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"text": "systematically Differentiating Functions for Alternatively Spliced Isoforms\nthrough Integrating-RNA-seg Data" + "text": "Novel Trial Design in a Clinical Study of Diaphragm Pacing (DPS) for ALS" }, { - "id": 77997, - "strid": "0b688f0a-8776-43b7-83c0-a380cf84f66d", - "image_id": 203544, - "image_name": "120444.png", + "id": 3, + "strid": "64e28d4c-4aeb-4b30-90c6-8788ba3f6345", + "image_id": 1, + "image_name": "10003.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 199.858, - 498.922, - 4198.537, - 196.03999999999996 + 146.733, + 217.79, + 3016.763, + 427.17600000000004 ], "priority": 2, "parents": [ - 78034 + 1 ], "children": [], - "area": 99713.55307600001, + "area": 31956.98007, "iscrowd": 0, "segmentation": [], - "text": "Ridvan Eksi', Hongdong Li’;,Rajasree Menon’, Yuchen Wen’, Gilbert S. Omenn’?, Matthias Kretzler’:2, Yuanfang Guan’:23\n1 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Department of Internal Medicine;University of Michigan, Ann\nArbor, Michigan, United States of America, 3 Department of Electrical Engineéring and Computer Science, University.of Michigan, Ann Arbor, Michigan, United)States of America" + "text": "Robert G. Miller+2, David L. Ennist?, Liberty Jenkins, Jeff Thompson‘, Michael Fritz*+, Dan H. Moore?\n\n1Forbes Norris ALS/MDA Research Center, San Francisco, CA\n*Stanford University, Department of Neurology and Neurological Sciences\n3Origent Data Sciences, Vienna, VA, USA\nORIGENT 4Synapse Biomedical, Oberlin, OH, USA Oct" }, { - "id": 77998, - "strid": "ff5cc25a-144d-4c50-a1c6-08c5a3923fe0", - "image_id": 203544, - "image_name": "120444.png", + "id": 4, + "strid": "c2d576ff-fffb-4836-8542-0314e5414d78", + "image_id": 1, + "image_name": "10003.png", "category_id": 5, "category_name": "Section", "bbox": [ - 207.012, - 840.891, - 209.163, - 47.97900000000004 + 685.882, + 793.301, + 337.33299999999997, + 51.20600000000002 ], "priority": 3, "parents": [ - 78034 + 1 ], "children": [ - 78005 + 6, + 5 ], - "area": 174074.527692, + "area": 544110.876482, "iscrowd": 0, "segmentation": [], - "text": "Abstract" + "text": "BACKGROUND" }, { - "id": 78005, - "strid": "1b6b44bf-42ac-4b3d-90be-1a32aa44661b", - "image_id": 203544, - "image_name": "120444.png", + "id": 5, + "strid": "53facfa4-a905-4293-9a6f-c7a2af567e7e", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 204.723, - 904.197, - 890.6780000000001, - 1097.7469999999998 + 94.492, + 855.744, + 1519.165, + 204.64800000000002 ], "priority": 4, "parents": [ - 77998 + 4 ], "children": [], - "area": 185109.922431, + "area": 80860.962048, "iscrowd": 0, "segmentation": [], - "text": "Integrating large-scale functional genomic data has\nsignificantly accelerated our understanding of gene\nfunctions. However, no algorithm has been developed to\ndifferentiate functions for isoforms of the same*gene using\nhigh-throughput genomic data. This is because standard\nsupervised learning requires ‘ground-truth’ functional\nannotations, which are lacking at the\\isoform level. We\ndeveloped a generic framework,that interrogates public\nRNA-seq data at the transcript level to differentiate functions\nfor alternatively spliced isoforms. For a specific function, our\nalgorithm identifies the ‘responsible’ isoform(s) of a gene and\ngenerates classifying models at the isoform level instead of at\nthe gene level. Through cross-validation, we demonstrated\nthat our algorithm is effective in assigning functions to\ngenes, especially the ones with multiple isoforms, and robust\nto gene expression levels and removal of homologous gene\npairs.(We identified genes in the mouse whose isoforms are\npredicted to have disparate functionalities and\nexperimentally validated the ‘responsible’ isoforms using\ndata from mammary tissue. With protein structure modeling\nand experimental evidence, we further validated the\npredicted isoform functional differences for the\n\ngenes Cdkn2aand Anxa6. Our generic framework is the first\nto predict and differentiate functions for alternatively spliced\nisoforms, instead of genes, using genomic dataNt'is\nextendable to other species with alternatively_spliced\nisoforms, and shifts the current gene-centered function\nprediction to isoform-level predictions." + "text": "NeuRx DPS was FDA approved in 2011 for persons with ALS (PALS). Results from an open label post-\napproval study showed a survival advantage for DPS patients compared to matched placebo groups from\nother US trials. However, results from two randomized European trials suggested DPS could be harmful in\npatients not on NIV. To learn more about the value of DPS, particularly in relation to NIV, we developed a\nprotocol (PARADIGM study) with novel design and control groups." }, { - "id": 77999, - "strid": "8955091c-59a8-44e2-918c-3ee4e4ed5f15", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 5, - "category_name": "Section", + "id": 6, + "strid": "7513875f-fad0-410b-acc5-06d5ac70dec1", + "image_id": 1, + "image_name": "10003.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 212.829, - 2176.678, - 553.578, - 57.8159999999998 + 171.561, + 1121.899, + 1393.404, + 995.8250000000003 ], "priority": 5, "parents": [ - 78034 - ], - "children": [ - 78007, - 78021, - 78032, - 78027, - 78033, - 78029, - 78014, - 78006, - 78028, - 78030, - 78015, - 78031 - ], - "area": 463260.202062, - "iscrowd": 0, - "segmentation": [], - "text": "Materials and_methods" - }, - { - "id": 78006, - "strid": "3943b8f0-7a4a-4457-8be3-a1c3df49a2e9", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 216.504, - 2257.863, - 873.063, - 499.6300000000001 - ], - "priority": 6, - "parents": [ - 77999 + 4 ], "children": [], - "area": 488836.37095199997, + "area": 192474.114339, "iscrowd": 0, "segmentation": [] }, { - "id": 78027, - "strid": "fd4c5172-2979-42d3-a1ff-2ae1cdce1880", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 3, - "category_name": "Text", + "id": 7, + "strid": "60f352b4-53b2-4334-a3f6-f7ebe3932c6c", + "image_id": 1, + "image_name": "10003.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 216.274, - 2761.203, - 154.514, - 71.69999999999982 + 719.687, + 2204.234, + 276.254, + 50.92399999999998 ], - "priority": 7, + "priority": 6, "parents": [ - 77999 + 1 ], - "children": [], - "area": 597176.417622, + "children": [ + 8 + ], + "area": 1586358.554758, "iscrowd": 0, "segmentation": [], - "text": "RNA-seq dala are colectad from\nSequence Read Archive (SRA);\nfunctional amotatons from Gene\nOntology (GO) ae se to constuc\nthe genedevel \"gold standard’" + "text": "OBJECTIVES" }, { - "id": 78028, - "strid": "eab6abf3-8a7e-462a-b96c-090e75b67fcb", - "image_id": 203544, - "image_name": "120444.png", + "id": 8, + "strid": "b5e78533-544c-44e0-9061-0089f247d6f8", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 215.005, - 2882.497, - 149.09500000000003, - 29.059999999999945 + 94.658, + 2263.701, + 1519.857, + 116.29599999999982 ], - "priority": 8, + "priority": 7, "parents": [ - 77999 + 7 ], "children": [], - "area": 619751.267485, + "area": 214277.409258, "iscrowd": 0, "segmentation": [], - "text": "Partitioning data for testing models\nand generating predictions:" + "text": "To further examine the impact of DPS upon survival of PALS already stabilized on noninvasive ventilation\n(NIV). Survival of those who elect to receive DPS will be compared to that for concurrent controls, historical\ncontrols, and virtual controls." }, { - "id": 78032, - "strid": "06f48653-9f86-4050-8b04-cfd0e28cb887", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", + "id": 9, + "strid": "d69063fd-752c-45d2-a0aa-bfba1e36814e", + "image_id": 1, + "image_name": "10003.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 216.154, - 2909.908, - 140.77999999999997, - 69.80400000000009 + 734.472, + 2379.995, + 240.47399999999993, + 47.146999999999935 ], - "priority": 9, + "priority": 8, "parents": [ - 77999 - ], - "children": [], - "area": 628988.253832, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 78029, - "strid": "69a8de92-bc4d-444b-af82-72d37cf2185e", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 216.515, - 3073.211, - 152.93200000000002, - 41.46900000000005 + 1 ], - "priority": 10, - "parents": [ - 77999 + "children": [ + 12, + 11, + 10 ], - "children": [], - "area": 665396.2796649999, + "area": 1748039.68764, "iscrowd": 0, "segmentation": [], - "text": "An iterative strategy to generate\n‘soformlevelclassfication models\nusing the training set." + "text": "METHODS" }, { - "id": 78030, - "strid": "5ba2c81a-fc09-416a-b14f-3cf5f3d80c36", - "image_id": 203544, - "image_name": "120444.png", + "id": 10, + "strid": "74a64b0a-b035-4729-a924-ef73b8f6455c", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 218.652, - 3278.944, - 149.05400000000003, - 59.3130000000001 + 91.244, + 2439.521, + 1526.302, + 162.1790000000001 ], - "priority": 11, + "priority": 9, "parents": [ - 77999 + 9 ], "children": [], - "area": 716947.6634879999, + "area": 222591.65412400002, "iscrowd": 0, "segmentation": [], - "text": "Predictions are madeon'én,\nindependenttest Set (used ether for\ncross-yalicatiorvor bootstrap-\nbagi)" + "text": "Enroll 106 PALS who are using NIV and meet FDA-approved DPS indications of chronic hypoventilation and\nstimulatable diaphragm. PALS who decline DPS will be monitored as concurrent controls. All PALS will be\nfollowed until death, tracheostomy or 2-year follow-up. Other measures of ALS progression and adverse\n\nevents will also be monitored." }, { - "id": 78031, - "strid": "78908f1c-8f46-4d4f-b5b4-d253596ed91d", - "image_id": 203544, - "image_name": "120444.png", + "id": 11, + "strid": "ddd3589e-af66-49dd-9396-964ddbe1e4e4", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 218.678, - 3374.143, - 94.80899999999997, - 16.146999999999935 + 405.201, + 2628.195, + 877.685, + 112.71099999999979 ], - "priority": 12, + "priority": 10, "parents": [ - 77999 + 9 ], "children": [], - "area": 737850.842954, + "area": 1064947.2421950002, "iscrowd": 0, "segmentation": [], - "text": "Model validation using:" + "text": "Study Design\n\nProspective, non-randomized, open-label, interventional study" }, { - "id": 78033, - "strid": "d60f0401-1b8c-4849-8fe0-4dd297430661", - "image_id": 203544, - "image_name": "120444.png", + "id": 12, + "strid": "4a2fedf8-4789-4efd-a50f-f62b71d14b79", + "image_id": 1, + "image_name": "10003.png", "category_id": 4, "category_name": "List", "bbox": [ - 218.927, - 3388.465, - 78.83899999999997, - 44.72600000000011 + 104.552, + 2755.485, + 1481.103, + 444.43499999999995 ], - "priority": 13, + "priority": 11, "parents": [ - 77999 + 9 ], "children": [], - "area": 741826.477055, + "area": 288091.46772, "iscrowd": 0, "segmentation": [] }, { - "id": 78021, - "strid": "94a12636-277b-47e1-b9b5-cf93470de5f0", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 2, - "category_name": "Figure", + "id": 13, + "strid": "5cca8d67-2f51-4d88-bdc7-d07eaaa913a8", + "image_id": 1, + "image_name": "10003.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 393.545, - 2758.643, - 352.373, - 687.3319999999999 + 666.202, + 3261.958, + 365.539, + 53.827999999999975 ], - "priority": 14, + "priority": 12, "parents": [ - 77999 - ], - "children": [], - "area": 1085650.159435, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 78014, - "strid": "b26d00d3-9657-4d4d-9354-d149c4174c2c", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 769.529, - 2768.374, - 269.3409999999999, - 37.79500000000007 + 1 ], - "priority": 15, - "parents": [ - 77999 + "children": [ + 15, + 14 ], - "children": [], - "area": 2130344.0758459996, + "area": 2173122.943516, "iscrowd": 0, "segmentation": [], - "text": "MIB.assumptions:" - }, - { - "id": 78007, - "strid": "a2607539-3060-4f24-8b04-701e70343f66", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 779.265, - 2807.151, - 319.3470000000001, - 358.721 - ], - "priority": 16, - "parents": [ - 77999 - ], - "children": [], - "area": 2187514.5240149996, - "iscrowd": 0, - "segmentation": [] + "text": "ANALYTIC PLAN" }, { - "id": 78015, - "strid": "befb9397-351b-460a-9a6a-8f9c17df8271", - "image_id": 203544, - "image_name": "120444.png", + "id": 14, + "strid": "83d62369-64fa-4d0d-a388-c55c4bd653e7", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 768.75, - 3210.878, - 336.7149999999999, - 158.58399999999983 + 91.888, + 3326.206, + 1525.501, + 593.5590000000002 ], - "priority": 17, + "priority": 13, "parents": [ - 77999 + 13 ], "children": [], - "area": 2468362.4625, + "area": 305638.41692800005, "iscrowd": 0, "segmentation": [], - "text": "Ambiguity: Which\nsubset of isoforms of a\npositive gene will be\npositive?" + "text": "For the primary outcome of death or tracheostomy, a log-rank test will be used to compare survival post\nenrollment among those who elected versus refused DPS. We will also test whether DPS treatment or\nrefusal predicts survival in a Cox Proportional Hazards model that includes other covariates suspected to\ninfluence survival.\n\nSecondary tests will be to compare DPS treated survival with that for a matched group of historical controls\nassembled from the PRO-ACT database; and to compare observed survival with survival predicted for a\nvirtual set of patients whose baseline characteristics match those who selected DPS. Survival predictions\nfor the virtual controls will be based on baseline values and 3-month slopes for FVC and ALSFRS-R. The\nprediction model will first be validated using the outcomes of the patients who refused DPS, the null\nhypothesis being that the patients who refused DPS will not differ significantly from their predictions.\nOnce validated, the model will be applied to the DPS implanted cohort to determine whether the DPS\nimplanted patients differed significantly from their predicted survival and ALSFRS-R outcomes. Results from\nthe three control populations will be compared to determine which is the most efficient in terms of sample\nsize and power." }, { - "id": 78016, - "strid": "b150f970-a4c1-4388-a47a-ae773169f7aa", - "image_id": 203544, - "image_name": "120444.png", + "id": 15, + "strid": "1941b501-e06d-4b94-b140-dfccda4c378a", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1306.637, - 847.865, - 825.2229999999997, - 39.42700000000002 + 105.969, + 3966.118, + 1482.553, + 390.99299999999994 ], - "priority": 18, + "priority": 14, "parents": [ - 78034 + 13 ], "children": [], - "area": 1107851.780005, + "area": 420285.55834199995, "iscrowd": 0, "segmentation": [], - "text": "Two basic formulations of the MIL algorithm are tested." - }, - { - "id": 78008, - "strid": "3a7a20af-9c13-43a7-957a-ff591299fb7f", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 1348.11, - 887.467, - 829.729, - 284.00300000000004 - ], - "priority": 19, - "parents": [ - 78034 - ], - "children": [], - "area": 1196403.13737, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 78020, - "strid": "1c8e464b-1e38-40a0-9ecd-8937eb4bffd7", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1314.146, - 1186.894, - 853.5350000000001, - 279.4870000000001 - ], - "priority": 20, - "parents": [ - 78034 - ], - "children": [], - "area": 1559752.002524, - "iscrowd": 0, - "segmentation": [] + "text": "Virtual Controls\n\nRandom forest (RF) and gradient boosting machine models (GBM) will be used to predict ALSFRS-R\nprogression and survival at time points up to two years into the future. The RF and GBM models have been\ntrained using the Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) Database. PRO-ACT, first\nreleased in 2012, was recently (Dec, 2015) updated and now contains over 10,700 de-identified ALS patient\nrecords derived from 23 phase 2 and 3 ALS clinical trials . The RF progression model to predict function as\nreflected by the ALSFRS-R score was trained on 3,594 records in PRO-ACT containing complete records for\nALSFRS-R and either FVC or SVC. The GBM model to predict log-likelihood of survival was trained using\n5,737 records (including 1,737 deaths) containing ALSFRS or ALSFRS-R and FVC." }, { - "id": 78000, - "strid": "e043bd8b-2bc3-402b-86fe-971a35aad032", - "image_id": 203544, - "image_name": "120444.png", + "id": 16, + "strid": "1a657735-3c7f-4ecc-b995-3c97f708f8ba", + "image_id": 1, + "image_name": "10003.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1309.201, - 1513.885, - 186.42799999999988, - 45.19100000000003 + 593.199, + 4403.683, + 535.535, + 50.97900000000027 ], - "priority": 21, + "priority": 15, "parents": [ - 78034 + 1 ], "children": [ - 78009, - 78023, - 78012, - 78022, - 78017 + 17 ], - "area": 1981979.755885, + "area": 2612260.351917, "iscrowd": 0, "segmentation": [], - "text": "Results" + "text": "ACKNOWLEDGEMENTS" }, { - "id": 78009, - "strid": "5728fb14-b857-4e47-ad45-e4fb74107b44", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", + "id": 17, + "strid": "28662e8c-9f01-48ff-b400-7e9e7796e5f4", + "image_id": 1, + "image_name": "10003.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1309.205, - 1579.548, - 835.0990000000002, - 277.6200000000001 + 102.878, + 4476.742, + 1517.198, + 77.8109999999997 ], - "priority": 22, + "priority": 16, "parents": [ - 78000 + 16 ], "children": [], - "area": 2067952.13934, + "area": 460558.263476, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Data used in the preparation of this presentation were obtained from the publicly available Pooled\nResource Open-Access ALS Clinical Trials Database." }, { - "id": 78017, - "strid": "30d95931-c329-4267-a780-3dd19a644d14", - "image_id": 203544, - "image_name": "120444.png", + "id": 18, + "strid": "463eacae-1feb-4c5e-b2c6-b06974eb17cf", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1307.329, - 1866.448, - 821.9939999999999, - 39.73900000000003 + 1837.909, + 835.235, + 1234.9140000000002, + 184.414 ], - "priority": 23, + "priority": 17, "parents": [ - 78000 + 1 ], "children": [], - "area": 2440061.5973920003, + "area": 1535085.9236150002, "iscrowd": 0, "segmentation": [], - "text": "Cross-validation of the function prediction algorithm." + "text": "Sample Size and Power for Upcoming Paradigm Study\n\nPower to detect a reduction in the\nhazard ratio with N=106 DPS treated" }, { - "id": 78022, - "strid": "d427a366-9f7a-4497-8215-cbb1e1b2f447", - "image_id": 203544, - "image_name": "120444.png", + "id": 19, + "strid": "833bc3cb-340c-4495-b2e0-1da8fe4464c1", + "image_id": 1, + "image_name": "10003.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1423.379, - 1928.457, - 635.8200000000002, - 553.7529999999999 + 1987.457, + 1028.668, + 948.1879999999999, + 535.874 ], - "priority": 24, + "priority": 18, "parents": [ - 78000 + 1 ], "children": [], - "area": 2744925.196203, + "area": 2044433.417276, "iscrowd": 0, "segmentation": [] }, { - "id": 78012, - "strid": "e3172999-6cad-4285-a796-11ff012d5abc", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", + "id": 20, + "strid": "99977456-e5d1-4517-af1b-b7afdccef573", + "image_id": 1, + "image_name": "10003.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1306.838, - 2505.278, - 869.6360000000002, - 401.11500000000024 + 1811.926, + 1654.131, + 1274.0499999999997, + 79.2349999999999 ], - "priority": 25, + "priority": 19, "parents": [ - 78000 + 1 ], "children": [], - "area": 3273992.4909639996, + "area": 2997162.966306, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Calculations are for logrank test based on 53 treated and 53 control with 20% survival at 24\nmonths post DPS implant." }, { - "id": 78023, - "strid": "dc55a655-7d78-4a79-85b0-e930ef290667", - "image_id": 203544, - "image_name": "120444.png", + "id": 21, + "strid": "3e6c5893-897a-4df1-83fa-7d2ab7894416", + "image_id": 1, + "image_name": "10003.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1410.29, - 2923.767, - 661.7829999999999, - 513.5929999999998 + 1755.027, + 1836.36, + 1246.7110000000002, + 491.42600000000016 ], - "priority": 26, + "priority": 20, "parents": [ - 78000 + 1 ], "children": [], - "area": 4123359.3624299997, + "area": 3222861.38172, "iscrowd": 0, "segmentation": [] }, { - "id": 78018, - "strid": "f712064b-5f73-44a8-b795-2fdb0f2a510f", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 3, - "category_name": "Text", + "id": 22, + "strid": "138cea9b-e495-4460-bca2-4e8233394f62", + "image_id": 1, + "image_name": "10003.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2404.001, - 847.421, - 836.7219999999998, - 79.21299999999997 + 1758.442, + 2352.245, + 790.9180000000001, + 413.97699999999986 ], - "priority": 27, + "priority": 21, "parents": [ - 78034 + 1 ], "children": [], - "area": 2037200.9314210003, + "area": 4136286.4022899996, "iscrowd": 0, - "segmentation": [], - "text": "Robustness of predictions with respect to gene\nexpression levels.and exclusion of homolog gene pairs" + "segmentation": [] }, { - "id": 78019, - "strid": "f867c9a4-11a4-4541-98df-21cf88abc7c7", - "image_id": 203544, - "image_name": "120444.png", + "id": 23, + "strid": "7f527899-542d-40b1-9c28-a2942b5409b6", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2403.555, - 967.045, - 735.5320000000002, - 81.1160000000001 + 2577.316, + 2345.949, + 619.9110000000001, + 434.1460000000002 ], - "priority": 28, + "priority": 22, "parents": [ - 78034 + 1 ], "children": [], - "area": 2324345.844975, + "area": 6046251.892883999, "iscrowd": 0, "segmentation": [], - "text": "Two factors‘are further considered to validate the\nrobustness,of our algorithm." - }, - { - "id": 78010, - "strid": "8381e3ba-a438-4e69-8115-709d92adcb7c", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 2443.766, - 1087.373, - 827.3609999999999, - 522.752 - ], - "priority": 29, - "parents": [ - 78034 - ], - "children": [], - "area": 2657285.166718, - "iscrowd": 0, - "segmentation": [] + "text": "Performance metrics for predictive models\nto be used as secondary outcomes in this\nstudy. A. The ALSFRS-R functional model\ndisplays an RMSD of 4.979 (48 point range)\nand a close correlation between predicted\nand observed scores. B. The survival model\nROC curve has an AUC of 0.826. C. The vital\ncapacity model has an RMSD of 0.553 over a\nrange of 7L and also exhibits close\ncorrelation between predictions and\nobservations." }, { - "id": 78024, - "strid": "691c8838-0a31-4fc8-b214-957e623ff6f8", - "image_id": 203544, - "image_name": "120444.png", + "id": 24, + "strid": "d179399f-f3a5-4bb3-ac14-f7d781ef2c6e", + "image_id": 1, + "image_name": "10003.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2405.462, - 1617.003, - 870.6489999999999, - 370.461 + 1718.775, + 2872.656, + 1486.366, + 580.7799999999997 ], - "priority": 30, + "priority": 23, "parents": [ - 78034 + 1 ], "children": [], - "area": 3889639.2703859997, + "area": 4937449.3164, "iscrowd": 0, "segmentation": [] }, { - "id": 78011, - "strid": "447974ce-47fe-4af2-8654-f70298ce0268", - "image_id": 203544, - "image_name": "120444.png", + "id": 25, + "strid": "76d63a79-e2f6-4593-bc80-7cdbe68105fe", + "image_id": 1, + "image_name": "10003.png", "category_id": 4, "category_name": "List", "bbox": [ - 2401.654, - 2006.214, - 875.085, - 402.62199999999984 - ], - "priority": 31, - "parents": [ - 78034 - ], - "children": [], - "area": 4818231.877956, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 78026, - "strid": "8904f824-40ae-4878-bd8c-824e58e7cbc9", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 7, - "category_name": "Table", - "bbox": [ - 2407.953, - 2446.991, - 865.0790000000002, - 961.018 + 1798.515, + 3485.846, + 1187.117, + 118.71199999999999 ], - "priority": 32, + "priority": 24, "parents": [ - 78034 + 1 ], "children": [], - "area": 5892239.319423, + "area": 6269346.31869, "iscrowd": 0, "segmentation": [] }, { - "id": 78013, - "strid": "6942b366-dfc4-4315-87db-cdc55d247fca", - "image_id": 203544, - "image_name": "120444.png", + "id": 26, + "strid": "8195fb34-a1bb-49c4-8d9c-e834c8e2ecef", + "image_id": 1, + "image_name": "10003.png", "category_id": 4, "category_name": "List", "bbox": [ - 3500.232, - 846.736, - 870.9459999999999, - 680.226 - ], - "priority": 33, - "parents": [ - 78034 - ], - "children": [], - "area": 2963772.442752, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 78025, - "strid": "f97d3bb2-c6af-4411-b108-7a7050b047e8", - "image_id": 203544, - "image_name": "120444.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 3540.183, - 1576.042, - 781.6890000000003, - 703.9470000000001 + 1800.734, + 3624.528, + 1353.5350000000003, + 166.41800000000012 ], - "priority": 34, + "priority": 25, "parents": [ - 78034 + 1 ], "children": [], - "area": 5579477.095686, + "area": 6526810.803551999, "iscrowd": 0, "segmentation": [] }, { - "id": 78001, - "strid": "a203b649-9aec-4060-b327-d9a8baa9d32d", - "image_id": 203544, - "image_name": "120444.png", + "id": 27, + "strid": "3d7ed427-03ac-47d6-ae28-a8fcf15289f0", + "image_id": 1, + "image_name": "10003.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3501.062, - 2486.224, - 276.7020000000002, - 44.934999999999945 + 2321.325, + 3898.727, + 267.0819999999999, + 52.777000000000044 ], - "priority": 35, + "priority": 26, "parents": [ - 78034 + 1 ], "children": [ - 78003 + 28 ], - "area": 8704424.369888, + "area": 9050212.453274999, "iscrowd": 0, "segmentation": [], - "text": "References" + "text": "COMMENT" }, { - "id": 78003, - "strid": "17064c82-e55e-40ce-b70f-03bcadf0a6c1", - "image_id": 203544, - "image_name": "120444.png", + "id": 28, + "strid": "90304900-c77f-4a51-a1fc-103d34b74ddc", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3500.657, - 2560.784, - 872.2280000000001, - 365.2539999999999 + 1694.235, + 3959.004, + 1526.9040000000002, + 174.558 ], - "priority": 36, + "priority": 27, "parents": [ - 78001 + 27 ], "children": [], - "area": 8964426.435088001, + "area": 6707483.14194, "iscrowd": 0, "segmentation": [], - "text": "S. Andrews, I. Tsochantaridis and T. Hofmann, \"Support Vector\nMachines for Multiple-Instance Learning,\" Proc. Advances in Neural\nInformation Processing Systems, 2003\n\nTrapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. (2012)\nDifferential gene and transcript expression analysis of RNA-seq,\nexperiments with TopHat and Cufflinks. Nat Prot 7: 562-578. doi:\n10.1038/nprot.2012.016\n\nLiontos M, Pateras IS, Evangelou K, Gorgoulis VG(2012) The tumor\nsuppressor gene ARF as a sensor of oxidative stress»Curr Mol Med 12:\n704-715. doi: 10.2174/156652412800792633" + "text": "This is the first study to enroll only PALS who are already on NIV. In this way, the impact of DPS can be\nmore clearly examined in the presence of NIV. Moreover, this design will speed recruitment by\nempowering patient choice to obtain concurrent controls and thereby increase participation of PALS in\nclinical research. The use of virtual controls is also innovative and shows great promise for ALS trials." }, { - "id": 78002, - "strid": "27f0a4b6-4e2e-4ba1-8845-3bfb47145bf8", - "image_id": 203544, - "image_name": "120444.png", + "id": 29, + "strid": "e927bf59-4566-448a-8e0a-28c1d3fd3722", + "image_id": 1, + "image_name": "10003.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3502.358, - 3095.833, - 447.36299999999983, - 52.965000000000146 + 2310.365, + 4155.629, + 292.7739999999999, + 53.23199999999997 ], - "priority": 37, + "priority": 28, "parents": [ - 78034 + 1 ], "children": [ - 78004 + 30 ], - "area": 10842715.474214, + "area": 9601019.794584999, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgments" + "text": "REFERENCES" }, { - "id": 78004, - "strid": "0bd26a09-5dda-4e5e-b6b1-260844f70bd6", - "image_id": 203544, - "image_name": "120444.png", + "id": 30, + "strid": "23951a32-b95a-4e33-b9a4-7cf764fc0e66", + "image_id": 1, + "image_name": "10003.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3498.983, - 3157.603, - 872.0159999999996, - 257.7600000000002 + 1697.426, + 4225.927, + 1518.3579999999997, + 293.1109999999999 ], - "priority": 38, + "priority": 29, "parents": [ - 78002 + 29 ], "children": [], - "area": 11048399.217749001, + "area": 7173198.363901999, "iscrowd": 0, "segmentation": [], - "text": "This work is supported by NIH 1R21NS082212-01 and EU-\nFP VII Systems Biology of Rare Disease\n\nAll prediction results are stored in MySQL databases and\ndelivered through a searchable website:\n\nhttp?//euanlab.ccmb.med.umich.edu/isoPred" + "text": "Kuffner R, Zach N, Norel R, Hawe J, Schoenfeld D, Wang L, Li G, et al. Crowdsourced analysis of clinical trial\ndata to predict amyotrophic lateral sclerosis progression. Nat Biotechnol 2015;33:51-57.