 bacteria isolated from bamboo shoot fermentation products produced 88.776 mg/l exopolysaccharide after incubation for 48 hours using MRS medium supplemented with 4% glucose and 0.3% yeast extract.68\n\nMolecular techniques based on DNA restriction fragments have been widely used to classify LAB isolated from various food products.69 This was validated through gene sequencing of the 16S rRNA genes from samples of bacteria. P. pentosaceus is an LAB that has thick cell walls, produces no spores, is negative for catalase, has a coccus shape, does not have cytochromes, and has facultatively anaerobic growth. P. pentosaceus can be isolated from the gastrointestinal tract. P. pentosaceus 4I1, a known LAB, was isolated once from the intestinal microorganisms of a sample of Zacco koreanus.70 LAB can also be isolated from fermented buffalo milk known as “dadih”, cereal fermentation, digestive organs of Bali cattle, tamarind fermentation, dried sausage, fermented “kombucha”, fermented freshwater fish and corn silage.41,45,47,48,71–74\n\n\nConclusions\n\nIn testing 56 LAB isolates from budu fish, as many as 29 isolates were demonstrated to be Pediococcus sp. Based on bacterial characterization, one potential isolate was determined to be Pediococcus pentosaceus. These bacteria showed resistance to gastric acid conditions, with a survival rate of 60.68% at pH 2.5. These bacteria inhibited dangerous microbes such as S. aureus, E. coli, and S. thypi from multiplying and were able to produce exopolysaccharides. After being identified molecularly, this bacterium was shown to have 100% similarity with Pediococcus pentosaceous strain 4942.\n\n\nData availability\n\nFigshare: Underlying data for ‘Characterization of lactic acid bacteria isolated from budu, a West Sumatra fish fermentation product, and their ability to produce exopolysaccharides’. https://doi.org/10.6084/m9.figshare.19612677\n\nThis project contains the following underlying data:\n\n• Table 1. Pedicoccus sp. bacteria resistance to gastric pH (2, 3, 4, 5, 6, 7, 8, 9, 10, and 11) using MRS broth fter incubation 36 hours\n\n• Table 2. Row data: Growth curve of Pediococcus sp. bacteria incubated on MRS broth medium for 36 hours\n\n• Table 3. Row data: Inhibitory ability of Pediococcus sp. bacteria against pathogenic bacteria (Escherichia coli, Staphylococcus aureus and Salmonella thypi)\n\n• Table 4. Row data: The sequence of nitrogen bases from the sequencing of Pediococcus sp.\n\n• Supplementary Figure 1. PCR gel image.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\nNCBI Gene: Pediococcus pentosaceus strain 4942 16S ribosomal RNA. Accession number MT512069.1. https://www.ncbi.nlm.gov/nuccore/MT512069.1",
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Publisher Full Text\n\nBungenstock L, Abdulmawjood A, Reich F: Evaluation of antibacterial properties of lactic acid bacteria from traditionally and industrially produced fermented sausages from Germany. PLoS One. 2020; 15: 1–15. Publisher Full Text\n\nDasari S, Shouri RND, Wudayagiri R, et al.: Antimicrobial activity of Lactobacillus against microbial flora of cervicovaginal infections. Asian Pac. J. Trop. Dis. 2014; 4: 18–24. Publisher Full Text\n\nHamida F, Wiryawan KG, Meryandini A: Selection of lactic acid bacteria as probiotic candidate for chicken. Media Peternakan. 2015; 38(2): 138–144. Publisher Full Text\n\nPorto MC, Kuniyoshi TM, Azevedo POS, et al.: Pediococcus spp.: an important genus of lactic acid bacteria and pediocin producers. Biotechnol. Adv. 2017; 35(3): 361–374. PubMed Abstract | Publisher Full Text\n\nKomora N, Maciel C, Pinto CA, et al.: Non-thermal approach to Listeria monocytogenes inactivation in milk: the combined effect of high pressure, pediocin PA-1 and bacteriophage P100. BMC Microbiol. 2020; 86: 103315–103319. Publisher Full Text\n\nOlaoye OA, Onilude AA, Dodd CER: Identification of Pediococcus spp. from beef and evaluation of their lactic acid production in varying concentrations of different carbon sources. Adv. Nat. Appl. Sci. 2008; 2(3): 197–207.\n\nMelia S, Juliyarsi I, Kurnia YF, et al.: Characteristics of antibacterial activity stability of crude bacteriocin Pediococcus acidilactici BK01. International Conference on Agriculture, Environment and Food Security: 2020. IOP Conf. Series: Earth and Environmental Science 2021; 782. 032074.\n\nSong YR, Lee CM, Lee SH, et al.: Evaluation of probiotic properties of Pediococcus acidilactici M76 producing functional exopolysaccharides and its lactic acid fermentation of black raspberry extract. Microorganisms. 2021; 9(7): 1–17. Publisher Full Text\n\nOgunsakin AO, Vanajakshi V, Anu-Appaiah KA, et al.: Evaluation of functionally important lactic acid bacteria and yeasts from Nigerian sorghum as starter cultures for gluten-free sourdough preparation. LWT-Food Sci.Technol. 2017; 82: 326–334. Publisher Full Text\n\nMin WH, Fang XB, Wu T, et al.: Characterization and antioxidant activity of an acidic exopolysaccharide from Lactobacillus plantarum JLAU103. J. Biosci. Bioeng. 2019; 127(6): 758–766. PubMed Abstract | Publisher Full Text\n\nDo TBT, Tran TAL, Tran TVT, et al.: Novel exopolysaccharide produced from fermented bamboo shoot-isolated Lactobacillus fermentum. Polym. J. 2020; 12(7): 1531.\n\nSimpson PJ, Stanton C, Fitzgerald GF, et al.: Genomic diversity within the genus Pediococcus was revealed by randomly amplified polymorphic DNA PCR and pulsed-field gel electrophoresis. Appl. Environ. Microbiol. 2002; 68(2): 765–771. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBajpai VK, Han J, Rather IA, et al.: Characterization of lactic acid bacterium Pediococcus pentosaceus 4I1 from freshwater fish Zacco koreanus and its antibacterial mode of action. Peer. J. Prepr. 2016; 4: e2121v1.\n\nSamuel O, Mavis O, Frederick O: In vitro studies of the probiotic properties of lactic acid bacteria isolated from akamu-a Nigerian weaning food. J. Immunol. Infect. Dis. 2019; 7(2): 13–20.\n\nRadwika M, Suardana IW, Sukrama IDM: Studies on species of lactic acid bacteria isolate Sr 12 from Bali cattle gastric with conventional method and Api Kit 50ch. J. Vet. Anim. Sci. 2019; 2(1): 18–23. Publisher Full Text\n\nSun F, Hu Y, Chen Q, et al.: Purification and biochemical characteristics of the extracellular protease from Pediococcus pentosaceus isolated from Harbin dry sausages. Meat Sci. 2019; 156: 156–165. PubMed Abstract | Publisher Full Text\n\nGowda SGS, Narayan B, Gopal S: Antioxidant properties and dominant bacterial community of fermented rohu (Labeo rohita) sauce produced by enzymatic and fermentation method. Turk. J. Fish. Aquat. Sci. 2020; 20(8): 583–592. Publisher Full Text"
}
|
[
{
"id": "203606",
"date": "25 Sep 2023",
"name": "Aybike Kamiloğlu",
"expertise": [
"Reviewer Expertise lactic acid bacteria",
"characterization",
"exopolysaccharide production",
"biotechnology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, the characterization and exopolysaccharide production abilities of lactic acid bacteria isolated from West Sumatra fermented fish were examined. However, when the study is evaluated, its purpose cannot be fully understood. What was wanted, what was sought, what was targeted.\nFirst of all, the concept of probiotics is included. However, in order to use the word probiotic, it is insufficient to only determine their antimicrobial and resistance in the gastric environment. Therefore, in this study, the concept of probiotics should have been stated only as a potential.\n\n56 isolates were mentioned in the study. On what basis was the selection made? However, no biochemical tests for these isolates were mentioned (except DNA isolation).\n\nCharacterization of the produced exopolysaccharide is not included.\nThis study does not meet the appropriate criteria for indexing. It does not express originality other than the microorganism source.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1139
|
https://f1000research.com/articles/11-503/v1
|
09 May 22
|
{
"type": "Research Article",
"title": "The Arizona Sexual Experiences Scale-the Thai Translation (ASEX-Thai): Reliability and validity in Thai patients with mental disorders",
"authors": [
"Natthaphon Charoenmakpol",
"Mayteewat Chiddaycha",
"Sorawit Wainipitapong",
"Natthaphon Charoenmakpol",
"Mayteewat Chiddaycha"
],
"abstract": "Background: Sexual dysfunction is common among patients with mental disorders but receives less clinical attention, especially in Thailand and other Asian countries. The Arizona Sexual Experiences Scale-the Thai Translation (ASEX-Thai), a self-rated, brief, questionnaire is a potential tool for screening for sexual dysfunction in this population. Our study aimed to assess the reliability and validity of ASEX-Thai in Thai patients with mental disorders. Methods: We enrolled 202 patients from an outpatient psychiatric department at a tertiary hospital in Bangkok, Thailand. Demographic data, clinical data, and diagnosis of sexual dysfunction were assessed. ASEX-Thai was done, and we analyzed the test’s psychometric properties. Results: Most participants were diagnosed with major depressive disorder (48%). A score of ≥ 17 points of the ASEX-Thai was the most suitable for sexual dysfunction screening (sensitivity 77.23 %, and specificity 58.42 %). For reliability, the Cronbach’s alpha coefficient (0.831) showed good internal consistency. Conclusions: The ASEX-Thai is a valid and reliable self-rated questionnaire for screening for sexual dysfunction among Thai patients with mental disorders. The test could help clinicians to evaluate this undetected condition and deliver proper interventions.",
"keywords": [
"Arizona Sexual Experiences Scale",
"ASEX",
"sexual dysfunction",
"Thai",
"mental disorder",
"psychiatric disorder"
],
"content": "Introduction\n\nThe World Health Organization (WHO) has emphasized the importance of mental health with its famous statement ‘without mental health there can be no true physical health’.1 There has been stronger evidence of the bidirectional linkage between mental and physical health. Mental disorders are significantly associated with higher hospitalizations, longer length of stay, and increased healthcare costs due to physical diseases.2 Additionally, certain physical diseases may precede the onset of mental disorders and vice versa.3 The adverse effects of medications for these two conditions also portray the same interaction. Apart from other physical causes, sexual problems are also commonly found among those receiving psychotropic medications.4 Sexual dysfunction (SD) is not only a frequent adverse effect but could also be a manifestation of some psychiatric disorders. Moreover, SD itself could be comorbid with other non-sexual mental disorders.5 Sexual dissatisfaction markedly affects the quality of life and mental health,6 therefore it may be reasonable to add to the WHO’s statement that ‘there also can be no true mental health without sexual health’.\n\nSD has been underrecognized in some Asian countries according to different cultures and attitudes toward sexuality.7 The prevalence of SD is mainly studied in some specific physical morbidities and tends to receive less academic attention in psychiatric populations. Some studies reported a great number of SD (60.7-82.7%) among those with schizophrenia,8,9 but related findings are still lacking in Asians with other mental disorders. A validated, especially a self-rated, SD measurement would be beneficial in terms of research and clinical application in the Asian culture where sexual issues are considered forbidden.\n\nThe Arizona Sexual Experiences Scale (ASEX) is a 5-item self-rated, brief questionnaire with a 6-point Likert scale assessing SD components including desire, arousal, penile erection or vaginal lubrication, ability to achieve orgasm and orgasmic satisfaction.10 The ASEX can be used regardless of sexual orientation and individual or partnered sexual activity. However, some items are not suitable for specific populations, such as transgender people, especially after the transition. The score is positively correlated with the severity of SD, and it can be implemented in various clinical settings with good reliability.11 The cutoff score is varied due to the methodology and study populations in each study.10–14 Validation studies have been done in some psychiatric and physical diseases. The ASEX is available in 43 languages and a few non-English versions, including Thai, of ASEX have been examined for their psychometric properties. However, only the Arabic and French versions of the ASEX have been validated in patients with psychiatric disorders.12,15 Psychometric properties from these two versions are highly acceptable. However, the application of the Arabic and French versions is limited since the study was done in patients with schizophrenia and depression, respectively. Only the original ASEX was assessed its reliability and validity in those with several mental disorders, so the generalizability of other translated versions in this certain population is still lacking.\n\nThe ASEX- Thai Translation (ASEX-Thai) was assessed for its reliability and validity among patients with Parkinson’s disease.14 The study included a forward/backward translation, and cross-cultural modifications for assuring content validity. The Cronbach’s alpha of all items with values of 0.948 at baseline and 0.962 at 2-month follow-up confirmed the reliability of the ASEX-Thai. Those with scores over fifteen would be considered positive for SD with 96.2% and 92.9% of sensitivity and specificity, respectively. However, the generalizability of the cutoff point is limited regarding the study population. Patients with Parkinson’s disease also contain ample SD risk factors, including age, motor deterioration, psychiatric comorbidities, and neuropsychiatric medications. A validation of ASEX-Thai in disparate populations would be profitable in clinical practices, especially among patients whose risks for SD are critically high, including psychiatric patients. Hence, our study aimed to examine the validity and reliability of ASEX-Thai in Thai patients with mental disorders.\n\n\nMethods\n\nWe enrolled participants aged at least 18 years old, from the psychiatric outpatient department at King Chulalongkorn Memorial Hospital in Bangkok, Thailand. All participants received a steady dosage of medications for at least one month and were diagnosed with mental disorders including schizophrenia, major depressive disorder, bipolar disorder, obsessive-compulsive disorder, or anxiety disorders. Those who were unable to communicate properly and had unstable medical or psychiatric conditions were excluded. Sample size calculation was done based on sensitivity, specificity and the results from the previous study.10,16 With SD prevalence of 31%, 82% and 90% of sensitivity and specificity, respectively, we used Buderer’s method for sample size calculation, which required a minimum total sample of 202 patients. Kaiser-Meyer-Olkin (KMO) and Barlett’s sphericity test confirmed that the sample size was adequate for the factor analysis. Written informed consent for participation and publication of the participants’ details was obtained from all participants was obtained, and the study was approved by the Institutional Review Board of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 430/2020).\n\nDemographic data, including sex, age, body mass index, psychotropic medications, and medical history were collected. The severity of their mental disorder was assessed using the Brief Psychiatric Rating Scale (BPRS). We used the second version of BPRS, which consists of 18 items measuring multidimensions of psychiatric symptoms, and categorized into two grades of severity with a cutoff score of 36.17\n\nThe ASEX-Thai was used under the permission of the original researcher. Diagnosis of SD based on the Diagnostic and Statistical Manual of Mental disorder, Fifth edition (DSM-5) was evaluated for establishing criterion validity for SD of ASEX-Thai. After completing the questionnaire, all participants were assessed their SD diagnosis by the psychiatric interview, while the ASEX-Thai result remained concealed. Test-retest reliability was not done since SD is impacted by multiple factors and may suddenly occur within a short period.18 Content validity was proved in the previous study.14\n\nDescriptive statistics were used to report the demographic data of all participants. Categorical variables were presented as counts and percentage, and continuous variables were shown as appropriate. In order to determine the criterion validity, we used Pearson’s correlation to assess the correlation between SD diagnosis based on ASEX-Thai and DSM-5. Exploratory factor analysis with principal-components method and varimax rotation was conducted to test the construct validity. Internal consistency was tested by the Cronbach’s alpha coefficient. Receiver operating characteristic (ROC) analysis was used to determine the area under curve (AUC). The sensitivity, specificity, and Youden J index were calculated for every cut-off point of the ASEX-Thai to find the optimal cut-off for sexual dysfunction screening. A p value of < 0.05 was considered statistically significant. STATA-IC Version 16.1 was used for analysis.\n\n\nResults\n\nIn total, 202 participants were recruited throughout our study period. Male participants were slightly greater in number (54.9%) and the median age was 28 years old. Most participants had normal body weight (Body mass index 23.8 kg/m2) and hypertension was the most frequent medical comorbidity (2.9%). As for psychiatric disorders, major depressive disorder remained the highest in number (48.0%) followed by anxiety disorder (18.3%) and schizophrenia (15.3%). According to the BPRS, the majority appeared to have mild symptoms (92.1%). The demographic data and psychiatric history are displayed in Table 1.\n\nRegarding the DSM-5 criteria, SD was found in 101 participants (50.0%). Pearson’s correlation portrayed a weak correlation between the ASEX-Thai positive for SD and clinical diagnosis according to the DSM (r = 0.402, p < 0.001).\n\nThe KMO coefficient was 0.77, which was above 0.50, and the result of Barlett’s sphericity test was found to be statistically significant (χ2 = 409.76; p = 0.000). Therefore, the sample size was sufficient for the analysis. Exploratory factor analysis showed one factor that explained 60.2% of the total variance. Factor loadings ranged from 0.72 to 0.86.\n\nArea under the curve (AUC) of the ROC analysis showed the ability to distinguish between those with and without SD (0.75 ± 0.03, p < 0.001). Among patients with mental disorders, we found that a cutoff score of ≥ 17 points of the ASEX-Thai was the most suitable for SD screening (sensitivity 77.23 %, specificity 58.42%, Youden J index 0.40). According to the manual of the ASEX, two additional proposed criteria, which indicated positive SD screening, were calculated with the ROC analysis. Evaluating participants who (1) had three or more items with an individual score of 4, or (2) any individual score of either 5 or 6, we found that the AUC for (1) and (2) was 0.68 (95% CI 0.61-0.74) and 0.75 (95% CI 0.69-0.81) respectively.\n\nFor the reliability, the Cronbach’s alpha coefficient was greater than 0.7, which indicated good internal consistency.\n\n\nDiscussion and conclusion\n\nSD among patients with mental disorders is common but undetected.19 Sexuality assessment is considered uncomfortable for healthcare providers because of stigmatization and limited opportunities for practice20 especially in Asian cultures, which are comparatively more conservative.21 This important problem can potentially be avoided by the use of a self-rated questionnaire.\n\nThe ASEX-Thai, a brief and self-rated measurement, showed good reliability and validity for SD assessment among patients with Parkinson’s disease and mental disorders (Table 2).\n\na BISF Brief Index of Sexual Functioning.\n\nWith a cutoff score of 17, the ASEX-Thai revealed constraints regarding its inferior psychometric properties. However, the purpose of the questionnaire was for SD screening, therefore lower specificity is considered acceptable, as one previous study had selected its cutoff for screening at 11 (sensitivity 100%, specificity 52%).13 Proper psychiatric assessment should be further evaluated for the diagnosis of SD. Adding two more criteria for a positive ASEX-Thai (those who had three or more items with individual score of 4 or had any 5 or 6 for at least one item) could improve the questionnaire’s property (sensitivity 82.2% specificity 55.4%).\n\nThe lower specificity found in our study could be explained by the use of DSM-5 for validation. The diagnosis of SD according to DSM-5 consists of one essential criterion regarding the individual’s clinically significant distress; meanwhile, the ASEX-Thai defines a positive screening by persistence of other symptoms alone, which may not fulfill the DSM-5 SD diagnostic criteria. This linkage was confirmed by a weak correlation from Pearson’s correlation. Also, the repression of sexual satisfaction and sex guilt among the Asian population is common, and lower desire is reported.22,23 Consequently, the distress of each individual may be obscured, and the diagnosis cannot be fulfilled. Our participants were also mostly young and single; thus, distress or impairment in interpersonal function might be absent. Supplemental items underpinning participants’ distress or impairment could further enhance the psychometric property of ASEX-Thai.\n\nAll participants were assessed by one clinician, so interrater bias of DSM-5 diagnosis was subtle. Our study reported poorer Cronbach’s alpha when compared with the previous ASEX-Thai and original ASEX studies. Since the ASEX-Thai measured every aspect of sexual function according to the human sexual response cycle, the extent of the participants’ sexual experiences could be a limitation, especially for those who have never engaged in partnered sexual activities. Their scores from these associated items might then be lower. We collected a large sample size that included psychiatric patients with various diagnoses, age, age of onset, and severity. These variables might impact the patient’s self-disclosure and cause self-reporting bias, which can interfere with the reliability of the ASEX-Thai, which is a self-rated questionnaire.24\n\nOur participants were diagnosed with certain mental disorders and were prescribed psychotropic medications from their attending psychiatrists. Multiple studies suggested that psychiatric illness and its treatment are related to the development of SD.25–27 However, receiving substances or medications able to induce SD does not exclude its diagnosis.28 Therefore, the nature of our participants does not confound the validity of the ASEX-Thai but increases its utility because of the high prevalence of SD among this population.29\n\nCompared to prior versions of ASEX studies in other languages, our study covered the greatest sample size and diversity in psychiatric diagnoses. The severity of psychiatric symptoms of all participants were assessed with the same, standardized, questionnaire by a sole investigator and a rater bias was minimized.\n\nSome limitations should be mentioned. The number of each psychiatric diagnosis was not distributed equally and could limit the generalizability to the whole psychiatric outpatient department. The majority of our participants were diagnosed with major depressive disorder, similar to the original version of the ASEX in psychiatric patients.10 However, the ASEX-Thai can be implemented as a screening tool and can facilitate psychiatrists to further evaluate SD and make a diagnosis using the psychiatric interview and gold-standard DSM-5 criteria. Some items of the ASEX-Thai cannot assess SD in specific populations, such as transitioned transgender people. Limitation and complications of gender-affirming therapy include lubrication in neovagina or erection in neophallus constructed by phalloplasty.30,31 Future studies focusing on clinical applications of the ASEX-Thai are needed to evaluate SD, both primary and medication-induced in etiology, among patients with mental disorders and gender diversity.\n\nPatients with mental disorder suffer from their mental health and underrecognized sexual problems, which may partly be caused by treatment complications. This undetected and untreated condition should be emphasized congruently with the cultural context and comfort of both patients and clinicians. The ASEX-Thai is a brief, self-rated, valid, and reliable questionnaire for SD screening among Thai patients with mental disorders.\n\n\nData availability\n\nThe data that support the findings of this study are not publicly available due to the containing information that is highly sensitive (participants’ mental and sexual health). However, the data can be available on request via email to the corresponding author. The access to the dataset is granted only for the purpose of reviewing and academic reasons.",
"appendix": "Acknowledgements\n\nWe appreciate Dr. Onanong Phokaewvarangkul for her dedicated work on the ASEX-Thai translation and permission to further validate this tool in our patients. We thank Dr. Chavit Tunvirachaisakul for his kind and patient statistical advice. We also thank Dr. Yanin Thipakorn for her grammatical reviews.\n\n\nReferences\n\nKolappa K, Henderson DC, Kishore SP: No physical health without mental health: lessons unlearned?. Bull. World Health Organ. 2013 Jan 1; 91(1): 3–3A. PubMed Abstract | Publisher Full Text\n\nRichmond-Rakerd LS, D’Souza S, Milne BJ, et al.: Longitudinal Associations of Mental Disorders With Physical Diseases and Mortality Among 2.3 Million New Zealand Citizens. JAMA Netw. Open. 2021 Jan 13; 4(1): e2033448. PubMed Abstract | Publisher Full Text\n\nTegethoff M, Stalujanis E, Belardi A, et al.: Chronology of Onset of Mental Disorders and Physical Diseases in Mental-Physical Comorbidity - A National Representative Survey of Adolescents. PLoS One. 2016 Oct 21; 11(10): e0165196. PubMed Abstract | Publisher Full Text\n\nMontejo AL, Montejo L, Navarro-Cremades F: Sexual side-effects of antidepressant and antipsychotic drugs. Curr. Opin. Psychiatry. 2015 Nov; 28(6): 418–423. Publisher Full Text\n\nPiontek A, Szeja J, Błachut M, et al.: Sexual problems in the patients with psychiatric disorders. Wiad. Lek. 2019 Oct 31; 72(10): 1984–1988. PubMed Abstract\n\nMontejo AL: Sexuality and Mental Health: The Need for Mutual Development and Research. J. Clin. Med. 2019 Oct 26; 8(11): 1794. PubMed Abstract | Publisher Full Text\n\nIrfan M, Hussain NHN, Mohd NN, et al.: Epidemiology of Male Sexual Dysfunction in Asian and European Regions: A Systematic Review. Am. J. Mens Health. 2020 Jul 6; 14(4): 1557988320937200. PubMed Abstract | Publisher Full Text\n\nHou C-L, Zang Y, Rosen RC, et al.: Sexual dysfunction and its impact on quality of life in Chinese patients with schizophrenia treated in primary care. Compr. Psychiatry. 2016 Feb; 65: 116–121. PubMed Abstract | Publisher Full Text\n\nHuang Y-H, Hou C-L, Ng CH, et al.: Sexual dysfunction in Chinese rural patients with schizophrenia. BMC Psychiatry. 2019 Jul 12; 19: 218. PubMed Abstract | Publisher Full Text\n\nMcGahuey CA, Gelenberg AJ, Laukes CA, et al.: The Arizona Sexual Experience Scale (ASEX): reliability and validity. J. Sex Marital Ther. 2000 Mar; 26(1): 25–40. PubMed Abstract | Publisher Full Text\n\nElnazer HY, Baldwin DS: Structured review of the use of the Arizona sexual experiences scale in clinical settings. Hum. Psychopharmacol. 2020 May; 35(3): e2730. PubMed Abstract | Publisher Full Text\n\nBriki M, Haffen E, Monnin J, et al.: Sexual dysfunction and depression: Validity of a French version of the ASEX scale. Encéphale. 2014 Apr; 40(2): 114–122. PubMed Abstract | Publisher Full Text\n\nSoykan A: The reliability and validity of Arizona sexual experiences scale in Turkish ESRD patients undergoing hemodialysis. Int. J. Impot. Res. 2004 Dec; 16(6): 531–534. PubMed Abstract | Publisher Full Text\n\nJitkritsadakul O, Jagota P, Bhidayasiri R: The Arizona Sexual Experiences Scale: a validity and reliability assessment of the Thai translation (ASEX-Thai) in Parkinson’s disease. J. Parkinsons Dis. 2014; 4(2): 205–210. PubMed Abstract | Publisher Full Text\n\nNakhli J, El Kissi Y, Bouhlel S, et al.: Reliability and validity of the Arizona sexual experiences scale-Arabic version in Tunisian patients with schizophrenia. Compr. Psychiatry. 2014 Aug; 55(6): 1473–1477. PubMed Abstract | Publisher Full Text\n\nNegida A, Fahim NK, Negida Y: Sample Size Calculation Guide - Part 4: How to Calculate the Sample Size for a Diagnostic Test Accuracy Study based on Sensitivity, Specificity, and the Area Under the ROC Curve. Adv. J. Emerg. Med. 2019; 3(3): e33. PubMed Abstract | Publisher Full Text\n\nOverall JE, Gorham DR: The Brief Psychiatric Rating Scale. Psychol. Rep. 1962 Jun 1; 10(3): 799–812. Publisher Full Text\n\nNguyen HMT, Gabrielson AT, Hellstrom WJG: Erectile Dysfunction in Young Men-A Review of the Prevalence and Risk Factors. Sex Med. Rev. 2017 Oct; 5(4): 508–520. PubMed Abstract | Publisher Full Text\n\nKumar PNS, Radhika MK, Suresh R, et al.: Comparative Study of Sexual Side Effects in Female Patients With Schizophrenia Receiving Risperidone or Olanzapine. Prim Care Companion CNS Disord. 2021 Jul 22; 23(4): 20m02835. Publisher Full Text\n\nTennille J, Bohrman C, Barrenger S, et al.: Behavioral Health Provider Attitudes and Beliefs about Sexuality and Intimacy: Findings from a Mixed Method Design. Community Ment. Health J. 2021 Jun 3.\n\nMeston CM, Ahrold T: Ethnic, Gender, and Acculturation Influences on Sexual Behaviors. Arch. Sex. Behav. 2010 Feb; 39(1): 179–189. PubMed Abstract | Publisher Full Text\n\nYang Q, Hu P: Chinese Women’s Sexual Desire in the Patriarchal Society. J. Sex. Med. 2017 May 1; 14(5): e285–e286. Publisher Full Text\n\nWoo JST, Brotto LA, Gorzalka BB: The role of sex guilt in the relationship between culture and women’s sexual desire. Arch. Sex. Behav. 2011 Apr; 40(2): 385–394. Publisher Full Text\n\nAlthubaiti A: Information bias in health research: definition, pitfalls, and adjustment methods. J. Multidiscip. Healthc. 2016 May 4; 9: 211–217. PubMed Abstract | Publisher Full Text\n\nde Boer MK , Castelein S, Wiersma D, et al.: The Facts About Sexual (Dys) function in Schizophrenia: An Overview of Clinically Relevant Findings. Schizophr. Bull. 2015 May; 41(3): 674–686. PubMed Abstract | Publisher Full Text\n\nBasson R, Gilks T: Women’s sexual dysfunction associated with psychiatric disorders and their treatment. Womens Health (Lond). 2018 Apr 12; 14: 174550651876266. Publisher Full Text\n\nMontejo AL, de Alarcón R , Prieto N, et al.: Management Strategies for Antipsychotic-Related Sexual Dysfunction: A Clinical Approach. J. Clin. Med. 2021 Jan 15; 10(2): 308. PubMed Abstract | Publisher Full Text\n\nAvasthi A, Grover S, Sathyanarayana Rao TS: Clinical Practice Guidelines for Management of Sexual Dysfunction. Indian J. Psychiatry. 2017 Jan; 59(Suppl 1): S91–S115. PubMed Abstract | Publisher Full Text\n\nOsasona SO, Ehimigbai M: Sexual dysfunction: prevalence and associated factors in patients with mental illness receiving psychotropic medication in Nigeria. Afr. Health Sci. 2019 Dec; 19(4): 2973–2984. PubMed Abstract | Publisher Full Text\n\nBizic M, Kojovic V, Duisin D, et al.: An Overview of Neovaginal Reconstruction Options in Male to Female Transsexuals. Sci. World J. 2014; 2014: 1–8. Publisher Full Text\n\nDjordjevic ML: Novel surgical techniques in female to male gender confirming surgery. Transl. Androl. Urol. 2018 Aug; 7(4): 628–638. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "144417",
"date": "25 Aug 2022",
"name": "Chotiman Chinvararak",
"expertise": [
"Reviewer Expertise Psychiatry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you very much for inviting me to be a reviewer of this article.\nThis article is the first study aimed to validate ASEX-Thai questionnaire in Thai patients with mental disorders.\n\nThe writing style was done with a standard academic English.\nThe authors demonstrated an appropriate rationale, study design and statistical analysis.\nI have few comments that may improve the scientific value of this article.\n1) According to “The KMO coefficient was 0.77, which was above 0.50, and the result of Barlett’s sphericity test was found to be statistically significant (χ2 = 409.76; p = 0.000)” please change the p-value to p<0.001\n2) please mention and explain more detail about DSM-5 diagnostic interview for sexual dysfunction in the methods (as the authors have discussed already in the discussion part)\n3) please discuss more on the comparison between this study and the study of Jitkritsadakul et al. And the reason why there is a difference in the sensitivity and specificity.\nI think this article has a sufficient value for Indexing.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8850",
"date": "04 Oct 2022",
"name": "Sorawit Wainipitapong",
"role": "Author Response",
"response": "Thank you for your kind and helpful comments. Please find my point-by-point responses below: 1) According to “The KMO coefficient was 0.77, which was above 0.50, and the result of Barlett’s sphericity test was found to be statistically significant (χ2 = 409.76; p = 0.000)” please change the p-value to p<0.001 Response – Thank you. We have changed as your suggestion in our revised version. 2) please mention and explain more detail about DSM-5 diagnostic interview for sexual dysfunction in the methods
(as the authors have discussed already in the discussion part) Response – Thank you for this point. Additional details about DSM-5’s sexual dysfunction and our clinical interview have been stated in the method section. 3) please discuss more on the comparison between this study and the study of Jitkritsadakul et al. And the reason why there is a difference in the sensitivity and specificity. Response – The psychometric properties from previous ASEX-Thai study were studied among patients with Parkinson’s disease whose clinical and demographical profiles were totally different. Our participants were younger and most of them were single. SD then could not be diagnosed for absence of functional/interpersonal impairment, and this explained a difference of our sensitivity and specificity, compared to previous study. We have mentioned this in Table 2 and the fourth paragraph of the discussion section."
}
]
},
{
"id": "140559",
"date": "29 Sep 2022",
"name": "Pakawat Wiwattanaworaset",
"expertise": [
"Reviewer Expertise Psychiatry"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is interesting and will be useful for screening people with sexual dysfunction in Thailand. However, I have some comments that may improve the scientific value of this article.\nMost participants were diagnosed with major depressive disorder, in other words, most of them received antidepressants which could cause sexual dysfunction. Did it confound the result of this study?\n\nMost participants had mild BPRS. Do you think that the result of this study can apply in all levels of psychiatric patients (mild to severe symptoms)? Please give further discussion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8851",
"date": "04 Oct 2022",
"name": "Sorawit Wainipitapong",
"role": "Author Response",
"response": "We appreciate your advice on our manuscript. Hereby, please find our response to your queries. 1) Most participants were diagnosed with major depressive disorder, in other words, most of them received antidepressants which could cause sexual dysfunction. Did it confound the result of this study? Response – Thank you for this interesting question. As your opinions, those receiving antidepressants might have poorer sexual function and SD could be diagnosed. According to DSM-5, medication-induced SD was included in our study. We believe that our psychometric properties would not be confounded from this nature. We have mentioned about this point in the sixth paragraph of the discussion section. 2) Most participants had mild BPRS. Do you think that the result of this study can apply in all levels of psychiatric patients (mild to severe symptoms)? Please give further discussion. Response – Thank you for this point. Generalizability of the tool was limited to those with mild symptoms. We have now clarified about this in the limitation."
}
]
},
{
"id": "151715",
"date": "30 Sep 2022",
"name": "Gonzalo R Quintana",
"expertise": [
"Reviewer Expertise Sex",
"sexual behavior and function"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall\nCharoenmakpol et al. Provided the psychometric evaluation (reliability and validity) for the Arizona Sexual Experiences Scale in Thai for patients with mental disorders. They showed that the instrument has adequate sensitivity and reliability, yet not good specificity, which relates to the low correlation with the criterion. The authors discuss why these results do not replicate previously reported better specificity.\nSpecific comments\nAbstract\n\nIt is well formatted. I would include information regarding the model fit and its validity assessed.\n\nIntroduction\n\nI believe the last sentence of the 1st paragraph may benefit by changing “add” to “expand” or “derive from the WHO...”\n\nA citation seems necessary for the last sentence of the 2nd paragraph. Otherwise, reconsider \"forbidden”\n\nIn the last sentence of the 3th paragraph, it says “Only the original ASEX was assessed its reliability...” This needs rewording. It appears that is missing the “for” before “its”.\n\nMethods\n\nThe study does not include a description of a Ethical Evaluation. This is of great concern, especially due to the sample characteristics\n\nSome readers would benefit from an explanation of the IQR acronym\n\nThere is no reason not to include the Omega’s calculation for reliability\n\nDiscussion\nThe authors do a good job discussing the findings and limitations.\n\nWhereas the scale may not instruct researchers to exclude not-sexually active people, to include these people in the analysis using other sexual function scales has shown to be problematic (e.g., IIEF). If the authors can redo their analysis excluding these individuals, it may be a hypothesis worth considering. If indeed the authors have this information, they must include it, and assess if it may partially explain the results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8852",
"date": "04 Oct 2022",
"name": "Sorawit Wainipitapong",
"role": "Author Response",
"response": "Thank you for your immensely helpful suggestions. Please find my point-by-point responses below: Abstract 1) It is well formatted. I would include information regarding the model fit and its validity assessed. Response –Thank you for your suggestion. Information was added into the abstract. Introduction 1) I believe the last sentence of the 1st paragraph may benefit by changing “add” to “expand” or “derive from the WHO...” Response – Thank you. We have now changed to “derive from” as your suggestion. 2) A citation seems necessary for the last sentence of the 2nd paragraph. Otherwise, reconsider \"forbidden” Response – Thank you for this crucial point. We have changed to “underreported and untreated” and the citation has been added. 3) In the last sentence of the 3th paragraph, it says “Only the original ASEX was assessed its reliability...” This needs rewording. It appears that is missing the “for” before “its”. Response – Thank you. “For” has now been added. Methods 1) The study does not include a description of a Ethical Evaluation. This is of great concern, especially due to the sample characteristics Response – Ethical issue is also our major concern. Our study received the approval from our institution’s IRB. We have mentioned about this in the last sentence of the first paragraph of the method section. 2) Some readers would benefit from an explanation of the IQR acronym Response – Thank you very much. The acronym has now been clarified. 3) There is no reason not to include the Omega’s calculation for reliability Response – Thank you for your suggestion. We have calculated the Omega’s reliability. The result of Omega’s reliability was 0.83 and we have added it into the method and result section. Discussion 1) Whereas the scale may not instruct researchers to exclude not-sexually active people, to include these people in the analysis using other sexual function scales has shown to be problematic (e.g., IIEF). If the authors can redo their analysis excluding these individuals, it may be a hypothesis worth considering. If indeed the authors have this information, they must include it, and assess if it may partially explain the results. Response - Thank you for the suggestion. We totally agree that our result would be much more interesting regarding additional analysis. Unfortunately, active sexual activity was not collected in our dataset. However, we will recruit your suggested variables in our further studies."
}
]
}
] | 1
|
https://f1000research.com/articles/11-503
|
https://f1000research.com/articles/11-908/v1
|
08 Aug 22
|
{
"type": "Research Article",
"title": "Sustainability of the regional financial system: a case study of the Northwestern Federal District",
"authors": [
"Sergey Evgenievich Barykin",
"Alexey Aleksandrovich Mikheev",
"Elena Grigorievna Kiseleva",
"Yuriy Evgenievich Putikhin",
"Elena De La Poza Plaza",
"Natalia Sergeevna Alekseeva",
"Alexey Aleksandrovich Mikheev",
"Elena Grigorievna Kiseleva",
"Yuriy Evgenievich Putikhin",
"Elena De La Poza Plaza",
"Natalia Sergeevna Alekseeva"
],
"abstract": "Background: This article provides an assessment of the sustainability of Russian regions’ financial systems. The study is based on the methods of generalization and synthesis, correlation-regression analysis, and multivariate classification. Since the structure of the regional financial system is complex, several works are devoted to studying its sustainability issues. The relevance of the study topic is confirmed by the lack of a systematic approach to assessing the integral index of sustainability and the possibility of using various tools in determining the complex indicator. Methods: This methodology with application of mathematical statistics methods makes it possible to assess the financial system sustainability in four sectors, to include the leading indicators in the assessment, and to identify regions with extreme values of debt burden indicators. The method was tested for the regions of the Northwestern Federal District (NWFD) for the period 2010 - 2019 to classify the regions according to three levels of debt sustainability. Data collection from the 1st January to 30th April 2022 included statistical data from government open internet sources, sectors studied relate to government, and municipal budgets in the NWFD. Authors analyzed regional debt sustainability indicators and identified themes in the field of sustainability studies for the NWFD. Results: An increased level of financial system sustainability was observed among the NWFD regions in the corporative and personal finance sectors, indicating a significant contribution of businesses and households to maintaining the balance and sustainability of the financial system in Russia as a whole. The results of the study also identified that the NWFD regions belong to three clusters: cluster 1 - high debt sustainability; cluster 2 - medium debt sustainability; and cluster 3 - low debt sustainability. Conclusions: The study results allowed the identification of regions with a constantly high level of debt, financial, and corporative sustainability.",
"keywords": [
"Financial Stability",
"Integral Index",
"Regional Financial System",
"Regions of Russia",
"Indicators",
"The Northwestern Federal District"
],
"content": "Introduction\n\nFinancial stability is one of the critical tasks in the functioning of the financial system of a country. National financial systems have significant differences in their development, structure, and approaches to regulation. The issues of assessing sustainability and stability of financial systems are relevant for different countries (Mazanec and Bartosova, 2021; Străchinaru and Dumitrescu, 2019; Jiang et al., 2019; Santos, Lisboa, and Eugénio, 2021; Chupina et al., 2021). The use of financial resources in various sectors of the economy, on the one hand, contributes to an increase in investment activity and an increase in the stability of the financial system, but, on the other hand, it may lead to its destabilization in case of low and untimely financing of its various sectors. In this regard, the issues of assessing the sustainability of regional financial systems are the subject of debate (Schinasi, 2004) and are actively discussed by the world scientific community (Schellhorn, 2020; Checherita-Westphal, Hughes Hallett, and Rother, 2014; Baharumshah, Soon, and Lau, 2017; Ghosh and Sahu, 2021).\n\nDuring the study, the authors concluded that changes in financial stability could not be summarized in one quantitative indicator. Unlike, for example, price stability, there is still no unambiguous unit for measuring financial stability. This reflects the multifaceted nature of the financial system, related to financial institutions' resilience and sustainability and the smooth functioning of financial markets and settlement systems. Therefore, the authors divided financial system stability into four sectors: the public finance sector, which characterizes the development of the budget system and its debt sustainability; the financial sector, which represents the state and sustainability of the banking sector, the insurance sector, the non-state pension funds, microfinancing entities, and cooperatives; the corporative sector, which takes into account the stability of cash flows of small businesses and the scale of large regional enterprises; and the personal finance sector, which takes into account the contribution of the households to the stable functioning of the financial system.\n\nWe would like to note that changes in financial stability are inherently difficult to predict. The state of financial system sustainability should assess violations as they occur and indicate the risks and vulnerabilities that may lead to such violations in the future. Therefore, an integrated approach is necessary to determine the growth of risks and imbalances and consider the time lag when using the integral financial system sustainability index to develop the public financial policy.\n\nBesides the time delays, the policy instruments of financial stability are often indirect. In some cases, disagreements may occur on the original purpose of the device and the implications of its application for the stability of the regional financial system. At the same time, policies aimed at financial stability often involve a trade-off between sustainability and efficiency. Measures to improve financial stability include, on the one hand, striving for efficient allocation of financial resources, and on the other hand, are designed to reduce the risks or vulnerabilities of the financial system. So, for example, foreign exchange restrictions can reduce or eliminate certain risks associated with international capital flows while reducing the efficiency of the domestic financial market (He, Korhonen, and Qian, 2021; Gurrea-Martínez, 2021; Rendon, 2019).\n\nThe issues of assessing financial stability and vulnerability of financial systems are widely discussed in the scientific literature. For example, in Khalatur et al.’s study (2021), the method of deriving regression equations in multivariate regression analysis is used to test the model for assessing the financial system's sustainability. Based on the data from several Eastern European countries from 2010 to 2019, a model of the modern business space ‘Volatility, uncertainty, complexity and ambiguity’ (VUCA) was developed on the example of the banking sector. The driving forces, consequences, requirements, and macroeconomic indicators of countries’ activities under the conditions of ‘VUCA-world’ were determined. The analysis showed that with an increase in GDP growth factors, growth in gross national income per capita, research and development costs, foreign direct investment, and net capital inflows by 1%, the effective ratio of the bank capital to the assets also increases by 1%.\n\nThe scientific works also note that there are no uniform worldwide standards, methods, or indicators for assessing financial sustainability (Babar et al., 2019; Nasreen and Anwar, 2019; Jadoon et al., 2021; Shkolnyk et al., 2021). A broad scope is employed in order to evaluate and test system sustainability based on different indicators and standards. The results obtained in the scientific works are diverse and interesting in terms of data coverage and other assessment methods. So, for example, in the study by Ukrainian scientists (Shkolnyk et al., 2021) on big data related to the structure of the financial system of Ukraine, a matrix of the financial system sustainability characteristics was developed, according to the 4x2 principle proposed by experts of the International Monetary Fund (Schinasi, 2004). The list of indicators for calculating the integral indicator characterizing the stability of the financial system of Ukraine covers the period from 2007 to 2019. It includes 29 indicators that consider the peculiarities of its formation and development. Harrington’s desirability function is used to determine an integral indicator that characterizes the state of financial stability. As a result, intermediate calculations obtained by modeling groups of indicators showed that the level of access to the financial system and its depth were balanced during the study period. The financial system’s efficiency is low and characterized by high volatility (the range of variations is 0.51).\n\nAn important aspect is a statement made by the scientists that it is essential to study the stability of the financial system from the point of view of resistance to a crisis (Gustiana and Nasrudin, 2021; Albulescu, 2010). The paper substantiates the thesis that instability faced by the countries is a consequence of the vulnerability of the financial system. As a method for assessing the sustainability of the financial system, the aggregate financial index (AFSI) is used, which takes into account the influence of other countries on the stability of the Indonesian banking system, and the Indonesian financial system stability index (ISSK), which takes into account the internal stability of the banking system of this country. Using the principal component analysis (PCA) method, one of the multivariate statistical analysis methods, the authors established specific weights for each index, which allowed to refine the index values for the period from 2000 to 2019. As a result, the paper concludes that each period of a crisis is always accompanied by pressure from the global economic environment, which significantly affects the sustainability of the regional financial system in Indonesia. The index developed by the scientists will serve as the basis for changing the regional policy of the Indonesian authorities.\n\nAlso, the study separately raises questions on the quality of the banks’ accounting, which plays a decisive role in assessing the financial sustainability of the banking system (Acharya and Ryan, 2016; Arzamasov and Penikas, 2014). The world scientific community is coming to understand the high role of transparency and openness of accounting information as a guarantee of objectivity in assessing the financial system sustainability. The scientists actively discuss how banking accounting and information disclosure can affect the assessment of the financial system's sustainability. The articles pay particular attention to recommendations for developers of accounting standards and policymakers of the financial system (Badertscher, Burks, and Easton, 2012; Grassa, Moumen, and Hussainey, 2021; Acharya and Ryan, 2016).\n\n\nMethods\n\nThe assessment of the sustainability of the financial system of the regions of the Russian Federation is carried out using the author’s methodology, which is a set of stages and assessment methods and a specific algorithm for their application. The developed method assumes: a) justification of choice and systematization of indicators of the debt sustainability, financial sustainability, corporative sustainability, and personal sustainability; b) standardization of the indicator values based on the method of Euclidean distances; c) calculation of the integral indicator in each sustainability sector, its ranking using the multivariate mean formula; d) division of regions into three sustainability groups: low, medium and high; and e) determination of the limit values (threshold values, limits) for the debt sustainability group using the hierarchical cluster analysis (Figure 1).\n\nAt the first stage of the study, using open data from the Federal State Statistics Service, a database of the Russian economy's statistical financial and economic indicators was formed. Next, a calculation of about 45 indicators of the financial system sustainability in four sectors was carried out. Then, at the second stage of the study, using the correlation analysis method, six indicators of debt sustainability, nine financial sustainability indicators, seven corporative sustainability indicators, and four personal sustainability indicators were selected. All indicators were highly correlated with the integral sustainability index for each financial system sector, respectively.\n\nAt the third stage of the study, all indicator values were standardized. To consider the degree of differences of each indicator across the federal districts, the method of Euclidean distances was applied. At the fourth stage of the study, the standardized values of six indicators were averaged over a dynamic series using the multivariate mean formula. A composite index (an integral indicator) across four sectors was calculated for each region of the Northwestern Federal District (NWFD). At the fifth stage of the study, a hierarchical cluster analysis was carried out, and the limit boundaries were obtained for the six indicators for the debt sustainability sector. Control of budget constraints within the boundaries found by us will increase the debt sustainability of the budget system of the Russian regions. We also used a distance matrix of indicators over the regions of the NWFD for each analyzed period and divided the data set into three clusters according to the type of debt, financial, corporative, and personal sustainability: low, medium, and high.\n\nThe study is based on the open data from the Federal State Statistics Service and the Ministry of Finance of the Russian Federation: 53 absolute indicators (the most typical indicators for the mentioned regions) of the socio-economic development of Russian regions were selected for the period from 2010 to 2019 (in 11 regions of the Northwestern Federal District (NWFD) which includes: Republic of Karelia, Republic of Komi, Arkhangelsk region, Vologda region, Kaliningrad region, Leningrad region, Murmansk region, Novgorod region, Pskov region, Saint Petersburg, Nenets Autonomous region), such as the local government debt, the volume of exports and imports, the gross domestic product, the population, the income of people per capita, the expenses for repayment and servicing of the local government debt, the amount of insurance premiums and payments, the level of the overdue debt on loans, the amount of deposits, the amount of loans granted to individuals and legal entities, the actual average wages, the consumer price index, the amount of payable and receivable accounts of enterprises, the profit of enterprises, etc. On the basis of the absolute indicators, 26 relative indicators of sustainability were calculated (for the calculations please see Barykin et al., 2022) across four sectors (the public finance sector, the financial sector, the corporative sector, and the personal finance sector) for 11 regions of the NWFD. Authors calculated indices for the debt, financial, corporative, and personal sustainability. The study uses the methods of comparison and grouping, correlation analysis, Euclidean distances, calculation of the multivariate mean, and hierarchical cluster analysis. Selection of the sustainability indicators was carried out using the correlation analysis, which has proven itself as a method for studying the relationship between the debt sustainability of the budget system and the risk of the government debt (Eberhardt and Presbitero, 2015; Égert, 2015; Li et al., 2021). Data on the selected indicators were collected from 1st January 2022 to 30th April 2022. The open service of the Federal State Statistics Service contains both separate information on statistical indicators and statistical reports for different time periods. Statistical reports used for this study were ‘Russia in numbers’ (https://fedstats.ru/, accessed 30th March 2022) and’Regions of Russia’ (Federal State Statistics Services, n.d.-b) to collect financial data while socio-economic indicators were collected from the’Russian Statistical Yearbook’ (Federal State Statistics Services, n.d.-c). Translation of all reports from Russian to English were undertaken by the authors in this study. In order to get data from 2010 to 2019, these reports were collected for various years. In the process of collecting information, some variables were excluded because they were partially presented, since it was not possible to find data for each year from the study period (the data from the period from the year of 2010 till the end of the year of 2015 has been excluded for the purpose of making conclusions regarding regional comparisons). Figure 1 shows the stages methodology for assessing the sustainability of the financial system.\n\nThe calculation of the integral sustainability indicator was carried out using the multivariate mean formula, which has proven itself for ranking indicators of digital potential (Kiseleva, 2020). To determine the budget constraints for the debt sustainability sector for each region of the NWFD, the hierarchical cluster analysis was applied since it is one of the methods of multivariate classification that allows to select areas of congestion of objects from the aggregate data and to combine them into groups (segments) with homogeneous characteristics (Kurushin and Vasilyeva, 2017). The authors used the method of Euclidean distances and cluster analysis to standardize the obtained values. Both methods are widely used in natural and social sciences to standardize and classify panel data (Barykin et al., 2021b; Bagirova and Shubat, 2021; Zolkover et al., 2020). In studying debt sustainability, using a distance matrix of indicators over the regions of the NWFD for each analyzed period, we divided the data set into three clusters: cluster 1 - high debt sustainability; cluster 2 - medium debt sustainability; and cluster 3 - low debt sustainability. Then the authors identified the cluster centroids for each indicator. Cluster centroids were determined based on the values of cluster centroids of indicators for each year of the study period, taking into account their average number, as well as the dynamics of change over the last four periods (the year of 2016, the year of 2017, the year of 2018, and the year of 2019). This allowed confirming the results obtained at the previous stage of the study and solve the problem of targeted statistical justification of the norms of budget restrictions on the debt burden. On the one hand, the values of cluster centroids were compared with the actual values of debt sustainability indicators, which allowed us to confirm the results obtained earlier. On the other hand, using clustering, the criteria values of debt sustainability indicators were justified. As a method of clustering, we used the method of intergroup communication, and as a measure of the similarity between objects, we used the Euclidean distance. The application of the author’s methodology using the standardization of indicator values and the multivariate mean formula allowed the authors of the study to rank the regions according to the level of the debt, financial, corporative, and personal sustainability, and the use of the hierarchical cluster analysis allowed to group the regions by three types of the debt sustainability and to determine the acceptable boundaries of the debt sustainability indicators for each cluster. All calculations in our study were performed using MS Excel 2016 for calculations.\n\n\nResults\n\nThe debt sustainability indicators included were: the ratio of the government debt to gross regional product (GRP); the amount of the local government debt on per capita; the share of the government debt in regional export; the ratio of the government debt to total budget revenues; the percentage of expenditures on servicing of the government and municipal debt in regional budget expenditures; the balance of annual payments for servicing and repayment of the government debt to total budget revenues. The last three indicators refer to the regulated indicators of the Budget Code of the Russian Federation (Federal State Statistics Services, n.d.-a).\n\nThe nine financial sustainability indicators included were: the ratio of deposits of legal entities to the number of registered enterprises and organizations; the deposits of individuals per capita; the ratio of loans granted to legal entities to the number of registered enterprises and organizations; the loans given to individuals per capita; the amount of debt on loans of legal entities and individuals to the loans granted; the volume of overdue debt on loans of legal entities to the number of registered enterprises and organizations; insurance premiums; and insurance payments.\n\nThe sector of corporative finance (business statistics) is represented by seven indicators: profitability of enterprises; unprofitability of enterprises; accounts receivable turnover; accounts payable turnover; the ratio of overdue accounts payable to revenue; the ratio of overdue receivables to revenue; and the share of unprofitable organizations in the total number of organizations.\n\nThe sector of personal finance (population statistics) includes four indicators: average per capita money income; average monthly wages; the average amount of assigned pensions; average per capita consumer expenditures of the population; and overdue wage arrearages.\n\nThus, the values of the indicators were calculated for the regions of the NWFD for the period from 2010 to 2019 (Barykin et al., 2022). A fragment of the obtained results for 2016-2019, containing sample data by years for the debt sustainability sector, is provided in Table 1. Full results are available in the underlying data in the index ids tab (Barykin et al., 2022). Similar tables were calculated for the other sectors but are not provided here because of the limited scope of the work (Barykin et al., 2022). According to Table 1, we can see that two regions stand out from the others by the low values of the indicators, allowing us to preliminarily classify them as regions with a high level of debt sustainability: Saint Petersburg and the Leningrad Region (LR). High values of the indicators for the analyzed period are most often observed in the Republic of Karelia (RKA), the Republic of Komi (RKO), the Vologda (VR), Arkhangelsk (AR), and Pskov regions (PR), therefore, most likely, these regions of the Russian Federation will be classified as regions with a low level of debt sustainability.\n\n* Abbreviations: NWFD - Northwestern Federal District, RKA - Republic of Karelia, RKO - Republic of Komi, AR - Arkhangelsk region, VR - Vologda region, KR - Kaliningrad region, LR - Leningrad region, MR - Murmansk region, NR - Novgorod region, PR - Pskov region, SPb - Saint Petersburg, NAR - Nenets Autonomous region, UCR - uncompensated receipts.\n\n+ GRP - gross regional product.\n\n** The maximum and minimum values of the indicators are highlighted in bold.\n\nStandardization of the indicator values using the method of Euclidean distances and further ranking of the resulting base of standardized estimates using the multivariate mean formula made it possible to obtain the debt, financial, corporative, and personal sustainability indices for each region of the NWFD (Tables 2–5). The use of the multivariate mean formula in our study correlates the value of a standardized indicator with the average value for the regions in the assessed year and allows us to identify the regions where the level of sustainability is significantly higher than the average value, close to the average value and significantly lower than the average value.\n\n- Three maximum values of indicators are highlighted.\n\n- Three minimum values of indicators are highlighted.\n\nAbbreviation: NWFD - Northwestern Federal District.\n\n- Three maximum values of indicators are highlighted.\n\n- The minimum values of indicators are highlighted.\n\n* Since when calculating the indicators I8, I9 a high differentiation of the NWFD regions is observed in relation to the city of Saint Petersburg, the latter was forcedly assigned a high sustainability level (1), and further ranking was carried out without taking Saint Petersburg into account.\n\nAbbreviation: NWFD - Northwestern Federal District.\n\n- Three maximum values of indicators are highlighted.\n\n- The minimum values of indicators are highlighted.\n\nAbbreviation: NWFD - Northwestern Federal District.\n\n- Three maximum values of indicators are highlighted.\n\n- The minimum values of indicators are highlighted.\n\nAbbreviation: NWFD - Northwestern Federal District.\n\nThe standardized values of the indicators reflect the high level of sustainability of the Saint Petersburg, Leningrad, and Kaliningrad regions, which naturally affects the value of the integral sustainability rating of these regions. The regions with a low level of debt sustainability include the Republic of Karelia, the Republic of Komi, and the Pskov region. The rest of the NWFD regions at this stage of the study can be considered as the regions with medium debt sustainability. Due to the developed gradation scale, all regions are well classified into three groups: with high, medium, and low debt sustainability (Table 6). The integral values of the debt sustainability index for the NWFD regions allow determining the regions with the level of sustainability higher than medium. Over the period of four years, such regions have consistently included Saint Petersburg, the Leningrad, and the Kaliningrad regions.\n\nThe preliminary calculated standardized indicator values reflect the high level of sustainability of Saint Petersburg, the Murmansk and Kaliningrad regions, and the Nenets Autonomous Region, which will subsequently affect the calculation of the integral sustainability index for the financial sector. For this type of analysis, the regions with a low level of debt sustainability include the Republic of Karelia, the Pskov, Leningrad, and Novgorod regions. The rest of the NWFD regions at this stage of the study can be considered as the regions with medium debt sustainability.\n\nThe integral index of financial sustainability shows that the regions with the level of sustainability higher than medium have consistently included Saint Petersburg, the Arkhangelsk, and the Vologda regions for the period of four years. In order to carry out a gradation of the studied regions according to three types of debt sustainability, it is necessary to set up the intervals for such assessment: the regions with the debt sustainability index equal to or greater than one were assigned to the group with high debt sustainability; the subsequent gradation was carried out taking into account the differentiation of annual values within two groups. So, for example, in 2019, the maximum value of the indicator for Saint Petersburg was 1.92, and the minimum value for the Pskov region was 0.58. The average value between 1 and 0.58 is 0.22, therefore, the border of the group with a medium level of the financial sector sustainability is determined from 1 to 0.78, and for groups with low sustainability, the values of the integral indicator will range from 0.78 to 0.\n\nThe regions with high financial sustainability include Saint Petersburg, the Arkhangelsk, and Vologda regions. The regions with medium financial sustainability include the Kaliningrad, Leningrad, Murmansk, and Novgorod regions, the Republic of Karelia and the Republic of Komi, and the Nenets Autonomous Region. The only region with low financial sustainability is the Pskov region. Here, it is important to note that the sustainability of the financial sector as a whole is higher than the debt sustainability.\n\nThe standardized values of indicators for the corporate finance sector reflect the high level of sales profitability of enterprises in the Leningrad and Murmansk regions, and the Republic of Karelia, which will subsequently affect the calculation of the integral index of sustainability of the regional financial system for this sector. The regions with low levels of sales profitability include the Pskov and Kaliningrad regions. The rest of the NWFD regions can be considered as regions with medium sustainability. As for the first indicator of the personal-finance sector, a higher level of per capita money income is accounted for by the Nenets Autonomous Region, the city of Saint Petersburg, the Murmansk, Arkhangelsk regions, and the Republic of Komi. Lower values of the indicator are typical for the Pskov and Novgorod regions. Later on, such differentiation for each standardized indicator will affect the calculation of the integral rating of sector sustainability for the region.\n\nThe regions with high sustainability according to the integral index for the corporative finance sector include the Republic of Komi, and the Vologda, Kaliningrad, Novgorod, and Pskov regions. The corporative finance sector of the Nenets Autonomous Region has low sustainability. The corporative finance sectors for the rest of the regions have medium sustainability. In general, the results for the corporative finance sector differ from the financial sector and the sector of debt sustainability, other regions play a leading role in this sector.\n\nIt is important to note here that the sustainability of the personal-finance sector is higher than all the sectors of sustainability identified in the study, namely, higher than the sectors of debt, financial, and corporative sustainability. In addition to this, in the personal finance sector, there are no regions with a low level of sustainability, which indicates a high contribution of households to the stable functioning of the region’s financial system. According to the results obtained, the regions with high sustainability include the Republic of Komi, the Arkhangelsk and Murmansk regions, the city of Saint Petersburg, and the Nenets Autonomous Region. The rest of the regions belong to the group of regions with medium sustainability.\n\nAt the final stage of assessment, the criteria values of the debt sustainability indicators were determined based on the values of the cluster centroids (Table 7).\n\nThe results of the study also identified that the NWFD regions belong to three clusters: cluster 1 - high debt sustainability: Saint Petersburg, the Leningrad region, and the Nenets Autonomous region; cluster 2 - medium debt sustainability: Saint Petersburg, the Vologda, Murmansk, and Kaliningrad regions; and cluster 3 - low debt sustainability: the Republic of Komi, the Republic of Karelia, the Arkhangelsk, Novgorod, and Pskov regions.\n\n\nDiscussion\n\nThe issues of sustainability within the financial system of the Russian Federation are of decisive importance for maintaining the country’s debt security and investment-driven development. The authors suppose that the term ‘stability’ means the invariability of parameters, while the term ‘sustainability’ is used in a broader and more complex sense (Barykin et al., 2021b). In this article, authors proposed a reliable and understandable methodological apparatus for assessing the sustainability of the financial system of the Russian regions and tested it on data from 11 regions of the NWFD. At the same time, our results need to be validated on a wider data set, for which we can recommend other researchers use our methodology. The chiefs of municipal entities can use the data on the debt sustainability standards to objectively assess the acceptable level of the debt burden and manage the size of the government debt in the event of a decrease in the debt sustainability of budgets. To develop a financial policy aimed at sustainable and stable functioning of the financial system, heads of municipalities can focus on the value of integral indices across the four sectors of sustainability. It is necessary to point out the limitations of the study. The developed methodology has been tested in 11 regions of the NWFD. For a more reliable evidence base, the number of regions should be expanded. The need to increase the sample of Russian regions to confirm the methodology presented in the article is related to the directions of further research. The directions of further research within the framework of the given topic are determined by the need for an annual statistical justification of the differentiated values of the upper limits of the local government debt, taking into account the macroeconomic situation in Russia and the regional priorities of socio-economic development.\n\nThe calculations showed the paramount importance of assessing the debt sustainability of the regional financial system since it is debt stability that is the key to stability and sustainability of the entire financial system. According to the results of the study, the debt sustainability of five regions of the NWFD (the Republic of Karelia, the Republic of Komi, and the Vologda, Pskov, and Arkhangelsk regions) is at a low level, as a result of which the authorities need to pursue a balanced debt policy aimed at increasing the sustainability and solvency of the region, reducing the credit risks, focusing on standards of the debt burden obtained during the study of each cluster, as well as the standards established by Art. 107.1 of the Budget Code of the Russian Federation (Official internet portal of legal information (n.d.).\n\n\nConclusions\n\nIn general, summing up the results of the assessment of the sustainability of the regional financial system across the four selected sectors, we can note the following:\n\n• When testing the methodology obtained, the authors faced the need for more thorough empirical indicators based on annual statistics, since not all indicators have passed empirical tests for adequacy of the values presented in the collections of values.\n\n• Across the different sectors of sustainability, there is a difference between the regions belonging to one group or another according to the type of sustainability. So, for example, the sustainable regions in the public finance sector (debt sustainability) include the Kaliningrad and Leningrad regions, and the city of Saint Petersburg; in the financial sector, the sustainable regions include the Arkhangelsk and Vologda regions, and the city of Saint Petersburg; in the corporative sector - the Republic of Komi, the Vologda, Kaliningrad, Novgorod, and Pskov regions; in the personal finance sector - the Republic of Komi, the Arkhangelsk, Murmansk regions, the city of Saint Petersburg and the Nenets Autonomous Region. Saint Petersburg is the only region that belongs to the high sustainability group according to each integral index. The personal finance sector is represented by five sustainable regions for the period from 2016 to 2019, which is higher than the number of regions with high sustainability in other sectors and reflects the high contribution of households of the NWFD regions to the sustainability of the financial system.\n\n• In general, the values of the integral indices of financial, corporative, and personal sustainability exceed the value of the integral index of debt sustainability, which indicates higher sustainability of the three sectors in comparison with the public finance sector. Such a conclusion can be made based on the values of integral indicators for different sectors: for example, the tables show that the minimum value of the personal-finance index for the period from 2016 to 2019 for the NWFD regions is not less than 0.5, while the minimum value of the debt sustainability index for the same period is 0.19. It can also be seen that the number of high values of the financial, corporative, and personal integral indices by years for 11 NWFD regions is generally greater than the number of high values of the debt sustainability integral index.\n\n• In the course of the study, the authors also realized the impossibility of calculating a general (aggregate, unified) sustainability index for the four sectors of the financial system, since each sector has its own type of sustainability in terms of homogeneous indicators included in it, which is confirmed by the results of the study. Also, the authors believe that the resulting summary estimate would be difficult to interpret logically. High scores in one of the sectors may overlap with low scores in another sector, as the result of which the region will be assessed as a region with a medium level of sustainability, and such an overall estimate will in no way reflect the detrimental processes of decreasing financial stability in one of the sectors. In our study, this thesis is fully actualized in the assessment of debt sustainability. Therefore, the calculation of the integral index for each sector of sustainability is an advantage of the developed methodology.\n\n\nData availability\n\nFigshare: Sustainability of the regional financial system ENG(1).xlsx. https://doi.org/10.6084/m9.figshare.20278098.v1 (Barykin et al., 2022).\n\nThis project contains the following underlying data:\n\n• Sustainability of the regional financial system ENG (1).xlsx (Data for the calculation of indicators with tabs for ‘Debt of the NWFD regions’, ‘indicators’, ‘index lds’, ‘index lfs’, ‘table’, ‘index lcs’, and ‘index lps’)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nWe are thankful to the Ministry of Science and Higher Education of the Russian Federation for the financial support of this project.\n\n\nReferences\n\nAcharya VV, Ryan SG: Banks’ Financial Reporting and Financial System Stability. J. Account. Res. 2016; 54(2): 277–340. Publisher Full Text\n\nAlbulescu CT: Forecasting the Romanian Financial System Stability Using a Stochastic Simulation Model. Rom. J. Econ. Forecast. 2010; 13(1).\n\nArzamasov V, Penikas H: A Financial Stability Index for Israel. Procedia Comput. Sci. 2014; 31: 985–994. Publisher Full Text\n\nBabar S, Latief R, Ashraf S, et al.: Financial Stability Index for the Financial Sector of Pakistan. Economies. 2019; 7(3): 81. Publisher Full Text\n\nBadertscher BA, Burks JJ, Easton PD: A Convenient Scapegoat: Fair Value Accounting by Commercial Banks during the Financial Crisis. Account. Rev. 2012; 87(1): 59–90. 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Publisher Full Text\n\nSantos E, Lisboa I, Eugénio T: Economic Sustainability in Wastewater Treatment Companies: A Regional Analysis for the Iberian Peninsula. Appl. Sci. 2021; 11(21): 9876. Publisher Full Text\n\nSchellhorn C: Financial System Stability, the Timing of Climate Change Action and the Federal Reserve. J. Cent. Bank. Theory Pract. 2020; 9(3): 45–59. Publisher Full Text\n\nSchinasi GJ: Defining Financial Stability. International Capital Markets Department. Washington:International Monetary Fund;2004. Accessed on 26th January 2022Reference Source\n\nShkolnyk I, Kozmenko S, Kozmenko O, et al.: Modeling of the Financial System’s Stability on the Example of Ukraine. Equilibrium. 2021; 16(2): 377–411. Publisher Full Text\n\nStrăchinaru AI, Dumitrescu BA: Assessing the Sustainability of Inflation Targeting: Evidence from EU Countries with Non-EURO Currencies. Sustainability. 2019; 11(20): 5654. Publisher Full Text\n\nState system of legal information. Official internet portal of legal information: Budget code of the Russian Federation as of July 31, 1998, No.145-FZ.n.d.. Accessed on 30th March 2022.Reference Source\n\nZolkover AO, Rusina YO, Bielialov TE, et al.: The Influence of Innovative Potential on Gross Production and Economic Security: Regional Analysis. Int. J. Manag. 2020; 11(4): 439–452. Publisher Full Text"
}
|
[
{
"id": "146837",
"date": "16 Aug 2022",
"name": "Muhammad Ibrar",
"expertise": [
"Reviewer Expertise Social Sciences i.e. Developmental Research",
"Management",
"/Administration",
"Public Policy",
"International Relations",
"Socio-Cultural Studies",
"Political Science related Research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPaper title: Sustainability of the regional financial system: a case study of the Northwestern Federal District Thank you so much for the opportunity to read and review your paper. This is a very interesting and informative paper. The authors have put efforts for the best. However, some points need to be cleared in the manuscript.\nOverall comments:\nIn the Methodology for assessing the debt sustainability of the regional budget system section on page 5 of the article, it is said that 45 financial sustainability indicators were selected at the first stage of the study. However, in section 2.3. Materials and Methods on the same page talk about 53 absolute indicators of the socio-economic development of Russian regions, of which 26 relative indicators were selected. How are indicators, absolute and relative indicators related in this study? The study says that it is based on data on socio-economic development indicators from 2010 to 2019. What is the reason for the choice of the study period? Why was a more extended period taken, for example, over the last 20-40 years? Tables 2,3,4,5 show sustainability indices from 2016 to 2019. Have such indices been calculated for an earlier period, given that macroeconomic indicators have been collected since 2010? The study states in Section 2.3, \"The study uses the methods of comparison and grouping, correlation analysis, Euclidean distances, calculation of the multivariate mean, and hierarchical cluster analysis.\" In these methods, for calculating the stability index of the financial system, the use of the multivariate average formula is of crucial importance; therefore, in our opinion, the formula should be given according to the text of the scientific work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8818",
"date": "04 Oct 2022",
"name": "Sergey Evgenievich Barykin",
"role": "Author Response",
"response": "Answer 1: Thank you for your comment. Indeed, there was a typo in section 2.3, only 45 absolute variables of financial sustainability were selected for research at the initial stage. This is the most typical variables of the socio-economic development of Russian regions, collected annually by the Federal Statistics Service. Absolute variables and relative indicators are interrelated, since relative indicators were calculated on the basis of absolute variables. For example, when calculating the ratio of the government debt to gross regional product, two absolute variables are used: GRP and public debt. Answer 2: Thank you for your comment. Indeed, the study of debt indicators in the long term is of greater interest. And we also regret it. However, we could not find data on the selected 45 absolute variables in the public domain. This is due to the fact that the set of macroeconomic indicators collected by the Federal State Statistics Service in the Russian Federation changes from time to time, as well as the fact that only in the last decade this information has been presented openly on special resources. We were able to collect the full number of indicators only for the period from 2010 to 2019. Answer 3: Thank you .Yes, the same indicators for four blocks were calculated for the period from 2010 to 2015, but due to the large volume of data, it is not possible to compactly fit the indicators from 2010 to 2019 in one table. Therefore, the results of the study are partially presented. Answer 4: In the paper, in the Data Analysis section, after the quote \"The calculation of the integral sustainability indicator was carried out using the multivariate mean formula ...\", a link is given to the article where this formula is given on page 77. The entire bibliography of the article is in the list of references and the article is publicly available in the international database Scopus. If, after reading the comment, the reviewer deems it necessary to add the multivariate mean formula to the text of the paper, we will definitely do it."
}
]
},
{
"id": "146838",
"date": "23 Aug 2022",
"name": "Alexey Petrovich Zhabko",
"expertise": [],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper explores the sustainability of Russian regions’ financial systems in the Northwestern federal district of Russia. I can see that it is an interesting title and deserves some merits. However, there are minor issues to be solved in the manuscript.\nMy comments:\nThe discussion section is too small; it needs to be deepened and expanded, referring to the results of previous studies in assessing the stability of regional financial systems. How would you explain the choice of indicators in each of the four sectors of the financial system? Why exactly did they go there? The composition of the indicators is well described at the beginning of Section 3, but it is not clear how the choice of indicators within each sector was made. Clarify, please. One of the blocks for assessing the financial system’s stability is debt sustainability. However, the authors do not discuss the concept of a country's debt sustainability in detail. Are our debt management practices similar between developed and developing countries? Especially the issues of debt sustainability of the country's budgets are essential for the federal structure of the state. The article says that the indicators R4, R5, and R6 refer to indicators that regulate the debt burden in the Russian Federation and are regulated by the Budget Code. Still, a more detailed description of holding the debt burden of the budget in the Russian Federation is not presented. What is the fiscal autonomy, in particular, the budgetary autonomy of regional and local governments and the spending autonomy of regions, and what types of transfers, under what conditions and criteria do regional governments (local governments) receive transfers from the federal government (from the regional government) of Russia? It may be worth presenting the debt potential of regions with fiscal transfers of the federal government and comparing it with the debt potential of regions without fiscal transfers of the federal government, as already studied in the international literature in question. The article does not present the foreign trade competencies of Russian regions. Can the governments of Russian regions actively pursue their foreign trade policy, especially exports and imports, without the federal government's approval? What is the share of export revenues of the studied regions in their regional budget? Suppose Russian regions have no such foreign trade competence. In that case, the increase or decrease of a region's exports is not due to its decision but to the federal government’s conclusion. When the federal government decides on exports and gets most of its income from them, then what justification and informative value does indicator 3 (R3) have?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8817",
"date": "01 Dec 2022",
"name": "Sergey Evgenievich Barykin",
"role": "Author Response",
"response": "Thank you. The composition of the indicators is explained by the accumulated experience of other scientists who presented research results and justified the choice of indicators of the sustainability of the financial system, as well as the availability of data collected by the State Statistics Service of the Russian Federation. The distribution of indicators by sector should have been logical. If the indicator characterizes the state of public debt and the microeconomics of the country as a whole, then such indicators were attributed to the debt sustainability sector. If the indicator characterizes the development of the banking system, then it was assigned to the financial sustainability sector. If the indicator describes personal finances (various incomes and expenditures of the population), then it was assigned to the personal sustainability sector. If this indicator characterizes the financial condition of enterprises and corporations in the region, then it was assigned to the corporate sustainability sector. Yes, indeed, the main issue in assessing the sustainability of the financial system is the debt sustainability block. And one of the directions of this topic is the assessment of the acceptable level of public debt. This is an interesting and at the same time quite complex topic. In this paper, we really did not present target values for indicators of the debt level regional budgets, focusing on the methodology for assessing the sustainability of the country's financial system and describing the results obtained, as well as discussing them. At the same time, the authors conduct a study of the safe level of public debt and describe the results in another article. It can be found on the website of the MDPI publishing house (https://www.mdpi.com/2227-7099/10/5/106) The issues of fiscal autonomy are interesting, but in our opinion, it should be the subject of a separate paper. The authors did not conduct research on how the presence or absence of fiscal transfers affects the state of debt sustainability of the financial system of the Russian Federation. Fiscal transfers of the federal government are carried out only under certain conditions and are unevenly distributed across the regions of the Northwestern Federal District. Some regions of the Northwestern Federal District do not have fiscal transfers from the federal budget (federal government) at all. Inclusion in the assessment of the sustainability of regional financial systems is problematic, since there is no publicly available information on the amounts of fiscal transfers. The foreign trade competencies of the Russian regions are quite broad. Since the products for export are produced by enterprises located in a particular region, then most of the income from the sale of export products goes to the regional budget, but not to the federal budget. That is why regions with a high volume of exports have less debt dependence and greater sustainability of regional financial systems. This is confirmed by the results obtained in the paper. Therefore, it is advisable to include R3 indicators in the assessment. At the same time, the value of this indicator R3 in most regions of the Northwestern Federal District (Table 1) is very high, which we assess negatively. This is due to the fact that only a few regions of the Northwestern Federal District sell products for export in high volumes."
}
]
}
] | 1
|
https://f1000research.com/articles/11-908
|
https://f1000research.com/articles/11-1130/v1
|
03 Oct 22
|
{
"type": "Case Report",
"title": "Case Report: Case report: Non-invasive mechanical ventilation in combination with bronchoscopy in the treatment of respiratory failure of lung cancer patient.",
"authors": [
"Katarzyna Guziejko",
"Łukasz Minarowski",
"Robert Mróz",
"Łukasz Minarowski",
"Robert Mróz"
],
"abstract": "Background: Respiratory failure (RF) is a common medical problem among cancer patients. Particularly active or ex-smokers diagnosed with chronic obstructive pulmonary disease (COPD) or lung cancer may develop severe hypoxemic and hypercapnic respiratory failure. Moreover, pneumonitis as a complication of the currently widely used immunotherapy of various cancers, may cause respiratory disorders requiring ventilation support. Non-invasive ventilation (NIV) is recommended as the first-line treatment for this type of respiratory failure and reduces the need for endotracheal intubation. Case presentation: We present a case report of lung cancer patient, who received NIV in the treatment of RF due to an infectious exacerbation of COPD. In addition, NIV enabled assisted flexible bronchoscopy (NIV-FB) to be performed. During the procedure tumor samples were collected for further molecular diagnosis of lung cancer. Improvement of the patient general condition and quality of life was also achieved. Conclusions: NIV can be used at any stage of oncological management in patients with lung cancer. It can also be implemented during endoscopic procedures of the respiratory system, as well as support in palliative care of patients with lung cancer at the end of life. Further studies should evaluate the use of NIV in conjunction with various oncological treatments and identify the exact contradictions for BF with NIV support in advanced cancer patients with RF.",
"keywords": [
"cancer",
"respiratory failure",
"non-invasive ventilation",
"flexible bronchoscopy",
"palliative care"
],
"content": "Introduction\n\nRespiratory failure (RF) is one of the most common complications associated with cancer.1 Acute RF is a life-threatening condition that requires immediate treatment. The use of non-invasive ventilation (NIV) reduces the need for endotracheal intubation in these cases, also in lung cancer patients.2,3 Another common recommendation in clinical practice is the use of NIV in exacerbations of chronic obstructive pulmonary disease (COPD), cardiogenic pulmonary edema, acute lung injury, acute respiratory distress syndrome, bacterial or viral pneumonia, and post-extubation failure.4–6 Immunotherapy currently plays an important role in the treatment of cancer patients, and the range of indications for this treatment is constantly expanding.7 Pneumonitis, as its complication may also cause respiratory disorders that require non-invasive ventilation.8 Moreover, the implementation of NIV during invasive endoscopic procedures among patients with RF is a new indication for this type of ventilation support4,5,9 We present a case of a patient with lung cancer who was treated with NIV in the course of an infectious exacerbation of COPD. NIV allowed for RF management, assisted flexible bronchoscopy (NIV-FB) performance obtaining tissue samples for molecular testing, and improving the patient’s general condition and quality of life. Thanks to this, oncological treatment could be started.\n\n\nCase description\n\nA 67-year-old female Caucasian patient, retired teacher, severe cigarette smoker (40 pack-years), with advanced lung cancer (adenocarcinoma cT4N3M1c CS IV), was admitted to the 2nd Department of Lung Diseases and Tuberculosis for oncological treatment. The diagnosis of lung cancer was made in the Department of Internal Medicine of the General Hospital using fine-needle biopsy of metastases to the subcutaneous tissue. No tissue samples were available for molecular diagnostics. Severe acute respiratory syndrome coronavirus-2 infection was ruled out by negative reverse transcription polymerase chain reaction (RT-PCR) on nasopharyngeal swabs.\n\nShe had a history of chronic obstructive pulmonary disease (Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 4D), paroxysmal atrial fibrillation on anticoagulant treatment with apixaban (5 mg, twice a day).\n\nAt the time of admission, the patient was in poor condition. The Eastern Cooperative Oncology Group Scale of Performance Status (ECOG PS) was rated at 3. She reported progressive dyspnoea, severe pain in the right scapula and spine of 7/8 points on the numerical rating scale (NRS).\n\nPhysical examination revealed tachypnoea (respiration rate 30 breaths per minute), peripheral cyanosis, multiple wheezing and rales on auscultation over the lungs. Oxygen saturation (SpO2) was 85% with 6 L per minute oxygen therapy with the nasal cannula (fraction of inspired oxygen (FiO2): 0.44).\n\nLaboratory tests have shown elevated levels of C-reactive protein, mild thrombocytopenia. In arterial blood gas (ABG) type 2 RF was found (pH: 7.303; carbon dioxide partial pressure (pCO2): 67.6 mmHg; oxygen partial pressure (pO2): 66.2 mmHg, HCO3: 27.9 mmol/L; SatO2: 90.5%).\n\nChest radiograph and computed tomography confirmed a tumor in the lower lobe of the left lung, metastases to the right lung, lymph nodes, bones and subcutaneous tissue (Figure 1).\n\nRounded mass in the left lung at the level of the lower pole of the hilum (A). Partial regression of opacities during (B) and after anti-inflammatory treatment (C).\n\nChest computed tomography (D-F lung window, axial scans; G-I abdomen window, axial scans): mass of the posterior chest wall on the right side size 7.5×3.4 cm, infiltrating the posterior segment of the fifth rib (D, G); rounded metastasis up to 10 mm in diameter in both lungs, tumor in the right dorsal muscle size 6×5 cm (E, H); tumor in the 6, 9 and 10 segments of the left lung size 9×6×6 cm, infiltrating eighth and ninth rib, with bone destruction (F, I).\n\nNIV was implemented for treatment. The target ventilation settings were: spontaneous/timed (S/T) mode, inspiratory positive airway pressure (IPAP) 16 cmH2O, expiratory positive airway pressure (EPAP) 7 cmH2O, VT 450 mL, FiO2 55%, backup rate 14 breaths per minute. For the first three days it was used around the clock, with breaks only for meals, drinking and care activities, during which passive oxygen therapy was used with a nasal cannula (FiO2: 0.3). The therapy was well tolerated. ABG control confirmed systematic, gradual improvement (pH: 7.416; pCO2: 58.9 mmHg; pO2: 66.5 mmHg, HCO3−: 33.7 mmol/L; SatO2: 93.0%). During the next seven days, ventilation time was reduced to the night and approximately 4 hours during the day. Oxygen therapy (FiO2: 0.28) was administered for the remainder of the day.\n\nFB at NIV support was also performed during hospitalization. A Philips Respironics Trilogy 100 device was used with a Philips Respironics AF531 naso-oral mask and a bronchoscopy elbow (S/T mode, IPAP 20 cmH2O, EPAP 7 cmH2O, VT 450 mL, FiO2: 90–95%, backup rate 18 breaths per minute). The minimum SpO2 value during the procedure was 85%. A sample was taken by forceps biopsy from a neoplastic mass in the lower lobe of the left lung. Additional molecular testing did not confirm the presence of predictive markers (epidermal growth factor receptor, anaplastic lymphoma kinase, c-ROS oncogene 1) and programmed death receptor-1 expression allowing the use of targeted therapy or immunotherapy.\n\nPharmacological treatment included broad-spectrum antibiotics (meropenem 3 g intravenously daily, levofloxacin 500 mg twice daily), systemic and inhaled glucocorticosteroids, short acting bronchodilators, mucolytics. Pain management based on NRS was escalated. Combination of non-steroidal anti-inflammatory drugs (ketoprofen 100 mg twice daily), oxycodone with naloxone (20 mg + 10 mg twice daily), fentanyl (50 μg transdermally every 72 hours), pregabalin (150 mg twice daily) and glucocorticosteroid (dexamethasone 8 mg daily) allowed for good pain control (2/3 points on the NRS). Palliative radiotherapy was also performed to the area of the right scapula and surrounding chest wall (a single dose of 8 Gy in one fraction).\n\nCombined pharmacological treatment, NIV and palliative radiotherapy of the chest wall significantly improved the patient’s condition. ECOG PS 2 has been achieved. After an acute phase of an infectious exacerbation of COPD complicated with type 2 respiratory failure, the patient was qualified to palliative chemotherapy based on the decision of multi-disciplinary team, initially with pemetrexed as monotherapy. NIV and oxygen therapy were continued on an outpatient basis. A timeline with all relevant data from this clinical case is available in Figure 2.\n\n\nDiscussion\n\nCancer complications may affect nearly one in four cancer patients. Among them RF is one of the most common. A study of 2028 patients with solid tumors and hematological malignancies showed that complications were more common in patients with metastatic solid tumors, especially lung and breast cancers. Moreover, RF was independently associated with in-hospital mortality.1 Previous studies have shown that NIV is effective in COPD exacerbations, cardiogenic pulmonary edema, acute lung injury, acute respiratory distress syndrome, bacterial or viral pneumonia, and post-extubation failure.4–6,10\n\nUnfortunately, NIV-assisted palliative care at the end of life is not a fully researched issue.3 In a randomized feasibility study by Nava et al.,11 200 participants with solid tumors and acute respiratory failure and a life expectancy of less than 6 months were randomized to receive either NIV or oxygen treatment. The study found that NIV is more effective than oxygen in reducing dyspnoea and the dose of morphine needed in patients with end-stage cancer.11 A study by Wilson et al.12 showed that many patients with do-not-intubate order who received NIV survived until hospital discharge. Similar results have been observed in a Kızılgöz et al.3 study. Most lung cancer patients, even those with short life expectancy, who received NIV as supportive therapy, were discharged from the hospital.\n\nIn the described case, the NIV treatment of RF in the course of an infectious exacerbation of COPD resulted in a reduction in dyspnoea. Moreover, the patient’s clinical condition improved from 3 to 2 according to ECOG PS. The daily ventilation time was determined on the basis of the ABG values. NIV therapy and oxygen therapy were continued on an outpatient basis.\n\nHowever, little is known about the use NIV during endoscopic procedures of the respiratory system in patients with RF.5,13 The use of NIV may enable management of patients who are initially ineligible for invasive respiratory diagnostics.14\n\nIn our report, the patient at the beginning of NIV therapy, was unstable in the respiratory system due to high hypercapnia. Effective ventilation allowed to reduce the partial pressure of carbon dioxide and maintain its stable level in ABG control. NIV combined with comprehensive analgesic and anti-inflammatory treatment reduced the severity of symptoms and allowed FB to be performed, which initially seemed impossible. Ventilation settings have been individualized based on clinical data and ABG values. Molecular tests on tissue samples collected during the procedure determined the type of lung cancer treatment.\n\nUltimately, we do not yet have enough information about the risks and complications of NIV-FB. The narrowing of the tracheal lumen by a bronchoscope may lead to RF exacerbation, which may cause further complications.15 Studies conducted on small groups of patients have shown that NIV-FB is safe, helps to avoid intubation, has a low complication rate, but should be performed by experienced teams.16 However, there are still no precise recommendations regarding NIV-FB in high-risk patients, including RF.10 In a study involving 50 patients, Skoczyński et al. also confirmed that NIV-FB is safe even in severely ill patients, but the risk associated with the procedure should always be taken into account.5 They highlight the need of further studies in large study groups to assess the exact level of hypoxemia and hypercapnia, the risk of NIV-FB, setting modalities, indications and contraindications.\n\nOur case emphasizes the key importance of the correct treatment of RF in cancer patients with NIV. Effective NIV therapy allowed not only to reduce dyspnoea, but also to perform FB in a patient previously disqualified due to RF and possible complications. The achieved clinical improvement influenced the further oncological treatment.\n\n\nConclusions\n\nNIV can be the mainstay of first-line treatment of acute or chronic respiratory failure. In addition, it can be used at any stage of oncological management in patients with lung cancer. NIV can also be implemented during endoscopic procedures of the respiratory system, as well as support in palliative care of patients with lung cancer at the end of life. Further research should evaluate the use of NIV in conjunction with various oncological treatments and identify the exact contradictions for FB with NIV support in RF patients with advanced cancer.\n\n\nConsent for publication\n\nWritten informed consent for the publication of identifying images or other personal or clinical details of participant that compromise anonymity was obtained.\n\n\nData availability\n\nNo data are associated with this article.\n\n\nAuthors’ contributions\n\nKG, ŁM, RMM – analyzed and prepared the data, wrote the manuscript; ŁM – was the leading doctor; KG, RMM – was involved in the clinical management of the patient. Our manuscript reporting adheres to CARE guidelines. All authors read and approved the final manuscript. Katarzyna Guziejko and Łukasz Minarowski contributed equally to the manuscript.",
"appendix": "Acknowledgements\n\nNot applicable.\n\n\nReferences\n\nTorres VBL, Vassalo J, Silva UVA, et al.: Outcomes in Critically Ill Patients with Cancer-Related Complications. PLoS One. 2016; 11(10): e0164537. PubMed Abstract | Publisher Full Text\n\nChawla R, Dixit SB, Zirpe KG, et al.: ISCCM Guidelines for the Use of Non-invasive Ventilation in Acute Respiratory Failure in Adult ICUs. Indian J. Crit. Care Med. 2020; 24(Suppl 1): S61–S81. PubMed Abstract | Publisher Full Text\n\nKızılgöz D, Akın Kabalak P, Kavurgacı S, et al.: The success of non-invasivemechanical ventilation in lung cancer patients with respiratory failure. Int. J. Clin. Pract. 2021; 75: e14712. PubMed Abstract | Publisher Full Text\n\nRochwerg B, Brochard L, Elliott MW, et al.: Official ERS/ATS clinical practice guidelines: noninvasive ventilation for acute respiratory failure. Eur. Respir. J. 2017; 50: 1602426. PubMed Abstract | Publisher Full Text\n\nSkoczyński S, Ogonowski M, Tobiczyk E, et al.: Risk factors of complications during noninvasive mechanical ventilation-assisted flexible bronchoscopy. Adv. Med. Sci. 2021 Sep; 66(2): 246–253. PubMed Abstract | Publisher Full Text\n\nOsadnik CR, Tee VS, Carson-Chahhoud KV, et al.: Non-invasive ventilation for the management of acute hypercapnic respiratory failure due to exacerbation of chronic obstructive pulmonary disease. Cochrane Database Syst. Rev. 2017 Jul 13; 2017(7): CD004104. PubMed Abstract | Publisher Full Text\n\nCable J, Greenbaum B, Pe’er D, et al.: Frontiers in cancer immunotherapy-a symposium report. Ann. N. Y. Acad. Sci. 2021 Apr; 1489(1): 30–47. PubMed Abstract | Publisher Full Text\n\nBalaji A, Hsu M, Lin CT, et al.: Steroid-refractory PD-(L)1 pneumonitis: incidence, clinical features, treatment, and outcomes. J. Immunother. Cancer. 2021 Jan; 9(1): e001731. PubMed Abstract | Publisher Full Text\n\nSaksitthichok B, Petnak T, So-Ngern A, et al.: A prospective randomized comparative study of high-flow nasal cannula oxygen and non-invasive ventilation in hypoxemic patients undergoing diagnostic flexible bronchoscopy. J. Thorac. Dis. 2019 May; 11(5): 1929–1939. PubMed Abstract | Publisher Full Text\n\nDu Rand IA, Blaikley J, Booton R, et al.: British Thoracic Society guideline for diagnostic flexible bronchoscopy in adults: accredited by NICE. Thorax. 2013; 68(Suppl 1): i1–i44. PubMed Abstract | Publisher Full Text\n\nNava S, Ferrer M, Esquinas A, et al.: Palliative use of non-invasive ventilation in end-of-life patients with solid tumours: a randomised feasibility trial. Lancet Oncol. 2013 Mar; 14(3): 219–227. PubMed Abstract | Publisher Full Text\n\nWilson ME, Majzoub AM, Dobler CC, et al.: Noninvasive Ventilation in Patients With Do-Not-Intubate and Comfort-Measures-Only Orders: A Systematic Review and Meta-Analysis. Crit. Care Med. 2018 Aug; 46(8): 1209–1216. PubMed Abstract | Publisher Full Text\n\nScala R, Naldi M, Maccari U: Early fiberoptic bronchoscopy during non-invasive ventilation in patients with decompensated chronic obstructive pulmonary disease due to community-acquired-pneumonia. Crit. Care. 2010; 14: R80. PubMed Abstract | Publisher Full Text\n\nSkoczyński S, Minarowski Ł, Tobiczyk E, et al.:Noninvasive ventilation-facilitated bronchofiberoscopy in patients with respiratory failure.Pokorski M, editor. Advances in pulmonary medicine: research and innovations. Cham:Springer International Publishing; 2019; vol. 1160. : pp. 53–64. Publisher Full Text\n\nEsquinas A, Zuil M, Scala R, et al.: Bronchoscopy during non-invasive mechanical ventilation: a review of techniques and procedures. Arch. Bronconeumol. 2013; 49: 105–112. PubMed Abstract | Publisher Full Text\n\nCabrini L, Nobile L, Cama E, et al.: A. Non-invasive ventilation during upper endoscopies in adult patients. A systematic review. Minerva Anestesiol. 2013 Jun; 79(6): 683–694. PubMed Abstract"
}
|
[
{
"id": "152867",
"date": "07 Nov 2022",
"name": "Artur Szlubowski",
"expertise": [
"Reviewer Expertise bronchology",
"including all endosonographic methods"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nA presented case report of a lung cancer patient, who received NIV in the treatment of RF due to an infectious exacerbation of COPD, is well reported.\n\nStill, little is known about the use of NIV during endoscopic procedures of the respiratory system in patients with RF.\n\nMoreover there are still no precise recommendations regarding NIV-FB in high-risk patients.\n\nIt would be nice to add what was the final histopathological result of the neoplastic mass based on forceps biopsy.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "191698",
"date": "04 Aug 2023",
"name": "Habib Md Reazaul Karim",
"expertise": [
"Reviewer Expertise Noninvasive Ventilation",
"Pain",
"Sedation",
"Perioperative Care",
"Critical Care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read the manuscript with interest and applaud the work. While NIV use in lung cancer and palliative patient is not unknown, nor is the endoscopy use during NIV, the case bears importance because such literature is still minimal. The authors have used NIV to manage RF arising from AECOPD and have performed bronchoscopy during ongoing NIV.\nThe title is, however, not distinct to indicate so, and the title delivers as if both NIV and bronchoscopy were continuous throughout. So, I suggest revising the title.\nFurther, the author should indicate the need for sedation during the bronchoscopy, monitoring of NIV tolerance, and success/failure during the therapy.\nIn my opinion, the author can also indicate the histopathology report and follow-up of the patient details, if they have any.\n\nBest of luck\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
},
{
"id": "191677",
"date": "18 Aug 2023",
"name": "Jacek Nasiłowski",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGuziejko and coworkers presented the exciting case of a COPD patient with stage IV lung cancer who developed hypercapnic respiratory failure due to exacerbation of COPD. During treatment, diagnostic flexible bronchoscopy NIV-assisted was performed to perform molecular investigation looking for other therapeutic options for treating advanced cancer.\nThe procedure was uneventful, proving the efficacy of NIV in endoscopic procedures of airways, even in acute exacerbation.\nThe minor points of criticism are the following:\nThe authors gave a very rough estimation of the severity of COPD (GOLD 4D), which refers to the former version of GOLD before 2023. I propose adding the most recent result of the patient's spirometry, namely FEV1.\n\nI would avoid giving FiO2 when the patient has oxygen therapy by nasal cannula because it only estimates FiO2, not an exact value.\n\nWhat kind of NIV machine was used for the treatment before bronchoscopy? Was it the same, Trilogy 100?\n\nIn the ST mode of ventilation, Vt is not titrated. The value of Vt changes from breath to breath depending on pressure support, work of breathing and resistance and compliance of the respiratory system.\n\nThe sequence of the chest X-rays should be given (e.g.day of hospitalization).\n\nIf chest X-ray A was done on admission, you can note the development of new opacities in the subsequent figures. Was it hospital-acquired pneumonia?\n\nIf it was the case, the patient did not suffer only from exacerbation of COPD but from pneumonia as well.\n\nThe description of the chest x-ray and CT scan is not entirely informative. The particular described findings should be enhanced with the markers (arrows, circles) on the pictures.\n\nThe choice of antibiotics should be explained because the combination of meropenem and levofloxacin is not the first choice of treatment for pneumonia.\n\nThe information about bronchoscopy is given before information about antibiotics treatment. Did pneumonia develop after bronchoscopy? Could pneumonia be a consequence of the procedure?\n\nThe NIV-assisted bronchoscopy should be described more precisely: what day of hospitalization, what was the blood gas analysis at the time of bronchoscopy, was there a need to change the ventilation settings after insertion of the bronchoscope, how long was the procedure, was sedation necessary, etc.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1130
|
https://f1000research.com/articles/11-1129/v1
|
03 Oct 22
|
{
"type": "Research Article",
"title": "Addressing the construct validity of the “individual problems and strengths” scale",
"authors": [
"Rune Zahl-Olsen",
"Nicolay Gausel",
"Åshild Tellefsen Håland",
"Terje Tilden",
"Nicolay Gausel",
"Åshild Tellefsen Håland",
"Terje Tilden"
],
"abstract": "Background: Routine Outcome Monitoring (ROM) systems have been used to monitor how a client’s life changes over the course of therapy. However, if a ROM system is to be used, the system should have sufficient construct validity to warrant its usage. In the current study we sought to test the construct of the “individual problems and strengths” (IPS) measurement scale, a sub-section of the “Systemic Therapy Inventory of Change” (STIC). Methods: We used a factorial construct validation procedure utilizing a stepwise confirmatory factor analysis approach on a sample of 841 clients of couple and family therapy. Results: We found support for the original “8-factor” version of the IPS but failed to find support for the “1-factor” version and the “higher order factor structure”. Conclusions: The investigation uncovered that the measurement tool is still under development and since the factorial construct (and the scale-reliability) was only supported for the original \"8-factor\" model, we encourage a pause in administering the IPS in clinical practice.",
"keywords": [
"Validity",
"Reliability",
"Confirmatory Factor Analysis",
"Cronbach",
"Routine Outcome Monitoring",
"STIC",
"IPS",
"Measurement",
"Therapy",
"Feedback instruments",
"Clinical tool"
],
"content": "Introduction\n\nEven though psychotherapy has been found to be effective for a large portion of clients seeking help (Sexton et al., 2013), not all benefit from therapy; in fact, some even get worse (Ogles, 2013). Attempting to better understand and explain why some clients benefit while others do not, quantitative systems consisting of standardized questionnaires (i.e., Routine Outcome Monitoring systems – “ROM”) have been developed over the last years (Lambert, 2010; Ogles, 2013; Tilden & Wampold, 2017). These ROM systems tap into various aspects of the client’s life, and if regularly responded to, the calculated mean score of these aspects will enable the therapist (and the client) to monitor change over the course of therapy (Duncan et al., 2004; Zahl-Olsen & Oanes, 2017). However, to administer a ROM system to monitor change, one needs reassurance that the ROM system is measuring what it is supposed to be measuring (i.e., its construct validity) and that the results of the measurement can be trusted (i.e., its scale-reliability). One of the ROM systems increasingly applied within the field of psychotherapy, and especially within couple and family therapy settings (Tilden & Wampold, 2017), is the “Systemic Therapy Inventory of Change” (STIC) (Pinsof et al., 2009).\n\nThe STIC addresses therapeutic change through a battery of six larger thematic sets of questionnaires, where one of these, the clinically important “individual problems and strengths” (IPS), taps into 8 typical aspects of distress and everyday difficulties that clients experience as they go through therapy. These include, for example, the degree to which the client can change plans and cope with changes (i.e., Flexibility/resilience), being able to express and share feelings (i.e., Open expression), managing daily tasks such as work and household (i.e., Life functioning), or coping with negative emotional states (i.e., Negative affect).\n\nThe 8-factorial structure of the IPS was first validated by the developers of STIC (Pinsof et al., 2009) on 188 clients seeking outpatient therapy in the Chicago area using confirmatory factor analysis (CFA). The factorial model yielded a good fit of data (The Root Mean Square Error of Approximation (RMSEA) = .06 and Comparative Fit Index (CFI) = .94) with low to good reliability for the 8 factors (α ranging from .54 to .89). Some years later, the same team (Pinsof et al., 2015) tried to replicate their “8-factorial” IPS structure, only now with more statistical power increasing their sample to 581 clients. However, this time the CFA did not fare so well with the “8-factorial” structure. It received poor fit of data (RMSEA = .117 and CFI = .59) with low to good reliability (α ranging from.45 to.85). In this paper, they also designed a factorial structure where all items loaded onto a global “single factor” (i.e., a “1-factor” solution) of IPS, arguing that all items were essentially a representation of the same psychological experience of individual problems and strengths. However, like the 8-factorial structure, this “1-factorial” structure also fit the data poorly (RMSEA = .099 and CFI = .71). Consequently, Pinsof and colleagues proposed a factorial solution they termed a “higher order factor structure.” This was a CFA where all items were loaded onto the 8 individual factors and then loaded onto a global “higher-order” IPS factor. This factorial solution yielded a borderline decent fit of data (RMSEA = .069 and CFI = .86) which Pinsof et al. (2015) viewed as a validation of their factorial solution.\n\nIn 2018, the same research team, only now led by Zinbarg et al. (2018), addressed the IPS and its relationship with other ROMs based on reports from 476 outpatient clients in the Chicago area. This time, however, they reported means and standard deviations for the 8 different factors along with their reliabilities (α ranging from .66 to .87) but failed to report any analysis or statistical support for an 8-factorial structure merely stating that the IPS “load on eight factors” (p.737). In our view, it is unclear why they did not report the statistical results of the original “8-factorial” solution but reported results from CFA on a “2-factor” solution in which they received mixed to fairly good support (RMSEA = .111 and CFI = .98) and on a “1-factor” solution which provided almost identical results (RMSEA = .115 and CFI = .98).\n\nTaken together, despite its growing popularity, the factorial structure of STIC has been replicated only twice, and its clinically important “8-factor” solution of IPS has been validated only once, in the original 2009 paper (Pinsof et al., 2009). The failure to replicate the 8-factorial structure in 2015 (Pinsof et al., 2015) and the lack of reporting CFA results on the “8-factor” structure in 2018 (Zinbarg et al., 2018), along with mixed levels of scale-reliability, all indicate that construct validation (and development) of the IPS is an ongoing and continuous process. Moreover, to date, no attempts to replicate the IPS have been published on samples outside the US or in a language other than English.\n\n\nThe current study\n\nIn the current study, we aimed to see if we could replicate the factorial structure of the IPS (Pinsof et al., 2009) in a Norwegian cultural context using the Norwegian language. Specifically, it would mean we would first test the hypothesis that IPS represents an “8-factor” solution. Secondly, as Pinsof et al. (2009) suggest, the IPS can be collapsed into a “1-factor” solution, so we decided to test this “1-factor” structure. Finally, as Pinsof and colleagues presented a “higher order factor structure” in 2015, we decided to test this alternative factor solution as well.\n\nTo test these factorial structures, we decided to follow the stepwise approach to construct validity as laid out by Gausel and colleagues (Gausel et al., 2012, 2016, 2018; Pardede et al., 2021). This approach recommends a four-step procedure where the preferred hypothesized factorial structure serves as a point of reference (in our case, the original 8-factorial structure). All other factorial solutions are compared against the preferred hypothesized model and each other. The best-fitting model (which should be the hypothesized model) would “win”. However, should the hypothesized model “lose” (i.e., fail to achieve the best fit), then more exploration of data is needed; ideally using exploratory factor analyses for the latter to return to a revised, hypothesized model to be tested with the same Gausel et al., procedure (for a discussion and practical example of this approach, see Pardede et al. (2021)).\n\nOur aim to test and attempt to replicate these various factors is primarily motivated by the fact that the IPS is increasingly deployed in various clinical settings. For instance, the 8-factorial solution is used by therapists to calculate eight different individual mean values used to monitor change throughout therapy, and the 1-factor solution is used to calculate an overall mean value to trace change more easily throughout therapy. Naturally, if we fail to replicate the factorial structure of the increasingly deployed IPS in therapy, therapists should be informed that the ROM they are using to interpret and trace change in client’s life throughout the therapy is flawed. Thus, it is of great importance for therapists to know this, but most of all for the well-being of our clients.\n\n\nMethods\n\nThis study's data were collected in Norway, where couple and family therapy treatment is offered to the general public in stepped levels of care. Two agencies provide the initial level of care, for which no referral is required. An outpatient agency represents the second level of care, for which a referral is required. A referral is required for the third and final level of care, which is represented by an inpatient facility. Since the data is derived from standard clinical practice, no inclusion or exclusion criteria were applied, other than the criteria each site uses to accept patients for treatment. The data was collected from clients of over 40 therapists at all three levels of couple and family therapy in Norway through online questionnaires1.\n\nThe PhD work that led to this manuscript was approved by the Modum Bad Ombudsman for Data Protection and the Regional Ethics Committee for Medical Research (2017/96/REK Sør-øst C, approved March 6, 2017). The primary study was also approved by the Modum Bad Ombudsman for Data Protection and the Regional Ethics Committee for Medical Research with human subjects; the pilot study was approved Nov. 13, 2009 (2009/927/REK Sør-øst C) and the RCT study was approved Jun. 13, 2016. Written informed consent was obtained from participants. For participants under the age of 16, consent was obtained from parents or guardians. This study investigated data from one of the questionnaires used in both a multi-site RCT study investigating the effects of the use of online feedback in therapy, registered at ClinicalTrials.gov (NCT01873742), as well as from a prior pilot study (Tilden et al., 2015). Ethical recommendations have been followed.\n\nThe RCT and pilot studies recruited 841 clients (51.8% women; mean age: 40; age range: 12-72) through ordinary clinical practice from March 2010 to April 2016. Written informed consent was obtained from each participant. Data is available for download (Zahl-Olsen et al., 2021a) and the variables and the data are described in more detail by Zahl-Olsen et al. (2021b). Data was collected as the clients began their therapeutic process.\n\nThe original “individual problems and strengths” (IPS) thematic subscale (Pinsof et al., 2009) has a total of 22 items theorized to tap into 8 different subscales (see Table 1 for correlations and descriptive statistics). Flexibility/resilience consisted of three items (α = .67) measured with a scale ranging from 1 (1st item: “very easy”, 2nd and 3rd items “strongly disagree”) to 5 (1st item: “very hard”, 2nd and 3rd items “completely disagree”): “How easy is it for you generally to overcome difficulties?”, “When what I’m trying doesn’t work out, I can change my approach or my plans” and “When I get upset, I find healthy ways to make myself feel better”. Life functioning measure consisted of two items (α = .78) measured with a scale ranging from 1 (“really bad”) to 5 (“really good”): “Performing work/school/household tasks” and “Managing day-to-day life”. Open expression consisted of two items (α = .68) measured with a scale ranging from 1 (“completely disagree”) to 5 (“completely agree”): “I can openly express my feelings” and “I can speak up for myself when the situation calls for it”. Self-acceptance consisted of two items (α = .71) measured with a scale ranging from 1 (“completely disagree”) to 5 (“completely agree”): “I can be myself in every situation” and “I am comfortable with who I am”. Disinhibition consisted of three items (α = .53) measured with a scale ranging from 1 (“never”) to 5 (“all the time”): “Thought about seriously harming or killing someone”, “Had fits of rage you could not control”, and “Had urges or impulses that you could not control”. Negative affect consisted of six items (α = .86) measured with a scale ranging from 1 (“never”) to 5 (“all the time”): “Had thoughts or images over and over again that you could not get rid of”, “Felt tense or anxious”, “Felt sad most of the day”, “Thought about ending your life”, “Felt hopeless about the future”, and “Not enjoyed things as much as you used to”. Self-misunderstanding consisted of two items (α = .66) measured with a scale ranging from 1 (“completely disagree”) to 5 (“completely agree”): “I don’t understand why I do the things I do” and “It’s tough for me to know what I’m feeling”. Substance abuse consisted of two items (α = .20) measured with a scale ranging from 1 (“never”) to 5 (“all the time”): “Drank too much alcohol” and “Used illegal drugs/misused prescribed medication”. The original English STIC version was translated into Norwegian according to the procedures outlined by Wild et al. (2005), which included preparation, forward translation by two independent interpreters, reconciliation, back translation, back translation review, harmonization, cognitive debriefing, and finalization. No test of the reliability of the back translation was performed before implementation in this study.\n\n* p<.001.\n\nWe used AMOS 25 from IBM to test our hypothesis with a confirmatory factor analysis (CFA) using maximum likelihood estimation. We adopted Gausel et al.’ (2012, 2016, 2018) stepwise “construct validity” (p. 945) approach by first testing the fit of the preferred model. Then, in a second step, testing the fit of the competing model. In a third step, comparing the fit of the competing model up against the preferred model, and finally, in a fourth step, by comparing the fit of the preferred model up against the fit of other plausible alternatives. In line with the recommendations of Gausel et al. (2012, 2016), we first tested the preferred “8-factor” model. Then, in the second step, we tested the “1-factor” model. In the third step, we compared the fit of the “8-factor” model against the fit of the “1-factor” model. In the fourth step, we compared the “8-factor” model against other plausible, data-driven alternatives, as well as the “higher order factor structure” as suggested by Pinsof et al. (2015). In line with recommendations by Gausel and colleagues, latent factors were allowed to correlate, but no items were allowed to cross-load on any of the factors, and no error terms were allowed to correlate.\n\n\nResults\n\nIn a first step, we tested the “8-factor” version of the IPS. Despite a significant chi-square, χ2 (181) = 605,994, p <.001, χ2/df = 3.35, the “8-factor” model fit the data well as indicated by the other fit-indices: IFI = .936, CFI = .935, RMSEA = .053 [.048 - .058], AIC = 793.994. As seen in Figure 1, all factor loadings were significant (all p values < .001), ranging from standardized λ = .30 to .86, with most above .55 or higher indicating that factors were well defined by their respective items (Gausel et al., 2012, 2016, 2018). The correlations among the eight different factors ranged from low (r = .06, p = .398) to high (r = .89, p < .001) with more than half of the items producing an explained variance of around 50% reaching an ideal level for a CFA (Kline, 2016).\n\nIn a second step, we tested the “1-factor” version of the IPS. Here, all items are theorized to be representative of the single construct. As such, we allowed all items to load onto a single “IPS factor”. This model fit the data poorly as indicated by a significant chi-square, χ2 (209) = 1949,931, p <.001, a very high χ2/df = 9.33, very low IFI = .736, very low CFI = .734, and a high RMSEA = .100 [.096 - .104], AIC = 2081.93. Not only did this “1-factor” model represent the data poorly, only half of the 22 items had factor loadings larger than λ .55, and only three of the items in the undifferentiated model reached the suggested 50% level of explained variance (Kline, 2016).\n\nEven though the fit indices clearly communicated that the “1-factor” model should be rejected, we decided to continue to follow Gausel et al.’ (2012, 2016, 2018) recommendations comparing the “1-factor” model up against the “8-factor” model. The “8-factor” model fit data significantly better than the “1-factor” model; ∆ χ2 (28) = 1343.937, p < .001. Moreover, the difference in AIC was substantial, ∆ AIC = 1287.937, demonstrating that the “8-factor” model was indeed superior to the “1-factor” model.\n\nIn the final step of the recommendations by Gausel et al. (2012, 2016, 2018), we compared the “8-factor” version of IPS up against other meaningful alternatives. Looking at the four correlations in Figure 1 that are higher than or equal to r = .70, we identified five alternative models that represented plausible data-driven alternatives to the 8-factor model. However, the “8-factor” model proved superior to all these alternative models. First, it fit better than a model collapsing “open expression” with “self-acceptance”, ∆ χ2 (7) = 149.44, p < .001 and ∆ AIC = 135.440. Second, it fit better than a model collapsing “flexibility/resilience” with “self-acceptance”, ∆ χ2 (7) = 27.761, p < .001 and ∆ AIC = 13.761. Third, it fit better than a model collapsing “flexibility/resilience” with “self-misunderstanding,” ∆ χ2 (7) = 75.735, p < .001 and ∆ AIC = 61.735. Forth, it fit better than a model collapsing “self-misunderstanding” with “self-acceptance.” ∆ χ2 (7) = 95.713, p < .001 and ∆ AIC = 81.713. Finally, it fit better than a model where all four mentioned factors were collapsed, ∆ χ2 (18) = 301.710, p < .001, and ∆ AIC = 260.71.\n\nIn 2015, Pinsof and colleagues tested a so-called “higher order factor structure” where they allowed their individual factors “like IPS Negative Affect and Open Expression” to load onto “a single second-order general factor like IPS” (p.470). They underlined that this analysis was “theoretically and methodologically important because finding support for a higher order model (…) demonstrates that each of the scale’s group factors links to a single higher order factor that underlies the scale and its factors” (p. 470). Consequently, we decided to test the “higher order factor structure” where each of the 8-factors is allowed to load independently onto a “higher-order” IPS-factor. This model approached a borderline acceptable fit of data, χ2 (201) = 818,833, p < .001, χ2/df = 4.07, IFI = .906, CFI = .906, RMSEA = .060 [.056 - .065], AIC = 966.833. However, when we compared this “higher order” model up against the original “8-factor” model, the “8-factor” model fit data significantly better than the “higher order” model; ∆ χ2 (20) = 212.839, p < .001, with a large difference in AIC; ∆ AIC = 212.839. Hence, the original “8-factor” model was superior to the suggested “higher order factor structure”.\n\n\nDiscussion\n\nOver recent years, research on psychotherapy has focused on how best to monitor clients' change throughout therapy using ROMs — Routine Outcome Monitoring (Duncan et al., 2004; Lambert, 2010; Pinsof et al., 2009). Naturally, it is important for a therapist (and a researcher) to be reassured that the ROM administered will represent the clients’ experiences in the best way possible. One of the ROMs believed to do this just so is the STIC system developed by Pinsof et al. (2009). However, the STIC system has been validated only twice, and the highly clinically-relevant sub-section, the IPS, has been successfully validated only once, only in the Chicago area and only in the English language. Thus, there were ample grounds to test the construct validity of the IPS and do so in a different culture and a different language.\n\nIn the current study, we employed Gausel et al.’ (2012, 2016, 2018) stepwise approach to “construct validation.” The advantage of their approach is that it is a clear-cut, step-by-step construct validation procedure where one can test a factorial structure up against other factorial structures in order to establish which is the best fitting model. Our first step was to test the fit of the original “8-factor” model as suggested by Pinsof et al. (2009). This first step was important because if it failed to fit well, it would be pointless to compare it to any other models (2018; 2012; 2016). As expected, the “8-factor” model did represent the data well. In fact, whichever way we tried to modify the combination of factors in the different steps of the CFA approach, the “8-factor” model always came out as the superior factorial solution. By such, the step-by-step analysis provided validating support to the original “8-factor” model as developed by Pinsof et al. (2009), and it supports Zinbarg et al.’ (2018) argumentation that a multi-faceted version of the IPS (and STIC) would provide the most accurate information about the complex lives of clients.\n\nWe also tested the proposed “1-factor” model (Pinsof et al., 2009) and the “higher order factor structure” (Pinsof et al., 2015). In terms of the “1-factor” model, we found it to be representing the data very poorly. In fact, when we compared this model up against the “8-factor” model, the “1-factor” proved to be inferior in all ways. This result goes against Pinsof et al.’ (2009, 2015) argumentation that all items in the IPS are indifferently representative of the overall construct, and it goes against the common therapeutic practice to calculate an overall mean in order to trace change in therapy (Oanes et al., 2015; Spanier, 1988). In terms of the “higher order factor structure,” we found it to achieve borderline acceptable fit. However, as it fit significantly worse than our “8-factor” model, the “higher order factor structure” was found to be an inferior alternative to the better fitting “8-factor” model.\n\nIn terms of scale-reliability, only one of the 8 IPS sub-scales achieved a Cronbach’s alpha more than .80 (i.e., Negative Affect), two achieved more than .70 (i.e., Life functioning and Self-acceptance), three more than .60 (i.e., Flexibility/resilience, Open expression, and Self-misunderstanding), one more than.50 (i.e., Disinhibition), and one barely made it to.20 (i.e., Substance abuse). Clearly, a measurement model obtaining low to mainly moderate and acceptable levels of scale-reliability levels indicates a need for further development of the various measurement scales (Schmitt, 1996). That said, finding levels of scale-reliability to be low in our study did not come as a surprise. As earlier communicated by the developers of the measurement tool (Pinsof et al., 2009), the low reliability of their scales constitutes “a major methodological concern” (p. 151). Due to this, they aimed “to increase the reliability of the subscales with low alphas” (p. 151) in future studies. However, six years later, Pinsof et al. (2015) still struggled with low reliabilities, reiterating that it “is concerning” (p. 478) that so many subscales of their measurement tool suffer from poor levels of scale-reliability. In light of our study, we cannot but agree: it is concerning, especially as the IPS (and STIC) is increasingly used in clinical practice to measure and monitor how clients’ change over the course of therapy (Pinsof et al., 2015).\n\n\nPossible limitations\n\nWe have to admit that the current study tested only one (the IPS) of six sub-themes within a comprehensive ROM system, the STIC (Pinsof et al., 2009). Therefore, we cannot say much in terms of the remaining other sub-themes but encourage future testing of the remaining five. Moreover, we are unable to have opinions about the construct validity or scale reliability of other ROM systems, such as the Systemic Clinical Outcome and Routine Evaluation (Carr & Stratton, 2017). Nevertheless, we generally encourage developers and independent researchers to test other ROM systems' construct validity and scale reliability. After all, the focus should be on the client and how best to understand and care for her/him as they go through therapy. This demands a measurement tool that can be trusted.\n\n\nConclusion\n\nTaken together, our study supports an “8-factor” solution of the IPS as originally developed by Pinsof et al. (2009) both cross-culturally (in the Norwegian culture) and cross-linguistically (the Norwegian language). We see this as a major step forward in construct validation of their IPS outside the US and the English language. However, our positivity comes with a fair amount of soberness. As we see it, the IPS may have achieved support for its “8-factorial” structure, but it has failed to live up to acceptable standards in terms of scale reliability. We have sympathy for the developer’s eagerness to put the measurement tool into practice, but as long as the tool is under development, we call on developers to pause the practical use of it until more research has clarified its construct validity and, importantly, increased its scale reliability.\n\n\nData availability\n\nMendeley Data: Dataset of the Individual Problems and Strengths scale (IPS): A clinical sample, https://doi.org/10.17632/fk5v8n726c.1 (Zahl-Olsen, Tellefsen Haaland and Tilden, 2021a).\n\nThis project contains the following underlying data:\n\n- Data_IPS.sav\n\n- Data_IPS.csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe data key for these files can be found in: Zahl-Olsen, R., Haaland, A. T., & Tilden, T. (2021b). Data on the individual problems and strengths scale from the systemic therapy inventory of change. Clinical samples from Norway. Data in Brief, 39. https://doi.org/10.1016/j.dib.2021.107577",
"appendix": "References\n\nCarr A, Stratton P: The SCORE family assessment questionnaire: a decade of progress. Fam. Process. 2017; 56(2): 285–301. PubMed Abstract | Publisher Full Text\n\nDuncan BL, Miller SD, Sparks J: The heroic client: a revolutionary way to improve effectiveness through client-directed, outcome-informed therapy. Rev. ed.Jossey-Bass;2004.\n\nGausel N, Leach CW, Mazziotta A, et al.: Seeking revenge or seeking reconciliation? How concern for social-image and felt shame helps explain responses in reciprocal intergroup conflict. Eur. J. Soc. Psychol. 2018; 48(1): O62–O72. Publisher Full Text\n\nGausel N, Leach CW, Vignoles VL, et al.: Defend or repair? Explaining responses to in-group moral failure by disentangling feelings of shame, rejection, and inferiority. J. Pers. Soc. Psychol. 2012; 102(5): 941–960. Publisher Full Text\n\nGausel N, Vignoles VL, Leach CW: Resolving the paradox of shame: Differentiating among specific appraisal-feeling combinations explains pro-social and self-defensive motivation. Motiv. Emot. 2016; 40(1): 118–139. Publisher Full Text\n\nKline RB: Principles and practice of structural equation modeling. 4th ed.Guilford publications;2016.\n\nLambert MJ: Yes, it is time for clinicians to routinely monitor treatment outcome.2010. Publisher Full Text\n\nOanes CJ, Borg M, Karlsson B: Significant Conversations or Reduced Relational Capacity? Exploring Couple and Family Therapists' Expectations for Including a Client Feedback Procedure. Aust. N. Z. J. Fam. Ther. 2015; 36(3): 342–355. Publisher Full Text\n\nOgles BM:Measuring change in psychotherapy research.Lambert MJ, editor. Bergin and Garfield's Handbook of psychotherapy research and behavior change. 6th ed.Wiley;2013; pp. 134–166.\n\nPardede S, Gausel N, Høie MM: Revisiting the “the breakfast club”: Testing different theoretical models of belongingness and acceptance (and social self-representation). Front. Psychol. 2021; 11: 3801. PubMed Abstract | Publisher Full Text\n\nPinsof WM, Zinbarg RE, Lebow J, et al.: Laying the foundation for progress research in family, couple, and individual therapy: The development and psychometric features of the initial Systemic Therapy Inventory of Change. Psychother. Res. 2009; 19(2): 143–156. PubMed Abstract | Publisher Full Text\n\nPinsof WM, Zinbarg RE, Shimokawa K, et al.: Confirming, Validating, and Norming the Factor Structure of Systemic Therapy Inventory of Change Initial and Intersession. Fam. Process. 2015; 54(3): 464–484. PubMed Abstract | Publisher Full Text\n\nSchmitt N: Uses and abuses of coefficient alpha. Psychol. Assess. 1996; 8(4): 350–353. Publisher Full Text\n\nSexton TL, Datchi C, Evans L, et al.:The effectiveness of couple and family-based clinical interventions.Lambert MJ, editor. Bergin and Garfield’s handbook of psychotherapy and behavior change. 6th ed.John Wiley & Sons;2013; pp. 587–639.\n\nSpanier GB: Assessing the strengths of the Dyadic Adjustment Scale. J. Fam. Psychol. 1988; 2(1): 92–94. Publisher Full Text\n\nTilden T, Håland ÅT, Hunnes K, et al.: Utprøving av systematisk tilbakemelding i par- og familieterapi: Barrierer og utfordringer. Fokus på familien. 2015; 43: 292–312. Publisher Full Text\n\nTilden T, Wampold BE: Routine Outcome Monitoring in Couple and Family Therapy: The Empirically Informed Therapist. Springer;2017.\n\nWild D, Grove A, Martin M, et al.: Principles of good practice for the translation and cultural adaptation process for patient-reported outcomes (PRO) measures: report of the ISPOR task force for translation and cultural adaptation. Value Health. 2005; 8(2): 94–104. PubMed Abstract | Publisher Full Text\n\nZahl-Olsen R, Haaland AT, Tilden T: Dataset of the Individual Problems and Strengths scale (IPS): A clinical sample. Mendeley Data. 2021a; V1. Publisher Full Text\n\nZahl-Olsen R, Haaland AT, Tilden T: Data on the individual problems and strengths scale from the systemic therapy inventory of change. Clinical samples from Norway. Data Brief. 2021b; 39: 107577. PubMed Abstract | Publisher Full Text\n\nZahl-Olsen R, Oanes CJ:An Anthill of Questions that Made Me Prepare for the First Session: A Clinical Vignette of the Usage of STIC Feedback System.Tilden T, Wampold BE, editors. Routine Outcome Monitoring in Couple and Family Therapy. Springer;2017; pp. 189–209. Publisher Full Text\n\nZinbarg RE, Pinsof WM, Quirk K, et al.: Testing the convergent and discriminant validity of the Systemic Therapy Inventory of Change Initial scales [Empirical paper]. Psychother. Res. 2018; 28: 734–749. PubMed Abstract | Publisher Full Text\n\n\nFootnotes\n\n1 The current manuscript originates from the first author’s PhD-thesis. The thesis consisted of a theoretical introduction with three different articles presenting findings of the thesis. The current manuscript is one of these three, only reworked and modified from how it was originally presented in the thesis."
}
|
[
{
"id": "152469",
"date": "18 Nov 2022",
"name": "Peter Stratton",
"expertise": [
"Reviewer Expertise Family therapy",
"outcome measurement"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe well-written study tackles essential issues in the development and application of ROMs, of reliability and validity. Without good evidence of these, a measure cannot be depended on for general usage. Data from an acceptably large sample were used to investigate the “individual problems and strengths” (IPS) subscale of the STIC.\nThere is no indication of how many in the sample were members of the same couple or family. This would create a risk of non-independence in the sample. Although the items in IPS are individually directed, so not asking about functioning in the relationship, the possibility of correlations within families should be considered.\nThe statistical procedures are well-referenced and described. They consistently point to the superiority of the 8-factor solution to any measure derived by coalescing the items with the combined measures that will be preferred as a measure of progress in the therapy, showing poor construct reliability. This robust finding suggests that the 8 subscales are measuring different aspects of clients' reports of their lives rather than alternative indicators of any underlying reality. Indicated by the low intercorrelations of Table 1 in which 22 of the 30 coefficients are less than 4.5 so accounting for less than 20% of the variation.\nIt seems possible that the low Cronbach for substance abuse may have been due to a consistently extreme rating of Mean 4.81 / 5 = ‘all the time’. Were nearly all of the sample really drunk or drugged all the time or have I misunderstood?\nThere is little comment on the potential usefulness to clinicians of a client’s scores on the 8 different factors. There is no discussion of how a clinician might make use of the information provided by the IPS. In practice, clinicians often want to make use of the scores of an individual client as an indication of where to focus in the therapy.\nThe core question addressed by the paper is whether the IPS is useful for a clinician. The conclusion is that, because none of the proposals for creating a summary measure out of the 8 subscales creates an acceptable level of statistical coherence, the IPS is not ready to be used as an outcome measure. This is an important conclusion for an SRM that is being widely promoted.\nTypo: End p.6 \"Forth, it fit better than a model...\" - Fourth\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1129
|
https://f1000research.com/articles/11-777/v1
|
12 Jul 22
|
{
"type": "Study Protocol",
"title": "Long-term health after Severe Acute Malnutrition in children and adults- the role of the Pancreas (SAMPA): Protocol",
"authors": [
"Sana Ahmed",
"George PrayGod",
"Nanette R. Lee",
"Paul Kelly",
"Geeta Trilok-Kumar",
"Molly Chisenga",
"Belinda Kweka",
"Daniel Faurholt-Jepsen",
"Rikke Krogh-Madsen",
"James AM Shaw",
"Dixi M. Paglinawan-Modoc",
"Juan Solon",
"Mette Frahm Olsen",
"Darko Stefanovski",
"Sharon Cox",
"Dorothea Nitsch",
"Ruth Keogh",
"Suzanne Filteau",
"George PrayGod",
"Nanette R. Lee",
"Paul Kelly",
"Geeta Trilok-Kumar",
"Molly Chisenga",
"Belinda Kweka",
"Daniel Faurholt-Jepsen",
"Rikke Krogh-Madsen",
"James AM Shaw",
"Dixi M. Paglinawan-Modoc",
"Juan Solon",
"Mette Frahm Olsen",
"Darko Stefanovski",
"Sharon Cox",
"Dorothea Nitsch",
"Ruth Keogh",
"Suzanne Filteau"
],
"abstract": "Background: Prenatal growth retardation may increase the risk of later chronic non-communicable diseases (NCDs), including diabetes; however, long-term effects of wasting malnutrition in childhood or adulthood are less studied. Pancreatic exocrine and endocrine functions, both critical for nutrition and NCD aetiology, may not fully recover following malnutrition. However, the evidence and mechanistic information is piecemeal. We hypothesise that wasting malnutrition at any age has long-term detrimental effects on endocrine and exocrine pancreatic structure and function. Methods: The SAMPA international research programme will assess pancreatic structure and function in 3700 participants from ongoing observational nutrition cohorts, two adolescent and four adult, in Zambia, Tanzania, Philippines, and India. Pancreas size, structure, and calcification will be assessed by ultrasound and computed tomography (CT) scan; exocrine function by faecal elastase and serum lipase; and endocrine function by haemoglobin A1c (HbA1c) and blood glucose, insulin and C-peptide concentrations during an oral glucose tolerance test (OGTT). In-depth hormonal analyses of incretins, glucagon, proinsulin and trypsinogen during OGTT and intravenous glucose tolerance tests will be done in subsets of adult participants. Pancreatic size and function outcomes will be compared between people with and without prior wasting malnutrition. Analyses will investigate effect modification by sex, current age, time since malnutrition, current body mass index and dietary patterns. Mathematical modelling of OGTT data will be used to estimate the relative contribution to glucose dysregulation of decreased insulin production, changes in insulin clearance and increased insulin resistance. Proinsulin/insulin ratio will be analysed in archived samples from the Tanzanian cohort using a nested case-control design to investigate whether abnormal values precede diabetes. Conclusions: SAMPA, a large-scale multi-centre research programme using data from people with or without prior wasting malnutrition to assess several aspects of pancreatic phenotype, will provide coherent evidence for future policies and programmes for malnutrition and diabetes.",
"keywords": [
"Malnutrition",
"wasting",
"diabetes",
"pancreas",
"non-communicable diseases",
"oral glucose tolerance test"
],
"content": "Introduction\n\nThere is an increasing prevalence of overweight and obesity worldwide which is associated with increases in non-communicable diseases (NCDs), including diabetes.1 Meanwhile, wasting malnutrition remains common in low- and middle-income countries (LMICs).2 It is well-documented that prenatal malnutrition, usually measured as low birth weight, can increase the risk of NCDs in later life,3 but how wasting malnutrition in childhood or adulthood may affect long-term health is less studied.4 The issue of child or adult malnutrition's long-term implications is becoming increasingly important because more children survive severe acute malnutrition as a result of improved care, while pharmacological treatments for infections, such as HIV and tuberculosis, that commonly cause or are linked with malnutrition, have increased patient survival among all age groups. Evidence from a recent systematic review suggests pancreatic endocrine and exocrine functions may not recover fully after childhood or adult wasting malnutrition.5 Such long-term effects on the pancreas may contribute to the different phenotype of diabetes common in LMICs with prevalent malnutrition, compared with the diabetes phenotype in high-income countries. Diabetes in LMICs often has a relatively early disease onset (<50 years) and may occur at a low or normal body mass index (BMI).6 There are heterogeneous reports of atypical diabetes in LMICs, describing an entity of malnutrition-related, insulin-deficient diabetes related to pancreatic damage, for example, a phenotype termed fibrocalculous pancreatic diabetes,7 but these studies often report highly selected patients, which can provide mechanistic but not epidemiologic information,8 or precede the availability of modern assessment methods.9 Our own work has shown that prior malnutrition in Tanzanian adults is associated with lower insulin production in men10 and that insulin deficiency is a more common cause of diabetes than insulin resistance.11 If malnutrition is associated with an atypical form of diabetes, driven by insulin deficiency and not resistance, then this has major implications for health policy, planning, investigation and treatment of diabetes in LMICs, because current first-line treatments of diabetes in these settings usually use treatments such as metformin which would be inappropriate for insulin-deficient diabetes.\n\nBoth pancreatic endocrine (i.e. production of hormones such as insulin) and exocrine (i.e. production of enzymes to aid digestion) functions are critical for nutritional metabolism and in chronic diseases including diabetes. Furthermore, deficits in exocrine and endocrine functions may interact such that diabetes is common among people with exocrine pancreas insufficiency12 and low faecal elastase is common in patients with type 2 diabetes, especially those with poor glycaemic control.13 There is a dearth of studies explaining the mechanisms of the exocrine-endocrine interactions leading to abnormalities in both functions.\n\nIn spite of its central importance, there has been surprisingly little research on pancreatic function following recovery from wasting malnutrition. This is likely due, in part, to there being no validated, easily measurable indicator of prior wasting malnutrition, in contrast to studies of poor early linear growth, resulting in largely irreversible stunting, short legs, and increased sitting/standing height ratio in adulthood. There is thus an urgent need for prospective cohort studies to investigate long-term effects of wasting malnutrition.\n\nThe central hypothesis of the severe acute malnutrition in children and adults - the role of the pancreas (SAMPA) study is that an episode of wasting malnutrition, irrespective of age of occurrence, affects endocrine and exocrine pancreatic size, structure and function. The study will recall for cross-sectional investigations participants from established cohorts recruited for the research team’s previous studies in Tanzania, Zambia, India and the Philippines. Many cohort members were originally recruited because of an episode of severe malnutrition or their infection with HIV or tuberculosis; their prior nutritional status, plus those of well-nourished controls, is documented. The cohorts now range in age from adolescence to late middle age and live in places with a wide range of access to foods high in fat and sugar which, combined with a more sedentary lifestyle, could affect their risk of diabetes. We will assess the association of prior wasting malnutrition with current pancreas structure and function, taking into account factors such as sex, current age, time since malnutrition, current BMI and body composition, and infections which could affect pancreas functions. Figure 1 shows the conceptual framework guiding the programme of research.\n\nThe above relationships may be subject to modification by sex, age at pancreas assessment, time since malnutrition, BMI, diet, or HIV status.\n\n\nProtocol\n\nOverall hypothesis\n\nWasting malnutrition at any age has medium- and long-term detrimental effects on endocrine and exocrine pancreatic function and structure.\n\n1. Specific objective 1: To investigate whether wasting malnutrition at various ages is associated with abnormalities of pancreas structure and function later in life.\n\na. Hypothesis 1: Prior wasting malnutrition is associated with later abnormal pancreatic structure and endocrine and exocrine function.\n\nb. Pancreatic phenotype of interest: Diabetes assessed by oral glucose tolerance test (OGTT) and haemoglobin A1c (HbA1c), exocrine pancreatic function tests (serum lipase, faecal elastase), pancreatic size and architecture measured using ultrasound for all participants and measured using computed tomography (CT) scans for a subset of participants (non-pregnant adult participants).\n\n2. Specific objective 2: To investigate whether pancreatic abnormalities in participants with prior malnutrition and diabetes are analogous to a previously described entity of fibro-calculous diabetes.\n\na. Hypothesis 2: Prior wasting malnutrition is associated with pancreatic calcification which in turn is associated with diabetes.\n\nb. Pancreatic phenotype of interest: Pancreatic calcifications determined from CT scans among non-pregnant adult study participants.\n\n3. Specific objective 3: To investigate the relative importance of decreased insulin production or increased insulin resistance in malnutrition-associated diabetes.\n\na. Hypothesis 3: The abnormal glucose regulation seen after wasting malnutrition is associated with relative insulin deficiency with or without insulin resistance.\n\nb. Pancreatic phenotype of interest: Indices of glucose metabolism and insulin kinetics based on mathematical models of glucose and hormone concentrations during OGTT and intravenous glucose tolerance tests (IVGTT). Homeostasis model assessment of insulin resistance (HOMA-IR) and liver fat (insulin resistance) will also be assessed.\n\n4. Specific objective 4: To investigate whether a prior abnormal pro-insulin/insulin ratio is associated with diabetes in adults infected or not with HIV or previously with tuberculosis.\n\na. Hypothesis 4: An abnormal pro-insulin/insulin ratio is associated with later development of diabetes in adults who had malnutrition earlier in life in association with HIV or tuberculosis infection.\n\nb. Pancreatic phenotype of interest: Fasting proinsulin/insulin ratio among Chronic Infections, Co-morbidities and Diabetes in Africa (CICADA) cohort participants measured several years before the SAMPA investigations.\n\nThis study brings together diverse cohorts (Table 1) under a common theme providing participants with prospectively assessed and clearly defined malnutrition exposure across populations and life-course and not previously malnourished controls, all from LMICs at various stages of the nutrition transition but with ongoing burden of infectious disease. Flow charts for each cohort are given in Figures 2–7.\n\n\n\n• Birth: 2079 total, all LBW\n\n• Age 5 y: 912 total, 764 (84%) BMIZ>-2, 138 (15%) BMIZ -2 to -3, 9 (1%) BMIZ<-3; 1 no anthropometry\n\n• Age ~13 y (ongoing): 647 total, 482 (75%) BMIZ>-2, 117 (18%) BMIZ -2 to -3, 48 (7%) BMIZ<-3\n\n• Expected for SAMPA: 750 total\n\n\n\na) 100 children who were hospitalised with malnutrition at University Teaching Hospital (UTH) between 2010 and 2014 when they were < 2 years\n\nb) 85 never-malnourished neighbourhood controls.\n\n\n\n• Age < 2 y: 100 malnutrition\n\n• Age 9 y: 185 total, 100 previous malnutrition, 85 no malnutrition; currently 17 (9%) BMIZ <-2\n\n• Expected for SAMPA: 180 total\n\n\n\na) Tuberculosis patients and controls from the TB-NUT study whose HIV and nutritional status ~16 years ago at recruitment are known (50% BMI<18.5 kg/m2) as well as more recently recruited HIV-infected and uninfected people (controls)18,19\n\nb) NUSTART, conducted 2010-2014, was a two-site (Mwanza and Lusaka) trial of food supplements for malnourished (BMI<18.5 kg/m2) HIV-infected adults, recruited when starting antiretroviral therapy.20 In Mwanza, 704 participants were recruited, 409 were alive and followed at the 12-week NUSTART end-point; 273 were available at a follow-up two-three years after starting ART and 206 were recruited to the CICADA study.\n\nc) HIV-infected and uninfected people, both malnourished and well-nourished, recruited 3-four years ago for HIV, nutrition and diabetes assessments\n\n\n\n• 73 (16.2%) BMI <17 kg/m2\n\n• 74 (16.4%) BMI 17 to 18.5 kg/m2\n\n• 303 (67.4%) BMI > 18.5 kg/m2\n\n\n\n• 105 (50.5%) BMI <17 kg/m2\n\n• 103 (49.5 %) BMI 17 to 18.5 kg/m2\n\n\n\n• 109 (8.4%) BMI <17 kg/m2\n\n• 171 (13.3 %) BMI 17 to 18.5 kg/m2\n\n• 1009 (78.3%) BMI >18.5 kg/m2\n\n\n\n• 10 y prior: 1111 total, 437 (39%) BMI 17 to 18.5 kg/m2, 674 (61%) BMI<17 kg/m2\n\n• Expected for SAMPA: 300 total\n\n\n\n• 1-2 y prior: 900 total, 495 BMI >18.5 kg/m2, 189 (21%) BMI 17.0-18.5 kg/m2, 216 (24%) BMI <17 kg/m2\n\n• Expected for SAMPA: 600 total\n\n\n\n• Birth: 28 LBW of the 143 with childhood malnutrition\n\n• Age ≤ 2 y: of 420 total to be included, 143 (34%) WHZ<-3\n\n• Expected for SAMPA: 420 total\n\nCohort members or their guardians (in case of children) will be contacted by the site principal investigators using the participant contact details from their most recent follow-ups. They will be asked if they wish to participate in SAMPA, and written informed consent will be obtained. For NUSTART, Lusaka, we will need to recruit never-malnourished controls. There are several possible levels of participation in SAMPA, based on cohort, sample size needed for testing specific hypotheses, and individual participants’ willingness to consent to specific tests. The potential different levels of participation are below. People not consenting to either version of the OGTT, a) or b), will be considered as not consenting to SAMPA overall and thus ineligible:\n\na) Questionnaires for socio-economic demographic and dietary assessment; anthropometry and body composition; medical exam; urine and stool sample collection; abdominal ultrasound and OGTT with blood sampling at baseline (fasting), and 15, 30, 45, 60, 90 and 120 minutes after glucose ingestion;\n\nb) Questionnaires for socio-economic demographic and dietary assessment; anthropometry and body composition; medical exam; urine and stool sample collection; abdominal ultrasound and minimal OGTT only, that is, with blood sampling at baseline (fasting), and 60 and 120 minutes after glucose ingestion;\n\nc) Addition of CT scans to a) or b). Children will not be asked to have CT scans. Women of childbearing age will not be asked to have CT scans unless they consent to a pregnancy test and have a negative result;\n\nd) Addition of IVGTT. This will be requested only for subsets of participants in the CICADA cohorts, as detailed below; glucose infusion will be at 0 minutes and samples will be collected at -10, -1, 2, 4, 6, 8, 10 minutes using an indwelling cannula.\n\nRegarding point c) above, although children in the DIVIDS cohort will not have CT scans, 100 of them will have MRI scans, funded by a separate project, which will be able to assess pancreas size and structure, as well as visceral fat.\n\nPrimary outcome measures\n\n1. Pancreatic endocrine function: diabetes or impaired glucose tolerance (pre-diabetes) by OGTT or HbA1c, defined using World Health Organization (WHO) cut-offs23\n\n2. Pancreatic exocrine function: faecal elastase and serum lipase\n\nSecondary outcome measures\n\n1. Pancreas size and structure: Pancreas size and architecture using ultrasound and CT (subsets from all adult cohorts)\n\n2. Pancreatic calcification: Calcification determined by CT scan (subsets from all adult cohorts)\n\n3. Insulin production and insulin resistance:\n\na. Mathematical modelling of blood glucose, insulin and C-peptide at three (for children) or seven (for adults) times during a 120-minute OGTT to determine first phase, second phase and total insulin release, insulin kinetics and insulin resistance;\n\nb. Mathematical modelling of data from analytes from IVGTT measured in blood samples collected at -10, -1, 2, 4, 6, 8, 10 minutes: glucose, insulin, and C-peptide (subset from CICADA).\n\n4. Other hormonal contribution to glucose metabolism and diabetes: Incretins (gastric inhibitory polypeptide (GIP) and glucagon-like peptide-1 (GLP-1)) and glucagon at 0, 30, 60, 90 and 120 minutes during an OGTT (subsets from CICADA and St-ATT).\n\n5. Proinsulin: Proinsulin in baseline samples before OGTT.\n\n6. Abnormal prior pro-insulin/insulin ratio and diabetes (subset): From the CICADA cohort, measurement of pro-insulin and insulin in fasting samples collected four years previously and comparison with current diabetes by OGTT.\n\nThe following assessments will be carried out on all consenting participants across the cohorts. Target sample sizes are as in Table 1.\n\n1. OGTT: The primary outcome for comparing those with and without prior malnutrition across all cohorts will be glucose ≥ 7.8 mmol/L at 2 hours in a standard OGTT with 75 g glucose (in children, 1.75 g/kg body weight up to 75 g) that is, diabetes plus impaired glucose tolerance by WHO criteria.23 Glucose in one hour samples in all participants will also be measured since this may be a better predictor of progression to diabetes due to insulin deficiency than the two-hour time point.24 Those with OGTT compatible with diabetes will be called back for a repeat OGTT in order to determine need for referral for clinical care. Urine dipstick will also be done for ketones to assess potential need for (short-/long-term) insulin replacement therapy. Indices of beta-cell function, insulin kinetics, and insulin resistance will be modelled from glucose, insulin and C-peptide during OGTT.25,26 Proinsulin will be measured in baseline samples only. Autoantibodies will be measured in participants with OGTT indicative of diabetes to confirm/exclude autoimmune type-1 diabetes.\n\n2. HbA1c: This will be by point-of-care test (Hemocue, Angelholm, Sweden) using fingerprick blood samples for most cohorts to indicate long-term glycaemic control; for the DIVIDS cohort, HbA1c will be measured in venous blood by a commercial lab (Dr. Lal Path Labs, Delhi).\n\n3. Abdominal ultrasound: Ultrasound scans will be performed by trained sonographers or radiologists in identified health facilities. The participant will be asked to lie on the ultrasound examination bed. They will be asked to breathe in and hold their breath in order to optimise visualization of the pancreas. A curvilinear ultrasound probe (2-5 MHz) will be placed onto the participant’s abdominal wall in the upper abdomen to image the pancreas. Images of the pancreas will be recorded and saved. Parameters obtained from the scans will be pancreas size, duct size, calcification, or other abnormality.\n\n4. Exocrine pancreas markers: These will be serum lipase in baseline OGTT samples and faecal elastase: Participants will collect faecal samples either in the clinic or bring them from home.\n\n5. Urine glucose and ketones by dipstick: These will be from random urine collection.\n\n6. Anthropometry: Anthropometry will use standard methods27 conducted by trained staff. At each site technical error of measurement will be assessed and further training provided so that all staff reach acceptable levels of agreement with the local criterion anthropometrist.28 Anthropometric measurements will be weight, height, sitting height, tibia length, circumferences of waist, hip and mid-upper arm, and triceps and subscapular skinfold thicknesses.\n\n7. Body composition: All sites will use bioelectrical impedance (BIA) for body composition assessment. Lusaka will additionally use air displacement plethysmography (BodPod) and can assess its agreement with BIA.\n\nThe following assessments will be conducted in only subsets of consenting participants.\n\n8. Detailed OGTT: The same OGTT protocol will be used as above but, for 80 participants in each of the CICADA and St-ATT cohorts, referred to as the in-depth subset, we will measure additional hormones: glucagon, gastric inhibitory peptide (GIP), glucagon-like peptide-1 (GLP-1) at multiple time points and trypsinogen in baseline samples.\n\n9. IVGTT: This test is the gold standard for estimating the early insulin response. It will be done only in the in-depth subset from CICADA. Results will be compared with OGTT in the same participants in order to better understand the OGTT results. For this test a solution of sterile 50% dextrose, in amounts 0.3 g/kg body weight, will be injected into the antecubital vein over 60 seconds starting at time 0 minutes. Blood samples will be taken at -10, -1, 2, 4, 6, 8, 10 minutes for measurement of glucose, insulin, C-peptide and glucagon.\n\n10. CT scans: The CT studies will be performed in 100 participants from each of the adult cohorts by qualified and experienced radiologists in identified health facilities. Scans will be taken without use of contrast agents. The protocol will assess the following:\n\n• Pancreatic volume (in cm3)\n\n• Abnormalities in duct size\n\n• Presence of cysts or calcification.\n\nStandardisation of the measurements between sites will be assured by consultation among all site radiologists of 10 scans from each cohort. The studies will be conducted and reviewed for incidental findings at the local site in accordance with the relevant standard operating procedure (SOP).\n\n11. Proinsulin-insulin ratio: This will be done in 120 archived samples from the CICADA cohort which were collected from fasting participants about four years prior to the SAMPA visit.\n\nThe DIVIDS child cohort will not have CT scans but 100 children will have MRI scans, funded through a separate project, which will permit examination of pancreas size and structure as well as quantification of visceral fat. Also, in the DIVIDS cohort only, we will measure full blood count, blood lipids and C-reactive protein in baseline samples from the OGTT; this is done for purposes of local ethics and family desire for the information.\n\nGlucose as part of OGTT and IVGTT tests and HbA1c will be measured using either point-of-care analysers or local labs, depending on the site, in order to provide rapid feedback to participants to enable medical care. Urine ketones will be measured by dipstick in those with suspected diabetes in order to assess the need for short or long-term insulin replacement therapy. Serum lipase, CRP and lipids will be measured at accredited commercial laboratories. Fecal elastase will be measured at each site using stool preparation and ELISA kits from ScheBo (Biotech UK, Lyme Regis, UK).\n\nOther laboratory assays (glucagon, insulin, pro-insulin, C-peptide, GIP, GLP-1 and auto-antibodies) for samples from Mwanza, Lusaka and the Philippines will be conducted together at Rigshospitalet, University of Copenhagen. Since it is not possible to ship samples from India to the UK, Dr. Krogh-Madsen of Rigshospitalet will arrange quality assurance with the Delhi laboratory.\n\nData will be collected using computer-assisted personal interviews. Structured questionnaires programmed in REDCap will be accessed by trained interviewers through tablets. Data will be transmitted to a secure database storage server hosted at the London School of Hygiene and Tropical Medicine (LSHTM). Quality control will be applied at each stage of data handling in accordance with Good Clinical Practice (GCP) requirements to ensure that all data are reliable and have been processed correctly. Access to the data (as uploaded in the database) will be granted to authorised representatives from the sponsor, host institution and the regulatory authorities to permit study-related monitoring, audits and inspections.\n\nFat and fat-free mass in kg will be divided by height in meters-squared, analogous to determining BMI from weight and height, to give fat mass index (FMI) and fat-free mass index (FFMI).\n\nSocioeconomic status (SES) indices will be derived separately for each site using principal component analysis (PCA) of individual or family assets; the specific assets will differ by site since they have been chosen to be locally appropriate. The first component from the PCA will be divided into terciles for use in analyses.\n\nSite-specific diet patterns will be calculated by PCA of food groups; the number of components to include will be based on eigenvalues and scree plots.29 The level of adherence to individual patterns will be calculated by dividing the components in terciles.\n\nDescriptive analysis will be conducted within cohorts and divided by sex. Means and standard deviations (SDs) will be used to summarise normally distributed data and medians and interquartile ranges (IQR) for non-normally distributed variables. Categorical variables will be described as proportions.\n\nAnalyses related to individual hypotheses are described below. Primary analyses will be conducted for each cohort separately. Pooled analyses using all or some cohorts combined will be conducted based on the individual cohort results, and in order to investigate how age at malnutrition and length of time between malnutrition and outcome assessment influence the associations between malnutrition and pancreas structure and function. Analyses will be guided by the conceptual framework in Figure 1. Sample sizes for the specific hypotheses indicate that, with the available number of participants in the cohorts, we have sufficient power for the main analyses with all participants. For some expensive or labour- and participant-intensive outcomes, we had to consider cost and feasibility and have calculated power for analyses in subsets.\n\nPrior malnutrition is associated with later abnormal pancreatic structure and endocrine and exocrine function.\n\nParticipants with and without prior wasting malnutrition, the SAMPA study primary exposure, will be compared within each cohort for all pancreas structure and function outcomes: diabetes by OGTT or HbA1c, exocrine function as indicated by faecal elastase and serum lipase, and pancreas size and presence of abnormalities detected by ultrasound or CT scan. We will initially fit regression models for each outcome with prior malnutrition as the main exposure, controlling for sex and for age as a continuous variable. We will investigate whether there are interactions between prior malnutrition and sex, which is known to be associated with both prior malnutrition and diabetes. We will then investigate whether the associations between malnutrition and the outcomes differ by the following variables:\n\n• Time since malnutrition\n\n• Sitting/standing height ratio as an indicator of early life stunting\n\n• HIV status for African cohorts only (SAM Lusaka, NUSTART Lusaka, CICADA)\n\nSeveral variables – BMI, FMI, FFMI and diet pattern (using components from PCA as defined above) – have potentially complex relationships with the exposure and outcomes. These variables will be measured at the time of outcome assessment, but are assumed to reflect participants’ nutritional status and diet prior to the outcome. We will start by investigating the associations among diet patterns, BMI, FMI and FFMI at the time of pancreas testing. We will then explore several relationships between these variables, the prior malnutrition exposure, and the outcomes. First, BMI and FMI may be on the causal pathway from wasting malnutrition to diabetes since recovery from wasting malnutrition associated with infection may lead to excess fat deposition,30,31 and since people previously severely malnourished may, if it becomes possible later, choose to gain weight as a buffer against future food shortages. Second, BMI, FMI and diet patterns could be modifiers of the association between prior malnutrition and diabetes, as seen previously for diet pattern and BMI in Chinese famine survivors.32 Third, exocrine pancreas abnormalities which result in fat malabsorption or intestinal discomfort may induce participants to modify their diets which could result in changes to BMI, FMI or FFMI.\n\nWe will conduct exploratory analyses to investigate the mechanisms through which the exposure variable, malnutrition, is associated with pancreas outcome variables. For example, decreased production of incretins by gut epithelial cells may be associated with both exocrine pancreas function, which could affect rate of absorption of nutrients which trigger incretin secretion, and insulin secretion.\n\nSample size: Large variations in prevalence of impaired glucose tolerance (OGTT≥7.8 mmol/L) or high fasting glucose in never malnourished (2%-11%) make estimates imprecise. The absolute difference in prevalence of hyperglycaemia in those with prior malnutrition versus those without was 3% to 9% in these studies.32–34 Assuming an intermediate prevalence of OGTT ≥7.8 mmol/L of 7% in those without malnutrition, the CICADA and St-ATT cohorts individually have 80% power to detect a difference in prevalence of 7.5% in those with malnutrition. For continuous variables, i.e. glucose, hormones, faecal elastase and serum lipase, the available sample size in the smallest cohort will be sufficient to determine differences of 0.4 times the standard deviation with 90% power. Expected differences in pancreas volume were calculated using volume normalised to kg body weight to account for the participant age and size range.35 A total of n=100 per cohort (assuming a standard deviation of 0.3 mL/kg) will provide 90% power to detect differences of 0.2 mL/kg between those with/without prior malnutrition, which is a smaller difference than that expected between people with and without diabetes.35,36\n\nPrior malnutrition is associated with pancreatic calcification which in turn is associated with diabetes.\n\nTo investigate whether prior malnutrition is associated with pancreas calcification, from each adult cohort we will randomly select for CT scans 50 participants who were exposed to malnutrition and 50 controls who were not exposed. The presence of calcification or other pancreas abnormalities on CT will be compared between those with or without prior malnutrition.\n\nIn order to increase sample size for this and for the second part of the hypothesis comparing calcification with diabetes, results from CT scans in the subset of participants with these will be compared with the ultrasound results from the same participants to indicate whether abnormalities determined by ultrasound, e.g. pancreas body or duct shape, correspond to calcification by CT scan. We will then compare the proportion of abnormalities based on ultrasound or CT scan among those with and without diabetes.\n\nSample size: Population prevalence estimates for pancreatic calcification appear unavailable so we have not performed any sample size calculations. Pancreatic calcifications are seen in fibro-calculous pancreatic diabetes7 but these studies have been conducted on participants selected for their clinical presentation.\n\nThe abnormal glucose regulation seen after malnutrition is associated with relative insulin deficiency with or without insulin resistance.\n\nA deeper understanding of associations between prior malnutrition and the underlying glucose metabolic pathways will be explored through modelling biochemical measures over the course of the two-hour OGTT. Glucose, insulin and C-peptide data from OGTT will be used to model pancreatic cell functionality according to published methods in order to determine a set of indices quantifying: first phase, second phase, and total insulin secretion,37 whole-body and hepatic insulin clearance,38 and insulin sensitivity.25,39 For the child cohorts for whom only three blood samples are available over the two-hour OGTT, we will use methods designed to determine insulin sensitivity from sparsely sampled OGTTs.26 The IVGTT data from the CICADA cohort subset can be similarly modelled to estimate insulin sensitivity and insulin secretion. Comparison of the indices estimated from the two tests will provide information as to whether altered intestinal function, e.g. glucose absorption or incretin secretion, influences insulin secretion or sensitivity in participants previously malnourished or not.\n\nSample size: We will use individual data from all SAMPA adult participants and, for children who have only three sample points during OGTT, we will combine data from groups of participants.26 Most previous studies in this area include 10-100 people per group, whereas we will be able to study all SAMPA participants.\n\nAn abnormal fasting pro-insulin/insulin ratio is associated with later development of diabetes in adults who had malnutrition and infection.\n\nAnalysis: We will use the detailed data and samples available from CICADA to investigate whether the proinsulin/insulin ratio in CICADA samples collected from fasted participants about four years prior to the SAMPA visit is associated with diabetes or prediabetes at the SAMPA visit. This will be a nested case-control study where cases are 60 CICADA participants with current diabetes by OGTT and controls are 60 CICADA participants with normal OGTT. These participants will be selected by stratified random sampling. Logistic regression will be used, controlling for age and sex, to determine if prior proinsulin/insulin ratio is associated with later diabetes.\n\nSample size: The sample size was a function of available cases and consumable costings. A sample of 120 (1:1 ratio of cases and controls) will provide 90% power to detect a difference of 0.04 in the fasting proinsulin/insulin ratio (assuming an SD of 0.07) which is smaller than that found between people with and without type 2 diabetes.40\n\nLead investigators from each of the study sites will disseminate the study findings to the participants and their families, to local clinicians working in nutrition, diabetes or related fields, and to the relevant government departments. Academics will learn about the research methods and findings through open-access, peer-reviewed journal articles, conference presentations, both international and in the participant countries, and seminar series and other platforms for exchanging information with staff and students within the partner institutions. They will then be able to take the results in various directions which will have impact beyond the study team’s expertise.\n\nData can be made available on request from the Principal Investigator for bona fide research conducted in accordance with protocols and stipulations in the project’s ethical approvals.\n\nThe study will be conducted in compliance with the Declaration of Helsinki's principles, as well as all applicable regulations and the 1996 ICH Guidelines for Good Clinical Practice (CPMP/ICH/135/95). The protocol, informed written consent and assent forms, participant information sheet and other required materials have been approved by the appropriate Research Ethics Committees (Table 2). If required, the investigators will obtain approval from these committees for all substantial amendments to the original approved documents. Permission has already been obtained from previous cohort follow-ups to use data and samples for subsequent research and has been agreed for SAMPA as well.\n\nChildren will have only three-sample OGTT and neither they nor pregnant women will be offered CT scans. All participants found during clinic visits or on later review of ultrasound and CT scans to have diabetes or other illnesses requiring treatment will be referred to local clinical facilities and, if required, offered a consultation with an appropriate specialist.\n\n\nConclusions\n\nThere is some evidence that wasting malnutrition in children and adults may leave lasting pancreatic damage and increase the risk of diabetes later in life, although little is known about the mechanisms involved. SAMPA will lead to better understanding of the long-term impacts of malnutrition as well as the manifestation and underlying metabolism of diabetes in Africa and Asia. Even if no significant link between wasting malnutrition and later diabetes is established, the research will improve understanding of both the long-term consequences of malnutrition and the phenotype of glucose dysregulation in Africa and Asia. It will thus result in better health care for both malnourished individuals and people with diabetes.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nWe are grateful to the SAMPA participants who have given their time, data and samples over the years and also to the SAMPA site clinical and administrative staff for their excellent work.\n\n\nReferences\n\nWorld Health Organization: Obesity and overweight, Fact sheet 2021.Reference Source\n\nPopkin BM, Corvalan C, Grummer-Strawn LM: Dynamics of the double burden of malnutrition and the changing nutrition reality. Lancet. 2020; 395(10217): 65–74. PubMed Abstract | Publisher Full Text\n\nFall C, Sachdev H:Developmental origins of health and disease: implications for developing countries.Gluckman PD, Hanson MA, editors. Developmental Origins of Health and Disease. Cambridge:Cambridge University Press; 2006; p. 456–470.\n\nGrey K, Gonzales GB, Abera M, et al.: Severe malnutrition or famine exposure in childhood and cardiometabolic non-communicable disease later in life: a systematic review. BMJ Glob. Health. 2021; 6(3): e003161. 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PubMed Abstract | Publisher Full Text\n\nPrayGod G, Range N, Faurholt-Jepsen D, et al.: Weight, body composition and handgrip strength among pulmonary tuberculosis patients: a matched cross-sectional study in Mwanza, Tanzania. Trans. R. Soc. Trop. Med. Hyg. 2011; 105(3): 140–147. PubMed Abstract | Publisher Full Text\n\nFilteau S, PrayGod G, Kasonka L, et al.: Effects on mortality of a nutritional intervention for malnourished HIV-infected adults referred for antiretroviral therapy: a randomised controlled trial. BMC Med. 2015; 13: 17. PubMed Abstract | Publisher Full Text\n\nCox S, Edwards T, Faguer B, et al.: Patterns of non-communicable comorbidities at start of tuberculosis treatment in three regions of the Philippines: The St-ATT cohort. PLoS Global Pub Health. 2021; 1: e0000011. Publisher Full Text\n\nAdair LS, Popkin BM, Akin JS, et al.: Cohort profile: the Cebu longitudinal health and nutrition survey. Int. J. Epidemiol. 2011; 40: 619–625. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Definition and diagnosis of diabetes mellitus and intermediate hyperglycaemia 2006.Reference Source\n\nTrico D, Galderisi A, Mari A, et al.: One-hour post-load plasma glucose predicts progression to prediabetes in a multi-ethnic cohort of obese youths. Diabetes Obes. Metab. 2019; 21(5): 1191–1198. PubMed Abstract | Publisher Full Text\n\nDalla Man C, Campioni M, Polonsky KS, et al.: Two-hour seven-sample oral glucose tolerance test and meal protocol: minimal model assessment of beta-cell responsivity and insulin sensitivity in nondiabetic individuals. Diabetes. 2005; 54(11): 3265–3273. PubMed Abstract | Publisher Full Text\n\nStefanovski D, Vellanki P, Smiley-Byrd DD, et al.: Population insulin sensitivity from sparsely sampled oral glucose tolerance tests. Metabolism. 2020; 110: 154298. PubMed Abstract | Publisher Full Text\n\nGibson RS: Principles of Nutritional Assessment. 2nd Edition.Oxford:Oxford University Press;2005.\n\nUlijaszek S, Kerr D: Anthropometric measurement error and the assessment of nutritional status. Br. J. Nutr. 1999; 82: 165–177. Publisher Full Text\n\nRichter A, Heidemann C, Schulze MB, et al.: Dietary patterns of adolescents in Germany--associations with nutrient intake and other health related lifestyle characteristics. BMC Pediatr. 2012; 12: 35. PubMed Abstract | Publisher Full Text\n\nPrayGod G, Blevins M, Woodd S, et al.: A Longitudinal Study of Systemic Inflammation and Recovery of Lean Body Mass among Malnourished HIV-infected Adults Starting Antiretroviral Therapy in Tanzania and Zambia. Eur. J. Clin. Nutr. 2016; 70: 499–504. PubMed Abstract | Publisher Full Text\n\nSchwenk A, Hodgson L, Wright A, et al.: Nutrient partitioning during treatment of tuberculosis: gain in body fat mass but not in protein mass. Am. J. Clin. Nutr. 2004; 79(6): 1006–1012. PubMed Abstract | Publisher Full Text\n\nLi Y, He Y, Qi L, et al.: Exposure to the Chinese famine in early life and the risk of hyperglycemia and type 2 diabetes in adulthood. Diabetes. 2010; 59(10): 2400–2406. PubMed Abstract | Publisher Full Text\n\nvan Abeelen AF , Elias SG, Bossuyt PM, et al.: Famine exposure in the young and the risk of type 2 diabetes in adulthood. Diabetes. 2012; 61(9): 2255–2260. PubMed Abstract | Publisher Full Text\n\nFrancis-Emmanuel PM, Thompson DS, Barnett AT, et al.: Glucose metabolism in adult survivors of severe acute malnutrition. J. Clin. Endocrinol. Metab. 2014; 99(6): 2233–2240. PubMed Abstract | Publisher Full Text\n\nBurute N, Nisenbaum R, Jenkins DJ, et al.: Pancreas volume measurement in patients with Type 2 diabetes using magnetic resonance imaging-based planimetry. Pancreatology. 2014; 14(4): 268–274. PubMed Abstract | Publisher Full Text\n\nVirostko J, Williams J, Hilmes M, et al.: Pancreas Volume Declines During the First Year After Diagnosis of Type 1 Diabetes and Exhibits Altered Diffusion at Disease Onset. Diabetes Care. 2019; 42(2): 248–257. PubMed Abstract | Publisher Full Text\n\nBreda E, Cavaghan MK, Toffolo G, et al.: Oral glucose tolerance test minimal model indexes of beta-cell function and insulin sensitivity. Diabetes. 2001; 50(1): 150–158. PubMed Abstract | Publisher Full Text\n\nWatanabe RM, Bergman RN: Accurate measurement of endogenous insulin secretion does not require separate assessment of C-peptide kinetics. Diabetes. 2000; 49(3): 373–382. Publisher Full Text\n\nDalla Man C, Caumo A, Cobelli C: The oral glucose minimal model: estimation of insulin sensitivity from a meal test. IEEE Trans. Biomed. Eng. 2002; 49(5): 419–429. PubMed Abstract | Publisher Full Text\n\nKim NH, Kim DL, Choi KM, et al.: Serum insulin, proinsulin and proinsulin/insulin ratio in type 2 diabetic patients: as an index of beta-cell function or insulin resistance. Korean J. Intern. Med. 2000; 15(3): 195–201. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "147874",
"date": "19 Aug 2022",
"name": "David J. Hill",
"expertise": [
"Reviewer Expertise Diabetes",
"pancreatic islet development and function. fetal programming of adult metabolic disease",
"diabetes in pregnancy",
"beta cell biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe hypothesis is that wasting malnutrition either in childhood or adulthood will cause long-term impacts on exocrine and endocrine pancreatic function following nutritional recovery, and that this will result in an increased risk of diabetes. This study will examine almost 4,000 individuals who experienced serious malnutrition from a number of existing study cohorts recruited in Zambia, Tanzania, Philippines, and India under the SAMPA International Program. Pancreas size, structure, and degree of calcification will be assessed by ultrasound and CT scan; exocrine function will be assessed by fecal elastase and serum lipase measurements and endocrine function by HbA1c measurement, blood glucose, insulin and C-peptide concentrations during an OGTT. Sub-sets of patients will be selected for analysis of insulin, pro-insulin, glucagon and incretin excursions during GTTs. Pancreatic size and function outcomes will be compared between subjects with and without prior wasting malnutrition. The impact of sex, age, time since malnutrition, current BMI and diet will be analyzed.\nThis is a very ambitious study covering a number of existing longitudinal cohorts. A major strength is the real-world approach to health outcomes in populations that experience serious famine, which is important for the planning of future health provision. The sample size is impressive but needs to be given the number of confounders that will exist. I may have missed it but will subjects who have already developed clinical diabetes be excluded?\nWith respect to pancreatic function I think better justification needs to be provided as to why ultrasound and CT estimation of anatomy and ductal structure need to be undertaken. Is there evidence that total pancreas volume is associated with either endocrine or exocrine sufficiency. Certainly pancreas size does not give any indication of endocrine cell mass since the islets represent less than 5% of pancreas cell mass. It is stated that CT will allow an estimate of duct size, but what does this imply? The degree of calcification will be measurable but it is not explained why this might cause an alteration in either exocrine or endocrine function. What might be useful if possible is to use contrast micro-CT to measure changes in the vascular density of the pancreas.\nThe timing and duration of malnutrition relative to age is likely to be very important with respect to the risk of adult diabetes and should be given more attention. Beta cell mass in the pancreas increases until adolescence through the potential for beta cell proliferation although this declines with age. After adolescence gain of beta cell mass is minimal. In terms of plasticity of beta cell mass this can recover during childhood from a metabolic insult such as malnutrition but this is likely to be minimal after adolescence. This, documentation of the age of onset of the malnutrition, duration and intensity, and recovery will be crucial to the metabolic phenotype and risk of adult diabetes. As four of the six cohorts are already adults it should be made clear what degree of precision around the historical documentation of these measurements will be available.\nWhile the detailed analysis from OGTT and i.p.GTT will be very informative in the sub-group analysis it is not clear how the sub-groups will be selected. Will they sample from the subjects found to have the most abnormal pancreas parameters, or from a group that represents median measurements? It is stated that both glucagon and insulin/proinsulin excursions will be measured during GTTs but the biological relevance of these measurements is not given. Is the proinsulin/insulin ratio meant to be a measure of beta cell stress? If so then there should also be changes in the ratio of first to second phase insulin release as the stressed pancreas will likely have a smaller pool of readily releasable insulin granules. Is the glucagon measurement meant to indicate a hyperglucagonemia as often found in T2D?\nThese comments are made in the constructive spirit of getting the most out of this very important study and how it is portrayed in the manuscript.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "8837",
"date": "03 Oct 2022",
"name": "Sana Ahmed",
"role": "Author Response",
"response": "Thank you for your thorough and insightful review of our manuscript. We sincerely appreciate your invested time and efforts. Please find below our detailed responses (in bold) to your comments: The sample size is impressive but needs to be given the number of confounders that will exist. I may have missed it but will subjects who have already developed clinical diabetes be excluded? We have not excluded those with diabetes. However, very few participants were known in advance to have diabetes since in only two of the six cohorts, CICADA and St-ATT, had there been previous studies of diabetes. Furthermore, for St-ATT participants, diabetes screening was undertaken when participants were acutely ill with tuberculosis which may have impacted on the diagnosis. For all cohorts, we are collecting data on whether participants have been previously diagnosed with diabetes and whether they are on any diabetes medication. With respect to pancreatic function I think better justification needs to be provided as to why ultrasound and CT estimation of anatomy and ductal structure need to be undertaken. Is there evidence that total pancreas volume is associated with either endocrine or exocrine sufficiency. Certainly pancreas size does not give any indication of endocrine cell mass since the islets represent less than 5% of pancreas cell mass. It is stated that CT will allow an estimate of duct size, but what does this imply? The degree of calcification will be measurable but it is not explained why this might cause an alteration in either exocrine or endocrine function. What might be useful if possible is to use contrast micro-CT to measure changes in the vascular density of the pancreas. There is no doubt that pancreas size is considerably reduced in type 1 diabetes despite this being a beta-cell targeted autoimmune disease, with islets constituting less than 5% of the overall pancreas volume. There is also accruing evidence for reduced pancreatic volume in type 2 diabetes; see, for example, Al-Mrabeh et al. Lancet Diabetes Endocrinology 2020; 8(12): 939-948, or Virostko et al., Diabetes Care 2019; 42(2): 248-257. We hypothesise that smaller pancreas size may reflect reduced islet mass - due to reduced growth during development in those with malnutrition occurring under the age of 20 years or due to loss of previously acquired mass. Pancreatic calcification is associated with a 3-fold increased risk of diabetes in chronic pancreatitis and ductal structure will be examined to further characterise the potential underlying pancreatic disease. Our ethical approvals at the sites do not permit contrast CT scans. Our purpose here is to define, we believe for the first time, whether, and what sort of, changes develop in the pancreas attributable to prior malnutrition. We, therefore, have to try and capture all possible changes which may occur. The timing and duration of malnutrition relative to age is likely to be very important with respect to the risk of adult diabetes and should be given more attention. Beta cell mass in the pancreas increases until adolescence through the potential for beta cell proliferation although this declines with age. After adolescence gain of beta cell mass is minimal. In terms of plasticity of beta cell mass this can recover during childhood from a metabolic insult such as malnutrition but this is likely to be minimal after adolescence. This, documentation of the age of onset of the malnutrition, duration and intensity, and recovery will be crucial to the metabolic phenotype and risk of adult diabetes. As four of the six cohorts are already adults it should be made clear what degree of precision around the historical documentation of these measurements will be available. We agree completely that the potential for beta cell proliferation declines with age, but hypothesise that malnutrition may have a greater effect on beta cell mass in those affected during growth and development due to reduced final beta-cell mass persisting into adulthood. The data on malnutrition were collected prospectively for 5 of the 6 cohorts and thus exact ages and degrees of malnutrition are known. The cohorts were either recruited based on being malnourished (DIVIDS, NUSTART Lusaka, St-ATT) or were recruited for longitudinal studies (CICADA, CLHNS) so we have nutritional status documented over several years in the past. For SAM Lusaka we recruited from hospital records when the children were admitted for severe acute malnutrition several years before our first contact with the children. While the detailed analysis from OGTT and i.p.GTT will be very informative in the sub-group analysis it is not clear how the sub-groups will be selected. Will they sample from the subjects found to have the most abnormal pancreas parameters, or from a group that represents median measurements? It is stated that both glucagon and insulin/proinsulin excursions will be measured during GTTs but the biological relevance of these measurements is not given. Is the proinsulin/insulin ratio meant to be a measure of beta cell stress? If so then there should also be changes in the ratio of first to second phase insulin release as the stressed pancreas will likely have a smaller pool of readily releasable insulin granules. Is the glucagon measurement meant to indicate a hyperglucagonemia as often found in T2D? In order to test our primary hypothesis that prior malnutrition has long-term effects on pancreas function, we will randomly select, stratified by prior malnutrition or not, from the full list of recruits to the relevant cohorts. This information, for CT scans as well, has been added to the section on tests performed in subsets of participants. Proinsulin will be measured in fasted samples just before the OGTT and its ratio with insulin calculated; this will indeed be used as a measure of beta-cell stress or potentially phenotypic shift induced by the beta-cell-specific impact of malnutrition. Our models of the full glucose, insulin and C-peptide data from all OGTT time points will provide further details of early and later phase insulin release. Several of the authors are building the models from their clinical studies in cystic fibrosis, a model disease likely to have a similar pancreatic phenotype as we look for in SAMPA. We recognise that the underlying pathophysiology of cystic fibrosis is completely different; cystic fibrosis is, however, also a disease of malnutrition combined with exocrine dysfunction. We suggest the proinsulin-to-insulin ratio is a good general indicator of stressed beta cells, as previous studies reported increased proinsulin-to-insulin ratios in both persons with and without cystic fibrosis with insufficient insulin secretion. We hypothesize that dysfunctional beta cells play an important role in the progression of abnormal glucose tolerance towards diabetes. Yes, the glucagon measurement is to detect whether an oral intake of glucose results in inappropriately high plasma concentrations of glucagon as in T2D. It is as yet unknown whether the same aberrant response will be seen in patients with prior malnutrition or current pancreas dysfunction. We have added text to the section on outcome measures to clarify our reasons for choosing these."