\nDOI:10.1038/nbt.3051\n\nD Friedman JH. 2001. Greedy Function Approximation: A Gradient Boosting Machine. Ann. Stat Taylor A,\nMiller R, Onders R and Ennist D. Analysis of function and survival in ALS patients with diaphragm pacing\nusing virtual controls (poster P108). Amyotrophic Lateral Sclerosis, 16:sup1, p130. DOI:\n10.3109/21678421.2015.1098811/009" }, { - "id": 179875, - "strid": "cf5a0af0-db31-478a-9b3b-9bc453e7c81a", - "image_id": 207525, - "image_name": "8368.png", + "id": 31, + "strid": "981a3558-c863-41b1-b916-bd8c5e167d64", + "image_id": 2, + "image_name": "10041.png", "category_id": 9, "category_name": "Root", "bbox": [ - 61.78, - 85.76, - 117.34, - 163.56 + 65.72, + 82.75, + 88.71000000000001, + 96.09 ], "priority": -1, "parents": [], "children": [ - 179869, - 179868, - 179867, - 179849, - 179850, - 179874, - 179873, - 179870, - 179872, - 179871 + 32, + 33, + 44, + 49, + 36, + 47, + 34 ], - "area": 5298.2528, + "area": 5438.33, "iscrowd": 0, "segmentation": [] }, { - "id": 179849, - "strid": "2d0b69c6-6446-4dd7-a73a-df6fa5d5664c", - "image_id": 207525, - "image_name": "8368.png", + "id": 32, + "strid": "a51b7e38-6991-4423-8b67-3fcb1be7c93d", + "image_id": 2, + "image_name": "10041.png", "category_id": 1, "category_name": "Title", "bbox": [ - 552.889, - 101.645, - 2375.053, - 179.96800000000002 + 263.856, + 118.232, + 2782.9620000000004, + 288.722 ], "priority": 1, "parents": [ - 179875 + 31 ], "children": [], - "area": 56198.402405, + "area": 31196.222592, "iscrowd": 0, "segmentation": [], - "text": "Trabectome-Mediated Ab Interno Trabeculectomy for Steroid-\nInduced Glaucoma" + "text": "Motor Unit Number Index (MUNIX) of six muscles:\nNormal values and effects of age and gender" }, { - "id": 179850, - "strid": "5d5a272d-934a-4606-acbf-9504cdeced2b", - "image_id": 207525, - "image_name": "8368.png", + "id": 33, + "strid": "c484b6e9-0931-4bb5-ae99-a295e51ec940", + "image_id": 2, + "image_name": "10041.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 629.84, - 315.034, - 2222.053, - 111.76499999999999 + 642.804, + 513.22, + 2119.301, + 370.928 ], "priority": 2, "parents": [ - 179875 + 31 ], "children": [], - "area": 198421.01456, + "area": 329899.86888, "iscrowd": 0, "segmentation": [], - "text": "Yalong Dang’, Hardik A. Parikh*?, Pritha Roy’, Igor |. Bussel*, Ralitsa T. Loewen’, Nils A. Loewen*\n1. Dept of Ophthalmology, University of Pittsburgh School of Medicine 2. Dept of Ophthalmology, Rutgers NJMS" + "text": "Taha Omer*?!, B Nasseroleslami?\nFiona Molloy? Gerard Mullins*, Orla Hardiman?\n1. Academic Unit of Neurology, Trinity College &\n2. Clinical Neurophysiology Dept, Beaumont Hospital, Dublin, Ireland" }, { - "id": 179867, - "strid": "e3788571-4cac-416d-9b29-1b250928bb37", - "image_id": 207525, - "image_name": "8368.png", + "id": 34, + "strid": "de29f0c4-789f-4570-ab13-07c5cea6fcf9", + "image_id": 2, + "image_name": "10041.png", "category_id": 5, "category_name": "Section", "bbox": [ - 120.638, - 517.532, - 142.374, - 38.85699999999997 + 100.375, + 1115.311, + 355.577, + 66.57199999999989 ], "priority": 3, "parents": [ - 179875 + 31 ], "children": [ - 179851 + 35 ], - "area": 62434.025416000004, + "area": 111949.34162499999, "iscrowd": 0, "segmentation": [], - "text": "Purpose" + "text": "Background:" }, { - "id": 179851, - "strid": "3c74de4c-3f11-40fc-bc06-57ed6afe74de", - "image_id": 207525, - "image_name": "8368.png", + "id": 35, + "strid": "936d66cf-8fda-4aef-92ee-9cfc66254473", + "image_id": 2, + "image_name": "10041.png", "category_id": 3, "category_name": "Text", "bbox": [ - 117.951, - 573.369, - 1000.152, - 79.793 + 101.098, + 1193.461, + 886.072, + 1574.2860000000003 ], "priority": 4, "parents": [ - 179867 + 34 ], "children": [], - "area": 67629.446919, + "area": 120656.520178, "iscrowd": 0, "segmentation": [], - "text": "To evaluate outcomes of ab-interno trabeculectomy in cases of steroid-\ninduced glaucoma." + "text": "Motor Unit Number index\n(MUNIX) is a neurophysiological\nmeasure estimated by a\nnoninvasive method that\nrequires minimal electric\nstimulation. It provides an index\nof the number of lower motor\nneurons in a muscle. The\ntechnique involves utilizing the\nsurface-recorded compound\nmuscle action potential (CMAP)\nand electromyographic (EMG)\ninterference pattern to compute\nthe motor unit number index\n(MUNIX). Previous studies\nestablished its role in\nlongitudinal follow up of lower\nmotor neuron loss and in\nmonitoring disease progression\nin ALS." }, { - "id": 179874, - "strid": "ea0a3c37-2b7f-440e-abe6-14d6fd171291", - "image_id": 207525, - "image_name": "8368.png", + "id": 36, + "strid": "42787380-de51-478b-b518-0ede9c03cbf5", + "image_id": 2, + "image_name": "10041.png", "category_id": 5, "category_name": "Section", "bbox": [ - 120.777, - 720.417, - 384.97, - 34.24699999999996 + 102.888, + 2935.902, + 269.81899999999996, + 64.39800000000014 ], "priority": 5, "parents": [ - 179875 + 31 ], "children": [ - 179852 + 42, + 40, + 37, + 38 ], - "area": 87009.804009, + "area": 302069.084976, "iscrowd": 0, "segmentation": [], - "text": "Patients and Methods" + "text": "Methods:" }, { - "id": 179852, - "strid": "00a6a5e1-1355-48f4-b7c1-8a794105ffa5", - "image_id": 207525, - "image_name": "8368.png", + "id": 37, + "strid": "31c4ea35-89c0-4d4e-936d-1a9451ccea7d", + "image_id": 2, + "image_name": "10041.png", "category_id": 3, "category_name": "Text", "bbox": [ - 116.518, - 773.212, - 1006.2469999999998, - 410.2550000000001 + 97.743, + 3013.788, + 888.8420000000001, + 1265.8709999999996 ], "priority": 6, "parents": [ - 179874 + 36 ], "children": [], - "area": 90093.115816, + "area": 294576.680484, "iscrowd": 0, "segmentation": [], - "text": "All cases diagnosed with steroid glaucoma were included. Cases that\nhad concurrent surgery other than cataract surgery and/or no follow-\nup records were excluded. The main outcomes measure was the\nchanges of IOP, numbers of medications and surgical success. Kaplan-\nMeier was used for survival analysis with success defined as |OPS21\nmmHg, at least 20% IOP reduction from baseline for any two\nconsecutive visits after 3 months and no secondary glaucoma surgery.\nSecondary outcomes included complication rate, secondary\nprocedures." + "text": "We have performed MUNIX ina\ncohort of 40 healthy controls\naged 23-80 (Table1) in\nBeaumont Hospital, Dublin,\nIreland. The same examiner\nperformed MUNIX test using\nKeypoint. NET® software. The\nright APB, ADM, BB, TA, EDB &\nAH muscles were investigated.\nMUNIX, CMAP & MUSIX\nmeasures were obtained for\neach muscle.\n\nDescriptive statistics, ANOVA\nand Spearman’s correlation\ntests were used as appropriate\nfor statistical analysis of data." }, { - "id": 179868, - "strid": "52ce0154-a9ea-4436-b69b-0d360ff414b0", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 5, - "category_name": "Section", + "id": 38, + "strid": "f1a03858-53fb-4a6e-b9f5-040b0975cf7f", + "image_id": 2, + "image_name": "10041.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 121.212, - 1212.984, - 126.146, - 32.88000000000011 + 1081.649, + 1084.525, + 934.261, + 875.3209999999999 ], "priority": 7, "parents": [ - 179875 + 36 ], "children": [ - 179853, - 179854 + 39 ], - "area": 147028.216608, + "area": 1173075.381725, "iscrowd": 0, - "segmentation": [], - "text": "Results" + "segmentation": [] }, { - "id": 179853, - "strid": "36d7b1c2-aec3-47b9-a7ea-baa046c8bfb4", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 3, - "category_name": "Text", + "id": 39, + "strid": "81d88f94-94e4-401b-ac99-1f091d152e46", + "image_id": 2, + "image_name": "10041.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 116.734, - 1267.165, - 1006.862, - 270.663 + 1097.328, + 1973.128, + 821.942, + 151.9559999999999 ], "priority": 8, "parents": [ - 179868 + 38 ], "children": [], - "area": 147921.23911, + "area": 2165168.601984, "iscrowd": 0, "segmentation": [], - "text": "A total of 69 cases were included in this study after applying inclusion\nand exclusion criteria. Mean IOP was reduced from a baseline of 31.6\n+10.1 mmHg to 15.8+3.5mmbHg at 12 months (p<0.01*), while number\nof glaucoma medication was reduced from 3.9+0.9 to 2.9+1.3 (p=0.12).\nSurvival rate was 86% at 12 months with 4 cases required additional\nglaucoma surgery." + "text": "Figure 1: MUNIX value is strongly determined\nby CMAP, a relation not affected by age or\ngender" }, { - "id": 179854, - "strid": "b0067b3b-fbb4-4e8f-b51b-7129d022de47", - "image_id": 207525, - "image_name": "8368.png", + "id": 40, + "strid": "856f5517-b450-4efe-a7a3-01673b1633e8", + "image_id": 2, + "image_name": "10041.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 185.648, - 1603.093, - 778.544, - 831.5470000000003 + 2055.978, + 1085.964, + 480.6880000000001, + 875.0250000000001 ], "priority": 9, "parents": [ - 179868 + 36 ], - "children": [], - "area": 297611.009264, + "children": [ + 41 + ], + "area": 2232718.092792, "iscrowd": 0, "segmentation": [] }, { - "id": 179869, - "strid": "057b16a0-b048-49ba-988c-5de8ec7c09ce", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 5, - "category_name": "Section", + "id": 41, + "strid": "8d46a865-1096-4fb8-a30e-a76b311dd0ad", + "image_id": 2, + "image_name": "10041.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1231.662, - 514.578, - 535.559, - 35.88599999999997 + 2055.913, + 1978.031, + 511.32699999999977, + 142.1010000000001 ], "priority": 10, "parents": [ - 179875 - ], - "children": [ - 179855 + 40 ], - "area": 633786.168636, + "children": [], + "area": 4066659.647303, "iscrowd": 0, "segmentation": [], - "text": "Key Steps of Surgical Technique" + "text": "Figure 2: a negative\ncorrelation exists\nbetween MUNIX and MUSIX" }, { - "id": 179855, - "strid": "5e0e92f6-2d5f-437d-9e34-c6014ce58bfe", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 2, - "category_name": "Figure", + "id": 42, + "strid": "b974af81-05bc-4e24-8f8f-8f23b79404c4", + "image_id": 2, + "image_name": "10041.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1238.216, - 592.605, - 949.672, - 556.963 + 1082.914, + 2156.571, + 1464.787, + 720.4560000000001 ], "priority": 11, "parents": [ - 179869 + 36 ], - "children": [], - "area": 733772.9926799999, + "children": [ + 43 + ], + "area": 2335380.927894, "iscrowd": 0, "segmentation": [] }, { - "id": 179873, - "strid": "262db913-3297-46c4-a98f-b35452cce3c3", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 5, - "category_name": "Section", + "id": 43, + "strid": "0f7f6f30-a4e7-4769-a42b-3b8d10dbb8c6", + "image_id": 2, + "image_name": "10041.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1251.037, - 1219.581, - 322.105, - 41.13499999999999 + 1096.744, + 2906.616, + 702.864, + 48.597999999999956 ], "priority": 12, "parents": [ - 179875 - ], - "children": [ - 179856, - 179858, - 179863, - 179860, - 179861, - 179859, - 179857, - 179862 + 42 ], - "area": 1525740.955497, + "children": [], + "area": 3187813.658304, "iscrowd": 0, "segmentation": [], - "text": "Subgroup Analysis" + "text": "Table 1: Participants’ demgraphics" }, { - "id": 179856, - "strid": "64dd9d96-30f2-46e4-87ac-8ee7d042a786", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 4, - "category_name": "List", + "id": 44, + "strid": "12799ac8-c3f3-47be-9e37-5584b18fec26", + "image_id": 2, + "image_name": "10041.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1250.891, - 1278.806, - 980.3589999999999, - 177.42599999999993 + 1127.101, + 3025.977, + 224.35300000000007, + 62.80000000000018 ], "priority": 13, "parents": [ - 179873 + 31 ], - "children": [], - "area": 1599646.9161460001, + "children": [ + 46, + 45 + ], + "area": 3410581.7026770003, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Results:" }, { - "id": 179857, - "strid": "9dccfc78-8d92-4880-9533-caf69cb56c1e", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 2, - "category_name": "Figure", + "id": 45, + "strid": "a90c3996-ba6a-4c4b-b4c9-3e437f7a6f3e", + "image_id": 2, + "image_name": "10041.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1255.59, - 1524.534, - 844.3949999999998, - 347.69799999999987 + 1123.873, + 3107.244, + 1360.232, + 1185.7050000000004 ], "priority": 14, "parents": [ - 179873 + 44 ], "children": [], - "area": 1914189.64506, + "area": 3492147.6360120005, "iscrowd": 0, "segmentation": [] }, { - "id": 179858, - "strid": "f72437ca-d758-4049-9cf3-8935455e858a", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 4, - "category_name": "List", + "id": 46, + "strid": "719c9afe-5e12-4ea3-9fb5-710ebe1cfbf1", + "image_id": 2, + "image_name": "10041.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1260.37, - 1943.412, - 974.3240000000001, - 82.37599999999998 + 2622.108, + 1127.593, + 566.1309999999999, + 785.258 ], "priority": 15, "parents": [ - 179873 + 44 ], "children": [], - "area": 2449418.1824399997, + "area": 2956670.6260440005, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Aims: To establish\nMUNIX normative\ndata profile of\ncontrols and to\ndetermine the\ndegree of variance,\nthe effect of gender,\nand whether MUNIX\ndeclines in normal\nageing." }, { - "id": 179859, - "strid": "9cab83f9-555f-4265-b540-8597a810cae1", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 2, - "category_name": "Figure", + "id": 47, + "strid": "5db8fe10-6037-410b-829d-78ae86477c5a", + "image_id": 2, + "image_name": "10041.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1251.781, - 2103.331, - 854.98, - 353.4200000000001 + 2642.81, + 2211.449, + 351.64300000000003, + 64.97800000000007 ], "priority": 16, "parents": [ - 179873 + 31 ], - "children": [], - "area": 2632909.782511, + "children": [ + 48 + ], + "area": 5844439.53169, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Conclusions:" }, { - "id": 179860, - "strid": "b05c1294-8fb9-476b-a3a8-cfb3c6a3f9b9", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 4, - "category_name": "List", + "id": 48, + "strid": "c2902edf-eb6f-46b2-9570-b099b490b4e9", + "image_id": 2, + "image_name": "10041.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2319.175, - 531.196, - 1065.2380000000003, - 171.264 + 2640.711, + 2285.039, + 554.6240000000003, + 1668.223 ], "priority": 17, "parents": [ - 179873 + 47 ], "children": [], - "area": 1231936.4833000002, + "area": 6034127.622729, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Our study\nestablished MUNIX\ndata profile of a\ncohort of normal\ncontrols and\ndetermined the\ndegree of variance\nas well as the\neffects of gender\nand age, in line with\nprevious findings by\nNeuwirth et al in\n2011 (ref 3).\n\nWe propose MUNIX\nas an alternative to\nother invasive and\ntime consuming\nmethods of\nmeasuring lower\nmotor neurons in\nmuscles." }, { - "id": 179861, - "strid": "fa9df7b0-d728-41b6-9b33-58271cddb801", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 2, - "category_name": "Figure", + "id": 49, + "strid": "9395ad60-8159-4623-b577-b57b15e7332b", + "image_id": 2, + "image_name": "10041.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2429.286, - 741.475, - 840.6149999999998, - 354.53599999999994 + 86.069, + 4370.412, + 3106.678, + 234.23400000000038 ], "priority": 18, "parents": [ - 179873 + 31 ], "children": [], - "area": 1801254.83685, + "area": 376156.99042800005, "iscrowd": 0, "segmentation": [] }, { - "id": 179862, - "strid": "73b32c4b-8f64-4038-98d8-4fbb5250ba26", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 4, - "category_name": "List", + "id": 50, + "strid": "4fbf0d20-7f2d-4f67-90fb-7ff13495df83", + "image_id": 3, + "image_name": "10043.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 2319.352, - 1134.349, - 1065.3360000000002, - 175.58300000000008 + 46.87, + 40.41, + 87.26999999999998, + 82.13000000000001 ], - "priority": 19, - "parents": [ - 179873 + "priority": -1, + "parents": [], + "children": [ + 96, + 82, + 99, + 97, + 66, + 76, + 103, + 62, + 51, + 94, + 54, + 63, + 101, + 52, + 53, + 78, + 69, + 74, + 80, + 100, + 90, + 98, + 57, + 95, + 73, + 64, + 86, + 67, + 60, + 84, + 88, + 71, + 92 ], - "children": [], - "area": 2630954.6218479997, + "area": 1894.0166999999997, "iscrowd": 0, "segmentation": [] }, { - "id": 179863, - "strid": "f844aa5a-2a4c-42f4-80b7-2192b0614b86", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 2, - "category_name": "Figure", + "id": 51, + "strid": "cd1e50a3-1c7b-4af2-9669-2f6667a8151a", + "image_id": 3, + "image_name": "10043.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 2429.02, - 1349.128, - 874.143, - 355.799 + 206.487, + 183.943, + 3182.53, + 263.22300000000007 ], - "priority": 20, + "priority": 1, "parents": [ - 179873 + 50 ], "children": [], - "area": 3277058.89456, + "area": 37981.838241000005, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Guide to Cyprinid Fish Larvae and Early Juveniles\n\nof the Upper Colorado River Basin with Computer-Interactive Key" }, { - "id": 179870, - "strid": "9b3c0447-b0e0-457c-93a0-a5a88bfca8f2", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 5, - "category_name": "Section", + "id": 52, + "strid": "2e896716-6140-4224-b097-d6773f7b3e71", + "image_id": 3, + "image_name": "10043.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 2321.022, - 1763.365, - 191.89800000000014, - 34.58999999999992 + 176.173, + 511.241, + 3247.8600000000006, + 144.45500000000004 ], - "priority": 21, + "priority": 2, "parents": [ - 179875 - ], - "children": [ - 179864 + 50 ], - "area": 4092808.95903, + "children": [], + "area": 90066.860693, "iscrowd": 0, "segmentation": [], - "text": "Conclusion" + "text": "By Darrel E. Snyder, Sean C. Seal, Jennifer A. Charles, and C. Lynn Bjork (illustrator)\n\nLarval Fish Laboratory, Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins (darrel.snyder @colostate.edu)" }, { - "id": 179864, - "strid": "6bb82d8c-8ff7-45a0-b9bf-df96d5acae37", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 3, - "category_name": "Text", + "id": 53, + "strid": "97bc2ef1-40fe-40de-9a60-4c775ed96b03", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2320.762, - 1836.5, - 1087.8629999999998, - 174.49399999999991 + 139.777, + 836.937, + 1014.6779999999999, + 1355.978 ], - "priority": 22, + "priority": 3, "parents": [ - 179870 + 50 ], "children": [], - "area": 4262079.413000001, + "area": 116984.54304899999, "iscrowd": 0, - "segmentation": [], - "text": "Trabectome reduced the IOP by a mean of 50% in 69 cases of steroid-induced\nglaucoma on 1 less medication after 1 year, suggesting trabectome with or\nwithout cataract surgery is a safe and effective surgical option for persistent\nsteroid-induced glaucoma." + "segmentation": [] }, { - "id": 179871, - "strid": "dcf1d6df-0cdd-433a-9fd6-5cc3e95771dc", - "image_id": 207525, - "image_name": "8368.png", + "id": 54, + "strid": "250a3c8c-de8f-4bcb-9fa0-e350a2fe01e6", + "image_id": 3, + "image_name": "10043.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3032.787, - 2038.765, - 196.42000000000007, - 32.7679999999998 + 1735.478, + 868.884, + 123.12699999999995, + 30.336000000000013 ], - "priority": 23, + "priority": 4, "parents": [ - 179875 + 50 ], "children": [ - 179865 + 55, + 56 ], - "area": 6183139.988055, + "area": 1507929.0665520001, "iscrowd": 0, "segmentation": [], - "text": "Disclosures" + "text": "Summary" }, { - "id": 179865, - "strid": "2fa1f7ba-e265-4b1b-9a7d-5049c02b7278", - "image_id": 207525, - "image_name": "8368.png", + "id": 55, + "strid": "a7281bb6-b16f-4067-b028-b4dd69388186", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3034.777, - 2097.359, - 339.8649999999998, - 27.061999999999898 + 1307.414, + 932.691, + 477.80600000000004, + 1188.544 ], - "priority": 24, + "priority": 5, "parents": [ - 179871 + 54 ], "children": [], - "area": 6365016.853943, + "area": 1219413.271074, "iscrowd": 0, "segmentation": [], - "text": "NAL: trabectome trainer" + "text": "During the past decade, 68 species of fish\nhave been found in the Upper Colorado River\nBasin (UCRB). Although they represent 14\nfamilies, over a third of the fish belong to just\none family, Cyprinidae. Of all the fish, only 13\nspecies (4 families) are native, and nearly a third\nof these are federally endangered and subject to\nrecovery efforts by the Upper Colorado River\nEndangered Fish Recovery Program—one\ncatostomid, razorback sucker = Xyrauchen\ntexanus, and three cyprinids, humpback chub\nGila cypha, bonytail G. elegans, and Colorado\npikeminnow Prychocheilus lucius.\n\nCollections of the early life stages of fish are\nessential for researching and monitoring fish\nspawning sites and seasons, production,\ntransport, distribution, nursery habitat, survival,\nand other aspects of early life history. Such\ninvestigations require accurate identification of\nat least the target species among collected\nspecimens. However, the larvae of most fishes\nchange dramatically as they grow and develop,\nwhich can make diagnosis especially difficult\nand complicated (e.g., the 60-page key for the\nlarvae of just six catostomids in Snyder and\nMuth 1990).\n\nOur objectives for this guide were to better\ndescribe and facilitate identification of the larvae\nand early juveniles of 15 cyprinids in the UCRB.\nThese included the three endangered cyprinids,\ntwo remaining native cyprinids—roundtail chub\nG. robusta and speckled dace Rhinichthys\nosculus, and ten non-native cyprinids (see Table\nof Contents). Nine other non-native cyprinids in\nthe UCRB were either not recognized as present\nwhen the guide was planned or considered\nunlikely to be encountered as larvae in Recovery\nProgram investigations. However, larval\ndescriptions were referenced for all but two of\nthese non-natives (two Lepidomeda species\nremain undescribed)." }, { - "id": 179872, - "strid": "9cf411f2-fc00-43a8-b711-8390bf8cc222", - "image_id": 207525, - "image_name": "8368.png", + "id": 56, + "strid": "7e8dbb20-5087-4e07-9663-d2ffb7e67de5", + "image_id": 3, + "image_name": "10043.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 1810.371, + 930.74, + 481.4229999999998, + 1190.3 + ], + "priority": 6, + "parents": [ + 54 + ], + "children": [], + "area": 1684984.70454, + "iscrowd": 0, + "segmentation": [], + "text": "The guide was built upon a foundation of\ninformation, species accounts, and keys\npreviously assembled for Snyder (1981), Muth\n(1990), and Snyder et al. (2005). In doing so, we\nstudied developmental series of reared and\ncollected specimens to more completely\ndocument differences in size relative to\ndevelopmental state, morphology, meristics, and\npigmentation. Newly acquired or re-examined\ndata were summarized for over 1,700 specimens.\nAlso, 66 new three-view drawings were prepared\nto complete sets of 8 illustrations per species\nwhich document typical body form and\npigmentation from recently hatched larvae\nthrough early juveniles. The results are\npresented in detailed descriptive species\naccounts, comparative summary tables, and an\nassociated computer-interactive key.\n\nFor complex data sets (e.g., those covering\nthe early developmental stages of various taxa),\ncomputer-interactive keys are much more user\nfriendly and flexible than printed dichotomous\nor polychotomus keys. They are also much\neasier to prepare, correct, and update. In\naddition to the key for cyprinid larvae and\njuveniles, a second associated computer-\ninteractive key (Snyder and Seal 2008) is\nprovided for identification of all larvae at the\nfamily level. Also, to complement the subset of\nfamilies specifically defined for the UCRB in\nthat key, applicable portions of a pictorial guide\nto families by Wallus et al. (1990) were modified\nas an appendix to the guide.\n\nThe guide was peer-reviewed as a final report\nof the Recovery Program and published by\nColorado Parks and Wildlife as Technical\nPublication 47. Together with a similar\npreviously published guide for catostomids\n(Snyder and Muth 2004), it completes a series of\ndescriptive investigations begun over 35 years\nago on cypriniform larvae in the UCRB." + }, + { + "id": 57, + "strid": "6b9c89c4-f57a-42e3-b3b7-049b1e39ddea", + "image_id": 3, + "image_name": "10043.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2325.739, - 2211.342, - 140.86000000000013, - 39.914999999999964 + 2838.613, + 867.006, + 222.01600000000008, + 27.21199999999999 ], - "priority": 25, + "priority": 7, "parents": [ - 179875 + 50 ], "children": [ - 179866 + 58, + 59 ], - "area": 5143004.331738001, + "area": 2461094.502678, "iscrowd": 0, "segmentation": [], - "text": "Funding" + "text": "Table of Contents" }, { - "id": 179866, - "strid": "1f029e7e-1017-4c24-9799-3a24f80a4530", - "image_id": 207525, - "image_name": "8368.png", - "category_id": 3, - "category_name": "Text", + "id": 58, + "strid": "eeda4bac-7cef-4730-86d3-39d1831b04b2", + "image_id": 3, + "image_name": "10043.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2325.661, - 2265.515, - 757.232, - 43.47400000000016 + 2460.423, + 924.912, + 485.81399999999985, + 1010.328 ], - "priority": 26, + "priority": 8, "parents": [ - 179872 + 57 ], "children": [], - "area": 5268819.880415, + "area": 2275674.757776, "iscrowd": 0, - "segmentation": [], - "text": "NAL: Grateful recipient of KO8-EY022737 and a departmental P30.\nHAP: Grateful recipient of the Alpha Omega Alpha Carolyn L Kuckien Student Research Fellowship" + "segmentation": [] }, { - "id": 136703, - "strid": "b7f1ec87-607c-44a4-ada8-1e655335380d", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 9, - "category_name": "Root", + "id": 59, + "strid": "f03b8718-f3de-4d71-9add-000dd288270a", + "image_id": 3, + "image_name": "10043.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 0, - 60.98, - 88.02, - 217.38000000000002 + 2961.529, + 921.9, + 490.6399999999999, + 1012.7880000000001 ], - "priority": -1, - "parents": [], - "children": [ - 136677, - 136679, - 136675, - 136678, - 136673, - 136674, - 136676 + "priority": 9, + "parents": [ + 57 ], - "area": 0.0, + "children": [], + "area": 2730233.5851, "iscrowd": 0, "segmentation": [] }, { - "id": 136673, - "strid": "fe50fb19-45a4-4675-9f9a-3b4bf3c732cc", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 1, - "category_name": "Title", + "id": 60, + "strid": "606bd036-b124-4d11-857b-8c11ef6a421a", + "image_id": 3, + "image_name": "10043.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 106.59, - 104.64, - 1916.876, - 178.123 + 2874.311, + 1989.656, + 148.7260000000001, + 29.593000000000075 ], - "priority": 1, + "priority": 10, "parents": [ - 136703 + 50 ], - "children": [], - "area": 11153.5776, + "children": [ + 61 + ], + "area": 5718890.127016, "iscrowd": 0, "segmentation": [], - "text": "Challenges and Success of Rowing Across the Atlantic\nby an Individual with ALS" + "text": "Availability" }, { - "id": 136674, - "strid": "ea18891b-3c82-47ca-bccc-4fd1ad63abf8", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 0, - "category_name": "Author Info", + "id": 61, + "strid": "bcef64b6-5408-4bac-bb86-dfeb1f7e117c", + "image_id": 3, + "image_name": "10043.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 426.817, - 321.29, - 1153.804, - 129.591 + 2463.0, + 2047.624, + 950.1909999999998, + 111.11800000000017 ], - "priority": 2, + "priority": 11, "parents": [ - 136703 + 60 ], "children": [], - "area": 137132.03393, + "area": 5043297.9120000005, "iscrowd": 0, "segmentation": [], - "text": "H. Hayes*, A. Alderman, S. Gibson**, M. Bromberg**\n\n*University of Utah College of Health, Department of Physical Therapy, Salt Lake City, UT\n**University of Utah School of Medicine, Department of Neurology, Salt Lake City, UT" + "text": "A PDF copy of the guide is available on the Colorado Parks and Wildlife (CPW) and Larval Fish\nLaboratory (LFL) websites, the latter at http://warnerenr.colostate.edu/Ifl-downloadable-keys-\nguides-and-bibliography; printed copies are available upon request from CPW. The associated\ncyprinid computer-interactive key and a family-level key are available at the same LFL website." }, { - "id": 136675, - "strid": "2b901a9a-1eeb-40b6-bd2f-9cdcdadb53dd", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 5, - "category_name": "Section", + "id": 62, + "strid": "304bd6c8-24e5-4056-862a-7c1adf8d481f", + "image_id": 3, + "image_name": "10043.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 54.155, - 519.908, - 268.89300000000003, - 41.347999999999956 + 989.936, + 2288.587, + 532.7579999999999, + 28.152000000000044 ], - "priority": 3, + "priority": 12, "parents": [ - 136703 + 50 ], - "children": [ - 136693, - 136692, - 136680 - ], - "area": 28155.61774, + "children": [], + "area": 2265554.660432, "iscrowd": 0, "segmentation": [], - "text": "Introduction" + "text": "1 of 15 Descriptive Species Accounts in the Guide" }, { - "id": 136680, - "strid": "966cbd10-b513-460f-a368-87ddb71e8b2f", - "image_id": 205802, - "image_name": "15961.png", + "id": 63, + "strid": "6f75a22a-c0f9-488d-bd4d-8e9d10f9774f", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 40.543, - 627.867, - 3117.044, - 102.928 + 319.85, + 2395.484, + 313.08900000000006, + 16.019999999999982 ], - "priority": 4, + "priority": 13, "parents": [ - 136675 + 50 ], "children": [], - "area": 25455.611781, + "area": 766195.5574, "iscrowd": 0, "segmentation": [], - "text": "The TaliskerTM Whisky Atlantic Challenge is the premiere ocean rowing event, requiring 3000 miles of rowing across the Atlantic Ocean, from the Canary Islands to\nAntigua (Figure 1), with no external support. When an individual (Figure 2) with ALS desires to row across the Atlantic there are extra challenges and successes!" + "text": "Species Account - Gila cypha, humpback chub" }, { - "id": 136692, - "strid": "9ad74cc7-0098-47ec-886d-1eb74d1e9044", - "image_id": 205802, - "image_name": "15961.png", + "id": 64, + "strid": "daa8f070-3ca7-41b6-8338-c5a9f4941e7e", + "image_id": 3, + "image_name": "10043.