}
]
},
{
"id": "149409",
"date": "16 Sep 2022",
"name": "Ishu Kataria",
"expertise": [
"Reviewer Expertise Noncommunicable Diseases",
"NCD policy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study will assess the association of prior wasting malnutrition on endocrine and exocrine pancreatic structure and function. It will include 3700 participants from existing observational cohorts in four LMICs.\n\nBased on reviewing the protocol manuscript, here are some suggestions that would strengthen the paper; and overall study:\nWith regards to participant recruitment, there are two cohorts out of six, where the sample will include adolescents. Although it is mentioned that parental consent will be obtained, an assent is recommended in case of adolescents.\n\nFor the OGTT analysis, how will the sub-groups be selected?\n\nThe investigators mention in their dissemination strategy for the project that they will be sharing the findings with participants and their families as well as with the relevant government departments. While there is clarity on the methods identified to reach academics and local clinicians, it is pertinent that there is a plan for dissemination for the abovementioned groups as the methods would be completely different.\n\nIt will be important to consider inclusion of patient perspectives in the research. Patients have multiple ongoing interactions with the health system over long periods of time and can provide useful inputs in terms of patient acceptability of aspects of study design, and also review draft patient information materials.\n\nThe study aims to generate evidence for future policies and programmes for malnutrition and diabetes; however, description about how that linkage will happen is missing. Suggest adding a paragraph on policy implications of research in the protocol paper.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "8838",
"date": "03 Oct 2022",
"name": "Sana Ahmed",
"role": "Author Response",
"response": "We appreciate you taking the time to read over and thoughtfully comment on our work. We are really grateful for your contribution. Below are the detailed answers (in bold) to your remarks: With regards to participant recruitment, there are two cohorts out of six, where the sample will include adolescents. Although it is mentioned that parental consent will be obtained, an assent is recommended in case of adolescents. As we have mentioned under ‘ethical considerations and regulatory approvals’ we would be getting assent from the adolescent participants in addition to the parental consent. For the OGTT analysis, how will the sub-groups be selected? All participants will have OGTT undertaken, the main difference being that there will be only 3 blood sampling time points for children, 7 for adults. For the in-depth sub-samples in some of the adult cohorts, we will randomly select these, stratified by whether or not they were previously malnourished, as recorded in our databases from earlier cohort follow-ups. This information, which also applies to the subsets for CT scans, has been added to the description of tests performed only on subsets of participants. The investigators mention in their dissemination strategy for the project that they will be sharing the findings with participants and their families as well as with the relevant government departments. While there is clarity on the methods identified to reach academics and local clinicians, it is pertinent that there is a plan for dissemination for the abovementioned groups as the methods would be completely different. All the reports from the several investigations that will be conducted will be duly shared and discussed with the participants, their families, local clinicians, and health care managers. The format for this dissemination will vary by study site and will be done according to usual practice at the sites. This information has been added to that section of the text. It will be important to consider inclusion of patient perspectives in the research. Patients have multiple ongoing interactions with the health system over long periods of time and can provide useful inputs in terms of patient acceptability of aspects of study design, and also review draft patient information materials. While formal patient input into research is becoming common in some places, it is not currently the norm at any of the study sites. We are developing such approaches and setting up Community Advisory Boards in several sites; however, this strategy was not in place when SAMPA was being designed. On the other hand, SAMPA participants are all from cohorts with whom the researchers at each site have had long contact. Participants are thus comfortable talking to the staff and the staff thus gains insight into their perspectives. We often use such information gathered to generate or modify research plans. The study aims to generate evidence for future policies and programmes for malnutrition and diabetes; however, description about how that linkage will happen is missing. Suggest adding a paragraph on policy implications of research in the protocol paper. We have added the following paragraph on policy implications near the end of the manuscript: If low insulin production, either with or without insulin resistance, is an important cause of diabetes in populations in which prior wasting malnutrition is common, then diagnosis and treatment regimens may require modification. By providing insights into hormonal changes during an OGTT, the project will provide information as to how diagnostic protocols could be modified, e.g. by looking at other time points than 120 minutes in an OGTT or including measurement of insulin or C-peptide. The usual current first-line treatment in many settings is metformin but modified treatment protocols could include drugs promoting insulin secretion with earlier progression to injected insulin therapy."
}
]
}
] | 1
|
https://f1000research.com/articles/11-777
|
https://f1000research.com/articles/11-906/v1
|
05 Aug 22
|
{
"type": "Opinion Article",
"title": "A general theory of multistable systems in pathophysiology",
"authors": [
"Bruno Burlando"
],
"abstract": "Despite intensive investigations numerous diseases remain etiologically puzzling and recalcitrant to treatments. A theory is proposed here assuming that these difficulties are due to an unsuitable approach to the mechanisms of life, which is subjugated by an apparent complexity and fails to grasp the uniformity that lays behind. The stability of metabolism, despite the enormous complex of chemical reactions, suggests that reciprocal control is a prerequisite of life. Negative feedback loops have been known for a long time to maintain homeostasis, while more recently, different life processes involved in transitions or changes have been modeled by positive loops giving rise to bistable switches, also including various diseases. The present theory makes a generalization, by assuming that any functional element of a biological system is involved in a positive or a negative feedback loop. Consequently, the theory holds that the starting mechanism of any disease that affects a healthy human can be conceptually reduced to a bistable or multistationary loop system, thus providing a unifying model leading to the discovery of critical therapeutic targets.",
"keywords": [
"bistable switch",
"feedback loops",
"pathogenesis",
"pathophysiology",
"systems and control theory",
"systems biology"
],
"content": "Introduction\n\nComplexity is one of the most addressed features of life and a possible major hindrance to the advancement of knowledge in life science. This inevitably makes life science a non-exact scientific field largely operating through qualitative, verbose descriptions, as opposed to the quantitative, mathematical models of physics. Consequently, the predictivity of theoretical models in life science is generally low, posing serious limits to their application to the real world. This is mirrored by serious difficulties in biomedical investigations, with several diseases remaining etiologically puzzling and recalcitrant to treatments, including tumor malignancies, neurodegenerative diseases, immune disorders, metabolic syndromes, and different infectious diseases. However, rather than being due to the excessive complexity of life, these drawbacks could derive from an unsuitable approach to the study of life processes, including transitions from physiological to pathological conditions.\n\nThe human body is believed to consist of about 1013 cells (Bianconi et al., 2013), while about 1010 s-1 chemical reactions can be roughly calculated to occur inside each cell, considering basal metabolism and the energy released per mole by ATP hydrolysis (Wackerhage et al., 1998), thus making up a total of about 1023 s-1 chemical reactions in the whole body. The ability of maintaining a metabolic steady state, despite such a huge complex of events, seems statistically paradoxical. However, this would be true if metabolic processes were uncorrelated from each other, whereas they are supposed to be strictly regulated and cross-adjusted (Burlando, 2017; El-Samad, 2021). Hence, if reciprocal control is the prerequisite of life processes, their study cannot be exempted from an appropriate analysis of control mechanisms.\n\nSeminal theoretical work by Ludwig Von Bertalanffy has led to the development of systems theory (von Bertalanffy, 1968), which in the beginning was inspired by living systems, and thereafter was widely applied to engineering. Thereafter, systems and control theory has developed the study of dynamic systems consisting of negative or positive feedback loops, i.e. sequences of interactions among functional agents arranged as closed chains (Blanchini et al., 2014). Negative loops have an uneven number of inhibitory steps, in addition to possible activation steps, and one stable equilibrium point or a limit cycle with oscillatory behavior. By contrast, positive loops have an even number of inhibitory steps, or none, and admit multiple stable equilibrium points.\n\nPhysiological mechanisms based on negative feedback loops are known to maintain homeostasis, or induce oscillations within fixed boundaries, thus ensuring the body’s steady state (Blanchini et al., 2014; Burlando et al., 2019). Conversely, positive feedback loops have been classically underestimated and assumed to occur sparingly, due to their supposed destabilizing effect in need of compensation by negative loops. However, the advent of systems biology has favored a new analysis of life complexity, by focusing not so much on the biodiversity of life constituents, but rather on the interactions that are established between them (Wolkenhauer and Mesarovic, 2005; Wolkenhauer et al., 2005). Such a new trend has proved that several life processes, especially those that produce irreversible changes, can be modeled by positive loops. A noncomprehensive list includes bistable gene expression (Olivenza et al., 2019), cell cycle (Mochida et al., 2016; Vigneron et al., 2018; Stallaert et al., 2019), mitosis (Hutter et al., 2017), cell migration (Nguyen et al., 2018), cell differentiation (Wang et al., 2009), and axon growth (Padmanabhan and Goodhill, 2018).\n\n\nA loopomic theory in pathophysiology\n\nThe accumulating evidence that loops play an essential role in several functions accomplished by living beings (El-Samad, 2021) has inspired the loopomics paradigm, i.e. the assumption that any functional element of a biological system is somehow involved in a loop mechanism, while the whole system can be conceptualized as an intertwined array of loops (Burlando, 2017). Hence, the dynamics of the whole system obey to a restricted number of rules, but nevertheless, they give rise to a highly complex biodiversity, expressed in terms of epiphenomena occurring at different dimensional scales, e.g. subcellular organelles, cells, tissues, human beings, etc. Hence, given the above dynamical behavior of functional loops, any change or transition that can be observed within the human body would be the result of a multistable positive loop system switching among different equilibrium points (Laurent and Kellershohn, 1999).\n\nThis is a completely new redefinition of life, shifting from complexity to uniformity through a comprehensive and unifying modeling in terms of loops. Such a new paradigm has deep repercussions in the field of medicine because any disease that affects a healthy organism must have at its origin an early event in the form of a change that drives the system from a physiological to an altered functional regimen. Therefore, according to the present theory this change must be driven by a positive loop.\n\nA rapidly increasing number of pathogenic processes are being modeled as bistable switches, a few representative examples of which include cancer (Kim et al., 2007; Huang et al., 2014), prion infections (Kellershohn and Laurent, 2001), immunological disorders (Beutler, 2009), dermatitis (Dominguez-Huttinger et al., 2017), neurological problems (Mucci et al., 2020), and neurodegenerative diseases (De Caluwe and Dupont, 2013; Burlando et al., 2020). In other cases, a bistable model has not been explicitly used to describe pathogenesis, but a positive loop has been nevertheless invoked (Beutler, 2009; Norwitz et al., 2019). However, this kind of approach is generally conducted on a case-by-case basis, without making any attempt at proving generalizability, despite long established evidence that could be used to move towards this direction, as explained below. First, it is obvious that diseases affecting a healthy human must involve at their origin pathophysiological changes leading to transitions from a physiological to pathological condition. Second, diseases are classifiable (e.g. https://www.who.int/standards/classifications/classification-of-diseases), i.e. they make up an ordered set, showing that the above changes are predictable. Third, diseases are recurrent through human generations, showing that pathophysiological changes depend on the activity of clonable physiological pathways that have been selected for by natural selection. Therefore, these changes must admit stability as a starting point, otherwise their selection would not have been possible. However, stability must also characterize their ending point, otherwise disease classification would not be possible. In summary, diseases depend on predictable changes carried out by multistable systems, and therefore a generalization of these processes can be achieved by using theoretical models able to develop transitions between different stable equilibrium points.\n\nA new theory can therefore be proposed, stating that any disease that affects a healthy human involves at its primary causal event a change that can be conceptually reduced to a multistable system (typically a bistable one) depending on a positive functional loop consisting of cellular, molecular, or biochemical elements interplaying with each other. Also, the mathematical study of loop dynamics can allow the identification of bifurcation parameters that drive the transition from monostability to multistability, thus allowing the switching of the system from a “physiological” to a “pathological” stable equilibrium point, or steady state. Hence, the physical correspondents of these parameters, which could be single factors or pathways, are to be recognized as best therapeutic targets, potentially allowing the achievement of disease manageability via pharmacological or non-pharmacological treatments. Moreover, this kind of system is characterized by hysteresis, i.e. the transitions from physiological to pathological steady states occur at different threshold values of the bifurcation parameter, according to the direction of movement along the steady state trajectory, and therefore, irreversibility is also possible for a strengthening of the interactions among the functional agents of the loop (Figure 1).\n\nThe illustrated system captures the essential elements of the proposed theory, though more complex loops are likely to occur in real pathophysiological processes. The loop (inset below) consists of two functional agents, indicated by X1 and X2, which may represent the amounts or activities of cells (e.g. lymphocytes), enzymes (e.g. kinases), signal molecules (e.g. interleukins), etc. In the mathematical analysis of the loop, the dynamical interactions between the functional agents are described by a system of differential equations yielding the rate of change of the functional agents. In commonly used models of biological systems dynamics, each functional agent Xi is assumed to undergo spontaneous inactivation and evolve along time with time constant τXi. The system of differential equations, in a schematic form, is the following:\n\n\n\nA possible example for the functions appearing in the differential equations is the Hill function fx=αxp1+βxp, which is a suitable model for different stimulus-response relationships in biological systems (Ferrante et al., 2009; Huang et al., 2014). However, f(X1) and f(X2) need not have the same form. By solving the system of differential equations, the trajectories followed by the system in the X1/X2 phase portrait can be traced (small plots at the top), showing the attraction basins of the stable equilibrium points (full dots), i.e. the system steady-states, and an unstable equilibrium point (empty dot). The bifurcation diagram (large plot below) shows the plot of the equilibrium values of X1 as a function of a bifurcation parameter, represented by one of the parameters of the differential equations. A similar plot can be derived for X2. The continuous lines represent stable equilibrium points and the dashed line unstable equilibrium points. As the bifurcation parameter increases (or decreases, depending on cases), the system can change from monostable (left), i.e. having a single stable equilibrium point, to bistable (middle), i.e. with two stable equilibrium points and an intermediate unstable equilibrium point, and eventually to monostable again (right). The two alternative stable equilibrium points represent the physiological and pathogenic conditions. Therefore, depending on the direction of variation, the bifurcation factor creates the conditions for the switch from physiological to pathogenic condition, or promotes the backward transition, respectively. The system also shows hysteresis, i.e. as shown in Figure 1, as the bifurcation parameter increases, and in the absence of other stimuli, the system is forced to abruptly jump from the physiological to the pathological condition at bifurcation point 2. However, once the system resides on the pathological condition, the reverse transition to physiological condition requires that the bifurcation parameter decreases until it reaches bifurcation point 1.\n\nIn operational terms, if a completely new disease is discovered, what is the main question to be addressed in order to manage it? Of course, this question concerns etiology, i.e. identifying the pathophysiological process leading to the primary causes of the disorder. Until we have an answer to this question, few possibilities exist to find a complete solution to the disease, and this is the main drawback that frequently affects biomedical research. According to the herein proposed theory, the above unexplored disease should be investigated by using currently available and newly acquired knowledge through the following steps from bench to bed: (i) localize the site of insurgence, (ii) identify major biological (molecular) factors involved, (iii) identify a positive loop (or a loop system collectively behaving as a positive loop) that could allegedly drive the pathogenic transition, (iv) develop formal mathematical analysis of the loop leading to the identification of critical bifurcation parameter(s), (v) design in vitro and/or in vivo experiments to verify that the loop and its bifurcation parameter(s) are responsible for the development of the disease. If successfully accomplished, these investigations would open the way to finely oriented pharmacological and pharmaceutical research directed to bifurcation parameter(s), followed by clinical trials.\n\nThe described approach is assumed to be the most suitable to fit the nature of life processes and therefore, given that health problems also derive from life processes, it is expected to maximize the chance of finding solutions to diseases. Although not intentionally hinged in the present theory, a study in this direction has already been done through a large-scale characterization of bistable switch-like, gene-gene interactions in cancer progression (Shiraishi et al., 2010).\n\n\nConclusions\n\nA huge set of data from systems biology suggests that changes occurring within living systems are the result of the activity of multistable switches depending on positive functional loops. The theory of systems and control provides a description of loop system dynamics in terms of a restricted set of mathematical rules, providing a basis for bypassing the drawbacks caused by the biodiversity of life constituents, spanning from molecules to individuals. Such a new conceptualization, focused on interactions rather than on objects, results in a recodification of life in terms of biouniformity, instead of biodiversity, allowing the application of unifying formal analyses on a ground where this approach seemed almost impossible. Accordingly, provided that pathogenic processes affecting healthy individuals must themselves be the result of functional changes, a general theory of pathogenesis can be formulated. Based on this theory, the enormous diversity of pathologies that have been described in the human body can be essentially reduced to a single, unifying pathogenic model, of which any disease would represent a variant. Consequently, each disease can be approached by a standard procedure of analysis aimed at identifying positive loops and their bifurcation parameters, thus addressing critical pharmacological targets. Such a theoretical framework could have a huge impact on pharmacology, medicinal chemistry, and clinical practice. Therefore, given the impasse of many approaches to the study of pathogenesis, this theory would deserve to be validated on specific cases by preclinical and clinical studies, in order to explore the extent to which it can be generalized and represent a turning point in biomedical and pathophysiological research.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgments\n\nI wish to thank Giulia Giordano and Franco Blanchini for their advice and suggestions.\n\n\nReferences\n\nBeutler B: Microbe sensing, positive feedback loops, and the pathogenesis of inflammatory diseases. Immunol. Rev. 2009; 227(1): 248–263. PubMed Abstract | Publisher Full Text\n\nBianconi E, Piovesan A, Facchin F, et al.: An estimation of the number of cells in the human body. Ann. Hum. Biol. 2013; 40(6): 463–471. Publisher Full Text\n\nBlanchini F, Franco E, Giordano G: A structural classification of candidate oscillatory and multistationary biochemical systems. Bull. Math. Biol. 2014; 76(10): 2542–2569. PubMed Abstract | Publisher Full Text\n\nBurlando B: Loopomics: a new functional approach to life. J. Appl. Physiol. (1985). 2017; 123(4): 1011–1013. PubMed Abstract | Publisher Full Text\n\nBurlando B, Blanchini F, Giordano G: Loop analysis of blood pressure/volume homeostasis. PLoS Comput. Biol. 2019; 15(9): e1007346. PubMed Abstract | Publisher Full Text\n\nBurlando B, Milanese M, Giordano G, et al.: A multistationary loop model of ALS unveils critical molecular interactions involving mitochondria and glucose metabolism. PLoS One. 2020; 15(12): e0244234. PubMed Abstract | Publisher Full Text\n\nDe Caluwe J, Dupont G: The progression towards Alzheimer's disease described as a bistable switch arising from the positive loop between amyloids and Ca(2+). J. Theor. Biol. 2013; 331: 12–18. PubMed Abstract | Publisher Full Text\n\nDominguez-Huttinger E, Christodoulides P, Miyauchi K, et al.: Mathematical modeling of atopic dermatitis reveals “double-switch” mechanisms underlying 4 common disease phenotypes. J. Allergy Clin. Immunol. 2017; 139(6): 1861–1872.e7. PubMed Abstract | Publisher Full Text\n\nEl-Samad H: Biological feedback control-Respect the loops. Cell Syst. 2021; 12(6): 477–487. PubMed Abstract | Publisher Full Text\n\nFerrante M, Migliore M, Ascoli GA: Feed-forward inhibition as a buffer of the neuronal input-output relation. Proc. Natl. Acad. Sci. U. S. A. 2009; 106(42): 18004–18009. PubMed Abstract | Publisher Full Text\n\nHuang B, Lu M, Jolly MK, et al.: The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition. Sci. Rep. 2014; 4: 6449. PubMed Abstract | Publisher Full Text\n\nHutter LH, Rata S, Hochegger H, et al.: Interlinked bistable mechanisms generate robust mitotic transitions. Cell Cycle. 2017; 16(20): 1885–1892. PubMed Abstract | Publisher Full Text\n\nKellershohn N, Laurent M: Prion diseases: dynamics of the infection and properties of the bistable transition. Biophys. J. 2001; 81(5): 2517–2529. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKim D, Rath O, Kolch W, et al.: A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK pathways. Oncogene. 2007; 26(31): 4571–4579. PubMed Abstract | Publisher Full Text\n\nLaurent M, Kellershohn N: Multistability: a major means of differentiation and evolution in biological systems. Trends Biochem. Sci. 1999; 24(11): 418–422. PubMed Abstract | Publisher Full Text\n\nMochida S, Rata S, Hino H, et al.: Two Bistable Switches Govern M Phase Entry. Curr. Biol. 2016; 26(24): 3361–3367. PubMed Abstract | Publisher Full Text\n\nMucci V, Indovina I, Browne CJ, et al.: Mal de Debarquement Syndrome: A Matter of Loops? Front. Neurol. 2020; 11: 576860. PubMed Abstract | Publisher Full Text\n\nNguyen LK, Kholodenko BN, von Kriegsheim A : Rac1 and RhoA: Networks, loops and bistability. Small GTPases. 2018; 9(4): 316–321. PubMed Abstract | Publisher Full Text\n\nNorwitz NG, Mota AS, Norwitz SG, et al.: Multi-Loop Model of Alzheimer Disease: An Integrated Perspective on the Wnt/GSK3beta, alpha-Synuclein, and Type 3 Diabetes Hypotheses. Front. Aging Neurosci. 2019; 11: 184. PubMed Abstract | Publisher Full Text\n\nOlivenza DR, Nicoloff H, Sanchez-Romero MA, et al.: A portable epigenetic switch for bistable gene expression in bacteria. Sci. Rep. 2019; 9(1): 11261. PubMed Abstract | Publisher Full Text\n\nPadmanabhan P, Goodhill GJ: Axon growth regulation by a bistable molecular switch. Proc. Biol. Sci. 2018; 285(1877): 20172618. PubMed Abstract | Publisher Full Text\n\nShiraishi T, Matsuyama S, Kitano H: Large-scale analysis of network bistability for human cancers. PLoS Comput. Biol. 2010; 6(7): e1000851. PubMed Abstract | Publisher Full Text\n\nStallaert W, Kedziora KM, Chao HX, et al.: Bistable switches as integrators and actuators during cell cycle progression. FEBS Lett. 2019; 593(20): 2805–2816. PubMed Abstract | Publisher Full Text\n\nVigneron S, Sundermann L, Labbe JC, et al.: Cyclin A-cdk1-Dependent Phosphorylation of Bora Is the Triggering Factor Promoting Mitotic Entry. Dev. Cell. 2018; 45(5): 637–650.e7. PubMed Abstract | Publisher Full Text\n\nvon Bertalanffy L : General System Theory: Foundations, Development, Applications. New York, NY, USA:George Braziller Inc;1968.\n\nWackerhage H, Hoffmann U, Essfeld D, et al.: Recovery of free ADP, Pi, and free energy of ATP hydrolysis in human skeletal muscle. J. Appl. Physiol. (1985). 1998; 85(6): 2140–2145. PubMed Abstract | Publisher Full Text\n\nWang L, Walker BL, Iannaccone S, et al.: Bistable switches control memory and plasticity in cellular differentiation. Proc. Natl. Acad. Sci. U. S. A. 2009; 106(16): 6638–6643. Publisher Full Text\n\nWolkenhauer O, Mesarovic M: Feedback dynamics and cell function: Why systems biology is called Systems Biology. Mol. BioSyst. 2005; 1(1): 14–16. PubMed Abstract | Publisher Full Text\n\nWolkenhauer O, Sreenath SN, Wellstead P, et al.: A systems- and signal-oriented approach to intracellular dynamics. Biochem. Soc. Trans. 2005; 33(Pt 3): 507–515. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "146862",
"date": "18 Aug 2022",
"name": "Rodrigo A. Mora-Rodríguez",
"expertise": [
"Reviewer Expertise Systems Biology",
"miRNA research",
"cancer",
"virology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a beautiful opinion article accurately summarizing what we, many systems biologists think and see biological complexity.\n\nComplexity implies that almost everything is connected within an interaction network and the influence of a perturbation could impact other parts of that network. This network could offer robustness but also, beyond certain level of perturbation lead to a different steady state.\n\nAlthough very interesting, I think that the problem is the word theory. To speak about a general theory, more systematic (and directed) validation is required. I would suggest to change that word to \"hypothesis\" in the title and along the text.\nApart from that, this hypothesis is fantastic and I would just like to see something more about how the author suggest that bistability can be identified, specially in complex loops since this is one the main limitations of the study of bistability. Perhaps the work of Angeli et al could be of some interest for the author.1\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "8654",
"date": "23 Aug 2022",
"name": "Bruno Burlando",
"role": "Author Response",
"response": "I wish to thank the reviewer for the appreciation of my article. Based on the peer review comments, I have prepared a new version of the article. Responses to the reviewer's comments and main changes in the new version follow (author in bold): Rev. Complexity implies that almost everything is connected within an interaction network and the influence of a perturbation could impact other parts of that network. This network could offer robustness but also, beyond certain level of perturbation lead to a different steady state. Author. In the new version I have more accurately addressed the problem of complexity in the interactions among biological functional agents. Specifically, input/output monotonicity has been addressed, being a distinctive feature of these interactions and a key element for the possibility of realizing mathematical models able to provide information for operational interventions on these systems, e.g. resolving a pathological condition. Rev. Although very interesting, I think that the problem is the word theory. To speak about a general theory, more systematic (and directed) validation is required. I would suggest to change that word to \"hypothesis\" in the title and along the text. Author. The word \"theory\", when referred to the present proposal, has been substituted with \"hypothesis\". By this way, also the title has been modified. Rev. Apart from that, this hypothesis is fantastic and I would just like to see something more about how the author suggest that bistability can be identified, specially in complex loops since this is one the main limitations of the study of bistability. Perhaps the work of Angeli et al could be of some interest for the author. Author. Together with complexity, the issue of bistability has also been addressed and it has been explained more clearly how it is linked to the identification of bifurcation parameters. These latter are a crucial element of the proposed hypothesis, as being considered main sites of \"engineering\" interventions on biological systems, obviously including pathological conditions. The suggested reference has been quoted, together with a few others."
}
]
}
] | 1
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https://f1000research.com/articles/11-906
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https://f1000research.com/articles/11-766/v1
|
11 Jul 22
|
{
"type": "Case Report",
"title": "Case Report: Nasopharyngeal carcinoma has metastasis to the orbit, consequences in anaemia: A paediatric unusual case of Bangladesh.",
"authors": [
"Mohammad Ashraful Amin",
"Sabrina Nahin",
"Atia Sharmin Bonna",
"Mohammad Delwer Hossain Hawlader",
"Sabrina Nahin",
"Atia Sharmin Bonna",
"Mohammad Delwer Hossain Hawlader"
],
"abstract": "Background: Although nasopharyngeal carcinoma (NPC) has a significant risk of spreading to other parts of the body early, orbital and ocular surrounding tissues metastases are uncommon. Case Report: This paper described a 16-year-old patient diagnosed with a locally advanced NPC and ocular metastasis and was treated with neoadjuvant chemotherapy treatment. One of the rare early presentations is orbital metastases with vision problems. Discussion: Orbital metastases in children are considerably more uncommon. Cachexia and malnutrition are prevalent problems in people with cancer, affecting life and longevity. Anaemia is a severe issue for nasopharyngeal cancer patients undergoing chemotherapy or radiotherapy. Conclusion: Orbital metastases frequently arise in advanced stages of the disease and in the scenario of many metastases the persistence of therapy and the nasopharyngeal cancer patient's standard of living is linked to the occurrence of anaemia. In addition, to predict the prognosis of individuals with NPC, pretreatment laboratory profiles should be evaluated.",
"keywords": [
"Chemotherapy",
"Imaging",
"Nasopharyngeal Carcinoma",
"Orbital Metastases",
"Radiotherapy."
],
"content": "Introduction\n\nEach year, around 129,000 new instances of nasopharyngeal carcinoma (NPC) are discovered around the world,1 a number of cases have been found in Asia.2 Heritability, environmental exposures, and Epstein-Barr virus (EBV) infection are all potential causes for NPC (EBV).3 The prevalence of Epstein-Barr virus (EBV)-associated nasopharyngeal carcinoma (NPC) in endemic Epstein-Barr virus (EBV)-infected people varies widely around the world.4 NPC affects one out of every 100,000 people worldwide.5 There was only one case of nasopharyngeal cancer incidence (0–14 years) and four cases (15–19 years) by diagnosis period in Bangladesh from 2001 to 2014.6 The common sites of distant metastasis of NPC are the bones, lungs, liver, and retroperitoneal lymph nodes.7 Nasopharyngeal carcinoma (NPC) is a tumour that develops from the nasopharyngeal epithelial cells. The nasal chamber, nasopharynx, pterygopalatine fossa, and apex of the orbital could all be affected by NPC.8 Ocular metastasis, on the other hand, is uncommon. Patients having NPC possess 1-year and 5-year overall survival of 92% and 70%, correspondingly, based on current screening and diagnostic procedures, and 20% to 25% of survivors will demonstrate metastatic diseases.9 In this case, we gathered information from patients with NPC eye metastasis (EM) and analyzed blood concentrations of EBV potential variables to determine their predictive usefulness for identifying NPC. Merely very few cases of paediatric nasopharyngeal carcinoma (NPC) disseminated to the ocular have been reported to our knowledge.\n\n\nCase description\n\nA 16-year-old child was admitted to the hospital with nasopharyngeal carcinoma metastasis to the eye. The patient had no known significant medical, family cancer or smoking history. In 2019, a 14-year-old child had a growing lump in his right cervical region below the right ear. He had gradually developed pain on that swelling. Then his family member obtained homoeopathy medicine treatment because of these concerns. One week later, he developed significant bleeding from the mouth and nose. As his complaints were not cured, his family went to ENT Head & Neck Specialist, Anwar khan modern hospital, Dhaka. Examination revealed mental wellbeing and several lymphadenopathies of which the largest was seen in the right cervical region. The subject’s entire system evaluations were also normal. Then Fiber Optic Laryngoscopy (FOL) was done on 8 July, 2019 was normal. Later CT of Nasopharynx done on 22 July 2019 revealing soft tissue inflammatory mass at the nasopharynx and suspected for carcinoma (Table 1). Excisional biopsy was recommended by an ENT Head and Neck Specialist resulting in Metastatic carcinoma, nasopharyngeal type (Table 1). In mid-August 2019, blood test for EBV ab (Epstein Barr Virus Antibody) revealed IgG- 112 (Positive) IgM- <5.0 (Negative) and a Biochemistry of the blood was performed (Table 2). From 20 August 2019, He had a minor hearing impairment, so an audiogram was performed, but the results were normal. On 31 August 2019, he went to National Institute of Cancer Research & Hospital (NICRH) and started chemotherapy (Table 3). Next cycle he went to Bangabandhu Sheikh Mujib Medical University (BSMMU) and Radiation treatment on NICRH (Table 3).\n\n\n\n• Mass at right frontal sinus & anterior part of the ethmoidal sinus with epidural extension into the lower part of right anterior cranial fossa & extraconal compartment of right orbit.\n\n• Bilateral maxillary, ethmoidal, sphenoidal & right frontal sinusitis.\n\n• No remarkable abnormality in the brain.\n\n\n\n• No focal brain lesions.\n\n• Suggestive of maxillary, ethmoidal and frontal sinusitis with possible neoplastic lesion in the frontoethmoidal sinuses.\n\n\n\n• Metastatic nasopharyngeal carcinoma.\n\n\n\n• Normal hearing in left ear\n\n• Mild conducting hearing loss in right ear\n\n\n\n• Soft tissue inflammatory mass at Nasopharynx with congenital lymphadenopathy (II, III level)\n\n• Right sided maxillary sinusitis\n\n\n\n• Inj. Cisplatin (120 mg)\n\n• 5FU (1500 mg)\n\n\n\n• Inj. Paclitaxel (270 mg)\n\n• Inj. Cisplatin (35+35+35)\n\n• Inj. G-CSF (Granulocyte colony-stimulating factor)\n\n\n\n• Inj. Gemcitabine (1200 mg)\n\n• Inj. Oxaliplatin (120 mg)\n\n\n\n• Inj. Paclitaxel (270 mg)\n\n• Inj. Cisplatin (35+35+35)\n\n• Inj. G-CSF\n\nThe patient was diagnosed with nasopharyngeal cancer in July 2019, and treatment began in August 2019 with cisplatin, Fluorouracil (5FU), Paclitaxel (PTX), Granulocyte colony-stimulating factor (G-CSF or GCSF), Gemcitabine and radiotherapy for seven sessions (Table 3). Previously regarded was used in two further cycles of adjuvant chemotherapy. After two courses of palliative chemotherapy, a partial response was observed. Complete blood count, peripheral blood smear and biochemical examinations were normal until December 2019.\n\nUnilateral uncomfortable palpable globs in the medial canthal area were noticed four months after the chemotherapy was finished in December 2019. He had history of eye bleeding, diplopia, and headaches. He arrived at the emergency room with a severe red eye and edema on his right side. He had noticed uncomfortable eyelid redness and swelling in his right eye, which was quickly obscuring his vision. He described involuntary tear production and complete visual impairment in his right eye, but no purulent discharges the patient had reported a decrease of appetite and weight loss in the prior three months. The right conjunctiva exhibited a vast, raised, and rough lesion that completely obscured the right eye on examination (Figure 1). The ulcerated tumor was painful.\n\nAn MRI of Brain & PNS with the base of the skull with contrast, Bone Scintigraphy (Figure 2), Histopathology (Sinonasal mass frontal right), positron emission tomography (PET)/CT scan, Echocardiography, Chest X-ray were all performed, which revealed in the (Table 1).\n\nHowever, his health deteriorated for four months from August to December 2021, with complete loss of right eye vision, low nutritional intake, lethargy, cachexia, and weight loss. In the right eye, ocular motion revealed unilaterally limited movement and no light perception. According to a CT scan and histology, the nasopharyngeal mass had increased, and there were metastases to the eye. A continuation of chemoradiotherapy cycle was started for him. He had a history of considerable fresh blood loss from the eye without any contact or trauma from August to December 2021, for which he received four blood transfusions because his Hb was 4.2 mg/dl at the time. Patient is now residing at home and receiving chemotherapy, blood transfusions, and other essential investigations in the hospital on an out-of-hospital basis.\n\n\nDiscussion\n\nNPC is rare cancer that affects just a small percentage of Bangladeshis. In terms of disease presentation, it is complex and one-of-a-kind. Neck swelling is the most prevalent presenting complaint (57.2%), followed by nasal symptoms (19.5%), headache (14.3%), and auditory symptoms (14.3%), aural symptoms (7.2%) and about 5.4% of people had ophthalmic manifestations.10 NPC has the highest tendency for rapid distant metastases among all head and neck cancers, with the probability increasing with progressive disease and recurring tumors, particularly in lymph node involvement of the primary tumor, which is consistent with our case.11 Orbital metastases in children is considerably more uncommon. The most prevalent primary tumors of these paediatric age group are sarcomas and neural embryonal tumors like neuroblastoma.12 According to the most advanced N classification, individuals with lymphatic metastases and a high probability of metastatic disease had the worst outcome.13 The most common cause of therapy failure in people with NPC is distant metastases. After completing radiation and chemotherapy, around 15% to 30% of patients with NPC develop metastases.14 The lungs, liver, bones, and retroperitoneal lymph nodes are frequent locations for distant metastases.15 The median duration of survival from the discovery of distant metastasis has been estimated to be 11.2 months for bone metastasis, 16.3 months for lung metastasis, and 3.2 months for liver metastasis.7 There were no metastases in the common areas in the case report mentioned here. On the other side, orbit intervention, may arise by direct extension through various paths, based on the surface area of the initial tumor. The pterygopalatine fossa and infratemporal fossa are the most common, followed by the inferior orbital fissure, in which most posterior section corresponds to the orbital apex. These ocular metastases have a wide range of clinical manifestations.11 Practically, orbital tumors and orbital metastases often present with an early onset of rapidly progressing symptoms. Most metastases entered intra/extraconal orbital soft tissues unilaterally, leading to globe dislocation with proptosis, diplopia, and reduced eye movement. Direct compression of the optic nerve, most usually at the ocular apex, resulted in Relative Afferent Pupillary Defect (RAPD) and vision loss, both of which significantly influenced on the victims’ clinical status.16 Nasal endoscopy is used to detect the presence of a mass, followed by cross-sectional imaging such as a CT scan, MRI, or PET for TNM staging. When detecting distant metastases, PET is more sensitive and accurate than MRI. Biopsy offers the necessary histopathological diagnostic for therapy planning. The results of radiological and histological tests are used to guide treatment decisions. The preferred treatment for NPC and associated regional nodal metastases is radiotherapy. Chemotherapy is used as an adjuvant for cancers that have progressed. Biopsy is the most common reason for surgery.17 Almost all metastases will emerge within three years, even with adequate treatment. The major component of NPC death is tumor metastasis.18 Radiotherapy is still the most common treatment for NPC. Because of the tumor’s deep anatomical position, a substantial cumulative amount of radiation is required to provide good therapeutic benefits. However, because the tumor is close to the eyes, radiation may affect the structure and function of the eyes.19 Eye discomfort caused by EM is indistinguishable from radiation-induced eye issues in people with NPC. As a result, efficient biological indicators with high specificity and sensitivity would be beneficial in determining whether radiation or NPC EM caused the eye symptoms.\n\nChemotherapy is one of the treatments for nasopharyngeal cancer that has progressed. The medications used in cancer treatment act by harming, inhibiting, or stopping the spread of cancer cells that are rapidly growing. On the other hand, chemotherapy medications damage both cancer cells and healthy tissue. They can harm the oral and gastrointestinal mucosa, hair follicles, reproductive system, and erythroid system in high enough doses. Malnutrition in cancer patients has many causes that are complex and multifactorial. Tumour cells secrete the chemicals serotonin and bombesin, which decrease appetite and cause anorexia. Nasopharyngeal cancer can also lead to inflammation of the oral mucosa and digestive mucous membranes, discomfort, decreased salivary gland secretion, psychologic distress, and tooth decay. Reduced oral intake can lead to a loss of strength, infection, and malnutrition. The tumour on NPC is weak, with enhanced neovascularization and a high risk of bleeding. Anaemia may develop as a result of chronic bleeding.20 In patients with nasopharyngeal cancer, anaemia is recognized as one of the predictive variables that affect numerous markers of life expectancy. A study in China discovered a substantial difference in overall survival between patients with Hb less than 11 g/dl and those with more than 11 g/dl, with 70% and 78%, respectively. Another Chinese study discovered a substantial difference in response to intensity-modulated radiation therapy among patients with and without anaemia. Anaemia patients had a complete response of 69.8% and a partial response of 30.2%, respectively, whereas non-anaemia patients had a complete response of 85.7% and partial response 14.3%. This was a statistically significant difference (p=0.02).20 In our patient’s case, he had a history of blood loss while touching the mass, even though it was a modest fresh quantity of blood loss, and he had a history of a decrease in food taste and losing weight while undergoing chemotherapy. He might develop anaemia due to external blood loss and chemotherapy, for which he had received blood transfusions multiple times.\n\nThe radiographic examination is necessary for the diagnosis of the disease as well as the evaluation of local bone and extra-bony expansion. The most common methods of examining suspected ocular lesions are computed tomography (CT) and magnetic resonance imaging (MRI). MRI provides the best resolution of orbital soft tissues, despite CT being frequently the primary choice in examining the orbit. A CT scan may be more effective in patients with suspected bone involvement. The anterior region of the orbit is where metastatic lesions are most frequent. These lesions are distinguished by their local aggressiveness, as evidenced by extraocular muscles and bone invasion.12\n\nThe uncommon occurrence of NPC metastasis in the eye poses a significant challenge to doctors, and at its early stage, it can be fatal.21 Due to a lack of specifics on radiation dosimetry, this study has a limitation. More detailed research into this area of interest is needed to help manage this severe consequence and offer the best and safest method for ocular metastatic surveillance. In most cases, histological proof is not required after a thorough radiological examination. In fact, in patients with advanced disease, a biopsy is rarely required to demonstrate metastasis. Biopsy may be required in some cases to make therapy decisions. This may interest in newly metastatic breast cancer, especially if ocular biopsy is proven to be more accessible, similar to executing novel targeted therapy by giving genetic studies of the tumour. In light of our patient’s unilaterality, we regarded his orbital involvement as metastatic after of the extension assessment.\n\nA comprehensive history, a careful ophthalmological examination, and an overall physical assessment are required when orbital or ocular metastases is anticipated. It is vital to refer patients with no known history of cancer to an oncologist for a simultaneous broad extension screening to investigation of the main tumor. The goal of orbital metastasis treatment is to improve the patient’s quality of life while preserving their functional prognosis. Radiotherapy and chemotherapy may be used. Since NPC is recognized for its radio sensitivity, the most common treatment for orbital metastases from NPC is radiotherapy. However, chemotherapy is still used in certain individuals. Limitation, the presence of cranial nerve palsy is not evaluated in our study.\n\n\nConclusion\n\nNasopharyngeal cancer can cause a wide range of symptoms which are not always associated to the nose. One of the rare early presentations is orbital metastases with vision problems. However, it is important to keep in mind that tumor recurrence and eye metastasis are also conceivable. Orbit is a unique location. Nasopharyngeal carcinoma seldom invades the orbit. Ophthalmic symptoms from orbital invasion, on the other hand, can be the first sign of NPC. As a result, it is critical to distinguish this disease entity, particularly in younger individuals, where malignancy is often overlooked as a possible differential diagnosis. The prognosis is generally dangerous and varies depending on the source malignancy. Furthermore, orbital metastases frequently arise in advanced stages of disease and in the scenario of many metastases. In terms of improving the function and quality of life, palliative radiation and chemotherapy are used. Despite recent therapy advancements, these individuals’ expectancy remains limited.\n\n\nConsent\n\nThe patient’s written informed consent for publishing of this case report, as well as images, was acquired.\n\n\nAuthor contributions\n\nMohammad Ashraful Amin: Conceptualization, Writing- Original draft preparation: Mohammad Ashraful Amin, Sabrina Nahin: Visualization and Supervision.: Mohammad Delwer Hossain Hawlader, Mohammad Ashraful Amin, Sabrina Nahin, Atia Sharmin Bonna, Mohammad Delwer Hossain Hawlader: Writing- Reviewing and Editing.\n\n\nData availability statement\n\nData can be shared based on the reader’s reasonable request and priority base and some restrictions will apply. All data related to the case are available; Amin, Mohammad Ashraful (2022), “Nasopharyngeal carcinoma has metastasis to the orbit, consequences in anaemia: A paediatric unusual case of Bangladesh.”, Mendeley Data, V1, doi: https://doi.org/10.17632/kw4fdmdgy8.1.\n\n\nEthical approval\n\nThe article is about a case study. As a result, our Ethics Committee’s consent was not required.",
"appendix": "References\n\nWorld Cancer Research Fund International: World Cancer Research Fund International:[cited 2021 06/12/2021].Reference Source\n\nZhang L, Chen Q, Liu H: Emerging treatment options for nasopharyngeal carcinoma. Drug Des. Devel. Ther. 2013; 7: 37–52. PubMed Abstract | Publisher Full Text\n\nTsao SW, Yip YL, Tsang CM, et al.: Etiological factors of nasopharyngeal carcinoma. Oral Oncol. 2014; 50(5): 330–338. PubMed Abstract | Publisher Full Text\n\nMiller JA, Le Q-T, Pinsky BA, et al.: Cost-effectiveness of nasopharyngeal carcinoma screening with Epstein-Barr virus polymerase chain reaction or serology in high-incidence populations worldwide. JNCI: Journal of the National Cancer Institute. 2021; 113(7): 852–862. PubMed Abstract | Publisher Full Text\n\nAzizah A, Hashimah B, Nirmal K, et al.: Malaysia National cancer registry report (MNCR).2019.\n\nChoudhury N, Selimuzzaman M, Belayet M: Childhood cancer a big burden of low middle income settings in Bangladesh: evidence from cross sectional study in Dhaka, Bangladesh. IOSR. J. Dent. Med. Sci. 2019; 18(5): 52–61.\n\nHuang C-J, Leung SW, Lian S-L, et al.: Patterns of distant metastases in nasopharyngeal carcinoma. Kaohsiung J. Med. Sci. 1996; 12(4): 229–234. PubMed Abstract\n\nHsu W-M, Wang A: Nasopharyngeal carcinoma with orbital invasion. Eye. 2004; 18(8): 833–838. PubMed Abstract | Publisher Full Text\n\nChen L-C, Chen C-C, Liang Y, et al.: A novel role for TNFAIP2: its correlation with invasion and metastasis in nasopharyngeal carcinoma. Mod. Pathol. 2011; 24(2): 175–184. PubMed Abstract | Publisher Full Text\n\nSuzina S, Hamzah M: Clinical presentation of patients with nasopharyngeal carcinoma. Med. J. Malaysia. 2003; 58(4): 539–545.\n\nGuezar M, Khalfi S, Erraisse M, et al.: Orbital Metastasis of a Pediatric Nasopharyngeal Carcinoma: A Rare Case Report.\n\nAllen RC: Orbital metastases: When to suspect? When to biopsy? Middle East Afr. J. Ophthalmol. 2018; 25(2): 60–64. PubMed Abstract | Publisher Full Text\n\nLee A, Au J, Teo P, et al.: Staging of nasopharyngeal carcinoma: suggestions for improving the current UICC/AJCC Staging System. Clin. Oncol. 2004; 16(4): 269–276. PubMed Abstract | Publisher Full Text\n\nChen X, Li J, Lin S, et al.: Expert consensus on the diagnosis of recurrent or metastatic nasopharyngeal carcinoma. Chin. J. Radiat. Oncol. 2018; 27(1): 7–15.\n\nZeng L, Tian Y-M, Huang Y, et al.: Retrospective analysis of 234 nasopharyngeal carcinoma patients with distant metastasis at initial diagnosis: therapeutic approaches and prognostic factors. PLoS One. 2014; 9(9): e108070. PubMed Abstract | Publisher Full Text\n\nPalmisciano P, Ferini G, Ogasawara C, et al.: Orbital Metastases: A Systematic Review of Clinical Characteristics, Management Strategies, and Treatment Outcomes. Cancers. 2022; 14(1): 94. Publisher Full Text\n\nLee AW, Lin JC, Ng WT: Current management of nasopharyngeal cancer. Seminars in radiation oncology. Elsevier;2012.\n\nBagatzounis A, Erakleous E, Michaelides I: Epidural metastasis in nasopharyngeal carcinoma. Strahlenther. Onkol. 2003; 179(2): 123–128. PubMed Abstract | Publisher Full Text\n\nPeng S-J, Wang C-F, Yu Y-J, et al.: CYFRA21-1/TG ratio as an accurate risk factor to predict eye metastasis in nasopharyngeal carcinoma: A STROBE-compliant article. Medicine. 2020; 99(46): e22773. PubMed Abstract | Publisher Full Text\n\nKadriyan H, Sulaksana MA, Lestarini IA, et al., editors: Incidence and characteristics of anemia among patients with nasopharyngeal carcinoma in Lombok, Indonesia.AIP Conference Proceedings.AIP Publishing LLC;2019.\n\nLi J-X, Lu T-X, Huang Y, et al.: Clinical characteristics of recurrent nasopharyngeal carcinoma in high-incidence area. Sci. World J. 2012; 2012: 1–8. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "149096",
"date": "23 Sep 2022",
"name": "Muhtarum Yusuf",
"expertise": [
"Reviewer Expertise oncology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGenerally, the case report is unique, because it is a rare case, nasopharyngeal carcinoma with orbital metastasis in paediatric. The introduction is sufficient.\nAbstract:\n\nThe conclusion of the abstract is overwritten, it should be shorter and relevant to the title. Minor point -The last sentence should be deleted\n\nCase description:\n\nMinor Point - The date, month, and year should only be mentioned at the beginning of the case, then use the description of time by mentioning the length of time, such as 2 months later, one week later\n\nDiscussion :\nThere are several major points:\nIn the discussion, there was no further explanation about the importance of EBV IgM and IgG antibodies analysis, even though it was mentioned in the introduction. If there is no relevance, this point in the introduction should be removed.\n\nIt’s not mentioned about the patient’s response to therapy in this patient, whether it is complete response, partial response, no response, or progressive.\n\nConclusion:\nMajor point: The conclusion is too long, and should be more relevant to the title of this case.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "8835",
"date": "30 Sep 2022",
"name": "Mohammad Ashraful Amin",
"role": "Author Response",
"response": "Dear Muhtarum Yusuf, Airlangga University, Surabaya, Indonesia, Greetings! First of all, we would like to express our sincere thanks and gratitude for giving us the opportunity to revise our manuscript F1000Research. We found your comments to be helpful and have carefully considered and responded to each suggestion. We have gone through all comments and concerns raised by our respected reviewer and incorporated them. All responses to the comments can be found below. Sincerely yours *Corresponding author: Dr. Mohammad Ashraful Amin, Abstract: The conclusion of the abstract is overwritten, it should be shorter and relevant to the title. Minor point -The last sentence should be deleted Response: Thank you for your response. As per your suggestion, we have modified it as required in the manuscript. Case description: Minor Point - The date, month, and year should only be mentioned at the beginning of the case, then use the description of time by mentioning the length of time, such as 2 months later, one week later Response: Thank you for your response. As per your suggestion, we have modified it as required in the manuscript. Discussion: There are several major points: In the discussion, there was no further explanation about the importance of EBV IgM and IgG antibodies analysis, even though it was mentioned in the introduction. If there is no relevance, this point in the introduction should be removed. Response: Thank you for your response. As per your suggestion, we have modified it as required in the discussion part of the manuscript. It’s not mentioned about the patient’s response to therapy in this patient, whether it is complete response, partial response, no response, or progressive. Response: Thank you for your response. As per your suggestion, we have modified it as required in the case report part and discussion part of the manuscript. Conclusion: Major point: The conclusion is too long, and should be more relevant to the title of this case. Response: Thank you for your response. As per your suggestion, we have modified it as required in the conclusion part of the manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/11-766
|
https://f1000research.com/articles/11-133/v1
|
02 Feb 22
|
{
"type": "Method Article",
"title": "Laboratory protocol for the digital multiplexed gene expression analysis of nasopharyngeal swab samples using the NanoString nCounter system",
"authors": [
"Marilina García Aranda",
"Inmaculada López-Rodríguez",
"Susana García-Gutiérrez",
"Maria Padilla-Ruiz",
"Vanessa de Luque",
"Maria Luisa Hortas",
"Tatiana Diaz",
"Martina Álvarez",
"Isabel Barragan-Mallofret",
"Maximino Redondo",
"Research Network on Health Services in Chronic Diseases (Red de Investigación en Servicios Sanitarios y Enfermedades Crónicas, REDISSEC)",
"Inmaculada López-Rodríguez",
"Susana García-Gutiérrez",
"Maria Padilla-Ruiz",
"Vanessa de Luque",
"Maria Luisa Hortas",
"Tatiana Diaz",
"Martina Álvarez",
"Isabel Barragan-Mallofret",
"Maximino Redondo"
],
"abstract": "This paper describes a laboratory protocol to perform the NanoString nCounter Gene Expression Assay from nasopharyngeal swab samples. It is urgently necessary to identify factors related to severe symptoms of respiratory infectious diseases, such as COVID-19, in order to assess the possibility of establishing preventive or preliminary therapeutic measures and to plan the services to be provided on hospital admission. At present, the samples recommended for microbiological diagnosis are those taken from the upper and/or the lower respiratory tract. The NanoString nCounter Gene Expression Assay is a method based on the direct digital detection of mRNA molecules by means of target-specific, colour-coded probe pairs, without the need for mRNA conversion to cDNA by reverse transcription or the amplification of the resulting cDNA by PCR. This platform includes advanced analysis tools that reduce the need for bioinformatics support and also offers reliable sensitivity, reproducibility, technical robustness and utility for clinical application, even in RNA samples of low RNA quality or concentration, such as paraffin-embedded samples. Although the protocols for the analysis of blood or formalin-fixed paraffin-embedded samples are provided by the manufacturer, no corresponding protocol for the analysis of nasopharyngeal swab samples has yet been established. Therefore, the approach we describe could be adopted to determine the expression of target genes in samples obtained from nasopharyngeal swabs using the nCOUNTER technology.",
"keywords": [
"respiratory infection",
"nasopharyngeal swab",
"gene expression",
"Immunology",
"Digital RNA quantification"
],
"content": "Introduction\n\nNasopharyngeal swabs are essential for the accurate diagnosis of respiratory infectious diseases such as coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The samples currently recommended for the microbiological diagnosis of respiratory infectious diseases are those obtained from the upper respiratory tract (nasopharynx and oropharynx) and/or the lower respiratory tract, such as sputum, endotracheal aspirates, bronchoalveolar lavages or bronchial aspirates, especially in patients with severe respiratory disease.\n\nAlthough specimen collection can be an uncomfortable procedure for the patient it provides a valuable mixture containing biological material both from the infectious agent and from the patient. The high viral load obtained,1 the simplicity of the procedure involved and the ready availability of this type of sample in laboratories performing routine microbiological analyses make surplus biospecimens a valuable source of biologic material for conducting molecular or genetic studies of the infectious agent and the host.\n\nIn recent years, the study of selected genes by real-time PCR or genome-wide gene expression microarray analysis has been used in genetic research to detect associations between specific gene expression profiles and particular diseases. Within these technologies, the nCOUNTER® platform (NanoString Technologies, Seattle, WA) delivers direct and multiplexed measurement of gene expression, providing digital readouts of the relative abundance of mRNA transcripts simultaneously2 in a single assay, without the need for cDNA conversion or amplification of target RNA. This platform, which offers reliable sensitivity, reproducibility, technical robustness and utility for clinical application,3 is also capable of analysing RNA samples of poor quality such as fragmented RNA (35 to 50-base target-specific sequences) or cell lysates with total RNA concentrations as low as 100 ng,4 as is foreseeably the case with samples from nasopharyngeal swabs.\n\nThe nCOUNTER Human Immunology V2 CSO panel, which facilitates the study of 594 genes, including the major classes of cytokines, chemokine ligands, interferons and their receptors, the TNF-receptor superfamily, the KIR family genes and genes involved with the anti-fungal immune response, is recommended for the study of the immune response to infectious disease in samples with fragmented RNA or low RNA inputs.5 This panel can also be combined with an additional panel of 55 genes related to the human inflammatory response. Although the protocols for the study of blood or formalin-fixed paraffin-embedded samples are well known and provided by the manufacturer, no protocol for the analysis of nasopharyngeal swab samples has yet been established.\n\n\nProtocol\n\nOur study will include 250 patients admitted to the Hospital Costa del Sol (Marbella, Spain) with severe COVID-19 and positive PCR results for SARS-CoV-2. To participate in the study, all patients will receive a patient information sheet and will be asked to sign the corresponding informed consent form.\n\nThe procedure for the routine determination of SARS-CoV-2 by PCR includes taking a nasopharyngeal sample with the sterile, fine, flexible swab that is included in the specific respiratory sampling kit for viruses. According to the protocol stipulated by the Spanish Ministry of Health,1 during sampling, the swab must be introduced through the nostril, parallel to the palate, to a depth equal to the distance from the nostrils to the outer opening of the ear. The swab should be maintained inside the nostril for five seconds to allow absorption of the secretions and should then be withdrawn slowly while making 180° rotations. After taking the sample, the swab should immediately be placed in a sterile tube with 2-3 ml of viral transport medium and kept refrigerated at +4°C until it is analysed at the molecular biology and microbiology laboratory.\n\nVarious kits are currently marketed for the collection, transport, and maintenance of clinical samples until the laboratory analysis is performed, some of which include transport media with an inactivator. In the subsequent analysis of the results, it must be considered whether the use of one or other means of transport might affect the final result.\n\nWe have performed a local validation study of a subset of samples to confirm that the viral transport media brands used in our laboratory (δ-SwabTM; UTMTM-Viral Transport Media; Viroclinics Biosciences, Mwe Viral Transport Media, Vircell Transport Media) do not compromise the results obtained.\n\nTo safely handle biological samples, they must first be inactivated. With samples obtained from nasopharyngeal swabs for molecular analysis, this is usually accomplished by the addition of a chemical quencher or by heat treatment.\n\nGiven the low concentration of genetic material in nasopharyngeal swabs, together with the high presence of biologic contaminants in upper respiratory airways, we recommend heat-treatment inactivation. Various techniques have been described to perform this task without affecting the integrity of the RNA, including inactivation at 56°C for 30 minutes, at 65°C for 15 minutes, at 95°C for 5 minutes or at 98 °C for 2 minutes.6,7\n\nBefore processing the samples, it is necessary to ensure that thermal inactivation does not impair RNA integrity, which can be performed by comparing the performance of RT-PCR analysis for SARS-CoV-2 after treating a set of samples to each of the heat inactivation protocols. In our study, we performed a local validation of a subset of samples with a volume of 400 μl, which confirmed that RT-PCR sensitivity is not compromised by heat inactivation at 98°C for 2 minutes.\n\nWe performed the local validation of a subset of samples to assess the performance of both the manual and the automated procedures considered. In the first case, the extraction was performed using the RNEasy kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions, using an initial sample volume of 500 μl and a final volume of 10 μl. For automated extraction, we tested the Biorobot EZ1, also obtained from Qiagen, with an initial sample volume of 200 μl and a final volume of 60 μl. Finally, RNA extraction was performed in the MagCore robot (Magcore Lamination India Pvt. Ltd), with an initial sample volume of 200 μl or 400 μl and a final volume of 40 μl.\n\nNanoString input recommendations stipulate a total RNA concentration range of 100-125 ng and specific purity ratios of absorbance measured by spectrophotometry at 260, 280 and 230nm. Since aromatic proteins have a strong UV absorbance at 280 nm, the A260/280 ratio is generally used to assess protein contamination in a nucleic acid sample. A260/280 ratios under 1.7 indicate the presence of contaminants that can affect the result, being the A260/280 ratio of ~2.0 as the generally accepted as “pure” for RNA. In such a manner, the A260/230 ratio is used to reveal the presence of organic contaminants such as phenol or TRIzol. Generally acceptable A260/230 ratios are those in the range of 2.0-2.2.\n\nIn our local validation study, we obtained varying results for RNA concentration and purity (Table 1). As can be seen, the eluates obtained by manual extraction had neither the concentration nor the purity required by the equipment. Automated extraction with the Qiagen EZ1 kit also produced aliquots of insufficient purity, which could invalidate the analysis results in the nCounter. Finally, using the MagCore equipment, for the same final eluate volume of 40 μl, initial sample volumes of 200 μl and 400 μl were tested, with the latter obtaining the best results.\n\nWe performed a local validation study in a subset of purified RNA aliquots from heat-inactivated nasopharyngeal swabs, in order to evaluate the performance of the NanoString nCounter platform in analysing the expression of our target genes, and obtained satisfactory results.\n\nWe followed the manufacturer’s instructions, using 100 ng of total RNA. In summary, the protocol consists of the following steps:\n\n1. Preheat the thermocycler to 65°C. Thaw the kit reagents and samples for 30 minutes.\n\n2. Add 70 μl of hybridisation buffer + 28 μl of Reporter Plus to the Reporter Codeset tube. Mix gently.\n\n3. Aliquot 10 μl of Master Mix to each well of the 12-tube strip.\n\n4. Add 5 μl of the samples to each corresponding well (RNA concentration should be 100 μg/μl. Dilute out-of-range samples with RNAse-free water).\n\n5. Spin the Capture ProbeSet and Capture Plus tubes.\n\n6. Add 14 μl of Capture Plus to the Capture ProbeSet tube to create the Master Capture. Mix gently and spin the Master Mix.\n\n7. Add 3 μl of Master Capture to each well of the 12-tube strip.\n\n8. Cover the tube strip with a corresponding plug strip. Mix gently and spin slowly so that the entire volume drops to the bottom of the well, leaving no bubbles.\n\n9. Use the thermocycler to perform hybridisation with the reporter and capture probes that carry the fluorescent signals, for 16-24 hours.\n\n10. Combine pairs of probes specific for the selected genes with a series of internal controls to form a molecular barcoding, or CodeSet, allowing downstream digital detection.\n\n11. Remove excess probes, align the probe/target complexes, immobilise them in the nCounter Cartridge, and then insert them into the nCounter Digital Analyser for data collection.\n\nThe differential expression analysis data model preferentially applies the optimal statistical method per gene given the following variable distribution: 1) Mixture negative binomial model, 2) Simplified negative binomial model, 3) Log-linear model, in that order. FDR p-value adjustment will be performed according to the Benjamini-Hochberg method. All samples will be normalised using the geometric mean of the housekeeping genes.\n\n\nConclusions\n\nCOVID-19 is a major global health problem, making it necessary to develop tools to optimise healthcare and facilitate personalised treatment. From a clinical perspective, the identification of gene transcripts related to the poor prognosis of patients hospitalised with SARS-CoV-2 has undeniable practical value. This complementary information would be straightforward to design multiplexed panels and prediction tools that can be incorporated into computers used in daily practice, helping clinicians predict and identify possible outcomes and facilitating decision-making in this respect.\n\nOur study may also provide useful information to help establish the protocols of other studies based on the analysis of nasopharyngeal swab samples using the NanoString nCOUNTER platform.\n\n\nData availability\n\nNormalisation, differential expression analysis and pathway analysis can be performed with Nanostring nCounter nSolver™ 4.0 (RRID:SCR_003420), using the Nanostring Advanced Analysis Module 2.0 plugin and following the Nanostring Gene Expression Data Analysis Guidelines. Advanced Analysis Module 2.0 software uses open-source R programs for quality control, normalisation, differential data analysis, pathway scoring and gene-set enrichment analysis.\n\n\nAuthor contributions\n\nMGA, SGR, IBM, MR conceptualization of the study. SGR, MGA, MR funding acquisition. MGA, ILR, TD, VDL, IBM, MA, MLH investigation and methodology. MPR, IBM, MGA, MA contributed to data analysis. MGA, IBM, MR supervised the study and revised the manuscript. All authors read and approved the final manuscript.\n\n\nEthics\n\nOur Institutional Review Board (CEI Costa del Sol exp.003_JUL20_PI-IMMU-COVID19) approved this study in July 2020. All patients will be informed of the study and invited to participate. All participation will be subject to the provision of informed written consent.",
"appendix": "Acknowledgments\n\nWe thank Ms Alicia Aguilera and Ms Belén Sojo for their excellent technical assistance.\n\n\nReferences\n\nMinisterio de Sanidad, C.y.B.S: Documento técnico: toma y transporte de muestras para diagnóstico por PCR de SARS-CoV-2 (technical document: Collection and transport of samples for PCR diagnosis of SARS-CoV-2). Health, Ed.2020.\n\nNanoString: nCounter(R) Analysis System and FFPE Samples for Gene Expression Analysis.2012.\n\nVeldman-Jones MH, Brant R, Rooney C, et al.: Evaluating Robustness and Sensitivity of the NanoString Technologies nCounter Platform to Enable Multiplexed Gene Expression Analysis of Clinical Samples. Cancer Res. 2015; 75: 2587–2593. PubMed Abstract | Publisher Full Text\n\nKulkarni MM: Digital multiplexed gene expression analysis using the NanoString nCounter system. Curr. Protoc. Mol. Biol. 2011; Chapter 25: Unit25B.10. PubMed Abstract | Publisher Full Text\n\nNanoString: nCounter® Immunology Panel. (accessed on December 21, 2021). Reference Source\n\nBatéjat C, Grassin Q, Manuguerra J-C, et al.: Heat inactivation of the severe acute respiratory syndrome coronavirus 2. J. Biosaf. Biosecur. 2021; 3: 1–3. PubMed Abstract | Publisher Full Text\n\nAuerswald H, Yann S, Dul S, et al.: Assessment of inactivation procedures for SARS-CoV-2. J. Gen. Virol. 2021; 102. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "122369",
"date": "21 Feb 2022",
"name": "Jan Weber",
"expertise": [
"Reviewer Expertise Virology and molecular biology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors here described their protocol for RNA preparation from nasopharyngeal swabs for subsequent analysis using the NanoString nCounter Gene Expression Assay. This article is a combination of method development with a description of a study on 250 SARS-CoV-2 positive patients with severe COVID-19.\nMajor issues\nThe major criticism here is that readers will not be able to assess if the RNA preparation from nasopharyngeal swab and subsequent evaluation by NanoString platform delivered good and reliable data. Reviewer assumes that it will be part of future publication, but without this data it is difficult to judge that nasopharyngeal swabs can be used as source material for this platform. Ideally, authors can post a preprint into archives and put link here.\n\nAuthors compared manual RNEasy kit that purifies total RNA (usually from cells, tissue, etc.) with automated kits specialized for purification of viral nucleic acid. Authors should have used e.g. QIAamp MinElute Virus kit or similar for a fair comparison.\n\nAuthors mentioned the nCounter Human immunology V2 CSO panel that can analyze 594 host genes. For this panel, total RNA isolation kit would be a better choice.\n\nDid authors test the platform also with the RNAs purified from EZ1 Virus Mini kit? The A260/A230 ratio is not very good, but high A260/A280 does not necessarily indicate contaminants. Did authors get chance to check the whole UV range spectrum?\n\nIt would be beneficial to show more data about different viral transport medium, heat inactivation, different nucleic acid extraction protocol and compare their impact on results from several internal controls, rather than showing manufacturer’s instruction for NanoString assay. Was there really any change in the protocol in the case of RNA from nasopharyngeal swabs? If yes, please stress the differences only.\nMinor issues:\nAuthors should change the future tense to past tense when describing their study in paragraphs “Patients”, “Data analysis” and “Ethics”.\n\nTable 1 correct ARN to RNA.\n\nInclude number of samples “n” per each isolation method in the Table 1.\n\nMake clear protocol point no. 4. At the protocol beginning, it is mentioned using 100ng of total RNA, but no.4 talks about using 5µl of sample and RNA concentration 100µg/µl.\n\nIn the protocol include temperature and other details (such as conditions of each spin).\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Partly\n\nAre sufficient details provided to allow replication of the method development and its use by others? Partly\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? No",
"responses": [
{
"c_id": "8027",
"date": "20 Apr 2022",
"name": "Marilina García Aranda",
"role": "Author Response",
"response": "We thank the reviewer for taking the time and effort necessary to review the manuscript and sincerely appreciate all valuable comments and suggestions which will help us to improve the quality of the paper. Please find below our point-by-point responses to each of the comments: Authors here described their protocol for RNA preparation from nasopharyngeal swabs for subsequent analysis using the NanoString nCounter Gene Expression Assay. This article is a combination of method development with a description of a study on 250 SARS-CoV-2 positive patients with severe COVID-19. Major issues The major criticism here is that readers will not be able to assess if the RNA preparation from nasopharyngeal swab and subsequent evaluation by NanoString platform delivered good and reliable data. Reviewer assumes that it will be part of future publication, but without this data it is difficult to judge that nasopharyngeal swabs can be used as source material for this platform. Ideally, authors can post a preprint into archives and put link here. We agree with the reviewer. However, we would like to point out that, as a pre-protocol study, we only have preliminary results. We are currently generating additional data and we will be able to stablish more consolidated conclusions in the protocol paper. Authors compared manual RNEasy kit that purifies total RNA (usually from cells, tissue, 0etc.) with automated kits specialized for purification of viral nucleic acid. Authors should have used e.g. QIAamp MinElute Virus kit or similar for a fair comparison. We agree with the reviewer, however, due to shortage of RNA extraction kits during the COVID-19 pandemic, we were not able to use the QIAmp MinElute Virus kit. Instead, we decided to use RNeasy Mini kit based on previously published papers reporting its use as a valid alternative strategy for viral detection in sputum (DOI: 10.1016/s0166-0934(01)00284-1) or nasopharyngeal samples (https://www.biorxiv.org/content/10.1101/2020.03.20.001008v1.full.pdf), Besides, the RNeasy Mini Kit is one of the most common commercial kits and the Gold Standard for RNA extraction. We will modify the corresponding paragraphs in the text accordingly. Authors mentioned the nCounter Human immunology V2 CSO panel that can analyze 594 host genes. For this panel, total RNA isolation kit would be a better choice. We agree with the reviewer. Indeed, we used RNEasy kit that purifies total RNA. We will modify the corresponding paragraph to make this point clearer. Did authors test the platform also with the RNAs purified from EZ1 Virus Mini kit? The A260/A230 ratio is not very good, but high A260/A280 does not necessarily indicate contaminants. Did authors get chance to check the whole UV range spectrum? We are sorry we did not. Despite its affordability, rapidity and ease of use, the NanoDrop usually does not give perfect and reliable readings, especially in samples with contaminants. For this reason, we measured the A260/280 ratios to get a general idea about the best RNA extraction method within the equipment available in the molecular biology laboratory of our hospital. Once we chose the method that best suited our criteria of 260/280 ratios (1.80-2.0 nm), we assessed the quality and quantity of RNA eluates with the Agilent 2100 Bioanalyzer. We will include a new table with the corresponding results in the manuscript. It would be beneficial to show more data about different viral transport medium, heat inactivation, different nucleic acid extraction protocol and compare their impact on results from several internal controls, rather than showing manufacturer’s instruction for NanoString assay. Was there really any change in the protocol in the case of RNA from nasopharyngeal swabs? If yes, please stress the differences only. Following the recommendations of the Reviewer, we have added information regarding the impact of transport medium and the heat inactivation protocol. While the former did not influence the experiment performance, the heat inactivation protocol was selected based on the reported standards (DOI: 10.1099/jgv.0.001539). Regarding our in house modifications of the manufacturers protocol to adapt it to this specific type of sample, as the reviewer emphasizes, it is important to make them clear in the manuscript. Therefore, we have modified it including and highlighting the optimized processes. This is of high relevance given that RNA from remnant nasopharyngeal exudates is present at very low concentrations and is highly degraded; indeed the RNA integrity number was less than 6 and the DV200 was less than 30% in most of the samples, what would make them inadequate for RNAseq. These samples are also highly heterogeneous, present great variability from patient to patient, and have been transported with several types of transportation medium. Also sampling procedure varies from center to center. Moreover, the fact that only diagnostic remnants were used implied that only limited volumes were available. For these reasons, the optimization of such a method that detects enough number of genes with this type of diagnostic residual samples is of high importance for performing research in the field. Minor issues: Authors should change the future tense to past tense when describing their study in paragraphs “Patients”, “Data analysis” and “Ethics”. The original version of the manuscript corresponds to the development phase of the technique, which was carried out prior to patient recruitment, reason why “Patients” and “Ethics” sections were written in future tense. We will modify the corresponding paragraphs accordingly. Table 1 correct ARN to RNA. We apologize for the mistake and will correct the typo in the new version of the manuscript. Include number of samples “n” per each isolation method in the Table 1. We appreciate the Reviewer’s suggestion, and will include the corresponding information in the new version. Make clear protocol point no. 4. At the protocol beginning, it is mentioned using 100ng of total RNA, but no.4 talks about using 5µl of sample and RNA concentration 100µg/µl. We apologize for the mistake and will change the corresponding paragraph. In the protocol include temperature and other details (such as conditions of each spin). We agree with the Reviewer’s suggestion and will modify the protocol accordingly."
}
]
},
{
"id": "122366",
"date": "22 Mar 2022",
"name": "Tara K. Sigdel",
"expertise": [
"Reviewer Expertise Organ transplantation",
"kidney"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe method on the digital multiplexed gene expression analysis of nasopharyngeal swab samples using the NanoString nCounter system is adequately presented in the manuscript. This could be of interest to the readers of F1000Research and researchers working with gene expression of immune signature and SARS-CoV-2.\n\nI find the rationale of the protocol adequate. I find the protocol not quite complete. Such as:\n\nThe authors should provide information on any failure in extracting enough total RNA as demanded by the method.\n\nIn real-life situations it is hard to get enough RNA from 100% samples. If it was the case then it has to be stated clearly.\n\nThere is some ambiguity on the amount of total RNA. From the manuscript it appears that only 100 ng is needed. The following statement is contradicting:\n\n\"4. Add 5 μl of the samples to each corresponding well (RNA concentration should be 100 μg/μl. Dilute out-of-range samples with RNAse-free water).\"\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "8026",
"date": "20 Apr 2022",
"name": "Marilina García Aranda",
"role": "Author Response",
"response": "We thank the reviewer for the constructive comments which will help us to improve the quality of our work. We hope that the revisions in the manuscript and our accompanying responses will be sufficient to make our manuscript suitable for acceptance. Please find below our point-to-point responses to the comments. The method on the digital multiplexed gene expression analysis of nasopharyngeal swab samples using the NanoString nCounter system is adequately presented in the manuscript. This could be of interest to the readers of F1000Research and researchers working with gene expression of immune signature and SARS-CoV-2. I find the rationale of the protocol adequate. I find the protocol not quite complete. Such as: The authors should provide information on any failure in extracting enough total RNA as demanded by the method. In real-life situations it is hard to get enough RNA from 100% samples. If it was the case then it has to be stated clearly. We agree with the Reviewer and will include the success rate of the extractions performed with the MagCore robot: The success rate of extractions performed with the MagCore robot has been 86%. There is some ambiguity on the amount of total RNA. From the manuscript it appears that only 100 ng is needed. The following statement is contradicting: \"4. Add 5 μl of the samples to each corresponding well (RNA concentration should be 100 μg/μl. Dilute out-of-range samples with RNAse-free water).\" We agree with the reviewer and apologize for error. We will modify the corresponding paragraphs and will also include additional information: NanoString input recommendations stipulate a total RNA amount range of 100-300 ng and specific ratios of absorbance at 260nm and 280nm (A260/280) measured with NanoDrop within the range 1.8-2nm. Given the characteristics of the samples, we decided to hybridize the nCounter probes with 100 ng to 200 ng of total RNA per assay, reason why we only assessed gene expression on eluates with total RNA concentration > 2.5 ng/µl measured with the bioanalyzer. Samples were prepared following manufacturer’s instructions. When necessary, we diluted samples in order to obtain 100-200ng of total RNA to each corresponding well. Time of hybridization was set between 16 and 21 hours. Results were obtained with the nCounter Prep Station and Digital Analyzer set at high sensitivity."
}
]
}
] | 1
|
https://f1000research.com/articles/11-133
|
https://f1000research.com/articles/11-938/v1
|
16 Aug 22
|
{
"type": "Research Article",
"title": "Parents’ perceptions on policies of early childhood care and education programmes in selected states of Malaysia",
"authors": [
"Dandan Tang",
"Fong Peng Chew",
"MohdNazri Abdul Rahman",
"Mogana Dhamotharan",
"Dandan Tang",
"Fong Peng Chew",
"Mogana Dhamotharan"
],
"abstract": "Background: The 2030 agenda for sustainable development proposed global equitable quality education and lifelong learning opportunities for all children. The quality of early childhood care and education (ECCE) programs helps shape children’s minds, attitudes and behaviors, and has short and long-term effects on a child, a family and a country. In Malaysia, the government has formulated some policies and laws to protect children’s rights. However, ECCE is facing some challenges. The purpose of this study is to investigate parents’ perceptions of the quality of ECCE programs implemented by Malaysian government. Methods: A mixed method was used to collect data on parents’ perceptions of ECCE policies in selected states in Malaysia. The questionnaires, (P1/POL) from the research project “Development of a Comprehensive and Integrated Model of Quality Malaysian ECCE”, were distributed among 629 respondents who have a child in a preschool, and 22 participants were randomly selected to take part in five focus group interviews Results: The key findings of the study revealed 68% parents were not familiar with ECCE Malaysian government policy, however 84.3% stressed it is important for the government to educate them about ECCE. Thus findings indicated that the majority of parents lack awareness of the ECCE policies and quality of early childhood care and education programs related to the policies remain the issue. While interviewing the focus group ,most of them were not aware of ECCE and pointed out parents are stressing children’s academic learning in particular preschools. Conclusions: It is concluded that parents’ awareness regarding the ECCE program must be part of the policies and needs to improve. It is recommended that the government of Malaysia should supply more information on ECCE policies to parents and focus on policy implementation. Moreover, the quality of ECCE programs should be improved based on the parents’ perceptions.",
"keywords": [
"Policies",
"Challenges",
"Parents’ perceptions",
"ECCE programs"
],
"content": "Introduction\n\nThe definition of early childhood care and education (ECCE) is the “holistic development of a child’s social, emotional, cognitive and physical needs in order to build a solid and broad foundation for lifelong learning and wellbeing.” (UNESCO, 2005). The 2030 Agenda for Sustainable Development meeting proposed that all countries should ensure inclusive and equitable quality education and facilitate lifelong learning opportunities for all (UNESCO, 2015, p.21). In addition, the State of the World’s Children reported that efforts to protect and expand an individual’s right to education should begin in early childhood. Moreover, it is the right of every child to receive a quality education (UNICEF, 2016). ECCE programs are places that enable children to shape their minds, attitudes and often behaviors (Ortiz, 2015).\n\nOn the other hand, parents’ engagement and education in early childhood is the foundation of all the education and has significant implications for a child’s well-being and success in later life (Alameda-Lawson, 2014; Barnes, et al., 2016). The influence of parents on children's growth process has basic, enlightening, subtle and natural characteristics (Goodall, 2017). Early childhood programs and parents share the responsibility to make contributions to the partnership for the benefit of the child. The relationship between parent and school is evolving to pay attention to partnerships and two-way communication (Epstein, 2010; Barnes et al., 2016). Therefore, parents have important implications for the ongoing process of evaluating, monitoring and improving the quality of ECCE programs.\n\nMoreover, early childhood care and education have the policies and procedures on a whole range of practice issues (Fitzgerald and Kay, 2016, p.6). Fitzgerald and Kay (2016) stress the importance of early years policy for practitioners, children, and parents. Early years policies are aimed at children and families, they impact practitioners significantly to have appropriate qualifications and skills to work with children. Moreover, the policy changes and implementations have implications for children’s diverse developmental needs. Parents can make contributions to the work of providers. Leonidas Kyriakides (2005) found that the implementation of an active partnership policy can provide parents with the opportunity to be involved in the development of school policy. Parents have an active response concerning the impact of school policy. It is suggested that working effectively with parents demands policies that meet the parents’ requirements (Fitzgerald and Kay, 2016, p.138).\n\nCurrently, countries around the world have recognized the importance of early childhood development and its impacts on the countries’ long-term economic and social developments (Hardin et al., 2017; Foong et al., 2018). The quality of early childhood education has been improved across the world since the Millennium Development Goals and Education for All targets were proclaimed (UNESCO, 2014; Engdahl, 2015; Shaeffer, 2016). Considerable progress has been achieved in promoting the well-being and development of young children, especially in European countries and the United States, where they account for the best practices of their early childhood education. The improved quality and equality of early childhood education in European countries and the United States have put much focus on the development and establishment of effective policies and practices (Hägglund, & Johansson, 2014; Shaeffer, 2016).\n\nAccording to UNESCO (2021) globally early child education enrolment rate in school has increased by 27% from 34% in 2001 to 61% in 2019. Although there is significant progress of early child education enrollment in 2019, globally however about 175 million children 3-6 years old are out of the school and have not received quality education.\n\nAbudu and Fuseini (2013) have also stressed that the increasing income gap has slowly enlarged the gap in early childhood education (ECE) quality in Asian countries, especially the quality of early childhood education between rural and urban areas. It is necessary for the government to establish and set effective policies to protect children’s rights to acquire high-quality early childhood care and education (Shaeffer, 2016; Samuelsson & Park, 2017; Shakeel, & Aslam, 2019).\n\nIn Malaysia, various approaches have been taken by the government to ensure and enhance the high quality of ECCE. ECCE is treated as a precondition to quality education as it is the primary factor for developing and improving young children’s knowledge, social skills, and attitudes toward life during one’s early childhood years (Myers, 2004; Eleventh Plan Malaysia 2016-2020: Anchoring Growth on People, 2015). ECCE consists of preschools for children aged 4 to 6 years old, and childcare centers for younger children aged 0 to 4 years old. The enrollment in preschool has increased from 46.24% in 2000 to 83.2% in 2013(McCool, 2013) In 2016, there were 200,684 pupils enrolled in preschool programs (Malaysia National Education for All Review Report, 2015; Samuel & Tee, 2017). However, the Education Blueprint of Malaysia acknowledges that serious problems remain with the quality of education and the investment in education is not as high as expected (Malaysia Education Blueprint 2013-2025, 2013). In addition, parents’ awareness of the positive impact of preschool and their expectations for preschool programs has increased in Malaysia (Siti Naziera, Jati Kasuma, & Irwan Shahrinaz, 2017; Tang et al., 2021).\n\nParental perspectives related to the quality of early childhood care and education programs are critical because parental perceptions reflect parental involvement and directly influence the quality of education (Ortiz, 2015). However, parents are rarely included as participants in research in the field of early education (Vuorinen, 2018). According to the Malaysia National Education for All Review Report (2015), the majority of parents were not satisfied with the quality of education in preschool and they argue that ECCE is mostly like a playground for their children.\n\nThe history of early childhood care and education started in the 1950s. From 1950 to 1960, kindergartens in Malaysia were opened by socialist Christians as part of church activities. Almost all kindergartens were owned by individual or private agencies in town areas. The fees were expensive to serve the children who were from rich families. Around 1969, the Asia Foundation contributed financial assistance to the Worker Society of Malaysia to develop a model of kindergarten called Taman Didikan Kanak-Kanak (TADIKA) in the Malay language similar to a project in the United States (Hutchins, 1995) In 1970, the launching of the New Economic Policy which focused on the eradication of illiteracy by the Department of Community Development (KEMAS) was established. The department of Neighbourhood and National Unity and the Ministry of Federal Territory made a decision to establish Taman Didikan Kanak-Kanak (TADIKA) or Taman Bimbingan Kanak-Kanak (TABIKA) for children aged 4 to 6 years. In 1972, the Ministry of Education enacted a special parliamentary act for early childhood education called Education Act 1961 (Ministry of Education, 2020).\n\nFrom 1972 to 1976, Maktab Perguruan Ilmu Khas (MPIK) (Special Education Teaching College) offered a course to train teachers in early childhood education. After that, the same programs were developed by the teaching colleges and government universities in Malaysia. In 1984, the Children Centre Act was established and in 1986 the Preschool Teachers Guide Book was published. This book was published for the purpose of enhancing the skills and creativity of preschool teachers.\n\nFrom 1990, government departments were actively developing early childhood education, and the number of early childhood education institutions continued to increase, broadening the education of children. In 1993, the Malaysian Preschool Education Guidelines were introduced and adopted by preschools under the Ministry of Education (Heng, 2008; Suseela Malakolunthu, & Nagappan. Rengasamy, 2012). According to the Malaysian Education Blueprint (2012-2025), clear targets were set in terms of quality early childhood education. One of the first stage targets is that the enrollment rate reaches 92% in preschools. All the preschools must be registered and abide by the regulations of the Ministry of Education. The National Early Childcare & Education Curriculum (PERMATA, 0-4 years) and National Preschool Curriculum Standards (KSPK, 4-6 years) are the main references for early childhood curriculum in a preschool. In accordance with the guidelines of the preschool education curriculum, teachers inspire children's intelligence and creativity by playing games and playing with teaching. The education bureaus in the states supervise whether the kindergartens comply with educational guidelines (UPSI National Education Museum, Tanjung Malim, Malaysia; Shaeffer, 2016).\n\nThe Malaysian government has put forth various laws and guidelines in the field of ECCE. There are educational policies and practices to address cultural diversity in Malaysia including issues and challenges (Malakolunthu, Rengasamy, 2012; Hooi San Phoon et al.,2013). The Education Development Master Plan 2001-2010, the Education Blueprint 2006-2010, and the Education Blueprint 2013-2015 have become the main guidelines for the education sector and securing funding for this sector. The 1984 Child Care Act, amended in 2007, refers to all early childhood care and education programmes for children under the age of 4 (Child Care Centre Act 1984, 1984). Convention on the Rights of the Child 1989 and Child Act 2001 (amendment in 2016) emphasized a child’s right to gain an education. The Education Act (1996) has included preschool education as part of the national school system. The National Education Act and Childcare Centre Regulation 1972 (revised draft 2012) formally integrated pre-primary education into the education system. In addition, some guiding policies which are related to early education were formulated such as Malaysian Education Blueprint (2012-2025), Eleventh Malaysian Plan (2016-2020), Country Health Plan 2015, and National Early Childcare and Education Policy 2008. However, the implementation of these policies is less than satisfactory (Ng, 2010; Hooi San Phoon et al., 2013).\n\nAccording to the policy, ECCE in Malaysia is broadly divided into two age groups including 0-4 years old and 4-6 years old (Early Childhood Care and Education Policy Implementation Review, 2008). Ministry of Women, Family and Community Development takes over responsibility for child care and coordinates national programs on the growth and development of children ages zero to four years old in childcare centers (also known as Taman Asuhan Kanak-Kanak). Preschool education (also known as Taman Didikan Kanak-Kanak) for the children who are four to six years old comes under three ministries, namely the Ministry of Education, the Ministry of Rural and Regional Development, as well as the National Unity Department. Moreover, to ensure quality teaching, the National Preschool Curriculum Standards and National Early Childcare and Education Curriculum used in preschools are standardised to ensure that all pupils are able to become literate and calculate before beginning formal education at the primary level (Mid-term Review Ninth Malaysia Plan 2006-2010, 2010).\n\nA significant change was made in preschool education in Malaysia in 2001. “The Council of Ministers gave its approval for the expansion of Preschool Programmes in education and also articulated in the National Preschool Curriculum that learning and teaching would be enacted in a more holistic, interesting and more orderly way” (Abdul Halim Masnan, 2010, p.3). To guarantee children’s health and safety, National Child Policy and Action Plan, National Family Policy and Action Plan, National Nutrition Policy as well as Child Health Services Policy were carried out. The National Preschool Quality Standard (SKPK) and National Quality Assurance System (PERMATA Q) are important policies implemented for the assessment of quality standards for preschools in Malaysia (Raman & Sua, 2010; Zalizan, Ali Manisah Mohd, 2014; Cheong, Hill & Leong, 2016).\n\nLassalle and Nektarios (2018) stated that several conditions contribute to the quality ECCE programs such as the learning environment, professional teachers and caregivers, the relationships among families and teachers as well as communities. Moreover, ECCE policy implementation is important in preschools. Bennett and Neuman (2004) argued that one of the main means of ensuring high-quality education for children is to formulate national education frameworks and policies and provide teachers and parents with intensive in-service training so that they can understand and comply with relevant laws and regulations. It is necessary to pay attention to parents’ perspectives and the interaction between parents and teachers. However, parents are rarely included as participants in research (Vuorinen, 2018) and therefore parents are not aware of the policies. Lack of correct parenting perspectives involving cultural, ethnic or personal values, or lack of interest in acquiring early childhood knowledge that could benefits parents to understand children rights for the education, can result in the the short and long term lack of educational awarness. (Vargas-barón, 2016). Some ECCE policies are brief “policy statements”, formally establishing the country’s intention on young child development. Inadequate attention of parents’ and children’s rights organzations is the reason ECCE polices are not sucessfully implemented (Vargas-barón, 2016). Haddad (2002) concluded an overview of the current situation and recent changes in ECCE policy in developed and developing countries and reported that new government policies have brought about a wide range of reforms addressing the family influence on children’s development in a developed country.\n\nIn Malaysia, many comprehensive policies are in place. However, the implementation of the policies is less than satisfactory (Ng, 2010). Although inclusive education was implemented at the policy level for more than ten years, Malaysia is far from reaching the goal of providing a responsive education path for every child (Zalizan & Manisah Mohd Ali, 2014, p.997). On the other hand, parents lack “political will” which is linked to political interests; cultural, national, or personal values, and they are concerned about the information and resources of early education (Kunagaratnam, & Loh, 2010; Vargas-barón, 2016). This paper focuses on the perspectives of parents on the policy implementation of ECCE programs.\n\nThe general aim of the study is to investigate parents’ perspectives of quality ECCE programs related to policies. The study aims to answer the following questions:\n\n1. Do parents know the policies of early childhood care and education?\n\n2. In what way do parents know the policies of ECCE?\n\n3. What are the main challenges of quality early childhood care and education programs related to policies from parents’ perspectives?\n\nAn explanatory mixed research design was employed in this study to investigate parents’ perceptions on the policy of the ECCE, and the main challenges faced in the implementation of ECCE. The first intent of the research was to collect and analyze quantitative data to find out parents’ views of existing ECCE policies. For this purpose, a questionnaire was distributed to parents in the selected states of Malaysia and provided the general outcomes of the study. Then the researcher engaged in a qualitative phase by doing focus group interviews to help explain the quantitative research results. The triangulation of the data helps to capture the overall picture of ECCE policy implementation of quality ECCE programs in Malaysia and evaluate the policy implementation in preschools based on parents’ perceptions which is beneficial for preschools to improve the quality of education and promote the further implementation of the ECCE policy in Malaysia.\n\n\nMethods\n\nThis study examined government policies for the early childcare education in Malaysia under the national research project titled “Development of a Comprehensive and Integrated Model of Quality Malaysian ECCE”. This study is approved by the Institutional Review Board from the SEGI University with the approval number: SEGi/LRGS/2015-0024-106-04 on 6 September 2017. Informed written (questionnaires) and oral (focus groups) consent was taken from participants who wished to take part in this study.\n\n30 participants were approached for the focus group interviews. 22 gave consent to participate and 8 refused and were not included further. The COREQ guidelines were followed in reporting this research.\n\nThe researchers are familiar with the study location and did not face any problems e reaching out to the participants. Researchers first established a good rapport with participants and explained the purpose of the study. This way we developed the trust of the participants in the researchers. The researchers and participants did not have a relationship prior to the study.\n\nThree authors hold PhDs, and one author is in the final year of their PhD. All authors have prior experience with ECCE research and practice.\n\nThe participants are parents who have children in an ECCE programme in the selected states of Malaysia: Selangor, Kuala Lumpur, Pulau Pinang, Kedah, Perak, Kelantan, Terengganu, Johor, Negeri Sembilan, Pahang, Sarawak, and Sabah. Tadika and Taska schools for the ECCE in the urban and rural areas among the 12 states were selected using a systematic sampling method to cover maximum number of parents. While picking up or dropping off their children to the schools, parents were approached by the research team to take part in the study. The study purpose was explained to them and questionnaires distributed in-person to those who consented to take part.\n\nThe questionnaire (P1/POL for parents) from the national research project entitled “Development of a Comprehensive and Integrated Model of Quality Malaysian ECCE” which is used to examine current government policies, regulations and legislation pertaining to Malaysian ECCE in the context of integration between policy and practice was used in this study. The questionnaire consisted of demographics, parents’ views of policy including nine items, and parents’ views of ECCE programs including 62 items. The validity and reliability of the questionnaire were measured and considered excellent (Cronbach’s alpha= 0.932). A total of 629 questionnaires were distributed to participants and 543 usable valid questionnaires were used in this research study. Statistical Package for the Social Sciences (SPSS.20) was used to conduct the analysis of the quantitative data to answer the research questions “do parents know the policies of early childhood care and education, and in what way do parents know the policies of ECCE”. Table 1 shows the demographics of the respondents.\n\n30 participants were randomly selected to take part in the focus group interviews. 8 refused to participate without giving a reason and were not included further. A total of 22 participants took part in focus group interviews. The interviews were conducted in a private meeting room in a nearby school. There was no one present beside the participants and researchers. Field notes were taken in all interviews, and the groups who consented to it were audio recorded (groups 1-3). Interviews lasted approximately 20 minutes.\n\nThere were five participants from Selangor, six participants from Kuala Lumpur, six participants from Sarawak, two participants from Melaka, two participants from Pahang, and one participant from Sabah, and they were in five interview groups. The audio recordings were transcribed and the transcriptions and field notes were analyzed by using Nvivo V.10 software. The portion of data was coded during the first and second cycle coding process. Codes were established for key concepts related to the research and based on what outcomes from the parents’ perceptions. The themes were derived from the codings, categorization and analytic reflection based on parents’ perceptions on the policies and challenges of quality ECCE programmes.\n\n\nResults\n\nTable 1 indicates the demographic information of the participants and shows most of the respondents (N=330) are female. Half (N=271) of the respondents are aged 31-40 years old, and the highest qualifications are SPM (Malaysian Certificate of Education; N=247) followed by a degree (N=184). Half of the respondents are Chines (N=269) followed by Malay race (N=174), and among 12 states of the Malaysia most of the respondents are from the Selangor and Kuala Lumpur. In Malaysia, two major early child care education programs approved by the government are called Taska and Tidka; Taska mainly deals with early child care for ages 0-4 years and a nursing program, while Tidka accepts children age 4. In this study most of the parents were registered with Tidka schools.\n\nTo investigate whether parents know the policies of ECCE, the frequency and percent of policy documents were analyzed. For the answers to the item “It is important for parents to know the policy documents”, 457 (84.2%) chose “Yes” and 86 (15.8%) chose “No”. It is obviouhs that the majority of parents thought they should know the policy about early education.\n\nTable 2 presents the results of item “In your search for a quality ECCE setting/center for your child, which of the following policy documents have you referred or consulted?”. 21% (n=116) of parents refer to policy documents Malaysian Education Blueprint (2012-2025)17) and National Preschool Curriculum Standards (KSPK) (n=116, 21.4%). 20% of parents would like to refer to the Education Act 1996 (Act 550) (n=110, 20.3%) and National Preschool Quality Standard (SKPK) (n=109, 20.1%).\n\nLike other policy documents, a minority of parents refer to them. The number of respondents (parents) who refer to the policy documents was below 30%. That means more than 70% of parents do not refer to the policy documents about ECCE in Malaysia.\n\nTable 3 shows the analysis results of the item “In your view, which of these policy documents are important for parents to know?”. 33% (n=177) of parents reported that the policy about the curriculum of “National Preschool Curriculum Standards (KSPK)” (n=177, 32.6%) is the most important. Parents also cared more about Childcare Centre Regulation 1972 (revised draft 2012) (n=172, 31.7%), the Malaysian Education Blueprint (2012-2025) (n=170, 31.3%), the Childcare Centre Act 1984 (revised 2012) (n=167, 30.8%), Education Act 1996 (Act 550) (n=145, 26.7%) as well as National Preschool Quality Standard (SKPK) (n=142, 26.2%) and Child Health Services Policy (n=140, 25.8%). This indicates that parents consider the importance of policies that are directly related to their children’s ECCE center.\n\nFor the answers to the item ‘Information about the policy documents can be disseminated to parents through’, most of the parents (N=392) stated school can disseminate policy documents for them. However, N=111 parents stated policy documents can be propagated through the channel of social medial and N=40 parents chose option for community disseminating, hospital conducting awareness program.\n\n40% (n=249) of parents reported that policy documents can be propagated through the channel of social media. 16% (n=16) of parents chose others such as community disseminating, hospital conducting propaganda and government.\n\nInterview: qualitative data analysis\n\nDemographic information of the parents involved in the interview process are given in Table 4 below. A total of 22 respondents volunteered for the interview program.\n\nTo investigate in-depth information on parents’ perceptions of ECCE policy in Malaysia, the researchers conducted focus group interview with 22 parents. Three themes regarding parents’ perceptions on ECCE policy were obtained from qualitative data, and the results are presented in Table 5.\n\nThemes are policy awareness, policy implementation, and challenges of policy implementation. Two categories are under the theme of policy awareness: lack ECCE policy awareness and knowing little ECCE policy. During the focus group interviews, when the interviewer asked the questions ‘what are some of the policies that you are familiar with?’, 15 (68%) parents stated that they were not familiar with the policies of ECCE. Moreover, when the interviewer asked that ‘how did you know about the policy and legislative documents?’ 12 parents (54%) reported they do not know the policy and legislative documents.\n\n“Something [inaudible segment] but not I don’t know how they (policies) apply this in education.” (P1.4)\n\n“We don’t know the about this policy. We heard about this is a strategy.” (P3.2)\n\n“Err I don’t know about locally la because I also hardly get the opportunity to know err most of the time …” (P5.5)\n\n(Focus group interview)\n\nFor the theme of policy implementation, two categories including good practice and expectations were obtained. 16 parents have shown satisfaction on the early child care education center registration and reported good environment in urban areas compared to rural location, moreover, they reported that centers provide healthy food while schooling and ECCE centers are more safe for the children in urban areas because of the policy implementation in ECCE. Moreover, parents expected the quality of teachers to be improved. Some parents pointed out that there were teachers screaming in a particular preschool. Parents thought teachers should be trained to be able to go beyond teaching children through books but also to understand the children who have issues such autism or dyslexia. Parents described that teachers and principals need to be sent for training. A good teacher must acquire some knowledge about psychology. If the teachers understand psychology, they can get the children out of a bad situation. It is better for children to learn how to cope with life problems from teachers. The lessons need to be related to real experiences and teachers should explore suitable teaching methods based on parents’ perceptions. At the same time, parents thought the principals and teachers need to stay relevant, they have to upgrade their facilities constantly and also their own qualifications.\n\n“Some teachers they scream, even in kindergartens in preschools. Even the quality of the teachers should be improved.” (P5.1)\n\n“I think that’s why teachers need to be sent out for training coz I understand now a lot of children also have issues like they get autistic and dyslexia like maybe 10% 20% children … I think teachers have to be trained to be able to go beyond teaching them through books but have to understand the child. You know teaching them how to cope with life measures, I don’t know. You know all sorts of things go beyond that because teachers are the only person who can go up from the situation so the teacher must be quick enough to notice them and to help them at this age. Do you get what I mean ahh? (P3.6)\n\n“So you know teacher should know a bit about psychology, coz it’s very important as they don’t get to, they have to get out, and school is the place where they have to explore, and the teacher is the one who should be sharp enough that they are able to get the children out of that situation.” (P1.2)\n\n“I think the principal and the teacher need to stay relevant, they have to upgrade their facility constantly and also their own qualification. Maybe you are teaching only using paper, but now need to use a computer and videos for teaching but now you may want to explore with other materials. Lessons need to be very relevant to today’s world as children are very clever nowadays.” (P2.2)\n\nThe theme of challenges of policy implementation combines three categories: issues, quality standard and assessment of preschool, and parental involvement. When parents talked about the issues raised by centers, they expressed some views on developing quality ECCE programs. They stressed the importance of children’s health and safety. Based on their opinions, centers should provide children with nutrition and a balanced diet. However, parents lamented that there is a poor hygienic environment, particularly in some preschools and no clear action has been taken by the welfare department.\n\n“There’re more erm mosquito. [inaudible segment] they can’t really take care of their hygiene. Sometimes, other than no. I think I will always complain of the mosquito bringing in all that …” (P5.3)\n\n“It also depends on the place right and who runs the place … some teachers in preschool think that the setting in their preschools is fine. The children have safeguarded regards to hygiene. However, we do not think so. It is common if anything falls on the floor. But for our children, we are so particular about. If children’s bottle falls on the ground, they (the teacher or caregiver) just pick it up and brush it and put it in the children’s month. We think it is serious not good for children.” (P4.2)\n\nMoreover, six parents emphasized that the quality of kindergartens in rural areas was poor and some preschools did not register at all or registrations were not renewed. Five parents pointed the disparity in preschools between rich and poor areas.\n\n“Urban schools are still ok, but I am very worried about, concerned about rural. Even in, within KL there are so many other schools like she said “dirty, unsafe … (cross talk).” (P3.2)\n\n“But those are government schools, but not all lah, there was one in PJ that I went to, WOW! Its posh, really cool, air conditioned all over, beautiful! Compared to the other one I went to, there is a vast difference, it’s like you walk out in Singapore and then back to Johor.” (P1.6)\n\n“But I have seen so many childcare around my house you know, those are run down, dirty, I don’t know how to help those, those are super dirty, especially the unregistered child cares so the government needs to work towards that.” (P5.3)\n\nIn addition, to the quality standard and assessment of preschool, five parents mentioned that cultural diversity remains an issue. Three parents stated that discrimination still happens in particular preschools. Furthermore, seven parents complained that nobody checks the quality of the center.\n\n“Says she was ahh being discriminated upon because of the color. She got a very dark- quite a dark complexion and ahh all-all the other children keep teasing her and all that and all that… So my wife ask her whether you talk to the teacher, she said she doesn’t tell the teacher, afraid that ahh that the children will [inaudible segment] on this type of thing.” (P5.2)\n\n“Actually we have the Malaysian standard which is very good already, if you go through the whole document, all the kindergartens do very good things (inaudible segment), it’s just that nobody check what should I follow and I think that is the issue.” (P3.5)\n\nOn the other hand, four parents commented that they are putting too much emphasis on academic success for children in their early years’ education. They described that they hope their children could learn more and have good preparation in kindergarten for transitioning to primary school. Some parents suggested that preschools should slowly improve their academic skills by using suitable approaches.\n\n“I guess Malaysia parents will give more importance to academic based curriculum instead of play based because they don’t believe that children learn just through play. Now you see when they go to school they care about the skills of writing and reading. However, it needs to consider when children study in a primary school. Some parents often ask teachers why they are playing all the time. So it’s different.” (P3.1)\n\n“What I heard even the year 1 and year 2 schools, government school is pretty much … umm academic oriented so I think we should ummm slow down specially at the kindergarten level. I mean you can have academic but probably slow the approach and not too much classroom oriented.” (P3.6)\n\n\nDiscussions\n\nBased on the findings, 84.2% of parents agree on the importance of knowing ECCE policy documents. However, the fact is that 70% of parents did not refer to the ECCE policy documents because 68% of parents were not familiar with ECCE policy documents. This revealed that some parents lacked awareness of the ECCE policies. Some parents even complained that they knew nothing about the policies of early childhood care and education because they do not have the opportunities to learn. This indicates that the policy implementation should be enhanced by the Malaysian government which should supply more information of ECCE policy to parents and follow the National Child Policy and Action Plan, National Family Policy and Action Plan, National Nutrition Policy as well as Child Health Services Policy to guarantee children’s health and safety. Abide the National Preschool Quality Standard (SKPK) and National Quality Assurance System (PERMATA Q) to do the assessment of quality standards of preschools (Abdul Halim, 2010; Raman & Sua, 2010; Zalizan, Ali Manisah Mohd, 2014; Cheong, Hill & Leong, 2016).\n\nFindings show parents focus on the policies which directly related to children’s ECCE center. This is similar to the study of Nagasangari Kunagaratnam and Loh (2010) who found that parents emphasize the importance of the information and resources of the preschool. According to findings, 72.2% (n=392) of parents hold the view that preschool can provide them with information about ECCE policy documents. A total of 20% (n=111) of parents preferred using digital, social and newspaper meda for the awareness of early child care education policy while 73% (n=40) thought other channels can disseminate policy documents such as community channels, hospitals conducting propaganda and government. This indicates that the government should improve the implementation of policy documents in preschools and parents can learn the policies from the workshops conducted by preschools. Beside, social media such as the internet, public news and TV can spread the policies of ECCE to parents. Bennett and Neuman (2004) claim that the principal means of ensuring the quality of provision of policies is to provide intensive in-service training of teachers and parents. Therefore, it is necessary for the government to offer training opportunities for parents to learn and understand the policies of ECCE and know how to apply and follow the principles.\n\nAccording to the findings from focus group interviews with 22 parents, themes that were derived are policy awareness and policy implementation as well as challenges of policy implementation. A total of 15 parents were not familiar with ECCE policies and 12 parents were unaware of the ECCE policies. This reveals that some parents lack awareness of policy in Malaysia. Parents proposed some issues of policy implementation in preschool from their perspectives such as poor hygiene and lack of direction by the welfare department in particular centres, and the situation of different policy implementation in preschools between rich and poor areas. However, the National Nutrition Policy, as well as the Child health Services Policy, were carried out to guarantee children’s health and safety (Early Childhood Care and Education Policy Implementation Review, 2008). As the quality standard and assessment of policy implementation, the issue is that nobody checks the quality of ECCE centers from parents’ perceptions. Moreover, some parents point out there is the phenomenon of stressing children’s academic learning in particular preschool.\n\nThe key finding of the study is that stressing the importance of the government early child care education polices implementation should create awareness among the parents where most of the parents reported to have no idea about the government policy documents. Therefore, this study strongly recommends the government take on board the parents’ reports, and that polices regarding early child care eduation should engage the public via directly involving them or through media. The study finding is limited to the early child care education policy only and does not deal with high school or other educational subjects.\n\n\nConclusions\n\nBased on parents’ perceptions, ECCE policy is important. However, the majority of parents lack awareness towards the ECCE policies in Malaysia. The government of Malaysia should supply more information of ECCE policies to parents and focus on policy implementation. There are good practices of policy implementation from parents’ views. They expected quality early childhood care and education programs. The challenges of policy implementation of quality early childhood care and education programs remain. Without any doubt, the policy regarding parents’ awareness and implementation should be improved. There was the phenomenon of discrimination in some particular preschools. Also, there were gaps in quality in different preschools in the rich and poor areas. The government still faces problems as to how to standardise the policy implementation and assessment of the preschools’ practice. Therefore, the government should provide professional training for the teachers as well as provide training and learning opportunities to parents. Furthermore, the government should enforce the laws of the National Quality Assurance System and develop new policies that strongly support parent-preschool relationships to ensure the quality of preschool education.\n\nIn order to promote the quality of ECCE in public and private preschools, it is suggested that the Ministry of Education, the Ministry of Rural and Regional Development, as well as the National Unity Department and other related departments should enforce the implementation of the minimum standards and operational guidelines such as National Preschool Quality Standard (SKPK). The standards should outline essential components for preschools. National and District ECCE departments should be responsible for the integration of early childhood care and education and specific activities such as supervision of preschools. The government should provide professional training for the current and new teachers as well as provide training and learning opportunities to parents.\n\nBesides that, the Ministry of Education and other educational departments should enforce the laws of the National Quality Assurance System and develop new policies that strongly support parent-preschool relationships to ensure the quality of preschool education such as the formulation of policy statements that clearly outline the roles of parents, teachers, and principals in children’s early education. Furthermore, the Quality Assurance Office should constantly assess the existing quality of ECCE of preschools in rural and urban areas in order to ensure that the licensed preschools meet the required minimum quality standards which should be developed and evaluated regularly to ascertain preschools owners adhere to and implement.\n\n\nAuthors’ contributions\n\nDandan Tang; original draft and methodology, Fong Peng Chew; original draft and software, MohdNazri A.R; original draft and validation, Mogana Dhamotharan; Original draft, supervision, formal analysis. All authors have read and agreed to the published version of the manuscript.\n\n\nData availability\n\nfigshare: data spss11.22.sav. https://doi.org/10.6084/m9.figshare.19848607.v1 (Abdul Rahman, 2022a)\n\nThis project contains the following file:\n\n- data spss11.22.sav (raw SPSS data set)\n\nFocus group data is not available without the relevant government department’s permission because this study is based on a government project. Because of this, and the detailed nature of the data, it is only available on request. To access the focus group transcript data, please contact the corresponding author mohdnazri_ar@um.edu.my. Any researcher affiliated with a university must show affiliation proof. Interview data is currently in Malay language and will be translated to English on request.\n\nfigshare: questionnaire.pdf. https://doi.org/10.6084/m9.figshare.19848604.v1 (Abdul Rahman, 2022b)\n\nThis project contains the following file:\n\n- questionnaire.pdf: (Questionnaire for the research and the focus group schedule)\n\nfigshare: excel spreadsheet SPSS Coding.xlsx. https://doi.org/10.6084/m9.figshare.20141057.v1 (Abdul Rahman, 2022c)\n\nThis project contains the following file:\n\n- excell spreadshet SPSS Coding (1).xlsx (data key for qualitative data file)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthor information\n\nDandan Tang is a final year doctorate student at the Faculty of Education, University of Malay (UM), Malaysia and about to submit her PhD Thesis. She is the author of a few research papers on the role of early child education and sustainable education polices published in Scopus and SSCI indexed journals.\n\nFong Peng Chew is a senior lecturer at Faculty of Education, University of Malaya (UM), Malaysia, teaching Malay language education and early childhood education program, and has presented approximately 160 working papers international and international seminars and conferences in Malaysia and foreign.\n\nMohd Nazri Abdul Rahman is senior lecturer at Faculty of Education, University of Malaya (UM), Malaysia. Teaching Malay language education and early childhood education, the author has been actively involved in the academic administrative duties with current active position Deputy of Dean and involved in more than 70 research projects on the education subjects, presented and attended multiple local and international conferences.\n\nMogana Dhamotharan is a full professor at the Faculty of Education, Segi University, Malaysia. She is the author of several research papers published in the Scopus and WOS indexed journals.",
"appendix": "References\n\nAbdul Halim M: Malaysian Preschool Education. Malaysia:2010.Reference Source\n\nAbudu AM, Fuseini MN: Influence of single parenting on pupils’ academic performance in basic schools in the Wa municipality. International Journal of Education Learning and Development. 2013; 1(2): 85–94.\n\nAbdul Rahman MN: data spss11.22.sav. figshare. [Dataset].2022a. Publisher Full Text\n\nAbdul Rahman MN: questionnaire.pdf. figshare. [Dataset].2022b. Publisher Full Text\n\nAbdul Rahman MN: excell spreadshet SPSS Coding.xlsx. figshare. [Dataset].2022c. Publisher Full Text\n\nAlameda-Lawson T: A pilot study of collective parent engagement and children's academic achievement. Child. Sch. 2014; 36(4): 199–209. Publisher Full Text\n\nBarnes JK, Guin A, Allen K, et al.: Engaging parents in early childhood education: Perspectives of childcare providers. Fam. Consum. Sci. Res. J. 2016; 44(4): 360–374. Publisher Full Text\n\nBennett J, Neuman MJ: Early childhood, major challenges: Review of early childhood education and care policies in oecd countries. Prospects. 2004; 34(4): 423–433. Publisher Full Text\n\nCheong K, Hill C, Leong Y: Malaysia's education policies and the law of unintended consequences. Journal of International and Comparative Education. 2016; 5(2): 73–86. Publisher Full Text Reference Source\n\nChild Care Centre Act 1984:1984.Reference Source\n\nEarly Childhood Care and Education Policy Implementation Review:2008.Reference Source\n\nEducation Act 1996:2012.Reference Source\n\nEleventh Plan Malaysia 2016-2020: Anchoring Growth on People:2015. Publisher Full Text\n\nEngdahl I: Early childhood education for sustainability: The OMEP world project. Int. J. Early Child. 2015; 47(3): 347–366. Publisher Full Text\n\nFitzgerald D, Kay J: Understanding Early Years Policy. SAGE Publications Ltd.;2016.\n\nFoong L, Veloo PK, Dhamotharan M, et al.: Private sector early child care and education in Malaysia: workforce readiness for further education. Kajian Malaysia: Journal of Malaysian Studies. 2018; 36(1): 127–154. Publisher Full Text\n\nGoodall J: Narrowing the achievement gap: Parental engagement with children’s learning. Taylor & Francis;2017.\n\nHägglund S, Johansson EM:Belonging, value conflicts and children’s rights in learning for sustainability in early childhood.Davis J, Elliott S, editors. Research in early childhood for sustainability: International perspectives and provocations. London:Routledge;2014; (pp. 38–48).\n\nHaddad L: An integrated approach to early childhood education and care. early childhood and family policy series. Young Child and the Family Education Section, ED/BAS/ECF, UNESCO, 7 Place de Fontenoy, 75352 Paris 07 SP, France. Education Collection. 2002.Reference Source\n\nHardin BJ, Bergen D, Busio DS, et al.: Investigating the psychometric properties of the ACEI global guidelines assessment, third edition (GGA) in nine countries. Early Childhood Educ. J. 2017; 45(3): 297–312. Publisher Full Text\n\nHeng KC: Child care in malaysia: Then and now. Int. J. Child Care Educ. Policy. 2008; 2(2): 31–41. Publisher Full Text\n\nJelas ZM, Ali MM: Inclusive education in Malaysia: policy and practice. Int. J. Incl. Educ. 2014; 18(10): 991–1003. Publisher Full Text\n\nPhoon HS, Abdullah MNLY, Abdullah AC: Multicultural early childhood education: Practices and challenges in malaysia. Aust. Educ. Res. 2013; 40(5): 615–632. Publisher Full Text\n\nHutchins T: The influence of Western models of service delivery on the development of services for young children in Malaysia.1995.Reference Source\n\nMinistry of Education: Imbasan Sejarah.2020.Reference Source\n\nLassalle LMM, Nektarios S: OMEP-policy forum: Financing early childhood care and Education—Justice for early childhood. Int. J. Early Child. 2018; 50(2): 139–142. Publisher Full Text\n\nKyriakides L: Evaluating School Policy on Parents Working With Their Children in Class. J. Educ. Res. 2005; 98(5): 281–298. Publisher Full Text\n\nMalakolunthu S, Rengasamy NC: Education policies and practices to address cultural diversity in Malaysia: Issues and challenges. Prospects. 2012; 42: 147–159. Publisher Full Text\n\nMalaysia Education Blueprint 2013-2025: Education (Vol. 27).2013. Publisher Full Text\n\nMalaysia National Education for All Review Report: World Education Forum. efa2015reviews@unesco.org.2015.\n\nMcCool YD: Scientifically based reading research strategies in the preschool classroom: An investigation into quality early childhood reading practices and literacy acquisition in one northern Michigan early reading first program. Eastern Michigan University;2013.\n\nMid-term Review Ninth Malaysia Plan 2006-2010:2010.Reference Source\n\nMyers RG: In Search of Quality in Programmes of Early Childhood Care and Education (ECCE). EFA Global Monitoring Report 2005.2004.Reference Source\n\nKunagaratnam N, Loh SC: Parental concerns regarding a centre-based early intervention programme for down syndrome in malaysia: A case study. Asia Pac. Educ. Rev. 2010; 11(4): 489–496. Publisher Full Text\n\nNg SB: Governance of education related ECCE policies in malaysia. Int. J. Child Care Educ. Policy. 2010; 4(1): 45–57. Publisher Full Text\n\nOrtiz J: A Comparison Study of Parents’ Perceptions of Quality in Early Childhood Programs By. Nevada, Las Vegas:2015.Reference Source\n\nRaman SR, Sua TY: Ethnic segregation in malaysia's education system: Enrolment choices, preferential policies and desegregation. Paedagog. Hist. 2010; 46(1-2): 117–131. Publisher Full Text Reference Source\n\nSamuel M, Tee MY: Education in Malaysia Developments and Challenges. Lorraine PS, editor.Singapore:Springer Nature Singapore Pte Ltd.;2017. Publisher Full Text\n\nSamuelsson IP, Park E: How to educate children for sustainable learning and for a sustainable world. Int. J. Early Child. 2017; 49(3): 273–285. Publisher Full Text\n\nShaeffer S: The demand for and the provision of early childhood services since 2000: Policies and strategies. Prospects. 2016; 46(1): 55–71. Publisher Full Text\n\nShakeel N, Aslam A: Challenges primary school teachers face in the implementation of early childhood education: Teachers perception. J. Early Child. Care Edu. 2019; 3.Reference Source\n\nSiti Naziera MD, Jati Kasuma A, Irwan S: The Study of Parent’ s Satisfaction Towards Kindergarten Center. Empirical Evidence Among Muslim Parents in Kuching, Sarawak. 2017; December: 137–142.Reference Source\n\nTang DD, Dhamotharan M, Abdul Rahman MN: Unveiling Malaysian parents’ perspectives on existing quality of early childhood care and education. Perspektivynaukiiobrazovania – Perspectives of Science and Education. 2021; 49(1): 318–328. Publisher Full Text\n\nUNESCO: Teaching and learning: Achieving quality for all. EFA Global Monitoring Report 2013/4. Paris:UNESCO;2014.\n\nUNESCO Bangkok: Parenting education guidebook and the facilitators’ handbook for parenting education. Bangkok:UNESCO;2015.\n\nUNESCO: Guidelines for inclusion: Ensuring access to Education for All, 40.2005. Publisher Full Text\n\nUNESCO: Early Childhood Care and Education.2015.Reference Source\n\nUNESCO: Education: From disruption to recovery.2021, 01.Reference Source\n\nUNICEF: The state of the world’s children 2016: A fair chance for every child. New York:UNICEF;2016.Reference Source\n\nUPSI National Education Museum: Tanjung Malim, Malaysia.2019.\n\nVargas-barón E: Policy planning for early childhood care and education: 2000-2014. Prospects. 2016; 46(1): 15–38. Publisher Full Text\n\nVuorinen T: ‘Remote parenting’: parents’ perspectives on, and experiences of, home and preschool collaboration. Eur. Early Child. Educ. Res. J. 2018; 26: 201–211. Publisher Full Text"
}
|
[
{
"id": "147731",
"date": "18 Aug 2022",
"name": "Abdul Halim Masnan",
"expertise": [
"Reviewer Expertise Pedagogy in Early Childhood Education"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAfter careful reading of the manuscript, I concluded that the paper has the potential to be 'Approved'. Authors have covered the Malaysian parents’ perception of government established policies for early child care education in the country. Parents' involvement in the educational policies is a remarkable step and it is parents’ right to know and understand what governments have planned and how schools are practically implementing them. This study is comprehensively drafted and well written, however, I have a few protentional but minor questions and directions for the authors to improve the paper more before it can be 'Approved':\nReview comments:\n\nMention key contributions of the study in the ending section of the introduction.\n\nProvide a reference for “The history of early childhood care and education started in the 1950s. From 1950 to 1960, kindergartens in Malaysia were opened by socialist Christians as part of church activities. Almost all kindergartens were owned by individual or private agencies in town areas”.\n\nIn my opinion, research aims and questions should be part of the introduction, however, it's also dependent on the publisher's policies if they do accept as a part of the literature review, authors are free to decide or refer to the publisher's policies.\n\nSection Method “Reflexivity”, “did not face any problems e reaching out to the participants” remove or rewrite the sentence.\n\nWhy Tadika schools are more than Taska? Table 1 shows the difference is very high – any reason please explain?\n\nResults presented very well along with constructive discussion, however, if there is any study limitation, can explain it.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "147732",
"date": "05 Sep 2022",
"name": "Hannah Ajayi",
"expertise": [
"Reviewer Expertise Early Childhood Education"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author(s) clearly pointed out the main problem of the study as the poor implementation of ECCE policies in Malaysia and lack of parental engagement. It is imperative to consider parents’ perception because it is a variable that can influence their engagement in the ECCE policies implementation and can boost the quality of ECCE. The author(s) therefore presented a succinct background on the policies on early childhood care and education in Malaysia in connections to the global agenda.\nHowever, the author(s) did not provide occasions that made them arrive at the conclusion that ‘the implementation is less than being satisfactory’. Is it that the quality is below standard? Who lacked ‘political will’? Parents or the government?\nTo make the paper better, the author(s) can suggest the advantages of parents’ awareness of ECCE Policy. Of what benefits will it be to children, families and the nation at large. The author(s) should provide adequate information about the variables in Research Questions 2 and 3 in the Background – What are the ways that parents may know about the policies and of what benefits will it be if those ways are made available? What challenges surround quality ECCE that parents need to be aware of and what part can the parents play if they are aware?\nThe mixed-methods adopted for the study is appropriate in that the focus group discussion helps to get an in-depth perception of parents beyond the surface level of using questionnaire only which may be subjective in nature. The results and findings were well presented, but the author(s) could take a step further to determine the factors that are responsible for a lack of awareness using the available data in the study. The findings are well presented. The study was well concluded however, the study’s limitation is that the experience in other countries have not been brought to bear. What obtains in other countries as regards parents' perception of ECCE policies implementation and quality may serve as future research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-938
|
https://f1000research.com/articles/11-1126/v1
|
29 Sep 22
|
{
"type": "Research Article",
"title": "Machine learning-based heart attack prediction: A symptomatic heart attack prediction method and exploratory analysis",
"authors": [
"Neha Nandal",
"Lipika Goel",
"ROHIT TANWAR",
"Lipika Goel",
"ROHIT TANWAR"
],
"abstract": "Background; Heart attack prediction is one of the serious causes of morbidity in the world’s population. The clinical data analysis includes a very crucial disease i.e., cardiovascular disease as one of the most important sections for the prediction. Data Science and machine learning (ML) can be very helpful in the prediction of heart attacks in which different risk factors like high blood pressure, high cholesterol, abnormal pulse rate, diabetes, etc... can be considered. The objective of this study is to optimize the prediction of heart disease using ML. Methods: In this paper, we are presenting a machine learning-based heart attack prediction (ML-HAP) method in which the analysis of different risk factors and prediction for heart attacks is done using ML approaches of Support Vector Machines, Logistic Regression, Naïve Bayes and XGBoost. The data of heart disease symptoms has been collected from the UCI ML Repository and analysis has been performed on the data using ML methods. The focus has been on optimizing the prediction on the basis of different parameters. Results: XGBoost provided the best prediction among the four. The Area under the curve achieved with XGBoost is .94 and Logistic Regression is .92. The prediction with ML models in identifying heart attack symptoms is highly efficient, especially with boosting algorithms. The prediction was done to evaluate accuracy, precision, recall, and area under the curve. ML models are being trained to perform optimized predictions. Conclusions: This prediction can help clinically in analyzing the risk factors of the disease and interpretation of the patient scenario. Boosting the algorithm provided promising results to predict symptoms of heart disease. It can further be optimized by working further on risk factors associated with this condition.",
"keywords": [
"Disease prediction",
"Machine Learning",
"XGBoost",
"Logistic Regression",
"Performance measures."
],
"content": "Introduction\n\nA heart attack which is analogous to acute myocardial infarction (AMI) is one of the most serious diseases in the segment of cardiovascular disease. It occurs due to the interruption of blood circulation to muscle of the heart which damages the heart the muscle. Diagnosing heart disease is also a crucial task. The symptoms, physical examination, and understanding of the different signs of this disease are required to diagnose heart disease. Different factors including cholesterol, genetic heart disease, high blood pressure, low physical activity, obesity, and smoking can be reasons for the occurrence of heart disease. The major reason for heart attacks is the stoppage of blood to the coronary arteries. The red blood cells (RBC) start getting low when blood flow is reduced; due to this the human body stops getting necessary oxygen and loses consciousness. The early diagnosis through symptoms and signs can help prevent patients of heart attacks if the prediction is accurate enough. Figure 1 shows different symptoms of a heart attack. The work presented takes 13 features/attributes as input having number values. It has been stated that little modifications in lifestyle including quitting smoking/alcohol/tobacco, having healthy food habits, and routine exercises can help in the prevention of heart attacks. Any person living a healthy lifestyle with early treatment after diagnosis can greatly increase the positive results. However, it is difficult to identify the high risk of heart disease where different risks like diabetes, high blood pressure, and cholesterol problems are present. In these types of scenarios, ML can help in the early diagnosis of disease.\n\nPrevious works have declared that prediction can be improved with the application of feature selection and proper engineering.1 An experiment with different machine learning approaches and models by tuning various hyper-parameters has been performed and improved the performance with optimized accuracy.1 Neural networks performed well when compared to other machine learning classifiers i.e., Naïve Bayes, J48, CART, Grading, and SVM with nearly 79% accuracy.\n\nOther researchers worked on the reduction of cardiovascular features and extracted nonlinear features with discriminant analysis.2 Fisher was utilized for the experiment’s purpose to tackle overfitting problems and to improve the training speed. Results stated that 100% accuracy has been shown for the detection of coronary disease. Table 1 represents the summary of literature survey done for the work.\n\nAnother study has been done on the classification of arrhythmias for variations of heart rate.3 Classification was performed by using a multi-layer perceptron neural network. The results stated that the accuracy achieved was 100% with Gaussian discriminant analysis (GDA). GDA optimization and heart rate variability (HRV) signal feature reduction were done later which then went up to 15 from 13.4\n\nIt has been stated in the work by Zhang et al., in 20185 that 100% precision has been achieved with the support vector machines classifier. Many researchers utilized principal component analysis (PCA) to deal with high dimensional data. The Adaboost model was utilized in another study by using PCA for breast cancer detection.5\n\nIn this work, the focus is on optimizing the model of ML for the prediction of heart disease and the overfitting problem. It is certainly possible to address overfitting problem while working with Logistic Regression. A random sample can be drawn from the complete dataset to avoid overfitting issues. Also, the work focuses on training the model on samples of data obtained from the UCI Machine Learning repository. So, the aim of this study is to improve the prediction of heart disease.\n\nIn this section the description of methods implemented and the techniques used in machine learning research (MLR) are provided. The ML approach and the challenges related to the same are discussed and then selected methods are described.\n\nAn active learning approach is utilized to implement the model. Figure 2 shows the base framework to the active approach of learning.\n\nIn the digital world, electronic health records have taken over to gather health data digitally which made it easier to collect data and allowed for data to become cheaper and more accessible in terms of availability. However, along with the easy availability of the data, there is also the issue of unstructured data which contains a lot of issues including redundancy, noise, heterogeneity, and diversity in scale.\n\nHealth care and diseases comprise of different outcomes including binary i.e., 0 or 1 which means 0 as ‘death’ or any other events, and 1 as continuous outcomes i.e., staying duration. Other outcomes include ordinal ones such as tumor grading, life quality, survival outcomes i.e., any clinical trials or survival from cancer, etc.\n\nML provides versatility in analyzing these data and providing some more precise results.\n\n\n\n- ML is an effective way to optimize the prediction of heart disease and the related effects.\n\n- A good understanding of the required parameters for the diagnosis of the disease can be highly helpful in making precise and accurate predictions.\n\n- Cardiovascular (CV) disease research and treatment coupled with some high-performance tools for analysis can improve the knowledge about the domain.\n\n\nLiterature survey\n\nA thorough search has been done of the previous work on the domain of the heart disease using different algorithms. The previous 21 years of work has been considered for study and their shortcomings are noted down to further extend our research. A total of 50 papers from Web of science, Science direct, and Scopus were collected from which 27 were selected for final study after removal of duplicates and same domain-based papers.\n\nThe literature survey has been started from January 1, 2021 until December 31, 2021 from Scopus, Web of Science, and Science Direct and thorough analysis has been performed on the collected papers. The analysis is done to understand the challenges in the field of heart disease prediction. Collected papers were studied and pros and cons of the work were being observed on the basis of the evaluation parameters, methodology, and utilization of algorithms.\n\nThe inclusion criteria was based on identifying the papers which are of related domain, utilization of latest machine learning algorithms, challenging area in domain of heart disease. Search terms for identifying papers are “machine learning based health disease prediction”, “optimization of Health disease prediction”, “Challenges in identifying health disease”. The exclusion criteria included removing duplicate papers, papers which presented inferior work in terms of evaluation parameter values, and obsolete work.\n\nIn one study, an electronic health record (ehr) model based on sequential modeling was designed with the utilization of a neural network.6 The EHR was applied for experiment conduction and predicting of heart disease. Researchers in this work used word vectors and hot encryption for modeling diagnostic situations and predicting cardiac failure. Along with the same approach, an extended memory model based on the network was utilized. The work stated that it is very necessary for taking care of the sequential character of healthcare with the help of results analysis. The sequential character of healthcare includes tracking of a behavior of person like his/her health-based activities, change in healthcare providers during sickness, exercise routine, diet routine etc.\n\nThe artificial neural network (ANN), random forest, K-Nearest Neighbor (KNN), and support vector machine techniques were used in another work.7 It stated that ANN produced the highest accuracy for heart disease predictions compared to the earlier classification algorithms. The work presented highly efficient results in terms of accuracy and other evaluation measures included in the study.\n\nAnother work stated that PCA as a dimensionality reduction technique can be utilized to deal with data having high dimensions and variance. More information can be stored utilizing this approach in new components.8 When working with data with high dimensionality, many researchers choose to employ PCA. Five unsupervised (linear and nonlinear) dimensionality reduction techniques were utilized, as well as NN as a classifier, to classify cardiac arrhythmia.9 With a minimum of 10 components, an F1 score of 99.83% was achieved with fast independent component analysis (FastICA) which was used for the ICA for breast cancer diagnosis.\n\nAnother researcher employed the AdaBoost algorithm, based on PCA.10 A combination of uncorrelated discriminant analysis and PCA was applied to select the optimal features for controlling upper limb motions.11\n\nUsing PCA approaches to time-frequency representations, another researcher attempted to minimize heart sounds to improve performance.12 A scale-invariant feature, Principle Component Analysis-K-Nearest Neighbor (PCA-KNN), was used in medical pictures for scaling to develop a new approach for diverse medical images that achieved an 83.6% accuracy with 200 images used for training the machine.13 A gray-level threshold of 150 was utilized as a result of PCA and Return on Investment (ROI), all of which were used to reduce X-ray picture characteristics.14\n\nDiabetics are more likely to suffer from cardiovascular (CV)disease. In determining CV risk-assessment methods, both fasting glucose levels and glycosylated hemoglobin have been used. The evidence that these components are being used is inconclusive. According to the cardiovascular heart study,15 the relationship between fasting blood glucose and CV risk is relatively weakly associated. Similarly, multiple studies were done by other researchers15,16 which have shown a correlation between glycosylated hemoglobin and CV risk, as well as postprandial glucose levels.\n\nBecause of our genetic diversity, cultures, dietary habits, and social and behavioral features, available risk-assessment measures are not universal. In a review of the worldwide burden of CV illness, researchers discovered that various populations have varied disease burdens as well as different main Rheumatic fever (RFs) that contribute to this burden. The Asia Pacific Cohort studies sought to compare the Asian and Framingham cohorts in terms of risk factors and illness incidence and discovered that the Framingham group had greater systolic blood pressure, total cholesterol, and CV events, whereas the Asian cohort had higher smoking rates.17,18 There has been no consensus on the risk-assessment tools to employ in Asian populations for risk stratification. As a result, clinicians are perplexed and are unable to use risk stratification to prioritize individuals for primary prevention strategies. So, it has been stated that it will be beneficial to develop a predictive equation from the population-based on gathered data on a contemporary and representative basis. The current mixture of known and unknown RF based on genetic traits has been considered.19 As a result, we must be aware of the limits of each of these risk-assessment techniques and interpret the results with caution.20\n\nAnother work presented on different ML classifiers on which later comparative analysis is also performed.21 This work was performed on data mining approaches like Sequential minimal optimization (SMO), naïve Bayes, and J48 decision trees.\n\nThe maximum accuracy has been achieved with SMO with 89%. The J48 decision tree experiment provided an accuracy of 86% and naïve bayes classifier gave an accuracy of 87%.\n\n\nMethods\n\nEach step of this study is outlined below. Exploratory data analysis (EDA) is used for mistake detection, finding appropriate data, and checking the relationship between variables of exploratory analysis. In this work the heart disease-based risk factors are taken into consideration and ultimately the prediction of the heart attack. The ML classifiers utilized for the work are logistic regression, support vector machines, naïve Bayes, and XGBoost. A detailed literature survey has been performed considering the previous experiments conducted to predict the heart disease and the classifiers SVM, Logistic Regression, Naïve Bayes, and XGBoost are taken into consideration on the basis of their performance attributes. The experiment is carried out on a Cleveland dataset which contains 294 tuples having 14 attributes. A flowchart of the process is presented in Figure 3.\n\n1. The first step is gathering data which is represented as ‘acquisition’. This included evaluating physical conditions and considering the numeric data by converting the samples which will be utilized by the computer to manipulate.\n\na. The data collected is taken from the UCI ML repository28 as outlined in the data collection section, having multiple attributes to study the risk factors for heart disease.\n\nb. All experiments in this study are performed on Python 3.8.3.\n\n2. The second step is ‘pre-processing’ where we tackled issues in the data such as missing values, outlier detection, and redundancy removal to clean the dataset. Predictive analysis has been performed for the uniform environment which also takes the application towards EDA.\n\na. The collected data has been cleaned using pre-processing techniques including missing values replacement, outlier detection, and duplicacy removal.\n\nb. Missing values (if any) are being replaced with Mean values.\n\nc. Outliers in the data has been detected using Boxplots by understanding minimum, maximum, and interquartile ranges of data.\n\nd. Duplicacy removal in the data was performed by using a function dict() for generating dictionary to remove the duplicates.\n\n3. The third step is ‘integration’ where libraries and different subsets were combined by importing independent modules in python and merging them to perform necessary experiments.\n\na. First part of the experiment was to have the preprocessed data.\n\nb. The cleaned data was then integrated to apply ML algorithms.\n\n4. The fourth step is ‘analysis’ where EDA was done to understand the relationship between different attributes of data (Table 2).28\n\na. Analysis works on the concept of learning from data, pattern identification and making decisions with least intervention of human beings.\n\nb. EDA is being utilized to understand the relationship between attributes.\n\nc. Variable were compared to understand the correlation and the same variables were analyzed using boxplots and heatmaps.\n\n5. The fifth step was ‘intervention’ to get into the decision-making policies i.e., search strategy for understanding previous experimental studies to determine when it becomes efficient to utilize models for real-world problems effectively.\n\na. A detailed literature survey was done to know the utilization of ML models for the same domain and to understand which are the most promising ones to optimize our results. The most promising papers were selected on the basis of their performance in previously implemented work in the similar domains for heart disease.\n\n6. The sixth step was’application’ of ML algorithms in making the predictions. In this work, four machine learning models were utilized i.e., SVM, Naïve Bayes, Logistic Regression, and XGBoost.\n\na. SVM was applied on the data utilizing scikit learn with svm extension of python.\n\nb. Naïve Bayes classifier is being applied by using Scikit learn library of neighbors in python.\n\nc. Logistic regression was utilized with linear model class of sklearn in python.\n\nd. XGBoost is a boosting algorithm which utilizes weak classifications and provide optimized results.\n\nThe work is conducted step wise starting from gathering the data. Pre-processing has been done on the data to clean it including duplicacy removal, detection of Outliers, and filling up missing values with mean. Then the four machine learning classifiers has been applied i.e., Support Vector machines, Naïve Bayes, Logistic Regression and XGBoost to further classify the outputs.\n\nThe dataset utilized is composed of four parts or sub-databases i.e., Hungary, Switzerland, Cleveland, and Long Beach which has 76 different attributes. In this work a subset of 14 attributes is utilized because all the published experiments in the literature review referred to these selected 14 attributes which helps to understand the major risk factors of heart disease. This dataset is available online in UCI repository to be availed freely for experimental purpose.28 The last column i.e., target value represents absence or presence of disease in the patient represented by binary of O or 1 respectively.\n\nThe prediction is being performed on whole dataset and to present the attributes and behavior of dataset, the sample of the data set is shown in Table 2 (whole dataset is not presented because of the size).27,28\n\nThe dataset contains attributes and integer values which are distributed in a file (heart.csv)29 whose link is provides at the end of the paper in the section of data availability.27 The behavioral and attributes information of the complete dataset is given in Table 3. The attributes of the dataset utilized (risk factors of heart attack)28 are discussed below:\n\n1. Age (age): This is a highly crucial risk factor for the occurrence of heart attacks because the risk of getting heart attacks can double as age increases. In adults, the fatty streaks indicative of coronary artery disease starts to develop and it is proven that more than 80% cases of heart attacks due to coronary heart disease are in patients aged 65 or above.16\n\n2. Sex (sex): It has been proven that there is a higher risk of heart attack in men compared to women aged 50 or less.17 After the menopause in women, there is a debate of equal risk of heart attack in both men and women. The disease of diabetes in women increases the risk of a heart attack.\n\n3. Chest pain (cp): This happens when the muscle of the heart doesn’t get enough blood with oxygen and is called angina. The feeling of squeezing or high pressure builds up in the chest and an uncomfortable feeling in shoulder, jaw, back, or neck can also develop along with the feeling of indigestion in angina. The pain can be felt in the hands. Different types of Angina include stable angina, pectoris, unstable angina, prinzmetal angina, and microvascular angina.\n\n4. Blood pressure (trtbps): Arteries can be affected by high blood pressure. This can occur because of different reasons like imbalanced cholesterol, high sugar, obesity etc. which can enhance the risks.\n\n5. Cholesterol (chol): Arteries again can get affected due to imbalanced or bad cholesterol. It narrows the arteries especially the low-density lipo-protein cholesterol. Another cause is the blood fat i.e., triglycerides with high levels of cholesterol which can also enhance the risk of heart attacks. So, it is advisable to maintain good cholesterol to lower the risk of a heart attack.\n\n6. Fasting blood sugar (fbs): High blood sugar can become a cause of a heart attack. It may happen due to lower hormone production by the pancreas or no response to insulin in the body.\n\n7. Resting Electrocardiographic (restecg): For medium to high risk of heart attack, the present scenario is not sufficient to understand the screening disadvantages. For those having less risk of disease, the screening harmful effects including a rash or irritation on skin can balance up with exercise.\n\n8. Heart rate (thalach): The increase in the heart rate with the enhanced risk of heart disease is being parallelized with risk increment with blood pressure enhancement.23It is proven in research25that if the heart rate increases by 10 bpm, then the chances of cardiac death increase by 20%. This is also the same with the enhancement in the blood pressure of 10 mm Hg.\n\n9. Angina (exng): The discomfort from Angina which is an Exercise-induced makes the person feel gripped, squeezed and tight which can carry from mild to serious. The pain is usually felt in the chest’s center and it can spread up in the shoulders, back, jaw, arm or neck. Angina plays a crucial role in identifying coronary disease which makes it worthwhile to consider it a separate category for analysis.\n\n10. Thalium Stress Test (thall): Duration of the segment is very important because it needs to be checked that after peak stress, the recovery is happening constantly or not with a positive treadmill test. The abnormal values come under the downslope of depression with less than or equal to 1 mm with 60 to 80 ms. The equivocal tests i.e., with up-sloping segments are also there in the exercise.\n\nRest 4 attributes, oldpeak, slope, number of major vessels, and output are the numeric values related to heart disease in the dataset and were not included in the 10 variables of this study.\n\nThe study was completed with four ML models: XGBoost, support vector machines, naïve Bayes, and logistic regression.\n\n1. Logistic regression: One of the very popular algorithms is considered as logistic regression which is a supervised learning model. It performs categorical predictions which can be ‘true’ or ‘false’. This model provides probabilistic values instead of exact ones. This algorithm works on both continuous and discrete values. A simple S-Shaped curve can elaborate the logistic regression very precisely.\n\n2. Naïve Bayes: A bayes theorem based algorithm, Naïve Bayes is a supervised learning model which works for fast predictions. It is a probabilistic classifier and works very accurately on high dimensional data.\n\n3. Support vector machines (SVM): It is a supervised learning model which works on the concept of decision boundary or hyper plane. The aim of the algorithm is to maximize the margin of the hyper planes which helps in minimizing the misclassification problem. Model chooses extreme points to create the decision boundary which are called as support vectors.\n\n4. XGBoost: It is a decision tree classifier which has been implemented on gradient boosting framework. This model works on the principle that weak learners should be combined to produce best predictions. Ensembling is performed in sequential manner.\n\n\nResults\n\nIn this work, the evaluation of the performance metrices are being done with four machine learning classifiers i.e., SVM, Naïve Bayes, XGBoost, and logistic regression.\n\nXGBoost classifier provided best training and test scores of.91 and.89 along with the 92% accuracy. The results achieved are discussed below. Figures 4 and 5 represents the interface for taking input from users and predicting using machine learning.\n\nFigure 6 represents distribution of attribute values. Figure 7 shows the box plots to understand the median values of data.\n\nThe training and testing was evaluated for each machine learning classifier and results achieved are shown in Figure 8. The training score came up maximum with XGBoost as 91% and Test score also came maximum with XGBoost as 89%.\n\nFigure 9 shows the results for different evaluation metrics and Table 4 provides the evaluated values for different machine learning classifiers.\n\nOn the basis of the evaluation, the area under the curve has been generated for the work which is shown in Figure 10 and Figure 11. Figure 10 compares True Positive Rate (TPR) and False Positive Rate (FPR). Figure 11 shows area under the curve for all machine learning classifiers.\n\nIn the work, maximum accuracy was achieved through XGBoost algorithm. Area under the curve, precision, and recall are also evaluated to understand the performance of algorithms.\n\n\nDiscussion\n\nSome previous researchers proposed that the datasets should be small to deploy ML classifiers, which has been proved in this work. Additionally, the computation time was reduced, which is significant when the model has been deployed. The requirement for the normalization of the dataset has also been felt during the work and the overfitting can be there while training the model. Minimal accuracy has been achieved during evaluation of the real world problem based data. The data can be normalized in a range of methods, and the results can be compared. More techniques to connect heart-disease trained ML models with specific multimedia for the convenience of patients and clinicians could be discovered. The optimized results have been achieved in the presented work and XGBoost provided best results when it came on to accuracy as 92 % and Area under the curve as 94%. Future work will be on optimizing the performance of algorithms with hybrid approach for the prediction of heart disease.\n\n\nConclusion\n\nThe comparative evaluation of four machine learning algorithms for the heart disease prediction was carried out in this study, with promising outcomes. In this investigation, the performance of ML approaches has been better. When data pre-processing was used, XGBoost performed better in the ML technique for the 13 features in the dataset. The training and test score achieved for the XGBoost was highest with the values 91% and 89% respectively. Similar results of 92% accuracy and AUC score of 0.94 was achieved with XGBoost.\n\nIn the future, this research will be expanded by identifying and integrating new features from total of 76 features of heart disease. It also intends to employ other classification methods, such as deep learning to optimize the prediction. The goal is to study and merge more datasets in order to create a more relevant dataset that encompasses a broad range of population types. The feature selection can be used to generate more relevant features and effective results for the prediction of heart disease.\n\n\nData availability\n\nFigshare: heart.csv. https://doi.org/10.6084/m9.figshare.20236848.v1.27\n\nThe project contains the following underlying data:\n\n• heart.csv (underlying data contains 14 features).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nSoftware availability\n\nSoftware available from: https://ipython.org/notebook.html\n\nSource code available from: https://github.com/nandalneha/heart_disease\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.6934185.\n\nLicense: GNU General Public License 3",
"appendix": "References\n\nFatima M, Pasha M: Survey of machine learning algorithms for disease diagnostic. J. Intell. Learn. Syst. Appl. 2017; 09: 1–16. Publisher Full Text\n\nSingh RS, Saini BS, Sunkaria RK: Detection of coronary artery disease by reduced features and extreme learning machine. Med. Pharm. Rep. 2018; 91(2): 166–175. PubMed Abstract | Publisher Full Text\n\nYaghouby F, Ayatollahi A, Soleimani R: Classification of cardiac abnormalities using reduced features of heart rate variability signal. World Appl. Sci. J. 2009; 6(11): 1547–1554.\n\nAsl BM, Setarehdan SK, Mohebbi M: Support vector machine-based arrhythmia classification using reduced features of heart rate variability signal. Artif. Intell. Med. 2008; 44(1): 51–64. PubMed Abstract | Publisher Full Text\n\nZhang D, Zou L, Zhou X, et al.: Integrating feature selection and feature extraction methods with deep learning to predict clinical outcome of breast cancer. IEEE Access. 2018; 6: 28936–28944. Publisher Full Text\n\nJin B, Che C, Liu Z, et al.: Predicting the Risk of Heart Failure With EHR Sequential Data Modeling. IEEE Access. 2018; 6: 9256–9261. Publisher Full Text\n\nAlex MP, Shaji SP: Predictionand Diagnosis of Heart Disease Patients using Data Mining Technique. 2019 International Conference on Communication and Signal Processing (ICCSP). 2019; pp. 0848–0852. Publisher Full Text\n\nGuyon I, Gunn S, Nikravesh M, et al.: Feature Extraction: Foundations and Applications. Cham, Switzerland:Springer;2008.\n\nRajagopal R, Ranganathan V: Evaluation of effect of unsupervised dimensionality reduction techniques on automated arrhythmia classification. Biomed. Signal Process Control. 2017; 34: 1–8. Publisher Full Text\n\nZhang D, Zou L, Zhou X, et al.: Integrating feature selection and feature extraction methods with deep learning to predict clinical outcome of breast cancer. IEEE Access. 2018; 6: 28936–28944. Publisher Full Text\n\nNegi S, Kumar Y, Mishra VM: Feature extraction and classification for EMG signals using linear discriminant analysis. Proceedings of the 2016 2nd International Conference on Advances in Computing, Communication, & Automation (ICACCA) (Fall); September 2016; Bareilly, India. IEEE.\n\nAvendaño-Valencia D, Martinez-Tabares F, Acosta-Medina D, Godino-Llorente I, Castellanos-Dominguez G: TFR-based feature extraction using PCA approaches for discrimination of heart murmurs. Proceedings of the 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society; Minneapolis, MN, USA. IEEE September 2009; pp. 5665–5668.\n\nKamencay P, Hudec R, Benco M, Zachariasova M: Feature extraction for object recognition using PCA-KNN with application to medical image analysis. Proceedings of the 2013 36th International Conference on Telecommunications and Signal Processing (TSP); Rome, Italy. IEEE July 2013; pp. 830–834.\n\nRatnasari NR, Susanto A, Soesanti I, et al.: Thoracic X-ray features extraction using thresholding-based ROI template and PCA-based features selection for lung TB classification purposes. Proceedings of the 2013 3rd International Conference on Instrumentation, Communications, Information Technology and Biomedical Engineering (ICICI-BME); Bandung, Indonesia. IEEE November 2013; pp. 65–69.\n\nConti AA, Minelli M, Gensini GF: Global management of high risk patients: integrated primary cardiovascular prevention in diabetics. Int. Congr. Ser. 2003; 207: 10–20.\n\nKhaw K-T, Wareham N, Luben R, et al.: Glycated haemoglobin, diabetes and mortality in men in Norfolk Cohort of European Perspective Investigation of Cancer and Nutrition (EPIC-Norfolk). BMJ. 2001; 322: 15–18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYusuf S, Reddy S, Ounpuu S, et al.: Global Burden of Cardiovascular Diseases: Part II: Variations in cardiovascular disease by specific ethnic groups and geographic regions and prevention strategies. Circulation. 2001; 104: 2855–2864. Publisher Full Text\n\nLiu J, Hong Y, Ralph B, et al.: Predictive value for the Chinese population of the Framingham CHD risk assessment tool compared with the Chinese Multi-provincial Cohort Study. JAMA. 2004; 291: 2591–2599. Publisher Full Text\n\nTonkin AM, Lim SS, Schirmer H: Cardiovascular risk factors: when should we treat?. Med. J. Aust. 2003; 178: 101–102. Publisher Full Text\n\nBrahmi B: Mirsaeid Hosseini Shirvani, “Prediction and Diagnosis of Heart Disease by Data Mining Techniques”. J. Multidiscip. Eng. Sci. Technol. 2015 February; 2(2): 164–168.\n\nSultana M, Haider A: Heart Disease Prediction using WEKA tool and 10-Fold cross-validation. The Institute of Electrical and Electronics Engineers;March 2017.\n\nBeyene C, Kamat P: Survey on Prediction and Analysis the Occurrence of Heart Disease Using Data Mining Techniques. Int. J. Pure Appl. Math. 2018.\n\nMooney SJ, Pejaver V: Big data in public health: Terminology, Machine Learning, and Privacy. Annu. Rev. Public Health. 2018; 39: 95–112. PubMed Abstract | Publisher Full Text\n\nMohan S, Thirumalai C, Srivastava G: Effective Heart Disease Prediction Using Hybrid Machine Learning Techniques. IEEE Access. 2019; 7: 81542–81554. Publisher Full Text\n\nSalhi DE, Tari A, Kechadi MT:Using Machine Learning for Heart Disease Prediction.Senouci MR, Boudaren MEY, Sebbak F, et al., editors. Advances in Computing Systems and Applications. CSA 2020. Lecture Notes in Networks and Systems. Cham.:Springer;vol. 199. Publisher Full Text\n\nJindal H, Agrawal S, Khera R, et al.: IOP Conf. Ser.: Mater. Sci. Eng. 2021; 1022: 012072. Publisher Full Text\n\nNandal N: heart.csv. Figshare. Dataset.2022. Publisher Full Text\n\nJanosi A, Steinbrunn W, Pfisterer M, et al.: Heart Disease. UCI Machine Learning Repository.1988.\n\nNeha N: nandalneha/heart_disease: (heart.csv). Zenodo. Software.2022. Publisher Full Text"
}
|
[
{
"id": "204980",
"date": "21 Sep 2023",
"name": "Farouk Gambo Lawan",
"expertise": [
"Reviewer Expertise Application of machine learning techniques for disease prediction",
"more especially cardiovascular diseases."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nINTRODUCTION The authors have introduced the work very well.\n\nLITERATURE The authors have done well in trying to correlate the literature with their work. However, it would have been helpful if they could look into the following:\nHeart disease is a general term for a range of cardiac related complications, such as the heart attack (topic of the article), stroke, coronary artery disease, valvular heart disease, cardiomyopathy, etc. In this regard, I think the title of the article is more specific than the literature, even though both need to reflect each other.\n\nThe authors made mentioned of reviewing previous studies conducted for the past 21 years that used latest machine learning algorithms. I think the correlation between 21 year old literature and latest machine learning algorithms can help other researchers understand the work better.\n\nConsidering the period covered for the literature survey (21 years), presenting more specific literature will go a long way in paving the way for other researchers to have a clearer direction of the study.\nMETHODOLOGY In their effort to optimize the prediction, the authors have beautifully selected 10 heart disease features upon which the XGBoost classifier performed better than the others. For the benefit of other researchers, it will be more beneficial if the authors could provide the details of the optimization technique(s) used in the work.\nRESULTS The authors have presented a very good result, with no overfitting or underfitting, which shows the correlation between training and testing results. However, other researchers may be interested in knowing the ratio of training set to testing set of the data utilized that arrived at this beautiful result.\n\nCONCLUSION The authors have given a very brief and precise conclusion. However, readers of the article may require more clarification about the 13 features mentioned here against 10 features utilized in training and evaluation of the selected algorithms.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1126
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https://f1000research.com/articles/11-1124/v1
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29 Sep 22
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{
"type": "Research Article",
"title": "Disease and viruses as negative factor prohibiting the growth of broiler chicken embryo as research topic trend: a bibliometric review",
"authors": [
"Maslichah Mafruchati",
"Akhmad Kusuma Wardhana",
"Wan Iryani Wan Ismail",
"Akhmad Kusuma Wardhana",
"Wan Iryani Wan Ismail"
],
"abstract": "Background\nBroiler chickens have properties as meat-producing poultry and produce meat with soft fiber quality. Broiler’s embryo needs to be given attention, especially against disease. The purpose of the study was to observe the trend of the research topic and external factors which could affect the embryo’s growth of broiler. Methods This study used meta-data from Scopus. There were 162 samples started from 2006-to 2022. The data were analyzed using a bibliometric method with two software, Vosviewer, and Biblioshiy from R studio. Results It was found that the study of broiler chicken embryos had developed well, especially those related to genetics, disease, and also the immunity system. But the result showed that topics about the disease, viruses, and bacteria were more popular than topics about the gene. The result also showed that based on the importance and development of topics, the words such as “chicken”, “genes”, “development”, “effect”, growth”, and “control” had importance for the study and developed well in research. It means that genes influenced the growth of the embryo of a chicken. But still, even though a chicken gene was predetermined, the genetic engineering of chicken insemination to produce a superior breed with a fast-growing rate of the embryo could be used. Conclusions It could be stated that disease, especially research about the virus is one of the main determinants that could affect the growth of the embryo of broiler chicken.",
"keywords": [
": Chicken",
"Embryo",
"Food security",
"Illness",
"Immunology"
],
"content": "Introduction\n\nBroiler chickens are meat-producing chickens that are kept until the age of 6–7 weeks with a weight of 1.5–2 kg. Broiler chicken meat is used as a source of animal protein (Puspita et al., 2021). Broilers have dominant characteristics as meat-producing poultry and produce meat with soft fiber quality. (Puvača et al., 2019).\n\nThe characteristics of broiler chickens are calm, large body shape, fast chicken growth, white chicken skin, and low egg production. In addition, broiler chickens have a weakness that is very sensitive to changes in environmental temperature and infection of various diseases (Qi et al., 2018).\n\nEmbryoid eggs as a dynamic biological system are expected to describe in vivo conditions. The intended in vivo condition is the continuous metabolism and development of embryonic cells in the egg. Chemicals, including antiviral agents, can also be inoculated into eggs (Wilson et al., 2003). The effect of these substances on viruses and embryos is influenced by the age of the embryo, the application of the route of administration to parts of the egg (embryo, allantois, yolk sac, air sac, and amnion), the ability to absorb substances by the embryo, and the pharmacological structure of the substance itself. Other chemical substance which was consumed through the hen also could become the factor in deciding the growth of the embryo (van den Brand et al., 2021).\n\nBesides viruses and chemical substances, the temperature limit that will kill the developing embryo is -1.7°C to -1.11°C for 70–95 minutes. Younger embryos are more resistant to these cold temperatures and require a longer exposure time to cause death. In addition, the temperature required to cause embryo death ranged from 41.1°C to 48.3°C. Within this high-temperature range, higher temperatures are required to cause death in older embryos (Sato et al., 2006).\n\nThe most ideal air temperature for an incubator is 37.5°C. This temperature range is very important for temperature selection to test the potential for manipulation of the sex ratio of broilers. (Stern, 2018). The aim of the study was to analyze broiler embryos based on the Scopus database, as well as the most important topics that need to be paid attention to related to the embryo of broiler chicken.\n\n\nMethods\n\nData gathered from Scopus website with subscription service. Subscription service was different from free service in Scopus because by paying the subscription fee to Scopus, that institution would receive access to all kinds of metadata related to all papers published in journals indexed by Scopus., while free access cannot (Harzing & Alakangas, 2016). This study limited the data related to the embryo of broiler chicken and focused the analysis of the data on disease and viruses which could affect the growth rate and survivability of the embryo. The data were collected using the keyword of “EMBRYO”, “BROILER CHICKEN”, and “VIRUS”. The duration of data gathering was 2006–2022 with all types of publications included. There were 1348 samples found.\n\nThe keywords were typed into advanced search in Scopus website. Those keywords were SRCTITLE (EMBRYO), (BROILER CHICKEN), (VIRUS). This study only included papers using English as the samples. The source type were open access articles, and document type were abstract, review article and research article. After being scrutinized to only related to “BROILER CHICKEN”, the remaining samples were 162. The collected samples are then exported to specific files, so that they could be analyzed by software.\n\nThe analysis of the data from a CSV file would be divided into two steps. The first step of analysis used Vosviewer version 1.6.16 to see the affiliation of the authors and keywords related to the study of the embryo of broiler chicken. The affiliation included the name of the institution, city, and country where the author resides. It also included the number of citations from their affiliations. The data were presented in a table. For the analysis of the keywords, Vosviewer could visualize the keywords related to the intended topics along with their connection to each other, shown by the strings attached. It also could show the keywords that had become the trend in a certain year indicated by color (Polley, 2016).\n\nThe second step of the analysis was using Biblioshiny feature from R studio software. Biblioshiny was a powerful tool for analyzing the metadata of publications using the bibliometric method. Using biblioshiny software that could provide many forms of analysis in bibliometrics, this study analyzed the data using four features. First was the “word cloud” feature to see the important word from the abstracts of each paper. The second was the “trend topic” feature to see what topic that was trend each year from 2013 to 2022. The third was the “thematic map” feature to see the importance and how well a keyword was developed in the research field. The fourth was the “thematic evolution” feature to know the frequency of keywords included in papers used as samples and their relationship with the countries and authors of the papers.\n\n\nResults\n\nTable 1 showed that three universities in France had publications with high citations. The country with publications with the highest citation was Canada, but only in one university. Other countries with more than one university that had publications related to the topic of the embryo of broiler chicken with high citations were Netherland and Germany. It means that the trend of publication related to the intended topic was more popular in European countries than in Asia or America.\n\nSource: Data processed using Vosviewer\n\nFigure 1 showed that there were some major keywords used in published papers such as “animal”, “article”, “animal tissue”, “chicken”, “controlled study”, and “genetic embryo”. The keyword “embryo” was connected to some keywords, such as “controlled study”, “genetics”, “immunology”, “poultry disease”, “chicken”, and “unclassified drug”. The appearance of those keywords means that several factors could affect the development of the embryo of broiler chicken, such as immunity against disease, some drugs given to hen, and genetics.\n\nSource: Data processed using Vosviewer.\n\nFigure 2 showed that the word “genes” and “chicken” were the major words used as the topic in published papers. Ate the right side of the word “chicken”, there was a word “messenger Ribonucleat acid”, “cell”, and “data”. It means that mRNA also had some kind of influence on the embryo. There were some words, such as “day”, “heat”, and “liver”. It means that besides daylight and heat that could affect the growth of the embryo, the liver condition of the hen of broiler chicken also contributed to the growth of the embryo too.\n\nSource: Data processed using biblioshiny from R studio.\n\nFigure 3 showed that topics of “chickens” had the biggest frequency come out from the web-based search than other topics used in published papers. It was because the chicken was the main topic of this study, which means that it had the biggest one. Besides the topic “chicken”, other topics that had a frequency of more than 100 were “genes”, and “expression”. Interestingly, there were topics like “virus” and “response” that had 100 frequency of occurrence from 2014 to 2016.\n\nSource: Data processed using biblioshiny from R studio.\n\nFigure 4 showed there were 4 areas of theme based on how important and how well some words developed in research fields. Those words were taken from abstract papers that became samples of this study. The motor theme area was only for words that have the important aspect and are well developed in the research field. Contrary to the motor theme, emerging or declining themes was an area where the keywords were neither developed well enough nor important for their research fields. The niche and the basic theme were different from each other. While Niche themes area for the topics which were not important to the research field but well developed, basic themes were the opposite of niche themes (Radha & Arumugam, 2021).\n\nSource: Data processed using biblioshiny from R studio.\n\nIn the motor theme, there were some words such as “chicken”, “genes”, “development”, “effect”, “growth”, and “control”. It means that genes influenced the growth of the embryo of a chicken. But still, even though a chicken gene was predetermined, the genetic engineering of chicken insemination to produce a superior breed with a fast-growing rate of the embryo could be used. Other factors such as disease and types of feeders also had a significant effect on embryo growth.\n\nFigure 5 showed that the word “chicken” was still the one that has grown most than other words used in published papers. The word “gene” was also the second most growing word. It means that the gene of the chicken itself, whether from hen or cock of broiler-type determines the growth rate of the embryo along with how resistant its embryo against disease. Because broiler chicken was the type of chicken raised for its egg and meat, it would grow faster than other types of chicken, so the output rate of meat production would be faster too.\n\nSource: Data processed using biblioshiny from R studio.\n\nBroiler chicken was one of the main sources of meat in many countries. The demand for meat from chicken, especially from fast-food chain restaurants caused many breeding houses and farms to raise more broiler because broiler could grow fast. Figure 5 showed that words besides “chicken”, such as “genes” and “growth” had raised higher than other types of words included in publications published by which was indexed by Scopus. It means that genes and growth become the major concern of authors around the world who were interested in observing embryos of broiler chickens.\n\n\nDiscussion\n\nFigure 1 showed some keywords such as “chicken”, “embryology”, and “immunology”. In particular, the chicken has uniqueness in the process of regulation of B cell production by B-cell receptor complex (BCR). Marrow Bone does not play a role in the formation of B cells in fowl, but the bursa of Fabricius, a GALT . organ specifically, in which there is B-cell lymphopoiesis. However, the surface expression of BCR has been maintained as an important checkpoint both on mammals and birds amidst variations in the microenvironment (Liu et al., 2019). After colonization of the bursal follicle by B cells expresses the prediversified sIg receptor, program induced gene conversion to diversify the VDJH . gene and VJL through gene conversion. It is at this stage that the repertoire premium is generated. Some evidence suggests that this repertoire is generated in an independent manner antigens. Most convincingly, this evidence comes from repertoire development among B cells supported by messenger T cell receptors. (Puspita et al., 2021).\n\nIn addition, the use of different pseudogenes in these B cells are correlated closely related to the use of pseudogenes in development normal B cells (Wirth et al., 2017). It also supports a model in which primary repertoire development is encouraged by the availability of pseudogene sequences without selection substantial for certain V gene sequences. Obviously, kind this analysis will not be able to detect subtle differences in the repertoire that may occur as consequences of negative selection from reactive specificity self. (Patel et al., 2021).\n\nSo, in Figure 1, the word \"immunology\" is also associated with the word \"unclassified drug\". Antibiotics in animal feed have been used since 1946 with the aim of increasing livestock productivity and health. In poultry, Antibiotics are used with the aim of increasing feed digestibility, growth and egg production, improve feed conversion, reduce mortality and maintain health conditions. Currently, the use of antibiotics is not only in broilers, but also other intensively reared birds (Gadde et al., 2017; Puvača et al., 2016).\n\nFigure 2 showed that there were some words related to “genes”, “chicken”, “mRNA”, and “cell”. It could be said that different genes of chicken stored in M-RNA played important role in the characteristics of the embryo itself. For example, laying hens are chickens reared to produce lots of eggs and are the final product of purebred chickens and should not be re-crossed (Aengwanich & Suttajit, 2010). Laying hens are adult hens that are specially reared for their eggs. This type of chicken is a species of “Gallus Domesticus”. The first chickens to enter and start breeding in Indonesia were white leghorn laying hens, which were thin and generally turned into chicken pieces after their productive period (Coyne et al., 2020).\n\nLaying hens are divided into three types, namely the light type from the white leghorn breed, the medium type from the Rhode Island Reds, and Barred Plymouth Rock, and the heavy type from the New Hampshire, white Plymouth Rock, and Cornish breeds (Puspita et al., 2021). The origin of laying hens is from partridges that have been domesticated and selected so that they lay quite a lot of eggs. The direction of partridge selection is aimed at large production. However, because the jungle fowl can be taken for eggs and meat, the direction of the selection is starting to be specific. Chickens selected for meat production are known as broilers, while for egg production, known as laying hens (Tamburawa et al., 2018).\n\nFigure 2 also showed that there was a word “vaccine” near two words, “body” and “distributed”. It could mean that broiler chicken needs a vaccine to get immunity from disease. One of the viruses caused by birds that had become famous before was bird flu.\n\nBird Flu (H5N1), classified as orthomyxoviruses that attack the respiratory or nervous system. This bird flu has a mortality rate up to 100%, so it is often called highly pathogenic avian influenza (Butler, 2006). The bird flu virus can cause human death, because the nature of this virus is easy to mutate to form new types of viruses that are dangerous, and death if bird flu meets human flu (Malek & Hoque, 2022)\n\nTransmission of the bird flu virus by means of the salivary glands (saliva) and chicken manure (excreta), and this virus can live to 30 days with temperature of 0°C, but this virus can die at a temperature of 80 ° C within 1 minute. This disease can be spread through the respiratory tract, conjunctiva, and feces (excreta) by being transmitted through direct contact between sick and healthy chickens. In addition, it can be through air contact, it can also be through vehicles, equipment, feed, drinking water that have been contaminated with AI. Blood Defecation Disease (Coccidiosis), was protozoa of Eimeria, causes diarrhea and inflammation of the intestines (enteritis). Feeder and drinking water that has been contaminated with AI. Blood Defecation Disease (Coccidiosis), is a disease caused by protozoa of the genus Eimeria which causes diarrhea and inflammation of the intestines (enteritis) (Butler, 2006).\n\nCoccidiosis attacks young chickens and occurs due to warm litter conditions or high humidity (wet litter). This disease disrupts the absorption process of intestinal nutrients so that the metabolic process does not run perfectly which causes impaired growth in chickens (Butler, 2006). Coccidiosis spreads in the form of single cells (oocysts) that are excreted in the feces (excreta) so that they are brownish or blood-red in color due to intestinal inflammation. Coccidiosis is grouped into three, namely “Eimeria Acervulina” which attacks the front intestine, “Eimeria Necratix” which attacks the middle intestine, and “Eimeria Tenella” which attacks the appendix or back intestine (Butler, 2006). “Protozoa Oocysts” can live outside the chicken's body for 2–4 days and are eaten by chickens into the intestinal tract, then develop and divide with a developmental process of 4–7 days. The clinical symptoms of the affected chickens include poor appetite but high appetite, brownish or reddish excreta, wrinkled and dull skin, and decreased bodyweight of the chickens.\n\nFigure 3 showed that trend topics per year that had high frequency were “genes”, and “expression”, as well as “virus”. It means that the virus also became a concern for a research topic to learn more about the embryo of chicken. It means that response against the virus was important for the hen to create immunity for its embryo.\n\nThe main problem which is the toughest challenge in chicken farming is the emergence of disease, so its management needs to be done efficiently and professionally. Diseases that attack chickens are many and often have almost the same symptoms. Chronic Respiratory Disease (CRD), often called snoring, is a disease caused by the bacterium “Mycoplasma Gallisepticum” that infects the respiratory tract. Snoring disease is also known as complex CRD, which is a combination of “Tetelo” disease, bronchitis, or mixed bacteria (Timms et al., 1989)\n\nSymptoms of chickens that are attacked by CRD are mucus in the nostrils that cause blockage and often shaking their heads to remove the mucus blockage, swelling in the eye and face area, drowsiness, decreased appetite, and a snoring sound in breathing. Complex CRD occurs due to “Mycoplasma Gallisepticum” infection which lasts longer and is clearer, and there are wounds in the respiratory tract, inflammation of the lungs (pneumonia), and thickening of the air sacs (airsaculitis). This disease attacks quickly in a long time with a morbidity rate of 70–90%, the incubation period lasts 24–48 hours after being contaminated through the nose (intranasal) or the nasal cavity (intranasal) (Abbas et al., 2018).\n\nAnother type of virus that could affect the embryo of chicken was the virulent strain of Newcastle Disease Virus (VND). It caused disturbances in the nervous, digestive, and respiratory systems of poultry, while infection in chicken embryos causes growth disturbances which can lead to death. A study conducted by Purnasari, Adi, and Winaya observed the effect of the APMV-1 virus isolate from Badung-2/AK/2014 on embryo weight and brain histopathological features of chicken embryos. This study used 18 embryonic chicken eggs (TAB) aged 11 days which were divided into two treatment groups, namely Group A and Group B, each of which consisted of nine eggs. Group A was inoculated with Phosphate Buffer Saline (PBS) and group B was inoculated with isolate Badung-2/AK/2014. Three days after inoculation, allantoic fluid from all treatment groups was collected.\n\nTo prove that the two groups did not contaminate each other, hemagglutination (HA) and hemagglutination inhibition (HI) tests were carried out. Chicken embryos were removed from the eggshells, then weighed and the average weight of the embryos of groups A and B were analyzed by independent sample T-test. After that, the chicken embryos were necropsied for brain organs and put into 10% Neutral Buffer Formalin (NBF). Subsequently, preparations were made using the Hematoxylin Eosin (HE) staining technique. Histopathological lesions were observed under a microscope and the results were presented descriptively. The results showed that the isolates caused histopathological lesions in the form of vasculitis and perivascular edema in the brain and resulted in weight loss of chicken embryos (Purnasari et al., 2017).\n\nFigure 4 showed some words related to embryo growth such as “growth” and “genes”. According Mukandungutse et al, Aflatoxins are toxic compounds that are mutagenic, teratogenic, and carcinogenic and are generally found in foodstuffs derived from grains such as corn, rice, and beans of poor quality. Its presence in foodstuffs, including food from livestock in Indonesia, has been widely disclosed by various researchers, but research on its toxicity is still very limited.\n\nA study by Mukandungutse et al tried to observe the effect of aflatoxin B1 on chicken embryos. It also observed effect of various doses of aflatoxin B1 on not alive and the ability to hatch the embryos, as well as complementing the previous information. In this study, the dose of AFB1 used was 0; 15.6; 31.2; 62.5; 125; and 250 ng AFB1 per embryonic egg administered via airbag to 25 5-day-old sprouted eggs each. The results obtained showed that the hatchability of embryos up to day 21 was 66, 28, 26, 16, 0 and 0% for dose 0; 15.6; 31.2; 62.5; 125; and 250 ng AFB1. Administration of AFB1 has also caused embryonic abnormality in the form of bleeding, egg yolk malabsorption, dwarfism, weakness, and mild leg defects. the body weight of hatched chicks did not have a significant difference between groups, although there was a lower tendency for giving high doses of AFB1 (Mukandungutse et al., 2020).\n\n\nConclusions\n\nBased on article review that the publications about the embryo of broiler chicken had more concern about immunity, virus, and disease as external factors that could impede the embryo’s growth. Moreover, for internal factors, some words have become a trend in publications, such as “gene”. But still, the study about diseases and viruses that could affect an embryo’s growth was more dominant. It could be seen from Figure 2, Figure 3, and Figure 4 that virus and disease became the trending words in publications. It means that the focus on how to prevent disease, the characteristic of viruses or bacteria, and the incubation period of microorganisms inside the embryo had become the hot trending topic for publications of papers published with the intended topic. Further study suggested focusing more on the nutrition needed for broiler’s hen as one of the external factors in deciding the growth rate of the embryo.",
"appendix": "Data availability\n\nZenodo. dataset of scopus. DOI: 10.5281/zenodo.6375278 (mafruchati, 2022)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbbas N, Suleman M, Khan NA, et al.: Prevalence of Mycoplasma Gallisepticum in Poultry and Wild Life Birds Suspected of Chronic Respiratory Disease in Northern Pakistan. Pak J Zool. 2018; 50(3): 1071–1077. Publisher Full Text\n\nAengwanich W, Suttajit M: Effect of Polyphenols Extracted from Tamarind (Tamarindus Indica L.) Seed Coat on Physiological Changes, Heterophil/lymphocyte Ratio, Oxidative Stress and Body Weight of Broilers (Gallus Domesticus) under Chronic Heat Stress. Anim Sci J. 2010; 81(2): 264–70. PubMed Abstract | Publisher Full Text\n\nButler D: Bird-Flu Experts Question Advice on Eating Poultry. Nature. 2006; 440(7086): 850–1. PubMed Abstract | Publisher Full Text\n\nCoyne L, Patrick I, Arief R, et al.: The Costs, Benefits and Human Behaviours for Antimicrobial Use in Small Commercial Broiler Chicken Systems in Indonesia. Antibiotics (Basel). 2020; 9(4): 154. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGadde U, Kim WH, Oh ST, et al.: Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Anim Health Res Rev. Cambridge University Press, 2017; 18(1): 26–45. PubMed Abstract | Publisher Full Text\n\nHarzing AW, Alakangas S: Google Scholar, Scopus and the Web of Science: A Longitudinal and Cross-Disciplinary Comparison. Scientometrics. 2016; 106(2): 787–804. Publisher Full Text\n\nLiu S, Tan JZ, Hu Y, et al.: Dietary L-arginine Supplementation Influences Growth Performance and B‐cell Secretion of Immunoglobulin in Broiler Chickens. J Anim Physiol Anim Nutr (Berl). 2019; 103(4): 1125–1134. PubMed Abstract | Publisher Full Text\n\nMafruchati M: dataset of scopus. [Data set]. Zenodo. 2022. http://www.doi.org/10.5281/zenodo.6375278\n\nMalek A, Hoque A: Mathematical Modeling of Bird Flu with Vaccination and Treatment for the Poultry Farms. Comp Immunol Microbiol Infect Dis. 2022; 80: 101721. PubMed Abstract | Publisher Full Text\n\nMukandungutse IB, Tuitoek JK, King’ori AM, et al.: The Effect of Fermented Aflatoxins Contaminated Feed on Digestibility and Performance of Broiler Chickens. Anim Prod. 2020; 22(1): 55–60. Publisher Full Text\n\nPatel NH, Padhiyar JK, Raval RC: A Cluster of Differentiation 19+ B-Lymphocyte Cell as a Predictor of Relapse in Pemphigus Vulgaris. Indian J Dermatol Venereol Leprol. 2021; 87(2): 237–38. PubMed Abstract | Publisher Full Text\n\nPolley DE: Visualizing the Topical Coverage of an Institutional Repository with VOSviewer. Data Visualization: A Guide to Visual Storytelling for Libraries. 2016; 111. Reference Source\n\nPurnasari ME, Adi AAA, Winaya IBO: Pengaruh Virus Newcastle Disease Isolat Virulen Terhadap Gambaran Histopatologi Otak Dan Berat Embrio Ayam. Maret. 2017; 6(2): 101–108. Reference Source\n\nPuspita UE, Saragih HTS, Hartatik T, et al.: Body Weight Gain and Carcass Quality of the Hybrid Chicken Derived from the Crossing between Female F1 Kampung Super and Male F1 Kampung-Broiler. J Tropical Biodiversity Biotechnology. 2021; 6(2): 60934. Publisher Full Text\n\nPuvača NM, Kostadinović LM, Đuragić OM, et al.: Influence of Herbal Drugs in Broiler Chicken Nutrition on Primal Carcass Cuts Quality Assessments. Food Feed Res. 2016; 43(1): 43–49.\n\nPuvača N, Peulić T, Ikonić P, et al.: Effects Of Medicinal Plants In Broiler Chicken Nutrition On Selected Parameters Of Meat Quality. Maced J Anim Sci. 2019; 9(2): 45–51. Publisher Full Text\n\nQi B, Wang J, Ma YB, et al.: Effect of dietary β-alanine supplementation on growth performance, meat quality, carnosine content, and gene expression of carnosine-related enzymes in broilers. Poult Sci. 2018; 97(4): 1220–28. PubMed Abstract | Publisher Full Text\n\nRadha L, Arumugam J: The Research Output of Bibliometrics Using Bibliometrix R Package and VOS Viewer. Humanities. 2021; 9(2): 44–49. Reference Source\n\nSato M, Tachibana T, Furuse M: Heat Production and Lipid Metabolism in Broiler and Layer Chickens during Embryonic Development. Comp Biochem Physiol A Mol Integr Physiol. Elsevier, 2006; 143(3): 382-8. PubMed Abstract | Publisher Full Text\n\nStern CD: Staging Tables for Avian Embryos: A Little History. Int J Dev Biol. 2018; 62(1–3): 43–48. PubMed Abstract | Publisher Full Text\n\nTamburawa MS, Ogundipe SO, Olugbemi TS, et al.: Effect Of Cooked African Locust Bean Seed Meal Diets On Performance, Haematological Profile And Nutrient Digestibility Of Finisher Broiler Chickens. J Anim Prod Res. 2018; 30(1): 179–87.\n\nTimms LM, Marshall RN, Breslin MF: Evaluation of the Efficacy of Chlortetracycline for the Control of Chronic Respiratory Disease Caused by Escherichia Coli and Mycoplasma Gallisepticum. Res Vet Sci. 1989; 47(3): 377–82. PubMed Abstract\n\nvan den Brand H, Meijerhof R, Heetkamp MJW, et al.: Interaction between Eggshell Temperature and Carbon Dioxide Concentration after Day 8 of Incubation on Broiler Chicken Embryo Development. Animal. Elsevier, 2021; 15(6): 100223. PubMed Abstract | Publisher Full Text\n\nWilson HR, Neuman SL, Eldred AR, et al.: Embryonic Malpositions in Broiler Chickens and Bobwhite Quail. J Appl Poult Res. Elsevier, 2003; 12(1): 14–23. Publisher Full Text\n\nWirth MD, Andrew ME, Burchfiel CM, et al.: Association of Shiftwork and Immune Cells among Police Officers from the Buffalo Cardio-Metabolic Occupational Police Stress Study. Chronobiol Int. 2017; 34(6): 721–31. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "159463",
"date": "16 Jan 2023",
"name": "Andre Chwalibog",
"expertise": [
"Reviewer Expertise Poultry nutrition",
"embryogenesis"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe work is interesting, providing a bibliometric review of publications related to chicken embryo. Methods are comprehensively described.\nNevertheless, I have a few comments.\nIn the introduction, the significant part is related to temperature effects on embryogenesis. The subject is important but not evaluated in the following results.\n\nIn the results, it is initiated that Canada has the highest citation rate, followed by the Netherlands and Germany. However, the second number of citations is from Poland (Bydgoszcz is not a country by a town in Poland – Table 1.).\n\nFig. 2 shows topics related to embryos, but it is unclear whether “Topics” are from titles, abstracts or keywords.\n\nFig. 3 is based on abstracts. The question is about the main differences between these figures.\n\nFig. 4 is difficult to comprehend.\n\nFig. 5 is entitled Word growth, but other words are demonstrated as well.\n\nIn the discussion, the use of antibiotics is underlined, but antibiotic additives have not been allowed in the European Union and some other countries for years.\n\nThe paragraph “Laying hens..” is general and not directly related to embryogenesis.\n\nThere is an extended description of different diseases in poultry. However, it is not clear why the particular diseases are described in detail but not referred to bibliographic evaluations.\n\nIt is concluded “it could be seen from figures 2, 3 and 4 that virus and disease become the trend words…” Explain the background of the word “trend”. How the “trending topic” is characterised?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "9252",
"date": "16 Feb 2023",
"name": "maslichah mafruchati",
"role": "Author Response",
"response": "Thank you for your time to give comment to this paper. I gladly accept your suggestion about what is trend, what should be added more in the description of each figure in my paper, as well as the paragraph that should be omitted because it was not too important for my result at all."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1124
|
https://f1000research.com/articles/11-653/v1
|
14 Jun 22
|
{
"type": "Study Protocol",
"title": "Protocol for the perioperative outcome risk assessment with computer learning enhancement (Periop ORACLE) randomized study",
"authors": [
"Bradley Fritz",
"Christopher King",
"Yixin Chen",
"Alex Kronzer",
"Joanna Abraham",
"Arbi Ben Abdallah",
"Thomas Kannampallil",
"Thaddeus Budelier",
"Arianna Montes de Oca",
"Sherry McKinnon",
"Bethany Tellor Pennington",
"Troy Wildes",
"Michael Avidan",
"Christopher King",
"Yixin Chen",
"Alex Kronzer",
"Joanna Abraham",
"Arbi Ben Abdallah",
"Thomas Kannampallil",
"Thaddeus Budelier",
"Arianna Montes de Oca",
"Sherry McKinnon",
"Bethany Tellor Pennington",
"Troy Wildes",
"Michael Avidan"
],
"abstract": "Background: More than four million people die each year in the month following surgery, and many more experience complications such as acute kidney injury. Some of these outcomes may be prevented through early identification of at-risk patients and through intraoperative risk mitigation. Telemedicine has revolutionized the way at-risk patients are identified in critical care, but intraoperative telemedicine services are not widely used in anesthesiology. Clinicians in telemedicine settings may assist with risk stratification and brainstorm risk mitigation strategies while clinicians in the operating room are busy performing other patient care tasks. Machine learning tools may help clinicians in telemedicine settings leverage the abundant electronic health data available in the perioperative period. The primary hypothesis for this study is that anesthesiology clinicians can predict postoperative complications more accurately with machine learning assistance than without machine learning assistance. Methods: This investigation is a sub-study nested within the TECTONICS randomized clinical trial (NCT03923699). As part of TECTONICS, study team members who are anesthesiology clinicians working in a telemedicine setting are currently reviewing ongoing surgical cases and documenting how likely they feel the patient is to experience 30-day in-hospital death or acute kidney injury. For patients who are included in this sub-study, these case reviews will be randomized to be performed with access to a display showing machine learning predictions for the postoperative complications or without access to the display. The accuracy of the predictions will be compared across these two groups. Conclusion: Successful completion of this study will help define the role of machine learning not only for intraoperative telemedicine, but for other risk assessment tasks before, during, and after surgery. Registration: ORACLE is registered on ClinicalTrials.gov: NCT05042804; registered September 13, 2021.",
"keywords": [
"Anesthesiology",
"Machine Learning",
"Postoperative Complications",
"Protocol",
"Surgery"
],
"content": "Introduction\n\nEach year, more than four million people worldwide die within 30 days after surgery, making perioperative events the third-leading cause of death.1 One common postoperative complication that is associated with an increased risk of death is acute kidney injury (AKI).2–6 In one retrospective study, postoperative AKI occurred in 39% of hospitalized surgical patients who had their creatinine checked after surgery.7 In-hospital mortality increased from 0.6% among those without AKI to 8.8% among those who experienced AKI.\n\nSome postoperative deaths and AKI may be prevented through identification and modification of risk factors. Although some risk factors (e.g., age8–10) are not modifiable and other risk factors (e.g., preoperative glycemic control8,11,12) are no longer modifiable once surgery has begun, several important risk factors are under the anesthesiologist’s control during surgery. For example, intraoperative hypotension is a well-established risk factor both for postoperative death13–15 and for postoperative AKI.15–17 Interventions on such risk factors may therefore affect outcomes.18,19 Appropriate adjustments to the postoperative care plan may also impact outcomes.19\n\nTelemedicine has successfully improved mortality and other outcomes in the intensive care unit (ICU), and similar results may be expected in the operating room. In a stepped-wedge trial across units in a single medical center, tele-ICU implementation was associated with an absolute mortality reduction of nearly 2%.20 In a subsequent multi-center pre-post study, tele-ICU was associated with reduced in-hospital mortality and length of stay.21 Improved outcomes were associated with enhanced compliance with best clinical practice guidelines.20,21 The effect of telemedicine on outcomes may depend on characteristics of the patients in question—in one study, tele-ICU implementation improved mortality only among patients with higher illness severity scores.22\n\nThe effectiveness of a telemedicine intervention depends on how well clinicians working in the telemedicine setting can assess patient risk and identify potential interventions to reduce risk. Accurate intraoperative risk assessment by clinicians is challenging for the following reasons. First, the sheer volume of data available is more than the human brain can comprehend with its limited data processing capacity.23,24 Competing clinical demands reduce the cognitive capacity available to process these data.25,26 Second, anesthesiology clinicians frequently use the available data to make decisions that are not based on sound logic.27 Clinicians may anchor on the first diagnosis that comes to mind, only seek out data that confirm a previously suspected diagnosis, or interpret ambiguous findings with a false sense of certainty.27 These concerns become increasingly significant as clinicians monitor increasing numbers of patients and have less time to review each patient’s information.\n\nClinicians in telemedicine settings may use machine learning (ML) tools to address their innate cognitive deficiencies. Computers can process larger quantities of data more quickly than a human, model more complex relationships and interactions among inputs, and will not fatigue.28–30 The ability of clinicians to integrate the output of ML tools into their overall assessment of the patient depends on the ML output being presented in a manner that makes sense to the clinician and caters to the clinician’s information needs.31,32 These needs will vary depending on the clinician’s background and the context in which the clinician is working.\n\nThis study is possible because the investigators have previously developed ML algorithms for predicting postoperative death and AKI. They used a retrospective cohort of approximately 110,000 patients who underwent surgical procedures at Barnes-Jewish Hospital between 2012 and 2016.33 This dataset was divided into a training set (for model parameter tuning), a validation set (for hyperparameter tuning), and a test set (for quantifying model performance) in a ratio of approximately 7:1:2. Inputs to the models included patient characteristics, health conditions, preoperative vital signs and laboratory values, and intraoperative vital signs and medications. The resulting model predicted postoperative death with excellent accuracy (area under the receiver operating characteristic curve of 0.91, 95% confidence interval 0.90-0.92).34,35 A separate model predicted AKI with good accuracy (area under the receiver operating characteristic curve of 0.82, 95% confidence interval 0.81-0.84).36\n\nIn addition, the investigators have recently conducted a series of focus groups and user interviews with anesthesiology clinicians (unpublished data) to learn about their workflows and information needs when working in the intraoperative telemedicine unit at Barnes-Jewish Hospital. Based on these insights, the investigators have designed a display interface that shows ML predictions for postoperative death and AKI in real-time during surgery.\n\nTo determine whether anesthesiology clinicians in a telemedicine setting can predict postoperative death and AKI more accurately with ML assistance than without ML assistance. The hypothesis is that clinician predictions will be more accurate with ML assistance than without ML assistance.\n\nThe Perioperative Outcome Risk Assessment with Computer Learning Enhancement (Periop ORACLE) study will be a sub-study nested within the ongoing TECTONICS trial (NCT03923699). TECTONICS is a single-center randomized clinical trial assessing the impact of an anesthesiology control tower (ACT) on postoperative 30-day mortality, delirium, respiratory failure, and acute kidney injury.37 As part of the TECTONICS trial, clinicians in the ACT perform medical record case reviews during the early part of surgery and document how likely they feel each patient is to experience postoperative death and AKI. In Periop ORACLE, these case reviews will be randomized to be performed with or without access to ML predictions.\n\n\nMethods: Participants, interventions, and outcomes\n\nThe study will be conducted at Barnes-Jewish Hospital, a 1,252-bed university-affiliated tertiary care facility in St. Louis, MO. About 19,000 inpatient surgeries are performed in the hospital’s 58 operating rooms each year.\n\nThe participants will include all patients enrolled in the TECTONICS trial during the 12-month sub-study period for whom the ACT clinicians conduct a case review. The inclusion criteria for TECTONICS include (1) surgery in the main operating suite at Barnes-Jewish Hospital, (2) surgery during hours of ACT operation (weekdays 7:00am-4:00pm), and (3) age ≥ 18. Exclusion criteria include procedures performed without anesthesiology services.\n\nParticipants are currently enrolled in TECTONICS via a waiver of consent. The investigators have obtained a waiver of informed consent to include these patients in Periop ORACLE as well.\n\nClinicians in the ACT currently conduct case reviews by viewing the patient’s records in AlertWatch (AlertWatch, Ann Arbor, MI) and Epic (Epic, Verona, WI). AlertWatch is an FDA-approved patient monitoring system designed for use in the operating room. Clinicians in the ACT use a customized version of AlertWatch that has been adapted for use in a telemedicine setting.38 Epic is the electronic health record system utilized at Barnes-Jewish Hospital. For patients included in Periop ORACLE, each case review will be randomized in a 1:1 fashion to be completed with or without ML assistance. If the case review is randomized to ML assistance, the clinician will access a display interface (currently deployed as a web application on a secure server) that shows real-time ML predicted likelihood for postoperative death and postoperative AKI. Study staff will be immediately available in the ACT during all case reviews to assist with accessing the display interface if needed to improve adherence to the protocol. If the case review is not randomized to ML assistance, the clinician will not access this display. This choice of comparator mimics current practice more closely than using an active comparator. After viewing the patient’s data, the clinician will complete a case review from in AlertWatch (as described in the data collection section later in this document).\n\nThe co-primary outcomes will be clinician accuracy in predicting postoperative death and clinician accuracy in predicting postoperative AKI. Clinician predictions will be retrieved from the case review forms completed in AlertWatch. Observed death and observed AKI will be retrieved from Epic. Death will be defined as 30-day in-hospital mortality. AKI will be defined as a creatinine increase ≥0.3 mg/dl above baseline within 48 hours or an increase to ≥ 1.5 times baseline within seven days, consistent with the kidney disease: improving global outcomes definition.39\n\nNo direct interactions between study staff and the participants are planned, and no anesthetic interventions will be prohibited based on participation in this trial. The initial medical record review and clinician predictions will occur during the participants’ surgery. Additional data retrieval to obtain observed death and AKI will occur at least 30 days after surgery (and may occur in bulk 30 days after the final participant’s surgery).\n\nThe sample size calculation is based on the assumption that ML-assisted clinicians would predict each outcome with receiver operating curve area under curve (AUC) similar to the published AUC of the ML algorithms.34,36 Incidences of death and AKI were also taken from these previous publications. A simulation population of 100,000 patients was generated. ML-assisted and -unassisted clinician predictions were simulated with beta distributions whose parameters were adjusted to achieve the specified AUC. For each sample size tested, 1,000 random samples were drawn and the difference in AUC between the assisted and unassisted clinician predictions was determined.40 Power at each sample size was defined as the fraction of samples for which the two sets of predictions had significantly different AUC at α = 0.025. The minimum clinically meaningful difference (MCMD) in AUC was defined as 0.07.\n\nAs shown in Figure 1, a sample size of 4,500 will provide 80% power to detect a difference in AUC from 0.91 to 0.84 (the MCMD) for death and 95% power to detect a difference from 0.91 to 0.81. This sample size will give >99% power to detect a difference in AUC from 0.82 to 0.75 (the MCMD) for AKI (Figure 2).\n\nPower achieved in simulations of various sample sizes and effect sizes for postoperative death. Blue line is minimum clinically meaningful difference.\n\nPower achieved in simulations of various sample sizes and effect sizes for postoperative AKI. Blue line is minimum clinically meaningful difference.\n\nTo allow for 15% missing data, we will enroll 5,300 cases. Currently, about 20 case reviews are performed in the ACT on a typical day. We should therefore be able to complete enrollment over a period of 12 months.\n\n\nMethods: Assignment of interventions\n\nEach participant case review will be randomized in a 1:1 fashion to be completed with or without ML assistance. Randomization will be stratified by intervention/control status of the parent trial because clinicians may be biased to perform case reviews more carefully in the TECTONICS intervention group than in the TECTONICS control group (Figure 3). The allocation sequence will be generated by computer-generated random numbers within the AlertWatch software. The allocation will be automatically displayed on the case review form when the clinician opens it. The study staff will not have access to the allocation sequence before the case review.\n\nPeriop ORACLE participants will be randomizated to ML assistance or no ML assistance, stratified by intervention or control status of the parent TECTONICS trial.\n\nBy necessity, the clinician completing the case review and the other study staff in the ACT will not be blinded to treatment allocation. Study personnel who retrieve observed postoperative complications from the electronic health record will be blinded.\n\n\nMethods: Data collection, management, and analysis\n\nClinician predictions will be collected via an existing case review form in AlertWatch that contains two sections (Figure 4). In the first section, the clinician documents how likely the patient is to experience postoperative death within 30 days, postoperative AKI within seven days, and a few other complications. The clinician selects their choice from a five-point ordered categorical scale (very low risk, low risk, average risk, high risk, and very high risk). In the second section (which is part of the parent TECTONICS trial but not used for this sub-study), the clinician selects treatment recommendations (e.g., blood pressure goals, medications to administer or avoid). An additional question asks the clinician to confirm whether they reviewed the ML display interface prior to documenting their predictions in section one. Finally, clinicians are asked whether the ML predictions on the display interface agree with their previous opinion and whether the display interface caused the clinician to change their opinion.\n\nThe first two sections contain fields for documentation of clinician predictions of postoperative complications, and the Periop ORACLE randomization allocation is disclosed in the header of the second section. The treatment recommendations documented in the third section are utilized for the parent TECTONICS trial but not for this sub-study.\n\nObserved death and observed AKI will be retrieved from Epic via a query of the Clarity database. Observed outcomes will be retrieved for all randomized participants, including those with protocol deviations.\n\nThe clinical applications used in this project (AlertWatch and Epic) can only be accessed over the secure institutional internet network or using virtual private network, and user authentication is required for access. Computations for the ML models will occur on institutional servers that meet the standards of the Health Insurance Portability and Accountability Act. The ML display interface is also hosted on an institutional server, can only be accessed over the secure institutional internet network or using virtual private network, and requires user authentication for access. For data analysis, the amount of protected health information retrieved will be limited to the minimum amount necessary to achieve the aims of the study. All study data will be stored on institutional servers, and access will be limited to study personnel.\n\nTo compare the accuracy of clinician predictions with and without ML assistance, the investigators will construct logistic regressions for death and for AKI. Separate models will be constructed for the ML-assisted and -unassisted groups. The only inputs will be dummy variables encoding the clinician predictions (Table 1). The regression coefficients will be restricted to positive values, thus modeling a monotonic increasing relationship between the clinician predictions and the true incidence of death and AKI. The AUC of the model constructed from ML-assisted cases will be compared to the AUC of the model constructed from ML-unassisted cases,40 using the Holm method to ensure the family-wise error rate remains less than a two-sided α = 0.05 across the two co-primary outcomes—accuracy of death prediction and accuracy of AKI prediction. The null hypothesis is that the AUCs will be equal.\n\nThe primary analysis will follow an intention-to-treat principle, and all case reviews will be included in the group to which they were randomized. In a secondary per-protocol analysis, case reviews will be grouped according to whether the clinician reported viewing the ML display or not. Exploratory analyses stratified by sex and race will evaluate for biases learned during training.41 If either clinician predictions or observed outcomes are missing for a given case, then the case will be excluded from the analysis. No interim analyses are planned. To determine whether different levels of clinician engagement in the TECTONICS intervention group versus the TECTONICS control group impact the findings, sensitivity analyses will be conducted stratified by TECTONICS intervention status.\n\n\nEthics and dissemination\n\nThis study has been approved by the Human Research Protection Office at Washington University in St. Louis (approval #202108022) on August 26, 2021. Any protocol amendments will be approved by the study steering committee and communicated with the institutional review board. This study presents patients with minimal risks, other than a small risk for a breach of confidentiality if protected health information were to become unintentionally available to individuals outside the study team. To protect against this risk, all electronic data will be kept in an encrypted, password-protected environment accessible only to the research team (see Data Management section). Because the risks are minimal, no dedicated safety monitoring committee is planned for Periop ORACLE. However, the parent TECTONICS trial does have a safety monitoring committee. The institutional review board has granted a waiver of informed consent to enroll patients in this study.\n\nStudy results will be presented at national or international scientific meetings and published in a peer-reviewed publication. Individuals who meet the International Committee of Medical Journal Editors authorship guidelines (https://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html) will be included as authors on any publications resulting from this work. To comply with data sharing recommendations, de-identified individual participant data underlying the study results will be made available to researchers who provide a methodologically sound proposal for utilizing that data.\n\nThis project has multiple strengths. First, this protocol has been prepared in accordance with Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) guidelines.42,43 Second, the sample size of predictions made by experienced anesthesia clinicians will be large. The pragmatic design of superimposing Periop ORACLE on the established TECTONICS trial where many case reviews are already being conducted on a daily basis makes it feasible to achieve such a large sample size. Third, the ML models to be used have very good AUC, which enhances the likelihood that ML assistance can increase the accuracy of clinician predictions. Fourth, the ML display interface has been created using a human-centered design framework informed by the clinicians who work in the ACT, which maximizes the chances that clinicians will integrate the ML display interface into their workflows and their decision-making.\n\nThis project also has limitations. First, data collection in a telemedicine setting rather than in the operating room may limit the generalizability of the findings to institutions that do not utilize intraoperative telemedicine. However, multiple clinicians have stated during focus group interviews that their workflows for performing case reviews in the ACT closely mimic their workflows for preparing to provide bedside anesthesiology care. Thus, the findings may be relevant in the operating room as well. Second, this is a single-center study, so differences in patient population or practice patterns at other institutions may limit generalizability. However, many large academic medical centers care for patient populations similar to those seen at Barnes-Jewish Hospital. Third, some of the outcomes may be incompletely measured. While in-hospital vital status should always be available, some patients may not have a postoperative creatinine measurement available to distinguish whether AKI has occurred. However, AKI is expected to be extremely uncommon among patients without postoperative labs, minimizing the effect of this potential bias. Fourth, AKI is defined using creatinine only and not urine output, based on anticipated data availability. This may cause some cases of AKI to be missed. However, during ML model training, the incidence of AKI using this definition was compatible with the incidence of AKI reported in other studies. Finally, clinicians may give the ML display interface varying degrees of weight during case reviews randomized to ML assistance. Understanding this variability is of interest to the research team, which is why the case review form will ask the clinician how the ML display impacted their decision-making.\n\nThe expected result is that prediction accuracy for death and for AKI to be greater with ML assistance than without ML assistance. If the null hypothesis is rejected for only one of the two co-primary outcomes, this result will still be viewed as evidence that the ML assistance is beneficial. A possible unintended consequence would be if false negative ML predictions lead telemedicine clinicians to pay less attention to some patients who are actually at high risk for death or AKI.22 Even if ACT clinicians monitor these patients less intensely, these patients will still receive standard-of-care monitoring and care by clinicians in the operating rooms. Thus, the reduction in telemedicine monitoring should not result in patient harm. The telemedicine clinicians supplement, but do not replace, standard care.\n\nIntraoperative telemedicine has the potential to improve postoperative outcomes if interventions can be targeted to patients most at-risk for complications, and ML may be able to help clinicians distinguish which patients those are. Periop ORACLE will test the hypothesis that anesthesiology clinicians in a telemedicine setting can predict postoperative complications more accurately with ML assistance than without ML assistance. By nesting this study within the ongoing TECTONICS randomized clinical trial of intraoperative telemedicine, the investigators will efficiently assemble a large dataset of clinician predictions that will be used to achieve the study objective. Successful completion of this study will help define the role of ML not only for intraoperative telemedicine, but for other risk assessment tasks before, during, and after surgery.\n\n\nData availability\n\nNo data are associated with this article.\n\n\nReporting guidelines\n\nThis protocol is presented according to the SPIRIT guidelines.\n\nOpen Science Framework: “Protocol for the Perioperative Outcome Risk Assessment with Computer Learning Enhancement (Periop ORACLE) Randomized Study”. https://doi.org/10.17605/OSF.IO/GC4ES.43\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
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Proc. Natl. Acad. Sci. U. S. A. 2011; 108(27): 11252–11255. PubMed Abstract | Publisher Full Text\n\nGaba DM, Lee T: Measuring the workload of the anesthesiologist. Anesth. Analg. 1990; 71(4): 354–361. PubMed Abstract\n\nZenati MA, Leissner KB, Zorca S, et al.: First reported use of team cognitive workload for root cause analysis in cardiac surgery. Semin. Thorac. Cardiovasc. Surg. 2019; 31(3): 394–396. PubMed Abstract | Publisher Full Text\n\nStiegler MP, Tung A: Cognitive processes in anesthesiology decision making. Anesthesiology 2014; 120(1): 204–217. Publisher Full Text\n\nSinha A, Singh A, Tewari A: The fatigued anesthesiologist: A threat to patient safety? J. Anaesthesiol. Clin. Pharmacol. 2013; 29(2): 151–159. PubMed Abstract | Publisher Full Text\n\nHoward SK, Rosekind MR, Katz JD, et al.: Fatigue in Anesthesia: Implications and Strategies for Patient and Provider Safety. Anesthesiology 2002; 97(5): 1281–1294. Publisher Full Text\n\nGander PH, Merry A, Millar MM, et al.: Hours of Work and Fatigue-Related Error: A Survey of New Zealand Anaesthetists. Anaesth. Intensive Care 2000; 28(2): 178–183. PubMed Abstract | Publisher Full Text\n\nLintern G, Motavalli A: Healthcare information systems: the cognitive challenge. BMC Med. Inform. Decis. Mak. 2018; 18(1): 3. PubMed Abstract | Publisher Full Text\n\nJohnson CM, Johnson TR, Zhang J: A user-centered framework for redesigning health care interfaces. J. Biomed. Inform. 2005; 38(1): 75–87. PubMed Abstract | Publisher Full Text\n\nFritz BA, Chen Y, Murray-Torres TM, et al.: Using machine learning techniques to develop forecasting algorithms for postoperative complications: protocol for a retrospective study. BMJ Open 2018; 8(4): e020124. PubMed Abstract | Publisher Full Text\n\nFritz BA, Cui Z, Zhang M, et al.: Deep-learning model for predicting 30-day postoperative mortality. Br. J. Anaesth. 2019; 123(5): 688–695. PubMed Abstract | Publisher Full Text\n\nFritz BA, Abdelhack M, King CR, et al.: Update to ‘Deep-learning model for predicting 30-day postoperative mortality’(Br J Anaesth 2019; 123: 688–95). Br. J. Anaesth. 2020; 125(2): e230–e231. PubMed Abstract | Publisher Full Text\n\nCui Z, Fritz BA, King CR, et al.: A factored generalized additive model for clinical decision support in the operating room. AMIA Annu. Symp. Proc. 2019; 2019: 343–352.\n\nKing CR, Abraham J, Kannampallil TG, et al.: Protocol for the Effectiveness of an Anesthesiology Control Tower System in Improving Perioperative Quality Metrics and Clinical Outcomes: the TECTONICS randomized, pragmatic trial. F1000Res 2019; 8: 2032. PubMed Abstract | Publisher Full Text\n\nMurray-Torres T, Casarella A, Bollini M, et al.: Anesthesiology Control Tower—Feasibility Assessment to Support Translation (ACTFAST): Mixed-Methods Study of a Novel Telemedicine-Based Support System for the Operating Room. JMIR Hum. Factors 2019; 6(2): e12155. PubMed Abstract | Publisher Full Text\n\nKellum JA, Lameire N: Diagnosis, evaluation, and management of acute kidney injury: a KDIGO summary (Part 1). Crit. Care 2013; 17(1): 204. PubMed Abstract | Publisher Full Text\n\nDeLong ER, DeLong DM, Clarke-Pearson DL: Comparing the Areas under Two or More Correlated Receiver Operating Characteristic Curves: A Nonparametric Approach. Biometrics 1988; 44(3): 837–845. Publisher Full Text\n\nZou J, Schiebinger L: AI can be sexist and racist—it’s time to make it fair. Nature 2018; 559(7714): 324–326. PubMed Abstract | Publisher Full Text\n\nChan A-W, Tetzlaff JM, Altman DG, et al.: SPIRIT 2013 statement: defining standard protocol items for clinical trials. Ann. Intern. Med. 2013; 158(3): 200–207. PubMed Abstract | Publisher Full Text\n\nFritz B: Perioperative Outcome Risk Assessment with Computer Learning Enhancement (Periop ORACLE) Randomized Study.2022, May 19. Publisher Full Text"
}
|
[
{
"id": "143767",
"date": "22 Jul 2022",
"name": "Michael Robert Mathis",
"expertise": [
"Reviewer Expertise Machine learning applied to healthcare",
"anesthesiology",
"prediction modeling",
"large observational database research",
"acute kidney injury prediction."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study is a protocol a sub-study nested within the TECTONICS RCT (assessing the impact of telemedicine approaches to preoperative risk assessment), seeking to understand the impact of machine-learning based prediction models to improve the accuracy of such preoperative risk assessments.\n\nThe study follows SPIRIT guidelines for reporting, and is overall well-written and of great clinical significance to anesthesiologists. Strengths of the study include its rigorous design; weaknesses include its single-center nature and perhaps limited exploration of unintended consequences of machine learning algorithm implementation.\n\nOverall I believe this study will be an important scientific contribution to the field of anesthesiology, and look forward to its execution. However as the protocol is currently written, I have several critiques for the authors to address:\n1) There limitations of using solely a creatinine-based AKI endpoint (as opposed to creatinine + UOP + dialysis), but on balance I recognize the choice to focus on simply creatinine, given it is widely available within the EHR. However, there are other unusual circumstances that the authors might consider, that may lead to misguided conclusions if left unaddressed:\na. How are patients with stage 4 or 5 CKD handled? Perhaps they are included, but it is misleading to think that AKI in such patients has anything to do with perioperative care, as most will develop AKI simply due to their native pathophysiology. b. If there is an EGFR-based cut-off for inclusion, how is EGFR computed? Would recommend the 2021 CKD-EPI formula which addresses racial bias. c. How are patients with no preoperative creatinine available handled? d. How are patients undergoing procedures which by definition impair renal function handled? (e.g. renal artery embolization; nephrectomy for RCC, etc.). e. Are dialysis access procedures (e.g. AV fistula placements) included in this study?\n\n2) I agree from both a study power / and clinical significance standpoint in using AKI Stage 1 or greater as AKI outcome (and of course mortality is more challenging to power); however you might consider breaking down AKI by stages as a secondary outcome (e.g. Stage 2 or greater; Stage 3 or greater), given their greater clinical significance (although even Stage 1 is important).\n3) It could be helpful to explore unintended consequences of the machine learning algorithm implementation. For example, workload/efficiency metrics may be useful to track: the authors may wish to track the total amount of ‘active review time’ used by clinicians in performing preoperative assessments with and without aid of the machine learning algorithm. If implemented in clinical care, there should be a plan (perhaps covered by the DSMB of the TECTONICS trial) to understand unexpected outcomes (for example, increased risk of stroke or MI, at the expense of decreased risk of AKI).\n4) As the AKI and mortality prediction algorithms are imperfect, do the clinicians performing preoperative risk assessments have insight into the performance characteristics of the algorithm (for example, do they know the algorithm’s positive predictive value, negative predictive value; perhaps Shapley values, AUROC, AUPRC, etc.), in order to better understanding exactly how much they should be trusting it? It may be interesting to study the impact of the machine-learning based risk assessments, for the cases in which the algorithm was *wrong*… in order to understand the potential impact of automation bias induced by machine learning algorithms on clinical decision-making.\n5) One of the major issues confronting ML-based algorithm support in healthcare decision-making is dataset shift – defined as an evolving mismatch between the data upon which the algorithm is trained upon, versus the data the algorithm is using in real-time to make predictions (PMID 34260843). Maintaining algorithm robustness over time remains very challenging, and decreases in algorithm performance can be seen whenever there are changes to practice patterns, EHR documentation patterns, or shifts in the patient population being studied. Although this study is limited by its single-center nature, it is not limited in its ability to assess temporal trends / algorithm de-tuning (and potential effects of algorithm re-tuning, if the authors wish to incorporate this into the study) over the time period studied. I would suggest assessing temporal trends in (i) AKI and mortality prediction algorithm performance, which if decreased may lead to a temporal trend in (ii) outcomes of this study.\n\n6) Whereas the study protocol appropriately follows SPIRIT guidelines, when this study is executed and reported, this study will most likely need to follow DECIDE-AI guidelines (PMID 35585198), although I could be mistaken. The study team may wish to consider that downstream study now, and have the trial protocol written in such a way that the downstream study will be able to best adhere to DECIDE-AI reporting guidelines.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "8808",
"date": "23 Sep 2022",
"name": "Bradley Fritz",
"role": "Author Response",
"response": "Thank you for your thoughtful review of this protocol. We have revised the protocol to address your concerns, and we feel these changes have made the protocol stronger. Please see our point-by-point response below: COMMENT 1a. How are patients with stage 4 or 5 CKD handled? Perhaps they are included, but it is misleading to think that AKI in such patients has anything to do with perioperative care, as most will develop AKI simply due to their native pathophysiology. Patients who are on dialysis preoperatively and patients with baseline creatinine level > 4.0 mg/dl will be excluded from the analyses of AKI, but other patients with CKD will be included. We agree that AKI will be highly prevalent among patients with CKD. Although some (many?) cases of AKI in this population will not be preventable, other cases will be driven at least partly by modifiable risk factors. All patients, including those on dialysis preoperatively and those with baseline creatinine > 4.0 mg/dl, will be included in the analyses of postoperative death. We have added a sentence to make this clearer: “Patients on dialysis preoperatively, undergoing dialysis access procedures, or with baseline creatinine > 4.0 mg/dl will be excluded from the AKI analysis but included in the death analysis.” (Methods/Statistical Methods) COMMENT 1b. If there is an EGFR-based cut-off for inclusion, how is EGFR computed? Would recommend the 2021 CKD-EPI formula which addresses racial bias. We agree that historically common EGFR equations can introduce racial bias, and we appreciate the reviewer’s suggestion for an alternative. As noted above, we will not use an EGFR-based cut-off for inclusion. COMMENT 1c. How are patients with no preoperative creatinine available handled? If no preoperative creatinine was available, then the upper limit of the laboratory’s reference range (1.2 mg/dl) was used as the baseline. We felt this was a reasonable approximation because patients with abnormal renal function before surgery would most likely have a creatinine value available. We have added a sentence to make this clearer: “If no preoperative creatinine is available, then the upper limit of the laboratory’s reference range (1.2 mg/dl) will be used as the baseline.” (Methods/Outcomes) COMMENT 1d. How are patients undergoing procedures which by definition impair renal function handled? (e.g. renal artery embolization; nephrectomy for RCC, etc.). These patients will be included in the AKI analyses. Although it may frequently not be possible to prevent AKI in these situations, it may be possible to lessen its severity. Therefore, a clinician would want to be aware of the elevated risk in these patients. COMMENT 1e. Are dialysis access procedures (e.g. AV fistula placements) included in this study? Patients undergoing dialysis access procedures will be excluded from the analyses of AKI. However, they will be included in the analyses of postoperative death. We have added a sentence to make this clearer: “Patients on dialysis preoperatively, undergoing dialysis access procedures, or with baseline creatinine > 4.0 mg/dl will be excluded from the AKI analysis but included in the death analysis.” (Methods/Statistical Methods) COMMENT 2. I agree from both a study power / and clinical significance standpoint in using AKI Stage 1 or greater as AKI outcome (and of course mortality is more challenging to power); however you might consider breaking down AKI by stages as a secondary outcome (e.g. Stage 2 or greater; Stage 3 or greater), given their greater clinical significance (although even Stage 1 is important). Thank you for this suggestion. We have added these as secondary outcomes: “Secondary outcomes will include AKI stage 2 or greater (creatinine increase to ≥ 2 times baseline within seven days) and AKI stage 3 (creatinine increase to ≥ 3 times baseline within seven days, an increase to ≥ 4.0 mg/dl, or initiation of renal replacement therapy).” (Methods/Outcomes) COMMENT 3. It could be helpful to explore unintended consequences of the machine learning algorithm implementation. For example, workload/efficiency metrics may be useful to track: the authors may wish to track the total amount of ‘active review time’ used by clinicians in performing preoperative assessments with and without aid of the machine learning algorithm. If implemented in clinical care, there should be a plan (perhaps covered by the DSMB of the TECTONICS trial) to understand unexpected outcomes (for example, increased risk of stroke or MI, at the expense of decreased risk of AKI). We agree it would be insightful to investigate the time spent reviewing each case. If the machine learning algorithms have an impact on active review time, then the impact could plausibly be in either direction: clinicians may spend less time in the patient’s chart for ML-assisted cases because the algorithms have expedited the risk assessment process, or they may spend more time because the algorithms have pointed out concerns the clinicians otherwise would not have noticed. We have added this to the data collection and analysis plans: “The amount of time the clinician in the ACT spends completing each case review will be retrieved from the Epic audit log.” (Methods/Data collection) “To estimate the effect of the ML predictions on case review efficiency, chart review duration (approximated using the time the Epic chart was open, retrieved from the audit log) will be compared between case reviews performed with ML assistance and those performed without ML assistance, using either an unpaired T test or Wilcoxon rank sum test as appropriate.” (Methods/Statistical methods) Information from the case reviews performed in ORACLE will only be communicated to bedside clinicians in the operating room if the patient is in the intervention arm of the parent TECTONICS trial. (All patients in ORACLE are also enrolled in TECTONICS.) The TECTONICS trial has a data safety monitoring committee that reviews adverse events. COMMENT 4. As the AKI and mortality prediction algorithms are imperfect, do the clinicians performing preoperative risk assessments have insight into the performance characteristics of the algorithm (for example, do they know the algorithm’s positive predictive value, negative predictive value; perhaps Shapley values, AUROC, AUPRC, etc.), in order to better understanding exactly how much they should be trusting it? It may be interesting to study the impact of the machine-learning based risk assessments, for the cases in which the algorithm was *wrong*… in order to understand the potential impact of automation bias induced by machine learning algorithms on clinical decision-making. We have added a new paragraph to explain what pieces of meta-data are provided along with the predictions: “For each patient, the machine learning predictions are presented in the form of predicted probabilities of each outcome (e.g., 4.5% chance of AKI). In addition, a list of features contributing most to the prediction is shown, along with Shapley values. During the focus group meetings, most users said they would find it overwhelming to see confidence intervals around the predicted probabilities. A fact sheet about each model is available on demand, including the receiver operating characteristic curve, precision-recall curve, and calibration curve.” (Methods/Interventions – Machine Learning Algorithms) To address the impact of “wrong” predictions, we have added a sensitivity subgroup analysis: “To examine the potential impact of inaccurate ML predictions, we will conduct the following sensitivity analysis. First, the predicted probabilities output by the ML algorithms will be converted to dichotomous predictions by using the cutoff value that maximizes the Youden index. Second, the cases will be categorized as having correct or incorrect ML dichotomized predictions. Finally, the primary analysis will be repeated in the subgroup with correct ML predictions and in the subgroup with incorrect ML predictions.” (Methods/Statistical methods) COMMENT 5. One of the major issues confronting ML-based algorithm support in healthcare decision-making is dataset shift – defined as an evolving mismatch between the data upon which the algorithm is trained upon, versus the data the algorithm is using in real-time to make predictions (PMID 34260843). Maintaining algorithm robustness over time remains very challenging, and decreases in algorithm performance can be seen whenever there are changes to practice patterns, EHR documentation patterns, or shifts in the patient population being studied. Although this study is limited by its single-center nature, it is not limited in its ability to assess temporal trends / algorithm de-tuning (and potential effects of algorithm re-tuning, if the authors wish to incorporate this into the study) over the time period studied. I would suggest assessing temporal trends in (i) AKI and mortality prediction algorithm performance, which if decreased may lead to a temporal trend in (ii) outcomes of this study. This is an important point that we had considered but failed to mention in the previous version of the protocol. At the time the study was initiated, we were utilizing models that had been trained on a retrospective cohort of patients who had surgery at Barnes-Jewish Hospital between 2012 and 2016. Approximately six months after study initiation, we retrained the models using patients who had surgery between 2018 and 2020. We have added two new paragraphs to the methods section to explain this clearly: “The machine learning models used in this study were originally trained and validated on a retrospective cohort of approximately 110,000 adult patients who underwent surgery with general anesthesia at Barnes-Jewish Hospital between 2012 and 2016. Input features included demographic characteristics, comorbid conditions, preoperative vital signs, surgical service, functional capacity as documented during the preoperative assessment, and most recent values of selected laboratory tests. A random forest model was implemented in scikit-learn. In the holdout validation cohort of 21,171 patients, the incidence of postoperative death was 2.2% and the model predicted this outcome with receiver operating characteristic area under curve (AUC) of 0.939 and precision-recall AUC of 0.161. The incidence of postoperative AKI was 6.1% and the model predicted this outcome with receiver operating characteristic AUC of 0.799 and precision-recall AUC of 0.275. In February 2022, the models were retrained using a newer cohort of 84,455 patients who underwent surgery with general anesthesia at Barnes-Jewish Hospital between 2018 and 2020. This time period was after the hospital had transitioned from its previous electronic health record systems (including MetaVision as its anesthesia information management system) to Epic (Epic, Verona, WI). Input features were the same as the previous models, with the addition of the planned surgical procedure text field. A regularized logistic regression was used to predict the outcome from the words in the planned surgical procedure text field. This was used to initialize a gradient boosted decision tree, which was trained using the remaining features. Hyperparameters were selected by 10-fold cross validation. Models were implemented in XGBoost. In the holdout validation cohort of 16,891 patients, the incidence of postoperative death was 1.9% and the model predicted this outcome with receiver operating characteristic AUC of 0.91 and precision-recall AUC of 0.27. The incidence of postoperative AKI was 13.3% and the model predicted this outcome with receiver operating characteristic AUC of 0.90 and precision-recall AUC of 0.66.” (Methods/Interventions – Machine Learning Algorithms) To examine the effects of dataset shift on model performance and trends over time, we will report the prospective performance (i.e., AUC) of each model for each month of the study. To examine the effects of model retraining, we will also conduct subgroup analyses repeating the primary analyses in the subgroups who had surgery before and after the retraining event. We have added these steps to the statistical methods: “To examine the effects of dataset shift and model retraining, the prospective performance of the models will be reported for each month of the study, and sensitivity analyses will be conducted in the subgroups who had surgery before and after the February 2022 retraining event.” (Methods/Statistical methods) COMMENT 6. Whereas the study protocol appropriately follows SPIRIT guidelines, when this study is executed and reported, this study will most likely need to follow DECIDE-AI guidelines (PMID 35585198), although I could be mistaken. The study team may wish to consider that downstream study now, and have the trial protocol written in such a way that the downstream study will be able to best adhere to DECIDE-AI reporting guidelines. Thank you for this suggestion—we agree the study results will be reported according to DECIDE-AI guidelines. To make it easier for the results manuscript to adhere to DECIDE-AI guidelines, we have expanded the methods section of this protocol to add details that are required by the DECIDE-AI guidelines. In particular, we have broken up the Intervention subsection into two new sections describing the AI system (checklist item 4) and describing the implementation (checklist item 5), which are mentioned in our responses to your earlier comments. In addition, we have added statistical methods that will allow us to report on human-computer agreement (checklist item 12): “To examine human-computer agreement, the proportion of cases for which the clinician reported being surprised by the ML prediction will be determined. Among those cases for which the clinician was surprised, the proportion for which the clinician self-reported agreeing or disagreeing with the ML prediction will be determined.” (Methods/Statistical methods)"
}
]
}
] | 1
|
https://f1000research.com/articles/11-653
|
https://f1000research.com/articles/11-474/v1
|
29 Apr 22
|
{
"type": "Research Article",
"title": "Critical delay factors for construction projects in Central Aceh District, Indonesia",
"authors": [
"Anita Rauzana",
"Aghnia Zahrah",
"Wira Dharma",
"Aghnia Zahrah",
"Wira Dharma"
],
"abstract": "Background: Construction development in Indonesia is growing rapidly, especially in Central Aceh District. Construction projects have distinctive characteristics and are very complex, so that risk events can have a serious impact on the viability of the project. A lack of attention to the risks faced will affect project implementation by creating delays, resulting in losses. The purpose of this study was to (1) identify the risk factors that cause delays in construction projects and (2) determine those particular risk factors that have a greater influence on construction projects. The location of this research was Central Aceh District, Indonesia. Methods: The data in this study were primary data in the form of a questionnaire and secondary data obtained from the literature related to this particular type of research. Questionnaires were distributed to respondents, namely contractor companies located in the Central Aceh District. The questionnaires were distributed to determine respondents' opinions about the level of influence of risk factors causing project delays. We used a validity test, reliability test, and descriptive analysis for data processing. Results: Based on the results of the study from 47 respondents, the “very high influence” category (Mode=5) for the tool malfunction factor was chosen by 21 respondents (44.68%), cost estimation inaccuracy by 20 respondents (42.55%), increased work costs by 22 respondents (46.81%), implementation of new technologies by 25 respondents (53.19%), details, accuracy and conformity to specifications that are not appropriate by 20 respondents (42.55%), worker quarrels by 20 respondents (42.55%), poor project planning and management by 22 respondents (46.81%), poor condition at locations and accessibility difficulty by 20 respondents (42.55%). Conclusions: Of the 80 risk factors that caused project delays, eight risk factors were found to have a very high influence on the implementation of construction projects in Central Aceh District.",
"keywords": [
"delay factors",
"project management",
"risk management",
"construction industry",
"schedule delays"
],
"content": "Introduction\n\nThe Central Aceh Regency is one of the regions in Aceh Province, Indonesia, experiencing rapid growth. This can be observed in the number of construction projects currently underway.1 The implementation of construction projects in the Central Aceh Regency often experiences failures and delays,1 which can cause project losses. Construction projects are dynamic and consist of limited resources. A complex project can cause high-risk and uncertain events that can cause delays and cost overruns on projects,2 thus allowing for uncertainty in the implementation process, which leads to various types of risks that ultimately cause losses to the parties involved in the construction project and affect the achievement of the desired goal. Risk is a condition in which there is a possibility of gain/loss,3 with losses, such as cost losses, injuries, and delays caused by uncertainty during project implementation. One of the most influential risk factors is changing the order.4 Delays in the implementation of projects are among the risks that often occur in the implementation of construction projects, especially in developing countries.5–8 Project delays and cost overruns can harm projects.9\n\nAn increase in fuel prices can cause cost increases, losses, and delays in construction projects.6,10 There are five causes for a project loss: (1) improper planning and scheduling, (2) many changes to orders by clients, (3) incompetent site management and supervision, (4) inexperienced subcontractors, and (5) poor contractor finances.11 Experienced contractors can accelerate a project schedule.12 The most influential risk factor for projects in Jordan (the Middle East) is poor soil/site conditions in construction projects.13\n\nPrevious research has shown that delays in project implementation can lead to cost overruns.14 Delays affect planning and control,15 especially during project implementation.16 Project delays can lead to losses, legal problems, and contract termination.17,18 The contractor suffers losses owing to cost overruns. For example, in Nigeria, cost overruns and delays are frequent factors affecting projects.19 It is important to apply risk management to avoid project failure because construction projects are complex and involve many risks.20 Project risk is defined as an unforeseen event or situation that can harm a project.21 Risk management is an important process for achieving project objectives.22,23 Identifying, assessing, and managing construction project risks is indispensable for risk management. A successful project is time- and cost-effective, and has good construction quality.24 Managing risk is an important mechanism in the construction sector, which is performed to obtain project objectives in the form of cost, time, safety, and good quality25; the most influential risk factor is material.26\n\nDevelopment projects globally often involve considerable risk. Inflation causes delays and losses.27 Risks can affect the time, cost, quality, and performance of a construction project.28 Time risk affects project costs. Project risk management aims to increase profits and reduce losses.29\n\nFor construction projects, overtime or delays are common during project implementation. Time delays can be described as events or interruptions that result in a project not being completed within the time specified in the contract. Defining delays as actions or activities that increase the time required by the contractor to conduct the project is referred to as time contingency.30\n\nOnly 30% of Saudi Arabian construction projects implemented require an average additional time of approximately 10–30%, where there are nine main groups of risk factors causing delays: costs, resources, contracts, schedule, government relations, personnel, planning, equipment, and environmental factors. Funding delay is the most important delay factor.31 In project implementation, the contractor company does not know the risk of project delays. Therefore, to avoid losses and delays in construction projects, research is needed to identify and analyze the factors causing delays in construction projects, particularly in Indonesia and the Central Aceh District, given the complex conditions of the district, including socio-cultural diversity, high inflation rates, low public education, frequent disasters, community economy weakness, geographic location, social and political conflicts, and economic crises.32\n\nRisk identification is conducted by collecting all information related to activities and analyzing it to find every possible risk that could result in a loss. Risk identification can be performed using several techniques.33 Identifying risks in a project consists in compiling (1) a list of risks that can cause losses, (2) a list of potential losses, and in this checklist compiling (3) a list of losses and (4) a ranking of losses occurring, and then (5) classifying losses. Project delays also occur owing to work accidents.34 The type of soil and rock at the project site is one of the main risk factors for project delay.35\n\n\nMethods\n\nThe primary data in this study was questionnaire data; the questionnaire was distributed to 47 respondents and contained 80 questions about project delays. Secondary data were obtained from studies in the literature such as journals, books, and other literature related to this research, as well as data about contractor companies obtained from the National Construction Services Association. The distribution of questionnaires aimed to determine the level of influence of risk factors causing project delays; a closed questionnaire was used, where answer choices had been determined in advance, and respondents were given the opportunity to choose the most appropriate answer.36 For data processing, we used a validity test, a reliability test, and descriptive analysis.\n\nThe questionnaire was composed of two parts: questionnaire A and questionnaire B. Questionnaire A concerned the characteristics of respondents, and questionnaire B concerned the level of influence of factors causing project delays. Assessment of the level of influence of 80 project delay risk factors was carried out using a Likert scale, which consists of five points as defined in previous studies (e.g., References 31,37,38). The Likert scale has previously been used to measure the perceptions of respondents about social events39–41 and can be seen in Table 1.\n\nThe data collected for this research were questionnaire data, from questionnaire tools distributed to respondents, namely contractor companies located in Central Aceh District. The collection of data was carried out over two months by the researchers. This study used probability sampling, namely simple random sampling in distributing questionnaires. Simple random sampling technique is a technique consisting in taking samples randomly from members of the population.42 The targeted respondents were contractors from the Central Aceh Regency, which has a population of 53 contractor companies. The experimental procedures were approved by the Institutional Review Board at Syiah Kuala University (IRB protocol number 99). All of these experimental methods were carried out in accordance with the regulations of the Institutional Review Board of Syiah Kuala University in Indonesia, and all participants gave their informed consent. The total sample size was 47 companies, calculated from the total population with an inaccuracy allowance of 5%, then by using the Slovin formula.43 Data collection was performed by distributing questionnaires to respondents directly.\n\nTable 2 shows that based on the identification of risk factors for delay, there were 80 causes of construction project delays, which were categorised into seven main factors.\n\nDescriptive statistics are used to collect, organize and process data to be presented and provide a clear picture, regarding a particular condition or event where the data is taken. Descriptive statistics are to present data clearly, in order to be taken or certain meanings.44 Descriptive statistics provide an overview of the object under study through sample or population data without analyzing and making conclusions that apply to the public.45 Quantitative descriptive research describes data in the form of numbers, and the size of the data includes the mean value, mode, and median. The size of the data deployment includes variance and standard deviation.46 Descriptive statistical analysis determines the most influential factors on project delays, and uses mode value, which is the data that appears most often.\n\n\nResults and discussion\n\nThe validity test is a tool to test whether each question item truly reveals the factors or indicators that need to be investigated.47 Validity testing was performed by distributing the questionnaires to 20 respondents. A validity test was performed for each variable using Pearson's product moment analysis. The variable was considered valid if the rxy value was greater than the r-table value. The r-table value obtained was 0.288, with degrees of freedom (df) associated with or an error level of 0.05, in both directions. The question had a value greater than 0.288; therefore, the questionnaire was deemed feasible and valid.\n\nA reliability test was conducted to determine whether the questionnaire was reliable, with a coefficient of ≥ 0.6. If the value was above 0.60, the questionnaire was considered reliable and feasible to use.48\n\nAs shown in Table 3, a reliability coefficient of 0.958 was obtained. This shows that the coefficient of Cronbach's alpha for the variable causing the delay was greater than 0.6. Therefore, the questionnaire was deemed to be reliable.\n\nQuestionnaires were distributed to 47 respondents; their characteristics are presented in Table 4.\n\nQuestionnaires were distributed to 47 respondents, and the results of distributing questionnaires on the characteristics of the respondents can be concluded based on the results of the research in Table 4. It was found that most companies, that is, 18 companies (38.30%) had over 15 years of experience in the construction sector, and the majority (26 companies, 55.32%) had handled several construction projects above 10. The majority, i.e.41 companies (87.23%) had estimated project durations of 0–6 months per year.\n\nA descriptive analysis was used to determine the level of influence of the delay risk variable. The descriptive analysis uses the mode value to determine the data that appear most often, and thus the responses that are most chosen by the respondents are obtained. The results of the levels of the factors influencing project delays are shown in Table 5.\n\nTable 6 shows that of the 80 variables causing project delays, based on the respondents' opinions, there were eight risk factors in the very high influence category (Mode = 5), 71 factors of high influence category (Mode = 4), and one factor that belonged to the medium influence category (Mode = 3).\n\nFigure 1 shows that the research results identified eight factors causing project delays that had a mode value of 5, including the very high influence category: tool malfunction, cost estimation inaccuracy, increased work costs, implementation of new technologies, details, inappropriate accuracy and conformity to specifications, workers quarrel, poor project planning and control, poor condition at locations, and accessibility difficulty.\n\nFigure 1 shows that of the 47 respondents, 21 (44.68%) chose the very high influence category (mode =5) for the tool malfunction factor. Cost estimation inaccuracy was chosen by 20 respondents (42.55%), increased work costs by 22 respondents (46.81%), implementation of new technologies by 25 respondents (53.19%), details, accuracy, and conformity to specifications that were not appropriate by 20 respondents (42.55%), workers quarrel by 20 respondents (42.55%), poor project planning and control by 22 respondents (46.81%), poor condition at locations, and accessibility difficulty by 20 respondents (42.55%).\n\nBased on the results of the questionnaire distribution, Figure 2 shows that 89% of respondents chose the high influence category, 10% chose the very high influence category, and 1% chose the medium influence category. The results of the descriptive statistics on the influence level of each delay factor are shown in Table 5.\n\nFactor 1: Tool malfunction\n\nThe distribution of ratings for the mode value for tool malfunction was 5 (very high influence). Therefore, the results of the study indicate that the majority of respondents rated the tool malfunction indicator as having a very high influence on project delays.6,49,50 Equipment damage can cause losses and endanger workers. One of the problems that often occurs is the tool’s age; the tool becomes damaged if it is too old. To avoid damage to the tool, it is best to perform routine and periodic maintenance such that the tool is more durable in operation.\n\nFactor 2: Cost estimation inaccuracy\n\nThe mode value for the cost estimation inaccuracy was 5 (very high influence). Therefore, the results of the study show that the majority of respondents rated the cost estimation inaccuracy indicator as having a very high influence over project delays. Cost estimation inaccuracies can result in delays and losses.49 Cost estimation is a calculation of the costs required to complete an activity or work in accordance with the requirements or contract; therefore, if the cost calculation is not appropriate, risk increases and can cause losses to the project. Therefore, accurate cost estimation is required to avoid risk. The main risk and uncertainty factor in a project is the estimated cost.51\n\nFactor 3: Increased work costs\n\nThe mode value for the increased work cost indicator was 5 (very high influence). Therefore, the results of the study indicate that the majority of respondents assess the indicator of increased work costs as having a very high influence on project delays. Cost overruns often occur in a project because the project implementation costs are greater than the project budget planning that has been set at the initial stage (estimated), which can cause significant losses for the project contractor. An increase in work costs is one of the causes of project delays.6,52 The increase in the cost of work needs to be considered because it involves the amount of investment that must be made by the owner, where the cost overrun is vulnerable to the risk of failure. Therefore, project costs must be managed properly to minimize the possibility of cost overruns. Cost control is the final step of the project cost management process, which ensures that the use and expenditure of costs are in accordance with the planning in the form of a predetermined budget, and thus there is no increase in work costs.\n\nFactor 4: Implementation of new technologies\n\nThe mode value for the implementation of new technologies was 5 (very high influence). Therefore, the results of the study indicate that the majority of respondents assessed the implementation of new technologies as having a very high influence on project delays. The development of new technological innovation and creativity is key to winning over competition and building resilience in the construction industry.53 Mastery and utilization of technology is needed by construction industry players to compete globally.53 The application of new and special technology that is not well known is a risk factor for project implementation because if the contractor does not know or understand new technology, it can hinder the implementation of the project, cause the project to fail or not be in accordance with the plans and losses, and can cause project delays.6,49\n\nFactor 5: Details, accuracy and conformity to specifications that are inappropriate\n\nInappropriate details, accuracy, and conformity to specifications have a mode value of 5 (very high influence). Therefore, the results of the study indicate that the majority of respondents assess the indicators of detail, accuracy, and conformity to specifications that are inappropriate as having a very high influence on project delays. However, inappropriate specifications can hinder the implementation of construction projects.49\n\nFactor 6: Workers quarrel\n\nThe workers’ quarrel factor had a mode value of 5 (very high influence). Therefore, the results of this study indicate that the majority of respondents assessed the indicator of workers’ quarrels as having a very high influence on project delays. Workers’ quarrels are a risk factor that can disrupt the project because if there is a fight between workers, project implementation will automatically stop and cause delays.6,50 A method often used to resolve conflicts occurring between workers and in human resources on projects is a problem-solving approach, namely, discussing openly and directly using dialogue between the parties involved, identifying problems that cause conflict, seeking and collecting information on the causes of conflict, and analyzing various alternatives that are considered to be the best solution.54\n\nFactor 7: Poor project planning and controlling\n\nPoor project planning and controlling factors had a mode value of 5 (very high influence). Therefore, the results of this study indicate that the majority of respondents assessed poor project planning and control as having a very high influence on project delays. Poor project planning and control are weaknesses that can lead to the possibility of a project not going as planned, and the project results are also likely not to run as expected. Therefore, poor project planning and control can result in delays and losses for the contractors. Contracting companies have a significant influence on project delays.55,56 The views of clients and contractors on the causes of delays differ as they tend to blame each other for unfortunate incidents.14,50,57\n\nFactor 8: Poor conditions at locations and accessibility difficulty\n\nThe majority of respondents rated poor conditions and accessibility difficulty at locations as having a very high influence on project delays, where the distribution of ratings for the mode value was 5 (very high influence). Construction locations can be in poor conditions and inaccessible in the Central Aceh District, which is hilly and surrounded by mountains, making access to project sites quite difficult. Poor and difficult-to-reach project site conditions can affect project delays and potentially cause project failures6,58 because of (1) a lack of initial information on field conditions, (2) contractors not conducting initial surveys, and (3) the work environment not being prepared, such as land clearing and acquisition, fresh air supply, and adequate lighting.59 To avoid project delays and failures, it is expected that the contractor can collect information and conduct an initial survey regarding the condition of the project site before implementing the project such that the contractor can plan strategies for the project to run smoothly.\n\n\nConclusions\n\nThe Indonesian government is actively engaged in construction in various sectors to create prosperity and welfare for its people. However, there are still many obstacles to working on construction projects that are not in accordance with the planned schedule. One of these obstacles is delays in construction projects. Obstacles and risks often occur during project implementation, resulting in project delays and losses. Delay in the implementation of construction projects is one of the risks that often occurs in the implementation of construction projects, especially in developing countries. Project delays for contractors can cause time and cost losses because the profits expected by the contractor are reduced, the contractor does not obtain the expected profits, or there may even be no profits at all. For project owners, delays in completing work can cause losses. Various methods have been implemented to avoid the problems that result in delays and losses. Identifying the root causes of delays is an important first step in mapping the problems that can cause project delays. The correct solution or strategy to overcome delays will be easier to obtain if the project has a map of the main factors that can cause the project to experience delays in the schedule. In this study, 80 factors causing project delays were identified, of which eight main factors were categorized as having a very high influence (=5) in causing project delays.\n\nThe findings of this study are useful for academics and construction practitioners with potentially deeper insights into the root causes of project schedule delays. The continuous expansion of knowledge and understanding of the importance (criticality) of the causes of delays will assist stakeholders in reducing the incidence of delays, lead to appropriate strategies, and can be used as comparisons or benchmarks in development planning; thus, by knowing the causes of these delays, the contractor can properly calculate these risks to avoid losses impacting the project. However, further research should be conducted with a wider study area to increase the number of respondents.\n\nThis study has limitations, namely, sampling was only conducted in the Central Aceh District, and the scope of the study is not wide enough; therefore, the results of the study cannot be generalized to a wider population. The results of this study are specific to Central Aceh Regency, and are not expandable to other regions in Indonesia. Thus, similar studies can be conducted in other districts, provinces, and cities in Indonesia, and the results of the research can be generalized to other regions. Further research is needed to increase the number of respondents such that the results are more comprehensive.\n\nOur future research will aim to determine the effects of delay factors on construction project costs using the ordinal logistic regression method. Future research will be conducted to determine the delay factors that have a significant effect on construction project costs. These delay factors are expected to serve as a reference for contractor companies carrying out construction projects such that they can avoid construction project losses.\n\n\nData availability\n\nZenodo: Raw data for the study of the f1000 manuscript entitled: Critical Delay Factors for Construction Project in Central Aceh District, Indonesia\n\nThis project contains the following underlying data:\n\n- Raw Data(1).xlsx\n\nZenodo: Raw data for the study of the f1000 manuscript entitled: Critical Delay Factors for Construction Project in Central Aceh District, Indonesia\n\nThis project contains the following extended data:\n\n- Questionnaire1.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nSyam F: Community Leader of Central Aceh Regency: If the Multiyear Project Is Canceled, We Can Ask for Separation. Aceh Journal National Network. 2020. (accessed Feb. 07, 2021). Reference Source\n\nQazi A, Quigley J, Dickson A, et al.: Project Complexity and Risk Management (ProCRiM): Towards modelling project complexity driven risk paths in construction projects. Int. J. Proj. Manag. 2016; 34: 1183–1198. Publisher Full Text\n\nGray CF, Larson EW: Project Management: The Managerial Process. Singapore: McGraw-Hill; 2000.\n\nRauzana A: The effect of the risk factors on the performance of contractors in Banda Aceh, indonesia. ARPN J. Eng. Appl. Sci. 2016; 11(15): 9496–9502.\n\nAlsuliman JA: Causes of delay in Saudi public construction projects. Alex. Eng. J. 2019; 58(2): 801–808. Publisher Full Text\n\nAziz RF, Abdel-Hakam AA: Exploring delay causes of road construction projects in Egypt. Alex. Eng. J. 2016; 55(2): 1515–1539. Publisher Full Text\n\nMahdi I, Soliman E: Significant and top ranked delay factors in Arabic Gulf countries. Int. J. Constr. Manag. 2019; 21(14): 167–180. Publisher Full Text\n\nMpofu B, Godfrey E, Moobela OC, et al.: Profiling causative factors leading to construction project delays in the United Arab Emirates. Eng. Constr. Archit. Manag. 2017; 24(2): 346–376. Publisher Full Text\n\nAl Amri T, Marey-Pérez M: Towards a sustainable construction industry: Delays and cost overrun causes in construction projects of Oman. J. Proj. Manag. 2020; 5: 87–102. Publisher Full Text\n\nRumimper R: Risk Analysis on Housing Construction Projects in Minahasa-North Regency. Sci. J. Media Eng. 2015; 5(2): 381–389.\n\nYap JB, Goay PL, Woon YB, et al.: Revisiting critical delay factors for construction: Analysing projects in Malaysia. Alex. Eng. J. 2021; 60(1): 1717–1729. Publisher Full Text\n\nAlwi S, Hampson K: Identifying the important causes of delays in building construction projects. Proceedings Ninth EastAsia-Pacific Conference on Structural Engineering and Construction, Bali, Indonesia. 2003; pp. 1–6.\n\nAbu Salem ZT, Suleiman A: Risk factors causing time delay in the Jordanian construction sector. Int. J. Eng. Res. Technol. 2020; 13(2): 307–315. Publisher Full Text\n\nYap JBH, Skitmore M: Investigating design changes in Malaysian building projects. Archit. Eng. Des. Manag. 2018; 14(3): 218–238. Publisher Full Text\n\nZarei B, Sharifi H, Chaghouee Y: Delay causes analysis in complex construction projects: a Semantic Network Analysis approach. Prod. Plan. Control. 2018; 29(1): 29–40. Publisher Full Text\n\nShahsavand P, Marefat A, Parchamijalal M: Causes of delays in construction industry and comparative delay analysis techniques with SCL protocol. Eng. Constr. Archit. Manag. 2018; 25(4): 497–533. Publisher Full Text\n\nGbahabo PT, Ajuwon OS: Effects of project cost overruns and schedule delays in Sub- Saharan Africa. Eur. J. Interdiscip. Stud. 2017; 3(2): 46–58. Publisher Full Text\n\nSambasivan M, Deepak TJ, Salim AN, et al.: Analysis of delays in Tanzanian construction industry: Transaction cost economics (TCE) and structural equation modelling (SEM) approach. Eng. Constr. Archit. Manag. 2017; 24(2): 308–325. Publisher Full Text\n\nAibinu AA, Jagboro GO: The effects of construction delays on project delivery in Nigerian construction industry. Int. J. Proj. Manag. 2002; 20(8): 593–599. Publisher Full Text\n\nWu Y, Zhou J: Risk assessment of urban rooftop distributed PV in energy performance contracting (EPC) projects: An extended HFLTS-DEMATEL fuzzy synthetic evaluation analysis. Sustain. Cities Soc. 2019; 47(1): 101524. Publisher Full Text\n\nPMI: A guide to the project management body of knowledge (PMBOK guide). 6th ed.USA: Newton Square, USA: Project Management Institute; 2017.\n\nQazi A, Dikmen I: From risk matrices to risk networks in construction projects. IEEE Trans. Eng. Manag. 2019; 68(12): 1449–1460. Publisher Full Text\n\nAnsah RH, Sorooshian S: Effect of lean tools to control external environment risks of construction projects. Sustain. Cities Soc. 2017; 32: 348–356. Publisher Full Text\n\nHwang B, Ngo J, Her PWY: Integrated Digital Delivery: Implementation status and project performance in the Singapore construction industry. J. Clean. Prod. 2020; 262: 121396. Publisher Full Text\n\nEskander RFA: Risk assessment influencing factors for Arabian construction projects using analytic hierarchy process. Alex. Eng. J. 2018; 57(4): 4207–4218. Publisher Full Text\n\nRauzana A: Identification and Assessment of Risk Factors Affecting Construction Projects in North Aceh, Indonesia. IOSR J. Bus. Manag. 2016; 18(09): 72–77. Publisher Full Text\n\nRauzana A: The Influence of Uncertainty Variables on Cost Estimation Lesson Learned From Construction Industry in Indonesia. Aust. J. Basic Appl. Sci. 2015; 9(April): 380–385.\n\nLeu SS, Chen AT, Yang CH: A GA-based optimal model for construction time-cost trade-off. Int. J. Proj. Manag. 2001; 19(1): 47–58. Publisher Full Text\n\nPMI: Construction Extension to the PMBOK® Guide. Project Management Institute, Inc.; 2016.\n\nStumpf GR: Schedule delay analysis. Cost Eng. Arbor Then Morgant. 2000; 42(7): 32–32.\n\nAssaf SA, Al-Hejji S: Causes of delay in large construction projects. Int. J. Proj. Manag. 2006; 24(4): 349–357. Publisher Full Text\n\nCentral Aceh District Government: Integrated Plan And Medium-Term Infrastructure Investment Plan, Central Aceh District, 2016-2020. Central Aceh District; 2020.\n\nKasidi: Risk Management. Bogor: Ghalia Indonesia; 2010.\n\nRauzana A, Dharma W: The knowledge and awareness of occupational health and safety requirements among civil engineering students in an Indonesian university. vol. 23(no. 3): pp. 210–215. 2021.\n\nSuárez M, García-Romero E, Baz A, et al.: Smectites: The key to the cost overruns in the construction of the third set of locks of the Panama Canal. Eng. Geol. 2021; 284: 106036. Publisher Full Text\n\nNasution S: Research Methods (Scientific Research). Jakarta: Bumi Aksara; 6th ed.2003.\n\nLe-Hoai L, Lee YD, Lee JY: Delay and cost overruns in Vietnam large construction projects: A comparison with other selected countries. KSCE J. Civ. Eng. 2008; 12(6): 367–377. Publisher Full Text\n\nBagaya O, Song J: Empirical study of factors influencing schedule delays of public construction projects in Burkina Faso. J. Manag. Eng. 2016; 32(5): 05016014. Publisher Full Text\n\nSugiyono: Combined Research Methods (Mixed Methods). Bandung: Alfabeta; 2013.\n\nRiduwan and Sunarto: Introduction to Statistics for Research: Education, Social, Communication, Economics, and Business. Bandung: Alfabeta; 2014.\n\nVagias WM: Likert-type scale response anchors. Clemson International Institute for Tourism & Research Development. Department of Parks, Recreation and Tourism Management, Clemson University; 2006.\n\nSugiyono: Combination Research Methods. Bandung: Alfabeta; 2015.\n\nRauzana A, Dharma W: Causes of delays in construction projects in the Province of Aceh, Indonesia. PLoS One. 2022; 17(1): e0263337. PubMed Abstract | Publisher Full Text\n\nHasan I: Research Data Analysis with Statistics. Jakarta: PT Bumi Aksara; 2004.\n\nJaya I: Application of Statistics for Educational Research. jakarta, Indonesia: Prenadamedia Group; 2019.\n\nKaur P, Stoltzfus J, Yellapu V: Descriptive statistics. Int. J. Acad. Med. 2018; 4(1): 60–63. Publisher Full Text\n\nArikunto S: Research Management. Jakarta: Rineka Cipta; 2013.\n\nSekaran U: Research methods for business: A skill building approach. 4th ed.John Wiley & Sons; 2006.\n\nSangari F, Tjakra J: Risk Analysis of Housing Construction Projects in Manado City. Sci. J. Media Eng. 2011; 1(1): 29–37.\n\nAziz RF: Ranking of delay factors in construction projects after Egyptian revolution. Alex. Eng. J. 2013; 52(3): 387–406. Publisher Full Text\n\nAidil M, Rauzana A, Muhammad N: A Study on Drinking Water Distribution Project in Banda Aceh. J. Phys. Conf. Ser. 2021; 1933(1): 012091. Publisher Full Text\n\nRodrigues-da-Silva LH, Crispim JA: The project risk management process, a preliminary study. HCIST J. 2014; 16: 943–949. Publisher Full Text\n\nKusumawanti R: Construction Industry Needs New Technology. Portonews; 2019. (accessed Jun. 07, 2021). Reference Source\n\nSusila H: Conflict Handling Methods In The Implementation Of Building Construction Projects In Surakarta. J. Civ. Archit. Eng. 2012; 12(16): 6–10.\n\nMydin MAO, Sani NMM, Taib NM, et al.: Imperative causes of delays in construction projects from developers’ outlook.2014. Publisher Full Text\n\nRao PB, Camron CJ: Causes of delays in construction projects: A case study. Int. J. Curr. Res. 2014; 6(6): 7219–7222.\n\nAl-Kharashi A, Skitmore M: Causes of delays in Saudi Arabian public sector construction projects. Constr. Manag. Econ. 2009; 27(1): 3–23. Publisher Full Text\n\nMuka I: Risk Analysis in the Sulawesi Denpasar Road Basement Parking Development Project. J. Civ. Eng. Commun. Media. 2012; 19(2): 155–165. Publisher Full Text\n\nPrice D, Andy K: Causes Leading to Poor site Coordination in Building Projects. Organ. Technol. Manag. Constr. - An Int. J. 2010; 2(2): 167–172."
}
|
[
{
"id": "142319",
"date": "20 Jul 2022",
"name": "Christopher Amoah",
"expertise": [
"Reviewer Expertise Construction project management"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract\nThe abstract omitted the implication of the study and the value of the paper\n\nThe author can state the factors without stating the number of participants and percentages in the result section.\nKeywords should be arranged in an alphabetical order\nIntroduction\nThe introduction is not well-written, and the research objective is not clearly stated. The authors did not discuss problem implementation challenges in the case study district that are needed to be addressed by this study. The authors discussed project delay factors in other countries without focusing on the case study area/country. The author must address these deficiencies.\nLiterature\nThis section was omitted. The author should discuss the following topics\nCauses of project delays\n\nEffects of project delays on stakeholders\n\nProject risk factors\n\nThe description of the case study district\n\nMethodology\n\nThe author claimed to have studied literature, yet there was no literature review section\n\nThe author should explain how the 80 factors were arrived at.\n\nThe author should back the efficacy of the sample size used for this study with some authorities in the literature.\n\nThe author should explain the procedures used in collecting the data\n\nThe author should explain why the Central Aceh district was chosen for the study\n\nTable 2 should be removed from this section.\nResult and discussion\n\nThe demographic data should include experience in the construction industry, educational level and nature of projects executed\n\nI suggest the author calculate the mean and standard deviation values for all the factors to see if the top 8 factors mentioned will suffice.\n\nCreate another column in table 5 and indicate the influence levels\n\nThe discussions of the top factors are shallow. The authors should also discuss the implications of the findings\n\nThe author should separate results from discussions\n\nThe discussion should be based on the 2 main research objectives, namely\nidentify the risk factors that cause delays in construction projects\n\ndetermine those particular risk factors that have a greater influence on construction projects.\n\nConclusion\nRecommendations should be given to the concerned stakeholders\nCommunication\nThe quality of communication is good, but proofreading is required\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8617",
"date": "16 Aug 2022",
"name": "Anita Rauzana",
"role": "Author Response",
"response": "ABSTRACT REVIEWER COMMENT: The abstract omitted the implication of the study and the value of the paper RESPONSE: Thank you very much. We agree with the reviewer and we have added study implication in the abstract REVIEWER COMMENT: The author can state the factors without stating the number of participants and percentages in the result section. RESPONSE: Thank you very much. We have stated the factors without stating the number of participants and percentages in the result section. REVIEWER COMMENT: Keywords should be arranged in an alphabetical order RESPONSE: Thank you very much. We agree with the reviewer and we've fixed the writing of keywords in alphabetical order INTRODUCTION REVIEWER COMMENT: The introduction is not well-written, and the research objective is not clearly stated. RESPONSE: Thank you very much. We have corrected the writing of the Introduction and the research objectives have been clearly stated. REVIEWER COMMENT: The authors did not discuss problem implementation challenges in the case study district that are needed to be addressed by this study. The authors discussed project delay factors in other countries without focusing on the case study area/country. The author must address these deficiencies. RESPONSE: Thank you very much. We agree with the reviewer and we have written a discussion of the challenges of implementing the problems in the case study districts that need to be addressed by this research. LITERATURE REVIEWER COMMENT: This section was omitted. The author should discuss the following topics 1. Causes of project delays 2. Effects of project delays on stakeholders 3. Project risk factors 4. The description of the case study district RESPONSE: Thank you very much. We agree with the reviewer, we have added Literature Review to discuss the following topics: 1. Causes of project delays 2. Effects of project delays on stakeholders 3. Project risk factors 4. The description of the case study district METHODOLOGY REVIEWER COMMENT: The author claimed to have studied literature, yet there was no literature review section RESPONSE: Thank you very much. We agree with the reviewer, we have added Literature Review REVIEWER COMMENT: The author should explain how the 80 factors were arrived at RESPONSE: Thank you very much, we have explained how the 80 factors were arrived at REVIEWER COMMENT: The author should back the efficacy of the sample size used for this study with some authorities in the literature. RESPONSE: Thank you very much, we have added literature to support the efficacy of the sample size used for this study by several authorities in the literature. REVIEWER COMMENT: The author should explain the procedures used in collecting the data RESPONSE: Thank you very much, we have added an explanation of the procedure used in collecting the data REVIEWER COMMENT: The author should explain why the Central Aceh district was chosen for the study RESPONSE: Thank you very much, we have added an explanation of why the Central Aceh district was chosen for the study REVIEWER COMMENT: Table 2 should be removed from this section. RESPONSE: Thank you very much. we agree with the reviewer, we already deleted Table 2 in the methodology section. RESULT AND DISCUSSION REVIEWER COMMENT: The demographic data should include experience in the construction industry, educational level, and nature of projects executed RESPONSE: Thank you very much, we've added experience in the construction industry, level of education, and nature of projects executed to the demographic data. REVIEWER COMMENT: I suggest the author calculate the mean and standard deviation values for all the factors to see if the top 8 factors mentioned will suffice. RESPONSE: Thank you very much. We appreciate the suggestion given by the reviewer to calculate the mean and standard deviation values for all the factors to see if the top 8 factors mentioned will suffice. However, in this study, we use the mode value to obtain the most influential delay factors (Mode=5) on a construction project, where the results show that of the 80 variables causing project delays, based on the respondents' opinions, there were eight risk factors in the very high influence category (Mode = 5), 71 factors of high influence category (Mode = 4), and one factor that belonged to the medium influence category (Mode = 3). REVIEWER COMMENT: Create another column in table 5 and indicate the influence levels RESPONSE: Thank you very much. We have created a column in table 4 which shows the level of influence of the factors that have been made in Table 4, namely in the fifth column REVIEWER COMMENT: The discussions of the top factors are shallow. The authors should also discuss the implications of the findings. RESPONSE: Thank you very much. We have added a discussion of the implications of the research findings REVIEWER COMMENT: The author should separate results from discussions RESPONSE: Thank you very much. We have separated the results from the discussion REVIEWER COMMENT: The discussion should be based on the 2 main research objectives, namely: identify the risk factors that cause delays in construction projects determine those particular risk factors that have a greater influence on construction projects. RESPONSE: Thank you very much. We have added a discussion based on 2 main research objectives, namely: Identify the risk factors that cause delays in construction projects Determine those particular risk factors that have a greater influence on construction projects. CONCLUSION REVIEWER COMMENT: Recommendations should be given to the concerned stakeholders RESPONSE: Thank you very much. We agree with the reviewer and we have added recommendations to concerned stakeholders in the conclusion section COMMUNICATION REVIEWER COMMENT: The quality of communication is good, but proofreading is required RESPONSE: Thank you very much. We have proofread this article"
}
]
},
{
"id": "143751",
"date": "01 Aug 2022",
"name": "Atasya Osmadi",
"expertise": [
"Reviewer Expertise Construction Project Management"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract\nThere is a lack in explaining why this article is interesting.\nIntroduction\nThe problem or issues to why this research is conducted in Central Aceh District is not properly discussed. The authors mainly discussed the project delay factors in other countries and not discussing on the case study area/country.\n\nMethodology\nThe author claimed that secondary data obtained from the literature related to this particular type of research and yet there was no section on literature review and how the 80 factors were determined. The reviewer could not tell which articles is being referred by the authors to determine this 80 factors.\n\nThe author should explain why the Central Aceh district was chosen for this research and where do they get the list or if there is any database for the 53 contractor companies. It is hard to tell if this research is significant without proper explanation\nResults\nA Research Article should be no more than 20,000 words but this research article has only around 5000 word. Results should be provided as required from the journal's format which includes: Preliminary pilot testing and any changes implemented resulting from preliminary testing\nConclusion/Discussion\nThere is lack of discussion in this section. Discussion based on the results should be here\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8618",
"date": "16 Aug 2022",
"name": "Anita Rauzana",
"role": "Author Response",
"response": "ABSTRACT REVIEWER COMMENT: There is a lack in explaining why this article is interesting. RESPONSE: Thank you very much. We agree with the reviewer and we've added an explanation in the abstract of why this article is interesting. INTRODUCTION REVIEWER COMMENT: The problem or issues to why this research is conducted in Central Aceh District is not properly discussed. The authors mainly discussed the project delay factors in other countries and not discussing on the case study area/country. RESPONSE: Thank you very much. We agree with the reviewer and we have added an explanation of why this research was conducted Central Aceh District METHODOLOGY REVIEWER COMMENT: The author claimed that secondary data obtained from the literature related to this particular type of research and yet there was no section on literature review and how the 80 factors were determined. The reviewer could not tell which articles is being referred by the authors to determine this 80 factors. RESPONSE: Thank you very much. We agree with the reviewer and we have added a literature review section and have defined the literature referring to the 80 factors of delay in Table 1 in the Literature Review section. REVIEWER COMMENT: The author should explain why the Central Aceh district was chosen for this research and where do they get the list or if there is any database for the 53 contractor companies. It is hard to tell if this research is significant without proper explanation RESPONSE: Thank you very much. We agree with the reviewer and we have explained why the Central Aceh district was chosen for this research, and also explained where to get the list of 53 contractor companies. RESULTS REVIEWER COMMENT: A Research Article should be no more than 20,000 words but this research article has only around 5000 word. Results should be provided as required from the journal's format which includes: Preliminary pilot testing and any changes implemented resulting from preliminary testing RESPONSE: Thank you very much. We agree with the reviewer and we have added words to this research article and it has reached 11068 words, and we have separated the results section from the discussion section. CONCLUSION/DISCUSSION REVIEWER COMMENT: There is lack of discussion in this section. Discussion based on the results should be here RESPONSE: Thank you very much. We agree with the reviewer and we have added a discussion section based on research results"
}
]
}
] | 1
|
https://f1000research.com/articles/11-474
|
https://f1000research.com/articles/10-943/v1
|
20 Sep 21
|
{
"type": "Study Protocol",
"title": "A study protocol to prepare an RBD protein for vaccine against COVID-19",
"authors": [
"ZMG Sarwar Jahangir",
"Arleta Helena Marnik",
"Arleta Helena Marnik"
],
"abstract": "Background: The SARS-CoV-2 pandemic is a global threat to humans and the world’s economy. Effective and safe vaccines against this virus are essential to control and eradicate the pandemic. The currently applied vaccines carry SARS-CoV-2 spike-protein mRNA/cDNA. These vaccines go through several cellular processes in the recipients for producing antigens. On the contrary, the SARS-CoV-2 RBD (receptor binding domain)-protein is an antigen. It will directly stimulate antibody production against SARS-CoV-2. Hence, we propose to produce SARS-CoV-2 RBD-protein as a fast acting, effective and safe vaccine. Methods: We propose to reconstruct a plasmid carrying three types of DNA sequences: RBD cDNA, FP (fusion peptide) DNA and sfGFP(superfolder green fluorescent protein), cDNA creating the RBD-FP-sfGFP DNA within an orf (open reading frame). Escherichia coli, C2566H, transformed with the reconstructed plasmid will express RBD-FP-sfGFP fusion protein producing green fluorescent cfu (colony forming unit). The RBD-protein will be separated from the sfGFP using an FP specific enterokinase, and eluted by HIC (hydrophobic interaction chromatography), detected with a BioVision Elisa kit, and quantified by spectrophotometry at UV280nm. Results: The plasmid reconstruct will carry ampr (ampicillin-resistant) gene as a selective marker and a T7 promoter controlling the expression of RBD-FP-sfGFP fusion protein. The transformed Escherichia coli will efficiently express the RBD-FP-sfGFP fusion protein. The highly efficient sfGFP fused within the RBD-FP-sfGFP will produce green fluorescent cfu. The RBD-FP-sfGFP protein extract from the green cfu, digested by enterokinase and separated by the HIC will produce pure RBD protein. Conclusion: A positive BioVision ELISA test detects <10 pg RBD protein/ml of the sample. A larger sample of the purified RBD protein can be used as a vaccine following a standard formulation and safety protocols. Once administered, the RBD protein will stimulate antibody production against the SARS-CoV-2 virus. The RBD protein has no potential to recombine with human genome.",
"keywords": [
"receptor angiotensin-converting enzyme 2",
"amino acids",
"colony forming unit",
"hydrophobic interaction chromatography",
"Luria Bertani microbial culture medium containing ampicillin",
"fusion peptide",
"open reading frame",
"receptor binding protein",
"Spike protein",
"severe respiratory syndrome coronavirus 2",
"superfolder green fluorescent protein."
],
"content": "Introduction\n\nUsing the “RNA-Dependent RNA Polymerase Molecular Clock”, it was estimated that the common ancestor of coronavirus (CoV) appeared about 10,000 years ago.2,3 The first human upper respiratory tract infection (URTI) caused by human CoV (H-CoV) was reported in 1965.4-7 The first severe acute respiratory syndrome caused by CoV (SARS-CoV) was reported from Guangdong, China, in 2002, that ultimately spread over many countries causing an epidemic in the Americas, Europe, and Asia, infecting over 8,098 people and killing about 774 of the infected.6,8 SARS-CoV has 99.6% genome sequence homology to CoV found in masked palm civets (Paguma larvata) and 88% – 95% homology to CoV found in several horseshoe bats, Rhinolophus pussilius, R. macrotis, R. pearsoni and R. sinicus.9-11\n\nThis was followed by another outbreak of a CoV epidemic in 2012 that started in Saudi Arabia, which is known as Middle East respiratory syndrome (MERS) and is caused by MERS-CoV.12,13 It spread over 27 countries, reaching Western Africa to the west and South Korea to the east, infecting over 2,400 and killing over 850 people.12,13 The survivors suffered from many diseases including heart, kidney, and multiorgan failures.12,14,15 In November 2019, another CoV epidemic emerged in Wuhan, China, found to be caused by SARS-CoV-2 infections, leading to a global pandemic. That epidemic infected over 179 million people and killed over 3.8 million as of June 2021.16\n\nCoronavirus infections are not a new challenge to human survival. Some of those challenges, we know, others are unknown to us. However, it is clear that the recent pandemic of 2019 will not be the last, and we have to be alert and keep us ready to be safe for the future.\n\nAll types of viruses mutate and evolve as they replicate. Their prolonged presence in an uncontrolled environment favors development of new variants. That ability to generate de novo diversity in a short period of time, as well as the rate of spontaneous mutation, vary among viruses. Furthermore, mutation rates in RNA viruses are higher than DNA viruses, and are higher in single-stranded viruses than double-stranded viruses.17\n\nHence, vaccinating a smaller segment of a population against SARS-CoV-2 may favor generation of new variants with new infectivity. In that scenario, even the vaccinated individuals would face risks from arrivals of new variants. This may only be brought under control by administering a safe and effective vaccine as soon as possible to a significantly large part of the population. Successes of such efforts will reduce the development of new variants and, thus, help the global human population attain herd immunity.18\n\nAs cases of coronavirus disease 2019 (COVID-19) were growing globally, it brought together the efforts of worldwide biotechnologists, scientists, experts, pharmaceuticals, and investors to develop effective vaccines against SARS-CoV-2 as soon as possible. More than 50 such vaccine candidates were put into human trials in 2020, and a total of 250 vaccine candidates were in the process of being developed.19 The safety and effectiveness of a vaccine are measured by the vaccine’s long-term antigenicity and immunogenicity for its therapeutic application as a vaccine. However, we still do not have direct evidence of the long-term efficacy of the short life mRNA and long-life cDNA antigenic vaccines.\n\nSARS-CoV-2 mutates at a rate four times slower than the influenza virus, and the new variants have a minimal effect on antigenicity of the virus.20,21 Although the coronaviruses mutate at a slower rate, some of the new variants of SARS-CoV-2, such as D 614 G, that mutated outside the receptor-binding domain (RBD) residue have a higher rate of infectivity by boosting viral replication in lung and respiratory tract tissues.22,23 This suggests that the RBD residue is more conserved and, hence, the RBD protein vaccines will be effective against multiple SARS-CoV-2 variants.\n\nThe RBD is a small segment of the spike protein (S-protein) located on the outer membrane of the SARS-CoV-2 virion. It plays a critical role in binding the virus to the angiotensin-converting enzyme 2 (ACE-2) receptors on human mucosal cells, causing infection leading to COVID-19. Hence, an antibody generated against the RBD protein will be able to strongly prevent any SARS-CoV-2 infection.\n\nAccording to Huang, et al.,24 the S-protein located on the SARS-CoV-2 virus envelope is composed of 1273 amino acids (aa). The S-protein consists of a 13 aa long signal peptide (1–13 residues), followed by a 672 aa long S1 domain (14-685 residues), and a 588 aa long S2 domain (686–1273 residues). The S1 domain contains a 292 aa long N—terminal domain (14–305 residues) and a 223 aa long RBD domain (319–541 residues). The SARS-CoV-2 encapsulating membrane holds many trimeric S-proteins, each containing three RBD protein monomers, that binds to the ACE-2 receptors present in human cells.25 Furthermore, Yang, et al.,26 also demonstrated that the S1 domain of the SARS-CoV-2 spike protein directly binds to ACE-2 receptors expressed by the undifferentiated human alveolar cells (A549) facilitating the entry of SARS-CoV-2 into these cells. It was also reported that the SARS-CoV-2 receptor-blocking human antibody, HA001, attaches to amino acid residues A475 and F486 in the RBD of the SARS-CoV-2 spike protein.27 In this process, a 71 aa long segment of the RBD, known as receptor binding motif (RBM), tightly binds to the ACE-2 receptor.28 Furthermore, the RBD contains nine cysteine (Cys) residues making four pairs and keeping one free Cys. The three pairs are Cys336–Cys361, Cys379–Cys432, and Cys391–Cys525 residues that form the core RBD β sheet related to its 3D structure. The remaining pair, Cys480–Cys488 residue, binds to the N-terminal peptidase domain of ACE-2.29 All the above information supports that the RBD protein will be a highly effective antigen for vaccine production against SARS-CoV-2.\n\nWe propose to reconstruct an ampr plasmid expression vector carrying RBD and superfolder green fluorescent protein (sfGFP) cDNAs linked by an oligo DNA, coding for a fusion peptide (FP), Asp-Asp-Asp-Asp-Lys.1 The construct will be expressed using Escherichia coli, C2566H, producing the RBD-FP-sfGFP fusion protein. The RBD protein will be separated from the RBD-FP-sfGFP fusion protein by digestion with an enterokinase (specific for the FP) and isolated by hydrophobic interaction chromatography (HIC). The RBD eluate will be analyzed to determine its size by SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis), tested for its immuno-reactivity with SARS-CoV-2 S-protein antibody using a BioVision ELISA kit, and quantified by spectrophotometry. The purified RBD protein will be available to study its efficacy following approved vaccine formulation and clinical trials.\n\n\nProposed methods\n\nThis study protocol is a meticulously derived scientific procedure without involving any test animals or test subjects. Hence, it does not require ethical approval at this time. Any further information on this matter, may be obtained from the “Institutional Review Board” (IRB). Once we are ready to submit a grant application and execution of the protocol, we will seek the IRB approval in due course.\n\nThe following specialized reagents and materials (from the same or alternate sources) will be required in addition to regular materials and reagents available in a running biotechnology laboratory.\n\n1. RBD cDNA: Addgene plasmid, Cat #141184, pcDNA3-SARS-CoV-2-S-RBD-sfGFP (AmpR, NeoR/KanR).\n\n2. Prokaryotic host cells: Escherichia coli, NEB, Cat # C2566H.\n\n3. Plasmid DNA extraction kit: Promega PureYield Plasmid Miniprep System I and a Protocol. Promega, Cat # A1222, and Promega Technical Bulletin # TB374.\n\n4. Custom made linker oligo DNA coding for the FP to be used for plasmid recombination: It is a double-stranded linker oligo DNA with ss (single-stranded) 5′ overhangs. This will contain a forward strand, 5′ GATCGGATGATGATGATAAAC 3′, and a reverse strand, 3′ CCTACTACTACTATTTGCTAG 5′, each carrying a ss 5′ GATC 3′ overhang at the 5′ end, Figure 1, to be obtained from GenScript, NJ. The working concentration will be adjusted to 105 units in 1 μl.\n\n5. A chromatography kit: Green Fluorescent Protein Chromatography Kit, Bio-Rad, Cat # 1660005EDU. It is a HIC (hydrophobic interaction chromatography) kit.\n\n6. Protein dialysis tubing: SnakeSkin dialysis tubing with 10 kDa molecular weight cut-off, Thermo Fisher Scientific, Cat # 88243.\n\n7. Power supply unit: Invitrogen PowerEase Touch 600W Power Supply. Thermo Fisher Scientific, Cat # PS0601.\n\n8. Electrophoretic unit: Mini Gel Tank, Thermo Fisher Scientific, Cat # A25977.\n\n9. Protein electrophoresis gel slabs: NuPAGE 4-12%, Bis-Tris, 1 mm, 12-well mini protein gradient gel. Thermo Fisher Scientific, Cat # NP0322PK2.\n\n10. Protein sample buffer: NuPAGE LDS Sample Buffer (4×), Thermo Fisher Scientific, Cat # NP0007.\n\n11. Protein electrophoresis buffer: NuPAGE MES SDS Running Buffer (20×), Thermo Fisher Scientific, Cat # NP0002.\n\n12. Protein standard: Unstained Protein Standard, Broad Range (10-200 kDa) (NEB #P7717).\n\n13. Immunodetection kit: ELISA Kit, BioVision, Cat # E4877.\n\n14. Culture media and other reagents: LB (Luria-Bertini)-agar and LB broth, and SOC (Super Optimal broth with Catabolite repression medium) bacterial cell culture media; Isopropyl-β-D-1-thiogalactopyranoside (IPTG), from Thermo Fisher Scientific or NEB.\n\n15. Enzymes: BamHI (NEB, Cat # R3136S); Enterokinase (NEB, Cat #P8070); Enterokinase removal kit (Sigma-Aldrich, Cat # PRKE); Lysozyme solution (Millipore-Sigma, Cat # L3790); Proteinase K, 800 u/ml (NEB, Cat # P8107S); T4 DNA Ligase (NEB, M0202).\n\n16. Tris-EDTA (TE) Buffer (20×, pH 9.2): Composed of 0.2M Tris-HCl and 20mM EDTA, pH 7.5 at 25°C, Promega, Cat # A2651; pH to be adjusted to 9.2 by adding 0.1 M NaOH.\n\n17. Tris-buffer containing 20 mM Tris, 200 mM NaCl, pH 8.0, Sigma-Aldrich, Cat # 93283.\n\n18. Protein stain: InstantBlue stain, 1 L, VWR, Cat # 95045-070. It is a Coomassie blue protein stain, ready to use for SDS-PAGE.\n\nA 17 bp (base pair) double-stranded DNA with 4 bases long single-stranded (ss) overhangs at the 5′ends. Forward strand, 5′ GATCGGATGATGATGATAAAC 3′ and the reverse strand, 3′ CCTACTACTACTATTTGCTAG 5′, each carrying a ss (single stranded) 5′ GATC overhang.\n\nBellow, we provide a unique study protocol for the production of SARS-CoV-2 RBD protein antigen using recombinant DNA technology. The RBD protein thus produced can be used as a COVID-19 vaccine after formulation, and evaluation for clinical efficacy and safety.\n\nA sample of Escherichia coli from a stock carrying the Addgene plasmid, Cat #141184, will be grown overnight at 37°C in 10 ml LB-ampicillin broth. The plasmid DNA will be isolated from the cells using PureYield Plasmid Miniprep System I (Promega, Cat #A1222 and a Technical Bulletin #TB374). The purity of the plasmid DNA will be determined by the UV OD260nm/OD280nm (OD = optical density) absorption ratio. A ratio of ≥1.8 is generally accepted as a value for “pure” DNA.30 If the ratio is <1.8, we will add 0.1 μl (0.8 units) Proteinase K to the sample, incubate it at room temperature for 15 minutes, add two volumes of ice-cold 95% ethanol, mix well, centrifuge at 10,000 g at 4°C for five minutes, pour off the supernatant, bring the DNA into solution in TE, and determine the purity of the DNA following its OD260nm/OD280nm absorption ratio. The plasmid DNA concentration will be equal to, OD260nm × the dilution factor × 50 = μg plasmid DNA/ml.\n\nLinearizing the plasmid. The plasmid in solution will be digested with BamHI in BamHI buffer at 37°C for 2 hours, heat denatured at 65°C for one minute, and chilled at 4°C for 10 minutes. Then, two volumes of ice-cold 95% ethanol will be added into it, mixed well, chilled for 10 minutes at –20°C, and centrifuged at 10,000 g using a Sorvall SS34 Fixed Angle Rotor, at 4°C for five minutes. The supernatant containing the linearized plasmid will be transferred into a fresh microfuge tube. The linearized plasmid will carry the RBD cDNA at one end and the sfGFP cDNA at the other end, as shown in Figure 2.\n\nLigating covalently the linker oligo DNA (FP-DNA) into the linearized plasmid. We will add 1 μl of the linker oligo to the linearized plasmid in the microfuge tube. Then, we will add 1 μl T4 DNA (NEB, M0202) ligase containing 400 – 500 units in 1 × T4 DNA ligase buffer, incubate at 16°C for 2 hours, deactivate the ligase by heating at 65°C for 10 minutes, chill at 4°C for five minutes, add two volumes of ice-cold 95% ethanol, mix well, and centrifuge at 10,000 g at 4°C for five minutes. The supernatant containing the ligated plasmid will be transferred into a fresh microfuge tube and the purity of the plasmid DNA will be determined following UV absorption ratio at OD260nm/OD280nm reaching ≥ 1.8. If the ratio is <1.8, add 0.1 μl (0.8 units) Proteinase K, incubate at room temperature for 15 minutes, add two volumes of ice-cold 95% ethanol, mix well, centrifuge at 10,000 g at 4°C for five minutes, pour off the supernatant, bring the DNA into solution in TE, and then again determine the purity of the DNA following its OD260nm/OD280nm absorption ratio. The plasmid DNA concentration will be equal to: OD260nm × the dilution factor × 50 in μg plasmid DNA/ml.\n\nThe incorporation of the oligo DNA (Figure 1), into the plasmid (Addgene, 141184) will be accomplished following a standard protocol for plasmid linearization, insertion of the oligo DNA, and ligation using T4 DNA ligase. The insertion of the oligo DNA will take place at the BamHI site located terminally at the RBD cDNA, and 21 bp upstream to the sfGFP cDNA as in Figure 3.\n\nThe oligo DNA insert will code for a heptapeptide, DDDDKRS, fused in-between the RBD-sfGFP fusion protein, coding for a novel RBD-FP-sfGFP fusion protein (Figure 4).\n\nThe fusion peptide, DDDDKRS (underlined), is shown in the “Recombined translated”, RBD-FP (underlined) -sfGFP fusion protein produced by the recombined plasmid.\n\nThe original plasmid carries RBD cDNA-sfGFP cDNA is shown in Figure 5A, and the ligated plasmid reconstruct will carry the RBD cDNA-FP DNA-sfGFP cDNA linked in order within one orf, as shown in Figure 5B.\n\nThe fusion peptide (FP) carrying a 17 bp long ds oligo, with 4 bases long ss 5′ GATC BamHI linker DNA sequence at either ends.\n\nThe Escherichia coli, C2566H, carrying T7 RNA polymerase gene will be used as a host. The host, transformed with the recombined plasmid, will express the orf producing RBD-FP-sfGFP fusion protein.\n\nTransformation. We will thaw a sample of competent Escherichia coli, C2566H, cells for 10 minutes in ice at 4°C, mix well gently, pipette out 50 μl of the cells in suspension into an ice-cold fresh 1.5 ml microfuge tube in ice, add 100 pg reconstructed plasmid DNA, mix well gently without vortexing, chill the microfuge tube in ice for 30 minutes, place the microfuge tube into a Styrofoam holder, transfer the holder into a 42°C water bath, wait for 15 seconds, take out the microfuge tube, and chill it in ice for five minutes without mixing.\n\nThen, we will add 950 μl SOC,31 maintained at room temperature, into the microfuge tube containing the transformed cells, incubate at 37°C for 60 minutes, and shake vigorously while under incubation using a rotator. This will complete the transformation process.\n\nPlating the transformed Escherichia coli. We will warm up prepared petri dishes/plates (100 mm × 15 mm) containing 20 ml LB-Amp-Agar (1.5%) at room temperature for 15 minutes. Using a sterile pipette, we will add aseptically 250 μl SOC medium containing the transformed E. coli cells into the petri dish and add 80 μl filter sterilized 100 mM IPTG solution into the dish over the SOC medium. Then, we will spread the SOC medium with the transformed cells evenly over the agar throughout the dish/plate with a sterilized spreader and incubate it overnight at 37°C. The E. coli cells transformed with the reconstructed plasmid will produce green fluorescent cfu, when observed using a 300 nm UV lamp.\n\nGrowing cells from green fluorescent cfu to produce the RBD-FP-sfGFP fusion protein. We will select a 15 ml (16 mm × 125 mm) microbial culture tube containing 5 ml sterile LB-Amp broth, warm it up at 37°C for five minutes and add 16 μl filter sterilized 100 mM IPTG solution into the tube reaching a concentration of 0.4 mM IPTG. Then, we will select a green fluorescent cfu from the culture plate, add the cells into the tube, mix gently and grow the cells overnight at 37°C.\n\nTranscription of the SARS-CoV-2 RBD-FP-sfGFP containing ORF from the recombined plasmid will be stimulated by the T7 promoter and regulated by the T7 RNA polymerase produced by E. coli, C2566H, that carries a genomic copy of the T7 RNA polymerase gene inducible by IPTG. Hence, the transformed E. coli, C2566H, will produce SARS-CoV-2 RBD-FP-sfGFP fusion protein from the reconstructed plasmid.32-34\n\nSimilar to the RBD-sfGFP fusion protein, the RBD-FP-sfGFP fusion protein will retain its green fluorescence at UV 300 nm. This is supported by the fact that the RBD-sfGFP fusion protein produced by the Addgene plasmid, 141184, expresses green fluorescence in E. coli carrying T7 RNA polymerase.35-37\n\nA comparison of the recombinant RBD protein with the Addgene, 141184, RBD protein sequences are presented in the results section.\n\nPipette out 1.5 ml cell culture from the tube into a 1.5 ml microfuge tube, centrifuge it at 5,000 g for 10 minutes at 4°C, pour off the supernatant, add 250 μl 1X TE buffer into the cell pellet, gently resuspend the cells in the pellet by pipetting up and down the buffer along with the cell pellet, add 50 μl lysozyme solution (Millipore-Sigma, Cat # L3790) reaching a final concentration of 0.2 mg lysozyme/ml, mix well, and incubate in a shaker at room temperature for 15 minutes. This will break open the cells and release the RBD-FP-sfGFP fusion protein into the buffer, centrifuge the solution at 2000 g for 10 minutes at 4°C, collect the supernatant containing the RBD-FP-sfGFP fusion protein, and observe the solution using UV 300 nm. The presence of RBD-FP-sfGFP fusion protein in solution will be indicated by a fluorescent green colour in UV 300 nm. Hold the tube containing the extract at 4°C for further use.\n\nThe RBD-FP-sfGFP fusion protein will be separated by HIC (hydrophobic interaction chromatography) using a BIO-RAD protein extraction kit (Cat #166-0005EDU), https://www.bio-rad.com/webroot/web/pdf/lse/literature/4006099.pdf, using the following steps:\n\n\n\n1. Using a pair of scissors, cut off the bottom of the hydrophobic resin prefilled HIC column.\n\n2. Place the column into a 5 ml test tube in a stable rack.\n\n3. Remove the top cap of the column and allow the buffer to drain out up to the top level of the resin in the column.\n\n4. Add 2 ml 2 M (NH4)2SO4 solution on top of the resin and allow it to drain out up to the top level of the resin.\n\n5. Put back the cap on top of the column to stop draining.\n\n6. Side-by-side, add 250 μl RBD-FP-sfGFP fusion protein extract into another microfuge tube.\n\n7. Add 250 μl 4 M (NH4)2SO4 solution and mix well.\n\n8. Transfer the solution into the column (Figure 6, Step 1).\n\n9. Allow the buffer to drain out up to the top level of the resin in the column into a collection tube; discard the fluid from the collection tube.\n\n10. Add 250 μl 1.3 M (NH4)2SO4 solution into the column and drain out the fluid up to the top level of the resin into the collection tube; discard the fluid (Figure 6, Step 2).\n\nThe discards will contain all unwanted bacterial protein contaminants while the RBD-FP-sfGFP fusion protein will remain attached to the resin beads in the column.\n\n11. In a separate microfuge tube, add 2 μl enterokinase (NEB, Cat #P8070) in 8 μl of its reaction buffer, 20 mM Tris-HCl, 50 mM NaCl, 2 mM CaCl2, pH 8.0, and mix well. Add 2 μl buffered enterokinase (NEB Cat #P8070) into the column (Figure 6, Step 3).\n\n12. Incubate the column at 25°C for two hours. This will degrade the FP and thus separate the RBD from the sfGFP from the fusion protein.\n\n13. Add 750 μl 1.3 M (NH4)2SO4 solution into the column and elute the RBD protein into a UV transparent collection tube and save (Figure 6, Step 4). The sfGFP will remain bound to the resin.\n\n14. Take out the collection tube with the eluate, view the eluate using a UV 300 nm lamp. Pure eluate will not emit green fluorescence. The top of the resin column holding the sfGFP will emit green fluorescence at UV 300 nm.\n\nStep 1. Protein extract from Escherichia coli, C2566H, cells transformed with the recombined plasmid and treated with the equilibrium buffer (4M (NH4)2SO4)) is being pipetted into the hydrophobic ion exchange column, already equilibrated with a high salt buffer (2M (NH4)2SO4)). This will allow RBD-FP-sfGFP fusion protein to bind tightly into the resins in the column.\n\nStep 2. A low salt buffer (1.3 M (NH4)2SO4)) is added to wash away the unwanted cell extract, while keeping the RBD-FP-sfGFP fusion protein bound to the column resins.\n\nStep 3. Enterokinase is being added to digest the FP to separate the RBD from the sfGFP proteins.\n\nStep 4. A low salt buffer (1.3 M (NH4)2SO4)) is added to elute the RBD proteins, keeping the sfGFP protein bound to the resins in the column.\n\nSeparation of the RBD protein from the RBD-FP-sfGFP fusion protein after the enterokinase (NEB Cat #P8070) digestion of the FP will be completed by HIC. This is a routine technique to isolate non-hydrophobic proteins from hydrophobic proteins. In this digestion, the enterokinase will digest the DDDDKRS fusion peptide in between DDDDK and RS, leaving DDDDK fused with the RBD protein at its C-terminal. The remaining RS dipeptide will remain fused with the GGSGSG, forming RSGGSGSG. This residue will remain fused with the sfGFP at its N-terminal. Since the sfGFP present in the RBD-FP-sfGFP fusion protein is strongly hydrophobic, the RBD-FP-sfGFP fusion protein will bind to the resins in the HIC column. Once the enterokinase completes the digestion, the RBD protein will become separated from the sfGFP. The separated RBD protein will be eluted by 1.3 M (NH4)2SO4 buffer from the hydrophobic resins in the column, leaving the sfGFP protein bound to the resins (Figure 6).\n\nThe RBD protein eluate from the hydrophobic column will contain approximately 1.3 M (NH4)2SO4 and stray molecules of enterokinase. The enterokinase molecules will be removed by using an enterokinase removal kit (Sigma-Aldrich, Cat # PRKE) followed by the removal of (NH4)2SO4 as follows:\n\n1. Add 50 μl anti-enterokinase–agarose conjugate pellet (following Sigma-Aldrich, PRKE protocol) to the RBD eluate, mix gently; centrifuge at 1000 g for 2 minutes at 4°C; collect the supernatant containing RBD and <1.3 M (NH4)2SO4. Add v/v Tris-buffer containing 20 mM Tris, 200 mM NaCl, pH 8.0 to the RBD eluate.\n\n2. Take a SnakeSkin dialysis tube prehydrated with the above buffer and close one of its ends with a clip.\n\n3. Place the RBD eluate into the SnakeSkin dialysis tube and close the other end with another clip.38,39\n\n4. Place the dialysis tube in the Tris-buffer at 4°C in a dish for two hours.\n\n5. Transfer the dialysis tube into fresh Tris-buffer two more times and run the dialysis for two hours each.\n\n6. Transfer the dialyzed eluate into a fresh sterile proteinase-free sterile tube and store at 4°C for further tests.\n\nRemoval of (NH4)2SO4 from a protein extract using dialysis is a routine procedure.40–42 Berndt, et al.,43 ligated cDNAs of an RBD protein of SARS-CoV-2 with a cDNA coding for a 5’mClover green fluorescent protein gene, which was expressed by a transformed Chlamydomonas reinhardtii. The RBD-mClover fusion protein, expressed by C. reinhardtii, was separated by HIC.43 The eluate RBD molecules retained its full immunogenic activity, as observed by its ability to bind to ACE-2 receptor proteins.43 This supports that (NH4)2SO4 does not affect the structural integrity of the RBD proteins. Furthermore, (NH4)2SO4 is known to stabilize the 3D structure of proteins.44 Park, et al.,45 isolated recombinant colorectal cancer vaccine protein, GA733-FcK, using 50% (5.05M) (NH4)2SO4 in its active form. Hence, we predict 1.3 M (NH4)2SO4 solution used in this protocol will have no impact on the 3D structure of the RBD protein.\n\nTan, et al.,42 dialyzed RBD-SpyVLP eluate for 16 hours in Tris-buffered saline (TBS). In our protocol, we propose to use a Tris-buffer (20 mM Tris, 200 mM NaCl, pH 8.0) to the RBD eluate, v/v, and put it into a SnakeSkin dialysis tube (Thermo Fisher Scientific, Cat #88243) with a 10 kDa cut-off, following Tai, et al.39 Since the molecular weight of RBD protein monomer is 25 kDa, the porosity of the SnakeSkin dialysis tube will save the RBD protein inside the tube while allowing (NH4)2SO4 to leach out. Upon completion of the dialysis, storing RBD protein in Tris-buffer, pH 8.0, at 4°C will save the RBD protein from bacterial and enzymatic degradation.\n\nWe will be using SDS-PAGE NuPAGE 4-12% gradient gel for the electrophoresis as follows:\n\n1. Place the NuPAGE into a Mini Gel Tank, Thermo Fisher Scientific, Cat # A25977.\n\n2. Fill in the chamber with 1× NuPAGE MES SDS Running Buffer up to the designated level.\n\n3. Put 5 μl Protein Standard in 1× solution buffer into a well of SDS-PAGE gel.\n\n4. Put 5 μl dialyzed RBD protein sample in 1× sample buffer into a parallel well in the SDS-PAGE gel.\n\n5. Run the electrophoresis using an Invitrogen PowerEase Touch 600W Power Supply, Thermo Fisher Scientific, Cat # PS0601, at 200 V and 30 – 40 mAmp for 40 minutes.\n\n6. Remove the NuPAGE gel slab and stain it with InstantBlue, following the supplier’s protocol.\n\n7. Measure in cm, using a ruler, the distances traveled by each of the Protein Standard bands as well as by the RBD protein bands and record them in a notebook to be used next for plotting and measurement.\n\n8. Plot a protein standard graph in a semi-log paper using the distance, in cm, traveled by each standard protein band on the Y (log) axis and their respective molecular sizes on the × (linear) axis.\n\n9. Determine the molecular sizes of the RBD protein bands using the protein standard graph, prepared above. The expected sizes of the RBD proteins will be 221 aa (24.3 kDa) for monomers, 442 aa (48.6 kDa) for dimers and 663 aa (72.9 kDa) for trimers.\n\nThe SDS-PAGE procedure separates proteins primarily by mass, since SDS denatures and binds to proteins to make them negatively charged. Hence, in an electric field, the SDS-bound RBD proteins will migrate through the gel toward the positively charged electrode based on its mass. A protein molecule of a lower mass size will have higher mobility in comparison to a protein molecule of higher mass size.\n\nThis procedure will help us determine the molecular sizes of the RBD proteins in the eluate and compare them with known values.\n\nWe will test 1 μl sample of the dialyzed RBD protein for immunoactivity using a SARS-CoV-2 RBD Elisa kit, BioVision, Cat # E4877, for a qualitative determination of the RBD protein, following the supplier’s protocol.\n\nThis procedure follows the ELISA principle. It contains SARS-CoV-2 RBD protein samples in solutions, detection solutions, pre-coated RBD antibodies, and all necessary ingredients. This technique is known to be highly sensitive, detecting <10 pg RBD/ml.\n\nIn this protocol, a standard RBD concentration graph will be plotted using OD450 nm of RBD samples of known concentrations. This will be accomplished by a tagged RBD-antibody-RBD-antigen binding, followed by a chromogenic reaction. An RBD sample from the dialyzed eluate will be tested using the same RBD-antibody-RBD-antigen binding followed by the chromogenic reaction and OD450 nm measurement. Based on the OD450 nm of the dialyzed RBD protein sample, its concentration will be determined from the standard graph. This procedure will help vaccine development in two ways: it will detect the presence of RBD protein in the HIC eluate that is purified by dialysis, and it will measure the concentration of RBD protein antigen present in the dialyzed sample.\n\nThe modification of the RBD protein will not affect its immunogenic ability as demonstrated by Keng, et al.47 Keng, et al.,47 in an antibody neutralization experiment demonstrated that fragmented spike protein DNA containing variable lengths of RBD proteins, expressed by transformed E. coli, retained the immunogenic ability against SARS-CoV-2 virus. Furthermore, this modification will not affect the internally located RBM, the epitope of the RBD protein.29 The RBD antigen thus produced can be applied as a safer vaccine after formulation for trials as described by Batty, et al.48\n\nWe will take a 10 μl sample of the dialyzed RBD protein and determine its concentration by measuring OD at UV 280nm using a UV-Vis spectrophotometer following Arbeitman, et al.49 The total amount of RBD protein in the dialyzed sample will be equal to M = (OD ÷ L) x D. (Where, M = amount of RBD protein present in mg per ml in the original sample; OD = Optical density at 280nm; L = the length of cuvette light path in cm; D = dilution factor.)50,51\n\nThe RBD protein sequences, before (Figure 7) and after modification (Figure 8) will be tested for their alignments with known 2019-nCoV RBD protein sequence available through a computerized program, UniProt Protein Blast (UniProtKB: P00750): https://www.uniprot.org/blast/.\n\nThe details of the alignment are presented in the results section following Figure 9 and Figure 10, below:\n\nAlignment of the RBD protein encoded by Addgene, 141184, with the RBD protein generated by 2019-nCoV, SARS-CoV-2 virus, for comparison, using UniProtKB: P00750.\n\nAlignment of modified RBD protein encoded by the recombinant plasmid with the RBD protein generated by 2019-nCoV, SARS-CoV-2 virus, for comparison, using UniProtKB: P00750.\n\nAdd a measured volume of glycerol to the dialyzed RBD solution, reaching a final concentration of 10% (v/v) glycerol in the solution and mix well. Make aliquots of the RBD solution in separate pre-laveled micro-vials, freeze them quickly in liquid nitrogen, and store them in a –80°C freezer following Tee, et al.46\n\nThe aliquots of RBD can be reused for vaccine formulations as needed. Edwards, et al.,52 have observed under electron microscopy that RBD molecules stored at 22°C or 37°C in a buffer (2 mM Tris, pH8.0, 200 mM NaCl, 0.02% sodium azide) for one week displayed well-ordered trimeric structure.52 Hence, we anticipate that the quick-frozen RBD monomers, isolated in the protocol, will form dimers and trimers after thawing at 22°C or 37°C, as a natural phenomenon. Since both the RBD dimers and trimers have higher ACE-2 binding activity than its monomers, the dimerization and trimerization will increase vaccination efficacy of the isolated RBD proteins.53,54\n\n\nProjected results\n\nThe original plasmid, Addgene, 141184, carries a 639 bp long RBD cDNA linked with a 714 bp long sfGFP cDNA (Figure 5A). The RBD cDNA will code for a 221 amino acid long RBD protein as shown in Figure 7.\n\nThe modified RBD protein encoded by the recombined plasmid is shown in Figure 8. As mentioned earlier, the modified RBD protein will have a five amino acid long FP (DDDDK) replacing six amino acids (GGSGSG) at its C-terminal (Figure 8).\n\nThe RBD protein β sheet, critical for its 3D structure, will also remain fully stable since the modification of the RBD protein at the C-terminal has no effect on the pairing of the sulfur containing amino acid Cys336–Cys361, Cys379–Cys432, and Cys391–Cys525.29 We proved this by aligning the RBD protein sequences, before and after modification, with the RBD sequence produced by the 2019-nCoV genome using a computerized program, UniProt Protein Blast (UniProtKB: P00750), https://www.uniprot.org/blast/as), as shown in Figure 9 and Figure 10.\n\nAs shown in Figure 9, the RBD protein encoded by the RBD cDNA, Addgene, 141183, matches perfectly with the respective RBD protein sequence produced by 2019-nCoV strain of the SARS-CoV-2 coronavirus. Three pairs of Cys-Cys residues, Cys336-Cys361, Cys379-Cys432 and Cys391-Cys525, encoded by the RBD cDNA, responsible for the core RBD protein β sheet formation, match perfectly with the respective RBD protein sequence produced by the 2019-nCoV strain. The total amino acid length of the RBD protein encoded by the RBD cDNA, Addgene, 141183, is 221, which has 99.0% identity match and 99.5% positivity match with the RBD protein sequence produced by the 2019-nCoV (Figure 9).\n\nSimilarly, as shown in Figure 10, the RBD protein encoded by the modified RBD cDNA matches perfectly with the respective RBD protein sequence generated by 2019-nCoV strain of the SARS-CoV-2 coronavirus. Three pairs of Cys-Cys residues, Cys336-Cys361, Cys379-Cys432 and Cys391-Cys525, encored by the modified RBD cDNA, that form the core RBD protein β sheet, match perfectly with the respective RBD protein sequence produced by the 2019-nCoV strain. The total amino acid length of RBD protein encoded by the modified RBD cDNA is 220, which has 98.5% identity match and 99.5% positivity match with the RBD protein sequence produced by the 2019-nCoV.\n\n\nDiscussion\n\nThe protocol we designed to produce the SARS-CoV-2 RBD antigen, which is responsible for recognition and attachment to the ACE-2 receptors in human cells, is a novel one. Since the RBD protein is not linked to the S2 domain protein, the RBD protein, after binding to ACE-2, will not allow any free-floating virions to enter any human cell. Additionally, the RBD protein alone was found to have effective immunological integration with eight types of ACE-2 variants in human cells.55 This observation supports that the RBD protein produced by this protocol will remain effective in multiple human recipients, despite their ACE-2 variations. Other authors reported that a single dose of the RBD antigen vaccine delivered to mice has produced a high titer of antibodies effective against both mutant and non-mutant variants of the SARS-CoV-2 virus.56\n\nAn RBD protein sample, similar to the RBD protein produced by this protocol, was found to induce a potent and functional antibody production in mice, rabbits, and non-human primates (Macaca mulatta) within seven to 14 days following single dose administrations.57 It was also found that the SARS-CoV-2 RBD protein is a highly effective antigen to work as a vaccine by Dai and Gao.53 Both RBD-dimer and RBD-trimer proteins have been found to increase the immunogenicity of RBD-protein based vaccines effectively, in comparison to RBD protein monomers.53 RBD proteins, produced by this protocol, will form trimers in a solution as supported by Edwards, et al.52 All the above reports support that the RBD protein produced by this protocol has the full potential to be an effective vaccine against the SARS-CoV-2 and some of its mutants.\n\nThe purified RBD protein molecules become dimers by forming four disulfide bonds between two RBD monomers.46 Furthermore, the RBD dimers are also much more effective than its monomers in stimulating antibody production (10-100 times immunogenicity) and in neutralizing SARS-CoV and SARS-CoV-2 antibodies.54 Hence, the RBD protein is a strong vaccine candidate and also potentially effective against multiple coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2.54 The yield of RBD dimerization from its monomer is high and its production level may be scaled up in order to meet clinical demands.54\n\nDevelopment of a more effective vaccine is the main target of this study protocol. The RBD vaccine antigen, once recognized by the T-cells, will promote secretion of cytokine interferon gamma and interleukin-2 biomarkers, which will stimulate the helper and cytotoxic T cells, B cells, and protective IgG antibodies.58\n\nFurthermore, since the glycan shield of the beta-coronavirus (β-CoV) spike glycoprotein acts as a steric block that prevents host immune responses (and thus reduces antibody production), the RBD monomer does not need to be glycosylated, as supported by Henderson, et al.59\n\n\nConclusion\n\nThe RBD protein is an excellent choice for developing a vaccine to prevent COVID-19. The vaccines composed of antigenic mRNA and cDNA are required to go through cellular processes to produce antigens. The RBD protein itself is an antigen and, hence, it will be direct and quick in stimulating the recipients’ immune systems to produce antibody against SARS-CoV-2 virions quickly.\n\nThe SARS-CoV-2 RBD protein vaccine can generate a strong immune response and can be used by almost everyone, including people with weakened immune systems and long-term health problems as supported by the United States Department of Health and Human Services. Furthermore, the RBD protein vaccines cannot cause the COVID-19 disease. However, while using the RBD protein vaccine, booster shots may be necessary for immunome compromised recipients to gain sufficient protection against the ongoing SARS-CoV-2 infections.\n\nThe RBD protein production and purification protocol that we are proposing is seamless. Hence, the RBD protein thus produced can be used to prepare a vaccine following a standard formulation procedure and clinical trials.\n\n\nDissemination\n\nThe authors are planning to apply for a National Institutes of Health grant in due course to support this project and execute it. After receiving a grant and access to the academic laboratory for the authors is released from the pandemic restrictions, the authors will conduct their research based on this protocol, approved by the IRB, and make their findings available through open access, online, present in conferences and publish in peer reviewed journals.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nWe would like to acknowledge the contributions made by the editors, Arnab Z. Jahangir, B.Sc. and Dr. Arthee E. Jahangir, Ph.D., and thank them for their editorial support.\n\nA previous version supporting this article can also be found on preprints.org.1 One of the authors, Arleta H. Marnik, presented “A Protocol for Producing SARS-CoV-2 RBD Vaccine” at a three-day long 2021 CUNY Research Scholars Summer Symposium, held during July 27-29, 2021. The protocol was highly accepted by the CUNY research scholars present and Mrs. Marnik was one of the winners in the competition receiving a certificate of an award. A list of the winners is available here.\n\n\nReferences\n\nJahangir ZS, Marnik AH: A Review of SARS-CoV-2, Responsible for COVID-19: History, Biology, Infection Mechanism, Antigenic Vaccines, Their Risks and how an Alternate RBD Vaccine is Safer? Preprints. 2021, 2021060377. 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}
|
[
{
"id": "118898",
"date": "12 Jan 2022",
"name": "Wen-Hsiang Chen",
"expertise": [
"Reviewer Expertise Recombinant protein production. Vaccines. Protein biophysical characterization. Protein science"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript, the authors described the procedure to produce a recombinant RBD protein as the COVID-19 vaccine antigen. This manuscript is relevant to the current COVID-19 pandemic. However, the overall design of the antigen, the procedure to purify the antigen, the characterization of purified RBD seemed to indicate that the procedure was not very efficient. This manuscript requires major improvement. The following comments are suggested:\nIn the Abstract section:\nThe advantage of mRNA/DNA vaccines is to avoid the production process of protein recombinantly, as recombinant protein production sometimes can be very challenging, considering each protein has unique biophysical characteristics which makes the expression/purification much more complex, versus for DNA or RNA vaccines, the purification process of DNA and RNA can typically remain very similar and straightforward. Thus, the background rationale addressing generating RBD protein as a fast-acting strategy may not make too much sense. Please consider re-write the rationale.\n\nIn the Introduction section:\nThe introduction section is extremely lengthy with disjointed information. Please consider removing unnecessary paragraphs and making them more concise. Under “the benefits and importance of SARS-CoV-2 vaccines” section, the fourth paragraph: Authors stated that RBD residue is more conserved, however, based on the mutation maps of the current SARS-CoV-2 variants of concern (VoC; https://asm.org/Articles/2021/December/How-Ominous-is-the-Omicron-Variant-B-1-1-529), one can find that all the VoCs contain mutations within the RBD region, the most recent VoC- Omicron even has 15 mutations. Thus, stating RBD is more conserved seems incorrect. Authors, please address accordingly.\nUnder “Advantages for using the RBD protein vaccine”, the 2nd paragraph: Authors listed several properties of RBD proteins, and stated that all these properties support the RBD protein as an effective antigen; one being the 4 cysteine bridges that RBD possesses. However, it is hard to correlate the effectiveness of this antigen with the Cys bridges. Could the authors clarify? Otherwise, please consider removing such info. Additionally, using RBD as the vaccine antigen against COVID-19 is not a new concept, and one can easily find articles describing similar ideas (e.g., Yang et al., Nature, 2020; Zhang et al., Cell Discov, 2021; Chen et al., BBA-Gen Subj. 2021; Dalvie, PNAS, 2021). This manuscript lacks the description of the advantages, the novelty, or a good rationale over the other published articles. Please consider providing reasons why your RBD design is better than the others to make your manuscript stronger.\nComments on the overall design of the antigen:\nThe authors designed an antigen that consists of the RBD protein, a linker (FP), and a GFP. However, it is unclear why GFP is required. Also, to remove the GFP, an additional enzyme had to be employed, which adds an extra step to the process and can potentially make it more difficult to purify. Authors should also beware that by using E. coli expression system, a complex protein such as RBD (containing many Cys bridges), may not have a correctly folded structure, as it can easily form an inclusion body instead of a soluble protein, which may explain why the overall yield was so low.\nIn the whole manuscript, no SDS-PAGE image was presented to demonstrate the expression of the protein actually occurred. The yield of the purified protein also seemed extremely low (<10 pg/mL out of 1.5mL cell culture) when quantified by BioVision ELISA kit. Authors should reconsider the production process, as this process did not seem efficient enough for protein production.\nThe authors used several in silico analyses to evaluate the structure of the expressed protein. But when the protein is expressed and purified, more sophisticated analyses should be performed. Minimally, a functionality test by evaluating the binding of RBD to ACE-2 should be considered. Additionally, for secondary structure analysis, circular dichroism can be used, and for Cys-bond formation, mass spectrometry should be considered.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "7714",
"date": "17 Jan 2022",
"name": "ZMG Sarwar Jahangir",
"role": "Author Response",
"response": "Professor Wen-Hsiang Chen, Baylor College of Medicine, Houston, Texas, USA Dear Professor Chen: Thank you for reviewing our submission to F1000, “A study protocol to prepare an RBD protein for vaccine against COVID-19”, and for your suggestions. We will address all issues you suggested to enrich the article. However, we will wait to get responses from two additional reviewers before we make the revision. Yours truly. ZMG Sarwar Jahangir, Ph.D. Molecular, Cellular and Developmental Biology and Director, AS in Biotechnology Program, Department of Biological Sciences KCC-CUNY and Arleta H. Marnik, M.S. in Biotechnology, GDANSK University of Technology, Poland, Research Scientist, Department of Biological Sciences, KCC-CUNY."
}
]
},
{
"id": "136859",
"date": "31 May 2022",
"name": "A. H. M. Nurun Nabi",
"expertise": [
"Reviewer Expertise Genetics",
"Immunoinformatics",
"Biochemistry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors are proposing the use of purified RBD protein as a vaccine formulation. The question that arises here is why are you using the whole RBD protein instead of predicting the most antigenic epitopes and constructing a multi epitope vaccine. Does their whole protein usage have any plus point over that?\n\nIn the introduction ‘This suggests that the RBD residue is more conserved and hence, the RBD protein vaccines will be effective against multiple SARS-CoV-2 variants.’ – this statement seems rather contradictory. RBD is a hot spot for mutations of the new variants. Kindly provide supporting references on behalf of your statement.\n\nThere have been several variants of SARS-CoV-2 with mutations in the RBD of the spike protein. Will this RBD vaccine be effective against all the variants? Furthermore, what is the significance of this study? The constructed RBD vaccine will serve as a subunit vaccine? Won’t the RBD of the spike protein bind with ACE-2? It may serve as a competitive inhibitor.\n\nAdministration of this whole protein might induce the innate immune response by producing antibodies. The authors have mentioned in the discussion section “Other authors reported that a single dose of the RBD antigen vaccine delivered to mice has produced a high titer of antibodies effective against both mutant and non-mutant variants of the SARS-CoV-2 virus”\nHowever, it is suggested that authors should perform some analysis that may demonstrate the immune simulation and represent the results to validate the probable effect of their designed vaccine.\n\nDid the authors perform any allergen test for the vaccine?\n\nThe authors mentioned “Additionally, the RBD protein alone was found to have effective immunological integration with eight types of ACE-2 variants in human cells” in the discussion section. Although, a detailed population coverage analysis is recommended.\n\nThe protein was aligned and compared with the RBD protein generated by 2019- nCoV, SARS-CoV-2 virus (UniProtKB: P00750) only. What about the specific variants? Will the vaccine be effective against all possible variants?\n\nIt is suggested to write about any subunit or purified protein vaccine that was subjected to trial against SARS-CoV-2 or other viruses and their outcomes in the introduction.\nThe manuscript is well written. I have no comments regarding the proposed wet lab methodology. Although an extensive immunoinformatics based validation of their proposed outcome must be added in the projected results section. They are suggested to perform protein modeling and docking, in addition to immune simulation analysis to demonstrate the probable outcome of the vaccine. Thus I would suggest a major revision including these proposed analyses.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "8759",
"date": "04 Nov 2022",
"name": "ZMG Sarwar Jahangir",
"role": "Author Response",
"response": "Dear Professor Dr. Nuran Nabi, Thank you for reviewing our article and also for your questions, suggestions, and comments. Please find below specific answers in response to your peer review. In the revision, the text may remain modified to match the format of the article. We have included answers to all your questions in the 3rd revised version of the article. Q1. \"The authors propose using purified RBD protein as a vaccine formulation. The question that arises here is why are you using the whole RBD protein instead of predicting the most antigenic epitopes and constructing a multi-epitope vaccine. Does their whole protein usage have any plus point over that?\" Answer: The entire RBD amino acid chain restores the integrity of the RBD epitope. Otherwise, the epitope may change its 3D structure. It has been demonstrated that an altered RBD amino acid chain elucidates phenotypic variation of the RBD protein. That allows the SARS-CoV-2 virus to escape binding to potently neutralizing anti-RBD antibodies which may relate to the altered epitopes (Deshpande, et al., 202139, Greaney, et al., 202144; Harvey, et al., 202145). Hence, in this protocol, we will use the entire RBD coding sequence to preserve the epitope structure, instead of using the binding site alone. Q2. \"In the introduction ‘This suggests that the RBD residue is more conserved and hence, the RBD protein vaccines will be effective against multiple SARS-CoV-2 variants.’ – this statement seems rather contradictory. RBD is a hot spot for mutations of the new variants. Kindly provide supporting references on behalf of your statement.\" Answer: The RBD residue carries the SARS-CoV-2 binding epitope that binds to the ACE-2 receptors in human cells. However, recent findings of the RBD structure of mutant delta strain vary with omicron strain in their 3D structures, but both the variants can bind to the same ACE-2 receptors infecting patients (Kumar, et al., 2021) 30. Hence, we assume the RBD sequence we have included in the protocol will be effective against multiple variants. Furthermore, the VH3-53/3-66 class-derived public neutralizing antibodies (NAbs) are effective against multiple SARS-CoV-2 variants (Xu et al, 2021)24. Hence, the RBD protein vaccine will be effective against multiple SARS-CoV-2 variants, without claiming it to be effective for all and forever. Once again, following the same protocol, the RBD DNA sequence is open for modification to match an altered variant if needed. Q3. \"There have been several variants of SARS-CoV-2 with mutations in the RBD of the spike protein. Will this RBD vaccine be effective against all the variants? Furthermore, what is the significance of this study? The constructed RBD vaccine will serve as a subunit vaccine? Won’t the RBD of the spike protein bind with ACE-2? It may serve as a competitive inhibitor.\" Answer 1: We gave a part of the answer to this question in the previous paragraph. The VH3-53/3-66 class-derived public neutralizing antibodies (NAbs) are effective against multiple SARS-CoV-2 variants (Xu et al, 2021)24. Hence, the RBD protein vaccine will be effective against multiple SARS-CoV-2 variants, without claiming it to be effective for all and forever. Furthermore, following the same protocol, the RBD DNA sequence is open for modification to match an altered variant if needed. 24Xu, H., Wang, B., Zhao, T., Liang, Z., Peng, T., Song, X., Wu, J., Wang, Y., & Su, X. (2021). Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-Cov-2 RBD variants. Cell Research, 31(10), 1126-1129. https://doi.org/10.1038/s41422-021-00554-1 Answer 2: The RBD vaccine has the following significance (Hernández-Bernal, et al. 202246, Mabrouk et al. 202147, Fliesle, N. 202148). Production of protein vaccine specific against SARS-CoV-2 without any potential for genomic recombination into the recipient’s genome. Production of the safer vaccine. The RBD DNA will have the scope for alteration to produce new RBD matching the new SARS-C0V-2 variants. Answer 3: The RBD vaccine will work as a fully effective vaccine against the SARS-CoV-2 virus. The amount of RBD molecules per vaccine will be limited and they will have no self-regenerating ability. Most of the titer will bind to T cells and then instruct the B cells to produce plasma cells for making antibodies against the SARS-CoV-2 virus. While the memory B cells will be involved in any future infection by the SARS-CoV-2. However, there will be limited opportunities for RBD vaccine molecules to bind the ACE-2 receptors. This opportunity of the RBD protein vaccine is much less in comparison to the currently administered spike protein mRNA antigenic vaccine. The mRNA vaccine continuously produces spike protein for a prolonged period which also binds to the ACE-receptors as well (Angeli, et al., 2021)49. Hence, the RBD spike protein vaccine will have little competition in comparison to the spike protein produced by the mRNA vaccines. Furthermore, spike proteins produced by the mRNA vaccine have an S2 segment that has the potential for facilitating fusion of the free-floating SARS-CoV-2, while the RBD protein vaccine has no potential for viral fusion into human cells (Belouzard, et al., 201250; Jackson, et al., 202251). Hence, the RBD protein vaccine is safer. Q4. \"Administration of this whole protein might induce the innate immune response by producing antibodies. The authors have mentioned in the discussion section “Other authors reported that a single dose of the RBD antigen vaccine delivered to mice has produced a high titer of antibodies effective against both mutant and non-mutant variants of the SARS-CoV-2 virus” However, it is suggested that authors should perform some analysis that may demonstrate the immune simulation and represent the results to validate the probable effect of their designed vaccine.\" Answer: Following your suggestion, we included that “the purified RBD will be tested for immune simulations in 7 weeks old mice Female C57BL mice and tested for neutralizing antibodies produced against SARS-CoV-2 following as described by Seephetdee et al., (2021)72. Q5. \"Did the authors perform any allergen tests for the vaccine?\" Answer: We are not completing the allergen testing in this protocol. Once the RBD protein meets the immunity generation test, the authors will contact agencies interested in using it as a vaccine. At that time, after vaccine formulation following a standard protocol, it will go through allergen tests before application to patients following US FDA recommended vaccine evaluation and management protocol (Goepfert, et al., 202173; Greenhawt, et al., 202174) Q6. \"The authors mentioned “Additionally, the RBD protein alone was found to have effective immunological integration with eight types of ACE-2 variants in human cells” in the discussion section. Although, a detailed population coverage analysis is recommended.\" Answer: Human ACE-2 variants are rare and mostly found in European non-Finnish and African populations except one in the Latino and one in finish populations, none in Ashkenazi Jewish, East and South Asian populations (Othman, et al., 2020)83. 83Othman H, Bouslama Z, Brandenburg JT, et al.: Interaction of the spike protein RBD from SARS-CoV-2 with ACE-2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. Biochem Biophys Res Commun. 2020;527(3):702–708. 32410735 10.1016/j.bbrc.2020.05.028 PMC7221370 Q7. \"The protein was aligned and compared with the RBD protein generated by 2019- nCoV, SARS-CoV-2 virus (UniProtKB: P00750) only. What about the specific variants? Will the vaccine be effective against all possible variants?\" Answer: Yes, the RBD protein thus generated should be compared with other variants before vaccine formulation. Although there exist variations in the spike protein, variations in the RBD region are relatively limited. When neutralization antibodies interact with naturally occurring SARS-CoV-2 RBD variants tested using structure-based analyses the VH3-53/3-66 class-derived public antibodies largely remain effective against most of the RBD variants studied (Xu, et al., 202124). The RBD variants lineages include the B.1.1.7 (UK) lineage that emerged in the United Kingdom (UK), the B.1.351 (South Africa-SA), and the P.1 and P.2 lineages in Brazil and others. The most abundant RBD variant mutations are N501Y in B.1.351, K417N (or T)/E484K/N501Y co-mutation in the SA and Brazil and are reported to be highly transmissible (Xu, et al., 202124). Furthermore, the VH3-53/3-66 class-derived public neutralizing antibodies (NAbs) antibodies were the most prevalent NAbs identified in COVID-19 patients worldwide (Cao, et al., 202085 Yuan, et al., 202086). Yes, the RBD protein will be still effective against more variants and justified in the review. Q8. It is suggested to write about any subunit or purified protein vaccine that was subjected to trial against SARS-CoV-2 or other viruses and their outcomes in the introduction. Answer: We included the following information in the 2nd and 3rd revisions. There are several reports on SARS-CoV-2 RBD and spike protein vaccines on trial (Formica, et al., 202140; Kyriakidis, et al., 202141). Vaccinating across the globe against SARS-CoV-2 is a great scientific, logistical, and moral challenge. Manufacturing protein-based vaccines are potentially more cost-effective than mRNA vaccines and do not require ultra-cold storage ( Hernández-Bernal, et al. 202246, Mabrouk et al. 202147, Fliesle, N. 202148, Kleanthous, et al., 202138). This would help with safe, potent, high-volume, and affordable vaccines for a large part of the world, especially in low- and middle-income countries, including Africa where vaccination rates are currently very low. Given a predominance of key biomarker neutralizing antibodies (NAbs) that target RBD following natural infection or vaccination, there is a great justification for selecting RBD as the sole vaccine immunogen. It has high-yielding potential, temperature-stable and cost-effective. In addition, the RBD focuses on the immune response to the potent and cross-protective domains which is central to the development of future pan-sarbecovirus vaccines (Kleanthous, et al., 202138). Kleanthous, et al., (2021)38 also reported that the RBD protein vaccines are equally effective in comparison to full-length S-protein vaccines concerning immune responses against the prototype pandemic SARS-CoV-2 isolate as well as emerging variants of concern. In a clinical trial in CUBA, 792 subjects received the SARC-CoV-2 RBD protein vaccine named ABDALA on Dec 7, 2020, and Feb 9, 2021. The ABDALA vaccine was found to be safe, well tolerated, and induced humoral immune responses against SARS-CoV-2. For the emergency COVID-19 pandemic the results support a 50 μg vaccine dose, applied in a 0-14-28 days schedule was highly effective. (Hernanadez-Bernal, et al., 202246). A trial study was conducted on the efficacy and safety of a dimeric tandem repeat of RBD of the SARS-CoV-2 spike protein (derived from the Wuhan-Hu-1 strain) vaccine among a total of 28,873 participants conducted on December 12, 2020, and December 15, 2021, at 31 clinical centers across Uzbekistan, Indonesia, Pakistan, and Ecuador with a safety assessment center in China Dai, et al., (2022)42. In this large cohort of adults, the RBD dimeric vaccine was found to be safe and effective for at least 6 months after full vaccination against symptomatic as well as severe-to-critical Covid-19, without any vaccine-related death (Dai, et al., 2022)42. Again, a SARS-CoV-2 recombinant spike protein nanoparticle vaccine in phase 1-2 trials where 83 participants received the vaccine with adjuvant, 25 received the vaccine without the adjuvant, and 23 participants received placebo, at random. At 35 days, the nanoparticle vaccine was found to be safe and elicited immune responses that exceeded levels in Covid-19 convalescent serum (Keech, et al., 2020)43. Peer Reviewer’s comments: \"The manuscript is well written. I have no comments regarding the proposed wet lab methodology. Although an extensive immunoinformatics-based validation of their proposed outcome must be added in the projected results section. They are suggested to perform protein modeling and docking, in addition to immune simulation analysis to demonstrate the probable outcome of the vaccine. Thus, I would suggest a major revision including these proposed analyses.\" Answer: Thank you very much for going through our manuscripts and making helpful comments and suggestions. We did our best to answer all your questions. We are looking forward if you have any other questions for us to answer."