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 28.105, - 762.372, - 1480.517, - 855.8670000000001 + 148.992, + 2406.433, + 317.918, + 151.76800000000003 ], - "priority": 5, + "priority": 14, "parents": [ - 136675 + 50 ], "children": [ - 136690 + 65 ], - "area": 21426.46506, + "area": 358539.26553599996, "iscrowd": 0, "segmentation": [] }, { - "id": 136690, - "strid": "537bce7b-4fac-473c-ae75-5a4228f06b85", - "image_id": 205802, - "image_name": "15961.png", + "id": 65, + "strid": "1150b23f-65fe-4f58-90a5-4145fd91b693", + "image_id": 3, + "image_name": "10043.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 43.339, - 1644.991, - 1279.933, - 29.826999999999998 + 150.099, + 2559.655, + 271.121, + 15.043999999999869 ], - "priority": 6, + "priority": 15, "parents": [ - 136692 + 64 ], "children": [], - "area": 71292.264949, + "area": 384201.655845, "iscrowd": 0, "segmentation": [], - "text": "Figure 1. Challenge starts in the Canary Islands and ends at Antigua (3000 miles across the Atlantic Ocean)." + "text": "Figure 36. Gila cyphe adult (© Joseph R. Tomelleri)." }, { - "id": 136693, - "strid": "4d76c1ed-b529-48c9-b103-3a4ee8daeeb0", - "image_id": 205802, - "image_name": "15961.png", + "id": 66, + "strid": "28014d80-85e9-45fa-9086-28a144e37e20", + "image_id": 3, + "image_name": "10043.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 149.477, + 2584.676, + 316.78700000000003, + 290.0129999999999 + ], + "priority": 16, + "parents": [ + 50 + ], + "children": [], + "area": 386349.614452, + "iscrowd": 0, + "segmentation": [], + "text": "Adult description: Up to 35-48 cm TL Body stcamlined.\ncompressed, with ‘ypically prominent anrerodorsal nuchal hump,\nabrupt and trmcate aver occiput. Head dorsally flatencd ce concave\nwith very small eyes (as litle a¢ §% HL) and Tong. fleshy snout\noverhanging subteraunal to infericr nearly horizontal, mouth, Caudal\npeduncle slender (least depth ~21% HL). Fins expansive, faleate\ncandaltin lobes moderately long_and pointed: dorsal cigin well\nbehind pelvic origin. Angle of line fiom along base of anal fin extends\nalong upper margin of caudal fin to middle of upper lobe. Scales,\nnearly licking or well embedded over uucal buuap and sometimes\nelsewhare except laterally. Gray or olivaceous deisally. silvery or\nwhite venolateally. Breeding mes orange-red along veateolaveral\nsurfaces with small tabercles an anterior body. (Also, Table 14.)\nReproduction: Nov-giauding, open-substatelihophil. Matureataze\n3.5. Spawn shorty after peak spring flows dung late April eatly\nsly at 12-23°C. typically 16-19°C, probably in near-shore areas af\nunodeate velocity and depth over sand, gravel or cobble, Wate\nhardened egas dewsrsal, acliesive, aud 2.3-)2.6-3.1(-3.3) mum in\ndiameter (nieans 2.7 & 2.9 (onig.) ma),\n\nYoung: Hatch in 3-7 d and swim up 3—4 dlares at 19-20°C. Young\ndiuraily active: in near-shore. low-velocity habitats. esecially at\nseh ce ‘torn oobi xx tages enedenie ated cage" + }, + { + "id": 67, + "strid": "814a6f10-a0a0-4363-abe8-424523702508", + "image_id": 3, + "image_name": "10043.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1544.005, - 758.609, - 865.0329999999999, - 865.7209999999999 + 486.857, + 2419.492, + 316.708, + 416.59699999999975 ], - "priority": 7, + "priority": 17, "parents": [ - 136675 + 50 ], "children": [ - 136691 + 68 ], - "area": 1171296.089045, + "area": 1177946.6166440002, "iscrowd": 0, "segmentation": [] }, { - "id": 136691, - "strid": "d9c55c0a-bdec-4218-84d4-30dd717b1170", - "image_id": 205802, - "image_name": "15961.png", + "id": 68, + "strid": "b35b2a17-cdf9-4d9f-a0b1-3ccd97e2fdb6", + "image_id": 3, + "image_name": "10043.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1549.756, - 1644.416, - 582.2340000000002, - 32.41000000000008 + 487.335, + 2847.076, + 315.536, + 26.409000000000106 ], - "priority": 8, + "priority": 18, "parents": [ - 136693 + 67 ], "children": [], - "area": 2548443.562496, + "area": 1387479.78246, "iscrowd": 0, "segmentation": [], - "text": "Figure 2. AA photo before and after race" + "text": "Figure 37. Recent distribution of Gila cypha in the Colorado\nRiser Genin toa tien weadiblr coerce icles," }, { - "id": 136676, - "strid": "4d906706-0ee7-4c18-986f-4608b936492c", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 5, - "category_name": "Section", + "id": 69, + "strid": "b245cdca-ee64-4b97-b22b-95192fceeada", + "image_id": 3, + "image_name": "10043.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 58.879, - 1741.744, - 104.04600000000002, - 40.1579999999999 + 149.195, + 2923.651, + 654.49, + 131.23000000000002 ], - "priority": 9, + "priority": 19, "parents": [ - 136703 + 50 ], "children": [ - 136689, - 136681, - 136694, - 136688 + 70 ], - "area": 102552.144976, + "area": 436194.11094499996, "iscrowd": 0, - "segmentation": [], - "text": "Case" + "segmentation": [] }, { - "id": 136688, - "strid": "841152e5-560f-4b82-b450-4700168c6c47", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 4, - "category_name": "List", + "id": 70, + "strid": "ce13d079-9800-4516-8aa2-ede0c77ed8de", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 69.294, - 1856.02, - 1034.216, - 417.36900000000014 + 149.269, + 2883.573, + 655.224, + 39.87300000000005 ], - "priority": 10, + "priority": 20, "parents": [ - 136676 + 69 ], "children": [], - "area": 128611.04987999999, + "area": 430428.058137, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Table 14. Selected juvenile and adult meristics for Gila c:pha. (P= principal rays: R:\nlateral series or line When complete Font added 10 vertebalconat for Weberitn complex. Pharyngea tet\njaiek iii, Caled, Sikencitox enelal ialaes suale nad lacie a htadenntiine mcicvalane Sxucizelbaaes)" }, { - "id": 136689, - "strid": "fec07911-d8a6-4b52-915b-10091fccd1b4", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 4, - "category_name": "List", + "id": 71, + "strid": "fb027f7f-4620-44a7-af1b-3f494e6a2697", + "image_id": 3, + "image_name": "10043.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1138.291, - 1847.836, - 852.31, - 419.4150000000002 + 149.547, + 3083.641, + 654.603, + 140.48100000000022 ], - "priority": 11, + "priority": 21, "parents": [ - 136676 + 50 ], - "children": [], - "area": 2103375.0882759998, + "children": [ + 72 + ], + "area": 461149.260627, "iscrowd": 0, "segmentation": [] }, { - "id": 136694, - "strid": "dd2babd0-6205-4668-9f15-309fe8f02da1", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 2, - "category_name": "Figure", + "id": 72, + "strid": "a6b20e9e-0dc7-4058-b73c-567974c7df9a", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2037.583, - 1712.816, - 638.2950000000001, - 679.0579999999998 + 149.651, + 3056.311, + 654.9279999999999, + 26.570999999999913 ], - "priority": 12, + "priority": 22, "parents": [ - 136676 + 71 ], "children": [], - "area": 3490004.763728, + "area": 457379.99746100005, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Table 15. Size at apparent ouset of selected developmental events for Gila eypha. (As apparent under low power magnification, P = principal\nrays; R= rudimentary rays. Scales are lateral series. Rare values in parentheses. Includes re-examined daia as per foomote for Table 14.)" }, { - "id": 136681, - "strid": "46aa624d-b488-4548-9ca7-b5c7ced78db1", - "image_id": 205802, - "image_name": "15961.png", + "id": 73, + "strid": "a6e4076c-003b-4625-ae64-9e150cae3a92", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2720.833, - 1849.112, - 488.3130000000001, - 203.19999999999982 + 149.135, + 3225.895, + 654.483, + 76.37199999999984 ], - "priority": 13, + "priority": 23, "parents": [ - 136676 + 50 ], "children": [], - "area": 5031124.950296001, + "area": 481093.850825, "iscrowd": 0, "segmentation": [], - "text": "RACING SCHEDULE\n\n2 hours of rowing and 2\nhours of sleep, repeated for\n35-60 days" + "text": "References. Balon 1975; Behnke and Benson 1983: Beimke ct al. 1982; Bulkicy ct al. 1982: Carison and Muth 1989: Gaufin ct al. 1960;\nHanuman 1982b; Holden 1968: Holden and Stalnaker 197%, 1975; Johnson 1987. Joseph et a. 1977: Kaceling and Zimmerman 1983; Lce ct al\n1980, Marsh 1985, Miller 1946, Miler aud Lowe 1964, Minckley 1973, Minckley and Marsh 2009, Moore 1968, Muth 1990; Page and Burt\n1991, Sigler and Millet 1963, Snuth tal, 1979, Snyder 1581, Stanford and Ward 1986; Stone and Gorman 2006, Suitkus and Clenuner 1977,\n\nTrys and Karp 1989: Tyus etal. 1983, 1987; LISEWS 1990, 2002c: Valdez T987, 1988; Valdez and Cemmer 1982\nOther larval descriptions: Muth 1990: Snyder 1981," }, { - "id": 136677, - "strid": "4414e01f-eedc-402c-8090-5116b6e47ed1", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 5, - "category_name": "Section", + "id": 74, + "strid": "07ca2b2f-4d25-4ce1-982d-4561ecd18874", + "image_id": 3, + "image_name": "10043.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 55.72, - 2325.452, - 489.009, - 52.58399999999983 + 929.368, + 2426.86, + 654.3960000000001, + 92.79899999999998 ], - "priority": 14, + "priority": 24, "parents": [ - 136703 + 50 ], "children": [ - 136698, - 136682, - 136684, - 136702, - 136683, - 136685, - 136696, - 136699, - 136695, - 136697 - ], - "area": 129574.18544000002, - "iscrowd": 0, - "segmentation": [], - "text": "Challenges - Solutions" - }, - { - "id": 136695, - "strid": "88d3a88f-0773-4f13-ac2f-40bd87fe5874", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 53.556, - 2429.407, - 863.857, - 1071.0259999999998 - ], - "priority": 15, - "parents": [ - 136677 + 75 ], - "children": [], - "area": 130109.32129200001, + "area": 2255446.02448, "iscrowd": 0, "segmentation": [] }, { - "id": 136682, - "strid": "3bf7f529-bc50-4ed4-8341-72d1b45cd944", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 3, - "category_name": "Text", + "id": 75, + "strid": "efe5705b-c03e-461f-95ce-b0511a12e696", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 57.68, - 3509.878, - 837.879, - 88.88900000000012 + 929.307, + 2399.251, + 655.4190000000001, + 27.8449999999998 ], - "priority": 16, + "priority": 25, "parents": [ - 136677 + 74 ], "children": [], - "area": 202449.76304000002, + "area": 2229640.749057, "iscrowd": 0, "segmentation": [], - "text": "THE BOAT: 28 feet long and 70-inches wide,\nwith a cabin at each end." + "text": "Table 16. Size at developmental interval (left) and gut phasc (right) transitions for Gila cypha. (Sec Figure 5 for phases of gut folding. Rare\nvalues in parentheses. Includes re-examined data originally prepared for Snyder 1981 or Muth 1990, and supplements and updates those accounts.)" }, { - "id": 136696, - "strid": "8110b7f7-166f-4d31-9e82-e15f066ede0d", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 2, - "category_name": "Figure", + "id": 76, + "strid": "a1c3179a-47b3-4eae-88f0-77557bf5da93", + "image_id": 3, + "image_name": "10043.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1004.282, - 2435.527, - 678.88, - 512.9090000000001 + 928.139, + 2594.045, + 655.8570000000001, + 709.9279999999999 ], - "priority": 17, + "priority": 26, "parents": [ - 136677 + 50 ], - "children": [], - "area": 2445955.926614, + "children": [ + 77 + ], + "area": 2407634.3322550002, "iscrowd": 0, "segmentation": [] }, { - "id": 136697, - "strid": "bad2ed9b-ba23-4296-8833-2be74790b153", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 2, - "category_name": "Figure", + "id": 77, + "strid": "fb7bd34a-089e-4ec5-a3cc-f9404856d987", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1713.477, - 2432.807, - 779.4890000000003, - 516.7039999999997 + 928.363, + 2542.053, + 656.9860000000001, + 41.722999999999956 ], - "priority": 18, + "priority": 27, "parents": [ - 136677 + 76 ], "children": [], - "area": 4168558.839939, + "area": 2359947.949239, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Table 17. Summary of morphometrics and myomere counts by developmental phase for Gila cypia. (See Figure 4 for abbreviations and methods\nof measurement and counting. Protolarvae with unpigmented eyes excluded. Standard deviation (SD) of 0 represents a valte “0.5, Includes e-\nexamined data originally prepared for Suyder 1981 or Muth 1990\", and supplements and updates those accounts.)" }, { - "id": 136698, - "strid": "77492ee5-7292-4a2a-bbd1-119d19a88351", - "image_id": 205802, - "image_name": "15961.png", + "id": 78, + "strid": "505f7a85-0b1f-424c-abc0-1f27dbafb422", + "image_id": 3, + "image_name": "10043.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2529.886, - 2429.398, - 724.3389999999999, - 513.7420000000002 + 1733.757, + 2396.379, + 605.2599999999998, + 410.9989999999998 ], - "priority": 19, + "priority": 28, "parents": [ - 136677 + 50 ], - "children": [], - "area": 6146099.988628, + "children": [ + 79 + ], + "area": 4154738.865903, "iscrowd": 0, "segmentation": [] }, { - "id": 136683, - "strid": "54a26b98-1961-4a3c-90ca-ea5e08ceca11", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 3, - "category_name": "Text", + "id": 79, + "strid": "1163f4b2-58dd-4f5d-931e-07db23d8bea3", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1008.378, - 2974.185, - 1376.935, - 88.1210000000001 + 1734.543, + 2824.841, + 603.1679999999999, + 30.213000000000193 ], - "priority": 20, + "priority": 29, "parents": [ - 136677 + 78 ], "children": [], - "area": 2999102.72193, + "area": 4899808.182662999, "iscrowd": 0, "segmentation": [], - "text": "EMERGENCY SUIT: Needed to learn to don the emergency suit quickly if\nneeded." + "text": "Figure 38. Gila cypha protolarva with yolk, recently hatched, 6.3 mm SL, 6.6 mm TL. (Cultured in 1960 by Willow Beach\nNational Fish Hatchery, Arizona, with stock from the Celorado River, Célorade. From Snyder 1981 and Muth 1980.)" }, { - "id": 136699, - "strid": "021fe83c-6db1-4629-965d-68f0a344393e", - "image_id": 205802, - "image_name": "15961.png", + "id": 80, + "strid": "b298ecfe-6819-4aaf-8249-38f2aab99ea8", + "image_id": 3, + "image_name": "10043.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2530.492, - 2953.366, - 726.5799999999999, - 460.15599999999995 + 1732.179, + 2877.185, + 606.8130000000001, + 381.67300000000023 ], - "priority": 21, + "priority": 30, "parents": [ - 136677 + 50 ], - "children": [], - "area": 7473469.036072001, + "children": [ + 81 + ], + "area": 4983799.436115, "iscrowd": 0, "segmentation": [] }, { - "id": 136702, - "strid": "ea19fbba-4ce2-4eac-8c54-4bc673843324", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 2, - "category_name": "Figure", + "id": 81, + "strid": "a9e9ae2f-4879-41f9-a875-b536d876fbc8", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1006.875, - 3084.34, - 1106.8140000000003, - 616.8249999999998 + 1734.859, + 3273.975, + 603.3830000000003, + 27.898999999999887 ], - "priority": 22, + "priority": 31, "parents": [ - 136677 + 80 ], "children": [], - "area": 3105544.8375000004, + "area": 5679884.9945249995, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 39. Gila cypha protolarva vith yolk, 8.3 mm SL, 8.7 mm TL. (Cultured in 1980 by Willow Beach National Fish\nHatchery, AZ, with stock from Colorado River, Black Rocks area, CO, near UT border. From Snyder 1981 and Muth 1990.)" }, { - "id": 136684, - "strid": "592b97c7-8e29-43cc-8b4f-94e9dea4b0ce", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 3, - "category_name": "Text", + "id": 82, + "strid": "78fb56c8-414d-4704-8c91-79241a77d2f9", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2156.482, - 3153.691, - 350.60699999999997, - 363.2350000000001 + 173.995, + 3423.591, + 606.747, + 407.058 ], - "priority": 23, + "priority": 32, "parents": [ - 136677 + 50 ], - "children": [], - "area": 6800877.875061999, + "children": [ + 83 + ], + "area": 595687.716045, "iscrowd": 0, - "segmentation": [], - "text": "THE BOAT: The\nspace was limited\nand required quick\nmovements in and\nout of cabin door to\nprevent water from\ncoming in." + "segmentation": [] }, { - "id": 136685, - "strid": "1039958d-8f7d-473e-8bbd-3ecbe8cbd0cb", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 3, - "category_name": "Text", + "id": 83, + "strid": "b0327304-8b99-4d35-afc6-8f3630b38887", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2533.866, - 3435.378, - 677.1210000000001, - 202.1260000000002 + 176.027, + 3843.059, + 603.6699999999998, + 28.019999999999982 ], - "priority": 24, + "priority": 33, "parents": [ - 136677 + 82 ], "children": [], - "area": 8704787.511348, + "area": 676482.146593, "iscrowd": 0, "segmentation": [], - "text": "ROWING SEAT: The rowing seat\nrequired adjustment to account for\ndecreased range of motion in hips due\nto spasticity." + "text": "Figure 40. Gila cypha flexion mesolarva with yolk, recently transformed, 8.6 mm SL, 9.3 mm TL. (Cultured in 1980 by\nWillow Bleach National Fish Hatchery, AZ: stock from Colo. R., Black Rocks area, CO. From Snyder 1981 and Muth 1990.)" }, { - "id": 136678, - "strid": "668cb56d-a32d-4d3e-88e6-13bf6b1f8bb6", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 5, - "category_name": "Section", + "id": 84, + "strid": "a7d990dd-472e-422f-8944-68967b082087", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 70.751, - 3670.548, - 169.83, - 41.00500000000011 + 171.23, + 3905.226, + 609.649, + 381.3390000000004 ], - "priority": 25, + "priority": 34, "parents": [ - 136703 + 50 ], "children": [ - 136686, - 136701, - 136700 + 85 ], - "area": 259694.941548, + "area": 668691.84798, "iscrowd": 0, - "segmentation": [], - "text": "Success" + "segmentation": [] }, { - "id": 136686, - "strid": "4f073f5e-fbbd-4166-b681-07850197b1db", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 3, - "category_name": "Text", + "id": 85, + "strid": "a291d821-9bb3-44b7-aae6-7587afad0c0e", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 55.892, - 3771.162, - 3030.524, - 109.79599999999982 + 174.145, + 4304.621, + 605.634, + 28.127000000000407 ], - "priority": 26, + "priority": 35, "parents": [ - 136678 + 84 ], "children": [], - "area": 210777.786504, + "area": 749628.224045, "iscrowd": 0, "segmentation": [], - "text": "The team used 5-individuals compared to the traditional 4 to assist with variation of the standard rowing shifts. This helped with decreasing mental and\nphysical fatigue. The team made it in 51 days, 11 hours, 57 minutes. The team rowed 3548 miles." + "text": "PERERA). Cher ype posta comets, 6)4 tare fl, 71-7 ie Th. (Conant eae oy Wow Bendy Metical Fits\nHatchery, AZ, with stock from Colorado River, Black Rocks area, CO, near UT border. From Snyder 1981 and Muth 1990.)" }, { - "id": 136700, - "strid": "57c964ac-2be8-493e-b544-c023f9b8a840", - "image_id": 205802, - "image_name": "15961.png", + "id": 86, + "strid": "e5b1b06a-7ebd-4beb-b709-e26e4e0a919c", + "image_id": 3, + "image_name": "10043.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 41.674, - 3905.314, - 704.64, - 694.6430000000005 + 952.035, + 3426.954, + 608.1170000000001, + 380.87300000000005 ], - "priority": 27, + "priority": 36, "parents": [ - 136678 + 50 ], - "children": [], - "area": 162750.055636, + "children": [ + 87 + ], + "area": 3262580.1513900002, "iscrowd": 0, "segmentation": [] }, { - "id": 136701, - "strid": "3741578c-6cd2-494c-ad95-ea9dce3bfc39", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 2, - "category_name": "Figure", + "id": 87, + "strid": "1922b889-15b7-4072-853d-4742340df939", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 805.54, - 3905.062, - 1509.616, - 703.5290000000005 + 954.14, + 3817.458, + 604.862, + 41.240999999999985 ], - "priority": 28, + "priority": 37, "parents": [ - 136678 + 86 ], "children": [], - "area": 3145683.6434799996, + "area": 3642389.37612, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 42. Gila cypha pastfiexion mesolarva near transition to metalarva (lacks second elements of last dorsal and anal\nfin rays), 12:2.mm SL, 14.0mm TL. (Cultured in 1980 by Willow Beach National Fish Hatchery, Anzona, with stock from\nColorado River, Black Rocks area, Colorado, near Utah border. From Muth 1990, modified from Snyder 1981.)" }, { - "id": 136679, - "strid": "89ff694c-6757-4576-bfd4-bd4d2bfe04b3", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 5, - "category_name": "Section", + "id": 88, + "strid": "8d056b51-fa8b-4440-9d63-0976660c821c", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2424.492, - 3937.716, - 247.55099999999993, - 41.534999999999854 + 954.107, + 3880.772, + 605.528, + 416.96399999999994 ], - "priority": 29, + "priority": 38, "parents": [ - 136703 + 50 ], "children": [ - 136687 + 89 ], - "area": 9546960.940272, + "area": 3702671.730604, "iscrowd": 0, - "segmentation": [], - "text": "Conclusion" + "segmentation": [] }, { - "id": 136687, - "strid": "8882d4c8-ce0d-478b-8b9b-d237b5b08c74", - "image_id": 205802, - "image_name": "15961.png", - "category_id": 3, - "category_name": "Text", + "id": 89, + "strid": "819b1929-540d-4293-8c38-c3f2325a3a60", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2409.495, - 4042.461, - 808.723, - 466.11100000000033 + 954.856, + 4304.345, + 603.2439999999999, + 27.81800000000021 ], - "priority": 30, + "priority": 39, "parents": [ - 136679 + 88 ], "children": [], - "area": 9740289.567194998, + "area": 4110029.6493200003, "iscrowd": 0, "segmentation": [], - "text": "For many individuals with ALS purpose\nand quality of life include fulfilling\ndreams even when the dreams require\nextreme physical and psychological\ndemands. AA demonstrates that even a\ndisease characterized by progression of\nphysical decline and degeneration does\nnot have to limit goals in life." + "text": "Figure 43. Gila cypha metalarva, 15.0 mm SL, 18.4 mm TL. (Cultured in 1980 by Willow Beach National Fish Hatchery,\nAZ. with stock from Colorado River, Black Rocks area, Colorado, near Utah border. From Snyder 1981 and Muth 1990 }" }, { - "id": 142975, - "strid": "79a23412-55a1-405a-bde7-449b68d58a30", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 9, - "category_name": "Root", + "id": 90, + "strid": "15c48fcb-ada4-4975-91b1-e91d0d912268", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 193.07, - 145.3, - 111.34000000000003, - 64.64999999999998 + 1735.062, + 3426.534, + 606.6620000000003, + 375.2950000000001 + ], + "priority": 40, + "parents": [ + 50 ], - "priority": -1, - "parents": [], "children": [ - 142962, - 142958, - 142960, - 142956, - 142959, - 142957, - 142961 + 91 ], - "area": 28053.071, + "area": 5945248.9351079995, "iscrowd": 0, "segmentation": [] }, { - "id": 142956, - "strid": "68701155-df0d-4041-bdfe-122950b01d61", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 1, - "category_name": "Title", + "id": 91, + "strid": "af57a841-a219-4d25-9a5e-d61c4586956e", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 393.601, - 33.323, - 783.243, - 82.40899999999999 + 1734.573, + 3830.203, + 607.5199999999998, + 26.934000000000196 ], - "priority": 1, + "priority": 41, "parents": [ - 142975 + 90 ], "children": [], - "area": 13115.966123, + "area": 6643766.708319, "iscrowd": 0, "segmentation": [], - "text": "Protein-guided nucleotide viral genome\nassembly for huge metagenomic datasets" + "text": "Figure 44. Gila cypha juvenile, recently transformed, 20.1 mm SL, 25.0 mm TL. (Cultured in 1980 or 1981 by Willov\nBeach Neiional Fish Halchety, Arizona, with stock froma Colorado River, Black Rocks ere, Colorado. From Mulh 1900.)" }, { - "id": 142957, - "strid": "232a3658-8e93-4103-9524-3d5ab291adb3", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 0, - "category_name": "Author Info", + "id": 92, + "strid": "9acff52f-c472-4e01-83cc-193969c65917", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 404.506, - 122.925, - 736.5849999999999, - 117.669 + 1734.99, + 3868.039, + 606.1649999999997, + 431.88300000000027 ], - "priority": 2, + "priority": 42, "parents": [ - 142975 + 50 ], - "children": [], - "area": 49723.90005, + "children": [ + 93 + ], + "area": 6711008.984610001, "iscrowd": 0, - "segmentation": [], - "text": "Annika Seidel’, Johannes Séding', Martin Steinegger***\n\n‘Max-Planck Institute for Biophysical Chemistry, Géttingen, Germany\n? School of Biological Sciences, Seoul National University, Seoul, Korea\n\n$ Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea\n‘ Artificial Intelligence Institute, Seoul National University, Seoul, Korea" + "segmentation": [] }, { - "id": 142958, - "strid": "09aa9943-7262-4094-8471-083a26477283", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 5, - "category_name": "Section", + "id": 93, + "strid": "0475d002-f56a-4575-8118-076b04db5aef", + "image_id": 3, + "image_name": "10043.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 149.293, - 273.47, - 121.41399999999999, - 27.976999999999975 + 1735.269, + 4304.452, + 606.327, + 29.98999999999978 ], - "priority": 3, + "priority": 43, "parents": [ - 142975 - ], - "children": [ - 142963, - 142964 + 92 ], - "area": 40827.15671, + "children": [], + "area": 7469382.117588, "iscrowd": 0, "segmentation": [], - "text": "Abstract" + "text": "Figure 45. Gila cypha juvenile, 33.6 mm SL, 44.2 mm TL. (Cultured in 1980 by Willow Beach National Fish Hatchery.\nAZ, with stock from Colorado River, Black Rocks area, Colorado, near Utah border. From Snyder 1981 and Muth 1990.)" }, { - "id": 142963, - "strid": "ccd2bbf4-444d-470b-8267-56c9d5242070", - "image_id": 206054, - "image_name": "17136.png", + "id": 94, + "strid": "f03c01c1-eec4-4e3d-aba9-7951be8e98f4", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 19.9, - 322.957, - 387.275, - 212.22699999999998 + 2584.937, + 2384.189, + 840.598, + 284.105 ], - "priority": 4, + "priority": 44, "parents": [ - 142958 + 50 ], "children": [], - "area": 6426.8443, + "area": 6162978.361093, "iscrowd": 0, "segmentation": [], - "text": "Viruses are the most abundant\nentities on earth. Metagenomic\nstudies offer an unique opportunity to\ndetect them. Their genomes can be\nassembled by tying together short\nnucleotide sequence reads _ into\ncontinuous genomic stretches.\nHowever, their high mutation rates\nand large viral communities make this\nparticular challenging for assemblers." + "text": "Computer-Interactive Key to\nEggs, Larvae, and Early Juveniles\nof Cyprinid Fishes in the\nUpper Colorado River Basin" }, { - "id": 142964, - "strid": "39a85a85-b177-4e54-80c6-e42a95e4c149", - "image_id": 206054, - "image_name": "17136.png", + "id": 95, + "strid": "66d3f365-0ce8-422b-af0c-75d5b5cfe76a", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 18.044, - 763.144, - 387.416, - 251.793 + 2601.407, + 2737.352, + 397.2710000000002, + 279.86400000000003 ], - "priority": 5, + "priority": 45, "parents": [ - 142958 + 50 ], "children": [], - "area": 13770.170336000001, + "area": 7120966.654264, "iscrowd": 0, "segmentation": [], - "text": "With our new _ protein-guided\nnucleotide assembler (PenguiN) we\nare able to assemble long contigs and\nwhole viral genomes. On a simulated\nmetagenome, we obtain a 3 to 11\nfold increase in sensitivity compared\nto MEGAHIT at similar precision. On a\nmetatranscriptomic dataset from 82\nsludge samples, PenguiN assembles\nabout 75-90% more complete ssRNA\nphage genomes than the state-of-\nthe-art tools." + "text": "Darrel E. Snyder\nand Sean C. Seal\nLarval Fish Laboratory\nColorado State University\nFort Collins, Colorado 80523\n(August 2015 onwards)" }, { - "id": 142961, - "strid": "93116773-0ad6-4675-8208-5fe5238419d2", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 5, - "category_name": "Section", + "id": 96, + "strid": "f9b93bd7-df08-4e0e-b77b-f113f4ad4fa1", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 96.463, - 1048.808, - 230.10300000000004, - 34.00299999999993 + 3063.033, + 2725.597, + 345.49900000000025, + 278.8670000000002 ], - "priority": 6, + "priority": 46, "parents": [ - 142975 - ], - "children": [ - 142974 + 50 ], - "area": 101171.16610399999, + "children": [], + "area": 8348593.555701001, "iscrowd": 0, - "segmentation": [], - "text": "Code availability" + "segmentation": [] }, { - "id": 142974, - "strid": "26350bf6-47d2-4fe9-9ca3-3167ccc106ad", - "image_id": 206054, - "image_name": "17136.png", + "id": 97, + "strid": "40661dfa-20fd-439f-b6f0-c9baef50393c", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 21.471, - 1103.23, - 302.3, - 94.02800000000002 + 2742.858, + 3082.112, + 512.625, + 29.81399999999985 ], - "priority": 7, + "priority": 47, "parents": [ - 142961 + 50 ], "children": [], - "area": 23687.45133, + "area": 8453795.556096, "iscrowd": 0, "segmentation": [], - "text": "PenguiN is GPLv3-licensed\nopen source software\n\nplassmmseqs.com" + "text": "Example of Intkey Screen During Identification" }, { - "id": 142959, - "strid": "5945080a-4b03-4c87-8129-4cbc059ea881", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 5, - "category_name": "Section", + "id": 98, + "strid": "814136f1-f2f3-4b75-86b6-7ae855ddda33", + "image_id": 3, + "image_name": "10043.