}
]
}
] | 1
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https://f1000research.com/articles/10-943
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https://f1000research.com/articles/11-1121/v1
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29 Sep 22
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{
"type": "Software Tool Article",
"title": "A flexible open-source processing workflow for multiplexed fluorescence imaging based on cycles",
"authors": [
"Guillaume Potier",
"Aurélie Doméné",
"Perrine Paul-Gilloteaux",
"Guillaume Potier",
"Aurélie Doméné"
],
"abstract": "Background Multiplexing tissue imaging is developing as a complement for single cell analysis, bringing the spatial information of cells in tissue in addition to multiple parameters measurements. More and more commercial or home-made systems are available. These techniques allow the imaging of tens of fluorescent reporters, where the spectral overlap is solved by imaging by cycles the fluorophores using microfluidics to change the reporters between each cycle.\nMethods For several systems, the acquisition system coupled to the microfluidic system is a wide field microscope, and the acquisition process is done by mosaicking to cover a large field of view, relying on image processing to obtain the data set to be analysed in intensity. The processed data set allows the identification of different populations, quite similarly to cytometry analysis, but with spatial information in addition. To obtain the final image for analysis from the raw acquisitions, several preprocessing steps are needed for inter-cycle registration, tissue autofluorescence correction or mosaicking. We propose a workflow for this preprocessing, implemented as an open source software (as a library, command line tool and standalone).\nResults We exemplify the workflow on the commercial system PhenoCycler® (formerly named CODEX®) and provide a reduced size data set for testing.\nConclusions We compare our processor with the commercially provided processor and show that we solve some problems also reported by other users.",
"keywords": [
"Bio image analysis",
"workflow",
"registration",
"signal processing",
"segmentation",
"fluorescence microscopy",
"multiplexing"
],
"content": "Introduction\n\nMammalian cells are organized in tissues and organs. They are assemblies of multiple cell types that can interact together. The tissue microenvironnment has been recognised as important during organisms’ development or for processes of deregulation such as cancer1–5. Understanding the spatial architecture or the heterogeneity in the tissue environment is key to understanding for example, the biology and progression of cancer or complex immune system disorders.\n\nSingle-cell technologies, like Next Generation Sequencing-based tools and flow or mass cytometry enable the detection of numerous parameters. However, biological samples are destroyed for the study and they don’t provide the associated spatial dimension.\n\nIn clinical practice, tissue samples are usually cut and then stained with conventional immunohistochemistry or immunofluorescence technologies but this is limited to measuring a few parameters simultaneously with the use of consecutive tissue sections, due in particular to the spectral overlap of fluorophores.\n\nA number of technologies have emerged in the last years with different strategies for multiple epitope detection on a single slide. The commercial system PhenoCyclerTM (formerly named CODEX® for co-detection by indexing) is a technology that uses DNA-conjugated antibodies with fluorescent nucleotides6,7. Associated to a fluorescence microscope, a multiplexed imaging device cycles through sample washing and marker substitution, allowing an important number of markers to be acquired using only a few fluorochromes. This technology solves the problem of spectral overlap and panel composition but requires an image processing software reconstituting the entire data from the raw acquired data.\n\nHere we focus on the processing step to process raw images out from the microscope (Figure 1 (A)) to obtain the full stitched image (Figure 1 (B)), including segmentation based on nuclei staining. The output of our workflow can then be used in different analysis software to analyse the different populations of cells (Figure 1 (C)). Our workflow is very similar to the original Codex Processor software provided by the vendor, or to the open source CODEX Toolkit Uploader6,8. Briefly, this software computationally concatenates and drift-compensates the images using nuclear stain as a reference, removes out-of-focus light using the Microvolution deconvolution algorithm, subtracts the background (using blank imaging cycles without fluorescent oligonucleotides), and creates hyperstacks of all fluorescence channels and imaging cycles. A Codex Segmenter was also made available by the same team to identify the cells incorporating recent advances in the segmentation methods9. However, as we encountered several issues with the original software provided along with the device, we developed our own processing pipeline, to solve in particular issues regarding the stitching, the intensity normalisation and the segmentation.\n\n(A) Raw images tiles before processing step: examples of tiles 5 and 65 extracted from 117 (13x9) mosaic acquisition. For each tile, one image was obtained for each plane of Z-stack, for each fluorescent channel and for each cycle acquisition. (B) Stitched image after processing: combined channels for visualisation with CD20 in magenta, CD21 in yellow, CD3e in green, CD31 in blue and CD45RO in cyan. (C) Color-coded populations as identified from the output of our pipeline by x-shift clustering using the Multiviewer Analysis Viewer (MAV), the Akoya Biosciences analysis software.\n\nThe cell phenotyping and identification of population usually relies on the crowded nuclei segmentation and intensity measurements8,10–12 and then on the quality of the processing step. In particular one needs to take into account the non-perfect flatness of the tissue, the mechanical drift between the subsequent acquisitions of the same position for different cycles, the non-uniformity of the microscope fields, the correction of the autofluorescence signal to make intensity measurement measurable, the stitching for the full mosaic to identify uniquely nuclei, and the segmentation of crowded nuclei in tissue.\n\n\nMethods\n\nWe have developed a new implementation of the processor, in particular adapted to the PhenoCyclerTM, but that could be used for any other system relying on cycles of acquisition. In particular our goal was to solve some problems encountered by the original software provided with the PhenoCycler as demonstrated in Figure 2 (C) and Figure 3 (B).\n\n(A) Processed data as generated by the original vendor software v1.8.2. White square shows the position of the insets shown in panels (C) and (D), at the intersection of four tiles. (B) The same area processed by our software. (C) Zoomed area on the intersection showing defect in stitching. (D) The same area after our processing.\n\nScale bar is 5 millimeters. (A) Stitched intensity image generated by our processor. (B) Color-coded x-shift generated populations generated by the MAV based on the segmentation and intensity measured by the vendor processed pipeline. (C) Color-coded x-shift generated populations generated by the MAV based on the segmentation and intensity measured by our pipeline. Grey means no cells detected.\n\nOur pipeline is written using the JAVA programming language. Our code is organised around a core library providing main functionalities and consumed by a command line interface (CLI) as well as a GUI (Graphical User Interface). The CLI application exposes each processing step independently whereas the GUI provides an easy interface to start the entire pipeline, with the option to select a subpart of the workflow to be run. The different dependencies and required packages are listed in https://gitlab.in2p3.fr/micropicell/multiplexprocessor/-/blob/master/README.md. Maven is used for software dependencies. A binary version compiled for Windows is provided with instructions for reader convenience, at https://gitlab.in2p3.fr/micropicell/multiplexprocessor/-/wikis/Install-from-binary (Figure 2).\n\nThe workflow was run on a laptop with Intel® CoreTM i7-7Y75, CPU @ 1.30 GHz, 16 Gb of RAM, with Windows 10 64-bit. Image processing performed includes deconvolution, extended depth of field, shading correction, background subtraction, cycle registration, stitching and segmentation (Figure 4).\n\nDeconvolution is included using DeconvolutionLab213 and PSFGenerator14 from EPFL BIG. However this step can be performed using any deconvolution software, and an example implementation with the commercial licensed software Microvolution®15 is provided as a branch in the code repository. Extended depth of field is provided using EPFL BIG implementation16. Shading correction is performed by dividing a profile image computed using median intensities. Background correction is performed by subtracting signal from the blank cycles. Cycle registration is performed using TurboReg17 from EPFL BIG. Position-wise tiles from reference channel are registered against tiles from reference cycle. Computed translations are then applied to all the remaining channels. Finally, registered tiles are cropped by the greatest computed translation. Stitching is performed using MIST18 from NIST. Stitched positions are computed using reference channel of the reference cycle and then applied to all remaining channels and cycles. Segmentation of nuclei is performed using Stardist19,20. The output directory structure is compatible with the original analysis software provided with the device CODEX® multiplex analysis viewer (MAV). Furthermore FCS files are generated using Flow Cytometry Data Standards21 and can be analyzed using any other tool.\n\n\nUse case\n\nWe provide an example dataset acquired in our lab using Formalin-Fixed Paraffin-Embedded (FFPE) human tonsil and describe the step-by-step operation using the GUI to call the core functions and the provided dataset, described in Data Availability.\n\nFFPE tonsil human sample was obtained from the tissue bank of the Nantes university hospital. FFPE tonsil human was sectioned at a thickness of 5 µm and directly adhered onto poly-L-lysine (Sigma Aldrich) coated coverslips (Akoya Biosciences). Tissue coverslips were stored at 4°C until staining.\n\nStaining and imaging with PhenoCyclerTM were performed using the Akoya Biosciences protocol available in https://www.akoyabio.com/wp-content/uploads/2021/01/CODEX-User-Manual.pdf\n\nThe sample cover slip was placed on a 55°C hot plate for 20 minutes. Tissue section was cooled down before deparaffinization and hydration steps. Tissue was immersed in the following solvent series for 5 minutes by step: twice in Xylene, twice in 100% Ethanol, once in 90%, 70%, 50%, 30% Ethanol and twice in ddH2O. Antigen retrieval was performed in a hot water bath at 94°C in a 1X Citrate Buffer (Sigma Aldrich) for 20 minutes.\n\nAfter cooling at room temperature, tissue was briefly washed twice in ddH2O for 2 minutes, twice in Hydration buffer (Akoya Biosciences), then was incubated in Staining buffer (Akoya Biosciences) at room temperature for 20 minutes. The antibody cocktail (10 antibodies and DAPI nuclear stain - Table 1) was prepared in a blocking solution according to the Akoya Biosciences instructions and tissue section was incubated with 190 µL of this solution at room temperature for 3 hours in humidity chamber. Stained tissue was washed twice in Staining buffer (Akoya Biosciences) for 2 minutes, then was post-fixed with 1.6% PFA in Storage Buffer (Akoya Biosciences) for 10 minutes. After an incubation in a cold methanol solution for 5 minutes, tissue section was successively washed three times in PBS 1X and fixed with a PhenoCyclerTM fixative solution at room temperature in humidity chamber for 20 minutes. Finally, tissue cover slip was washed three times in PBS 1X and stored in Storage Buffer (Akoya Biosciences) at 4°C before PhenoCyclerTM multi-cycle imaging.\n\nSample and reagents were equilibrated at room temperature before the PhenoCyclerTM run. According with Akoya Biosciences recommendations, a 96-well plate of PhenoCyclerTM reporters complementary to the bar-codes used in the antibody panel with a nuclear stain was prepared.\n\nSolutions (PhenoCyclerTM 1X buffer, dimethyl sulfoxide, water) required for the PhenoCyclerTM fluidic instrument automate were loaded into the PhenoCyclerTM and the tissue coverslip was installed onto the stage insert. Multi-imaging was performed using a Zeiss Axio Observer inverted microscope with Colibri 7 light source, coupled with the ORCA Flash 4.0 LT camera (Hamamatsu) and associated at the Filter Set 112 HE LED from Zeiss. The multiplex imaging run was executed with the PhenoCyclerTM Instrument Manager (CIM) software. Nuclear DAPI staining was used to design tiled regions of the human tonsil section of interest at the 5x magnification (N-Achroplan 5x/0.15 M27, Zeiss). The focus of tissue was performed using a Plan-Apochromat 20x/0.8 M27 objective (Zeiss), with every image being 2048x2048 pixels, and a x-y pixel size of 0.325 micrometers. Led intensity and light exposure times were for each channel respectively: 50% and 500 milliseconds for AlexaFluorTM750 and Cy5 dyes, 50% and 400 milliseconds for ATTO550 dye, and 30% and 5 milliseconds for the DAPI dye. For each antibody, images were acquired per tile for each of 4 channels with an 11 plane Z-stack and an acquisition step in Z of 1.5 micrometers.\n\nA total of 117 (13x9) tiles were acquired in snake order, but the example data set is a sub-sampling of 4 tiles (Figure 5) created by renaming image files and creating new experiment files.\n\nScale bar is 2 millimeters.\n\nHere we describe the use of the Multiplex Processor graphical user interface, exemplified on the data set provided (Figure 6). The GUI has no parameters exposed, since metadata related to the acquisition are read from the file generated by the PhenoCycler CIM and other parameters have been optimized on different types of tissue. They can be modified if needed in a special java class for every step for parameters, but in our case are kept the same for all experimentation by the PhenoCyclerTM users. Note that the workflow can be started and ended at any step, assuming that data are organised as expected in the input description in the wiki https://gitlab.in2p3.fr/micropicell/multiplexprocessor/-/wikis/MultiplexProcessor-Usage-documentation. Error and log files are generated and can be used to monitor the processing.\n\nAll scale bars are 200 micrometers if not specified on the figure. (A) One example of tile slice before deconvolution (slice 8 position 2, CD20 in magenta and DAPI in cyan). (B) The same position and channels after deconvolution by Microvolution and extended field of view (from these steps all data are 2D). (C) The same view after shading and background correction. (D, F) The shading profile from cycle 1 (D) and the last cycle 6 (F) for the same position. (E, G) Contrast-adjusted blank cycles 1 (E) and 6 (G) used to correct the autofluorescence in each wavelength of the tissue, here for channel 2, after shading correction. (H, I) Cycle registration uses DAPI staining to correct the drift that can occur between cycles: (H) shows the discrepancy between cycle 1 in red and 2 in green, (I) is the same field of view after drift correction. (J) Stitching result of the 4 tiles examples used with only CD20 in magenta and DAPI in cyan. The white rectangle shows the area corresponding to panel (K). (K) Regions of interest obtained by Stardist superimposed on DAPI (cyan) and CD20 (magenta). (L) Color-merged image from stitching with CD20 in magenta, CD21 in yellow, CD3e in green, CD31 in blue and CD45RO in cyan.\n\nStep 0: Deconvolution\n\nThe data having been acquired with a wide-field microscope as 3D stack (an example of one slice is shown in Figure 6 (A)), the deconvolution step is a classical step to ameliorate the quality and resolution of data. Two options are offered in the Multiplex Processor as two different branches of the software. The compiled version relies on DeconvolutionLab213. The point spread function for each wavelength is generated based on the parameters contained in the experiment json file (wavelengths, voxel size, aperture). By default when using DeconvolutionLab2 in our workflow, Richardson Lucy algorithm is used with 10 iterations. The option can be changed in our DeconvolutionProcessor class.\n\nThis step is very long using Deconvolutionlab2 (96 stacks of 11 slices each, 2048x2048, take 8 hours to be processed, at 5.10 minutes per 3D stack on a laptop). A processed deconvolved data set using Microvolution commercial software is provided as a companion data set. To use it, unzip bu_deconvolution.zip and rename the extracted directory to \"out\".\n\nStep 1: Extended depth of field (EDF)\n\nThe purpose of this step is to create a 2D image from the 3D stack to get the in-focus information (the resulting processed slice from one stack using Microvolution followed by EDF is shown in Figure 6 (B)). We rely on the BIG EPFL plugin16 for this step, with quality HIGH and topology NO_MEDIUM in the GUI implementation used here, where the full list of associated parameters are defined in the ParametersFactory class from our processor. This step should take about 1.22 minutes per stack on a laptop.\n\nStep 2: Shading correction\n\nA shading profile for the first and the last cycle of each channel is computed (Figure 6 (D-E)) by dividing the median of all positions by its convolution with a Gaussian blur (sigma 64 pixels) kernel. For each cycle and each channel, a specific shading profile is computed by linear interpolation of the shading profile of the first cycle and the last cycle. Each tile is then corrected by dividing the EDF image by this normalised interpolated profile. This step should take about 1 second per stack.\n\nStep 3: Background correction\n\nThe first and the last cycle of acquisition are acquired without marker, to create blank cycles images (Figure 6 (F-G)). After a Gaussian blur of sigma 10 pixels, we assume these images represent the autofluorescence intensity. This autofluorescence is then linearly interpolated between the first and last cycle and subtracted for each cycle and channel to be processed. This step should take about 0.74 seconds per stack.\n\nStep 4: Cycle registration\n\nBecause the acquisition is done by cycles, coming back to the same position but moving the microscope stage, a mechanical drift due to the accuracy of stage repositioning is likely to occur, as exemplified in Figure 6 (H). For these reasons, all cycles have a nuclei marker acquisition, that will then serve as a reference channel for inter-cycle registration. We used the automatic mode of Turboreg17, constraining the transformation to be a translation. This step took 168 seconds in total on a non-CUDA-enabled desktop.\n\nStep 5: Remove negative values\n\nAfter the registration step, we have added a \"Remove negative values\" step. All negative intensity values in the images are replaced by 0 and the minimal intensity value of every image is subtracted to the non-zeros values.\n\nStep 6: Stitching\n\nStitching is performed using the MIST software18 based on the information contained in the experiment json file. This file contains the percentage of overlap during acquisitions between tiles and the number of rows and columns of tiles, as well as the reading order (by default in snake row order). We have made here the controversial choice to generate one mosaic per channel and cycle, instead of tiles (regions in MAV) due to the usage of the MAV software provided by Akoya Biosciences, free but not open source, afterwards (Figure 6 (J)), which was re-correcting the regions’ positions.\n\nStep 7: Segmentation\n\nNuclei are segmented from the nuclei stained channel of the first cycle stitched image, on which all other cycles have been registered during step 4. We used Stardist pre-trained model \"2D_versatile_fluo\" with image normalisation19,20 to segment the nuclei as exemplified in Figure 6 (K)). An imageJ22 set of ROIs is then generated and saved as zip.\n\nStep 8: Create Mask from ROI\n\nThis optional step allows the creation of an RGB image corresponding to the segmented nuclei perimeter with a correct naming for visualisation only.\n\nStep 9: Measure\n\nEvery cell is analyzed as an ImageJ ROI using the ImageJ analyzer plugin to measure their spatial location and intensity values, but also other parameters that we did not use in the analysis, but which could be of interest for other analysis such as nuclei shape descriptors, orientation, intensity statistics in every channel. These measurements are then stored in both a csv file compatible with the MAV software, and in standard FCS format using the CSVtoFCS functionalities offered by the Flow Cytometry Data standard project21.\n\nStep 10: Create MAV Project\n\nThis last optional step allows the use of the MAV software afterwards, as in our lab routine workflow usage of the PhenoCyclerTM. This simply reorganised our output to make it compatible with the expected input experiment and file organisation for MAV.\n\nFor the clustering analysis in this paper, we used the freely available CODEX MAV, provided by Akoya Biosciences as a Fiji plugin. All files are prepared in MAV compatible format by the last step of our workflow. The directory selected as output directory can then be used directly in the \"open experiment\" field from MAV. Note that any other analysis tools could be used, including histocat23, qupath24 or other tools, as well as any population analysis based tools usually used in cytometry thanks to the FCS output.\n\n\nConclusions\n\nIn this paper we present an open source workflow, based on an optimised sequential arrangement of existing steps. This workflow is now used routinely in our lab, replacing the commercial solution provided by the vendor and solving the problems encountered of stitching or intensity normalisation. Recently a generalist software suite was implemented for multiplexed data processing25, which also incorporated the processing step26. The MCMicro software is conceived in order to be ready to host different implementation of steps because it is based on Galaxy and Nextflow. Our command line implementation would ease this implementation in the future, and would also facilitate the extension of usage to other multiplexed tissue imaging systems. However we provide here an out of the shell tool for other labs using the PhenoCyclerTM that may fix problems encountered.",
"appendix": "Data availability\n\nExample data are available from: https://doi.org/10.5281/zenodo.646161127.\n\nThis project contains the following underlying data in one 6.5 Gb zipped file. The imaging was generated from a larger acquisition by sub-selecting 6 cycles and 4 fields of view by rewriting the metadata files accordingly.\n\n6 cycles, organised in folders by cycles, each folder 1.37Gb. Each folder contains 2D tif experimentname_image -position1-4_Z01-11_CH1-4.tif (176 files in each folder). 2048x2048 image in 16 bits; each image 8Mb\n\nExperiment.json was generated by the PhenoCyclerTM acquisition and modified. Note that the path under the experiment json has no importance, but the raw data should be at the same level.\n\nchannelNames.txt contains the list of fluorescent reporters used. Blank means no reporters.\n\nLicence: Creative Commons Attribution 4.0 International.\n\n\nAcknowledgements\n\nWe acknowledge the Tumorothéque from the \"service d’anatomie cytologie pathologiques du CHU de Nantes\" for providing samples. We acknowledge the IBISA MicroPICell facility (Biogenouest), member of the national infrastructure France-Bioimaging, in particular Steven Nedellec, and the \"Région Pays de la Loire\". We are grateful to Nicolas Jouand from the Cytocell facility for providing expertise in cytometry file preprocessing. Most of the figures were generated using FigureJ28.\n\n\nReferences\n\nQuail DF, Joyce JA: Microenvironmental regulation of tumor progression and metastasis. Nat Med. 2013; 19(11): 1423–1437. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorrison SJ, Spradling AC: Stem cells and niches: Mechanisms that promote stem cell maintenance throughout life. Cell. 2008; 132(4): 598–611. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nForster B, Van De Ville D, Berent J, et al.: Extended depth-of-focus for multi-channel microscopy images: A complex wavelet approach. In: 2004 2nd IEEE International Symposium on Biomedical Imaging: Macro to Nano (IEEE Cat No. 04EX821). IEEE, 2004; 2: 660–663. Publisher Full Text\n\nThévenaz P, Ruttimann UE, Unser M: A pyramid approach to subpixel registration based on intensity. IEEE Trans Image Process. 1998; 7(1): 27–41. PubMed Abstract | Publisher Full Text\n\nChalfoun J, Majurski M, Blattner T, et al.: MIST: Accurate and scalable microscopy image stitching tool with stage modeling and error minimization. Sci Rep. 2017; 7(1): 4988. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchmidt U, Weigert M, Broaddus C, et al.: Cell detection with star-convex polygons. In: Med Image Comput Comput Assist Interv - MICCAI 2018 - 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part II. 2018; 11071: 265–273. Publisher Full Text\n\nWeigert M, Schmidt U, Haase R, et al.: Star-convex polyhedra for 3d object detection and segmentation in microscopy. In: IEEE Winter Conf Appl Comput Vis (WACV). 2020. Publisher Full Text\n\nSpidlen J, Shooshtari P, Kollmann TR, et al.: Flow cytometry data standards. BMC Res Notes. 2011; 4(1): 50. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchneider CA, Rasband WS, Eliceiri KW: NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012; 9(7): 671–675. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchapiro D, Jackson HW, Raghuraman S, et al.: histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data. Nat Methods. 2017; 14(9): 873–876. 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PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "152007",
"date": "21 Oct 2022",
"name": "Anna H. Klemm",
"expertise": [
"Reviewer Expertise Bioimage analysis"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a pipeline for PhenoCycler(CODEX)/similarly structured data sets that run preprocessing, segmentation, and parameter extraction using open-source tools. Based on a limited demonstration in Fig.2 it seems to perform better than the vendor-provided software. Also, using open-source, free tools come with the advantages of higher availability and the possibility to adjust to own needs. The description of the tool is easy to follow and it comes with an example dataset and description to run the pipeline on this dataset.\nMinor comments to the text:\nFig 1A: z-stacks should be indicated by either drawing an axis or visualizing bigger steps between slices.\n\nStitching: How big is the typical translation needed and how much is a typical overlap?\n\nFig. 6: Show B, C, J, and L with comparable adjusted brightness/contrast in order to better inspect the contrast.\n\nRegistration/corrections: Eventually, it could help to include a table with all cycles and recordings for displaying which images were used for registration, etc.\n\nPost-processing/Fig 3C: I suggest including a short description of how cell classification was done.\n\nTool:\nI run the binary version from https://zenodo.org/record/6773173#.Y1KHQWdBxD8 on the example data, starting with the deconvolved data.\nComments:\nRunning it requires Java 11. The information could be found on https://gitlab.in2p3.fr/micropicell/multiplexprocessor/-/tree/master/, but not on the instruction of the binary version or the workflow description so it should be included there.\n\nWorkflow description https://gitlab.in2p3.fr/micropicell/multiplexprocessor/-/wikis/MultiplexProcessor-Usage-documentation ends with Step 6: Stitching.\n\nRunning the processor on the example data generated stitched datasets, but no further output (segmentation, MAV project, FCS file).\n\nThe output stitched results don’t show the expected quality - see image.\n\nThere is relatively little dialog when running the processor. Some brief information about the progress of processing would help.\n\nhttps://gitlab.in2p3.fr/micropicell/multiplexprocessor/-/tree/master/ misses description of Usage and Codex Splitter.\nThis needs to be double-checked before indexing.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "8951",
"date": "28 Oct 2022",
"name": "Perrine Paul-Gilloteaux",
"role": "Author Response",
"response": "Dear Dr. Klemm, Many thanks for your constructive and useful comments. Before answering your review point by point and providing an adequately revised new version, could you upload or copy the log and error files that you should find in the same directory as the binary software? Indeed, I was not able to reproduce the bug reported about the stitching having crashed, these log files would be very useful. Best regards, Perrine Paul-Gilloteaux"
},
{
"c_id": "8999",
"date": "16 Nov 2022",
"name": "Anna Klemm",
"role": "Reviewer Response",
"response": "Yes, happy to do so. Please let me know if you need more information. Error message: okt. 21, 2022 3:53:18 EM com.sun.javafx.application.PlatformImpl startup WARNING: Unsupported JavaFX configuration: classes were loaded from 'unnamed module @3c95b7a5' java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space at wavelets.ImageAccess.(ImageAccess.java:165) at wavelets.ImageAccess.duplicate(ImageAccess.java:294) at wavelets.ComplexWavelet.analysis(ComplexWavelet.java:54) at edf.EdfComplexWavelets.process(EdfComplexWavelets.java:91) at fr.univ_nantes.codex_processor.core.extended_depth_of_field.ExtendedDepthOfField.process(ExtendedDepthOfField.java:73) at fr.univ_nantes.codex_processor.core.extended_depth_of_field.ExtendedDepthOfFieldProcessor.run(ExtendedDepthOfFieldProcessor.java:23) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.lambda$run$0(DatasetExtendedDepthOfFieldProcessor.java:58) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor$$Lambda$408/0x0000000800389440.run(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask$AdaptedRunnableAction.exec(ForkJoinTask.java:1407) at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space at wavelets.ImageAccess.(ImageAccess.java:165) at wavelets.ImageAccess.duplicate(ImageAccess.java:294) at wavelets.ComplexWavelet.analysis(ComplexWavelet.java:54) at edf.EdfComplexWavelets.process(EdfComplexWavelets.java:91) at fr.univ_nantes.codex_processor.core.extended_depth_of_field.ExtendedDepthOfField.process(ExtendedDepthOfField.java:73) at fr.univ_nantes.codex_processor.core.extended_depth_of_field.ExtendedDepthOfFieldProcessor.run(ExtendedDepthOfFieldProcessor.java:23) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.lambda$run$0(DatasetExtendedDepthOfFieldProcessor.java:58) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor$$Lambda$408/0x0000000800389440.run(Unknown Source) at java.base/java.util.concurrent.ForkJoinTask$AdaptedRunnableAction.exec(ForkJoinTask.java:1407) at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290) at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1020) at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1656) at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1594) at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183) java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError at java.base/java.util.concurrent.ForkJoinTask.get(ForkJoinTask.java:1006) at fr.univ_nantes.codex_processor.gui.DatasetExtendedDepthOfFieldProcessor.run(DatasetExtendedDepthOfFieldProcessor.java:69) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:96) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Caused by: java.lang.OutOfMemoryError at java.base/jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source) at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490) at java.base/java.util.concurrent.ForkJoinTask.getThrowableException(ForkJoinTask.java:603) ... 49 more Caused by: java.lang.OutOfMemoryError: Java heap space WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by gov.nist.isg.mist.lib.libraryloader.LibraryUtils (file:/C:/Users/IT-WL-annkl878/Documents/notes/Codex_Analysis/MultiplexProcessor/gui-0.1.0-SNAPSHOT.jar) to field java.lang.ClassLoader.usr_paths WARNING: Please consider reporting this to the maintainers of gov.nist.isg.mist.lib.libraryloader.LibraryUtils WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Python was not found; run without arguments to install from the Microsoft Store, or disable this shortcut from Settings > Manage App Execution Aliases. java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\MultiplexProcessor\\labels.tif at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileCopy.move(WindowsFileCopy.java:326) at java.base/sun.nio.fs.WindowsFileSystemProvider.move(WindowsFileSystemProvider.java:292) at java.base/java.nio.file.Files.move(Files.java:1422) at fr.univ_nantes.codex_processor.gui.StardistDatasetSegmentationProcessor.run(StardistDatasetSegmentationProcessor.java:36) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:144) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.gui.CreateSegmentationMaskFromRois.run(CreateSegmentationMaskFromRois.java:32) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:152) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) java.nio.file.NoSuchFileException: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\rois_cy002_ch1.zip at java.base/sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:85) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:103) at java.base/sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:108) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:53) at java.base/sun.nio.fs.WindowsFileAttributeViews$Basic.readAttributes(WindowsFileAttributeViews.java:38) at java.base/sun.nio.fs.WindowsFileSystemProvider.readAttributes(WindowsFileSystemProvider.java:198) at java.base/java.nio.file.Files.readAttributes(Files.java:1764) at java.base/java.util.zip.ZipFile$Source.get(ZipFile.java:1259) at java.base/java.util.zip.ZipFile$CleanableResource.(ZipFile.java:733) at java.base/java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:850) at java.base/java.util.zip.ZipFile.(ZipFile.java:248) at java.base/java.util.zip.ZipFile.(ZipFile.java:177) at java.base/java.util.zip.ZipFile.(ZipFile.java:191) at fr.univ_nantes.codex_processor.core.measure.MeasureProcessor.run(MeasureProcessor.java:43) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:45) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) Exception in thread \"JavaFX Application Thread\" java.lang.IllegalArgumentException: Column cy001_ch1_DAPI_Area is not present in table Measure results at tech.tablesaw.api.Table.columnIndex(Table.java:437) at tech.tablesaw.table.Relation.doubleColumn(Relation.java:379) at fr.univ_nantes.codex_processor.gui.DatasetMeasureProcessor.run(DatasetMeasureProcessor.java:62) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:160) at fr.univ_nantes.codex_processor.gui.MainController$1.handle(MainController.java:64) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Node.fireEvent(Node.java:8889) at javafx.scene.control.Button.fire(Button.java:203) at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208) at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.Scene$MouseHandler.process(Scene.java:3856) at javafx.scene.Scene.processMouseEvent(Scene.java:1851) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299) at java.base/java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446) at com.sun.glass.ui.View.handleMouseEvent(View.java:556) at com.sun.glass.ui.View.notifyMouse(View.java:942) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174) at java.base/java.lang.Thread.run(Thread.java:829) ^C"
},
{
"c_id": "9000",
"date": "16 Nov 2022",
"name": "Anna Klemm",
"role": "Reviewer Response",
"response": "output_gui9 Extended depth of field - completed : 0 / 96 Extended depth of field - completed : 1 / 96 Extended depth of field - completed : 2 / 96 Extended depth of field - completed : 3 / 96 Extended depth of field - completed : 4 / 96 Extended depth of field - completed : 5 / 96 Extended depth of field - completed : 6 / 96 Extended depth of field - completed : 7 / 96 Shading correction - completed : 0 / 72 Shading correction - completed : 1 / 72 Shading correction - completed : 2 / 72 Shading correction - completed : 3 / 72 Shading correction - completed : 4 / 72 Shading correction - completed : 5 / 72 Shading correction - completed : 6 / 72 Shading correction - completed : 7 / 72 Shading correction - completed : 8 / 72 Shading correction - completed : 9 / 72 Shading correction - completed : 10 / 72 Shading correction - completed : 11 / 72 Shading correction - completed : 12 / 72 Shading correction - completed : 13 / 72 Shading correction - completed : 14 / 72 Shading correction - completed : 15 / 72 Shading correction - completed : 16 / 72 Shading correction - completed : 17 / 72 Shading correction - completed : 18 / 72 Shading correction - completed : 19 / 72 Shading correction - completed : 20 / 72 Shading correction - completed : 21 / 72 Shading correction - completed : 22 / 72 Shading correction - completed : 23 / 72 Shading correction - completed : 24 / 72 Shading correction - completed : 25 / 72 Shading correction - completed : 26 / 72 Shading correction - completed : 27 / 72 Shading correction - completed : 28 / 72 Shading correction - completed : 29 / 72 Shading correction - completed : 30 / 72 Shading correction - completed : 31 / 72 Shading correction - completed : 32 / 72 Shading correction - completed : 33 / 72 Shading correction - completed : 34 / 72 Shading correction - completed : 35 / 72 Shading correction - completed : 36 / 72 Shading correction - completed : 37 / 72 Shading correction - completed : 38 / 72 Shading correction - completed : 39 / 72 Shading correction - completed : 40 / 72 Shading correction - completed : 41 / 72 Shading correction - completed : 42 / 72 Shading correction - completed : 43 / 72 Shading correction - completed : 44 / 72 Shading correction - completed : 45 / 72 Shading correction - completed : 46 / 72 Shading correction - completed : 47 / 72 Shading correction - completed : 48 / 72 Shading correction - completed : 49 / 72 Shading correction - completed : 50 / 72 Shading correction - completed : 51 / 72 Shading correction - completed : 52 / 72 Shading correction - completed : 53 / 72 Shading correction - completed : 54 / 72 Shading correction - completed : 55 / 72 Shading correction - completed : 56 / 72 Shading correction - completed : 57 / 72 Shading correction - completed : 58 / 72 Shading correction - completed : 59 / 72 Shading correction - completed : 60 / 72 Shading correction - completed : 61 / 72 Shading correction - completed : 62 / 72 Shading correction - completed : 63 / 72 Shading correction - completed : 64 / 72 Shading correction - completed : 65 / 72 Shading correction - completed : 66 / 72 Shading correction - completed : 67 / 72 Shading correction - completed : 68 / 72 Shading correction - completed : 69 / 72 Shading correction - completed : 70 / 72 Shading correction - completed : 71 / 72 Shading correction - completed : 72 / 72 Background subtraction - completed : 0 / 48 Background subtraction - completed : 1 / 48 Background subtraction - completed : 2 / 48 Background subtraction - completed : 3 / 48 Background subtraction - completed : 4 / 48 Background subtraction - completed : 5 / 48 Background subtraction - completed : 6 / 48 Background subtraction - completed : 7 / 48 Background subtraction - completed : 8 / 48 Background subtraction - completed : 9 / 48 Background subtraction - completed : 10 / 48 Background subtraction - completed : 11 / 48 Background subtraction - completed : 12 / 48 Background subtraction - completed : 13 / 48 Background subtraction - completed : 14 / 48 Background subtraction - completed : 15 / 48 Background subtraction - completed : 16 / 48 Background subtraction - completed : 17 / 48 Background subtraction - completed : 18 / 48 Background subtraction - completed : 19 / 48 Background subtraction - completed : 20 / 48 Background subtraction - completed : 21 / 48 Background subtraction - completed : 22 / 48 Background subtraction - completed : 23 / 48 Background subtraction - completed : 24 / 48 Background subtraction - completed : 25 / 48 Background subtraction - completed : 26 / 48 Background subtraction - completed : 27 / 48 Background subtraction - completed : 28 / 48 Background subtraction - completed : 29 / 48 Background subtraction - completed : 30 / 48 Background subtraction - completed : 31 / 48 Background subtraction - completed : 32 / 48 Background subtraction - completed : 33 / 48 Background subtraction - completed : 34 / 48 Background subtraction - completed : 35 / 48 Background subtraction - completed : 36 / 48 Background subtraction - completed : 37 / 48 Background subtraction - completed : 38 / 48 Background subtraction - completed : 39 / 48 Background subtraction - completed : 40 / 48 Background subtraction - completed : 41 / 48 Background subtraction - completed : 42 / 48 Background subtraction - completed : 43 / 48 Background subtraction - completed : 44 / 48 Background subtraction - completed : 45 / 48 Background subtraction - completed : 46 / 48 Background subtraction - completed : 47 / 48 Background subtraction - completed : 48 / 48 Cycle registration compute - completed : 0 / 20 Cycle registration compute - completed : 1 / 20 Cycle registration compute - completed : 2 / 20 Cycle registration compute - completed : 3 / 20 Cycle registration compute - completed : 4 / 20 Cycle registration compute - completed : 5 / 20 Cycle registration compute - completed : 6 / 20 Cycle registration compute - completed : 7 / 20 Cycle registration compute - completed : 8 / 20 Cycle registration compute - completed : 9 / 20 Cycle registration compute - completed : 10 / 20 Cycle registration compute - completed : 11 / 20 Cycle registration compute - completed : 12 / 20 Cycle registration compute - completed : 13 / 20 Cycle registration compute - completed : 14 / 20 Cycle registration compute - completed : 15 / 20 Cycle registration compute - completed : 16 / 20 Cycle registration compute - completed : 17 / 20 Cycle registration compute - completed : 18 / 20 Cycle registration compute - completed : 19 / 20 Cycle registration compute - completed : 20 / 20 Cycle registration apply - completed : 0 / 96 Cycle registration apply - completed : 1 / 96 Cycle registration apply - completed : 2 / 96 Cycle registration apply - completed : 3 / 96 Cycle registration apply - completed : 4 / 96 Cycle registration apply - completed : 5 / 96 Cycle registration apply - completed : 6 / 96 Cycle registration apply - completed : 7 / 96 Cycle registration apply - completed : 8 / 96 Cycle registration apply - completed : 9 / 96 Cycle registration apply - completed : 10 / 96 Cycle registration apply - completed : 11 / 96 Cycle registration apply - completed : 12 / 96 Cycle registration apply - completed : 13 / 96 Cycle registration apply - completed : 14 / 96 Cycle registration apply - completed : 15 / 96 Cycle registration apply - completed : 16 / 96 Cycle registration apply - completed : 17 / 96 Cycle registration apply - completed : 18 / 96 Cycle registration apply - completed : 19 / 96 Cycle registration apply - completed : 20 / 96 Cycle registration apply - completed : 21 / 96 Cycle registration apply - completed : 22 / 96 Cycle registration apply - completed : 23 / 96 Cycle registration apply - completed : 24 / 96 Cycle registration apply - completed : 25 / 96 Cycle registration apply - completed : 26 / 96 Cycle registration apply - completed : 27 / 96 Cycle registration apply - completed : 28 / 96 Cycle registration apply - completed : 29 / 96 Cycle registration apply - completed : 30 / 96 Cycle registration apply - completed : 31 / 96 Cycle registration apply - completed : 32 / 96 Cycle registration apply - completed : 33 / 96 Cycle registration apply - completed : 34 / 96 Cycle registration apply - completed : 35 / 96 Cycle registration apply - completed : 36 / 96 Cycle registration apply - completed : 37 / 96 Cycle registration apply - completed : 38 / 96 Cycle registration apply - completed : 39 / 96 Cycle registration apply - completed : 40 / 96 Cycle registration apply - completed : 41 / 96 Cycle registration apply - completed : 42 / 96 Cycle registration apply - completed : 43 / 96 Cycle registration apply - completed : 44 / 96 Cycle registration apply - completed : 45 / 96 Cycle registration apply - completed : 46 / 96 Cycle registration apply - completed : 47 / 96 Cycle registration apply - completed : 48 / 96 Cycle registration apply - completed : 49 / 96 Cycle registration apply - completed : 50 / 96 Cycle registration apply - completed : 51 / 96 Cycle registration apply - completed : 52 / 96 Cycle registration apply - completed : 53 / 96 Cycle registration apply - completed : 54 / 96 Cycle registration apply - completed : 55 / 96 Cycle registration apply - completed : 56 / 96 Cycle registration apply - completed : 57 / 96 Cycle registration apply - completed : 58 / 96 Cycle registration apply - completed : 59 / 96 Cycle registration apply - completed : 60 / 96 Cycle registration apply - completed : 61 / 96 Cycle registration apply - completed : 62 / 96 Cycle registration apply - completed : 63 / 96 Cycle registration apply - completed : 64 / 96 Cycle registration apply - completed : 65 / 96 Cycle registration apply - completed : 66 / 96 Cycle registration apply - completed : 67 / 96 Cycle registration apply - completed : 68 / 96 Cycle registration apply - completed : 69 / 96 Cycle registration apply - completed : 70 / 96 Cycle registration apply - completed : 71 / 96 Cycle registration apply - completed : 72 / 96 Cycle registration apply - completed : 73 / 96 Cycle registration apply - completed : 74 / 96 Cycle registration apply - completed : 75 / 96 Cycle registration apply - completed : 76 / 96 Cycle registration apply - completed : 77 / 96 Cycle registration apply - completed : 78 / 96 Cycle registration apply - completed : 79 / 96 Cycle registration apply - completed : 80 / 96 Cycle registration apply - completed : 81 / 96 Cycle registration apply - completed : 82 / 96 Cycle registration apply - completed : 83 / 96 Cycle registration apply - completed : 84 / 96 Cycle registration apply - completed : 85 / 96 Cycle registration apply - completed : 86 / 96 Cycle registration apply - completed : 87 / 96 Cycle registration apply - completed : 88 / 96 Cycle registration apply - completed : 89 / 96 Cycle registration apply - completed : 90 / 96 Cycle registration apply - completed : 91 / 96 Cycle registration apply - completed : 92 / 96 Cycle registration apply - completed : 93 / 96 Cycle registration apply - completed : 94 / 96 Cycle registration apply - completed : 95 / 96 Cycle registration apply - completed : 96 / 96 Remove negative values - completed : 0 / 24 Remove negative values - completed : 1 / 24 Remove negative values - completed : 2 / 24 Remove negative values - completed : 3 / 24 Remove negative values - completed : 4 / 24 Remove negative values - completed : 5 / 24 Remove negative values - completed : 6 / 24 Remove negative values - completed : 7 / 24 Remove negative values - completed : 8 / 24 Remove negative values - completed : 9 / 24 Remove negative values - completed : 10 / 24 Remove negative values - completed : 11 / 24 Remove negative values - completed : 12 / 24 Remove negative values - completed : 13 / 24 Remove negative values - completed : 14 / 24 Remove negative values - completed : 15 / 24 Remove negative values - completed : 16 / 24 Remove negative values - completed : 17 / 24 Remove negative values - completed : 18 / 24 Remove negative values - completed : 19 / 24 Remove negative values - completed : 20 / 24 Remove negative values - completed : 21 / 24 Remove negative values - completed : 22 / 24 Remove negative values - completed : 23 / 24 Remove negative values - completed : 24 / 24 gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy001_ch1.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=false globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true STITCHING BEGINS! Successfully loaded plan from file Loading FFTW Plan... Saving plan to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\MultiplexProcessor\\lib\\fftw\\fftPlans\\2032x2032MeasurePlan.dat Finished loading/saving FFTW plan. Commencing stitching. memory pool size: 16 Writing relative positions (no optimization) to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\relative-positions-no-optimization-0.txt Computed North overlap: 5.0% Computed West overlap: 4.0% Warning: no good translations found for North direction. Estimated translations generated from the overlap. Warning: no good translations found for North direction. Repeatability has been set to zero. Please check the statistics file for more details. Repeatability for North: 0 pixels Repeatability for West: 0 pixels Calculated Repeatability: 3 pixels Completed Stitching in 3864ms Writing global positions to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt Writing relative positions to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\relative-positions-0.txt Writing relative positions (no optimization) to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\relative-positions-no-optimization-0.txt Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Saving Statistics to \"C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt\" Saving Log to \"C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt\" Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy001_ch2.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 13ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy001_ch3.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy001_ch4.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 0ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy002_ch1.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy002_ch2.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 2ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy002_ch3.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 2ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy002_ch4.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 0ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy003_ch1.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy003_ch2.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy003_ch3.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy003_ch4.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy004_ch1.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy004_ch2.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy004_ch3.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy004_ch4.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy005_ch1.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 0ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy005_ch2.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy005_ch3.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy005_ch4.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 0ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy006_ch1.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 0ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy006_ch2.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy006_ch3.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 0ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done gridwidth=2 gridheight=2 starttile=1 imagedir='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' filenamepatterntype=SEQUENTIAL filenamepattern={ppppp}_cy006_ch4.tif gridorigin=UL numberingpattern=HORIZONTALCONTINUOUS assemblefrommetadata=true globalpositionsfile='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\global-positions-0.txt' assemblenooverlap=false startrow=0 startcol=0 extentwidth=2 extentheight=2 timeslices=0 istimeslicesenabled=false outputpath='C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out' displaystitching=false outputfullimage=true outputmeta=true outputimgpyramid=false outfileprefix= blendingmode=LINEAR blendingalpha=1 numfftpeaks=100 isusedoubleprecision=true translationrefinementmethod=EXHAUSTIVE programtype=FFTW headless=true Checking args for stitching: Arg check passed Warning: the following files will be overwritten: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\log.txt C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\statistics.txt STITCHING BEGINS! Completed Stitching in 1ms Writing full image to: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Width: 3929 Height: 3965 Saving tiles to file: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Finished saving full image: C:\\Users\\IT-WL-annkl878\\Documents\\notes\\Codex_Analysis\\test_multiplxProcessor\\out\\stitched-0.tif Completed output options for slice 0. Done Measure - completed : 0 / 24 Measure - completed : 1 / 24 Measure - completed : 2 / 24 Measure - completed : 3 / 24 Measure - completed : 4 / 24 Measure - completed : 5 / 24 Measure - completed : 6 / 24 Measure - completed : 7 / 24 Measure - completed : 8 / 24 Measure - completed : 9 / 24 Measure - completed : 10 / 24 Measure - completed : 11 / 24 Measure - completed : 12 / 24 Measure - completed : 13 / 24 Measure - completed : 14 / 24 Measure - completed : 15 / 24 Measure - completed : 16 / 24 Measure - completed : 17 / 24 Measure - completed : 18 / 24 Measure - completed : 19 / 24 Measure - completed : 20 / 24 Measure - completed : 21 / 24 Measure - completed : 22 / 24 Measure - completed : 23 / 24 Measure - completed : 24 / 24"
}
]
},
{
"id": "230519",
"date": "28 Dec 2023",
"name": "Mark Zaidi",
"expertise": [
"Reviewer Expertise Multiplexed Immunohistochemistry",
"Image Analysis",
"Digital Pathology",
"Image Registration",
"Pipeline Development"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper essentially presents a new open-source (excellent!) software workflow for processing multiplexed fluorescence images. It addresses the challenges in existing commercial software, particularly around image stitching, intensity normalization, and segmentation. The authors demonstrate the workflow using the PhenoCycler (formerly CODEX) system, and compare its performance with the commercial processor, highlighting improvements in various processing aspects.\nSome of it's strengths are that this is open-source, adaptable to other cyclic imaging systems (not just PhenoCycler), and does a head-to-head comparison with commercial software.\nSome of the weaknesses include that they're not using the latest version of the CODEX processor for comparison (paper shows v1.8.2, newest release is 1.8.3). This should not be considered a valid negative criticism, because in the period during manuscript write up, the commercial software profiled in this study has been updated. It is not feasible to expect this manuscript to be constantly revised for each software release. Instead, the authors should take note of the differences between 1.8.2 and the current release, to see if any of their criticisms have been resolved in the new release (such as improved stitching, if it has been). Also, the repository has not been sufficiently populated with documentation and code necessary to replicate this study. Under post-processing analysis, histoCAT and QuPath should have the correct case sensitivity in its spelling.\nFig.2C - please include arrows highlighting where the defect in stitching is. While it seems quite apparent (huge cross in the middle of the FOV), Fig. 2D seems to have an additional channel displayed not present in Fig.2C which may confuse the reader as to what this defect is. Also, consider increasing the font size for this and all subsequent figures (fig 1 is good).\nAside from these otherwise minor issues, I don't see anything that would bar this manuscript from being published. The meticulous nature of the author in describing the technical detail at each step of the workflow, is greatly appreciated and seldom seen in similar studies. Running this pipeline on a laptop highlights how robust this workflow is, in its capacity to operate with limited computational resources. The CLI interface allows this tool to run in high-performance headless environments such as a SLURM cluster, highlighting its potential for scalability. Future studies can include integrating this workflow as an extension to other java-based applications such as QuPath. Excellent work!\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
},
{
"id": "230517",
"date": "19 Jan 2024",
"name": "Asier Antoranz",
"expertise": [
"Reviewer Expertise Spatial -omics",
"bioinformatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary The authors present a computational workflow for the analysis of cyclic multiplexing images. They pipeline cover from the raw data acquisition to the segmentation based on a nuclear staining. Their implementation is similar to that of the CODEX Processor software provided by the vendor with a few improvements regarding stitching, intensity normalization, and segmentation.\nThis is a timely and interesting work since the analysis of multiplexing images remains challenging and commercial platforms do not often perform properly.\n\nComments The description of the software tool is very shallow. They provide a wiki page, but this is not extensively descriptive.\nIn the introduction, the authors mention they introduce improvements with respect to the commercial software. However, all the results are presented visually (no quantifications) and are based on a single tonsil image.\nThe authors mention that the workflow is parameter free. However, it seems that a large number of parameters have been hard coded in the individual steps which can reduce generalizability to other imaging platforms, tissue types.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1121
|
https://f1000research.com/articles/11-1120/v1
|
29 Sep 22
|
{
"type": "Research Article",
"title": "Evaluation of the relationship between dermatoglyphics and mandibular third molar impaction: A cross-sectional study",
"authors": [
"Ashish Kapoor",
"Premalatha Shetty",
"Sameep S. Shetty",
"Srikant N.",
"Nancy Aggarwal",
"Yash Merchant",
"Seyed Mohammed Riahi",
"Ashish Kapoor",
"Sameep S. Shetty",
"Srikant N.",
"Nancy Aggarwal",
"Yash Merchant",
"Seyed Mohammed Riahi"
],
"abstract": "Background: Dermatoglyphics can be utilised in clinical settings to identify those who are more likely to have impacted teeth. Additionally, dermatoglyphics looks to have potential as a non-invasive diagnostic method for predicting the presence or absence of an impacted tooth. The goal of this study was to look at the most common dermatoglyphic pattern in people who had or didn't have an impacted mandibular third molar teeth and see if there was a dermatoglyphic signature. Methods: A cross-sectional study with 180 participants was conducted (90 cases and 90 controls). The rolling impression technique was used to apply blue duplicating ink to participants' fingertips, which was then recorded. There was an increase in the frequency of the whorl-plain pattern in the right-hand ring finger (60%; p=0.028) and left-hand little finger (33.3%; p=0.009), as well as the loop-ulnar pattern in the right-hand middle finger (74.4%; p=0.024) in individuals with a predisposition to the presence of impacted teeth. Results: The left-hand little finger was found to be the most predictive for impaction in a forward stepwise binary logistic regression analysis. Conclusions: Dermatoglyphics could be used as a non-invasive sign to predict whether or not a tooth is affected. Its value comes in early detection, which helps to avoid the surgical problems that come with symptomatic extraction of an impacted tooth.",
"keywords": [
"Dermatoglyphics",
"impacted tooth",
"third molar",
"fingerprint",
"young adult"
],
"content": "Introduction\n\nCumins and Midlo invented the term dermatoglyphics, which is taken from two Greek words – derma and glyphics. Glyphe means “carve” and derma means “skin” in English.1 Dermatoglyphics is the study of the patterns of dermal ridges on the fingertips, palms, soles, and toes of the feet. During the sixth and seventh weeks of pregnancy, the baby develops thick pads called volar pads on the fingers, hands, and feet. Volar pads are derived from the mesenchyme and form on the extremities of the fingers, palms, and feet. After week 10 of pregnancy, the pads stop expanding, but the phalanges continue to extend, causing pattern orientation. Around the 13th week of pregnancy, ridge formation begins, and pattern formation is completed by the 19th week of pregnancy.2\n\nFinger, palm, and sole impressions are thought to be influenced by both the environment and heredity. It has been proven scientifically that no two people, including monozygotic twins, have the same fingerprints or other dermal ridge characteristics. As a result, fingerprints are unique to each person and do not change over time as a result of disease, ageing, or other factors.1\n\nGalton (1892) was one of the first to use distinct fingerprint ridgeline patterns or minutiae to investigate fingerprint individuality. Fingerprints are influenced by genetic and environmental variables. Dermatoglyphics are beneficial in a variety of ways, including assisting in the diagnosis of single-gene illnesses. The fact that each person’s fingerprint is unique adds to the argument that a person’s genetic features will be revealed by his or her fingerprint.3\n\nAn impacted tooth is one that is unable to erupt into its normal functional position due to malposition, insufficient space, or other factors. A multitude of local and systemic factors that can act as roadblocks in an impacted tooth’s path to eruption prohibit it from erupting into its functional position within the projected chronological age. The interaction of local factors, such as the ectopic position of the tooth bud; ankylosis of the primary tooth; arch size-tooth size discrepancy; systemic factors, such as genetic, environmental, and endocrine disorders; and inherent genetic susceptibility, appears to be the driving force behind the impaction process.4 There have been reports of racial and demographic differences in impacted teeth. Asian and Black populations had a lower prevalence rate of impaction, but those in Greece and Turkey had a greater prevalence rate.5\n\nThe third molar is the last tooth to form and erupt in humans, as well as the tooth that is most likely to become impacted. Previous study has connected impacted third molars to pericoronitis, caries, periodontal issues, root resorption, and cysts or tumours of the jaw. The extraction of the impacted third molar has consequently become the most common treatment in the Department of Oral and Maxillofacial Surgery.6 These changes are influenced by genes, developmental processes, and a refined diet. Nonetheless, a small number of studies have revealed a relationship between the mandible and a higher occurrence of impacted third molars.7\n\nAside from radiographic diagnosis, an investigation strategy that is quick, cost-effective, and accurate is necessary. In this case, clinicians may profit from anticipating impaction and intervening at an early stage. There has been a paucity of research on predicting an individual’s likelihood of getting impaction in the field of dermatoglyphics. Teeth and fingerprints are both ectodermal. As a result, dermatoglyphics can be utilised as a marker to predict a variety of genetically susceptible disorders, bolstering the genetic basis.\n\nThis study’s purpose is to answer the following clinical question: is there a specific fingerprint pattern associated with impacted third molars? According to our hypothesis, there is a relationship between dermatoglyphics and mandibular tooth impaction. This study aimed to analyse the most common pattern of dermatoglyphics present in an individual with/without impacted mandibular third molar tooth and find the dermatoglyphic marker if any.\n\n\nMethods\n\nThis comparative cross-sectional study was conducted in the city of Mangalore, in the district of Dakshin Kannada, in the southern Indian coastline region. The study was authorized by the Institutional Ethics Committee, Manipal College of Dental Sciences, Mangalore (Approval Date: 13.10.2018; Protocol Reference Number: 18061), and the subjects gave their written informed consent before participating.\n\nIndividuals aged 20 years or older, residents of Karnataka and Kerala states, seeking dental care at Manipal College of Dental Sciences, Mangalore between 2018 and 2020 were eligible to participate. Those with physical limitations such as amputation of forelimbs or scars on their fingers, as well as those with impacted third molars with cystic lesions or neoplasms, were not allowed to participate.\n\nSample size: 180 (90 * 2)\n\nthe following formula was used to calculate the sample size:\n\nq = 100 − p\n\np1 = proportion of first group q1 = 100 − p1\n\np2 = proportion of second group q2 = 100 − p2\n\nZα = 1.96 at 95% confidence level ZB = 1.28 at 90% power\n\nWith 95% confidence level and 90% power by assuming 47% will give whorl fingerprint pattern in first group and 24% will give in the second group8 the sample size comes to be 90 for each group.\n\nIndividuals with impacted third molars/partially erupted third molars/missing third molars with no history of extraction were included in the case group, which consisted of 90 subjects, whereas individuals with the full complement of erupted teeth (32 teeth) were included in the control group, which consisted of 90 subjects.\n\nNon-probability quota sampling was utilized as the sample method. With blue duplicating ink, the ink process was employed to record the impression of fingerprints. The following supplies were used: a magnifying glass (×5), a cotton applicator, soap, water, tissue paper, and a study proforma sheet.\n\nThe hands of the participants were cleansed with soap and water, then dried with tissue paper to eliminate sweat, oil, and grime from the fingertips, ensuring a high-quality dermatoglyphic print. After that, a small dab of blue duplicating ink was put to the cotton applicator, and a thin coating of ink was smeared evenly on the fingertip. To record the impression on the research proforma sheet, the rolling impression technique was preferred. By rotating the finger from one side to the other (nail to nail), complete imprints were recorded.9,10\n\nEach digit was firmly pushed into the proforma sheet with constant and adequate pressure to achieve a high-quality impression. To minimize duplication, the blocks on the proforma sheet were numbered 1 to 5 for the right hand, beginning with the thumb and ending with the little finger, and 6 to 10 for the left hand, beginning with the thumb and ending with the little finger. A panoramic radiograph was taken for participants who had missing tooth/teeth without a history of surgery/extraction to confirm the presence of impacted tooth/teeth or congenital missing tooth/teeth.\n\nDemographic variables were recorded. Impaction was used as a dependent variable, with all versions of fingerprints from all fingers being used as independent variables. All of the fingerprints were categorized into five different categories: loop-radial, loop-ulnar, whorl-plain, whorl-pocket, whorl-double loop, and arch-plain. Under the guidance of the forensic expert, the recorded prints were examined with a hand-magnifying glass. The patterns visualized were:\n\nWhorl pattern: It has a concentric design in which the majority of the ridges make circuits around the core. They are further divided into: i) plain (concentric circles form the pattern around a core); ii) double loop (two loops form an S-shaped pattern); iii) accidental (irregular shaped pattern); and iv) central pocket loop (a loop with a whorl pattern at one end).\n\nLoop pattern: It has ridges that are open and curve around only on the single extremity of the pattern and flow to the margin of the digit. They are further divided into: i) radial (loop ends towards the radial side); and ii) ulnar (loop ends towards the ulnar side).\n\nArch pattern: It has ridges passing from one margin of the digit to the other with a distally bowed sweep. They are further subdivided into: i) plain (the wave in the centre is blunt/low in height); and ii) tented (the wave in the centre is sharp/high in height).1\n\nStatistical analysis was performed using IBM SPSS Statistics (RRID:SCR_016479) version 22.0 (IBM Inc., New Armonk, NJ, USA). The impaction with sex and the pattern of dermatoglyphics with each finger was compared using the chi-squared test. The prediction of impaction was analysed using forward stepwise binary regression analysis. Impaction was taken as the dependent variable, and the patterns of each finger of the individual were taken as the independent variables for prediction. The level of significance was set at p<0.05 in all analyses.\n\nAn earlier version of this article can be found on Research Square (doi: https://doi.org/10.21203/rs.3.rs-951125/v1).\n\n\nResults\n\nA total of 180 subjects were engaged in the study (90 cases and 90 controls). Female participants made up the majority (n=123; 68.3%) (Table 1) (23). Mesioangular impaction was more common in mandibular teeth (38:42%; 48:44.1%), while distoangular impaction was more common in maxillary teeth (38:42%; 48:44.1%) (18:31.7%; 28:46.4%). The maxilla had missing tooth buds more frequently (18:16.7%; 28:16.1%) than the mandible (38:13%; 48:10.3%) (Figure 1). A total of 42 of the 90 people (46.7%) with impacted teeth had all four teeth impacted, followed by 21 (23.3%) who had two impacted teeth (Table 2).\n\n* p<0.05. R, Radical; U, Ulnar.\n\nThe most common fingertip pattern amongst research participants was loop-ulnar, which was seen more than 50% of the time in eight fingers (right and left thumb, index, middle, and little fingers), followed by whorl-plain, which was seen more than 50% of the time in two fingers (ring finger of both right and left-hands). Less than 10% of the respondents reported seeing the other patterns (Table 3).\n\nThe significance of the association with impaction was evaluated for all of the study variables. Sex, right-hand middle finger, right-hand ring finger, and left-hand little finger all revealed substantial impaction results. In terms of sex, female subjects and impacted third molars had a 76.7% association (p=0.016). Loop-ulnar and impacted third molar were related with 74.4% in the right-hand middle finger (p=0.024). The whorl-plain and impacted third molar with 60% were related with the right-hand ring finger (p=0.028). Similarly, the loop-ulnar fingerprint was related with both non-impacted and affected third molar teeth with 61.1%; whereas the whorl-plain fingerprint was identified with 33.3% in the impacted third molar tooth group (p=0.009). All of the other study factors, on the other hand, were not linked to impaction (Table 1).\n\nTo predict impaction, a forward stepwise binary logistic regression analysis was used. Impaction was used as a dependent variable, with all versions of fingerprints from all fingers being used as independent variables. All of the fingerprints were grouped into five categories: loop radial, loop-ulnar, whorl-plain, whorl-pocket, whorl-double loop, and arch-plain. The indicator variable was chosen as the first variable-loop radial, and all the others were compared to it. Using impaction as the dependent variable and fingerprints as the predictor variables (categorical), we discovered that the dermatoglyphic pattern of the left-hand little finger pattern was the single most important predictor of impaction, followed by the whorl-plain with an odd ratio of 1 (give the odd ratio with confidence intervals and p-value). Although the whorl-pocket pattern had a high odds ratio, it was not statistically significant. When compared to the loop radial group, whorl-plain had an odds ratio of 6.250 and was more significant for predicting impaction (Table 4).\n\n\nDiscussion\n\nThe purpose to conduct this study was to answer the following clinical question: is there a specific fingerprint pattern linked to impacted third molars? There is a link between dermatoglyphics and mandibular tooth impaction, according to our hypothesis. The aim of this study was to identify the most common dermatoglyphic pattern in people with and without impacted mandibular third molar teeth, as well as any dermatoglyphic markers.\n\nTeeth have a unique histology, making this biomatrix a time capsule for research of prenatal and early life exposure.11 The mandibular third molars are located near the mandible’s posterior and ramus intersection. It is often impacted in the current generation due to various factors and a lack of space. Dermatoglyphics, on the other hand, can be utilized to detect any environmental problems during the foetal stage due to their ectodermal origin. Environmental influences on the symmetry and size of the volar pads, which affects the dermatoglyphic pattern, have been studied in a few studies.12 Dermatoglyphic patterns, like all physical characteristics of the body, are the consequence of a person’s genes and are passed down the generations.\n\nDermatoglyphics have been linked to a variety of chromosomal abnormalities in a number of studies. In chromosomal illnesses such Patau’s syndrome, Edwards’ syndrome, Down syndrome, and Cri du Chat syndrome, atypical dermatoglyphic patterns can be detected. Dermatoglyphics research in dentistry is still in its early stages, with only a small amount of literature available. Caries, cleft lip and palate, bruxism, malocclusion, periodontal disease, oral submucous fibrosis, and head and neck squamous cell carcinomas are only a few of the dental problems connected to dermatoglyphics.2,13,14\n\nFemale subjects had higher mandibular third molar impaction than male subjects, according to our findings, and comparable findings were found in a study of the Swedish population.15\n\nWhen compared to the control group, the whorl-plain pattern in the right-hand ring finger, the loop-ulnar pattern in the right-hand middle finger, and the whorl-plain pattern in the left-hand little finger were found to be significantly linked with the presence of impacted teeth. The single most important predictor for the whorl-plain pattern was the left-hand little finger, which was validated using forward stepwise binary logistic regression. Ramesh et al., discovered a higher frequency of the whorl pattern on the ring and index fingers of the right hand in people with impacted teeth, as well as an increased frequency of the ulnar loop on the index and little finger of the left hand in people who didn’t have any impaction.16 In a similar study investigating for a link between dermatoglyphics and tooth impaction, Narang et al., reported contradicting results, albeit with a small sample size (20 participants). They concluded that in the group with impacted teeth, the tented arch pattern in both hands’ index fingers was more common.8\n\nThe non-randomization of the sampling in our study resulted in an unbalanced sex distribution, with female subjects being more likely than male subjects to be in the impacted third molar group. The compliance and patience of the subject during the procedure were the flaws in this investigation. Furthermore, one must be vigilant while recording, as excessive ink use or, on the other side, little ink makes interpreting the pattern harder. The proclivity for finger patterns varies from person to person. Abnormalities in dermal ridges, according to Carter and Matsunaga, can only occur when a combination of inherited and environmental variables exceeds a particular threshold level.17\n\nVarious methods to record fingerprints have been discussed in the literature. A few such methods are as follows: i) Ink method (most common method, uses ink and paper); ii) Inkless method (use of a biometric scan machine); iii) Adhesive tape method (uses lead/graphite powder and transparent tape); and iv) Photographic method (use of a digital camera).18–20\n\nThe ink approach has been chosen above other existing technologies because of its advantages of being simple, cost-effective, user-friendly, reproducible, safe, and non-invasive. Alternative procedures have their own set of advantages, but the necessary equipment is time-consuming and expensive. Individual fingerprints, including monozygotic twins, are unique and different for each person. Dermatoglyphics can be a reasonably reliable instrument for investigations with a suspected genetic basis. Their benefits, including as ease of use, mass screening, and rapid interpretation, make them a valuable diagnostic tool. From infancy until adulthood, they may be simply recorded.18\n\nWhen decoding skin carvings, the preference of certain finger patterns to the presence of an impacted tooth may serve as a clinical signal. Impacted molars are more difficult to remove than other diseased teeth, particularly those that are low horizontally and buccally impacted mandibular third molars, which have a high risk of intraoperative and postoperative complications.6 Furthermore, an impacted mandibular third molar reduces the angle of the jaw, making it more prone to fracture, and has been linked to lower arch crowding, temporomandibular joint disorders, vague oro-facial pain, and neuralgias, according to numerous studies.21\n\nIn addition, large-scale, multi-racial, multi-geographical population research should be done to reduce variation in a heterogeneous population, as well as to discover the exact process of dermatoglyphic pattern inheritance and its preference for the type of impaction.22 This could help us fine-tune our understanding of differences and allow us to replicate similar studies across human ethnicities. When paired with genetic study, dermatoglyphics research has the potential to uncover more about the genesis and agenesis of third molars. We feel that our findings will give the scientific community a boost, as well as a greater knowledge of how dental anomalies link to dermatoglyphic patterns.\n\n\nConclusions\n\nAn impacted tooth can be diagnosed with a clinical examination and a clear radiograph. Dermatoglyphics is used as a preventative approach to forecast the presence of tooth impaction rather than to confirm a diagnosis. The evaluation of the dermatoglyphic pattern is simple, inexpensive, and produces speedy findings. In contrast to symptomatic removal of an impacted tooth, dermatoglyphics could serve as a non-invasive screening method for predicting the existence of impaction, have applications in forensics, and aid in early diagnosis, allowing for more efficient surgical operations with fewer consequences.\n\nPredicting the type of impaction can assist surgeons and patients in understanding the risks of maintaining a distoangular impacted tooth, a horizontally impacted tooth with a high difficulty index and a strong desire to erupt in the usual anatomical position after growth is completed.\n\nUntil definitive marker genes for impacted teeth are identified, dermatoglyphic investigation can be combined with other diagnostic techniques and markers to improve diagnosis. DNA testing may be a viable alternative to dermatoglyphics.15\n\n\nData availability\n\nFigshare: Supplemental Information, https://doi.org/10.6084/m9.figshare.21065809.23\n\nThis project contains the following underlying data:\n\n- IMPACTION DATA.xlsx (spreadsheet data)\n\n- English information.pdf (information sheet)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nTikare S, Rajesh G, Prasad KV, et al.: Dermatoglyphics—a marker for malocclusion? Int. Dent. J. 2010 Aug; 60(4): 300–304. PubMed Abstract\n\nSoni A, Singh SK, Gupta A: Implications of dermatoglyphics in dentistry. J Dentofacial Sci. 2013; 2: 27–30.\n\nShirali A, Chowta KN, Ramapuram JT, et al.: A “Handy” tool for hypertension prediction: Dermatoglyphics. Indian Heart J. 2018 Dec 1; 70: S116–S119. Publisher Full Text\n\nJacoby H: The etiology of maxillary canine impactions. Am. J. Orthod. 1983 Aug 1; 84(2): 125–132. Publisher Full Text\n\nAllareddy V, Caplin J, Markiewicz MR, et al.: Orthodontic and surgical considerations for treating impacted teeth. J. Maxillofac. Oral Surg. 2020 Feb 1; 32(1): 15–26. PubMed Abstract | Publisher Full Text\n\nZheng X, Lin X, Wang Z: Extraction of low horizontally and buccally impacted mandibular third molars by three-piece tooth sectioning. Br. J. Oral Maxillofac. Surg. 2020 Sep 1; 58(7): 829–833. PubMed Abstract | Publisher Full Text\n\nLima CJ, Silva LC, Melo MR, et al.: Evaluation of the agreement by examiners according to classifications of third molars. Med. Oral Patol. Oral Cir. Bucal. 2012 Mar; 17(2): e281–e286. PubMed Abstract | Publisher Full Text\n\nNarang D, Das A, Kumar P, et al.: Dermatoglyphics (finger prints) as predilection marker for impacted teeth: A randomized blind trial. Int. J. Bioassays. 2016; 5: 4851–4857. Publisher Full Text\n\nDai J, Feng J, Zhou J: Robust and efficient ridge-based palmprint matching. IEEE Trans. Pattern Anal. Mach. Intell. 2011 Dec 27; 34(8): 1618–1632. Publisher Full Text\n\nVaidya P, Mahale S, Badade P, et al.: Dermatoglyphics in periodontics: An assessment of the relationship between fingerprints and periodontal status-A cross-sectional observation study. Indian J. Dent. Res. 2017 Nov 1; 28(6): 637–641. PubMed Abstract | Publisher Full Text\n\nYu M, Tu P, Dolios G, et al.: Tooth biomarkers to characterize the temporal dynamics of the fetal and early-life exposome. Environ. Int. 2021 Dec 1; 157: 106849. PubMed Abstract | Publisher Full Text\n\nMulvihill JJ, Smith DW: The genesis of dermatoglyphics. J. Pediatr. 1969 Oct 1; 75(4): 579–589. PubMed Abstract | Publisher Full Text\n\nPolat MH, Azak A, Evlioglu G, et al.: The relation of bruxism and dermatoglyphics. J. Clin. Pediatr. Dent. 2000 Jan 1; 24(3): 191–194. PubMed Abstract\n\nAtasu M, Kuru B, Firatli E, et al.: Dermatoglyphic findings in periodontal diseases. Int. J. Anthropol. 2005 Jan; 20(1): 63–75. Publisher Full Text\n\nHugoson A, Kugelberg CF: The prevalence of third molars in a Swedish population. An epidemiological study. Community Dent. Health. 1988 Jun 1; 5(2): 121–138. PubMed Abstract\n\nRamesh DN, Thriveni R, Rachel BB, et al.: Comparative study to analyse the correlation between dermatoglyphics and impacted teeth. J. Indian Acad. Oral Med. Radiol. 2020 Apr 1; 32(2): 145. Publisher Full Text\n\nMatsunaga E: Perspectives in mutation epidemiology 1. incidence and prevalence of genetic disease (excluding chromosomal aberrations) in human populations. Mutation Research/Reviews in Genetic. Toxicology. 1982; 99(1): 95–128. PubMed Abstract | Publisher Full Text\n\nAase J, Lyons R: Technique for recording dermatoglyphics. Lancet. 1971 Feb 27; 297(7696): 432–433. PubMed Abstract | Publisher Full Text\n\nPrabhu N, Issrani R, Mathur S, et al.: Dermatoglyphics in health and oral diseases-A review. JSM Dent. 2014; 2(4): 1044.\n\nGupta RK, Gupta AK: New, easy and effective method to take dermatoglyphic prints. Nat. J. Med. Res. 2013 Jan; 3(1): 45–47.\n\nHashemipour MA, Tahmasbi-Arashlow M, Fahimi-Hanzaei F: Incidence of impacted mandibular and maxillary third molars: a radiographic study in a Southeast Iran population. Med. Oral Patol. Oral Cir. Bucal. 2013 Jan; 18(1): e140–e145. PubMed Abstract | Publisher Full Text\n\nBarrantes R, Segura-WW M: Dermatoglyphic traits of six Chibcha-speaking Amerindians of Costa Rica, and an assessment of the genetic affinities among populations. Rev. Biol. Trop. 2009 Nov; 57: 357–369.\n\nKapoor A, Shetty P, Shetty S, et al.: Supplementary Information. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "187581",
"date": "23 Aug 2023",
"name": "Nisha Ashifa",
"expertise": [
"Reviewer Expertise Periodontology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the authors for presenting a well-conducted and well-written study. The article explains dermatoglyphics and their uses/associations in detail. The methodology is clearly interpreted which allows for reproducibility. Statistical analysis seems to be appropriate. The discussion and conclusion are adequate. There are a few suggestions/remarks I would like to add, to improve the current article.\n\nCan the possibility of future impactions be diagnosed before the eruption of wisdom teeth since the fingerprints are developed at birth and remain stable throughout the life span?\n\nPhotos of each type of fingerprint pattern could've been added to the article, enabling easy visualization and interpretation for the readers.\n\nCan you please explain why such study populations have been included in the study? Have you included patients with clinically and radiographically missing third molars in the study group? I feel that area needs clarification.\n\nWas any criteria used to diagnose Impactions? Like WAR lines or Winters classification?\n\nDoes the results of the study give insight to the surgeons in predicting the difficulty of impaction?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "178068",
"date": "29 Aug 2023",
"name": "Kalyani Bhate",
"expertise": [
"Reviewer Expertise Impacted Teeth",
"minor oral surgery",
"anthropology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article by Kapoor et al. discusses common dermatoglyphic patterns to predict the presence of impacted teeth. Different patterns on different fingers are associated with a predictive value. The article appears to positively co-relate certain fingerprint patterns on certain fingers to the presence of impacted teeth. This is statistically significant in their paper and this unique finding needs to be corroborated with larger sample sizes. While it may not aid clinicians clinically in managing impacted teeth, the theoretical treatise seems unique and adds value to the literature. It appears to be an unexplored venue and needs further exploring to ascertain whether it is a coincidence.\nMajor Comments: Statistical analysis seems robust. The findings seem to be backed by a sound statistical methodology. References are relevant and buttress the article. A simple ink approach was used that appears to be effective. Dermatoglyphics are certainly more cost effective than DNA testing for prediction. However, how this prediction may help has to come out more clearly in the paper.\nMinor Comments: The authors could expand on how this knowledge and findings could translate to benefit patients and clinicians.\nThe article is well drafted and follows a clear flow of thought. The language is lucid. The article is a theoretical treatise but it seems to be done following due protocol and an appropriate analysis.\nWhile it may not have huge impact on translation, it serves to facilitate discussion on an interesting aspect of the relation of finger prints to impacted third molars. The area needs to be further explored with RCTs and it is this purpose that the article serves.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1120
|
https://f1000research.com/articles/11-1119/v1
|
29 Sep 22
|
{
"type": "Case Report",
"title": "Case Report: Hemophagocytic lymphohistiocytosis associated with acute polymyositis",
"authors": [
"Mohammad Azmain Iktidar",
"Nowshin Jabin",
"Md. Tajwar Rahman Khan",
"Subrina Anjum",
"Nowshin Jabin",
"Md. Tajwar Rahman Khan",
"Subrina Anjum"
],
"abstract": "Hemophagocytic lymphohistiocytosis (HLH) is a rare condition marked by uncontrolled histiocyte proliferation and activation, and phagocytosis of normal hematopoietic cells. This disease is rare, and a concurrent presentation with acute polymyositis is rare. A 14-year-old male was admitted to Chattogram Medical College Hospital with a high-grade fever for 25 days, generalized severe body aches, and multiple large joint pain in the lower limb for the same duration. On examination, the patient was found to have splenomegaly, tenderness in both knee joints, symmetrical proximal weakness of both lower limbs, several sensory losses, and loss of bowel and bladder control. The laboratory data showed that he had anemia, thrombocytopenia, hyperferritinemia, hypertriglyceridemia, hypofibrinogenemia, hypoalbuminemia, raised D-dimer, and serum creatine phosphokinase (S. CPK). Along with these, a bone marrow biopsy revealed hemophagocytic cells, and he was diagnosed with HLH with acute polymyositis (PM). The patient was treated with intravenous (IV) hydrocortisone and dexamethasone. Clinical stability was achieved with gradual improvement of initial symptoms and biochemical markers. The patient was discharged with oral steroids at a tapering dose and was advised to regularly follow-up.",
"keywords": [
"acute polymyositis",
"case report",
"hemophagocytic lymphohistiocytosis",
"HLH"
],
"content": "Introduction\n\nHemophagocytic lymphohistiocytosis (HLH) is a rare immunological syndrome characterized by an uncontrolled hyperinflammatory response coupled with excessive lymphocyte and macrophage activation.1 People with this condition have a substantial risk of death and disability because of its severity and difficulty to diagnose. HLH can be grouped into two main types: primary and secondary, each of which has its own subtypes. Primary or familial HLH is an autosomal recessive inheritance often manifesting in infants and children. The main pathogenesis lies in genetic mutations or variations impacting the cytotoxic functions of natural killer cell (NK cell) and cytotoxic T cells.2 On the other hand, secondary HLH usually affects adolescents and adults;there are no known underlying genetic defects, and it rather occurs as a consequence of infections, malignancies, autoimmune diseases, among others.3,4 Rheumatological diseases have been linked to a significant number of cases of HLH around the world, with systemic lupus erythematosus (SLE) and systemic juvenile idiopathic arthritis (sJIA) being the most common; but very few cases have been reported with polymyositis.5 Our case report aims to highlight a rare and unique association between HLH and polymyositis so that the disease is identified and treated early and effectively to assure long-term survival.\n\n\nCase presentation\n\nA 14 year-old Bengali male was admitted to Chattogram Medical College Hospital with a high-grade fever for 25 days, generalized severe body aches, multiple large joint pain in the lower limbs for 20 days, ulceration at lips for three days and loss of bowel and bladder control for one day. Before being admitted to our hospital, the patient was taken to a local hospital. He was diagnosed with enteric fever and was treated with intravenous (IV) third-generation cephalosporin (ceftriaxone) but didn’t improve clinically and was referred to a tertiary care hospital. The patient was non-diabetic and normotensive, and had a previous history of asthma.\n\nOn examination, his temperature was 102°F (38.9°C), pulse 150 bpm, and blood pressure 80/60 mmHg. He had tenderness in both knee joints, proximal myopathy of both lower limbs, and several sensory losses.\n\nHis initial investigation revealed bicytopenia with elevated inflammatory markers, i.e., Erythrocyte sedimentation rate (ESR), C-reactive protein, and serum ferritin. Patient showed altered liver and renal function test; with elevated serum alanine aminotransferase (s. ALT), decreased serum albumin, decreased serum fibrinogen, elevated serum bilirubin, and elevated serum creatinine level. Moreover, serum creatine phosphokinase (s. CPK), serum lactate dehydrogenase (LDH), serum triglyceride, and serum d-dimer were found abnormally high. Serum electrolytes revealed hyponatremia (Table 1).\n\nUltrasonography of the whole abdomen indicated renal parenchymal disease, pleural effusion, and mild splenomegaly (10.7×5.1 cm) (Figure 1). Peripheral blood film revealed microcytic hypochromic anemia with neutrophilic leukocytosis with thrombocytopenia; bone marrow examination presented reactive marrow with erythroid hyperplasia with an increased number of lymphocytes. Investigations for screening autoantibodies, i.e., perinuclear anti-neutrophil cytoplasmic antibodies, anti-neutrophil cytoplasmic antibodies, rheumatoid factor, Antistreptolysin O titer, direct Coombs’s test, anti dsDNA, antinuclear antibodies, anti-cyclic citrullinated peptide antibody tests were negative. Sepsis screening for hepatitis B, C, human immunodeficiency virus (HIV), malaria, salmonella, rickettsia, and brucella was also negative. CSF study revealed no significant abnormalities, and a magnetic resonance imaging (MRI) of the Lumbosacral spine showed no significant finding.\n\nA. Urinary Bladder is well filled with normal wall thickness. Prostate is normal in size with intact capsule. B. Spleen was mildly enlarged in size (10.7x5.1 cm). C. Liver is normal in size measuring about 11.4 cm at the level of right anterior mid clavicular line (normal up to 14 cm) & normal parenchymal echotexture all over. D. Both kidneys were swollen, parenchymal echogenicity was increased, and corticomedullary differentiation was altered. E, F: Gall Bladder is well outlined, normal in size and wall thickness is within normal limit. Common bile duct and intrahepatic biliary channels are not dilated. Visible part of pancreas appears normal.\n\nBy the judgment of clinical presentation and investigation, we diagnosed the case as HLH syndrome with polymyositis. The patient was treated with IV hydrocortisone and dexamethasone. Clinical stability was achieved with gradual improvement of initial symptoms and biochemical markers. ESR and s. ferritin were reduced and liver and renal function tests were improved. Furthermore, s. CPK was also reduced (Table 1). The patient was discharged with oral steroids at a tapering dose and advised for regular follow-up with no clinical relapse that needed hospital admission.\n\n\nDiscussion\n\nIn a normal immune response, natural killer cells (NK cells) and cytotoxic lymphocytes (CTL) suppress macrophages and CD8 cells to attenuate the immune response. However, deficient NK cell activity and CTL fail to suppress the immune response and result in profuse activation and release of interferon-gamma and inflammatory cytokines, causing organ damage. This pathogenesis plays a central role in HLH.6–8 Primary HLH is due to mutations in different genes such as PRF1, UNC13D, STX11, RAB27A, LYST, AP3B1, and SH2D1A that regulate perforin expression in immune cells and regulates synthesis, maturation, and release of cytotoxic and cytolytic granules in lymphocytes.9 Most of these are inherited as autosomal recessive form secondary associated with infections, autoimmune or malignant disorders.8,10,11\n\nAccording to the HLH-2004 trial criteria,12 diagnosis of HLH is established if one of either (1) or (2) below (Table 2) is fulfilled.\n\nThe present case fulfilled five out of eight diagnostic criteria of HLH; fever, splenomegaly, bicytopenia, hypertriglyceridemia, and hyperferritinemia. Furthermore, hepatopathy with altered liver function test, coagulopathy, raised d-dimer, hypoalbuminemia, and hyponatremia strengthen the diagnosis of HLH.6,13,14 Furthermore, markedly elevated skeletal muscle-related enzymes (i.e., s. CPK, s. LDH, and s. ALT) in association with symmetrical proximal muscle weakness, severe myalgia, and absence of rash indicate acute polymyositis.\n\nThe collapse of immunological tolerance against muscle antigen is the fundamental mechanism of polymyositis.15 Hence, the combination of the two autoimmune diseases of seemingly unrelated systems in this patient could be a reflection of the widespread impairment of immune functioning in the patient as a whole. HLH has been reported in systemic lupus erythematosus, Still’s disease, rheumatoid arthritis, systemic juvenile arthritis, dermatomyositis, Kawasaki disease, systemic sclerosis, Bechet’s disease, polyarteritis nodosa, ankylosing spondylitis, mixed connective tissue disease, sarcoidosis, Sjogren’s syndrome, Wegener’s granulomatosis in previous case reports but very few care reports were indexed with polymyositis.16,17\n\n\nConclusions\n\nThere are exceedingly few reported occurrences of HLH linked with acute PM. This article seeks to add to the existing knowledge by describing the characteristics of a probable HLH presentation with PM. HLH with PM should be suspected in a patient with unexplained fever, cytopenia, hepatitis, proximal muscle weakness, and myalgia. The diagnosis is difficult because patients may appear with symptoms that are indistinguishable from those of sepsis or multiple organ failure syndrome. Priority should be given to quick workup using complete blood count (CBC), inflammatory markers, liver function test, triglycerides, and bone marrow examination. Early diagnosis and prompt treatment are the key to improving survival in this patient group.\n\nThe mother of the patient (since the patient was a minor) provided written informed consent for this report. Since this is a case report that maintains the anonymity of the patient, ethical clearance from our Institutional Review Board was not necessary. This report was prepared in accordance with the CARE guidelines.18\n\nThe patient was requested to provide his written perspective, but he politely refused.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
"appendix": "References\n\nDunn T, Cho M, Medeiros B, et al.: Hemophagocytic lymphohistiocytosis in pregnancy: a case report and review of treatment options. Hematology. 2012; 17: 325–328. PubMed Abstract | Publisher Full Text\n\nHenter JI: Biology and treatment of familial hemophagocytic lymphohistiocytosis: importance of perforin in lymphocyte-mediated cytotoxicity and triggering of apoptosis. Med. Pediatr. Oncol. 2002; 38: 305–309. PubMed Abstract | Publisher Full Text\n\nFisman DN: Hemophagocytic syndromes and infection. Emerg. Infect. Dis. 2000; 6: 601–608. Publisher Full Text\n\nFilipovich AH: Hemophagocytic lymphohistiocytosis (HLH) and related disorders. Hematology Am. Soc. Hematol. Educ. Program. 2009; 2009: 127–131. Publisher Full Text\n\nKarjigi U, Plant M: Acute polymyositis associated with hemophagocytic lymphohistiocytosis syndrome. BMC Musculoskelet. Disord. 2013; 14: 1–2. Publisher Full Text\n\nUsmani GN, Woda BA, Newburger PE: Advances in understanding the pathogenesis of HLH. Br. J. Haematol. 2013; 161: 609–622. PubMed Abstract | Publisher Full Text\n\nSchmid JP, Côte M, Ménager MM, et al.: Inherited defects in lymphocyte cytotoxic activity. Immunol. Rev. 2010; 235: 10–23. PubMed Abstract | Publisher Full Text\n\nKalinichenko A, Perinetti Casoni G, Dupré L, et al.: RhoG deficiency abrogates cytotoxicity of human lymphocytes and causes hemophagocytic lymphohistiocytosis. Blood. 2021; 137: 2033–2045. PubMed Abstract | Publisher Full Text\n\nEricson KG, Fadeel B, Nilsson-Ardnor S, et al.: Spectrum of perforin gene mutations in familial hemophagocytic lymphohistiocytosis. Am. J. Hum. Genet. 2001; 68: 590–597. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpessott WA, Sanmillan ML, McCormick ME, et al.: Hemophagocytic lymphohistiocytosis caused by dominant-negative mutations in STXBP2 that inhibit SNARE-mediated membrane fusion. Blood. 2015; 125: 1566–1577. PubMed Abstract | Publisher Full Text\n\nMeeths M, Chiang SCC, Wood SM, et al.: Familial hemophagocytic lymphohistiocytosis type 3 (FHL3) caused by deep intronic mutation and inversion in UNC13D. Blood. 2011; 118: 5783–5793. PubMed Abstract | Publisher Full Text\n\nHenter JI, Horne AC, Aricó M, et al.: HLH-2004: Diagnostic and therapeutic guidelines for hemophagocytic lymphohistiocytosis. Pediatr. Blood Cancer. 2007; 48: 124–131. PubMed Abstract | Publisher Full Text\n\nPadhi S, Sarangi R, Patra S, et al.: Hepatic Involvement in Hemophagocytic Lymphohistiocytosis. Hepatitis A and Other Associated Hepatobiliary Diseases. 28 November 2019. Publisher Full Text\n\nMalinowska I, Machaczka M, Popko K, et al.: Hemophagocytic Syndrome in Children and Adults. Arch. Immunol. Ther. Exp. 2014; 62: 385–394. PubMed Abstract | Publisher Full Text\n\nFye KH, Sack KE:Rheumatic diseases.Stites DP, Stobo JD, Fudenberg HH, et al., editors. Basic and Clinical Immunology. Los Altos:Lange Medical Publications;1982; 423–423.\n\nAtteritano M, David A, Bagnato G, et al.: Haemophagocytic syndrome in rheumatic patients. A systematic review. Eur. Rev. Med. Pharmacol. Sci. 2012; 16: 1414–1424. PubMed Abstract\n\nFreeman HR, Ramanan AV: Review of haemophagocytic lymphohistiocytosis. Arch. Dis. Child. 2011; 96: 688–693. Publisher Full Text\n\nGagnier JJ, Kienle G, Altman DG, et al.: The CARE guidelines: consensus-based clinical case reporting guideline development. BMJ Case Rep. 2013; 2013: bcr2013201554. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "219141",
"date": "07 Nov 2023",
"name": "Eric Mariotte",
"expertise": [
"Reviewer Expertise Internal medicine",
"clinical hematology",
"intensive care medicine"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDr Iktidar et al provide a case report of chidhood inflammatory myositis with features of haemophagocytic lymphohistiocytosis.\nI have several concerns about this case report :\nThe description of the case is too succinct. In particular the authors state that \"several sensitive loss\" are present in the patient, which is very unusual in polymyositis. This should be detailed and at least discussed. Was there a medical history suggestive of congenital immune deficiency in the child? Are all the investigations performed reported in the manuscript? Were any researches of other infectious or non-infectious etiologies of rhabdomyolysis performed (inflenza, toxoplasmosis, leptospirosis, trichinellosis, heavy metal poisoning...)? Was an electromyography performed? Was a muscular biopsy performed?\n\nSome details are required in the treatment and evolution paragraph: what dose of steroids was administered? For how long? how long after the onset of steroids was the \"post-treatment values\" of the table obtained? How fast did the patient recover?\n\nI doubt that this case can be useful to clinicians.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1119
|
https://f1000research.com/articles/11-422/v1
|
14 Apr 22
|
{
"type": "Research Article",
"title": "Study of bypassing Microsoft Windows Security using the MITRE CALDERA Framework",
"authors": [
"Nachaat Mohamed"
],
"abstract": "Background: Microsoft Windows Security is a recently implemented safeguard for the Windows operating systems, including the latest versions of Windows10 and 11. However, there is a major shortcoming in this system to stop Advanced Persistent Threat (APT). These are government-financed groups that are funded to attack other government entities. Following the initial security breach, the hacked Windows device is used to access the rest of the network devices in order to transfer data to external storage (Exfiltration). Methods: In this work, we have tested the Microsoft Windows Security system using MITRE CALDERA and ATT&CK frameworks and explain how APT groups are able to bypass Windows Security. Results: In this study we used \"54ndc47\" agent through GoLang feature in MITRE CALDERA platform to test and bypass Microsoft Windows Security systems (MS Windows 10). Through it, we were able to bypass the Windows Security system and display entire files in the victim's device. Conclusions: In this paper, we have provided recommendations to Microsoft to improve their Windows Security tool through the use of Artificial intelligence (AI).",
"keywords": [
"APT",
"CPU",
"Attack",
"Exploit",
"Detection",
"Cyberattack."
],
"content": "Introduction\n\nWindows 10 and 11 incorporate Windows Security, which provides users with the most recent antivirus assurance. Windows Security will begin operating and secure the system from the minute one begins Windows.1 It ceaselessly looks for malware (pernicious programs), infections, and security dangers.1 In addition to this real-time assurance, overhauls are downloaded automatically to assist in keeping the device secure from ongoing threats. Since this mode is streamlined for tighter security, the Infection & Danger assurance zone has fewer alternatives.2 Built-in security within this mode that naturally anticipates infections and other dangers running on user devices, and users then receive security overhauls as they continue using their device.\n\nAs with each previously released version, Windows 10 was intended to be the most secure Windows operating system. As part of that release, Microsoft presented Windows Security as a beneficial addition.3 This offered an improved approach to building, sending, and adjusting Windows data, and unused highlights are built persistently with each overhaul. Windows 10 also has more layers of assurance that assist in securing organizational information, as well as identifying unsafe behaviors and modern assaults. Windows 10 is therefore making a difference using superior secure data and with each subsequent release, Microsoft have built upon the existing security measures by including modern security highlights.3 They have consciously tended to dangers through iterative design, ensuring that improved security is one of the operating system’s greatest benefits.4 However, there is a huge shortcoming in this product, and traditional hackers and Advanced Persistent Threat (APT) groups are utilizing varying methods to bypass this improved level of Windows security.\n\nIn order to test the level of vulnerability, we simulated an APT attack to bypass the Windows security, using the CALDERA framework from MITRE. CALDERA is a tested framework to evaluate features of infrastructure security posture through penetration testing. It tests the entire suite of tactics and techniques used by APT.12,13 The CALDERA framework is used by red teams to protect organizations against sophisticated attacks, and adversary emulation is resource intensive and can present challenges. To combat these challenges, the CALDERA framework offers an intelligent, automated system of red teamwork, which can reduce the resources needed by penetration testing and security teams for routine testing. This then leads to providing the right solution/recommendation to the blue teams/organizations.14,15\n\nCALDERA can also be utilized to test endpoint security arrangements and evaluate a network’s security capability to withstand the common post-compromise, antagonistic strategies contained within the ATT&CK approach.14 CALDERA leverages the ATT&CK approach to distinguish and imitate enemy behaviors as if a genuine interruption is happening. This empowers computerized evaluations of a network’s defenselessness to enemy penetration, permitting organizations to see their systems through the eyes of a progressive, determined danger, on-demand and to confirm the strength of guards and security arrangements currently based upon known risk methods. It also employs an enemy representation dialect; the ATT&CK profile. This is a motor choice to prepare assembled information and select ensuing activities, and a specialist conducting the operation. Utilizing CALDERA can therefore decrease assets required for appraisals and permit groups to focus on modern approaches to more difficult issues.16 This can enable organizations to tune behavioral-based, interruption discovery frameworks more quickly as they are deployed.17\n\nCALDERA is also complementary to other types of security evaluation. The infrastructure security position is commonly surveyed based on program fix levels, security controls, and shield devices. Whereas numerous interruption location apparatuses depend on looking for known risk markers which alter as often as possible. Appraisals and enemy discovery are only typically based upon foe behavior.18 This can change how shields respond to, identify, and react to dynamic dangers. CALDERA can also make a difference to shield approaches as it can move past discovery of pointers of compromise, through to location and reaction of foe behavior.17 In addition to the expansion to the open-source adaptation of CALDERA, Miter maintains a closed-source form that highlights extra capabilities, creating superior adaptability to more endpoints. These are used to examine authorizing or collaboration exercises on closed-source CALDERA.18,19\n\nMicrosoft’s Protector is proficient at recognizing malware records, blocking misuses and network-based assaults, and hailing phishing destinations. It incorporates basic PC execution and wellbeing reports, as well as parental controls with substance sifting, utilization impediments, and area following. Antivirus software is fundamental if the user is utilizing a Mac or Windows device; both come with some level of infection assurance built in.3,4,7 In order to build upon these protections and develop endpoint security, protection against malware and possibly undesirable programs, it is best to introduce a third-party antivirus application. Microsoft Guard was not present in the old versions of Windows operating systems, so users of Microsoft operating systems purchased or acquired an antivirus program for device protection. This has changed over time, and Microsoft has integrated an antivirus program to protect its operating systems and software running under them 10.8,9\n\nMicrosoft now indirectly implies that when in the Microsoft system work environment, a user does not need the support of other companies for protection. Microsoft are now able to provide this protection to the end user utilizing Microsoft Protector. A user’s device, files, and data are under its protection from direct or indirect tampering.10,11 In addition, it is now true that Microsoft Shield is sometimes seen as a competitor with decent protection capabilities when compared to the large security systems in the free antivirus world.10 This product has evolved significantly since being first developed due to Microsoft’s relentless pursuit of this product. This could be because it would prevent the company’s end users from buying protection products from other companies, which was clearly noted in the latest evaluations conducted by the main independent laboratories that conduct tests at fixed intervals to measure the readiness of antivirus applications.7 A test of these available antivirus systems was conducted in July and October 2020 by AV-Comparatives, showing that Microsoft’s performance improved considerably, and Microsoft was rated overall as ‘good’ as it was able to stop 99.5% of the risks, and in this test it came in twelfth place among 17 competing anti-virus programs.22,23 In another similar evaluation conducted by SE Labs, Microsoft’s product scored 99%, making it the fifth out of 13 participants in the competition. In a further report on protection against intrusion, as of 2020, Microsoft ranked fourth; a result indicating its quality, especially considering the competition was with top providers in the antivirus industry.24 The overall picture, therefore, is that Microsoft Guard is now more than robust in terms of protecting the user from hacking and malware. In short, according to Avira, we can say that Microsoft Protector may be sufficient for the user to satisfactorily protect their data, but it is also clear that it represents a reputable and reliable ‘non-free’ antivirus option.25\n\nWith regards to users who do not have high levels of technical experience, it is difficult for them to correctly judge whether this product is sufficient to protect them or not. It can therefore represent an advantageous product for some, and a limited one for others. This difference depends on the way users navigate their computer hardware, software and the Internet.8 However, if the user can easily get a free protection program that meets their needs and does not put them at risk, then those can represent a suitable subscription for both experienced users and novice users.7,8,10 Unfortunately, the area of antivirus software can also be used by malicious groups to distribute agents used to penetrate users’ systems. This has and will continue to occur, and therefore improved access to reputable antivirus programs for both ends of the market is a positive change.11 However, it is also true that although Microsoft strives to maintain its reputation and increase the number of its users by providing products that meet user needs,30 the findings from this paper prove with conclusive evidence that it is possible to bypass Microsoft Anti-Virus and take control of the device, just as the same device can then be used to hack the rest of the devices in the same infrastructure.\n\n\nMethods\n\nThe objective of robotized/simulated APT attacks imitating adversaries (APT groups) is to detect weaknesses in the current systems and provide system defenders with an apparatus able to execute a full-scale evaluation of their organization, working in a way that is comparable to a genuine adversary. Such an apparatus has noteworthy utility for guards, ultimately providing a standard for what their network looks like to an enemy, producing preparedness data, identifying shortcomings and/or misconfigurations, and testing in-place security measures and devices. This provides a valuable experimental proof for a cautious blue team to build on.2,31 We differentiate this with a device that, for example, only distinguishes assault methods and approaches without actually executing them. This tool could provide an outline of what the organization looks like digitally, but typically will come up short to realize other utilization cases because it omits critical, hard-to-measure points of interest, and requires the authenticity of genuine execution. The objective of CALDERA therefore is to drive automated adversaries that do not just imitate, but also incorporate:\n\n1) Selecting and chaining actions in ways comparable to how an attacker would.\n\n2) Allowing shields to be able to utilize the tool without requiring express arrangement of points of interest. These are both time-intensive to gather and are nearly incomprehensible for guards to completely track.\n\n3) The framework executes the same techniques that a genuine enemy would, and, like a genuine adversary, should begin at initial compromise, and progress to their intended end after achieving (or coming up short to realize) a particular set of goals.\n\n4) Clients of the framework ought to be able to run appraisals with methods of their choosing, as well as have the capacity to include modern strategies.2,30,32\n\nCALDERA therefore offers and adds to the field of information security, as it automates the penetration-testing process and simulates the tactics and techniques used by state-funded hacking groups to attack other countries for the purposes of espionage or sabotage.16 As a consequence, it is used as a tool by red teams to simulate a real attack, and blue teams can then use realistic data to explain protection plans and methods to protect public and private institutions.18 It has also been designed to deal with aspects of the defensive and offensive systems of MITER ATT&CK. This system consists of two components: 1) the server that contains all the operations with an application interface to control all the operations that take place on the victim’s device.18 2) Additions. This is the main user interface through which it is possible to control the addition and deletion of components that serve the attack process, which must eventually lead to access and control of the largest possible amount of the target device’s resources.19,20 The end result therefore provides a product that will automatically test an organization’s infrastructure against the tactics and techniques used by currently operating hackers.15 It provides the red team a contemporary and informed ability to test the dangerous infrastructure in the shortest possible time and with as few people as possible, so one or two individuals can simulate an entire team of penetration testers. This is provided by CALDERA, produced and developed by MITER.17,32,37 It can be directly used to design a client and test it on potential victims to test if there is a vulnerability that hackers can use against the targeted network and the rest of the network devices.16,33 This paper presents an application of the CALDERA approach to Microsoft’s security systems. It demonstrates that the protections were bypassed, new permissions were added, and all files on the victim’s device were accessed.\n\nThe client used in the attack is called Sandcat, a small command generation program identified as “54ndc47”, which can evade and attack the opponent, and reconnect with the CALDERA server. This “54ndc47” agent was created in GoLang to be compatible with most existing operating systems. The operation of “54ndc47” requires port 8888 to be opened to communicate with the server. To run “54ndc47”, one of the commands included in this framework that corresponds to the operating system or the so-called potential target is used, which allows the user to run remote commands.15 These commands download the “54ndc47” executable compiled and provided by CALDERA and immediately run it on the victim or target machine. All commands and instructions can then be accessed through the Sandcat plugin. Once commands are executed on the target device, the attacker’s device appears to have successfully communicated with the victim’s device after sending it to CALDERA. With regards to the CALDERA server, every time a transfer command is run, the attack command forcefully reassembles itself and changes its source code to contact the attacker’s machine, so that it gets a “MD5” miscellaneous registry hash. This certainly helps bypassing command-dependent signature detections in files.17,38 When running “54ndc47”, important parameters can be used after the executable is running. The agent in this regard must be sent to at least one victim device within the target infrastructure.19 In addition, virtual groups will be used during the attack process and the communication between the victim’s device and the attacker. The attack process is organized and arranged to maintain the lightweight code, “54NDC47” or hack commands which are sometimes restrictive to avoid detection devices in general.\n\nThe work used in the attack process has powerful additional features, referred to as GoCat extensions. It also includes an extension to the existing GoCat module tokens to provide many benefits, such as the use of a peer-to-peer broker, additional proxies, and additional C2 communication protocols.13 To request other restricted plugins from GoCat, the client can perform a HTTP merge of all GoCat extensions when C2 is queried, which is called a custom assembler. The title should be a comma-separated list with technical considerations.34 The server includes additional extensions and is not required if their conditions are met (e.g., if extension A requires a specific GoLang that is not available on the server, then extension A is almost certainly not included at this point). It is possible to set default values for these alternatives when Sandcat is pulled from an attacker’s machine. Of course, this is highly valuable if hiding parameters from a method is required. This can be done by passing the values as headers instead of as parameters.\n\nFor illustration, the following will download a windows executable that will utilize http://192.168.1.14:8888 as the server address rather than http://localhost:8888.\n\nFirst step: update Kali Linux\n\nIn this step, we updated the Kali Linux system version 2022.1 to get the latest version of all the programs in the Kali Linux distribution; this can be done by typing the following command in the terminal “apt-get update”. Figure 2 shows the command used to update Kali Linux.\n\nSecond step: installing CALDERA\n\nThen, we proceeded to installing the CALDERA framework within the Kali distribution by using the following command “apt-get -y install caldera”. Figure 3 shows the command used to install CALDERA.\n\nThird step: running CALDERA\n\nSince CALDERA was integrated into the Kali repositories of the latest versions, this made it easy to install and run the CALDERA system from Kali Linux. After we installed CALDERA in the previous step, we then ran it via the command “caldera”. Figure 4 shows the command used to run CALDERA.\n\nFourth step\n\nAfter using the previous command, we obtained the login information to the CALDERA framework, red username and password, blue username and password. In this study, we logged in using the red user and password. Considering that CALDERA runs through port 8888, we could start CALDERA by going to the browser and typing the IP of the CALDERA device followed by the port as in the following example. http://192.168.0.14:8888/ or http://localhost:8888/\n\nRed:\n\nUSERNAME: red\n\nPASSWORD: je2nj8OypHUCp4fZiH08R9z0qDeKTD6vexftrOJ7Ru0\n\nAPI_TOKEN: Sugyhnx290IG3zAFgHh8wvx0zqWHh9yBICUHurcVkuk\n\nWe then logged into the CALDERA framework, and selected \"Navigate\", then \"Agent\", and then we chose the orange key on the left side “Click here to deploy an agent”; after that, we identified the agent kind “54ndc47. Finally, we specified the operating system as “Windows”. Depending on these settings, the CALDERA system generates a code to create a client to bypass the Windows Security system and get a direct connection to the victim’s machine as shown below:\n\n($server=\"192.168.0.14:8888/\";$url=\"$server/file/download\";$wc=New-Object System.Net.WebClient;$wc. Headers.add(\"platform\",\"windows\");$wc. Headers.add(\"file\",\"sandcat.go\");$data=$wc. DownloadData($url);$name=$wc. ResponseHeaders[\"Content-Disposition\"].Substring($wc. ResponseHeaders[\"Content-Disposition\"].IndexOf(\"filename=\")+9).Replace(\"`\"\",\"\");get-process|? {$_.modules.filename -like \"C:\\Users\\Public\\$name.exe\"}|stop-process -f;rm -force \"C:\\Users\\Public\\$name.exe\" -ea ignore;[io.file]::WriteAllBytes(\"C:\\Users\\Public\\$name.exe\",$data)|Out-Null;Start-Process -FilePath C:\\Users\\Public\\$name.exe -ArgumentList \"-server $server -group red\" -WindowStyle hidden;)).\n\nThis study was approved by Rabdan Academy (Homeland Security (HLS) department), Abu Dhabi, United Arab Emirates.\n\n\nResults\n\nOrganizations may fail if they do not implement a solid approach against apt attack and confirmation controls may then permit an aggressor to evade verification. In addition, enemies may also evade the verification component through taking substantial victim sessions and cookies. It is also possible to avoid authentication powerlessness, which appears to permit assailants to perform different noxious processes by avoiding the device verification method. After performing this process, the primary concern is verification bypassing abuse, solely because of a powerless confirmation structure. Companies that fail to maintain a robust and secure infrastructure may create many conditions that allow an attacker to bypass verification.5,6,38\n\nIn this study, CALDERA was used to send a single command to the victim’s device, and through it enable the opening of a session on the target device. This provided the hostname, username, privilege, group, and other sensitive information. Figures 3 and 4 show the command used to bypass Microsoft Windows security and take over the victim machine through got active session over victim machine. Figure 5 shows create agent from CALDEARA server for Windows operating system.\n\nFollowing this, the green color batten was utilized (agent 16232) to open the operations screen; this provides considerable possibilities with regards to implementing all the tactics and techniques used by the offensive groups’ APTs. All this was performed without any warnings or messages identifying suspicious activity on the victim’s device, even though the version installed was recently updated to the latest one available. Figure 6 shows bypassing Windows security (connected with victim machine and take over through the agent).\n\nAfter bypassing the Windows security system by agent that was created by CALDERA and then applying the Collection tactic, gives us the ability to collect the entre files from the victim’s machine as shown in the following figure. Taking into account that attacker can use the same device to penetrate the rest of the devices and servers in the target infrastructure trough applying lateral movement tactic, credential access tactic, credential dumping technique. Figure 7 shows results from victim machine (paths to aggregated files).\n\nThe next figure present example of results (paths to aggregated files).\n\nAs we can see, these paths have become compromised, and all files can be transferred to the attacker’s device.\n\nC:\\Users\\engcn\\Desktop\\Results of APT Attack\\\n\nC:\\Users\\engcn\\OneDrive\\Desktop\\CTIA\\CTIA Lab Prerequisites\\CTIA Lab Prerequisites\\CTIA Desktop\n\nC:\\Users\\engcn\\OneDrive\\Desktop\\\n\nThe following figures shows the final report that was generated by CALDERA after bypassing Windows Security and getting files from the victim’s machine as shown earlier. The full report has been uploaded to the GitHub website as shown in the Data Availability section. The entire code for this study has been uploaded to GitHub and archived in Zenodo.\n\n\nDiscussion\n\nAdversarial Tactics, Techniques, and Common Knowledge (ATT&CK) is a database used by information security professionals to understand the methods and techniques used by high-level attack groups utilizing APT, and these groups may be funded by state actors to attack other countries or regions.37 ATT&CK allows to develop new methods and plans to protect against attack groups. The most important thing distinguishing ATT&CK is that it is free and available for governments and private organizations.35 It is possible to take advantage of this approach in order to develop interception methods and defensive plans against offensives by attack teams funded by state actors for espionage or sabotage purposes.36 ATT&CK contains 14 tactics and more than 500 techniques to counter the attacks of these groups.38 Figure 1 shows which tactics and techniques are designed based on MITER. Figure 10 shows ATT&CK tactics and techniques.\n\nIn this scenario, Figures 8 and 9 illustrates how, through the application of CALDERA, it was possible to infiltrate all the data from the victim’s device after achieving the initial access, credential access, and using lateral movement tactics and techniques. Through using the indicial access (IA) tactic, the enemy attempts to create a ‘foothold’ inside the existing infrastructure to allow access into the target network. IA tactics are ultimately used to comprise the target infrastructure that access different passage paths, in order to establish an introductory, solid footing inside an arrangement. The strategies utilized to pick up a dependable balance incorporate a focus upon spear-phishing and abusing shortcomings on web servers’ interfaces. The privileges that were obtained at the beginning of the penetration stage greatly facilitated the upgrade process to obtain full privileges on the victim’s device, then completely manage the victim’s machine and use it to access the rest of the network resources. This may result in limited or no use after passwords have been changed. In this scenario, spear-phishing was conducted through normal commands, sent to the victim machine from the CALDERA attacker machine, in order to pick up get to casualty frameworks. Spear-phishing by incomes of value may be a particular variation of command execution. It is as diverse as most of the more common methods of spear phishing, in that it engages in taking advantage of third-party administrations, rather than specifically using project mail channels. All spear-phishing forms are electronically conveyed social building focused on a particular person, company, or industry. In this situation, enemies send messages through different social media administrations, individual webmail, and other non-enterprise-controlled administrations. These administrations are more likely to have a less-strict security arrangement than other undertakings. As with most types of spear-phishing, the objective is to create affinity with the target or develop the target’s intrigue and attention in a variety of ways. Figure 11 Windows defender, and firewall cannot detect the payload when APT used ATT&CK against target infrastructure.\n\n\nConclusions\n\nThis paper focused upon the application of the MITRE CALDERA framework to test Microsoft Windows security. Utilizing this framework, the paper explains and provides evidence on how to bypass Microsoft Windows security. A primary recommendation following this research, is that Microsoft specifically work to improve the level of security in recognizing commands written on devices by using artificial intelligence. The primary method for this can be through analyzing the commands before executing them. Finally, the paper advises researchers to study MITRE ATT&CK to develop security solutions against APT attacks.\n\n\nData availability\n\nAll data underlying the results are included as part of the article and no additional data are required.\n\nZenodo: Nachaat3040/CALDERA-Code-Bypassing-Microsoft-Windows-security-: Cyber Attack DOI: https://zenodo.org/record/6309927\n\nThis project contains the following extended data:\n\n- Agent 1.png\n\n- CALDERA Code - Bypassing Microsoft Windows security.txt\n\n- Collect info blugin 2.png\n\n- Files collected 4.png\n\n- README.txt\n\n- collect txt files 3.png\n\nAnalysis code available from: https://github.com/Nachaat3040/CALDERA-Code-Bypassing-Microsoft-Windows-security-/releases/tag/CALDERA\n\nArchived analysis code as at time of publication: https://zenodo.org/record/6309927\n\nLicense: MIT",
"appendix": "Acknowledgments\n\nThe authors express their gratitude and thanks to the Department of Internal Security at Rabdan Academy for their financial and moral support to complete this study. At the same time, we extend our sincere thanks and appreciation to all the reviewers and readers of this study for their valuable comments and suggestions, which improve the presentation of this research effort in a wonderful way that benefits the community and researchers.\n\n\nReferences\n\nSaleem S, Ullah S, Kwak KS: A study of IEEE 802.15. 4 security framework for wireless body area networks. Sensors. 2011; 11(2): 1383–1395. PubMed Abstract | Publisher Full Text\n\nMiller D, Alford R, Applebaum A, et al.: Automated adversary emulation: A case for planning and acting with unknowns. MITRE CORP MCLEAN VA MCLEAN; 2018.\n\nToorani M: On vulnerabilities of the security association in the IEEE 802.15. 6 standard. International conference on financial cryptography and data security. Berlin, Heidelberg: Springer; 2015, January; (pp. 245–260).\n\nManadhata PK, Wing JM: An attack surface metric. IEEE Trans. Softw. Eng. 2010; 37(3): 371–386. Publisher Full Text\n\nHuang Y, Arsenault D, Sood A: Closing cluster attack windows through server redundancy and rotations. Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID’06). IEEE; 2006, May; (Vol. 2. , pp. 12-pp).\n\nTomlinson A, Bryans J, Shaikh SA, et al.: Detection of automotive CAN cyber-attacks by identifying packet timing anomalies in time windows. 2018 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops (DSN-W). IEEE; 2018, June; (pp. 231–238).\n\nFurdek M, Natalino C, Lipp F, et al.: Machine learning for optical network security monitoring: A practical perspective. J. Lightwave Technol. 2020; 38(11): 1–2871. Publisher Full Text\n\nSambandam N, Hussein M, Siddiqi N, et al.: Network security for iot using sdn: Timely ddos detection. 2018 IEEE Conference on Dependable and Secure Computing (DSC). IEEE; 2018, December; (pp. 1–2).\n\nAlharbi F, Chang J, Zhou Y, et al.: Collaborative client-side DNS cache poisoning attack. IEEE INFOCOM 2019-IEEE Conference on Computer Communications. IEEE; 2019, April; (pp. 1153–1161).\n\nMohamed N, Belaton B: SBI Model for the Detection of Advanced Persistent Threat Based on Strange Behavior of Using Credential Dumping Technique. IEEE Access. 2021; 9: 42919–42932. Publisher Full Text\n\nLi F, Li Q, Zhang J, et al.: Detection and diagnosis of data integrity attacks in solar farms based on multilayer long short-term memory network. IEEE Trans. Power Electron. 2020; 36(3): 2495–2498. Publisher Full Text\n\nNazarov AN, Sychev AK, Voronkov IM: The Role of Datasets when Building Next Generation Intrusion Detection Systems. 2019 Wave Electronics and its Application in Information and Telecommunication Systems (WECONF). IEEE; 2019, June; (pp. 1–5).\n\nHassan WU, Bates A, Marino D: Tactical provenance analysis for endpoint detection and response systems. 2020 IEEE Symposium on Security and Privacy (SP). IEEE; 2020, May; (pp. 1172–1189).\n\nAjmal AB, Shah MA, Maple C, et al.: Offensive security: Towards proactive threat hunting via adversary emulation. IEEE Access. 2021; 9: 126023–126033. Publisher Full Text\n\nKaruna P, Hemberg E, O’Reilly UM, et al.: Automating Cyber Threat Hunting Using NLP, Automated Query Generation, and Genetic Perturbation. arXiv preprint arXiv:2104.11576. 2021.\n\nXiong W, Legrand E, Åberg O, et al.: Cyber security threat modeling based on the MITRE Enterprise ATT&CK Matrix. Softw. Syst. Model. 2021; 1–21.\n\nGolushko AP, Zhukov VG: Application of Advanced Persistent Threat ActorsTechniques aor Evaluating Defensive Countermeasures. 2020 IEEE Conference of Russian Young Researchers in Electrical and Electronic Engineering (EIConRus). IEEE; 2020, January; (pp. 312–317).\n\nHong S, Kim K, Kim T: The Design and Implementation of Simulated Threat Generator based on MITRE ATT&CK for Cyber Warfare Training. Journal of the Korea Institute of Military Science and Technology. 2019; 22(6): 797–805.\n\nEnoch SY, Huang Z, Moon CY, et al.: HARMer: Cyber-attacks automation and evaluation. IEEE Access. 2020; 8: 129397–129414. Publisher Full Text\n\nGianvecchio S, Burkhalter C, Lan H, Sillers A, et al.: Closing the gap with APTs through semantic clusters and automated cybergames. International Conference on Security and Privacy in Communication Systems. Cham: Springer; 2019, October; (pp. 235–254).\n\nSen Ö, van der Velde D , Peters SN, et al.: An Approach of Replicating Multi-Staged Cyber-Attacks and Countermeasures in a Smart Grid Co-Simulation Environment. arXiv preprint arXiv:2110.02040. 2021.\n\nBrangetto P, Veenendaal MA: Influence cyber operations: The use of cyberattacks in support of influence operations. 2016 8th International Conference on Cyber Conflict (CyCon). IEEE; 2016, May; (pp. 113–126).\n\nNaveen S, Puzis R, Angappan K: Deep Learning for Threat Actor Attribution from Threat Reports. 2020 4th International Conference on Computer, Communication and Signal Processing (ICCCSP). IEEE; 2020, September; (pp. 1–6).\n\nPerry L, Shapira B, Puzis R: No-doubt: Attack attribution based on threat intelligence reports. 2019 IEEE International Conference on Intelligence and Security Informatics (ISI). IEEE; 2019, July; (pp. 80–85).\n\nGeiger M, Bauer J, Masuch M, Franke J: An Analysis of Black Energy 3, Crashoverride, and Trisis, Three Malware Approaches Targeting Operational Technology Systems. 2020 25th IEEE International Conference on Emerging Technologies and Factory Automation (ETFA). IEEE; 2020, September; (Vol. 1. , pp. 1537–1543).\n\nSiadati H, Saket B, Memon N: Detecting malicious logins in enterprise networks using visualization. 2016 IEEE Symposium on Visualization for Cyber Security (VizSec). IEEE; 2016, October; (pp. 1–8).\n\nSiadati H, Saket B, Memon N: Detecting malicious logins in enterprise networks using visualization. 2016 IEEE Symposium on Visualization for Cyber Security (VizSec). IEEE; 2016; pp. 1–8.\n\nNoor U, Anwar Z, Rashid Z: An Association Rule Mining-Based Framework for Profiling Regularities in Tactics Techniques and Procedures of Cyber Threat Actors. 2018 International Conference on Smart Computing and Electronic Enterprise (ICSCEE). IEEE; 2018, July; (pp. 1–6).\n\nToker FS, Akpinar KO, Özçelik İ: MITRE ICS Attack Simulation and Detection on EtherCAT Based Drinking Water System. 2021 9th International Symposium on Digital Forensics and Security (ISDFS). IEEE; 2021, June; (pp. 1–6).\n\nKwon R, Ashley T, Castleberry J, et al.: Cyber Threat Dictionary Using MITRE ATT&CK Matrix and NIST Cybersecurity Framework Mapping. 2020 Resilience Week (RWS). IEEE; 2020, October; (pp. 106–112).\n\nYin M, Wang Q, Cao M: An Attack Vector Evaluation Method for Smart City Security Protection. 2019 International Conference on Wireless and Mobile Computing, Networking and Communications (WiMob). IEEE; 2019, October; (pp. 1–7).\n\nPark K, Ahn B, Kim J, et al.: An advanced persistent threat (apt)-style cyberattack testbed for distributed energy resources (der). 2021 IEEE Design Methodologies Conference (DMC). IEEE; 2021, July; (pp. 1–5).\n\nWang W, Zhang X, Dong L, et al.: Network Attack Detection based on Domain Attack Behavior Analysis. 2020 13th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI). IEEE; 2020, October; (pp. 962–965).\n\nFujimoto M, Matsuda W, Mitsunaga T: Detecting abuse of domain administrator privilege using windows event log. 2018 IEEE Conference on Application, Information and Network Security (AINS). IEEE; 2018, November; (pp. 15–20).\n\nDiffenderfer PA, Baumgartner DM, Long KM, et al.: Authentication and Authorization Challenges for Controller-Pilot Information Exchange Using Mobile Devices. 2020 AIAA/IEEE 39th Digital Avionics Systems Conference (DASC). IEEE; 2020, October; (pp. 1–8).\n\nNiakanlahiji A, Wei J, Chu BT: A natural language processing based trend analysis of advanced persistent threat techniques. 2018 IEEE International Conference on Big Data (Big Data). IEEE; 2018, December; (pp. 2995–3000).\n\nNisioti A, Loukas G, Laszka A, et al.: Data-driven decision support for optimizing cyber forensic investigations. IEEE Trans. Inf. Forensics Secur. 2021; 16: 2397–2412. Publisher Full Text\n\nAl-Shaer R, Spring JM, Christou E: Learning the Associations of MITRE ATT & CK Adversarial Techniques. 2020 IEEE Conference on Communications and Network Security (CNS). IEEE; 2020, June; (pp. 1–9)."
}
|
[
{
"id": "134931",
"date": "27 Apr 2022",
"name": "Abdullah Alabdulatif",
"expertise": [
"Reviewer Expertise information security"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author has done very good work and explained the problem, which is an Advanced Persistent Threat (APT) against Microsoft Windows Security with the last versions of Windows 10 &11. In this part of the paper, the author has studied and analyzed the problem clearly. However, there are some references that are a bit old. They should be updated with some references in this part.\nAfter that, the author explains the methodology for attaching APT and supports the explanation with great steps and pictures that make this part easy to follow and understand for the reader. Before the end, the author presented the results and discussed them, along with some pictures to prove these results and identify flaws in the APT. I recommend the author discuss the results in depth, as well as make the discussion more clear. Finally, the conclusion part should be expanded by adding more about the future work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8175",
"date": "04 May 2022",
"name": "Nachaat Mohamed",
"role": "Author Response",
"response": "I would like to thank the reviewer for the valuable comments and I assure that first, I will change the old reference for the year 2010 with a new one. Secondly, I will add the future work to the conclusion section as recommended. Thank you"
}
]
}
] | 1
|
https://f1000research.com/articles/11-422
|
https://f1000research.com/articles/11-1118/v1
|
29 Sep 22
|
{
"type": "Research Article",
"title": "Experimental study and machine learning model to predict formability of magnesium alloy sheet",
"authors": [
"Balaji Viswanadhapalli",
"Bupesh Raja V.K",
"Krishna Chythanya Nagaraju",
"Balaji Viswanadhapalli",
"Krishna Chythanya Nagaraju"
],
"abstract": "Background: Magnesium alloy is not only light in weight but also possesses moderate strength. Magnesium AZ31-H24 alloy sheet has many applications in the automotive and aerospace industries. Experimental stretch forming tests are performed on this sheet to measure the material’s formability by constructing forming limit diagrams. Methods: Several tests of Nakazima were carried out on rectangular samples at 24, 250, 350°C and 0.01, 0.001 mm/s using a hemispherical punch. The work done to predict the formability of magnesium alloys has not been recorded in recent literature on machine learning models. Hence, the researchers of this article choose to explore the same and build three models to predict the formability of magnesium alloy through Random Forest algorithm, Extreme Gradient Boosting, and Multiple linear Regression. Results: The Random Forest showed high accuracy of 96% in prediction. Conclusions: It is concluded that the need for physical experiments can be greatly minimized in formability studies by using machine learning concepts.",
"keywords": [
"Magnesium alloy sheet",
"Aerospace and automotive applications",
"Formability",
"Stretch forming",
"Forming Limit Diagram",
"Machine learning model."
],
"content": "Introduction\n\nMagnesium alloy sheet in rolled condition, is an emerging alternative material to aluminium in light weight applications. Magnesium alloys having applications in the aerospace and automotive industries.1 The low melting point of magnesium alloys as compared to steel alloys makes them suitable for casting. Standard automobile steel makeup is about 65% of its parts, which is important for safety reasons, but if the magnesium alloy is stronger and lighter the overall weight of automobile can be reduced to improve fuel efficiency. Fine-forming products can be produced with available metal-forming techniques to broaden the applications of magnesium alloys. In the past, due to the low ductility of magnesium sheets, the applications are limited. However, it was of particular interest because its low density could result in savings in vehicle weight, in turn fuel economy which is a major concern in the automotive and aerospace industries. Hot working can improve the ductility of the material when formed at elevated temperatures. The basal slip mechanism and twinning are the major deformation mechanisms. At temperatures of 200°C and above, some of these basal planes can get activated.2\n\nThe new version of the AZ31B magnesium alloy AZ31B-H24 was used in this present work. Formability, however, is limited by several factors such as poor elongation, alloying elements, and mainly by forming speed and temperature.\n\nThe key to effectively use light alloys like magnesium lies in understanding how they are structured at the atomic level. Magnesium, like Titanium, has a hexagonal close-packed (hcp) crystal lattice with a packing factor of 74%. These lattices are not perfect, but they have many defects such as spacing and linear defects.3 Linear defects such as edge dislocation and screw dislocation are important in metal forming processes. Dislocations mean that the number of atoms are offset from their normal position in the lattice. Edge dislocations have an additional half-plane of atoms that, when stress is applied to the lattice, the atomic bonds are broken and re-formed, allowing the additional half-plane atoms to glide through the lattice. Screw-dislocation, on the other hand, occurs when the entire block of atoms is shifted out of alignment with the correct lattice structure when shear stress is applied to it.\n\nThis displacement motion is irreversible when the tension is removed. The main concept behind plastic deformation is the movement of many dislocations at the atomic level. Material yield strength varies with dislocation density. Materials that contain many dislocations have improved strength, preventing each other from moving through the lattice. Figure 1 shows the effect of dislocation density on the material yield strength. The movement of dislocations through the lattice also affected by how the atoms are packed together. It is easiest for dislocations to move along the planes where the atoms are closest to each other which are the most densely packed planes because those bonds are easier to break and re-form. The denser plane in hcp is shown in Figure 2.4\n\nIn AZ31B-H24 magnesium alloy, H24 indicates one of the tempered designations. H24 means strain hardened and partially annealed.5 The molten metal moves along the channels into moulds to form huge slabs of magnesium, which in turn will roll the solid slab into sheets. From time to time a small sample of molten magnesium is taken for analysis. The metal is poured and left to solidify. As magnesium solidifies, tiny metal crystals begin to form and grow at several points in the liquid in a special film. Each crystal moves outward in all directions until it meets the surfaces of its neighbouring crystals. In engineering parlance, each fully grown crystal is called a grain. Once the magnesium is poured into the slab it is rolled into sheets. To reduce the metal to the desired thickness, it is now rolled several times while relatively cold, as the metal is crushed between the rollers as it is cold worked. Cold working influences the grain structure of magnesium. Changes in grain structure by cold working are accompanied by changes in the mechanical properties of the metal. Its hardness and tensile strength increase while ductility decreases. After cold working the metal is usually heated to a sufficiently high temperature. Heating influences the deformed grain structure. Nothing happens until the metal is heated to its recrystallization temperature, but after attaining its recrystallization temperature, new grains begin to grow rapidly at the grain boundaries and until a new identical grain is formed. The structure does not completely replace the old deformed one. This process is known as recrystallization. This influenced the mechanical properties. These newly formed grains are separated by grain boundaries. Since each grain has a specific plane along which it is easy to slip.6 The presence of grains impedes the movement of dislocations, so polycrystalline metals are stronger than metals composed of similar crystals. The smaller the grain size, the stronger the material.\n\nAll metals and metal alloys are composed of grains, although the grains are not visible. To make the grain visible, it’s a common practice to a give firstly a mirror-like finish and then carefully treating the finished surface with a very strong acid.7 Gloves are required for this operation. As soon as the acid has time to react, the metal must be washed. It is then given a second treatment with another special chemical, this process commonly called as etching. The chemical used for etching is dependent on the material. At the last wash, there are granules of similar size and shape. But in structure they appear as different shapes only because they reflect light. Etching is an important process as it reveals the grain structure. In this present work is AZ31B-H24 magnesium alloy, which is partially annealed, and strain hardened. Thus, the metal is softened and prepared for further work such as shaping, stamping, or forming. AZ31B magnesium alloys have major advantages such as good ductility and corrosive resistance.8 Good strength, high electrical and thermal conductivity at room temperature. AZ31B-H24 magnesium alloy is a newer version of AZ31B magnesium alloy, which has applications in the production of complex parts, chassis components and structural engine parts, etc., where low weight and high relative strength are required. It’s observed that the resistance to indentation on a piece of metal before and after recrystallization, recrystallization has restored softness which means a reduction in hardness. And the tensile strength of the recrystallized magnesium sample was also deceased when tested compared to the cold worked sample. It is noteworthy that the recrystallized sample is most stretched. Hence restored the flexibility. However, the resulting properties depend on the temperature at which recrystallization is performed. If the temperature is too high some grains will grow at the expense of their neighbours. This can lead to properties that are highly undesirable for most engineering applications.9\n\nBi-axial stretch forming test was performed on AZ31B-H24 magnesium alloy of 2 mm thick sheet.10 Rectangular specimens of different widths of 150 mm, 125 mm, 100 mm, and 75 mm are taken, fixing the other dimension as constant at 150 mm. However, other smaller widths such as 50 mm and 25 mm were not taken, as this work mainly focuses on biaxial stretching and plane strain conditions. CNC wire cut edm process has been preferred to cut the samples to the desired sizes. Shearing process, is not preferred for preparing the samples, as it associated with high cutting forces, thereby resulting reduced formability. To measure the deformations, a circular grid is etched on the samples with a laser engraving machine prior to stretching. The circles can take the shape of ellipses after being stretched. The major and minor diameters of the ellipses are measured to calculate the strains and predict the forming limits of the material. No lubricant is applied on the sample in this work. However, lubricant may have a marginal effect on formability of sheet metal.11 Many Nakazima tests are conducted using hemi-spherical punch of 50mm diameter. Hot forming equipment have been used in this work was shown in Figure 3. The equipment is connected to computer data acquisition system to interpret the data. Specimen is heated to reach desired temperature.\n\nA soaking time of 20-30 min is allowed as per standards for test specimen to attain equilibrium temperature inside the heating chamber. For this purpose, ceramic wool is used as insulating material to avoid heat losses from the heating chamber. An initial blank holder pressure of 120-140 bar is applied on the specimen by using a hydraulic pump with 300 bar capacity.12 The blank holder pressure essentially creates a bead on the flat sheet prior to start of actual stretch forming operation using upper and lower dies. The experiment is monitored by observing the load -displacement curve displayed on the computer screen via data acquisition system.\n\nIt’s a challenging task to predict the exact moment and time the fracture begins. It is common practice to stop the experiment by observing the load-displacement curve displayed on the monitor. Many yielding-like points are observed while stretched at temperatures 250°C and above and no such points appear when stretched at room temperature as shown in Figure 4. Reason behind these yielding points has yet to be investigated. Maximum load at fracture for different temperatures, at one fixed strain rate, on four different widths have been noted from the experiments and are analysed as shown in Figure 5.\n\nAt 150°C and 0.01mm/s, it is observed that maximum dome height and maximum load at fracture. However, specimen width has marginal effect on maximum load at fracture. Temperature and strain rate has got more impact on load carrying capacity. Temperature and speed are the two dominant parameters when compared to other parameters like width of the specimen, thickness, and lubrication. Blank holder pressure can be adjusted, otherwise would cause crack initiation near the bead even before the start of forming process.\n\nTo determine the formability of the material, forming limit diagrams are constructed by measuring the circle dimensions before and after the forming operation From Figure 6, it is clearly observed that the load-displacement curves are almost equal irrespective of specimen widths at room temperature and at other temperatures as well.13 At 0.01/s and RT, load and displacement peaks are much less observed compared to the highest values obtained when stretching at 0.01/s and 150°C. It is observed that even at 350°C, the maximum load on the fracture is much lower if the rate of formation is 0.001/s. Therefore, the impact of forming speed cannot be ignored. Figure 7 shows a magnesium etched specimen and another specimen with clear beading and necking after stretching. Fractography, a failure analysis method to study the fracture surface of materials. Studying fracture surface characteristics can help determine the cause of failure in an engineered product. Specific failure modes impart characteristic features on the fracture surface. A small piece of cut sample is taken at the fracture zone with CNC wire cut edm and tested for fractography. Scanning electron microscope pictures are shown in Figure 8 and Figure 9. Both the fractographs exhibiting the ductile fracture, which is associated with dimples and inclusions, a favourable condition for good formable material. Crack initiation is so gradual in ductile fracture.\n\nAny information related to a certain material can be obtained by an experimental tensile test. The Ultimate Tensile Strength as an example at which the necking occurs, cannot be used as a single failure criterion. Instead, forming limit diagram (FLD), used to predict the forming behaviour of sheet metal.14 The forming limit curve is a material parameter that reflects the limiting strains that cause necking failure as a function of the strain path. It is a function of the quality of the metal, the thickness and surface conditions of the sheet, as well as the methods used during its creation vide hemispherical or flat punch, test speed, temperature. It is applicable to any shape of part.\n\nFLD is a diagram contains major principal strain values that are always positive and minor principal strains that are either positive or negative. The shape of the curve can be obtained experimentally. To construct forming limit curve, test pieces of different geometry stretched by a punch with a diameter of 50 mm until fracture occurs. It is a regular practice to make a circular grid all over the structure or panel and after the metal forming process is carried out to see or monitor the behaviour of the circle at each region on the specimen panel. Up to 4 or 5 Nakazima tests can be performed using each of the specimens for the average point on the plot. It is observed that some regions are uniaxial state of stress, some regions are of biaxial state of stress and some other regions are of plane-strain condition as shown in Figure 10. Experimental forming limit diagrams have been plotted by considering 4 or 5 ellipses on either side of the necking zone from each specimen. Stereozoom optical microscope is used to measure major and minor diameters, which will be useful in calculating major and minor true strains. Figure 11, Figure 12, and Figure 13 shows experimental FLDs, when stretched at room, 150°C and 350°C temperatures and at strain rate 0.01/s respectively.\n\nHaving proven itself a better option for prediction in the fields of Finance, Natural Language Processing, weather forecasting, computer vision etc Machine Learning has slowly paved its path into Material Science as well in the recent years. With the advent of machine learning models and artificial intelligence once again gaining much ground in the research front, much of work is being carried out in developing machine learning models to study different alloy properties. The machine learning mechanisms is largely dependent on the data set used to train the model. The required features to calculate or measure a specific feature of the alloy are considered as the input set of features and the output variable is the feature in interest to be calculated. The model builds up a quantitative relationship between the input features and the target variable. Zhenxin Lu, in his work, predicted successfully the corrosivity of low alloy steel.15\n\nIn the recent past many researchers have given their contributions in developing machine learning models for prediction of metallic materials’ properties. D.Z. Xue studied accelerated search for materials with targeted properties by adaptive design.16 C. Wen studied Machine learning assisted design of high entropy alloys with large hardness.17 S. Feng identified the defects in stainless steel using deep neural network.18 Y.T. Sun carried out Prediction of glass forming ability in binary metallic alloys using machine learning approach.19 C. Wolverton in his studies used machine learning techniques to study Accelerating design of engineered metallic glasses.20 The study done by L W Hart, is an excellent work of review on current research happening on alloys based on Machine Learning.21 In the work carried out by Amar M Chheda, a ML model was developed to predict the forming limit diagrams of aluminium alloys.22 The researchers initially considered multi-dimensional data but after rigorous data reduction mechanism application and elimination of non-importance data in recursive method, it was concluded to use 12 features to train the ML Model. Out of 12 features ‘n’and ‘r’ values from tensile tests were used besides elemental composition being represented by six features and four parameters representing process. Accuracy calculation was done based on Root mean Square error ration with respect to R2 and a global genetic algorithm was used for fine tuning of parameters with leave-one-out cross validation score being used to calculate accuracy of model. The researchers claim to have around 93% accuracy. The study carried out by Zhenxin Lu, tried to predict the corrosion potential of magnesium alloy based on its chemical composition. The study was based on four machine learning models developed using Extreme Gradient Boosting, Random Forest, Support Vector Machine regression and Multiple linear regression. The work of Leyun Wang, builds two models based on Artificial Neural Networks and Support Vector Machine algorithms to predict the tensile properties of AZ31 Magnesium alloy.23 Tensile strength, Yield Strength and Ultimate Tensile Strength were predicted using above models. But, the models could not accurately predict the Elongation. The work made use of 112 data items. The authors considered 16 features as input for ANN model. However, the work carried to predict the formability of magnesium alloy was not recorded in the recent literature of Machine learning models being developed to study the alloy properties. Hence, the researchers of this article choose to explore the same and build a model to predict the formability of Magnesium alloy using Random Forest algorithm.\n\nThe data set is of 50534 rows and 7 columns. We used Temperature, Stain Rate, Time in Sec, Load in kN, Length, Width properties of experiment as input features for training and Displacement in mm as target variable. The description of the data can be found as shown in Figure 14. The data considered has got different temperatures viz, 24 (room), 150 and 350 degrees respectively and the Stain Rate (SRt) values are 0.01 and 0.001 mm/s. As it can be observed there were no data missing cases as we can observe each column having equal count of 5034 values. Hence, we can conclude there are no anomalies in data considered. The data visualization graphs that are Strain rate Vs displacement, Temperature Vs Displacement and load Vs displacement illustrated in Figure 15 and Figure 16, and Figure 17 respectively, to understand and interpret the data more clearly.\n\nThe Random Forest builds multiple Decision Trees and the output of multiple trees is averaged to get the final output of Random Forest. Random Forest is categorized under Supervised learning techniques of Machine Learning. The decision trees are evaluated parallel and it is also called as Bagging technique. Owing to the feature and subset randomization, this technique of random forest almost avoids over fitting of data. In this work authors explored three different machine learning models of Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Multiple Linear Regression (MLR). It was observed that the accuracy in RF was almost 94% and in case of EGBoost Root Mean Square Error (RMSE) was just 0.04 whereas in case of MLR it was observed that the accuracy is of only 86.62% and RMSE was 1.392, thus RF demonstrated better performance in predicting the formability of Magnesium Alloy in our experimentation. The graphs shown in Figure 18, Figure 19 and Figure 20 indicating the values, accuracy and RMSE of different algorithms. The regression plot for displacement in MLR is shown in Figure 21.\n\n\nResults and discussion\n\nStretch forming experiments were conducted on 2mm thick AZ31B-H24 magnesium alloy sheets to find material’s formability using hemi spherical punch at elevated temperatures.\n\nFor this purpose, many Nakazima tests are performed on each specimen for consistency. FLDs are constructed, which is the measure of formability.\n\nUsing the experimental data set,24 three Machine learning models are developed to predict the material’s formability. Results and observations from both experimental study and machine learning models are summarised below:\n\n\nExperimental results\n\n\n\n• Maximum height of the dome is achieved when formed at test temperatures of 150°C and at strain rate of 0.01 mm/s.\n\n• It is observed that the blank holder pressure of 120-140 bar can be successfully applied to the specimen, to create a good bead and to avoid cracks near the bead prior to forming happens.\n\n• Punch speed of 0.01/s and blank temperature of 150°C have been identified as excellent forming conditions.\n\n• Forming limit curve reveals the fact that the effect of sample temperature and strain rates are the major controlling factors for a good formability.\n\n• Scanning electron microscope images indicate the ductile fracture, a favourable condition for good formability.\n\n\n\n• In predicting material’s formability, Random Forest (RF) model shown almost 94% accuracy.\n\n• In case of XGBoost Root Mean Square Error (RMSE) was just 0.04.\n\n• It is observed that the accuracy in case of MLR is of only 86.62 and RMSE was 1.392\n\n• RF demonstrated better performance in predicting the material’s formability\n\n\nConclusion\n\nHigh temperature stretch forming tests are conducted on AZ31B-H24 magnesium alloy and the test results are used in developing and train the Machine learning models. The FLD curves and SEM images illustrated, demonstrating the fact that material’s formability can be significantly improved at high test temperatures, making suitable for temperature applications.\n\nMachine learning models are built to predict the material’s formability. The three algorithms predicting materials properties accurately, hence the requirement of physical experimentations can be greatly avoided, thereby, provide emission free environment, if we can use light magnesium alloy in aerospace and automotive applications.\n\n\nData availability\n\nFigshare:Stretch Forming _Data_Set, https://doi.org/10.6084/m9.figshare.20237529.v11.24\n\nThis project contains the following underlying data:\n\n- Temp_room_Strainrate_0.01_Samplesize_150X100mm.xls\n\n- Temp_150_Strainrate_0.001_Samplesize_150X75mm.xls\n\n- Temp_150deg_Strainrate_0.001_Samplesize_150X100mm.xls\n\n- Temp_150deg_Strainrate_0.01_Samplesize_150X125mm.xls\n\n- Temp_350deg_Strainrate_0.01_Samplesize_150X75mm.xls\n\n- Temp_350deg_Strainrate_0.01_Samplesize_150X150mm.xls\n\n- Temp_350deg_Strainrate_0.01_Samplesize_150x125mm.xls\n\n- Temp_room_Strainrate_0.01_Samplesize_150X150mm.xls\n\n- Temp_room_Strainrate_0.01_Samplesize_150X75mm.xls\n\n- Temp_room_Strainrate_0.01_Samplesize_150X125mm.xls\n\n- Temp_150deg_Strainrate_0.01_Samplesize_150X75mm.xls\n\n- Temp_150deg_Strainrate_0.01_Samplesize_150X100mm.xls\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nMordike BL, Ebert T: Magnesium: Properties — applications — potential, Materials Science and Engineering. Mater. Sci. Eng. 2001; A302: 37–45.\n\nWang L, Qiao Q, Liu Y, et al.: Formability of AZ31 Mg alloy sheets within medium temperatures. J. Magnes. Alloy. 2013; 1: 312e317Reference Source\n\nChang Q-F, Li D-Y, Peng Y-H, et al.: Experimental and numerical study of warm deep drawing of AZ31, magnesium alloy sheet. Int. J. Mach. Tool Manu. 2007; 47: 436–443. Publisher Full Text\n\nWang Q, Bertolini R, Bruschi S, et al.: Anisotropic fracture behavior of AZ31 magnesium alloy sheets as a function of the stress state and temperature. Int. J. Mech. Sci. 2019; 105146.\n\nLi Z, Zhou G, Li D, et al.: Forming limits of magnesium alloy AZ31B sheet at elevated temperatures. Int. J. Plast. 2020; 135: 102822. Publisher Full Text\n\nFentahun MA, Prof. Dr. Savaş MA : Materials Used in Automotive Manufacture and Material Selection Using Ashby Charts, International. J. Mater. Eng. 2018; 8(3): 40–54. Publisher Full Text\n\nBrabie G, Lupu R, Rizea AD, et al.: REVIEW OF RECENT STRETCH FORMING DEVELOPMENT. Proc. Manuf. Syst. 2018; 13(3): 147–152.\n\nCai Z-Y, Wang S-H, Xu X-D, et al.: Numerical simulation for the multi-point stretch forming process of sheet metal. J. Mater. Process. Technol. 2009; 209: 396–407. Publisher Full Text\n\nYi S, Bohlen J, Heinemann F, et al.: Mechanical anisotropy and deep drawing behaviour of AZ31 and ZE10 magnesium alloy sheets. Acta Mater. 2010; 58: 592–605. Publisher Full Text\n\nWinsberg E: Simulated Experiments: Methodology for a Virtual World. Philos. Sci. 2003; 70: 105–125. Publisher Full Text\n\nWatiti V, Labeas G: Analysis of the formability magnesium alloys using a new ductile fracture criterion. Int. J. Mater. Form. 2013; 6: 165–171. Publisher Full Text\n\nWatiti V, Labeas G: Finite Element Optimization of Deep Drawing Process Forming Parameters for Magnesium Alloys. Int. J. Mater. Form. 2010; 3: 97–100. Publisher Full Text\n\nAndar MO, Kuwabara T, Steglich D: Material modeling of AZ31 Mg sheet considering variation of r-values and asymmetry of the yield locus. Mater. Sci. Eng. A. 2012; 549: 82–92. Publisher Full Text\n\nSteglich D, Tian X, Bohlen J, et al.: Mechanical Testing of Thin Sheet Magnesium Alloys in Biaxial Tension and Uniaxial Compression. Exp. Mech. 2014; 54: 1247–1258. Publisher Full Text\n\nLu Z, Si S, He K, et al.: Prediction of Mg Alloy Corrosion Based on Machine Learning Models. Adv. Mater. Sci. Eng. 2022; 2022: 1–8. Publisher Full Text\n\nXue DZ, Balachandran PV, Hogden J, et al.: Accelerated search for materials with targeted properties by adaptive design. Nat. Commun. 2016; 7. PubMed Abstract | Publisher Full Text\n\nWen C, Zhang Y, Wang CX, et al.: Machine learning assisted design of high entropy alloys with desired property. Acta Mater. 2019; 170: 109–117. Publisher Full Text\n\nFeng S, Zhou HY, Dong HB: Using deep neural network with small dataset to predict material defects. Mater. Des. 2019; 162: 300–310. Publisher Full Text\n\nSun YT, Bai HY, Li MZ, et al.: Machine learning approach for prediction and understanding of glass-forming, ability. J. Phys. Chem. Lett. 2017; 8: 3434–3439. PubMed Abstract | Publisher Full Text\n\nWolverton C, Jelbert GR, O’Keeffe SC, et al.: A machine learning approach for engineering bulk metallic glass alloys. Acta Mater. 2018; 159: 102–111. Publisher Full Text\n\nHart GLW, Mueller T, Toher C, et al.: Machine learning for alloys. Nat. Rev. Mater. July 2021; 6: 730–755. Publisher Full Text\n\nChheda AM, Nazro L, Sen FG, et al.: Prediction of forming limit diagrams using machine learning, Amar M Chheda et al 2019 IOP Conf. Ser.: Mater. Sci. Eng. 651 012107.\n\nXu X, Wang L, Zhu G, et al.: Predicting Tensile Properties of AZ31 Magnesium Alloys by Machine Learning. JOM. 2020; 72: 3935–3942. Publisher Full Text\n\nViswanadhapalli B: Stretch Forming _Data_Set. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "151891",
"date": "12 Dec 2022",
"name": "Janaki Vinjamuri",
"expertise": [
"Reviewer Expertise Machine Learning",
"Deep Learning",
"Information Security",
"Network Security"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMagnesium alloy plays an important role in the automobile industry and understanding its formability is crucial hence the work is much useful. The prediction of formability of magnesium alloy can give a free hand for people in Industry to decide on the usage in different points while building the automobile. The work falls in the category of prediction of materials’ properties hence Machine Learning is a good research area to explore the possible methods and Authors have aptly chosen to implement. The work explored different research contributions and the drawbacks there which paved a path in that direction in defining the problem under consideration. Machine Learning methods to predict Magnesium alloy formability have been experimented using Python. The prediction in this work was done using a proper dataset and for rebuilding by any researchers it is also made openly available. The machine learning models explored includes XGBOOST, Multi Linear Regression and Random Forest which are suitable models for these types of tasks.\nA bit of more detailed discussion on concepts of Random Forest and XGBoost would help other researchers to further explore this kind of problems. The authors tried to demonstrate use of machine learning models in predicting the formability without actually needing to carry out the physical experimentation. The authors considered 7 parameters at 3 different temperatures giving a variety of training examples to train the ML model. The data set used is consisting of 50534 examples is considerably good size dataset for a model to learn the classification pattern. This was successfully demonstrated with the help of afore mentioned models. The results shown are promising and a good detailed discussion is done Random forest is an ensemble method and weighted voting would always leads to a more accurate classification of data. Hence the work can be considered as a good research work which can show some direction for future researchers as well.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "193630",
"date": "24 Aug 2023",
"name": "Kun Li",
"expertise": [
"Reviewer Expertise Intelligent manufacturing"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this research, high-temperature tensile forming tests were conducted on AZ 31 B-H24 magnesium alloy and the results were used to develop and train machine learning models. Three models were developed to predict the formability of magnesium alloys by RF, XGBoost and MLR. There are some major suggestions for this article as follows:\nComment 1: The paper lacks a reasonable explanation for the utilization of three machine learning methods.\nComment 2: The explanations of the diagrams in the text are too little explained, please add them. For example, Figures 4, 8, and 9.\nComment 3: The quality of the diagrams in the paper is terrible. It is not very impressive in terms of conveying what is stated as well as the clarity of the picture. Please replace it.\nComment 4: Figure 14 describes too little of the data. The 16 features described in the text as inputs are not described in detail.\nComment 5: For trained models, there is a lack of curves for the iterative process and there is a lack of validation results for the models. It is not possible to prove the actual accuracy of the trained model.\nComment 6: Although the article employed three machine learning algorithms for prediction, it fails to explain the reason behind the superior training effect of XGBoost compared to others. Was it due to the amount or type of data, or some other factor?\nComment 7: The descriptions of the models for machine learning and the presentation of the results in the paper are too rough. It is recommended to learn about machine learning model drawing and optimize the model schematic. For example, Li et al., (2023)1.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "193629",
"date": "25 Aug 2023",
"name": "Umer Masood Chaudry",
"expertise": [
"Reviewer Expertise Plastic deformation of Mg",
"physical metallurgy",
"Materials for extreme environments"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe present research utilized ML to predict the formability of AZ31-H24 Mg alloy. Overall, the manuscript looks interesting and can be Approved after addressing the following comments:\nThere are many grammatical mistakes throughout the manuscript.\n\nThe quality of most of the images is very poor.\n\nFor the predicted data set, it would be better to show the graph with experimental and predicted formability comparison.\n\nMore details about the algorithm used in the present study would be better for the reader.\n\nAuthors are suggested to add important literature about the mechanism controlling the formability of Mg alloys. A few suggestions are: Chaudry, Hamad & Kim (2019)1, Chaudry, Kim & Hamad (2019)2 and Masood Chaudry et al., (2022)3.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1118
|
https://f1000research.com/articles/11-1117/v1
|
28 Sep 22
|
{
"type": "Research Article",
"title": "The validity and reliability test of the leprosy life quality questionnaire in leprosy patients",
"authors": [
"Dhelya Widasmara",
"Dhany Prafita Ekasari",
"Santosa Basuki",
"Muhammad Mazaya Atif",
"Ramesh Bhat M",
"Dhany Prafita Ekasari",
"Santosa Basuki",
"Muhammad Mazaya Atif",
"Ramesh Bhat M"
],
"abstract": "Background: Leprosy is a public health problem because it potentially affects social life. In 2018, World Health Organisation (WHO) reported that Indonesia ranks third of new cases leprosy. Leprosy significantly influences patients' quality of life. Until now, there is still no specific questionnaire to assess the quality of life for leprosy patients. Leprosy Quality of Life Questionnaire (KUKUH) is a questionnaire to assess leprosy patients' quality of life, which includes questions about psychology, physical health, social environment, and treatment. The study aimed to assess the validity and reliability of the Leprosy Quality of Life Questionnaire (KUKUH) as a tool to assess the quality of life of leprosy patients in Indonesia. Methods: The study was conducted at Saiful Anwar General Hospital in Malang, East Java. The validity analysis using construct validity with a minimum correlation coefficient value considered valid by 0.3. Internal consistency assessment for the questionnaire utilized the Cronbach α value where a value greater than or equal to 0.60 is acceptable, and a value greater than or equal to 0.80 is considered good. Results: Based on the result of variable validity test, all items measuring each aspect have item correlation coefficient values with a total score (riT) > table correlation value (0.361). The results of reliability testing, the items that measure each aspect of the quality-of-life variable for leprosy patients have Cronbach's Alpha values greater than 0.6.\n\nConclusion: The validity test results of KUKUH Questionnaire are considered quite good, with a total score of 0.361 for the correlation coefficient for each question in KUKUH. The reliability test results were deemed satisfactory, with Cronbach's alpha > 0.6. The KUKUH questionnaire can be used to evaluate the quality of life of leprosy patients in Indonesia.",
"keywords": [
"Leprosy",
"Morbus Hansen",
"Questionnaire",
"Leprosy Quality of Life",
"KUKUH"
],
"content": "Introduction\n\nChronic infectious disease that is caused by Mycobacterium leprae is called Leprosy. This disease primarily affects the skin and peripheral nerves, resulting in sensory, motor, and autonomic dysfunction. Mycobacterium leprae can be found in high concentrations on the nasal mucosa of leprosy patients. Bacilli can survive outside the body for 36 hours to nine days.1 In 2019, 202,256 new cases of leprosy have been reported worldwide. India, Brazil, and Indonesia accounted for 79% of the most recent cases of leprosy patients globally.2 At the end of 2018, the South-East Asia region (SEAR) accounted for 71% of new leprosy cases globally, with India and Indonesia accounting for 92% of the location's case load.3\n\nLeprosy is one of the infectious diseases that causes extremely complex problems, not only from a medical standpoint but also from a socioeconomic standpoint. The negative stigma from society persists, with people viewing leprosy as a frightening disease. Leprosy patients frequently experience psychosocial problems because of negative stigma.4\n\nDelay in diagnosis and treatment of leprosy patients can result in permanent damage to the peripheral nerves and possibly lead to amputation and disability, this can occur due to many factors such as lack of awareness, poor access to leprosy diagnosis and treatment, neglect, poverty, social stigma, etc. Even today, many patients are diagnosed with leprosy after they become disabled.5\n\nLeprosy can cause physical disability, which can have severe psychological consequences and will almost certainly reduce one's quality of life. Disability-related leprosy can cause economic, social, and psychological issues that have a negative impact on one's quality of life.6\n\nThe study's findings also revealed that people with leprosy had lower mean quality of life scores than people without disabilities in all four domains of health relationships: physical, psychological, social, and environmental. Following this discovery, Tsutsumi et al. (2007) and Dinesh et al. (2016) discovered that people suffering from leprosy have a low quality of life.6–8 A 2015 study in Brazil with 106 leprosy patients found a lower quality of life, particularly in leprosy patients with disabilities. Disability was associated with a decrease in quality of life (p = 0.001).9\n\nThe European Academy of Dermatology and Venereology (EADV) believes that measuring quality of life in clinical practice can benefit patients, support physician decision-making, and contribute to the delivery of high-quality care. The goal of this Statement is to describe the various ways in which using quality of life measures can be beneficial in clinical practice.10\n\nData on quality of life can aid in therapeutic strategy decisions and encourage patient participation in joint decision-making with doctors. Patients' understanding of non-medical aspects of their illness supplements the physician's knowledge of medical factors. Medication adjustments can be made while viewing the patient's quality of life data, which can aid in clinical decisions such as dose adjustments and changes to follow-up therapy.11\n\nLeprosy can cause paralysis and deformity, which can lead to social stigma and exclusion, negatively impacting patients' quality of life.12 There is currently no specific quality of life assessment questionnaire available to assess the quality of life of leprosy patients. Information about people with leprosy's quality of life is expected to be the foundation for overcoming the problem of leprosy, which focuses not only on the physical but also on other factors that may lead to a decrease in the quality of life of people with leprosy.\n\nLeprosy Quality of Life (KUKUH) is a questionnaire that can be filled out by patients to assess the leprosy patients’ quality of life. It consists of ten questions on one sheet of paper and includes questions about aspects of psychology, physical health, social environment, and treatment. The Total Leprosy Quality of Life Score (KUKUH) is calculated by adding the scores for each question. Each question's score has its own interpretation. KUKUH is a short and simple acronym that can be used in clinical practice and research. The Leprosy Quality of Life (KUKUH) questionnaire must be tested for validity and reliability before it can be used in the Indonesian leprosy population. The goal of this study was to determine the validity and reliability of the Leprosy Quality of Life Questionnaire (KUKUH) so that it could be used widely in Indonesian leprosy patients. Among the various types of validity, the construct validity is the most used for various types of research to test the validity of the questionnaire. The external validity test, which correlated a questionnaire with a valid measuring instrument, was not performed because there was no gold standard questionnaire for assessing the quality of life of leprosy patients in Indonesian. As a result, in this study, the construction validity is evaluated to assess the validity of all questions in the Leprosy Quality of Life (KUKUH) questionnaire. The instrument was tested for reliability with an internal consistency test on the research subject once. The Cronbach Alpha technique can be used to perform this test.\n\n\nMethods\n\nThe research design tested the validity and reliability of the Leprosy Quality of Life Questionnaire (KUKUH) using a cross-sectional study design.\n\nPatients diagnosed with leprosy/Morbus Hansen with the type of Pausibacillary and Multibacillary with a degree of disability 0-2 were controlled at the Dermatology and Venereology Polyclinic, Saiful Anwar Regional General Hospital, and at the Primary Public Health Center, Malang East Java. The sample size is 30 people.\n\nThe inclusion criteria were that patients had to be between the ages of 18 and 60, have a clinical diagnosis of leprosy, be able to communicate in Indonesian, read, and be willing to participate in research by signing informed consent. Patients with psychiatric disorders were excluded from the study.\n\nThe researchers recorded the identity, diagnosis of leprosy type, and the degree of disability of patients who had signed the consent form. Research subjects were asked to fill out the Quality-of-Life Leprosy (KUKUH) Questionnaire after receiving an explanation on how to fill out the questionnaire. The research subjects filled out the questionnaires themselves, but the researchers accompanied the process of filling out the questionnaires to provide explanations if needed.\n\nUsing the Pearson product-moment correlation technique formula, validity analysis uses construction validity by calculating the correlation between each statement and the total score. The minimum correlation coefficient value that is considered valid is 0.3. Correlation numbers below the minimum value indicate an invalid argument, perhaps due to the arrangement of words or sentences that are not good, or the sentences give different interpretations that require evaluation. The corrected statement must be tested again for validity on a diverse sample until valid results are obtained.\n\nInternal consistency is used to test the reliability of the Leprosy Quality of Life (KUKUH) Questionnaire. Internal consistency is assessed using the Cronbach value, a value greater than 0.60 is acceptable, and a value greater than 0.80 is considered good.\n\nThe data is recorded in a particular format then edited and coded. The data was entered in the SPSS worksheet and then processed using the SPSS v. 21 program. Univariate analysis was to determine the distribution of the characteristics of the research subjects. The construction validity assessment uses Pearson's product-moment correlation technique to see the correlation value between each statement and the total score. Internal consistency is used to test the reliability of the Leprosy Quality of Life (KUKUH) Questionnaire18 and is assessed using the Cronbach α value.\n\n\nResults\n\nThe Pearson Correlation (Product Moment) technique was used to test the instrument's validity by correlating each score in each item with the total score. The Pearson Correlation technique test criteria state that if the correlation coefficient (riT) table correlation (rtable) is greater than one, the questionnaire item is declared valid or capable of measuring variables and can be used as a data collection tool.\n\nBased on the results of validity test of the research variables (Table 1), all items which measuring each aspect, have coefficient correlation values with a total score (riT) > table correlation value (0.361). As a result, the questionnaire items that measure every aspect of leprosy patients' quality of life are declared valid or capable of measuring these variables and will be used as a data collection tool in this study.\n\nAccording to a summary of the research instrument's reliability testing results (Table 2), the items that measure every aspect of the quality-of-life variable for leprosy patients have Cronbach's Alpha values greater than 0.6. As a result, the questionnaire items that measure every aspect of leprosy patients' quality of life have been declared reliable or consistent in measuring these variables and will be used as a data collection tool in this study.\n\nBased on the summary of the correlation coefficient and the value of Cronbach's alpha in each aspect (Table 3), the average value of the correlation coefficient in the psychological aspect is 0.862, and the value of Cronbach's alpha is 0.885. Then, the average value of the correlation coefficient on the physical health aspect is 0.843, and Cronbach's alpha value is 0.790. Furthermore, the average value of the correlation coefficient on social and environmental aspects is 1.000, Cronbach's alpha value is 1.000, and the average value of the correlation coefficient on the treatment aspect is 0.926, and Cronbach's alpha value is 0.828.\n\n\nDiscussion\n\nData on quality of life can help with therapeutic strategy decisions and encourage patient involvement in decision making. Patients' understanding of non-medical aspects of their illness supplements the physician's knowledge of medical factors. Medication adjustments made while viewing patient quality of life data can assist physicians in clinical decisions such as dose adjustments or changes to follow-up therapy, for example, to reduce the identified quality of life impacts more quickly. The treatment's effect can also have an impact on the quality-of-life score.11\n\nRegular quality of life measurements can aid in monitoring the progression of a condition or the efficacy of therapy. Changes in the score can be instructive and serve as a reminder to the doctor to reconsider changing treatment. For many patients and doctors, the most important outcome of care is improved quality of life. Quality of life measurement can be used as a screening tool to uncover “hidden” physical, psychological, and adjustment issues, as well as to identify patients who may need to be referred to other specialists or who may require additional support or care.11\n\nHealth questionnaires are generally designed to detect a psychological disorder and are reliable in dermatology patients. Quality of life measurement can show the effect of skin disease compared to other organ diseases.11\n\nThe European Academy of Dermatology and Venereology (EADV) summarizes at least 40 tools for measuring the quality of life and health status for skin diseases. Quality of life in dermatology is most often assessed with generic and specialized instruments for dermatology-specific conditions. Researchers and clinicians have a wide choice of tools in which several parameters can influence therapy for a patient. Doctors and patients prefer short instruments and a short time to complete them. Another critical parameter in assessing the quality of life is validation. A well-validated tool has a better chance of being widely used.13\n\nAn excellent measuring instrument or instrument must meet the requirements for testing its validity and reliability. Validity in the context of research instruments means that the validity of a study is related to the extent to which a researcher measures what is supposed to be measured. Moreover, the validity of quantitative research is rooted in empiricism, which emphasizes evidence, objectivity, truth, deduction, reason, facts, and numerical data. The measurement tools commonly used are questionnaires and tests. In this context, the questionnaire measuring instrument needs to be structured in such a way that it can be used as the right instrument to obtain, find, describe, explore, and compare various information, topics, and research variables.11 Construction validity relates to whether the research tools have been prepared based on an appropriate and relevant theoretical construct. Questionnaires with high construct validity are always based on the definition or limitations of experts on the concept, not on a dictionary definition. Based on these limitations, researchers can arrange appropriate statements and questions. With SPSS, questionnaires and test items need to be measured using factor analysis.14\n\nConstruct validity focuses on the extent to which a measuring instrument shows measurement results that conform to its definition. The definition of variables must be clear to facilitate the assessment of construct validity. The definition is derived from theory. If the definition is based on the correct theory and the question or item statement is appropriate, then the instrument is declared valid with construction validity.15\n\nUsing the Pearson product-moment correlation technique formula, validity analysis uses construction validity by calculating the correlation between each statement and the total score. The minimum correlation coefficient value that is considered valid is 0.3. Correlation numbers below the minimum value indicate an invalid statement, perhaps due to the arrangement of words or sentences that are not good, or the sentences give different interpretations that require evaluation. The corrected statement must be tested again for validity on a diverse sample until valid results are obtained.16\n\nAccording to the results of testing the validity of this research variable, all items measuring each aspect have item correlation coefficient values with a total score (riT) greater than the table correlation value (0.361). As a result, the questionnaire items that measure every aspect of the quality-of-life variable of leprosy patients are declared valid or capable of measuring these variables, and will be used as a data collection tool in this study.\n\nTrustworthiness, reliability, constancy, stability, and consistency are all synonyms for reliability. The main idea behind the concept of reliability is \"the degree to which measurement results can be trusted.\" The term reliability refers to the degree to which measurement results can be trusted. Furthermore, the concept of reliability refers to the consistency of the scores on the questionnaire items, so that the reliability test evaluates the accuracy of the research instrument's measurement scales.14\n\nTherefore, the main purpose of testing the reliability of research instruments is to measure the consistency of the measuring instruments used by quantitative researchers. In this context, the researcher wants to determine whether there is the accuracy of measurement results in the same sample at different times. A research instrument, such as a questionnaire, is reliable if it can provide consistent scores on each measurement. Then the measurement tool (items of statements/questions) still provides consistent measurement results at different times.14\n\nRe-measurement techniques, halving techniques, parallel techniques, and internal consistency can all be used to calculate reliability. Only questions with existing validity should be subjected to reliability calculations (Rahmatina, 2013). If the Cronbach's Alpha reliability coefficient is greater than 0.70 (ri > 0.70), the instrument is said to be reliable, and if the Cronbach's Alpha reliability coefficient is greater than 0.90 (ri 0.9), the instrument is said to be unreliable. Tavakol and Dennick (2011) recommend revising or eliminating items with low correlations if the Cronbach's Alpha reliability coefficient is less than 0.70 (ri 0.70).17 A computer program can be used to quickly determine the object of the question. They also have suggestions if the Cronbach's Alfa reliability coefficient is greater than 0.90 (ri > 0.90). They advocate for fewer questions with the same criteria, even if they are in different sentences.15\n\nAccording to a summary of the research instrument's reliability testing results, the items that measure each aspect of the quality-of-life variable for leprosy patients have Cronbach's Alpha values greater than 0.6. As a result, the questionnaire items that measure every aspect of leprosy patients' variable quality of life are declared reliable or consistent in measuring these variables, allowing them to be used as data collection tools.\n\n\nConclusion\n\nThe validity test results of the Indonesian language KUKUH Questionnaire to assess the quality of life of leprosy patients were considered good, with a total score of 0.361 for the correlation coefficient for each question. The reliability test results were deemed satisfactory, with Cronbach's alpha > 0.6. The KUKUH questionnaire can be used to evaluate the quality of life of leprosy patients in Indonesia.\n\n\nData availability\n\nZenodo: The validity and reliability test of the leprosy life quality questionnaire in leprosy patients.18\n\nhttps://doi.org/10.5281/zenodo.6817556\n\nThis project contains the following underlying data:\n\n‐ Analytic Data Revised/Raw Data.xlsx\n\n‐ Validity and Reliability Test Result.docx\n\n‐ Validity and reliability test.sav\n\nThis project contains the following extended data:\n\n‐ Quality of Life Questionnaire (KUKUH).docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nWidasmara D: Leprosy A Clinical Perspective. Poor. Malang:UB Press;first ed2018.\n\nWorld Health Organization: Towards zero leprosies. Global leprosy (Hansen's Disease) strategy 2021–2030.2021.\n\nSardana K, Khurana A: Epidemiology and World Distribution, Handbook Of Leprosy. 6th ed.2020; vol. 1: 4–5.\n\nAzizah N: Analysis of the Impact of Leprosy on the Social Interaction of Patients in Brondong, Lamongan. Statistics Paper ITS:Indonesia;2011.\n\nNery R, Ramond A, Pescarini JM, et al.: Socioeconomic determinants of leprosy new case detection in the 100 Million Brazilian Cohort: a population-based linkage study. Lancet Glob. Health. 2019; 7(9): e1226–e1236. PubMed Abstract | Publisher Full Text\n\nGovindharaj P, Srinivasan S, Darlong J: Quality of life of persons affected by leprosy in an endemic district, West Bengal, India. Indian J. Dermatol. 2018; 63(6): 459–464. PubMed Abstract | Publisher Full Text\n\nTsutsumi A, Izutsu T, Islam AM, et al.: The quality of life, mental health, and perceived stigma of leprosy patients in Bangladesh. Soc. Sci. Med. 2007; 64(12): 2443–2453. PubMed Abstract | Publisher Full Text\n\nDinesh G, John KR, Logaraj M: An assessment of quality of life among leprosy affected persons residing in leprosy settlements of Chengalpet Taluk, Kancheepuram, Tamil Nadu. Natl. J. Res. Community Med. 2016; 5: 149–154.\n\nSantos VS, Oliveira LS, Castro FD, et al.: Functional activity limitation and quality of life of leprosy cases in an endemic area in Northeastern Brazil. PLoS Negl. Trop. Dis. 2015; 9(7): e0003900. Publisher Full Text\n\nMokkink LB, Terwee CB, Patrick DL, et al.: The COSMIN checklist for assess-ing the methodological quality of studies on measurement properties of health status measurement instruments: an international Delphi study. Qual. Life Res. 2010; 19: 539–549. PubMed Abstract | Publisher Full Text\n\nFinlay AYPrinciples of measurement and assessment in dermatology. Rook's Textbook of Dermatology, Ninth Edition.2016; 1–13.\n\nEl-Refaei A, et al.: Health Related Quality of Life in Egyptian Leprosy Patients using DLQ and WHOQOL-BREF Questionnaires. J. Clin. Exp. Dermatol. Res. 2018; 9: 475.\n\nChernyshov PV: The evolution of quality of life assessment and use in dermatology. Dermatology. 2019; 235(3): 167–174. PubMed Abstract | Publisher Full Text\n\nBudiastuti D, Bandur A: Research validity and reliability. Equipped with Data Analysis using NVivo, SPSS, and AMOS. Jakarta:Mitra Wacana Media;2018.\n\nYusup F: Test the validity and reliability of quantitative research instruments. Tarbiyah: Scientific. J. Educ. 2018; 7(1).\n\nNotoatmodjo S: Develop research instruments. Medical research methodology. Jakarta:Rineka Cipta;2010; 152–170.\n\nTavakol M, Dennick R: Making sense of Cronbach’s alpha. Int. J. Med. Educ. 2011 Jun; 27(2): 53–55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWidasmara D, et al.: ‘The validity and reliability test of the leprosy life quality questionnaire in leprosy patients’ [Data].2022. Publisher Full Text"
}
|
[
{
"id": "203877",
"date": "22 Sep 2023",
"name": "Marília Brasil Xavier",
"expertise": [
"Reviewer Expertise Dermatology",
"tropical dermatology",
"leprosy",
"infectious diseases."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript proposes a specific questionnaire for evaluating the quality of life in leprosy patients and aims to assess the validity and reliability of the proposed tests in Indonesian patients. The addressed topic is relevant to clinical health assistance for leprosy patients. However, several areas need to be addressed before indexing:\nThe authors do not clearly indicate that this is the proposal of a novel questionnaire. Initially, it appears that they are testing a previously published method. If this is indeed a new questionnaire proposed by the authors, a thorough description of its development and composition is necessary, including the participation of experts in its creation, if it is the case.\n\nThe authors should provide more background information on other instruments used to assess the quality of life in leprosy patients, such as adapted WHO questionnaires. This context will help readers understand the significance of the proposed questionnaire.\n\nCitations for the statistical methodology used to evaluate the validity and reliability of the Leprosy Quality of Life Questionnaire (KUKUH) are mentioned in the discussion but not in the methodology section. It's important to include these citations in the methodology section for clarity and transparency.\n\nThere is inconsistency in the description of the Cronbach α reliability value. In one part, it is mentioned that a value greater than 0.60 is acceptable, and a value greater than or equal to 0.80 is considered good. However, in the discussion, it is stated that a value greater than 0.70 indicates reliability and a value greater than 0.90 indicates unreliability. This discrepancy needs clarification, as it affects the interpretation of the reliability of the Social and Environment questions, which were reported as (summarized) 1.000 in the results section. The same goes for the sentence \"The reliability test results were deemed satisfactory, with Cronbach's alpha > 0.6\", incoherent with the >0.70 cut-off mentioned.\n\nThe manuscript should clearly state that the study's population is small and composition, especially considering the diversity of disease and disability within the leprosy spectrum. This is important information for readers to understand the limitations of the study and the generalizability of the findings.\n\nThe discussion should be improved by incorporating relevant literature, even if it includes adapted questionnaires previously mentioned. This will help place the research in a broader context and provide more robust support for the study's findings and conclusions.\n\nPlease address these issues to enhance the quality and clarity of your manuscript before revising.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "210830",
"date": "17 Nov 2023",
"name": "Pitchaimani Govindharaj",
"expertise": [
"Reviewer Expertise Physiotherapy",
"Leprosy Rehabilitation",
"Sociology of Health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFirst, I appreciate the authors for developing the Leprosy Quality of Life Questionnaire (KUKUH) to assess the quality of life of patients with leprosy in Indonesia. However, there are several areas of concern that need to be addressed before the paper can be indexed.\nIt would be good if you changed the word to ‘people affected by leprosy’ instead of ‘leprosy patient’. The authors should provide the process of questionnaire development, such as identification of the domains and item generation. The authors do not consider content validity (theoretical analysis). Content validity is mainly assessed through evaluation by expert and target population judges. Items: How many items were collected? How was the process of item selection done? What criteria were used for item reduction? Pre-testing of the questionnaire is one of the processes of testing the measurement tools, and this process is missing in this study. Sample Size: The rule of thumb has been at least 10 participants for each scale item, i.e., an ideal ratio of respondents to items is 10:1. The small sample size is inadequate to draw a conclusion. This questionnaire includes domains of psychology, physical health, social environment, and treatment. The authors merely placed the items in the domains; no factor analysis was done to explore the domains. Furthermore, for a domain to be considered, a minimum of three items are required. In this questionnaire, only one item is present in the social and environmental domains, and two items are in the treatment domain. There is inconsistency in the description of the Cronbach α reliability value. In the methods, the authors stated that a Cronbach value greater than 0.60 is acceptable, and a value greater than 0.80 is considered good. In the discussion, it is stated that a value greater than 0.70 indicates reliability and a value greater than 0.90 indicates unreliability. Generally, an alpha coefficient of 0.70 has often been regarded as an acceptable threshold for reliability.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "210839",
"date": "17 Nov 2023",
"name": "Jane Rahedi Ong'ang'o",
"expertise": [
"Reviewer Expertise Public health research and health systems strengthening research for both communicable and non-communicable health conditions."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe tool for validation is based on the concept of QoL and includes physical activity, psychological condition, environment and social relationship and treatment.\nTo understand whether this tool was a comprehensive evaluation of different aspects of QoL, it would be important to indicate what were the details/questions of the different QoL domains for a reader to assess the appropriateness. Under the section of data availability the questionnaire is available but I did not have access to enable me review it.\nWas there any reference to the use of other instruments for assessing quality of life eg the WHOQOL-bref tool, the short form-36 (SF-36), the Dermatology life of quality index (DLQI)? In developing this tool, it would be important to understand this if at all as part of tool development.\n\nA mention of limitations of the tool may be important. For example this may apply to this tool or not; considering the quantitative data on QoL may only reflect the multidisciplinary nature of the domains of focus but may not capture their subjectivity so the inclusion of qualitative approaches may be important to understand the experience and needs of patients in specific contexts. Another limitation is that the validation is only limited to one language of Indonesia and for one to participate in using the tool they had to be able to read and write the language. The tool was self administered. This may limit response especially if the question is not well understood.\nWhat was the criteria to select the group of individuals that participated in the validation age 18-60 years? Was the stage of disease considered; a patient with advanced stage of disease could lead to bias on scores of poor QoL. Excluding children/their guardians to participate may miss out a specific context in relation to children/adolescents.\nIn the discussion section it is stated that if the Cronbach's Alpha reliability coefficient is greater than 0.70 (ri > 0.70), the instrument is said to be reliable, and if the Cronbach's Alpha reliability coefficient is greater than 0.90 (ri 0.9), the instrument is said to be unreliable. This needs to be consistent with what is indicated in the methods section that with Cronbach's alpha > 0.6 the instrument is reliable.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1117
|
https://f1000research.com/articles/11-1116/v1
|
28 Sep 22
|
{
"type": "Brief Report",
"title": "Therapeutic effect of herbal infusion on abnormal uterine bleeding: interventional non-randomized pilot study",
"authors": [
"Mejda Selmi",
"Latifa Lassoued",
"Badra Bannour",
"Chahra Chbili",
"Maha Ben Fredj",
"Ridha Charfeddin",
"Hedi Khairi",
"Latifa Lassoued",
"Badra Bannour",
"Chahra Chbili",
"Maha Ben Fredj",
"Ridha Charfeddin",
"Hedi Khairi"
],
"abstract": "Background: Abnormal uterine bleeding-menometrorrhagia due to uterine myomas is a health problem affecting women’s quality of life and it is considered a frequent cause of emergency visits for women. If first line medication fails to treat symptoms, surgical procedures, such as hysterectomy could be indicated, which could interfere with women's physical, social, emotional, and material quality of life. The purpose of this pilot study was to investigate the effect of a mixture of two medicinal plants, Mentha pulegium L and Artemisia abrotanum L, on 13 women with menometrorrhagia, who were candidates for hysterectomy. Methods: The herbs were taken as a tea infusion by the oral route. A total of 5 g of the dried aerial parts of the mixture were added to 100 ml of boiling water and the tea infusion was taken three times a day starting from the onset of menstruation for three consecutive days, and it was repeated for three consecutive months. Results: The study results showed that 10 out of the 13 women involved avoided the surgical procedures. The mean number of bleeding days declined from 11.50 (±3.77) at baseline to 7.60 (±2.11) (p=0.01). Participants confirmed a change in the bleeding intensity, regularization of their menstrual cycle, and improvement in their quality of life. Conclusions: This preliminary study explores a new approach to treat abnormal uterine bleeding- menometrorrhagia, based on tea infusion consumption of a mixture of two medicinal herbs, and it paves the way for future studies. Trial registration: This study is registered with ClinicalTrials.gov NCT05406960 (07/06/2022).",
"keywords": [
"Abnormal uterine bleeding",
"Menometrorrhagia",
"Tisane",
"Traditional Medicine",
"North Africa"
],
"content": "Introduction\n\nMenometrorrhagia, caused by uterine myomas, is defined as excessive uterine bleeding resulting from a combination of two different conditions, namely menorrhagia or hypermenorrhea, which is blood loss of more than 80 ml per cycle or having a cycle longer than seven days or both,1 and metrorrhagia, which is uterine bleeding at irregular intervals, particularly between the expected menstrual periods.2 It is defined as abnormal uterine bleeding (AUB) and known as prolonged and excessive uterine bleeding in irregular intervals.3 AUB is a worldwide health problem affecting 20% of adolescent girls and more than 50% of women older than 45 years.4 Management of AUB includes hormonal and non-hormonal treatments.5 If first line medication fails to treat women with AUB, surgical treatment, such as hysterectomy could be indicated. This solution is often used without a clear treatment strategy.6,7 The hypoestrogenic state of these therapies can lead to rapid bone demineralization and menopausal symptoms, such as vaginal dryness and hot flushes, having negative effects on women’s quality of life.1,8 Thus, because of these serious side effects, it seems logical to investigate other available sources. The therapeutic uses of Mentha pulegium L, known as Pennyroyal, and Artemisia abrotanum L, known as Southernwood, as traditional medicinal treatments for painful menstruation, pave the way for the possibility of new health-related uses.9,10 A mixture of these two herbs is recommended as a strong emmenagogue.11 Only few studies have explored the effect of Pennyroyal on menstruation,12 however, to the best of the authors’ knowledge, no scientific data highlighting the therapeutic effect of a mixture of Southernwood and Pennyroyal tea infusion on menometrorrhagia in women are available. It is a non-randomized, controlled trial to investigate the effect of a mixture of Pennyroyal and Southernwood tea infusion consumption on women with menometrorrhagia who are candidates for hysterectomy, in avoiding the surgical procedure, reducing the number of days of menstrual bleeding, and improving women’s quality of life.\n\n\nMethods\n\nThis is an interventional, non-randomized, controlled, single center pilot study. It was conducted in the department of Gynecology and obstetrics at Farhat Hached University Hospital, Sousse, Tunisia.\n\nRetrospective registration was acquired (Clinicaltrials.gov NCT05406960, 07/06/2022) because the study was taken to be low risk; however, the study was approved by the Human Research Ethics Committee at the Faculty of Medicine of Sousse, Tunisia and it was registered under the number (Ref: CEFMS 27/2019, 29/08/2019).\n\nAfter being informed about the research protocol, each participant signed a written informed consent form prior to the initiation of the study procedures. All clinical investigation procedures were conducted according to the principles expressed in the declaration of Helsinki guidelines. This study is reported in line with the Consolidated Standards of Reporting Trials (CONSORT) guidelines.26\n\nParticipants meeting the inclusion criteria were informed about the research protocol by their gynecologists. They underwent complete physical examination following their acceptance to be enrolled in the study (Figure 1). They were interviewed to complete a quality-of-life questionnaire to determine the impact of the illness on their daily life and to record all details of their gynecological and menstrual histories. All participants were asked to report all details with regard to the effect of the treatment on menstrual cycle, menstruation duration, and bleeding intensity measured using pictorial blood assessment chart (PBAC) during three consecutive menstrual cycles treatments and the three-month follow-up period. They were also asked to report any change in the bleeding pattern and any adverse effects. Participants were recruited between 2019 and 2021. The study was interrupted by the COVID-19 pandemic.\n\nThe herbal tea infusion was taken by the patients at home after providing them with a detailed oral and written explanation. Assistance was provided by phone or via visits if any participant had questions regarding the treatment.\n\nParticipants took 5 g of mixed herbs powder added to 100 ml of boiling water and infused for 10 to 15 min, in accordance with the traditional uses. Herbal tea infusion was taken through the oral route before food, three times a day at 4-hour intervals after the first administration for three consecutive days, starting from the first day of the onset of menstruation.\n\nInclusion criteria\n\nThe study included women with menometrorrhagia who were candidates for hysterectomy, aged between 30 and 55 years, not pregnant and not lactating and having a menstrual period for more than seven days with uterine bleeding at irregular intervals.\n\nExclusion criteria\n\nThe exclusion criteria included women suffering from abnormal uterine bleeding with menometrorrhagia but who were not candidates for hysterectomy, those suffering from gastrointestinal problems or any chronic diseases requiring long-term treatment, participants with increasing menstrual bleeding during the treatment requiring emergency surgical procedures, and those refusing the instructions given or who were participating in other clinical trials.\n\nMethod of herbs powder preparation\n\nPennyroyal and Southernwood were collected in July 2019 and 2020 from two different areas in the region of Sousse, Tunisia. The aerial parts (leaves and stems) of each plant were dried at room temperature in the shade; then, they were powdered in a rotating knife grinder. The powder was packaged in sachets, each containing 5 g, 2.5 g Pennyroyal and 2.5 g Southernwood, mixed according to the traditional uses of the herbs.13\n\nTreatment duration and follow-up\n\nThe treatment duration was up to three consecutive menstrual cycles and the total duration of the participants’ involvement in the study ranged between six and nine months.\n\nParticipants were followed via phone interview during and after the treatment. They were followed up for six months. Monitoring for efficacy and safety was performed every month starting from the treatment initiation until the treatment completion.\n\nRestriction parameters\n\nDuring the treatment period, participants were restricted to use just oral iron therapy, opioid analgesics, or acetaminophen. They were strictly asked to stop using any hormonal therapy, other herbal treatments, tranexamic acid, or any other treatment in relation to their disease.\n\nSafety assessments\n\nAll participants were asked to record any possible adverse effects occurring during the study period. The effect of mixed herbal tea infusion was evaluated in the first four days. If no improvement in bleeding intensity was noted, participants were asked to stop taking the infusion and to return to their gynecologist to undergo a surgical procedure.\n\nClinical criteria\n\nParticipants were evaluated based on the bleeding intensity using PBAC scores, the duration of menstrual bleeding in days, regularization of menstrual cycle, and the improvement in their quality of life.\n\nBiological criteria\n\nComplete blood count (CBC) was performed before the start of the trial and after the third cycle of taking the infusion to control anemia. The safety and hemostatic effects of the treatment were evaluated by the analysis of prothrombin time (PT), prothrombin ratio (INR), and fibrinogen (FIB) to detect bleeding disorders, and the analysis of serum creatinine to detect urinary toxicity. Laboratory tests were conducted in the department of hematology at Farhat Hached University Hospital, Sousse, Tunisia. A 4ml blood sample was collected from each participant during the first visit before the start of the trial and after the last infusion consumption (day 91) in the same laboratory. A heparinized catheter was inserted into the antecubital vein to collect venous blood samples in three different tubes: an EDTA-coated tube, used for the CBC analysis parameters that were assessed following the combining laser diffraction flow cytometry and spectrophotometric technique,14 a sodium citrate 3.2% tube used to collect blood samples for the hemostasis analysis FIB, PT, and INR that were assessed by the coagulometric method,15 and finally, a lithium heparin tube used for creatinine analysis that was determined by the Jaffe’s reaction.16\n\nSample size\n\nThe sample size was assessed according to the following formula Kang et al.17 N = (Zα/2) 2 s2/d2, where “s” is the standard deviation (SD = 2300.000), and “d” is the accuracy of estimate or how close it is to the true mean (d = 900.40). Given the pioneering nature of this study, the above two data were collected from a previous work including women suffering from abnormal uterine bleeding-menometrorrhagia, conducted by Qaraaty et al.,18 where the mean number of bleeding days was 10.6 ± 2.7 and 8.2 ± 1.9, respectively, before and after the consumption of myrtle syrup. “Zα/2” is the normal deviate for a two-tailed alternative hypothesis at a level of significance (Zα/2 equal to 1.44 at an error rate of 0.20%). The assessed sample size as N = (1.44)2 2,300.00 / (900.40)2 gives a sample of 14 women suffering from abnormal uterine bleeding-menometrorrhagia. Assumption of 40% for non-attendance during the second or the third session gives a revised sample of 24 women suffering from abnormal uterine bleeding-menometrorrhagia (24 = 14/ (1.0−0.40)).\n\nStatistical analysis\n\nData entry and analysis were performed using SPSS software version 10 to test for normality, distribution of the studied variables was examined in reference to Shaprio-Wilk test. The significance level was fixed at p<0.05. Descriptive statistics were used to examine the characteristics of the studied population (means, standard deviation). Comparison of the biological parameters and scores of PBAC between baseline and the end of treatment was performed using paired t-test when variables were normally distributed and Wilcoxon signed ranks test, as a non-parametric test, when variables were not normally distributed.\n\n\nResults\n\nA total of 24 women with abnormal uterine bleeding-menometrorrhagia were involved in this study. During the course of the study, the data of 11 participants were excluded from the final statistical analysis. Indeed, the study was interrupted by the Covid-19 pandemic during which five participants withdrew from the trial because they took other different species of plants in order to prevent or treat Covid-19. Among the 11 excluded participants, three underwent surgeries for other reasons and the remaining three withdrew for personal reasons. Therefore, 13 participants completed the study (Figure 1).\n\nBaseline characteristics, responses, and side effects of herbal tea infusion consumption on 13 Tunisian women with menometrorrhagia that are candidates for hysterectomy are shown in (Table 1). Participants’ ages ranged between 32 and 53 years. Among them, five were single. A total of nine participants were suffering from clot excretion. The infusion of mixed Pennyroyal and Southernwood extracts was effective in 10 participants; normal and less heavy bleeding flow and disappearance of blood clotting were noted. However, positive response means a decrease in bleeding intensity and duration, and recovery of the menstrual cycle regularity. Negative response corresponds to negative feedback reflecting patient unsatisfaction related to the absence of improvement in bleeding intensity and/or duration, and/or persistence of menstrual cycle irregularity. Negative feedback was noted in three participants after being treated for just two menstrual cycles. Persistence and an increase in bleeding was observed during the study, and they underwent hysterectomy. Strong uterine contraction, as a side effect, concomitant with bleeding cessation after three days of tea infusion consumption was reported by four participants. A total of two participants reported having a headache after using the herbal tea infusion in the first day. No other adverse effects or allergic reactions were observed.\n\n* Responses to the treatment of thirteen Tunisian women with menometrorrhagia candidate for hysterectomies treated with herbal infusion of 5 g mixed southernwood and pennyroyal plants 3 times a day, every 4h after the first administration by oral rout started from the onset of menstruation during 3.\n\nResults of the mean and standard deviation of the number of menstrual bleeding days before and after herbal treatment revealed a significant decline from 11.50 (±3.17) at baseline to 7.60 (±2.11) (p=0.01) to become close to the normal level (Table 2).\n\n* Data are expressed as median value.\n\n** Wilcoxon Signed Ranks Test, P ≤ 0.05.\n\nResults of the mean PBAC scores of the intensity of bleeding revealed a significant decrease from 219.30 (±57.03) at baseline to 79.60 (±31.09) (P=0.05) (Table 2).\n\nAll the participants reported regularization in the menstrual cycle, and improvement in their quality of life.\n\nAt the end of the study, herbal tea infusion consumption was found to help 10 participants out of the 13 women avoid the surgical procedure.\n\nResults of the hematologic laboratory evaluation to control anemia before and after herbal treatment are detailed in (Table 2). For each parameter, the mean and the standard deviation were defined. An increase in the mean hemoglobin value (Hgb), from 9.740 (±3.17) g/dl in baseline to 11.59 (±1.6) g/dl after 90 days of treatment was noted. However, the parameters did not achieve a statistically significant level.\n\nNo significant differences in PT and INR were observed before and after herbal treatment. They were at the normal level.\n\nThe serum creatinine levels at baseline and after three months were in the normal range but the difference was not statistically significant (p>0.05) (Table 3). The tea infusion consumed was well-tolerated and participants did not report any serious adverse events.\n\n\nDiscussion\n\nIn the present preliminary study, the effect of mixed herbal Pennyroyal and Southernwood tea infusion consumption in a small sample size of women with abnormal uterine bleeding-menometrorrhagia that are candidates for hysterectomy was investigated. Used according to the Tunisian traditional remedies, these two herbs are considered as menstrual regulators and are known to stimulate uterus muscles during painful or strong menstruation.11 Our results revealed that mixed herbal Pennyroyal and Southernwood tea infusion consumption was effective in regulating menstrual problems in 10 women. This result is consistent with that of Firdose et al.12 showing that Pennyroyal and other species are effective in reducing the number of days of menstrual flow and in normalizing the cycle in patients with infrequent periods of more than 35 days or with scanty flow, both in amount and duration.12 This positive correlation of the tea infusion of both herbs may be due to their richness in polyphenols and flavonoids, as found in our results.25 Several studies have demonstrated that polyphenols and flavonoids have an effect on hormone regulation in premenopausal women.19 A study conducted by Taamalli et al.20 revealed that gallocatechin is as a major compound in Pennyroyal from the north-west of Tunisia. Gallocatechin, as a phenolic compound, is a flavan-3-ol.20 According to a study performed by Ko et al.,21 this compound has an osteoblastic activity. It is responsible for synthesizing dense cross-linked collagen and proteins.21 This activity may be related to the side effect mentioned in the results. This ascertainment is supported by the findings of Alekel et al.,22 showing that bone mineral content increased by 10.1% in 40 postmenopausal women receiving Isoflavone extract.22 In their study, Baiceanu et al.23 showed that sinapic acid is a major active polyphenols compound in Southernwood.23 The most interesting effects of sinapic acid are its capacity to influence steroid hormone metabolism and its anti-inflammatory properties.24 The results of this study were similar to the results of Qaraaty et al.18 in the management of abnormal uterine bleeding-menometrorrhagia by myrtle fruit syrup.\n\nThis pilot study presents several limitations. First, it seems that there is a lack of information about the chemical composition of the aqueous extract of these two plants. Therefore, this study needs to be completed to identify the major active components of the two plants. Secondly, our study involved a small sample size of participants due to the inclusion criteria and the limited period of time of the study. Thirdly, investigation of the effect of herbal tea infusion would be strengthened if a placebo group was involved.\n\n\nConclusion\n\nThrough this pilot study, we tried to explore a new approach to treat menometrorrhagia in women candidates for hysterectomy, based on tea infusion consumption of a mixture of Pennyroyal and Southernwood extracts. The study demonstrated that consumption of this tea infusion during three consecutive menstrual cycles helped 10 out of the 13 participants avoid the surgical procedure and improve their quality of life with no major side effects. However, larger clinical trials involving placebo groups, variable doses, and extended treatment periods are required to investigate the effect of Pennyroyal and Southernwood herbal tea infusion on abnormal uterine bleeding.\n\n\nData availability\n\nZenodo: ‘Therapeutic effect of herbal infusion on Abnormal Uterine Bleeding Extended data’, https://doi.org/10.5281/zenodo.6821462.25\n\nThis project contains the following underlying data:\n\n• data update version.xlsx (study subjects results (baseline and after three months))\n\n• method of herbs powder preparation.pdf (the method used by subjects to prepare the herbal tea infusion)\n\n• Pictorial Blood Assessment Chart.pdf (method used to assess menstrual blood lose in clinical trials)\n\n• polyphenols and flavnoids content data.xlsx (data of total polyphenols and flavonoids content in the aerial parts (leaves and stems) of Tunisian Pennyroyal and Southernwood extracted by methanol solvent))\n\n• Study protocol.pdf (outlining the study design and describing the objectives and methodology)\n\n• Total polyphenol and flavonoïds compounds contents in the aerial parts of Tunisian Mentha Pulegium.pdf (the total polyphenol and flavonoids compounds contents in the aerial parts of Mentha pulegium (pennyroyal) and artemisia abrotanum (southernwood))\n\n• trendstatement_trend_checklist (1).pdf (Guide standardized reporting non randomized controlled trials)\n\n\nReporting guidelines\n\nZenodo: CONSORT checklist and flow chart for ‘Therapeutic effect of herbal infusion on Abnormal Uterine Bleeding: consort flowchart and checklist’: https://doi.org/10.5281/zenodo.6881765.26\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgments\n\nThe authors would like to express their sincere gratitude to Mr Samir Boukattaya for proof reading this work.\n\n\nReferences\n\nFathima A, Sultana A: Clinical efficacy of a Unani formulation ‘Safoof Habis’ in menorrhagia: A randomized controlled trial. Eur. J.Integr. Med. 2012; 4(3): 315–e322.\n\nSperoff L, Glass R, Kase N: Clinical gynecology endocrinology and infertility. 8th ed.Philadelphia. USA:2011.\n\nBereak, Break SJ: Novaks Gynecology. fifteenth ed.Philadelphia USA:2012.\n\nDonnez J: Menometrorrhagia during the premenopause: an overview. Gynecol. Endocrinol. 2012; 27: 1114–1119. Publisher Full Text\n\nPinkerton JV: Pharmacological therapy for abnormal uterine bleeding. Menopause. 2011; 18: 459–467. Publisher Full Text\n\nBone K, Mills S: Principles and practice of phytotherapy: Modern Herbal Medicine. 2nd ed.Churchill Livingstone:Elsevier;2013.\n\nIstre O, Qvigstad E: Current treatment options for abnormal uterine bleeding: an evidence-based approach. Best, Pract. Res.Clin. Obstet. Gynecol. 2007; 21: 905–913. PubMed Abstract | Publisher Full Text\n\nProtheroe J: Modern management of menorrhagia. J. Fam Plan.Reprod. Health Care. 2004; 30: 118–122. PubMed Abstract | Publisher Full Text\n\nJazani N, Ghasemnejad-Berenji H, Sadegpoor S: Antibacterial effects of Iranian Mentha pulegium essential oil on isolates of Klebsiella sp. Pakistan. J. Biol. Sci. 2009; 12: 183–185. Publisher Full Text\n\nKowalski R, Wawrzykowski J, Zawiślak G: Analysis of essential oils and extracts from Artemisia abrotanum L. and Artemisia dracunculus L. Herba Pol. 2007; 53: 246–254.\n\nBoukef MK: Les Plantes dans la Médecine Traditionnelle Tunisienne. Médecine Traditionnelle et Pharmacopée. Agence de Coopération Culturelle et Technique;1986.\n\nFirdose KF, Begum W, Shameem I, et al.: Clinical evaluation of Qillat tams and its Management with Unani formulation. Int. Res. J. Medical Sci. 2013; 1: 1–8.Reference SourceReference Source\n\nLi W, Zhou CH, Lu QL: Effects of Chinese materia medica in activating blood and stimulating menstrual flow on the endocrine function of ovary-uterus and its mechanisms. Chung Kuo. Chung Hsi I Chieh Ho Tsa Chih. 1992; 516: 734168–734624. Publisher Full Text\n\nSudnitsyna JS, Skverchinskaya EA, Zubina IM, et al.: Alterations in Erythrocyte Deformability and Functions Associated with End-Stage Renal Disease. Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology. 2022; 16: 79–90. Publisher Full Text\n\nDati F, Barthels M, Conard J, et al.: Multicenter evaluation of a chromogenic substrate method for photometric determination of Prothrombin Time. J. Thromb. Haemost. 1987; 58(03): 856–865. Publisher Full Text\n\nSlot C: Plasma Creatinine Determination A New and Specific Jaffe Reaction Method. Scand. J. Clin. Lab. 1965; 17(17): 381–387. PubMed Abstract | Publisher Full Text\n\nKang M, Ragan BG, Park JH: Issues in outcomes research: An overview of randomization techniques for clinical trials. J. Athl. Train. 2008; 43(2): 215–221. PubMed Abstract | Publisher Full Text\n\nQaraaty M, Kamali SH, Dabaghian FH, et al.: Effect of myrtle fruit syrup on abnormal uterine bleeding: A randomized double-blind, placebo-controlled pilot study. DARU J. Pharm. Sci. 2014; 22(1). PubMed Abstract | Publisher Full Text\n\nWilliamson G, Manach C: Bioavailability and bio-efficacy of polyphenols in humans. II. review of 93 intervention studies. A.J.C.N. 2005; 81(1): 243S–255S. Publisher Full Text\n\nTaamalli A, Arráez-Román DA, Abaza L, et al.: LC-MS-based metabolite profiling of methanolic extracts from the medicinal and Aromatic Speciesmentha pulegiumandoriganum Majorana. Phytochem Anal. 2015; 26(5): 320–330. PubMed Abstract | Publisher Full Text\n\nKo CH, Lau KM, Choy WY, et al.: Effects of tea catechins, epigallocatechin, Gallocatechin, and Gallocatechin gallate, on Bone metabolism. J. Agric. Food Chem. 2009; 57: 7293–7297. Publisher Full Text\n\nAlekel DL, Germain AS, Peterson CT, et al.: Isoflavone-rich soy protein isolate attenuates bone loss in the lumbar spine of perimenopausal women. A.J.C.N. 2000; 72: 844–852. Publisher Full Text\n\nBaiceanu E, Vlase L, Baiceanu A, et al.: New polyphenols identified in Artemisiae Abrotani Herba extract. Molecules. 2015; 20: 11063–11075. PubMed Abstract | Publisher Full Text\n\nVon. Danwitz A, Schulz C: Effects of dietary rapeseed glucosinolates, sinapic acid and phytic acid on feed intake, growth performance and Fish Health in Turbot (Psetta maxima L). Aquac. Res. 2020; 516: 734624–734624. Publisher Full Text\n\nSelmi M, Lassoued L, Bannour B, et al.: Therapeutic effect of herbal infusion on Abnormal Uterine Bleeding Extended data [Data set]. Zenodo. 2022. Publisher Full Text\n\nSelmi M, Lassoued L, Bannour B, et al.: Therapeutic effect of herbal infusion on Abnormal Uterine Bleeding: consort flowchart and checklist. Zenodo. 2022. Publisher Full Text"
}
|
[
{
"id": "193046",
"date": "15 Aug 2023",
"name": "Abhishek Tiwari",
"expertise": [
"Reviewer Expertise Cancer"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have reported the therapeutic effect of herbal infusion on abnormal uterine bleeding: interventional non-randomized pilot study. The text in Figure 1 is not clear The research is at very preliminary stage.\nProvide more comprehensive details about the selection criteria for participants, including any specific characteristics or conditions they had.\nDescribe the rationale behind choosing Mentha pulegium L and Artemisia abrotanum L for the herbal mixture, considering their potential benefits and historical use.\nElaborate on any potential safety considerations related to consuming the herbal infusion, including any known contraindications or side effects.\nClearly state how the tea infusion was prepared, ensuring that all steps are well-documented for reproducibility.\nSpecify the process for measuring bleeding days and how the mean number of bleeding days was calculated.\nProvide more context when discussing the results, explaining the clinical significance of the observed reductions in bleeding days and improvements in quality of life. Why are these changes important for the participants' overall well-being?\nDiscuss potential directions for future research based on these findings. Are there plans for larger trials, mechanisms of action exploration, or investigating long-term effects?\nAlongside the ClinicalTrials.gov registration identifier, provide additional information such as the principal investigator.\nProofread the manuscript carefully to correct grammatical mistakes and ensure the text is clear and coherent.\nReference related studies or prior research that support the rationale for using the specific herbal mixture and the potential effects observed.\nSample size chosen is very small. Among 13 women, 6 reported side effects, few of them are serious.\nGrammatical mistakes are noticed, kindly check.\nNo information regarding phytoconstituent as well as characterization of herbal infusion is missing, which is absolutely required. Other iron supplement has been allowed, justify it.\nAll in all, the manuscript needs extensive modification.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "198664",
"date": "25 Sep 2023",
"name": "Malarvili Selvaraja",
"expertise": [
"Reviewer Expertise Immunopharmacology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study overall is good. Here are some limitations that authors should take note of:\n\nThe problem statement is not well explained. Maybe the statistics for the prevalence or incidence of this condition should be included specifically in Tunisia.\n\nThe rationale why this plant has been selected? How widely it has been used? Where is the plant widely available? Are any preliminary studies conducted for the plants in vitro or in vivo models? What is the effect on menometrorrhagia? Is any toxicity information available?\n\nNot much information is available on the Figure 1. More information is required here in terms of patients' conditions if they have any other complications. These will be points to be included in the selection criteria.\n\nHow the bleeding days were calculated and differentiated from one to another individual? An individual who is active in physical activities and one who is least active will have different bleeding patterns and times, how this be controlled/assessed?\n\nWhat kind of improvement was observed in terms of quality of life?\n\nA sample size of 13 is too small to conclude on the effectiveness of the mixed plants.\n\nAs mentioned in the conclusion it is important to include a placebo group in non-randomized control trials.\n\nThe discussion is very brief.\n\nMost references are more than 5 years old. Try to include more on the latest publications to cite.\n\nProofreading required.\n\nGrammatical errors to be corrected.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1116
|
https://f1000research.com/articles/9-1228/v1
|
12 Oct 20
|
{
"type": "Research Article",
"title": "Identification of selected primary bloodstream infection pathogens in patients attending Kisii level five and Homa Bay county hospitals",
"authors": [
"Ronald Kirera",
"Erick Kipkirui",
"Margaret Koech",
"Abigael Ombogo",
"Janet Ndonye",
"Mary Kirui",
"Cliff Odhiambo Philip",
"Nancy Kipkemoi",
"Elizabeth Odundo",
"Alexander F. Flynn",
"Christine Hulseberg",
"Judd Walson",
"Joseph Nganga",
"Daniel Kariuki",
"Erick Kipkirui",
"Margaret Koech",
"Abigael Ombogo",
"Janet Ndonye",
"Mary Kirui",
"Cliff Odhiambo Philip",
"Nancy Kipkemoi",
"Elizabeth Odundo",
"Alexander F. Flynn",
"Christine Hulseberg",
"Judd Walson",
"Joseph Nganga",
"Daniel Kariuki"
],
"abstract": "Background: Bloodstream infection (BSI) contributes to a substantial proportion of mortality in sub-Saharan Africa and is marked by the presence of bacterial and/or fungal microorganisms in the blood. Because BSI can be life threatening, it requires a timely, reliable and accurate diagnosis. This study retrospectively analyzed data of identified BSI pathogens and compared the performance of the different diagnostic technologies used in terms of accuracy, sensitivity, turnaround time (TAT) and cost. Methods: Currently, culture followed by analytical profile index biochemical strips (API), (BioMerieux) are used as the conventional standard diagnostics in Kenyan public hospitals and labs. We compared the results of this standard to that of the BioFire FilmArray (FA) (BioFire Diagnostics) and MicroScan WalkAway-40 plus System (MS) (Beckman Coulter) used in diagnosis of BSI. The FA technology was able to identify 150/152 bacterial and yeast isolates with an overall accuracy of 99.04% (95% CI: 96.59-99.88%), sensitivity of 98.68% (95% CI: 95.33-99.84%), mean TAT of 8 hours 40 minutes per eight samples and running cost per sample of USD 140.11. The MS identified 150/152 isolates with an overall accuracy of 98.56% (95% CI: 95.86-99.70%), sensitivity of 98.68% (95% CI: 95.30-99.84%), mean TAT per sample was 42 hours and running cost per sample of USD 28.05. API detected 150/152 isolates, with an overall accuracy of 99.04% (95% CI: 96.59-99.88%), sensitivity of 98.68% (95% CI: 95.33-99.84%) and the mean TAT per sample was 53 and 103 hours for bacterial and yeast samples, respectively, with a running cost per sample of USD 28.05.Conclusions: The findings in this paper suggest that the FA and MS platforms should be able to perform adequately in Kenya referral hospitals and medical clinics as a rapid diagnostic tool.",
"keywords": [
"Bloodstream infection",
"FilmArray",
"MicroScan",
"Resistance genes"
],
"content": "Introduction\n\nBacteremia accounts for a large number of hospital admissions and results in high morbidity and mortality1. In sub-Saharan Africa, there is limited information on bloodstream infections (BSI)2,3, which can be partly attributed to the paucity of studies conducted in developing countries lacking high throughput BSI diagnostic technology. The availability of such equipment would facilitate widespread BSI detection in patients, help close this critical knowledge gap, and potentially save lives4,5.\n\nBlood culture and analytical profile index (API, BioMerieux) strip analysis has been the conventional standard for bacteremia diagnosis in many hospitals throughout the world, including Kenya6,7. Using this technique has been a challenge because it is a labor intensive process that requires experienced laboratory technologists and has a reportedly lower level of accuracy than other techniques such as conventional cultures2–6. To address this issue, diagnostic platforms such as the BioFire FilmArray (FA) and MicroScan WalkAway 40 plus (MS) are now widely used in Europe and the United States2–8.\n\nThe FA is a sophisticated closed-automated polymerase chain reaction (PCR) system that utilizes specific commercial pouches such as FA blood culture ID panel to identify BSI causative agents and antimicrobial resistance markers within 1 hour of a positive blood culture9. This platform can identify 24 causative agents of BSI (eight gram-positives, 11 gram-negatives, and give yeast species) and three antimicrobial resistance genes: mecA for methicillin, vanA/B for vancomycin and blaKPC for carbapenem by nested multiplex PCR5–8. The MS system can provide identification of bacteria within 16 to 20 hours, phenotypic antimicrobial profile (AST) and extended-spectrum beta lactamase (ESBL) using negative combo panel type 66 for gram negatives and positive combo panel type 39 for gram positives10,11 and identification of yeast within 4 hours using a rapid yeast panel (Beckman Coulter, United States).\n\nThe use of conventional methods requires considerably long turnaround time (TAT) from 12–72 hours. In potentially life-threatening cases of BSI, the microbial cause of infection must be identified as quickly as possible to ensure proper treatment and management of the disease. The newly employed methods FA® and MS® have never been used before in Kisii and Homa Bay hospitals.\n\nIn this paper, we compared the accuracy, sensitivity, turnaround time (TAT) and cost of new technologies against the conventional API strip technique based on past data from blood culture isolates. Based on our findings, we will identify whether these automated platforms would be capable of providing a rapid diagnosis of BSI in Kenya hospitals.\n\n\nMethods\n\nStored blood culture samples received from Kisii Teaching and Referral Hospital and Homa Bay County Referral hospital were analyzed at Microbiology Hub Kericho. These collection sites were selected because they do not have the capacity to identify BSI pathogens to the species level. Kisii Teaching and Referral Hospital is a public hospital located in Kitutu Chache Constituency, Kisii County. It is located in Kisii town Central Business, District Hospital Road, and serves a population of over 1 million. Homa Bay County Referral Hospital is a government health center located in Homa Bay Township Sub-location, Homa-Bay Location, Asego Division, and Rangwe Constituency in Homa Bay County. It has a population of over 1 million. The common diseases in these areas are malaria, upper respiratory tract infections, typhoid, pneumonia, tuberculosis and HIV12.\n\nThis study analyzed BSI isolates data tested using FA, MS technologies and culture followed by API strip analysis. A total of 152 isolates data (122 blood culture isolates and 30 control isolates were analyzed. The study focused on the identification of BSI, accuracy, sensitivity, TAT as well as the cost of the items. Isolate analysis was performed at the Microbiology Hub Kericho (MHK), a United States Army Medical Research Directorate-Africa (USAMRD-A) facility working in collaboration with Kenya Medical Research Institute (KEMRI). The MHK performs surveillance and clinical research diagnosis of enteric pathogens causing acute diarrhea across Kenya in addition to screening blood culture samples for BSI agents.\n\nFormula n = Z2 × P (1-P)/d2, n = Sample size, Prevalence (p) = 10.4%\n\n95% confidence interval (z) = 1.96\n\nPrecision d2 = 0.05\n\nn = 1.962 × 0.104(1-0.104)/0.052\n\nCalculated sample size (n) = 143 isolates.\n\nThe prevalence was taken from the study by Maze et al. (2018)13 “The epidemiology of febrile illness in sub-Saharan Africa: implications for diagnosis and management”. The prevalence rate is based on East Africa data which is part of Kenya, the ranges in prevalence is between 10-20% in Kenya.\n\nBlood samples were collected into BACTEC Plus Aerobic/F, Peds Plus Aerobic/F, Anaerobic/F and Lytic/10 Anaerobic/F vials (BD, United States) and incubated using the BacTec 9050 instrument (BD, United States) for 5 days to account for slow-growing pathogens. A positive signal was indicated by an increased fluorescence caused by the carbon dioxide released by an organism reacting with the vial dye. Positive blood culture samples were removed and processed to identify the organism. Samples were processed directly using the FA without need for prior subculture. As for the MS and the API strip method, samples were first gram-stained and sub-cultured on MacConkey agar, Blood agar plate, Sabouraud Dextrose agar, Hektoen enteric agar and Tryptic soy agar (Becton Dickson).\n\nFor identification by FA, samples were tested per the manufacturer’s instructions. First, the blood culture identification panel was inserted in the loading chamber, then hydration solution was added to the sample and then the panel was placed into the FA. The results were checked after 1 hour.\n\nPure colonies were used for the MS identification procedure. An inoculum of 0.5 McFarland standard equivalents was prepared by selecting 1 to 3 discrete colonies from pure culture on MacConkey agar (MAC) or blood agar plate (BAP) or Sabouraud dextrose agar (SDA) and suspended in 3 ml of the MS inoculum water (Beckman Coulter). From the solution, 100 μl was transferred and mixed with 25 ml of the MS inoculum water with pluronic and then poured into the sterile inoculator D set tray. The solution (140 μl) was transferred into a gram-negative or a gram-positive panel (Beckman Coulter), and then loaded into the MS and results checked after 18–24 hours and 4 hours for yeast organisms.\n\nFor manual biochemical analysis method, the API strips (BioMerieux, United States) and media (MacConkey agar, blood agar, Hektoen enteric agar, triple sugar irons and Sabouraud dextrose agar plates) were brought to room temperature. After this, 5 mL of deionized water was added to the tray along with the strips. The API ampules or equivalent suspension medium was inoculated with a single colony. The inoculation of wells for gram negative, gram positive and yeast organisms was done as per manufacturer’s instruction. The incubation box was closed and incubated at 36°C for 18–24 hours for bacterial while for the yeast it was incubated at 29°C for 48 to 72 hours. A positive signal was indicated by a colorimetric change that was interpreted using the API guidelines.\n\nOverall accuracy was calculated as the (number of individual isolate identified using evaluated technique) / (total number of same isolates identified) x 100%), sensitivity values and the 95% confidence intervals (CI) for both of these metrics were analyzed using the Graphpad Prism 8.2.1 software. The TAT was defined as the time taken from sample preparation to identification14. The average cost per samples included consumable reagents and disposable supplies and was defined as the total cost of each assay per sample run.\n\nThe indeterminate results were resolved by comparing the two techniques FA and MS, where the two techniques agreed was taken as a true positive, the discordant results were repeated using the API technique (gold standard).\n\nEthical review for this work was obtained from the Kenya Medical Research Institute Scientific and Ethical review Unit-Scientific Steering Committee (KEMRI SERU-SSC) #3686 and Walter Reed Army Institute Research (WRAIR) Institutional Review Boards (IRBs) #2513. Consent was not sought for this study since it was determined that there was no interaction with human subjects.\n\n\nResults\n\nThe overall accuracy and sensitivity of each platform is shown in Table 1. For the FA, the calculated accuracy was 99.04% (95% CI, 96.59-99.88%). Out of the total 152 isolates identified, FA technology was able to correctly identify 150 isolates resulting in a calculated sensitivity of 98.68% (95% CI: 95.33-99.84%). Similar to the accuracy computation for the FA instrument, the accuracy of the MS instrument was determined based on the number of isolates correctly identified by the MS out of the total number of isolates correctly identified. This yielded an overall accuracy of 98.56% (95% CI: 95.86-99.70%). The MS technology identified 149 true isolates, which produced a calculated sensitivity of 98.68% (95% CI: 95.30-99.84%). The API strip analysis identified 150 isolates with an accuracy of 99.04% (95% CI: 96.59-99.88%) with no significant difference in overall accuracy to the FA and MS. The sensitivity of API method was 98.68% (95% CI: 95.33-99.84%).\n\nThe accuracy and sensitivity for the evaluated three techniques is shown above. The bold values listed are the calculated accuracy or sensitivity means for each method. Shown in parentheses are the 95% CI values.\n\nFA, FilmArray; MS, MicroScan; API, Analytical Profile Index.\n\nNext, we decided to breakdown which microbes that each platform correctly identified (Table 2). The FA and API were able to identify 150/152 BSI pathogens. Interestingly, the FA platform was able to identify 4/4 of Enterobacter cloacae isolates as opposed to API technique, which detected only 2/4. However, the FA only recognized Staphylococcus at the genus level. In addition, the system could not characterize Streptococcus anginosus and Streptococcus bovis at the species level as these bacteria were not in its database, and therefore, were identified as Streptococcus spp. The FA identified Salmonella isolates as Enterobactericiae while the API and the MS were able to identify these isolates as Salmonella spp. The MS was able to accurately identify the presence of all other isolates similar to the API method except with Staphylococcus spp. (93.75%) and Acinetobacter baumanii (85.71%), while the API method was 100% accurate for both. In addition, the MS correctly identified all other Streptococcus isolates besides S. pneumoniae, whereas the FA and API standard had accuracies of 83.3% and 85.7%, respectively. Results of identification using each technique are available (see Underlying data15).\n\nThe accuracy broken down by microorganism was calculated for each platform. The total number of isolates identified followed by accuracy percentage of FA, MS and API is listed above. For the FA, the “n/a” indicates that the isolates could not be identified beyond the family level (Enterobactericeae). Those rows with a dash mark (-) indicate those identified at specific genus level (Salmonella) and not group level (Enterobactericeae).\n\nFA-FilmArray, MS- MicroScan, API-Analytical Profile Index.\n\nWe limited the running time for each platform to the length of a normal working day (8 hours) (Table 3). Under this condition, the FA could only run eight samples. We therefore established this limit to ensure an equal number of samples per run across all the techniques. The turnaround time (TAT) for the FA per sample run was 1 hour 6 minutes, with an average of 5 minutes processing time and 1 hour identification and results analysis. The average time for FA was 8 hours 40 minutes and significantly less (p < 0.0001) compared to the MS and API. The MS had a mean TAT of 42 hours per sample run, with 27 hours processing time and the mean TAT was significantly more (p < 0.0001) compared to the FA. Breaking this down, the culture process and incubation required 24 hours, which could be more depending on the bacteria and purity of culture. The API method had a mean TAT of 53 hours per sample run for bacterial isolates while for yeast was 103 Hrs. The mean TAT was significantly more (p < 0.0001) compared to the FA. Sample processing data are available for each technique (see Underlying data15).\n\nFor each platform being analyzed, turnaround times were broken into processing and ID analysis. The time shown for each of these categories is the mean of multiple runs, which had eight samples each. The processing column shows the time taken to prepare the samples for culture and then selection of isolates for identification. Of note, the FA did not require gram staining or culture and selection of an isolate from a blood culture. Identification analysis was based on the time each platform required to complete their respective protocols. The p-value showed the significance of the mean difference among the techniques.\n\np-value <0.0001 for mean TAT: FA vs. MS/API, MS vs. FA, and API vs. MS\n\nFA-FilmArray, MS-MicroScan, API-Analytical Profile Index, ID-Identification.\n\nThe total average cost of processing one sample using the FA technique was 140.11 USD (Table 4). The total average cost of running one isolate per sample using the MS instrument was 38.75 USD while API technique was 29.17 USD. Extra equipment required but not included were biosafety cabinet, incubators, autoclaves, hot plates, conical flasks, stirrers and spatulas as well as the annual preventive maintenance for this equipment. Only the costs of the consumable items needed for each method were evaluated. As expected, the cost of the items used for the API technique was lower than for those used by the MS and FA.\n\nThe average cost of running sample was broken down into biochemical reagents/media used. Reagents not used by a platform as designated N/A (non-applicable). Not included in the cost breakdown were the equipment aforementioned above. The periodic maintenance required for the automated platforms was also not included.\n\nFA-FilmArray, MS-MicroScan, API-Analytical Profile Index.\n\n\nDiscussion\n\nIn resource-limited settings, the use of conventional methods in diagnosis of bacteremia has been a challenge to most public health facilities leading to misclassification of the diagnosis of BSI8,16. The automated methods FA and MS proved to be more efficient, reliable and faster in the identification of a wide range of microorganisms than API. The technologies are reliable with a short turnaround time. These positive factors outweigh the use of API strips for microbial identification, which is considered the conventional standard in Kenya for diagnosis of BSI. In comparison to the FA and MS, the API method was more labor intensive. Furthermore, fastidious bacteria might not be identified if they fail to grow on culture media but can be identified directly from blood culture using FA.\n\nOverall, the sensitivity of FA (98.68%), MS (98.68%) and API (98.68%) were identical, with an overall accuracy of 99.04%. Moreover, the sensitivity of FA demonstrated in this study was similar to the sensitivity observed in a previous study carried out in Kazulu-Natal17. The differences in sensitivity came in inability of FA and MS to agree in terms of genus and species individual identification of BSI pathogens.\n\nThe higher accuracy by FA in individual identification of BSI pathogens could be because it is a molecular-based platform. The FA identified Enterobacter cloacae with a higher accuracy than the other two methods, which could not identify the two isolates. This is probably because the FA identified two isolates as Enterobacter cloacae complex, which neither of the other methods could identify. However, the accuracy of FA was limited when identifying Streptococcus spp. where the accuracy was 83.3%, the organisms in question (Streptococcus anginosus and Streptococcus bovis) are not available in the FA database and are not common causes of BSI2. We believe that these organisms were actually skin contaminants. Still, the overall accuracy demonstrated by the FA is in line with previous paper evaluating the diagnostic capabilities of the system18.\n\nThe MS was able to accurately identify the presence of BSI bacteria with similar accuracy to the API method, except for the identification of Staphylococcus spp. where the accuracy was 93.75% and Acinetobacter baumanii with an accuracy of 85.71% for MS. The MS surpassed the API strip method in the identification of Streptococcus spp. where the accuracy was (100%) compared to API method (85.71%). These issues with MS in identifying Staphylococcus spp. and Acinetobacter baumanii is in line with previous studies, where the MS misidentified Acinetobacter baumanii19,20. For this study, the misidentified Streptococcus spp. were actually Staphylococcus spp.\n\nIn past studies, the API strip analysis had a lower accuracy identifying microorganisms such as Citrobacter species, Escherichia coli, Pseudomonas aeruginosa and Enterobacter species than automated platforms21. Interestingly, this did not occur with this study, and could partly be because the lab technician performing the assay had extensive clinical microbiology experience. Microbiology labs typically address this lower accuracy by adding biochemical tests such as oxidase and catalase to increase accuracy. We, however, did not incorporate these assays into the API strip analysis.\n\nThe mean TAT difference per run of eight samples among the technologies was significant at p<0.0001. The FA technology required 8 hours 48 minutes per eight samples compared to the MS, which required 42 hours and the API method, which required 53 hours for bacterial species and 103 hours for yeast. The major factor contributing this difference was time needed to prepare the isolates, which require gram-staining then culturing for 24/48 hours prior to identification by MS or API21. It should be noted that the MS has higher throughput and can process 40 or more panels in one run. In addition, the API method can test more samples and is only dependent on availability of incubators, reagents and the experience of the technician. The shorter TAT for FA is a very attractive feature for under-developed areas with poor infrastructure and inaccessible areas where field clinical/research activities are undertaken and do not necessarily require a high-throughput machine. Though not a metric evaluated in this study, the FA requires considerably less training and skill compared to the other methods, which help to balance its throughput limitations.\n\nThe average cost of testing one sample using FA was noticeably higher than the cost of the MS and API methods. This was expected as the FA test kits cost more than the MS panels and the API reagents. While the FA is more expensive, it is able to identify co-infection in one sample, which would require separate runs for the MS and API5.\n\nOf note, the FA is able to identify resistant genes such as methicillin resistance common with Staphylococcus aureus, vancomycin resistance common with Enterococcus spp. and carbapenem resistance common with Klebsiella pneumoniae and other Enterobactericiae8. While the MS has no capability to identify antimicrobial resistant genes commonly associated with BSI, it is able to perform phenotypic drug sensitivity. In fact, the MS has a wider range of antimicrobial testing capabilities with regularly updated software database in line with CLSI guidelines.\n\n\nConclusion\n\nWhile the evaluated methods were similar in accuracy and sensitivity, there were appreciable differences in TAT and cost. The FA cost more, but had a quicker TAT compared to the MS and API methods. This is a significant concern when using the machine in areas with limited financial resources. However, the FA requires minimal training prior to use and is able to identify co-infections. Furthermore, the FA requires a small space, and therefore, the cost of the FA panels should not be considered a major drawback since early detection of BSI has shown to reduce medical costs, hospital stays, and help guide the clinicians on the best treatment approach5, which lower overall economic costs.\n\nThe FA and MS have not been evaluated at Kenya hospitals and further evaluation using a larger sample size is recommended. However, these preliminary results clearly suggest that both the FA and MS platforms are valuable tools in rapid identification of BSI. Each technology has its advantages and disadvantages, which must be considered. Still, implementation of either platform could result in reduction of hospital stays, lower cost, better patient management and more appropriate use of antibiotics by clinicians.\n\n\nData availability\n\nFigshare: IDENTI~1.DOC. https://doi.org/10.6084/m9.figshare.12948533.v415.\n\nThis project contains the following underlying data:\n\nIdentification of Selected Primary Bloodstream Infection Pathogens in Patients Attending Kisii Level Five and Homa Bay County Hospitals- FA.xlsx. (Data obtained using Film Array.)\n\nIdentification of Selected Primary Bloodstream Infection Pathogens in Patients Attending Kisii Level Five and Homa Bay County Hospitals-MS.xlsx. (Data obtained using Microscan.)\n\nIdentification of Selected Primary Bloodstream Infection Pathogens in Patients Attending Kisii Level Five and Homa Bay County Hospitals-Api.xlsx. (Data obtained using analytical profile index.)\n\nIdentification of Selected Primary Bloodstream Infection Pathogens in Patients Attending Kisii Level Five and Homa Bay County Hospitals-FA raw data.xlsx. (Pathogen count data obtained using Film Array.)\n\nIdentification of Selected Primary Bloodstream Infection Pathogens in Patients Attending Kisii Level Five and Homa Bay County Hospitals-MS raw data.xlsx. (Pathogen count data obtained using Microscan.)\n\nIdentification of Selected Primary Bloodstream Infection Pathogens in Patients Attending Kisii Level Five and Homa Bay County Hospitals-Api raw data.xlsx. (Pathogen count data obtained using analytical profile index.)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe acknowledge the role of United States Army Medical Research Directorate-Africa, Kenya, the Microbiology Hub – Kericho, and Kenya Medical Research Institute for facilitating this study. Ethics committees from both WRAIR and KEMRI-SERU played a critical role in ensuring that this study is feasible and meets the required standards and invaluable gratitude also goes to Walter Reed Project-Kericho Regulatory office, Michael Obonyo, Mary Leelgo and Judith Bosuben for unrelenting support in their guidance, our thanks also goes to Benson Singa for the support during regulatory process and Rukia Kibaya for continued review and guidance.\n\n\nAuthor contributions\n\nRonald Kirera was responsible for conceptualization, study design, data analysis, and drafting of the manuscript. Daniel Kariuki, Joseph Nganga, Judd L. Walson, Christine Hulseberg and Alexander Flynn contributed in the manuscript review. Elizabeth Odundo, Erick Kipkirui, Cliff Odhiambo, Nancy Kipkemoi, Abigael Ombogo, Janet Ndonye, Mary Kirui, and Margaret Koech contributed in data analysis and manuscript review.\n\n\nReferences\n\nDagnew M, Yismaw G, Gizachew M, et al.: Bacterial profile and antimicrobial susceptibility pattern in septicemia suspected patients attending Gondar University Hospital, Northwest Ethiopia. BMC Res Notes. 2013; 6(1): 283. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAltun O, Almuhayawi M, Ullberg M, et al.: Clinical evaluation of the Filmarray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J Clin Microbiol. 2013; 51(12): 4130–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAkoua-Koffi C, Tia H, Plo JK, et al.: Epidemiology of community-onset bloodstream infections in Bouaké, central Côte d’Ivoire. New Microbes New Infect. 2015; 7: 100–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nViscoli C: Bloodstream Infections: The peak of the iceberg. Virulence. 2016; 7(3): 248–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRay STJ, Drew RJ, Hardiman F, et al.: Rapid Identification of Microorganisms by FilmArray Blood Culture Identification Panel Improves Clinical Management in Children. Pediatr Infect Dis J. 2016; 35(5): e134–8. PubMed Abstract | Publisher Full Text\n\nBerkley JA, Lowe BS, Mwangi I, et al.: Bacteremia among Children Admitted to a Rural Hospital in Kenya. N Engl J Med. 2005; 352(1): 39–47. PubMed Abstract | Publisher Full Text\n\nPrakash KP, Arora V, Geethanjali PP: Bloodstream bacterial pathogens and their antibiotic resistance pattern in Dhahira region, Oman. Oman Med J. 2011; 26(4): 240–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlaschke AJ, Heyrend C, Byington CL, et al.: Rapid Identification of Pathogens from Positive Blood Cultures by Multiplex PCR using the FilmArray System. Diagn Microbiol Infect Dis. 2013; 74(4): 349–55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAltun O, Almuhayawi M, Ullberg M, et al.: Clinical evaluation of the Filmarray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J Clin Microbiol. 2013; 51(12): 4130–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSnyder JW, Munier GK, Johnson CL: Direct comparison of the BD phoenix system with the MicroScan WalkAway system for identification and antimicrobial susceptibility testing of Enterobacteriaceae and nonfermentative gram-negative organisms. J Clin Microbiol. 2008; 46(7): 2327–33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSt.-Germain GG, Beauchesne D: Evaluation of the MicroScan Rapid Yeast Identification panel. J Clin Microbiol. 1991; 29(10): 2296–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIntegrated FC, Plan D: COUNTY GOVERNMENT OF HOMA BAY ‘ A County of Choice ’ FIRST COUNTY INTEGRATED. 2017. Reference Source\n\nMaze MJ, Bassat Q, Feasey NA, et al.: The epidemiology of febrile illness in sub-Saharan Africa: implications for diagnosis and management. Clin Microbiol Infect. 2018; 24(8): 808–814. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPhilip CO, Koech M, Kipkemoi N, et al.: Evaluation of the performance of a multiplex reverse transcription polymerase chain reaction kit as a potential diagnostic and surveillance kit for rotavirus in Kenya. Trop Dis Travel Med Vaccines. 2019; 5: 12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKirera R, Kipkirui E, Kirui M, et al.: IDENTI~1.DOC. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.12948533.v4\n\nPradhan R, Shrestha U, Gautam SC, et al.: Bloodstream Infection among Children Presenting to a General Hospital Outpatient Clinic in Urban Nepal. PLoS One. 2012; 7(10): e47531. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFhooblall M, Nkwanyana F, Mlisana KP: Evaluation of the BioFire® FilmArray® blood culture identification panel on positive blood cultures in a regional hospital laboratory in KwaZulu-Natal. Afr J Lab Med. 2016; 5(1): 411. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalimnia H, Fairfax MR, Lephart PR, et al.: Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial. J Clin Microbiol. 2016; 54(3): 687–98. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJin WY, Jang SJ, Lee MJ, et al.: Evaluation of VITEK 2, MicroScan, and Phoenix for identification of clinical isolates and reference strains. Diagn Microbiol Infect Dis. 2011; 70(4): 442–7. PubMed Abstract | Publisher Full Text\n\nPatteet L, Goossens H, Ieven M: Validation of the MicroScan-96 for the species identification and methicillin susceptibility testing of clinical significant coagulase-negative staphylococci. Eur J Clin Microbiol Infect Dis. 2012; 31(5): 747–51. PubMed Abstract | Publisher Full Text\n\nO’Hara CM, Tenover FC, Miller JM: Parallel comparison of accuracy of API 20E, Vitek GNI MicroScan Walk/Away Rapid ID and Becton Dickinson Cobas Micro ID-E/NF for identification of members of the family Enterobacteriaceae and common gram-negative, non- glucose-fermenting bacilli. J Clin Microbiol. 1993; 31(12): 3165–9. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "72842",
"date": "23 Nov 2020",
"name": "Ciira Kiiyukia",
"expertise": [
"Reviewer Expertise Medical microbiology-Bacteriology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe evaluation of the various analytical techniques available for the BSI in Kenya was timely. The methods used and the the results obtained are reliable. However, the abstract need some revision since the section on Methods contains more about the results than methodology. This section can be split to include a section on Results.\nIn the abstract 3rd line from the top, the authors claim that - This study retrospectively analyzed data of identified BSI pathogens. Which means that the they did not isolate and identify the pathogens as described in the Methods section. It is not clear whether they used already identified pathogens or used stored blood culture samples from Kisii Referral Hospital and identified the pathogens.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6138",
"date": "24 Nov 2020",
"name": "Ronald Kirera",
"role": "Author Response",
"response": "Dear reviewer, Thank you for the review and taking the time to go through the paper, The question on results and methods in the abstract section Response: This was combined to meet the allowable minimum number in the abstract section as per journal requirement however I had to limit the explanation on results and methods to meet the required number. On abstract 3rd line on “this study retrospectively analyzed data of identified BSI pathogens” Response: a) I used archived BSI isolates which I had processed/analyzed before using the same methods under analysis for comparison. b) The explanation in the method section was to show how the isolates were processed and how the techniques work. Thank you, Ronald Kirera Corresponding author."
}
]
},
{
"id": "85225",
"date": "20 May 2021",
"name": "Josette Raymond",
"expertise": [
"Reviewer Expertise Infectious diseases (pediatric mainly) andd Helicobacter infection"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study compare three methods of identification of pathogens growth in blood culture samples: API, Film Array and MS. All the 3 methods show excellent sensitivity and accuracy. What was the specificity?\nSome comments:\nIt should be clearly noted that due to the technology and the price, these techniques (FA and MS) cannot be used in any laboratory in Africa (or low income countries).\nUnfortunately, the FA method is not able to identify the Salmonella. This is a real problem, since the isolated Enterobacteriaceae were mainly Salmonella knowing that Salmonella is the major pathogen in Africa.\nIn the discussion, the authors state that S. anginosus and S. bovis are contaminant. I do not agree since these Streptococcus may be responsible of endocarditis or other (abdominal) infections.\nThe identification of the bacteria is not enough. More data on antimicrobial susceptibilities are required since antimicrobial resistance is a major problem in Africa. So, more data are needed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6727",
"date": "28 Sep 2022",
"name": "Ronald Kirera",
"role": "Author Response",
"response": "Dear reviewer, Thank you for taking time to review our journal. We appreciate comments and suggestions. The study compare three methods of identification of pathogens growth in blood culture samples: API, Film Array and MS. All the 3 methods show excellent sensitivity and accuracy. What was the specificity? Response: The overall specificity was 98%. We did not include specificity in the journal because consultation with my co-authors we decided to use sensitivity and accuracy. Some comments: It should be clearly noted that due to the technology and the price, these techniques (FA and MS) cannot be used in any laboratory in Africa (or low income countries). Response: In Kenya, the government has invested a lot in the health sector through county governments under devolution and universal health initiative. These technologies will be embraced in the referral hospitals and research institutions, also the non-governmental organizations and private sector have also invested much in this institutions. With the emergence of drug resistant microorganisms these technologies will help in early diagnosis and reduce on multidrug resistant. Unfortunately, the FA method is not able to identify the Salmonella. This is a real problem, since the isolated Enterobacteriaceae were mainly Salmonella knowing that Salmonella is the major pathogen in Africa. Response: FA BCID 1 panel is not able to identify the Salmonella (genus) but it identifies up to the family level, following manufacturers' recommendations and inhouse standard procedures this can be identified further to genus level using salmonella antisera. The FA identification panel keeps on improving and the current panel (BCID2) identifies Salmonella at genus level using the same machine/platform. The turnaround time for FA is really helpful in early diagnosis of Salmonella. In the discussion, the authors state that S. anginosus and S. bovis are contaminant. I do not agree since these Streptococcus may be responsible of endocarditis or other (abdominal) infections. Response: Thank you for pointing this out, These microorganisms cause bacteremia taking advantage of immunocompromised patients though not common in immunocompetent individuals. The identification of the bacteria is not enough. More data on antimicrobial susceptibilities are required since antimicrobial resistance is a major problem in Africa. So, more data are needed. Response: We agree, in our recommendation we suggested more studies with big number. Our study was limited by timelines and resources. Thank you, Ronald Kirera, Corresponding author."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1228
|
https://f1000research.com/articles/11-1114/v1
|
28 Sep 22
|
{
"type": "Research Article",
"title": "Investigation of knowledge management and firm competitiveness: core competence as a mediator",
"authors": [
"Iffat Aziz",
"Muhammad Shafiq",
"Iram Fatima",
"Iffat Aziz",
"Muhammad Shafiq"
],
"abstract": "Background: The objective of the current study is to empirically investigate interrelationships among three variables; knowledge management (KM), core competence (CC), and firm competitiveness (FC), and to develop a framework based on empirical evidence for developing countries in South Asia. Methods: This is a cross-sectional quantitative study using the Pakistan stock exchange (PSX) enlisted manufacturing and service organizations having a sample size of 136 companies. A questionnaire was self-administered to the respondents by executing a comprehensive strategy to get a high response rate. A total of 201 valid and complete responses from four manufacturing (automobiles, food & cosmetics, textile, and pharmaceutical) and one service organization (banks) were received using a Likert scale of five points in the questionnaire to examine the subject agreement level against statements. All hypothesized relationships were analyzed by employing SEM using AMOS ver. 20. Results: Results of the study confirmed the positive and significant influence of four constructs of knowledge management processes on four constructs of firm competitiveness (innovation, delivery, quality, and financial performance). Further, knowledge management significantly impacts the firm's competitiveness through the mediation of technology, organization and people (TOP) core competence. The findings also supported that managing the intangible resource of the organization can influence the firm's competitiveness and resource-based TOP competence. Conclusions: The SEM analysis confirmed all hypothetical relationships and supported the knowledge management's direct and indirect effects through core competence on firm competitiveness. The findings showed that the effectiveness of knowledge management will increase the organizations' competitiveness in developing countries' research perspective.",
"keywords": [
"Knowledge management (KM)",
"TOP competence (CC)",
"Firm competitiveness (FC)"
],
"content": "Introduction\n\nGlobally the fast-changing business environments and uncompromising competition for innovative products and services has evolved high in domestic and international markets. Competition based on uniqueness has become requisite to business success. Organizations are looking for new strategic ways to strengthen their economies and extend their agility (Teece et al., 2016). In such a scenario, modern organizations change their directions from faded philosophies to lasting management approaches. Therefore, knowledge management (KM) and building core competence are becoming new management attitudes in the knowledge era. Organizations' particular knowledge stock and capability differentiate them over rivals (Grant, 1996). Moreover, KM is a firm strategic process, taking a central pace for firms' competitiveness either through managing and utilizing existing knowledge or integrating existing knowledge with new knowledge (Chetty et al., 2021; Bloodgood, 2018). In other words, competitiveness can only be accomplished when a firm manages its knowledge processes effectively.\n\nWhile going through the academic literature, many scholars considerably investigated the impact of varied KM processes on firm performance. However, among these, several studies observed either no effect of KM processes on firms' performance (Sahibzada et al., 2022; Ferraresi et al., 2012) or mixed results (Obeso et al., 2020; Dzenopoljac et al., 2018; Wang et al., 2014; Zack et al., 2009). Consistently, in an issue of frequent conflicting and ambiguous findings, scholars now agree that KM has not remained a sufficient direct contributing strategic factor to increase organizational performance without influencing the intervention of competence or capabilities (Migdadi, 2020; Obeso et al., 2020; Shahzad et al., 2016; Wu & Chen, 2014; Wang et al., 2014; Villar et al., 2014). Therefore, scholars stressed the role of the mediator variable to increase the effectiveness of KM on firm performance (López-Nicolás & Meroño-Cerdán, 2011; Hsu, 2008).\n\nMoreover, in a similar vein, a stream of studies also observed the significant effect of KM on organizational performance in varied economic contexts. Among these findings are from high financially stable countries (Kassou, 2019; Tan & Wong, 2015), developed and economic countries (Tubigi & Alshawi, 2015; Kiessling et al., 2009; Tseng & Lee, 2014), and non-industrialized or low-income countries (Migdadi, 2020; Al-Sa’di et al., 2017). Since, KM has been verified as a socially embedded phenomenon that varies from country to country (Hussinki et al., 2017; Andreeva & Kianto, 2012). The universality of KM could be affected by other contexts, like managerial, institutional, and cultural (Hussinki et al., 2017). Based on the fact many scholars limited their empirical evidence of the significant and insignificant impact of KM in developed and developing countries to another social, economic, and geographical context.\n\nContinually, the high pressure of competition stressed companies to develop and identify unique and distinctive competencies and core competence (Mahdi et al., 2019). The factors like technology, organization, and people (TOP) have been identified as core competence and supported the influence on firm competitive advantages (Hafeez et al., 2019; Hafeez et al., 2010; Hafeez et al., 2006; Hafeez et al., 2002). In KM literature, enormous studies examined the role of TOP factors using terms like knowledge infrastructural capabilities or knowledge assets as an antecedent to KM processes to influence competitive performance (Kassou, 2019; Nguyen et al., 2018; Pérez‐López & Alegre, 2012; Donate & Guadamillas, 2011; Lee & Choi, 2003). However, mediation of TOP-enabled core competence or capabilities has not yet been viewed as a necessary intervention condition for the KM to achieve high competitive success.\n\nFirm success can be depicted by its unique functional and operational capabilities (Eldridge, 2019). Therefore, KM's relationship with competitiveness carries a growing interest. Indeed, four dimensions of competitiveness are generally involved in the extent of KM literature for operational performance (non-financial), such as cost, quality, flexibility, and delivery (Mohamad & Zin, 2019; Al-Sa'di et al., 2017; Aboelmaged, 2014). However, innovation is argued as a non-financial indicator (Jalil et al., 2017) and has not frequently been used in KM literature besides the four components of competitiveness. Alongside dimensions, i.e., cost, quality, delivery, and flexibility, firm innovation also are among the primary sources of competitive advantages and a crucial part of international competitiveness (Laosirihongthong et al., 2015). On the flip side, studies employed multiple performance measures, including firm financial performance, to comprehend the full benefits of KM implementation. Such as Migdadi (2020) studied the firms' performance through operational, financial and product quality. Andreeva & Kianto (2012) suggested two performance outcomes from the role of effective KM practices, including competitiveness and financial performance. The financial benchmarks determine the firm quantifiable competitiveness.\n\nParticularly in the context of KM in Pakistan, scholars focused on varying performance measures. For example, the research work of Shujahat et al. (2019) examined the impact of KM processes on organizational performance through the mediation of knowledge worker productivity in the IT industry. Shahzad et al. (2016) studied the manufacturing and service firms listed on the Lahore stock exchange and analyzed the knowledge creation process capabilities and their relationship with organizational creativity and performance. Abbas et al. (2020) empirically investigated the KM impact on sustainable innovation in the garment industry. Iqbal et al. (2020) explored the KM effect on the innovation capability of the banking sector. However, these studies do not give sufficient information on the extent of KM on firm competitiveness in larger manufacturing and service organizations.\n\nTherefore, the main focus of the study is to provide empirical evidence on the interrelations between the KM process, core competence (TOP), and firm competitiveness. Further, the study will bridge gaps, add value to the existing KM literature, and address the empirical spectacle in the developing country context of Pakistan.\n\nIn this research paper, KM is defined by four constructs, using four items to measure knowledge creation (KC), three variables for knowledge sharing (KSH), two measures for knowledge application (KAPP), and two for knowledge storage (KST). This study formulated a research model to establish at first a direct KM relationship with firm competitiveness (FC) using four (operational and financial) constructs such as innovation (IN), delivery (D), quality (Q), and financial performance (FP). The second relationship is between KM and TOP core competence (CC), and the third is the relationship between CC and FC. The fourth is knowing about the effect of KM on FC through the mediation of CC. Using the underpinning of the knowledge-based view (KBV), we argue that KM processes of manufacturing and service organizations in Pakistan have considerable direct and indirect capacity to increase the firm competitiveness.\n\nAccording to the knowledge-based view (KBV), the knowledge possessed by a firm is a strategic intangible asset and critical to long-term success (Grant, 1996). The effective management of knowledge leads organizations to perform better than competitors (Martín‐de Castro et al., 2011). That means the existence of resources (employees) is not remained enough without managing knowledge through processes at the firm level (Kiessling et al., 2009). Creation, sharing, storage, and application determine common KM abilities to create and capture value (Martelo-Landroguez & Cepeda-Carrión, 2016). Under the theoretical pinning of KBV, previous studies suggest that KM processes can significantly impact competitive advantages and performance (Kassou, 2019; Al-Ahbabi et al., 2019; Tan & Wong, 2015; Kiessling et al., 2009; Gold et al., 2001).\n\nMohamad & Zin (2019) have shown a positive association between KM and competitiveness in the service context (innovation, cost, quality, and flexibility). Ali et al. (2019) indicated a significant impact of knowledge-sharing practices on firm competitive tangible (cost reduction, organization growth) and intangible advantages. Investigating the manufacturing firms, Liu et al. (2004) also revealed significant connections between KM process capabilities and competitiveness. Aboelmaged (2014) found a positive linkage with firm operational competitive measures (cost, quality, delivery, and flexibility) through KM capabilities. In line with the above, here this study postulates,\n\nH1. Knowledge management processes are positively related to the firm competitiveness.\n\nKnowledge is the critical source of distinctive tangible and intangible competence, competencies, and capabilities (Tseng & Lee, 2014; Momeni et al., 2011). Many empirical studies have also shown a positive relationship between KM processes and intellectual capital as an organization intangible competence (Wang et al., 2014; Hsu, 2008). KM studies argue that tacit and explicit knowledge sharing influences human (people-based skills, expertise, training, teamwork), structural (organizational factors and processes and technology), and relational (external) competence (Wang et al., 2014).\n\nIt has also directed that organizational competency development in terms of learning (internal and external competence) highly depends on knowledge integrating, converting, creating, acquiring, exchanging (Cooper et al., 2016), dissemination, and storage (Villar et al., 2014), or generation, storage and flow (Obeso et al., 2020). Kassou (2019) empirically estimated that the generation of competency (employee satisfaction, skills, and staff retention) is mainly attributed to KM activities.\n\nEmpirical research on achieving resources, capabilities, core competence, and competencies attained less attention from KBV literature. Studies established that acquisition, conversion, application, and protection are the knowledge management process that positively and significantly influence the types of core competencies (marketing, technological, and integrative) in the corporate sector context (Momeni et al., 2011). While examining the service sector, Mahdi et al. (2019) confirmed the impact of knowledge management processes (generate, store, share, and apply) on sustainable competitive advantages involving resources, capabilities, competencies, and core competence. So, it is also important to propose that,\n\nH2: There is a positive relationship between knowledge management processes and core competence.\n\nFirm competence offers a capacity to benchmark other organizations generating high profits, innovation, and competitive advantages (Brown et al., 2019; Hafeez et al., 2002). According to Hafeez et al. (2019), the TOP competence should be flexible enough to meet the changing demands. In the notion of TOP-associated factors, technological capabilities are empirically revealed mostly as the prominent predictors of organizational performance (financial and non-financial) relative to the organization and people in many studies (Hafeez et al., 2010; Hafeez & Essmail, 2007; Hafeez et al., 2006).\n\nFurthermore, in the wake of the knowledge economy, companies are retaining core knowledge infrastructure capabilities through developing an understanding of the management of technology (tangibles), culture, structure, and people (intangibles) practices for competitive performance outcomes (Nguyen et al., 2018; Andreeva & Kianto, 2012; Pérez-López & Alegre, 2012; Mills & Smith, 2011; Chen & Huang, 2009; Lee & Choi, 2003; Gold et al., 2001). Others emphasized intellectual capital and human resources practices (Hafeez & AbdelMeguid, 2003). Under a similar view, the studies of Hsu (2008) and Andreeva & Kianto (2012) empirically reported human resource practices and people competencies as a prominent source to increase firm competitiveness. Therefore, in line with the significant consequences of TOP on competitive advantages, the proposed hypothesis is that:\n\nH3: There is a positive relationship between TOP-associated core competence and firm competitiveness.\n\nVillar et al. (2014) argued that without companies' dynamic capabilities like internal and external learning competence, knowledge management practices do not provide sufficient conditions for firm performance. Many studies empirically validated that the measurements of knowledge management are insufficient to generate competitive advantages and firm performance (Obeso et al., 2020; Durmuş-Özdemir & Abdukhoshimov, 2018; Tubigi & Alshawi, 2015). Recently, Aghaegbuna & Ukoha (2020) empirically show that not all knowledge processes contribute directly to firm performance.\n\nCorrespondingly, using operational and financial performance outcomes, studies observed mixed results, such as Zack et al. (2009) performed a significant direct relationship between knowledge management practices and operational performance relative to financial performance. Wang et al. (2014) also found two different results that reported the positive effect of tacit knowledge sharing on financial performance, while an insignificant relationship between explicit knowledge sharing and operational performance.\n\nTherefore, prior research confirmed the successful role of knowledge management on competitive advantages and firm performance incorporated through building internal and external competencies such as learning and innovation capability (Migdadi, 2020; Obeso et al., 2020; Villar et al., 2014; Aboelmaged, 2014). Wang et al. (2014) noted a full mediation effect of intellectual competence (structure, culture, and relation) on the relationship between explicit knowledge sharing and operational performance than financial performance, while intellectual capital has shown a full mediation between tacit knowledge sharing and financial performance. Cooper et al. (2016) exhibited the impact of knowledge management on organizational performance through competence such as learning culture and human capital. The hypothesis generated as,\n\nH4: There is a positive mediating role of core competence (TOP) between knowledge management and competitiveness.\n\n\nMethods\n\nThe researchers have employed a cross-sectional survey strategy and a deductive quantitative research method to perform a cause and effect analysis of the hypothesized relationships. Close-ended structured questionnaires were manipulated with predetermined options on a multi-item instrument using 5 points Likert scale (strongly disagree-strongly agree) to gather first-hand information for this particular study issue. Respondents were from the manufacturing and service sectors enlisted in PSX. For the generalizability issue of the study, it has tried to collect data from different departments like quality, R&D, production, human resource, finance, sales & marketing, procurement, and others. Respondents were requested to participate with at least 2-5 responses from different departments in each firm to reduce the respondents’ bias.\n\nThe reliability and validity of the questionnaire is the fundamental aspect and established related to their respective constructs in variables through SPSS ver.20. In the following steps, a detailed descriptive analysis provided on the sample profile of the respondents, which included the respondents’ demographic information like gender, job position, sector, experience etc. Convergent and discriminant validity was also conducted by using MS Excel for the reconfirmation of latent constructs. Confirmatory factor analysis (CFA) was executed for the measurement and structural model. Towards the end, the outcome of structural equation modelling (SEM) has integrated with the research model alongside model fit indices using AMOS ver.20. SEM analysis was used to test the proposed research hypothesis.\n\nWritten informed consent was taken before filling the questionnaire. The study was sent for ethical approval to the Institute of Quality & Technology Management (IQTM), University of the Punjab, Lahore, Pakistan and got waiver IRB (Ref. No: D/218/IQTM) dated 17-08-2020. Therefore, we are thankful to all the volunteer respondents and their organizations who helped us without any conflict of interest and supported the industry academia relationship.\n\nThe target population for the current study was the managers or senior officers of manufacturing and service organizations listed on the Pakistan stock exchange (PSX). PSX-listed companies, which determine the share exchange-based companies in Pakistan, were the study data source. Initially, this study utilized purposive sampling for companies and approached them conveniently. Therefore, out of the 544 manufacturing and service companies, 210 innovative manufacturing (automobiles, food & cosmetics, textile, and pharmaceuticals) and service (banks) organizations were selected as participants. Figure 1 shows the participants’ (companies) selection and eligibility criteria. The sample size has then calculated with a 95% confidence interval and a 0.05% margin for error in Yamane formula (Yamane, 1967). According to Saunders et al. (2009), if the population size is 200, the sample size at a ±5% confidence interval should be 132. In our case, the population size is 210, and the sample size is 136, which shows a sufficient sample size eligible to obtain a ±5% confidence interval. Afterward, the researcher of the current project adopted a stratified sampling technique for data collection amongst 136 listed manufacturing and service companies (Table 1) with at least 100 employees and ISO certification.\n\nOrganizations located in different provinces of Pakistan were contacted to acknowledge their participation. A list of contacts (addresses, emails, telephone numbers) has arranged from the PSX website. Initially, the organizations have contacted via given email addresses and phone contacts in the list, and five questionnaires to each organization besides research information were sent. Data collection was performed through a self-administered survey and followed a comprehensive strategy of emails, phone contacts, physical visits, and google form link sending on corresponding emails and WhatsApp to enhance the response rate. Afterward a continuous follow-up process was carried out from August 2020 to February 2021. Only targeted innovative sectors of PSX. The innovative nature of large firms shows enough ability to create and use knowledge and invest more in KM activities to outperform (Sukumar et al., 2020). The sectors like automobiles, food & cosmetics, textiles, and pharmaceuticals in manufacturing, and banks in service lines are becoming innovative and changing their products and services at short intervals. For example, the textile sector is a cornerstone in developing and boosting Pakistan's economy and contributing about 60% of the total export. Pakistan is the 8th largest exporter of textile products in Asia. The government of Pakistan investing its time and efforts in providing policy support like textile policy 2025 with an investment of $ 3 billion in new projects. After textile food & beverage processing industry is the 2nd largest in Pakistan. Halal products (food & cosmetics) are taking new horizons of opportunity. Pakistan halal food products authority is an endeavor to capture the international markets as a competitive edge over other non-muslim countries that offer halal products.\n\nThe automobile industry in Pakistan is one of the large-scale manufacturing (LSM) sector and the fastest-growing industry. Fetching technological advancements and increasing the national economy, employing a workforce of over 1.8 million people, and generating revenue through taxes and duties. Continuous-based production of automobile products is a sign that the auto industry is increasing at a regular speed. Pakistan is looking to introduce its first national electric vehicle as a solution to green Pakistan and climate concerns soon. This industry is expanding with buyer choice and providing safe, modern, and cost-effective vehicles. Pharmaceutical is a highly technological and R&D incentive sector. Top pharmaceutical companies in Pakistan adopt and use new technologies, good manufacturing practices (GMP), striving for the latest equipment and production technologies to sustain economic health and gain productivity. Apart from direct contribution to Pakistan's GDP, banks contribute to many economic and social development activities. In the coming years banking sector is anticipated to develop long-term financing, investment products, and green banking products.\n\nA total of 680 (136*5) questionnaires were disseminated consisting of 99 items to the potential respondents of the sampling frame. Initially, all responses were entered on an MS Excel sheet. At the end of the span, a total of 281 responses were in hand, which enabled the scholars to proceed to the next step of the data analysis phase. Among these, 80 questionnaires were excluded from the final analysis using the screening process because a major part of the data was incomplete and missing. For data screening, all responses were entered against the respective ID under every post-coded item to check consistency, completeness, and legitimacy. In addition to the procedure, to ensure the coding accuracy and precision of the data entry, every 10th record has to recheck using a double-entry technique.\n\nThe study cast items from previous literature to measure the variables KM processes, CC, and FC. Table 2 (constructs and measures) shows the selection of items from existing literature. Before the final execution of the original research questionnaire, the measurement instrument was refined and tested by using methods like pilot testing to identify uncertainty, problems, wording errors, or confusing questions from the contents of the questionnaire. The pilot study shows with 73 participants randomly selected from manufacturing and service organizations. Respondents were allowed to comment on the difficulty or any improvement suggestions in open-ended questions provided at the end of the questionnaire or send their valuable advice via email or phone contacts. Finally, the researcher considered the best items to have high Cronbach’s alpha values for the final version of the questionnaire (see Extended data, Fatima et al., 2022).\n\nBefore moving towards SEM analysis of the hypothesized relationships in the proposed model, reliability and validity had measured. For the internal consistency of the constructs in the questionnaire, accessed a reliability test through Cronbach's alpha value using through SPSS ver.20. The value of Cronbach's alpha could vary between 0 and 1. The 0.8 value is generally considered the acceptable level. While, in literature, for any construct reliability, the value must be 0.7 or above is recommended as adequate (Pallant, 2010). For this study, the value of each construct varies between 0.7 and 0.8. All values are in the range of the specified threshold limit (>0.7) of Cronbach alpha, shown in Table 3.\n\nAccording to Hair et al. (2010), for the establishment of convergent validity (CV) of variables, the value of average variance extracted (AVE) should be > 0.5. All AVE values of latent variables are in their specified ranges except knowledge application (0.44), knowledge storage (0.44), and quality (0.49) which are < 0.5. Whereas the AVE value of 0.44 is acceptable when the value of composite reliability (CR) is > 0.6 (Fornell & Larcker, 1981). So the value of the CV is in the acceptable range. The CR values of all latent constructs are far > 0.6, as indicated in Table 3.\n\n\nResults\n\nOut of the 680 questionnaires sent to the 136 companies, 201 filled questionnaires were returned from 119 companies, as shown in Figure 2 (Fatima et al., 2022). It represents a useable response rate of 87.5% (119/136*100) company wise and 29.5% (201/680*100) respondent wise. The earlier response is higher than the study of Shafiq (2011), while the latter is close to the study of Aboelmaged (2014).\n\nTable 4 indicates the respondents varied characteristics of job position, no. of employees, nature of the organization, job experience, gender, ISO certification, and types of organization sector. The study established a descriptive analysis of the demographic characteristic. The results of job position indicates the majority of respondents were quality managers (26.37%), followed by sales & marketing managers (13.43%), production managers (11.94%), R&D managers (10.95%), procurement managers (10.45%) finance managers (6.46%), the human resource manager (4.48%), and 15.92% respondents were performing other responsibilities. These mixed responses from different departments give confidence to the researcher that the data will not be biased (Kumar et al., 1993). The response rate of 33.33% and 31.84% broadly came from medium to large firms that had number of employees > 500. This result gave much confidence to the researcher. Most of the organizations listed on the PSX are manufacturing companies. Therefore, 83.08% of responses were received from manufacturing organizations and 17% (16.92%) from the service sector. The analysis showed that 48.26% of respondents had a job experience of 11-15 years, and only 9.45% had job experience of 2-5 years. The maximum response rate was obtained from well-experienced employees of the sample organizations. Only 8.46% of respondents calculated as female, and 91.54% were male. The results indicate that nearly 80% (79.60%) of Pakistan organizations are ISO certified. The majority of data, like 40% (39.80%), was collected from the textile sector as it is one of the largest leading manufacturing sectors in Pakistan.\n\nThe CFA analysis of measuring KM, CC, and FC shows all the estimated values in the specified threshold ranges as given in outcome summary Table 5. This first measurement model examines the relationships among measures of the independent variable (IV), comprised of 4 KM processes (creation, sharing, application, and storage). The results of parameter re-estimates, fit indices, and observed residuals imply that the dimensions of KM provide the best fit for the observed co-variances among the collection of measures. Measurement model of FC constructs (innovation, delivery, quality, and financial performance) at the loss of cost and flexibility constructs (due to low Cronbach’s alpha values), others are in specified range value of thresholds and demonstrating uni-dimensional (Gaskin & Lim, 2016). Afterward, CFA confirmed the measurements in such constructs with low factor loadings. It is also interesting to mention that constructs like technology (T) and organization (O) competence were deleted during the construction of the CC measurement model and remained with 1 item of technology and 1 item of organization factors competence. However, people (P) construct stayed with a good number of items. In this way, only the variable CC came into existence with all TOP.\n\nAfter performing the reliability and validity successfully, measurement models remained with a total of 29 items (KM = 11 items, CC= 7 items, FC = 11 items) used to measure the four constructs of KM and four constructs of FC (Table 2).\n\nDirect effect (D)\n\nThe proposed three direct relationships (KM->FC, KM->CC, and CC->FC) were tested by using structural equation modelling (SEM). Predominantly, the revealed first direct relationship is a path between the measured KM processes and outcomes of FC. It had noticed that the path coefficient of the estimated model supports the hypothesized relationship of fit in all directions and magnitudes. Table 5 indicates all the main results and goodness of fit indices for direct relationships on standardized estimates are in acceptable ranges and at the significance level of p=0.000. So, the results of the regression coefficient of the direct path exhibited the effect of KM on FC and endorsed that the KM implementation practices significantly encourage FC at a standardized value (β =0.78). This significant and positive result supported H1. Furthermore, the effect of KM on CC was observed positively and significantly at standardized estimates (β =0.89). The last direct effect of CC on FC also indicated a significant and positive relationship with standardized value (β =0.84) and supporting H2 and H3.\n\nIndirect effect (IND) structural model of mediation analysis\n\nFor testing the mediation, the researcher followed the method of Baron & Kenny (1986). The bootstrapping technique with 5000 bootstraps (number of samples) was employed to examine the indirect relationship (Zhao et al., 2010). SEM testing of the relationship between KM and FC through the mediating role of measured CC exhibited perfect goodness of fit indices (Table 6). According to Baron & Kenny (1986), mediation exists if the independent variable (IV) does not affect the dependent variable (DV), and the mediator variable controls the influence of the IV on the DV.\n\nSo, in this study, the CC (mediator TOP) has dominated the effect of KM (IV) on FC (DV). That determines, in the presence of core competence related to technology, organization, and people, that the direct influence of KM does not remain more on the FC (Figure 3). Table 6 shows that the presence of a mediator (indirect effect) suppressed the KM direct effect on FC and remained less with a standardized estimate (β = 0.3), and analysis remained statistically significant at 0.001 (<0.005). Results established CC (TOP) mediation between KM and FC and supported H4.\n\n\nDiscussion and conclusion\n\nThe findings of this study have proved KM effectiveness in FC and that all four processes are equally important to address the KM performance to impact organizational competitiveness in the context of manufacturing and service organizations of Pakistan. The results of the H1 ascertained a positive and significant relationship between KM and the FC (KM -> FC). All four measurements of KM (creation, sharing, application, and storage) statistically verified the contribution toward competitiveness. While the strategic value of knowledge substituted the theoretical assumptions suggested in KBV, management of knowledge mechanisms as intangible firm resources is a fundamental source of competitive performance.\n\nGenerally, the finding agrees with previous empirical studies that KM significantly impacts firms' performance. No difference emerges while comparing the existing result of H1 with studies performed by Al Yami et al. (2021), Al Ahbabi et al. (2019), Dzenopoljac et al. (2018), and Aboelmaged (2014) validated all KM processes significantly affect organizational performance in UAE and Kuwait. The result is similar to Mohamad & Zin (2019) who found a direct influence of KM on the performance of Malaysian construction firms. The conclusion is constant with Kiessling et al. (2009) who established that KM at the firm level has more capacity to increase organizational performance in manufacturing and service firms in Croatia. Gold et al. (2001) empirically proved the influence of knowledge process capability on organizational effectiveness in the USA manufacturing industries context.\n\nThe results of four KM constructs demonstrated on the scale lead to FC. Knowledge creation (KC) exhibits KM performance to attain firms' competitiveness (β=0.90). In other words, this study experienced that when a firm deploys knowledge creation and generates new knowledge (internal and external) may improve its performance. These findings are in line with prior studies. Like collecting data from Spanish service firms, Obeso et al. (2020) observed the significant connection between knowledge generation and firm performance. Tubigi & Alshawi (2015), in the UK service industry, also observed the positive impact of knowledge creation.\n\nThe positive role of knowledge sharing (KSH) shows a better understanding through KM, and the result is constant with past findings (Migdadi, 2020; Ali et al., 2019; Dzenopoljac et al., 2018; Durmuş-Özdemir & Abdukhoshimov, 2018). In contrast, explicit knowledge sharing shows less support than the previous study conducted by Wang et al. (2014). Their study found the only positive relationship of explicit knowledge sharing with financial performance except for the operational performance of technology firms in China.\n\nKnowledge application (KAPP) is significant in the prediction of KM as (β=0.97) used to enhance performance shows agreement with past research performed by Tubigi & Alshawi (2015). There is a fundamental role of knowledge usage in firm performance (Tubigi & Alshawi 2015). If firms deploy their knowledge in the new products and services and apply knowledge to critical competitive needs will perform better than competitors.\n\nKnowledge storage (KST) is pivotal in KM performance (β=0.81). Several studies confirmed the significant connection between knowledge storage and firm performance. Migdadi (2020) found a direct and positive relationship between knowledge storage and the manufacturing and service companies' performance in Jordan. In contrast, Obeso et al. (2020) and Durmuş-Özdemir & Abdukhoshimov (2018) did not find a relationship between knowledge storage and firm performance. In this study, systematically administered knowledge and the knowledge stored in the databases are necessary for making the task easier. In a nutshell, while going through the literature review, the extent showed the relationship between KM and firm performance remained inconsistent. However, the current impact of knowledge processes such as creation, sharing, application, and storage will increase the firm's competitiveness.\n\nThe findings show significant and positive impacts of KM on CC and supported H2. In other words, the firm supposed to implement KM (creation, sharing, application, and storage) will increase its competencies. This finding is in line with Mahdi et al. (2019), who significantly supported the implementation of KM processes for resources, capacities, competence, and core competence in the universities of Iraq. The result is constant with Momeni et al. (2011), who found that KM processes contribute significantly to core competencies in Iranian automotive industries. Consistently Tseng & Lee (2014) study showed the influence of KM capability on the dynamic capability of China. The result is similar to those that examined the intellectual capital as an organization's intangible competence against KM impact (Wang et al., 2014). The finding is comparable with prior studies that established the direct relationship between KM and organizational learning competence. Such as Obeso et al. (2020) successfully examined the effect of KM in Spain on organizational learning. Data from Spain and Italy Villar et al. (2014) found that knowledge management practices significantly determine internal and external learning capabilities.\n\nThe results show CC (TOP) significantly influenced FC, and H3 is accepted. This relationship indicates that people-based practices (P) are the most prominent core competencies of manufacturing and service organizations in Pakistan compared to technology (T) and organization (O) factors. The outcomes of people factors support studies done in the past, and those empirically suggested similar results (Hafeez & Essmail, 2007; Hafeez & AbdelMeguid, 2003). In the KBV, the findings of H3 are constant with Tan & Wong (2015) for KM factors to significantly enhance manufacturing performance and Andreeva & Kianto (2012) as they observed a strong influence of technology and people practices on firm competitiveness. Similarly, finding supports others like Cooper et al. (2016), Mills & Smith (2011), and Gold et al. (2001) discovered that the level of firm knowledge-based capabilities (structure, culture, people) exhibit an improved level of organizational effectiveness.\n\nFinally, the SEM results also showed a significant relationship between KM and FC through the mediating role of CC (TOP) and supported H4. The finding suggests that the more manufacturing and service firms develop core competence, the more firm increases their competitiveness and lead performance of their unique and distinctive products and services. Previously, technology (T) and organization (O) factors remained a significant core competence of competitive advantages in many previous studies from different countries (Hafeez et al., 2010; Hafeez & Essmail, 2007). While in Pakistan, this result indicates that T and O are less contributing factors to competitiveness in larger sectors of Pakistan. The less or no impact of technological competence are consistent with the studies conducted on another cultural context in larger firms (Mills & Smith, 2011; Pérez‐López & Alegre, 2012).\n\nThe findings of this study will contribute to existing literature that knowledge management significantly determines competitiveness in developing countries' research perspective. Results found statistically significant direct and indirect effects of knowledge management on firm competitiveness. Respondents of the organizations tend to believe that the more knowledge management implementation initiatives and improvement practices generate facts, the more firms will be competitive.\n\nKnowledge management has been an emerging competitive global trend and incorporates all the sectors in developed and knowledge-economic countries. However, the organizations of developing countries are still in their struggling phase to find out the business ways for the full potential of knowledge management. Hence, organizations in developing countries like Pakistan must comprehend the importance of knowledge management in response to being more competitiveness.\n\nMost importantly, the limitation may affect the generalizability issue. However, the findings are not generalized to the manufacturing and service sectors other than Pakistan. The current study is cross-sectional and performed in one go (snapshot) and conducted the data using a self-administered close-ended questionnaire design. It would be interesting to conduct a longitudinal study to measure the knowledge management effect over periods with a chronological break. Similarly, it would also be interesting for future scholars to use qualitative research studies by implementing multiple experiment methods in a similar domain to reduce the chance of variance in the data method. Further, future studies should examine the obstacles facing Pakistan’s larger sectors in knowledge management implementation.\n\n\nData availability\n\nUK Data Service ReShare: Impact of Knowledge Management on Firm Competitiveness: Core Competence as Mediator, 2020-2021. https://dx.doi.org/10.5255/UKDA-SN-855898 (Fatima et al., 2022).\n\nThis project contains the following underlying data:\n\n- Data file.xlsx\n\n- Spss data file.sav\n\nUK Data Service ReShare: Impact of Knowledge Management on Firm Competitiveness: Core Competence as Mediator, 2020-2021. https://dx.doi.org/10.5255/UKDA-SN-855898\n\nThis project contains the following extended data:\n\n- KM Questionnaire\n\n- Data coding file\n\n- Short methodology paper\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAbbas J, Zhang Q, Hussain I, et al.: Sustainable innovation in small medium enterprises: the impact of knowledge management on organizational innovation through a mediation analysis by using SEM approach. Sustainability. 2020; 12(6): 2407. Publisher Full Text\n\nAboelmaged.: Linking operations performance to knowledge management capability: the mediating role of innovation performance. Prod. Plan. Control. 2014; 25(1): 44–58. Publisher Full Text\n\nAghaegbuna AJ, Ukoha O: Developing organizational innovation capabilities through knowledge management: Evidence from refining companies in Nigeria. Int. J. Adv. Acad. Res. 2020; 6(3): 14–30.\n\nAl Ahbabi SA, Singh SK, Balasubramanian S, et al.: Employee perception of impact of knowledge management processes on public sector performance. J. Knowl. Manag. 2019; 23(2): 351–373. Publisher Full Text\n\nAl Yami M, Ajmal MM, Balasubramanian S: Does size matter? 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Knowledge Management & E-Learning: An International Journal. 2021; 13(2): 225–249.\n\nCooper AL, Huscroft JR, Overstreet RE, et al.: Knowledge management for logistics service providers: the role of learning culture. Ind. Manag. Data Syst. 2016; 116(3): 584–602. Publisher Full Text\n\nDonate MJ, Guadamillas F: Organizational factors to support knowledge management and innovation. J. Knowl. Manag. 2011; 15(6): 890–914. Publisher Full Text\n\nDurmuş-Özdemir E, Abdukhoshimov K: Exploring the mediating role of innovation in the effect of the knowledge management process on performance. Tech. Anal. Strat. Manag. 2018; 30(5): 596–608. Publisher Full Text\n\nDzenopoljac V, Alasadi R, Zaim H, et al.: Impact of knowledge management processes on business performance: Evidence from Kuwait. Knowl. Process. Manag. 2018; 25(2): 77–87. Publisher Full Text\n\nEldridge H: Improving productivity through strategic alignment of competitive capabilities. Int. J. Product. Perform. Manag. 2019; 68(3): 644–668. Publisher Full Text\n\nFatima I, Aziz I, Shafiq M: Impact of Knowledge Management on Firm Competitiveness: Core Competence as Mediator, 2020-2021. [Dataset]. Colchester, Essex: UK Data Service.2022. Publisher Full Text\n\nFerraresi AA, Quandt CO, dos Santos SA , et al.: Knowledge management and strategic orientation: leveraging innovativeness and performance. J. Knowl. Manag. 2012; 16(5): 688–701. Publisher Full Text\n\nFornell C, Larcker DF: Structural equation models with unobservable variables and measurement error: Algebra and statistics.1981; 18(3): 382–388.\n\nGaskin J, Lim J: Model fit measures. Gaskination’s StatWiki. 2016; 1–55.\n\nGold AH, Malhotra A, Segars AH: Knowledge management: An organizational capabilities perspective. J. Manag. Inf. Syst. 2001; 18(1): 185–214. Publisher Full Text\n\nGrant RM: Toward a knowledge-based theory of the firm. Strateg. Manag. J. 1996; 17(S2): 109–122. Publisher Full Text\n\nHafeez K, AbdelMeguid H: Dynamics of human resource and knowledge management. J. Oper. Res. Soc. 2003; 54(2): 153–164. Publisher Full Text\n\nHafeez K, Essmail EA: Evaluating organisation core competences and associated personal competencies using analytical hierarchy process. Manag. Res. News. 2007; 30(8): 530–547. Publisher Full Text\n\nHafeez K, Foroudi P, Nguyen B: An integrated core competence evaluation framework for portfolio management in the oil industry. Int. J. Manag. Decis. Mak. 2019; 18(3): 229–256. Publisher Full Text\n\nHafeez K, Keoy KHA, Zairi M, et al.: E-supply chain operational and behavioural perspectives: an empirical study of Malaysian SMEs. Int. J. Prod. Res. 2010; 48(2): 525–546. Publisher Full Text\n\nHafeez K, Malak N, Abdelmeguid H: A framework for TQM to achieve business excellence. Total Qual. Manag. Bus. Excell. 2006; 17(9): 1213–1229. Publisher Full Text\n\nHafeez K, Zhang Y, Malak N: Core competence for sustainable competitive advantage: A structured methodology for identifying core competence. IEEE Trans. Eng. Manag. 2002; 49(1): 28–35. Publisher Full Text\n\nHair JF, Anderson RE, Babin BJ, et al.: Multivariate data analysis: A global perspective. Pearson Upper Saddle River;2010.\n\nHsu.: Knowledge sharing practices as a facilitating factor for improving organizational performance through human capital: A preliminary test. Expert Syst. Appl. 2008; 35(3): 1316–1326.\n\nHussinki H, Kianto A, Vanhala M, et al.: Assessing the universality of knowledge management practices. J. Knowl. Manag. 2017; 21(6): 1596–1621. Publisher Full Text\n\nIqbal S, Rasheed M, Khan H, et al.: Human resource practices and organizational innovation capability: role of knowledge management. VINE Journal of Information and Knowledge Management Systems. 2020; 51(5): 732–748. Publisher Full Text\n\nJalil F, Shafiq M, Rehman W, et al.: Assessing the Mediating Role of manufacturing competitive strategies in the relationship of Quality Management System and Financial Performance. J. Manag. Sci. 2017; 11(3): 415–432.\n\nKassou I: Performance measurement for knowledge management project: model development and empirical validation. J. Knowl. Manag. 2019; 23(7): 1403–1428. Publisher Full Text\n\nKiessling TS, Richey RG, Meng J, et al.: Exploring knowledge management to organizational performance outcomes in a transitional economy. J. World Bus. 2009; 44(4): 421–433. Publisher Full Text\n\nKumar N, Stern LW, Anderson JC: Conducting interorganizational research using key informants. Acad. Manag. J. 1993; 36(6): 1633–1651.\n\nLaosirihongthong T, Prajogo DI, Adebanjo D: Erratum: The relationships between firm's strategy, resources and innovation performance: resources-based view perspective (Production Planning and Control (2013)). Prod. Plan. Control. 2015; 26(3): 248.\n\nLee H, Choi B: Knowledge management enablers, processes, and organizational performance: An integrative view and empirical examination. J. Manag. Inf. Syst. 2003; 20(1): 179–228. Publisher Full Text\n\nLiu PL, Chen WC, Tsai CH: An empirical study on the correlation between knowledge management capability and competitiveness in Taiwan’s industries. Technovation. 2004; 24(12): 971–977. Publisher Full Text\n\nLópez-Nicolás C, Meroño-Cerdán ÁL: Strategic knowledge management, innovation and performance. Int. J. Inf. Manag. 2011; 31(6): 502–509. Publisher Full Text\n\nMahdi OR, Nassar IA, Almsafir MK: Knowledge management processes and sustainable competitive advantage: An empirical examination in private universities. J. Bus. Res. 2019; 94: 320–334. Publisher Full Text\n\nMartelo-Landroguez S, Cepeda-Carrión G: How knowledge management processes can create and capture value for firms? Knowl. Manag. Res. Pract. 2016; 14(4): 423–433. Publisher Full Text\n\nMartín-de Castro G, López-Sáez P, Delgado-Verde M: Towards a knowledge-based view of firm innovation. Theory and empirical research. J. Knowl. Manag. 2011; 15(6): 871–874.\n\nMigdadi MM: Knowledge management processes, innovation capability and organizational performance. Int. J. Product. Perform. Manag. 2020; 71(1): 182–210. Publisher Full Text\n\nMills AM, Smith TA: Knowledge management and organizational performance: a decomposed view. J. Knowl. Manag. 2011; 15(1): 156–171. Publisher Full Text\n\nMohamad MR, Zin NM: Knowledge management and the competitiveness of small construction firms: Innovation as mediator. Competitiveness Review: An International Business Journal. 2019; 29(5): 534–550. Publisher Full Text\n\nMomeni M, Monavarian A, Shaabani E, et al.: A conceptual model for knowledge management process capabilities and core competencies by SEM the case of Iranian automotive Industry. Eur. J. Soc. Sci. 2011; 22(4): 473–489.\n\nNguyen TN, Que LV, Ngo GN, et al.: Realising the value of knowledge resources and capabilities: an empirical study. J. Knowl. Manag. 2018; 23(2): 374–395. Publisher Full Text\n\nObeso M, Hernández-Linares R, López-Fernández MC, et al.: Knowledge management processes and organizational performance: the mediating role of organizational learning. J. Knowl. Manag. 2020; 24(8): 1859–1880. Publisher Full Text\n\nPallant J:PART FIVE-Statistical techniques to compare groups.Pallant J, editor. SPSS Survival Manual: A Step by Step Guide to Data Analysis Using SPSS. 4th edn.Berkshire:Open University Press McGraw-Hill Education;2010; 25.\n\nPérez-López S, Alegre J: Information technology competency, knowledge processes and firm performance. Ind. Manag. Data Syst. 2012; 112(4): 644–662. Publisher Full Text\n\nSahibzada UF, Jianfeng C, Latif KF, et al.: Interpreting the impact of knowledge management processes on organizational performance in Chinese higher education: mediating role of knowledge worker productivity. Stud. High. Educ. 2022; 47(4): 713–730. Publisher Full Text\n\nSaunders M, Lewis P, Thornhill A: Research methods for business students. Pearson education;2009.\n\nShafiq M: An Investigation of Total Quality Management Practices in Pakistan (Doctoral dissertation, University of York).2011.\n\nShahzad K, Bajwa SU, Siddiqi AFI, et al.: Integrating knowledge management (KM) strategies and processes to enhance organizational creativity and performance: An empirical investigation. J. Model. Manag. 2016; 11(1): 154–179. Publisher Full Text\n\nShujahat M, Sousa MJ, Hussain S, et al.: Translating the impact of knowledge management processes into knowledge-based innovation: The neglected and mediating role of knowledge-worker productivity. J. Bus. 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Manag. 2014; 27(2): 158–179. Publisher Full Text\n\nTubigi M, Alshawi S: The impact of knowledge management processes on organisational performance: The case of the airline industry. J. Enterp. Inf. Manag. 2015; 28(2): 167–185. Publisher Full Text\n\nVillar C, Alegre J, Pla-Barber J: Exploring the role of knowledge management practices on exports: A dynamic capabilities view. Int. Bus. Rev. 2014; 23(1): 38–44. Publisher Full Text\n\nWang Z, Wang N, Liang H: Knowledge sharing, intellectual capital and firm performance. Manag. Decis. 2014; 52(2): 230–258. Publisher Full Text\n\nWu L, Chen JL: Knowledge management driven firm performance: the roles of business process capabilities and organizational learning. J. Knowl. Manag. 2014; 18(6): 1141–1164. Publisher Full Text\n\nYamane T: Statistics, an introductory Analysis. 2nd ed.New York:Horper and Row;1967.\n\nZack M, McKeen J, Singh S: Knowledge management and organizational performance: an exploratory analysis. J. Knowl. Manag. 2009; 13(6): 392–409. Publisher Full Text\n\nZhao X, Lynch JG Jr, Chen Q: Reconsidering Baron and Kenny: Myths and truths about mediation analysis. J. Consum. Res. 2010; 37(2): 197–206. Publisher Full Text"
}
|
[
{
"id": "169748",
"date": "21 Apr 2023",
"name": "Jyoti Verma",
"expertise": [
"Reviewer Expertise organizational ambidexterity",
"social entrepreneurship",
"knowledge sharing",
"job performance",
"leadership",
"emotional intelligence"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOriginality: This paper is about already a well-researched but interesting topic. The current form of the manuscript has exhibited minor shortcomings which impairs the overall quality of the study. I suggest you to state explicitly what the problem statement of this study is instead of writing ‘the objective of the current study is to empirically investigate interrelationships among three variables; knowledge management (KM), core competence (CC), and firm competitiveness (FC)…………..’ please refer to the background within the abstract, starting line. It should be based on the research gaps which have been identified from the literature. Further, the literature on the variables that your paper deals with are voluminous. It is unnecessarily increasing the length of the manuscript.\nRelationship to Literature: The author(s) should also add some updated (2022-2023) relevant papers to the research. While discussing the constructs at individual level, I suggest to include some recent studies. In my opinion, the development of the research problem needs some explanations; thus, more references should be added to support the research goals (as stated in paper).\n\nMethodology: The methodology is clear and the methods appropriated. How has the data been collected (i.e. CAWI?) and how have the firms have been selected? Language can be refined by adding more clarity towards adopted methods.\n\nImplications for research, practice and/or society: The implications proposed are relevant. They should be aligned with the premises presented in the introduction. Need to specify more clearly, as mentioned above.\n\nResults: The results are clearly presented. The discussion of the results include important issues related to the relevance of KM, firm competitiveness, and core competence that have not been previously included in the paper - in the theoretical section or in the motivation concerning the choice of testing the HPs in the health care system.\n\nQuality of Communication: I found the manner of expression in this presentation a bit problematic. It seems that the author(s) used local English and not Standard English which makes it sometimes difficult to figure out. It affects readability. At some places it is difficult to follow the arguments. The paper requires more linguistic editing, such as:\n\nText referencing and style of referencing- As per journal’s guidelines\n\nRemove ambiguity, break large sentences into smaller ones.\nThe author can work on structure and flow more. As mentioned above, I would suggest to rearrange the theoretical section as well as the methodology to align the different parts of the paper and strengthen the results obtained.\n\nFinal Comment: Yes the paper contains interesting and significant information that justifies indexing. Recommendation: Minor Revision\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1114
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https://f1000research.com/articles/11-1112/v1
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28 Sep 22
|
{
"type": "Research Article",
"title": "Medication-related burden among patients with diabetes mellitus and its relation to diabetic control parameters: an observational study",
"authors": [
"Ayman Jamal Noori",
"Dheyaa Jabbar Kadhim",
"Muqdad Abdulhasan Al-Hilal",
"Dheyaa Jabbar Kadhim",
"Muqdad Abdulhasan Al-Hilal"
],
"abstract": "Background: Diabetes mellitus (DM) refers to a group of metabolic abnormalities that are linked with significant morbidity, death, and health-care costs. Management options for patients with chronic illnesses such as diabetes are growing more complicated, which may result in a therapeutic burden for patients. The purpose of this research was to quantify the forms of concerns diabetic individuals have with medication that influence overall burden, as well as to examine the sociodemographic and clinical factors linked with negative medication use experiences and increased levels of burden. Methods: The present research was a cross-sectional study of diagnosed diabetes patients who attended the Specialized Center for Endocrinology and Diabetes between 1st of December 2021 and 30th April 2022 in Baghdad, Iraq. The Living with Medicines Questionnaire (LMQ) was used to assess medication-related burden (MRB). Results: The study recruited 193 patients with diabetes mellitus. The participants were adults with an average age of 50±15 years. More than half (52.8%) of the participating patients were women, and more than half (51.3%) also had one or more other chronic diseases. Additionally, 23.3% of patients had polypharmacy (≥ 5 medications). More than one-third had diabetes complications: neuropathy (45.6%) or retinopathy (38.9%). The mean LMQ score was (122.8±15.5). The research revealed that most of the DM patients experienced a moderate degree of medication burden (72.5%), followed by high burden (14.5%), minimum burden (12.4%), and no burden at all (0.5%) with no patient experiencing extremely high burden (0.0 %). Patients with uncontrolled blood glucose (high HbA1c), neuropathy, or retinopathy had a significantly higher medication burden. Conclusions: The MRB among diabetic patients is at a very high level. This information may be helpful to health care professionals and policymakers seeking to understand MRB for patients with diabetes. Future studies should focus on developing interventions that help reduce such burdens.",
"keywords": [
"Diabetes mellitus",
"medication-related Burden",
"Living with Medicines Questionnaire",
"diabetic control parameters",
"Iraq"
],
"content": "Introduction\n\nDiabetes is a series of metabolic abnormalities characterized by hyperglycemia which are caused by abnormalities in insulin activity, production, or even both. Type 1 and type 2 diabetes are the most common types of diabetes.1 Type 2 diabetes is a chronic disease defined mostly by insulin resistance and high blood glucose levels, which may lead to increased morbidity and mortality.2 Type 1 diabetes is characterized by autoimmune destruction of the pancreas' beta cells, leading to absolute insulin deficiency.3 Diabetes constitutes a severe public health care issue. According to the international diabetic federation, in 2021 the total global number of adult diabetic patients was 537 million, which represents 9.8% of the total population; 73 million live in the Middle East and North Africa (MENA), which include the highest regional prevalence of 16.2%.4,5 In Iraq, studies suggested the prevalence of diabetes (13.9%). However, some Iraqi cities have a high diabetes mellitus (DM) prevalence of as much as one in five adults.6,7\n\nMany patients find it burdensome to take many medications for long-term diseases. This burden is complex and influenced by various aspects, such as medicine formulation, regimen, adverse outcomes, socioeconomic burden, and healthcare influences.8–11 Medicine has been demonstrated to make patients' everyday life more difficult, including medication administration, controlling, and traveling.8,10 Medication-related burden (MRB) affects patients' health and well-being, as well as their views and behaviors regarding treatments.8 Diabetes is a non-communicable chronic disease that needs lifelong treatment, mostly with more than one medication to achieve the target blood glucose. The prevalence of many comorbidities and diabetic complications increase the number and burden of medication use.12 Extra medication and much more complicated prescription programs have been associated with poorer patient outcomes, notably higher patient non-adherence.13,14 Increased medication complexity or burden has also been associated with higher HbA1c, healthcare costs, and death rates among elderly individuals.15–18\n\nThe purpose of this research was to quantify the sorts of concerns diabetic people have with medication that relate to total burden, as well as to examine the socio-demographic and clinical factors related with unfavourable medication use situations and high levels of burden.\n\n\nMethods\n\nOn March 23, 2021, the scientific and ethical committee of Baghdad University's College of Pharmacy reviewed and approved the research proposal that explains the aims of the present study as well as the anticipated procedures for data collection (ethics board approval code: 2615). Additionally, on November 11th, 2021, clearance was acquired from the Iraqi Ministry of Health (ethical board approval code: 110483). Before giving the questionnaire, the investigator described the goal of the research to each participant and got written consent to participate in the study. The participants were not offered any incentives.\n\nThis research was a descriptive cross-sectional study carried out on individuals who had been diagnosed with diabetes.\n\nThis study was carried out at a single location, and participants were recruited from patients who were seen at the Specialized Center for Endocrinology and Diabetes at the Al-Rusafa Health Directorate in Baghdad, Iraq, during the period from the first of December 2021 to the end of April 2022.\n\nThe statistical tool G*Power (RRID:SCR 013726) edition 3.1.9.7 was utilized to determine the sample size. To a 95% confidence level, the following have been the calculated results: Df = 194, noncentrally parameter = 3.3087, critical t = 1.6527 The sample size required to be in the range of 196 individuals (f).\n\nThe inclusion criteria of the study were diabetic patients aged 18 years and above of either sex that were diagnosed with DM at least one year before this study and used at least one pharmacological treatment for DM and were able to communicate and willing to participate in the study.\n\nThe study's exclusion criteria were patients with cognitive, hearing, or speech deficits that affect their understanding level, pregnancy or lactation, and patients who give incomplete information.\n\nSampling error may arise throughout sample selection. This is especially noticeable in retrospective cohort studies when exposure and result have already occurred. In this research, sampling error is less likely. In order to get the desired conclusion, the ideal research population is well-defined, accessible, highly reliable, and reasonable. To avoid bias, participants were recruited in such a way that persons with hearing, speech, or cognitive problems that restrict topic understanding were excluded. We also used standard words to prevent confusion.\n\nThe study questionnaire is divided into two parts. The first part contains questions about patients' demographical and clinical information, including gender, age, duration of illness, social status, education level, residence, diabetes type, other chronic diseases, monthly income, emergency attendance, and several chronic medications currently used. The second part is the Living with Medicines Questionnaire (LMQ). The Arabic version19 of LMQ version 3 was used to measure MRB experienced by the DM patients. The LMQ-3 consists of 41 items about which participants expressed their overall degree of agreement using a 5 Point Likert scale [ranging from (strongly agree) through to (strongly disagree)]. It contained eight domains: interactions and communication with health care providers (HCPs) regarding medications (five items), practical difficulties (seven items), medications cost burden (three items), side-effects burden of drugs (four items), belief about the efficacy of medicines (six items), concern about medicine use (seven items), interferences of medications with daily life (six items), and control of drug use (three items). The sum of domain scores yields a total scale score (LMQ-3 overall score) measuring the general degree of MRB, varying from 41 to 205, with higher values suggesting greater pharmaceutical loads.19–22\n\nThe researcher gathered all of the data needed for this study. After briefly describing the goal of the research and obtaining an informed consent form, the patients completed the questionnaire, which took around 15-20 minutes.\n\nAdditionally, the researcher (after patients’ permission) ordered blood sample withdrawal for the analysis of glycosylated hemoglobin in all patients involved in this study. Also, the researcher requested examining the patients for diabetic neuropathy using United Kingdom Screening Test,23 while eye examination was performed by dilated fundus examination by a specialist physician.\n\nDuring the statistical analysis, version 25 of the IBM SPSS Statistics (RRID: SCR 016479) software for Microsoft Windows was used. All research items were analyzed using descriptive statistics (means, standard deviations, frequencies, and percentages). The association between biological parameters and MRB Score was determined using Pearson correlation. Using independent T-tests and one-way analysis of variance (ANOVA) testing, the effect of patients' demographic and clinical features on MRB was determined (total LMQ Score). Furthermore, an independent T-test was employed to assess the associations between medication burden (total LMQ score) and DM control/complications (neuropathy & retinopathy). A P-value below 0.05 was considered statistically meaningful.\n\n\nResults\n\nThe study recruited 193 patients with diabetes mellitus.33 The participants were adults with an average age of (50.15±13.6 years). More than half (52.8%) of the participating patients were women, and more than three-quarters were married with primary/secondary school education. In addition, the majority (95.3%) have lived in urban areas and had low income (65.8%) (Table 1).\n\nThe mean disease duration was (9.32±7.33 years). More than three quarters (83.4%) of the participating patients had type 2 DM, and more than half (51.3%) also had one or more chronic diseases. Additionally, 23.3% of patients had polypharmacy (≥ 5 medications). Less than one-quarter (16.1%) were admitted to the emergency room during the last 12 months. More than one-third had diabetes complications: neuropathy (45.6%) or retinopathy (38.9%) (Table 2).\n\nThe mean LMQ score was (122.8±15.5). The findings showed that most of the DM patients experienced a moderate degree of medication burden (72.5%), followed by a high burden (14.5%) and a minimum burden (12.4%), and no burden at all (0.5%), with no patient experiencing extremely high burden (0.0 %) as illustrated in Table 3.\n\nFour LMQ domains had the lowest mean of burden scores (below the average): domain 1 (relationships with HCPs), domain 2 (practical difficulties in using medicines), domain 5 (effectiveness of prescribed medications), and domain 6 (concerns about drugs use). In other words, the patients had good relationships with HCPs, low practical difficulties in using medicine, reasonable belief in their effectiveness, and shared concerns about medicine use. On the other hand, four domains had the highest mean of burden scores: domain 3 (cost related burden), domain 4 (side effects of medicines), domain 7 (impact of using medications on daily life), and domain 8 (autonomy to vary regimen). In other words, the patients had difficulty with medicine costs, could not change their regimen, and their medicine impacted their daily life (Table 4).\n\nThere were no significant differences in medication burden (total LMQ) according to patient demographic characteristics (Table 5).\n\nPatients who were admitted to the emergency department (ED) last year had a significantly (P-value <0.05) higher medication burden (total LMQ) compared to not admitted patients (Table 6).\n\n* Significant (P-value <0.05) according to independent T-test; DM: diabetes mellitus; ED: emergency department; LMQ: Living with Medicines Questionnaire.\n\nThere were significant (P-value <0.05) differences in medication burden in terms of total LMQ scores according to diabetes control (HbAlc) and complications (neuropathy and retinopathy). In other words, patients with uncontrolled blood glucose (high HbA1c), neuropathy, or retinopathy had a significantly (P-value <0.05) higher medication burden (total LMQ) (Table 7).\n\n* Significant (P-value <0.5) according to independent T-test. DM: diabetes mellitus; HbA1c: haemoglobin A1c; LMQ: Living with Medicines Questionnaire.\n\n\nDiscussion\n\nDiabetes is a chronic condition requiring long-term medical treatment. Whenever lifestyle adjustments alone fail to achieve or maintain the desired glycemic control, the majority of patients are routinely recommended prescription medicine.12 The vast majority of published studies have understood the biological viewpoint of MRB as the quantity of pills or treatments frequently taken by specific patients to treat their conditions, ignoring the patient’s views.9,24 To our knowledge, no published research has quantified MRB amongst diabetic patients in Iraq. Consequently, the purpose of this research was to assess the problems diabetic patients encounter with drugs that contribute to the overall MRB and the variables that affect them.\n\nThe current study indicated that nearly all the participants (99%) suffered from varying degrees of MRB. A study in Qatar found that 90% of DM patients were suffering from MRB.19 Utilization of prescription medication to manage glucose levels and manage concomitant illnesses is an important aspect of diabetes therapy and might even greatly contribute to the MRB for this disease. The most frequent degree of MRB in the current study was moderate burden (72.5%); however, inconsistent with the results of the present study, most DM participants in Qatar were of minimum burden (66.8%). The high level of services administered to DM patients in Qatar at low cost and in one clinical setting19 may explain such findings.\n\nFour domains had the highest mean of burden scores: cost-related burden, side effects of medicine, the impact of using medication on daily life, and autonomy to vary regimen. Traditionally the focus of guidelines for clinical practice on specific diseases, the growing coexistence of various chronic conditions, and the lack of systematic strategies for addressing issues related with the implications of therapies supposed that patients with long-term illnesses such as DM had to deal with complex medication-related instructions and tasks for the remainder of their lives.25 Dealing with the unpleasant effects of medication and needing to adjust daily activities to meet the requirements of therapeutic interventions imposes an additional stress on individuals.26–28 On the other hand, the patients had good relationships with HCPs, low practical difficulties in using medicine, reasonable belief in their effectiveness, and shared concerns about medicine use. The preponderance of patients with T2DM in Iraq (76.3%) according to a prior research were adamant about the requirement of anti-diabetic therapy for ensuring constant glycemic control (scores of specific-necessity were more significant than the score of specific-concern).29\n\nThere were no significant differences in medication burden (total LMQ) according to patient demographic characteristics. However, a study in Qatar found that unmarried, female gendered DM patients demonstrated significantly higher scores of medication burden.19 Patients admitted to ED last year had substantially higher MRB (total LMQ) compared to not admitted patients. Previous studies showed that high MRB leads to decreased medication adherence,19,22 and the non-adherence to medication increases emergency room visits and hospitalization.30 Patients with uncontrolled blood glucose (high HbA1c), neuropathy, or retinopathy had significantly higher medication burdens. Diabetes-related microvascular and macrovascular complications in many patients with type 2 diabetes result in polypharmacotherapy and a high pill burden.31,32\n\nThe limitations of the present research demand examination. First, an MRB measurement was patient-reported and hence subjective. The research sample was limited to a single site; therefore, the results may not be representative of the population of individuals with DM in Iraq. Thirdly, due to the cross-sectional design of the research, we were unable to examine how these patient experiences evolved over time.\n\n\nConclusions\n\nThe medicine burden for diabetic people is at a very high level. This knowledge may assist pharmacists, doctors, nurses, and other clinicians, as well as policymakers, in comprehending MRB for people with diabetes. Accordingly, future studies should continue to measure MRB while moving the science toward developing interventions aimed at reducing such burdens.\n\n\nData availability\n\nZenodo: Demographic details, as well as questionnaire responses, https://doi.org/10.5281/zenodo.6968395.33\n\nThis project contains the following underlying data:\n\n- Article’s data.xlsx (Demographic details, as well as questionnaire responses)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThe authors thank the participants and the Specialized Center for Endocrinology and Diabetes, Alrusafa Health Directorate, Baghdad/Iraq team for their continuous support during data collection and patient interviews.\n\n\nReferences\n\nAmerican Diabetes A: Diagnosis and classification of diabetes mellitus. Diabetes Care. 2013; 36(Suppl 1): S67–S74. PubMed Abstract | Publisher Full Text\n\nCarrillo-Sepulveda MA, Maddie N, Johnson CM, et al.: Vascular hyperacetylation is associated with vascular smooth muscle dysfunction in a rat model of non-obese type 2 diabetes. Mol. Med. 2022; 28(1): 1–14.\n\nCare D: Care in Diabetes—2022. Diabetes Care. 2022; 45: S17.\n\nRashad BH, Abdi BA, Naqid IA, et al.: Risk Factors Associated with Poor Glycemic Control in Patients with Type Two Diabetes Mellitus in Zakho City. J. Contemp. Med. Sci.|Vol. 2021; 7(3): 167–170.\n\ndiabetesatlas.org: Iraq diabetes report 2000.[cited 2022 Jul 23].Reference Source\n\nAlogaily MH, Alsaffar AJ, Hamid MB: Prevalence of prediabetes among adults in Baghdad/Iraq. Editorial Board Members. 2000; 17(3&4): 215–222.\n\nMansour AA, Al-Maliky AA, Kasem B, et al.: Prevalence of diagnosed and undiagnosed diabetes mellitus in adults aged 19 years and older in Basrah, Iraq. Diabetes Metab. Syndr. Obes. 2014; 7: 139. Publisher Full Text\n\nMohammed MA, Moles RJ, Chen TF: Medication-related burden and patients’ lived experience with medicine: a systematic review and metasynthesis of qualitative studies. BMJ Open. 2016; 6(2): e010035. Publisher Full Text\n\nKrska J, Morecroft CW, Rowe PH, et al.: Measuring the impact of long-term medicines use from the patient perspective. Int. J. Clin. Pharm. 2014; 36(4): 675–678. PubMed Abstract | Publisher Full Text\n\nSav A, Kendall E, McMillan SS, et al.: ‘You say treatment, I say hard work’: treatment burden among people with chronic illness and their carers in Australia. Health Soc. Care Community. 2013; 21(6): 665–674. PubMed Abstract | Publisher Full Text\n\nSav A, King MA, Whitty JA, et al.: Burden of treatment for chronic illness: a concept analysis and review of the literature. Health Expect. 2015; 18(3): 312–324. PubMed Abstract | Publisher Full Text\n\nAb Rahman N, Lim MT, Thevendran S, et al.: Medication regimen complexity and medication burden among patients with type 2 diabetes mellitus: a retrospective analysis. Front. Pharmacol. 2022; 883.\n\nClaxton AJ, Cramer J, Pierce C: A systematic review of the associations between dose regimens and medication compliance. Clin. Ther. 2001; 23(8): 1296–1310. PubMed Abstract | Publisher Full Text\n\nde Vries ST , Keers JC, Visser R, et al.: Medication beliefs, treatment complexity, and non-adherence to different drug classes in patients with type 2 diabetes. J. Psychosom. Res. 2014; 76(2): 134–138. PubMed Abstract | Publisher Full Text\n\nLabib ALM, Martins AP, Raposo JF, et al.: The association between polypharmacy and adverse health consequences in elderly type 2 diabetes mellitus patients; a systematic review and meta-analysis. Diabetes Res. Clin. Pract. 2019; 155: 107804.\n\nRodbard HW, Green AJ, Fox KM, et al.: Impact of type 2 diabetes mellitus on prescription medication burden and out-of-pocket healthcare expenses. Diabetes Res. Clin. Pract. 2010; 87(3): 360–365. PubMed Abstract | Publisher Full Text\n\nWimmer BC, Bell JS, Fastbom J, et al.: Medication regimen complexity and polypharmacy as factors associated with all-cause mortality in older people: a population-based cohort study. Ann. Pharmacother. 2016; 50(2): 89–95.\n\nAbdelaziz TS, Sadek KM: Effect of reducing medication regimen complexity on glycaemic control in patients with diabetes. Rom. J. Intern. Med. 2019; 57(1): 23–29. PubMed Abstract | Publisher Full Text\n\nZidan A, Awaisu A, El-Hajj MS, et al.: Medication-related burden among patients with chronic disease conditions: perspectives of patients attending non-communicable disease clinics in a primary healthcare setting in Qatar. Pharmacy. 2018; 6(3): 85. PubMed Abstract | Publisher Full Text\n\nKatusiime B, Corlett SA, Krska J: Development and validation of a revised instrument to measure burden of long-term medicines use: the Living with Medicines Questionnaire version 3. Patient Relat. Outcome Meas. 2018; 9: 155–168. PubMed Abstract | Publisher Full Text\n\nZidan A, Awaisu A, Hasan S, et al.: The Living with Medicines Questionnaire: translation and cultural adaptation into the Arabic context. Value Health Reg. Issues. 2016; 10: 36–40. PubMed Abstract | Publisher Full Text\n\nAwad A, Alhadab A, Albassam A: Medication-related burden and medication adherence among geriatric patients in Kuwait: a cross-sectional study. Front. Pharmacol. 2020; 11: 1296. PubMed Abstract | Publisher Full Text\n\nSoheilykhah S, Rashidi M, Dehghan F, et al.: Prevalence of peripheral neuropathy in diabetic patients. Iranian Journal of Diabetes and Obesity. 2013; 5(3): 107–113.\n\nKrska J, Corlett SA, Katusiime B: Complexity of medicine regimens and patient perception of medicine burden. Pharmacy. 2019; 7(1): 18. PubMed Abstract | Publisher Full Text\n\nGallacher K, Morrison D, Jani B, et al.: Uncovering treatment burden as a key concept for stroke care: a systematic review of qualitative research. PLoS Med. 2013; 10(6): e1001473. PubMed Abstract | Publisher Full Text\n\nTran V-T, Montori VM, Eton DT, et al.: Development and description of measurement properties of an instrument to assess treatment burden among patients with multiple chronic conditions. BMC Med. 2012; 10(1): 1–10.\n\nTran V-T, Barnes C, Montori VM, et al.: Taxonomy of the burden of treatment: a multi-country web-based qualitative study of patients with chronic conditions. BMC Med. 2015; 13(1): 1–15.\n\nTran V-T, Harrington M, Montori VM, et al.: Adaptation and validation of the Treatment Burden Questionnaire (TBQ) in English using an internet platform. BMC Med. 2014; 12(1): 1–9.\n\nHussein EA, Kadhim DJ, Al-Auqbi TF: Belief About Medications Among Type 2 Diabetic Patients Attending the National Diabetes Center in Iraq. Iraqi Journal of Pharmaceutical Sciences. 2017; 66–74. (P-ISSN: 1683-3597, E-ISSN: 2521-3512).\n\nPolonsky WH, Henry RR: Poor medication adherence in type 2 diabetes: recognizing the scope of the problem and its key contributors. Patient Prefer. Adherence. 2016; 10: 1299–1307. PubMed Abstract | Publisher Full Text\n\nMorrish NJ, Wang SL, Stevens LK, et al.: Mortality and causes of death in the WHO Multinational Study of Vascular Disease in Diabetes. Diabetologia. 2001; 44(2): S14–S21. PubMed Abstract | Publisher Full Text\n\nStamler J, Vaccaro O, Neaton JD, et al.: Multiple Risk Factor Intervention Trial Research G. Diabetes, other risk factors, and 12-yr cardiovascular mortality for men screened in the Multiple Risk Factor Intervention Trial. Diabetes Care. 1993; 16(2): 434–444. PubMed Abstract | Publisher Full Text\n\nNoori AJ: Demographic details, as well as questionnaire responses. [Dataset]. Zenodo.2022. Publisher Full Text"
}
|
[
{
"id": "151759",
"date": "16 Dec 2022",
"name": "Ahmed Awaisu",
"expertise": [
"Reviewer Expertise Medication use optimization and outcome research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents an interesting study about patient-reported medication burden in patients with diabetes in Iraq and its relationship with diabetes control. However, major revisions are needed for the paper to be indexed. I suggest some recommendations for improvement.\nGeneral\nThe manuscript is fairly well-written. However, it requires significant editing, syntax improvement and attention to detail in several places. Definitely, this paper should undergo professional language editing by experts in the area in order to be considered for indexing.\n\nThroughout the manuscript, poor and inappropriate scientific terminologies were used. For example, \"diabetic patients\" instead of patients with diabetes, \"diabetic people\", \"complicated prescription program\", \"pharmaceutical loads \" etc.\n\nThis is a single-center study with a very small sample (193 patients) and one cannot draw generalizations from the findings; therefore, I doubt the usefulness of this study.\n\nThe Introduction needs significant improvement to identify gaps in the literature and the rationale for the conduct of the study.\n\nThe Methods section requires improvement as will be explained later.\n\nThe data require more robust statistical analysis, specifically multivariate regression analysis.\n\nFinally, the results, particularly the tables, need better presentation.\nAbstract\nThe Abstract is fairly well-written, but syntax and readability can be better in places.\n\nThe study objective is not clear and not SMART (Specific, Measurable, Achievable, Reliable, Time-framed). Please revise in the Abstract and the main manuscript.\nIntroduction\nThe Introduction and other parts of the paper contain several grammatical errors in places. Several sentences need syntax and readability improvement. Therefore, the paper should undergo language editing before it can be considered for indexing.\n\nAn Introduction should reflect “what is known”, “the gap in the literature”, “the research problem and rationale” and “the study objectives”. The Introduction has provided some insight into what is known in the literature. However, the gaps are not clearly presented and the rationale for the conduct of the study is not presented.\n\nThe following sentence is poorly written: “Medicine has been demonstrated to make patients' everyday life more difficult, including medication administration, controlling, and traveling.8,10”\n\nAgain, I would like to stress that the study objective is not SMART and not well-written.\nMethods\nThe Methods contain most of the elements required; however, most sub-sections require improvement.\n\nSetting: The study setting is not adequately described. What is this center for? How many patients attend the center monthly and annually? Who or which population in Iraq does the center serve? What about the services, facilities, and specialties available? Please also write the dates of patients' recruitment using proper conventions of writing dates.\n\nSample size: How were the parameters used for sample size estimation determined? I am not very convinced as these were unconventional parameters for a cross-sectional study.\n\nSampling technique: The sampling technique has not been described, yet the investigators concluded that there was no bias in their study.\n\nBias: As a reader, I do not agree with the content of this section. For a study that is single-centered and with no description of sampling technique, how could you assume that its findings are free of bias?\n\nStudy questionnaire: Describe the psychometrics of the original LMQ and the Arabic-translated version. What are “pharmaceutical loads”?\n\nStatistical analysis: I am very certain that the data analysis is suboptimal. The investigators should consult with an experienced biostatistician to conduct more robust analysis. For example, multivariate logistic regression analysis may be needed in order to relate the medication burden and other factors (demographic and clinical) with glycemic control. In this case, univariate regression may be warranted before the multivariate regression analysis.\nResults\n\nAuthors try to explain the finding, which is not needed.\n\nAll tables need to be revised and improved to meet the standard of tables in published articles.\n\nTable 1: Merge the column of frequency with that of %. \"Illiterate\"? Do you mean 'No formal education'?\n\nTable 2: Merge the column of frequency with that of %. I am very surprised that no patients with “nephropathy (kidney damage)” among the whole study population. It is surprising to see that in a population of patients with diabetes, there was no patient with a complication of nephropathy or CKD, which is highly prevalent.\n\nTable 3: It is really confusing how the ranges of burden were determined. Are these based on a validated method or reference?\n\nTable 5: Merge the column of mean with that of SD (it should be mean±SD). Remove the column with “Total LMQ” as it is unnecessary.\n\nTable 6: Merge the column of mean with that of SD (it should be mean±SD). Remove the column with “Total LMQ” as it is unnecessary.\n\nTable 7: Same as above\nDiscussions\nThe Discussion should be improved to focus on the major findings and to cite relevant literature. Several important previous studies are not cited. The authors should be able to do a more thorough literature search. There are several studies from USA, Malaysia, and Europe.\nConclusion\nCan be better written to reflect the study objectives and findings.\n\nDecision: MAJOR REVISION\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1112
|
https://f1000research.com/articles/11-1108/v1
|
28 Sep 22
|
{
"type": "Data Note",
"title": "Crude oil hydrocarbons' effect on soil microbial metagenome from Niger Delta polluted soils",
"authors": [
"Chidinma Peace Okafor",
"Chioma Blaise Chikere",
"Onyewuchi Akaranta",
"Khayalethu Ntushelo",
"Chioma Blaise Chikere",
"Onyewuchi Akaranta",
"Khayalethu Ntushelo"
],
"abstract": "Crude oil pollution is an endemic environmental problem in the Niger Delta region of Nigeria with background pollution levels greater than the regulatory intervention limit of 5000mg/kg of soil as stipulated in the Environmental Guidelines and Standards for Petroleum Industry in Nigeria (EGASPIN) in most polluted sites. Hence, the essence of this study was to evaluate the extent of damage caused by the pollutant (crude oil hydrocarbons) on the soil physicochemical parameters and microbial communities as well as to determine pollution effects on soil microbial ecosystem services. The soil microbial community composition, diversity, functional genes, and metabolic pathways were studied to evaluate the pollutant effect on soil microbiomes and their ability to utilize petroleum hydrocarbons as carbon and energy sources. Two sites Bodo (N4.620134, 7.282998E) and Ngia-Ama Tombia (N4.9816667; 7.0608333E) were chosen for the study. The America standard testing methods (ASTM International) were used in measuring physicochemical parameters of the soil influencing microbial response and pollutant behavior in the soil environment. Soil pH was measured using a pH meter, total petroleum hydrocarbons (TPH) using gas chromatography with a mass spectrophotometer (GC-MS), polycyclic aromatic hydrocarbons (PAHs) (ASTM D5412-93(2017) e1), Heavy metals analysis (ASTM D8404-21), soil texture (ASTM D6913/D6913M-17). Shotgun metagenomic analysis was used to determine microbial community composition, following “DNA extraction”, library preparation (Nextera® DNA Flex Library Prep Kit (Illumina, San Diego, CA), and sequencing using Illuminana NovaSeq® 6000. The results were analyzed using bioinformatics pipelines. The sequences generated were deposited in the European nucleotide Archive (ENA) with project accession number PRJEB53529.",
"keywords": [
"crude oil hydrocarbons",
"Pollution",
"Niger Delta",
"Shotgun metagenomics",
"Soil microbiomes."
],
"content": "Introduction\n\nSuccessful microbial remediation of polluted environments depends largely on the prevailing baseline physicochemical parameters, ecological conditions, available microbial community structure and their numbers and how the pollutant influences the interaction of these factors. For this study crude oil polluted soils were monitored prior to a microbial remediation project. Crude oil is a major pollutant of environmental concern. At certain concentrations it is toxic to microorganisms and other life forms within the receiving environmental compartment. It contains compounds like the polycyclic aromatic hydrocarbons (PAHs) which are priority chemicals of concern according to the United States Environmental Protection Agency (USEPA). PAHs are reported to be toxic, mutagenic, teratogenic to mammals. They bioaccumulate along the food chain and can persist in the environment. Crude oil hydrocarbons also alter the physicochemical parameters like pH, oxygen tension, and nutrient composition of receiving environment thereby affecting microbial activities within the impacted site. The Niger Delta region of Nigeria has a high incidence of crude oil pollution due to the heightened oil and gas industry activities within the region (Nwilo & Badejo, 2005). Most polluted environments within the region exceed both the regulatory intervention value of 40 mg/kg of soil or 70 μg/L for ground waters of PAHs and total petroleum hydrocarbons (TPH) concentration of 5000 mg/kg of soil or 600 μg/L for groundwater as contained in the Environmental Guidelines and Standards for the Petroleum Industry in Nigeria (EGASPIN) (Okafor et al., 2021; UNEP, 2011).\n\nThe data collected were to address the specific objectives of the study which were to:\n\n1. Investigate the effect of crude oil hydrocarbons on diversity, distribution, and functional profile of indigenous microbial communities in the polluted soils. It also sought to determine metabolic pathways utilized by the indigenous microbial population in the degradation of the pollutant.\n\n2. Determine the change if any on the physicochemical parameters occasioned by the crude oil spill.\n\n\nMethods\n\nThe data were collected from two polluted sites in Rivers State, Nigeria, namely Bodo community (N4.620134, 7.282998E) and Ngia-Ama Tombia Community (N4.9816667; 7.0608333E) within the Niger Delta region of Nigeria. The Ngia-Ama Tombia site is a moderate low land in close proximity to mangroves and creeks whereas Bodo is an upland environment. Eight (8) samples per 1000 sqm of soil at the depth of 0-30 cm were collected from each site and used for this study. The eight samples were collected, four (4) from points around the pollution point and another four (4) samples about 200m away from the point source. The samples were pooled and homogenized into duplicates per site according to proximity before analysis. The physical properties of the polluted soil were analyzed according to regulatory recommended test methods for physicochemical parameters as contained in (APPENDIX VIII-E1, EGASPIN) (Resources, 2018). Sieve analysis and hydrometer method were used to determine the proportion of sand, salt, clay and sand using the standard test methods for particle-size distribution of both soils and fine-grained soils (ASTM, 2017b; ASTM, 2021a). The soil density, specific gravity and water content by gravimetric method, were also determined to project pollutant movement within the soil. Other parameters within the polluted soil were determined and these physicochemical parameters included pH of the soil, soil conductivity, soil nutrients (nitrates and phosphate concentration) of the polluted soil. pH was analyzed according to the United States Environmental Protection Agency (USEPA, 2004) using the pH meter (Hanna multimeter reader), soil conductivity was by a modification of the APHA 145 method, whereas the nutrients, nitrates and phosphates were determined using the spectrophotometer method (PG, T60) and nutrient pillows from HACH®. The concentration of extractable total petroleum hydrocarbon (eTPH) in the soil was determined using the GC-FID protocol. The residual petroleum hydrocarbons were extracted from the samples by hexane (for slightly contaminated soils) or chloroform (for heavily contaminated soils) and the extract cleaned in activated charcoal column prior to spectrophotometry. Agilent 1760 spectrophotometer with flame ionizing radiation was used for TPH concentration determination. GC-MS protocol was used in the determination of the PAHs concentration in the soil samples after sample clean-up (ASTM, 2017a). Heavy metals analysis was done using the ASTM-D8404-21 method (ASTM, 2021b). The practice covered drying, homogenization, ammonium bifluoride-nitric acid digestion of soil samples and associated quality control (QC) samples for the determination of metals and metalloids using laboratory flame atomic absorption spectrometry (FAAS).\n\nFor microbial community analysis, shotgun metagenomic sequencing was used to determine the composition, diversity, spread and functional profile of extant microbial population within the polluted environment. The samples were processed and analyzed with the ZymoBIOMICS® Shotgun Metagenomic Sequencing Service for Microbiome Analysis (Zymo Research, Irvine, CA). Sample processing included DNA extraction, library preparation, and metagenomic DNA sequencing.\n\nDNA extraction was done using the ZymoBIOMICS®-96 MagBead DNA Kit (Zymo Research, Irvine, CA), Cat. No D4308 using an automated platform according to the manufacturers’ instructions. Following the extraction, 50 μL of extracted DNA was then used for library preparation.\n\nGenomic DNA samples were profiled with shotgun metagenomic sequencing. Sequencing libraries were prepared with the Nextera® DNA Flex Library Prep Kit (Illumina, San Diego, CA) Cat.No. 20018704 with up to 100 ng DNA input following the manufacturer’s protocol using internal dual-index 8 base pairs (bp) barcodes with Nextera® adapters (Illumina, San Diego, CA). All libraries were quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and then pooled in equal abundance. The final pool was quantified using quantitative polymerase chain reaction (qPCR). This step amplifies the Bead-linked Transposomes (BLT) tagmented DNA using a limited-cycle PCR program. The PCR step adds the Enhanced PCR mix (EPM), Nextera® DNA CD indexes (24 indexes, 24 samples) Cat.No. 20018707 and sequences required for sequencing cluster generation. Amplification was by five (5) cycles of: 98°C for 45 seconds, 62°C for 30 seconds, 68°C for 2 minutes, 68°C for 1 minutes and held at 10°C on the Applied Biosystems™ SimpliAmp™ Thermal cycler. The metagenomic library had no visualization of Ct value.\n\nSequencing depth, or coverage, refers to the number of times a reference base is represented within a set of sequencing reads. The higher the sequencing depth, the more sensitive the detection. Sequencing depth can critically affect the profiling of polymicrobial animal and environmental samples when using shotgun metagenomics. The depth needed will be determined by the sensitivity of detection required for an application.\n\nThe final library was sequenced on the Illumina NovaSeq® with a sequence depth of >15 M.\n\nRaw sequence reads were trimmed by sliding window with 6bp window size and a quality cutoff of 20 to remove low-quality fractions with size lower than 70 bp and adapters with Trimmomatic-0.33 (Bolger et al., 2014).\n\nThe ZymoBIOMICS® microbial community standard (Zymo Research, Irvine, CA) was used as a positive control for each DNA extraction, ZymoBIOMICS® microbial community DNA standard (Zymo Research, Irvine, CA) was used as a positive control for each targeted library preparation. Negative controls (i.e. blank extraction control, blank library preparation control) were included to assess the level of bioburden carried by the wet-lab process.\n\nThese data set were collected as part of the polluted site characteristic project to determine various effects of hydrocarbon pollution on soil and its indigenous microbial communities. They are also to serve as polluted site reference genomes for comparison on effect of climate and other variables on microbial response to perturbations.\n\n\nData availability\n\nThe results obtained are deposited with the European Nucleotide Archive (ENA) of the European Molecular Biology Laboratory (EMBL) repository.\n\nEuropean Nucleotide Archive: Crude oil hydrocarbon polluted soil metagenomes. Accession number: PRJEB53529 (Okafor et al., 2022).\n\nThis project contains the following underlying data:\n\n• Data file 1. Contains raw sequences of soil metagenomes from Bodo sample (BSP1) with sample accession number ERS12263116\n\n• Data file 2. Contains raw sequences of soil metagenomes from Bodo sample (BSP2) with sample accession number ERS12263117\n\n• Data file 3. Contains raw sequences of soil metagenomes from Tombia sample (TSP1) with samples accession number ERS12257751\n\n• Data file 4. Contains raw sequences of soil metagenomes from Tombia sample (TSP2) with sample accession number ERS12257752\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nASTM: Standard Test method for particle-size distribution (Gradation) of Fine-Grained soils using the sedimentation (Hydrometer) Analysis. Standard No. D7928-21e1.2021a.\n\nASTM: Standard Practice for Preparation of Soil Samples by Ammonium Bifluoride-Nitric Acid Digestion for Subsequent Analysis for Metals and Metalloids. Standard No. D8404-21.2021b.\n\nASTM: Standard Test Method for Quantification of Complex Polycyclic Aromatic Hydrocarbon Mixtures or Petroleum Oils in Water. Standard No. D5412-93(2017) e1.2017a.\n\nASTM: Standard Test Method for Particle size Distribution (Gradation) of soils using sieve analysis. Standard No. D6913/D6913-17.2017b.\n\nBolger AM, Lohse M, Usadel B: Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–2120. PubMed Abstract | Publisher Full Text\n\nNwilo PC, Badejo OT: Oil spill problems and management in the Niger Delta. 2005 International Oil Spill Conference, IOSC 2005. 2005; 11400–11403. Publisher Full Text\n\nOkafor CP, Chikere CB, Akaranta O, et al.: Crude oil polluted soil metagenomes. European Nucleotide Archive [Dataset].2022.Reference Source\n\nOkafor CP, Udemang NL, Chikere CB, et al.Indigenous microbial strains as bioresource for remediation of chronically polluted Niger Delta soils. Scientific African. 2021; 11: e00682. Publisher Full Text\n\nResources, D. of P: Environmental Guidelines and Standards for the Petroleum Industry in Nigeria. (3rd ed.).2018.\n\nUNEP: Environmental Assessment of Ogoniland. 2011; 39: 205."
}
|
[
{
"id": "269822",
"date": "17 May 2024",
"name": "Raghavendran Sivasubramanian",
"expertise": [
"Reviewer Expertise 1. Wastewater treatment2. Aerobic sludge3. Linear regression statistics4. Algae biodiesel5. Advanced reduction process6. Environmental Sustainability"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nVerdict: Rejected The study wanted to evaluate the extent of damage caused by crude oil hydrocarbons on the soil physicochemical parameters and microbial communities as well as to determine pollution effects on soil microbial ecosystem services. This article is not approved. For the following reasons: 1.\n\nThe primary reason for the rejection of this article is the lack of results and analysis. The results are tagged to a different repository and are not discussed at all. Journal publications require extensive discussion of results and findings with ample support of evidence. This paper does not show any such efforts. 2.\n\nThere is no introduction to the paper. Journal papers require a detailed introduction ranging to a couple of pages. The paper should have been structured around the concerns of crude oil soil contamination of the environment, types of remediation reported in the literature and their challenges, and why the authors’ study adds benefits to the existing literature. 3.\n\nThe study overall is incomplete. The objective seems to be limited to understanding the effects of crude oil on the microbial communities for which there is ample information in the literature. The intent of the paper should focus on the remediation strategies to mitigate crude oil pollution in the Niger Delta and investigate the effects on microbial communities in the process. Those findings would enhance the paper.\n\nIs the rationale for creating the dataset(s) clearly described? No\n\nAre the protocols appropriate and is the work technically sound? No\n\nAre sufficient details of methods and materials provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1108
|
https://f1000research.com/articles/11-1106/v1
|
27 Sep 22
|
{
"type": "Research Article",
"title": "Design And Development of a Remote Monitoring Agent For Energy Service Companies In The Telecommunication Industry",
"authors": [
"Sunkanmi Oluwaleye",
"Francis Idachaba",
"Francis Idachaba"
],
"abstract": "Background: Energy Service Companies (ESCOs) for telecommunication sites operate by providing reliable power supply at 100% uptime and billing the mobile operators accommodated on their sites for power usage. To achieve this, there is a need for them to accurately meter the power consumed by connected telecommunication equipment. Method: This work focused on the design and implementation of a remote monitoring agent (RMA) that will pool both power and environmental data from a telecommunication site. The data pool can be presented as real-time data on the RMA’s webpage, it can be downloaded as historical data, and it can be sent to a remote cloud server at regular intervals. The RMA collects both power and environmental data over an RS485 Modbus network and I2C bus respectively. An alternating current (AC) energy meter and a direct current (DC) energy meter were used to harvest the energy data while the environmental data were harvested using a developed Input/Output controller board based on an Atmega328P microcontroller. Raspberry pi was used as the master controller and Node.js was used to build the application running on the master controller. Result: The result showed how both power and environmental data can be harvested from a telecommunication site and locally presented on the web dashboard for real-time monitoring of the site power system. The data could be saved locally on the RMA and downloaded for future use. Conclusion: The implementation of this work provided a prototype of the remote monitoring agent (RMA) that can be deployed by Energy Service Companies (ESCOs) in the telecommunication industry to monitor the usage of the power systems on a cell site.",
"keywords": [
"Monitoring",
"Raspberry pi",
"Atmega328P",
"Node.js",
"RS485 Modbus",
"Power",
"Telecommunication",
"Programming",
"Communication."