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 548.257, - 274.354, - 348.48300000000006, - 33.423 + 2499.1, + 3120.182, + 1007.3980000000001, + 710.444 ], - "priority": 8, + "priority": 48, "parents": [ - 142975 - ], - "children": [ - 142968 + 50 ], - "area": 150416.50097799997, + "children": [], + "area": 7797646.836199999, "iscrowd": 0, - "segmentation": [], - "text": "Protein-guided assembly" + "segmentation": [] }, { - "id": 142968, - "strid": "d9aa41aa-64aa-4b21-bfd1-a7de512ddf15", - "image_id": 206054, - "image_name": "17136.png", + "id": 99, + "strid": "c56b3c62-4ad6-44d1-a5dc-ea51ecc3e39f", + "image_id": 3, + "image_name": "10043.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 416.255, - 322.251, - 554.777, - 485.058 + 2497.389, + 3848.283, + 596.326, + 855.0710000000004 ], - "priority": 9, + "priority": 49, "parents": [ - 142959 + 50 ], "children": [], - "area": 134138.59000499998, + "area": 9610659.633087, "iscrowd": 0, "segmentation": [] }, { - "id": 142962, - "strid": "af41b04d-fce3-4364-aa7e-cd48dae61f60", - "image_id": 206054, - "image_name": "17136.png", + "id": 100, + "strid": "22a142dd-fc96-4f6a-9b80-c890d4010732", + "image_id": 3, + "image_name": "10043.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 3123.569, + 3939.262, + 360.5920000000001, + 85.11799999999994 + ], + "priority": 50, + "parents": [ + 50 + ], + "children": [], + "area": 12304556.666078001, + "iscrowd": 0, + "segmentation": [], + "text": "Example of an Attribute-selection\nWindow for an Illustrated\nMultistate Character" + }, + { + "id": 101, + "strid": "84866a39-7164-4867-9b64-263cec35991f", + "image_id": 3, + "image_name": "10043.png", "category_id": 5, "category_name": "Section", "bbox": [ - 431.009, - 819.319, - 535.047, - 58.436000000000035 + 509.582, + 4479.71, + 285.975, + 23.511000000000422 ], - "priority": 10, + "priority": 51, "parents": [ - 142975 + 50 ], "children": [ - 142972, - 142973 + 102 ], - "area": 353133.862871, + "area": 2282779.58122, "iscrowd": 0, "segmentation": [], - "text": "Assembly of 2550 HIV genomes\nfrom simulated reads at 1x, 10x, 100x" + "text": "Acknowledgment of Sponsors" }, { - "id": 142973, - "strid": "cfc81632-bb72-48de-ac1e-bc7b641bdb3f", - "image_id": 206054, - "image_name": "17136.png", + "id": 102, + "strid": "f3b9aad4-7750-44c5-a034-181d56655095", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 415.335, - 883.322, - 496.638, - 35.557000000000016 - ], - "priority": 11, + 144.078, + 4519.868, + 1020.9080000000001, + 140.79799999999977 + ], + "priority": 52, "parents": [ - 142962 + 101 ], "children": [], - "area": 366874.54287, + "area": 651213.5417040001, "iscrowd": 0, "segmentation": [], - "text": "Sensitivity = Fraction of assembly aligned to a reference genome\nPrecision = Fraction of reference genomes aligned to to assembly" + "text": "This project was funded primarily by the Upper Colorado.\nRiver Endangered Fish Recovery Program through the U.S.\nBureau of Reclamation (Upper Colorado Regional Office, Salt\nLake City, Utah). It was co-sponsored by the Glen Canyon\nNational Recreation Area through the National Park Service\nColorado Plateau Cooperative Ecosystem Studies Unit. Work\n\non four shared species accounts and completion of associated\nportions of the guide and key were also partially funded as part\nof a similar project for cypriniform larvae of the Middle Rio\nGrande by the Middle Rio Grande Endangered Species Act\nCollaborative Program, also through the U.S. Bureau of\nReclamation." }, { - "id": 142972, - "strid": "d98932ec-ba10-4628-9347-a10fffaab883", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 2, - "category_name": "Figure", + "id": 103, + "strid": "21520519-f86e-489b-8f7f-f5e081d1c603", + "image_id": 3, + "image_name": "10043.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 427.168, - 923.578, - 535.313, - 286.15200000000004 + 1516.678, + 4477.474, + 160.43900000000008, + 21.284999999999854 ], - "priority": 12, + "priority": 53, "parents": [ - 142962 + 50 ], - "children": [], - "area": 394522.967104, + "children": [ + 105, + 104 + ], + "area": 6790886.311372001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Literature Cited" }, { - "id": 142960, - "strid": "18102413-8e55-465c-a891-e6338e3e358e", - "image_id": 206054, - "image_name": "17136.png", - "category_id": 5, - "category_name": "Section", + "id": 104, + "strid": "52867645-6674-47d0-b71c-16d9a94cea0d", + "image_id": 3, + "image_name": "10043.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1033.527, - 271.641, - 497.221, - 34.093999999999994 + 1345.389, + 4509.789, + 502.34799999999996, + 160.36499999999978 ], - "priority": 13, + "priority": 54, "parents": [ - 142975 - ], - "children": [ - 142970, - 142967, - 142969, - 142966, - 142971, - 142965 + 103 ], - "area": 280748.307807, + "children": [], + "area": 6067420.512920999, "iscrowd": 0, "segmentation": [], - "text": "Assembly of ssRNA phage genomes" + "text": "Dallwitz, M. J, T. A. Paine, and E. J. Zurcher. 1995 (onwards). User's guide to Tntkey: a program for\ninteractive identification and information retrieval, [st edition, Commonwealth Scientific and Industrial\nReseareh Org. Dep. Fntomol. Available: itp /delt-inkey.comy, under \"Programs and documentation”.\n\n‘Muth, R-T. 1990. Onfogeny and taxonomy of humpback chub, Boustal, and roundtail chub larvae and eatly\njuveniles. Doctoral dissertation, Colorado State University, Fort Collins.\n\nSyder, D.E. 1981. Coutibutions to @ guide to the eypriniform fish larvae of the Upper Colorado River\n‘stem in Colorado. US. Bur Land Management Biol Se. Series 3, Deaver, CO.\n\nSnyder D-E..and RT. Muth. 1990, Description and identification of razorback, flannelmouth, white, Uta,\nbielead, and mountain sucker larvae and eatty juveniles. Colorado Division of Wildlife Tech. Publ. 38.\n\nSayder, D.E.,and R. T. Muth. 2004. Catostomid fish larvae and easly juveniles ofthe Upper Colorado River\n\n‘Basin —morphological descriptions, comparisons, and computer-interactive key. Colorado Division of\n‘Wildlife Technical Publication 42." }, { - "id": 142965, - "strid": "085470b3-d343-46b9-bd4d-09cd0d43f5fd", - "image_id": 206054, - "image_name": "17136.png", + "id": 105, + "strid": "ef0fd518-d944-488f-a10e-c80c798684cb", + "image_id": 3, + "image_name": "10043.png", "category_id": 3, "category_name": "Text", "bbox": [ - 996.142, - 326.023, - 553.03, - 45.110000000000014 + 1865.283, + 4472.969, + 496.797, + 184.5060000000003 ], - "priority": 14, + "priority": 55, "parents": [ - 142960 + 103 ], "children": [], - "area": 324765.203266, + "area": 8343353.035227, "iscrowd": 0, "segmentation": [], - "text": "ssRNA phage genomes consists of three core genes in\ndifferent variations (Callanan et al)" + "text": "Snyder, D. E., and S.C. Seal. 2008 onwards. Computer-ineractive key to families of larval fishes in\nfeshwaters of the United States and Cannda (dataset for use with DELTA Jnkey) Laval Fish\nLaberatry, Colorado State Univesity, Fort Collins. Available: np wanes eolostateedui-\ndovwoadable-keys-guides-and-biblioraphy.\n\nSnyder, D Ean S.C. Sea. 2015 onwards. Computer-ineractive key o eggs larvae, and early juveniles of\n‘yprinid Hshes inthe Upper Colorado River Basin data st forse with DELTA Inkey) Laval ish\nLaberaiery, Colorado State University, Fort Collins. Available: hp /wamerencolstate edu I-\n300 ng/ml), troponin T (0.109\nng/ml), and anuria. The level of myoglobin\ndetermined on day 2 of the patient’s ICU stay\nwas > 30,000 ng/ml." }, { - "id": 15387, - "strid": "0f4bfff6-74da-499c-901e-1d57f1d675cd", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 170, + "strid": "979ef95b-e3b9-4ee3-b9a2-5b37e0166698", + "image_id": 7, + "image_name": "10316.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 269.411, - 3975.416, - 562.675, - 41.903999999999996 + 265.83, + 1310.705, + 241.66500000000002, + 47.39200000000005 ], - "priority": 17, + "priority": 5, "parents": [ - 15353 + 165 ], - "children": [], - "area": 1071020.799976, + "children": [ + 171 + ], + "area": 348424.71014999994, "iscrowd": 0, "segmentation": [], - "text": "Post-processing for noise removal" + "text": "" }, { - "id": 15358, - "strid": "b8ed466c-ade5-4731-909b-811c74059eb6", - "image_id": 201106, - "image_name": "116600.png", + "id": 171, + "strid": "d5b9c9d9-e79d-49a1-b2ce-ebfcf6f52531", + "image_id": 7, + "image_name": "10316.png", "category_id": 3, "category_name": "Text", "bbox": [ - 86.671, - 4075.625, - 925.176, - 282.15499999999975 + 33.323, + 1371.96, + 705.999, + 703.875 ], - "priority": 18, + "priority": 6, "parents": [ - 15353 + 170 ], "children": [], - "area": 353238.494375, + "area": 45717.82308, "iscrowd": 0, "segmentation": [], - "text": "Each image was processed twice, once with central\nlight reflex (CLR) removal (Marin et al, 2011) and once\nwithout. The two resulting images were combined after\nthe noise removal stage. Most of the remaining pre-\nand post-processing steps were based on (Saleh and\nEswaran, 2011)." + "text": "The treatment administered to the patient led\nto establishing a diuresis of over 400 ml/day on\nday 6 after admission. CVVHD was discontinued\non day 11 of hospitalization, when the patient’s\nspontaneousdiuresiswas 1,600 ml/day. Following\nCVVHD discontinuation, diuresis was aided\nby the intake of mannitol and the continuous\ninfusion of furosemide. The AST, CK and ALT\nlevels returned to the normal range on days\n11, 12 and 21 of hospitalization, respectively.\nThe level of myoglobin decreased steadily,\nand was 233.4 ng/ml, 149.6 ng/ml and 72.57\nng/ml on hospitalization days 8, 11 and 15,\nrespectively. The patient was discharged on\nday 17 of hospitalization, in the polyuric phase\nof up to 9,300 ml/day (eGFR 17.40 ml/min/1.73\nm?), for further treatment in the Nephrology\nUnit. A week later, upon being discharged from\nthe Nephrology Unit, the patient’s renal function\nwas satisfactory (eGFR 72.3 ml/min/1.73 m?)." }, { - "id": 15341, - "strid": "3b36749f-2d9f-4618-acd8-39e1db8168f6", - "image_id": 201106, - "image_name": "116600.png", + "id": 172, + "strid": "b99a782f-29f7-4caa-9721-fd39dafb1a77", + "image_id": 7, + "image_name": "10316.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1348.684, - 547.57, - 616.201, - 98.94500000000005 + 981.596, + 392.444, + 267.337, + 50.125999999999976 ], - "priority": 19, + "priority": 7, "parents": [ - 15334 + 165 ], "children": [ - 15344, - 15374, - 15379, - 15377, - 15342, - 15373, - 15375, - 15378, - 15372, - 15376 + 177, + 174, + 175, + 176, + 178, + 173 ], - "area": 738498.8978800001, + "area": 385221.460624, "iscrowd": 0, "segmentation": [], - "text": "VESSEL EXTRACTION:\nGABOR FILTER APPROACH" + "text": "METHODS" }, { - "id": 15373, - "strid": "71699f93-6902-4950-9f60-66c1d761bcdd", - "image_id": 201106, - "image_name": "116600.png", + "id": 173, + "strid": "1604d800-0401-41b4-a885-2138a891f4cc", + "image_id": 7, + "image_name": "10316.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1472.308, - 690.242, - 370.001, - 38.210000000000036 + 762.125, + 456.961, + 706.4479999999999, + 488.259 ], - "priority": 20, + "priority": 8, "parents": [ - 15341 + 172 ], "children": [], - "area": 1016248.818536, + "area": 348261.402125, "iscrowd": 0, "segmentation": [], - "text": "Grey-scale conversion" + "text": "Aside from standard treatment, with a view\nto managing hyperkalaemia and _ protecting\nthe kidneys from further damage, CVVHD CiCa\nhaemodialysiswithanEMIC2filterwas performed,\nleading to a rapid stabilization of the patient's\nclinical condition including sinus rhythm recovery.\nThe EMIC2 filter and/or the CVVHD CiCa kit\nwas/were initially replaced every 12-24 hours.\nAt the same time, the patient, who was monitored\nhaemodynamically, despite anuria received fluid\ntherapy soasto achieve mild arterial hypertension\ndue to hypervolaemia (fluid delivery rate: 4,000\nml/day). The rate of ultrafiltration was adjusted\nto the patient’s hydration level." }, { - "id": 15374, - "strid": "8484ef3b-701a-4d53-90d3-913c4af0f515", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 174, + "strid": "2cfb0956-f2ce-48d3-a58c-89ef30258e39", + "image_id": 7, + "image_name": "10316.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1508.924, - 791.971, - 294.82500000000005, - 40.23599999999999 + 763.673, + 967.962, + 699.6180000000002, + 442.33799999999997 ], - "priority": 21, + "priority": 9, "parents": [ - 15341 + 172 ], "children": [], - "area": 1195024.049204, + "area": 739206.444426, "iscrowd": 0, - "segmentation": [], - "text": "Invert grey-levels" + "segmentation": [] }, { - "id": 15375, - "strid": "0dbc207a-8e27-4d08-a0c8-c2a546c9d316", - "image_id": 201106, - "image_name": "116600.png", + "id": 175, + "strid": "1797d22f-a2ff-4f27-85e9-e9ebb4fd0061", + "image_id": 7, + "image_name": "10316.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1454.571, - 901.296, - 403.4850000000001, - 41.60400000000004 + 975.513, + 1416.759, + 78.01100000000008, + 19.701999999999998 ], - "priority": 22, + "priority": 10, "parents": [ - 15341 + 172 ], "children": [], - "area": 1310999.024016, + "area": 1382066.8223670002, "iscrowd": 0, "segmentation": [], - "text": "Background subtraction" + "text": "" }, { - "id": 15376, - "strid": "b10124a8-15ca-43ea-8fb0-678502b0499b", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 176, + "strid": "41ea0523-3413-4062-a91b-562532ffed7c", + "image_id": 7, + "image_name": "10316.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1235.123, - 1013.06, - 842.5279999999998, - 42.31099999999992 + 763.71, + 1441.264, + 701.623, + 284.202 ], - "priority": 23, + "priority": 11, "parents": [ - 15341 + 172 ], "children": [], - "area": 1251253.7063799999, + "area": 1100707.72944, "iscrowd": 0, - "segmentation": [], - "text": "Assign non-ROI pixel mean intensity of ROI pixels" + "segmentation": [] }, { - "id": 15377, - "strid": "a3104609-ba99-47f8-b1b6-15fd9476b42f", - "image_id": 201106, - "image_name": "116600.png", + "id": 177, + "strid": "4120a8ce-0f17-44e4-8c2d-3c29283053e3", + "image_id": 7, + "image_name": "10316.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1530.99, - 1124.386, - 249.48199999999997, - 41.708000000000084 + 974.773, + 1732.406, + 80.09000000000003, + 18.99000000000001 ], - "priority": 24, + "priority": 12, "parents": [ - 15341 + 172 ], "children": [], - "area": 1721423.72214, + "area": 1688702.593838, "iscrowd": 0, "segmentation": [], - "text": "Gabor filtering" + "text": "" }, { - "id": 15378, - "strid": "fe819d1d-9d4c-4689-8657-ce2c0bdb0445", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 178, + "strid": "e4458e24-edd4-47f9-8d68-9daa7dbc97c5", + "image_id": 7, + "image_name": "10316.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1226.422, - 1235.507, - 861.7599999999998, - 33.815000000000055 + 764.598, + 1757.439, + 701.623, + 286.866 ], - "priority": 25, + "priority": 13, "parents": [ - 15341 + 172 ], "children": [], - "area": 1515252.9659540001, + "area": 1343734.344522, "iscrowd": 0, - "segmentation": [], - "text": "Normalisation to unit mean and standard deviation" + "segmentation": [] }, { - "id": 15379, - "strid": "fbfe19f0-9414-4ee9-ae18-432dd703f95c", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 179, + "strid": "7763aa62-3884-492f-afbd-88c973b5fc35", + "image_id": 7, + "image_name": "10316.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1248.881, - 1344.804, - 816.4959999999999, - 43.59899999999993 + 186.546, + 2110.644, + 398.22100000000006, + 50.126000000000204 ], - "priority": 26, + "priority": 14, "parents": [ - 15341 + 165 ], - "children": [], - "area": 1679500.1643240002, + "children": [ + 180 + ], + "area": 393732.1956239999, "iscrowd": 0, "segmentation": [], - "text": "Thresholding and combination of different scales" + "text": "" }, { - "id": 15342, - "strid": "09f5def5-2f51-4a1f-a60f-1149f01f13fc", - "image_id": 201106, - "image_name": "116600.png", + "id": 180, + "strid": "85af1923-53dc-4e5d-8a2f-fcdf7f25b90d", + "image_id": 7, + "image_name": "10316.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1191.042, - 1417.925, - 929.8240000000001, - 184.8209999999999 + 32.32, + 2173.301, + 705.609, + 450.6399999999999 ], - "priority": 27, + "priority": 15, "parents": [ - 15341 + 179 ], "children": [], - "area": 1688808.22785, + "area": 70241.08832, "iscrowd": 0, "segmentation": [], - "text": "Each image was filtered with differently oriented Gabor\nfilters. For each scale only the maximum response of\nthe differently oriented filters was kept. The Gabor fil-\nters were defined as in Oloumi et al (2007)." + "text": "Acombination of intensive fluid therapy provided\nunderhaemodynamic monitoring with continuous\nrenal replacement therapy using a large pore\nfilter ensuring myoglobin filtration in patients\nwith acute renal failure caused by exertional\nrhabdomyolysis is a safe method of patient\nmanagement which may reduce kidney damage\nand speed up the recovery of normal renal\nfunction after exercise-induced rhabdomyolysis.\nAlso, it appears beneficial to determine the CK\nand myoglobin levels in the blood on a routine\nbasis during the first 12 hours after the end\nof ultramarathons." }, { - "id": 15344, - "strid": "b6de48fb-1b0f-41d5-97ba-361421a4cbdd", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 2, - "category_name": "Figure", + "id": 181, + "strid": "e7312163-837d-488c-987c-2f1986b160db", + "image_id": 7, + "image_name": "10316.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1189.996, - 1669.982, - 931.989, - 419.05600000000004 + 936.124, + 2110.749, + 358.1780000000001, + 44.85600000000022 ], - "priority": 28, + "priority": 16, "parents": [ - 15341 + 165 ], "children": [ - 15343 + 182 ], - "area": 1987271.9000720002, + "area": 1975922.7968759998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 15343, - "strid": "2ace2c18-af59-4d3a-b060-3fdff2e75d63", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 6, - "category_name": "Caption", + "id": 182, + "strid": "a8804f6b-c4ed-4933-b440-9d9624b63b5e", + "image_id": 7, + "image_name": "10316.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1191.036, - 2112.788, - 903.2089999999998, - 81.70699999999988 + 761.6, + 2171.909, + 705.938, + 452.5239999999999 ], - "priority": 29, + "priority": 17, "parents": [ - 15344 + 181 ], "children": [], - "area": 2516406.568368, + "area": 1654125.8944, "iscrowd": 0, - "segmentation": [], - "text": "FIGURE 2: Two examples of differently oriented Ga-\nbor filters" + "segmentation": [] }, { - "id": 15372, - "strid": "7e121a58-4627-4e05-9d0d-fe00c7e492f3", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 183, + "strid": "79d60547-7096-4cbd-a527-9704c8bffa30", + "image_id": 8, + "image_name": "10356.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 1191.346, - 2225.044, - 894.2739999999999, - 43.40599999999995 + 1422.99, + 57.53, + 342.28, + 213.92999999999998 ], - "priority": 30, - "parents": [ - 15341 + "priority": -1, + "parents": [], + "children": [ + 192, + 186, + 206, + 203, + 190, + 185, + 184 ], - "children": [], - "area": 2650797.2692239997, + "area": 81864.6147, "iscrowd": 0, - "segmentation": [], - "text": "Left: Filter oriented at 0°. Right: Filter oriented at 135°." + "segmentation": [] }, { - "id": 15361, - "strid": "300d5fe1-199e-4ef3-ae7b-892eca423a3b", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 5, - "category_name": "Section", + "id": 184, + "strid": "bd29aa3b-738f-4c0d-b71d-24431c6f7c6c", + "image_id": 8, + "image_name": "10356.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 1403.524, - 2348.402, - 502.02, - 96.57600000000002 + 64.394, + 44.835, + 1110.471, + 255.617 ], - "priority": 31, + "priority": 1, "parents": [ - 15334 - ], - "children": [ - 15354, - 15364, - 15356, - 15362 + 183 ], - "area": 3296038.568648, + "children": [], + "area": 2887.1049900000003, "iscrowd": 0, "segmentation": [], - "text": "VESSEL EXTRACTION:\nRESULTS" + "text": "Metabolic pathway\nextraction from text" }, { - "id": 15356, - "strid": "a9f97bf4-cf91-45ca-af03-d2df6d06f70e", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 2, - "category_name": "Figure", + "id": 185, + "strid": "d4e703f9-e475-400c-b8dc-10d6b9b5a045", + "image_id": 8, + "image_name": "10356.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1195.982, - 2490.972, - 921.06, - 468.067 + 523.24, + 378.339, + 1872.474, + 337.66299999999995 ], - "priority": 32, + "priority": 2, "parents": [ - 15361 + 183 ], - "children": [ - 15363 - ], - "area": 2979157.674504, + "children": [], + "area": 197962.09836, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Cécile Pereira', Ana Conesa!?\n'Microbiology and Cell Science Dept, Institute for Food and Agricultural Sciences,\nUniversity of Florida, Gainesville, USA\nGenomics of Gene Expression Lab, Centro de Investigacion Principe Felipe,\nValencia, Spain" }, { - "id": 15363, - "strid": "6e1d8545-c423-4768-9c8f-c1772e16c25b", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 6, - "category_name": "Caption", + "id": 186, + "strid": "b85c80f2-3319-4e51-a9f4-60f35d3908e0", + "image_id": 8, + "image_name": "10356.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1191.198, - 3003.699, - 666.6589999999999, - 32.39399999999978 + 318.22, + 746.764, + 220.712, + 48.63599999999997 ], - "priority": 33, + "priority": 3, "parents": [ - 15356 + 183 ], - "children": [], - "area": 3578000.241402, + "children": [ + 188, + 187 + ], + "area": 237635.24008000002, "iscrowd": 0, "segmentation": [], - "text": "FIGURE 3: Automatic vessel extraction" + "text": "Abstract" }, { - "id": 15354, - "strid": "aedd2bdc-4a6e-4276-aa14-35d7fce6c254", - "image_id": 201106, - "image_name": "116600.png", + "id": 187, + "strid": "4e9aa629-58f1-49ef-bcba-eb1bdf7c5437", + "image_id": 8, + "image_name": "10356.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1190.817, - 3049.62, - 920.5500000000002, - 189.89699999999993 + 39.709, + 823.007, + 1552.002, + 557.2120000000001 ], - "priority": 34, + "priority": 4, "parents": [ - 15361 + 186 ], "children": [], - "area": 3631539.33954, + "area": 32680.784963000002, "iscrowd": 0, "segmentation": [], - "text": "The automatic extraction for the fundus image shown\nin figure 1 using the noise removal (left) and Gabor fil-\nter (right) approaches. Green: True positives. Red: False\nnegatives. Blue: False positives." + "text": "There exist at least 35 databases listing metabolic pathways or reactions [1]. These databases differ\nby the organisms and processes represented. It was shown that even for the same organism, the\nrecovery between these databases is smaller than 16% (figure 1) [2]. Furthermore, some processes,\nlike plant response to stress, are still not well integrated in databases even though a large number\nof publications are available.\n\nWe propose to automatically extract metabolic reactions involved in a list of processes given\nby the user. Our method combines abstract selection methods (MedlineRanker [3]) with text\nmining methods (Banner [4], tmChem [5], TEES [6]) and databases of metabolic reactions (Brenda\n[7]) to provide a complete and accurate set of compounds, genes and reactions involved in the\nprocesses of interest.\n\nWe tested the methodology on two well described pathways in plants and bacteria. Using this\nmethodology we recovered more than 90% of the genes and compounds described in MetaCyc [8].\nMoreover, even for these well known pathways, our results proposed new entities and reactions\npossibly involved in the process and actually described in the literature." }, { - "id": 15364, - "strid": "447c03dd-cd4b-439f-94b6-e47d7d43fae8", - "image_id": 201106, - "image_name": "116600.png", + "id": 188, + "strid": "d310c2a6-1e38-4b67-9ac0-b28a5a509826", + "image_id": 8, + "image_name": "10356.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1225.884, - 3365.749, - 866.779, - 544.2260000000001 + 1681.091, + 875.465, + 1221.989, + 366.82499999999993 ], - "priority": 35, + "priority": 5, "parents": [ - 15361 + 186 ], "children": [ - 15359 + 189 ], - "area": 4126017.847116, + "area": 1471736.332315, "iscrowd": 0, "segmentation": [] }, { - "id": 15359, - "strid": "82ce308a-a327-43ea-8ac3-e6588681138b", - "image_id": 201106, - "image_name": "116600.png", + "id": 189, + "strid": "eb18f3cc-e5ec-4bb0-94c1-9bf42e9f9df1", + "image_id": 8, + "image_name": "10356.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1190.693, - 3961.705, - 867.4489999999998, - 40.702000000000226 + 1696.626, + 1264.988, + 973.981, + 30.136999999999944 ], - "priority": 36, + "priority": 6, "parents": [ - 15364 + 188 ], "children": [], - "area": 4717174.411565, + "area": 2146211.5304880003, "iscrowd": 0, "segmentation": [], - "text": "FIGURE 4: Accuracy of automatic vessel extraction" + "text": "Figure 1: Comparison of 5 databases (BiGG, EHMN, HumanCyc, KEGG, Reactome) [2]" }, { - "id": 15362, - "strid": "09a0ba94-fd4b-4f57-a374-ab0594044181", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 190, + "strid": "c985c07d-066f-4047-a405-31ad9177eecd", + "image_id": 8, + "image_name": "10356.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1190.267, - 4008.844, - 910.3219999999999, - 383.7659999999996 + 1402.987, + 1435.78, + 196.14200000000005, + 47.2349999999999 ], - "priority": 37, + "priority": 7, "parents": [ - 15361 + 183 ], - "children": [], - "area": 4771594.721348001, + "children": [ + 191 + ], + "area": 2014380.6748600001, "iscrowd": 0, "segmentation": [], - "text": "Both approaches were of similar accuracy (noise re-\nmoval approach: 94.50%, Gabor filter approach:\n94.07%) when applied to the DRIVE database. The\nnoise removal approach extracted a greater proportion\nof the vessels (72.33%) than the Gabor filter approach\n(68.07%). In terms of segmentation noise, both ap-\nproaches performed similarly (percentage of correctly\nsegmented background pixels: ~98%)." + "text": "Method" }, { - "id": 15345, - "strid": "87b8c962-73e8-4251-b65e-83ef39cd809f", - "image_id": 201106, - "image_name": "116600.png", + "id": 191, + "strid": "1c261cac-b134-47f4-8d30-049d70d0af10", + "image_id": 8, + "image_name": "10356.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 35.69, + 1507.641, + 2928.757, + 461.79399999999987 + ], + "priority": 8, + "parents": [ + 190 + ], + "children": [], + "area": 53807.70729, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 192, + "strid": "dd7aec98-8065-47cb-a78c-40f62bc1bade", + "image_id": 8, + "image_name": "10356.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2494.566, - 579.507, - 529.4659999999999, - 34.936000000000035 + 1409.319, + 2019.458, + 188.18499999999995, + 48.253999999999905 ], - "priority": 38, + "priority": 9, "parents": [ - 15334 + 183 ], "children": [ - 15340, - 15348, - 15366, - 15346, - 15368, - 15360 + 193, + 201, + 198, + 200, + 196, + 202, + 199, + 195, + 194, + 197 ], - "area": 1445618.4589619997, + "area": 2846060.529102, "iscrowd": 0, "segmentation": [], - "text": "IMAGE REGIST\n\nRATION." + "text": "Results" }, { - "id": 15340, - "strid": "bf5ed3ce-f74a-4b54-8221-090318b93034", - "image_id": 201106, - "image_name": "116600.png", + "id": 193, + "strid": "a2fb5291-7034-4433-be19-6ce8d4eb54c4", + "image_id": 8, + "image_name": "10356.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2361.476, - 689.956, - 764.6839999999997, - 405.88 + 36.609, + 2091.409, + 692.824, + 1240.069 ], - "priority": 39, + "priority": 10, "parents": [ - 15345 - ], - "children": [ - 15347 + 192 ], - "area": 1629314.535056, + "children": [], + "area": 76564.39208100001, "iscrowd": 0, "segmentation": [] }, { - "id": 15347, - "strid": "854b624d-424b-4856-bcba-8e1bc4139748", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 6, - "category_name": "Caption", + "id": 194, + "strid": "29bf641a-acdb-4faa-98a3-6c08445dafa9", + "image_id": 8, + "image_name": "10356.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2295.221, - 1107.846, - 877.431, - 90.2059999999999 + 769.735, + 2116.245, + 726.8089999999999, + 858.7399999999998 ], - "priority": 40, + "priority": 11, "parents": [ - 15340 + 192 ], "children": [], - "area": 2542751.403966, + "area": 1628947.8450749998, "iscrowd": 0, - "segmentation": [], - "text": "FIGURE 5: Schematic diagram of apparatus used to\nobtain spectroscopic fundus images" + "segmentation": [] }, { - "id": 15346, - "strid": "fec4891b-3b06-4798-b5e2-76a44e4521a2", - "image_id": 201106, - "image_name": "116600.png", + "id": 195, + "strid": "8e854438-5674-4c84-96a1-753732a4b097", + "image_id": 8, + "image_name": "10356.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2294.378, - 1220.201, - 926.54, - 427.8430000000001 + 781.695, + 3000.263, + 477.62800000000004, + 37.802999999999884 ], - "priority": 41, + "priority": 12, "parents": [ - 15345 + 192 ], "children": [], - "area": 2799602.3299780004, + "area": 2345290.585785, "iscrowd": 0, "segmentation": [], - "text": "A tungsten halogen light (Light Source) produced\nwhite light (black arrows), which were filtered by a\nVariSpec filter (Filter). The filtered light (red arrows)\nwas fed into the fundus camera via a fibre optic cable.