],
"content": "Introduction\n\nThe global increase and acceptance of mobile technology has dramatically led to demand for internet penetration by both mobile operator companies and end-users. In other to meet this demand without increasing the environmental pollution the proliferation of masts that individual mobile operators would have caused.1,2 The government of countries like Nigeria has made rules to encourage infrastructure sharing among the mobile operators and the tower companies (Towercos) or energy service company (ESCOs) have availed themselves of this opportunity.3 The ESCO provides the platform for multiple mobile operators to share passive infrastructures such as mast, shelter, space, and the required power supply system.4 This also reduces the initial cost of building site infrastuture by new entance.5 The ESCOs make revenue from the rent and power consumption fees paid by the mobile operators. However, the ESCOs pay fines when failing to meet up with the 100% power uptime required by the mobile operators’ equipment.6 Hence, for the ESCOs’ operation model to be profitable, one of the important measures that must be ensured is that each tenant’s equipment is well metered so that mobile operators can be accurately billed for the power consumed by their equipment.\n\nIn this work, a remote monitoring agent (RMA) that will pool both power and environmental data from mobile operators’ equipment was developed. The data pool could be presented as real-time data on the RMA’s webpage, it can be downloaded as historical data, and it can be sent to a remote cloud server at regular intervals. The remote monitoring agent (RMA) hardware was designed and built using Raspberry Pi 3 B+, IO board built on Atmega328P microcontroller, AC energy meter (Hop energy meter model: DTZ1737), DC energy meter (Hop Energy meter model: DJZ1737), and 3G USB modem as shown in Figure 1. The energy meters were manufactured by Chengdu HOP Telecom Co., Ltd. Node.js (Node.js, OpenJS Foundation) was used to develop the application running on the Raspberry Pi (master controller) and the C programming language was used to program Atmega328P microcontroller using Arduino IDE (Arduino IDE 1.8.19, Arduino).7 One RMA was deployed for one telecommunication site in Lagos, Nigeria, to monitor the pattern of power consumed by all the mobile operators accommodated at the site.\n\n\nLiterature review\n\nProviding a reliable and affordable power solution for telecommunication sites has been a major source of concern in the industry.8 The power solution architecture generally implemented is shown in Figure 2.9 Typically, the power solution will have AC-DC converters (rectifiers) that convert the AC power source coming from either the grid power supply or the AC Genset to DC power that charges the battery and powers the tenant loads.6,10 The optional DC-DC converter in the power solution will be an MPPT (maximum power point t racking) solar charge controller for sites implementing hybrid power solutions.10,11 The DC-DC converter delivers DC power in an acceptable voltage range to the output power bus of the power equipment. The power from the DC-DC converter can be complemented with the battery bank to reduce Genset run hours, which provides financial savings and a reduction in the emission of carbon dioxide into the atmosphere.\n\nDC: direct current, AC: alternating current, PV: photovoltaic.\n\nMany works have been done to provide reliable and cost-saving power solutions to telecommunication sites. A study12 designed and implemented a solar hybrid power solution for off-grid telecommunication sites; a diesel generator was used to support the site whenever there was insufficient energy harvested from the solar system. The system, after implementation, reduces operation costs by 80%. To further avoid the environmental pollution caused by the diesel gensets,8,13 presented the use of proton exchange membrane fuel cell (PEMFC) as an optimized and environmentally friendly power solution for the telecommunication site.\n\nA remote monitoring system is just as crucial for ESCOs involved in the telecommunication tower industry as putting in place a reliable power solution for the sites under their management.8 Utilize monitoring of power distribution and consumption to keep tabs on the installed power solution's energy and performance parameters. For the purpose of gathering environmental information, such as internal and external temperatures and relative humidity, a wireless sensor network based on the ZigBee standard was used.14 Similarly, the power consumption by the telecommunication equipment, cooling devices, and other auxiliary devices were all collected. This data was used to analyze the energy balance of the solution, which revealed how energy was distributed at the site.15\n\nAnother study,16 focused on building a low-cost remote monitoring system for a solar plant using RS485 Modbus RTU communication with Raspberry Pi. To efficiently monitor the system for preventive maintenance, the raspberry pi pooled operational data from the plant's solar charge controller and uploaded it to a dedicated central server. RS485 RTU communication protocol is frequently used for data transfer between the main controller and other peripheral devices in embedded solution. Its key benefits are long-distance data transfer and great robustness to an electrically noisy environment… Multiple nodes (up to thirty-two) can be connected and communicate over the RS485 RTU bus.17,18 demonstrated a master-slave RS485 communication network using a Raspberry Pi as a Modbus master and Arduino Pro minis as slave nodes. The user could edit the programs of the master and slave nodes from the built mobile application using a graphical language. The Raspberry Pi acted as the master and the server for the web application, while the Arduino boards served as the slave nodes.19 used the I2C communication protocol to integrate legacy equipment to the industrial internet of things (IIoT) infrastructure. I2C communication is also like RS485 Modbus but I2C is a synchronous serial communication protocol that can have multiple masters and slaves on the same bus network of connected devices.20 The use of these communication protocols enables the remote monitoring agent to collect data from multiple sensors installed on the telecommunication.21,22\n\nThe aim of this work is to implement most of the technologies reviewed above to develop a RMA that meet the need of ESCOs in the telecommunication industry. The RMA served as data collection unit and was able to present real-time power and environmental data locally over its web interface. The RMA should also send data and alarm events to a cloud server for remote monitoring over the cloud. The unique identification of the telecommunication site can be done on the configuration page in the RMA’s local web page.\n\n\nMethods\n\nThis work can be categorized into two major developments; the development of the RMA’s hardware and the development of the RMA’s software. A Raspberry Pi 3 B+ board and Atmega328P microcontroller are the controllers used for the development of the RMA. The Atmega328P was used to develop an IO controller board that interfaced with field devices such as temperature sensors, voltage measurement circuits, digital input sensors, and digital output actuators. The Raspberry Pi was used to pool site power data from RS485 Modbus enabled energy meters, as shown in Figure 3. Arduino IDE (integrated development environment) was used to program the Atmega328P, while the Raspberry Pi was programmed with bash shell scripting and Node.js.\n\nRemote monitoring agent (RMA), Input/output (IO). DC: direct current, AC: alternating current, I2C: Inter-Integrated Circuit, RS485: ANSI/TIA/EIA-485, USB: universal serial bus.\n\nThis involves the design and implementation of both the hardware and software required to build the RMA. It included the design and implementation of the data acquisition controller board and programming the Raspberry Pi as the master controller to pool data from the data acquisition controller board and the connected energy meters. The Raspberry Pi locally stored the site data and also upload the data to a cloud server every two minutes. The software tools used to design and develop the data acquisition controller board or input/outpot (IO) board are EasyEDA and Arduino IDE. The EasyEDA software23 was used for the electronics design and generating the printed circuit board (PCB) Gerber file format was used for the PCB production. Arduino IDE version 1.8.19 was used to program the Atmega328P for digital and analog input processing that produced the digital output signals that controlled the actuators connected to the RMA. The digital input states and the analog input values captured by the RMA were shared with the master controller (the Raspberry Pi) over I2C serial communication. Windows 10 OS HP intel Core i5 8th generation PC (personal computer) was used as the programming device and for the PCB design.\n\nAs shown in Figure 4, the Atmega328P was the principal component of the IO board, the digital input circuitry was built with 12Vdc relays. The digital output circuitry was built with 5Vdc relays, BC547 transistors, 1N4007W diodes, and 1kΩ resistors. The programming device, PC used the programable universal synchronous/asynchronous receiver/transmitter (USART) port of the microcontroller for program data transfer and serial data monitoring for debugging purposes. The IO board was powered with 5Vdc. The main hardware materials required to build the IO board (Table 1), are Atmega328P microcontroller (with preloaded bootloader), 16MHz crystal, 10kΩ resistor, 1kΩ resistor, 100Ω resistor, 5.1kΩ resistor, 5Vdc PCB board relay, 12Vdc PCB board relay, BC547 transistors, 1N4007W diodes, 47pF ceramic capacitor, 10uF electrolytic capacitor, and WJ2EDGV-5.08-8P terminal connectors.\n\nDC: direct current.\n\nS/N: Item Number, DC: direct current, Conn: connector, PCB, printed circuit board.\n\nEasyEDA, an online electronics design and PCB development platform, was used because it does not require local software installation on the PC.23 The design was done online and saved in the cloud, to be accessed with any PC in the future that has minimum specification of Windows 7 and above, 1 gigahertz (GHz) processor, 1 gigabyte (GB) (32-bit) or 2 GB (64-bit) RAM (random access memory), 16 GB (32-bit) or 20 GB (64-bit) Hard disk space, Microsoft DirectX 9 graphics device with a Windows Display Driver Model graphics card, and internet access. The electronic circuitries of the IO board were designed with EasyEDA using the available electronics components on the platform and component packages were also created for the components that were not available on the platform to create mounting space for it on the PCB board. The most important component of this design was the Atmega328PU microcontroller, and all other circuitry was built around this microcontroller as shown in Figure 8. This microcontroller is based on the Advance Virtual RISC (AVR), developed by Microchip. It supports 8-Bit data processing with 32kB internal flash memory, 1kB electrically erasable programmable read-only memory (EEPROM), and 2kB static random-access memory (SRAM).\n\nThe Atmega328PU microcontroller component was first picked on the EasyEDA design sheet. Each component placed on the sheet was linked to other components using the wire tool. To avoid the complexity of the wiring arrangement, a tool called netPort was used to connect one point of a component to another component without drawing wires on the design sheet. The important circuitries to consider in this design are the digital output circuitries, digital input circuitries, and the DC voltage measurement circuitry.\n\nThe digital output circuitry is functionally called the relay driver circuit. The circuit consist of a 5Vdc relay which was controlled by the digital output of the Atmega328P to switch relatively larger current and higher voltage on its dry contact. The relay driver circuit consists of a transistor, resistor, and diode. The transistor was used as an amplifier; it amplified the small current flowing from the microcontroller output pin so that full current from the 5Vdc power supply source can energize the coil of the connected relay. The resistor was used to bias the transistor, and the diode was used to prevent reverse current produced on the relay’s inductor coil from damaging the output pin of the microcontroller. Finally, an LED (light emitting diode) was added to show the state of the IO board digital output pin. In operation, the incoming voltage source to be switched is connected to the common of the relay labeled C and the outgoing end is connected to the normally open terminal labeled NO. This drawing schematic for this circuitry is shown in Figure 5.\n\nGND: ground, NC: normally close, NO: normally open.\n\nThe digital input circuitry is comprised of a 12Vdc relay. The coil of the relay was driven by the 12Vdc voltage supply, one terminal of the relay coil was already terminated to the positive 12Vdc source on the board while the negative 12Vdc ground (GND) was wired to pass through the digital sensor switch to close the circuit that energized the relay coil when the signal event was sensed. The relay common terminal was connected to the 5Vdc GND, when the relay would be energized the common terminal became connected to the normally open terminal on which the microcontroller digital input pin was connected. This schematic is shown in Figure 6.\n\nThe DC voltage measurement circuitry was designed with 100kΩ and 5.1kΩ resistors, and a Zener diode. The resistors were wired to serve as the required voltage divider circuit that ensured that the voltage to the microcontroller analog input pin did not exceed 5V when the DC voltage range of 0–100V was measured. The Zener diode served as a protection for the microcontroller if the supplied input voltage was higher than the acceptable voltage range the circuit could measure. The schematic is shown in Figure 7. The formula to to calculate resistor labelled 8 (R8) in the Figure 7 is given in equation 1.\n\nWhere Vin is the maximum voltage that can be measured. The general formula to find the Vin is given in equation 2.\n\nThe components listed in Table 1 were locally purchased in an electronics shop and soldered to the printed PCB board according to the design in Figure 8. The soldering was carefully done to avoid possible short circuits that excessive soldering lead could cause. After soldering, the PCB board was properly cleaned to remove unwanted leads that could affect the operation of the board.\n\nGND: ground.\n\nVin: voltage input, GND: ground, R: resistor.\n\nThe IO board’s microcontroller was programmed with C programming language using Arduino IDE, an open-source IDE that makes it easy to program and upload code to Arduino boards. The software was installed on an Intel Core i5 HP computer. An Arduino Uno revision 2 board hat had no Atmega328P installed was used as the programming interface for the microcontroller on the IO Board. The program data transfer was done via the programmable USART (universal synchronous asynchronous receiver transmitter) port of the Atmega328P microcontroller at Tx (transmitter) and Rx (receiver) pins. From Figure 9, the Arduino Uno board was acting as the USB to transistor-transistor logic (TTL) Converter doing the required level shifting.\n\nTX: Transmitter, RX: Receiver, USB: universal serial bus, GND: ground.\n\nThe C code was written and compiled on the Arduino IDE. The program structure is described by the flow chart algorithm given in Figure 10. The program entry point started from loading all the required libraries. These libraries were prewritten software that was used to extend the functionality of the sketch (Arduino code) written for the IO Board microcontroller. The libraries were as follows:\n\n➢ Wire library: the library was used to access the SDA (Data line) and SCL (clock line) pins on the microcontroller for I2C communication with other connected I2C devices. In this case, the I2C device to communicate with was the master controller built on Raspberry Pi 3B.\n\n➢ MillisDelay library: a part of the SafeString V3+ library; the library was used to implement non-blocking delay timers in the Arduino IDE sketch. These non-blocking delay timers were used to control when the I2C data byte would be read by the master device and when the sensor values would be captured from the connected sensors\n\n➢ TinyDHT library: from Adafruit; this library was used to read temperature and humidity values from the DHT22 temperature and humidity sensor.\n\nI2C: inter-integrated circuit.\n\nAfter loading all required libraries, all variables’ initializations were done and the program endless loop began as shown in Figure 10.\n\nIn other to work with power and energy measurement values that can be industrially trusted and acceptable, AC and DC energy meters were purchased from Chengdu HOP Telecom Co., Ltd, a company with certification and necessary compliance to produce energy meters. Both the DC and AC energy meters supported the RS485 RTU communication protocol. The DC meter came with six current sensors for six channels of power metering function using advanced measurement chip technology such as SMT (surface–mount technology). The AC meter was a three-phase four-wire smart meter with a single channel, primarily dedicated to capturing the Genset's energy values. The meter has performance compliance with GB/T 17215.321-2008 (AC measuring special equipment requirements). Also, its communication protocol complied with DL/T 645-2007 (Multi-function Energy Meter Communication Protocol) and YD/T 1363.3-2005 (Communication station power, air conditioner, and environment concentrated monitoring management system). The meter was supplied with three current sensors that measured each phase current of the Genset.\n\nThe AC meter had a single channel of three-phase input current measurement for the three-phase output power supplied from the Genset. Table 2 shows the properties of the AC meter; it could measure AC input current up to 400A per phase. The working voltage was within DC 40V~273V or AC 40V~264V. 48VDC was used to power the AC meter since it was deployed in a telecommunication site where the available nominal voltage was 48VDC. The wiring of the AC meter was done as shown in Figure 17. The labels L1, L2, L3, and N, were for the three-phase voltage sampling for the AC meter; the meter measured the phase voltages from this port. Power to the three current sensors and the measured current values from the sensors were respectively connected to ports labeled L1CT, L2CT, and L3CT. The connection points labeled A and B was the port for the RS485 communication with the master controller.\n\nDC: direct current, A: amperage, RTU: remote terminal unit.\n\nThe AC meter shared its measured and calculated values with the master controller (Raspberry Pi) via an RS485 communication protocol. The protocol communication para meters for the established RS485 network were given as 9600, 8, N, and 1 are respectively the baud rate, data length, parity, and the stop bit. All the devices communicating over the network were set to have this same communication protocol parameters. The AC meter Modbus communication parameter was set using the Modbus register map supplied by the manufacturer manual24,25\n\nThe DC meter features are shown in Figure 13. It had six power monitoring channels, and each channel had a current sensor of type hall sensor, which was developed using the open-loop Hall effect. The specification of the current sensor is given in Table 4. The nominal operating voltage of the DC meter was -48V having its positive terminal grounded as required in a typical telecommunication site power design.6 However, the DC meter could still operate within the voltage range of -60Vdc to -40Vdc. Both the energy measurement range and power range, as shown in Table 3, are sufficient for the application. Each current sensor was expected to measure the current consumed by the equipment installed by a particular mobile operator (tenant) on the site. The maximum current the hall sensor (model number: HL01-40-400P104) can measure was 400A, far higher than what a single tenant could consume. The wiring between a single hall sensor and the DC meter is shown in Figure 12. The DC meter powers the hall sensor with 12VDC, the GND of the meter and the hall sensor were connected, and the hall sensor signal output Vout is connected to the DC meter Vin signal input. All the six current sensors were wired as shown in Figure 13, the meter was powered from the 48Vdc source connected to its power supply port. The meter was connected to the Modbus network using its RS485 port.\n\nL1: Line 1, GND: ground, AC: alternating current, L1CT: line 1 current transformer.\n\nDirect current (DC), ground (GND). Vin: voltage in, Vout: voltage out.\n\nLCD: liquid crystal display, RTU: remote terminal unit.\n\nA: amperage, V: voltage, DC: direct current, Hz: Hertz, Ω: omhs, C: Celsius.\n\nThe first thing to do in integrating the DC meter was to set the meter’s Modbus communication parameter to 9600bps baud rate, 8 data bits, none parity check and 1 stop bit. The procedure used was similar to how the Modbus communication parameter of the AC meter was set. The only differences were that register addresses and acceptable register values were different. Relevant energy data were pooled using the Modbus register map supplied with the meter. With this parameter setting, the DC meter was able to communicate on the Modbus network.25,26\n\nThe master controller was built with Raspberry Pi B 3+, a mini microcomputer running on the Raspbian operating system developed from the Linux distribution Debian. Raspberry Pi has a lot of hardware peripherals that made it suitable for this project as shown in Table 5; it has four USB ports, 2.4 GHz and 5.0 GHz IEEE 802.11ac wireless onboard and 40 GPIO (general-purpose input/output) pins.25,27\n\nCPU: central processing unit, SoC: system on chip, RAM: random access memory, GPU: graphics processing unit, USB: universal serial bus, GPIO: general purpose input/output.\n\nThe master controller was wired to other sub-units, as shown in Figure 1. The USB to RS485 converter was used to connect the master controller to the Modbus network using one of its USB ports.28 The Modbus network was made of two wires that were looped across the RS485 interface of the three devices (the DC meter, AC meter, and Raspberry Pi) connected to the network. The IO board was connected to the Raspberry Pi via the I2C serial communication interface. The I2C interface on SDA1 and SDL1 on pin 3 and 5 of the Pi GPIO were connected to the CN2 terminal, pin 5 and 4, routed on the PCB board to pin 27 and 28 of the Atmega328P microcontroller respectively.\n\nThe 3G USB modem was plugged into one of the free UBS ports on the Pi to provide internet access, as shown in Figure 20. 5Vdc was supplied to Pi from a 12/5Vdc DC-DC converter to power it.\n\nAPI: application programming interface, DC: direct current, AC: alternating current, IO: input/output, USB: universal serial bus, 3G: third generation, VPI: virtual private internet.\n\nI2C: inter-integrated circuit.\n\nPPP: point to point protocol, USB: universal serial bus.\n\nNPM: node package manager, I2C: inter-integrated circuit.\n\nRMA: remote monitoring agent.\n\nThe software architecture used for the development of the RMA is shown in Figure 14. The software component can be divided into two parts. The Node.js application and the shell script or Linux-based terminal commands. The shell script was used to configure the Pi’s hardware peripheral operations. As shown in Figure 15, the function of the shell script programs used in the development could be categorized as 3G USB modem initialization and configuration, node.js application startup scripts, I2C hardware configuration, the configuration of Wi-Fi hardware as Wi-Fi hotspot spot to connect other Wi-Fi devices. Terminal commands were used to install node.js and MongoDB (MongoDB Inc) (RRID:SCR 021224) server.\n\nThe software development depended on some already existing libraries in the node.js ecosystem and Linux OS-based libraries compatible with the Raspberry Pi platform. The Linux OS-based libraries were developed using bash shell scripts/programs, while the node.js libraries were developed with JavaScript programming language. Figure 16 shows the development pattern; apt-get command was used to install all the Linux-based dependencies for the development, and node package manager (NPM) was used to install all the dependencies/libraries required for the developed node.js application.29\n\nIn this work, both the executable bash shell script files and the terminal commands used for the development were referred to as shell scripts. This shell script was fundamental to getting the Raspberry Pi to function as expected. Figure 17 shows how the Raspberry Pi was connected to the internet using the USB modem. Three Linux-based libraries were required as follows:\n\n➢ USB-modeswitch: This library was used to set the 3G USB device to modem mode instead of storage mode.\n\n➢ PPP (point-to-point protocol): This is a TCP/IP protocol library used to connect one computer system to another over the internet.\n\n➢ Wvdial; This is a Linux OS-based intelligent point-to-point protocol dialer library used for modem-based internet connection.\n\nWhen initiating an internet connection, a custom shell script was developed with the algorithm shown in Figure 18. At boot-up or if the internet connection was not detected after 40 minutes, the script initiated the wvdial program that started the PPP to try a modem-based connection to the internet. This connection procedure was possible because the USB-modeswitch had forced the USB modem to the modem mode as shown in Figure 24.\n\nCN: connector, SCL: serial clock line, SDA: serial clock line, AC: alternating current, DC: direct current.\n\nThe Node.js programming environment was set up by installing both the Node.js and MongoDB with the apt-get command, as shown in Figure 16.30,31 Installation of the Node.js package automatically comes with the node package manager (NPM) software. NPM was used to install all the application dependencies or libraries. The application's information and dependencies were stored in the package.json file. Visual Studio Code (Microsoft, 2015) (vscode) was the code editor used to develop the Node.js program on an intel core i5 HP computer running on Windows 10. Putty was the secure shell (SSH) client software used to connect to the terminal console of the master controller (Raspberry Pi) via the Wi-Fi connection or LAN connection through an ethernet cable. WinSCP, an SSH File Transfer Protocol (SFTP), was used to share programming files between the Windows PC and the Raspberry Pi. All the codes were written in vscode and uploaded to the pi using the WinSCP software.\n\nThe Node.js application building blocks are shown in Figure 19. Express.js was the web framework used; it was integrated with passport.js to support the implemented authentication; it was also integrated with body-parser.js to provide access to the middleware passed data from incoming requests. Finally, express.js handled all HTTP (Hypertext Transfer Protocol) requests and responses that the application covered.\n\nThe critical part of this application was the data handling; how data were captured from external devices like the energy meters, the IO controller board, and the web application front-end. Also, this includes how data were stored and retrieved from the database, and how real-time data were shared with the application front-end (user interface) and the application programming interface (API) calls.\n\nThe two programming files that contain the algorithm that handled this data management were tool.js and operationData.js. The tool.js imports mongoose.js, a library that provided API endpoints to interface with MongoDB databased in the node environment.32 Tool.js has several functional modules that carry out database-related operations. These functions were exported to the index.js where they were to serve requests and make API calls.\n\nThe operationData.js imported modbus-serial.js and i2c-bus.js to connect to the RS485 Modbus network and I2C Bus respectively. There were functions on operationData.js that were called from index.js to retrieve data from the RS485 network and I2C Bus, these real-time data were shared with the user interface every two seconds. Also, these real-time data were uploaded to a cloud application and stored on the local database every two minutes. If the cloud data upload failed, the data would be stored on the buffered data collection in the database until the cloud data upload was successful, then the buffered data collection would be uploaded to the cloud, and the buffered collection data would be deleted from the database.\n\nFigure 20 shows the MongoDB data structure developed for the project. The data collections were created automatically on the MongoDB server when the tool.js used the data model created from user.js, operation.js, deviceStatus.js, configuration.js, and bufferedData.js files in the model’s folder. Successful connection to these models from the tool.js made it possible to insert data into the collection, read or find data from the collection, update data in the collection and delete data from the collection.\n\nThe algorithms that powered the node.js application could be divided into three parts for better understanding as follows36:\n\n1) The first part was the collection of codes that runs only once after the program has started. Figure 21 shows the flow chart of the set of algorithms that ran once when the application started. All the dependencies/libraries were first loaded into the application from the node module folder, also other created program files were loaded from their respective files. Libraries like passport.js and body-parser.js were initialized and integrated to express.js (node.js web application development framework). The next step was to declare the application’s global variables, the most important ones are the currentOperationData and deviceStatus variables. Both are objects, the currentOperationData holds all the data pooled from the Modbus network and the I2C bus. The Modbus network comprised the AC meter and DC meter, data from these meters were pooled and temporarily kept in currentOperationData. Similarly, data from the I2C bus were pooled from the IO board and also kept in currentOperationData. The deviceStatus object holds the state of the RMA, such as, the number of items in the buffer, commissioning status, the site ID, server connectivity, internet connectivity, etc. Other data kept in the currentOperationData were some of the data in the deviceStatus object and the controller time captured. The freshStart function would be called to retrieve previous deviceStatus data saved in the database before the last shutdown. The data retrieved were passed into the newly created deviceStatus object. The last part of the flow chart for this set of algorithms that run once was starting the server with express.js using the process environment port (if the application is deployed to the cloud) or using port 8080. For the RMA, port 8080 will always be used. The server continuously listens to HTTP requests on this port if the application was running. Now, the RMA’s node.js application was ready to serve both GET and POST requests coming from the RMA front-end or coming from RMS (The remote monitoring server installed in the cloud).\n\n2) The second set of algorithms were ran every four seconds. The flow chart for this set of algorithms is shown in Figure 22. The primary function of these algorithms was to update the currentOperationData object. The loop starts by calling the handleInitialization function; this function was used to ensure that the version of site configuration details on the RMA was the same as the one in the RMS. If there was a difference, the function that updates the site configuration details was called. The internet connectivity was checked, and its state was updated in the currentOperationData object. Then the function getOperationData was called; this function was imported from the operationData.js file into the index.js file. The function pooled data from the AC meter and DC meter over the Modbus network, the data retrieved was used to update the currentOperationData object. Function handleAlarm was called to update the alarm array and the algorithm checks if the system time has been updated. If the time was not updated, the function getDate4rmMeter would be called, and the date value retrieved from the meter was used to set the Raspberry Pi time. Furthermore, function getI2CData was called to pool data from the IO board over the I2C bus to update the currentOperationData. Finally, the deviceStatus object was updated in the database and the program waited for four seconds for the loop to start again.\n\n3) The third set of algorithms is shown in Figure 23, its primary function was to manage how operation data held in the currentOperationData object were uploaded to the cloud and saved locally on the master controller. The first step was to check for internet connectivity, if the internet connection was not available, the currentOperationData data object was stored in the buffered data collection and operation data collection on the database, and the bufferedItem value was incremented. If there was internet connectivity, the program checked if the value of bufferedItem was greater than 0, if this was true, it uploaded the buffered data to the cloud and empty the buffered data collection if the data upload was successful. If the buffered data collection was successfully emptied, the bufferedItem would be reset to 0 value. Then the program proceeds to save the currentOperationData to the operation data collection on the local database, the program also returned to this same point directly if the value of bufferedItem was not greater than 0. Finally, the currentOperationData object was uploaded to the cloud, and if the data upload failed, the data would be stored in the buffered data collection as shown in Figure 23.\n\nThe electrical components for RMA were wired as shown in Figure 24. The 48VDC from the output of the rectifier installed on the site was connected to the incoming terminal of the surge protection enabled circuit breaker (CB-S). The outgoing of the CB-S was connected to power both AC and DC meters and it was also wired as input to 48/12V DC-DC converter. The output of the 48/12V DC-DC converter was connected as an input to a 12/5V DC-DC converter and wired to power the red and green pilot lamps. The output of the 12/5VDC-DC converter powered both the IO board and master controller (Raspberry Pi).\n\nThe 12VDC relay soldered to the IO board needed 12V power for the relay coil to be energized, hence, 12V output from the 48/12V DC-DC converter was also wired to the 12V terminal port of the IO board. The negative of the 12VDC was wired through the door switch to CN1 pin 3 as an input signal that senses the state of the door.\n\nFour current sensors were connected to the DC meter as shown in Figure 13, while three current sensors were connected to the AC meter as shown in Figure 11. The Modbus network connection was made with a 1mm two-core cable, one of the cores looped all the RS485-A terminals of all the Modbus devices together, and the second core looped all the RS485-B terminal of the Modbus devices together as well as shown in Figure 13. All the components were assembled on a 400mm by 300mm by 200mm outdoor panel as shown in Figure 24B shows the final assembly of RMA.\n\nI2C: inter-integrated circuit.\n\n\nResults\n\nAll the hardware was connected and assembled in the panel as shown in Figure 24B. The final assembly picture is shown in Figure 25B, extended from the RMA panel were three current sensors for the genset three-phase power supply. Also, four DC current sensors extended from RMA were for current measurements, met to capture the current consumed by the mobile networks’ equipment and the installed battery bank. The cables available for external connections were two core cables that supplied 48Vdc power to the RMA. And a four-core cable that should be connected to the three-phase plus neutral of the AC source for the AC meter’s voltage sampling. The humidity and temperature sensor hung below the RMA panel and the battery temperature sensor was dropped inside the battery cabinet. A standing frame was built for the RMA panel as shown in Figure 26A to make the site installation easy.\n\nThe installation permission was requested for the unit to be installed on a live telecommunication site. This was granted after the installation process was reviewed and it was confirmed to be traffic not affecting. The unit was moved to the site and all the necessary cables were connected as shown in Figure 25. The current sensors shown in Figure 25A could be clamped to the connected equipment cables without disconnecting the cables making the installation seamless without disconnecting tenants’ equipment from power during the installation.\n\nThe RMA was powered with 48Vdc after the site installation, the main controller booted up for about 45 seconds and the RMA Wi-Fi interface was available for connection as shown in Figure 27. The Wi-Fi connection was enabled with WPA2 (Wi-Fi Protected Access 2) authentication to prevent the connection from an unauthorized user. After a successful WiFi connection was made to the RMA, the user could access the web interface by typing the IP address 192.168.50.10 to the address bar of any web browser. To further prevent unauthorized users and establish access control, the user had to login to the RMA web page as shown in Figure 28. The user could either log in as Admin or Operator username with their respective passwords. The Admin has access to the configuration page, export data page, and robot the main controller button while the Operator user does not have access to these operations but can only view the site details.\n\nAfter successful login, the user would be redirected to the dashboard shown in Figure 29. The dashboard contains the overview of site operation data and presented the tabs to access other functionalities.\n\nThe top of the dashboard gave information about the site status, if the site was already commissioned, the site name and site ID text value will be shown as presented in the dashboard shown in Figure 29. The site name was Lagos Central, and the site ID was Ts_LG_1210A, these values will be “Not Available” if the site has not been commissioned. The value for the label server connection could be “Connected” or “Not Connected” if the RMA was able to upload site operation data to the cloud server, the value of server connection would be “Connected” and the value would be “Not Connected” otherwise. The label System Voltage gave the value of the DC voltage captured on the site. This voltage was common to the voltage of the battery bank, the tenant’s equipment voltage, rectifier output voltage, and the voltage connected to power the RMA. The local time captured was the time of the main controller, this time was always corrected at boot up using the time of the DC meter pooled over the RS485 network. The DC meter has a complementary metal-oxide semiconductor (CMOS) battery that accurately kept the time at no power. The internet status label displayed “Online” when the RMA was connected to the internet and “Offline” would be displayed if there was no internet connection. There was an algorithm on the main controller that checked the internet connectivity at every four seconds interval.\n\nThe genset line voltages, currents, energy consumed, power consumed, and frequency were shown under the genset section of the dashboard. If the site was commissioned, the section for each tenant will display the tenant’s name and the tenant equipment power data such as current, power, and energy consumed by the equipment. The ambient temperature and humidity were shown, and the battery temperature value was also displayed as well. There are navigation tabs listed on the left side of the dashboard, the first one to access during the first installation when the site has not been commissioned was the Configuration tab. This tab is shown in Figure 30, the user can set the site parameters from this page. The fields included the site name, ID, region, longitude, latitude, talents names, and the capacity of the Genset installed. The already configured data could be edited and deleted using the buttons below the configuration form. When this form was submitted, the site configuration collection in the database was updated and the site configuration version value was incremented, the RMA tracked this value to know when to update the site configuration details of the site ID on RMS so that the same site parameters would be on the RMA and the RMS.\n\nThe diagnostics tab has three sub-tabs for the AC meter, DC meter, and other information. These three tabs categorized the real-time data pooled from the AC meter, DC meter, and the IO board respectively. The information on this tab was met for fault troubleshooting. The AC meter real-time data pooled over RS485 Modbus is shown in Figure 31. Similarly, the DC meter real-time data pooled over RS485 Modbus is shown in Figure 32. The IO board real-time data were pooled over the I2C bus and other operational data like internet connectivity, the number of items that were buffered, site and server configuration version values, and many more were shown when the Other Info tab was clicked as shown in Figure 33. These data were continuously pooled at four seconds intervals from the RMA backend application and updated on this page. The same data was saved to the RMA database every two minutes and uploaded to the RMS every two minutes as well. Only the Admin user has access to this page.\n\nAC: alternating current, DC: direct current.\n\nFor quick monitoring of historical data, the Trendline tab shows the AC power chart as shown in Figure 34. Operation data from the last twenty-four hours were queried from the database and only the latest 100 points (number chosen arbritarily) of these data were sent to this page to be plotted on these charts. The first chart displayed the AC power source line voltage, current, and power. The second chart displayed the total dc power consumed by all the tenant’s equipment installed on the site and the DC voltage. The last chart displayed the battery temperature, ambient temperature, and ambient humidity.\n\nAC: alternating current.\n\nLocally from the site, when connected to the RMA, the user can download the site operational data as shown in Figure 35. The user could select the start date and the end date for the required data, clicking on the “Get Data” button queried the operational data from the database using the date selected as the query selector. The data within the date range were retrieved and sent to this page and displayed as the table shown in Figure 35. This data could be downloaded in excel format for further analysis.35\n\nAC: alternating current, DC: direct current, RMA: remote monitoring agent, L1: line 1, L2: line 2, L3: line 3.\n\nThe accuracy of the current and voltage measurement captured by the RMA was benchmarked by taking a manual reading with UNI-T UT203+ digital multimeter. The corresponding currents and voltages manually measured for the captured values on the RMA’s webpage in Figure 29 are shown in Tables 6 and 7. The percentage error for the current and voltage measurements was calculated with equation 3 and the values are shown in column %Error in Tables 6 and 7 respectively. Equations 4 and 5 were used to calculate the total error for the current and voltage measurements respectively. TEc was 1.97 and TEv was 0.54.\n\nRMA: Remote Monitoring Agent, DC: Direct Current, AC: Alternating Current, L1: Line 1, L2: Line 2, L3: Line 3.\n\nRMA: Remote Monitoring Agent, DC: Direct Current, AC: Alternating Current, L1: Line 1, L2: Line 2, L3: Line 3.\n\n\n\nWhere M is the manually measured value using the digital multimeter and R is the captured value from the RMA webpage.\n\nTEc is the total error for the measured current values, MCi is the manually measured current at a point, and RCi is the current value captured on the RMA webpage for the point.\n\nWhere TEv is the total error for the measured voltage values, MVi is the manually measured voltage at a point, and RVi is the voltage valued captured on the RMA webpage for that point.\n\nFigures 36 and 37 show the charts that compare the values of currents and voltages measured manually and the corresponding values captured on the RMA’s webpage.\n\nAC: alternating current, DC: direct current, RMA: remote monitoring agent, L1: line 1, L2: line 2, L3s: line 3.\n\n\nDiscussion\n\nThe RMA master controller developed with Raspberry Pi 3 controller has proven that this microcomputer is a powerful credit-card size alternative for a personal computer with the ability to integrate effectively with peripheral hardware as shown by.33 The possibility of setting up the RS485 Modbus communication network on Raspberry Pi provided the flexibility required to simultaneously integrate the microcomputer with up to thirty-two industrial devices on the same network using just two wires as mentioned under the literature review section. This has made it possible to integrate the Raspberry Pi microcomputer (the master controller) with the two energy meters, and with the developed IO board over the I2C communication protocol. This work extended was done in the cited litetrature papers by using raspberry pi to implement both synchronous and asynchronous serial communication in a single application. With the energy meters and their connected current sensors, the master controller could pool real-time data of all power/energy data captured from the connected mobile operators’ equipment and the genset. This made the RMA suitable for energy service companies (ESCOs) in telecommunication industry to monitor individual power/energy profile of mobile operators connected to an example of power solution developed by.12\n\nFurthermore, since the main controller was a computer with an onboard WiFi chip, it was possible to build and host a web application on it that could locally serve the connected users through the web application frontend and also send data to a cloud server.34 Similar to what was done by16 for a solar plant. Data captured by the main controller were saved in its database which could be retrieved to serve locally connected users or the cloud server. The internet connection to the main controller was provided using a 3G USB model, the RMA had been online since it was installed and the custom-built shell script on the master controller ensured internet connectivity by restarting the modem whenever there is no internet connection. Having the master controller connected to the internet was critical for the RMA to serve its purpose. The web application hosted on the master controller started up whenever the main controller (Raspberry Pi) booted up successfully. Both the WiFi hotspot and the internet modem started up as well during the controller boot-up session. The automatic startups of these applications were handled by the shell scripts running on the Raspberry Pi.\n\n\nConclusions\n\nThe implementation of this work provided a platform for Energy Service Companies (ESCOs) in the telecommunication industry to accurately meter the power consumed by the accommodated mobile operators’ equipment on their site. The web application on the RMA provided access to site information. Harvested data can be locally stored and uploaded to a cloud server for further information processing. This study could be extended to capture other important data on the telecommunication site, such as rectifier information, fuel level measurement and site surveillance. Also, it can be extended to take commands from the remote server to start/stop the generator set remotely or control the whole power system.\n\nThe solution developed in this work looked a bit bulky, future research could perform similar tasks while being much more smaller and cost effective if the input/output (IO) board can be enabled to measure both AC and DC currents and voltages.\n\n\nData availability\n\nZenodo: Design and development remote monitoring agent for energy service companies in the telecommunication industry. https://doi.org/10.5281/zenodo.6829361.35\n\nThis project contains the following underlying data:\n\n- rma data.csv. (Data set downloaded from the remote monitoring agent (RMA) over its local webpage using WiFi connection)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nSoftware availability\n\nSource code available from: https://github.com/skcareer/Software-for-RMA\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.682829136\n\nLicense: GNU Affero General Public License v3.0.",
"appendix": "References\n\nNomamidobo Amadasun K, et al.: Transitioning to Society 5.0 in Africa: Tools to Support ICT Infrastructure Sharing. Data. Jun. 2021; 6(7): 69. Publisher Full Text\n\nAdebayo EA, Adeeyo AO, Ogundiran MA, et al.: Bio-physical effects of radiofrequency electromagnetic radiation (RF-EMR) on blood parameters, spermatozoa, liver, kidney and heart of albino rats. J. King Saud Univ. - Sci. 2019; 31(4): 813–821. Publisher Full Text\n\nFrancis P, Idachaba E: Telecommunication Cost Reduction in Nigeria through Infrastructure Sharing between Operators. Pac. J. Sci. Technol. 2010; 11.\n\nMamushiane L, Lysko AA, Dlamini S: SDN-enabled Infrastructure Sharing in Emerging Markets: CapEx/OpEx Savings Overview and Quantification.2018.\n\nA. A. SAmeh KTOOJ: Significant Factors Causing Cost Overruns in Telecommunication Projects in Nigeria. J. Constr. Dev. Ctries. 2010; 15(2).\n\nFerraro M, Brunaccini G, Sergi F, et al.: From Uninterruptible Power Supply to resilient smart micro grid: The case of a battery storage at telecommunication station. J. Energy Storage. 2020; 28(April 2019): 101207. Publisher Full Text\n\nKondaveeti HK, Kumaravelu NK, Vanambathina SD, et al.: A systematic literature review on prototyping with Arduino: Applications, challenges, advantages, and limitations. Comput. Sci. Rev. 2021; 40: 100364. Publisher Full Text\n\nLi H, Li K, Zafetti N, et al.: Improvement of energy supply configuration for telecommunication system in remote area s based on improved chaotic world cup optimization algorithm. Energy. 2020; 192: 116614. Publisher Full Text\n\nKaldellis JK, Ninou I: Energy balance analysis of combined photovoltaic-diesel powered telecommunication stations. Int. J. Electr. Power Energy Syst. 2011; 33(10): 1739–1749. Publisher Full Text\n\nOkundamiya MS, Emagbetere JO, Ogujor EA: Design and control strategy for a hybrid green energy system for mobile telecommunication sites. J. Power Sources. 2014; 257: 335–343. Publisher Full Text\n\nWibowo WW, Astuti YDRW, Hudaya C: Solar-Powered Base Transceiver Station. Proc. - 2018 2nd Int. Conf. Green Energy Appl. ICGEA 2018. 2018; pp. 108–112. Publisher Full Text\n\nSalihoddin MABM, Muhtazaruddin MNB, Bani NA, et al.: UTM Razak School of Engineering and Advanced Technology, Universiti Teknologi Malaysia, Kuala Lumpur, “Hybrid Power Supply System for Telecommunication Base Station.Publisher Full Text\n\nZhai Z, Martínez JF, Beltran V, et al.: Decision support systems for agriculture 4.0: Survey and challenges. Comput. Electron. Agric. 2020; 170(January): 105256. Publisher Full Text\n\nOmpal VMM, Kumar A: FPGA integrated IEEE 802.15.4 ZigBee wireless sensor nodes performance for industrial plant monitoring and automation. Nucl. Eng. Technol. 2022; 54(7): 2444–2452. Publisher Full Text\n\nD’Aniello F, Sorrentino M, Rizzo G, et al.: Introducing innovative energy performance metrics for high-level monitoring and diagnosis of telecommunication sites. Appl. Therm. Eng. 2018; 137(February): 277–287. Publisher Full Text\n\nSiva M, Krishna R, Dinesh K, et al.: Low Cost Remote Monitoring of Solar Plant through RS485 Communication. Int. J. Innov. Technol. Explor. Eng. 2019; 8(9): 3034–3037. Publisher Full Text\n\nJian YW: Application of RS-485 Bus in Warehouse Communication Technology.2021. Publisher Full Text\n\nHung PD, Van Chin V, Chinh NT, et al.: A flexible platform for industrial applications based on RS485 networks. J. Commun. 2020; 15(3): 245–255. Publisher Full Text\n\nNguyen V, Dugenske A: An I2C based architecture for monitoring legacy manufacturing equipment. Manuf. Lett. 2018; 15: 67–70. Publisher Full Text\n\nŁukasz P, Marcin O, Dariusz K, et al.: I2C interface design for hardware master devices. IFAC Proc. Vol. 2012; 45(PART 1): 163–168. Publisher Full Text\n\nMcBride WJ, Courter JR: Using Raspberry Pi microcomputers to remotely monitor birds and collect environmental data. Ecol. Inform. 2019; 54(October): 101016. Publisher Full Text\n\nNadafa RA, Hatturea SM, Bonala VM, et al.: Home Security against Human Intrusion using Raspberry Pi. Procedia Comput. Sci. 2020; 167(Iccids 2019): 1811–1820. Publisher Full Text\n\nEasyEDA: Online electronics design software tools.Reference Source\n\nRholam O, Tabaa M, Monteiro F, et al.: Smart device for multi-band industrial IoT communications. Procedia Comput. Sci. 2019; 155: 660–665. Publisher Full Text\n\nHsiao CH, Lee WP: OPIIoT: Design and Implementation of an Open Communication Protocol Platform for Industrial Internet of Things. Internet of Things (Netherlands). 2021; 16(August): 100441. Publisher Full Text\n\nHuang Y, Li C: Real-time monitoring system for paddy environmental information based on DC powerline communication technology. Comput. Electron. Agric. 2017; 134: 51–62. Publisher Full Text\n\nPereira RIS, Dupont IM, Carvalho PCM, et al.: IoT embedded linux system based on Raspberry Pi applied to real-time cloud monitoring of a decentralized photovoltaic plant. Meas. J. Int. Meas. Confed. 2018; 114(August 2017): 286–297. Publisher Full Text\n\nMudaliar MD, Sivakumar N: IoT based real time energy monitoring system using Raspberry Pi. Internet of Things. 2020; 12: 100292. Publisher Full Text\n\nBesada-Portas E, Bermúdez-Ortega J, de la Torre L , et al.: Lightweight Node.js & EJsS-based Web Server for Remote Control Laboratories. IFAC-PapersOnLine. 2016; 49(6): 127–132. Publisher Full Text\n\nWisnusenna S, Yonatan MS, Wibisurya A, et al.: Model of Web Based Application to Control Bridge Traveler Using Raspberry Pi. Procedia Comput. Sci. 2018; 135: 518–525. Publisher Full Text\n\nZhou K, Yuan Y: A smart ammunition library management system based on raspberry pie. Procedia Comput. Sci. 2020; 166: 165–169. Publisher Full Text\n\nKumar JV, Moeed SA, Kumar CM, et al.: Integration patterns of MongoDB GridFS for advanced data science and big data processing. Mater. Today Proc. 2021. no. xxxx. Publisher Full Text\n\nOguntosin V, Oluwaleye S, Idachaba F: Conceptual design of smart multi-farm produce dehydrator using a low-cost programmable logic controller and raspberry pi. F1000Res. 2021; 10: 810–825. PubMed Abstract | Publisher Full Text\n\nVujović V, Maksimović M: Raspberry Pi as a Sensor Web node for home automation. Comput. Electr. Eng. 2015; 44: 153–171. Publisher Full Text\n\nOluwaleye S, Idachaba F: Design and development remote monitoring agent for energy service companies in the telecommunication industry [Data set]. Zenodo.2022. Publisher Full Text\n\nOluwaleye S, Idachaba F: Design and development remote monitoring agent for energy service companies in the telecommunication industry (To develop a software for a remote monitoring unit for telecommunication site.). [Source code] Zenodo.2022. Publisher Full Text"
}
|
[
{
"id": "151658",
"date": "29 Sep 2022",
"name": "Kenneth Eloghene Okedu",
"expertise": [
"Reviewer Expertise Energy Systems."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper presents the implementation of energy service companies in the telecommunication industry to accurately carryout the monitoring and metering of the consumed power by the equipment of mobile operators in a site. Lagos state in western Nigeria, was used as the site in this study. The concept of the paper is interesting, however, there are some shortcomings. The following comments would help the authors in improving the readership of this work.\nThe paper should be checked for grammatical and typo errors; e.g., \"In other...\" instead of in order. Also, some statements are not clear in the introduction, as it is difficult to comprehend them.\n\nIn order to boost the theory of this work, more mathematical formulations of the model and its design are required.\n\nFigure 8 is not readable.\n\nA detailed model system of the topology of the study should be shown before the description of each components. Readers would like to have a holistic view or a bigger picture of the energy service companies in the telecommunication industry and the link with remote monitoring agent for proper monitoring, and the variables been monitored, with detailed parameters of the components. This is required in order to bring out the contribution of the paper.\n\nFigure 17 should be properly captioned.\n\nThe work is basically describing only the hardware techniques employed in this research. A simulation result section is required and it should be robust. A more rigorous simulation study showing graphically the various variables of the system over time is imperative. The responses or dynamic behaviors of the voltages, currents, temperature, humidity, energy consumed, power consumed and frequency of the proposed model system earlier requested should be given in this paper.\n\nThe data in Figure 35 are constant and seem not to change over time.\n\nThe paper is too long. It should be concise.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "151660",
"date": "25 Oct 2022",
"name": "Abel E. Airoboman",
"expertise": [
"Reviewer Expertise Renewable Energy",
"Power Systems",
"Electrical Machines"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: The section is void of results. This reviewer upholds that authors should include salient results in the abstract while stating their significance and implication\nIntroduction: Given the length of the paper, this reviewer upholds that the introduction as presented has not done justice to the subject matter. This reviewer therefore affirmed that authors should give a background on RMA, ESC etc. taking cognizance of their operations, challenges etc.\nLiterature Review: There are some misconceptions particularly in the last paragraph under this section. Authors claimed to have implemented the technologies of other researcher as their aim. This reviewer struggles to understand the notion behind the statement. This reviewer therefore affirmed that authors should point out the gap saliently from literature. This “gap” should be “gap” and not a generalized aim as claimed by the authors.\nMethod: More information on the type of data, year/duration of collection, method of collation are needed. This information will assist other researchers in the same field when carrying out similar research. This researcher also affirmed that a distribution pattern should be established to show if such data can be used for the analysis as presented\nThe design part of the research is hanging and missing. Authors are supposedly to justify the size of each component that makes up the system. If otherwise, this reviewer suggests that the term “design” should be expunged from the title.\n\nToo much of theoretical concepts in the methodology and this has contributed to making the research too lengthy. Majority of the flow chart presented if not all are fundamentally faulty. This researcher can affirm that (All flow chart MUST begin with a “START” and end with a “STOP”). Where a process is continuous then a connector should be used. However there must be a “Start” and a “Stop”. Likewise, the conditions for “success” must be stated in the entire chart.\n\nFigure 11 is hanging? Where are the output strings connected to or going?\n\nFrom fig 26, this reviewer may like to ascertain if the authors got the appropriate clearance to carry out this study in form of grant or otherwise. If otherwise, authors should avoid displaying logos and names of industries in their work for ethical reasons\n\nThe header title in Figure 36 & b37 should be deleted\n\nThis reviewer is of the opinion that a relationship between power and time should has been presented taking into cognizance how it affect the energy management in the study. Further, the relationship between other key parameters like voltage, current and frequency is inevitable and MUST be discussed as far this study is concerned.\n\nAuthors’ have not shown the energy demand and how it was established.\nOverall, it is a good work for research and scientific community in this line of interest.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1106
|
https://f1000research.com/articles/11-1101/v1
|
27 Sep 22
|
{
"type": "Brief Report",
"title": "Hair greying in castrated mice",
"authors": [
"Aoi Matsumoto",
"Junko Kawabe",
"Natsumi Kawakami",
"Koichi Node",
"Makoto Akashi",
"Aoi Matsumoto",
"Junko Kawabe",
"Natsumi Kawakami",
"Koichi Node"
],
"abstract": "Depigmentation of hair shafts is a hallmark of human aging. However, it remains unclear how aging causes human hair to grey. Here, we found that a single session of hair plucking via waxing causes hair to grey in castrated mice. Moreover, this hair greying continued for several hair cycles. Given that androgen secretion decreases with age in both male and female humans, the present result suggests that this decrease may contribute to age-related hair greying. In addition, our experimental procedure may represent an effective way to generate a new mouse model of hair greying without the need for genetic engineering.",
"keywords": [
"hair greying",
"androgen",
"hair plucking",
"castrated mice",
"mouse model"
],
"content": "Introduction\n\nHair greying is a common and ubiquitous feature of human aging.1 Although the rate of hair greying varies among individuals, almost all males and females experience depigmentation of hair shafts with age. Because the color in hair shafts is provided by melanin granules, which are supplied to the trichocytes of growing hair shafts by melanocytes,2 age-related hair greying is thought to involve some dysfunction to these processes.3\n\nIn contrast to humans, mice do not show any obvious hair greying, probably because they have a much shorter lifespan. However, hair greying in mice is experimentally inducible by genetic manipulation3 or ionizing radiation,4 suggesting that hair greying in humans may also involve genetic variation and genomic damage. Very recently, a report demonstrated that strong acute stress leads to hair greying in mice through depletion of melanocyte stem cells.5 Consistent with this, another report indicated that hair greying in humans likely occurs in parallel with psychological stressors.6 Given that genomic damage and psychological stress are likely to accumulate with age, these factors may explain the mechanism of age-related hair greying in humans. However, the true mechanism remains unclear due to the lack of direct evidence for this hypothesis and the presence of multiple other factors related to aging that may be involved in human hair greying.\n\nMany previous studies have demonstrated a relationship between sex hormones and hair physiology and drastic changes in the secretion of sex hormones with age.7,8 Therefore, in this study, we focused on the causal link between sex hormone secretion and hair greying.\n\n\nMethods\n\nAll protocols for animal experiments refer to the 3R principle and were approved by the Animal Research Committee of Yamaguchi University (approval number: 437). Animal studies were performed in compliance with the Yamaguchi University Animal Care and Use guidelines. All animals were assessed as healthy prior to commencement of experiments and handled by experienced researchers in such a way as to minimize stress. All efforts were made to ameliorate any suffering of animals.\n\nC57BL6J mice were purchased from Japan SLC, maintained under standard laboratory conditions (room temperature: 24 ± 2°C), with a regular 12:12 light-dark cycle, and allowed ad libitum access to food and water. Each mouse was housed singly in a standard mouse cage (W 213 mm, D 324 mm and H 131 mm) and transferred to a clean cage every two weeks. ALPHA-dri (Shepherd Specialty Papers, Inc., U.S.A.), made from alpha cellulose and having high absorbency, was used as animal bedding. Mice were acclimatized to laboratory conditions for at least 7 days before the commencement of experiments. They had never received any experimental treatment previously. Mice with abnormalities were excluded from the study. To evaluate hair regrowth, mice were anesthetized with isoflurane gas, and their dorsal hair shafts were trimmed and then completely removed by waxing.\n\nNo statistical methods were used to predetermine the sample size due to the lack of available estimation. A Fisher’s exact test was performed to compare the probability of hair greying between sham-operated and castrated males. P < 0.05 indicated statistical significance.\n\n\nResults and discussion\n\nIntact male and female C57BL6 mice did not show any visibly obvious signs of hair greying over their lifetime, probably because their lifespan was too short for depigmentation to begin in the hair shaft. Based on a previous report demonstrating that repetitive shaving or plucking accelerates hair greying,9 we applied this method to increase the susceptibility of hair shafts to greying in response to experimental intervention. As expected, neither a single shaving nor waxing session to pluck hair shafts from the back was sufficient to induce hair greying (shaving, 16-week-old males (n = 12) and females (n = 12); plucking, 16-week-old males (n = 52) and females (n = 12)). Next, to simply and directly test the involvement of androgen in hair greying, we examined whether or not a single session of plucking hair shafts from the back caused hair to grey in castrated male mice (Figure 1a). We found that while sham-operated mice did not show any visible signs of greying, one-third of castrated mice showed hair greying in a small area on the surface of the back (16-week-old sham-operated (n = 12) and castrated males (n = 18)). A Fisher’s exact test showed that there was a significant difference in the incidence of hair greying between sham-operated and castrated males (0 out of 12 sham-operated versus 6 out of 18 castrated males, P < 0.01). Taken together, these results suggest that loss of androgen substantially accelerates hair greying. Grey hair shafts were still present after more than 100 days post-hair plucking (Figure 1b). Given that the length of each hair cycle in mice is about 25 days,10 this result indicates that hair greying continued across at least four hair cycles. Therefore, just a single session of hair plucking in castrated mice caused long-lasting damage to the pigmentation of hair shafts.\n\n(a) Representative images of the back of sham-operated and castrated male mice 24 days after hair plucking. The operation and waxing were performed when mice were 5 and 16 weeks old, respectively. Hair shafts were removed from almost the entire area of the back in the image. The area containing greying hairs is enlarged two-fold and shown at the bottom.\n\n(b) An image showing the back of a castrated mouse with greying hair 103 days after hair plucking. The animal in this image is the same as that shown in the rightmost image in (a).\n\nConsidering that androgen secretion decreases with age in both male and female humans,8 a possible interpretation of the present findings is that this decrease contributes to age-related hair greying in humans. While it is well known that androgen is involved in the pathogenesis of androgenetic alopecia,11 the present study is the first to show that androgen is also involved in hair greying. Further studies are required to elucidate the mechanism underlying how loss of androgen causes depigmentation of hair shafts.\n\nA potential limitation of the present study is that our experimental results may not directly explain age-related hair greying in humans because hair greying in mice was induced by hair plucking. However, it is difficult to overcome this technical limitation in animal experiments due to the creatures’ short lifespan, thus, unavoidably requiring some artificial induction of hair greying. Another potential limitation is that we cannot currently explain why a single session of hair plucking causes hair to grey in only about 33% but not all castrated mice, and in just a small area but not the entire surface of the back.\n\nThe present method may be useful for generating a new mouse model of hair greying that differs from most previous models in that it does not require genetic manipulations. However, our experimental procedure needs to be modified to improve the success rate and increase the body surface across which hair greying is induced. It is possible that a second session of hair plucking may overcome these limitations. Successful modification of the procedure for hair greying will provide a useful mouse model for studying the mechanism and prevention of human hair greying.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAuthor contributions\n\nA.M., J.K. and N.K. performed experiments. K.N. provided a wide range of general support. M.A. conceived and supervised the project and wrote the manuscript.",
"appendix": "Acknowledgments\n\nWe express our appreciation to Nanami Yasumune, Yuna Yamamoto, Ritsuko Matsumura and Junko Sumino for providing technical assistance.\n\n\nReferences\n\nPanhard S, Lozano I, Loussouarn G: Greying of the human hair: a worldwide survey, revisiting the ‘50’ rule of thumb. Br. J. Dermatol. 2012 Oct; 167(4): 865–873. eng. PubMed Abstract | Publisher Full Text\n\nTobin DJ: The cell biology of human hair follicle pigmentation. Pigment Cell Melanoma Res. 2011 Feb; 24(1): 75–88. eng. PubMed Abstract | Publisher Full Text\n\nO’Sullivan JDB, Nicu C, Picard M, et al.: The biology of human hair greying. Biol. Rev. Camb. Philos. Soc. 2021 Feb; 96(1): 107–128. eng. PubMed Abstract | Publisher Full Text\n\nInomata K, Aoto T, Binh NT, et al.: Genotoxic stress abrogates renewal of melanocyte stem cells by triggering their differentiation. Cell. 2009 Jun 12; 137(6): 1088–1099. eng. PubMed Abstract | Publisher Full Text\n\nZhang B, Ma S, Rachmin I, et al.: Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells. Nature. 2020 Jan; 577(7792): 676–681. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRosenberg AM, Rausser S, Ren J, et al.: Quantitative mapping of human hair greying and reversal in relation to life stress. elife. 2021 Jun; 10: 10. Epub 2021/06/23. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOhnemus U, Uenalan M, Inzunza J, et al.: The hair follicle as an estrogen target and source. Endocr. Rev. 2006 Oct; 27(6): 677–706. eng. PubMed Abstract | Publisher Full Text\n\nLamberts SW, van den Beld AW , van der Lely AJ : The endocrinology of aging. Science. 1997 Oct 17; 278(5337): 419–424. eng. PubMed Abstract | Publisher Full Text\n\nEndou M, Aoki H, Kobayashi T, et al.: Prevention of hair graying by factors that promote the growth and differentiation of melanocytes. J. Dermatol. 2014; 41(8): 716–723. eng. PubMed Abstract | Publisher Full Text\n\nMüller-Röver S, Handjiski B, van der Veen C , et al.: A comprehensive guide for the accurate classification of murine hair follicles in distinct hair cycle stages. J. Invest. Dermatol. 2001 Jul; 117(1): 3–15. eng. PubMed Abstract | Publisher Full Text\n\nHeilmann-Heimbach S, Hochfeld LM, Henne SK, et al.: Hormonal regulation in male androgenetic alopecia-Sex hormones and beyond: Evidence from recent genetic studies. Exp. Dermatol. 2020 Sep; 29(9): 814–827. eng. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "161200",
"date": "13 Feb 2023",
"name": "Shungo Adachi",
"expertise": [
"Reviewer Expertise cell biology",
"molecular biology",
"proteomics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript by Matsumoto et al. describes that wax depilatory treatment of castrated male mice can induce graying of newly growing body hair. Since graying does not occur in untreated mice, the authors suggest that it may be due to sex hormone effect. The results are valuable not only because it provides new insights into graying research, but also it provides an experimental model for graying. However, several concerns need to be addressed before this paper can be accepted for publication.\n1. Please provide more details about the hair removal method in the METHOD section.\n2. Since normal epilation does not cause graying in male castrated mice, it is likely that the artificial epilation process itself is also responsible for graying. Please provide experimental results as to whether the chemical stimulation of Wax or the physical stimulation of wiping the hairs (or both) is responsible for graying.\n3. Since graying does not occur in female mice, it is possible that it is caused by sex hormones other than androgens, please provide a discussion in the text as to why graying does not occur in females. Or, In order to confirm whether the induction of graying is due to the effect of androgens, please provide an experiment result to see if gray hairs develop when male castrated mice are administered androgens.\n4. Since graying after epilation does not occur in all castrated male mice and the shape of the areas varies, it seems likely that graying is related to the hair growth cycle. Please discuss that in the discussion section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "191777",
"date": "14 Aug 2023",
"name": "Sekyu Choi",
"expertise": [
"Reviewer Expertise Hair follicle stem cells",
"Adult stem cells",
"Aging."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors showed plucking a small area of the back skin in castrated male mice can lead to hair greying, whereas the entire back skin area did not exhibit the same effect. However, this report's scientific credibility is deficient and it needs to be addressed in the following points.\nThe Methods sections should encompass the details of mouse castration procedure.\n\nTestosterone levels should be measured in both sham-operated and castrated male mice.\n\nStatistical analysis, accompanied by mouse images, should be integrated into Figure 1.\n\nAuthors should provide the results of plucking across the entire skin area of castrated mice in main figures.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate? No\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1101
|
https://f1000research.com/articles/11-1099/v1
|
27 Sep 22
|
{
"type": "Systematic Review",
"title": "Recent advancements in machine vision methods for product code recognition: A systematic review",
"authors": [
"Jarmo Koponen",
"Keijo Haataja",
"Pekka Toivanen",
"Keijo Haataja",
"Pekka Toivanen"
],
"abstract": "Background: Manufacturing markings printed on products play an important role in the handling and use of pharmaceuticals and perishable foods. Currently, optical character recognition, neural networks, deep learning-based methods, and combinations of these methods are used to recognize these codes. Methods: This systematic review was performed to find papers that can answer the following research questions: How have machine vision methods that can recognize product texts evolved over the past eight years? What are the most common difficulties in recognizing product texts? Articles published between 2012 and 2020 were systematically searched from Science Direct/SCOPUS, and Google Scholar in November-December 2020. Ten studies were eligible, with inclusion criteria: details about the recognition method used, performance analysis result, imaging method, product and the text printed on it. Results: Product text recognition methods have evolved significantly over the last two years to tolerate the most common difficulties in the field. This is due to the ability of the deep learning neural network (DNN) architectures such as convolutional neural networks (CNN) to extract and learn salient character features straight from packaging surface images. Four of the most recent methods use two consecutive deep learning networks, one detecting the text area based on an image captured from the product package's surface and the other recognizing the characters within. Furthermore, this paper presents solutions to the most common product text recognition difficulties. Conclusions: There were a limited number of studies that met the eligibility criteria for this systematic review. The study's aim was to evaluate the development of machine vision methods for recognizing manufacturing marking texts printed on the surface of products. The study results demonstrated how methods have evolved over time, beginning with optical character recognition, and advancing to methods which can recognize texts despite the field's most common problems.",
"keywords": [
"Machine Vision",
"Imaging System",
"Character Recognition",
"OCR",
"Deep Learning",
"Product",
"Packaging",
"Manufacturing"
],
"content": "Introduction\n\nThe reported value of food and pharmaceutical production sold in the European Union (EU) in 2020 was over €105 billion and over €30 billion respectively. 1 The manufactured product moves through the supply chain from the factory to its end users. The product requires primary packaging for its handling, secondary packaging may be required for storage, and tertiary packaging for its transport. 2 The packaging has multiple functions, to protect the product during handling, storage, and transport, as well as prevent contamination and spoilage of the product. 3 On the other hand, it should increase the usefulness and convey information for the many uses of the product. 2 , 3 Production information, such as batch code, serial number, or expiration date, is printed on specific fields of the product, or its package at the manufacturing stage. Each of these consists of numbers and letters with a defined structure and length.\n\nOne key point in EU food safety legislation is the ability to trace products throughout the food chain. 4 All perishable food products intended for human consumption must be marked with the date which their consumption is no longer considered safe. 5 Likewise, finished medicinal products must be identifiable by the labels required by national law, including the expiry date in uncoded form and the batch number provided by the manufacturer. 6\n\nHowever, even today, the traditionally necessary step to check the expiration date information printed on packages is done by a human operator who manually picks up the package and checks the date. This is an everyday, monotonous, and high precision task, placing the human in an error-prone working environment. 7 Instead of a human operator, machine vision could be used for product codes text recognition without contact with higher accuracy and speed.\n\nConverting these product codes into a machine-coded format is more difficult than optical text recognition of paper documents. However, it enables storage and processing of package-specific production data as well as search and extraction of codes and dates electronically.\n\nExisting optical character recognition (OCR) techniques work effectively only with clear characters in high-quality images on an uncomplicated background, while requiring character consistency in terms of format and viewing angle. 7 Common problems in recognizing the texts are caused by the complexity and deformation in the facet where the codes are printed, its problematic illumination, rich color information, insufficient contrast of the text, different printing types, and inconsistency of text characters. 5 , 7 – 10 Although the package is regular in shape after the product has been manufactured, character distortion and warping during the storage duration can cause challenges for traditional OCR. 9 Changes in physical conditions, such as different sizes and shapes of product packages, different positions, and angle of placement of the package in the camera view, and work environments lighting conditions make text recognition more difficult. When capturing images of packets moving on a conveyor belt, due to the motion blur caused by speed, the images may be blurred, making the recognition more difficult. 11 The recognition of product codes from natural images is still a challenging task, as images may contain text with arbitrary perspective deformations in a complex background due to its unknown 3D position and orientation. 7 , 11\n\nNeural networks modeled from brain structure are today very widely used in text recognition applications that require complex and large numbers of feature classification capabilities. At the same time, the graphics cards required for model training of neural networks are constantly evolving in terms of computing power and storage capacity. Several researchers propose neural network-based methods for detecting and recognizing packaging texts in recent studies. 7 , 10 , 11 However, training in the deep neural network (DNN) model required familiarity with the subject and a large number of experiments to determine what is a viable way to solve the text recognition problem in question.\n\nIn recent years, machine vision technology has been increasingly used in a wide range of product codes recognition: it is used in the design of sustainable food systems to reduce food waste, 12 , 13 improving safety in the use of perishable food and pharmaceutical products, 4 , 9 and in developing faster and more accurate methods for the retail supply chain. 5 , 14 , 15 Electronic processing of product-specific serial numbers is also suitable for electronic inventory management systems, 16 development of intelligent product code recognition systems to help the daily lives of visually impaired people, 10 development of intelligent household refrigerator food management systems, 17 and also for the needs of metal industry to automatically verify the serial numbers of metal products at different stages of production. 18\n\nFor individual photosensitive sensors used in digital imaging, the dominant arrangement is a 2D array form. The imaging system (see Figure 1c) collects the incoming energy and focus it onto the image plane (see Figure 1d). In bright illumination lens at the front end of the imaging system projects the scene being viewed onto the lens focal plane. The sensor array is coincident with the focal plane, it produces output proportional to the integral of the light received at each sensor. Electronic circuits sample the outputs, and another part of the imaging system digitizes the signal and produces an output image (see Figure 1e). 19\n\n(a) Energy source. (b) Product package. (c) Imaging system. (d) Projection of the scene onto image plane. (e) Digitized image. (f) Computer. (g) Character recognition software.\n\nWith good illumination, the imaging system captures a clear image of the flat surface of the packages. The computer (see Figure 1f) and its character recognition software (see Figure 1g) are used to recognize the codes printed on it. Regularly shaped characters with good contrast against a simple background can be recognized with OCR software. 20 Imperfections in the orientation of the target surface, in its flatness, in the contrast of the text, in the consistency of the characters, or in the regularity of the printed text on the packaging surface complicates the recognition task. In addition to OCR, 21 the subject of product code recognition has been approached in a number of methods. To extract representative features of characters, binary large object detection (BLOB), 16 Histograms of Oriented Gradients (HOG), 18 and Gabor-filtering 8 , 9 have been utilized, whereas classifiers and neural networks have been used to categorize them. Recently, the topic has been addressed utilizing end-to-end execution with Deep learning, such as fully Convolutional Neural Network, Mask R-CNN neural network, and Connectionist Text Proposal Neural Network (CTPN), for text region detection and recognition. 7 , 10 , 11 , 15\n\nThis research aims to advance the knowledge base in developing smart product handling methods for future researchers by:\n\n• Providing detailed knowledge of current algorithms for text recognition methods for product codes.\n\n• Systematically analyzing and presenting an overview of machine vision- based product code recognition techniques for each stage, (Code characters: extraction, segmentation when applicable, and recognition), with a brief description of the techniques used in each stage.\n\n• Summarizing the performance of algorithms developed by various researchers and used and tested for product code recognition.\n\n• Providing knowledge of the associated imaging environment used and tested for product code recognition, with details on the surface properties of product packaging and printed texts.\n\n\nMethods\n\nThe systematic review method used in this study can be considered as somewhere between the traditional and meta-analysis review approaches. This method has been chosen to reduce the risk of bias and increase reliability. The evaluation was conducted in accordance with the guidelines known as PRISMA statement [Reporting guidelines].\n\nThis work examines the literature to answer the following research questions:\n\n• How have machine vision methods capable of recognizing product texts evolved over the last eight years?\n\n• What are the most common difficulties in recognizing product texts?\n\nAnswers are sought by formulating a research question and collecting data from a scholarly database, primarily Scopus, and secondly searching for related publications in the Google Scholar database. The search strategy for Scopus used in this study was a string of characters composed specifically of the following terms: batch code, batch, expiration date, expiry date, serial number, manufacturing, OCR, machine vision, computer vision, detection, recognition, and combinations thereof. The search was limited to literature published during the last eight years (2012-2020). Publications related to manufacturing, retail chain, and serial production were retrieved from the Google Scholar. The following criteria were used to select the appropriate studies to review:\n\n• The studies which include predefined keywords in the article title, abstract or keywords.\n\n• Those who deal with product codes text recognition which are based on computer vision.\n\n• Those that provided details of the performance analysis with details of the imaging method, product, printed text, and the method of text recognition itself.\n\n• Those studies that were published between 2012 and 2020.\n\n• Those that can be accessible.\n\nThe following criteria were used to exclude the studies from the scope of review:\n\n• The studies which are not written in English.\n\n• The studies with unidentified reference.\n\n• The studies published before the year 2012.\n\nIn total, 138 articles were extracted. The following is a detailed analysis of the product text recognition methods used in the 10 studies, as well as the recognition results achieved with them.\n\nAccording to the Althobaiti et al., 20 OCR is the process of converting text in images into a machine-coded form. The first step in OCR is to find the optical characters in the input image. OCR works by collecting detected dots (pixels) from an image, which are then compared to a model taught to the system. This is used to identify a detected character, which can be a letter, number, or special character. If characters form a group, this group is compared with possible grammatical words, and the correctness of the recognition can be automatically concluded. An OCR- based expiration date recognition system for the visually impaired is described in Peng et al. 21 It recognizes date codes of consumer products using cell phone camera and guides the user with voice feedback. This method works in two steps: First, the product barcode is detected. Next, the date code location information for the corresponding available facet and surface area is retrieved from the database and the date code is recognized therefrom by OCR. The accuracy of the proposed method reached 100% in all tests, while it is only 10-20% for the baseline system, which detects date-like texts from the wrong range and often misses the expiration date completely due to missing text location information.\n\nGabor energy response based expiration code detection and recognition method for food packaging has been proposed in Zaafouri et al. 8 Method use source images captured from the packages with a standard digital camera. The expiration code is localized based on the local energy calculation of the images, the determination of the maximum energy difference, and the analysis of connected components. Characters found are binarized, and further segmented characters are convolved with a bank of Gabor -filters to extract three Gabor features: Fourier magnitude, imaginary response, and Gabor energy- response. Characters are classified by a sparse representation-based classifier using the Gabor energy -response. The method was tested with different backgrounds, code directions, and contrasts. It consistently located codes from images but suffered limitations with complex backgrounds and when the characters composing the code derived from location and isolation modules are very distorted. Moreover, it is sensitive to parameter selection, especially Gabor filter parameter settings. Furthermore, comparing the execution time of the proposed algorithm of 4.6 s with the execution time of the edge-based algorithm of 2.1 s in the corresponding task shows the slowness of the method.\n\nA method based on Stretched Gabor features was proposed in Zaafouri, Sayadi, and Fnaiech 9 for expiration dates recognition of products. In pre-processing input image is binarized, skewness of the code is corrected, and the thickness of the touching characters are reduced. Character strings are segmented using a vertical projection technique to extract character images. Individual character images are normalized and convolved with a bank of 2D S-Gabor filters for feature extraction. Feature indexes consisting of the difference between local energy feature maps on subsequent orientation channels, the norm of the difference between subsequent magnitude responses, and the difference between subsequent complex moments magnitude of order one, are used in four filter orientations composing the feature vector used as input for multilayer neural networks for number recognition. The number of output nodes in the neural network is 10 corresponding to the number of digits, the number of nodes in the hidden layer is 50, the learning speed is 0.1, the network learns using the Backpropagation-method, and the number of maximum iterations is set to 5,000 in the method. The achieved average recognition rate reaches 99.3%. The method consistently locates the expiration code of images, and its degraded digit detection rate is high.\n\nThe binary large object (BLOB) algorithm with K-nearest neighborhood (KNN) classifier was proposed in Mishra and Jain 16 for the recognition of serial numbers printed on labels. Numbers are detected using BLOB-algorithm with filters by color parameters. The KNN classifier used for recognition was first trained with the corresponding numbers. The classifier recognizes detected blobs by comparing them to its trained internal models. The method achieved a detection rate of 88%, and the recognition accuracy of the classifier was 100%. With the inexpensive Linux-based system, the processing speed of the method was 10 frames per second.\n\nIn Xiang et al. 18 a multidirectional illumination and image fusion method for recognition of metal stamping characters on metal surfaces of industrial products was proposed. In the method, the difference in surfaces grayscale values in four source images taken from different lighting directions is used to fuse the images and to eliminate the effect of background brightness differences with enhancing the contrast between the text and the background. Fused images’ character strings are binarized and segmented using the horizontal projection function. Further connected component labeling algorithm is used for single characters separation. For single character histogram of oriented gradients (HOG) -feature extraction, the block of four cells is traversed through the input image in horizontal and vertical directions. Direction and amplitude of the gradient are calculated in each cells in the block. Images’ spatial histogram is obtained by dividing the gradient direction into nine bins in each cell and merging them into a 36-dimensional block feature. By traversing the image, a feature matrix composed of all block features is obtained. The feature vector describing the features of the whole image is obtained by concatenating each row and column of the feature matrix. Backpropagation -neural network is used as a classifier for character recognition. The method achieved a recognition accuracy of 99.6% with an execution time of 2.4 s with a cell size of four pixels with stride three.\n\nA method based on fully convolutional network (FCN) and Tesseract OCR was proposed in Gong et al. 14 for food packages expiration date detection and recognition. For date region detection Fully Convolutional Network structure decomposing into three parts is used: First branch, the feature extractor stem composing of interleaving convolution and pooling layers is used to extract four levels of feature maps from the input image. Features from different scale levels detects date code regions with different sizes. In the second phase, the feature merging branch, the feature outputs from a different layers of the Feature extractor stem are concatenated, and convolution layer is applied to produce the final feature map. Final feature map is fed into the third branch, the output layer, which contains multiple 1x1 convolution operations to project 32 channels of feature maps into score map, geometry map, and angle map. Score map gives likely-hood that a pixel belongs to the expiry date region, and multi-channel geometry map defines the boundary of the text box, which can be either a rotated box or quadrangle. Network is trained based on the defined loss function using the adaptive moment estimation (ADAM) -optimization tool until performance improves. Location of the final text region area is determined by the locations of the values that are greater than the score map threshold. Geometries associated with these locations on the geometry map are then combined with location-aware non-maximum suppression (NMS) to determine the final text region. Tesseract OCR is used to recognize texts from detected expiry date regions. First, using the maximally Stable Extremal regions (MSER) algorithm, the extracted date code region is binarized with characters being differentiated from the background. Connected component analysis is used to find blobs representing different characters while filtering out small noisy spots. Each candidate blob boundary with the corresponding shape features is extracted for character classification. In the nearest neighbor (NN) classifier blob features are compared to the prototypes representing different characters and classified as the character for which the relative distance is smallest. The proposed system is trained and tested using different types of food package images taken in a natural food store environment. The method achieved a text recognition rate of 98%. However, text recognition errors occurred with blurred characters.\n\nCNN-based deep learning method for water bottle dot matrix characters recognition is described in Muresan, Szabo, and Nedevschi. 15 A controlled imaging environment was used for bottle imaging. Transparent and curved plastic bottles are back illuminated, with text area oriented directly to the camera. Mask R-CNN algorithm is used to detect the bottle from the image, returning the bottle shaped bounding box, mask, label, and score of the recognition. The bottle-shaped image is scaled to a predefined size and processed using a morphological gradient operation to outline the objects it contains and further binarized. To find the text area in the image, the white pixels it contains are morphologically processed to form rectangular shaped blobs. By only using the extreme outer contour extraction function, contours are extracted and drawn on a new black image. The properties of the bounding box areas of each contour object are verified, and the original image is cropped using the bounding box coordinates resulting from the included contours. Cropped image with texts in a bounding box is zoomed to twice the size of the original and processed with a sharpening operation before binarization, and morphological processing with the aim of connecting the dots, keeping the characters separate while expanding the number of character pixels. Characters are segmented from the image using vertical and horizontal projections. In post-processing phase often missing dot matrix character parts are reconstructed using morphological dilation. For feature extraction, post-processing phase images, used as features for classification, are equally padded and resized forming a 32x32 pixel square that conforms to CNN’s constraints. Segmented digits are recognized using the LeNet-5 CNN - architecture. Network is trained with a set of ~22500 images in 10 epochs and with batch size of 1000, achieving 97,5% test accuracy.\n\nEnd-to-end deep learning methods for batch codes recognition printed on cardboard boxes was proposed in Singh et al. 11 A set of three images is captured at a time in three orientations from a box moving on a conveyor. After pre-processing with motion blur removal of and image sharpening, pre-processed images are subsequently used for the text localization. The connectionist text proposal neural network algorithm is used to detect the text in the image, recognizing the lines of text as a series of fine text proposals. The methods vertical anchoring mechanism predicts the location and text/non-text scores of each fixed-width proposal. The localized text sequences are cropped, and the resulting image is enhanced and adaptively thresholded. Discontinuities in the pixels of the characters are removed before connected components-based contour detection, after which contours with very small width and unexpectedly large height are removed. Each of the contour features are extracted, contours are compared with each other, and groups are formed based on the features belonging within empirically selected values. The objective is to find the character contours for batch codes of a finite length. All characters of the localized text are sent in batches to the capsule-based modified caps net-network, whose structure consists of two feature blocks and two layers of capsules for recognition. Input features extracted by successive convolutions of feature blocks are used to create feature vector, which is then fed to capsule blocks for character prediction. The feature vector enables the network to learn the spatial relationship between features. The achieved recognition accuracy is 85.6% with the real world dataset and 91.3% with the synthetic dataset.\n\nIn Ashino and Takeuchi 10 the combination of two deep neural networks for dot matrix printing recognition of food drink cartons is proposed. Faster R-CNN, used for expiration date digit location and recognition, first obtains the position and size of characters in an image. The system then scans the expiration date area using a raster scanning method and crops out the area of recognized characters in the image. Character recognition Le-Net network is used for character recognition from the cropped image. The system then combines the results of both neural networks to get a final result based on the spacing of the digits. The limited size of the training data set limited the method's recognition accuracy to 97%, according to the researchers.\n\nThe dual DNN method, FCN for text region detection, and convolutional recurrent neural network (CRNN) for text recognition of food packaging is proposed in Gong et al. 7 Source images of the methods are captured in the real food industry/retail environment, which includes different colors/textures, and low-quality images. A fully connected CNN as in Gong et al. 14 is used in the text region detection method. Text recognition is performed using CRNN-composed of three parts including the feature extraction part, bidirectional long short-term memory recurrent neural network (LSTM RNN) part, and transcription layer part. In feature extraction, convolution and pooling layers thereof are used to partition the input image into image patches. Feature vectors corresponding to the number of patches are fed to the bidirectional recurrent neural network with the LSTM unit to predict the label distribution. Recurrent layers in Bi-directional LSTM-RNN capture the contextual dependencies between consecutive image patches. Bi-directional LSTM-RNN operates on arbitrary length text sequencies, recognizing texts of different lengths in different formats. The transcription layer of the CRNN converts the predictions of the second LSTM-RNN into a label sequence that maximizes the conditional probability given by the bidirectional LSTM-RNN predictions. Comparing the text recognition performance of the proposed method with Tesseract OCR used to recognize similarly detected texts, the CRNN network performs better in recognizing blurry characters, with OCR being able to misclassify them.\n\nTable 1 summarizes the details of the product code recognition methods analyzed in Section 2, and the recognition rates achieved.\n\nTable 1 summarizes the character extraction and recognition algorithms from various products, and description of their surfaces, recognition accuracies, and training data sets. It can be concluded that machine vision can accurately recognize characters of various shapes printed using various methods on various product surfaces. It should be noted that controlled imaging environments are used during the imaging phase of the product surfaces in. 11 , 15 Product codes printed on products can now be recognized on surfaces that traditionally normally require human vision using current state-of-the-art methods.\n\n\nResults\n\nThe results are based on a detailed analysis of 10 studies published between 2012 and 2020 which presented state-of-the-art product code recognition methods. 22 The PRISMA-based flowchart of this systematic review 23 is shown in Figure 2.\n\nIn this section, we examine the development of product text recognition methods over the past eight years. Based on the analyzed articles, six relevant aspects can be identified that affect the recognition accuracy:\n\n(1) Changes in the shape, size, position, and placement angle of the packages in the camera view.\n\n(2) Changes in the shape of the packaging surface on which the codes are printed.\n\n(3) Changes in the illumination of the packaging surface.\n\n(4) Low contrast between the text printed on the surface of the product and the background or its variation.\n\n(5) Inconsistencies in the character shapes of the text.\n\n(6) The effect of motion blur caused by the movement of the package.\n\nFor the results, the text recognition performance, imaging methods, products, texts printed on them, and printing methods of the articles published during the research period were compared with those of the first year.\n\nDeep learning methods with two consecutive networks are the most tolerant to the most common problems in the field. Despite variations in physical circumstances, changes in the curvature of the package's surface, and changes in illumination, the study's deep learning algorithms recognize the characters. In a controlled imaging environment, they also recognize low-contrast characters, characters with irregular character formats, and images captured from moving packages. Recognition accuracies of the methods are despite these imperfections over 91%.\n\nConventional recognition methods have evolved to tolerate variations in surface shape and illumination, as well as low contrast between the text and background, during the period of the research. On the other hand, the rate of recognition of regular characters on a plain background has increased. They have a recognition accuracy of more than 99%. Table 2 shows the results of the method development for the most common recognition difficulties in the field.\n\nDeep learning has outperformed other recognition methods in the past two years, while no conventional methods have been proposed. The following numbers of deep learning character recognition algorithms have been proposed:\n\nFive of them utilize deep learning to detect text regions. 7 , 10 , 11 , 14 , 15 Four of them 7 , 10 , 11 , 15 use two separate deep networks for text area detection and character recognition. Table 3 represents the number of papers published each year by method of recognition.\n\nA significant result for this field is the comparison of the performance of conventional character recognition with deep learning when recognizing characters that are inclined, affected by lighting, and printed with low printing quality from food packaging images: The CRNN method has a recognition rate of 95.4%, whereas the Tesseract OCR method has a rate of 31.1%. 7\n\nIn this research, deep learning is used to recognize characters in a wide range of food packaging, beverage cans, transparent water bottles, and moving boxes. Conventional recognition methods in the study 8 , 9 , 16 , 18 , 21 included multi-directional illumination of the text area to enhance low-contrast characters, recognition of regularly shaped characters by a computationally efficient BLOB algorithm with the KNN classifier, character recognition based on energy differences in different areas of the image, and the OCR method. The performance of conventional recognition methods has improved in terms of the speed of recognition of clear characters in clear backgrounds, as well as in the recognition of degraded characters.\n\nFigure 3 illustrates the evolution of methods in terms of publication years, used source images, character characteristics, and packaging surfaces.\n\nWith the set search criteria, ten studies containing performance analysis were found, of which seven proposed methods for expiration date code detection, two for serial numbers, and one for batch code recognition. In addition to them, four research papers from the years 2012-2020 were examined in order to obtain a sufficient knowledge base of the field, they deal with: OCR performance in a variety of environments, 17 dot-matrix character segmentation, 5 deep neural networks in impaired character recognition, 13 and the effect of pre-processing methods in improving general-purpose OCR performance. 12\n\nThis section will explore of which are the most common difficulties in recognizing product text. The search strategy used made state-of-the-art product text recognition methods available. Studies of the latest methods include solutions to overcome the most common problems in the field. Analysis of the research material provided answers to the second research question:\n\nThe main problems in product code recognition are:\n\nScene complexity: Variations in physical conditions while capturing images of product packages: Changes in the shape, size, location, and angle of placement of the packages. A natural scene image from package may contain text with arbitrary perspective deformation in a complex background due to its unknown 3D position and orientation.\n\n(1) To solve this problem, Table 4 shows the solutions to the variations caused by physical conditions.\n\n(2) Due to the change in the shape of the package surface, the intensity of the light varies in different locations, which is reflected as different shades of gray on the same surface, leading to an incorrect recognition result. To solve this problem, Table 5 shows the solutions to alleviate the problem caused by the change in the surfaces shape.\n\n(3) Low contrast of text printed on the surface of the package. Variations in product label formats. Caused by uneven illumination of a complex package background (not a flat surface). Background colored texts. Complex background with writing style. To solve this problem, Table 6 shows solutions to alleviate the problem caused by the low contrast of the text.\n\n(4) Fonts and print style. Inconsistencies in character shapes in manual ink stamping and in dot matrix printed texts. Variations in printing styles such as blurred code due to manual printing, such as ink stamping. 11\n\nSome printing methods may produce blurry texts and texts without common features from any other font family. During to the storage duration, texts may be distorted and warped.\n\nTable 7 presents solutions to inconsistency in the shapes of the fonts.\n\n(5) Motion blur due to movement:\n\nMotion blur caused by acquiring an image of the product package as it moves on the conveyor. To solve this problem, Table 8 shows the solutions to the motion blur.\n\nThe answers to the research question have been found through an in-depth literature review of recent research and analysis of the papers included in the research.\n\n\nDiscussion\n\nThis paper provided a detailed literature review of state-of-art product code recognition methods proposed and tested in recent relevant studies. The research questions focused on finding solutions for the development of methods for product text recognition in the last 8 years, and for the most common problems of product text recognition.\n\nRecognition techniques were divided into a previous conventional recognition method period of 6 years, and a deep learning methods period into the last two years. Increased application of deep neural networks for product text recognition since 2018 has made possible to recognize inconsistent characters, detect and recognize text of different sizes in images captured in real-world conditions and recognize text from moving packaging.\n\nMethods with two separate consecutive deep neural networks has made it possible to recognize distorted text and irregular characters on surfaces exposed to light, even in low-quality images. In these methods, deep-learning neural networks have been defined for use in text area detection and in character recognition algorithms. The methods use this structure to extract and learn the features of text regions and characters from a large set of training images, and then recognize the characters in subsequent images using the model they have learnt. Such methods greatly contribute to the recognition of packaging texts in real-life conditions. Conventional recognition methods in the study included multi-directional illumination of the text area to enhance low-contrast characters, recognition of regularly shaped characters by a computationally efficient BLOB algorithm with the KNN classifier, and character recognition based on differences in energy in different areas of the image. The performance of conventional recognition methods has improved in terms of the speed of recognition of clear characters in clear backgrounds, as well as in the recognition of degraded characters.\n\nThis study demonstrated that product text recognition techniques have evolved to address the most common research problems presented in the results section of this study.\n\nIn the first phase of the study, a comprehensive literature search on state-of-the-art methods was carried out, which was analyzed, and the individual method details were presented with a recognition performance analysis. The results section answers research questions and presents the methods tolerances to the most common difficulties in the field, identified based on analyzes performed on research articles. At the end of the results section, the most common difficulties in this area are presented in detail, together with the proposed solutions from the literature.\n\nThis research topic is relatively new, and although studies have been published in this area, there are not many. It would be of particular interest to find further studies where experimental results were obtained with real products and environments. Successful product text recognition also requires consistent thinking when designing the product imaging phase, how to capture an image of each package such that the source image's image analysis can effectively recognize the characters contained within it. Since objects of interest (characters) are imaged with visible light from the surface of the product, the research area itself, the development of recognition algorithms would be facilitated by a well-known standard imaging environment. Similarly, it would be useful for research development to have a data set in which the codes are printed using different printing methods. Such as laser and dot matrix printing, stamping, character pressing, and character pressing with ink marking. In addition, a research topic that deserves attention is the contextual handling of recognized characters. In this field of research, publications often propose solutions for the classification of digits, letters, or combinations thereof. In the packaging handling industry, there is a need to convert a variety of well-defined character sets into electronic form, so research should focus on the contextual understanding of different length codes. With OCR, which has been used for decades, this is done by comparing the result with the grammatical words.\n\n\nData availability\n\nOpen Scientific Framework: Summary of References for Recent advancements in machine vision methods for product code recognition. A systematic review. https://doi.org/10.17605/OSF.IO/8Z54T 22\n\nThis project contains the following underlying data:\n\n• Summary of References Reviewed for Recent advancements in machine vision methods for product code recognition. A systematic review.xlsx (Summary of references).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nOpen Scientific Framework: PRISMA checklist for ‘Recent advancements in machine vision methods for product code recognition: A systematic review’ https://doi.org/10.17605/OSF.IO/CN42Q 23\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nEuropean Commission, Eurostat: [Retrieved 25.05.2022].Reference SourceReference Source\n\nBix L, de la Fuente J , Sundar R, et al.:2009. Book: Packaging Design and Development.859–866. 978-0-470-08704-6. Publisher Full Text\n\nKotler P, Wong V, Saunders J, et al.: Book: Principles of Marketing.2005.9781292269566\n\nEuropean Union, EUR-Lex:[Retrieved 25.05.2022].Reference Source\n\nRodríguez-Rodríguez JC, Quesada-Arencibia A, Moreno-Díaz R, et al.: A character segmentation proposal for high-speed visual monitoring of expiration codes on beverage cans. Sensors (Switzerland). 2016; 16(4). PubMed Abstract | Publisher Full Text\n\nWorld Health Organization, Guidelines on Packaging for Pharmaceutical Products:[Retrieved 25.05.2022].Reference Source\n\nGong L, Thota M, Yu M, et al.: A novel unified deep neural networks methodology for use by date recognition in retail food package image. SIViP. 2020; 15(3): 449–457. Publisher Full Text\n\nZaafouri A, Sayadi M, Fnaiech F, et al.: A new method for expiration code detection and recognition using gabor features based collaborative representation. Adv. Eng. Inform. 2015; 29(4): 1072–1082. Publisher Full Text\n\nZaafouri A, Sayadi M, Fnaiech F: A vision approach for expiry date recognition using stretched gabor features. Int. Arab. J. Inf. Technol. 2015; 12(5): 448–455.\n\nAshino M, Takeuchi Y: Expiry-date recognition system using combination of deep neural networks for visually impaired.2020. Publisher Full Text\n\nSingh CK, Gangwar VK, Singh HV, et al.: Deep capsule network based automatic batch code identification pipeline for a real-life industrial application. Paper presented at the Proceedings of the International Joint Conference on Neural Networks. 2019-July. Publisher Full Text\n\nScazzoli D, Bartezzaghi G, Uysal D, et al.: Usage of hough transform for expiry date extraction via optical character recognition. Paper presented at the 2019 Advances in Science and Engineering Technology International Conferences, ASET 2019. 2019. Publisher Full Text\n\nKhan T: Expiry date digits recognition using deep learning. Paper presented at the Proceedings of the IEEE National Aerospace Electronics Conference, NAECON, 2019-July 302-304. 2019. Publisher Full Text\n\nGong L, Yu M, Duan W, et al.: A novel camera-based approach for automatic expiry date detection and recognition on food packages.2018. Publisher Full Text\n\nMuresan MP, Szabo PA, Nedevschi S: Dot matrix OCR for bottle validity inspection. Paper presented at the Proceedings - 2019 IEEE 15th International Conference on Intelligent Computer Communication and Processing, ICCP 2019, 395-401. 2019. Publisher Full Text\n\nMishra RK, Jain P: A system on chip based serial number identification using computer vision. Paper presented at the 2016 IEEE International Conference on Recent Trends in Electronics, Information and Communication Technology, RTEICT 2016 - Proceedings. 2016; 278–283. Publisher Full Text\n\nHosozawa K, Wijaya RH, Linh TD, et al.: Recognition of expiration dates written on food packages with open-source OCR. Int. J. Comput. Theory Eng. 2018; 10(5): 170–174. Publisher Full Text\n\nXiang Z, You Z, Qian M, et al.: Metal stamping character recognition algorithm based on multi-directional illumination image fusion enhancement technology. EURASIP J. Image Video Process. 2018; 2018(1). Publisher Full Text\n\nGonzalez RC, Woods RE: Digital Image Processing. 4th ed.Hudson Street, New York:Pearson;2018.9780133356724.\n\nAlthobaiti H, Lu C: A survey on arabic optical character recognition and an isolated handwritten arabic character recognition algorithm using encoded freeman chain code. Paper presented at the 2017 51st Annual Conference on Information Sciences and Systems, CISS 2017. 2017. Publisher Full Text\n\nPeng E, Peursum P, Li L: Product barcode and expiry date detection for the visually impaired using a smartphone. Paper presented at the 2012 International Conference on Digital Image Computing Techniques and Applications, DICTA 2012. 2012. Publisher Full Text\n\nKoponen J: Summary of References Reviewed for Recent advancements in machine vision methods for product code recognition. A systematic review. [Dataset].2022. Publisher Full Text\n\nKoponen J: PRISMA Checklist Recent advancements in machine vision methods for product code recognition A systematic review. [Reporting guidelines].2022, September 1. Publisher Full Text"
}
|
[
{
"id": "183263",
"date": "31 Jul 2023",
"name": "Mehwish Leghari",
"expertise": [
"Reviewer Expertise Pattern Recognition",
"Fingerprint Recognition",
"Online Signature Recognition",
"Machine Learning and Deep Learning."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study reviews the text recognition techniques in last eight years particularly from the products related with pharmaceuticals and perishable foods. There were 138 search results returned to the authors from various sources and ten articles were shortlisted for this research.\nOverall the methods used by different researchers have been analyzed and presented systematically in this work. Research works using both the traditional recognition techniques like KNN and modern recognition techniques like deep learning methods have been analyzed. A detailed account of extraction methods, segmentation methods, recognition and results have been presented for all the studies reviewed in this research.\nThis research also highlighted that some of the deep learning based techniques use a combination of two networks: one for text area detection and other for character recognition. The research presents a detailed discussion on different problems in text recognition that have been solved in recent years. The solutions to the various problems have been presented from the literature in forms of tables. This research concludes that the deep learning has outperformed the conventional methods in recent years.\nOverall the research work is acceptable though there are two points needed to be clear:\nUsing a deep neural network models, able to automatically learn effective features for text detection and recognition under variety of scenes. (This statements need a justification, that how the use of a deep learning method will solve the said problem i.e. the irregular fonts)\n\nThe paper claims to deal the text recognition for perishable food and pharmaceutical however it only cited the research using food and food packages. Pharmaceuticals have not been cited in any of the 10 research works.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "10011",
"date": "16 Nov 2023",
"name": "Jarmo Koponen",
"role": "Author Response",
"response": "Thank you for your insightful feedback on my research work. I appreciate your positive assessment of the overall quality of the research. To clarify the Point 1): \"Using deep neural network models, capable of automatically learning effective features for text detection and recognition across a variety of scenes.\" The text in question appears in the publication's chapter discussing solutions to the most common problems in the field. Each text contains reference numbers to the source articles (15, 11, 10, and 7) of the study, which utilize deep learning neural networks for text detection and recognition. Page 9 indicates that their recognition accuracy is over 91%. In Figure 3, it is observed that in article 15, the texts on the bottle are printed using a dot-matrix method. In article 11, the surfaces of the imaged products are non-planar, and the objects are positioned obliquely relative to the camera, resulting in imperfections in the printed characters on their surfaces. Method 10 detects inconsistently formed dot-matrix characters, while method 7 causes glare on the surface of the packaging due to view imperfections. Automatic feature learning from different scenes and irregular fonts relies on the ability of deep neural networks to process large amounts of diverse training data. When a deep neural network model is exposed to a wide and varied collection of images, it learns to recognize and abstract meaningful features that are common across different text types and irregular fonts. Point 2) : The researchers included cardboard medicine packages in the \"Consumer products\" category, as they can have critical consequences if used incorrectly, such as with expired medication. The study highlights the potential harm that can arise from using an expired product, especially if it is intended for human consumption like medicine. Ahmed Zaafouri, Mounir Sayadi, and Farhat Fnaiech wrote about product code inspection as quality control of the label of medical products, further emphasizing the relevance of pharmaceuticals in the context of the study. The paper discusses various products such as perishable food items, opaque labels on flat surfaces, metallic liquefied petroleum gas cylinders, cardboard boxes moving on a conveyor, and consumer products packaged in cardboard. The \"Consumer products\" category encompasses a diverse range of products, including pharmaceuticals."
}
]
},
{
"id": "192361",
"date": "22 Aug 2023",
"name": "Zobeir Raisi",
"expertise": [
"Reviewer Expertise Computer Vision",
"Deep learning",
"Text Detection",
"and Recognition in the Wild."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nUpon a thorough review of the manuscript, it is gratifying to note that the paper aligns with the required criteria for acceptance. The authors have demonstrated a comprehensive understanding of the subject matter and have effectively presented their research methodologies and findings. The study's focus on text recognition techniques in the context of pharmaceuticals and perishable foods is well-aligned with the aims and scope of our journal. Including traditional and modern recognition methods and a detailed account of extraction, segmentation techniques, and results showcases a rigorous approach to the research. Furthermore, exploring deep learning techniques and their outperformance in recent years adds valuable insights. Given these strengths, the paper is acceptable for indexing with minor revisions to address some points raised earlier. The authors' work contributes significantly to our understanding of text recognition and its applications and will undoubtedly enrich the scholarly dialogue in this domain.\nTo further enhance the strength of the paper, the authors are encouraged to consider the following suggestions:\nWhile the authors have concentrated on text instances associated with pharmaceuticals and perishable foods, it is worth acknowledging that benchmark datasets within the scene text detection community encompass many images featuring related content. The authors might consider incorporating recent deep learning methodologies with readily available pre-trained models on platforms like GitHub to augment the research. By evaluating these models on text instance images related to pharmaceuticals and perishable foods, the paper could provide a broader perspective on the performance of the chosen techniques within a more diverse context.\n\nTo provide a more comprehensive understanding of the applications under study, it is recommended that the authors include qualitative results for the challenges that exist in these types of text instances. This could involve showcasing examples of successful text recognition instances from their research. Additionally, for each application, including detailed captions that specify the encountered challenges would enrich the readers' comprehension. Such qualitative insights can offer a nuanced view of the complexities faced in real-world scenarios, enhancing the overall impact of the paper.\n\nAddressing the challenge of occlusion in product text instance spotting and its potential impact on the performance of trained models could enhance the paper's comprehensiveness. Therefore, the inclusion of a discussion regarding this aspect would be beneficial.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1099
|
https://f1000research.com/articles/11-296/v1
|
10 Mar 22
|
{
"type": "Research Article",
"title": "Characterizing gene expression in an in vitro biomechanical strain model of joint health",
"authors": [
"Anthony Hung",
"Genevieve Housman",
"Emilie A. Briscoe",
"Claudia Cuevas",
"Yoav Gilad",
"Anthony Hung",
"Genevieve Housman",
"Emilie A. Briscoe",
"Claudia Cuevas"
],
"abstract": "Background: Both genetic and environmental factors appear to contribute to joint health and disease. For example, pathological levels of biomechanical stress on joints play a notable role in initiation and progression of osteoarthritis (OA), a common chronic degenerative joint disease affecting articular cartilage and underlying bone. Population-level gene expression studies of cartilage cells experiencing biomechanical stress may uncover gene-by-environment interactions relevant to human joint health. Methods: To build a foundation for population-level gene expression studies in cartilage, we applied differentiation protocols to develop an in vitro system of chondrogenic cell lines (iPSC-chondrocytes). We characterized gene regulatory responses of three human iPSC-chondrocyte lines to cyclic tensile strain treatment. We measured the contribution of biological and technical factors to gene expression variation in this system. Results: We identified patterns of gene regulation that differ between strain-treated and control iPSC-chondrocytes. Differentially expressed genes between strain and control conditions are enriched for gene sets relevant to joint health and OA. Furthermore, even in this small sample, we found several genes that exhibit inter-individual expression differences in response to mechanical strain, including genes previously implicated in OA. Conclusions: Expanding this system to include iPSC-chondrocytes from a larger number of individuals will allow us to characterize and better understand gene-by-environment interactions related to joint health.",
"keywords": [
"Genomics",
"joint health",
"biomechanical stress",
"iPSC-derived cells",
"gene regulation"
],
"content": "Introduction\n\nDisorders of the joints can often lead to pain and disability and have far-reaching impacts on quality of life. For example, osteoarthritis (OA) is a chronic degenerative joint disease characterized by defects in articular cartilage integrity and alterations to underlying bone structure.1 OA is a major cause of disability in older adults and impacts approximately 300 million people worldwide.2 There are no disease-modifying treatments for this painful disorder, and its specific pathogenic mechanisms are still under investigation.\n\nGenome-wide association studies (GWAS) have identified over 86 genetic loci associated with OA risk.3 Most of these loci fall within non-coding regions of the genome and have eluded functional characterization. Therefore, it remains unclear how associated genetic factors modulate OA onset and progression. One possibility is that regulatory changes in key structural and metabolic genes may modulate OA-related outcomes. Regulatory changes occurring in response to relevant environmental factors, including biomechanical stress, may be particularly important. Indeed, gene expression studies have identified broad patterns of gene expression that differ markedly between healthy and osteoarthritic human cartilage.4,5 These gene expression differences reflect activation of biological pathways associated with joint disease, suggesting that studies of gene regulation in cartilage and other skeletal tissues are valuable for understanding normal joint health and joint disease and pathogenesis in joint conditions like OA.\n\nHowever, few studies have measured gene regulatory phenotypes in human skeletal tissues or cells. Even the Genotype-Tissue Expression (GTEx) Project, one of the largest efforts to examine gene expression variation across human tissues and cell types, does not include samples from cartilage.6 This is partially due to the practical limitations and ethical issues associated with collecting healthy, high-quality cartilage samples from human donors. Nevertheless, protocols to differentiate induced pluripotent stem cells (iPSCs) into cells relevant to joint health and disease, such as chondrocytes (the primary cells of cartilage), exist,7,8 and these methods can circumvent some of the challenges associated with inaccessible primary tissues.\n\niPSC-derived cells also allow for the study of dynamic cellular responses to specific environmental conditions. It has become increasingly evident that studying gene regulation in disease-relevant states is crucial for understanding the genetic basis of disease.9 Thus, numerous studies have begun identifying dynamic regulatory expression quantitative trait loci (eQTLs) in various cell types and contexts, including drug-induced cardiotoxicity,10 cardiomyocyte differentiation,11 vitamin D exposure,12 and response to infection.13–17 These studies highlight the merits of exploring gene regulation beyond steady-state conditions.\n\nIn human joints, biomechanical stress is a particularly relevant environmental condition. Joint health deteriorates in response to excessive or insufficient amounts of mechanical loading.18–22 Further, biomechanical factors may impact gene expression regulation in joint tissues and may interact with genetic factors to impact risk for joint diseases.23 Such interactions are difficult to examine in vivo. However, iPSC-derived chondrogenic cells (iPSC-chondrocytes) provide an alternative system in which to study the effects of cyclic tensile strain (CTS), a type of controlled biomechanical stress regimen designed to induce joint disease-like phenotypes.24–27 Thus, iPSC-chondrocytes offer an opportunity to study gene expression responses to joint disease-relevant states. Studies of iPSC-chondrocytes may also help uncover mechanisms through which OA-associated genetic loci modulate OA outcomes.\n\nBoth chondrocyte differentiation protocols and methods for inducing CTS in vitro existed prior to this study. Still, little is known about the suitability of this system for studies of gene regulatory dynamics. Therefore, we designed a study using human iPSC-chondrocytes to examine the combined effects of genetic variation and biomechanical stress on gene regulation during CTS. Through this study, we evaluated whether the process of chondrocyte differentiation is robust to individual differences. We also ascertained whether iPSC-chondrocytes exhibit a robust gene expression response to CTS. Finally, we determined whether expanding the sample size of this experimental system might further improve our understanding of gene-by-environment interactions within joint health.\n\n\nMethods\n\niPSCs in this study were previously generated from lymphoblastoid cell lines (LCLs) derived from three Yoruba individuals (NA18855, female; NA18856, male; and NA19160; male).28 These LCLs were originally derived from individuals collected as part of the HapMap project.29 Undifferentiated iPSCs were cultured on Matrigel-coated plates (Corning 356230) in Essential 8 (E8) medium at 37°C, 5% CO2, and atmospheric O2 until iPSCs reached 30% confluency. E8 medium was subsequently changed to mesenchymal stem cell (MSC) culture medium, which consists of low glucose Dulbecco’s Modified Eagle Medium (DMEM) with 20% stem cell-qualified fetal bovine serum (FBS), and 100 mg/mL Penicillin/Streptomycin. The MSC medium was changed every day for 3 days, at which point cells were 80-100% confluent. On day 3, cells were detached from the Matrigel-coated petri dishes using a 0.05% Trypsin/EDTA solution and cultured on uncoated polystyrene flasks in MSC medium. The medium was changed every 2-3 days until the cells reached 90% confluency. The cells were then sub-cultured at a ratio of 1:3 until passage 4, at which point cells were classified as iPSC-derived MSCs (iPSC-MSCs). iPSC-MSCs were cryopreserved with cryopreservation media (80% FBS, 10% MSC culture medium, 10% Dimethyl Sulfoxide) in liquid nitrogen at passage 5 to 7.\n\niPSC-MSCs were detached from culture flasks using 0.05% Trypsin/EDTA and seeded at a density of 250,000 cells/well onto the center of wells of BioFlex Type I Collagen coated 6-well Culture Plates (FlexCell International BF-3001C) using BioFlex cell seeders (FlexCell International). Cells were seeded using a regimen of 15% elongation for 2 hours followed by overnight culture in MSC culture medium. After seeding, cells were cultured in serum-free chondrogenic differentiation medium,7 consisting of high glucose DMEM, 100 mg/mL Penicillin/Streptomycin, 50mg/mL L-Proline, 200 mM GlutaMax, 50 mg/mL L-Ascorbic acid-2-Phosphate, 11g/L Sodium pyruvate, 5mM Dexamethasone, 1x ITS Premix, and supplemented with 10 ng/mL TGF-β3. The chondrogenic medium was changed every 2-3 days for 14 days.\n\nFlow cytometry of iPSC-MSCs was performed using the BD Biosciences Human MSC Analysis Kit (BD Biosciences 562245), in combination with the Zombie Violet Fixable Viability Kit (BioLegend 423113). The Human MSC Analysis Kit assesses the surface markers CD90, CD105, CD73, CD34, CD45, CD11b or CD14, CD19, CD79α, and HLA-DR. In each flow experiment, matched iPSCs from the same line as each iPSC-MSC were included as a negative staining control. Samples were run on a BD LSRII Special Order System machine at the University of Chicago Cytometry and Antibody Technology Core Facility.\n\niPSC-chondrocytes were fixed using 4% paraformaldehyde in phosphate-buffered saline (PBS) before staining using Alcian blue and Nuclear Fast Red. Alcian blue binds proteoglycans, which are found in connective tissue, particularly in cartilage.30 Stained iPSC-chondrocytes and matched iPSC-MSCs from the same individuals were imaged using an Olympus dissecting microscope.\n\niPSC-chondrocytes differentiated in chondrogenic media from MSCs for 14 days in either monolayer or pellet culture, MSCs, and primary cartilage tissue were fixed using 4% paraformaldehyde in PBS. iPSC-chondrocyte pellets were generated as in Nejadnik et al. (2015),7 fixed in 4% paraformaldehyde in PBS, dehydrated sequentially in 15% sucrose in PBS and 30% sucrose in PBS, and then embedded in optimal cutting temperature compound (OCT). Primary human articular cartilage samples were obtained from a patient undergoing hip replacement surgery (University of Chicago BSD/UCMC IRB Protocol 19-0990). The IRB granted a waiver of informed consent for these samples as they were deidentified. Under sterile conditions, cartilage scrapings were obtained from the medial portion of the femoral head and cut into small pieces using a scalpel. Samples were washed with PBS twice and flash frozen. Primary cartilage tissues were then thawed and embedded in OCT. Cartilage tissue and iPSC-chondrocyte pellets were sectioned on a cryostat to a thickness of 18 μm and 5 μm respectively and sections were mounted on slides prior to staining. Cells and sections were immunostained using a rabbit Collagen II polyclonal primary antibody (Thermo PA5-85108, RRID:AB_2792256) and a secondary antibody HRP/DAB detection IHC kit (Abcam ab64261, RRID:AB_2810213). Immunostained cells and sections were imaged using an EVOS microscope under the brightfield setting.\n\niPSC-chondrocytes were treated with a cyclic tensile strain (CTS) regimen that is known to induce an OA-like phenotype using the Flexercell FX6000 Tension System (Flexcell International).24–27 Plates were loaded onto the Flexercell baseplate (located in an incubator at 37°C, 5% CO2, and atmospheric O2), and a vacuum was used to deform the cell culture plate membrane and create uniform biaxial cyclic tensile strain. Specifically, 2.5% elongation (15kPa) of CTS was applied to the cells at a rate of 0.5 Hz for 24 hours.\n\nRNA was extracted from iPSC-chondrocytes following CTS or control treatments using the ZR-Duet™ DNA/RNA MiniPrep kit according to manufacturer instructions (Zymo D7001). To quantify target gene expression of GUSB, MMP1, MMP13, and TIMP2, we used RT-PCR with a QuantStudio 6 Flex Real-Time PCR System and SYBR Green reagents according to manufacturer instructions (Applied Biosystems). The sequences of primers used for each marker gene are shown in Extended Data Table 988. The cycle threshold (Ct) values were measured, and relative transcript levels were calculated for each target gene in each sample. The efficiency (E) of each PCR amplification reaction was calculated based on the slope of a linear curve of a series of dilutions of target DNA with known concentrations (E =10(-1/slope)). Data were plotted as relative expression, which is calculated as E(− ΔΔCt), using GUSB as a housekeeping gene in all cases.31\n\niPSC-chondrocytes were dissociated from adherent conditions into single cell suspension as follows: first, cells were rinsed once with 1X PBS. Then, 1mg/mL of collagenase II) in 1X HBSS was added to cell culture wells at room temperature for 5 minutes. The collagenase II was neutralized with MSC medium and removed before further processing of the cells. Cells were rinsed once again with 1X PBS. A 0.25% Trypsin/EDTA solution was added to wells at room temperature for 2 minutes until cells detached. The trypsin was neutralized with MSC culture medium, and the cells were pelleted at 1000 rpm for 5 minutes and resuspended in FBS Stain Buffer. Cells were counted separately for each sample and combined in equal proportions before loading into a Chromium Single Cell A Chip kit according to manufacturer instructions (10X Genomics, 120236). To ensure that collection batch, individual, and treatment conditions were not confounded, samples were pooled strategically. One GEM well of a Chromium single cell chip targeting a collection of 5000 cells contained NA19160 control, NA18856 control, and NA18855 strain-treatment cells. A second GEM well of the same Chromium single cell chip targeting a collection of 5000 cells contained NA19160 strain-treatment and NA18855 control cells. The cells collected from sample NA18856 strain-treatment were not processed due to viability issues. Single cell cDNA libraries were established following the 10x Genomics Chromium Single Cell protocol.32 In brief, the RNA of the captured cells was released by lysis, barcoded via a reverse transcription process, and amplified to produce gene expression libraries. The libraries were sequenced to 100 base pairs, paired-end on one lane using the Illumina HiSeq4000 at the University of Chicago Genomics Core Facility according to manufacturer instructions.\n\nFastQC (RRID:SCR_014583) was used to confirm that the reads were of high quality. Using an in-house computational pipeline, we extracted 10X cell barcodes and UMIs from raw scRNA-seq reads and mapped remaining reads to genes in the hg38 genome using STARsolo from the STAR software with default parameters (version 2.6.1b, RRID: RRID:SCR_004463).33 The software demuxlet was used to deconvolute sample identity of individual cell droplets and detect multiplets in multiplexed samples with default parameters.34 Previously collected and imputed genotype data for the three Yoruba individuals from the HapMap and 1000 Genomes Project were used as input for demuxlet.29,35\n\nProcessed gene count per cell barcode matrices were imported into R using the Seurat package (v3.2.0, RRID:SCR_007322).36,37 Data were filtered to remove cells with fewer than 2000 UMIs detected and more than 10% of reads mapping to mitochondrial genes. Cells assigned as multiplets by demuxlet were also removed. A Uniform Manifold Approximation and Projection (UMAP) plot of the merged and unintegrated data shows that cells originating from the same individual cluster with each other (Extended Data Figure 1188).\n\nFiltered scRNA-seq data was integrated across individuals using Seurat. Cells that were assigned as singlets by demuxlet were treated as individual datasets. Specifically, we focused on just those datasets deriving from control cell culture conditions (n = 3), as opposed to strain-treated conditions (n = 2). Using Seurat, the SCTransform normalization function was applied to each of these datasets, and then datasets were integrated using integration anchors identified using the FindIntegrationAnchors function. Five-thousand features were selected as integration features for the SCT integration.\n\nSeurat’s FindClusters function was used with 38 gene expression principal components (PCs) and a resolution of 0.4 as parameters to perform unsupervised clustering of transformed and integrated data. Thirty-eight gene expression PCs were chosen by locating the elbow in an elbow plot of PCs. To characterize the resulting three clusters that emerged, a Poisson adaptive shrinkage model was fit to the raw count data from the cells in each pseudo-sample described above using the ashR package.38 Poisson ashR models were fit separately for cell droplets assigned to each unsupervised cluster or separately for cell droplets from each individual. The cumulative density function of the inferred prior distributions for each of the fitted Poisson ashR models was plotted as in Sarkar and Stephens 2020,39 for chondrogenic gene markers.\n\nAn unsupervised topic model with k = 7 topics was fit to the scRNA-seq raw count data from several published sources and data from iPSCs and iPSC-derived cell types generated by our laboratory. Briefly, single cell data from iPSCs, iPSC-MSCs, iPSC-chondrocytes, and iPSC-osteoblasts collected by our group from a single human cell line were combined with single cell data from primary human hepatocytes,40 iPSC-chondrocytes from an iPSC-chondrogenic pellet time-course,41 primary human chondrocytes,42,43 and the iPSC-chondrocytes from the present study.\n\nFirst, the 10X Genomics Chromium Single Cell Gene Expression platform was used to collect scRNA-seq data from iPSCs, iPSC-MSCs, iPSC-chondrocytes, and iPSC-osteoblasts. All of these cells, which were derived from a single human cell line, were included in the topic modeling analysis. This human iPSC line was previously generated and characterized in our lab.44 The same protocol used to generate other iPSC-MSCs in the current study was also used to generate iPSC-MSCs here, with the exception that DMEM:F-12 (Thermo fisher 11330032) was used instead of low glucose DMEM (See Methods). The same chondrogenic media formulation was used to differentiate iPSC-chondrocytes here as in this current study. iPSC-osteoblasts were generated by culturing iPSC-MSCs in osteogenic differentiation medium, consisting of high glucose DMEM (Gibco 11965092), 100 mg/mL Penicillin/Streptomycin (Corning 30002Cl), 10% stem cell-qualified fetal bovine serum (FBS, Thermo fisher 10567014), 50ug/mL Vitamin C, 100nM Dexamethasone, 10mM β-glycerophosphate, and 1uM Vitamin D. The osteogenic medium was changed every 2-3 days. Our iPSC-chondrocyte and iPSC-osteoblast protocols each included a total of 21 days of differentiation in their respective media before isolation and data collection, compared to 14 days for iPSC-chondrocytes in the current study.\n\nAlso included in the analysis were single-cell data from 3,490 hepatocytes published in MacParland et al., 2018, which were subset from a larger dataset of single cell results from whole liver homogenate.40 Data from MacParland et al., 2018 are accessible using the R package HumanLiver and were originally obtained using the 10X Genomics Chromium Single Cell Gene Expression platform. These cells belong to clusters 1, 3, 5, 6, 14, and 15, identified in the original paper as showing enriched ALB (Albumin) expression, a hallmark of hepatocytes.\n\nAdditionally, data from iPSC-derived chondrocytes from a time-course of iPSC-chondrocyte pellet differentiation published in Wu et al., 2021 were obtained from GEO (GEO SRP290799).41 Data from single cells collected on day 7, day 14, day 28, and day 42 of differentiation were used to fit the topic model. Wu et al. chondrogenic pellets were treated with C59 for WNT inhibition during chondrogenesis to improve homogeneity of hiPSC chondrogenesis and avoid off-target cells.\n\nFinally, data from 6,200 and 1,464 primary human chondrocytes were obtained from Chou et al., 2020 and Ji et al., 2018, respectively,42,43 for use in the topic modeling analysis. Cells from Chou et al. 2020 were isolated from the intact outer lateral tibial plateau of a single male individual and processed using the 10X Genomics Chromium Single Cell Gene Expression platform. Data from these cells were downloaded from GEO (GEO Sample GSM4626766). Cells from Ji et al., 2018 were obtained from 10 patients with OA undergoing knee arthroplasty and underwent a modified single cell tagged reverse transcription (STRT) protocol for single cell transcriptional data collection. Data from all cells included in the original study were used. In both primary chondrocyte studies, isolated chondrocytes were not cultured in vitro before processing for scRNA-seq.\n\nGenes with non-zero counts in at least one cell in any of the six single cell datasets were included in the raw count matrix used to fit the topic model. A Poisson non-negative matrix factorization (NMF) model with 7 ranks was fit to the data using the fit_poisson_nmf function in the fastTopics R package with default parameters (v0.4.35).45 After fitting the Poisson NMF model, the fitted loadings and factors matrices were rescaled to sum to a total of 1 across each barcode for the loadings matrix and across each gene for the factors matrix to convert the Poisson NMF model into a topic model. The rescaled loadings matrix became the topic probabilities, and the rescaled factors matrix became the word probabilities in the resulting topic model.\n\nThe diff_counts_analysis function in fastTopics was applied to the topic model to evaluate differential expression of individual genes in each topic. Briefly, the function calculates a β statistic, which represents the log-fold change in relative occurrence of a gene in a single topic compared to its occurrence in all other topics. The function also calculates a standard error and z-score for each β statistic based on a Laplace approximation to the likelihood at the MLE.\n\nRNA was extracted from cells following CTS or control treatments using the ZR-Duet™ DNA/RNA MiniPrep kit (Zymo D7001). RNA concentration and quality were measured using the Agilent 2100 Bioanalyzer. Library preparation was performed over two batches using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 & -2002, Illumina). Samples were sequenced to 50 base pairs, single-end on one lane using the Illumina HiSeq4000 at the University of Chicago Genomics Core Facility according to manufacturer instructions. A minimum of 17,284,094 raw reads were generated per sample. We used FastQC to confirm that the reads were of high quality. One bulk RNA-seq sample was found to have a very low proportion of mapped reads (38.40%) and was excluded from subsequent analyses.\n\nReads were mapped to the hg38 genome using STAR (version 2.6.1b).33 Gene expression levels were quantified using the featureCounts function in Subread (v1.6.5 RRID:SCR_009803) using standard parameters.46 All downstream processing and analysis steps were performed in R (v3.6.1, RRID:SCR_001905) unless otherwise stated.\n\nLog2-transformed counts per million (CPM) were calculated from raw counts for each sample using the edgeR package (RRID:SCR_012802).47 Lowly expressed genes were filtered such that only genes with an expression level of log2(CPM) > 2.5 in at least 4 samples were kept for downstream analyses. For the remaining 10,486 genes, the raw read counts were normalized using the relative log expression (RLE) method to account for the median number of reads sequenced across samples.\n\nTo account for batch effects arising between technical replicates before differential expression analysis, we modeled factors of unwanted variation using the RUVs correction method (RRID:SCR_006263)48 with k = 2. RUVs is a method that uses technical replicate samples to estimate factors of unwanted variation from RNA-seq data. Individual-treatment pairs were constant within replicate blocks, which are used for the RUVs correction. RUVg is distinct from RUVs in that it uses negative control genes to estimate factors of unwanted variation from RNA-seq data rather than knowledge of technical replicate samples in the data.\n\nDifferential expression (DE) was measured using a linear-model-based empirical Bayes method in the limma R package (RRID:SCR_010943). The voom function from the limma package was also used to calculate weights to account for the mean-variance relationship in the RNA-seq count data.\n\nReplicate batch was modeled as a random effect while treatment, individual, two RUVs coefficients, and RIN score were modeled as fixed effects in the linear mixed model for DE comparisons as in equation (1). The ashR package38 was used to perform multiple testing correction on the DE tests using an adaptive shrinkage method. Genes with an FDR-adjusted p value < 0.05 were considered DE.\n\nUsing topGO (RRID:SCR_014798), we assessed enrichment of Gene Ontology (GO) biological processes among DE genes. A Kolmogorov-Smirnov test using ashR adjusted p-values was used for assessing enrichment of GO processes, and the top 20 most enriched terms were reported. To test for enrichment of sets of OA-related genes in our DE genes,3,5 a Fisher’s exact test was used. In all enrichment tests, the background gene set was the complete set of genes tested for DE in our analyses (n = 10,486 genes).\n\nThere is the possibility that the enrichment of DE genes for GO categories and outside gene sets is driven by differential power due to some genes having higher expression in our samples. We therefore repeated the DE and enrichment analyses ten times, permuting the treatment condition labels for the samples each time.\n\nPrincipal component analysis (PCA) was performed on the normalized log2(CPM) values from above. A linear regression analysis was then performed between each of the top 5 PCs and several biological and technical variables. These variables included number of reads sequenced, library preparation batch, RIN score, treatment condition, replicate, and individual. P values from the regression were corrected using the Benjamini Hochberg (BH) procedure. Results with a BH-adjusted p value < 0.05 were considered significant.\n\nThe variancePartition (RRID:SCR_019204) package was applied to the filtered and RLE-normalized CPM values.49 variancePartition uses a linear mixed model to quantify the contribution of variance from different sources. Our linear mixed model included variation due to individual cell line, treatment status, replicate batch, and library preparation batch. In addition, a single coefficient of unwanted variation was determined using the RUVg correction method48 with k = 1; this coefficient was also included in the model. The RUVg correction method estimates factors of unwanted variation in RNA-seq data through negative control genes, which have the lowest variation in expression between samples. The 100 least variable genes in the data ranked by coefficient of variation were used as the set of control genes for the RUVg correction.\n\nTo ascertain the power to detect eQTLs and dynamic eQTLs across a range of sample sizes and standardized effect sizes, we followed the example presented in Ward et al., 2021.50 In brief, for the power analysis we assumed a simple linear regression for eQTL mapping and a conservative Bonferroni correction for multiple testing (FWER = 0.05). Standardized effect sizes are defined as the true additive effect size of genotype on gene expression divided by the phenotype standard deviation. To estimate the false positive rate of calling a dynamic eQTL, we computed the probability of a SNP being called as significant in only one of the two treatment conditions, assuming the standardized effect size was in fact identical in both conditions.\n\nWe used summary statistics from eQTL mapping in three prior dynamic eQTL studies13,50,51 to determine standardized effect sizes for eQTL association tests in each treatment condition. Briefly, p values from association tests were converted into Z-scores using the appropriate quantile function. Z-scores were then converted to standardized effect sizes by adjusting for the square root of the sample size of the study. For summary statistics from Alasoo et al., 2018, and Caliskan et al., 2015, an adaptive shrinkage model was fit to the distribution of effect sizes and standard errors using ashR.38 The ashR posterior estimates of effect sizes and standard deviations were used to compute the standardized effect size. Standardized effect size thresholds for at least 0.8 power under a sample size of 10, 30, 58, or 100 individuals were determined as described above. The number of genes with at least one association test that meets each of these thresholds in each condition were tabulated. Empirical distribution functions were fit to the distributions of the standardized effect sizes from each condition in each of the three studies. The 99th percentile of these standardized effect sizes was determined from the empirical distribution function.\n\nThe analysis code used in this study is available on GitHub and is archived with Zenodo.81\n\n\nResults\n\nWe designed this study to determine whether iPSC-chondrocytes are a useful system for studying gene-by-environment regulatory interactions relevant to joint health. First, we asked whether the efficiency of chondrocyte differentiation is similar in different individuals. Next, we evaluated the effects of CTS on gene regulation in iPSC-chondrocytes to determine whether this system is suitable for studying gene regulatory effects on joint health. Finally, we estimated the contribution of sample and batch effects to variation in gene expression response to CTS, to assess the suitability of our iPSC-chondrocyte system for response eQTL mapping studies.\n\nWe used three human iPSC lines that were previously established and characterized as part of a panel of iPSCs derived from Yoruba individuals.28 We differentiated the iPSCs along the chondrogenic lineage with an intermediate differentiation step into mesenchymal stem cells (MSCs; Figure 1a) using previously established protocols.7 iPSC-derived MSCs (iPSC-MSCs) exhibited phenotypes and cell surface marker expression patterns characteristic of primary MSCs52 (Extended Data Figure 188). iPSC-chondrocytes showed a modest increase in collagenous extracellular matrix (ECM) production as compared to matched iPSC-MSCs (Figure 1b; Extended Data Figure 2a88). Additionally, immunostaining for COL2A1 of iPSC-chondrocytes from one individual demonstrated increased expression compared to matched iPSC-MSCs (Extended Data Figure 2b88).\n\n(a) In our study design, iPSCs generated from three Yoruba individuals were first differentiated along the chondrogenic lineage with an intermediate differentiation step into mesenchymal stem cells (MSCs). iPSC-derived MSCs from each individual were cryopreserved. For each replicate of the experiment, iPSC-MSCs from the same cryopreservation batch were differentiated into iPSC-chondrocytes over a period of 14 days. Subsequently, we treated iPSC-chondrocytes from each individual with 24 hours of a CTS treatment that is known to induce an OA-like phenotype. We simultaneously kept a second, matched control set of iPSC-chondrocytes in the same incubator for the same period of time, but without CTS treatment. We performed three technical replicates of this experiment, starting with MSCs from the same cryopreservation batch. Following strain-treated and control conditions, we extracted bulk RNA from all biological and technical iPSC-chondrocyte replicates and collected scRNA-seq data from one technical replicate from each cell line using the 10X Genomics Chromium Single Cell Gene Expression platform. (b) Representative images of Alcian blue staining of 14 day iPSC-chondrocytes and matched iPSC-MSCs demonstrating increased proteoglycan production in iPSC-chondrocytes. Images are cropped to show the central seeded area of wells of BioFlex Type I Collagen coated 6-well Culture Plate (seeded area diameter 25mm). Additional images for other cell lines are available in Extended Data Figure 2.\n\nWe treated iPSC-chondrocytes from each individual with 24 hours of CTS, which is known to induce a hypertrophic phenotype in cartilage24–27; Methods). We simultaneously kept a second, matched set of untreated iPSC-chondrocytes in the same incubator for the same period as a control. We performed three technical replicates of this experiment, starting with MSCs from the same cryopreservation batch and carrying out an independent differentiation of the MSCs to iPSC-chondrocytes in each replicate. We extracted bulk RNA from all biological and technical iPSC-chondrocyte treated and untreated replicates (n = 9). We also collected single cell RNA sequencing (scRNA-seq) data from one technical replicate (n = 3) using the 10X Genomics platform.\n\nWe could not detect differential expression between treatment conditions for markers of chondrocyte degeneration and hypertrophy in the bulk RNA sequencing data. This is because these genes are expressed at a low level across all samples and are filtered out in pre-processing steps. To evaluate the changes in the expression of these gene markers between treatment conditions more sensitively, we performed quantitative real-time reverse transcription PCR (RT-PCR) on control and strained iPSC-chondrocytes. We detected modest increases in expression of gene markers of chondrocyte hypertrophy MMP1 and MMP13 in response to CTS,25,53 while gene marker TIMP2 did not change in expression, in line with previous reports (Extended Data Figure 3, Extended Data Table 188).25\n\nAs a next step in our analysis, we confirmed that iPSCs successfully differentiated to chondrogenic cells. Using standard staining protocols (Methods), we demonstrated that our cells produce glycosaminoglycan ECM, a hallmark of chondrogenesis (Figure 1b; Extended Data Figure 2a88). Our cells also produce the collagen COL2A1, a protein that is almost exclusive to cartilage tissues54,55 (Extended Data Figure 2b88). We also used our scRNA-seq data to address two major questions: First, what is the approximate proportion of iPSCs that differentiated into chondrogenic cells in each individual? Second, what is the relative maturity of iPSC-chondrocytes?\n\nWe expected that chondrocyte differentiation might result in heterogeneous populations of cells at different stages along the chondrogenic lineage and that iPSC-chondrocyte purity might differ across cell lines. We used scRNA-seq data to assess potential differences in differentiation efficiency among the three individuals. Following standardization and normalization (Methods), unsupervised clustering of the single cell data revealed three clusters of cells in our untreated control samples (Figure 2a). The proportion of cell membership in each cluster is comparable across individuals (Figure 2b). Five percent of cells from individual NA18855 fall into cluster 2, along with 8% of cells from NA18856 and 7% of cells from NA19160. Based on gene expression patterns, cluster 2 consists of cells that are most like chondrocytes; for example, these cells show high expression of COL11A1, an essential gene for normal cartilage collagen fibril formation56 (Figure 2c; Methods; additional genes shown in Extended Data Figure 488). We found no substantial difference in COL11A1 expression between individuals. Thus, based on staining and gene expression patterns, iPSC-chondrocytes are undergoing chondrogenesis, and importantly, cell type composition does not differ substantially among the three individuals in this study.\n\n(a) Uniform Manifold Approximation and Projection (UMAP) of normalized and integrated single cell RNA sequencing data from control samples from all three individuals included in the study. (Left) UMAP colored by sample label. Cells from different samples are well-integrated. (Right) UMAP colored by Seurat cluster determined from normalized gene expression data. (b) Proportion of membership of cells from each individual in each Seurat cluster. The relative membership in each Seurat cluster is comparable between individuals. (c) Cumulative distribution function (CDF) of marginal distributions of latent gene expression of COL11A1 determined through fitting a Poisson adaptive shrinkage model to raw gene expression counts in each sample. (Left) CDF curves colored by Seurat cluster. Cells in cluster 2 contain a higher latent gene expression of COL11A1 on average. (Right) CDF curves colored by Individual. (d) STRUCTURE plot representing the relative proportional membership of single cells (columns) in 7 different topics in a topic model fit to scRNA-seq data derived from iPSC-chondrocytes collected in this study (“Current Study iPSC-Chondrocytes”); matched iPSCs, iPSC-MSCs, iPSC-osteoblasts, and iPSC-chondrocytes collected from a single individual (“GH iPSCs, GH iPSC-MSCs, GH iPSC-Osteoblasts, GH iPSC-Chondrocytes”); primary hepatocytes (“MacParland et al. Hepatocytes”); a time-course of iPSC-Chondrocyte pellet culture differentiation through the use of pellet culture (“Wu et al. iPSC-Chondrocytes (day 7 – day 42)”; and primary adult chondrocytes described in two separate publications (“Chou et al. Chondrocytes”, “Ji et al. Chondrocytes”). The ordering of individual cells within each study are determined through a one-dimensional tSNE algorithm applied to topic memberships of each cell. For each data source and cell type on the x-axis, a random subset of 800 cells is plotted with the exception of Current Study iPSC-Chondrocytes, for which all 1,815 cells are plotted.\n\nIn addition to discerning heterogeneity in our samples, we also evaluated the relative maturity of our iPSC-chondrocytes. To do this, we used topic modeling, analyzing our single cell data along with single cell datasets from multiple cell types, including primary adult chondrocytes (Methods). Topic modeling is an unsupervised classification approach that, when applied to single cell gene expression data, allows one to find recurring patterns of gene expression, or topics, present across a collection of cells. By allowing each cell to have grades of membership in multiple topics simultaneously, rather than assigning cells to only one cluster,57 topic modeling can identify both discrete and continuous variation between cells.\n\nA model fit with seven topics to the combined dataset shows that both iPSC-chondrocytes and primary chondrocytes are equally reliably distinct from unrelated cell types (e.g., hepatocytes). iPSC-chondrocytes retain a large proportion of gene expression patterns characteristic of iPSC-MSCs (topic 1), but they also possess certain gene expression patterns seen in adult primary chondrocytes and in iPSC-chondrocytes differentiated through a chondrogenic pellet (topics 4, 6, and 7) (Figure 2d). Topics 4-7 display relatively high levels of expression of several markers of chondrogenesis or cartilage fate, including SOX9, SOX5, SOX6,58 and COL9A159 (Extended Data Figure 588). Furthermore, differential expression analyses across topics identified type IX collagen gene COL9A359 as highly occurring in topic 7 relative to all other topics (Extended Data Figure 588). Similarly, in topics 4 and 6, the chondrogenic marker COMP60 has a high occurrence relative to all other topics. Thus, we conclude our iPSC-chondrocytes are likely in the early stages of chondrogenesis and are readily distinguishable from iPSCs and iPSC-MSCs.\n\nAfter confirming we can generate chondrogenic cells from iPSCs, we next sought to understand gene expression variation in this system. For this we focused on bulk RNA-seq data collected from all replicates. We generated an average of 22.3M raw reads per sample (s.d. 4M reads). We excluded one sample from further analyses because it displayed a particularly low percentage of mapped reads (Extended Data Table 288). We note the mapped reads from this sample cluster as expected with other technical replicates from the same individual and treatment (Extended Data Figure 688), but we still excluded it because it failed standard QC metrics. We filtered the remaining data for lowly expressed genes and standardized gene counts with respect to library size (Methods).\n\nAs a first step of our analysis of the bulk data, we identified gene expression responses to strain treatment. We used the limma R package to fit a linear mixed model for each of the 10,486 expressed genes in the filtered bulk RNA-seq data, accounting for the random effect of experimental batch and the fixed effects for individual cell line, sex, treatment status, two factors of unwanted variation, and RIN score (Methods). Using this model, we tested for differential expression between treated and untreated cultures. At an FDR of 0.05, 987 genes are significantly differentially expressed (DE) between treated and untreated chondrogenic cells (Figure 3a-b; Extended Data Table 388).\n\nThe linear mixed model used to conduct the analysis also accounted for the random effect of experimental batch and the fixed effects of individual cell line, sex, treatment status, two factors of unwanted variation, and RIN score. (a) Histogram of raw p values from DE analysis conducted independently for each gene between control and strain-treated conditions. Highlighted in red are genes with an FDR-adjusted p value < 0.05 (987 of 10,486 tested genes). (b) Volcano plot of –log10 raw p values vs log-fold change between treatment conditions. Highlighted in red are genes with an FDR-adjusted p value < 0.05. Genes plotted to the right of 0 on the x-axis represent genes with higher average expression in control iPSC-chondrocyte samples compared to strain-treated samples. (c) Top 20 Biological processes enriched among DE genes compared to background set of 987 genes. These GO biological process terms include those related to extracellular matrix organization and metabolism of extracellular matrix structure.\n\nTo evaluate the potential relevance of the DE genes to joint health and OA, we first considered their enrichment among gene ontology (GO) terms. The top 20 most highly enriched GO biological process terms include those related to ECM organization and metabolism of ECM structure (Figure 3c). These functions make intuitive sense given that ECM homeostasis is important for joint cartilage health; moreover, imbalances in this homeostasis are associated with OA.61,62\n\nWe also determined whether the DE genes may be overrepresented in gene sets previously implicated in OA. We examined results from one of the largest GWAS for OA susceptibility, which identified 64 independent significant associations with OA.3 We used a Fisher’s exact test to assess enrichment of DE genes among a set of 553 genes located within 500 kb of the 64 associated loci. These 553 genes were also identified as having prior evidence of involvement in animal models of skeletal disease or human bone diseases.3 We found that DE genes in our study are significantly enriched within the set of 553 genes previously associated with OA (p = 0.002; Extended Data Table 488).\n\nNext, we evaluated results from a separate study, which profiled mRNA and protein samples in low-grade and high-grade osteoarthritic cartilage from 115 patients undergoing joint replacement.5 Steinberg et al., 2019 found 409 genes with evidence of significant differential expression between patients with low-grade and high-grade osteoarthritic cartilage, at both the RNA and protein levels. Though causality is difficult to infer, this observation suggests at least a subset of these genes is involved in OA cartilage degradation (Extended Data Table 5). A Fisher’s exact test reveals that our DE genes are also significantly enriched among this gene set (p = 0.02). Of note, the two genes that overlap between the two external gene sets, LTBP3 and LAMC1, are also DE our study. LTBP3 is a regulator of the TGF-ß signaling family, which plays roles in cartilage formation and development.63 LAMC1 has been identified as a blood-based biomarker for detecting mild knee OA, with lower RNA expression identifying mild OA.64 Based on these GO and gene set enrichment results we concluded that the DE genes identified between strain-treated and control iPSC-chondrocytes are relevant to joint health.\n\nDue to differential power, highly expressed genes are more likely to be detected as DE than lowly expressed genes in any RNA sequencing dataset.65 Therefore, it is possible the magnitude of expression of different genes in our data can explain our enrichment results. To assess the robustness of our findings, we permuted the labels of treatment condition among our samples and re-performed DE and enrichment analyses a total of ten times (Extended Data Table 688). In nine permutations, we failed to identify ECM-related GO terms among the top 20 enriched terms (one permutation revealed two ECM-related GO terms). Further, we did not find any enrichment of DE genes within the two OA-relevant gene sets using permuted data. As our permuted data do not display the same enrichment patterns as our actual data, we concluded our results are not due to differential power to detect DE.\n\nIn our DE analysis, we focused on identifying inter-treatment differences in gene expression rather than inter-individual differences. Ultimately, we would like to use this system to study gene-by-environment interactions, which occur at the intersection of inter-treatment and inter-individual differences. A gene-by-environment interaction occurs when the magnitude or direction of gene expression response to an environmental stimulus is associated with an individual’s genotype at a particular locus. The sample size of this current study is far too small to detect gene-by-environment interactions. Still, we identified several genes that exhibit inter-individual differences in expression in response to CTS (Figure 4).\n\n(a-c) MMP14, COPG1, and EXOSC8 each demonstrate inter-individual differences in gene expression in our dataset. Dot plots are the expression level (log2 cpm) of each gene in each sample, with each individual and treatment condition plotted separately. Lines represent ± one standard deviation. For each candidate gene, expression is relatively consistent between individuals in the control condition but differs in magnitude or direction between individuals in the strain condition (in response to CTS). These heterogenous responses do not all involve differing magnitudes of changes in the same direction. In the case of MMP14, while NA18855 does not seem to respond to CTS through altering MMP14 expression, NA18856 responds through upregulation of this gene and NA19160 responds through downregulation. If heterogenous responses to CTS such as these exist more broadly between individuals and are associated with genotypic differences, they should be identifiable in population-level eQTL studies using this experimental system.\n\nFor example, MMP14 displays a different pattern of expression in each cell line before and after CTS (Figure 4a): MMP14 expression remains constant between control and strain-treated NA18855 cells, is upregulated in strain-treated NA18856 cells, and is downregulated in strain-treated NA19160 cells. MMP14 is expressed constitutively in adult joint cartilage and upregulated in diseased states.66 In addition, EXOSC8 and COPG1 (Figure 4b-c) are both involved in the formation of secretory vesicles originating from the Golgi complex. These genes also display differences in direction or magnitude of gene expression response to CTS between individuals. If heterogenous responses to biomechanical stress exist more broadly and are associated with genotypic differences, this experimental system will be able to identify them in population-level eQTL studies.\n\nThus far, our results show that CTS elicits a robust, joint health-relevant gene expression response in iPSC-chondrocytes, and that, anecdotally, this response can differ between individuals. Next, we sought to more generally evaluate the utility of this system for studying the effects of genetic variation and biomechanical stress on gene regulation. Specifically, we considered dynamic expression quantitative trait loci (dynamic eQTLs), which are genetic variants associated with a change in gene expression in response to a treatment. For our system to be useful in identifying dynamic eQTLs, individual differences should drive a substantial amount of the variation in gene expression response to the treatment. To quantify the contribution of individual differences to gene expression variation in iPSC-chondrocytes, we estimated how much of this variation is attributable to technical and biological factors. Our study design allows us to do so, as we collected bulk RNA-seq data from three independent technical replicates of each cell line.\n\nFirst, we evaluated the contributions of experimental variables to major axes of variation in our bulk RNA-seq data by performing a principal components analysis (PCA; Extended Data Figures 7 and 8; Extended Data Table 788). Our results indicate the primary source of gene expression variation is individual (regression of PC1 by individual, p = 1.34 × 10-7, regression of PC2 by individual, p = 4.61 × 10-4). The second largest source of variation in the data is sex (regression of PC2 by sex, p = 2.67 × 10-4), which is unsurprising given our study included one female and two male cell lines. Although treatment shows a minor correlation with PC2 (R2 = 0.14), PC3 (R2 = 0.14), and PC4 (R2 = 0.3), none of these correlations are statistically significant.\n\nEncouragingly, we did not find technical replicate (or ‘batch’) to be significantly associated with any of the first five PCs in the data. Nevertheless, we took advantage of our replicated experimental design to account for two factors of unwanted technical variation in the data48; Methods). Following this we observed the top three sources of gene expression variation are individual (regression of PC1 by individual, p = 7.34 × 10-8, regression of PC2 by individual, p = 3.98 × 10-4), sex (regression of PC2 by sex, p = 1.79 × 10-4), and treatment effect (regression of PC3 by treatment, p = 3.92 × 10-2), all three of which are significant (Figure 5a-b, Extended Data Figure 988).\n\n(a) Principal components (PC) plot of normalized and RUVs-corrected bulk RNA sequencing samples colored by individual and shaped by treatment condition. Samples largely separate by Individual, with strain-treated samples from NA18856 showing a large separation from control samples from the same Individual. (b) Correlation between each of the first 5 PCs and several experimental variables, determined through linear regression analysis on normalized and RUVs-corrected bulk RNA sequencing data. Significant regressions (Benjamini-Hochberg corrected FDR < 0.05) are highlighted with an asterisk. (c) Violin-box plots displaying the fraction of variation explained by a number of experimental variables of the study design, including a single factor of unwanted variation fit using RUVg. Variables are ordered from largest to smallest by the median fraction of variation explained except for Residuals. The boxplots indicate the median, inner quartile range (IQR) and 1.5 times the IQR. Data beyond this are plotted as points. Violin plots indicate the density of data points based on their width.\n\nNext, we took a more systematic approach to modeling the contribution of biological and technical factors to gene expression variation. Our goal was to leverage the total amount of variation in our data rather than focusing only on a few major axes of variation, as in the PCA above. We quantified the contributions of several experimental variables to gene expression variation on the level of individual genes using a linear mixed model (Methods). To do so, we modeled a single factor of unwanted variation in the data by using a set of 100 genes with the least amount of variation in the data as negative control genes48 (Methods). We then included the filtered and normalized gene expression data and this single factor of unwanted variation in the model (Methods; Figure 5c).\n\nWe determined that individual cell line contributes the largest amount of variance to the data (median of 42% variance explained). The additional factor of unwanted variation explains a median of 3.6% of the variance, and treatment explains a median of 3.5% of the variance. In contrast, technical replicate batch and cDNA library preparation batch explain a negligible amount of variance (median of 8.7 × 10-7 % and 3.5 × 10-7 % variance explained, respectively). We observed similar results when running a model that did not include the factor of unwanted variation (Extended Data Figure 1088). Therefore, the biological variables of individual cell line and treatment contribute more to gene expression variation than technical variables. However, unwanted variation still seems to contribute to gene expression variation. Therefore, gene expression studies using this system should account for potential latent sources of variation.\n\nOur results are encouraging for our goal of verifying the feasibility of using iPSC-chondrocytes to study gene-by-environment interactions in joint health. One possible way to study these interactions would be to use this system to map static eQTLs and dynamic response eQTLs (i.e., eQTLs that emerge in response to CTS). We conducted a power analysis to determine the potential impact of expanding this system to include 58 iPSC lines (Figure 6; we chose n = 58 because this is the number of YRI iPSCs available to us). Under the assumptions of a simple linear regression to map eQTLs and a conservative Bonferroni correction for multiple testing (FWER = 0.05; Methods), we estimated that a sample of 58 individuals will provide 80% power to detect eQTLs with a standardized effect size of 0.7 in each of the control and treatment conditions. At this effect size, the power to detect eQTLs comes with a correspondingly low FDR (0.22).\n\nPower curves are derived under the assumption of a simple linear regression for expression quantitative trait locus (eQTL) mapping and plotted over standardized effect sizes (effect sizes divided by the phenotype standard deviation) for a range of sample sizes. Dynamic QTL false positive rates are computed as the probability of a SNP being called as significant in only one of two treatment conditions, assuming the standardized effect size was in fact identical in both conditions. The horizontal red line represents a power to detect eQTLs of 0.80. Vertical transparent lines represent the 99th percentile of the standardized effect size estimated from an empirical cumulative distribution function fit to eQTL summary statistics from 3 published dynamic eQTL studies from different contexts, with the mean value over all the conditions in each study plotted.\n\nTo contextualize these results, we reanalyzed eQTL summary statistics from a set of previous dynamic eQTL studies that come from a variety of different research contexts13,50,51 (Figure 6; Extended Data Table 888). In each of these studies, hundreds to thousands of genes in each treatment condition have at least one eQTL which meets the standardized effect size threshold of 0.7 above. While none of these examples perfectly recapitulates the results of our system, the fact these estimates are conservative and come from eQTL studies in three different stimulus conditions demonstrates the potential effectiveness of this approach.\n\n\nDiscussion\n\nWe conducted a study to establish the feasibility of an in vitro iPSC-chondrocyte model for studying gene-by-environment interactions in joint health. Gene-by-environment interactions, particularly those related to biomechanical stress, may play a role in pathogenesis in joint related diseases such as OA. However, numerous ethical and logistical obstacles limit the study of these interactions and their effects on gene regulation in human chondrocytes. iPSC-chondrocytes may be a suitable alternative to circumvent these obstacles when paired with in vitro CTS models. Overall, our in vitro system allows for both the precise control of iPSC-chondrocyte environmental exposures and measurement of gene expression responses relevant to human joint health. While no in vitro model can completely accurately mimic in vivo disease, our results demonstrate this system has tremendous potential to increase our understanding of human joint health.\n\niPSC-chondrocytes are a valuable system to address the current lack of gene expression studies in human joint cells. Although iPSC-chondrocytes do not completely emulate mature, primary human chondrocytes, they do exhibit protein and gene expression patterns characteristic of both adult chondrocytes and developing chondrocytes. The relatively early differentiation stage of our cells may be due to a variety of factors, including a shorter differentiation time and the culturing of cells as a monolayer as opposed to a 3-dimensional pellet.67 Nevertheless, iPSC-chondrocytes provide a unique opportunity to learn about gene regulation in human joints and the basis of adult joint disease phenotypes. For instance, the ability to generate cells along the trajectory between iPSC-MSCs and mature chondrocytes allows for gene expression studies at a level infeasible with human primary tissues. Furthermore, prior studies have shown that studying iPSC-derived cells can uncover potentially important and transient forms of gene regulation masked in terminal cell types.11\n\nOur results point to a robust gene expression response to CTS in iPSC-chondrocytes. We detected 987 DE genes in our study between treated and control cultures. These DE genes are enriched for gene sets relevant to joint health and OA. Thus, our results highlight the potential of this system as a platform for gene expression studies of human joint cells that circumvent the limitations of primary tissues. Our observations also suggest that studying gene regulation in this relatively simple system may provide insight into more complex biological processes relevant to human joint disease.\n\nOne potential cause for reservation in our GWAS analysis is the mismatch in population ancestries between our DE results (African ancestry) and OA GWAS results (European ancestry). However, prior studies have found that genetic associations between causal variants and complex traits are largely shared between populations.68–70 Furthermore, our analyses focus on the genes implicated in the OA GWAS results, rather than the causal variants themselves. As such, we expect the relevance of these gene sets to carry over more faithfully between populations. Finally, the population mismatch would likely have the effect of biasing our results towards the null rather than introducing false positive findings. Therefore, we believe the observed enrichment is meaningful despite the current lack of equivalent OA GWAS results from a more comparable African ancestry population.\n\nWe acknowledge that in vitro CTS models do not directly mimic the compressive biomechanical stress felt by joint chondrocytes in vivo. However, CTS models are recognized as a valid method for studying the effects of extra-physiological stresses in cultured cells. Others have previously used CTS models to measure responses of joint cells to controlled biomechanical stress treatments.24–27,71–75 Other groups have also developed models that use specific types and patterns of biomechanical strain to induce transcriptional and biochemical changes characteristic of early human OA.24–27 Our RT-PCR and bulk RNA-seq results further attest to the utility of CTS as a model of biomechanical stress in studies of human joint health.\n\nWe also found that an in vitro iPSC-chondrocyte system may be useful for studying the effects of genetic variation on gene regulation; moreover, it offers a way to study how biomechanical stress interacts with genetic factors to affect gene regulation. Indeed, individual-level differences drive a substantial amount of gene expression variation in this system. Therefore, eQTL and dynamic eQTL studies would be feasible using iPSC-chondrocytes. We identified specific differences in the gene expression response to CTS between individuals in this study. As such, iPSC-chondrocytes may be fruitful for uncovering gene-by-environment interactions involved in pathogenesis of joint diseases.\n\nInvestigating dynamic and context-specific gene regulatory effects may reveal the mechanisms contributing to joint disease development and progression, as this approach has been successfully applied to a variety of other cell types and trait contexts.10,13–17,51,76 Previous studies have found that dynamic eQTLs are more enriched for relevant significant GWAS alleles than non-dynamic (‘standard’) eQTLs, which show consistent effects between conditions.10,11,14,16 Our power analysis suggests that a study with a few dozen individuals may grant sufficient power to detect many static and dynamic eQTLs. Dynamic eQTLs may be more useful for identifying candidate susceptibility genes in joint diseases than steady state eQTLs, and they may also improve our understanding of gene-by-environment interactions related to joint health and disease.\n\nFuture studies using the iPSC-chondrocyte system should account for the possibility that transcriptional heterogeneity between and within individual iPSC-chondrocyte lines may confound association results in an eQTL study. Our analysis of the scRNA-seq data from control iPSC-chondrocytes suggests that differentiation efficiency does not differ substantially between individuals. Nonetheless, it is possible that differentiation efficiency may differ for other individuals not included in this study. There may also still exist transcriptional heterogeneity between iPSC-chondrocytes in their response to CTS that bulk RNA-seq would not adequately capture. Measuring and accounting for transcriptional heterogeneity in iPSC-chondrocytes will also allow future gene expression studies to focus specifically on iPSC-chondrocytes, which represent only a minority of cells in each culture. This will increase power to detect both standard and dynamic eQTLs.\n\nOur iPSC-chondrocyte system also facilitates investigations beyond those involving only human cells. The existence of panels of human and nonhuman primate iPSCs44 introduces the possibility of inter-species comparisons of response to CTS. Comparative studies may help uncover gene-by-environment interactions that contribute to the differential prevalence of OA and other joint diseases observed across primate species.77–79\n\nWe believe the in vitro iPSC-chondrocyte CTS model shows great promise when applied to studies of gene expression in human joints. We hope such a system enables future studies of gene regulation in joint cells and their connections to joint health and disease.\n\n\nData availability\n\nNCBI GEO: Characterizing gene expression responses to biomechanical strain in an in vitro model of osteoarthritis. Accession number: GSE165874; https://identifiers.org/geo:GSE165874.\n\nNCBI GEO: Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. Accession number: GSE167240; https://identifiers.org/geo:GSE167240.\n\nOpen Science Framework: Characterizing gene expression in an in vitro biomechanical strain model of joint health, DOI https://doi.org/10.17605/OSF.IO/YQRJM.80\n\nThis project contains the following underlying data:\n\n- Extended Data Table 1. Raw RT-PCR amplification\n\n- Extended Data Table 2. Bulk RNA sequencing library metadata and quality control metrics.\n\n- Extended Data Table 3. Differential expression results from limma analysis between strain-treated and control samples. Only genes that passed filters for low expression were kept.\n\n- Extended Data Table 4. Genes from Tachmazidou et al., 2019\n\n- Extended Data Table 5. Genes with significant cross-omics differences between high-grade and low-grade cartilage in Steinberg et al. 2019.\n\n- Extended Data Table 6. Results from 10 random permutations of sample treatment condition labels.\n\n- Extended Data Table 7. Full results of linear regression analysis between experimental variables and top 5 principal components in the bulk RNA sequencing data.\n\n- Extended Data Table 8. Results from reanalysis of prior dynamic eQTL studies for eQTL power analysis.\n\n- Extended Data Table 9. Nucleotide sequences of the primers used for RT-PCR\n\n- Extended Data Figures 1-11\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nAll computational scripts and analysis pipelines can be found on GitHub at: https://github.com/anthonyhung/invitrostrain_pilot_repository and in webpage format at: https://anthonyhung.github.io/invitrostrain_pilot_repository/index.html\n\nArchived analysis code at time of publication: https://doi.org/10.5281/zenodo.6095200.81\n\nLicense: MIT License",
"appendix": "Acknowledgements\n\nWe thank Natalia Gonzales for comments on the manuscript. We thank Abhishek Sarkar, Michelle Ward, Kenneth Barr, and other members of the Gilad Lab for helpful discussions. This work was completed in part by using computational resources provided by the University of Chicago Research Computing Center.\n\nAn earlier version of this article can be found on bioRxiv (DOI https://doi.org/10.1101/2021.02.22.432314)\n\n\nReferences\n\nAigner T, Schmitz N: 173 - Pathogenesis and pathology of osteoarthritis. 2011. Publisher Full Text\n\nKloppenburg M, Berenbaum F: Osteoarthritis year in review 2019: epidemiology and therapy. Osteoarthritis Cartilage. 2020; 28: 242–248. PubMed Abstract | Publisher Full Text\n\nTachmazidou I, et al.: Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank. Nat. Genet. 2019; 51: 230–236. 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PubMed Abstract | Publisher Full Text\n\nChubinskaya S, Kuettner KE, Cole AA: Expression of matrix metalloproteinases in normal and damaged articular cartilage from human knee and ankle joints. Lab. Investig. J. Tech. Methods Pathol. 1999; 79: 1669–1677.\n\nYoon HH, Bhang SH, Shin J-Y, et al.: Enhanced Cartilage Formation via Three-Dimensional Cell Engineering of Human Adipose-Derived Stem Cells. Tissue Eng. Part A. 2012; 18: 1949–1956. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGurdasani D, Barroso I, Zeggini E, et al.: Genomics of disease risk in globally diverse populations. Nat. Rev. Genet. 2019; 20: 520–535. PubMed Abstract | Publisher Full Text\n\nShi H, et al.: Localizing Components of Shared Transethnic Genetic Architecture of Complex Traits from GWAS Summary Data. Am. J. Hum. Genet. 2020; 106: 805–817. PubMed Abstract | Publisher Full Text\n\nMogil LS, et al.: Genetic architecture of gene expression traits across diverse populations. PLOS Genet. 2018; 14: e1007586. PubMed Abstract | Publisher Full Text\n\nTakahashi K, et al.: Hydrostatic pressure influences mRNA expression of transforming growth factor-beta 1 and heat shock protein 70 in chondrocyte-like cell line. J. Orthop. Res. Off. Publ. Orthop. Res. Soc. 1997; 15: 150–158. PubMed Abstract | Publisher Full Text\n\nTakahashi K, et al.: Hydrostatic pressure induces expression of interleukin 6 and tumour necrosis factor α mRNAs in a chondrocyte-like cell line. Ann. Rheum. Dis. 1998; 57: 231–236. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTakano-Yamamoto T, et al.: Comparison of the effects of hydrostatic compressive force on glycosaminoglycan synthesis and proliferation in rabbit chondrocytes from mandibular condylar cartilage, nasal septum, and spheno-occipital synchondrosis in vitro. Am. J. Orthod. Dentofac. Orthop. Off. Publ. Am. Assoc. Orthod. Its Const. Soc. Am. Board Orthod. 1991; 99: 448–455.\n\nMohtai M, et al.: Expression of interleukin-6 in osteoarthritic chondrocytes and effects of fluid-induced shear on this expression in normal human chondrocytes in vitro. J. Orthop. Res. Off. Publ. Orthop. Res. Soc. 1996; 14: 67–73. PubMed Abstract | Publisher Full Text\n\nBougault C, Paumier A, Aubert-Foucher E, et al.: Investigating conversion of mechanical force into biochemical signaling in three-dimensional chondrocyte cultures. Nat. Protoc. 2009; 4: 928–938. PubMed Abstract | Publisher Full Text\n\nMaranville JC, et al.: Interactions between Glucocorticoid Treatment and Cis-Regulatory Polymorphisms Contribute to Cellular Response Phenotypes. PLoS Genet. 2011; 7: e1002162. PubMed Abstract | Publisher Full Text\n\nJurmain R: Degenerative joint disease in African great apes: an evolutionary perspective. J. Hum. Evol. 2000; 39: 185–203. PubMed Abstract | Publisher Full Text\n\nVidean EN, Lammey ML, Lee DR: Diagnosis and Treatment of Degenerative Joint Disease in a Captive Male Chimpanzee (Pan troglodytes). J. Am. Assoc. Lab. Anim. Sci. JAALAS. 2011; 50: 263–266. PubMed Abstract\n\nLowenstine LJ, McManamon R, Terio KA: Comparative Pathology of Aging Great Apes: Bonobos, Chimpanzees, Gorillas, and Orangutans. Vet. Pathol. 2016; 53: 250–276. PubMed Abstract | Publisher Full Text\n\nHung A: Characterizing gene expression in an in vitro biomechanical strain model of joint health.2022, February 23. Publisher Full Text\n\nHung A: anthonyhung/invitrostrain_pilot_repository: Characterizing gene expression in an in vitro biomechanical strain model of joint health (v1.0.0). Zenodo. 2022. Publisher Full Text"
}
|
[
{
"id": "127025",
"date": "08 Apr 2022",
"name": "Alex Pollen",
"expertise": [
"Reviewer Expertise stem cell biology",
"gene regulation."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Hung et al seeks to build a foundation for measuring population-level gene expression responses to biomechanical stress in cartilage. This framework is important because recent studies indicate that genetic variation linked to physiological responses of relevant tissues relates better to disease traits than does baseline genetic variation. However, studying dynamic changes in gene expression in human tissue across many individuals is extremely challenging. This study uses pluripotent stem cells to generate chondrocytes and measure responses to biomechanical stress via cyclic tensile strain.\nThe major findings are that: 1) the chondrocyte differentiation protocol does produce a consistent, albeit low (5 – 8%) percentage of chondrocytes that share gene expression features with normal human chondrocytes and produce proteoglycans; 2) that cyclic tensile strain induces gene expression changes in relevant gene ontology categories; 3) that the induction of some genes varies; 4) given low technical variation the system is likely to enable dynamic eQTL mapping with reasonably high sensitivity in an available panel of 58 iPSC lines.\nThis feasibility study has a number of strengths – strong premise of studying dynamic responses to physiological stimuli, elegant topic modeling to examine the fidelity of iPS-derived chondrocytes to primary samples, and providing a careful feasibility rationale for larger-scale future QTL mapping studies.\nGiven that this represents a feasibility study for future QTL mapping, there are a few experiments/explanations that would strengthen the foundation:\n\nWhat is the nature of the cells that make up the majority of the chondrocyte differentiation? Are these simply cells in the right lineage, but in a more immature state? If so, the foundation for future studies would benefit from experimenting with longer differentiation times, or strategies to accelerate differentiation/maturation, or enrichment strategies (e.g., FACS or MACS) to focus more specifically on the cell type of interest. Indeed, 5% - 8% are relatively similar, but still represent a 60% difference in efficiency. Developing antibody markers of the on-target lineage would also be beneficial to future studies for assessing/enriching samples prior to sequencing.\n\nI am concerned that the NA18856 cells appear to be more dramatically changed by the cyclic tensile strain on the axes of PC1 and especially PC2 than the other cell lines. This is dismissed as “treatment shows a minor correlation with PC2 (R2 = 0.14), PC3 (R2 = 0.14), and PC4 (R2 = 0.3)”, but I wonder if this result implies concerted individual variability across many genes in this system, rather than random variability in responses across individuals at specific loci. It would help to also show the samples plotted along PC3 and PC4 to evaluate if the response of this single individual to treatment is driving the correlations, and to discuss possible implication of a single individual having distinct concerted responses.\nMinor comments:\n\nThis claim in the introduction is too strong “Through this study, we evaluated whether the process of chondrocyte differentiation is robust to individual differences” given that only used 3 individuals were used in the present study.\n\nThe authors could cite analyses of human sequence variation in chondrocyte regulatory elements: e.g. Richard et al. (2020).1\n\nFor the topic modeling, this is discussed in the text, but it would be helpful to show an additional panel in the figure or supplement on the key genes in each topic and their preservation, especially for markers characteristic of adult chondrocytes.\n\nThe authors could consider presenting Figure 5 before Figure 3 since Figure 5 makes it clear why using a linear model to account for the effects of individual, sex, etc is a useful approach for discovering the effect of treatment in this dataset.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8800",
"date": "27 Sep 2022",
"name": "Anthony Hung",
"role": "Author Response",
"response": "The point-by-point responses to comments: Reviewer comment 1: What is the nature of the cells that make up the majority of the chondrocyte differentiation? Are these simply cells in the right lineage, but in a more immature state? If so, the foundation for future studies would benefit from experimenting with longer differentiation times, or strategies to accelerate differentiation/maturation, or enrichment strategies (e.g., FACS or MACS) to focus more specifically on the cell type of interest. Indeed, 5% - 8% are relatively similar, but still represent a 60% difference in efficiency. Developing antibody markers of the on-target lineage would also be beneficial to future studies for assessing/enriching samples prior to sequencing. Author Response to comment 1: Based on the single-cell RNA sequencing data and phenotypic staining data collected from iPSC-chondrocytes, these cells represent an early differentiation stage distinct from MSCs and with some similarity to mature chondrocytes. We agree with the points listed here about the potential for differentiation of more mature chondrocytes in this system. However, the relative immaturity of iPSC-chondrocytes as they currently stand does not necessarily hamper their potential to yield useful insight into human joint health and disease. For instance, prior research has found that studying cells representing transient developmental timepoints can uncover forms of gene regulation that would be invisible to studies of terminal cell types (Strober et al 2019, Elorbany et al, 2022). Reviewer comment 2: I am concerned that the NA18856 cells appear to be more dramatically changed by the cyclic tensile strain on the axes of PC1 and especially PC2 than the other cell lines. This is dismissed as “treatment shows a minor correlation with PC2 (R2 = 0.14), PC3 (R2 = 0.14), and PC4 (R2 = 0.3)”, but I wonder if this result implies concerted individual variability across many genes in this system, rather than random variability in responses across individuals at specific loci. It would help to also show the samples plotted along PC3 and PC4 to evaluate if the response of this single individual to treatment is driving the correlations, and to discuss possible implication of a single individual having distinct concerted responses. Author Response to comment 2: While the small scale of this study makes it difficult to generalize to other individuals not included in the study, we anticipate that there will be some degree of heterogeneity in the severity of response to CTS in a larger group of individuals. We also think it is more likely that NA18856 does not represent concerted individual variability across many genes specific to this one individual but rather a more severe response that would be found across other individuals. Therefore, we do not expect this heterogeneity to limit our ability to map eQTLs in this system, especially if many other individuals show a similar large response to the strain treatment. We present PCA plots of samples plotted along additional PCs beyond PC1 and 2 in the Extended Data figures (Extended Data Figures 7 and 9), and in an updated version of this text, we include more details about the implications of a subset of individuals having strong responses to CTS in the Discussion section. Reviewer Minor comment 1: This claim in the introduction is too strong “Through this study, we evaluated whether the process of chondrocyte differentiation is robust to individual differences” given that only used 3 individuals were used in the present study. Author Response to Minor comment 1: Thank you for the suggestion. We modified the sentence to read: “Through this study, we evaluated whether the process of chondrocyte differentiation is robust to individual differences between three individuals.” Reviewer Minor comment 2: The authors could cite analyses of human sequence variation in chondrocyte regulatory elements: e.g. Richard et al. (2020).1 Author Response to Minor comment 2: Thank you for the suggestion. We mention prior studies of known variation in chondrocyte regulatory regions in an updated version of the text. Reviewer Minor comment 3: For the topic modeling, this is discussed in the text, but it would be helpful to show an additional panel in the figure or supplement on the key genes in each topic and their preservation, especially for markers characteristic of adult chondrocytes. Author Response to Minor comment 3: We present a heatmap of word probabilities of selected marker genes for different cell types across the topic model and volcano plots for relative occurrence of genes in each topic compared to all other topics presented in the Extended Data figures (Extended Data Figure 5). We emphasize the availability of these figures in an updated version of the main text. Reviewer Minor comment 4: The authors could consider presenting Figure 5 before Figure 3 since Figure 5 makes it clear why using a linear model to account for the effects of individual, sex, etc is a useful approach for discovering the effect of treatment in this dataset. Author Response to Minor comment 4: Thank you for the suggestion. We agree that the discussion of the sources of variation in the data does help to justify the linear model. However, because we want to conclude our paper with an emphasis on the potential for this system for future studies of gene expression in human joint cells, we feel that concluding with this figure is more impactful than presenting it earlier in the paper. References: Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y. Dynamic genetic regulation of gene expression during cellular differentiation. Science. 2019 Jun 28;364(6447):1287-1290. doi: 10.1126/science.aaw0040. PMID: 31249060; PMCID: PMC6623972. Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr K, Qi G, Gilad Y, Battle A. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genet. 2022 Jan 21;18(1):e1009666. doi: 10.1371/journal.pgen.1009666. PMID: 35061661; PMCID: PMC8809621."
}
]
},
{
"id": "138892",
"date": "29 Jun 2022",
"name": "Shireen Lamande",
"expertise": [
"Reviewer Expertise Genetic skeletal disorders",
"cartilage",
"bone",
"iPSC differentiation to chondrocytes",
"bulk RNAseq analysis and DE gene expression"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Hung et al manuscript seeks to define the gene regulatory responses of three human iPSC lines that have been differentiated into ‘chondrocytes’ to cyclic tensile strain treatment. The premise is that measuring how chondrocytes from different individuals respond to mechanical stress could uncover gene-environment interactions that are relevant to human joint health. This is a question worthy of study – understanding how individual differences influence joint health could identify new therapeutic targets to treat osteoarthritis, an increasingly common and debilitating disease.\nThe paper includes a lot of complex bioinformatic and statistical analyses of single cell RNAseq and bulk RNAseq data generated in this study and also includes new analyses of publicly available RNAseq data that, in the first instance, are designed to demonstrate that ‘the process of chondrocyte differentiation is robust to individual differences.’ It seems this complex analysis was undertaken because the cell populations being compared contain only a small proportion of chondrocytes.\nTo draw robust conclusions about how chondrocytes respond to mechanical forces it is critical to start the study with a well-defined chondrocyte population. Hence, my reservations about this manuscript stem from the cell population that was studied. The study uses iPSCs from three individuals, 2 male and 1 female. The iPSCs were first differentiated to mesenchymal stem cells (MSCs) and after several passages the MSCs were cryopreserved at passage 5-7. A single batch of cryopreserved MSCs from each iPSC line was used for multiple technical replicate experiments where the MSCs were differentiated in chondrogenic medium for 14 days.\nThe greatest source of variability in iPSC differentiation protocols are technical parameters (eg different differentiation batch) rather than the cell line (see Phipson et al (2018) and this means that comparisons must be made using samples from concurrent carefully matched differentiations.1 It is not clear if concurrent differentiations to MSCs were part of the experimental design but the images in extended data figure 1 show cells at very different densities suggesting differences in cell growth or seeding density. The MSCs differentiated from the three lines are compared by FACS using 8 different markers (extended data Fig 1) and this shows considerable variation between the three lines. Given the importance of starting the chondrocyte differentiation from matched cell populations it is imperative to show that this first step is robust and reproducible and that the cell population is similar at the start of the chondrocyte differentiation step. This is not shown in the manuscript. The authors conclude that “individual cell line contributes the largest amount of variance to the data” but this is based on a single differentiation to MSCs then technical replicates of the chondrocyte differentiation stage and it is unclear how reproducible the MSC differentiation is. The variance could have been generated by technical variation in the early differentiation stages.\nChondrocyte differentiation. Figure 1b and extended data Figure 2a show alcian blue staining. Alcian blue stains proteoglycan side chains so the staining doesn’t show a collagenous ECM as claimed in the results. The staining is localised and very weak and in one line, not visible at all in the mechanically unstimulated cells. Data from one individual shows slight collagen II staining (extended data figure 2b). This staining pattern suggests that the chondrocyte differentiation protocol has produced a small proportion of immature chondroprogenitors and the scRNAseq data confirms this. Between 5% and 8% of the cells from each line form a cluster that is ‘most like chondrocytes’. The only gene expression data shown that supports the chondrocyte like nature of this cell cluster is COL11A1 in figure 2c and TIMP2 and TIMP3 in extended data figure 4. It would be much easier to judge this if this is a chondrocyte population if expression data for a range of genes characteristically expressed in chondrocytes was shown – for example SOX9, SOX5, SOX6, COL2A1, ACAN, COL9A1, MATN3, SPARC, COL11A1, COL10A1, PRG4 – a comparison with the scRNAseq data published in the Wu et al 2021 paper would also be helpful when judging what stage of chondrocyte development has been induced.2 To substantiate any conclusions about how individual differences influence how chondrocytes respond to mechanical forces the authors would need to compare chondrocytes rather than a mixed population of cells where immature chondrocyte progenitors are <10% of the total cell population. When >90% of the cell population are not chondrocytes it is difficult to see how the differential gene expression in mechanically stimulated cultures can be attributed to the way chondrocytes respond.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "8801",
"date": "27 Sep 2022",
"name": "Anthony Hung",
"role": "Author Response",
"response": "Reviewer comment 1: The Hung et al manuscript seeks to define the gene regulatory responses of three human iPSC lines that have been differentiated into ‘chondrocytes’ to cyclic tensile strain treatment. The premise is that measuring how chondrocytes from different individuals respond to mechanical stress could uncover gene-environment interactions that are relevant to human joint health. This is a question worthy of study – understanding how individual differences influence joint health could identify new therapeutic targets to treat osteoarthritis, an increasingly common and debilitating disease. The paper includes a lot of complex bioinformatic and statistical analyses of single cell RNAseq and bulk RNAseq data generated in this study and also includes new analyses of publicly available RNAseq data that, in the first instance, are designed to demonstrate that ‘the process of chondrocyte differentiation is robust to individual differences.’ It seems this complex analysis was undertaken because the cell populations being compared contain only a small proportion of chondrocytes. To draw robust conclusions about how chondrocytes respond to mechanical forces it is critical to start the study with a well-defined chondrocyte population. Hence, my reservations about this manuscript stem from the cell population that was studied. The study uses iPSCs from three individuals, 2 male and 1 female. The iPSCs were first differentiated to mesenchymal stem cells (MSCs) and after several passages the MSCs were cryopreserved at passage 5-7. A single batch of cryopreserved MSCs from each iPSC line was used for multiple technical replicate experiments where the MSCs were differentiated in chondrogenic medium for 14 days. The greatest source of variability in iPSC differentiation protocols are technical parameters (eg different differentiation batch) rather than the cell line (see Phipson et al (2018) and this means that comparisons must be made using samples from concurrent carefully matched differentiations.1 It is not clear if concurrent differentiations to MSCs were part of the experimental design but the images in extended data figure 1 show cells at very different densities suggesting differences in cell growth or seeding density. The MSCs differentiated from the three lines are compared by FACS using 8 different markers (extended data Fig 1) and this shows considerable variation between the three lines. Given the importance of starting the chondrocyte differentiation from matched cell populations it is imperative to show that this first step is robust and reproducible and that the cell population is similar at the start of the chondrocyte differentiation step. This is not shown in the manuscript. The authors conclude that “individual cell line contributes the largest amount of variance to the data” but this is based on a single differentiation to MSCs then technical replicates of the chondrocyte differentiation stage and it is unclear how reproducible the MSC differentiation is. The variance could have been generated by technical variation in the early differentiation stages. Author Response to comment 1: The reviewer indicated that they believe that the study is not sound and that our conclusions are not supported by the data. We do not understand these statements considering the more specific concerns detailed by the reviewer. We agree with the reviewer that our cellular model is not optimal, and that the differentiated chondrocytes are not mature and represent a small proportion of the culture. These details, however, are known to the reviewer because we clearly reported them in our paper and explained our conclusions in relationship to these caveats. We are aware of the limitations of the study and believe we reported them accordingly. In our opinion, this is the requirement for a sound study – being aware of the limitations. We provide further details in our responses below. Cell heterogeneity is critically important to consider, and we appreciate the reviewer’s request for further clarification. While it is true that iPSC differentiation batch contributes greatly to variation in many complex organoid differentiation protocols, our observations in monoculture differentiations of iPSCs have not found this to be as sizeable of an issue. Data from Housman, Briscoe, and Gilad 2022 demonstrate that gene expression patterns between iPSC-MSC lines differentiated from the same individual but in different batches and even using different formulations of MSC media are remarkably similar (97% correlation between matched iPSC-MSC lines). This high degree of correlation is observed between human (98% correlation) and chimpanzee (93% correlation) iPSC-MSC lines, demonstrating the robustness of this observation. Furthermore, our gene expression measurements across technical replicates of the experiment allow us to measure the contribution of individual variables (encompassing both individual cell line differences and individual donor differences) to variation in the system. These technical replicates of the experiment also allow us to account for individual factors in downstream analyses, which demonstrate reliable differences between treatment groups. We have modified our textual descriptions of individual cell line contributions to gene expression variation to reflect the fact that this variable encompasses both cell line and donor variation in the Results section. If any of the individual level gene expression variation observed in this study segregates with genotype, this will be detected in an eQTL mapping study. While much can and has been achieved through this small scale study to determine the feasibility of an eQTL approach in this system, to definitively establish this feasibility, a full scale experiment will need to be performed. Therefore, we believe this study has achieved its intended purpose. In this study, we made the choice to pause the differentiation at the iPSC-MSC state for each individual by cryopreserving cells in order to facilitate the design of larger-scale experiments including many more individuals. During the differentiation of each individual to MSCs, we were careful to keep reagent lot numbers consistent to minimize technical differences between MSC lines. The differentiation from iPSC-MSC to iPSC-chondrocyte consistently occurs over a period of 14 days, and the differentiation from iPSC to iPSC-MSC occurs over a period of around 28 days but is variable between individuals. Cryopreservation of iPSC-MSC lines enables larger scale studies to more reliably synchronize the collection of data from multiple individuals simultaneously to reduce the impact of batch effects from multiple sample collections. Images of MSCs in Extended Data Figure 1 were taken prior to seeding of cells for differentiation and were not standardized to the same confluency, though this was not made adequately clear in the previous figure description. In Extended Data Figure 1, we now include images of iPSC-chondrocytes from each of the lines after 14 days of differentiation, demonstrating equal confluency of cells between individuals, in an updated version of the text. Reviewer comment 2: Chondrocyte differentiation. Figure 1b and extended data Figure 2a show alcian blue staining. Alcian blue stains proteoglycan side chains so the staining doesn’t show a collagenous ECM as claimed in the results. The staining is localised and very weak and in one line, not visible at all in the mechanically unstimulated cells. Data from one individual shows slight collagen II staining (extended data figure 2b). This staining pattern suggests that the chondrocyte differentiation protocol has produced a small proportion of immature chondroprogenitors and the scRNAseq data confirms this. Between 5% and 8% of the cells from each line form a cluster that is ‘most like chondrocytes’. The only gene expression data shown that supports the chondrocyte like nature of this cell cluster is COL11A1 in figure 2c and TIMP2 and TIMP3 in extended data figure 4. It would be much easier to judge this if this is a chondrocyte population if expression data for a range of genes characteristically expressed in chondrocytes was shown – for example SOX9, SOX5, SOX6, COL2A1, ACAN, COL9A1, MATN3, SPARC, COL11A1, COL10A1, PRG4 – a comparison with the scRNAseq data published in the Wu et al 2021 paper would also be helpful when judging what stage of chondrocyte development has been induced.2 To substantiate any conclusions about how individual differences influence how chondrocytes respond to mechanical forces the authors would need to compare chondrocytes rather than a mixed population of cells where immature chondrocyte progenitors are <10% of the total cell population. When >90% of the cell population are not chondrocytes it is difficult to see how the differential gene expression in mechanically stimulated cultures can be attributed to the way chondrocytes respond. Author Response to comment 2: We appreciate the note about Alcian blue staining indicating proteoglycan side chains rather than collagen production. This wording is changed in our revised manuscript. We now include expression plots for several other chondrogenic marker genes as suggested. However, we were not able to plot expression data for COL2A1, ACAN, or COL9A1 due to zero counts measured for these genes. Based on the topic model, Wu et al, 2021 iPSC-chondrocytes display gene expression patterns that are shared with our chondrogenic cells and with primary chondrocytes from Chou et al, 2020. While the iPSC-chondrocytes in Wu et al, 2021 do not explicitly move through an hMSC state as in our differentiation, the authors do observe MSC-like cells in their cultures. The presence of MSCs is reflected in the representation of topic 1 (iPSC-MSCs) in these samples in the topic model. The majority of cell types in the iPSC chondrogenic cell cultures are closer to a MSC state than to a chondrocyte state, but the responses of these chondrogenic cells are still relevant to joint health. DE genes between control and CTS-treated iPSC-derived cells are enriched for genes relevant to joint health as determined through prior differential expression studies of high and low grade OA cartilage and genes implicated in OA GWAS. Also, these relatively immature cells still hold potential utility for studies of genetic control of gene regulation. Transient forms of gene regulation present in these intermediate chondrogenic cells may be masked in mature cell types, yet may still play a role in OA development, either through regulating proper chondrogenesis or modifying joint growth trajectories in a way that predisposes a joint to developing OA (Pitsillides & Beier, 2011). Further evidence for this hypothesis is present in the implication of chondrogenic development genes, including SMAD3, TGFB1, and GDF5, in OA susceptibility through OA GWAS (Boer et al, 2021). Thus, we do agree with the fact that our model does not capture completely the responses of primary chondrocytes to mechanical strain, but that this does not necessarily invalidate it as a useful approach to study gene regulation in OA. References: Housman, G., Briscoe, E., & Gilad, Y. (2022). Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model. PLoS Genetics, 18(3), e1010073. https://doi.org/10.1371/journal.pgen.1010073 Wu, C.-L., Dicks, A., Steward, N., Tang, R., Katz, D.B., Choi, Y.-R., and Guilak, F. (2021). Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis. Nat. Commun. 12, 362. Chou, C.-H., Jain, V., Gibson, J., Attarian, D.E., Haraden, C.A., Yohn, C.B., Laberge, R.-M., Gregory, S., and Kraus, V.B. (2020). Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritis. Sci. Rep. 10, 10868. Pitsillides, A., Beier, F. Cartilage biology in osteoarthritis—lessons from developmental biology. Nat Rev Rheumatol 7, 654–663 (2011). https://doi.org/10.1038/nrrheum.2011.129 Boer CG, Hatzikotoulas K, Southam L, Stefánsdóttir L, Zhang Y, Coutinho de Almeida R, Wu TT, Zheng J, Hartley A, Teder-Laving M, Skogholt AH, Terao C, Zengini E, Alexiadis G, Barysenka A, Bjornsdottir G, Gabrielsen ME, Gilly A, Ingvarsson T, Johnsen MB, Jonsson H, Kloppenburg M, Luetge A, Lund SH, Mägi R, Mangino M, Nelissen RRGHH, Shivakumar M, Steinberg J, Takuwa H, Thomas LF, Tuerlings M; arcOGEN Consortium; HUNT All-In Pain; ARGO Consortium; Regeneron Genetics Center, Babis GC, Cheung JPY, Kang JH, Kraft P, Lietman SA, Samartzis D, Slagboom PE, Stefansson K, Thorsteinsdottir U, Tobias JH, Uitterlinden AG, Winsvold B, Zwart JA, Davey Smith G, Sham PC, Thorleifsson G, Gaunt TR, Morris AP, Valdes AM, Tsezou A, Cheah KSE, Ikegawa S, Hveem K, Esko T, Wilkinson JM, Meulenbelt I, Lee MTM, van Meurs JBJ, Styrkársdóttir U, Zeggini E. Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations. Cell. 2021 Sep 2;184(18):4784-4818.e17. doi: 10.1016/j.cell.2021.07.038. Epub 2021 Aug 26. Erratum in: Cell. 2021 Nov 24;184(24):6003-6005. PMID: 34450027; PMCID: PMC8459317."
}
]
}
] | 1
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https://f1000research.com/articles/11-296
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https://f1000research.com/articles/11-232/v1
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24 Feb 22
|
{
"type": "Research Article",
"title": "Can enhancement and suppression concurrently guide attention? An assessment at the individual level",
"authors": [
"Tomoya Kawashima",
"Kaoru Amano",
"Kaoru Amano"
],
"abstract": "Background: Although people can pay attention to targets while ignoring distractors, previous research suggests that target enhancement and distractor suppression work separately and independently. Here, we sought to replicate previous findings and re-establish their independence. Methods: We employed an internet-based psychological experiment. We presented participants with a visual search task in which they searched for a specified shape with or without a singleton. We replicated the singleton-presence benefit in search performance, but this effect was limited to cases where the target color was fixed across all trials. In a randomly intermixed probe task (30% of all trials), the participants searched for a letter among colored probes; we used this task to assess how far attention was separately allocated toward the target or distractor dimensions. Results: We found a negative correlation between target enhancement and distractor suppression, indicating that the participants who paid closer attention to target features ignored distractor features less effectively and vice versa. Averaged data showed no benefit from target color or cost from distractor color, possibly because of the substantial differences in strategy across participants. Conclusions: These results suggest that target enhancement and distractor suppression guide attention in mutually dependent ways and that the relative contribution of these components depends on the participants’ search strategy.",
"keywords": [
"Attention",
"Enhancement",
"Suppression",
"Visual search"
],
"content": "Introduction\n\nOwing to limitations in attentional capacity, we must attend selectively to goal-related items and ignore ones that are unrelated to our goals. Directing our visual attention toward an object with a specific feature dimension can help improve the detection of task-relevant items. The possession of prior information regarding the properties of a target is known to expedite visual search by enhancing the attention paid to target stimuli (Vickery, King, & Jiang, 2005; Wolfe, Horowitz, Kenner, Hyle, & Vasan, 2004). Another means of accelerating visual search is to guide attention away from task-irrelevant items (Arita, Carlisle, & Woodman, 2012; Woodman & Luck, 2007). For example, Arita et al. (2012) found that presenting prior information on a color to be ignored sped up the perceiver’s visual search. The participants in their study performed a visual search after providing a distractor color as a negative cue; target detection was found to be faster than in neutral trials, and the authors argued that observers can use their prior knowledge of distractor features to guide visual attention.\n\nThis distractor suppression has been reportedly achieved through extensive practice or learning (Cunningham & Egeth, 2016; Zehetleitner, Goschy, & Müller, 2012; Geng, Won, & Carlisle, 2019). Cunningham and Egeth (2016) asked participants to perform a visual search task with negative or neutral cues (such as the words “Ignore Red” or “Neutral”) and found that the reaction time (RT) to the target was increased by negative cues in the first block of 72 trials; however, this difference decreased in subsequent blocks. These results suggest that observers can learn to suppress specific to-be-ignored features through considerable practice.\n\nFurther studies have shown that even a salient distractor can be suppressed (Chang & Egeth, 2019, 2021; Gaspelin, Leonard, & Luck, 2015, Gaspelin & Luck, 2018a). Gaspelin et al. (2015) embedded probe tasks into visual search tasks to examine the distractor suppression effect. In the visual search task (70% of all trials), the target was defined by a shape (e.g., a diamond), and a singleton distractor was presented for half of the search trials. In the probe task (30% of all trials), alphabet letters were briefly presented (100 ms) among the search shapes, and the participants were asked to report as many letters as they could recall. The authors found that the RTs in the search task were faster when the singleton was presented (singleton-presence benefit). In the probe task, the recall accuracy for probes at the singleton location was lower, suggesting that the benefit was not due to the rapid disengagement from the singleton. From these results, Gaspelin et al. (2015) proposed that a physically salient item can be actively suppressed before attentional capture (signal-suppression hypothesis (Sawaki & Luck, 2010, 2013)).\n\nThis distractor suppression can be explained by two mechanisms: secondary inhibition or active suppression (Chelazzi, Marini, Pascucci, & Turatto, 2019; Gaspelin & Luck, 2018b; van Moorselaa & Slagter, 2020). In the first, ignoring task-unrelated stimuli is performed by focusing attention onto the target representation. Even where the distractor is salient, distractor interference can be diminished through a top-down attentional setting that focuses on target features (feature-search mode) relative to the set focusing on salient items (singleton-detection mode (Bacon & Egeth, 1994; Leber & Egeth, 2006)). Thus, target enhancement can indirectly suppress distractor representation simply because the distractors are not attended to (i.e., the attention is directed away or secondary inhibition). The second involves direct distractor suppression. Several studies that incorporate electroencephalography (EEG) have observed the distractor-suppression related distractor positivity (Pd) component in response to salient distractors without the N2pc (N2-posterior-contralateral) component, which represents attentional selection (Luck, 2012; Luck & Hillyard, 1994), suggesting that the distractor can be suppressed without attentional selection (Gaspelin & Luck, 2018a, b; Sawaki & Luck, 2010; Burra & Kerzel, 2013).\n\nChang and Egeth (2019, 2021) sought to determine whether singleton-presence benefit in visual search could be explained by target enhancement, distractor suppression, or both. Instead of using a memory-based probe task, as Gaspelin et al. (2015) did, Chang and Egeth (2019) asked participants to detect a probe target (“A” or “B”) presented in a probe in a forced-choice manner and found 9 milliseconds (ms) singleton-presence benefit in visual search. Critically, the probe target appeared in the target or distractor feature that had been presented in search trials such that target enhancement and distractor suppression could be assessed separately. Moreover, these authors revealed that the RT was faster when the probe target was in the target color (34 ms target-color benefit) and slower when it was in the distractor color (43 ms distractor-color cost), arguing that target enhancement and distractor suppression guide attention in separate and independent ways (enhancement-plus-suppression: Chang & Egeth, 2019). Thus, target enhancement and distractor suppression work in parallel (Andersen & Müller, 2010).\n\nAlthough Chang and Egeth (2019) concluded that “observers can concurrently maintain two different attentional control processes and use either one of them as the occasion demands” (p. 1731), this concurrent enhancement and suppression are cognitively demanding. Although such attentional templates can be created implicitly through successive practice, attention should be allocated at the beginning of the experimental session to a specific feature, particularly to the to-be-suppressed items (Cunningham & Egeth, 2016). Furthermore, several studies have shown that visual attention can be guided by only a single item in working memory (Olivers, Peters, Houtkamp, & Roelfsema, 2011; van Moorselaar, Theeuwes, & Olivers, 2014). van Moorselaar et al. (2014) required participants to conduct a visual search while holding a variable number of colors in working memory and found that attentional guidance through working memory representation was obtained only when a single color appeared. First, these results suggest that it is difficult to guide attention simultaneously by more than two representations, indicating a possible cognitive demand for maintaining representations for both enhancement and suppression (but see Bahle, Beck, & Hollingworth, 2018; Bahle, Thayer, Mordkoff, & Hollingworth, 2020). Second, attending to target information may be preferable to ignoring distractor features because enhancement and suppression do not have the same efficiency in attentional guidance. The effects of negative cues have been widely reported to be smaller than those for positive cues (Arita et al., 2012; Beck & Hollingworth, 2015; Becker, Hemsteger, & Peltier, 2016). Even within the same search settings, distractor inhibition mediated by negative cues has been shown to be inefficient relative to target enhancement mediated by positive cues (Kawashima & Matsumoto, 2018). When both positive and negative cues are provided, participants selectively encode positive information for visual search (Rajsic, Carlisle, & Woodman, 2020), although some studies suggest simultaneous guidance of target enhancement and distractor rejection (Stiwell & Vecera, 2020; Beck, Luck, & Hollingworth, 2018). Based on the reported individual differences in selecting a search strategy (Boot, Becic, & Kramer, 2009) and the tendency to avoid cognitive demands (Kool, McGuire, Rosen, & Botvinick, 2010), observers may rely on a single attentional control process instead of maintaining two simultaneous processes, as suggested by Chang and Egeth (2019), in the performance of visual search. Thus, it would be valuable to gain further insights into the mechanisms of attentional enhancement and distractor inhibition.\n\nIn the present study, we first repeated the work of Chang and Egeth (2019) with the intention of replicating their findings. We then modified their paradigm to re-investigate whether target enhancement and distractor suppression can guide attention independently. Experiment 1 was drawn from Chang and Egeth (2019) and was performed as an online experiment. In addition to group-level analyses, as performed in their work, we explored differences in behavior among individuals. Specifically, we investigated a correlation between target enhancement and the effects of distractor suppression. We obtained the raw data of Chang and Egeth (2019) and applied the same analysis, hypothesizing that if target enhancement and distractor suppression could guide attention independently, as Chang and Egeth (2019) argued, no negative correlation would be observed. Furthermore, Experiments 2 and 3 were intended to quantify the effects of target enhancement and distractor suppression separately by manipulating color combinations of the target and the distractor. In particular, unlike the use of fixed colors for the search target and distractor in Experiment 1, we altered the search target and distractor colors on a trial-by-trial basis in Experiments 2 and 3, respectively. Thus, the participants could expect only a target or a distractor color. Accordingly, we calculated the magnitude of the enhancement and suppression for each participant and compared the effect across experiments. We hypothesized that if two attentional-guidance elements, enhancement and suppression, competed for common processing resources, the magnitude of the effect in Experiment 1 would be smaller than those in Experiments 2 and 3 because Experiment 1 required both of these attentional controls.\n\n\nMethods\n\nSchematic illustrations of experimental trials are shown in Figure 1. Search trials (70% of all trials) and probe trials (30%) were randomly presented to participants. In the search trials, participants were asked to report whether a dot inside the search target (diamond) was presented on the left or right. In the probe trials, participants were required to detect a probe target (A or B). The probe target appeared in a critical color (either of the target or distractor color in search trials) or in a neutral color (a color that had not been presented in search trials). Experimental codes can be found at https://doi.org/10.5281/zenodo.5944534 (Kawashima & Amano, 2022a).\n\nIn the search trials (top panel), participants were asked to report whether a dot inside the search target (diamond) was presented on the left or right. In half of the trials, a different color (singleton) was presented. The target color was fixed (Experiments 1 and 3) or random (Experiment 2); the distractor color was also fixed (Experiments 1 and 2) or random (Experiment 3). In the probe trials (bottom panel), the task was to detect a probe target (A or B). In Experiment 1, in half of the trials, the target color (e.g., green) was presented, while in the other half, the distractor color (e.g., red) was presented. The probe target appeared in a critical color (either of the target or distractor color in search trials) or in a neutral color (a color that had not been presented in search trials). In Experiments 2 and 3, either the distractor or target color appeared in half of the probe trials, respectively, while all items were presented in neutral colors in the other half of the trials.\n\nThe research subjects were healthy adults between the ages of 20 and 35 living in Japan from the Center for Information and Neural Networks (CiNet)’s research participation pool. In total, 150 participants were enrolled in this study via the web-based SONA recruitment system (www.sona-systems.com) and were promised monetary compensation (1,000 Japanese Yen or approximately 10 US dollars). Three experiments were conducted, each with 50 different participants. The color combinations for the target and distractor differed across the three experiments. A minimum sample size of 25 was estimated via a priori power analysis using G*Power (Faul, Erdfelder, Buchner, & Lang, 2009: with settings of power = 0.80, alpha = 0.05, and ηp2 = .374) based on a previous report (Chang & Egeth, 2019). We doubled this number because of the possible large variability inherent in data collected through online experimentation.\n\nIn Experiment 1, four participants were removed owing to their probe task performance, which was below the level of chance. Ultimately, 46 participants, who were aged between 20 and 30 years (M = 22.3, SD = 2.04, 17 female participants), were included in the analyses. For the same reason, two and three participants were removed from Experiments 2 and 3, thereby resulting in 48 (M = 21.9, SD = 1.36, 26 female participants) and 47 (M = 22.8, SD = 2.63, 22 female participants) total participants, respectively.\n\nThe study was approved by the ethics and safety committee of the National Institute of Information and Communications Technology in Osaka, Japan (approval number: 20191031). Informed consent was obtained from all participants. The informed consent statement was displayed on the monitor at the beginning of the online experiment, with a full description of the study purpose, authors identification, and that data would be stored privately with authors. Participants expressed their willingness to participate in the experiment by pressing a predetermined key. All methods were performed in accordance with the relevant guidelines and regulations.\n\nAll experiments were performed online. Participants obtained the link to the online experiment through the SONA Systems recruitment website and, after clicking on the link, the experiment started. Participants were asked to participate in the experiment in a quiet room and not to use cell phones or listen to music during the experiment.\n\nStimuli and experiment design\n\nStimuli were generated and presented via Pavlovia.org based on PsychoPy (v2020.1: Peirce et al., 2019). At the beginning of the experiment, we calculated the pixel density (pixel/mm) of the participants’ monitors using a card task and then calculated their viewing distance with a blind spot task (Li, Joo, Yeatman, & Reinecke, 2020). The blind spot task featured three practice trials (repeated if needed), followed by five experimental trials. The same five trials of the blind spot task were presented in each half of the main task to obtain a reliable viewing distance throughout the experimental session. These parameters were used to determine the visual angle of the stimuli.\n\nWe created search and probe displays similar to those of Chang and Egeth (2019), as shown in Figure 1. The search (70% of trials) and probe trials (30% of trials) were presented to the participants randomly. The search and probe displays contained four geometric shapes presented at each corner of an imaginary diamond with a diagonal of 10.34°. The search displays contained one diamond, one circle, one square, and one hexagon (1.7° × 1.7°). The search target was the diamond. Each shape contained a black dot (0.15°) located 0.3° to the right or left side of the shape. The task was to report the dot location of the target shape by pressing the “F” or “J” keys for the left or right side, respectively, as quickly and accurately as possible. For 50% of the search trials, one randomly chosen distractor item was presented as a singleton (i.e., one shape was drawn in a different color). This point was explicitly mentioned in the instruction. In the remaining trials, no singleton was presented (i.e., all the shapes were drawn in the same color). The location of the target dot, target shape, and singleton varied randomly. The search trials began with a black screen (500 ms) followed by a fixation cross (800 ms) and then a search display (2,000 ms). A feedback display was subsequently presented for 500 ms with the word “correct!” or “error” based on the participants’ responses.\n\nThe target and distractor colors were fixed in the task in Experiment 1. These colors were assigned to the participants randomly. In Experiment 2, only the distractor color was fixed throughout the trials; the target color was varied randomly on a trial-by-trial basis. In Experiment 3, only the target color was fixed; the distractor color was changed for each trial.\n\nThe probe displays contained four different colored ovals (1.5° × 1.2°), inside which a letter (0.75° in height) was presented. The task was to detect the letter A or B in the display and to press F or J keys in response, respectively. The other three letters were randomly selected from other alphabets, with the exception of I and O. The probe trials began with a black screen (500 ms) and the subsequent fixation cross (800 ms) followed by a probe display for 100 ms. The observers had to press a key within 3,000 ms after the presentation of the probe. A feedback display was then presented for 500 ms with the word “correct!” or “error” based on the participant’s key press.\n\nThe target–distractor color combinations were manipulated in the experiments. For Experiment 1, 50% of the probe trials contained the target color in the search trials, where the target color that appeared in the search trials also appeared in the probe trials (i.e., the target-color-present trials). The probe target was presented on the target-colored items in 25% of this group of trials or on neutral-colored items in 75% of this group. The remaining 50% of probe trials included a distractor color in the search trials (i.e., the distractor-color-present trials) where the probe target appeared on a distractor-colored item in 25% of trials or on a neutral-colored item in 75% of trials. The location of the probe target was varied randomly. For Experiment 2, all the target-color-present trials in Experiment 1 were replaced with neutral trials where all probes were colored in neutral colors. Thus, the rate of distractor-color-present trials was maintained at the same level as that of Experiment 1. Namely, 50% of probe trials included a distractor color (25% featured a probe on a distractor-colored item, and 75% featured a probe on neutral-colored items). Conversely, the remaining 50% of probe trials included neutral-colored items. Similarly, for Experiment 3, 50% of the probe trials included the target color (25% had a probe on the target-colored item, and 75% had a probe on the neutral-colored items), and the remainder included neutral-colored items.\n\nFive distinctive colors (red, medium blue, forest green, dark orange, and magenta) were used as the target, distractor, and neutral colors. Their roles were randomly assigned across participants. Four other unique colors (white, light gray, dark gray, and dim gray) were used as the target color (Experiment 2) and distractor color (Experiment 3), respectively. We used grayscale as random colors to avoid potential confounds in the color space associated with fixed colors; target-to-target and distractor-to-distractor color similarity could affect the formation of the search template (Geng & Witkowski, 2019). The experiment was preceded by 10 practice trials for the search task and 10 practice trials for the probe task. The main experiment comprised 448 search trials and 192 probe trials (640 trials in total) with an opportunity given for a brief rest every 40 trials.\n\nAll data analysis was carried out using R (version 4.0.3). In the search task, a paired t-test was used to compare the reaction times (RTs) between singleton-present and singleton-absent trials. In the probe task, we conducted repeated-measures analysis of variance (ANOVA) with within-subject factor critical color and within-subject factor probe-target location on RTs and accuracy (Experiment 1). For Experiment 2 and 3, a paired t-test was used to compare the RTs and accuracy between probe conditions. A Pearson correlation analysis was conducted for evaluating the relationship between target enhancement and distractor suppression. Target enhancement effect was calculated by subtracting the RTs for critical-colored condition (probe on a target color) from those for neutral-colored condition, while distractor suppression effect was calculated by subtracting the RTs for critical-colored condition (probe on a distractor color) from those for neutral-colored condition.\n\nRe-analysis of Chang and Egeth (2019)\n\nWe obtained the raw data from Chang and Egeth (2019) and applied the same correlation analyses as those used in Experiment 1. Specifically, to assess the relationship between target enhancement and distractor suppression, we calculated the magnitude of enhancement by subtracting the RTs on target-color trials from those on neutral-color trials and the magnitude of suppression by subtracting the RTs in neutral-color trials from those in distractor-color trials. Furthermore, we combined correlation coefficients of those in Experiment 1 and in Chang and Egeth (2019) to better ascertain whether enhancement and suppression could guide attention independently.\n\n\nResults\n\nTrials with RTs faster than 100 ms or slower than 5,000 ms were excluded from the analysis. Further, we removed trials with RTs 3.5 standard deviations above or below the mean for each participant, resulting in the elimination of 0.4%, 0.6%, and 0.5% of all the search trials in Experiments 1, 2, and 3, respectively. Full raw data for all the experiments can be found under Underlying data (Kawashima & Amano, 2022b).\n\nAll participants performed well on the search task (n = 46, 48, and 47 for Experiment 1, 2, and 3, respectively). The mean accuracy was 96.5% (95.5%, 96.2%) and 96.9% (95.3%, 96.5%) for singleton-present and singleton-absent trials in Experiments 1, 2, and 3, respectively. Therefore, we did not examine accuracy owing to possible ceiling effects. A pairwise t-test was used to compare the RTs between the trials. Figure 2 shows the mean RTs in the visual search task. In Experiment 1, where target and distractor colors were fixed during the trials, the RTs were faster for singleton-present trials than in singleton-absent trials (−5.8 ms [95% CI, −0.23 to −11.3]; t (45) = 2.10, p = .041, d = 0.31). This singleton-presence benefit fits with earlier findings [8,10], allowing us to test target enhancement and distractor suppression for probe trials. Unexpectedly, however, in Experiment 2, where the target colors were randomized and the distractor color was fixed, no RT differences were observed between singleton-present and singleton-absent trials (2.8 ms [95%CI, −3.2 to 8.8]; t (47) = 0.94, p = .354, d = 0.14). However, in Experiment 3, where the target color was fixed and the distractor colors were random, singleton-present benefits were observed in the RTs (−14.0 ms [95% CI, −8.6 to −19.4]; t (46) = 5.20, p < .001, d = 0.76).\n\nEach dot represents the mean RT per participant. Error bars indicate standard errors of the mean. The RT was shorter in singleton-present trials than in singleton-absent trials for Experiments 1 and 3.\n\nThe same criteria were used to exclude trials in search tasks. We removed trials if two or more consecutive preceding trials were probe trials, because successive probe tasks could transiently disrupt the attentional set for target or distractor and thus distort probe responses (Chang & Egeth, 2019; Gaspelin & Luck, 2018a), which resulted in the elimination of 9.8%, 9.7%, and 10.0% of all probe trials in Experiments 1, 2, and 3, respectively. We performed a 2 (critical color: target color or distractor color presented on a probe trial) × 2 (probe-target location: neutral-colored or critical-colored item on which the target was present) repeated-measures analysis of variance for both RT and accuracy. Please note that target enhancement effect is calculated by subtracting the RTs for critical-colored condition (probe on a target color) from those for neutral-colored condition, while distractor suppression effect is calculated by subtracting the RTs for critical-colored condition (probe on a distractor color) from those for neutral-colored condition.\n\nIn Experiment 1 (Figure 3A and B), no significant main effect of critical color and probe-target location on RT was found (F (1, 45) = 1.00, p = .321, ηp2 = .02; F (1, 45) = 0.53, p = .471, ηp2 = .01), nor was there any significant interaction (F (1, 45) = 2.37, p = .130, ηp2 = .05). These results indicate no enhancement or suppression effects in the probe task (−13.4 ms [95% CI, −6.9 to −33.9]; −1.7 ms [95%CI, −19.4 to 16.0]: the scatter plot in Figure 5B). This remained true even when the target or distractor colors were presented randomly in the visual search task (Experiments 2 and 3): no difference was observed in the probe location for the suppression effect (Figure 3C: 8.5 ms [95%CI, −8.4 to 25.3]; t (47) = 1.01, p = .318, d = 0.15: the scatter plot in Figure 5A) and for the enhancement effect (Figure 3D: −8.1 ms [95%CI, −27.4 to 11.1]; t (46) = 0.85, p = .400, d = 0.12: the scatter plot in Figure 5C).\n\nThe probe-target color was either the critical color or neutral color. The critical color was either the distractor or target color in Experiment 1; it was always the distractor color in Experiment 2 or the target color in Experiment 3. The neutral color was one that had not been presented in search trials. Each dot represents the mean RT per participant.\n\nFor accuracy, in Experiment 1 (Figure 4A and B), there was neither a significant main effect of critical color and probe-target location (F (1, 45) = 1.00, p = .323, ηp2 = .02; F (1, 45) = 0.0002, p = .989, ηp2 = .00) nor a significant interaction (F (1, 45) = 0.06, p = .810, ηp2 = .00). These results indicate no enhancement or suppression effects in the probe task (−1.7 % [95% CI, −19.4 to 16.0]; −13.5 % [95%CI, −33.9 to 6.9]). In addition, we found no difference in the probe location in Experiments 2 and 3 (the suppression effect: Figure 4C, −0.008 % [95%CI, −0.04 to 0.02]; t (47) = 0.60, p = .551, d = 0.09; the enhancement effect: Figure 4D, 0.01% [95%CI, −0.02 to 0.05]; t (46) = 0.75, p = .455, d = 0.11).\n\nThe probe-target color was either the critical color or neutral color. The critical color was either the distractor or the target color in Experiment 1; it was always the distractor color in Experiment 2 or the target color in Experiment 3. The neutral color was one that had not been presented in search trials. Each dot represents the mean accuracy per participant.\n\nOur results in Experiment 1 showed no enhancement or suppression effects in either RT or accuracy in the probe task, which does not support the findings of Chang and Egeth (2019). This may be due to the larger variability across participants in search performances. Therefore, we assessed the relationship between target enhancement and distractor suppression effects in Experiment 1. The magnitude of enhancement was calculated by subtracting the RTs on target-color trials from those on neutral-color trials. The magnitude of suppression was obtained by subtracting RTs in neutral-color trials from those in distractor-color trials. As shown in Figure 5B, we found a significant negative correlation between them (r = −.46, 95% CI [–.66, –.20], p = .001, t (44) = 3.44). This negative correlation remained significant after Spearman’s rank-order correlations, which are less sensitive to outliers than Pearson’s product-moment correlation (rs = −.40, p = .006). This correlation indicates that those with larger RT benefits by target enhancement had less inhibition to the distractor color and vice versa.\n\n(A). Probe effect of all subjects in Experiment 2. Distractor suppression effect varied across subjects, and no group-level effect was observed. (B). Correlations between target enhancement and distractor suppression effects in Experiment 1 for reaction times (RTs). Target enhancement (distractor suppression) indicates a faster RT for the target-colored probe than the neutral probe, while distractor suppression indicates a faster RT for the distractor-colored probe than the neutral probe. The red line indicates the best fit line to the data. The target enhancement and distractor suppression were negatively correlated (Pearson’s r = −.46, p = .001), suggesting that they are not mutually independent. (C) Probe effect of all subjects in Experiment 3. Target enhancement effect varied across subjects, and no group-level effect was observed.\n\nTo improve the comparison of our findings to those of Chang and Egeth (2019), we obtained their raw data and applied the same correlation analyses. We found a numerically negative but nonsignificant correlation between target enhancement and distractor suppression (r = −.15, 95% CI [−.39, .11], p = .257, t (58) = 1.15). Further, we applied a meta-analysis of correlations between Chang and Egeth (2019) and Experiment 1 of the present study using the “meta” package in R (Schwarzer, 2007). As Figure 6 shows, the pooled correlation in this dataset is r = −.31 (95% CI [−.57, .02], for the random-effects model), which is marginally significant (z = −1.83, p = .068).\n\nForest plot indicates pooled individual-study Pearson’s correlation coefficients with corresponding 95% CIs. Random effect model showed a marginal negative correlation between target enhancement and distractor suppression (r = −.31, 95% CI [−.57, .02], p = .068), suggesting that they are not mutually independent.\n\nAlthough a negative correlation between the magnitude of distractor suppression and attentional enhancement was found for RT, no correlation was found for accuracy in Experiment 1 (r = −.13, 95% CI [−.40, .16], p = .378, t (44) = 0.89) and in Chang and Egeth’s (2019) data (r = .16, 95% CI [−.09, .40], p = .211, t (58) = 1.27). We checked for a possible speed-accuracy trade-off in Experiment 1, analyzing RT and accuracy together by computing inverse efficiency scores (RT/proportion correct: Bruyer & Brysbaert, 2011) for each participant and condition in Experiments 1, 2, and 3. The inverse efficiency score combines both RT and accuracy into a single measure. The ANOVA of the inverse efficiency index in Experiment 1 also revealed a non-significant probe effect reflected in no interaction between critical color and probe-target location (F (1, 45) = 0.12, p = .733, ηp2 = .003). Neither was any probe effect observed in Experiments 2 and 3 (t (47) = 1.32, p = .194, d = 0.19; t (46) = 1.29, p = .204, d = 0.19). This lack of probe effect in inverse efficiency scores indicates that faster RTs were not accompanied by a sharp decrease in accuracy in our task.\n\n\nDiscussion\n\nThe present study tested whether target enhancement and distractor suppression can work independently. We observed the singleton-present benefit of RTs in the visual search task, replicating previous findings (Chang & Egeth, 2019, 2021; Gaspelin & Luck, 2018a). This suggests that a salient distractor in a visual display can be excluded from selection, supporting the idea of a signal-suppression hypothesis (Sawaki & Luck, 2010, 2013). However, the RT benefits in visual search unexpectedly disappeared when the target color was varied from trial to trial (Experiment 2; Figure 2B). One possible reason for the lack of RT benefits is that, to some extent, the participants relied on attentional enhancement to target items rather than direct suppression to exclude the salient item. In Experiment 2, the participants could not expect target features due to its randomness, so the contribution of attentional enhancement in the visual display was lower than that in Experiment 1 and 3. This makes it plausible that target enhancement guides visual attention more effectively than distractor suppression.\n\nWe found a singleton-presence benefit in Experiment 3, where the distractor color varied on a trial-by-trial basis. However, this observation seems to be inconsistent with previous results suggesting that singletons are suppressed based on their color dimension (first-order suppression: Gaspelin & Luck, 2018a). Vatterott and Vecera (2012) asked participants to perform a visual search task where singleton color was constant for block 1 (48 trials) before changing to a different color in block 2. These authors found that the singleton captured the participants’ attention (singleton-presence cost) in the first half of block 1, while this cost was eliminated (singleton-presence benefit) in the second half of block 1, indicating that the participants learned to suppress the salient item (see also Vatterott, Mozer, & Vecera, 2018). Notably, the singleton-presence cost was observed again in the first half of block 2, where the singleton color was changed. Similarly, Gaspelin and Luck (2018a) demonstrated that oculomotor suppression effects (Gaspelin, Leonard, & Luck, 2017) were reduced when the singleton color was changed, suggesting that first-order feature suppression plays a crucial role. However, our results show that even when the singleton color was changed from trial to trial, a singleton-presence benefit was observed for the RTs (Figure 2C). One difference between the previous studies and ours is the frequency of changes in the singleton colors on a blocked or trial-by-trial basis. Following the observation that attentional capture by distractors can be suppressed by increasing repetitions (repetition suppression: Bonetti & Turatto, 2019; Thompson, 2009), our frequent changes in singleton color may have prevented this habituation-based inhibition, instead promoting a conceptual suppression of the singleton. Thus, our finding of a changing-color singleton-presence benefit suggests that singletons can be suppressed based not only on color information but also on a higher conceptual level of information, such as the semantic levels of the description of saliency (second-order suppression: Gaspelin & Luck, 2018a). This second-order suppression has also been reported in the domain of spatial attention (Won, Kosoyan, & Geng, 2019; Won, Forloines, Zhou, & Geng, 2020).\n\nThe participant-level analysis presented in Figure 5B shows a negative correlation between the RT effects of target enhancement and distractor suppression. This result does not support the idea of concurrent attentional guidance through enhancement and suppression proposed by Chang and Egeth (2019). Rather, this negative correlation indicates that the two are not independent. Combining the observations that the distributions of target enhancement and distractor suppression effects in Experiment 1 (Figure 5B) resembled those in Experiments 2 (Figure 5A) and 3 (Figure 5C), the results indicate that participants encountered difficulties in using the two representations for enhancement and suppression—that is, whether attentional enhancement or distractor suppression works depends on the observer’s choice of search strategy. Some participants would cease suppressing irrelevant distractors because of the effort required: an empirical study showed that participants selectively encode positive information for visual search even when both positive and negative cues are provided (Rajsic et al., 2020). Thus, those who attempt to focus more on the target dimension would be more drawn to the distractor and vice versa.\n\nThis difference in search strategy across individuals may be one reason why no attentional enhancement or distractor suppression was observed in group-level analysis. Although a singleton-presence benefit of RTs was observed in visual search, we found no target enhancement or distractor suppression in the probe task in Experiment 1 (Figures 3A and 4A). Thus, we failed to replicate the previous findings of Chang and Egeth (2019), thereby casting doubt on their claim that attention can be guided concurrently by enhancement and suppression. Here, we propose instead that differences in search strategy among the participants might have made group-level effects invisible.\n\nChang and Egeth’s (2019) data showed a numerically negative but nonsignificant correlation between target enhancement and distractor suppression. This was in contrast to our argument that participants select and rely on a single search strategy to perform the search task. Why were we unable to find group-level effects for enhancement and suppression, unlike Chang and Egeth (2019)? It is possible that our failure of replication was due to our less controlled setting—a result of the online constraints of our experiments. However, we believe that this account is incomplete because we replicated the singleton-presence benefit in visual search in experimental online settings, showing the precise measurements for RT (e.g., 5.7 ms benefit in Experiment 1). In addition, we found no probe effect in inverse efficiency scores, indicating that enhancement and suppression effects were still not observed even when a larger variability in accuracy was incorporated. Thus, we believe that a potential lack of complete engagement by the participants in the task because of the online setting cannot fully explain our results. Another possible reason is differences in instruction. Previous studies have shown that an awareness of distractors modulates the interference of the distractor (Chisholm & Kingstone, 2014: Huffman, Rajsic, & Pratt, 2019). Chisholm and Kingstone (2014) assessed the influence of awareness on attentional capture by informing some participants of the presence of the distractor (aware condition) and asking others to avoid attending to the distractor (avoid condition). Their results showed that the oculomotor capture of the distractor in the avoid condition was larger than that in the aware condition, suggesting that too much of an emphasis on distractor suppression could lead to a larger interference. Based on these findings, the slight differences in instructions between Chang and Egeth (2019) and our study might have resulted in the observed inconsistency in the results. For our online experiment, the instruction was presented as screen text, and understanding it was entirely dependent on the participants. For onsite experiments, as in Chang and Egeth (2019), generally, the instructions can be repeated several times, and their emphasis is dependent on the experimenter. Although this attribution is speculative, such a difference in instruction could yield a different attentional set to the task, which may be a reason for the failure of replication. Future research is required to control the attentional set through the instructions for exploring the mechanism of distractor suppression, particularly regarding the comparison of online and offline results. However, another possibility concerns methodological differences. Chang and Egeth (2019) gave 32 probe and 48 search practice trials; to save time, we gave 10 probe and search practice trials. These differences in the exposure to target and distractor prior to the task might have led to the weak enhancement and suppression in the current study. Future work should consider the role of practice in the mechanism of attentional guidance. Finally, the limitation of this study is that the sample size was rather small for observing the correlation between target enhancement and distractor suppression. Although the combined correlation coefficients of those in Experiment 1 and in Chang and Egeth (2019) showed a negative trend (Figure 6), future studies with a larger sample size and controlled settings might confirm our findings.\n\nOur current results constitute a contribution to the understanding of how target enhancement and distractor suppression are coordinated to allocate visual attention. Some have suggested that the two operate concurrently to guide visual attention (Andersen & Müller, 2010; Navalpakkam & Itti, 2007), leading to the idea of an enhancement-and-suppression model (Chang & Egeth, 2019). Our results, however, show that, instead of attentional guidance occurring independently through enhancement and suppression, it depends on the participants’ search strategy: some use target enhancement; others use distractor suppression for the guidance of visual attention. These findings suggest that maintaining these two control systems simultaneously would be cognitively demanding. Future research should examine the contributions of explicit learning (e.g., strategy choice) and implicit learning (e.g., excessive training) in suppressing distractors (Luck, Gaspelin, Folk, Remington, & Theeuwes, 2021).\n\n\nData availability\n\nOSF: Can enhancement and suppression concurrently guide attention? An assessment at the individual level. https://osf.io/bpz3k (Kawashima & Amano, 2022b)\n\nThis project contains the following underlying data:\n\n- raw_data.xlsx (Raw data from search trials and probe trials)\n\nThis project contains the following extended data:\n\n- Experiment files (JavaScript code for each Experiment 1, 2, and 3)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nSoftware availability\n\nSource code available from:\n\nExperiment 1 (https://gitlab.pavlovia.org/Kawashima/exp1_kawashima_amano)\n\nExperiment 2 (https://gitlab.pavlovia.org/Kawashima/exp2_kawashima_amano)\n\nExperiment 3 (https://gitlab.pavlovia.org/Kawashima/exp3_kawashima_amano)\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.5944534 (Kawashima & Amano, 2022a)\n\nLicense: GNU General Public License, version 3\n\n\nAuthor contributions\n\nT.K. performed experiments and analyzed data; and K.A. and T.K. designed experiments, defined and validated data analysis methods, and wrote the paper.",
"appendix": "Acknowledgements\n\nThe authors would like to thank Enago (www.enago.jp) for the English language review.\n\n\nReferences\n\nAndersen SK, Müller MM: Behavioral performance follows the time course of neural facilitation and suppression during cued shifts of feature-selective attention. Proc. Natl. Acad. Sci. 2010; 107: 13878–13882. PubMed Abstract | Publisher Full Text\n\nArita JT, Carlisle NB, Woodman GF: Templates for rejection: Configuring attention to ignore task-irrelevant features. J. Exp. Psychol. Hum. Percept. Perform. 2012; 38: 580–584. PubMed Abstract | Publisher Full Text\n\nBacon WF, Egeth HE: Overriding stimulus-driven attentional capture. Percept. Psychophys. 1994; 55: 485–496. PubMed Abstract | Publisher Full Text\n\nBahle B, Beck VM, Hollingworth A: The architecture of interaction between visual working memory and visual attention. J. Exp. Psychol. Hum. Percept. Perform. 2018; 44: 992–1011. 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}
|
[
{
"id": "138946",
"date": "09 Jun 2022",
"name": "Li Jingling",
"expertise": [
"Reviewer Expertise cognitive psychology",
"human attention",
"cognitive control"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study tried to replicate Chang and Egeth (2019) and extended their conditions to a randomized target color or distractor color in separate blocks. Their goal was to test whether attentional setting on the task demand and distractor suppression are related or separate processing. They replicated Chang and Egeth (2019) in that presenting a distractor actually facilitated the speed of target discrimination, suggesting there was target enhancement and distractor suppression occurred simultaneously. Such effect increased when the target color was fixed and distractor color varied trial-by-trial, suggesting a varied distractor induced a stronger suppression. Nevertheless, when target color varied trial-by-trial and distractor color was fixed across trials, there was no distractor suppression. Also, the interleaved probe task with the search trials did not reveal any significant effect. The author found a negative correlation between target enhancement and probe suppression in the probe task in experiment 1, suggesting that those who enhance the target more tend to suppress distractors less. The authors also provided a meta-analysis of their own data and that of Chang and Egeth (2019) and obtained a significant correlation effect. The author, therefore, concluded that the two operations, target enhancement and distractor suppression, are related.\n\nThis study is well-conducted in method, the data are well processed, and the conclusion is clear and potentially contributes to academic literature. I suggest accepting this article with minor revisions:\n1. I have difficulty understanding why non-significant probe data can generate a significant correlation in experiment 1, and why such corresponding analysis cannot apply to experiments 2 and 3. Does that mean a traditionally assumed distractor capture also occurred? Can probe data in experiments 2 and 3 also be considered separated into \"target\" or \"distractor\" colors even if they are varied?\n\n2. I like your strategy account, which is consistent with the definition of attention in resource control. Could it be possible that online data collection essentially probes a different group of participants compared to that recruited by Chang and Egeth (2019)? For instance, those who come to the lab to complete the task might be mainly graduate students while those who complete an online experiment are more close to the heterogeneous population? The authors may add some discussion on this point.\n\n3. I noticed that the accuracy of experiment 2 was a bit lower than that in experiments 1 and 3, is there any significance? Randomizing target color across trials may make the task more difficult, even if the target was not defined by color. This can also be a piece of evidence on the importance of strategy induced by different task settings.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8795",
"date": "16 Sep 2022",
"name": "Tomoya Kawashima",
"role": "Author Response",
"response": "I have difficulty understanding why non-significant probe data can generate a significant correlation in experiment 1, and why such corresponding analysis cannot apply to experiments 2 and 3. Does that mean a traditionally assumed distractor capture also occurred? Can probe data in experiments 2 and 3 also be considered separated into \"target\" or \"distractor\" colors even if they are varied? Thank you for the comment. Our interpretation of the observed negative correlation between target enhancement and distractor suppression is that “whether attentional enhancement or distractor suppression works depends on the observer’s choice of search strategy”. In other words, individuals will adopt a strategy to focus their attention on the target dimension, whereas others will adopt a different strategy to focus on the distractor dimension. This variability in strategy across participants may be “one reason why no attentional enhancement or distractor suppression was observed in group-level analysis.” We cannot apply the same analysis to Experiments 2 and 3 for distractor suppression and target enhancement, respectively, because different participants in each experiment were different. Therefore, we cannot consider the correlation between Experiments 2 and 3 (please see Figure 5). The probe data in Experiments 2 and 3 were obtained with a fixed distractor or target color, respectively. Therefore, we can consider the data from these experiments as producing the distractor suppression and target enhancement effects. I like your strategy account, which is consistent with the definition of attention in resource control. Could it be possible that online data collection essentially probes a different group of participants compared to that recruited by Chang and Egeth (2019)? For instance, those who come to the lab to complete the task might be mainly graduate students while those who complete an online experiment are more close to the heterogeneous population? The authors may add some discussion on this point. Thank you for the suggestion. We have added the following sentence: In addition, the online experimental settings enable the collection of various populations compared with laboratory experiments. Hence, the difference in data from online and laboratory experiments should be interpreted with caution. I noticed that the accuracy of experiment 2 was a bit lower than that in experiments 1 and 3, is there any significance? Randomizing target color across trials may make the task more difficult, even if the target was not defined by color. This can also be a piece of evidence on the importance of strategy induced by different task settings. Thank you for the suggestion. We performed the additional analysis to compare the accuracy of the experiments and found no significant difference. Therefore, we concluded that randomizing the target or distractor color did not change the overall difficulty of the probe task. We added the following sentences: We further compared the accuracy of the experiments to verify whether the overall task difficulty differed among the experiments. In the target-color present condition (Figure 4B and D), two-way ANOVA with between-subject factor (experiment) and within-subject factor (probe condition) demonstrated the lack of the main effect of the experiment or probe condition (F (1, 91) = 0.24, p = .629, = .00; F (1, 91) = 0.16, p = .695, = .00) or an interaction effect (F (1, 91) = 0.43, p = .512, = .00). The same analysis was performed for the distractor-color present condition (Figure 4A and C), which illustrated the absence of the main effect of the experiment or probe condition (F (1, 92) = 0.005, p = .944, = .00; F (1, 92) = 0.22, p = .639, = .00) or an interaction effect (F (1, 92) = 0.06, p = .809, = .00). Thus, randomizing the target or distractor color did not change the overall difficulty of the probe task."
}
]
},
{
"id": "140348",
"date": "27 Jun 2022",
"name": "Xiangyong Yuan",
"expertise": [
"Reviewer Expertise multisensory integration",
"selective attention"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe submitted paper re-examined an interesting issue whether target enhancement and distractor suppression in visual search are performed in parallel. The introduction was a thorough one, having reviewed several relevant studies, it raised a clear standpoint about why these two processes may not be weighted in an equal manner. Although failed to fully replicate a previous one, they observed a novel negative correlation between target enhancement and distractor suppression, and found that expecting only one target color compared with only one distractor color can benefit search. As the authors explained, online experiments may allow more personal strategies in search thus more individual variances than lab experiments. Overall, I agree with most of the authors’ opinion about the relationship between target and distractor suppression. Besides, I fell the experiments are well-conducted and the manuscript is well-written, and would be very glad to see it published after my minor concerns below are addressed:\nThe authors noticed that after few practice trials observers may not find a stable search strategies therefore have not shown simultaneous target enhancement and distractor suppression. Suppose the search strategies were stable for a particular observer only after enough practice trials, if the first few trials, or the first block in the formal experiment was abandoned, will these two processes be found like Chang and Egeth (2019)? Or alternatively, the author may split the data into first and second halves, examining how the search strategies change over time. This may also help to reveal the individual differences if they indeed have different strategies.\n\nThe mean accuracies of probe task in Chang and Egeth (2019) were above 90%. In contrast, the mean accuracies were below 80% in exp. 1–3. This may suggest that the participants in the current online experiments did not fully focus on the task, compared with in the lab. Is it possible that target enhancement and distractor suppression can only work in parallel with sufficient attention resources? The authors may select and analyze the data from those participants with higher accuracies that match those in Chang and Egeth (2019), and check if this is true. This possibility may be mentioned in the discussion.\n\nIn discussion, a conceptual suppression of the singleton has been proposed as a possible explanation of exp. 3. But it seems the search benefit in exp. 3 can be simply explained by a figure-background segregation. If all the targets share the same color across trials while the distractor is always distinguishable from the targets, the observers could learn to only search for the targets and simultaneously ignore the distractors as an irrelevant background. I am not sure whether we actually need to suppress the singleton on a conceptual (or semantic) level of saliency. The distractors can be easily excluded from the search pool due to their first order saliency.\n\nIn Page 4, the authors wrote: “Accordingly, we calculated the magnitude of the enhancement and suppression for each participant and compared the effect across experiments. We hypothesized that if two attentional guidance elements, enhancement and suppression, competed for common processing resources, the magnitude of the effect in Experiment 1 would be smaller than those in Experiments 2 and 3 because Experiment 1 required both of these attentional controls.” But I didn’t find this comparison in the result section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8796",
"date": "16 Sep 2022",
"name": "Tomoya Kawashima",
"role": "Author Response",
"response": "The authors noticed that after few practice trials observers may not find a stable search strategies therefore have not shown simultaneous target enhancement and distractor suppression. Suppose the search strategies were stable for a particular observer only after enough practice trials, if the first few trials, or the first block in the formal experiment was abandoned, will these two processes be found like Chang and Egeth (2019)? Or alternatively, the author may split the data into first and second halves, examining how the search strategies change over time. This may also help to reveal the individual differences if they indeed have different strategies. Thank you for the suggestion. We divided the trials and used the second half for analysis. The results illustrated that no distractor suppression was observed, although the target enhancement effect was significant. In a critical sense, a negative correlation once again exists between enhancement and suppression effects, which were observed for all data (Figure 5). Therefore, we deem that these data support our idea that attentional guidance is dependent on the search strategy of the participant. We added the following text: Chang and Egeth (2019) gave 32 probe and 48 search practice trials; to save time, we gave 10 probe and search practice trials. These differences in the exposure to target and distractor prior to the task might have led to the weak enhancement and suppression in the current study. To test this assumption, we divided trials into first and second halves and used the second half of the trials for analysis. The visual search performance pointed to the singleton-benefit effect (n = 40, −7.2 ms [95% CI: −12.68 to −1.81]; t (39) = 2.70, p = .010, d = 0.43). For RTs in the probe task, the study observed a significant interaction (F (1, 39) = 4.68, p = .037, = .11), which reflected a significant target enhancement effect (F (1, 39) = 4.47, p = .041, = .10) but not a distractor suppression effect (F (1, 39) = 1.07, p = .307, = .03). Importantly, the study also observed a significant negative correlation between enhancement and suppression effects (r = −.34, 95% CI [−.59, −.03], p = .031). Thus, the study noted no clear distractor suppression effect even in the second half of the trials, where the participants were sufficiently exposed to the target and the distractor. Instead, the data support our idea that attentional guidance is dependent on the search strategy of the participants. The mean accuracies of probe task in Chang and Egeth (2019) were above 90%. In contrast, the mean accuracies were below 80% in exp. 1–3. This may suggest that the participants in the current online experiments did not fully focus on the task, compared with in the lab. Is it possible that target enhancement and distractor suppression can only work in parallel with sufficient attention resources? The authors may select and analyze the data from those participants with higher accuracies that match those in Chang and Egeth (2019), and check if this is true. This possibility may be mentioned in the discussion. Thank you for the suggestion. In the current experiment, only a few particpants exhibited accuracies higher than 90%. We selected participants with relatively high accuracy rates (above 70%) in the probe task and assessed their RTs but found no target enhancement or distractor suppression effects. Therefore, high accuracy rates in the probe task do not seemingly guarantee the enhancement or suppression effect. We added the following text: Furthermore, the study observed that the mean accuracy of the probe task in Experiments 1–3 was less than 80%, whereas Chang and Egeth (2019) reported more than 90%. This difference may suggest that the participants in the online experiments only partially focused on the task compared with experiments conducted in laboratory settings. The current study investigated whether or not target enhancement and distractor suppression can work in parallel with sufficient attentional focus on the task in an exploratory manner. We selected participants with relatively higher accuracy (above 70%) on each condition of the probe task and re-analyzed their reaction times (see Figure 4 for the distribution of accuracy data). In Experiment 1, the study selected 19 out of 46 participants. They displayed no target enhancement effect (13.4 ms [95% CI: −16.2 to 43.0]; t (18) = 0.95, p = .353, d = 0.22) or distractor suppression effect (18.6 ms [95% CI: −13.7 to 50.9]; t (18) = 1.21, p = .243, d = 0.28). In Experiment 2, the study selected 28 out of 48 participants, which exhibited no distractor suppression (12.3 ms [95% CI: −24.7 to 25.7]; t (27) = 0.04, p = .969, d = 0.01). In Experiment 3, 27 out of 47 participants produced no target enhancement effect (12.2 ms [95% CI, −16.1 to 34.3]; t (26) = 0.74, p = .464, d = 0.14). Thus, even the participants who would have focused their attention on the task presented no target enhancement or distractor suppression. As such, higher accuracy in the probe task seemingly does not guarantee the enhancement or suppression effect. In discussion, a conceptual suppression of the singleton has been proposed as a possible explanation of exp. 3. But it seems the search benefit in exp. 3 can be simply explained by a figure-background segregation. If all the targets share the same color across trials while the distractor is always distinguishable from the targets, the observers could learn to only search for the targets and simultaneously ignore the distractors as an irrelevant background. I am not sure whether we actually need to suppress the singleton on a conceptual (or semantic) level of saliency. The distractors can be easily excluded from the search pool due to their first order saliency. Thank you for the suggestion. We added the following statement in the discussion: Another concept for the mechanisms underlying the singleton-presence benefit is figure-background segregation. In Experiment 3, where the target color was fixed, and the distractor color was varied across trials, the participants learned to search for the target color while segregating the distractor colors as background, which led to the singleton-presence benefit. Thus, future studies are required to elucidate the mechanisms underlying the singleton-presence benefit. In Page 4, the authors wrote: “Accordingly, we calculated the magnitude of the enhancement and suppression for each participant and compared the effect across experiments. We hypothesized that if two attentional guidance elements, enhancement and suppression, competed for common processing resources, the magnitude of the effect in Experiment 1 would be smaller than those in Experiments 2 and 3 because Experiment 1 required both of these attentional controls.” But I didn’t find this comparison in the result section. Thank you for the comment. We have planned but did not conduct this analysis, because we did not observe significant enhancement and suppression effects for all experiments. As suggested, we conducted this analysis with the following results. We added the following statement: Although the study observed no target enhancement or distractor suppression, we compared these effects across experiments. For the target enhancement effect, no significant difference was observed between Experiments 1 and 3 (Experiment 1: −1.7 ms; Experiment 3: −8.1 ms; t (91) = 0.49, p = .624, d = 0.10). Similarly, no significant difference was observed between Experiments 1 and 2 (Experiment 1: −13.5 ms; Experiment 2: 8.5 ms; t (92) = 1.68, p = .097, d = 0.35) for the distractor effect."
}
]
},
{
"id": "140483",
"date": "30 Jun 2022",
"name": "Ru-Yuan Zhang",
"expertise": [
"Reviewer Expertise Visual perception",
"cognitive neuroscience"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary:\nThis study focuses on the relative contributions of target enhancement and distractor suppression in visual search. In particular, the authors designed three experiments. In Experiment 1, the authors attempted to replicate the singleton-presence benefits as reported in Chang & Egeth, 2019 and found negative results. In Experiments 2 and 3, the randomness of target colors and distractor colors in the search task was systematically manipulated. However, these manipulations seem to exert no effects on reaction time and accuracy. Most importantly, the authors independently calculated the target enhancement effect and the distractor suppression effect (i.e., RT differences as compared to the neural conditions) and discovered a negative correlation between the two. This novel negative correlation suggests target enhancement and distractor suppression may act as the two sides of the same coin—the shared cognitive mechanisms.\nIn general, I like the overall experimental design and the arguments here, albeit the majority of the results being negative. I especially appreciate the authors’ efforts to replicate a published study and extend it. We should encourage reporting negative and replication results. I have several comments as below that may help improve the manuscript.\nMajor points:\nThe experimental design is OK, but the descriptions of the experimental details are hard to follow. Fig.1 is particularly confusing, and I have to read line-by-line in the methods part in a combination of Fig. 1 to comprehend what exactly the authors meant. I suggest substantially improving Fig.1 and the figure caption underneath.\n\nReaction time is usually highly skewed distributed. It seems to me that the authors performed stats on the raw RT values. I suggest trying to perform stats on log-transformed RT. That should better fit the intentions of t-tests and ANOVAs.\n\nIt remains unclear to me the rationales behind Experiments 2 and 3. The authors mentioned that “We hypothesized that if two attentional- guidance elements, enhancement and suppression, competed for common processing resources, the magnitude of the effect in Experiment 1 would be smaller than those in Experiments 2 and 3 because Experiment 1 required both of these attentional controls.” This argument is unclear to me. If either the target or distractor color is randomly selected, the advantage of color expectation should be diminished and that would lead to a smaller enhancement or suppression effect. Can the authors elaborate on the rationales and the predictions?\nMinor points:\n“This singleton-presence benefit fits with earlier findings [8,10], allowing us to test target enhancement and distractor suppression for probe trials. ” Here the numbered-style references should be replaced by inline-style references.\n\nThe figure captions should be improved. For example, in Fig. 2, does the black horizontal line in the box plot represent the mean or median of the group? What are the definitions of the upper and lower edges of the boxes and of the range of the whiskers?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8797",
"date": "16 Sep 2022",
"name": "Tomoya Kawashima",
"role": "Author Response",
"response": "The experimental design is OK, but the descriptions of the experimental details are hard to follow. Fig.1 is particularly confusing, and I have to read line-by-line in the methods part in a combination of Fig. 1 to comprehend what exactly the authors meant. I suggest substantially improving Fig.1 and the figure caption underneath. Thank you for the suggestion. We amended Figure 1 and added a few statements in the caption to further illustrate the experimental design. Figure 1. Schematic illustration of experimental trials. The search (70% of trials) and probe trials (30% of trials) were presented to the participants randomly. In the search trials (top panel), participants were asked to report whether a dot inside the search target (diamond) was presented on the left or right. The four stimuli had the same color in half of the trials (singleton absent), whereas one of the four stimuli had a different color (singleton present) in the other half of the trials. The singleton was never the search target; thus, it functioned as a distractor. The color of the target stimulus was fixed (Experiments 1 and 3) or random (Experiment 2); the color of the distractor (singleton) was also fixed (Experiments 1 and 2) or random (Experiment 3). Notably, the task was just to identify the location of a dot inside the target (diamond), and the assigned color was irrelevant to the task. We examined whether or not the singleton-presence benefit can be obtained even when the target or distractor color was changed on a trial-by-trial basis. In the probe trials (bottom panel), the task was to detect a probe-target letter (A or B). In Experiment 1, in half of the trials, the target color (e.g., green) in the visual search was presented, while in the other half, the distractor color (e.g., red: a singleton color in the visual search) was presented. The probe-target letter appeared in a critical color (either of the target or distractor colors in search trials) or in a neutral color (a color that had not been presented in search trials). The probe presentation in the target or distractor feature that was presented in the search trials enabled the assessment of the target enhancement and distractor suppression separately. In Experiments 2 and 3, either the distractor or target color appeared in half of the probe trials, respectively, while all items were presented in neutral colors in the other half of the trials. This process enabled the calculation of the distractor suppression and target enhancement effects in Experiments 2 and 3, respectively. Reaction time is usually highly skewed distributed. It seems to me that the authors performed stats on the raw RT values. I suggest trying to perform stats on log-transformed RT. That should better fit the intentions of t-tests and ANOVAs. Thank you for the suggestion. We used the same analysis using log-transformed RT data and obtained the same results. We added these analyses in Supplementary Analysis. Log-transformed RT was used for the analysis. Visual Search Experiment 1 RTs were faster for singleton-present trials than in singleton-absent trials (t (45) = 2.13, p = .039, d = 0.31). Experiment 2 No RT differences were observed between singleton-present and -absent trials (t (47) = 0.37, p = .716, d = 0.05). Experiment 3 RTs were faster for singleton-present trials than in singleton-absent trials (t (46) = 5.24, p < .001, d = 0.76). Probe Task Experiment 1 No significant main effect of critical color and probe-target location on RT (F (1, 45) = 1.23, p = .274, = .03; F (1, 45) = 0.74, p = .391, = .02) nor any significant interaction (F (1, 45) = 2.20, p = .144, = .05) was found. Experiment 2 No difference was observed in the probe location for the suppression effect (t (47) = 1.07, p = .290, d = 0.16). Experiment 3 No difference was observed in the probe location for the enhancement effect (t (46) = 0.42, p = .674, d = 0.06). It remains unclear to me the rationales behind Experiments 2 and 3. The authors mentioned that “We hypothesized that if two attentional guidance elements, enhancement and suppression, competed for common processing resources, the magnitude of the effect in Experiment 1 would be smaller than those in Experiments 2 and 3 because Experiment 1 required both of these attentional controls.” This argument is unclear to me. If either the target or distractor color is randomly selected, the advantage of color expectation should be diminished and that would lead to a smaller enhancement or suppression effect. Can the authors elaborate on the rationales and the predictions? Although we hypothesized that the target enhancement and distractor suppression will become larger in Experiments 2 and 3, a possibility indeed exists that these effects will become relatively smaller due to the smaller advantage of color expectation, as pointed out by the reviewer. In fact, we did not find larger target enhancement and distractor suppression in Experiments 2 and 3, which is partially due to the weaker color expectation effect. We included this aspect in the discussion. Although we hypothesized that the target enhancement and distractor suppression would increase in Experiments 2 and 3, a possibility exists that these effects would relatively decrease due to the smaller advantage of color expectation. The reason is that the target and distractor colors were fixed in Experiment 1, whereas the target or distractor color was randomized in Experiments 2 and 3. In fact, we were unable to identify large target enhancement and distractor suppression effects in Experiments 2 and 3, which is partially due to the weaker color expectation effect. “This singleton-presence benefit fits with earlier findings [8,10], allowing us to test target enhancement and distractor suppression for probe trials.” Here the numbered-style references should be replaced by inline-style references. Thank you for pointing out this aspect. We replaced the references as follows: This singleton-presence benefit fits with earlier findings (Chang & Egeth, 2019; Gaspelin et al., 2015), allowing us to test target enhancement and distractor suppression for probe trials. The figure captions should be improved. For example, in Fig. 2, does the black horizontal line in the box plot represent the mean or median of the group? What are the definitions of the upper and lower edges of the boxes and of the range of the whiskers? Thank you for the suggestion. We added the required information in the caption. For example, the caption for Figure 2 is presented as follows: Figure 2. The mean reaction times (RTs) in the visual search task as a function of the singleton condition. Each dot represents the mean RT per participant. The RT was shorter in singleton-present trials than in singleton-absent trials for Experiments 1 and 3. The box represents the interquartile range, which contains 50% of the values (median with midline), and the bottom and top edges of the whiskers represent the 1.5 × interquartile range. Figures were drawn using the “raincloudplots” package in R (Allen et al., 2021)."
}
]
}
] | 1
|
https://f1000research.com/articles/11-232
|
https://f1000research.com/articles/11-1097/v1
|
26 Sep 22
|
{
"type": "Genome Note",
"title": "The complete mitochondrial genome sequence of Chimarrogale leander (Insectivora: Soricidae)",
"authors": [
"Yongxin Miao",
"Yidi Li",
"Yaqing Mei",
"Cheng Chen",
"Liling Sun",
"Baowei Zhang",
"Hui Wang",
"Yongxin Miao",
"Yidi Li",
"Yaqing Mei",
"Cheng Chen",
"Liling Sun",
"Hui Wang"
],
"abstract": "Background: Chimarrogale leander is a species of the family Soricidae and is mainly distributed in southern China. Methods: Here, a complete mitochondrial genome for C. leander was assembled via high-throughput sequencing technology. Results The results showed that the complete mitogenome of C. leander is 17,357 bp and includes 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%. Through the phylogenetic analysis of complete mitochondrial genome, it is found that C. leander has a close genetic relationship with Nectogale elegans. Conclusions: The new mitogenome will hopefully prove useful for systematic analyses of genus Chimarrogale.",
"keywords": [
"Chimarrogale leander",
"mitochondrial genome",
"phylogenetic analysis"
],
"content": "Introduction\n\nThe Asiatic water shrew, Chimarrogale leander, belongs to the family Soricidae and is mainly distributed in southern China (Thomas 1902). They have large bodies, long noses, small eyes, well-developed ears, and hairy fingers, feet, and toes. They inhabit by mountain streams, swimming or diving in water (Wang 1986). In order to further understand its mitochondrial genome characteristics, phylogeny and evolutionary characteristics, this paper carried out its genomic analysis and characterized it.\n\n\nMethods\n\nThis experiment complies with Anhui University GB/T35892-2018 Guidelines for Ethical Review of Laboratory Animal Welfare. The approval committee name is Experimental Animal Ethics and Management Committee of Anhui University the approval number is IACUC (AHU)-2022-044, and approval date is April 13, 2022. The ethical approval included permission for us to take and sacrifice the animal.\n\nA specimen of C. leander was collected from Yaoluoping Nature Reserve (N: 30°57′57.06″, E: 116°04′04.96″) in the Dabie Mountains, Anhui, China and stored in Anhui University Museum (contact person and email: Baowei Zhang, zhangbw@ahu.edu.cn) under the voucher number AHU2010YLP01. We compared the morphological characteristics of the specimens and found that they were similar to C. leander (Wang 1986). Then DNA was extracted and PCR reaction was carried out. Blast comparison was carried out to ensure that this species belongs to C. leander. The genomic DNA extraction, library preparation and Illumina sequencing were done by Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China).\n\nWe sequenced the data using the Illumina HiSeq™ 2000 platform, pruned the sequencing results using Trimmomatic software (RRID:SCR_011848) (Bolger et al., 2014), and assembled them using the MITObim program (RRID:SCR_015056) (Hahn et al., 2013). The annotation was performed using MITOS WebServer (Bernt et al., 2013) for the entire mitogenome of C. leander, and manually adjusted it according to the published mitogenomes of the Soricidae family and submitted the complete sequence of mitochondrial gene to GenBank (Accession number ON646617).\n\nTo better understand the phylogenetic position of C. leander within Soricidae, we constructed a phylogenetic tree by using maximum likelihood (ML) method implemented in IQ-TREE v2.1.2 (RRID:SCR_017254) (Minh et al., 2020), which was based on 13 complete mitochondrial genome sequences of Soricidae. There was another species (Mogera wogura) included as the outgroup (GenBank accession numbers are shown in Figure 1).\n\nML analysis shows startup support values sequentially on nodes. ML, maximum likelihood.\n\n\nResults\n\nThe complete mitochondrial DNA (mtDNA) sequence of C. leander is a circular molecule, 17,357 bp in length and included 13 protein-coding genes, two rRNAs genes, 22 tRNAs genes and a D-loop region. The overall nucleotide composition is A: 33.1%, T: 31.5%, C: 22.5% and G: 12.9%, with a total A + T content of 64.6%. The mitogenome of C. leander shows the typical gene order observed in Soricidae mitogenomes (Li et al., 2016; Qing et al., 2019; Wang et al., 2016). Within 37 mitochondrial genes, the ND6 gene and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro) were encoded on the light strand and all other genes were encoded by the H-strand. Most mitochondrial protein-coding genes, have ATG as its start codon, whereas ND2 (1,042 bp), ND3 (348 bp) and ND5 (1,820 bp) begin with ATA. Eight genes use TAA as stop codons, whereas the ND1 (955 bp) and ND2 end with TAG, and Cyt b (1,140 bp) ends with AGA. COX3 (785 bp) uses TA, and ND4 (1378 bp) uses T as an incomplete stop codon, which are presumably completed as TAA by posttranscriptional polyadenylation (Ojala et al., 1981). In all 13 protein-coding genes, the shortest gene is ATP8 (204 bp) and the longest gene is control region (D-loop) (1,864 bp). The two rRNA genes were 968 bp (rrnS) and 1,564 bp (rrnL) in length, respectively.\n\nThe phylogenetic results show that C. leander is closely related to Nectogale elegans and these are sister to two species of Chodsigoa (Huang et al., 2014; Pu et al., 2019; Qing et al., 2019). Overall, the relationships inferred agree with those of Dubey et al. (2007). Mitochondrial DNA is a powerful tool for studying the evolution of the genome, which can help us speculate about evolution in ancient times (Boore 1999). This study provides useful data for further study of population evolution and phylogenetic relationships.\n\n\nData availability\n\nGenBank: Chimarrogale leander mitochondrion, complete genome. Accession number ON646617; https://www.ncbi.nlm.nih.gov/nuccore/ON646617.\n\nBioProject: Chimarrogale leander. Accession number PRJNA832022; https://identifiers.org/NCBI/bioproject:PRJNA832022.\n\nSRA: Chimarrogale leander. Accession number SRR19348878; https://identifiers.org/insdc.sra:SRR19348878.\n\nBioSample: Animal sample from Chimarrogale leander. Accession number SAMN27771023; https://identifiers.org/biosample:SAMN27771023.",
"appendix": "References\n\nBernt M, Donath A, Jühling F, et al.: MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 2013; 69(2): 313–319. Publisher Full Text\n\nBolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–2120. PubMed Abstract | Publisher Full Text\n\nBoore JL: Animal mitochondrial genomes. Nucleic Acids Res. 1999; 27(8): 1767–1780. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDubey S, Salamin N, Ohdachi SD, et al.: Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Mol. Phylogenet. Evol. 2007; 44(1): 126–137. PubMed Abstract | Publisher Full Text\n\nHahn C, Bachmann L, Chevreux B: Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucleic Acids Res. 2013; 41(13): e129. PubMed Abstract | Publisher Full Text\n\nHuang T, Yan C, Tan Z, et al.: Complete mitochondrial genome sequence of Nectogale elegans. Mitochondrial DNA Part B. 2014; 25(4): 253–254. PubMed Abstract | Publisher Full Text\n\nLi Q, Wang Q, Chen G, et al.: The complete mitogenome of Chinese Mole Shrew, Anourosorex squamipes (Soricidae). Mitochondrial DNA Part A. 2016; 27(1): 553–554. PubMed Abstract | Publisher Full Text\n\nMinh BQ, Schmidt HA, Chernomor O, et al.: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020; 37(5): 1530–1534. PubMed Abstract | Publisher Full Text\n\nOjala D, Montoya J, Attardi G: tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981; 290(5806): 470–474. PubMed Abstract | Publisher Full Text\n\nPu Y, Tan X, Wei H, et al.: The complete mitogenome of Smith’s shrew (Chodsigoa smithii). Mitochondrial DNA Part B. 2019; 4(2): 2553–2554. Publisher Full Text\n\nQing J, Liu H, Wei H, et al.: The complete mitochondrial genome of pygmy red-toothed shrew (Chodsigoa parva). Mitochondrial DNA Part B. 2019; 4(2): 2549–2550. PubMed Abstract | Publisher Full Text\n\nThomas O: XXIV-On two new mammals from China. J. Nat. Hist. 1902; 10(56): 163–166. Publisher Full Text\n\nWang Q, Fu C, Chen S, et al.: The complete mitogenome of Asiatic Short-tailed Shrew Blarinella quadraticauda (Soricidae). Mitochondrial DNA Part A. 2016; 27(1): 282–283. PubMed Abstract | Publisher Full Text\n\nWang QS: The Zoogeographical Division of Anhui Province. J. Anhui Agric. Univ. (Natural Science Edition). 1986. (in Chinese with English abstract)."
}
|
[
{
"id": "152050",
"date": "17 Oct 2022",
"name": "Chaochao Hu",
"expertise": [
"Reviewer Expertise Genomic resources."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript entitled “The complete mitochondrial genome sequence of Chimarrogale leander (Insectivora: Soricidae)” provided valuable data for further research. Miao et al. sequenced the complete mitogenome of C. leander, and analyzed the phylogeny of Soricidae family. I would like to thank the authors for the invested effort in generating new genomic resources, which is always a welcome thing to see and crucial to facilitate future research in various fields such as phylogenetics, population, conservation, functional genetics etc. I think authors had the ability to produce a nicer to read manuscript. Here are a few questions, and I hope my review gives justice to what this opus deserves:\nAbstract: I suggest adding the English name before the species name appears for the first time.\n\nIntroduction: needs to be slightly expanded to introduce the subject and the need for this research. Literature references should try to choose the scientific study in recent years, sufficient field background/context provided.\nThe methods should be specified and described in more detail. The method part lacks necessary data description, such as the total sequencing volume of each sample, the average sequencing depth of assembled mitochondria, etc. Such as:\n“Then DNA was extracted and PCR reaction” what kind of gene, and what condition was performed?\n\n“Blast comparison was carried out to ensure that this species belongs to C. leander.” Pay attention on the “belongs”.\n\nHow many raw reads were generated? After removing low quality sequences, how many clean Raw Data were used?\n\nThere were so many software used, please indicated the parameters for each analysis.\n\n“manually adjusted it according to the published mitogenomes of the Soricidae family”, please detail the species name and GenBank accession number. Phylogenetic relationship reconstruction usually does not require control regions.\n\n“constructed a phylogenetic tree by using maximum likelihood”, the method part lacks the description of sequence alignment.\n\n“another species”?\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? No\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes",
"responses": []
},
{
"id": "206019",
"date": "24 Oct 2023",
"name": "Adrian Marciszak",
"expertise": [
"Reviewer Expertise Zoology",
"Paleontology",
"ancient DNA"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is short, but well written and organised. All references are included, and database as well as present data well supported obtained results. Methods used by authors clearly confirmed that mitochondrial DNA is a powerful tool for studying the evolution of the genome.\nCan be indexed in the recent form.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1097
|
https://f1000research.com/articles/11-367/v1
|
30 Mar 22
|
{
"type": "Research Article",
"title": "Awareness of asthma and its management in primary school teachers in Baghdad, Iraq",
"authors": [
"Muhannad R. M. Salih",
"Arwa Y. Abd",
"Hayder Adnan Fawzi",
"Arwa Y. Abd",
"Hayder Adnan Fawzi"
],
"abstract": "Background: Asthma is a major global health issue characterized by chronic airway inflammation. It is linked to a high disease burden and disproportionately high healthcare utilization in severe, uncontrolled cases compared to non-severe asthma. We aimed to conduct this survey among primary school teachers in Baghdad, Iraq, to assess their level of knowledge about asthma and confidence in managing school children with asthma. Methods: This was a prospective cross-sectional study conducted in the Karkh and Rusafa areas of Baghdad. The study adopted a questionnaire for assessing the asthma knowledge and confidence scores regarding the management of asthmatic children. This questionnaire contained 29-multiple true-false questions based on different aspects, including facts about asthma and the management of asthma by teachers. Results: The questionnaire for testing teachers’ knowledge of asthma and confidence scores regarding the management of asthmatic children was distributed to 150 teachers. 103 (68%) teachers completed the questionnaire fully. Approximately 71% of teachers answered the question ‘What are the three main symptoms of asthma?’ correctly i.e., answering either one symptom (35.9%) or two symptoms (35.9%) correctly. A relatively smaller number of teachers (16.5%) mentioned all three symptoms correctly. Across the 29-multiple true-false questions, more than 75% of teachers answered 11 questions correctly, 50-74% of teachers answered the rest of eight questions appropriately, and <50% of teachers answered the remaining 10 questions properly. The statistical evaluation indicated that the mean total knowledge score about asthma for all the teachers was 20.27 ± 2.97 and the mean total confidence score regarding the management of asthmatic children was 72.44 ± 13.61. Conclusions: This study suggests that teachers from the schools in Karkh and Rusafa areas of Baghdad appear to be self-confident in their ability and knowledge to help and manage children with asthma.",
"keywords": [
"primary school",
"teachers",
"knowledge",
"confidence",
"asthma",
"management",
"children"
],
"content": "Introduction\n\nAsthma is one of the most common chronic diseases in children globally.1 During the last 40 years, there has been a significant rise in the prevalence, morbidity, and mortality related to asthma in children worldwide.2 As per the World Health Organization (WHO), there are more than 339 million asthmatic cases globally.3 The global death rate in asthmatic children is 0 to 0.7 per 100,000 people and asthma is listed in the top 20 conditions globally for disability-adjusted life years in children.2 The incidence of asthma in Baghdad, Iraq, is closely 22%.4 In a cross-sectional study carried out between October 2000 and June 2002 conducted by Al-Thamiri D et al., in Baghdad, Iraq, asthma was diagnosed in approximately 82% of primary-school children who had experienced wheezing and difficulty breathing in the last 12 months at the time of the administration of the questionnaire.5\n\nIt is an important causative factor for school absenteeism in children and decreased involvement of children in school activities.6,7 Meng YY et al.,6 reported that students with frequent asthmatic symptoms and those who were on asthma medications had increased likelihood of missing school. As per a review by Elif Isik RN et al.,7 uncontrollable asthma leads to a significant rise in visits to an emergency room, hospitalization, and school absenteeism that eventually contributes to emotional and financial problems for parents, and decreased school performance in children. School activities including extracurricular activities are restricted in asthmatic children, and uncontrollable asthma affects social interactions and self-confidence in children.\n\nMost of the schools in Baghdad do not have full-time nurses to manage children with asthma. These circumstances lead to imparting the responsibility of managing school children with asthma onto the non-medical staff or schoolteachers. Various studies have reported that schoolteachers have inadequate awareness about asthma and the management of asthma among school children.8–11 Therefore, it is recommended to train schoolteachers on specific aspects of asthma and its management for school children. The study aims to assess teachers’ current knowledge about asthma and to infer the need for teacher training around asthma and asthma management in school children. Therefore, we aimed to conduct this survey among primary school teachers in Baghdad, Iraq, to assess their level of knowledge about asthma and confidence in managing school children with asthma.\n\n\nMethods\n\nThe study has been approved by the Ethical Committee of the Ministry of Higher Education and Scientific Research Al-Rasheed University College, Department of Pharmacy (approval number 121) on the 3rd September, 2019. There was no established ethical committee for controlling such research purposes at the governmental authority in charge of primary schools in Iraq.\n\nWritten informed consent was obtained from all the participants. Oral consent was taken from the principal of each school before distributing the questionnaire to the teachers (since the principal of each school did not participate in the actual study, and only the ethical committee was responsible for approving the protocol, the approval of the principal was a courtesy from the research team to inform the principal about the study).\n\nParticipant recruitment\n\nThis was a prospective cross-sectional study. A sample of eight primary schools in both the parts of Baghdad (Karkh and Rusafa) was targeted during this investigation. All the teachers (excluding support staff, i.e., non-teaching staff) were invited to participate in the survey. The Ministry of Education provided us with a list of the primary schools in Baghdad, including urban and rural (all school must teach primary level students), private and public schools, and education level of the teachers. We randomly selected schools based on this list (we used the excel program to generate random model for selecting the school). The teachers received letters; the letters outlined the study’s purpose as well as the instructions for filling out the questionnaire that was attached. Before the teachers administered the questionnaire we went to the schools and explained the questions and directives in further detail. The selected schools must have students with asthma, the schools must be coeducational (both girls and boys), and the teachers must have at least five years’ experience in the education sector to be included in the study.\n\nThe study was conducted during the period of 1st October–30th November 2019. The aim was the assessment of asthma knowledge of schoolteachers and their confidence level in the management of children with asthma.\n\nThe study adopted the amended Newcastle asthma knowledge questionnaire from the Al-Motlaq and Sellick (2013)20 study, who amended the questionnaire developed by Fitzclarence and Henry (1990), from the University of Newcastle, New South Wales, Australia.12 This amendment changed the format of the questionnaire to true-false and replaces four of the questions; in total the questionnaire contained 29 multiple true-false questions based on different aspects, including facts about asthma and the management of asthma (see examples one and two below), and one open-ended question on the three symptoms of asthma resulting in 30 questions in total (20-22).\n\nTranslation and cross-cultural adaptation\n\nAl-Motlaq and Sellick’s score was translated and cross-culturally adapted in accordance with the ‘Guidelines for the Process of Cross-Cultural Adaptation of Self-Report Measures’.24 Two clinical pharmacists (Muhannad Salih and Arwa Abd) who are native Arabic speakers with outstanding English language skills translated the scale into Arabic. The original short form of the scale, as well as the two translations, were evaluated and discussed with a third clinical pharmacist (Hayder Fawzi) in order to fix any conceptual flaws or conflicts and create one Arabic version of the scale. The scale was then re-translated into English by two native English speakers with good Arabic language skills who were unaware of the original version of the questionnaire or the study’s goal.\n\nInterpretation of the questionnaire\n\nTwo of the 29 true-false questions regarding ‘knowledge’ of asthma are set out as follows in the examples: 1. ‘More than one in 10 children will have asthma at some time during their childhood’, and 2. ‘Children with frequent asthma should have preventive drugs’. The open-ended question on three symptoms of asthma is as follows: ‘What are the three main symptoms of asthma?’.\n\nEach question received a score ‘1’ if a correct answer is given for each of the 29 true/false questions, and the final open-ended question received a score of ‘1’ for each correctly identified symptom of asthma with a maximum of three points. Incorrect answers were given a score of ‘0’ for all 30 questions. This means the range of scores on ‘knowledge’ is 0-32 (0=no correct responses or symptoms identified; 32=all correct responses and three correct symptoms identified in the open-ended final question). The asthma knowledge questionnaire has been proven reliable in the previous studies prior to minor edits.12–15 Total asthma knowledge score was estimated based on the accurate responses given to each question by teachers with a maximum test score of 32, additionally we divided the answer into three groups based on percentage of answered correctly: more than 75%, between 50–74%, and less than 50%.21\n\nA questionnaire for confidence scores previously developed by Al-Motlaq and Sellick (2013)20 was also used in this study. The confidence scores of teachers regarding the management of asthmatic children were assessed by a questionnaire22 comprising nine questions as cited in Table 2, for example, a couple of questions are as follows: 1. ‘Keeping asthma from getting worse when the student starts to wheeze or cough’ 2. ‘Giving the appropriate medications to the student during an asthma attack’.\n\nNext, the participating teachers were questioned to rate their confidence level on each element/question by putting an ‘X’ spot on a visual analogue scale of 10 centimetres that ranged from one (means not confident at all) to 10 (means fully confident).20,23\n\nData collection and follow-up\n\nAs shown in Figure 1, teachers from eight schools participated in the study. The questionnaire was distributed to 150 teachers in total, the distribution and collection of the questionnaire was done in person by the investigators. 103 teachers (68%) completed the questionnaire in full, the questionnaires were distributed by the authors of this study by direct personal interview to ensure complete understanding of the content of the questionnaire by the teachers. The data were later entered to excel sheets to be sorted later, if there was any missing data the participant was excluded from the final analysis.\n\nAfter the data collection for this survey, the statistical analysis was done by using IBM SPSS Statistics (IBM Corp. Version 25.0. Armonk, N.Y., USA). The statistics helped to demonstrate the demographics. The categorical variables were denoted with percentages and frequencies. The continuous variables were denoted with the mean ± standard deviation, independent t-test and one way ANOVA were used in this study.\n\n\nResults\n\nThe socio-demographic characteristics of teachers have been demonstrated in Table 1. Teachers from both private (≈58%) and public (≈42%) schools with ≈50% of schools from both Karkh and Rusafa areas in Baghdad participating in the study (in public school the students fees are paid by the government, while private school the fees are paid by the parents). Participants were primarily female (83%), and reported having a diploma, a bachelor’s, or a master’s degree. A small percentage had diagnosed asthma (10.7%) or a family history of asthma (22.3%). A majority of respondents were over the age of 30 (65%).\n\nTeachers’ total knowledge score and the percentage of accurate answers on the asthma knowledge questionnaire are shown in Table 2. 71% of teachers answered the question ‘What are the three main symptoms of asthma?’ with either one symptom (35.9%) or two symptoms (35.9%) identified correctly. A relatively smaller number of teachers (16.5%) mentioned all the three symptoms correctly.\n\nMore than 75% of teachers answered the remaining 11 questions correctly (questions: 2, 3, 4, 7, 11, 17, 25, 26, 28, 29, and 3) and a few of those questions are cited as follows: ‘More than one in 10 children will have asthma at some time during their childhood’, ‘children with asthma have abnormally sensitive air passages in their lung’, and ‘if one child in a family has asthma, then all his/her brothers and sisters are almost certain to have asthma as well’, as shown in Table 2.\n\nMoreover, 50–74% of teachers answered remaining eight questions correctly (questions: 5, 6, 8, 10, 13, 14, 18, and 22) and some of those questions are mentioned as follows: ‘Most children with asthma have an increase in mucus production when they drink cow’s milk’, ‘influenza is a common cause or trigger of an asthma attack’, and ‘during an attack of asthma, wheezing may occur due to swelling in the lining of the air passage in the lungs’, etc. as shown in Table 2.\n\nFurthermore, less than 50% teachers answered the remaining 10 questions correctly (questions: 9, 12, 15, 16, 19, 20, 21, 23, 24, and 27) and few of those questions are cited as follows: ‘Asthma damages the heart’, ‘antibiotics are an important part of treatment for most children with asthma’, and ‘if a person dies from an asthma attack, this usually means that the final attack must have begun so quickly that there was no time to start any treatment’, etc. as shown in Table 2.\n\nThe mean total knowledge score for all the teachers was 20.27 (SD=2.97). There were no significant differences in asthma-related knowledge scores of teachers based on the types and areas of the schools, age, gender, teachers with an asthma diagnosis, family history of asthma, and academic achievements.\n\nAs shown in Table 3, teacher’s confidence scores in managing children with asthma ranged from 55.82 to 86.60 for various parameters and a few of those are cited as follows as examples: ‘Taking a student on a school camp or excursion’, ‘helping a student to use their inhaler during an asthma attack’, and ‘calming a student when they have the difficulty in breathing’. The teacher’s confidence score was the highest (86.6) for the parameter ‘helping a student to use their inhaler during an asthma attack’. The overall confidence score in managing children with asthma was 81.75. The mean total confidence score considering all the parameters was 72.44±13.61.\n\nAnalysis for the association between the total confidence score and sociodemographic characteristics of primary school teachers was performed and results are shown in Table 4. Female teachers showed a significantly higher mean total confidence score (p=0.02) than male teachers. Teachers who had a family history of asthma showed a significantly higher mean total confidence score (p=0.03) than those without such history.\n\na Independent Sample T-Test.\n\nb ANOVA.\n\nTeachers ≥50 years of age demonstrated a significantly higher mean total confidence score (p=0.003) than other age groups. On the contrary, no significant association was observed between the total knowledge score and sociodemographic characteristics of teachers (Table 5). Further analysis showed no significant correlation between the total confidence scores and total knowledge scores among primary school teachers (r=0.02, p=0.82).\n\n\nDiscussion\n\nSchool teachers have a responsibility to take care of children when they are at school, thus they need to be knowledgeable about asthma and to be confident about helping children suffering from asthma. School teachers’ knowledge about asthma may make a difference in the health condition of asthmatic children. Plenty of studies indicate that schoolteachers have limited knowledge about asthma.16–18\n\nIn the present study, the mean total knowledge score [20.27 (SD = 2.97)] about asthma for all the teachers appears to be relatively good in comparison with other studies. Though the teachers’ knowledge score appears to be relatively better than that which was observed in a study conducted by Gibson et al.19 (knowledge score = 14.90)’ the study was conducted in New South Wales, Australia and included 1,104 teachers and 4,161 students in 1995. But it was less than that (26.3) observed in a study conducted by Mohammad Al-Motlaq et al.,20 in Australia. Thus, it indicates key gaps in the knowledge about asthma in the schoolteachers involved in the present study.19,20\n\nThe current study indicates that teachers’ knowledge scores about asthma are not related to different variables viz. types and areas of the schools, age, gender, teachers with an asthma diagnosis, family history of asthma, and academic achievements. It indicates that these variables did not play a role as confounding variables.\n\nIn the current study, the overall confidence score was 81.75 in managing children with asthma. 65% of teachers were in the age group of above 30 years of age. Their maturity levels and experience may have contributed to a higher confidence score in the management of children with asthma. A finding from the current study also demonstrates a significantly higher mean total confidence score in teachers who had a family history of asthma, which is similar to that observed in the study conducted by Al-Motlaq et al.20 However, unlike the study by Al-Motlaq et al., female teachers showed a significantly higher mean total confidence score than male teachers in the present study.20 Thus, there could be some other factors that may have contributed to a significantly higher mean total confidence score in female teachers.\n\nThe mean total confidence score in managing children with asthma was 72.44 (SD 13.61) in the present study appears to be slightly greater than that observed in a study conducted by Mohammad Al-Motlaq et al., in the Gippsland region of Victoria in Australia.20 Though the mean confidence score with an item ‘your overall confidence in managing children with asthma’ was 81.75 (SD 22.81), an approximate score of ‘55’ with other parameters must have contributed in causing the mean total confidence score in the current study. Responses to these lower score parameters suggest areas for further improvement in the total confidence score of schoolteachers through education and training sessions.\n\nIt is encouraging to know that the knowledge related to asthma and confidence of teachers in the management of children with asthma were relatively satisfactory in the present study considering the results from other studies.19,20 However, training should be recommended to improve teachers’ knowledge score and such training may also help to take teachers’ confidence in managing children with asthma to the next level.\n\nThe limitations of this study are as mentioned previously; the study adopted an asthma knowledge questionnaire amended by Al-Motlaq and Sellick (2013) and was originally developed by Fitzclarence et al.,12 from the University of Newcastle, New South Wales, Australia with a translation into Arabic as outlined in the methods section. However, the asthma knowledge questionnaire was not pre-tested considering that the original version was validated in the Fitzclarence et al.,12 study and there were only minor amendments involved.21 However, the amended questionnaire used in this study from Al-Motlaq and Sellick (2013) was not validated in their study. In addition, the sample size for the study was not calculated so 150 teachers were considered based on convenient sampling.\n\n\nConclusions\n\nThis study suggests that teachers from schools in Karkh and Rusafa areas of Baghdad appear to be reasonably self-confident in helping to manage children with asthma. However, training may be recommended to improve teachers’ knowledge score and such training may help to take teachers’ confidence in the management of children with asthma to the next level.\n\n\nData availability\n\nZenodo: The modified Newcastle Asthma Knowledge Questionnaire. https://doi.org/10.5281/zenodo.5837458.21\n\nThis project contains the following extended data:\n\n• Arabic translation.pdf. (The amended Newcastle Asthma Knowledge Questionnaire translated into Arabic for this study).\n\n• Mohammad Al-Motlaq.png. (Amended Newcastle Asthma knowledge questionnaire from Al-Motlaq and Sellick (2013) in original English).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo. Confidence score (Arabic and English version). https://doi.org/10.5281/zenodo.6331672.22\n\nThis project contains the following extended data:\n\n• Confidence scores questionnaire – Ar (Arabic questionnaire in PDF and Word format).\n\n• Confidence scores questionnaire – EN (English questionnaire in PDF and Word format).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: SRQR checklist for ‘Awareness of Asthma and Its Management in Primary School Teachers of Baghdad, Iraq’. https://doi.org/10.5281/zenodo.5803507.23\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe acknowledge my colleagues Mohammed Khaleel Lafta, and Israa Ali Jawad for their appreciated effort in supporting this study during the data collection process.\n\n\nReferences\n\nAsher I, Pearce N: Global burden of asthma among children. Int. J. Tuberc. Lung Dis. 2014; 18(11): 1269–1278. Publisher Full Text\n\nSerebrisky D, Wiznia A: Pediatric asthma: a global epidemic. Ann. Glob. Health. 2019; 85(1): 1–6.\n\nWorld Health Organization (WHO): Chronic respiratory diseases: Asthma. Accessed on 8th June 2020. Reference Source\n\nMirzaei M, Karimi M, Beheshti S, et al.: Prevalence of asthma among middle eastern children: a systematic review. Med. J. Islam Repub. Iran. 2017; 31: 43–52.\n\nAl Thamiri D, Al Kubaisy W, Ali SH: Asthma prevalence and severity among primary-school children in Baghdad. East Mediterr. Health J. 2005; 11: 79–86.\n\nMeng YY, Babey SH, Wolstein J: Asthma-related school absenteeism and school concentration of low-income students in California. Prev. Chronic Dis. 2012; 9: E98. PubMed Abstract | Publisher Full Text\n\nIsik E, Isik IS: Students with Asthma and its Impacts. NASN Sch. Nurse. 2017; 32: 212–216. PubMed Abstract | Publisher Full Text\n\nMadsen LP, Storm K, Johansen A: Danish primary schoolteachers’ knowledge about asthma: results of a questionnaire. Acta Paediatr. 1992; 81(5): 413–416. PubMed Abstract | Publisher Full Text\n\nHussey J, Cahill A, Henry D, et al.: National school teachers’ knowledge of asthma and its management. Ir. J. Med. Sci. 1999; 168(3): 174–179. PubMed Abstract | Publisher Full Text\n\nBrookes JU, Jones KE: Schoolteachers’ perceptions and knowledge of asthma in primary schoolchildren. Br. J. Gen. Pract. 1992; 42(365): 504–507. PubMed Abstract\n\nBevis M, Taylor B: What do school teachers know about asthma. Arch. Dis. Child. 1990; 65(6): 622–625. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFitzclarence CA, Henry RL: Validation of an asthma knowledge questionnaire. J. Paediatr. Child Health. 1990; 26(4): 200–204. Publisher Full Text\n\nFinn A, Richard S: Asthma knowledge attitudes and quality of life in adolescents. Arch. Dis. Child. 1996; 74(4): 367. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAllen RM, Abdulwadud OA, Jones MP, et al.: A reliable and valid asthma general knowledge questionnaire useful in the training of asthma educators. Patient Educ. Couns. 2000; 39(2-3): 237–242. PubMed Abstract | Publisher Full Text\n\nHazell J, Henry RL, Francis JL: Improvement in asthma management practices in child care services: an evaluation of a staff education program. Health Promot. J. Austr. 2006; 17(1): 21–26. Publisher Full Text\n\nCanitez Y, Cekic S, Celik U, et al.: Health-care conditions in elementary schools and teachers’ knowledge of childhood asthma. Paediatr. Int. Child Health. 2016; 36(1): 64–71. PubMed Abstract | Publisher Full Text\n\nBruzzese JM, Unikel LH, Evans D, et al.: Asthma knowledge and asthma management behavior in urban elementary school teachers. J. Asthma. 2010; 47(2): 185–191. PubMed Abstract | Publisher Full Text\n\nGetch YQ, Neuharth-Pritchett S: Teacher characteristics and knowledge of asthma. Public Health Nurs. 2009; 26(2): 124–133. PubMed Abstract | Publisher Full Text\n\nGibson PG, Henry RL, Vimpani GV, et al.: Asthma knowledge, attitudes, and quality of life in adolescents. Arch. Dis. Child. 1995; 73(4): 321–326. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAl-Motlaq MA, Sellick K: Primary school teachers’ asthma knowledge and confidence in managing children with asthma. Health Educ. 2013; 31(2): 53–58.\n\nAl-Motlaq M, Sellick K: The modified Newcastle Asthma Knowledge Questionnaire. Zenodo. 2021. Publisher Full Text\n\nAl-Motlaq M, Sellick K: Confidence score (Arabic and English version).2021.Publisher Full Text\n\nHayder adnan fawzi: SRQR checklist. Zenodo. 2021. Publisher Full Text\n\nAlzhrani M, Alzahrani H, Alshehri YS: Arabic Version of the Short Anterior Cruciate Ligament-Return to Sport After Injury Scale: Translation, Cross-cultural Adaptation, and Validation. Orthop. J. Sports Med. 2022; 10(1): 23259671211066509. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "129353",
"date": "04 May 2022",
"name": "Ramadan Elkalmi",
"expertise": [
"Reviewer Expertise Clinical pharmacy practic"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI found it interesting to review this article on \"Awareness of asthma and its management in primary school teachers in Baghdad, Iraq\"\nAbstract Methods: the authors need to improve the methods in a way to give clear views about the methods, i.e. some of the methods' issues have been presented in the results, which could affect the scholarly of the manuscript. In general, rearrangement of the abstract, paragraphs is advised.\nIntroduction: The approach of leading your reader from the Awareness of Asthma and its management in primary school teachers to the goal of this paper was good.\nHowever, Construction and rearrangement of the last paragraph are recommended as;\n\"Various studies have reported that schoolteachers have inadequate awareness about Asthma and asthma management among school children.8–11 Therefore, it is recommended to train schoolteachers on specific aspects of Asthma and its management for school children. Therefore, we aimed to conduct this survey among primary school teachers in Baghdad, Iraq, to assess their knowledge about Asthma and confidence in managing school children with Asthma. The study aims to assess teachers' current knowledge about Asthma and to infer the need for teacher training around Asthma and asthma management in schoolchildren.\"\nMethods:\nThis section is well written, but you still need to arrange the sections to give an overview of the study design clearly, to ease the reader's follow-up and understanding of the steps of the study execution and avoid any ambiguity.\nDiscussion: Although the discussion section is well written, the summary of the article was good, and the comparisons were relatively coherent.\nTechnically: There is a clear and significant influence of the study of Mohammad Al-Motlaq on the design and theoretical frame of this study. Adding more references on the same topic at the national or regional level is imperative to give a closer picture of Asthma and its management in Iraq schools.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8289",
"date": "26 Sep 2022",
"name": "Muhannad R. M. Salih",
"role": "Author Response",
"response": "Dear Reviewer Greetings Thank you for your remarks. Regarding the abstract: We have separated the sentence in the results that is best represented in the methods in the abstract. Regarding the introduction: We have rearranged the last paragraph as recommended : \"Various studies have reported that schoolteachers have inadequate awareness about Asthma and asthma management among school children.8–11 Therefore, it is recommended to train schoolteachers on specific aspects of Asthma and its management for school children. Therefore, we aimed to conduct this survey among primary school teachers in Baghdad, Iraq, to assess their knowledge about Asthma and confidence in managing school children with Asthma. The study aims to assess teachers' current knowledge about Asthma and to infer the need for teacher training around Asthma and asthma management in schoolchildren.\" Regarding the methods: We rearrange it according to instructions. Regarding the discussion: We rearrange it according to instructions. Thank you for your notes"
}
]
},
{
"id": "140322",
"date": "22 Jun 2022",
"name": "Kosisochi Amorha",
"expertise": [
"Reviewer Expertise Clinical Pharmacy"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGENERAL COMMENTS\nAsthma is a common chronic disease in children. Children in primary school are usually dependent on their parents or caregivers. However, this responsibility shifts to the teachers when these children are in school. In acute asthma attacks, first responders who are knowledgeable and confident can prevent asthma-related deaths. The authors assessed the level of knowledge and confidence that primary school teachers in Baghdad, Iraq, have in managing school children with asthma. The relevance of this study is further buttressed by the findings of a previous study which reported that more than four-fifths of primary school children in Baghdad were diagnosed of asthma.\nOverall, the article is well-written. The findings of the research add to the body of knowledge. The recommendation of training of primary school teachers in the management of asthma cannot be overemphasized. Despite the knowledge-base of the teachers and their confidence in managing asthma being relatively satisfactory, there is always room for improvement.\nOTHER POINTS Few observations are outlined below:\nAbstract\nResults: Note: Do not start a sentence with figures.\n\nArrange keywords in alphabetical order.\nMethods\nPage 3 (Participant recruitment): …in both parts of Baghdad (Karkh and Rusafa)…\n\nPage 4 (Data collection and follow-up): Include level of statistical significance, with respect to p-value. This is necessary so readers can understand the implications of the p-values in the Results section.\nResults\nPage 5: More than half (71%) of teachers answered… (Note: Do not start a sentence with figures).\nDiscussion\nPage 10: More than three-fifths (65%) of the teachers were in the age group of above 30 years of age. (Note: Do not start a sentence with figures).\n\nPage 10: … were considered, based on convenience sampling.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-367
|
https://f1000research.com/articles/11-944/v1
|
17 Aug 22
|
{
"type": "Review",
"title": "The social prescribing of psychosocial interventions in the treatment of addictions and substance use disorders with military veterans: a reclamation of identity and belonging",
"authors": [
"Richard Mottershead"
],
"abstract": "Social prescribing is a way of connecting individuals to a source of support within the community to help improve their health and well-being. Social prescribing programmes are being widely promoted within the United Kingdom (UK) and United States as non-pharmaceutical interventions for those living with addiction and substance misuse needs. These needs have been exasperated by the recent COVID-19 pandemic and global economic crisis, with emerging research indicating short-term and long-term detrimental effects on physical and mental health due to substance misuse and addictions. Psychosocial interventions utilize psychological or social factors rather than an overreliance on biological interventions to treat the health impacts of mental illnesses such as addictions and substance use disorder. In this paper, I will discuss the associated determinants of addictions and substance for the military veteran population, as well as how the social prescribing of psychosocial interventions could be used to reaffirm participant’s identity and enhance their sense of belonging for military veterans, using a real-world example in Wales, UK.",
"keywords": [
"social prescribing",
"psychosocial interventions",
"addictions",
"substance misuse",
"military",
"veterans",
"identity",
"belonging"
],
"content": "Introduction\n\nIndividuals with addictions and substance use disorders are known to face a number of challenges and needs associated with social determinants of health including medical, social, emotional, financial, legal and housing. These challenges require innovative care pathways that create solutions, in addition to evidence based treatment for substance use problems (EMCDDA, 2016). As highlighted previously by the author (Mottershead and Ghisoni, 2021) psychosocial interventions are crucial in supporting the recovery of military veterans. Psychosocial interventions can also be adopted through social prescribing for effective management of addiction and related issues, and can be successfully used as independent treatment methods as well as adjuncts to pharmacological treatment plans for military veterans.\n\nThe 21st Century has seen the continuation of armed conflict, exposing military personnel to the rigours of warfare and the challenges of transition back to a civilian identity. There has been a renewed realisation that there exists a sub-group of service-personnel leaving the Armed Forces with underlying mental health problems, including addictions and substance misuse disorders. These issues become apparent during the transition to a civilian life, and an overreliance and use of alcohol or substances can often become a maladaptive coping mechanism. Previously, the author (Mottershead, 2019) has expressed concern that there was evidence that once military service personnel are discharged, there appears to be no communication to relevant health and social services to allow for rehabilitation and treatment of mental health conditions, including addictions and substance misuse disorders. Research by Fear et al. (2010) states that the prevalence of heavy drinking is higher with serving personnel than with their civilian counterparts. Hossain et al. (2020) explained that this is a concern, as following a major crisis or trauma an individual may be at an increased risk of using substances to manage stress related anxiety. Johnsen et al. (2008) found that for those participants identified as homeless, these participants believed that there was a link between their current alcohol abuse and the drinking culture that they had been exposed to within the Armed Forces.\n\nThe use of psychosocial interventions is not a new revelation. In 1942 in Birmingham, United Kingdom (UK) at the Northfield Military Hospital, a controversial approach was adopted that sought to rehabilitate neurotic casualties of war (Bridger, 1985). This therapeutic community was short-lived due to its operating parameters, which were outside of the normal treatment plans of that time. This seminal work along with the previous success in the Peckham experiment in the 1930s, which saw the creation of an “unintentional therapeutic community” (Bridger, 1985) began to establish an evidence base for a shift away from the dominant medical model. In this article, the author will present, within a review of literature, how the social prescribing of psychosocial interventions could enhance self-image and create a sense of belonging for military veterans struggling to adjust to the transition of a civilian identity.\n\n\nAlcohol and substance misuse within the veteran population\n\nWithin western nations, there appears to be a culture of reliance and overuse of alcohol within military services. This is highlighted within the research of Ames and Cunradi (2005) and Fear et al. (2010) within the United States and UK. This research evidence shows that alcohol consumption rates in military service personnel exceed those of civilian counterparts across all age groups. This does not appear to be a camouflaged concern in so much as to say that military leaders are aware of the negative impact that excessive drinking has on the health of their troops, their effectiveness and wider reputation of Armed Forces (Ames and Cunradi, 2005; Iversen et al. 2007; Fear et al., 2010).\n\nIn 2018, a report published by Combat Stress indicated that substance misuse issues were found to be higher within the veteran community than civilian counterparts. Within the 743 participants (veterans) included within the study, 8.6% had posttraumatic stress disorder (PTSD) and 57.5% had a diagnosis of another mental health problem. Alarmingly, there were higher rates of alcohol related problems (81.6%), with a lower use of illegal substances at 16.8%, and 2% prescription medications (Ashwick and Murphy, 2018). Previously collaborative research between Help for Heroes and the Kings Centre for Military Health Research (KCMHR) noted that for those that had served within a 20-year period, there was a 10% prevalence of mental health illnesses. These illnesses included alcohol dependency and substance misuse, which would need substantial interventions from health and social care providers (Help for Heroes & KCMHR, 2015).\n\nIndeed, the author’s own research and role within the Government Review on former members of the armed forces and the criminal justice system on behalf of the Secretary of State for Justice (Phillips, 2014) indicated that alcohol and substance use were common features noted within the arrest profile of veterans entering the criminal justice system. The Defence Analytical Services and Advice (DASA, 2010) explored the issue of substance misuse and found that within England and Wales, male veterans were less than 50% likely to be imprisoned for drug-related offences than that of the general population but no explanation or sample size was provided. However, Bird (2007) reported that there has been a four-fold increase in the number of veterans who are being discharged due to random sampling tests. According to Gillan (2007), the Ministry of Defence (MoD) explained that these results were significantly lower than the 7% of civilian workforce statistics, although it is unclear how they arrived at this conclusion as the source of the civilian statistics was unclear.\n\nA crucial factor to consider is that once military service personnel are discharged, there appears to be no communication to relevant health and social services to allow for rehabilitation and treatment for the offending behaviour, which is often linked to alcohol consumption. Indeed, no information was given to be able to ascertain how many of the reported 7% were veterans. Johnsen et al. (2008) found that for those participants identified as homeless, these participants believed that there was a link between their current alcohol abuse and the drinking culture that they had been exposed to within the Armed Forces. In support of this argument, Fear et al. (2010) stated that the prevalence of heavy drinking is higher with serving personnel than with their civilian counterparts.\n\nFear et al. (2010) identifies Early Service Leavers (ESLs) as experiencing an elevated risk of suicide and heavy alcohol consumption over that of longer serving veterans. Within Wales, UK, the Health Inspectorate of Wales (HIW, 2012) has expressed concerns that some ESLs had been discharged back into civilian life as the result of disciplinary issues, including substance misuse, without adequate liaison with statutory services and support from the MoD. There is a consensus that this group represents the most vulnerable and ineffectual at circumnavigating their transition back into civilian life especially for those exposed to combat related trauma. Kitchiner et al. (2012) undertook an analysis of 29 randomised controlled trials, examining the efficacy of psychosocial interventions for military veterans, and found psychosocial interventions to be beneficial for the treatment of depression and those at risk of alcohol consumption.\n\nExposure to armed conflict has a significant impact on those involved and can lead to PTSD. Iribarren et al. (2005) provides a historic account of 30 years of studies and explains that PTSD, whilst not confined to military combat, it has a higher rate for those that may have witnessed a life-threatening event or engaged in extended combat tours in warzones. Hoge et al. (2006) warns that anxiety and substance misuse are common comorbidities with military veterans. Similarly, Rytwinski et al. (2013) discusses within their research that there was a comorbidity rate of 52% with alcohol abuse being present with depression and PTSD. Sareen (2014) explains that a feature of PTSD with military veterans is the prevalence of physical health problems that are often aligned with excessive alcohol and substance misuse. Collaborating this evidence is Kessler et al. (1995) who notes that alcohol abuse is commonly associated with depression and PTSD within former members of the Armed Forces. The author (Mottershead, 2019) has previously called for the need for a greater understanding of the problems faced by those who have been exposed to military culture, particularly in relation to alcohol abuse, which becomes a common feature within veteran’s life stories as they struggle with transiting to a civilian identity. The social prescribing of psychosocial interventions offers a bespoke and holistic treatment pathway to enhance resilience and develop coping mechanisms for stress, which as the literature (Wemrell et al., 2020) indicates, can lead to a dependency on addiction and misuse of substances.\n\n\nPsychosocial interventions in the reclamation of identity and belonging\n\nA psychosocial intervention is a broad term used to describe different ways to support people to overcome challenges within their life and maintain good mental health (O’Shea et al., 2017). Psychosocial interventions have had success to aid in the normalization of the treatment process and this has relevance with military veterans who may have issues around stigma and associated shame in seeking assistance and struggling to relate to non-veteran civilian counterparts. This can be understood through Social Identity Theory (Tajfel and Turner, 1986) which highlighted the boundaries between ‘normals’ and ‘others’. Abrams and Hogg (1990) provide further insight and explain that these theories describe a psycho-social process by which individuals categorise themselves and others into groups in order to place comparative values on themselves, thus ranking their relative position in the social hierarchy. Such ranking enables self-monitoring and potentially facilitates the reclamation of self-image. The current author (Mottershead, 2019) has previously explained that issues around social identity are evident from his research with veterans in relation to stigma, as these individuals may strive to protect their veteran identities even if this means not mixing with non-veterans. He goes on to explain that language is important in enabling the division of individuals into categories, such as veteran and non-veteran, as the distinction can be made to ‘in’ groups and ‘out’ groups, which effectively categorises ‘us’ and ‘them’ who are divided by impenetrable boundaries that can inhibit a sense of belonging (Mottershead, 2019).\n\nRather than relying on the use of medication, psychosocial interventions can be delivered through in person face-to-face as high intensity psychological therapy or in a low-intensity format via the use of Cognitive Behavioural Therapy, self-help interventions, or a combination of these support modalities (O’Shea et al., 2017). For veterans the benefits of psychosocial interventions is that they allow for a process of engaging in therapy, but with a therapeutic intervention designed around a proactive activity. This has the positive outcome of allowing the veteran to see an output for their engagement. Crucially, these psychosocial interventions can be group-based, which allows shared veteran identity to support an establishment of belonging through the familiarity of comradeship, yet empowers confidence to explore and form ownership of new identities.\n\nThis need to belong is also a feature found within Social Identity Theory, as attested by Tajfel and Turner (1986). They explain that social identity consists of “those aspects of an individual’s self-image that derive from the social categories to which he perceives himself as belonging” (Tajfel and Turner, 1986 p.16). This inherent need to belong for military veterans could be seen to be indicative of the findings of Steger and Lopez (2011) who observed a continuing process to establish meaning through belonging. Indeed, Barron, Davies and Wiggins (2008) identify comradeship and associated societal support to be crucial in promoting a sense of belonging for military veterans. This is supported by Burnell et al. (2006) who cite the importance of comradeship in service personnel returning home and transitioning back to post-military identities as civilians. Indeed, the current author’s research infers that the absence of a sense of belonging can lead veterans into crime and often as a result of alcohol and substance misuse (Mottershead, 2019). Within a more recent study (Mottershead and Alonaizi, 2021), it was demonstrated that comradeship with fellow veterans support a reclamation of identity due to the shared life experience of a culture uniquely developed and understood by veterans within the Arabian Gulf. The results of this study have clear parallels with the UK and be understood through the use of Social Identity Theory. Additionally, this could lead to further understanding of Goffman’s (1961) mortification of self and perhaps desire to return to a pre-existing identity of veteran over other less favourable or less influential identities such as the civilian identity, which the individual may struggle to establish a sense of belonging to this transitioning identity. Consequently, the misuse of alcohol and substances become a coping mechanism within the life stories of post-military identities that fail to establish a belonging to a civilian identity.\n\n\nFuture considerations\n\nIt is the intention of the author that the review of this literature will inform the development of social prescribing for existing psychosocial interventions for military veterans, reservists, emergency service personnel and their families within Wales, UK. The author believes that this care pathway will support the well-being and rehabilitation of these sub-groups, and have a positive impact on their families. This is timely as in July 2022 the Welsh Government announced a consultation on developing a framework for social prescribing. Figures in Wales indicate that from 2018 to 2021 there was an increase from 10,000 to 25,000 people benefiting from social prescribing (Welsh Government, 2022).\n\nThis therapeutic alliance utilizes the countryside and invites the participants to join one of the regional rural hubs of the award-winning national charity - Woody’s Lodge. These rural hubs are at Ty Gwalia in North Wales, Penlan Farm in West Wales Amelia Farm in South Wales, and a recent development on Flat Holme Island within the Bristol Channel. Research by Detweiler et al. (2015) and Reisman (2016) supports the evidence base practice of using the countryside, gardens, greenhouses and other psychosocial interventions to facilitate relationship developments and social interaction. In addition, the sharing of real-life experiences of the challenges of combating alcohol and substance misuse will assist in developing healthy coping habits that will have a positive impact on physical and mental wellbeing (Detweiler et al., 2015). Research by Hall et al. (2020) and Tanagra et al. (2013) provides further reassurance that teamwork around a physical activity can have a positive impact on self-esteem and confidence for veterans who are transitioning to a civilian identity.\n\nWoody’s Lodge network of rural hubs support and mentor veterans, emergency service personnel, reservists and their families in safe, quiet and informal surroundings. This is achieved through the use of the shared veteran identity as an ability to create effective veteran peer-support schemes centered around the social prescription of psychosocial interventions that built on a belonging to this shared veteran identity. This process is an aid to those living with addiction and reliance on substances, whose traditional hospital admissions have not been effective. The project is carried out by the registered UK charities Woody’s Lodge and Wintergreen UK – CIC which collectively provide the psychological and social support holistically. Both organisations offer complementary psychosocial interventions, free of charge to people with lived experience of health and social care challenges. This approach uses an evidence base to create bespoke psychosocial interventions to personalise recovery without needing further access to increased medical or other interventions (Cipriani et al., 2017).\n\n\nConclusions\n\nThis review has highlighted an awareness of the benefits of psychosocial interventions, as a therapeutic treatment option for addictions, substance misuse and wider mental health. However, 21st Century practices persist to treat the health needs of military veterans with predominantly pharmaceutical interventions. The author advocates for a biopsychosocial approach as realised through the care pathway of the social prescribing of psychosocial interventions. The author also advocates for a broader approach that dovetails medical prescribing alongside social prescribing so that personal health needs link to the importance of acknowledging social relationships and their impact on personal health needs of military veterans.\n\nThe author has sought to highlight that military veterans with addiction- and substance-related problems can be treated using non-medical interventions that can be socially prescribed. A real-world solution has been presented with the presentation of a national project that uses psychological treatments and interventions to support improved mental health. This paper acknowledges the strength of the military identity and how transitional challenges can create an entrenched social identity, which can inhibit a sense of belonging to new roles and identities within civilian life. Through the proposed use of veteran peer-support structured around psychosocial interventions, the rural hubs of Woody’s Lodge will empower veterans and their families through the adoption of the proposed therapeutic framework. The use of psychosocial interventions via the rural hubs has the potential to become a fully integrated pathway for primary care and social prescribing practices in Wales for the veteran community. This integrated approach between healthcare providers, community, voluntary and statutory services means that there will be opportunities for cost-saving as well as multidisciplinary collaboration and cooperation around addictions with military veterans. Given the degrading economic climate within the UK and post-pandemic fallout it is likely that there will be a detrimental effect on veterans’ mental health.\n\nThis paper seeks to present alternatives to the traditional use of pharmaceutical treatments and how the additional use of psychosocial interventions through social prescribing will allow for an early intervention and support the rehabilitation of addictions for military veterans. The addition of social prescribing arms the health profession with an additional asset via access to community-based treatments and improved access to psychosocial therapies. The author advocates for interventions that seek to address the wider determinants of impoverished self-image and to create an awareness that embedded within veterans is a need to belong. A sense of belonging creates a positive self-image, which can lead to the development of a new civilian identity and a rewarding life.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "References\n\nAbrams D, Hogg MA: Social identity theory: Constructive and critical advances. Hemel Hempstead, England:Harvester Wheatsheaf;1990.\n\nAmes G, Cunradi C: Alcohol use and preventing alcohol-related problems among young adults in the military. Alcohol Res. Health. 2005; 28(4): 252–257.\n\nAshwick R, Murphy D: Reviewing the efficacy of case management for veterans with substance misuse problems. Combat Stress: for veterans mental health.2018.Reference Source\n\nBarron DS, Davies SP, Wiggins RD: Social integration, a sense of belonging and the Cenotaph Service: old soldiers reminisce about remembrance. Aging Ment. Health. 2008; 12(4): 509–516. PubMed Abstract | Publisher Full Text\n\nBird S: Compulsory Drugs Testing in the British Army: Assessing the data. RUSI J. 2007; 152(6): 54–59. Publisher Full Text\n\nBurnell KJ, Coleman PG, Hunt N: Falklands War veterans' perceptions of social support and the reconciliation of traumatic memories. Aging Ment. Health. 2006; 10(3): 282–289. PubMed Abstract | Publisher Full Text\n\nBridger H: The Discovery of the Therapeutic Community.1985. Last accessed 20th Oct 2011.\n\nCipriani J, Benz A, Holgren A, et al.: A Systematic Review of the Effects of Horticultural Therapy on Persons with Mental Health Conditions. Occup. Ther. Ment. Health. 2017; 33(1): 47–69. Publisher Full Text\n\nDefence Analytical Services and Advice (DASA): Estimating the proportion of prisoners in England and Wales who are ex- Armed Forces; a data matching exercise carried out by the MOD in collaboration with the MoJ.2010.Reference Source\n\nDetweiler MB, Self JA, Lane S, et al.: Horticultural therapy: A pilot study on modulating cortisol levels and indices of substance craving, posttraumatic stress disorder, depression, and quality of life in veterans. Altern. Ther. Health Med. 2015; 21(4): 36–41. PubMed Abstract\n\nEuropean Monitoring Centre for Drugs and Drug Addiction (EMCDDA): Health responses to new psychoactive substances. Luxembourg:Publications Office of the European Union;2016.Reference Source\n\nFear NT, Jones M, Murphy D: What are the consequences of deployment to Iraq and Afghanistan on the mental health of the UK armed forces? A cohort study. Lancet. 2010; 375(9728): 1783–1797. PubMed Abstract | Publisher Full Text\n\nGillan A: Army losing a battalion a year to drug abuse, The Guardian (14/12/2007).2007.\n\nGoffman E: Asylums: Essays on the social situation of mental patients and other inmates. London:Penguin Books;1961.\n\nHall KS, Morey CM, Beckham JC, et al.: Warrior Wellness: A Randomized Controlled Pilot Trial of the Effects of Exercise on Physical Function and Clinical Health Risk Factors in Older Military Veterans With PTSD. J. Gerontol. A Biol. Sci. Med. Sci. 2020; 75(11): 2130–2138. PubMed Abstract | Publisher Full Text\n\nHealth Inspectorate Wales (HIW): Healthcare and the Armed Forces Community in Wales. Crown copyright;2012.\n\nHelp for Heroes and King’s Centre for Military Health Research: Counting the Costs. King’s College London.2015; 3–4.\n\nHoge CW, Auchterlonie JL, Milliken CS: Mental health problems, use of mental health services, and attrition from military service after returning from deployment to Iraq or Afghanistan. JAMA. 2006; 295(9): 1023–1032. PubMed Abstract | Publisher Full Text\n\nHossain MM, Tasnim S, Sultana A, et al.: Epidemiology of mental health problems in COVID-19: a review [version 1; peer review: approved]. F1000Res. 2020; 9: 636. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIribarren J, Prolo P, Neagos N, et al.: Post-Traumatic Stress Disorder: Evidence-Based Research for the Third Millennium. Evid. Based Complement. Alternat. Med. 2005; 2(4): 503–512. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIversen A, Waterdrinker A, Fear N, et al.: Factors associated with heavy alcohol consumption in the UK Armed Forces: Data from a health survey of Gulf, Bosnia, and era veterans. Mil. Med. 2007; 172(9): 956–961. PubMed Abstract | Publisher Full Text\n\nJohnsen S, Jones A, Rugg J: The experience of ex-service Homeless personnel in London. York:University of York, Centre for Housing Policy;2008.\n\nKessler RC, Sonnega A, Bromet E, et al.: Posttraumatic stress disorder in the National Comorbidity Survey. Arch. Gen. Psychiatry. 1995; 52(12): 1048–1060. PubMed Abstract | Publisher Full Text\n\nKitchiner NJ, Roberts NP, Wilcox D, et al.: Systematic review and metaanalyses of psychosocial interventions for veterans in the military. Eur. J. Psychotraumatol. 2012; 3(1): 19267. PubMed Abstract | Publisher Full Text\n\nMottershead R: British Military Veterans and the Criminal Justice System in the United Kingdom: Situating the Self in Veteran Research. (Unpublished doctoral dissertation). University of Chester, Chester, UK.2019.\n\nMottershead R, Alonaizi N: A narrative inquiry into the resettlement of armed forces personnel in the Arabian Gulf: a model for successful transition and positive mental well-being. F1000Res. 2021 Dec 16; 10: 1290. Publisher Full Text\n\nMottershead R, Ghisoni M: Horticultural therapy, nutrition and post-traumatic stress disorder in post-military veterans: developing non-pharmaceutical interventions to complement existing therapeutic approaches. F1000Res. 2021; 10: 885. PubMed Abstract | Publisher Full Text\n\nO’Shea L, Watkins E, Farrand P: Psychological interventions for the treatment of depression, anxiety, alcohol misuse or anger in armed forces veterans and their families: systematic review and meta-analysis protocol. Syst. Rev. 2017; 6: 112. Publisher Full Text\n\nPhillips S: Former members of the armed forces and the criminal justice system: a review on behalf of the Secretary of State for Justice.2014.Reference Source\n\nReisman M: PTSD Treatment for Veterans: What’s Working, What’s New, and What’s Next. P T. 2016; 41(10): 623–634. PubMed Abstract | Free Full Text\n\nRytwinski NK, Scur MD, Feeny NC, et al.: The co-occurrence of major depressive disorder among individuals with posttraumatic stress disorder: a meta-analysis. J. Trauma. Stress. 2013; 26(3): 299–309. PubMed Abstract | Publisher Full Text\n\nSareen J: Posttraumatic stress disorder in adults: impact, comorbidity, risk factors, and treatment. Can. J. Psychiatr. 2014; 59(9): 460–467. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSteger MF, Lopez SJ:The pursuit of meaningfulness in life. Handbook of positive psychology. 2nd ed.Oxford:Oxford University Press;2011.\n\nTajfel H, Turner JC:The social identity theory of intergroup behaviour. Psychology of intergroup relations. 2nd ed.Chicago:Nelson-Hall;1986; 7–24.\n\nTanagra D, Panidis D, Tountas Y, et al.: Implementation of a worksite educational program focused on promoting healthy eating habits [version 2; peer review: 2 approved]. F1000Res. 2013; 2: 201. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWelsh Government: Consultation Document - National framework for social prescribing: Development of a national framework for social prescribing that enables delivery of social prescribing in Wales of a consistent, effective, high quality standard across the ‘whole system’. Crown Copyright;2022.Reference Source\n\nWemrell M, Olsson A, Landgren K: The Use of Complementary and Alternative Medicine (CAM) in Psychiatric Units in Sweden. Issues Ment. Health Nurs. 2020; 41(10): 946–957. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "147821",
"date": "26 Aug 2022",
"name": "Professor David Taylor",
"expertise": [
"Reviewer Expertise Qualitative research particularly in education"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a clear review of the literature surrounding the support needed for military veterans with addiction/drug-related problems. They reach the conclusion that specific psychosocial models of care should dovetail with the existing pharmaceutical approaches.\n\nFrom what the author writes, the strength of the approach stems from the potential for psychosocial support to help the veterans repair their impoverished self-image and through that regain an identity within society as a whole.\n\nThis review is well-researched, grounded in a clear understanding of the participants and the literature, and is to be highly commended.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "8731",
"date": "06 Sep 2022",
"name": "Dr. Richard Mottershead",
"role": "Author Response",
"response": "I would like to take this opportunity to thank Professor David Taylor for taking the time to review my article and acknowledging the importance and relevance of the content in supporting and treating military service personnel. His insight and guidance will allow me to write and publish with clarity and focus. Thank you Dr. Richard Mottershead"
}
]
},
{
"id": "147820",
"date": "02 Sep 2022",
"name": "Matt Fossey",
"expertise": [
"Reviewer Expertise I am a social scientist with an extensive portfolio of research with the military",
"veterans and their families"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for giving me the opportunity to review this paper. The subject matter is of great importance as the NHS seeks to increase and improve its psycho-social healthcare provision for veterans with the emergence of the Op Courage programme.\nThe debate in this article is stilted somewhat by the tight word-limit, which is a shame, as the author has quite a lot to say about a significant topic and this is a challenge within this restriction.\nI believe that this article is suitable for publication with a number of changes, that I will outline below. I hope that these changes will not take away from the substance of the argument that the author is trying to make, rather enhance it:\nIt would be helpful to give a clearer definition of social prescribing -it’s worth looking at some of the excellent material developed by the Kings Fund What is social prescribing? | The King's Fund (kingsfund.org.uk). However, this paper does not really focus on “social prescribing” per se, rather the use of psychosocial interventions. Consequently, the author may wish to drop the term “social” from the title. This, I believe, will help to better indicate the focus of the paper.\n\nThere needs to be consistency throughout the article – where the author is referring to research on PTSD from the USA, this needs to be made clear. It is quite a challenge to use this when formulating an argument for service improvement in the UK as the numbers of patients with PTSD are not comparable. I would urge the author to use UK-based data only.\n\nIssues relating to the challenges associated with military transition and substance abuse in the UK have been investigated in research funded by the Forces in Mind Trust 20210322-Galahad-Fall-Out-Briefing-Report-FINAL.pdf (pcdn.co) – this is the most up-to-date account in the UK and should be referenced – the figures within this report will be slightly more up-to-date than the Combat Stress ones cited.\n\nThe author needs to also consider the UK’s MOD attempts to engage with and provide support for more challenging SLs – please refer to JSP100 and the formation of the Defence Transition Service (DTS). It is also worth noting that the reduced provision for CDT failures was removed over 12 months ago – they are now entitled to support that is commensurate with their length of service.\n\nAs the author is proposing work with colleagues in Wales, it may also be worthwhile citing some of the work that currently being undertaken within the Principality and how the author would:\nSee this link to the existing mental health provision for veterans And outline how this service could be evaluated within the context of different models\n\nFinally, it would be helpful for the flow of the article if Woody’s Lodge and the nature and importance of their work were introduced at the start. The argument relates to the potential of this rural retreat for the treatment of veterans and their families and I think should have more prominence earlier.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly",
"responses": [
{
"c_id": "8730",
"date": "06 Sep 2022",
"name": "Dr. Richard Mottershead",
"role": "Author Response",
"response": "Response – Thank you for this suggestion and I have sought to include within the introduction a definition from a relevant document pertinent to social prescribing within the locality of the proposed initiative which has a relatable evidence base. I have not included Op Courage as this is a recent initiative within England and instead I have focused on initiatives within the country of Wales. Response - The articles abstract identifies a wider scope than just a UK perspective in highlights the inclusion of US data. I acknowledge my esteemed colleagues point regarding variation in numbers between UK and US. However, the presence of PTSD and most importantly the transatlantic evidence of the beneficial use of social prescribing of psychosocial interventions is a joint objective of the author and the journal to reach a wider demographic diversity. Response – I have included the relevant research study within my article which is strengthened by your suggestion. Thank you. Response – As you so correctly identity the allocated word limit within the article means that a fuller exploration of all suggested points becomes restricted. As the article indicates, this is the 2nd publication of a series and your points will be included with the subsequent publications. Response – the article highlights research and work being undertaken within Wales and I have sought to highlight this work by listing some collaborative work with additional psychological therapies services. I hope to publish a third article that will focus on the points you raise once the national rural hub network is established at the end of this year. Response – it was felt by myself and the editorial team that the presentation and discussion of the topic (theory) and subsequently the presentation of the charity (practice) would guide the reader to the importance and relevance to the proposed initiative. Overall response – I would like to thank Professor Matt Fossey for his review of my article. I acknowledge him to be one of the UK’s most highly regarded academics within the area of veteran affairs who has a genuine and heartfelt compassion to support military veterans and their families. My article has been enhanced through his review and guidance. I have submitted an updated version of my article which will be available shortly - Thank you. Dr. Richard Mottershead"
}
]
}
] | 1
|
https://f1000research.com/articles/11-944
|
https://f1000research.com/articles/11-739/v1
|
04 Jul 22
|
{
"type": "Brief Report",
"title": "The potential utility of an augmented data collection approach in understanding the journey to care of pregnant women for maternal and perinatal death surveillance and response",
"authors": [
"Aduragbemi Banke-Thomas"
],
"abstract": "Background: The Maternal and Perinatal Death Surveillance and Response (MPDSR) proposed by the World Health Organization recognises the importance for health systems to understand the reasons underpinning the death of a pregnant woman or her newborn as an essential first step in preventing future similar deaths. Data for the surveillance component of the MPDSR process are typically collected from health facility sources and post-mortem interviews with affected families, though it may be traumatising to them. This brief report aimed to assess the potential utility of an augmented data collection method for mapping journeys of maternal and perinatal deaths, which does not require sourcing additional information from grieving family members. Methods: A descriptive analysis of maternal and perinatal deaths that occurred across all 24 public hospitals in Lagos State, Nigeria, between 1st November 2018 and 30th October 2019 was conducted. Data on their demographic, obstetric history and complication at presentation, travel to the hospital, and mode of birth were extracted from their hospital records. The extracted travel data was exported to Google Maps, where driving distance and travel time to the hospital for the period of the day of travel were also extracted. Results: Of the 182 maternal deaths, most presented during the week (80.8%), travelled 5-10 km (30.6%) and 10-29 minutes (46.9%), and travelled to the nearest hospital to their places of residence (70.9%). Of the 442 pregnant women who had perinatal deaths, most presented during the week (78.5%), travelled <5 km (26.9%) and 10-29 minutes (38.0%). For both, the least reported travel data was the mode of travel used to care (>90.0%) and the period of the day they travelled (approximately 30.0%). Conclusion: An augmented data collection approach that includes accurate and complete travel data and closer-to-reality estimates of travel time and distance can be beneficial for MPDSR purposes.",
"keywords": [
"Maternal mortality",
"Perinatal mortality",
"Maternal and Perinatal Death Surveillance and Response",
"Audit",
"Emergency obstetric care",
"Travel",
"Access to healthcare",
"Nigeria"
],
"content": "Introduction\n\nApproximately 300,000 maternal deaths occur annually because of complications related to pregnancy and childbirth. These complications include abortion, pre-eclampsia/eclampsia, ante- or post-partum haemorrhage, and sepsis.1 In addition, these complications also increase the chance of pregnant women having babies born dead or dying within the first week of life (perinatal deaths). It is estimated that about three million perinatal deaths occur every year.2,3 Between 97% and 99% of these deaths occur in low- and middle-income countries (LMICs).1–3 To minimise the risk of maternal and perinatal deaths, pregnant women need to be able to promptly access emergency obstetric care (EmOC) provided by skilled health personnel.4,5 However, before pregnant women can access EmOC, they must first decide to seek the care, travel to a health facility with the capacity to provide EmOC and, upon arrival at the health facility, have a skilled health personnel who can actually provide the needed care or promptly refer them.6 Travel time and distance to care may lead to maternal or perinatal deaths.7–10\n\nThere is a global consensus that understanding the reasons underpinning the death of a pregnant woman or her unborn child is an important first step in forestalling future similar deaths. To reach this understanding, in addition to being able to label the obstetric complication that led to the death(s), it is crucial to capture the pregnant woman’s personal story to care and the precise circumstances around her death or that of her unborn child. To be comprehensive and useful for action, the story needs to capture the narrative and establish any obstacles that prevented the woman from accessing prompt care. In 2021, the World Health Organization (WHO) and partners launched the Maternal and Perinatal Death Surveillance and Response (MPDSR) to investigate maternal and perinatal deaths and act based on the findings.11 This new guide builds on two previous guides that focused on capturing the story of the mother and the newborn separately.12,13\n\nAs per the WHO MPDSR guide, data from the admission and discharge register, labour and childbirth ward register, and theatre or minor surgery record books will be helpful. In addition, patient records, including case notes, referral notes, postoperative notes, and laboratory results are deemed to contain relevant information to reflect the personal stories of women.11 However, while patient records have copious detail to understand factors that might have contributed to delays after the woman arrived at the health facility, they typically contain minimal information on the journey she travelled to care.14,15 The WHO recommends that though it is more difficult to obtain, such additional information could be sourced from the woman’s family.11 In practice, this might mean conducting post-mortem interviews for MPDSR purposes, as in Indonesia.16 However, the woman’s family are not always in the frame of mind to provide, and neither are the skilled health personnel to collect the necessary information when a death has occurred.17,18 Other challenges, including additional workload for skilled health personnel, have been mentioned in the literature.19 Indeed, issues related to travel to care are rarely specifically flagged as contributory factors to maternal or perinatal deaths reported in MPDSR audits conducted in LMICs.20 The objective of this brief report was to assess the potential utility of an augmented data collection method for mapping journeys of maternal and perinatal deaths, which does not require sourcing additional information from family members.\n\n\nMethods\n\nEthical approval for this study was obtained from the Research and Ethics Committees of the Lagos University Teaching Hospital (ADM/DCST/HREC/APP/2880) and Lagos State University Teaching Hospital (LREC/06/10/1226). This study was conducted with secondary data from hospital records with permission from the Ministry of Health to access these records. There was no direct interaction with patients at any point in time. The risk of identifying pregnant women in the study was substantially reduced by not collecting identifiers such as names and specific street numbers.\n\nThis descriptive study was conducted across all 24 public hospitals in Lagos State, Nigeria, that provided EmOC. Lagos is a principally urban state located in the southwestern part of Nigeria with a total population of 26 million as of 2019.21 For different reasons, including perceived higher concentration of skilled health personnel and equipment, availability of round-the-clock care, and in some instances ‘free’ or reduced fees, many pregnant women prefer to access EmOC in public hospitals.22 Institutional maternal mortality ratios in Lagos public hospitals have been reported to range between 987 and 2,111 per 100,000 live births. Over a third of maternal deaths are attributed to a delayed presentation at health facilities.23\n\nFor this study, pregnant women who presented in the emergency room of the different public hospitals between 1st November 2018 and 30th October 2019 were identified. The sample for this brief report was limited to those who resulted in maternal deaths or had perinatal deaths. Amongst these women, data on demographic characteristics, obstetric history, travel to the hospital, obstetric complication (as defined in the WHO’s Monitoring EmOC guidelines),5 and mode of birth were extracted.\n\nBased on the travel data extracted from the patient records, additional data were collected to estimate the driving distance (in kilometres (km)) and travel time (in minutes (mins)) of the pregnant women to the hospital using Google Maps (Alphabet Inc., Mountain View, California, US), which offers closer-to-reality estimates.24 To map the journeys in Google Maps, the street name of women’s self-reported addresses and referral points were geo-referenced for each woman who had traceable journeys in the application. The ‘typical time of travel’ feature in Google Maps was used for the period of the day of travel for specific time slots (9.00 a.m., 3.00 p.m., 6.00 p.m., and 9.00 p.m. for morning, afternoon, evening, or night journeys, respectively), based on awareness of peak and non-peak travel periods in Lagos.25 A check was subsequently conducted in Google Maps to ascertain whether there was an alternative public hospital closer to the pregnant woman’s self-reported address for the period of the day of travel to care.\n\nFor this study, maternal death was defined as “the death of a woman while pregnant or within 42 days of termination of pregnancy, irrespective of the duration and site of the pregnancy, from any cause related to or aggravated by the pregnancy or its management, but not from accidental or incidental causes”.26 Perinatal death was defined as a foetal death occurring on or after 28-week gestation but before birth or neonatal death within seven days of life.3 A perinatal death was recorded as long as a foetal death occurred even If the woman had multiple gestations (e.g. twins) and one baby survived.\n\nA descriptive analysis of the socio-demographic, obstetric, and travel characteristics of the women who ended as maternal deaths or had perinatal deaths was conducted. The data was disaggregated by referral status. Analysis was conducted using Stata SE version 16.1 (StataCorp, College Station, Texas, USA).\n\n\nResults\n\nIn all, there were 182 intra-facility maternal deaths amongst pregnant women who presented in the emergency rooms of the public hospitals during the study period. These maternal deaths included 140 (76.9%) pregnant women who travelled directly to hospitals where they received EmOC, and 42 (23.1%) were referred. Amongst all maternal deaths, the majority were pregnant women who were aged 20-34 years (68.1%), married (86.3%), self-employed as petty traders (37.4%), and had attained a secondary level of education (37.4%). In terms of obstetric history, most maternal deaths were pregnant women with complications in a previous pregnancy (93.4%) and multiparous at presentation (42.9%). For their index pregnancy, most maternal deaths were pregnant women who were un-booked (94.0%), had singleton pregnancies (98.9%), and presented with spontaneous abortion (40.1%). Regarding travel to care, most maternal deaths were pregnant women who presented during the week (80.8%), travelled 5-10 km (30.6%) and 10-29 mins (46.9%). Journeys of 4.9% of women who ended as maternal deaths could not be mapped. Most travelled to the nearest hospital to their places of residence (70.9%). Most of those referred before they died initially presented at a primary health centre (40.5%). It was not possible to extract data on what period of the day they travelled (29.7%) or what mode of travel they used to care (92.9%) for most women who ended as maternal deaths, as these were not reported in the patient records [Table 1].\n\nThere were 442 intra-facility perinatal deaths amongst pregnant women who presented in public hospitals requiring EmOC during the study period, including 269 (60.9%) who travelled directly to the hospital where they received EmOC and 173 (39.1%) referred. Most pregnant women who had perinatal deaths were aged 20-34 years (67.2%), married (94.3%), and self-employed as petty traders (43.0%). Most did not have the level of education attained reported in their case notes (52.3%). In terms of obstetric history, most perinatal deaths were delivered by pregnant women who did not have a complication in a previous pregnancy (93.4%) and were multiparous at presentation (43.4%). For the index pregnancy, most perinatal deaths were by un-booked mothers (81.2%) and were singleton pregnancies (96.8%). Regarding travel, most perinatal deaths were delivered by pregnant women who presented during the week (78.5%), travelled <5 km (26.9%) and 10-29 minutes (38.0%). Journeys of 4.8% of women with perinatal deaths could not be mapped. Most travelled to the nearest hospital to their places of residence (70.9%). Most of those referred before they died initially presented at a primary health centre (37.3%). For most pregnant who ended with a perinatal death, it was not possible to extract data on the period of the day they travelled (34.6%) or the mode of travel used to care (98.9%) as these were not reported in the patient records. Most foetuses that ended as perinatal deaths were delivered via spontaneous vaginal birth (56.6%) [Table 2].\n\n\nDiscussion\n\nThis brief report showed that for MPDSR, patient records are useful in capturing the personal stories relating to travel to care which might have contributed to maternal and perinatal deaths. However, their usefulness can be significantly improved if more thorough travel to care history is taken when the pregnant woman presents in an emergency. As per evidence gathered from this study, questions relating to the period of the day of travel to the facility and mode of transport are only minimally recorded. In addition, there were cases of incomplete, wrong, or difficult-to-read addresses, which made it impossible to locate residential addresses. For those referred, though the type of referral facility was reported in many instances (for example, by simply writing ‘private clinic’), it was not always possible to map the actual location of the referral facilities. The utility of the travel data when complete and reflective of the travel to care was further improved when complementary travel data, including travel time and distance, were subsequently collected using a web-based navigation application (Google Maps). This study showed that data was more detailed for maternal deaths compared to perinatal deaths.\n\nThese study findings have several implications for practice and policy, especially as issues related to travel to care are seldomly flagged in MPDSR audits conducted in LMICs.20 First, as with the recognised need for complete and accurate information on the circumstance and management of pregnant women and their newborns at all levels,27 skilled health personnel need to be trained and encouraged to collect detailed and accurate travel history of pregnant women at the point of presentation, with a guaranty of no blame at audit even if there was a delay in a referral or organising an ambulance for onward travel.17,28 These efforts need to include verification of points of origin from which the woman came to care, which may be their home or anywhere else in the community. In instances where the points of origin are difficult to establish, a nearby popular structure (for example, ‘beside the stadium’) should be inputted as a proxy. Indeed, this process of address localisation will be easier with electronic health information systems. However, challenges related to the cost of implementing and maintaining such systems have been raised.29 The alternative to this, which is also the status quo in many LMIC health systems, involves using hand-written paper-based platforms. However, this is prone to errors.29 As was observed in this study, errors related to accurate reporting of patient addresses limit the utility of the data for assessing delays that might have contributed to maternal or perinatal deaths. In deciding the health information management system to implement, the efficiency, accuracy, data safe-keeping, and decision-making gains that come with electronic systems need to be considered as they may guarantee value for money for such investments.29–33\n\nThe augmented data collection approach used for this research yielded additional information that would otherwise not have been available. Beyond understanding the journey to care preceding the death, insights garnered from this augmented approach can help provide the more robust evidence to support the planning of EmOC services.32 This approach of leveraging technology to estimate travel time and distance has been shown to offer closer-to-reality estimates, especially in urban areas.24 Indeed, there might still be a case for collecting additional information from family members. For example, to establish if there were notably worse traffic conditions beyond the ‘typical travel time’ reported by Google Maps or a motor vehicle breakdown that will not be captured in Google Maps in any case. However, this enquiry risks re-traumatising relatives after the death. Furthermore, an enquiry might still be required to establish circumstances which might have contributed to delays in the decision to seek care. This approach will reduce the number of families that need to be engaged and could potentially improve the efficiency of MPDSR committees. In instances in which an enquiry is still warranted, the augmented data collection proposed in this report could serve the purpose of data triangulation.\n\nThere are some limitations to consider in interpreting the findings of this study. First, though Google Maps has been shown to provide closer-to-reality estimates of travel time and distance in urban settings like Lagos, its applicability in rural settings remains questionable.24 Second, the study was conducted with retrospective health facility data. While this provided an actual case study in an unaltered environment, it did not allow exploration of the full potential of this augmented approach if instituted, building on complete and accurate data that could have been realised if the study had been conducted prospectively. Future prospective research needs to be undertaken, and the utility of this augmented data collection approach needs to be assessed from the perspective of MPDSR committee members.\n\n\nConclusions\n\nIn conclusion, while not the magic bullet, for MPDSR purposes, an augmented data collection approach that includes accurate and complete travel data collection and closer-to-reality estimates of travel time and distance can improve the understanding of travel experiences of pregnant women and their new-borns to care.\n\n\nData availability statement\n\nFigshare: Intra-facility_maternal_deaths_Lagos_2018-2019.csv. https://doi.org/10.6084/m9.figshare.20098148.v1.\n\nThis project contains the following underlying data:\n\n• Intra-facility_maternal_deaths_Lagos_2018-2019.csv, (Anonymised data on maternal deaths analysed in this study).\n\n• Intra-facility_perinatal_deaths_Lagos_2018-2019.csv, (Anonymised data on perinatal deaths analysed in this study).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nWHO, UNICEF, UNFPA, World Bank Group, UNDP: Trends in maternal mortality 2000 to 2017: estimates by WHO, UNICEF, UNFPA, World Bank Group and the United Nations Population Division. Geneva:World Health Organization;2019; 1–119.Reference Source\n\nUNICEF, WHO, World Bank, UNPD: A neglected tragedy: The global burden of stillbirths. New York:United Nations Children’s Fund;2020; 1–90.\n\nWHO: Neonatal and perinatal mortality: country, regional and global estimates. Geneva, Switzerland:World Health Organization;2006.\n\nUnited Nations: Sustainable Development Goals: 17 goals to transform our world. Sustainable Development Goals.2016 [cited 2020 Oct 12].Reference Source\n\nWHO, UNFPA, UNICEF, Averting Maternal Deaths and Disabilities: Monitoring emergency obstetric care: a handbook. Geneva, Switzerland:WHO Press;2009.\n\nThaddeus S, Maine D: Too far to walk: Maternal mortality in context. Soc. Sci. Med. 1994; 38(8): 1091–1110. PubMed Abstract | Publisher Full Text\n\nBanke-Thomas A, Avoka CK, Gwacham-Anisiobi U, et al.: Influence of travel time and distance to the hospital of care on stillbirths: a retrospective facility-based cross-sectional study in Lagos, Nigeria. BMJ Global Health. 2021; 6(10): e007052. PubMed Abstract | Publisher Full Text\n\nBanke-Thomas A, Avoka CK, Gwacham-Anisiobi U, et al.: Travel of pregnant women in emergency situations to hospital and maternal mortality in Lagos, Nigeria: a retrospective cohort study. BMJ Global Health. 2022 Apr 1; 7(4): e008604.\n\nPirkle CML, Fournier P, Tourigny C, et al.: Emergency obstetrical complications in a rural african setting (Kayes, Mali): The link between travel time and in-hospital maternal mortality. Matern. Child Health J. 2011 [cited 2021 May 31]; 15(7): 1081–1087. PubMed Abstract | Publisher Full Text\n\nvan Duinen AJ , Adde HA, Fredin O, et al.: Travel time and perinatal mortality after emergency caesarean sections: an evaluation of the 2-hour proximity indicator in Sierra Leone. BMJ Glob. Health. 2020; 5(12): e003943. Publisher Full Text\n\nWHO: Maternal and Perinatal Death Surveillance and Response: Materials to Support Implementation. Geneva, Switzerland:World Health Organization;2021; 1–140.Reference Source\n\nWHO, FIGO, E4A, UNFPA, CDC, ICM: Maternal death surveillance and response: technical guidance. Information for action to prevent maternal death. Geneva, Switzerland:World Health Organization;2013; 1–128.Reference Source\n\nWHO: Making every baby count: Audit and review of stillbirths and neonatal deaths. Geneva, Switzerland:2016; 1–144.Reference Source\n\nBanke-Thomas A, Balogun M, Wright O, et al.: Reaching health facilities in situations of emergency: qualitative study capturing experiences of pregnant women in Africa’s largest megacity. Reprod. Health. 2020; 17: 145. PubMed Abstract | Publisher Full Text\n\nRadovich E, Banke-Thomas A, Campbell OMR, et al.: Critical comparative analysis of data sources toward understanding referral during pregnancy and childbirth: three perspectives from Nigeria. BMC Health Serv. Res. 2021; 21: 927. PubMed Abstract | Publisher Full Text\n\nSupratikto G, Wirth ME, Achadi E, et al.: A district-based audit of the causes and circumstances of maternal deaths in South Kalimantan, Indonesia. Bull. World Health Organ. 2002; 80(3): 234.\n\nStabnick A, Yeboah M, Arthur-Komeh J, et al.: “Once you get one maternal death, it’s like the whole world is dropping on you”: experiences of managing maternal mortality amongst obstetric care providers in Ghana. BMC Pregnancy Childbirth. 2022; 22: 206. PubMed Abstract | Publisher Full Text\n\nMills TA, Ayebare E, Mukhwana R, et al.: Parents’ experiences of care and support after stillbirth in rural and urban maternity facilities: a qualitative study in Kenya and Uganda. BJOG. 2021; 128(1): 101–109. PubMed Abstract | Publisher Full Text\n\nKinney MV, Walugembe DR, Wanduru P, et al.: Maternal and perinatal death surveillance and response in low- and middle-income countries: a scoping review of implementation factors. Health Policy Plan. 2021 Jun 25 [cited 2022 May 19]; 36(6): 955–973. PubMed Abstract | Publisher Full Text Reference Source\n\nMerali HS, Lipsitz S, Hevelone N, et al.: Audit-identified avoidable factors in maternal and perinatal deaths in low resource settings: A systematic review. BMC Pregnancy Childbirth. 2014; 14: 280. PubMed Abstract | Publisher Full Text\n\nLASG: Abstract of local government statistics. Ikeja.2019 [cited 2022 Apr 17]. p. 1–113.Reference Source\n\nWright K, Banke-Thomas A, Sonoiki O, et al.: Opinion of women on emergency obstetric care provided in public facilities in Lagos, Nigeria: A qualitative study. Health Care Women Int. 2017; 38(6): 527–543. PubMed Abstract | Publisher Full Text\n\nOkonofua F, Imosemi D, Igboin B, et al.: Maternal death review and outcomes: An assessment in Lagos State, Nigeria. PLoS One. 2017; 12(12): e0188392. PubMed Abstract | Publisher Full Text\n\nBanke-Thomas A, Wong KLM, Ayomoh FI, et al.: “In cities, it’s not far, but it takes long”: comparing estimated and replicated travel times to reach life-saving obstetric care in Lagos, Nigeria. BMJ Glob. Health. 2021 [cited 2021 Jan 26]; 6(1): e004318. PubMed Abstract | Publisher Full Text\n\nAsiyanbola RA, Osoba SB, Adewale SS: Road traffic administration and management in the third world mega-city: Lagos, Nigeria. Int. J. Dev. Sustain. 2012; 1(2): 490–509.\n\nWHO: ICD-10: International Classification of Diseases and Related Health Problems. 2010 Edition. Geneva:World Health Organization;2010; 1–201.Reference Source\n\nSmith H, Ameh C, Roos N, et al.: Implementing maternal death surveillance and response: a review of lessons from country case studies. BMC Pregnancy Childbirth. 2017; 17: 233. PubMed Abstract | Publisher Full Text\n\nAchem F, Agboghoroma C: Setting up facility-based maternal death reviews in Nigeria. BJOG. 2014 Sep 1 [cited 2017 Jul 15]; 121(s4): 75–80. PubMed Abstract | Publisher Full Text\n\nKerber KJ, Mathai M, Lewis G, et al.: Counting every stillbirth and neonatal death through mortality audit to improve quality of care for every pregnant woman and her baby. BMC Pregnancy Childbirth. 2015; 15(Suppl 2): S9. Publisher Full Text\n\nBanke-Thomas A, Wright K, Sonoiki O, et al.: Multi-stakeholder perspectives on access, availability and utilization of emergency obstetric care services in Lagos, Nigeria: A mixed-methods study. J. Public Health Afr. 2017; 8(2): 717. PubMed Abstract | Publisher Full Text\n\nBanke-Thomas A, Madaj B, Kumar S, et al.: Assessing Value-for-Money in Maternal and Newborn Health. BMJ Glob. Health. 2017; 2: e000310. PubMed Abstract | Publisher Full Text\n\nBanke-Thomas A, Wong KLM, Collins L, et al.: An assessment of geographical access and factors influencing travel time to emergency obstetric care in the urban state of Lagos, Nigeria. Health Policy Plan. 2021; 36(9): 1384–1396. PubMed Abstract | Publisher Full Text\n\nQomariyah SN, Bell JS, Pambudi ES, et al.: A practical approach to identifying maternal deaths missed from routine hospital reports: lessons from Indonesia. Glob. Health Action. 2009; 2(1): 1905. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "143184",
"date": "26 Jul 2022",
"name": "Tope Olubodun",
"expertise": [
"Reviewer Expertise Public Health",
"Reproductive Health."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper explains how an augmented data collection approach that includes accurate and complete travel data collection and closer-to-reality estimates of travel time and distance can improve the practice of maternal and perinatal death surveillance and response. The paper has findings which can be important for practice. It is well written, passes the message across and is at the same time, concise.\nSuggestions for revisions are provided below:\nAbstract Please state that the study was carried out across all 24 public hospitals in Lagos State, that provided EmOC (emergency obstetric care). It is important to state that those public hospitals that provided EmOC were used, as some other public hospitals may exist that do not provide EmOC.\nMethods The correct name of the Lagos University Teaching Hospital ethics committee is Human Research and Ethics Committees of the Lagos University Teaching Hospital.\nDiscussion Please make it clearer, how this approach will reduce the number of families that need to be engaged (third paragraph).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8587",
"date": "04 Aug 2022",
"name": "Aduragbemi Banke-Thomas",
"role": "Author Response",
"response": "This paper explains how an augmented data collection approach that includes accurate and complete travel data collection and closer-to-reality estimates of travel time and distance can improve the practice of maternal and perinatal death surveillance and response. The paper has findings which can be important for practice. It is well written, passes the message across and is at the same time, concise. Response: Thank you for your thorough review. Deeply appreciated. Suggestions for revisions are provided below: Abstract \"Please state that the study was carried out across all 24 public hospitals in Lagos State, that provided EmOC (emergency obstetric care). It is important to state that those public hospitals that provided EmOC were used, as some other public hospitals may exist that do not provide EmOC.\" Response: Thank you for this important point, which has now been effected and will be reflected in the updated version when it is published. The statement now reads \"A descriptive analysis of maternal and perinatal deaths that occurred in 24 emergency obstetric care providing public hospitals in Lagos, Nigeria...\". Methods \"The correct name of the Lagos University Teaching Hospital ethics committee is Human Research and Ethics Committees of the Lagos University Teaching Hospital.\" Response: This is true. However, the sentence here was reflecting the two research and ethics committees for both Lagos University Teaching Hospital and Lagos State University Teaching Hospital. This was to keep the text succinct. To avoid confusion, both have been separated. It now reads \"Ethical approval for this study was obtained from the Human Research and Ethics Committee of Lagos University Teaching Hospital (ADM/DCST/HREC/APP/2880) and the Health Research and Ethics Committee of Lagos State University Teaching Hospital (LREC/06/10/1226)\". This change will be reflected in the updated version when it is published. Discussion \"Please make it clearer, how this approach will reduce the number of families that need to be engaged (third paragraph).\" Response: Thank you for this comment. Sections of this paragraph have been rephrased to improve clarity. It now reads \"For example, to establish if there were notably worse traffic conditions beyond the ‘typical travel time’ reported by Google Maps or a motor vehicle breakdown that will not be captured in Google Maps in any case. An enquiry might also still be required to establish circumstances which might have contributed to delays in the decision to seek care. However, these supplementary enquiries risk re-traumatising relatives after the death of their loved ones. The proposed augmented data collection approach in this study will reduce the number of families that need to be engaged and could potentially improve the efficiency of MPDSR committees\"."
}
]
},
{
"id": "143182",
"date": "04 Aug 2022",
"name": "Prestige Tatenda Makanga",
"expertise": [
"Reviewer Expertise Spatial Epidemiology",
"Health Geography"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an important report that furthers the conversation on ways to understand pathways to deaths for women due to complications of pregnancy and child birth. It's timely considering the 2021 development in maternal and perinatal deaths surveillance. It addresses the limitations of current methods of gathering data, that somewhat compromise privacy, still collecting limited and subjective information. That said, there are a few minor issues that the author needs to address before the report can be published.\nThe author needs to describe or define what they mean by an augmented approach early in the article. It becomes clear as one reads, but a definition would help.\n\nThough demographic characteristics and obstetric history serve as important information that gives context to any study of this kind, it is unclear how this is valuable for this specific report seeing that the author is emphasizing collecting data related to the women's travel. At the least, the author could minimize this information and make the tables smaller.\n\nWhy is it necessary to differentiate weekdays and weekends? The author should explain and also reflect on this in the discussion.\n\n\"self-employed as petty traders (37.4%)\" in results should be 44%.\n\n\"In terms of obstetric history, most maternal deaths were pregnant women with complications in a previous pregnancy (93.4%)\" in results. From the Table, it is \"NO\" with a score of 93.4% implying that 6.6 did not have complications in previous pregnancies'. Do check if my interpretation is correct.\n\nIt would be appropriate for the author to address in greater detail the impact of the 42 that were referred on modelling the travel times, since the current approach estimates travel directly to the facility where the woman died. Also since mode was not known for 93% of the record, what would be the implication on assuming that everyone was driven?\n\nAdd period of travel to table 1.\n\nIn the discussion or conclusion, I suggest that the author suggest specific fields that could be added to current data collection instruments to aid the augmentation that they are suggesting.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8630",
"date": "07 Sep 2022",
"name": "Aduragbemi Banke-Thomas",
"role": "Author Response",
"response": "\"This is an important report that furthers the conversation on ways to understand pathways to death for women due to complications of pregnancy and childbirth. It's timely considering the 2021 development in maternal and perinatal deaths surveillance. It addresses the limitations of current methods of gathering data, that somewhat compromise privacy, while still collecting limited and subjective information. That said, there are a few minor issues that the author needs to address before the report can be published.\" Response: Thank you for your thorough review which has really helped to strengthen the report and improve its clarity. Deeply appreciated. Comment 1: \"The author needs to describe or define what they mean by an augmented approach early in the article. It becomes clear as one reads, but a definition would help.\" Response: Thank you for this comment. The objective has been modified to include a phrase that describes the proposed augmented approach early on. The objective now reads, \"...to assess the potential utility of an augmented data collection method that uses data already collected in patient case notes to map journeys of maternal and perinatal deaths in navigation software without requiring additional information from family members\". Comment 2: \"Though demographic characteristics and obstetric history serve as important information that gives context to any study of this kind, it is unclear how this is valuable for this specific report seeing that the author is emphasizing collecting data related to the women's travel. At the least, the author could minimize this information and make the tables smaller.\" Response: Both demographic and obstetric data are critical for understanding the personal stories as described by the World Health Organization and better understanding the context before the travel. This has been highlighted in the discussion, where I added \"Data on some relevant socio-demographic and all obstetric history, which will be helpful for efforts in building travel-relevant context of the maternal and perinatal deaths, were reported\". Comment 3: \"Why is it necessary to differentiate weekdays and weekends? The author should explain and also reflect on this in the discussion.\" Response: Thank you for this comment. An explanation has been added to the discussion, writing, \"Data on the day of travel and whether this is a weekday or weekend, which is important because of varying availability of transport options and degrees of traffic,14 were available in all cases. Having data on specific travel dates will be helpful in contextualising strikes, periods of petrol scarcity, lockdowns, protests, road blockages etc. which may all affect travel\". Comment 4: \"\"self-employed as petty traders (37.4%)\" in results should be 44%.\" Response: Thank you for picking this error. This has now been changed in the results. Comment 5: \"\"In terms of obstetric history, most maternal deaths were pregnant women with complications in a previous pregnancy (93.4%)\" in results. From the Table, it is \"NO\" with a score of 93.4% implying that 6.6 did not have complications in previous pregnancies'. Do check if my interpretation is correct.\" Response: Thank you for picking this error. This has now been changed in the results. The statement now reads, \"In terms of obstetric history, most maternal deaths were pregnant women with no complication in their previous pregnancy (93.4%)\" Comment 6: \"It would be appropriate for the author to address in greater detail the impact of the 42 that were referred on modelling the travel times, since the current approach estimates travel directly to the facility where the woman died. Also since mode was not known for 93% of the record, what would be the implication on assuming that everyone was driven?\" Response: As described in the methods, \"To map the journeys in Google Maps, the street name of women’s self-reported addresses and referral points were geo-referenced for each woman who had traceable journeys in the application\". The journey of those referred followed their actual path to care. A note on the limitation of assuming that all women were driven has been added as a limitation, writing, \"Second, an assumption was made that all cases used a motor vehicle to reach the health facility where they received care. While this may not always be the case, available evidence shows that nine in 10 pregnant women in emergency situations travel to care in a four-wheel vehicle in Nigeria.35\" Comment 7: \"Add period of travel to table 1.\" Response: This is in the table. Comment 8: \"In the discussion or conclusion, I suggest that the author suggest specific fields that could be added to current data collection instruments to aid the augmentation that they are suggesting.\" Response: Thank you for this very important recommendation. The concluding statement now reads \"The usefulness of information already collected in patient records can be significantly improved if more thorough travel to care history that captures the period of the day of commencement of travel to the health facility, mode of travel, condition of road during travel, referral points, time of referral, major incidents that might have affected or delayed travel, and arrival time at the health facility are taken when the pregnant woman presents in an emergency. Once again, thank you very much for your detailed review."