\nThe light reflected back out of the subject’s eye (blue ar-\nrows) was captured by a CCD camera with 25° field-of-\nview. The images were then saved on a PC. The PC\nsynchronised the CCD camera (dotted double arrow)\nwith the filter (dotted arrow)." + "text": "Input: 122 PMID from MetaCyc" }, { - "id": 15348, - "strid": "8f1793a2-6992-4e2b-bfef-1efee885dd23", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 2, - "category_name": "Figure", + "id": 196, + "strid": "7dadb8de-10c7-4442-adbb-ec66bfa0cf86", + "image_id": 8, + "image_name": "10356.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2297.941, - 1708.966, - 922.0590000000002, - 358.0749999999998 + 780.437, + 3078.794, + 620.955, + 237.47800000000007 ], - "priority": 42, + "priority": 13, "parents": [ - 15345 + 192 ], - "children": [ - 15351 - ], - "area": 3927103.0390059995, + "children": [], + "area": 2402804.752978, "iscrowd": 0, "segmentation": [] }, { - "id": 15351, - "strid": "215837d1-0016-43ed-9f89-9f901d850d46", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 6, - "category_name": "Caption", + "id": 197, + "strid": "66152e0e-f5a3-4eb4-8291-9156dcde12e6", + "image_id": 8, + "image_name": "10356.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2295.45, - 2092.186, - 892.1210000000001, - 90.43299999999999 + 1537.378, + 2110.125, + 661.5249999999999, + 816.623 ], - "priority": 43, + "priority": 14, "parents": [ - 15348 + 192 ], "children": [], - "area": 4802508.3537, + "area": 3244059.75225, "iscrowd": 0, - "segmentation": [], - "text": "FIGURE 6: Aligning fundus images using automati-\ncally extracted surface vessels" + "segmentation": [] }, { - "id": 15366, - "strid": "569111ad-14af-45ce-943a-00e9180bdfa8", - "image_id": 201106, - "image_name": "116600.png", + "id": 198, + "strid": "46e24cbf-e5a2-41ce-88ac-25fa9c8cc114", + "image_id": 8, + "image_name": "10356.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2293.904, - 2187.908, - 929.1210000000001, - 384.5819999999999 + 1543.643, + 2921.969, + 640.8540000000003, + 118.72699999999986 ], - "priority": 44, + "priority": 15, "parents": [ - 15345 + 192 ], "children": [], - "area": 5018850.912831999, + "area": 4510476.993067, "iscrowd": 0, "segmentation": [], - "text": "The noise removal vessel extraction approach was ap-\nplied to spectroscopic images obtained with the appa-\nratus shown in figure 5 (yellow vessels: A = 605nm;\nblue vessels: A = 586nm). The alignment was obtained\nby shifting the yellow vessels relatively against the blue\nvessels. The shift resulting in the smallest difference\nwas considered to align the two images. Left: Una-\nligned images. Right: Aligned images." + "text": "Training: 122 PMID from MetaCyc\n\nMedlineRanker output: 1000 PMID of the\nlast 10 years" }, { - "id": 15360, - "strid": "a31f98b3-c278-472c-9060-cf1aa37b4017", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 2, - "category_name": "Figure", + "id": 199, + "strid": "660edeba-d025-4b65-aa34-4bfb7884b803", + "image_id": 8, + "image_name": "10356.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2378.912, - 2630.944, - 764.114, - 571.114 + 1547.994, + 3080.821, + 681.0409999999999, + 238.48700000000008 ], - "priority": 45, + "priority": 16, "parents": [ - 15345 - ], - "children": [ - 15355 + 192 ], - "area": 6258784.252927999, + "children": [], + "area": 4769092.423074, "iscrowd": 0, "segmentation": [] }, { - "id": 15355, - "strid": "cff20be3-8e9b-40c2-8b7f-d81bd563adcd", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 6, - "category_name": "Caption", + "id": 200, + "strid": "467deab4-2d57-443f-95de-5ae4e7f27889", + "image_id": 8, + "image_name": "10356.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2294.715, - 3214.735, - 612.8670000000002, - 40.91800000000012 + 2263.108, + 2117.86, + 695.7860000000001, + 699.1779999999999 ], - "priority": 46, + "priority": 17, "parents": [ - 15360 + 192 ], "children": [], - "area": 7376900.6255250005, + "area": 4792945.908880001, "iscrowd": 0, - "segmentation": [], - "text": "FIGURE 7: Aligning fundus images" + "segmentation": [] }, { - "id": 15368, - "strid": "42a760d6-3986-4c90-bb53-6b30e3d5ba38", - "image_id": 201106, - "image_name": "116600.png", + "id": 201, + "strid": "ec33e72d-6f81-46bb-b83e-9ae65062bf45", + "image_id": 8, + "image_name": "10356.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2294.625, - 3260.652, - 903.4719999999998, - 190.10899999999992 + 2269.003, + 2921.624, + 638.9470000000001, + 157.1959999999999 ], - "priority": 47, + "priority": 18, "parents": [ - 15345 + 192 ], "children": [], - "area": 7481973.5955, - "iscrowd": 0, - "segmentation": [], - "text": "The alignment of two spectroscopic fundus images (Ai\n= 586nm, A2 = 548nm). Each square is taken from one\nimage, while the 4 neighbouring squares belong to the\nalternate image." - }, - { - "id": 15365, - "strid": "4da76af1-1b09-437a-8c2c-96ed429c0db7", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 2586.085, - 3550.405, - 346.84799999999996, - 37.715000000000146 - ], - "priority": 48, - "parents": [ - 15334 - ], - "children": [ - 15369 - ], - "area": 9181649.114425, + "area": 6629173.620872, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Training: Pubmed request (Arabidopsis\nthaliana and stress and antibiotics)\n\nMedlineRanker output: 1000 PMID of the\nlast 10 years" }, { - "id": 15369, - "strid": "65573c22-c1a4-420b-8416-bced59566664", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 202, + "strid": "01cc2ead-313b-46f9-ad82-cfdd51b773d6", + "image_id": 8, + "image_name": "10356.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2294.393, - 3679.993, - 927.864, - 335.58399999999983 + 2273.064, + 3119.821, + 439.82299999999987, + 198.53899999999976 ], - "priority": 49, + "priority": 19, "parents": [ - 15365 + 192 ], "children": [], - "area": 8443350.179249, + "area": 7091552.801543999, "iscrowd": 0, - "segmentation": [], - "text": "Both automatic vessel extraction approaches resulted in\naccurate, binary masks of the surface vessels. The im-\nage registration algorithm was sufficiently robust to\ncorrect eye movements in spectroscopic datasets.\nAutomatic vessel extraction can also be used to select a\nspecific vessel segment for further processing, such as\nretinal oximetry measurements." + "segmentation": [] }, { - "id": 15367, - "strid": "556b8456-a8e4-454c-85cc-c3cfa87a01c8", - "image_id": 201106, - "image_name": "116600.png", + "id": 203, + "strid": "80a57d9e-2e43-4e46-bd4b-93aca0801137", + "image_id": 8, + "image_name": "10356.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2486.648, - 4139.071, - 545.7129999999997, - 37.460000000000036 + 37.881, + 3377.651, + 737.748, + 57.340000000000146 ], - "priority": 50, + "priority": 20, "parents": [ - 15334 + 183 ], "children": [ - 15370 + 205, + 204 ], - "area": 10292412.624008, + "area": 127948.79753099999, "iscrowd": 0, "segmentation": [], - "text": "ACKNOWLEDGEMENTS" + "text": "Conclusions and Perspectives" }, { - "id": 15370, - "strid": "9b9c90c4-e0cf-4f38-b4fe-89926ab8d497", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 204, + "strid": "dc7eaaf3-5d22-4a31-8b88-ac43f4c1226e", + "image_id": 8, + "image_name": "10356.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2294.801, - 4255.716, - 923.685, - 139.89000000000033 - ], - "priority": 51, + 41.083, + 3547.399, + 749.183, + 272.05099999999993 + ], + "priority": 21, "parents": [ - 15367 + 203 ], "children": [], - "area": 9766021.332516, + "area": 145737.793117, "iscrowd": 0, - "segmentation": [], - "text": "We would like to thank the BBSRC for funding this\ndoctoral work and Prof D. Henson for providing the in-\nfrastructure and equipment used." + "segmentation": [] }, { - "id": 15357, - "strid": "fc1d0631-e3b0-4c7f-a2a9-19bcaab7ffeb", - "image_id": 201106, - "image_name": "116600.png", + "id": 205, + "strid": "ed848d3f-5443-46c6-ae3f-5f2066cf6915", + "image_id": 8, + "image_name": "10356.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 814.328, + 3387.777, + 651.3319999999999, + 573.0160000000001 + ], + "priority": 22, + "parents": [ + 203 + ], + "children": [], + "area": 2758761.668856, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 206, + "strid": "57abeab0-28f7-477a-ba15-ce67654fc312", + "image_id": 8, + "image_name": "10356.png", "category_id": 5, "category_name": "Section", "bbox": [ - 397.101, - 4495.553, - 296.87, - 37.797999999999774 + 1560.104, + 3374.561, + 297.05399999999986, + 58.01899999999978 ], - "priority": 52, + "priority": 23, "parents": [ - 15334 + 183 ], "children": [ - 15371 + 207 ], - "area": 1785188.591853, + "area": 5264666.114344001, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Bibliography" }, { - "id": 15371, - "strid": "32748af3-d283-464c-9553-fd6842f30267", - "image_id": 201106, - "image_name": "116600.png", - "category_id": 3, - "category_name": "Text", + "id": 207, + "strid": "c7c2b289-5546-4658-93ec-951798fe307a", + "image_id": 8, + "image_name": "10356.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1029.769, - 4474.501, - 2196.295, - 90.04799999999977 + 1559.899, + 3460.961, + 1370.5279999999998, + 423.5909999999999 ], - "priority": 53, + "priority": 24, "parents": [ - 15357 + 206 ], "children": [], - "area": 4607702.420269, + "area": 5398749.602938999, "iscrowd": 0, - "segmentation": [], - "text": "Marin et al (2011), IEEE Trans Med Imaging, 30, 146-158 | Oloumi et al (2007), Conf Proc IEEE Eng Med Biol Soc., 6451-6454\nSaleh and Eswaran (2011), Comput Methods Biomech Biomed Engin., 1-9 | Staal et al (2004), IEEE Trans Med Imaging, 23, 501-509" + "segmentation": [] }, { - "id": 122027, - "strid": "ede09cde-3bcc-4047-89e5-53dbd0098740", - "image_id": 205249, - "image_name": "14510.png", + "id": 208, + "strid": "0752ded0-2fa3-40db-933b-70f14d5a0d9e", + "image_id": 9, + "image_name": "10415.png", "category_id": 9, "category_name": "Root", "bbox": [ - 5374.26, - 91.15, - 134.76999999999953, - 332.45000000000005 + 2200.7, + 105.49, + 229.35000000000036, + 206.42000000000002 ], "priority": -1, "parents": [], "children": [ - 122004, - 122019, - 122009, - 122002, - 122008, - 122005, - 122003, - 122006, - 122023, - 122025, - 122007 + 209, + 210, + 222, + 211, + 212, + 217 ], - "area": 489863.79900000006, + "area": 232151.84299999996, "iscrowd": 0, "segmentation": [] }, { - "id": 122002, - "strid": "d8e48452-dd1d-4804-9f1c-ecaf7c601621", - "image_id": 205249, - "image_name": "14510.png", + "id": 209, + "strid": "42e5eee1-11fe-4da0-a5fd-2591d8a0786c", + "image_id": 9, + "image_name": "10415.png", "category_id": 1, "category_name": "Title", "bbox": [ - 136.8, - 56.758, - 5209.3, - 231.052 + 184.405, + 111.908, + 1599.333, + 205.96999999999997 ], "priority": 1, "parents": [ - 122027 + 208 ], "children": [], - "area": 7764.494400000001, + "area": 20636.39474, "iscrowd": 0, "segmentation": [], - "text": "The true relative financial costs of Planned Caesarean Section (PCS) versus Planned Vaginal Birth (PVB) in England\ntaking into account litigation and compensation for harm" + "text": "" }, { - "id": 122003, - "strid": "427cf72d-7034-4e3a-a0ca-771fe469356f", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 0, - "category_name": "Author Info", + "id": 210, + "strid": "45f02be2-a86d-478d-9628-dc68b80528c1", + "image_id": 9, + "image_name": "10415.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 100.239, - 313.666, - 5085.296, - 81.82999999999998 + 104.557, + 722.816, + 731.354, + 755.952 ], "priority": 2, "parents": [ - 122027 + 208 ], "children": [], - "area": 31441.566174, + "area": 75575.47251200001, "iscrowd": 0, "segmentation": [], - "text": "AUTHORS:\nJonathan H West! ; Myles J Taylor? ; Michael Magro? +4Former NHS Consultant in Obstetrics & Gynaecology. 2 Trews Weir Reach, Exeter EX2 4EG; 2Consultant Obstetrician & Gynaecologist, Royal Devon & Exeter NHS Foundation Trust 3?ST7 O&G Registrar Queens Hospital BHR Trust. Darzi Fellow, NHS Resolution (2016-7)" + "text": "Participating organizations:\n\nAristotle University of Thessaloniki (AUTH)\nDemocritus University of Thrace (DUT)\nNational Technical University of Athens (NTUA)\nUniversity of Athens (UoA)\n\nUniversity of Crete (UoC)\n\nUniversity of loannina (Uol)\n\nUniversity of Patras (UoP)\n\nUniversity of Thessaly (UTH)\n\nAthena Research and Innovation Centre (ATHENA)\n\nBiomedical Research Foundation of the Academy of Athens (BRFAA)\nBiomedical Sciences Research Center \"Alexander Fleming\" (FLEMING)\nCentre for Research & Technology Hellas (CERTH)\n\nFoundation for Research and Technology Hellas (FORTH)\n\nHellenic Center for Marine Research (HCMR)\n\nHellenic Pasteur Institute (HPI)\n\nNational Hellenic Research Foundation (NHRF)\n\nGreek Research and Technology Network (GRNET)\nThe Hellenic Society for Computational Biology and Bioinformatics (HSCBB)\nHellenic Bioinformatics (HBIO)" }, { - "id": 122004, - "strid": "eca73ba3-3dab-4cb7-80e4-f8f47139a8bd", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 3, - "category_name": "Text", + "id": 211, + "strid": "7925c99c-4400-4159-900a-5fa19f58f573", + "image_id": 9, + "image_name": "10415.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 100.562, - 447.093, - 1720.369, - 113.57499999999999 + 104.494, + 1499.941, + 735.982, + 207.89200000000005 ], "priority": 3, "parents": [ - 122027 + 208 ], "children": [], - "area": 44960.566266, + "area": 156734.83485400002, "iscrowd": 0, - "segmentation": [], - "text": "AIM To determine the true financial costs of Planned Caesarean Section and Planned Vaginal\nBirth in England in 2017/18 after accounting for litigation and compensation for harm" + "segmentation": [] }, { - "id": 122005, - "strid": "c8f8cbd6-e9ca-422a-8f77-c6c849abcd1c", - "image_id": 205249, - "image_name": "14510.png", + "id": 212, + "strid": "1c1f33cb-241f-4021-838c-fc248713d724", + "image_id": 9, + "image_name": "10415.png", "category_id": 5, "category_name": "Section", "bbox": [ - 148.957, - 654.823, - 537.371, - 44.24199999999996 + 105.588, + 1760.971, + 515.133, + 129.72299999999996 ], "priority": 4, "parents": [ - 122027 + 208 ], "children": [ - 122010 + 216, + 213, + 215, + 214 ], - "area": 97540.469611, + "area": 185937.405948, "iscrowd": 0, "segmentation": [], - "text": "SUMMARY\n\nMESSAGE" + "text": "Node services\n\n(to be supported by a Structural Funds grant)" }, { - "id": 122010, - "strid": "756aa5b4-d409-4228-877e-c0b0abdf8c79", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 4, - "category_name": "List", + "id": 213, + "strid": "c10b5b75-5427-490e-ab8c-fa626463783b", + "image_id": 9, + "image_name": "10415.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 144.748, - 785.261, - 1763.484, - 1423.8889999999997 + 104.093, + 1912.318, + 740.947, + 156.7099999999998 ], "priority": 5, "parents": [ - 122005 + 212 ], "children": [], - "area": 113664.95922799999, + "area": 199058.917574, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Databases:\n\nBRIDEdb, DGP, FINDbase, LncBase, MESBL GC-MS,\nMjCyc, mirGEN, OMPdb, OpenAlRE, PICKLE,\nTCGA-Prognostic-Model-Collection, NGS-metadata-DB" }, { - "id": 122006, - "strid": "80105b33-bdfc-49bc-a4ef-dfd20e9b2391", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 5, - "category_name": "Section", + "id": 214, + "strid": "e8b141f8-9d73-451b-97b3-f0957a8ed2b0", + "image_id": 9, + "image_name": "10415.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1961.89, - 444.377, - 200.3230000000001, - 44.38900000000001 + 102.571, + 2093.307, + 785.68, + 285.43100000000004 ], "priority": 6, "parents": [ - 122027 - ], - "children": [ - 122012 + 212 ], - "area": 871818.7925300001, + "children": [], + "area": 214712.59229699997, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "°Tools:\n\nACT, AMYLPRED2, NGStool, CHRONOS, DEsubs,\nGprotPRED, GWA R, LifeWatchGreece/MicroCT vLab,\nMETAGEN, metaseqR, M-IOLITE DIANA-microT,\nDIANA-mictoTSS, DIANA-mirExTra, DIANA-mirPath,\nMagicMatch/Biolayout/CAST/RAGE/MCL,\n\nPCASNPs, Translational molecular analysis platform,\nPOTAMOS, PRED-TMBB, SweeD, SymCurve, VariantRanker" }, { - "id": 122012, - "strid": "edcf8a67-e9b4-4a7c-91b4-430971cc040b", - "image_id": 205249, - "image_name": "14510.png", + "id": 215, + "strid": "25830029-296a-4d4b-8149-306e73ec6659", + "image_id": 9, + "image_name": "10415.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1959.128, - 511.855, - 3532.7200000000003, - 270.52199999999993 + 102.082, + 2399.119, + 812.944, + 348.712 ], "priority": 7, "parents": [ - 122006 + 212 ], "children": [], - "area": 1002789.46244, + "area": 244906.865758, "iscrowd": 0, "segmentation": [], - "text": "The procedure was to estimate the proportion of LCFH costs attributable to three categories, namely: unaffected or equally affected by planned mode of delivery; solely or predominantly attributable to the choice of PVB;\nand, solely or mainly attributable to the choice of PCS. This was done by examining the breakdown of obstetric claims by value reported in the NHS Litigation Authority publication 'Ten Years of Maternity Claims: An Analysis of\nNHS Litigation Authority Data’ (October 2012)(9p17 Figure 6) and assuming that the proportions continue to hold sufficiently true as to be applicable to current costs. Figure 1 below reproduces this data. The resulting sub-\ncategorisation was then applied to overall obstetric LCFH costs, both those currently recovered through CNST funding and anticipated true costs for which financial provision must be made i.e. the ‘annual cost of harm’\n\nreported by NHS Resolution in its Annual Report and Accounts for 2017/18, being the most recent available (6) . Base costs were taken from published NHS Reference costs, which was also the method in the comparison of\nPCS and PVB performed by NICE in 2011 (2)." + "text": "Training:\n\n15 courses, among these:\n\nBioinformatics workflow management with Galaxy,\n\nNGS data analysis, Prediction of protein structure and function,\nComputational resources for membrane proteins,\nMeta-analysis of OMICs data,\n\nBiocuration and specialized protein databases,\n\nSystematic exploratory metagenomic analysis with Galaxy,\nComputer aided drug design and pharmacophore elucidation,\nOn line tutorial for ncRNA research" }, { - "id": 122007, - "strid": "c21d0a19-ffc9-4e72-ab93-beac3c7c7471", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 5, - "category_name": "Section", + "id": 216, + "strid": "f0ec9370-5a25-4dc3-9348-1f878183f2d3", + "image_id": 9, + "image_name": "10415.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1962.825, - 844.592, - 179.09500000000003, - 43.98299999999995 + 105.809, + 2819.791, + 1282.269, + 123.72400000000016 ], "priority": 8, "parents": [ - 122027 + 212 ], - "children": [ - 122017, - 122016, - 122014, - 122015, - 122018, - 122013 - ], - "area": 1657786.2924, + "children": [], + "area": 298359.265919, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "*Compute:\n\nComputational resources (1000 cores, 750TB disks, 1PB tape library) will be provided in a 'Green' Datacenter by\nGRNET (national e-Infrastructure providing high-quality international/national networking/computational services)" }, { - "id": 122013, - "strid": "39fda5f9-b5c9-46b2-9372-e9be8cadb134", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 3, - "category_name": "Text", + "id": 217, + "strid": "359f3625-9206-477f-802c-c14352ab3762", + "image_id": 9, + "image_name": "10415.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1959.357, - 912.148, - 3521.889, - 81.60299999999995 + 100.076, + 2997.262, + 525.041, + 127.20699999999988 ], "priority": 9, "parents": [ - 122007 + 208 ], - "children": [], - "area": 1787223.568836, + "children": [ + 218, + 221, + 219, + 220 + ], + "area": 299953.991912, "iscrowd": 0, "segmentation": [], - "text": "Our sub-categorisation and its impact on the relative risks is as follows, along with our justification. Figures following claim categories in brackets below are the proportionate values of the claims to the overall total. Weighted\ntotals have been calculated assuming a PCS rate of 9.7%, which was current at the time of the NHSLA report (10). Where deemed appropriate figures have been rounded to the nearest one or two decimal places." + "text": "Pilot actions\n\n(to be supported by a Structural Funds grant)" }, { - "id": 122014, - "strid": "be6062e0-4fb6-4475-898a-a1bbd3589e3f", - "image_id": 205249, - "image_name": "14510.png", + "id": 218, + "strid": "a989ba2a-2bf4-4ed4-987a-45a6aaefcdb6", + "image_id": 9, + "image_name": "10415.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1960.562, - 1050.736, - 229.45699999999988, - 36.57999999999993 + 107.135, + 3144.631, + 1522.974, + 178.00999999999976 ], "priority": 10, "parents": [ - 122007 + 217 ], "children": [], - "area": 2060033.073632, + "area": 336900.042185, "iscrowd": 0, "segmentation": [], - "text": "From Figure 1:" + "text": "*Data dependent exploration of marine biology\n\n(coordinator: HCMR)\nenvironmental sequencing, zooplankton community DNA barcoding and meta-barcoding, aquaculture fish species genomics ,\npopulation genomics of marine organisms." }, { - "id": 122015, - "strid": "7f70d83e-d581-4036-a1f9-c98b02643d84", - "image_id": 205249, - "image_name": "14510.png", + "id": 219, + "strid": "61642c6d-89d9-45e3-870d-87a6263b790e", + "image_id": 9, + "image_name": "10415.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1960.068, - 1098.38, - 3510.13, - 130.3789999999999 + 99.528, + 3337.856, + 1387.565, + 252.56100000000015 ], "priority": 11, "parents": [ - 122007 + 217 ], "children": [], - "area": 2152899.4898400004, + "area": 332210.13196800003, "iscrowd": 0, "segmentation": [], - "text": "Claim values from causes deemed unaffected or likely to be equally affected by planned mode of delivery:\nAccident (0.02%); Anaesthetic (0.61%); Antenatal Care (4.64%); Antenatal investigations (4.81%); Bladder (0.28%); Drug error (0.28%); Maternal Death (0.64%); Nursing Care (0.01%); Other (1.29%); Postpartum haemorrhage\n(0.1%); Psychological (0.02%); Retained swabs (0.1%); Stillbirth (0.5%); Cerebral Palsy (3.24%)* Subtotal: 16.55%" + "text": "Computational metabolomics & protein interactomics\n\n(coordinator: FORTH)\n\nStandardized repositories of metabolomic data from various biological systems,\n\nStandardized integration of metabolomic with proteomic and transcriptomic data repositories,\nCombined reconstruction and analysis of metabolic and protein interaction networks,\n\nTarget identification and validation via a systems-level multi-layer strategy" }, { - "id": 122016, - "strid": "d4b55f10-d29c-4e3f-b9b9-9364fda6a6b6", - "image_id": 205249, - "image_name": "14510.png", + "id": 220, + "strid": "2b814463-97f3-4b09-b3b3-61895f348f50", + "image_id": 9, + "image_name": "10415.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1957.668, - 1238.685, - 3526.2480000000005, - 129.86200000000008 + 106.89, + 3608.674, + 1105.161, + 211.43899999999985 ], "priority": 12, "parents": [ - 122007 + 217 ], "children": [], - "area": 2424933.98658, + "area": 385731.16386, "iscrowd": 0, "segmentation": [], - "text": "Sole or predominantly PVB causes:\nCaesarean Section (CS)** (5.93%); CTG interpretation (14.95%); Management of labour (13.6%); Operative vaginal delivery (3%); Perineal trauma (1%); Shoulder dystocia (3.32%); Uterine rupture (3.31%); Cerebral Palsy (CP) *\n(37.28%) Subtotal: 82.4%" + "text": "eNonCodingRNA biomarker identification\n\n(coordinator: UTH)\n\nHigh Throughput Functional Annotation of Epigenetic and Transcriptional Regulators,\nConstruction of molecular signatures,\n\nElucidation of Regulatory Networks in Homeostasis and Malignancy" }, { - "id": 122017, - "strid": "70993328-b596-4d55-a621-16d0181722e7", - "image_id": 205249, - "image_name": "14510.png", + "id": 221, + "strid": "ded80d0d-df60-4738-a1c8-4bdb7d3626e4", + "image_id": 9, + "image_name": "10415.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1959.099, - 1379.422, - 3460.062, - 128.82999999999993 + 108.011, + 3842.978, + 1007.847, + 243.80099999999993 ], "priority": 13, "parents": [ - 122007 + 217 ], "children": [], - "area": 2702424.260778, + "area": 415083.896758, "iscrowd": 0, "segmentation": [], - "text": "Sole or predominantly PCS causes\nThis figure has been calculated by excluding the 71% of claims values (i.e. 71% of 6.93%) related to CS attributed to delay, leaving 29%. 29% of 6.93% = 2.0097% attributable to complications of the procedures themselves.\nEmergency CS rates and PCS rates are sufficiently similar to make little or no significant difference to the subtotal so allocating half to PCS and half to PVB = 1.01% Subtotal = 1.01%" + "text": "ePathogen metagenomics\n\n(coordinator: HPI)\n\ninfectious diseases diagnosis support,\n\noutbreak and transmission pattern monitoring,\n\ntargeted vaccine development support,\n\ndetermination of pathogen-specific mechanisms of antimicrobial resistance" }, { - "id": 122018, - "strid": "209cdabb-645d-4831-8a24-b768e3402fda", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 3, - "category_name": "Text", + "id": 222, + "strid": "1958bf2d-63fa-405d-b8f2-b227212fea91", + "image_id": 9, + "image_name": "10415.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1961.043, - 1565.403, - 3527.977, - 642.374 + 854.612, + 703.069, + 2434.546, + 3442.998 ], "priority": 14, "parents": [ - 122007 + 208 ], "children": [], - "area": 3069822.5953289997, + "area": 600851.2042279999, "iscrowd": 0, - "segmentation": [], - "text": "Calculations\nApplying these figures to current (2017/18) CNST obstetric costs the amount unrelated to mode of delivery is 16.55% of £1,469/birth i.e. £243.12. The appropriate additional ‘premium’ for sole PCS causes is 1.01%, which\nweighted for a 9.7% PCS rate = £152.96. The appropriate additional ‘premium’ for PVB (rate = 100%-9.7%=90.3%) is 82.4% of £1,469/birth with weighting for a PVB rate of 90.3% = £1,340. This ratio (£1,340/£152.96) = 8.8:1.\n\nThe overall appropriate ‘premium’ for PVB is thus £243.12 + £1,340 = £1,583.6, and that for PCS £243.12 + £152.96 = £396.08 . The difference (£1,190.22) exceeds the difference in base costs of PCS and PVB (£4,016 - £3,265\n= £751) by £439/birth.\n\nAs previously mentioned current CNST funding and charges are set only to cover expected LCFH costs for the immediate future. The true anticipated cost based on ‘annual cost of harm’ is 2.83 to 3.23 higheri.e. £4,481.6 -\n£5,115.0 for PVB and £1,120 - £1,279.3 for PCS. Added to the ‘base’ costs the true overall costs are therefore found to be: PVB £7,747-£8,380; PCS £5,136-£5,295.\n\n* Although a relatively small proportion of all CP cases by far the most that lead to claims arise from brain damage caused during labour. In the 2017 NHS Resolution publication 'Five years of cerebral palsy claims’ (11,059) the\nauthor and co-author of this study analysed fifty CP claims in depth. Of these four (8%) including the only one delivered by elective CS arose from causes unrelated to the mode of delivery e.g. late deficiencies in neonatal care\n\n(review by the author MM of the case details). 8% of the Figure 1 amount for CP claims (8% x 40.53% = 3.24%) has thus been added to the 'unrelated causes' total with the remainder (37.28%) being attributed to PVB\n\n**the explanation for the allocation of 1% of CS causes to PVB prior to weighting is given above under 'PCS causes’. From Figure 1. 'Caesarean section’, 6.93% -1% = 5.93% to PVB." + "segmentation": [] }, { - "id": 122008, - "strid": "5aec14bc-4f35-4ff4-80a4-dee16a1383ad", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 5, - "category_name": "Section", + "id": 223, + "strid": "04f82313-b09d-4a6f-aac3-6126dc89e740", + "image_id": 10, + "image_name": "10434.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 103.528, - 2319.743, - 296.095, - 53.80099999999993 - ], - "priority": 15, - "parents": [ - 122027 + 33.28, + 47.37, + 255.42, + 351.2 ], + "priority": -1, + "parents": [], "children": [ - 122021, - 122011 + 224, + 247, + 251, + 226, + 253, + 225, + 228, + 230, + 252, + 249 ], - "area": 240158.35330400002, + "area": 1576.4736, "iscrowd": 0, - "segmentation": [], - "text": "Background" + "segmentation": [] }, { - "id": 122011, - "strid": "dc6ae387-8dd4-4fc1-804c-6132bb870935", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 3, - "category_name": "Text", + "id": 224, + "strid": "c102ef6a-4d70-4d89-87aa-309b2e6a6f8f", + "image_id": 10, + "image_name": "10434.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 97.429, - 2433.506, - 1791.875, - 2134.8919999999994 + 839.702, + 54.751, + 3355.322, + 299.054 ], - "priority": 16, + "priority": 1, "parents": [ - 122008 + 223 ], "children": [], - "area": 237094.056074, + "area": 45974.524202, "iscrowd": 0, "segmentation": [], - "text": "Caesarean section (CS) is often subject to negative perceptions by the public and health professionals, especially\nwith respect to its cost relative to planned vaginal birth. Examples of this include: newspaper headlines (‘NHS\npolicing pregnancies to put women off caesareans: Mothers-to-be are having to beg for the procedure as\nhospitals face pressure to cut costs')(1); the economic analysis accompanying the NICE Guideline on CS ('.. the\ncosts of birth and downstream costs associated with the outcomes... found that a planned vaginal birth was\napproximately £700 cheaper than a maternal request CS. This implies that the NHS could save £4.9 million for\nevery percentage point reduction in CSs')(2,p217); the National Audit Office ('.. the most common reasons for\nmaternity claims have consistently been mistakes in the management of labour and relating to caesarean\nsections.... The Department's objectives include decreasing the number of ‘unnecessary interventions’ by\npromoting normal births')(3,p16); and a plethora of journal publications e.g. 'FIGO position paper: how to stop\nthe caesarean section epidemic'(4).\n\nProviding balance to the above views NICE also assessed that Planned Caesarean Section (PCS) v Planned Vaginal\nBirth (PVB) may be cost-effective subject to different assumptions regarding downstream costs such as urinary\nincontinence (2p100) but either way despite the significant contribution that litigation and compensation for\nharm (LCFH) makes to maternity costs NICE has not considered it ‘appropriate’ to include these in its economic\n\nmodels (5,p94).\n\nNHS Resolution is tasked with the management of LCFH for NHS patients in England and runs the CNST schemes.\nIncome to defend or settle claims and provide compensation for harm is derived principally from members of the\nscheme and subscriptions are adjusted annually to cover payments expected to be required for the following\nyear. Charges to subscribers lag behind actual costs of harm however because of factors beyond NHS Resolution’s\ncontrol such as delays between incidents and claims and Periodic Payment Orders (PPO's). NHS Resolution and its\npredecessor the NHS Litigation Authority (NHSLA) produce annual reports and accounts as well as other\npublications analysing and detailing factors responsible for claims.\n\nFrom the NHS Resolution Annual Report and Accounts 2017/18 (6,025) the value of new clinical claims received\nfor the year was reported to be £4,513.2 million, of which the obstetric proportion was 48% i.e. £2,166.3 million.\nDivided by the number of births in England during the year (646, 794)(7) this amounts to an average of £3,348.8\nclaimed for every birth. By way of comparison ‘Reference Costs' published by NHS Improvement show that the\nentire cost of providing intrapartum care (i.e. all normal births, all assisted vaginal births, all emergency\nCaesarean sections and all elective Caesarian sections) in the same year amounted to £1,954.6 million ((8), sheet\n2 rows 1858-1893).\n\nApart from setting CNST charges to cover immediate needs NHS Resolution uses an actuarial methodology to\nmake financial provision for future cash flows. This takes into account known outstanding claims, provision for\nincidents incurred but not reported (IBNR), probability of settlement, adjustments for PPO's and HM Treasury\ndiscount rates. Taking these into account it was communicated in the 2017/18 report (6,p8) that 'At current\nprices the annual financial 'cost of harm' is now £7-8 billion, roughly double the figure prior to 2016/7'.\n\nAlthough obstetric claims accounted for 48% of the overall value of claims for 2017/8 the proportion charged to\nobstetric providers is currently lower. Overall CNST funding of all schemes in 2017/8 was £2,227.5 million (6,015)\nof which the obstetric proportion was 37% (NHS Resolution telephone personal communication to JW, November\n30 2018) i.e. £916.16 million, or £1,469.40 per birth. Applying the same proportion to the ‘annual cost of harm'\nthe true anticipated cost of obstetric LCFH at current prices can therefore be estimated to be 37% of £7-8 billion\n/646,794 i.e. £4,154 - £4,748 per birth." + "text": "Rapid learning curve assessment in an ex vivo training system\nfor microincisional glaucoma surgery" }, { - "id": 122021, - "strid": "16c90db9-50f9-4233-9e94-9e471c7f1a68", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 7, - "category_name": "Table", + "id": 225, + "strid": "7a06579d-cfcf-440d-827d-d0fc66da991b", + "image_id": 10, + "image_name": "10434.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 2000.317, - 2625.544, - 1236.3249999999998, - 1587.8289999999997 + 1055.753, + 359.457, + 2943.8860000000004, + 311.741 ], - "priority": 17, + "priority": 2, "parents": [ - 122008 - ], - "children": [ - 122020 + 223 ], - "area": 5251920.297448, + "children": [], + "area": 379497.806121, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Chao Wang *”, Yalong Dang ?, Susannah Waxman +, Hardik A. Parikh *, Igor Bussel ?,\nRalitsa T. Loewen ?, Xiaobo Xia 2, Kira L. Lathrop *, Richard A. Bilonick 3, Nils A. Loewen **\n1. Dept. of Ophthalmology, University of Pittsburgh School of Medicine 2. Dept. of Ophthalmology, Xiangya Hospital of Central South University\n3. Dept. of Biostatistics, University of Pittsburgh Graduate School of Public Health." }, { - "id": 122020, - "strid": "1646bdb3-d32a-488b-80c9-4f3d1e09d9ca", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 6, - "category_name": "Caption", + "id": 226, + "strid": "a82145f8-6147-46b6-813e-539c4ddc73ae", + "image_id": 10, + "image_name": "10434.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2004.587, - 2473.915, - 1159.4069999999997, - 82.49200000000019 + 139.53, + 687.231, + 228.86999999999998, + 71.23800000000006 ], - "priority": 18, + "priority": 3, "parents": [ - 122021 + 223 ], - "children": [], - "area": 4959177.848105, + "children": [ + 227 + ], + "area": 95889.34143, "iscrowd": 0, "segmentation": [], - "text": "Figure 1. Total number and value of claims reported by the NHS\nLitigation Authority according to category over a ten year period °" + "text": "Purpose" }, { - "id": 122019, - "strid": "52fbf3f2-099b-4e43-b25f-663c2f1360b7", - "image_id": 205249, - "image_name": "14510.png", + "id": 227, + "strid": "5a1f8827-ff34-4bdf-8efa-bba58723adf8", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3349.048, - 2218.583, - 2156.0189999999993, - 1348.5989999999997 + 139.724, + 776.972, + 1520.483, + 230.55700000000002 ], - "priority": 19, + "priority": 4, "parents": [ - 122027 + 226 ], "children": [], - "area": 7430140.958984, + "area": 108561.635728, "iscrowd": 0, "segmentation": [], - "text": "Critique\n\nIt is not possible to be precise about the total overall relative costs that we have investigated, but nevertheless we believe that the\namounts and differences are so stark as to provide sufficient indication that LCFH costs in obstetrics should not be ignored in health\neconomic models comparing PCS and PVB.\n\nIt may be argued that the values and causes of obstetric claims in Figure 1 are historic, referring as they do to events occurring between\n2000 and 2010. Unfortunately this NHSLA study has not been repeated and more up to date information is not available. Improvements\nfrom changes to some procedures e.g. the timing of PCS, changed practices regarding breech and twin births, routine use of\nprophylactic antibiotics and steroids, labour ward staffing, education and protocols may have had some effect since then in either\ndirection but the continued dominance of obstetrics in the overall cost of LCFH and its similar proportion by specialty then and now\nsuggests that significant changes in the categories and relative amounts are unlikely. Awards for brain damage to babies from obstetric\ncauses remain high as do obstetric indemnity costs both in the UK and some other countries where they may pose serious problems for\nthe provision of care (12). Indeed if they have increased at a higher rate than other LCFH costs then the PVB/PCS ratio of cost of harm\nmay be even greater than our analysis suggests.\n\nSub-categorisation of the claim types between PVB and PCS is of necessity somewhat subjective and approximate. Some, e.g.\n‘management of labour' and 'perineal trauma’ are self-evident. Some e.g. anaesthetic, retained swabs, or drug errors have required\nassumptions of equality. Where such assumptions have been made, however, it should be noted that the related claim values are a tiny\nproportion of the overall totals and may favour PVB since errors and complications are arguably more likely in an emergency rather than\nelective setting.\n\nWe have ignored the economic impact of clinical ‘adverse outcomes’ from choosing PCS or PVB. In the assessment by NICE in 2011\n(2p100) it was concluded that these depended on assumptions made about long-term effects e.g. urinary incontinence in particular.\nUnder one set of assumptions PVB had an advantage of £87 per birth but under other assumptions PCS was actually more cost-effective\noverall even without accounting for LCFH.\n\nThe PCS rate of 9.7% was applied as the average value for the years 2005-2010 reported in NHS Hospital Episode Statistics (10).\nModeling for different rates would alter the relative costs by approximately £100 per percentage point, lower rates reducing the\ndifference between PCS and PVB and vice versa." + "text": "Microincisional glaucoma surgeons operate in a highly confined space, making\nit difficult to learn by observation or assistance alone. An ex vivo model would\nallow for better refinement of technique, quantification of progress and\ncomputation of a learning curve." }, { - "id": 122009, - "strid": "0040c91b-beb0-4b41-abc0-5f4ff7e2ee5c", - "image_id": 205249, - "image_name": "14510.png", + "id": 228, + "strid": "91a9b931-e73e-43d5-9725-79f522e88a25", + "image_id": 10, + "image_name": "10434.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3352.437, - 3663.022, - 455.26900000000023, - 28.66300000000001 + 150.14, + 1054.029, + 604.763, + 71.23800000000006 ], - "priority": 20, + "priority": 5, "parents": [ - 122027 + 223 ], "children": [ - 122022 + 229 ], - "area": 12280050.484614, + "area": 158251.91405999998, "iscrowd": 0, "segmentation": [], - "text": "DISCUSSION & CONCLUSION" + "text": "Materials and Methods" }, { - "id": 122022, - "strid": "3c56d07c-33cd-4b80-9b0d-248e0ee6ffe7", - "image_id": 205249, - "image_name": "14510.png", + "id": 229, + "strid": "e0789cef-e97e-4a70-a800-7d4bee747a67", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3347.106, - 3756.901, - 2146.4060000000004, - 1529.1710000000003 + 134.519, + 1134.449, + 1502.501, + 513.453 ], - "priority": 21, + "priority": 6, "parents": [ - 122009 + 228 ], "children": [], - "area": 12574745.878506001, + "area": 152604.945031, "iscrowd": 0, "segmentation": [], - "text": "We do not believe it will come as much of a surprise to obstetricians, other health professionals or those involved with healthcare\nlitigation that planned vaginal birth should be so much more risky with respect to LCFH than planned Caesarean section. What may be\nsurprising to some, however, is the degree to which these risks and costs may now dominate the health economics of maternity care in\nEngland and that this has not so far been taken into consideration with respect to funding, improvement initiatives and other relevant\npolicies such as NHS Commissioning (13p14).\n\nThe reports and values used as the basis for our analysis are from authoritative sources. They are in the public domain and may easily\nbe accessed and checked. We believe our assumptions about the applicability of the data to be reasonable and in accordance with\nexperience. There is also, however, an alternative way of approaching the issue, which is to consider the number of additional CS\nprocedures required to prevent one case of cerebral palsy. In this regard any argument that intrapartum hypoxia does not cause CP is\nirrelevant since we are dealing with litigation costs and legal opinion does not support this. The figure is reported to be in the region of\n3,000-5,000 (14). That LCFH costs for individual cases now amount to £Emillions (in some cases tens of Emillions) provides separate\ncorroboration of our contention that obstetric LCFH costs have reached £thousands per birth and may be reduced by PCS.\n\nIn any normal business model indemnity costs would be included and insurers would adjust premiums according to risk. This is not\ncurrently the case with NICE economic models, which has implications for both obstetrics and the wider NHS. We believe we have\ndemonstrated PCS currently to be cost-effective or even more cost-effective than previously thought and that maternity LCFH costs\nmust surely be accounted for since they are so high relative to the costs of service provision. Until such time as these costs can be\nproved to be insignificant any analysis that ignores them risks criticism for not being rooted in the 'real world' potentially leading to\npolicies that are harmful, unfair, costly and missing out on opportunities for improvements.\n\nSerious adverse events in childbirth are rare. Women may truthfully be reassured that their risk of experiencing one is low but\nrisk/benefit evaluation also requires account to be taken of the severity of harm when it occurs. PCS has a different profile and\nincidence of medical complications from PVB and rational medical reasons may therefore inform and justify a woman's individual choice\naccording to her personal priorities, for which she deserves to be properly counselled. Failure to do so risks continuing the pattern and\nhistory of increasing claims for obstetric litigation and compensation for harm. The possibility and cost of medical error may be taken as\na proxy for risk and may reasonably form part of that choice. This may seem obvious in countries with variable or unpredictable\nstandards of obstetric care but appears to be a taboo subject in the UK. Against this background the promotion of 'normal birth' rather\nthan informed choice according to the views of health professionals and others as to what constitutes an ‘appropriate CS rate’ is thus\narguably patronising and perhaps consideration should be given as to whether as a notion it should be dropped.\n\nWhatever attitude is taken to CS rates and maternal choice Caesarean section in particular, however, this analysis shows that there is\ncurrently no justification to deny or discourage women from PCS on the grounds of cost." + "text": "Seven resident trainees without angle surgery experience performed nine ab\ninterno trabeculectomies in pig eyes after preparing with training slides and\nvideos. They placed the eyes on a tiltable mannequin head, visualized the\ntrabecular meshwork gonioscopically through an ophthalmic microscope and\nremoved it by trabectome-mediated plasma ablation. An expert surgeon\nobserved, guided, and rated the procedure using an Operating Room Score\n(ORS). The extent of accessed outflow beds was estimated with canalograms\nusing 0.5-micron fluorescent microspheres. Data was fit using mixed effect\nmodels." }, { - "id": 122023, - "strid": "da4a7828-0d57-4529-aa5c-8ede1ec40ac0", - "image_id": 205249, - "image_name": "14510.png", + "id": 230, + "strid": "7b89d836-7462-475e-9b99-9d47785a6ca3", + "image_id": 10, + "image_name": "10434.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3360.03, - 5384.841, - 796.0570000000002, - 37.94200000000001 + 149.329, + 1715.489, + 190.80599999999998, + 64.39699999999993 ], - "priority": 22, + "priority": 7, "parents": [ - 122027 + 223 ], "children": [ - 122024 + 244, + 245, + 232, + 231, + 238, + 239, + 242, + 236, + 235, + 234, + 241 ], - "area": 18093227.305230003, + "area": 256172.256881, "iscrowd": 0, "segmentation": [], - "text": "ACKNOWLEDGEMENTS/CONELICTS OF INTERESTS" + "text": "Results" }, { - "id": 122024, - "strid": "a5d74a35-8994-4539-8baf-fcb4de070a0d", - "image_id": 205249, - "image_name": "14510.png", + "id": 231, + "strid": "96177fc1-008a-4824-882e-553089874063", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3359.918, - 5435.647, - 2050.6149999999993, - 128.64800000000014 + 136.668, + 1794.129, + 1501.1169999999997, + 458.279 ], - "priority": 23, + "priority": 8, "parents": [ - 122023 + 230 ], "children": [], - "area": 18263328.196946, + "area": 245200.022172, "iscrowd": 0, "segmentation": [], - "text": "The authors have no conflicts of interest to declare.\nPauline Hull of the Caesarean Birth Organisation and Maria Booker of the Birthrights Charity kindly helped source some references\nNHS Resolution staff provided a helpful discussion of their published Annual Reports and Accounts" + "text": "Ex vivo training system\n\nSeven trainees without experience in angle surgery participated in this study.\nA) Trabectome stand with aspiration/irrigation pump and high frequency\ngenerator. B) Trainee surgeon with rotated mannequin head and tilted\nophthalmic microscope. C) Right-handed trainee using a surgical goniolens\nwith the left hand and the trabectome handpiece with the right. D) Under\ndirect view, the trabecular meshwork is engaged with the tip of the\ntrabectome and ablation is started (Figure 1)." }, { - "id": 122025, - "strid": "d22ff4af-f64a-4a17-946c-9c9828563321", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 5, - "category_name": "Section", + "id": 232, + "strid": "5ecc1164-abd2-477c-810e-a4e41022983a", + "image_id": 10, + "image_name": "10434.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 101.359, - 4598.468, - 240.515, - 39.63299999999981 + 215.196, + 2307.024, + 1325.402, + 1001.8789999999999 ], - "priority": 24, + "priority": 9, "parents": [ - 122027 + 230 ], "children": [ - 122026 + 233 ], - "area": 466096.11801199993, + "area": 496462.33670399996, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 233, + "strid": "2608b3a0-891d-41a9-9192-24718472e74c", + "image_id": 10, + "image_name": "10434.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 387.694, + 3332.656, + 926.7360000000001, + 60.853000000000065 + ], + "priority": 10, + "parents": [ + 232 + ], + "children": [], + "area": 1292050.735264, "iscrowd": 0, "segmentation": [], - "text": "References:" + "text": "Figure 1. Setup for microincisional glaucoma surgery" }, { - "id": 122026, - "strid": "eedfa5f4-a740-4446-ac7b-75409cd70f3c", - "image_id": 205249, - "image_name": "14510.png", - "category_id": 4, - "category_name": "List", + "id": 234, + "strid": "32f44910-e19b-4255-bf73-743c7162dcc8", + "image_id": 10, + "image_name": "10434.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 101.392, - 4655.206, - 3129.049, - 871.1620000000003 + 143.367, + 3459.246, + 1290.562, + 140.2420000000002 ], - "priority": 25, + "priority": 11, "parents": [ - 122025 + 230 ], "children": [], - "area": 472000.646752, + "area": 495941.72128199995, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Operating Room Score (ORS)\n\nORS was fit by an asymptotic nonlinear mixed effects model with a" }, { - "id": 120348, - "strid": "9d6db63b-eae2-490f-b1ce-1d43001e5e6c", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 9, - "category_name": "Root", + "id": 235, + "strid": "0feba964-8650-4b7b-bab5-3983a6135f86", + "image_id": 10, + "image_name": "10434.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 559.62, - 62.28, - 147.51, - 120.68 + 1768.523, + 746.155, + 1537.9929999999997, + 625.338 + ], + "priority": 12, + "parents": [ + 230 + ], + "children": [], + "area": 1319592.279065, + "iscrowd": 0, + "segmentation": [], + "text": "fixed upper asymptote, an estimated lower asymptote, and an estimated\nlogarithmic rate constant, and including random effects for the lower\nasymptote and for the rate constant. A half-maximum was achieved after 2.5\neyes. Scores were summed from the following operating room parameters:\narc of ablation (2120°=3, 90-119°=2, <90°=1), procedure time (<10 minutes=3;\n10-15 minutes=2; >15 minutes=1), number of questions asked (0-1\nquestion=3; 2-5 questions=2; >5 questions=1), confidence of movement\n(fluid=3; some hesitation=2; awkward=1), number of errors (none=3; 1-2\nerrors=2; 23 errors=1), number of entries into the anterior chamber (2\nentries=3; 3 entries=2; 24 entries=1), and scope movement (clear economy=3;\nmoderate=2; unnecessary movements=1) (Figure 2)." + }, + { + "id": 236, + "strid": "97392080-0646-4378-94d0-6cf9871a6bbc", + "image_id": 10, + "image_name": "10434.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 1774.349, + 1449.942, + 1506.624, + 756.9049999999997 + ], + "priority": 13, + "parents": [ + 230 ], - "priority": -1, - "parents": [], "children": [ - 120340, - 120345, - 120336, - 120332, - 120334, - 120333 + 237 ], - "area": 34853.1336, + "area": 2572703.137758, "iscrowd": 0, "segmentation": [] }, { - "id": 120332, - "strid": "1c52d5e2-1fad-4638-9eb9-7ccc6e349f3d", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 1, - "category_name": "Title", + "id": 237, + "strid": "f648901e-1f13-4d8a-8537-09bd53af3f79", + "image_id": 10, + "image_name": "10434.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 853.845, - 31.471, - 1773.7550000000003, - 182.3 + 2006.234, + 2213.267, + 1036.728, + 65.17700000000013 ], - "priority": 1, + "priority": 14, "parents": [ - 120348 + 236 ], "children": [], - "area": 26871.355995, + "area": 4440331.5064779995, "iscrowd": 0, "segmentation": [], - "text": "SPARQL-Powered Search Engine and RESTful APIs for\nProtein Ontology" + "text": "Figure 2. The Operating Room Score (ORS) and eye number" }, { - "id": 120333, - "strid": "66dfdefe-2aec-4127-908a-fe516a271519", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 0, - "category_name": "Author Info", + "id": 238, + "strid": "41fa652d-e208-4691-8154-7cb5f3d54b07", + "image_id": 10, + "image_name": "10434.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 828.821, - 223.615, - 1827.112, - 153.897 + 1768.127, + 2295.617, + 1488.667, + 138.14499999999998 ], - "priority": 2, + "priority": 15, "parents": [ - 120348 + 230 ], "children": [], - "area": 185336.807915, + "area": 4058942.3993590004, "iscrowd": 0, "segmentation": [], - "text": "Xiang Lit, Chuming Chen+, Hongzhan Huang}, Darren A. Natale2, Cecilia N. Arighit, Cathy H. Wut\n\n1 Protein Information Resource, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA\n2 Protein Information Resource, Georgetown University Medical Center, Washington, D. C., 20007, USA" + "text": "Time\nSurgical time decreased by 0.9 minutes per eye in a linear fashion (Figure 3)." }, { - "id": 120334, - "strid": "d0ad5214-3465-4e25-89ac-96fce145e4d3", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 5, - "category_name": "Section", + "id": 239, + "strid": "650efe0c-1b08-4796-b53d-41f6291c6744", + "image_id": 10, + "image_name": "10434.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1560.361, - 425.104, - 474.5640000000001, - 69.02800000000002 + 1779.93, + 2470.547, + 1511.1669999999997, + 745.1469999999999 ], - "priority": 3, + "priority": 16, "parents": [ - 120348 + 230 ], "children": [ - 120335 + 240 ], - "area": 663315.702544, + "area": 4397400.72171, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 240, + "strid": "d2b473b9-af99-4e15-8627-26a7beb516a4", + "image_id": 10, + "image_name": "10434.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 2186.943, + 3236.566, + 701.315, + 68.8789999999999 + ], + "priority": 17, + "parents": [ + 239 + ], + "children": [], + "area": 7078185.357738, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Figure 3. Surgical time and eye number" }, { - "id": 120335, - "strid": "8487fcef-e518-46e8-9aa1-a0d02a74fb11", - "image_id": 205186, - "image_name": "14414.png", + "id": 241, + "strid": "3121a61b-a1ac-4525-b908-ae04b3d30614", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 113.077, - 504.567, - 3373.193, - 441.26099999999997 + 1766.232, + 3334.888, + 1516.7889999999998, + 246.51000000000022 ], - "priority": 4, + "priority": 18, "parents": [ - 120334 + 230 ], "children": [], - "area": 57054.922659, + "area": 5890185.902016, "iscrowd": 0, "segmentation": [], - "text": "The Protein Ontology (PRO) represents protein-related entities, ranging from broad protein families down to very specific proteoforms, and protein complexes. We currently use a\nrelational database to store not only the ontology itself, but also other information, such as orthology, annotation and cross-reference information. Data integration and information\nretrieval can be efficiently achieved using the powerful Semantic Web technologies. Once data are converted into the widely used Resource Description Framework (RDF) format, they\ncan be queried using the SPARQL language. In this work, we investigate the use of Semantic Web technologies to power the PRO website. We studied the content and organization of\ndata source and extracted the relevant information. This was converted into RDF triples (10,657,089 in total, PRO release 56.0) and integrated into a Virtuoso RDF store. We then\ndeveloped a SPARQL-powered search engine to query the resulting RDF database to handle full-scale text search and hierarchy browsing for the PRO website. Tests reveal that we\nachieved a performance similar to the Apache Lucene-based search engine in current use. We also developed RESTful APIs for programmatic access to the PRO based on the new search\nengine. The SPARQL-powered PRO text search website and the PRO APIs are accessible at https://proconsortium.org/rdf_based." + "text": "Arc\n\nThe ablation arc followed a sigmoidal function with a half-maximum inflection\n\npoint after 5.3 eyes, and the mean arc improved from 73 to 135 degrees\n(Figure 4)." }, { - "id": 120336, - "strid": "c5470b11-2f8a-4b3b-bcba-28e61727d496", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 5, - "category_name": "Section", + "id": 242, + "strid": "375301fe-9e07-4858-b958-106c40a55c71", + "image_id": 10, + "image_name": "10434.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 156.126, - 1003.046, - 1366.473, - 87.99299999999994 + 3406.349, + 679.419, + 1422.589, + 710.2119999999999 ], - "priority": 5, + "priority": 19, "parents": [ - 120348 + 230 ], "children": [ - 120338, - 120337, - 120339 + 243 ], - "area": 156601.55979600002, + "area": 2314338.2312310003, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 243, + "strid": "a5bf063a-12cd-4a8e-9946-d4fedd9132f1", + "image_id": 10, + "image_name": "10434.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 3596.894, + 1396.127, + 1160.5899999999997, + 62.79299999999989 + ], + "priority": 20, + "parents": [ + 242 + ], + "children": [], + "area": 5021720.829538, "iscrowd": 0, "segmentation": [], - "text": "Data Integration and Semantic Web" + "text": "Figure 4. The improvement of ablation arc length and eye number" }, { - "id": 120338, - "strid": "48cf7256-5fe3-4214-8741-a2e4c7abe503", - "image_id": 205186, - "image_name": "14414.png", + "id": 244, + "strid": "459d2c60-d60e-4941-a118-2b0a68257b3f", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 118.871, - 1094.717, - 1445.068, - 483.1489999999999 + 3372.971, + 1491.134, + 1522.6920000000005, + 241.20000000000005 ], - "priority": 6, + "priority": 21, "parents": [ - 120336 + 230 ], "children": [], - "area": 130130.10450700001, + "area": 5029551.739114, "iscrowd": 0, "segmentation": [], - "text": "As the volume and diversity of data and the desire to share them increase, we\ninevitably encounter the problems of combining heterogeneous data\ngenerated from many different but related sources and providing users with a\nunified view of this combined data set. These problems emerge in the life\nsciences research community, where research data from different\nbioinformatics data repositories and laboratories need to be combined and\nanalyzed. The benefit of developing a data integration system is that it can\nfacilitate information access and reuse by providing a common access point. It\nalso provides users with more complete view of the available information." + "text": "Fluorescence\n\nCanalograms revealed that this progress did not correlate well with\nimprovement in outflow suggesting instead that about 30 eyes are needed for\ntrue mastery (Figure 5)." }, { - "id": 120337, - "strid": "2d2e0b7f-4468-4020-a56e-56196c2cb28d", - "image_id": 205186, - "image_name": "14414.png", + "id": 245, + "strid": "5cc85ce7-2d4e-4beb-9a0c-8106a335d75e", + "image_id": 10, + "image_name": "10434.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1592.569, - 1028.531, - 1870.455, - 561.741 + 3414.371, + 1749.274, + 1542.1459999999997, + 613.3719999999998 ], - "priority": 7, + "priority": 22, "parents": [ - 120336 + 230 ], - "children": [], - "area": 1638006.5861389998, + "children": [ + 246 + ], + "area": 5972670.416654, "iscrowd": 0, "segmentation": [] }, { - "id": 120339, - "strid": "247a3f5b-ed72-4149-94d5-a7a512f00698", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 3, - "category_name": "Text", + "id": 246, + "strid": "0ee3c204-e960-48ce-a91a-8f1f3563427a", + "image_id": 10, + "image_name": "10434.