}
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}
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https://f1000research.com/articles/11-739
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https://f1000research.com/articles/11-529/v1
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16 May 22
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{
"type": "Research Article",
"title": "Mental health, suicide attempt, and family function for adolescents’ primary health care during the COVID-19 pandemic",
"authors": [
"Indiana-Luz Rojas-Torres",
"Mostapha Ahmad",
"Juan Manuel Martín Álvarez",
"Antonio A Golpe",
"Richard de Jesús Gil Herrera",
"Mostapha Ahmad",
"Juan Manuel Martín Álvarez",
"Antonio A Golpe",
"Richard de Jesús Gil Herrera"
],
"abstract": "Background: The study’s purpose was to identify associations between mental health risk, suicide attempts, and family function.\n\nMethods: A correlational, descriptive, and cross-sectional study was carried out in a group of adolescents in the last grade of secondary school to establish the association between mental health risk, suicide attempt, and family functionality. The instruments used were the self-report questionnaire, the suicide risk assessment scale, and the family APGAR. Data analysis was performed using the artificial intelligence algorithm (gower clustering). Results: 246 adolescents responded to the three instruments, which made it possible to select those with correlations of sensitive interest and, based on these, an intervention plan. Psychological distress was found in 28%, psychotic symptoms in 85%, and problematic alcohol use in 9%. Good family functioning was identified in 34% and some type of family dysfunction in 66%. In terms of suicide risk, there was a low suicide risk of 74%, 24% medium risk, and 2% high risk. It could be shown that there is a correlation in a group of 15% of the respondents. Conclusions: The risk of suffering mental health deterioration and the suicide risk, during this pandemic period, seems to be related to family functionality.",
"keywords": [
"Adolescent",
"Mental Health",
"Family Relationships",
"attempted suicide",
"Primary care",
"clustering algorithms"
],
"content": "Introduction\n\nThe World Health Organization (WHO) conceives mental health as the state of well-being of a person for the performance of their activities of daily life in the environment in which they are, overcoming the stressors that can be seen exposed (WHO, 2001). Good mental health allows the individual to maintain balance and harmony both individually and as a group (Loaiza et al., 2019).\n\nDuring the life course of early and intermediate adolescence, which includes the ages between 12 to 18 years (Ministry of Health, 2016), and late adolescence, which can extend to 21 years (Brittany Allen, 2012), changes occur of a biological, psychological, and socio-cultural nature (Garcia et al., 2015), in which manifestations related to depression, anxiety, eating disorders, and negative feelings that can lead to harmful behaviors such as self-destructive thoughts and suicidal ideation that are frequent (Texeira et al., 2020), and those are considered as the main risks of suicidal behavior itself (Canón and Carmona 2018).\n\nAccording to the WHO (2016), depression is the most common mental disorder, affecting more than 350 million people worldwide. Mental disorders, state the same organization, represent 16% of the global burden of diseases in people aged 10 to 19, with suicide being the third leading cause of death in young people aged 15 to 19 (WHO, 2019).\n\nIn the case of Colombia, the number of people between the ages of 0 and 19 years who consult for mental disorders is increasing every day. According to data from the 2003 National Mental Health Survey, during adolescence there is an increase in the frequency of symptoms related to mental health, the most common being anxiety, phobia, anguish, post-traumatic stress, and panic disorder (Ministry of Health, 2003).\n\nThe National Mental Health Survey conducted in 2015 showed worrying results related to depression and anxiety in adolescents. Suicidal ideation is the most frequent event with 6.6%, followed by the attempt with 2.6% and 1.8% for the suicide plan (Ministry of Health, 2015).\n\nBetween 2009 and 2015 there were 10,325 cases of self-harm, a phenomenon that increased between 2010 and 2016; people aged 15 to 19 comprise the highest rates of attempted suicide (Ministry of Health, 2017). In the years 2009 to 2017, 2,128,573 schoolchildren and adolescents with diagnoses associated with mental pathologies were attended. With an average of 236,508 people served per year, the trend is towards an increase in cases each year, with a significant decrease in 2016 (Ministry of Health, 2018).\n\nFor Siguenza (2015), the family is considered as the main resource and support group because it is the first contact of an individual with society, which helps adaptation and contact with other social groups. The support that the family provides and allows the person will be essential in their development and balance for both individuals and family (López, 2009).\n\nThe expressions of affection within the family nucleus are considered a family function that favors not only the dynamics but also the family union between parents and children (Velez and Betancurth, 2016). On the contrary, a dysfunctional family becomes a risk factor for the adolescent, with a greater possibility of risk in their mental health (Rivera et al., 2018).\n\nRecent studies associated with mental health in adolescents (Meng et al., 2020; Lee, 2020) bring up the emphasis on these factors, which become particularly relevant due to the processes associated with the situation on the pandemic global, and its behaviors of this adolescent. Especially when the first year of limitations has passed (emphasis in 2020), due to mobility/traffic control, teleworking, online education, and confinements adopted by public administrations, as measures to counteract the spread of such a pandemic.\n\nThe more social support adolescents receive there is an improvement in their mental state which favours the maintenance of emotions even in adverse circumstances. This evidence supports the need to propose and implement strategies to promote mental health and increase social support in adolescents (Gallegos et al., 2020; Galiano et al., 2021).\n\nFrom the nursing discipline, some different models and theories allow professionals in this area to guide the practice of their professional tasks In this regard, it is pertinent to specifically mention the theory of critical care proposed by Adeline Falk-Rafael in 2005. This theory in turn allows integrating this care from the social determinants of health, facilitating the understanding of various risk factors, and addressing them comprehensively and holistically in the subject of care (Dickson and Lobo, 2018).\n\nIn the method (measurement) subsection, emphasis is placed on three survey/questionnaire instruments to be applied to the target population sample. Likewise, new techniques of data analytics (artificial intelligence) are used to address specific problems associated with the data of such adolescents and how the variables that these represent could be grouped (clustering) in a meaningful way.\n\nIn school-aged order, it is hypothesized that the risk of mental health and suicide attempt in adolescents is associated with family functioning. The purpose of this study is to verify the relationship between mental health risk, suicide attempt, and family functionality in a group of adolescents in school-aged 16 to 20 years to cope with relevant interventions based on the North American Nursing Diagnosis Association (NANDA), Nursing Interventions Classification (NIC), and the Nursing Outcomes Classification (NOC).\n\n\nMethods\n\nThis study was approved by the Research Ethical Committee of the Simón Bolívar University of Barranquilla-Colombia. In compliance with the recommendations of the Committee, the endorsement of the Project from which the postulated article is the product corresponds to CIE-USB-CE-0267-00, legalized on May 24, 2019. The purpose of the study was explained to directors, teachers, parents, and students. Likewise, it was explained all of them about the objective of the research, the ethical, and scientific component for their authorization and participation. The student as participants were told that by accepting their involvement in the study, they would remain anonymous regarding the associated information from the surveys. Once this authorization is obtained, the links of the instruments are delivered to each teacher and selected groups. It is explained that the study constitutes academic information, oriented to the creation of strategies that promote Mental Health Promotion. Permission from the educational institution, informed consent from the parents, and assent from the adolescents were required for this study. Due to the physical limitations of the COVID-19 pandemic, written informed consent was obtained digitally on the project’s webpage.\n\nThe present study is of a correlational, descriptive, and cross-sectional type carried out in a group of adolescents between 16 and 20 years old from 21 district educational institutions in the city of Barranquilla-Colombia. The adolescents were attending the last grade of secondary school and received complementary studies in a technical education institution. The inclusion criterion in this study were that participants had to be Colombian belonging to the age groups of 16 to 20 years and being in secondary school involved in the complementary studies from a program of the Ministry of Education of Colombia1 in the city of Barranquilla-Columbia.\n\nThe average number of students per institution was thirty students, for a total of 630.\n\nIt is intended to establish the association between risk of mental health, suicide attempt, and family functionality for subsequent strategy design intervention from nursing. The sampling carried out was for convenience or intentional. The selected study subjects were conveniently available to the researchers in one place. As seen in the previous paragraph, the students came from different educational institutions in the city but received complementary technical studies at the same educational institution, which was available to the research group.\n\nThe procedure for the selection of the participants was carried out in a technical institution for training for work and human development in a group of 11th-grade of secondary school. This grade was selected because it is the last year of studies that adolescents take before entering university and given the needs of the mental health approach, an immediate nursing intervention plan was required in this group of students. This group of students have been prioritized taking into account the increase in the numbers of mental health problems that affects this age group and the level of studies in which the young people were found, which for the Colombian educational system is the last level before entering to university, which requires preparation for the process of change. The need then arises to detect exposure to risk factors early in order to prevent them with nursing care in Primary Care or refer them for timely management.\n\nThe students participating in the study come from different educational institutions in the city. The 21 educational institutions selected that had an agreement with the educational corporation for complementary studies participated. The students of the 21 educational institutions pursue complementary studies in a technical institution ‘CODETEC’ different from the one in which they carry out their regular studies. In this institution they pursue complementary studies according to their interests as assistants in public health, pharmacy, administrative health, beauty, oral health, job security, and customs, among others through an agreement between the Mayor's Office of the city of Barranquilla and CODETEC.\n\nThe complementary studies correspond to a program of the Ministry of Education of Colombia that aims to prepare students for job performance in one of the productive sectors and graduate with two degrees: the first accredits them as high school graduates and the second as assistants or technicians of a specific area2. During the process of collecting information, managers, teachers, and students were informed of the objective of the research, ethical, and scientific component for their authorization and participation. Due to the limitations imposed by lockdowns due to the pandemic in the city, in order to achieve access to the adolescents and operators of the questionnaires, a small Google link (Rojas and Gil, 2020) for presenting the project was developed and, with the support of WhatsApp, it was possible to digitally show the project to both the adolescents participating and the interested community, however the questionnaire was only sent to students as participants.\n\nIn this process, participating students have been informed that the questionnaires would be processed anonymously and that the information would only be used for research purposes. Each one of the students was accompanied and informed by their professors regarding completion of the questionnaires, which were delivered through the WhatsApp technological application with prior informed consent. Once this authorization was obtained, the links of the instruments were given to each professor and they in turn deliver it to the students included in the study to be filled out by the participants. The data were collected between June to December 2020.\n\nThe total population consisted of 630 students, who have been assigned an identification code, which has been used in each instrument to preserve the identity of the participants which allowed them to be related to each other and to exclude those participants who did not fill out all the three instruments outlined in the measurement section. To estimate the sample size, the statistical equation 1, has been applied.\n\nEquation 1: Equation used to determine sample size required for this study.\n\nN = Total population 630 students\n\nZ2 = probabilistic confidence (distribution factor 1.96)\n\nE2 = Error 5% (0.05)\n\np = 50% (0.5)\n\nq = 50% (0.5)\n\nSample calculation with the case data:\n\nn = 239 (Sample size).\n\n276 students filled out or completed the three instruments, of which 30 samples were excluded because they did not meet the inclusion criteria for filling in all three proposed information collection instruments. Finally, a total of 246 valid samples were obtained; a correlation of the study variables was identified in 37 of them.\n\nThe research on the field consisted of five people: one woman and four men. Two of the members are nursing professionals with experience in the disciplinary area, reading the application of models, theories, and nursing process. One of the nursing professionals has community experience in Primary Health Care. Two researchers have Ph.Ds. in Economics and the main doctoral researcher in Computer Science and IT. All of them with numerous publications in high-impact journals. The interdisciplinarity of the team allowed each one to contribute from their investigative and disciplinary experience to the achievement of the main purpose of the investigation of correlating risk variables in mental health, family functionality and suicidal risk to timely detect health problems in adolescents and act from them throw Primary Care for its promotion and prevention.\n\nBased on the first results obtained from the application of the instruments proposed for data collecting, in which mental health risk, family dysfunction, and suicide attempt in adolescents were identified, a detailed intervention plan was designed.\n\nFor the design of the intervention plan, first, the NNN consult database was consulted, which is an online tool that allows quick consultation of the standardized diagnostic languages developed by NANDA, NOC, NIC and the links between them. For the mental health risk variable, the nursing diagnoses called: tendency to adopt risk behaviors for health and anxiety were selected. Based on the previously selected diagnoses, NOCs for health-promoting behaviors and anxiety self-control were proposed, with their respective evaluation indicators. For the NIC, nursing interventions for health education and anxiety reduction were selected with the activities to be carried out for each case.\n\nIn the suicidal risk variable, the chosen NANDA nursing diagnosis was suicidal risk, for the NOC self-control of suicidal impulse and the NIC prevention of suicide. The proposed activities were focused on teaching the patient coping strategies, discuss plans to deal with suicidal ideation and implement actions necessary to reduce immediate distress.\n\nFor the family functionality variable, based on NANDA, the nursing diagnosis of dysfunctional family processes, the NOC family functioning, and for the NIC the stimulation of family integrity were prioritized. The main activities proposed were focused on helping the family maintain positive relationships, facilitating communication, facilitating harmony within the family.\n\n117 adolescents participated, who were selected from seven educational institutions where the variables under study were correlated.\n\nAll the students who were in grade 11 of the 21 institutions studied were included in this intervention project regardless of whether there was a correlation between the variables so as not to discriminate against the rest of the group in the process and not to point out (mark) adolescents, at-risk and, because it was a strategy of primary health care with a focus on promotion of the health. In which a nursing care plan is established that contains health education interventions and activities to reduce anxiety, suicide prevention, and stimulation of family integrity. Of the 21 educational institutions characterized, 11 institutions were prioritized within which students with connections of the three variables of the study were found: mental health risk, suicide attempt and family functionality.\n\nFor the design of the action plan and to propose a relevant educational intervention strategy, the online tool NNN Consult, and NANDA taxonomy were consulted (NNN Consult, 2017). From this resource, the domains considered most affected were identified, which were supported based on the variables understudy in the following nursing diagnoses: (See Table 1). Similarly, regarding the design of the intervention, the nursing results classification taxonomy (NOC) was applied with its respective indicators and the detailed nursing interventions classification (NIC) with their respective activities. These were selected taking into account the nursing diagnoses identified in the analysis of the results obtained from the data collection instruments: tendency to adopt risk behaviours for health, anxiety, risk of suicide, and dysfunctional family processes.\n\n\n\n1. Incorporate strategies to enhance self-esteem.\n\n2. Develop written educational materials at an appropriate reading level.\n\n3. Teach strategies that can be used to deal with unhealthy or risky behavior, rather than giving advice to avoid or change the behavior.\n\n4. Help the patient to recognize and express feelings such as anxiety, anger, or sadness.\n\n\n\n1. Help the patient to identify the situations that precipitate anxiety.\n\n2. Instruct the patient on the use of relaxation techniques.\n\n3. Establish recreational activities aimed at reducing tensions.\n\n\n\n1. Teach the patient coping strategies (assertiveness training, control of impulsive acts, progressive muscle relaxation), as appropriate.\n\n2. Discuss plans for coping with suicidal ideation in the future (e.g. precipitating factors, who to contact, where to seek help, ways to alleviate impulses for self-harm\n\n3. Implement actions necessary to reduce the individual's immediate distress by negotiate a non-self-harm or safety contract\n\n\n\n1. Help the family maintain positive relationships.\n\n2. Facilitate open communication between family members.\n\n3. Facilitate harmony within/between the family.\n\n4. Establish a relationship of trust with family members.\n\nConsidering the proposed objective in terms of establishing the relationship between mental health risk, suicide risk, and family functionality in school adolescents for a subsequent educational proposal, the pertinent literature was first considered.\n\nSecond, the main instruments used in primary care in mental health at the national and international level were reviewed based on the following studies “critical review of the instruments for psychiatric evaluation in primary care” (Tejada et al., 2014), collection instruments and information from the national survey of Mental Health contained in the methodological document national survey of Mental Health (Ministry of salud, 2015), and the electronic database bank of instruments and methodologies in Mental Health. The Bank of Instruments and Methodologies in Mental Health is a universal and free electronic database developed within CIBERSAM at the beginning of 2008, which aims to collect all the instruments in Spanish related to Mental Health, with the aim of facilitating access to the questionnaires (Cibersam, 2015).\n\nThe search for instruments in the area of mental health was carried out through different filters proposed by the search tool: in the type of population to which it is directed, adolescents and children were selected; in the criteria of therapeutic area, risk factors and projects and diagnosis; in type of alteration, all were selected. The results of this search were organized in an Excel matrix that summarized the following information for each instrument: instrument name, objective, description, author, psychometric properties, and internet link. Those that partially or completely adapted to the needs of the study in terms of early detection of risks in mental health were preselected, excluding those that did not fit the age group of adolescents or psychiatric pathologies themselves.\n\nInitially, 11 instruments used in mental health were preselected: Beck Anxiety Inventory, a useful instrument in early screening for depression or subclinical depression; the Alcohol Consumption Disorders Identification Test (AUDIT), an instrument capable of detecting non-serious problems related to alcohol consumption; the Family Apgar, used to identify families with possible dysfunctions; The Altman Self-Rating Mania Scale (ASM) is a brief scale developed to measure the presence and severity of manic symptoms; Anxiety Screening Questionnaire (ASQ-15), useful for detecting generalized anxiety disorders; Forages Adult Self-Report 18-59 (ASR 18-59), the ASR for adults aged 18-59 belongs to the assessment system to assess psychopathology; Scale of Interpersonal Difficulties for Adolescents, the EDIA scale evaluates the perception of adolescents about the level of difficulty of the situations; Generalized Anxiety Disorder (GAD-7), this scale assesses the severity of anxiety globally in patients who meet criteria for anxiety or depression; Suicide Risk Assessment Scale (ERS) evaluation of the risk of suicide in adolescents; Adult Psychiatric Symptom Self-Report Questionnaire (SRQ), this instrument provides the ability to determine the user's health status and assess the presence of a condition that may be related to mental health; Symptom questionnaire for children – RQC (Reporting Questionnaire for Children) useful to identify children and adolescents between 5 and 15 years old, who present symptoms compatible with possible mental disorders; GHQ-12 The GHQ-12 is an effective screening measure for assessing psychological well-being and detecting non-psychotic psychiatric problems in people; ASSIST V3.0 (Alcohol, Tobacco and Substance Use Screening Test). Those instruments that evaluated psychiatric pathologies, not applicable to the age group under study, not exclusive to Primary Health Care or those that only allowed the identification of a specific risk factor were excluded. For the inclusion criteria in the selected instruments, their applicability in Primary Health Care and the identification of risks in mental health and family functionality were taken into account.\n\nAfter reading the description of each of them and the purpose of their application, three instruments were selected: the Family Apgar, the Suicide Risk Assessment Scale (ERS), and the Self-Report Questionnaire of Psychiatric Symptoms in Adults (SRQ), which were consulted as valid by three academic experts in the area (Rojas et al., 2022). The variables evaluated with the three selected instruments are listed below. The experts were identified for their expertise in the area of mental health. The professionals were two nurses and a psychologist who not only participated in the selection of the data collection instruments, but also in the planning of the nursing care plan, suggesting interventions and activities to address the diagnoses identified in adolescents.\n\nMental health risk\n\nFor the analysis of this variable, the self-reporting questionnaire (SRQ) of psychiatric symptoms (Ministry of salud, 2020), was used. No changes were made to the instrument for the present study. The instruments were translated to English in the extended data after data collection (Rojas et al., 2022). This instrument measures five specific areas: depression, anxiety, alcoholism, psychosis, and epilepsy. It is applied to adolescents from 16 years of age onwards and consists of 30 questions with answer options of YES and NO. It consists of two parts: an initial one with identification data about the respondent, a block of 20 questions on non-psychotic psychiatric symptoms (anxious/depressive); a second segment of 10 questions that refer to psychiatric symptoms of a psychotic type, convulsive or alcohol consumption.\n\nFamily functionality\n\nTo identify the type of family function, the family APGAR instrument was used (Suarez Cuba and Espinoza, 2014). To identify the type of family function, the family APGAR instrument was used (Suarez Cuba and Espinoza, 2014). This instrument was designed in 1978 by Dr. Gabriel Smilkstein, who, based on his experience as a family doctor, proposed the application of this test as a tool for professionals in the area of primary health care, in their analysis approach. of the family role. This test is based on the premise that family members perceive the functioning of the family and can express the degree of satisfaction with the fulfillment of its basic parameters.\n\nThis test has called ‘family APGAR’ because it is an easy word for health professionals to remember, given the similarity with the nearly universally used test in newborn screening proposed by Dr. Virginia Apgar. This instrument evaluates five basic functions of the family: adaptation, participation, gain, affection, and resources. Each of the responses has a score that ranges between 0 and 4 points. When adding the five parameters, the score fluctuates between 0 and 20, which indicates good family function, moderate family dysfunction, mild family dysfunction, and severe family dysfunction.\n\nSuicide risk\n\nSuicidal risk assessment was carried out using the instrument for suicide risk assessment in adolescents. It is a Likert-type scale designed and validated in Colombia by psychologists Marly Bahamón and Yolima Alarcón in their research work (Bahamón and Alarcón, 2018). It evaluates these factors: 1) depression and hopelessness, 2) ideation, planning, and self-harm, 3) isolation/social support, and 4) lack of family support. The variables high, medium, and low were defined in the global suicide risk score according to the authors' instructions. described in the document entitled design and validation of a scale to assess the risk of suicide (ERS) in Colombian adolescents provided by the authors at the time of authorizing the use of the ERS scale for research purposes.\n\nAs a research pilot test, the questionnaires proposed for this research were previously applied to a small sample corresponding to 29 adolescents enrolled in school, in order to detect biases in the processing and analysis of information. The adolescents selected for the pilot test were school students from the same participating educational institutions, they were not excluded from the main study. The selection of the sample was random with a raffle to select the educational institution and the participants for the pilot and for the convenience of the different educational institutions, the links of the questionnaires were distributed via Whatsapp to the participants who in turn filled them out.\n\nThe results obtained made it possible to identify that there was no way to relate the results of the instruments: family functionality/mental health risk/suicide risk. Based on this analysis, the identification document number is included in the instruments but in processing it is replaced by a sequential numerical code to preserve its identity. In this way, not only the previous aspect is corrected, but also the information of adolescents who did not complete the three proposed instruments: SRQ, family APGAR, and ERS scale is also excluded.\n\nTo establish the association of the variables studied, the results obtained were analysed using machine learning techniques (clustering), which are tools that help to understand the different subgroups that exist within the data set. These techniques aim to group elements that are close enough to each other and far enough from other elements (Rokach and Maimon, 2005).\n\nTherefore, the Gower distance technique was used which is a measure of distance that can be calculated for two individuals whose attributes are mixed. The Gower distance is calculated as the average of the differences between individuals. Each Gower distance lies between [0,1]. The partial dissimilarity d (i, j) (f) depends on the type of variable we are measuring. In the case of numerical variables, partial dissimilarity is the relationship between the absolute differences between the observations and the maximum observed range of all individuals. In the case of categorical variables, the partial dissimilarity is 1 if the observations are different and 0 otherwise (Asensio et al., 2022). The formula applied is the following in the equation 2\n\nEquation 2: Gower distance equation used in this study.\n\nThe clustering algorithm selected should fit well with the Gower distance. For this, the k-medoids algorithm was selected, which is a classic partitioning method like the well-known k-means method but, instead of iterating over the centroids, it iterates over the medoids that is, it tries to find the most representative object of each group (Rokach and Maimon, 2005).\n\nThe algorithm groups the objects into a total of k groups where k must be given a priori. The selection of the optimal number of clusters (k) should be made considering the statistical information obtained in the data, although if there is some reasoned justification a priori, the number of clusters may vary for different reasons. For the optimal number of clusters to divide our data into, we use the width of the silhouette. The width of the silhouette is one of the most used options to measure the similarity between each point of a group and compares this similarity with the closest point of the neighbouring group. This metric is between [-1, 1] where higher values mean greater similarities (Asensio et al., 2022).\n\nFigure 1 shows the result of the measurement for values of k between 2 and 10 where it can be observed that segmenting the students into eight groups of five or six maximizes the similarity within the clusters and the dissimilarity between the clusters. The sample has been divided into eight groups following the results found in the silhouette analysis.\n\nSource: self-made by authors.\n\nThis result can be seen in Figure 2, a visualization with the observations classified in six clusters.\n\nSource: self-made by authors.\n\nNow comparing the characteristics, it can be seen where the differences are concerning surveyed students and with data that can be used for proper segmentation, to apply intervention strategies, The group represented in Table 2 are those that correspond to these groupings resulting from applying the algorithm, which will become a focus group (of interest or reference) for the research.\n\nTo improve the reliability and credibility of the information, the verification of the participants has been established through interaction in remote meetings during the class sessions in order to also contrast the results obtained with what the students said and thought about the subject under investigation. Following the methodological rigor proposed by Guba and Lincoln (1981) in terms of auditability, the skills of the study researchers have been used for the respective follow-up. In this way, the data was examined by the different researchers, reaching complementary contributions and conclusions around the research topic.\n\n\nResults\n\nA total of 246 adolescents were included in this study after completed all three tools in full. In relation to the socio-demographic variables studied of sex and age in the 246 adolescents studied, there is a higher proportion of women (65%) compared to men (35%). The participants were aged 16 years (33%), 17 years (42%), 19 years (6%), and 20 years (5%) respectively (Rojas et al., 2022).\n\nRegarding the non-psychotic psychiatric symptoms of the SRQ instrument, it was found that the most frequently reported symptoms were disinterest (44%), nervousness (37%), trouble thinking clearly (37%), indecision (37%), headache (33%), and fatigue (25%). The most frequently reported psychotic psychiatric symptoms were the belief that your feelings are more important than what others think (76%) and the feeling that someone has tried to hurt you (40%). These results indicate significant psychological pain (28%), psychotic-type symptoms (85%), and problematic alcohol consumption (9%).\n\nConcerning the family functionality obtained from the application of the family APGAR. The good family function was 34% while the remaining 66% presented some type of family dysfunction: mild family dysfunction (31%), moderate family dysfunction (21%), and severe family dysfunction (15%).\n\nRegarding the global suicide risk score in the surveyed adolescents, it was found that 74% presented a low risk for this variable, while 24% presented a medium risk, and 2% showed a high risk. When analyzing the relationship between the variables of the present study, it was possible to show that there is a significant correlation in 15% (37) of those surveyed (See Table 3).\n\nIn three adolescents, a high suicide risk, severe family dysfunction, and mental health risk were found; specifically, with symptoms indicating distress and psychotic symptoms. Similarly, a marked correlation was identified in twenty-three adolescents with medium suicide risk, and in eleven of them a low suicide risk and correlation of the same variables (Rojas et al., 2022).\n\n\nDiscussion\n\nThe findings are related to preliminary studies that show the prevalence of the female gender to present symptoms related to anxiety crisis, mood alterations, deep sadness among other symptoms compared to the male gender (Riecher-Rossler, 2017; Odéhn and Goulding, 2018; Chaskel et al., 2015). This may be a trend in this population group (female) due to family overload and psycho-social stressors (Sol-Pastorino et al., 2017).\n\nRegarding the clinical characteristics related to non-psychotic psychiatric symptoms expressed by the participants such as headache, nervousness, disinterest, confusion, fatigue, and psychotic type, such as feeling that they have tried to hurt and primarily significant psychological anguish, the capacity for self-recognition is striking adolescents themselves, which reflects the felt need for mental health. In this regard (Gómez-Rest EPO et al., 2021) expresses that the perception of inadequate mental health would gain importance because it allows the professional involved room for planning and a timely approach, especially in this stage of life, in which they are going through various processes and changes of a biological, psychological, and social nature.\n\nIn González et al. (2017) and Guo et al. (2018) studies, they highlight both the importance of family support as well as the negative influence of family stressors such as intra-family violence, inappropriate parental roles, and the breakdown of family dialogue as risk factors in adolescent mental health.\n\nIn the case of suicidal behaviour, a major trigger is a depression. Approximately 60% of people with depression have thought of suicide as a way out of their experiences and 30% attempted suicide (Rey et al., 2015). This behaviour is potentiated if there are family stressors, aggressions, loneliness, or suicidal behaviours in the family nucleus, among other related factors.\n\nWang et al. (2020) state that adolescents with high degrees of family dysfunction are more exposed to suffering psychological conditions that can affect their mental health and trigger a high suicide risk. Some scientific literature confirms the relationship of the suicide attempt with factors such as anxiety, traumatic events, and the social environment, which has a significant impact on the public health of a region (Arenas et al., 2016).\n\nThe authors (Radovic et al., 2015; Rey et al., 2015) suggest motivational therapies between parents and children as the main recommendations for family functioning which provides adolescents with security, resources, and strengths to face challenges, demands, and threats to their mental health. The strengthening of emotional skills is considered a key element that undoubtedly improves not only their self-esteem but also their perspectives towards their life project (Bonet et al., 2020).\n\nThe strengthening of the primary level of health care is required, as well as community empowerment and interdisciplinary work. In the same way, consider the training of human talent in health. The use of technologies also becomes a key factor specific to this age group with ‘e-mental health’ or ‘telepsychiatry’ (Rojas-Bernal et al., 2018).\n\nDue to the fact that these types of technological tools cause good receptivity in these age groups, they offer multiple benefits not only in education and health promotion, but also in prevention, diagnosis, treatment and recovery. They become a challenge for health professionals, and especially for nurses who are in charge of direct care, leadership and management in health promotion and maintenance programs.\n\nThe ability to determine whether the correlation between suicide risk, mental health risk, and family dysfunction has been influenced by current circumstances, derived from confinement due to the pandemic and the underlying climate. Although the corresponding methodological process and explanations were carried out in the completion of the information collection instruments, these were completed online, which may cause bias in the results obtained.\n\n\nConclusion\n\nThe results obtained suggest an interdisciplinary approach given the correlation between suicide risk, mental health risk, and severe family dysfunction in a significant group of scholarhood adolescents. It is important to emphasize the need for urgent attention to them, firstly because of the repercussions that these have on the age group studied and secondly, because of the degree of chronicity they represent in adulthood, presenting problems and conditions not only of a biological nature but also of a social and family one.\n\nIn the same way, it is evidenced that the integration of the parental role and family dynamics play a fundamental role in the actors involved, not only in prevention but maintenance, recovery, and rehabilitation in adolescents. This process should not be isolated but must include the school, the family, and the adolescent.\n\n\nData availability\n\nZenodo. Mental health, suicide attempt, and family function for adolescents' primary health care during the COVID-19 pandemic. https://doi.org/10.5281/zenodo.6466538 (Rojas et al., 2022).\n\nThe project contains the following underlying data:\n\n• Adult Psychiatric Symptoms Self-Report Questionnaire (SRQ). (Anonymised results from the SRQ questionnaire with English and Spanish versions)\n\n• Suicide risk data. (Anonymised results from the suicide risk questionnaire with English and Spanish versions)\n\n• Family Apgar Instrument. (Anonymised results from the family Apgar questionnaire with English and Spanish versions)\n\n• Consolidated instruments results. (This file contains the consolidation of the results of the three instruments applied to the population under study with English and Spanish versions)\n\n• Consolidated codified instruments. (This file contains the consolidation and coding of data from the three instruments used in the present study\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo. Mental health, suicide attempt, and family function for adolescents' primary health care during the COVID-19 pandemic. https://doi.org/10.5281/zenodo.6466538 (Rojas et al., 2022).\n\n• Figure 1. Gower model optimal clusters. (Figure 1 shows the measurement result for values. Similarity within clusters and dissimilarity between clusters are maximized.)\n\n• Figure 2 Viewing Gower Clusters. (Figure 2 provides relevant information organized into six 6 clusters. It can be seen where the differences are in terms of the students surveyed and with data that can serve for an adequate segmentation, to apply intervention strategies)\n\n• Table 1. Nursing process based on searches NNN Consult. (Table 1 shows the nursing care plan with the diagnoses, interventions and activities to be carried out, as well as the objective to be achieved according to the needs identified in the participants)\n\n• Table 2. Focal group selected by Gower's algorithm. (Table 2 shows the results of the focus group selected by the Gower algorithm)\n\n• Table 3. Correlation of variables. (Table 3 shows the correlation of variables of the three instruments applied to the study participants)\n\n• Self report questionnaire. (Blank copy of the self-reporting questionnaire with English and Spanish versions).\n\n• ERS Suicidal Risk scale. (Blank copy of the ERS suicidal risk scale with English and Spanish versions)\n\n• Family Apgar instrument. (Blank copy of the Family Apgar instrument with English and Spanish versions).\n\n• Annex web link of project information. (Link to send information on project to participants, parents, and institutions)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReporting guidelines\n\nSRQR checklist for ‘Mental health, suicide attempt, and family function for adolescents' primary health care during the COVID-19 pandemic [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6466538 (Rojas et al., 2022).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAllen B, Waterman H: Stages of adolescence. 2012.2012. Reference Source\n\nArenas A, Gómez-Restrepo C, Rondón M: Factors associated with suicidal behavior in Colombia. Results of the National Survey of Mental Health 2015. Revista Colombiana de Psiquiatria. 2016; 45(S 1): 68–75. PubMed Abstract | Publisher Full Text\n\nAsensio E, Almeida A, Galiano A, et al.: Using Customer Knowledge Surveys to Explain Sales of Postgraduate Programs: A Machine Learning Approach. International Journal of Interactive Multimedia and Artificial Intelligence. 2022; 7. Publisher Full Text\n\nBahamón Muñetón MJ, Alarcón-Vásquez Y: Design and validation of a scale to assess Suicide Risk (ERS) in Colombian adolescents. Universitas Psychologica. 2018; 17(4): 1–15. Publisher Full Text\n\nBonet C, Palma C, Gimeno-Santos M: Suicide risk, emotional intelligence and basic psychological needs in adolescents supervised in residential centers. Journal of Clinical Psychology with Children and Adolescents. 2020; 7(1): 30–37. Publisher Full Text\n\nCañón S, Carmona J: Suicidal ideation and behaviors in adolescents and young people. Rev. Pediatr Aten Primaria. 2018; 20(80): 387–397. Reference Source\n\nChaskel R, Gaviria SL, Espinel Z, et al.: Mental health in Colombia. BJPsych. International. 2015; 12(4): 95–97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCibersam: Bank of Instruments and Methodologies in Mental Health.2015. Reference Source\n\nDickson E, Lobo ML: Critical caring theory and public health nursing advocacy for comprehensive sexual health education. Public Health Nursing (Boston, Mass.). 2018; 35(1): 78–84. PubMed Abstract | Publisher Full Text\n\nGallegos M, Zalaquett C, Luna Sánchez SE, et al.: How to face the Coronavirus (Covid-19) pandemic in the Americas: recommendations and lines of action on mental health. Revista Interamericana de Psicología/Interamerican Journal of Psychology. 2020; 54(1): e1304. Publisher Full Text\n\nGaliano Ramírez M, Prado Rodríguez R, Mustelier Bécquer R: Mental health in childhood and adolescence during the COVID-19 pandemic. Rev. Cuba. Pediatr. 2021; 92Reference Source\n\nGarcía E, Romero N, Gaquin K, et al.: Risk behaviors in adolescents. Cuban Journal of Military Medicine. 2015; 44(2): 218–229. Reference Source\n\nGómez-Restrepo C, Malagón NR, Eslava-Schmalbach J, et al.: Factors associated with the recognition of mental disorders and problems in adolescents in the National Mental Health Survey, Colombia. Colombian Journal of Psychiatry. 2021; 50(1): 3–10. PubMed Abstract | Publisher Full Text\n\nGonzález RM, Martínez García L, Ferrer Lozano DM: Family functioning and suicide attempt in schoolchildren. Cuban Journal of Comprehensive General Medicine. 2017; 33(3): 281–295. Reference Source\n\nGuba EG, Lincoln YS: Effective evaluation: improving the usefulness of evaluation result drought responsive and naturalist approach. Hoboken; Jossey-Bass Publishers; 1981; p. 103-127.\n\nGuo L, Tian L, Scott Huebner E: Family dysfunction and anxiety in adolescents: A moderated mediation model of self-esteem and perceived school stress. Journal of School Psychology. 2018; 69(April): 16–27. PubMed Abstract | Publisher Full Text\n\nLee J: Mental health effects of school closures during COVID-19. The Lancet Child & Adolescent Health. 2020; 4(6): 421. PubMed Abstract | Publisher Full Text\n\nLoaiza J, Albornoz E, Sotelo R, et al.: Characterization of the mental health of medical school students. University, Science and Technology. 2019; 2: 125–131. Reference Source\n\nLópez C: Family interaction and emotional development in boys and girls. Rev Latinoam en Ciencias Soc Niñez. 2009; 7(2): 785–802. Reference Source\n\nMeng Q, Shuang-Jiang Z, Zhao-Chang G, et al.: The Effect of Social Support on Mental Health in Chinese Adolescents During the Outbreak of COVID-19. Journal of Adolescent Health. 2020; 67(4): 514–518. PubMed Abstract | Publisher Full Text\n\nMinistry of health and social protection (Min salud): Mental health newsletter Mental health in boys, girls and teenagers.2003. Reference Source\n\nMinistry of health and social protection (Min salud): National Survey of Mental Health 2015.2015. Reference Source\n\nMinistry of health and social protection (Min salud): Life cycle.2016. Reference Source\n\nMinistry of health and social protection (Min salud): Mental health newsletter suicidal behavior Subdirectorate of Diseases No communicable.2017. Reference Source\n\nMinistry of health and social protection (Min salud): Integrated Management Group for Mental Health. Mental health bulletin Mental health in children and adolescents.2018. Reference Source\n\nMinistry of health and social protection (Min salud): Instruments suggested in the comprehensive assessment for early detection of risks or alterations.2020. Reference Source\n\nNNNConsult: Herramienta online para la consulta y diseño de Planes de Cuidados de Enfermería. Elsevier; 2017. Reference Source\n\nÖdéhn N, Goulding A: Schizotypy and mental health in women and men from the general population. Nordic Psychology. 2018; 70(3): 198–208. Publisher Full Text\n\nRadovic A, Reynolds K, McCauley HL, et al.: Parents’Role in Adolescent Depression Care: Primary Care Provider Perspectives. The Journal of Pediatrics. 2015; 167(4): 911–918. PubMed Abstract | Publisher Full Text\n\nRey JM, Bella-Awusah TT, Liu J, et al.: Mood disorders Depression in children and adolescents. IACAPAP Child and Adolescent Mental Health Manual. 2015; (pp. 1–41). Reference Source\n\nRiecher-Rössler A: Sex and gender differences in mental disorders. Lancet Psychiatry. 2017; 4(1): 8–9. Publisher Full Text\n\nRivera R, Arias L, Cahuana M: Family profile of adolescents with depressive symptoms in the city of Arequipa, Peru. Rev. Chile. Neuropsychiatry. 2018; 56(2): 117–126. Publisher Full Text Reference Source\n\nRojas I, Ahmad M, Martín A, et al.: Mental health, suicide attempt, and family function for adolescents' primary health care during the COVID-19 pandemic [Data set]. Zenodo. 2022. Publisher Full Text\n\nRojas, Gil: Educational Intervention in School Adolescents of the District of Barranquilla.2020. Reference Source\n\nRojas-Bernal LÁ, Castaño-Pérez GA, Restrepo Bernal DP: Mental health in Colombia. A critical analysis. Ces Medicine. 2018; 32(2): 129–140. Publisher Full Text\n\nRokach L, Maimon O: “Grouping Methods” in the Knowledge Discovery and Data Mining Handbook. Boston, MA: Springer; 2005. 321–352.\n\nSiguenza WG: Family Functioning according to Olson's circumplex model [Thesis to opt for the master's degree in child and family psychotherapy]. University of Cuenca; 2015. Reference Source\n\nSol-Pastorino M, Vanegas-López J, Florenzano-Urzúa R: Mental health with a gender perspective. Public Health of Mexico. 2017; 59(6): 601–602. Reference Source\n\nSuarez Cuba MA, Espinoza Ma A: Familial APGAR: a tool to detect family dysfunction. Rev. Méd. Peace. 2014; 20(1): 53–57. Reference Source\n\nTeixeira L, Freitas R, Moura N, et al.: Mental health needs of adolescents and the nursing cares: integrative review. Text & Context - Enfermagem. 2020; 29. Publisher Full Text\n\nTejada PA, Jaramillo LE, Sánchez-Pedraza R, et al.: Critical review of the instruments for psychiatric evaluation in primary care. Rev Fac Med. 2014; 62: 101–110. Publisher Full Text Reference Source\n\nVélez C, Betancurth D: Family functionality and affective dimensions in school adolescents. Caldas-Colombia, 2013-2014. Investigaciones Andina. 2016; 18(33): 1751–1766.\n\nWang Y, Tian L, Guo L, et al.: Family dysfunction and Adolescents' anxiety and depression: A multiple mediation model. Journal of Applied Developmental Psychology. 2020; 66(September 2018): 101090. Publisher Full Text\n\nWorld Health Organization (WHO): Report on world health. Mental health: new knowledge, new hope.2001. Reference Source\n\nWorld Health Organization: WHO Fact Sheet on Mental Disorders No. 396.2016. Reference Source\n\nWorld Health Organization: Adolescent mental health. Data and numbers.2019. Reference Source\n\n\nFootnotes\n\n1 More information available at https://www.mineducacion.gov.co/1780/w3-propertyvalue-56741.html?_noredirect=1 and http://200.24.48.52/educa/index.php/doble-titulacion .\n\n2 http://200.24.48.52/educa/index.php/doble-titulacion"
}
|
[
{
"id": "137986",
"date": "11 Jul 2022",
"name": "Valentina Lucia La Rosa",
"expertise": [
"Reviewer Expertise Clinical psychology",
"Mental health",
"Developmental psychology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read with great interest the Manuscript titled “Mental health, suicide attempt, and family function for adolescents’ primary health care during the COVID-19 pandemic”, which falls within the aim of F1000 Research.\n\nIn my honest opinion, the topic is interesting enough to attract the readers’ attention. The Authors aimed to identify associations between mental health risk, suicide attempts, and family function in a sample of 246 adolescents. The results underlined that the risk of mental health deterioration and suicide during the pandemic was related to family functionality. The study methodology is adequate, and the conclusions are consistent with the reported data. The manuscript can be improved expanding the references and citing some recently published articles on this topic.\nAuthors should consider the following recommendations:\nI recommend a linguistic revision of the Manuscript to improve its readability.\n\nI recommend better describing the scales used in the study and further specifying their psychometric properties.\n\nInclusion/exclusion criteria should be better clarified. More specifically, it is unclear whether the authors excluded adolescents with psychiatric or psychological comorbidities from the sample. I recommend specifying this point more clearly as it could constitute a bias for the study results.\n\nI suggest citing other studies that have investigated the psychological well-being of adolescents during the pandemic in other countries to compare the authors' findings with those of these studies. Some suggestions are the following: doi:10.3389/fpsyg.2020.559951; doi: 10.1016/j.psychres.2020.113264\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "147902",
"date": "06 Sep 2022",
"name": "Sebastián Gabini",
"expertise": [
"Reviewer Expertise Psychology",
"mental health",
"mental health in workplace",
"psychometric assessment",
"quantitative analysis."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe research problem is clear and current. The rationale is well developed and contains relevant citations. The description and selection of the sample, the selection of the measurement instruments and the ethical considerations are consistent. Although in the SRQ instrument the criterion to determine possible psychosis is too narrow (and this is reflected in the results).\nHowever, methodological design contains some aspects to review. It is maintained that it is a correlational study but no specific statistics are applied to assess it (eg.: Pearson or Spearman correlation). In this case, the type of instrument (which gives quantitative raw scores as a result) would suggest the application of a statistic of this style, rather than a cluster analysis that tends to form groups. Table 3 (referred to as correlation between variables) contains the absolute frequencies for each group. If you choose to work with contingency tables to see the relationship between the variables, you should use statistics such as the chi-square. Note, for example, that about 65% of those who scored low on suicidal risk were from a dysfunctional family.\nFinally, the proposed intervention plan could be part of the study's suggestions but not within the methodology chapter.\nAdditionally, it is suggested to review the use of English.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-529
|
https://f1000research.com/articles/11-171/v1
|
11 Feb 22
|
{
"type": "Research Article",
"title": "Bayes factor benefits for clinical psychology: review of child and adolescent evidence base",
"authors": [
"Thomas B. Bertelsen",
"Asle Hoffart",
"Sondre Sverd Rekdal",
"Rune Zahl-Olsen",
"Asle Hoffart",
"Sondre Sverd Rekdal",
"Rune Zahl-Olsen"
],
"abstract": "Background: Statistical methods are a cornerstone of research in clinical psychology and are used in clinical trials and reviews to determine the best available evidence. The most widespread statistical framework, frequentist statistics, is often misunderstood and misused. Even when properly applied, this framework can lead to erroneous conclusions and unnecessarily prolonged trials. The implications for clinical psychology are difficulties in interpreting best available evidence and unnecessarily costly and burdensome research. An alternative framework, Bayesian statistics, is proposed as a solution to several issues with current practice. Methods: Statistical tests of primary outcome measures were extracted from 272 studies, which were cited in 11 recent reviews in the Evidence-based updates series in the Journal of Clinical Child and Adolescent Psychology. The extracted tests were examined regarding relevant features and re-analyzed using Bayes Factors. Results: When statistical tests were significant, the majority (98%) of re-analyzed tests agreed with such claims. When statistical tests were nonsignificant almost half (43%) of re-analyzed tests disagreed with such claims. Equally important for clinical research, an average of 13% fewer participants per study would have been required if the studies had used Bayes Factors. Conclusions: Bayes Factors offer benefits for research in clinical psychology through intuitive interpretations, and less costly trials.",
"keywords": [
"evidence-based",
"Bayesian",
"Bayes Factor",
"clinical psychology",
"child and adolescent psychology"
],
"content": "Introduction\n\nStatistical methods are a cornerstone of research in clinical psychology and play an important role when assessing the evidence base of treatments. Such methods are intended to rigorously test posited hypotheses and inform researchers and clinicians whether a treatment is effective or not, why it is effective, and how to improve treatment. In clinical psychology, the importance of appropriate use of statistical methods has been formalized into criteria, which are necessary to evaluate the evidence base for a treatment (Chambless & Hollon, 1998; Silverman & Hinshaw, 2008). Through the assessment of evidence-based treatments, statistical methods thus have far-reaching impact on what research is further developed, and ultimately what treatment clients receive.\n\nHowever, researchers in the field of clinical psychology over-rely on a single set of methods, despite certain limitations of these. The vast majority of research within this filed is namely based on the frequentist statistical methods, typically the p-value and confidence intervals (Nuijten et al., 2016). Considering the popularity of these methods, it is problematic that they can easily be misinterpreted and lead to challenges in conducting and interpreting studies. When designing a study and using frequentist statistics, one must consider that the reliability of tests is affected by how many tests are performed (Greenland et al., 2016). As a consequence frequentist methods do not easily allow for monitoring data while it is gathered (Dienes & Mclatchie, 2018). Moreover, ascertaining reliability requires larger samples and introduce ethical issues when planning and executing a study. The researcher faces a dilemma between gathering enough data to make valid inferences and burdening many clients with research procedures as well as risking delivery of ineffective or potentially harmful treatment to more subjects than necessary. The challenges in interpreting findings based on frequentist methods are related to how these methods work over many repeated trials, and thus the individual trial should be interpreted cautiously (Greenland et al., 2016). The described challenges are important as clinical decisions on which treatment to deliver are based on such research (for a review see Bakker et al., 2012; Kruschke & Liddell, 2018; Simmons et al., 2011). More particularly, nonsignificant findings (e.g., p = .07) may be taken to indicate a lack of effect, when they more appropriately should be taken to indicate an uncertainty about the existence of an effect. This in turn may lead to premature discontinuation of further research and recommendations for practice that overlook potentially effective — but as yet uncertain — interventions.\n\nA promising solution to these issues is Bayesian statistics (Kruschke & Liddell, 2018). These methods have not been widely applied in clinical psychology, although they have been gaining interest (Oldehinkel, 2016; van de Schoot et al., 2017). Previous studies have evaluated how p-values have been misreported in the field of psychology in general and how Bayesian methods can be beneficial for evaluating evidence-based treatments in an adult population (Sakaluk et al., 2019; Williams et al., 2020). However, the clinical consequences in terms of potentially increased sample sizes and recommendations for practice have not been investigated. In this article, we motivate researchers in clinical psychology to adopt Bayesian statistics by describing and empirically investigating the practical benefits of using Bayes Factors compared to p-values. To accomplish this, we conducted a reanalysis of studies included in 11 recent evidence base updates on treatments published in the Journal of Clinical Child and Adolescent Psychology (JCCAP) to investigate how the current practice of frequentist statistics affects the conclusions that are reached in this field of research and how the field can benefit from adopting Bayes Factors in place of or in addition to existing methods. The overall aim is to assess the clinical consequences of employing Bayes Factors versus p-values in research.\n\nTo enter a discussion of the clinical consequences of statistical choices, preliminary clarification of frequentist and Bayesian methods is needed. The frequentist methods begin with the p-value developed by Ronald Fisher (1934). This represents the probability of observing the treatment effect one has observed (or larger treatment effects) if there is no treatment effect. The hypothesis of no treatment effect is H0. If H0 is true, the p-value will vary between 0 and 1, with equal probability of any value (Rouder et al., 2009). That is, if H0 is true, we are equally likely to observe a p of .01 and .56. If H0 is false, p-values will tend to be small. The p-value informs us of H0, the hypothesis of no treatment effect, but it cannot directly tell us anything about the alternative hypothesis (H1), that the treatment is effective.\n\nTo improve this situation, Neyman and Pearson (1933) elaborated on the p-value method. They proposed a decision rule for concluding that the treatment works or not, after conducting several independent studies (Berger, 2003; Christensen, 2005). This decision rule does not inform the researcher whether she has made the correct decision for each study individually, but she would know how often she would make the wrong decision if the experiment was repeated indefinitely (Dienes, 2011; Szucs & Ioannidis, 2017). The decision rule is based on deciding, before the trial, which specific effect-size value is expected if there is no treatment effect (H0), and which if there is a treatment effect (H1). One then decides on acceptable values for α and β. The measure α is the error rate, which is the proportion of times the researcher will be wrong in concluding the treatment does work if the experiment was repeated indefinitely. The measure β is the proportion of times the researcher would be wrong in concluding the treatment does not work if the experiment was repeated indefinitely. Based on the values of H0, H1, α, and β, one computes a sample size. If the researcher has followed this method carefully, she can choose to conclude that the treatment does work if the p-value is lower than the set α-level or choose to say the treatment does not work if the p-value is above the set α-level (Berger, 2003; Szucs & Ioannidis, 2017). The α-level and p-value criteria are typically set to.05 based on a rule of thumb introduced by Fisher (1934)\n\nBayesian methods are an alternative to frequentist. These are based on the theorem by Thomas Bayes (Bayes, 1763), which states that the conditional relationship between two variables A and B is defined by P(A|B) = [P(B|A)*P(A)]/P(B). The Bayes Factor (BF) is an essential aspect of this approach as it formalizes how the data inform us. The BF indicates the relative strength of evidence in the data for two competing theories (Dienes, 2014). When noted as BF10 the Bayes Factor denotes the ratio of evidence for the alternative hypothesis compared to the null hypothesis. An example could be comparing the theory of a treatment effect to the theory of no treatment effect. The BF10 varies between 0 and ∞, where 1 indicates that the data does not favor one hypothesis over the other. Values above 1 indicate evidence for the alternative hypothesis, whereas values below indicate evidence for the null hypothesis. The BF is considered a degree of evidence and scales with the number of observations confirming one theory over the other. Since the BF gives us degrees of evidence and considers two competing hypotheses, it can give us three possible conclusions based on a single experiment, depending on the BFs magnitude: (a) There is evidence of a treatment effect, (b) There is evidence of no treatment effect, and (c) There is equal evidence for there being an effect and there not being an effect (Dienes & Mclatchie, 2018). There are no set rules for what counts as strong evidence and what does not, and one must consider the gravity of decisions when deciding what constitutes the strength of evidence. In a life-or-death situation 25:1 odds that a treatment works may not suffice, whereas when deciding what day of the week to begin a therapy session, a 2:1 odds for a preferred day may be more than enough to base a decision on.\n\nThe difference between frequentist and Bayesian methods is important when considering how many participants to include in clinical trials, and when to stop recruiting. Particularly the praxis of conducting statistical tests before a study is finished (hereafter monitoring data) is treated differently by the frequentist and Bayesian methods. Because the p-value is equally distributed between 0 and 1 when there is no treatment effect (Rouder et al., 2009), some p-values will be below .05 and some will be above, even when there is no treatment effect. Thus, researchers will always be able to obtain p < .05 if they conduct enough tests. When performing one test and using p < .05 as a decision criterion, the error rate is 5%, but when performing 20 tests and using the same decision criterion the error rate increases to 25% (Armitage & Rowe, 1969). To prevent this and to keep the error rate stable, one must correct the p-value for the number of tests performed (Kruschke & Liddell, 2018). Thus, frequentist methods are penalized by the number of tests performed. As a consequence, researchers face an ethical dilemma with regard to the trade-off between sample size and ability to monitor data as it is collected. If the treatment is effective and not harmful, it would be unwise to monitor subjects often because this would lead to the unnecessary prolonging of the trial and more people receiving an inferior control treatment. However, if the treatment is not effective or even harmful, it would be unwise to monitor subjects infrequently. This would lead to more people receiving harmful or inferior treatment.\n\nBayesian statistics offer a solution to this dilemma, by questioning why it should matter how many, or when, tests are performed (Dienes, 2011). In frequentist methods, one assumes that H0 is true and then proceeds to describe the observed data with probability statements. The question asked is “what is the probability of observing these data, if there is no effect?”. In Bayesian statistics, one assigns probability statements to the hypothesis not the data. The question asked here is “What is the probability that there is a treatment effect when we have observed these data?”. Because of this difference in the view of the data, Bayesian analysis can be performed as many times as you want without jeopardizing the reliability of the results. You can stop sampling when results are convincing either way. Bayesian methods are affected by the how convincing the data are of a hypothesis and how much evidence one requires to make a satisfactory conclusion (Dienes & Mclatchie, 2018; Dienes, 2011; Wagenmakers et al., 2018).\n\nSince the BF does not depend on the testing plan of the researcher, it does not matter if researchers test hypotheses only at the end of a clinical trial or if one tests every time a new subject enters. Bayesian methods allow gradual decisions to be made based on continuous monitoring of data because the BF is not affected by testing intentions. The implication of this is that Bayesian methods may reach conclusions in clinical trials faster than classical methods. Thus, using the BF may pose less burden on participants.\n\nIn addition to the speed of trials, Bayesian methods, such as BFs offer advantages in terms of interpreting findings. After a trial, researchers wish to know whether the treatment works or not, that is, whether H1 or H0 is true. Such questions are however not easily answered using frequentist methods. The p-value assumes that H0 is true and gives the probability of our observation under that assumption. Thus, the p-value cannot be used to indicate whether a treatment works or not and is at best a weak heuristic for decision making. The method proposed by Neyman and Pearson does inform us whether the treatment works or not, however, only after many repeated trials. Indeed, using this method, we must accept that the single trial does not inform us.\n\nContrary to the frequentist methods, the BF allows us to make inferences based on each conducted study, with higher values indicating stronger support for the theory that there is a treatment effect. The BF also allow us to gather evidence for the theory that there is no treatment effect. This is underappreciated but highly advantageous for clinical research. Just as important as it is to know that a treatment works, it is equally important to know that it does not work and that it should be aborted. Another unique benefit of BFs is that they allow us to distinguish between evidence for a theory and lack of evidence (Gallistel, 2009; Morey et al., 2016; Wagenmakers et al., 2018). Imagine a researcher expecting a 40% rate of remission if there is no treatment effect (from pure placebo) and an 80% rate of remission if there is a treatment effect. If she in a study observes a 60% rate of remission, this will not seem to favor one theory over the other and the BF will inform the researcher about this. The approach by Fisher may conclude that the observed effect is improbable if there is no treatment effect. With several equal results, the method by Neyman-Pearson leads the researcher to reject the theory of no effect. Thus, data may lead to conclusions in the frequentist methods when the data does not suggest that one theory is more likely than the other. This difference between the statistical paradigms is of importance for clinical researchers since they will lead to different motivations for further research, and different recommendations for practicing clinicians. Non-significant findings may potentially lead to reduced interest in a research area and recommendations against using such interventions in practice. This is problematic if the BF suggest that the treatment may be effective.\n\nWe have described some major benefits of the Bayesian statistics, with emphasis on BFs, compared to frequentist approaches and highlighted the practical implications of these. To better understand the real-world implications of BFs versus frequentist we aim to empirically demonstrate how a specific subfield of clinical psychology has been affected by statistical choices. To investigate this, we selected the meta-analytic reviews in the evidence base updates on treatments published in the Journal of Clinical Child and Adolescent Psychology (JCCAP) between 2017 and 2019. From these we extracted the statistical tests on primary outcome measures, and reanalyzed these using BFs. The subfield of clinical child and adolescent psychology was selected for two reasons. First, within this subfield there is an inherent power imbalance between adult researchers and non-adult clients. Thus, it is of particular importance to follow the ethical imperative to not burden clients through research. Second, the evidence-base updates series in JCCAP has highly transparent reporting standards, allowing for easy identification of individual studies and primary outcomes within studies. We investigated two primary hypotheses:\n\n1. The conclusions reached in current practice would have been reached with a smaller sample size if data had been monitored using Bayes Factors.\n\n2. Current research practice indicates an effect or lack of effect when there is no evidence in the data for such conclusions.\n\n\nMethods\n\nThe study is a cross-sectional analysis of a strategic sample of articles that laid the foundation for the evidence base in child and adolescent clinical psychology between 2017–2019. The sample was selected to investigate what statistical analyses make up the evidence base in clinical child and adolescent psychology. The definition of evidence base was articles contained within the evidence base update series of Journal of Child and Adolescent Clinical Psychology. Thus it is important to note that our sample does not contain the entire evidence base for child and adolescent psychology. Rather it contains those articles that we believe have had substantial influence as evidence base.\n\nA set of 11 meta-studies, reporting on treatment effects, in the evidence base updates series of the Journal of Child and Adolescent Clinical Psychology published between 2017–2019 was selected to extract individual articles from. These include the evidence base updates on psychosocial treatments for: early childhood anxiety and related problems (Comer et al., 2019), children and adolescents exposed to traumatic events (Dorsey et al., 2017), children and adolescents with attention-deficit/hyperactivity disorder (Evans et al., 2014), pediatric obsessive-compulsive disorder (Freeman et al., 2018), self-injurious thoughts and behaviors in youth (Glenn et al., 2019), disruptive behaviors in children (Kaminski & Claussen, 2017), ethnic minority youth (Pina et al., 2019), child and adolescent depression (Weersing et al., 2017), and pediatric elimination disorders (Shepard et al., 2017) as well as outpatient behavioral treatments for adolescent substance use (Hogue et al., 2018) and treatments for youths who engage in illegal sexual behaviors (Dopp et al., 2017). Inclusion criteria for individual articles within meta-studies were the presence of a control group condition, the description of quantitative measures of treatment outcomes that allowed the calculation of Cohens d (Cohen, 1988) and Bayes factors from summary statistics. Summary statistics eligible for inclusion were contingency tables, regression models, generalized linear regression models, binary proportions, χ2 values, F-values, means, and SD or SE, t-tests, correlations, odds ratios, hedge’s g, and η2. The selection of studies was based on a full reading to assess eligibility. Study selection was conducted independently by the first and third authors on the evidence base update on early anxiety interventions (Comer et al., 2019), with complete agreement on which studies to include. Further information about which studies were included can be found in the extended data (Bertelsen, 2022).\n\nMeasures associated with primary outcomes within each study were extracted by hand. These included the effect size measure, how authors interpreted the p-value, and the n associated with the test. If multiple summary statistics were available for the same treatment outcome (e.g., reporting t-tests and means and standard deviations), the summary statistics that required the least assumptions about the data were preferred over those that required more assumptions. That is, means and standard deviations were preferred over t-values, which were preferred over F-values, which were preferred over regression models, and so on. A subset of 29 (11% of included) articles was independently assessed by the first and third authors, with complete agreement on the description and interpretation of p-values, and which effects were primary. For the effect-size measure and n associated with it, there was high inter-rater reliability (Cronbach’s α = 0.91). Disagreement between authors was handled through discussion.\n\nAn outcome was defined as primary if described as such within the article. If such information was not available, the definition was based on whether the evidence base update article, in which it was included, had treated it as a primary outcome. If this was not available, it was based on whether other studies within the same field had defined the present outcome as primary.\n\nAssessment of whether a test was treated as significant or not was based on authors’ reports. If such reports were not available, tests were supposed to be treated as significant based on the described cut-offs for significance elsewhere in the article. If this was not available, the cut-off of p < .05 was used.\n\nThe authors' interpretation of the p-value was coded as either indicating an effect of treatment, no effect of treatment, or a negative effect of treatment (e.g., the control group performs better). If authors described a significant treatment effect or described that the treatment was better or outperformed the control condition, this was taken as indicating a treatment effect. If authors reported no differences, not significantly different, or simply did not describe any outcome measure, this was taken as indicating equality. If authors described a treatment as worse than, or having a negative effect, or control groups being superior, this was taken to indicate a negative effect of treatment.\n\nThe n associated with a test was extracted for participants in the treatment condition and the control condition. If Intent-To-Treat analyses were available, these were used and the n associated with these was extracted.\n\nCalculation of Bayes factors from summary statistics was conducted in R (R Core team, 2020) using the BayesFactor package (Morey & Rouder, 2018). The aim of these methods is to calculate the Bayes Factor as a comparison between the likelihood of the null-model and the alternative using priors that have been developed to be sensitive to change, while becoming increasingly stable as sample size increases. These methods are described by Rouder et al. (2009) for outcomes that allowed the calculation of t-statistics (81% of summary statistics). For outcomes for which binomial proportions were available (13% of summary statistics), or computable, Bayes factors were calculated using the method described by Kass and Vaidyanathan (1992). In the case of χ2-statistics (5% of summary statistics), the method described by Johnson (2008) was used to calculate Bayes factors. In the cases of tests, in which only R2 values were available (0.4%), the method described by Rouder and Morey (2012) was applied to calculate Bayes factors. Finally, some outcomes only gave results as odds ratios (0.4% of summary statistics), without other available information. These outcomes were recalculated into Cohens d and interpreted as t-statistics and Bayes factors were calculated based on this.\n\nIn the presented analyses, the inferential statistic is either represented as the Bayes factor (BF) or credibility interval. The BF describes the hypothesis of an effect (H1) over the hypothesis of no effect (H0) unless otherwise specified. The credibility interval (CI) describes the interval where the parameter is with 95% probability, with values closer to the centre being more probable. For all analyses, priors were specified with the intent that conclusions should be primarily influenced by observed data. For continuous outcomes the prior distribution was Cauchy distribution with a location parameter of 0 and a scale of 0.7. For categorical outcomes the prior was a beta distribution with parameter a = 1 and b = 1.\n\nAnalysis of p-value reporting\n\nTo ensure that differences between BFs and p-values did not reflect erroneously reported p-values, the sample was checked for inconsistencies in reported statistics using the p-checker app (Schönbrodt, 2018). Tests that were reported as significant or nonsignificant at a set level but reported a statistic that would lead to a p-value in the opposite direction were coded as mismatched. Such situations would be when p < .05 was reported, but the test statistic resulted in p > .05 or vice versa. This implies that either the summary statistics, the reported p-value, or the assumptions underlying the tests were incorrect. After removing tests that indicated mismatched p-values, we calculated BFs based on the reported statistics. This was done to ensure that differences between BFs and p-values did not reflect erroneously reported p-values.\n\nSample size with Bayes Factors\n\nTo analyze the expected required n if Bayes Factors had been used in the studies, we used the BFDA package in R (R Core Team, 2020; Schönbrodt & Wagenmakers, 2018), to simulate 10,000 repeated studies based on the median observed effect size of the articles. We simulated a design where data was monitored continuously with stopping rules being either (a) achieving a BF > 9 or (b) achieving a sample size that would have 95% power to achieve a BF > 3 if the effect was present. In performing these simulations, we assumed a non-informative prior. The first stopping rule (BF > 9) was chosen based on preliminary testing suggesting this stopping rule would result in a false-positive rate below .05, which we believe would be reasonable to researchers accustomed to using α = .05. The second stopping rule (BF > 3, with 95% power) was chosen as a futility limit, based on our belief that researchers would not sample indefinitely if the data gave them no indication of an effect and they would expect to see an indication if there was an effect.\n\nCategorization of Bayes factors\n\nTo exemplify the difference between inference based on p-values and BF we divided the BFs into eight categories based on recommendations in common use (Wagenmakers et al., 2018). We describe BFs between 0.33 and 3 as “not worth a bare mention”, between 0.05–0.33 and 3–20 as moderate evidence for H0 and H1, respectively. BFs between 0.0066–0.05 and between 20–150 are seen as strong evidence for H0 and H1, respectively, whereas values below 0.0066 and above 150 are seen as very strong evidence for H0 and H1, respectively. These categorizations should not be seen as objective demarcations of truth, but rather a simplified model for the reader. In our analysis we mainly focus on whether a BF is above or below 1 and whether it is within the range of “not worth a bare mention” (0.33–3). The aim of this focus is to assess how results would have been interpreted differently using BFs both in terms of direction of conclusion and whether evidence was strong enough to draw a conclusion.\n\n\nResults\n\nIn the 11 evidence base updates assessed, 309 articles were described. Of these, we were unable to obtain 5 of the original articles. Additionally, 12 articles did not report summary statistics that allowed for the recalculation of Bayes factors. Finally, 5 articles did not include a control group or comparison condition (i.e. pre-treatment measures or benchmark) and were thus not selected for further evaluation. In the remaining 287 articles, 24 appeared in more than one evidence base update. In the final 263 articles, 272 studies were included for analysis, with 26170 participants (M = 96.5, Mdn = 65, min = 6, max = 832), and 2431 statistical tests were extracted, with a mean of 9.4 statistical tests on primary outcome measures per study (min = 1, max = 175). The mean observed power of the studies was 0.77 (min = .03, max = .99). Of the 2431 statistical tests, 171 showed indication of mismatched p-values and thus 2260 were used for further analysis. See Table 1 for a summary of descriptive statistics.\n\na A p-value mismatch indicates a mismatch between p-values calculated from summary statistics and those reported, that would have lead to a difference in interpretation.\n\nb The Bayes Factor (BF) indicates the ratio of evidence for an effect compared to evidence against an effect.\n\nOur first hypothesis was that conclusions reached in current practice would have been reached with a smaller sample size if data had been monitored using Bayes Factors. To assess this, simulated replications of each study were conducted based on the median observed effect size. The observed sample size and that required by Bayesian methods are shown in Figure 1. This shows that the Bayesian method requires smaller sample sizes than the observed studies as a function of effect size. Using Bayes Factors and monitoring data until reaching a BF > 9, studies would have reached conclusions with an average of 10.4 (95% CI [4.8, 16.1]) fewer participants per control group compared to what was observed. The average relative decrease in sample size was 12.7% (95% CI [5.0, 20.5]). Across studies, 1656 (95% CI [1649, 1664]) fewer participants would have been required if Bayes Factors had been applied. To understand the implications of a smaller required sample, a subset of studies that reported on suicide attempts (k studies = 17) were further analyzed. Within the Bayesian replication, using power equal to the described studies, an estimated 67 individuals who attempted suicide would not have been placed in a control group due to fewer required participants. Overall, these findings support the hypothesis that smaller sample sizes would be required if monitoring data using Bayes Factors.\n\nNote. Effect size is measured in Cohens d. Participants describes number of observed or required participants per group. The required N with Bayesian monitoring describes the expected participants per group if one monitored data and stopped collecting when reaching a Bayes Factor of > 9.\n\nOur second hypothesis was that current research practice indicates an effect or lack of effect when there is no evidence in the data for such claims. To assess this hypothesis, BFs were calculated on the basis of summary statistics and compared to the claims made in the articles. Results shown in Table 2 indicate that when findings were claimed to be support for H1 the majority of BFs were in agreement with that claim. Of the p-values deemed significant, only 1.8% (n = 21) were evidence in the direction of H0 (BF10 < 1), whereas 3.3% (n = 39) were “not worth a bare mention”. In the case of findings claimed to be support for H0, the BFs did not uniformly support such claims. Of the p-values deemed nonsignificant 43.6% (n = 470) were evidence in the direction of H1 (BF10 > 1) and 50% (n = 539) were “not worth a bare mention”. Among the tests that were reported as nonsignificant, but the BF indicated evidence in the direction of H1, 61.3% (n = 301) had used correction methods to lower the α-level. These findings indicate that when research indicates the presence of an effect there is evidence in the data for such a claim. However, these findings also suggest that when research indicates a lack of an effect the evidence in the data does not generally support such a claim.\n\nTo expand on these findings Table 2 depicts BFs in relation to what the authors of articles argued the test to indicate. When authors had argued for the existence of a treatment effect 94.6% of tests indicated support for this statement (BF > 3), whereas 4.3% indicated not much evidence (BF: 0.33–3) and 1.9% indicated evidence for lack of an effect (BF < 0.33). When authors had argued that a test indicated a lack of difference or an equality 23.4% of tests supported this statement, whereas 50.5% indicated not much evidence and 26.1% indicated evidence for the existence of an effect. When authors had argued that a test indicated superiority of the control group condition 71.4% of tests supported this statement, whereas 23.8% indicated not much evidence and 4.8% indicated evidence for the lack of superiority of control group condition.\n\n\nDiscussion\n\nThe purpose of this paper was to investigate how the widespread use of frequentist statistics affects research in clinical psychology, and what benefits the field may have from incorporating Bayesian methods, such as Bayes Factors. 11 recent evidence base updates were selected, and 2431 tests were extracted from 272 included studies. Sample size estimation with Bayesian methods using data-monitoring indicated that we would expect a decrease in the expected sample size per study of 12.7% due to being able to monitor the data while it was gathered. Among tests in which p-values were reported correctly, 55% of the tests did not strongly support the hypothesis claimed by the p-value when reanalyzed with Bayes Factors. Unfortunately, 22% of tests supported the opposite hypothesis of that stated by the p-value. Of clinical importance when statistical tests were used to argue for a lack of effect, only 23% of tests were in agreement with this, with slightly more (27%) indicating the existence of an effect.\n\nThe results indicate that the required sample size in studies could have been considerably reduced had Bayes Factors been adopted. This is due to the ability of these methods to allow for continuous monitoring of data and altering of the trial as it is in progress. These aims are difficult to attain with corresponding frequentist methods, which require a large and predefined sample size to allow for multiple comparisons (Berry, 2004). The ethical importance of requiring lower n is particularly poignant in the case when negative outcomes may befall participants in control group conditions. In the current study, it was found that 67 individuals who attempted suicide and were placed in a control group would not have been placed in a control group if Bayes Factors were applied. Although this does not directly support the statement that they would not have attempted suicide if Bayes Factors had been applied, one cannot preclude that allocation to the control instead of the treatment group contributed to demoralization and suicidality.\n\nOverall p-values described as significant indicated evidence in favor of H1 when reanalyzed with BF, with 96% (n = 1132) having a BF above 3. Of greater concern is the finding that only 23% (n = 244) of the nonsignificant findings showed evidence in the direction of H0 (BF10 < 0.33), with 27% (n = 296) showing evidence in favor of H1 (BF10 > 3) and 50% (n = 539) showing not much evidence at all (BF10 0.33-3). A substantive explanation for this is the low power of studies or using error-control procedures that lowered power. However, it remains that tests were used to conclude lack of effect or no difference, when in fact the data suggested the existence of an effect. This may at first glance seem confusing and leave researchers asking what to believe – the BF or the p-value? Such phenomena have been described as “Lindley's paradox” (Shafer, 1982), but do not constitute any real paradox. Instead, these showcase the difference in interpretation of data in the frequentist framework and the Bayesian. There is no paradox between (a) the frequentist interpretation: observing this data is not unlikely if H0 is true and (b) the Bayesian interpretation: H1 is more probable than H0 if we observe this data. Based on the articles analyzed, the impression is that researchers wish to assess whether treatments work or not, which fits well with the aims of Bayesian methods. Indeed, from a clinical perspective it seems intuitive and valuable to wish to know which hypothesis one should believe.\n\nA strength of the current study is that it evaluates the performance of frequentist methods and Bayesian methods on findings that are clinically meaningful. Previous studies have assessed p-values and BFs based on summary statistics regardless of whether these were supplementary (e.g., correlation tables or sample demographics) or of primary concern (clinical outcomes) (e.g., Nuijten et al., 2016; Wetzels et al., 2011). Other studies have evaluated the use of Bayesian statistics and their benefits for clinical practice from a theoretical perspective or using simulation studies (Dienes & Mclatchie, 2018; Kruschke & Liddell, 2018; Wagenmakers et al., 2018). To our knowledge, this is the first comprehensive empirical assessment of how frequentist compared to Bayesian methods affect the field of clinical psychology.\n\nSome limitations of the current study are important to note. The effect-measures and Bayes factors calculated in the present study are based on summary statistics from published articles and not on the observed data. Regarding the calculation of effect size measures and BFs, this should be of little consequence, given that the margin of error between summary statistics and observed data are generally inconsequential (Lin & Zeng, 2010).\n\nA second limitation of the current study relates to estimates of the required sample size if one had used Bayesian methods. These estimates are based on simulated replications of studies and not actual studies and thus only describe what we would expect to see if we repeated the studies, not what we necessarily would observe. In line with this, it is not possible to know whether fewer suicide attempts would have been made if a Bayesian design was employed. However, we can make the counterfactual argument that these suicide attempts were seen in control groups given the observed design, and we would not have expected them given the use of Bayesian methods.\n\nAnother possible limitation of the current study is the use of non-informed priors, that is, assuming that there was no pre-existent evidence for or against the hypotheses. One may rightfully raise the question that the findings would have been different had we used alternative, more informed, priors. This is correct, and it is important to acknowledge that the findings in this article are not intended to absolutely refute the findings of the analyzed articles. The intent is rather to question whether statistics are best represented as a dichotomous choice, as in frequentist methods, or as degrees of evidence, as in Bayesian methods. Indeed, the ability to specify priors is itself helpful for research as it allows a fruitful discussion of how knowledge accumulates. Specification of priors is further useful as they may increase the power of studies by incorporating information from previous studies or clinical experience. Additionally, Bayesian priors represent a more reasonable assumption than that of the p-value, which assumes that H0 is true. It seems odd that one would wish to carry out a study on the effect of a treatment if one from the onset assumes that there is no effect.\n\nThe presented findings have implications for current and future evidence-based clinical practice. Currently evidence-based practice is defined as the integration of best available research with clinical expertise (APA Presidential Task Force on Evidence-Based Practice, 2006). However, it is not specified how to integrate these two. Without systematic integration, meta-studies such as the evidence-based update series may be prioritized over sound clinical expertise. This is of particular concern given that 77% of nonsignificant findings from the evidence-based update series did not indicate a lack of effect. In addition to giving a non-dichotomized description of findings, Bayesian methods also allow a simple heuristic to integrate clinical expertise with research findings. This is done by specifying the BF and prior belief based on clinical experience. As an example, a researcher may have considerable experience with hypnotherapy for enuresis leading him to be 90% certain that this is an effective treatment. The researcher learns about a study that found nonsignificant effects of this treatment and calculates the BF to be 1.5, thus weak evidence that hypnotherapy is ineffective. His prior odd were 9:1, the BF is 1.5:1 which means his posterior odds is 13.5:1, expressed as a probability his posterior belief that the treatment is effective is 93%.\n\nThe implications for future evidence-base are related to the possibilities afforded by Bayesian methods due to the ability to continuously monitor data as it is collected and alter treatment while a study is ongoing. In addition to reducing sample size needed this also allows for studying domains that are otherwise difficult due to ethical concerns. An important case is studies of populations where suicide may be a potential outcome. Despite the ethical imperative to improve and find effective treatments for such populations they may be understudied due to ethical issues that are a consequence of frequentist design. Using Bayesian methods one can conduct studies on such population in a way that closer resembles clinical practice, where one continuously tweaks current practice based on available information. Such changes in research opportunities may lead to important discoveries with ramifications for clinical practice.\n\n\nConclusions\n\nClinical psychology seems to be comprised of researchers who are pragmatic, concerned with study ethics, and who want to know what works for whom. Frequentist methods are at odds with these characteristics: they place researchers in ethical dilemmas while collecting data, and force dichotomized thinking on researchers. Some suggest that researchers should suit their research to accommodate their statistics (Kerr, 1998); we suggest the opposite – researchers should suit their statistics to accommodate their research. By using Bayesian statistics, many of the practices which are currently problematic for the field (i.e., monitoring data, interpreting findings) will no longer be so. This does not imply that researchers should be careless. However, the type of considerations researchers make may become more clinically meaningful when switching to Bayesian methods.\n\nResearchers should not need to be reluctant to monitor data because this may alter the validity of their inference. Instead, they should assess intervention effects continuously and make appropriate alterations of studies as they are conducted. Researchers should not need to interpret findings in a binary fashion. Rather, they should test competing substantial hypotheses and assess to which degree these are supported.\n\n\nData availability\n\nOpen Science Framework: Bayes Factor Benefits for Clinical Psychology. https://doi.org/10.17605/OSF.IO/UB5PJ (Bertelsen, 2022)\n\nThis project contains the following underlying data:\n\n• BayesFactorOutcomeDataShare.csv (Contains data used for analysis of all tests performed, contains information on BFs of individual tests and whether the test was assessed as significant)\n\n• BFSpeedDatashare.csv (Summary data of data used to compare sample size required for Bayesian studies. Contains reported sample size and recalculated sample size as well as Mean cohens d)\n\n• DataKey.docx (Contains data key for variables in BayesFactorOutcomeDatashare.csv and BFSpeedDatashare.csv)\n\n• Supplement.docx (Contains references to all studies included and reanalyzed as well as which meta-analysis they were related to)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
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PubMed Abstract | Publisher Full Text\n\nHogue A, Henderson CE, Becker SJ, et al.: Evidence Base on Outpatient Behavioral Treatments for Adolescent Substance Use, 2014-2017: Outcomes, Treatment Delivery, and Promising Horizons. J. Clin. Child Adolesc. Psychol. 2018; 47(4): 499–526. PubMed Abstract | Publisher Full Text\n\nJohnson VE: Properties of bayes factors based on test statistics. Scand. J. Stat. 2008; 35(2): 354–368. Publisher Full Text\n\nKaminski JW, Claussen AH: Evidence base update for psychosocial treatments for disruptive behaviors in children. J. Clin. Child Adolesc. Psychol. 2017; 46(4): 477–499. PubMed Abstract | Publisher Full Text\n\nKass RE, Vaidyanathan SK: Approximate Bayes Factors and Orthogonal Parameters, with Application to Testing Equality of Two Binomial Proportions. Journal of the Royal Statistical Society: Series B (Methodological). 1992; 54(1): 129–144. Publisher Full Text\n\nKerr NL: HARKing: hypothesizing after the results are known. Personal. Soc. Psychol. Rev. 1998; 2(3): 196–217. PubMed Abstract | Publisher Full Text\n\nKruschke JK, Liddell TM: The Bayesian New Statistics: Hypothesis testing, estimation, meta-analysis, and power analysis from a Bayesian perspective. Psychon. Bull. Rev. 2018; 25(1): 178–206. PubMed Abstract | Publisher Full Text\n\nLin DY, Zeng D: On the relative efficiency of using summary statistics versus individual-level data in meta-analysis. Biometrika. 2010; 97(2): 321–332. PubMed Abstract | Publisher Full Text\n\nMorey RD, Romeijn J-W, Rouder JN: The philosophy of Bayes factors and the quantification of statistical evidence. J. Math. Psychol. 2016; 72: 6–18. Publisher Full Text\n\nMorey RD, Rouder JN: BayesFactor: Computation of Bayes Factors for Common Designs. R package version 0.9.12-4.2.2018. Reference Source\n\nNeyman J, Pearson ES: On the Problem of the Most Efficient Tests of Statistical Hypotheses. Philos. Trans. R. Soc. A Math. Phys. Eng. Sci. 1933; 231(694-706): 289–337. Publisher Full Text\n\nNuijten MB, Hartgerink CHJ, van Assen MALM , et al.: The prevalence of statistical reporting errors in psychology (1985-2013). Behav. Res. Methods. 2016; 48(4): 1205–1226. PubMed Abstract | Publisher Full Text\n\nOldehinkel AJ: Editorial: Bayesian benefits for child psychology and psychiatry researchers. J. Child Psychol. Psychiatry. 2016; 57(9): 985–987. PubMed Abstract | Publisher Full Text\n\nPina AA, Polo AJ, Huey SJ: Evidence-Based Psychosocial Interventions for Ethnic Minority Youth: The 10-Year Update. J. Clin. Child Adolesc. Psychol. 2019; 48(2): 179–202. PubMed Abstract | Publisher Full Text\n\nR Core Team, R: R: A language and environment for statistical computing. [Computer software]. R Foundation for Statistical Computing; 2020;\n\nRouder JN, Morey RD: Default Bayes Factors for Model Selection in Regression. Multivar. Behav. Res. 2012; 47(6): 877–903. PubMed Abstract | Publisher Full Text\n\nRouder JN, Speckman PL, Sun D, et al.: Bayesian t tests for accepting and rejecting the null hypothesis. Psychon. Bull. Rev. 2009; 16(2): 225–237. PubMed Abstract | Publisher Full Text\n\nSakaluk JK, Williams AJ, Kilshaw RE, et al.: Evaluating the evidential value of empirically supported psychological treatments (ESTs): A meta-scientific review. J. Abnorm. Psychol. 2019; 128(6): 500–509. PubMed Abstract | Publisher Full Text\n\nSchönbrodt FD: p-checker: One-for-all p-value analyzer.2018. Reference Source\n\nSchönbrodt FD, Wagenmakers E-J: Bayes factor design analysis: Planning for compelling evidence. Psychon. Bull. Rev. 2018; 25(1): 128–142. PubMed Abstract | Publisher Full Text\n\nShafer G: Lindley’s Paradox. J. Am. Stat. Assoc. 1982; 77(378): 325–334. Publisher Full Text\n\nShepard JA, Poler JE, Grabman JH: Evidence-Based Psychosocial Treatments for Pediatric Elimination Disorders. J. Clin. Child Adolesc. Psychol. 2017; 46(6): 767–797. PubMed Abstract | Publisher Full Text\n\nSilverman WK, Hinshaw SP: The second special issue on evidence-based psychosocial treatments for children and adolescents: A 10-year update. J. Clin. Child Adolesc. Psychol. 2008; 37(1): 1–7. Publisher Full Text\n\nSimmons JP, Nelson LD, Simonsohn U: False-positive psychology: undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychol. Sci. 2011; 22(11): 1359–1366. Publisher Full Text\n\nSzucs D, Ioannidis JPA: When null hypothesis significance testing is unsuitable for research: A reassessment. Front. Hum. Neurosci. 2017; 11: 390. PubMed Abstract | Publisher Full Text\n\nvan de Schoot R , Winter SD, Ryan O, et al.: A systematic review of Bayesian articles in psychology: The last 25 years. Psychol. Methods. 2017; 22(2): 217–239. PubMed Abstract | Publisher Full Text\n\nWagenmakers E-J, Marsman M, Jamil T, et al.: Bayesian inference for psychology. Part I: Theoretical advantages and practical ramifications. Psychon. Bull. Rev. 2018; 25(1): 35–57. PubMed Abstract | Publisher Full Text\n\nWeersing VR, Jeffreys M, Do M-CT, et al.: Evidence base update of psychosocial treatments for child and adolescent depression. J. Clin. Child Adolesc. Psychol. 2017; 46(1): 11–43. PubMed Abstract | Publisher Full Text\n\nWetzels R, Matzke D, Lee MD, et al.: Statistical Evidence in Experimental Psychology: An Empirical Comparison Using 855 t Tests. Perspectives on Psychological Science: A Journal of the Association for Psychological Science. 2011; 6(3): 291–298. Publisher Full Text\n\nWilliams AJ, Botanov Y, Kilshaw RE, et al.: Potentially harmful therapies: A meta-scientific review of evidential value. Clin. Psychol. Sci. Pract. 2020; 28: 5–18. Publisher Full Text"
}
|
[
{
"id": "135924",
"date": "11 May 2022",
"name": "Einar Baldvin Baldursson",
"expertise": [
"Reviewer Expertise Research in occupational health",
"clinical research focusing on diagnosis and treatment in everyday life",
"and philosophy/method of science."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI think that the researchers make a strong case for using Bayesian methods in clinical research. Few of the positives might profit from a bit stronger argumentation/illustration.\nThe point that Bayesian methods lend themselves to at more adaptable research strategy is mentioned. This is actually a quite strong argument. Frequentist methods force a discipline on clinical research that makes such research more difficult to do. More doable research will enhance the pace of empirical testing and improving existing methods, and increase the likelihood of clinical research focusing on novel ideas. Bayesian methods will strengthen explorative and innovative clinical research. The burden of doing frequentist research is so heavy, that it primes researchers and clinicians to bet on \"safe\" and well established methods. In short - it is worth emphasizing that adapting Bayesian methods will increase innovation in clinical treatment and research.\nSecondly. And this point is implicit in the paper, but could be spelled out in a bit more words. Frequentist methods work wonderfully in a classical experimental setting where the focus is on a distinct part of a system, and the measurements are both fairly exact and reliable. None of this is possible in clinical research. The phenomena we observe are fussy, the measurements we use are inherently imprecise, and no amount of experimental control can master the dynamic processes and changes characteristic of phenomena in clinical research. Here Bayesian methods promise a better and more suitable approach.\nThe final comment, also on something the authors mention. Frequentist methods increase the likelihood of false negatives. Bayesian methods decrease the likelihood of false negatives. The only real alternative to adopting the pragmatic approach of Bayesian methods, is to focus on more and more power. And that approach comes with a multitude of pitfalls.\nIn short. In my view this paper makes an important contribution to the debate about how to approach and evaluate clinical research. A bit stronger focus on the interaction between design and methods (the specific contribution of Bayesian methods) would strengthen the paper. On the other hand, maybe this part of the discussion merits a paper in its own right.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8806",
"date": "23 Sep 2022",
"name": "Thomas Bertelsen",
"role": "Author Response",
"response": "Thank you for your time and encouragement. You have wonderfully captured the essence of this paper. In response to your concerns and those of Stephen Senn, we attempted to highlight the pragmatic merits of Bayesian methods."
}
]
},
{
"id": "138920",
"date": "31 May 2022",
"name": "Stephen Senn",
"expertise": [
"Reviewer Expertise Biostatistics and statistical methodology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe strangest thing about this study is that it claims the opposite of the usual Bayesian criticism of frequentist approaches. The usual criticism is that frequentist approaches give significance too easily. See, for example, 1,2,3. This immediately raises the question, \"how have the authors come to their conclusion?\". I am not sure what the answer is. I note, however, that the circumstances under which frequentist tests \"give significance too easily\", as noted by Casella and Berger 4, is where there is a lump of probability on H0. See Stephen Senn: The pathetic P-value (Guest Post) | Error Statistics Philosophy for a discussion and also5.\nNow, in the simulation, it seems to me that the authors have simulated from the case where H1 is true. They state that they chose to \"simulate 10,000 repeated studies based on the median observed effect size of the articles\". But if the median observed effect size is not zero, then H0 is not true. However, the whole motivation of the proposal by Jeffreys of Bayes Factors in 1939 in his Theory of Probability was to be able to prove that scientific laws were true. This in turn required that a lump of probability should be placed on the null hypothesis. It is the fact that the probability under the alternative hypothesis is widely spread that causes some values under H1 to be less well supported (in terms of likelihood) than is the value under H1. It is this that leads to the Jeffreys-Lindley paradox6,7. The authors mention this but don't seem to appreciate its relevance for their examination. Thus, the simulation carried out by the authors does not reflect what Bayes factors were created to deal with.\nIt is unclear to me whether this is the origin of the discrepancy. Nevertheless, it seems to me that the set-up the authors have used is confusing. To judge classification methods one needs a gold standard. This is usually provided by simulators by assumption and by varying such assumptions, the performance of two systems may be compared.\nIn any case, to use either Bayes factors or P-values to make a decision to either accept or reject a hypothesis also requires the use of thresholds. Varying these will lead to different error rates. It is not clear to me that this aspect is properly addressed in this paper.\nI am also unhappy with the discussion of the history of statistics. P-values were in use before Fisher. For example, by Pearson8 in 1900. It was Fisher who gave them their modern interpretation, at least as early as 1925. The authors have Neyman and Pearson in 1933 improving on Fisher's approach of 1934, which would require a time machine.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "8807",
"date": "23 Sep 2022",
"name": "Thomas Bertelsen",
"role": "Author Response",
"response": "Thank you for your time and insightful remarks. We agree that our article may have been unclear on our goal, and especially in the discussion, we did not emphasize three critical aspects that you raised: 1. These findings are unexpected (opposite of usual critique) 2. The procedures are not applied in the conventional manner (we sample where H1 is assumed true) 3. All findings are contingent on thresholds (as are ours). In our new manuscript, we emphasize that our findings are unusual in the literature criticizing frequentism. The findings, however, are not surprising (at least in our profession), and it is crucial to highlight that clinical psychology research are often underpowered. We have also highlighted that our goal was not to see if Bayesian methods were more \"right\" than frequentist approaches, and that they were utilized in a particular case where we assumed that the initial findings were valid. Our goal was to see whether we could reach conclusions faster if the original study was correct. The paper's main point is that Bayesian approaches provide pragmatic advantages that are especially useful in clinical psychology. In the discussion, we sought to explain this point. In accordance with the aforementioned, we endeavored to emphasize that all conclusions are dependent on thresholds and that the benefits of Bayesian approaches are not better thresholds but rather more intuitive interpretation, which leads to more reasonable conclusions in the event of null results. We understand that our introduction to statistical methods is somewhat lacking. Our intent is that it should be readily available to researchers within the field of clinical psychology and therefore we wish to keep the background for the methods short. However, we have highlighted that this is an abridged history. If you would prefer, we could also include references to more in-depth discussions on the history of both Bayesian and frequentist methods. We appreciated your remark about time machines, and while Fisher caused innovation in many areas, I do not recall him being involved with time travel. The Fisher reference has been updated to the 1925 edition."
}
]
}
] | 1
|
https://f1000research.com/articles/11-171
|
https://f1000research.com/articles/11-1088/v1
|
22 Sep 22
|
{
"type": "Research Article",
"title": "The new educational paradigm in the COVID-19 era: Can Blackboard replace physical teaching in EFL writing classrooms?",
"authors": [
"Bandar Aljafen"
],
"abstract": "Background: Many changes are evident in classrooms in the COVID-19 times, but the most drastic perhaps has been the scramble to find substitutes for physical classrooms, a truly solemn challenge for the foreign language learning paradigm. In the meantime, many customized learning apps came to the educationists’ rescue: Blackboard being one of them. This study endeavors to investigate the effectiveness of Blackboard as an alternative to face-to-face writing instruction during the COVID-19 crisis and in the following period of precautionary distancing and other norms. Methods: The study used the final grades of Saudi male and female EFL undergraduates across two terms and with the Blackboard and face-to-face approaches in three compulsory English writing courses, and statistical tests were conducted on them. Results: The findings showed that female students (M=83.24, Std= 10.627) significantly outperform the male students (M=73.62, Std=16.011) in the final writing test (P=. 000). Furthermore, in face-to-face teaching (M=84.34, Std=10.752) was more statistically effective than when using Blackboard (M=75.65, Std=14.545) with the Sig value scored (P=. 000). Findings also showed that third level scored higher than the second and the first in writing (83.83, 78.17, 77.89) respectively. All the differences were significant (P=. 000). Conclusion: The implications of the study have a major bearing on curriculum and pedagogy planning for the coming times which may see more comebacks of the COVID-19 variants and warrant innovative teaching-learning tools and methods.",
"keywords": [
"Blackboard",
"COVID-19",
"EFL classroom",
"educational paradigms",
"physical teacher",
"writing"
],
"content": "Editorial note\n\nEditorial Note (26th July 2023): The F1000 Editorial Team is currently substantiating that this research was presented at an IIARP conference and should be included in the IIARP Gateway. The Editorial Team is currently requesting further information from the authors regarding this. This Editorial Note will be updated as new information is provided.\n\n\nIntroduction\n\nThe COVID-19 crisis disturbed different aspects of life in nearly every country worldwide, including, but not limited to, the economy, education, and social life at all levels. The pandemic hit every country at its core. The education sector was thrown into disarray as students and their families became targets of the viral infection.1 Social isolation became a priority, and as a result, alternative online educational platforms emerged to take the place of face-to-face communication to allow students to receive education even though at a skeletal level. Although this flexibility was necessary during this disruption, its effects could not be fully predicted given the fact that the new system was one that had never been tried before: it could affect the quality of education either way, and there is a need for further investigation to evaluate such experiments in real life.\n\nClosing down of educational institutions has had serious effects on the education, development, and well-being of the students: Apart from the deprivation of social contact with peers and teachers which are vital for promoting mental well-being, the new modes of learning were not authenticated to provide as much learning success as the conventional face-to-face method. The new dispensation also left behind the socially and/or economically disadvantaged students and students with different or heightened learning support needs. Emergency remote learning systems which have since been pressed into action, have struggles to minimize learning loss and increasing inequality in access to education. Among the educational institutions affected by the COVID-19 outbreak was the Department of English and Translation at Qassim University, Saudi Arabia, where, since the pandemic broke out, teaching has been carried out via Blackboard, and physical attendance has been limited to midterm and final exams subject to firm guidelines. To ensure the quality of online teaching and learning, this study sought to investigate the quality of writing instruction by examining students’ final English writing scores before (face-to-face) and after (Blackboard) the COVID-19 crisis and how this pandemic could affect the learning outcomes among Saudi male and female Saudi EFL students.\n\nQassim University, like most learning institutions not only in Saudi Arabia but across the world, rapidly transformed its learning system from in-class interaction to online learning due to the COVID-19 outbreak. This swift shift was not planned, although there is a Deanship of E-Learning that has been serving the university since 2013. The ultimate goal of the deanship from the day it was created until prior to the pandemic was to raise awareness of the use of Blackboard as an assistant tool alongside face-to-face learning, including by providing intensive courses to introduce Blackboard to faculty members and students explaining the features and benefits of E-learning that could change pedagogies and learning approaches. The sudden and unprecedented use of Blackboard as an alternative tool for teaching and learning before it was fully accepted by all faculty members and students raised vital concerns about the effectiveness of Blackboard in teaching. This paper sought to investigate the effectiveness of Blackboard and face-to-face teaching approaches in promoting writing proficiency among male and female Saudi students in the English Language and Translation department at Qassim University before and after the COVID-19 crisis.\n\nBlackboard as a potential learning system has been examined widely by numerous educators whose findings have highlighted many benefits, including students’ preference for online over face-to-face communication,2–6 positive effectiveness of online communication,6 the sharing and construction of knowledge,7 facilitation of students’ learning increased student participation,8,9 support of learning autonomy,10 increased student motivation,11 open access to information at all times,12 and decreased student anxiety.13\n\nFor teachers, virtual instruction through Blackboard helps instructors to manage course activities, planning, and evaluation more easily.14–17 On the other hand, a study conducted in Ghana by Okantey and Addo adopted the technology acceptance model (TAM) to measure the effectiveness of Blackboard in education.18 The results showed that instructors found Blackboard useful but not easy to use. Other studies have shown less positive results for Blackboard. For example, a study conducted by Gregory and Lodge concluded that online learning may interrupt students’ learning cognition due to the lack of physical communication with their instructors.19 Another study showed that students were unready to deal with online learning platforms because of their lack of online technology experience, or they required one-to-one attention that was not available through electronic programs such as Blackboard.19,20 Moreover, Hosamo’s findings showed that students and teachers were not interested in the online learning experience in general.21 One possible reason for this lack of interest could be faculty resistance to adopting new online teaching pedagogy22 or lack of time.20 Another possible reason for the resistance to technology adoption among faculty is the lack of institutional support.23 A study by Ben Bakr emphasized the need to revisit online strategic plans before applying them in the classroom to ensure their effectiveness.24 Some research has also indicated some cautions to be considered when adopting online platforms and devises. First, the teacher should carefully design the course content to be appropriate for online display.25,26 Furthermore, course activities and evaluations should be thoroughly considered because planning an online course may differ from planning for a face-to-face classroom. Hazaea et al. emphasized the need to make online learning programs more user-friendly.27\n\nEFL writing has only recently become a field of significant scholarly interest.28 The social learning approach has been adopted in teaching language skills, and more specifically writing, to engage students in a natural learning environment.29–31 The emergence of new technologies such as Blackboard has simplified social learning and promoted interaction and collaboration between students.32–34 Blackboard and many other online collaborative platforms exerts a positive impact on the study of academic writing among EFL/ESL students. Many studies have highlighted the effect of Blackboard on writing outcomes,12,35,36 peer interaction,37,38 peer feedback,39,40 and learning motivation.12,41,42 This study compared two learning strategies, traditional learning in a classroom and online learning via Blackboard, and examined students’ final scores to determine whether the different strategies were associated with differing results.\n\n\nTheoretical framework\n\nThe world wide web (www) witnessed dramatic expansion in the period of the COVID-19 pandemic with universities scrambling to reinvent the learning environments not only to expand the digital net but also, to effectively complement learning relationships. Looking back, Web 1.0 had little influence on education due to the isolation between receiver and sender.43 In contrast, the emergence of Web 2.0 validates information interaction and the negotiation of meaning in different ways through the use of technology to construct knowledge.43–45 The virtual learning platform Blackboard is a Web 2.0 program that has been widely accepted among educational institutions to achieve the ultimate goal of collaboration and interaction between students to enhance learning development. Blackboard also serves the constructivist learning theory. According to Vygotsky,46 the father of social learning theory, cognitive learning only occurs when interaction takes place between more knowledgeable students and less knowledgeable students.46 Social theory also supports a student-centered environment in which the students are responsible for their own learning, and the teacher’s role is merely to guide and facilitate learning. In this sense, Blackboard supports social learning since it enables students’ knowledge construction and learning accountability.\n\n\nMethods\n\nThis study investigates the effectiveness of Blackboard in promoting EFL students’ writing performance in the Department of English Language and Translation at Qassim University. The data were collected for two periods: before (spring 2019) and after (spring 2020) the spread of COVID-19 virus. The study analyzed the students’ final grades in three different levels of writing courses. The results were collected and analyzed across the two different teaching approaches (face-to-face and Blackboard) to evaluate the two learning experiences and to highlight suggestions for enhancing students’ and teachers’ experience in online learning in the future.\n\nThis study enlisted two groups of undergraduate male and female Saudi students who had applied for English language courses at Qassim University. Ethical approval was obtained (issued on, Sep. 25, 2020) from the ethics committee at the deanship of scientific affairs to the head of the departments. Verbal consent was obtained from the students (as the study did not involve interviews, observations or questionnaires, the ethics committee at the Qassim University approved verbal consent). Students were also assured that their information would be only used for the study and that they were not required to disclose their identity in any way. The ethical approval letter clearly stated: “This research meets the high ethical and scientific standards expected by society, and the participants have informed the Committee that they have no objection with the outcomes of the research work being published”.\n\nThe first group comprised students who took Writing 1, 2, and 3 prior to the pandemic, and the second group were those who took the same courses after the pandemic. The participants were assigned to take these three compulsory writing courses in the first three semesters after joining the program. The study sample thus included a total of 833 participants (287 males and 546 females). The students had prior experience with Blackboard as a learning tool. All freshman students, in traditional and pandemic times, are introduced to the most important features of Blackboard at the beginning of each semester. Additionally, three general courses were taught completely online during the first semester after students’ full enrolment in the program.\n\nThe current study was conducted to explore improvements, if any, in the writing proficiency of male and female Saudi EFL students who received instruction through two teaching approaches (face-to-face and Blackboard). The data were collected from the students’ final grades in three writing courses: Writing 1, Writing 2, and Writing 3 (henceforth referred to as level one, level two, and level three). The data were organized and analyzed through SPSS, (Version 26). Three main factors appeared in the study (gender, writing level, and teaching approaches). Three-way ANOVA was conducted to compare the means.\n\nThe data were analyzed in descriptive and inferential format. The descriptive analysis showed the total number of participants, the number in each group, the mean, and the standard deviation. Inferential analysis considers the p-value when comparing means to answer the research questions raised in this study. Data were considered statistically significant in the current study when the p-value was less than or equal to .05.\n\n\nResults\n\nThe descriptive data for gender were collected for a total of 833 participants (546 females and 287 males). The means of the final scores of the female participants (M = 83, SD = 11) were 9 points higher than those of the male participants (M = 74, SD = 16) (Table 1).\n\nTable 2 shows the sum of squares, degree of freedom, the mean square, the F-value, and the significance value between individual and among combined variables. To answer the first research question, whether the means of the male and female participants differed, the data showed that the main effect of gender on students’ writing scores was statistically significant (F(1, 821) = 125.227, p = .000), meaning that female students earned higher final grades in writing than the male students. These results are summarized in Table 2 below.\n\na R Squared = .301 (Adjusted R Squared = .292).\n\nInterpreting the results of Table 2 above, seven correlations were sought to be established using the students’ data in three writing exercises at two different periods of time. Significance probability indicates the probability that we would find the sample regression coefficient we have actually found in our sample if the null hypothesis is true, i.e. if it is true that the value of the population regression coefficient is 0. If this value is smaller than the chosen significance level, it implies that the null hypothesis is refuted and that there is no linear association between the relevant independent variable and the dependent variable.\n\nThe computation shows that the Sig. value for the factors of gender, level, learning approach, interaction between gender and level, between gender and learning approach, level and learning is.000, where the study had set the significance at p ≤ .05, implying that a significant relationship exists between the variables stated. In other words, gender, level, learning approach have a correlation with writing performance in the case of the participants in this study. It indicates strong evidence against the null hypothesis.\n\nThe descriptive data for the English writing levels displayed the number of all participants in each level. In this study, the total number of participants at level one was 249, at level two was 313, and at level three was 271. The mean of the third level was higher (M = 84, SD = 13) than those of levels two (M = 78, SD = 13) and one (M = 78, SD = 14) (Table 4).\n\nTo answer the second research question, about whether the means of the three participant levels differed, the results in Table 3 indicate that the main effect of the three levels of the English writing courses on students’ final scores was significant (F(2, 821) = 995.894, p = .000), indicating that the participants in the level-three English writing course scored higher than those in the first and the second levels. In other words, as the level of the writing course went higher, the writing performance also improved which goes to show that with time, students’ writing proficiency in the given sample tends to improve. This finding is borne out by the scores of the participants in all the three levels with each subsequent level reflecting a better output.\n\nThe descriptive data for learning approach indicated that the mean in the face-to-face teaching approach was 9 points higher (M = 84, SD = 11) than that of the online learning approach using Blackboard (M = 76, SD = 15) (Table 4).\n\nTo answer the third research question, about the students’ final writing scores in face-to-face vs. online writing classes, the results in Table 3 showed that the main effect of the learning approaches on students’ final scores was statistically significant (F(1, 821) = 132.612, p = .000), indicating that the students in the face-to-face classroom performed better than those engaging in online learning via Blackboard.\n\nTo answer the final research question, whether there is an interaction among the three independent variables (gender, English writing level, and learning approach), there was a significant interaction among the three variables (F(2, 821) = 3.565, p = .000), indicating that at levels two and three, female students had higher final scores than male students for face-to-face instruction and for online instruction via Blackboard. At level one, however, gender had no effect.\n\nTesting simple main effect. To determine whether the main effects of gender, writing course level, and learning approach on students’ final scores in writing are significant, a test of simple main effects is required (Table 3, pairwise comparisons). In Table 5, the test showed the following:\n\n- At level one, male and female students scored similarly for the face-to-face learning classroom (F(1,821 = 1.223, p = .269) and online learning platform (Blackboard) (F(1,821 = 1.418, p = .234). In other words, gender had no effect on students’ writing performance across the learning approaches in level one.\n\n- At level two, female students scored 6 points higher than male students for the face-to-face learning approach (F(1,821 = 9.097, p < 0.5) and 14 points higher for Blackboard (F(1,821 = 52.545, p < 0.5). In other words, gender showed an effect on students’ writing performance across the two learning approaches at level two.\n\n- At level three, female students’ mean was significantly higher (11 points) for the face-to-face classroom (F(1,821 = 28.687, p < .001) and was more than 21 points higher for Blackboard (F(1,821 = 94.759, p < .001). In other words, gender showed an effect on students’ writing performance across the two learning approaches at level three. These findings were displayed in Figure 1.\n\n* The mean difference is significant at the .05 level.\n\nb Adjustment for multiple comparisons: Bonferroni.\n\n\nDiscussion\n\nThis study revolved around three queries as indicated in the research questions. Inquiry showed that female students outperformed male students in the writing tests. This finding can be explained by the fact that the interest and time that female students allocated for their study and practice the writing skills and performing the tasks and assignments that the instructors gave them to respond to as a part of the assessment procedures of the course outweighed that of their male counterparts. This finding is in line with Al-Saadi's who found that Omani female students scored higher than the male students in the writing fluency test.47\n\nIt also reported that third level students scored higher than first and second level students. This finding is natural because third year students are exposed longer to the language than their counterparts in the first and second level. However, Almekhlafy found that first level students got higher perceptions than the second level students regarding pursuing online learning.11\n\nFinally, students in face-to-face learning did better than they did in online mode. This finding may be interpreted and related to the interest that students have in learning mode. Almekhlafy found that Saudi EFL students have the tendency to learn better in conventional classes than they do though the Blackboard.11 In contradiction, Hemdi reported that Saudi EFL postgraduate students preferred virtual learning than conventional methods during COVID-19 pandemic.48\n\nThe results of this study align with those of Gregory and Lodge, who questioned the effectiveness of online learning as a means for learning cognition.19 The students’ poorer performance online could be because Qassim University students were not prepared nor trained adequately to switch to online learning applications, drawbacks of online learning as also suggested by Almansour and Al-Ahdal, Allen and Seaman and Gregory and Lodge.19,20,49 Scarcity of the desire, time, and technology needed to promote beneficial online teaching among teachers could be another reason for this low performance, as suggested by many previous studies.20,22,23 This study’s conclusions support those of other studies that argue that the emergence of the shift from face-to-face to online instruction (e.g., through platforms such as Blackboard) requires that teachers consider that the course content may require modifications to be best applied in the online classroom.24,26 In this case, teachers may need to alter their pedagogical approaches, class activities, and evaluations to be applicable in the online context. This study also highlights the need to prepare students along with teachers to be introduced to online learning environments through extensive training sessions in order to feel comfortable with the new environment, as suggested by Hazaea et al.27\n\nIn conclusion, online instruction was compulsion replacing face-to-face classroom teaching during the COVID-19 crisis to ensure continued learning. In this study, English writing performance was evaluated, and the results suggested that face-to-face teaching and learning was more effective than online (e.g., via Blackboard). This study raised suggestions to be considered when applying online technologies to future teaching.\n\n\nConclusion\n\nThis study aimed to discuss the effectiveness of instruction via Blackboard versus face-to-face approaches on the enhancement of writing proficiency among male and female Saudi students across three levels of English writing courses at Qassim University, Saudi Arabia. First, the results generally showed that the female participants outperformed male participants in their final scores in English writing courses and at all levels except the first. This means that as the levels progressed, female students outperformed their male counterparts. Second, students at level three scored higher than those at levels one and two in writing performance. Third, both groups (male and female students) performed better in the face-to-face classroom than online via Blackboard across all three required English writing courses. Combining the three variables, the results demonstrated that females outperformed male students at all levels across both learning approaches: face-to-face and online learning via Blackboard.\n\nBased on the findings, the study has the following suggestions to make: Online learning apps should be carefully evaluated and assessed as learning tools before being imposed across board in the Saudi context. Greater weightage should be placed on the face-to-face learning approach till the Saudi university students are adequately prepared to be autonomous agencies in learning. When absolutely imperative to resort to online learning approaches such as Blackboard, teachers as much as students should be trained in effective use of the tools. Finally, periodic appraisals of fulfilment of learning objectives and student needs should be encouraged to ensure timely course correction, especially in the current special times. Any study has limitation, and the current study is not free from shortcomings. Quantitative studies help establish trends but as in the present case, they do not give a deeper understanding of the discerned phenomena. This was one limitation of the study, though the sample size was fairly large at 833 and one which could be ironed out by following mixed methods approaches.\n\n\nData availability\n\nFigshare: Scores of the writing performance from the three writing courses (Traditional and Online) https://doi.org/10.6084/m9.figshare.20182226.v1.50\n\nThis project contains the following underlying data:\n\n- 1-a Traditional writing test- level 1\n\n- 1-b Online writing test- level 1\n\n- 2-a Traditional writing test- level 2\n\n- 1-b Online writing test- level 2\n\n- 3-a Traditional writing test- level 3\n\n- 3-b Online writing test- level 3\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe authors would like to express a sincere word of gratitude and appreciation to the participants who spared their precious time to respond to the research instrument.\n\n\nReferences\n\nUN: Education during COVID-19 and beyond.2020. (accessed February 24, 2021). Reference Source\n\nAli J: Blackboard as a motivator for Saudi EFL students: A psycholinguistic study. International Journal of English Linguistics. 2017; 7(5): 144–151. Publisher Full Text\n\nAl-Mubireek A: E-learning in the English classroom: Comparing two e-learning platforms impacting preparatory year students’ language learning. CALL-EJ. 2019; 20(2): 19–37.\n\nAnas A: Perceptions of Saudi students to blended learning environment at the University of Bisha, Saudi Arabia. Arab World Journal (AWEJ) Special Issue on CALL. 2020; 6: 261–277. Publisher Full Text\n\nFageeh A, Mekheimer M: Effects of Blackboard on EFL academic writing and attitudes. JALT CALL Journal. 2013; 9(2): 169–196. Publisher Full Text\n\nMasino M: Integration of Blackboard in the online learning environment. Journal of Instructional Pedagogies. 2015; 16: 1–10.\n\nKaplan AM, Haenlein M: Users of the world, unite! The challenges and opportunities of social media. Business Horizons. 2010; 53(1): 59–68. Publisher Full Text\n\nAl Jarrah AA: Jordan University students' attitudes towards using blackboard software in their learning. Journal of Studies of Educational Sciences Jordan. 2011; 38(4).\n\nHuang X, Hsiao E -l: Synchronous and Asynchronous Communication in an Online Environment: Faculty Experiences and Perceptions. Q. Rev. Dist. Learn. 2012; 13: 15–30.\n\nMarsh D: Blended learning: Creating learning opportunities for language students. New York: Cambridge University Press; 2012.\n\nAlmekhlafy SSA: Online learning of English language courses via blackboard at Saudi universities in the era of COVID-19: perception and use. PSU Research Review.2020; 5(1): 16–32. Publisher Full Text\n\nLi X, Chu SK, Ki WW: The effects of a wiki-based collaborative process writing pedagogy on writing ability and attitudes among upper primary school students in Mainland China. Computers & Education. 2014; 77: 151–169. Publisher Full Text\n\nAdam S, Nel D: Blended and online learning: Student perceptions and performance. Interactive Technology and Smart Education. 2009; 6: 140–155. Publisher Full Text\n\nAl-Ahdal AAMH, Alqasham FH: Saudi EFL learning and assessment in times of Covid-19: Crisis and beyond. Asian EFL Journal. 2020; 27(4.3): 356–383.\n\nAlharbi S, Drew S: Using the technology acceptance model in understanding academics’ behavioral intention to use learning management systems. International Journal of Advanced Computer Science and Applications. 2014; 5(1): 143–155. Publisher Full Text\n\nOh E, Park S: How are universities involved in blended instruction? Educational Technology & Society 2009; 12(3): 327–342.\n\nPowell A, Watson J, Staley P, et al.: Blended learning: The evolution of online and face-to-face education from 2008–2015. Promising practices in online learning. Vienna: International Association for K-12 Online Learning; 2015.\n\nOkantey M, Addo H: Effect of theoretical and institutional factors on the adoption of E-learning. European Scientific Journal. 2016; 12(16): 462–473. Publisher Full Text\n\nGregory MS-J, Lodge JM: Academic workload: The silent barrier to the implementation of technology-enhanced learning strategies in higher education. Distance Education. 2015; 36(2): 210–230. Publisher Full Text\n\nAllen IE, Seaman J: Online nation: Five years of growth in online learning. Needham, MA: Sloan Consortium; 2008.\n\nHosamo SA: The reality of e-learning in Tishreen University from the viewpoint of faculty members and students. Journal of University of Damascus. 2011; 27: 243–278.\n\nAl-Shboul M: The level of E-learning integration at the University of Jordan: Challenges and opportunities. International Education Studies. 2013; 6(4): 93–113. Publisher Full Text\n\nSinclair TR, Purcell LC, Sneller CH: Crop transformation and the challenge to increase yield potential. Trends in Plant Science. 2004; 9: 70–75. PubMed Abstract | Publisher Full Text\n\nBen Bakr MBA: The requirement of activating E-learning technology (Web CT) among faculty members at girls collages at King Faisal University in Saudi Arabia: Reality and hope. Journal of the College of Education in Alexandria, Egypt. 2011; 21(2): 23–32.\n\nAlghamdi EA: Untangling multimedia effects on EFL incidental vocabulary learning via playing an online hidden-object game. IJCALLT. 2016; 6(1): 24–39. Publisher Full Text\n\nBousbahi F, Alrazgan MS: Investigating IT faculty resistance to learning management system adoption using latent variables in an acceptance technology model. The Scientific World Journal. 2015; 2015: 1–11. 375651. PubMed Abstract | Publisher Full Text\n\nHazaea AN, Bin-Hady WRA, Toujani MM: Emergency remote English language teaching in the Arab league countries: Challenges and remedies. Computer-Assisted Language Learning Electronic Journal (CALL-EJ). 2021; 22(1): 201–222.\n\nMatsuda PK: Second language writing in the twentieth century: A situated historical perspective. Exploring the Dynamics of Second Language Writing. 2003; 1: 15–34. Publisher Full Text\n\nLeki I: Understanding ESL writers: A guide for teachers. Portsmouth, NH: Boynton/Cook Publishers Heinemann; 1992.\n\nReid J: Teaching ESL writing. Englewood Cliffs. NJ: Prentice Hall Regents; 1993.\n\nStorch N: Collaborative writing in L2 contexts: Processes, outcomes, and future directions. Annual Review of Applied Linguistics. 2011; 31: 275–288. Publisher Full Text\n\nDucate LC, Anderson LL, Moreno N: Wading through the World of Wikis: An Analysis of Three Wiki Projects. Foreign Language Annals. 2011; 44(3): 495–524. Publisher Full Text\n\nPrensky M: Teaching digital natives: Partnering for real learning. London: Corwin; 2010.\n\nSheskey B: Creating learning savvy student.Jacobs HH, editors. Curriculum 21: Essential education for a changing world. Alexandria, VA: ASCD; 2010; (pp. 195–209).\n\nAlshumaimeri Y: The effects of wikis on foreign language students writing performance. Procedia - Social and Behavioral Sciences. 2011; 28: 755–763. Publisher Full Text\n\nWang Y: Using wikis to facilitate interaction and collaboration among EFL students: A social constructivist approach to language teaching. System. 2014; 42: 383–390. Publisher Full Text\n\nAhmadi SD, Marandi SS: Social software in the classroom: The case of wikis for scaffolding. Procedia - Social and Behavioral Sciences. 2014; 98: 100–108. Publisher Full Text\n\nSalaber J: Facilitating student engagement and collaboration in a large postgraduate course using wiki-based activities. International Journal of Management Education. 2014; 12: 115–126. Publisher Full Text\n\nDemirbilek M: Social media and peer feedback: What do students really think about using Wiki and Facebook as platforms for peer feedback? Active Learning in Higher Education. 2015; 16(3): 211–224. Publisher Full Text\n\nGielen M, Wever BD: Scripting the role of assessor and assessee in peer assessment in a wiki environment: Impact on peer feedback quality and product improvement. Computers & Education. 2015; 88: 370–386. Publisher Full Text\n\nÖzdemir E, Aydın S: The effects of blogging on EFL writing achievement. Procedia - Social and Behavioral Sciences. 2015; 199: 372–380. Publisher Full Text\n\nSura T: Infrastructure and wiki pedagogy: A multi-case study. Computers and Composition. 2015; 37: 14–30. Publisher Full Text\n\nWang S, Vásquez C: Web 2.0 and second language learning: What does research tell us? CALICO Journal. 2012; 29: 412–430. Publisher Full Text\n\nHoltzman S: Web 2.0 and CMS for second language learning. Thomas M, editor. Handbook of research on Web 2.0 and second language learning. Hershey, PA: Information Science Reference; 2009; (pp. 526–545).\n\nMotteram G, Brown S: A context-based approach to Web 2.0 and language education. Thomas M, editor. Handbook of research on Web 2.0 and second language learning. Hershey, PA: Information Science Reference; 2009; (pp. 119–136).\n\nVygotsky L: The development of scientific concepts in childhood. Hanfmann E, Vakar G (Eds.), Thought and language: Studies in communication. Cambridge, MA: MIT Press; 1962; (pp. 82–118).\n\nAl-Saadi Z: Gender differences in writing: The mediating effect of language proficiency and writing fluency in text quality. Cogent Education. 2020; 7(1): 1770923. Publisher Full Text\n\nHemdi A: Exploring the experiences of postgraduate students in the field of special education with remote online teaching amid COVID-19 pandemic: A mixed methods study. Journal of Educational and Social Research. 2021; 11(5): 237–252. Publisher Full Text\n\nAlmansour MI, Al-Ahdal AAMH: University education in KSA in Covid times: Status, challenges and prospects. International Journal of Innovation, Creativity and Change. 2020; 14(3): 971–984.\n\nAljafen B: The new educational paradigm in COVID era: Can Blackboard replace physical teaching in EFL writing classrooms? figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "176774",
"date": "27 May 2024",
"name": "Mohammad Mahyoob",
"expertise": [
"Reviewer Expertise ELE",
"E-learning",
"ELT",
"Linguistics",
"Computational Linguistics."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, the author needs to explore the application of modern frameworks in the context of online learning. What are the variables related to writing, the author focuses on? The significance of this study lies in its potential to enhance the understanding of how these frameworks can be utilized in the realm of online education, it needs to be added.\n\nThe novelty and contribution of this study lie in its examination of writing issues in both physical and online classes. The author must discuss a range of issues, including format, grammar, syntax cohesion, coherence, and word choice. By addressing these concerns, what are the unique challenges and opportunities presented by online and physical writing instruction?\nTo ensure the practicality of the findings, the author should plan to include samples from both modes of teaching. Given the large number of participants involved, the author must select a representative sample of approximately 30 to 50 pieces of writing. Through critical analysis, the author should present the results of the analysis, providing valuable insights for educators and researchers in the field.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "333761",
"date": "06 Nov 2024",
"name": "Wafa Hazaymeh",
"expertise": [
"Reviewer Expertise English Curriculum and PedagogyE-learning and Innovative English Language Teaching Methods"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, the author should focus on the following points:\nstudy variables, sampling procedure, and data analysis should all be included in the abstracts. The introduction must include some recent references. The author needs to research the usage of modern frameworks in online learning; thus, he should emphasize the significance of the study. In the literature review, the researcher should provide a description of educational abilities in his chosen region. This might be useful if the argument explains how to compare teaching skills in the region or with other institutions. The method includes, methods sampling, equipment, data analysis, and process. The difference between online and in-class writing should be discussed. The discussion just explains the tables; the author should investigate and align the findings with the benefit and research implications. The language can be comprehended but needs to be enhanced. The conclusion should include examples of both types of education. Recommendations should be made to provide substantial insights for educators and academics on the issue.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1088
|
https://f1000research.com/articles/9-286/v1
|
24 Apr 20
|
{
"type": "Case Report",
"title": "Case Report: Sudden death related to unrecognized cardiac hydatid cyst",
"authors": [
"Med Amin Mesrati",
"Yosra Mahjoub",
"Nouha Ben Abdejlil",
"Marwa Boussaid",
"Meriem Belhaj",
"Hiba Limem",
"Ali Chadly",
"Abdelfeteh Zakhama",
"Abir Aissaoui",
"Yosra Mahjoub",
"Nouha Ben Abdejlil",
"Marwa Boussaid",
"Meriem Belhaj",
"Hiba Limem",
"Ali Chadly",
"Abdelfeteh Zakhama",
"Abir Aissaoui"
],
"abstract": "Echinococcosis, also known as hydatid disease, is a common parasitic human infestation found in sheep-breeding areas. It is caused by the larvae stage of Echinococcus granulosus, and cysts develop mostly in the lungs and the liver. Cardiac involvement is unusual and silent until acute complications or a fatal outcome occurs. Herein, we report an autopsy case of a young healthy adult who died suddenly. The autopsy revealed an external bulging on the right heart ventricle outlet with a fluid-filled cystic cavity discovered on sectioning. Dissection of other organs did not reveal other cyst locations. Histological examination ascertained the diagnosis of hydatid cyst, and death was attributed to cardiac arrhythmias. Pathologists should keep in mind that hydatid cysts can develop anywhere in the body. Solitary cardiac cyst is rare and can simulate a “silent bomb”. Unfortunately, sudden death remains the frequent manner of revelation of this disease in endemic areas.",
"keywords": [
"sudden death",
"hydatid cyst",
"right ventricle",
"autopsy",
"pathology"
],
"content": "Introduction\n\nEchinococcosis, also known as hydatid disease, is a parasitic human infestation that commonly occurs in countries where sheep farming is widespread, such as Mediterranean countries1. In Tunisia, the prevalence and incidence of this contagion are estimated to be high (15/100000 individuals)2. It is attributed to the larval stage of a tapeworm, chiefly Echinococcus granulosus. The mature worm inhabits the intestines of the dog and humans are accidental hosts in their life cycle. Hydatid cysts can develop anywhere in the human body, predominantly in the lung and the liver3. Cardiac involvement is very scarce, even in endemic regions, and its clinical evolution is asymptomatic until acute complications or a fatal outcome occurs. Herein, we report an autopsy case of a young patient who died suddenly due to an unrecognized hydatid cyst located in the right heart ventricle.\n\n\nCase report\n\nA previously healthy 26-year-old man, without any relevant past medical family history, was discovered dead at home. A forensic medical examination and an autopsy were ordered by the judicial authorities. Information provided by the patient’s relatives revealed that the deceased was the owner of a large farm that he had been managing for the past 5 years. A few days ago, the patient had experienced mild chest pain with syncope but did not visit a cardiologist.\n\nDuring external examination, the corpse was that of a young white male, medium-build, 183cm of tall. There was no external evidence of violence or trauma, and examination of the skin revealed no rash. At autopsy, there was multi-visceral congestion without any internal haemorrhage. Internal organs were unremarkable except for the heart, which was found to be enlarged, weighing 530g (normal range: 260–350g) with an external bulging on the right ventricle outlet (Figure 1). Sectioning of the heart revealed a fluid-filled cystic cavity, measuring 5×4cm, occupying half the volume of the right chamber and spreading to the septum. The cyst was enveloped by a thick fibrous tissue, and it featured germinative membranes, which infiltrated the myocardium. There was no hypertrophy of the myocardium. The left ventricle was 12mm of thick (Figure 2).\n\nMicroscopic examination using haematoxylin and eosin staining of paraffin sections of the cyst revealed classic layers of a hydatid cyst; pericyst (fibrous outer layer), ectocyst (laminated, hyaline and acellular middle layer) and endocyst (inner germinative layer) (Figure 3). This ascertained the diagnosis of hydatid disease.\n\nHaematoxylin and eosin, x40 magnification.\n\nHistological findings of the left ventricle and coronary arteries were unremarkable. Examination of the lungs and liver did not reveal any abnormality, and no cysts were detected at dissection of these organs. The pulmonary arteries also did not display morphological changes, notably there were no fragments of membranes or vesicles obstructing the vessels. Toxicological screening was negative. Death was attributed to cardiac arrhythmias.\n\n\nDiscussion\n\nHydatid disease is a parasitic infection most often induced by the larval form of the tapeworm E. granulosus, for which dogs are the definitive host4. In rural areas, dogs are common companions for sheep farmers. Typically, dogs become infected with E. granulosus from eating carcasses of infected sheep in endemic areas. Adult parasites colonize the intestinal tract and the faeces of infected dogs. Humans are intermediate hosts and may accidentally acquire infection by eating contaminated food such as water or salad or after close contact, e.g. hand-to-mouth transmission, with an infected dog. After ingestion, the larvae pass through the duodenal wall, reach the portal blood system and shelter in the liver, where they are found in ~60% of cases5. Some larvae may escape via the hepatic filter and cross into the pulmonary circulation, while others may continue to the systemic circulation, resulting in the generation of hydatid cysts in other organs, e.g. the lungs, muscles, bones or kidneys.\n\nSecluded cardiac involvement by E. granulosus is very uncommon, and has not been described widely in the literature. Its incidence is estimated to be at about 0.4-3% of hydatid cyst cases6. This scarcity is attributed to the natural resistance of heart contraction. The first described case of cardiac hydatid cyst was reported in 18367. Most reports documented in the literature are of single cases, and a pervious literature review of the topic identified only 100 case presentations to date8.\n\nThe coronary circulation is the main pathway by which the parasitic larvae reach the heart. The second route of infestation is the pulmonary vein9. Due to their thickness and rich blood supply, the interventricular septum and the free wall of the left ventricular are the most common cardiac sites involved with hydatid cyst (55-60%). Pericardium, atria and right ventricle involvement have also been described; however, identification of an isolated right ventricle located hydatid cyst, like in our case, is atypical and quite rare10.\n\nCardiac hydatid cysts are often latent. They remain symptomless and silent for a considerable time and clinical manifestation of cardiac hydatid disease may vary and depends on the size and the location of the cysts11. The process of growth of cardiac cysts is slow because of the permanent traumatic action of myocardial contraction. After 2-7 years they can mimic the size of a chicken egg6. Unless it’s in a critical anatomic site, cardiac hydatid disease is usually diagnosed late, as patients can manifest non-specific symptoms such as cough, palpitations and chest pain. The cyst may affect cardiac function leading to conduction and rhythmic disturbances, chest pain or angina, acute myocardial infarction or valvular dysfunction and thus pulmonary hypertension may develop12. Cystic rupture is the most frequent complication (24-60%) and generally results in anaphylactic reaction with circulatory collapse. Other complications may occur leading to death, such as pericarditis, embolus, obstruction of cardiac chambers, cardiac tamponade and cardiac arrhythmias13.\n\nHydatid cysts located in the right cardiac chambers have special features, dissimilar from those of left sided cysts. In fact, right-sided cysts, such as in our case, have a tendency to extend subendocardially and intracavitarily14. In our case, the cyst seemed to extend to the septum. Cysts fissuration or rupture is more frequent, as this may trigger pulmonary embolic complication, anaphylaxis or sudden death. Chadly et al.1 reported a case of a 22-year old man who died of pulmonary artery emboli because of the rupture of right ventricle located hydatid cyst. Pansard et al.15 documented a case of progressive fissure of a hydatid cyst of the right ventricle, which led to a chronic pulmonary hypertension. The authors suggested that it was probably secondary to microemboli migration in the small vessels of the lung. Buris et al.16 reported a sudden death caused by hydatid embolism in a previously healthy man who died during a race, and at autopsy hydatid cysts in the right ventricle were detected. The necropsy revealed that the cysts had embolized into the pulmonary arteries.\n\nIn our case, ventricular arrhythmia seemed to be the fatal outcome of the cardiac cyst which was found macroscopically intact. Malamou-Mitsi et al.6 also have reported a case in which the cyst was found intact; they suggested that the death seemed to be due to fatal left ventricular arrhythmias. Singh et al.17 reported a case of a 57-year-old man who presented with syncope due to ventricular tachycardia, and imaging revealed a right ventricular hydatid cyst. In our case, although no allergic signs were observed, anaphylactic shock cannot be excluded from the scope of mechanisms of death beyond pulmonary embolism. This fact may be explained by the rapidity and unwitnessed death.\n\nPathologists should keep in mind that hydatid cysts can develop anywhere in the body. Solitary cardiac cyst is rare and can simulate a “silent bomb”. Unfortunately, sudden death remains the frequent manner of revelation of this disease in endemic areas.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication was obtained from the legally authorized representative of the decedent.",
"appendix": "References\n\nChadly A, Krimi S, Mghirbi T: Cardiac hydatid cyst rupture as cause of death. Am J Forensic Med Pathol. 2004; 25(3): 262–4. PubMed Abstract | Publisher Full Text\n\nPakis I, Akyildiz EU, Karayel F, et al.: Sudden death due to an unrecognized cardiac hydatid cyst: three medicolegal autopsy cases. J Forensic Sci. 2006; 51(2): 400–2. PubMed Abstract | Publisher Full Text\n\nCotran RS, Kumar V, Robbins SI: Infectious diseases: fungal, protozoal and helminthic diseases and sarcoidosis. In: Lichenberg F, editor, Robbins pathologic basis of disease. Philadelphia PA: WB Saunders; 1989; 385–433. Reference Source\n\nBudke CM, Carabin H, Ndimubanzi PC, et al.: A systematic review of the literature on cystic echinococcosis frequency worldwide and its associated clinical manifestations. Am J Trop Med Hyg. 2013; 88(6): 1011–27. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnderson WAD, Scotti TM: Mycotic, protozoan and helminthic infections. In: Anderson WAD, editor, Synopsis of pathology.10th ed.St. Louis, MO:the C.V.Mosby Company; 1980; 197–219.\n\nMalamou-Mitsi V, Papa L, Vougiouklakis T, et al.: Sudden death due to an unrecognized cardiac hydatid cyst. J Forensic Sci. 2002; 47(5): 1062–4. PubMed Abstract | Publisher Full Text\n\nWilliams WH: Hydatiden in demherzeneineskindes. Schmidts Jahrb. 1836; 9: 29.\n\nDibello R, Menendez H: Intracardiac rupture of hydatid cysts of the herat. A study based on three personal observations and 101 cases in the world literature. Circulation. 1963; 27: 366–74. PubMed Abstract | Publisher Full Text\n\nAmeli M, Mobarhan HA, Nouraii SS: Surgical treatment of hydatid cysts of the heart: report of six cases. J Thorac Cardiovasc Surg. 1989; 98(5 Pt 2): 892–901. PubMed Abstract | Publisher Full Text\n\nByard RW, Bourne AJ: Cardiac Echinococcosis With Fatal Intracerebral Embolism. Arch Dis Child. 1991; 66(1): 155–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLanzoni AM, Barrios V, Moya JL, et al.: Dynamic Left Ventricular Outflow Obstruction Caused by Cardiac Echinococcosis. Am Heart J. 1992; 124(4): 1083–5. PubMed Abstract | Publisher Full Text\n\nTrehan V, Shah P, Yusuf J, et al.: Thromboembolism: A Rare Complication of Cardiac Hydatidosis. Indian Heart J. 2002; 54(2): 199–201. PubMed Abstract\n\nBirincioğlu CL, Bardakci H, Küçüker SA, et al.: A clinical dilemma: cardiac and pericardiac echinococcosis. Ann Thorac Surg. 1999; 68(4): 1290–4. PubMed Abstract | Publisher Full Text\n\nDursun M, Terzibasioglu E, Yilmaz R, et al.: Cardiac hydatid disease: CT and MRI findings. AJR Am J Roentgenol. 2008; 190(1): 226–32. PubMed Abstract | Publisher Full Text\n\nPansard Y, De Brux JL, Cohen-Solal A, et al.: Kyste hydatique du coeur droit et hypertension pulmonaire post-embolique. Arch Mal Coeur Vaiss. 1987; 5: 667–669.\n\nBuris L, Takacs P, Varga M: Sudden death caused by hydatid embolism. Z Rechtsmed. 1987; 98(2): 125–8. PubMed Abstract | Publisher Full Text\n\nSingh SK, Singh V, Kumar S, et al.: Right ventricular hydatid cyst presented as tachyarrhythmia. Asian Cardiovasc Thorac Ann. 2019; 27(6): 489–491. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "63961",
"date": "02 Jun 2020",
"name": "Mejdi Ben Messaoud",
"expertise": [
"Reviewer Expertise interventional cardiology",
"valvular heart disease",
"echocardiography",
"heart failure"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nEditorial Note from F1000Research 7th September 2022 - This report has been updated to include a conflict of interest statement explaining the relationship between the reviewer and the author's institutional affiliations.\nI read with great interest the report written by Med Amine Mesrati et al. about a case of sudden death due to cardiac hydatic cyst of the right ventricle. Only few similar cases were reported in the literature. The authors attributed the sudden death to ventricular arrhythmia. I think that other causes, such as anaphylactic shock (although the cyst was intact) or pulmonary embolism or right ventricular obstruction are not excluded based on the lack of some data, especially imaging exams. Additionally, other cyst locations, such as cerebral or renal, should be excluded by authors (only lungs and liver were reported) to confirm the cardiac etiology of the death.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "5571",
"date": "05 Jun 2020",
"name": "med amin mesrati",
"role": "Author Response",
"response": "Dear Reviewer,Thank you for your considerations.Response to question 1: the autopsy findings and histological tests which are always more accurate than pre-mortem imaging had excluded a pulmonary embolism or obstruction of the RV. Thus we attributed the death to cardiac arrythmiasResponse to question 2: we report in the section of the case report that others organs were unremarkable. This is to say that kidney and brain didn't exhibit hydatid cyst.Cordially"
}
]
},
{
"id": "69471",
"date": "28 Aug 2020",
"name": "Omer Tanyeli",
"expertise": [
"Reviewer Expertise Cardiac surgery"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe cardiac hydatid disease is a relatively rare disease, especially causing symptoms in farmers. In this case report, the etiology of sudden death was attributed to possible arrhythmias caused by huge cyst in the right ventricle.\n\nIn the literature, the cardiac hydatid cyst is reported many times both for therapeutic options, and for its morbidity, e.g. arrhythmias. But in some Mediterranean countries, the disease is still a problem which should be kept in mind. The disease also seems to be in an increase, due to immigration/common travel policies all around the world; so that the disease can be seen in both urban and rural areas.\n\nI advise the authors to also read Tanyeli et al. (20171).\nAlthough it's not the first or the last case report in the \"cardiac hydatid cyst\" field, it may deserve indexing for the dramatic postmortem pictures of the heart.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "5876",
"date": "03 Sep 2020",
"name": "med amin mesrati",
"role": "Author Response",
"response": "Dear Tanyelli,Thank You very much for your comments. They are so pertinent and considered by all authors.It is true that many cases were reported in the literature about cardiac hydatid cyst but as you advanced, the exemplarity of our case remains in post-mortem pictures of the heart.We have read your article published in this field and we considered it very interesting.Cordially"
},
{
"c_id": "6155",
"date": "18 Dec 2020",
"name": "med amin mesrati",
"role": "Author Response",
"response": "Dear Dr. Tanyeli, Thank you very much for your comments. They are so pertinent and considered by all authors. It is true that many cases were reported in the literature about cardiac hydatid cyst but as you advanced, the exemplarity of our case remains in post-mortem pictures of the heart. We have read your article published in this field and we considered it very interesting. It was included in our references. Cordially"
}
]
}
] | 1
|
https://f1000research.com/articles/9-286
|
https://f1000research.com/articles/11-1087/v1
|
22 Sep 22
|
{
"type": "Research Article",
"title": "Circadian signatures of anterior hypothalamus in time-restricted feeding",
"authors": [
"Meiyu Zhou",
"Jianghui Chen",
"Rongfeng Huang",
"Haoran Xin",
"Xiaogen Ma",
"Lihua Li",
"Fang Deng",
"Zhihui Zhang",
"Min-Dian Li",
"Meiyu Zhou",
"Jianghui Chen",
"Rongfeng Huang",
"Haoran Xin",
"Xiaogen Ma",
"Lihua Li",
"Fang Deng"
],
"abstract": "Background: Meal timing resets circadian clocks in peripheral tissues, such as the liver, in seven days without affecting the phase of the central clock located in the suprachiasmatic nucleus (SCN) of the hypothalamus. Anterior hypothalamus plays an essential role in energy metabolism, circadian rhythm, and stress response. However, it remains to be elucidated whether and how anterior hypothalamus adapts its circadian rhythms to meal timing. Methods: Here, we applied transcriptomics to profile rhythmic transcripts in the anterior hypothalamus of nocturnal female mice subjected to day- (DRF) or night (NRF)-time restricted feeding for seven days. Results: This global profiling identified 128 and 3,518 rhythmic transcripts in DRF and NRF, respectively. NRF entrained diurnal rhythms among 990 biological processes, including ‘Electron transport chain’ and ‘Hippo signaling’ that reached peak time in the late sleep and late active phase, respectively. By contrast, DRF entrained only 20 rhythmic pathways, including ‘Cellular amino acid catabolic process’, all of which were restricted to the late active phase. The rhythmic transcripts found in both DRF and NRF tissues were largely resistant to phase entrainment by meal timing, which were matched to the action of the circadian clock. Remarkably, DRF for 36 days partially reversed the circadian clock compared to NRF. Conclusions: Collectively, our work generates a useful dataset to explore anterior hypothalamic circadian biology and sheds light on potential rhythmic processes influenced by meal timing in the brain (www.circametdb.org.cn).",
"keywords": [
"Circadian rhythm",
"time-restricted feeding",
"entrainment",
"anterior hypothalamus",
"transcriptomics",
"Hippo signaling",
"oxidative phosphorylation",
"amino acid degradation"
],
"content": "Introduction\n\nMeal timing resets circadian clocks in peripheral tissues (peripheral clocks), particularly in the liver.1–3 Day time-restricted feeding (DRF) in nocturnal rodents is misaligned with daily rhythms generated by the circadian clock. DRF reverses the liver clock within seven days in mice without altering the central clock located in the suprachiasmatic nucleus (SCN).4,5 DRF contributes to increased adiposity and glucose intolerance when combined with high-fat diet feeding.6–9 Conversely, night time-restricted feeding (NRF), is known to protect against metabolic diseases, such as obesity, insulin resistance, and fatty liver in rodents.10,11 Nevertheless, both DRF and NRF increase longevity in mice, when compared to arrhythmic feeding.12\n\nEmerging evidence shows that peripheral clocks entrain to DRF in a tissue-specific manner.13,14 Peripheral clocks in the heart and kidneys exhibit resistance to phase entrainment by DRF in female mice, so do the diurnal transcriptomes in these organs.14 This effect is also present in male mice.13 Of note, the liver clock seems to condition circadian rhythms in transcriptome in distant organs such as the lungs and adipose tissue.13 The tissue specificity of phase entrainment to DRF lends support to the proposed network organization or hierarchy of peripheral clocks.15–17\n\nAnterior hypothalamus is a center for circadian rhythm biogenesis, thermal regulation, endocrine functions, and energy metabolism. It includes the medial preoptic nucleus, supraoptic nucleus, SCN, anterior hypothalamic nucleus, and the paraventricular nucleus of the hypothalamus (PVH). While the SCN generates circadian rhythms, the PVH orchestrates circadian rhythms of metabolism and endocrine factors.18 In addition, the PVH is a hub for nutrient sensing and receives neural signaling from the hunger neurons located in the posterior hypothalamus.19,20 The SCN and PVH host cellular circadian clocks, and the former projects to the latter to output circadian signals.21 Perceivably, the SCN clock is coupled to the light/dark cycle, whereas the PVH clock integrates circadian signals from both light and food. Genome-wide transcript profiling studies have been done in the SCN or the hypothalamus for rhythmic transcripts in constant darkness.22,23 It remains to be elucidated whether and how anterior hypothalamus adapts its circadian biology to meal timing in mice.\n\nTo explore the regulation of anterior hypothalamic circadian biology by time-restricted feeding, we took a systems approach to profile rhythmic transcripts in this tissue from NRF and DRF female mice. We determined rhythmicity features of diurnal transcripts as well as the category and distribution of the enriched rhythmic pathways. This is followed by examining phase entrainment of the circadian clock, rhythmic transcripts and pathways found in both NRF and DRF tissues. Lastly, we compared the profiles of clock genes in the typical seven-day time-restricted feeding regimen to those in the 36-day long-term regimen in order to elucidate the dynamics of the circadian clock. In summary, we have defined circadian signatures of anterior hypothalamus in time-restricted feeding and generated a useful resource to explore the physiology and pathophysiology associated with different types of time-restricted feeding.\n\n\nMethods\n\nAnimal use was approved by the Laboratory Animal Welfare and Ethics Committee of the Third Military Medical University, China (No. AMUWEC20201106, approval date: 2020/04/15). All experiments conform to the relevant regulatory standards of the institution. All efforts were made to ameliorate harm to animals such as daily monitoring of food and water availability and routine husbandry. This study is reported in line with the ARRIVE guidelines.41\n\nSpecial pathogen-free (SPF) mice were purchased from Hunan SJT Laboratory Animal Co. and housed in a SPF barrier facility. C57BL/6J female mice at seven weeks of age were group housed and entrained to a 12h light:12h dark cycle with free access to normal chow diet and water during acclimation for one week. Animals were randomly assigned in a 1:1 ratio to time-restricted feeding groups and fed for seven or 36 days as previously described.24 The body weight statistics were balanced between groups before subjecting to time-restricted feeding so that there was no significant difference in body weight between experimental groups. DRF permits access to food from zeitgeber time 0 (ZT0, light-on time) to ZT12 (light-off time), and NRF allows food access from ZT12 to ZT0. At the end of time-restricted feeding, mice were euthanized by cervical dislocation, and subjected to tissue collection every 4 h for a complete 24-h cycle. Refer to doi:10.1016/j.xpro.2021.100701 for step-by-step procedures. Anterior hypothalamus was dissected, snap frozen in liquid nitrogen and stored in -80°C (n = 4 per group per time-point).\n\nTotal RNA from mouse anterior hypothalamus was extracted by TRIzol method (Invitrogen). RNA integrity (RIN > 7), purity and concentration were assessed and all samples passed the quality control. A total of 200 ng total RNA per sample was subjected to mRNA purification by poly-T oligo magnetic beads and the 150-bp pair-end RNA sequencing in the MGISEQ2000 (BGISEQ-500, RRID:SCR_017979) platform for a minimal coverage of 43.1 million reads by BGI (Shenzhen, China) as described.14 The RNA sequencing unit was blinded of the grouping information. Raw reads were cleaned via SOAPnuke (RRID:SCR_015025) (v1.5.2), mapped to the reference genome (GRCm38.p6) by HISAT2 (RRID:SCR_015530) (v2.0.4), aligned to the reference coding gene set by Bowtie (RRID:SCR_005476) (v2.2.5), and quantified using RSEM (RRID:SCR_013027) (v1.2.12). Raw counts were normalized by trimmed mean of M-values by edgeR (RRID:SCR_012802) (v3.30.3) and converted to Wagner’s transcripts per million (TPM). No sample was excluded (Pearson correlation coefficient per time point per group > 0.8). Transcripts with a TPM < 1 in more than 20% of samples were filtered. Data were then analyzed by MetaCycle (v1.2.0).25 The cutoff p-value for a rhythmic transcript was set to BH.Q-value < 0.05.\n\nPathway enrichment analysis was performed on rhythmic genes as described14,26 (Source file: c5.bp.v7.1.symbols.gmt from https://www.gsea-msigdb.org/gsea/msigdb). Mouse gene nomenclature was converted to human gene nomenclature via “Human and Mouse Homology Classes with Sequence information” (curated by http://www.informatics.jax.org). Domain was set from 0 to 24, indicating the minimal and maximal period length is 0 and 24 h, respectively. Minimal and maximal items per set are 10 and 10000, respectively. Kuiper’s test FDR q-value < 0.05 is considered as statistical significance.\n\nTissue RNA was isolated using Eastep Super Total RNA Extraction Kit (Promega). Complementary DNA (cDNA) was synthesized using the GoScript Reverse Transcription Mix (Promega). cDNA was amplified and analyzed using iTaq universal SYBR Green Supermix (Bio-Rad) and the Bio-Rad CFX96 Real-Time PCR Detection System (Bio-Rad). PCR protocol: DNA denaturation at 95°C for 3 min; denaturation at 95°C for 10 sec; annealing/extension and plate read at 60°C for 30 sec; 40 cycles of quantitative PCR. Results were normalized to u36B4. Period circadian protein homolog 2 (Per2)-forward (F), ATGCTCGCCATCCACAAGA; Per2-reverse (R), GCGGAATCGAATGGGAGAAT; Nuclear receptor subfamily 1 group D member 1 (Nr1d1)-F, TACATTGGCTCTAGTGGCTCC; Nr1d1-R, CAGTAGGTGATGGTGGGAAGTA; D site-binding protein (Dbp)-F, CGTGGAGGTGCTAATGACCTTT; Dbp-R, CATGGCCTGGAATGCTTGA; u36B4-F, AGATGCAGCAGATCCGCAT; u36B4-R, GTTCTTGCCCATCAGCACC. Experiments were repeated twice with similar results.\n\nStatistical analysis was conducted in R Project for Statistical Computing (RRID:SCR_001905) (v 4.0.2) and RStudio (RRID:SCR_000432) (v 1.2.5033). BH.Q-value < 0.05 (MetaCycle, v1.2.0), Kuiper test FDR q < 0.05 (phase set enrichment analysis), or p < 0.05 (Bonferroni test or circacompare, v0.1.027) was considered to be statistically significant. Heatmap of expression profile was visualized by R package: pheatmap (RRID:SCR_016418) (v1.0.12) with row-wise scaling and gene-specific clustering by Euclidean correlation.\n\n\nResults\n\nTo characterize whether and how diurnal rhythms in the anterior hypothalamus entrain to feeding rhythm, we performed RNA sequencing on samples dissected from nine week-old female C57BL/6J mice that had been subjected to either DRF or NRF for seven days. Seven days of DRF is sufficient to entrain peripheral clocks in female mice.14 Samples were collected every four hours for a complete diurnal cycle and assigned four biological replicates per time point. This is a commonly used study design used in global transcript profiling experiment. RNA sequencing reached a minimal depth of 43.1 million reads, which follows the guideline for genome-scale analysis of circadian rhythms.28 We applied an BH-adjusted p-value (meta2d_BH.Q) of 0.05 to filter rhythmic transcripts and acquired 128 and 3,518 rhythmic transcripts in DRF and NRF tissues, respectively (Figure 1A).41 Notably, DRF significantly decreased the number of rhythmic transcripts in anterior hypothalamus, compared to NRF. There were 83 rhythmic transcripts that are shared by DRF and NRF tissues (Figure 1B). As shown in Figure 1C, DRF rhythmic transcripts were clustered in the late active period (ZT18-ZT0), whereas NRF rhythmic transcripts exhibited a bimodal distribution that clustered in the pre-dawn hours (ZT23) and the late sleep phase (ZT9). Averagely speaking, rhythmic transcripts in DRF tissue exhibited a higher amplitude than those in NRF without any significant difference in the basal expression levels (midline estimating statistic of rhythm, MESOR) (Figure 1D).\n\n(A) Heatmap showing 24-h expression profiles of rhythmic transcripts in the anterior hypothalamus. Samples were dissected from time-restricted fed nine-week female mice every four hours for a complete daily cycle (n = 4 mice per time point). (B) Interaction of rhythmic transcripts between day time-restricted feeding (DRF) and night time-restricted feeding (NRF). (C) Distribution of the phase. (D) Midline estimating statistic of rhythm (MESOR) and amplitude of rhythmic transcripts. Data are presented as boxplots. Mann-Whitney test; ns, not significant, ****p < 0.0001.\n\nNext, we performed pathway analysis among rhythmic transcripts found in NRF tissue. As shown in Figure 2A, 990 pathways were significantly enriched and distributed towards the late active phase (ZT21) and the late sleep phase (ZT9). We examined these pathways by hour and found that ‘cotranslational protein targeting to membrane’ (ZT8), ‘electron transport chain’ (ZT9), ‘sterol biosynthetic process’ (ZT9), ‘primary alcohol metabolic process’ (ZT10), and ‘negative regulation of cell cycle g2 m phase tr’ (cell cycle G2-M phase transition) (ZT12) (Figure 2B). Compared to the late sleep phase, the late active phase is a rush hour for hundreds of rhythmic biological pathways, which are represented by ‘mRNA cis-splicing via spliceosome’ (ZT20), ‘regulation of translational initiation’ (ZT20), ‘protein k63 linked ubiquitination’ (ZT20), ‘protein k48 linked ubiquitination’ (ZT20), ‘de novo protein folding’ (ZT21), ‘phosphatidylinositol phosphorylation’ (ZT21), and ‘Hippo signaling’ (ZT22) (Figure 2C).\n\n(A) Phase distribution of enriched rhythmic pathways based on the anterior hypothalamic diurnal transcriptome. (B) Representative rhythmic pathways that peak around zeitgeber time 9 h (ZT9). (C) Representative rhythmic pathways that peak around ZT21. (D) Diurnal expression profiles of the rhythmic genes involved in electron transport chain. (E) Diurnal expression profiles of the rhythmic genes involved in Hippo signaling. (F) Representative rhythmic transcripts related to Hippo signaling. Data are presented as mean ± SEM (n = 4 mice per time point for seven time points). MetaCycle method, *BH adjusted p-value < 0.05, **p < 0.01, ***p < 0.001. NRF, night time-restricted feeding; DRF, day time-restricted feeding; GOBP, gene ontology biological processes; Nek8, NIMA related kinase 8; Yap1, Yes-associated protein 1; Tjp1, Tight junction protein 1.\n\nPreviously, microarray-based transcriptome profiling of the SCN has shown that the oxidative phosphorylation pathway exhibited circadian rhythm in ad libitum feeding and peaked in the late subjective night.23 Examination of the electron transport chain pathway revealed that transcripts related to three respiratory complexes (CI, CII, and CIV) are rhythmic in the NRF anterior hypothalamus and peak in the late active phase (Figure 2D). For example, these transcripts include NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (Ndufv1) (CI), NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (Ndufa9) (CI), Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (Sdhb) (CII), and Cox7a1 (CIV).\n\nHippo signaling is essential in organ size control through inhibiting cell proliferation and regulating apoptosis.29 We found that key components from the constituents and regulators of Hippo signaling (e.g., Transcriptional coactivator YAP1 (Yap1), Serine/threonine-protein kinase LATS2 (Lats2) and Wwc1) (Figure 2E). As shown in Figure 2F, representative transcripts encoding Serine/threonine-protein kinase Nek8 (Nek8), Yap1, and Tjp1 exhibited robust daily rhythm in NRF but lost the rhythmicity upon DRF.\n\nAs shown in Figure 1B, the number of rhythmic transcripts was reduced notably by DRF in the tissue, compared to NRF. Pathway analysis of the 128 rhythmic transcripts revealed 20 enriched rhythmic pathways with peak hours ranging from ZT17 to ZT20 (Figure 3A). These DRF rhythmic pathways include ‘response to endogenous stimuli’ (ZT17), ‘response to hormone’ (ZT18), ‘organophosphate metabolic process’ (ZT19), and ‘cellular amino acid metabolic process’ (ZT20) (Figure 3B). With respect to the magnitude of enrichment, amino acid metabolism is highly scored. Hierarchical analysis identified two clusters of rhythmic transcripts involved in cellular amino acid metabolism (Figure 3C).\n\n(A) Phase distribution of enriched rhythmic pathways based on the anterior hypothalamic diurnal transcriptome. (B) Representative rhythmic pathways that peak around zeitgeber time 18.5 h (ZT18.5). (C) Diurnal expression profiles of the rhythmic genes involved in cellular amino acid metabolism. (D) Representative rhythmic transcripts related to cellular amino acid metabolism. Data are presented as mean ± SEM (n = 4 mice per time point for seven time points). MetaCycle method, *BH adjusted p-value < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. NRF, night time-restricted feeding; DRF, day time-restricted feeding; GOBP, gene ontology biological processes; Pipox, Pipecolic acid and sarcosine oxidase; Prodh, Proline dehydrogenase 1; Csad, Cysteine sulfinic acid decarboxylase; Sds, Serine dehydrastase.\n\nPipox transcript encoding pipecolic acid and sarcosine oxidase, an essential enzyme in lysine degradation-forms one cluster by itself, which peaked in the late sleep phase (Figure 3D). Proline dehydrogenase 1 (Prodh) transcript encodes the first enzyme in proline degradation. Cysteine sulfinic acid decarboxylase (Csad) is an enzyme in cysteine and methionine degradation. Serine dehydrastase (Sds) catalyzes serine and threonine degradation. As shown in Figure 3D, transcripts of Prodh, Csad, and Sds exhibited robust diurnal oscillation in anterior hypothalamus of DRF mice. In particular, Csad and Sds did not oscillate in NRF. Thus, transcript signatures suggest that DRF entrains diurnal rhythms of cellular amino acid degradation.\n\nAfter examining circadian signatures of the anterior hypothalamus in each time-restricted feeding regimen, we determined the features associated with rhythmic transcripts found in both NRF and DRF tissues. Hierarchical analysis segregated the 83 dual-cycling transcripts into three clusters (Figure 4A). DRF reserved only 8.24% of rhythmic transcripts for more than 8 h compared to NRF, whereas more than 60% of the rhythmic transcripts remained phase-locked to the light/dark cycle (Figure 4B). This is consistent with the results of pathway analysis. In fact, none of the 37 enriched rhythmic pathways were shifted in phase for more than 2 h by DRF compared to NRF (Figure 4C). Representative enriched pathways include ‘lipid metabolic process’ (phase-shift 1 h), ‘regulation of phosphorylation’ (phase-shift 2 h), and ‘circulatory system development’ (phase shift 2 h) (Figure 4D).\n\n(A) Hierarchical clustering analysis of rhythmic transcripts found in both DRF and NRF anterior hypothalamus. (B-C) Distribution of the phase-shift between DRF and NRF among (B) rhythmic transcripts or (C) enriched rhythmic pathways. (D) Representative enriched pathways based on shared rhythmic transcripts between DRF and NRF. (E) Hierarchical clustering analysis of the circadian clock genes. (F-G) Diurnal expression of selected clock genes in the anterior hypothalamus from female mice subjected to DRF or NRF for (F) seven days or (G) 36 days. Data are presented as mean ± SEM (n = 4 mice per time point). MetaCycle, *BH adjusted p-value < 0.05; Circacompare method, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. NRF, night time-restricted feeding; DRF, day time-restricted feeding; GOBP, gene ontology biological processes; Per2, Period circadian protein homolog 2; Nr1d1, Nuclear receptor subfamily 1 group D member 1; Dbp, D site-binding protein.\n\nThe weak response in phase entrainment is matched with the response of the circadian clock. Hierarchical analysis segregated the core clock genes into two clusters. One cluster of genes, e.g., Brain-and-muscle ANRT-like 1 (Bmal1/Arntl) and Circadian locomotor output cycles protein kaput (Clock), reached the peak time in the dawn under NRF and damped under DRF (Figure 4E). The other cluster of genes, e.g., Per1, Per2, Per3, Nr1d1 and Nr1d2, reached the peak time in the dusk in both DRF and NRF (Figure 4E). As expected, representative transcripts encoding Per2, Nr1d1, and Dbp, was not shifted in phase by DRF (Figure 4F). After an extension of the time from seven days to 36 days, Per2 rhythm damped in DRF (Figure 4G). Remarkably, 36 days of DRF significantly inverted the phase and reduced the amplitude of Nr1d1 and Dbp in the anterior hypothalamus compared to NRF (Figure 4G).\n\n\nDiscussion/conclusions\n\nIn this study, we applied an unbiased approach to characterize circadian signatures of the anterior hypothalamus in time-restricted fed female mice. We found that DRF, the feeding rhythm that is mis-aligned with the circadian clock, decreased the number of rhythmic transcripts from 3,518 to only 128 compared to NRF within seven days. Pathway analysis identified synchronized rhythms among 990 and 20 biological processes in NRF and DRF, respectively. Typical NRF active pathways include ‘electron transport chain’ (peak time ZT9) and ‘Hippo signaling’ (ZT22). Meanwhile, DRF entrained robust diurnal oscillation among 43 transcripts including those related to ‘cellular amino acid catabolic process’ (ZT20). At the transcriptomic level, only 8.24% rhythmic transcripts were reversed in phase by DRF compared to NRF. This is matched with the resistance of the anterior hypothalamic clock to DRF. However, long-term DRF inverted the phase in some clock genes, such as Nr1d1 and Dbp.\n\nGlobal profiling of rhythmic transcripts and metabolites have been conducted in a few brain regions particularly including the SCN. In constant darkness, 365 and 642 rhythmic transcripts were identified in the SCN and hypothalamus, respectively.22,23 High-fat diet feeding increases the number of rhythmic metabolites in the SCN but not in the prefrontal cortex.30 Our transcriptome profiling of anterior hypothalamus uncovered 3,518 rhythmic transcripts in NRF, which suggests that synchronized rhythms from the light and food may markedly increase the prevalence of diurnal rhythms in the hypothalamus.\n\nAnterior hypothalamus is composed of different hub neural regions, such as the preoptic area, SCN and PVH. Our study identified distinct sets of circadian signatures in this tissue under different regimens of time-restricted feeding. Compared to previous studies elucidating the landscape of circadian rhythms in the SCN, hunger neurons, or the hypothalamus,22,23,31 NRF entrains diurnal rhythms among a similar set of biological pathways, including oxidative phosphorylation and intracellular trafficking among organelles. By contrast, DRF almost ablates the diurnal rhythms in anterior hypothalamus. This effect may come as a trade-off of two reverse rhythms originating from the light/dark cycles to the SCN and from the feed/fast cycle to the PVH, respectively. Cellular amino acid metabolism is a key circadian signature associated with DRF, which implies the robust daily activity and signaling related to amino acids in anterior hypothalamus. This is supported by a recent study reporting the role of tryptophan metabolism in the entrainment of the brain clock after integrating signals from the light and food.32\n\nThe PVH is emerging as a critical peripheral oscillator on top of its well-recognized role as a hub for nutrient sensing and energy homeostasis.19,20 It outputs circadian rhythm of energy expenditure, the rhythmicity of which is crucial for body weight homeostasis.33 PVH also mediates the circadian tone from the SCN to orchestrate daily rhythm of plasma glucose.34 Recently, it has been shown that corticotrophin-releasing hormone-producing neurons in the PVH receive circadian inputs from the SCN and drive daily release of glucocorticoids.35 Previously, olfactory bulb and cerebellum are proposed as food entrainable peripheral oscillators and involved in food anticipatory behavior induced by DRF.36–38 In our study, the anterior hypothalamus is partially food-entrainable as indicated by transcript rhythms of Nr1d1 and Dbp after a 36-day DRF. It could be due to the actions in the non-SCN brain area within the anterior hypothalamus, or the SCN. It has been shown recently that time-restricted feeding near the light-on time modulates the SCN functions and impacts thermal homeostasis, locomotor activity and wakefulness.39,40 These results suggest that brain regions within the anterior hypothalamus may entrain to the feeding rhythm after a long DRF.\n\nIn summary, we have determined circadian signatures of the anterior hypothalamus in time-restricted fed mice. The accessibility of the global transcript profiling data in CircaMetDB42,43 would provide a useful resource to study the physiological significance and the entrainment of circadian rhythms in anterior hypothalamus.\n\n\nData availability\n\nMendeley Data: F1000Research-125368, Zhou, Chen. https://doi.org/10.17632/h4bvgm2z6s.1.41\n\nThis project contains the following underlying data:\n\n- Raw data from RT-qPCR experiment, associated with Figure 4G\n\n- ARRIVE checklist – The ARRIVE Essential 10\n\n- Gene expression profile.csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe accession numbers for the global profiling dataset:\n\nGene Expression Omnibus: Global circadian transcript profile of mouse anterior hypothalamus entrained by inverted feeding. Accession number GSE150958; https://identifiers.org/geo:GSE150958.42\n\nChina National GeneBank DataBase: Global circadian transcript profile of mouse anterior hypothalamus entrained by inverted feeding. Accession number CNP0001601; https://db.cngb.org/search/project/CNP0001601/.43",
"appendix": "References\n\nReinke H, Asher G: Crosstalk between metabolism and circadian clocks. Nat. Rev. Mol. Cell Biol. 2019 Apr 11; 20(4): 227–241. Publisher Full Text Reference Source\n\nGuan D, Lazar MA: Interconnections between circadian clocks and metabolism. J. Clin. Invest. 2021 Aug 2; 131(15): e148278. PubMed Abstract\n\nLi MD: Clock-modulated checkpoints in time-restricted eating. Trends Mol. Med. 2022 Jan; 28(1): 25–35. Publisher Full Text\n\nStokkan KA, Yamazaki S, Tei H, et al.: Entrainment of the Circadian Clock in the Liver by Feeding. Science (1979). 2001 Jan 19; 291(5503): 490–493.Reference Source\n\nDamiola F, le Minli N , Preitner N, et al.: Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. Genes Dev. 2000; 14(23): 2950–2961. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYasumoto Y, Hashimoto C, Nakao R, et al.: Short-term feeding at the wrong time is sufficient to desynchronize peripheral clocks and induce obesity with hyperphagia, physical inactivity and metabolic disorders in mice. Metabolism. 2016; 65(5): 714–727. PubMed Abstract | Publisher Full Text\n\nArble DM, Vitaterna MH, Turek FW: Rhythmic leptin is required for weight gain from circadian desynchronized feeding in the mouse. PLoS One. 2011; 6(9): e25079. PubMed Abstract | Publisher Full Text\n\nArble DM, Bass J, Laposky AD, et al.: Circadian timing of food intake contributes to weight gain. Obesity. 2009; 17(11): 2100–2102. PubMed Abstract | Publisher Full Text\n\nKolbe I, Leinweber B, Brandenburger M, et al.: Circadian clock network desynchrony promotes weight gain and alters glucose homeostasis in mice. Mol Metab. 2019; 30(October): 140–151. PubMed Abstract | Publisher Full Text\n\nPetersen MC, Gallop MR, Flores Ramos S, et al.: Complex Physiology and Clinical Implications of Time-restricted Eating. Physiol. Rev. 2022 Jul 14: 9–25. Reference Source\n\nManoogian EN, Chow LS, Taub PR, et al.: Time-restricted eating for the prevention and management of metabolic diseases. Endocr. Rev. 2021 Sep 22; 43:405–436. Publisher Full Text\n\nAcosta-Rodríguez V, Rijo-Ferreira F, Izumo M, et al.: Circadian alignment of early onset caloric restriction promotes longevity in male C57BL/6J mice. Science (1979). 2022 Jun 10; 376(6598): 1192–1202. PubMed Abstract | Publisher Full Text\n\nManella G, Sabath E, Aviram R, et al.: The liver-clock coordinates rhythmicity of peripheral tissues in response to feeding. Nat. Metab. 2021 Jun 31; 3(6): 829–842. PubMed Abstract | Publisher Full Text\n\nXin H, Deng F, Zhou M, et al.: A multi-tissue multi-omics analysis reveals distinct kinetics in entrainment of diurnal transcriptomes by inverted feeding. iScience. 2021 Apr 23; 24(4): 102335. PubMed Abstract | Publisher Full Text\n\nAllada R, Bass J: Circadian Mechanisms in Medicine. Longo DL, editor. N. Engl. J. Med. 2021 Feb 11; 384(6): 550–561. PubMed Abstract | Publisher Full Text\n\nKoronowski KB, Sassone-Corsi P: Communicating clocks shape circadian homeostasis. Science (1979). 2021 Feb 12; 371(6530): eabd0951. PubMed Abstract | Publisher Full Text\n\nZhang Z, Shui G, Li MD: Time to eat reveals the hierarchy of peripheral clocks. Trends Cell Biol. 2021 Nov 14; 31(11): 869–872. PubMed Abstract | Publisher Full Text Reference Source\n\nLi MD, Xin H, Yuan Y, et al.: Circadian Clock-Controlled Checkpoints in the Pathogenesis of Complex Disease. Front. Genet. 2021 Sep 7; 12(September): 721231. PubMed Abstract | Publisher Full Text\n\nMorton GJ, Meek TH, Schwartz MW: Neurobiology of food intake in health and disease. Nat. Rev. Neurosci. 2014; 15(6): 367–378. PubMed Abstract | Publisher Full Text\n\nMyers MG, Affinati AH, Richardson N, Schwartz MW: Central nervous system regulation of organismal energy and glucose homeostasis. Nat. Metab. 2021 Jun 1; 3(6): 737–50. PubMed Abstract | Publisher Full Text\n\nMohawk JA, Green CB, Takahashi JS: Central and peripheral circadian clocks in mammals. Annu. Rev. Neurosci. 2012; 35: 445–462. PubMed Abstract | Publisher Full Text\n\nZhang R, Lahens NF, Ballance HI, et al.: A circadian gene expression atlas in mammals: Implications for biology and medicine. Proc. Natl. Acad. Sci. U. S. A. 2014 Nov 11; 111(45): 16219–16224. PubMed Abstract | Publisher Full Text\n\nPanda S, Antoch MP, Miller BH, et al.: Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 2002; 109(3): 307–320. PubMed Abstract | Publisher Full Text\n\nXin H, Huang R, Zhou M, et al.: Protocol for setup and circadian analysis of inverted feeding in mice. STAR Protoc. 2021 Sep; 2(3): 100701. PubMed Abstract | Publisher Full Text Reference Source\n\nWu G, Anafi RC, Hughes ME, et al.: MetaCycle: An integrated R package to evaluate periodicity in large scale data. Bioinformatics. 2016; 32(21): 3351–3353. PubMed Abstract | Publisher Full Text\n\nZhang R, Podtelezhnikov AA, Hogenesch JB, et al.: Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA). J. Biol. Rhythm. 2016; 31(3): 244–257. PubMed Abstract | Publisher Full Text\n\nParsons R, Parsons R, Garner N, et al.: CircaCompare: A method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms. Bioinformatics. 2020; 36(4): 1208–1212. PubMed Abstract | Publisher Full Text\n\nHughes ME, Abruzzi KC, Allada R, et al.: Guidelines for Genome-Scale Analysis of Biological Rhythms. J. Biol. Rhythm. 2017; 32(5): 380–393. PubMed Abstract | Publisher Full Text\n\nKoo JH, Guan KL: Interplay between YAP/TAZ and Metabolism. Cell Metabolism. Cell Press. 2018; 28: 196–206. PubMed Abstract | Publisher Full Text\n\nDyar KA, Lutter D, Artati A, et al.: Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks. Cell. 2018; 174(6): 1571–1585.e11. PubMed Abstract | Publisher Full Text\n\nCedernaes J, Huang W, Ramsey KM, et al.: Transcriptional Basis for Rhythmic Control of Hunger and Metabolism within the AgRP Neuron. Cell Metab. 2019; 29(5): 1078–1091.e5. PubMed Abstract | Publisher Full Text\n\nPetrus P, Cervantes M, Samad M, et al.: Tryptophan metabolism is a physiological integrator regulating circadian rhythms. Mol Metab. 2022 Oct; 64(July): 101556. PubMed Abstract | Publisher Full Text\n\nKim ER, Xu Y, Cassidy RM, et al.: Paraventricular hypothalamus mediates diurnal rhythm of metabolism. Nat. Commun. 2020 Dec 30; 11(1): 3794. PubMed Abstract | Publisher Full Text\n\nKalsbeek A, la Fleur S , van Heijningen C , et al.: Suprachiasmatic GABAergic inputs to the paraventricular nucleus control plasma glucose concentrations in the rat via sympathetic innervation of the liver. J. Neurosci. 2004 Sep 1; 24(35): 7604–7613. PubMed Abstract | Publisher Full Text\n\nJones JR, Chaturvedi S, Granados-Fuentes D, et al.: Circadian neurons in the paraventricular nucleus entrain and sustain daily rhythms in glucocorticoids. Nat. Commun. 2021 Dec 1; 12(1): 5763. PubMed Abstract | Publisher Full Text\n\nPavlovski I, Evans JA, Mistlberger RE: Feeding Time Entrains the Olfactory Bulb Circadian Clock in Anosmic PER2::LUC Mice. Neuroscience. 2018; 393: 175–184. PubMed Abstract | Publisher Full Text\n\nGranados-Fuentes D, Tseng A, Herzog ED: A circadian clock in the olfactory bulb controls olfactory responsivity. J. Neurosci. 2006; 26(47): 12219–12225. PubMed Abstract | Publisher Full Text\n\nMendoza J, Pévet P, Felder-Schmittbuhl MP, et al.: The cerebellum harbors a circadian oscillator involved in food anticipation. J. Neurosci. 2010; 30(5): 1894–1904. PubMed Abstract | Publisher Full Text\n\nZhang Z, Zhai Q, Gu Y, et al.: Impaired function of the suprachiasmatic nucleus rescues the loss of body temperature homeostasis caused by time-restricted feeding. Sci Bull (Beijing). 2020 Aug; 65(15): 1268–1280. PubMed Abstract | Publisher Full Text Reference Source\n\nZhai Q, Zeng Y, Gu Y, et al.: Time-restricted feeding entrains long-term behavioral changes through the IGF2-KCC2 pathway. iScience. 2022; 25(5): 104267. PubMed Abstract | Publisher Full Text\n\nLi M-D: “F1000Research-125368, Zhou, Chen”. Mendeley Data, V1. [Dataset].2022. Publisher Full Text\n\nLi M-D: Global circadian transcript profile of mouse anterior hypothalamus entrained by inverted feeding. Gene Expression Omnibus [Dataset]. 2021.Reference Source\n\nLi M-D: Global circadian transcript profile of mouse anterior hypothalamus entrained by inverted feeding. China National GeneBank DataBase [Dataset].2021.Reference Source"
}
|
[
{
"id": "151170",
"date": "12 Oct 2022",
"name": "Jeff R. Jones",
"expertise": [
"Reviewer Expertise Circadian biology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript by Zhou and Chen, et al., focuses on an important question in circadian biology and metabolism: how do clocks in the hypothalamus adjust to meal timing? To address this question, the authors use transcriptomics on anterior hypothalamus tissue taken from female mice every 4 h throughout the day. These mice were subjected to either day-restricted or night-restricted feeding. The authors found that there were many more cycling transcripts in the anterior hypothalamus from mice under night-restricted feeding compared to those under-day restricted feeding. Using pathway enrichment analysis, the authors found that many more rhythmic pathways were entrained in mice under night-restricted feeding compared to mice under day-restricted feeding. Night-restricted feeding-entrained pathways included those involved in oxidative phosphorylation and cell proliferation/apoptosis, and day-restricted feeding-entrained pathways included those involved in amino acid metabolism. Pathways associated with transcripts that cycled in both day-restricted and night-restricted feeding paradigms were largely resistant to food entrainment. Finally, and most excitingly, the authors find that extending day-restricted feeding from 7 d to 36 d inverts the phase of several core clock genes in the anterior hypothalamus. Overall, this study is novel and interesting. I greatly appreciate the online resource the authors developed. I do have a few minor concerns:\nMy largest concern is that the amount of tissue obtained for analysis is large and contains several brain regions including the SCN. Clock gene expression rhythms that are out of phase to those in the SCN have been reported in several of these regions (see, for instance, Figure 1 in Paul et al., Eur J Neurosci 20191). The authors mention that antiphase rhythms in the SCN and PVN may contribute to the blunting of diurnal rhythms in the anterior hypothalamus observed in mice under the day-restricted feeding paradigm. The authors should elaborate more on this limitation to their study in the Discussion section.\n\nThe authors should elaborate more on their pathway enrichment analysis findings in the Discussion. Why might different feeding paradigms entrain different metabolic pathways? The authors mention that oxidative phosphorylation has been previously demonstrated to be rhythmic, but what about Hippo signaling (or apoptosis, cell proliferation, etc.)? Why might feeding schedule entrain certain pathways such that they peak at different times of day (ZT 9 vs. ZT 21)? Why are pathways presumably unrelated to metabolism (e.g., prostate gland development) entrained by night-restricted feeding?\n\nWas the phase of any other transcript rhythm (including transcripts that aren’t core clock genes) inverted by 36 d of time-restricted feeding compared to 7 d?\n\nIt would be helpful for the authors to invert the colors on their heatmaps in Figs 2B, C, 3B, 4D. Typically “warmer” colors indicate a higher magnitude response.\n\nIn the Methods, the authors mention that for phase set enrichment analysis, they set domain from 0 to 24 to indicate that minimal and maximal period lengths were between 0 and 24 h. Is there a reason the authors didn’t examine periods that were longer than 24 h?\n\nWas there a reason the authors used female mice instead of a mix of male and female mice?\n\n\"We examined these pathways by hour and found that… (Figure 2B)” and “We found that key components from the constituents… (Figure 2E)” are sentence fragments.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "154353",
"date": "06 Dec 2022",
"name": "Christopher S. Colwell",
"expertise": [
"Reviewer Expertise Circadian rhythms",
"diseases of the nervous system. Time restricted feeding."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study, the authors used transcriptomics to profile rhythmic transcripts in the anterior hypothalamus of nocturnal female mice subjected to time-restricted feeding that was aligned (night-restricted feeding, NRF) or misaligned (day-restricted feeding, DRF) for seven days.\n\nThey found 3,518 diurnally rhythmic transcripts in the aligned feeding group while only 128 diurnally rhythmic transcripts in the misaligned feeding group. Impacted pathways were identified.\n\nStrengths:\nRNA-seq appears to be technically solid.\n\nThe authors appear to be well-versed in circadian rhythms and collected samples of the anterior hypothalamus every 4 hrs with n=4 per sample. This sampling frequency is sufficient to look at diurnal rhythms in transcriptions under the aligned (NRF) and misaligned (DRF) time-restricted feeding.\n\nAn unbiased hierarchical clustering analysis was used.\n\nThe dramatic loss of rhythmicity from the misaligned feeding group is a surprising finding.\n\nThe dataset has been deposited and this work may well guide future studies.\n\nWeaknesses:\nThe anterior hypothalamus is an anatomically heterogeneous region containing structures central to circadian rhythms like the SCN but also those involved with response to feeding like the PVH.\n\nThe authors just used female mice so sex differences cannot be explored.\n\nBulk RNA-seq used in this study captures the expression profiles averaged from thousands of cells and single-cell RNA-seq may have been more informative.\n\nControl data from mice on ad lib feeding and subjected to the same analysis would have added to the study.\n\nThe transcription factors driving the robust rhythms under aligned feeding and those compromised by the misaligned feeding were not explored.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1087
|
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