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 104.899, - 1600.849, - 3337.801, - 219.87400000000002 + 3729.547, + 2367.799, + 894.8979999999997, + 47.17099999999982 ], - "priority": 8, + "priority": 23, "parents": [ - 120336 + 245 ], "children": [], - "area": 167927.459251, + "area": 8830817.657053, "iscrowd": 0, "segmentation": [], - "text": "Semantic Web provides the requisite technologies to make such integration possible: 1) an abstract model for the relational graphs: RDF; 2) a query language adapted for the relational\ngraphs: SPARQL; and 3) various technologies to characterize the relationships and categorize resources: RDFS (RDF Schemas), OWL (Web Ontology Language) etc. In life sciences,\nSemantic Web technologies have been used to build and provide the largest network of Linked data by defining a set of simple conventions to create RDF(s) compatible Linked Data\nfrom a diverse set of heterogeneously formatted sources obtained from multiple data providers." + "text": "Figure 5. Fluorescent canalograms and eye number" }, { - "id": 120340, - "strid": "0e712601-76bf-4184-b3da-40bdb942bc7c", - "image_id": 205186, - "image_name": "14414.png", + "id": 247, + "strid": "4ce705c8-46b7-4797-aa76-195276bb9944", + "image_id": 10, + "image_name": "10434.png", "category_id": 5, "category_name": "Section", "bbox": [ - 390.965, - 1875.283, - 654.615, - 88.29300000000012 + 3386.628, + 2458.458, + 288.06100000000015, + 66.92300000000023 ], - "priority": 9, + "priority": 24, "parents": [ - 120348 + 223 ], "children": [ - 120343, - 120342, - 120341, - 120344 + 248 ], - "area": 733170.018095, + "area": 8325882.699624001, "iscrowd": 0, "segmentation": [], - "text": "Protein Ontology" + "text": "Conclusion" }, { - "id": 120341, - "strid": "82061758-36ea-46b5-9667-a6467d84b404", - "image_id": 205186, - "image_name": "14414.png", + "id": 248, + "strid": "76396e0c-f1a6-4244-8790-f5a8b9c299bd", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 114.79, - 1967.441, - 1199.533, - 474.1650000000002 + 3379.908, + 2534.028, + 1589.3960000000002, + 286.16899999999987 ], - "priority": 10, + "priority": 25, "parents": [ - 120340 + 247 ], "children": [], - "area": 225842.55239000003, + "area": 8564781.509424, "iscrowd": 0, "segmentation": [], - "text": "Protein Ontology (PRO) (https://proconsortium.org/pro/\npro.shtml) represents protein-related entities. Each PRO term\nrepresents a distinct class of entities (including specific modified\nforms, orthologous isoforms, and protein complexes) ranging\nfrom the taxon-neutral to the taxon-specific. In addition to the\nmain ontology file itself (in OBO or OWL format), PRO databases\ndraw on sources that provide orthology, annotation, and\nmapping information, as well as sequence-related data, including\namino acid and splice variants and multiple sequence alignments." + "text": "This inexpensive pig eye model provides a safe and effective training model for ab\ninterno trabeculectomy and allows for quantification of outcomes. Trainees\nwithout prior angle surgery experience proceeded quickly on the learning curve.\nActual outflow improvements progressed at a slower rate, a reminder to remain\nhumbly committed to training." }, { - "id": 120342, - "strid": "66b51754-f103-4783-bd95-333d264948dd", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 2, - "category_name": "Figure", + "id": 249, + "strid": "7f7e2684-807e-4dbc-bb30-2f415cb1c701", + "image_id": 10, + "image_name": "10434.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1349.123, - 1887.31, - 1129.042, - 568.7179999999998 + 3381.938, + 2846.972, + 296.8069999999998, + 60.11299999999983 ], - "priority": 11, + "priority": 26, "parents": [ - 120340 + 223 ], - "children": [], - "area": 2546213.32913, + "children": [ + 250 + ], + "area": 9628282.791736001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "References" }, { - "id": 120343, - "strid": "a171c68b-88f9-40b9-8dd7-6d5b03968215", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 2, - "category_name": "Figure", + "id": 250, + "strid": "ceb35ba0-2163-46bf-ad8b-f88713755a9c", + "image_id": 10, + "image_name": "10434.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2522.236, - 1885.211, - 904.4929999999999, - 581.3099999999997 + 3383.537, + 2909.413, + 1554.154, + 356.2420000000002 ], - "priority": 12, + "priority": 27, "parents": [ - 120340 + 249 ], "children": [], - "area": 4754947.0517959995, + "area": 9844106.533781, "iscrowd": 0, "segmentation": [] }, { - "id": 120344, - "strid": "a5ed152e-e2ca-4cb8-815b-002be79a1aa7", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 3, - "category_name": "Text", + "id": 251, + "strid": "e4718197-84e1-41b1-a1d8-8627b81a54b8", + "image_id": 10, + "image_name": "10434.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 103.387, - 2494.631, - 3302.839, - 165.57799999999997 + 3385.245, + 3294.271, + 299.192, + 68.45899999999983 ], - "priority": 13, + "priority": 28, "parents": [ - 120340 + 223 ], "children": [], - "area": 257912.415197, + "area": 11151914.431395, "iscrowd": 0, "segmentation": [], - "text": "These contribute to the underlying data, supporting the PRO website to provide PRO entry view, batch retrieval and search functionalities. The PRO website is currently hosted in two\nplaces: University of Delaware for entry page and visualization, and Georgetown University for text search and browse. The dual-site structure requires that data files be duplicated\nand overlapped, thus creating website maintenance issues." + "text": "Disclosures" }, { - "id": 120345, - "strid": "f3910a73-c20f-45d1-bdf8-91e6af87f7b1", - "image_id": 205186, - "image_name": "14414.png", + "id": 252, + "strid": "dfa34d14-8b78-49a7-a622-19286f408c8f", + "image_id": 10, + "image_name": "10434.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1153.402, - 2688.984, - 1194.1999999999998, - 87.99400000000014 + 3383.193, + 3476.871, + 402.97800000000007, + 64.16800000000012 ], - "priority": 14, + "priority": 29, "parents": [ - 120348 + 223 ], - "children": [ - 120347, - 120346 - ], - "area": 3101479.523568, + "children": [], + "area": 11762925.629103001, "iscrowd": 0, "segmentation": [], - "text": "Search Engine and RESTful APls" + "text": "Author Contact" }, { - "id": 120346, - "strid": "982ff199-f664-45a0-a37b-362c05267fd4", - "image_id": 205186, - "image_name": "14414.png", - "category_id": 2, - "category_name": "Figure", + "id": 253, + "strid": "a9049382-6ab8-466d-a45e-4d6cca1540b1", + "image_id": 10, + "image_name": "10434.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 220.18, - 2812.231, - 3084.156, - 1276.726 + 4128.115, + 3323.277, + 222.625, + 68.75199999999995 ], - "priority": 15, + "priority": 30, "parents": [ - 120345 + 223 ], - "children": [], - "area": 619197.0215800001, + "children": [ + 254 + ], + "area": 13718869.632855, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Funding" }, { - "id": 120347, - "strid": "1485be94-abed-4032-9e60-5ab95c43224f", - "image_id": 205186, - "image_name": "14414.png", + "id": 254, + "strid": "e5a2cd1f-0450-4f8b-8f91-385ec37dd441", + "image_id": 10, + "image_name": "10434.png", "category_id": 3, "category_name": "Text", "bbox": [ - 150.031, - 4108.77, - 2773.347, - 594.848 + 4128.483, + 3394.092, + 815.9840000000004, + 219.03999999999996 ], - "priority": 16, + "priority": 31, "parents": [ - 120345 + 253 ], "children": [], - "area": 616442.87187, + "area": 14012451.122436002, "iscrowd": 0, "segmentation": [], - "text": "To streamline the update process and to remove redundancy, we explored simplifying the data integration for the PRO database using Semantic Web\ntechnology. We studied the content and organization of each data source, identified and extracted relevant information, converted them into RDF\ntriples, and integrated them into a Virtuoso RDF triple store. We then developed a Virtuoso/SPARQL based search engine for the full-scale text search\nand hierarchy browsing of PRO website using Virtuoso full text search in SPARQL. Tests reveal that we achieved comparable performance as compared\nto the Apache Lucene-based search engine in current use. We also developed RESTful APIs for programmatic access to the PRO database based on the\nnew search engine. The API specification was designed using Swagger Editor based on Open API Specification 3. Swagger UI was used to visualize and\ninteract with the API’s resources automatically generated from API specifications. The PRO APIs include 8 API operation groups and 33 access paths,\nand are implemented using Django-REST framework.\n\nOur results indicate that: 1) RDF facilitates integration of the heterogeneous data for PRO database; 2) the SPARQL-based search engine is powerful\nenough to support PRO’s need for full-scale text search, hierarchy browsing and RESTful APIs." + "text": "National Eye Institute KO8EY022737 (NAL); Initiative to\nCure Glaucoma of the Eye and Ear Foundation of\nPittsburgh (NAL); Research to Prevent Blindness,\nDepartmental Grant (NAL); National Eye Institute\nP30EY08098 (KLL)." }, { - "id": 62347, - "strid": "85d48cb7-eabd-418d-9356-064899401bfd", - "image_id": 202956, - "image_name": "119500.png", + "id": 255, + "strid": "9452b650-5353-494f-8c06-984a0d1a064a", + "image_id": 11, + "image_name": "10502.png", "category_id": 9, "category_name": "Root", "bbox": [ - 430.78, - 162.5, - 220.09000000000003, - 289.59 + 71.35, + 418.74, + 297.87, + 132.39 ], "priority": -1, "parents": [], "children": [ - 62328, - 62326, - 62325, - 62329, - 62324, - 62327, - 62322, - 62323 + 271, + 264, + 265, + 281, + 262, + 278, + 258, + 274, + 256, + 270, + 277, + 283, + 276, + 260, + 272, + 263, + 261, + 284, + 267, + 280, + 266, + 273, + 269, + 275, + 268, + 257, + 279, + 282 ], - "area": 70001.75, + "area": 29877.099, "iscrowd": 0, "segmentation": [] }, { - "id": 62322, - "strid": "13185025-3119-48dd-a6c6-a6e8c12f3138", - "image_id": 202956, - "image_name": "119500.png", + "id": 256, + "strid": "fd5eb7d1-5732-4e37-9490-f0fce2786f33", + "image_id": 11, + "image_name": "10502.png", "category_id": 1, "category_name": "Title", "bbox": [ - 997.088, - 98.5, - 2787.74, - 225.27800000000002 + 492.217, + 118.372, + 2004.7939999999999, + 218.56799999999998 ], "priority": 1, "parents": [ - 62347 + 255 ], "children": [], - "area": 98213.16799999999, + "area": 58264.710724, "iscrowd": 0, "segmentation": [], - "text": "Depression Severity Predicts Striatat Reactivity to Positive\n7 . RN\nSocial Cues in Anxiety Disorders _.c®" + "text": "Comprehensive Gene Ontology annotation\nof ciliary genes in the laboratory mouse |" }, { - "id": 62323, - "strid": "10e9ab6c-b5ff-4705-afb4-686d57206ef1", - "image_id": 202956, - "image_name": "119500.png", + "id": 257, + "strid": "f569560b-7921-42ef-8bf7-1a438a4bb340", + "image_id": 11, + "image_name": "10502.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 934.652, - 339.825, - 2910.021, - 170.543 + 356.564, + 344.588, + 2283.952, + 42.19799999999998 ], "priority": 2, "parents": [ - 62347 + 255 ], "children": [], - "area": 317618.1159, + "area": 122867.67563200001, "iscrowd": 0, "segmentation": [], - "text": "Daniel A. Fitzgerald':2 K. Chau’, Christine A. Rabin Amy E. Kennedy'?, Heide Klumpp. Luan Phant2 q\n\n‘Mood and Anxiety Disorders Resbarch Program, Psychiatry, University of iRals at Chicago, Chicago, IL, @Mental Health e Line, Jesse Brown Veterans\nAdminiStration Medical Center, Chicago, IL, 7Department of Psychiatry, University of Michigan, Ann Atbor, MI, USA" + "text": "Karen R. Christie’ 2, Paola Roncaglia~ *, Teunis J. P. van Dam” ’, Toby J. Gibson®, Jane Lomax? ’, and Judith A. Blake” ¢" }, { - "id": 62324, - "strid": "64607c0e-a0cd-40a9-a13f-5f0578822829", - "image_id": 202956, - "image_name": "119500.png", + "id": 258, + "strid": "acc2a4e0-3fb0-47d1-a9be-95e8bf9783e5", + "image_id": 11, + "image_name": "10502.png", "category_id": 5, "category_name": "Section", "bbox": [ - 730.843, - 588.626, - 470.1829999999999, - 52.11699999999996 + 482.246, + 503.998, + 230.73199999999997, + 33.63799999999998 ], "priority": 3, "parents": [ - 62347 + 255 ], "children": [ - 62330 + 259 ], - "area": 430193.191718, + "area": 243051.019508, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 62330, - "strid": "1e2cd67a-60b8-49d5-88be-fd6d3abbf23b", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 4, - "category_name": "List", + "id": 259, + "strid": "68d78913-40df-4c8b-9b10-6ca46218c76d", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 78.796, - 673.818, - 1811.961, - 524.875 + 46.415, + 582.98, + 1093.263, + 1235.606 ], "priority": 4, "parents": [ - 62324 + 258 ], "children": [], - "area": 53094.163128, + "area": 27059.0167, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Interest in primary cilia has increased dramatically over the last ten years\nas it has become clear that ciliopathies are an underlying cause of\nnumerous human diseases including some types of retinitis pigmentosa\nand polycystic kidney disease. Once thought to be restricted to a few cell\ntypes, it is now clear that primary cilia are found on almost all vertebrate\ncells and are critical to Sonic hedgehog (Shh) signaling. Mouse models\nplay a key role in developing our understanding of the role of primary cilia\nin control of Shh signaling in development throughout the embryo and in\nongoing maintenance of structures such as photoreceptors.\n\nTo maximize the utility of the wealth of experimental data generated by\nthese mouse ciliopathy models, we have engaged in a project to\ncomprehensively annotate experimentally characterized ciliary genes of\nthe laboratory mouse using Gene Ontology (GO) terms to describe their\nmolecular functions, biological roles, and cellular locations, using the\nSYSCILIA gold standard of known human ciliary components as a starting\npoint. However, experimental annotations of mouse genes may allow\nadditional genes to be added to the SYSCILIA gold standard list. We have\nalso updated the Gene Ontology to add new terms and clarify existing\nterms to represent recent advances in our understanding of ciliary biology.\nThese improvements to the representation of cilia within GO greatly\nimproves our ability to make informative annotations for ciliary genes.\nComprehensive GO annotation of ciliary genes in the mouse will be a\ngreat resource to those doing high-throughput studies or comparative\ngenomic analysis across species.\n\nKRC, PR, and JAB were funded by NIH NHGRI grant U41 HG 002273 to\nthe Gene Ontology Consortium. TJPvD and TJG were funded by EU\nFP7/2009 (SYSCILIA grant agreement no: 241955). TJPvD was also\nfunded by the Virgo consortium (FES0908) and by the Utrecht\nBioinformatics Center. TJG and JL were supported by EMBL core funding." }, { - "id": 62325, - "strid": "cffc54d4-d7da-43a9-86c6-1010f22e7a25", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 5, - "category_name": "Section", + "id": 260, + "strid": "d1005a4d-d364-4765-8c7a-b94a0a1300de", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 859.269, - 1223.997, - 307.231, - 51.950000000000045 + 1317.286, + 481.518, + 1539.998, + 128.20099999999996 ], "priority": 5, "parents": [ - 62347 + 255 ], - "children": [ - 62332, - 62331, - 62333 - ], - "area": 1051742.6781930001, + "children": [], + "area": 634296.920148, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Identification of the mouse equivalents of the\nhuman genes in SYSCILIA Gold Standard version 1" }, { - "id": 62331, - "strid": "e1da4859-bb2f-4abb-997f-85788ef298e1", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 4, - "category_name": "List", + "id": 261, + "strid": "456002e2-0917-4406-a854-7a10bb4c8a5f", + "image_id": 11, + "image_name": "10502.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 78.011, - 1307.849, - 1634.031, - 325.297 + 1200.949, + 658.085, + 1149.397, + 391.144 ], "priority": 6, "parents": [ - 62325 + 255 ], "children": [], - "area": 102026.60833899998, + "area": 790326.522665, "iscrowd": 0, "segmentation": [] }, { - "id": 62332, - "strid": "b25ccbd1-9370-443c-bab6-579feca77af1", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 4, - "category_name": "List", + "id": 262, + "strid": "d7c77585-bfd0-4c6d-9b3f-37323151fbbf", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 77.945, - 1669.511, - 1830.698, - 458.3159999999998 + 2433.659, + 748.205, + 513.7670000000003, + 33.472999999999956 ], "priority": 7, "parents": [ - 62325 + 255 ], "children": [], - "area": 130130.03489499999, + "area": 1820875.8320950002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "302 unique human gene Ensembl IDs" }, { - "id": 62333, - "strid": "37dfde04-71ec-4fb1-9b0a-b602d4c542d1", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 4, - "category_name": "List", + "id": 263, + "strid": "5f61abf3-5e33-47d7-9c32-b35b0bc25f73", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 79.023, - 2165.724, - 1814.599, - 412.74699999999984 + 2486.839, + 847.751, + 412.8800000000001, + 28.001999999999953 ], "priority": 8, "parents": [ - 62325 + 255 ], "children": [], - "area": 171142.007652, + "area": 2108220.249089, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "ID Mapping at http:/Awww.uniprot.org/" }, { - "id": 62326, - "strid": "3aec35d9-702e-44a9-b673-db918c515048", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 5, - "category_name": "Section", + "id": 264, + "strid": "ad62d2bf-abb2-4024-ba10-fdd0e827aa9c", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 782.612, - 2639.213, - 462.3849999999999, - 53.766000000000076 + 2300.247, + 960.727, + 641.3250000000003, + 63.048 ], "priority": 9, "parents": [ - 62347 - ], - "children": [ - 62342, - 62343 + 255 ], - "area": 2065479.764356, + "children": [], + "area": 2209909.3995689997, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "302 UniProtKB IDs for human proteins\n\n(301 Reviewed records + 1 additional Unreviewed record)" }, { - "id": 62343, - "strid": "5f4d789a-6e13-4b25-91b4-237600689eb8", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 2, - "category_name": "Figure", + "id": 265, + "strid": "5b4546bf-cc9e-45e7-92ed-49942d0367af", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 113.818, - 2931.952, - 1004.512, - 595.1030000000001 + 1847.733, + 1075.312, + 457.0899999999999, + 57.256000000000085 ], "priority": 10, "parents": [ - 62326 + 255 ], - "children": [ - 62338 - ], - "area": 333708.912736, + "children": [], + "area": 1986889.4676959997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Identification of mouse homologs with\nMouseMine - http://www.mousemine.org/" }, { - "id": 62338, - "strid": "1b710ea6-16b8-461e-ad36-0a88da7cd6f1", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 6, - "category_name": "Caption", + "id": 266, + "strid": "db20f0bf-da8d-4686-a4b9-cb450f99a6c7", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 97.33, - 2736.578, - 1021.689, - 182.4029999999998 + 1216.743, + 1191.374, + 742.9580000000001, + 122.58400000000006 ], "priority": 11, "parents": [ - 62343 + 255 ], "children": [], - "area": 266351.13674, + "area": 1449595.974882, "iscrowd": 0, "segmentation": [], - "text": "emotional face trials (fear, angry, happy ated with\nblocks of geometric shape trials (circle, gle, square),\nwith each block lasting 20 seconds. . Q,\n\nBigure 1. Emotional face assessment task: ‘Blocks of\nae" + "text": "297 mouse genes with 1:1 homology with human gene\n263 — both Panther and HomoloGene\n29 — HomoloGene only\n4 — Panther only" }, { - "id": 62342, - "strid": "7b8110db-6681-435f-bad1-1ceb755ec9b9", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 7, - "category_name": "Table", + "id": 267, + "strid": "278a689d-26b3-4b0d-bbae-9ef69e39394b", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1194.945, - 2780.951, - 781.1189999999999, - 763.7129999999997 + 1267.688, + 1375.563, + 780.3959999999997, + 148.25 ], "priority": 12, "parents": [ - 62326 + 255 ], - "children": [ - 62337 - ], - "area": 3323083.492695, + "children": [], + "area": 1743784.7083440002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "11 mouse genes with 2 or more homologs to human gene\n(by a combination of Panther and HomoloGene)\n4-2 mouse to 1 human\n3-3 mouse to 2 human\n- 4—4 mouse to 1 human |" }, { - "id": 62337, - "strid": "7bf421b5-a9f7-4655-87fc-0a278f0b3856", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 6, - "category_name": "Caption", + "id": 268, + "strid": "61fa963f-21b8-4962-925b-1916227e9bfc", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1195.116, - 2734.16, - 766.1570000000002, - 37.072000000000116 + 2460.627, + 1146.46, + 456.36299999999983, + 56.49800000000005 ], "priority": 13, "parents": [ - 62342 + 255 ], "children": [], - "area": 3267638.36256, + "area": 2821010.43042, "iscrowd": 0, "segmentation": [], - "text": "Table 1. Participant Demographic Characteristics" + "text": "Additional research for human gene\nwith no mouse homologs via MouseMine" }, { - "id": 62329, - "strid": "04304a12-87a7-464f-8483-4de66d5b6d9d", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 5, - "category_name": "Section", + "id": 269, + "strid": "97786a41-cbee-4198-9a87-e7058f084de2", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3232.952, - 588.422, - 283.3760000000002, - 53.537000000000035 + 2127.103, + 1287.285, + 804.9850000000001, + 152.46800000000007 ], "priority": 14, "parents": [ - 62347 + 255 ], - "children": [ - 62345, - 62334, - 62346, - 62344 - ], - "area": 1902340.0817440003, + "children": [], + "area": 2738187.7853550003, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "No clear mouse homolog to 1 human gene (SLC47A2)\n2 human genes in the same Panther family (PTHR11206)\nonly HSSLC47A2 on SysCilia list\n2 mouse genes in cluster with HsSLC47A1\nboth added to candidate list as not clear which, if either, is equivalent" }, { - "id": 62344, - "strid": "051befe3-77ab-44e2-b786-9eb33d41f6cc", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 2, - "category_name": "Figure", + "id": 270, + "strid": "67ac74c4-ca85-421f-b64d-ac0b2190d65f", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2034.391, - 808.466, - 2641.597, - 806.398 + 1792.112, + 1624.519, + 575.9960000000001, + 33.024000000000115 ], "priority": 15, "parents": [ - 62329 - ], - "children": [ - 62339 + 255 ], - "area": 1644735.954206, + "children": [], + "area": 2911319.994128, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "310 mouse genes on cilia candidate list" }, { - "id": 62339, - "strid": "c9136cb2-34c7-4e54-adc6-42bf859a4268", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 6, - "category_name": "Caption", + "id": 271, + "strid": "74984b33-2ee4-4970-82bd-8ff22c59aa39", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2022.703, - 691.454, - 2704.9189999999994, - 102.11000000000001 + 53.336, + 1949.061, + 1327.399, + 132.89599999999996 ], "priority": 16, "parents": [ - 62344 + 255 ], "children": [], - "area": 1398606.080162, + "area": 103955.11749599999, "iscrowd": 0, "segmentation": [], - "text": "Fi 2. Happy > Shapes (Negative BDI & ID Correlations): Correlation maps s pyidg bilateral caudate with extracted para r\niaates from left and right caudate plotte inst BDI & HAMD scores\n\n," + "text": "improvements in the Gene Ontology to\nbetter represent ciliary structure & biology" }, { - "id": 62345, - "strid": "0558dc9a-3e76-4ed8-9bdf-820e4d0c49a8", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 2, - "category_name": "Figure", + "id": 272, + "strid": "0d60e653-9e4b-4122-acbb-cbcc5d729239", + "image_id": 11, + "image_name": "10502.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1992.42, - 1820.082, - 1577.795, - 527.7850000000001 + 77.304, + 2152.609, + 581.193, + 637.7379999999998 ], "priority": 17, "parents": [ - 62329 - ], - "children": [ - 62340 + 255 ], - "area": 3626367.7784400005, + "children": [], + "area": 166405.286136, "iscrowd": 0, "segmentation": [] }, { - "id": 62340, - "strid": "79142546-f13d-419b-99ef-6553b7803f8c", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 6, - "category_name": "Caption", + "id": 273, + "strid": "a1b17beb-426b-42be-9f94-083e5352dabe", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2020.633, - 1649.91, - 1493.543, - 155.71399999999994 + 48.743, + 2919.01, + 642.298, + 251.6329999999998 ], "priority": 18, "parents": [ - 62345 + 255 ], "children": [], - "area": 3333862.59303, + "area": 142281.30443000002, "iscrowd": 0, "segmentation": [], - "text": "Figure 3. Happy > Shapes (Negati 3D! Correlations): Correlation\nmaps showing A) Right Anterior-Cingulate and B) Left Medial-Frontal Gyrus\nwith extracted parameter ostimates. (fted against BDI scores" + "text": "Systematic classification of axonemal types\nFor the cellular component branch of GO, we\nbased our main classifications on two\ncharacteristics: 1) the structural aspects of\naxonemal configuration (9+2 or 9+0) and 2)\nmotility, producing four categories, and still\nallowing annotation of atypical structures." }, { - "id": 62346, - "strid": "b9649bcc-7f62-4315-853b-08f21af9903e", - "image_id": 202956, - "image_name": "119500.png", + "id": 274, + "strid": "1b95d0f6-91bc-4004-95db-e759796ee554", + "image_id": 11, + "image_name": "10502.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3612.147, - 1774.038, - 1107.7579999999998, - 529.183 + 36.479, + 3180.263, + 686.149, + 215.00300000000016 ], "priority": 19, "parents": [ - 62329 - ], - "children": [ - 62341 + 255 ], - "area": 6408086.039586, + "children": [], + "area": 116012.813977, "iscrowd": 0, "segmentation": [] }, { - "id": 62341, - "strid": "3a1d34b7-79f7-4d2c-a725-34948cb685f4", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 6, - "category_name": "Caption", + "id": 275, + "strid": "4dc76822-0d51-4b0c-ad7b-41bbf37c4eae", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3616.707, - 1645.247, - 1082.274, - 96.57500000000005 + 55.333, + 3419.199, + 663.909, + 206.54199999999992 ], "priority": 20, "parents": [ - 62346 + 255 ], "children": [], - "area": 5950376.341629, + "area": 189194.538267, "iscrowd": 0, "segmentation": [], - "text": "Figure Fear > Shapes (Control condition): Extracted parameter estimatés from A)\nRight Caudate, C) Right Anterior-Cingulate and D) Left Medi. ital Gyrus\npl d against BDI depression index" + "text": "Details of the Gene Ontology term ‘cilium’ and its\ndescendants. The term ‘cilium’ itself is highlighted in light\nblue. Dark blue arrows and “I” indicate is_a relationships.\n‘motile cilium’ is in bold to denote presence of a computable\ndefinition [PMID:20152934]. Obtained with the Graph Editor\nfunction of the OBO-Edit ontology editing tool [PMID:\n17545183]." }, { - "id": 62334, - "strid": "a338b977-bb9c-487e-bb4b-038f259cf78f", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 4, - "category_name": "List", + "id": 276, + "strid": "d78a9c63-dc2e-45bb-9866-866225e293ea", + "image_id": 11, + "image_name": "10502.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2021.496, - 2361.42, - 2659.0119999999997, - 260.0749999999998 + 668.016, + 2097.171, + 745.484, + 771.9470000000001 ], "priority": 21, "parents": [ - 62329 + 255 ], "children": [], - "area": 4773601.08432, + "area": 1400943.782736, "iscrowd": 0, "segmentation": [] }, { - "id": 62328, - "strid": "c50cfb24-a566-49ff-9e15-da0577f5ebe8", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 5, - "category_name": "Section", + "id": 277, + "strid": "fb55335f-2816-42e0-9d84-f38c920eceee", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2952.73, - 2669.474, - 726.1680000000001, - 55.05699999999979 + 759.194, + 2871.506, + 605.0410000000002, + 205.65599999999995 ], "priority": 22, "parents": [ - 62347 - ], - "children": [ - 62335 + 255 ], - "area": 7882235.964020001, + "children": [], + "area": 2180030.1261639996, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Schematic representation of the cilium\nComponents in bold indicate new terms in GO;\ncomponents in italics indicate pre-existing GO terms\nthat were modified to improve them. A, schematic\noverview of a cilium. B, cross-section of a cilium with a\n9+2 axoneme. *’Daughter centriole’ is a new synonym\nof ‘ciliary basal body’." }, { - "id": 62335, - "strid": "02cc11d2-0b75-4d63-a4d5-04b8081d465a", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 4, - "category_name": "List", + "id": 278, + "strid": "25da7fd4-fb81-4ca0-a272-dd80c726396f", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2022.257, - 2762.987, - 2706.806, - 546.288 + 744.031, + 3116.756, + 662.7550000000001, + 658.2570000000001 ], "priority": 23, "parents": [ - 62328 + 255 ], "children": [], - "area": 5587469.801659, + "area": 2318963.0834359997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Summary:\n\nBefore: 85 ciliary GO terms\nOur work: 48 existing ciliary GO terms improved\n7 ciliary terms merged into others\n69 new ciliary GO terms\n\n10 new or improved non-ciliary terms\nto clarify distinction between\nbacterial flagella, archaeal flagella,\nand eukaryotic cilia/flagella\n\n5 new non-ciliary terms to clarify\ndistinction between types of sperm\nmotility, e.g. flagellar vs. amoeboid\n\n4 other improved non-ciliary terms\n\nCurrent: 180 ciliary GO terms" }, { - "id": 62327, - "strid": "c11483cd-b031-426e-a4c5-a018411e1e77", - "image_id": 202956, - "image_name": "119500.png", - "category_id": 5, - "category_name": "Section", + "id": 279, + "strid": "1829cb48-4093-4692-8280-3d289cb4b7d6", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3136.017, - 3358.945, - 472.625, - 52.514000000000124 + 1460.912, + 1745.909, + 1444.818, + 129.1210000000001 ], "priority": 24, "parents": [ - 62347 + 255 ], - "children": [ - 62336 + "children": [], + "area": 2550619.409008, + "iscrowd": 0, + "segmentation": [], + "text": "Prioritizing curation of mouse genes by paucity\nof annotations and availability of literature" + }, + { + "id": 280, + "strid": "ac2ca541-79d0-4529-a1d1-6064163dcb8e", + "image_id": 11, + "image_name": "10502.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 1469.539, + 1879.274, + 1452.0160000000003, + 1289.0059999999999 ], - "area": 10533708.622065, + "priority": 25, + "parents": [ + 255 + ], + "children": [], + "area": 2761666.434686, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 281, + "strid": "aab9e287-2efe-412e-92c8-430a2784c9c8", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 1450.044, + 3135.499, + 81.03600000000006, + 29.07900000000018 + ], + "priority": 26, + "parents": [ + 255 + ], + "children": [], + "area": 4546611.511956, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgements" + "text": "" }, { - "id": 62336, - "strid": "26e23d38-424d-4b0a-aed4-527c594a66de", - "image_id": 202956, - "image_name": "119500.png", + "id": 282, + "strid": "29d2b8e2-2643-4c4d-9b0e-45b79abe3cf3", + "image_id": 11, + "image_name": "10502.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2021.96, - 3438.187, - 2702.0739999999996, - 112.39499999999998 + 1478.817, + 3173.663, + 1368.661, + 130.13099999999986 ], - "priority": 25, + "priority": 27, "parents": [ - 62327 + 255 ], "children": [], - "area": 6951876.58652, + "area": 4693266.796671, "iscrowd": 0, "segmentation": [], - "text": "This work was supported by the Department of Veterans Affairs Merit Review Program Award (to KLP) and by the National\nInstitutes of Health grants MHI 98 (to KLP) and MH903679 (to HK)" + "text": "To maximize the our annotation effort, we are focusing on mouse genes that are not currently annotated or only\npartially annotated with ciliary terms in the Cellular Component (CC) or Biological Process (BP) sections of the\nontology, based on the availability of literature for each gene. However, we will make additional annotations for\npreviously annotated genes when we come across supporting experimental data." }, { - "id": 172835, - "strid": "ca836a1a-f819-483d-bf54-27c14e4e8d0d", - "image_id": 207247, - "image_name": "7182.png", + "id": 283, + "strid": "017192b1-f9ae-4ede-8ce4-438c7c0d1c7d", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 1450.592, + 3324.931, + 1511.063, + 325.69799999999987 + ], + "priority": 28, + "parents": [ + 255 + ], + "children": [], + "area": 4823118.309152001, + "iscrowd": 0, + "segmentation": [], + "text": "Priorities: 134 Genes Completed (July 2013 — December 2016):\n\n \n\n \n\n \n\n \n\n \n\n \n\n \n\n{| 30 genes — no ciliary annotations; ciliary literature available 12 genes (40%)\n73 genes — no ciliary annotations; other literature available 42 genes (58%)\n\n33 genes — some ciliary annotations; ciliary literature available Q9genes (27%)\n\n| | 19 genes — some ciliary annotations; other literature available 4genes (21%)\n109 genes — no literature available 47 genes (43%)\n46 genes — already annotated with ciliary terms 20 genes (43%)" + }, + { + "id": 284, + "strid": "1455ec2b-7e9b-4643-9cc0-844da2ab7445", + "image_id": 11, + "image_name": "10502.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 1450.175, + 3667.054, + 1499.894, + 170.51800000000003 + ], + "priority": 29, + "parents": [ + 255 + ], + "children": [], + "area": 5317870.03445, + "iscrowd": 0, + "segmentation": [], + "text": "Summary: Our goal is to achieve comprehensive annotation of these ciliary genes based on experimental data from the\nlaboratory mouse. In our work so far, we have greatly improved the level of annotation of ciliary genes. This includes\nsome genes without any previous experimental annotations, in some cases due to publication of new papers providing\ninitial characterizations of these genes. This improved level of annotation of ciliary processes will be very helpful to\nthose conducting large scale experiments or bioinformatic analyses." + }, + { + "id": 285, + "strid": "e00537d2-68de-4082-b86b-1e1ddd11b33a", + "image_id": 12, + "image_name": "10539.png", "category_id": 9, "category_name": "Root", "bbox": [ - 2966.2, - 64.79, - 180.33000000000038, - 105.84999999999998 + 4.11, + 3.95, + 26.7, + 27.09 ], "priority": -1, "parents": [], "children": [ - 172816, - 172820, - 172817, - 172818, - 172819, - 172815, - 172821 + 290, + 292, + 286, + 302, + 288, + 303, + 287 ], - "area": 192180.098, + "area": 16.2345, "iscrowd": 0, "segmentation": [] }, { - "id": 172815, - "strid": "b0dc26f5-459e-4eb4-8021-942ae1e545f7", - "image_id": 207247, - "image_name": "7182.png", + "id": 286, + "strid": "57738d15-be7d-4a33-b968-e59b9842c211", + "image_id": 12, + "image_name": "10539.png", "category_id": 1, "category_name": "Title", "bbox": [ - 104.124, - 65.609, - 1158.34, - 46.057 + 93.902, + 10.976, + 663.415, + 82.927 ], "priority": 1, "parents": [ - 172835 + 285 ], "children": [], - "area": 6831.471515999999, + "area": 1030.6683520000001, "iscrowd": 0, "segmentation": [], - "text": "Effects of music on pain in patients with fibromyalgia" + "text": "GENETIC DIVERSITY ANALYSIS, SEQUENCE MOTIF\nCOMPARISON AND HOMOLOGY MODELING OF VPg FROM\nBANANA BRACT MOSAIC VIRUS" }, { - "id": 172816, - "strid": "78595e0c-6df0-47fb-8a58-5647a2c671e5", - "image_id": 207247, - "image_name": "7182.png", + "id": 287, + "strid": "8c117701-1ace-4605-a8dd-ab92a5ce209f", + "image_id": 12, + "image_name": "10539.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 94.27, - 113.065, - 2780.35, - 121.338 + 193.902, + 107.317, + 462.195, + 57.31699999999999 ], "priority": 2, "parents": [ - 172835 + 285 ], "children": [], - "area": 10658.63755, + "area": 20808.980933999996, "iscrowd": 0, "segmentation": [], - "text": "Giller Balci Alparslan'- Burcu Babadag'- Ayse Ozkaraman’: Pinar Yildiz?- Anmet Musmul® - Cengiz Korkmaz*\n‘Department of Nursing, Eskisehir Osmangazi University, Eskigehir School of Health @Department of Internal Medicine, Eskisehir Osmangazi University, School of Medicine\n8Department of Biostatistics, Eskisehir Osmangazi University, School of Medicine “Department of Internal Medicine and Rheumatology, Eskisehir Osmangazi University,School of Medicine" + "text": "Anuradha C and Selvarajan R\nMolecular Virology Lab, ICAR-National Research Centre for Banana\nThogamalai Road, Thayanur Post, Trichy-620102" }, { - "id": 172817, - "strid": "696d3e2b-e997-4afe-ab51-38043b627d87", - "image_id": 207247, - "image_name": "7182.png", + "id": 288, + "strid": "0e3d1fe2-bb4b-4023-b081-11b3dee143c0", + "image_id": 12, + "image_name": "10539.png", "category_id": 5, "category_name": "Section", "bbox": [ - 90.87, - 299.286, - 251.89099999999996, - 26.646000000000015 + 38.303, + 171.976, + 105.774, + 17.421999999999997 ], "priority": 3, "parents": [ - 172835 + 285 ], "children": [ - 172822 + 289 ], - "area": 27196.11882, + "area": 6587.196728, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "INTRODUCTION" }, { - "id": 172822, - "strid": "55ef8d57-a9ea-44ff-9487-d82236594110", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", + "id": 289, + "strid": "b0735c37-0e94-4e95-add8-e00c57d295d6", + "image_id": 12, + "image_name": "10539.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 88.018, - 342.173, - 854.057, - 343.783 + 25.236, + 190.02, + 390.742, + 123.196 ], "priority": 4, "parents": [ - 172817 + 288 ], "children": [], - "area": 30117.383114, + "area": 4795.34472, "iscrowd": 0, - "segmentation": [], - "text": "Fibromyalgia syndrome (FMS) is a chronic syndrome\ncharacterized by diffuse musculoskeletal system pain and\npainful tender points in certain areas of the body.It is\nsuggested that nonpharmacologic treatment may be also\neffective in addition to pharmacological treatment. Music\nmay be suggested as a nonpharmacological treatment for\nFMS. Therefore, this study was carried out to assess the\neffect of the music on the pain in FMS patients." + "segmentation": [] }, { - "id": 172818, - "strid": "bdc3dbe4-5043-4ae9-aa7d-f802cc058a50", - "image_id": 207247, - "image_name": "7182.png", + "id": 290, + "strid": "69d52e27-cc8d-4a05-b4a6-da700571ac37", + "image_id": 12, + "image_name": "10539.png", "category_id": 5, "category_name": "Section", "bbox": [ - 89.79, - 739.634, - 446.204, - 26.879999999999995 + 447.088, + 171.976, + 178.57099999999997, + 14.311000000000007 ], "priority": 5, "parents": [ - 172835 + 285 ], "children": [ - 172823 + 291 ], - "area": 66411.73686, + "area": 76888.40588800001, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "MATERIALS AND METHODS" }, { - "id": 172823, - "strid": "af98ce33-b29f-42ec-8c35-f6487942b323", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", + "id": 291, + "strid": "b6d17f94-612e-4ca1-a915-101f793b3658", + "image_id": 12, + "image_name": "10539.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 87.499, - 783.52, - 855.46, - 473.97399999999993 + 435.266, + 189.398, + 362.743, + 125.06199999999998 ], "priority": 6, "parents": [ - 172818 + 290 ], "children": [], - "area": 68557.21647999999, + "area": 82438.50986800001, "iscrowd": 0, - "segmentation": [], - "text": "This randomized clinical trial was carried out with 37\nfibromyalgia outpatients as an experimental group n=21\nand control group n=16 at a University Hospital Internal\nMedicine and Rheumatology Clinic between 1 June-1\nDecember 2014. The research instruments were used a\nDescriptive Characteristics Questionnaire, Visual\nAnalogue Scale(VAS), music CD which is including water\nand wave sounds is recommended by the Turkish\nPsychological Association for psychological relaxation\nand Pain Evaluation Form. Statistical analysis was\nperformed by using IBM SPSS 20.0 package program." + "segmentation": [] }, { - "id": 172819, - "strid": "9f5c4b96-369a-45e4-865b-54d90f18da80", - "image_id": 207247, - "image_name": "7182.png", + "id": 292, + "strid": "b3bbc7ec-cf9c-4f54-9420-05029183c8f1", + "image_id": 12, + "image_name": "10539.png", "category_id": 5, "category_name": "Section", "bbox": [ - 90.876, - 1310.016, - 149.848, - 27.54600000000005 + 37.058, + 327.474, + 166.75, + 14.363 ], "priority": 7, "parents": [ - 172835 + 285 ], "children": [ - 172827, - 172829, - 172830, - 172831, - 172825, - 172833, - 172824, - 172832 + 296, + 293, + 294, + 300, + 298 ], - "area": 119049.01401600002, + "area": 12135.531492, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "RESULT AND DISCUSSION" }, { - "id": 172824, - "strid": "9ae12493-7366-40b0-9880-13f6abcdcdac", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", + "id": 293, + "strid": "d86b0994-347c-4fb9-83c7-bf54ed90b81b", + "image_id": 12, + "image_name": "10539.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 87.111, - 1348.341, - 855.275, - 276.674 + 24.614, + 341.837, + 798.905, + 164.26099999999997 ], "priority": 8, "parents": [ - 172819 + 292 ], "children": [], - "area": 117455.332851, + "area": 8413.975918, "iscrowd": 0, - "segmentation": [], - "text": "Sociodemographic, Disease and _ Pain-Related\nFactors\n\nThe mean age for all patients was 43.59+10.30 years\nwith 94.6% are being female, 40.5% are being primary\nschool graduates and 81.1% are being married.The\nmean disease duration of the patients was 23.62+45.58\nmonths (min:1; max:20 years)." + "segmentation": [] }, { - "id": 172830, - "strid": "a03e013f-2d45-46df-9ddc-10be5eb4936e", - "image_id": 207247, - "image_name": "7182.png", + "id": 294, + "strid": "4001f6bd-dfb0-4c01-b269-3e77a2a91fbb", + "image_id": 12, + "image_name": "10539.png", "category_id": 7, "category_name": "Table", "bbox": [ - 978.418, - 343.807, - 900.1149999999999, - 602.111 + 32.39, + 543.545, + 530.431, + 78.73199999999997 ], "priority": 9, "parents": [ - 172819 + 292 ], "children": [ - 172812 + 295 ], - "area": 336386.95732600003, + "area": 17605.42255, "iscrowd": 0, "segmentation": [] }, { - "id": 172812, - "strid": "56ff4106-1f57-455b-9aca-ee3cafb048c1", - "image_id": 207247, - "image_name": "7182.png", + "id": 295, + "strid": "641859f2-c592-4a67-8ce8-e6d3c26e68e6", + "image_id": 12, + "image_name": "10539.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 987.163, - 285.356, - 663.74, - 34.384000000000015 + 31.49, + 510.702, + 528.182, + 30.59299999999996 ], "priority": 10, "parents": [ - 172830 + 294 ], "children": [], - "area": 281692.885028, + "area": 16082.00598, "iscrowd": 0, "segmentation": [], - "text": "Table 1 Sociodemographic characteristics" + "text": "Table 1: Analysis of evolutionay distance, SNP, Indels and Ks/Ka rat\nVP gene of BBrMV isolate\n\nand percentage sequence identity of" }, { - "id": 172829, - "strid": "0942e996-419b-4786-96f2-92db7529f3ca", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 4, - "category_name": "List", + "id": 296, + "strid": "46ae08f7-7bef-4024-9386-07b45024234c", + "image_id": 12, + "image_name": "10539.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 986.503, - 951.138, - 212.67700000000002, - 53.87800000000004 + 34.039, + 644.072, + 556.976, + 151.61599999999999 ], "priority": 11, "parents": [ - 172819 + 292 ], - "children": [], - "area": 938300.4904140001, + "children": [ + 297 + ], + "area": 21923.566808, "iscrowd": 0, "segmentation": [] }, { - "id": 172825, - "strid": "beaf1907-787a-48ab-8c52-50753aaa211b", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", + "id": 297, + "strid": "8ebc8715-27f3-4023-889f-1ec934a1129e", + "image_id": 12, + "image_name": "10539.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 983.635, - 1059.119, - 877.0240000000001, - 586.8610000000001 + 33.74, + 624.527, + 471.045, + 16.645999999999958 ], "priority": 12, "parents": [ - 172819 + 296 ], "children": [], - "area": 1041786.5175649999, + "area": 21071.54098, "iscrowd": 0, "segmentation": [], - "text": "In the initial interview with the patient, general pain severity\nwas evaluated by using VAS in which a mean score of\n6.89+1.64 was obtained. Of the patients, 56.8% reported\nthat they have another disease other than fibromyalgia.\nControl and intervention groups were found to be similar in\nterms of sociodemographic characteristics such as age\nand gender (p>0.05) (Table 1).\n\nVAS scores comparations\n\nThe mean VAS score in the intervention group changed\nfrom 5.45+2.73 on Day 1 to 4.57+2.71 on Day 7 and\n4.14+2.45 on Day 14 with a significant decrease in pain\nseverity in the intervention group of patients who had\nlistened to the music (p=0.026) (Table 2)." + "text": "1 Multiple sequence alignment of VPg from different potyviruses including BBrMV isolates" }, { - "id": 172831, - "strid": "68caae05-4c37-4b9c-bec2-2a4f2a528c81", - "image_id": 207247, - "image_name": "7182.png", + "id": 298, + "strid": "a11e7109-2270-4b7d-a260-d27a8160ad88", + "image_id": 12, + "image_name": "10539.png", "category_id": 7, "category_name": "Table", "bbox": [ - 1940.731, - 431.651, - 843.5359999999998, - 339.768 + 601.163, + 548.444, + 214.60199999999998, + 310.43100000000004 ], "priority": 13, "parents": [ - 172819 + 292 ], "children": [ - 172813 + 299 ], - "area": 837718.476881, + "area": 329704.240372, "iscrowd": 0, "segmentation": [] }, { - "id": 172813, - "strid": "49f553d2-0274-42b1-a5c9-c8c2e38588c6", - "image_id": 207247, - "image_name": "7182.png", + "id": 299, + "strid": "22203c3f-283f-4a39-8f03-71578bc9965e", + "image_id": 12, + "image_name": "10539.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1924.478, - 297.555, - 845.8240000000001, - 35.678 + 567.87, + 511.602, + 244.745, + 27.44399999999996 ], "priority": 14, "parents": [ - 172831 + 298 ], "children": [], - "area": 572638.0512900001, + "area": 290523.42774, "iscrowd": 0, "segmentation": [], - "text": "Table 2 VAS scores in the intervention group by days" + "text": "Table 2: The sequence motifs identified in VPg of\nBanana Bract Mosaic Virus" }, { - "id": 172833, - "strid": "da5cc424-c4dc-4709-8cb5-d8e7330c8471", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", + "id": 300, + "strid": "c03bd004-be02-4fa6-b5ab-3ae0028887ad", + "image_id": 12, + "image_name": "10539.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1947.759, - 782.116, - 113.99299999999994, - 20.851999999999975 + 33.29, + 841.728, + 472.844, + 152.966 ], "priority": 15, "parents": [ - 172819 - ], - "children": [], - "area": 1523373.478044, - "iscrowd": 0, - "segmentation": [], - "text": "° Tukey Test" - }, - { - "id": 172827, - "strid": "d6dbb807-cc8f-4474-8cab-45bffbb3f546", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 1947.184, - 848.219, - 815.4799999999998, - 233.4090000000001 - ], - "priority": 16, - "parents": [ - 172819 - ], - "children": [], - "area": 1651638.465296, - "iscrowd": 0, - "segmentation": [], - "text": "Repeated measures showed a significant difference\nbetween VAS scores on Day 1 and 14 (p=0.022)(Table\n2). The mean VAS score in the control group changed\nfrom 6.25+2.41 on Day 1 to 5.68+3.28 on Day 7 and\n5.40+3.11 on Day 14 with no statistically significant\ndifference (p=0.853)(Table 3)." - }, - { - "id": 172832, - "strid": "4e12796e-044b-4c2f-bb4f-30db81398afb", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 7, - "category_name": "Table", - "bbox": [ - 1932.003, - 1126.668, - 872.992, - 256.5429999999999 - ], - "priority": 17, - "parents": [ - 172819 + 292 ], "children": [ - 172814 + 301 ], - "area": 2176725.956004, + "area": 28021.125119999997, "iscrowd": 0, "segmentation": [] }, { - "id": 172814, - "strid": "b39cc2a0-8559-4e47-b3c4-7251d0c5d4dc", - "image_id": 207247, - "image_name": "7182.png", + "id": 301, + "strid": "a993e83d-8063-49cf-a1f3-3e8253fdf8db", + "image_id": 12, + "image_name": "10539.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1924.916, - 1389.529, - 486.38699999999994, - 22.207000000000107 - ], - "priority": 18, - "parents": [ - 172832 - ], - "children": [], - "area": 2674726.604564, - "iscrowd": 0, - "segmentation": [], - "text": "2Friedman Repeated measures Analysis of Variance" - }, - { - "id": 172820, - "strid": "b037de80-bfe5-4e2f-bfeb-a4a1008bef9e", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 1938.783, - 1446.201, - 223.9409999999998, - 26.873000000000047 - ], - "priority": 19, - "parents": [ - 172835 - ], - "children": [ - 172826, - 172828 - ], - "area": 2803869.913383, - "iscrowd": 0, - "segmentation": [], - "text": "" - }, - { - "id": 172826, - "strid": "8cc10f76-f2ca-4405-855f-64102a4703a0", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 1938.972, - 1526.452, - 870.3529999999998, - 114.92200000000003 + 33.74, + 798.988, + 545.278, + 41.84100000000001 ], - "priority": 20, + "priority": 16, "parents": [ - 172820 + 300 ], "children": [], - "area": 2959747.6873439997, + "area": 26957.855120000004, "iscrowd": 0, "segmentation": [], - "text": "Pain is one of the most important symptoms of FMS and\nmany other diseases and the pain management includes\nseveral non-pharmacological methods" + "text": "23D Structure of BBrMV HC-Pro. (a) Diagram of the BBrMV RNA genome, the domain orgar\nVPs, and the region used for modelling. (b) 3D structural model of BBrMV VPg. (c) 3D model of BBrMY VPg\nshowing the Tyr and Tyr! (blue) are shown as sticks. (d) Ramachandran plot for the BBrMV VPg." }, { - "id": 172828, - "strid": "5f94817b-69f2-4c43-b61e-172173752178", - "image_id": 207247, - "image_name": "7182.png", - "category_id": 3, - "category_name": "Text", + "id": 302, + "strid": "dda88e3d-c60f-4de5-91cd-6808cc90bd4a", + "image_id": 12, + "image_name": "10539.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2838.54, - 308.163, - 773.556, - 436.289 + 509.833, + 868.972, + 304.58199999999994, + 91.33000000000004 ], - "priority": 21, + "priority": 17, "parents": [ - 172820 + 285 ], "children": [], - "area": 874733.00202, + "area": 443030.601676, "iscrowd": 0, - "segmentation": [], - "text": "Physicians and Nurses provide the painful\nfibromyalgia patients to use the music therapy as a\ncomplementary treatment method, helping to\nreduce the complaints and to increase the\nrelaxation, happiness and competence feelings.\n\nIn conclusion, music therapy being a _non-\npharmacological nursing intervention for pain\nmanagement in fibromyalgia patients is\nrecommended to be used in this group of patients\nand to be studied on larger study samples." + "segmentation": [] }, { - "id": 172821, - "strid": "ac8234b2-ea77-4464-bedb-c07eca0dc2fc", - "image_id": 207247, - "image_name": "7182.png", + "id": 303, + "strid": "f4dc2163-41c1-4773-8eca-5d18249d0615", + "image_id": 12, + "image_name": "10539.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2840.859, - 789.704, - 225.42799999999988, - 27.30499999999995 + 35.489, + 1002.142, + 107.226, + 14.996999999999957 ], - "priority": 22, + "priority": 18, "parents": [ - 172835 + 285 ], "children": [ - 172834 + 304 ], - "area": 2243437.715736, + "area": 35565.017438, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "CONCLUSION" }, { - "id": 172834, - "strid": "0ef1b352-53cd-4a92-bba4-b06c4880cc48", - "image_id": 207247, - "image_name": "7182.png", + "id": 304, + "strid": "14d8ca63-4e5e-46bf-b6cc-a2ba7cf94395", + "image_id": 12, + "image_name": "10539.png", "category_id": 4, "category_name": "List", "bbox": [ - 2845.043, - 917.828, - 788.7710000000002, - 658.826 + 24.242, + 1021.638, + 794.822, + 62.23599999999999 ], - "priority": 23, + "priority": 19, "parents": [ - 172821 + 303 ], "children": [], - "area": 2611260.126604, + "area": 24766.548396000002, "iscrowd": 0, "segmentation": [] }, { - "id": 40957, - "strid": "bdc4745e-6a7b-4253-b3b5-af00feba3fe0", - "image_id": 202109, - "image_name": "118146.png", + "id": 305, + "strid": "690ce945-fb16-42b1-8168-32f3ebf1bc06", + "image_id": 13, + "image_name": "10595.png", "category_id": 9, "category_name": "Root", "bbox": [ - 3564.05, - 107.87, - 302.6999999999998, - 302.71 + 345.98, + 316.05, + 185.17999999999995, + 172.40999999999997 ], "priority": -1, "parents": [], "children": [ - 40938, - 40936, - 40948, - 40944, - 40937 + 314, + 307, + 328, + 306, + 322, + 310, + 332, + 308, + 312, + 325, + 319, + 330, + 316 ], - "area": 384454.07350000006, + "area": 109346.979, "iscrowd": 0, "segmentation": [] }, { - "id": 40936, - "strid": "bd808bf8-ae89-4501-a220-3284dcf048f9", - "image_id": 202109, - "image_name": "118146.png", + "id": 306, + "strid": "3d858ecd-0e88-499a-aeb5-f49eb5f7752a", + "image_id": 13, + "image_name": "10595.png", "category_id": 1, "category_name": "Title", "bbox": [ - 197.469, - 186.59, - 3290.727, - 288.42999999999995 + 715.473, + 97.569, + 2560.519, + 273.629 ], "priority": 1, "parents": [ - 40957 + 305 ], "children": [], - "area": 36845.74071, + "area": 69807.985137, "iscrowd": 0, "segmentation": [], - "text": "a\nACO EL\n=> = s €\nhe a= Y c rc JS\n—=— Yr 2 Te" + "text": "Evolutionary conservation of Ebola virus proteins\npredicts important functions at residue level" }, { - "id": 40937, - "strid": "c2dbfc8a-7726-4dfc-b626-aac40e79cfec", - "image_id": 202109, - "image_name": "118146.png", + "id": 307, + "strid": "284a891d-63a9-4036-af0a-0218228c686b", + "image_id": 13, + "image_name": "10595.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 232.43, - 625.179, - 3548.566, - 222.87800000000004 + 735.091, + 409.722, + 1844.0790000000002, + 167.17200000000003 ], "priority": 2, "parents": [ - 40957 + 305 ], "children": [], - "area": 145310.35497, + "area": 301182.954702, "iscrowd": 0, "segmentation": [], - "text": "i a ee ee —\nJianjun Wang*, Ji Shen1, Yucheng-Wu, Chen Tu,Janne Soininen, James C. Stegen, Jizheng He,.Xingqi Liu, Lu Zhang, Enlou Zhang\nState Key Laboratory of Lake Science and Environment Ze Institute of pS an ll EIS) eS ave eu) of Salley Tal Lal 210008 China\n*Contact: JJWang@niglas.ac.cn; COE Te" + "text": "A. Arslan* and V. van Noort\nCentre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S),\nKU Leuven, Kasteelpark Arenberg 22 —box 2460, 3001 Leuven, Belgium. *presenting author, ahmed.arslan@biw.kuleuven.be" }, { - "id": 40938, - "strid": "3c3f17bd-b770-4e5b-8007-ab736d9dcc58", - "image_id": 202109, - "image_name": "118146.png", + "id": 308, + "strid": "29167688-c788-4b67-8da1-ebcb97e9c6e7", + "image_id": 13, + "image_name": "10595.png", "category_id": 5, "category_name": "Section", "bbox": [ - 84.781, - 914.198, - 459.743, - 91.65300000000002 + 63.212, + 710.796, + 316.784, + 61.48299999999995 ], "priority": 3, "parents": [ - 40957 + 305 ], "children": [ - 40940, - 40941, - 40939 + 309 ], - "area": 77506.62063800001, + "area": 44930.836752, "iscrowd": 0, "segmentation": [], "text": "Background" }, { - "id": 40939, - "strid": "38893910-4e3d-42f1-9c42-d7634d315752", - "image_id": 202109, - "image_name": "118146.png", + "id": 309, + "strid": "c1cf3018-0a91-402d-aa8e-db04ffe0eeeb", + "image_id": 13, + "image_name": "10595.png", "category_id": 3, "category_name": "Text", "bbox": [ - 71.447, - 1051.689, - 2377.983, - 683.2259999999999 + 65.541, + 857.114, + 979.988, + 599.635 ], "priority": 4, "parents": [ - 40938 + 308 ], "children": [], - "area": 75140.023983, + "area": 56176.108674, "iscrowd": 0, "segmentation": [], - "text": "Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge ~\nof the processes that cause variation in microbial assemblage among ecosystems is lacking. For ’\ninstance, some studies showed that deterministic processes such as habitat specialization are\nimportant, while other studies hold that bacterial communities are assembled by stochastic forces.\n\nHere we examine the relative influence of deterministic and stochastic processes for bacterial\ncommunities from subsurface environments, stream biofilm, lake water, lake sediment and soil using\npyrosequencing of the 16S rRNA gene. We characterized patterns of spatial turnover in the\nphylogenetic composition of microbial communities, and inferred processes by comparing phylogenetic\nturnover to null model expectations based on the detection of phylogenetic signal in microbial habitat\nassociations." + "text": "Ebola Virus (EBOV), a member of Filoviridae family,\ncauses severe hemorrhagic fever known as Ebola Virus\nDisease (EVD) with a mortality rate of up to 90%.\n\nThe recent outbreak of EVD resulted in a large number of\nhuman deaths; moreover there is no suitable medicine\ncommercially available to date for EVD. Due to this dev-\nastation and lack of medication, EBOV has attracted re-\nnewed interest as model for virus evolution.\n\nRecent literature on EBOV has improved our under-\nstanding of the underlying genetics and its scope with ref-\nerence to the 2014 outbreak. But no study yet, has fo-\ncused on the conservation patterns of EBOV proteins\nthat can contribute to the virus fitness and onset of EVD." }, { - "id": 40940, - "strid": "48f7de22-2ac0-42a5-b93c-52a74094e49f", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 2, - "category_name": "Figure", + "id": 310, + "strid": "179c8cf3-ef7f-4b09-827a-7ecac02e57ca", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2413.493, - 862.041, - 918.8710000000001, - 655.6140000000001 + 77.118, + 1566.558, + 108.95999999999998, + 49.317999999999984 ], "priority": 5, "parents": [ - 40938 + 305 ], "children": [ - 40942 + 311 ], - "area": 2080529.919213, + "area": 120809.819844, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Aim" }, { - "id": 40942, - "strid": "098405b5-188b-4772-924b-5cf262089577", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 6, - "category_name": "Caption", + "id": 311, + "strid": "8d065f7e-8174-4a30-9be6-6345f710a077", + "image_id": 13, + "image_name": "10595.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2551.105, - 1718.867, - 928.674, - 42.89300000000003 + 59.573, + 1670.902, + 989.4130000000001, + 184.76 ], "priority": 6, "parents": [ - 40940 + 310 ], "children": [], - "area": 4385010.198035, + "area": 99540.64484600001, "iscrowd": 0, "segmentation": [], - "text": "Figure 1. The sampling locations from various habitats." + "text": "The aim is to understand the molecular biology of\nEVD by discovering most conserved regions of EBOV\nproteins and predicting their functional annotations\nwith computational tools." }, { - "id": 40941, - "strid": "58fb4267-85c1-412f-aa56-a65205c2e8b6", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 7, - "category_name": "Table", + "id": 312, + "strid": "2540df85-ff4a-4944-a65c-6f0c4948da42", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 3055.677, - 1362.592, - 874.0480000000002, - 337.2629999999999 + 39.288, + 1975.632, + 194.72899999999998, + 48.39499999999998 ], "priority": 7, "parents": [ - 40938 + 305 ], "children": [ - 40943 + 313 ], - "area": 4163641.0347840004, + "area": 77618.630016, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Results" }, { - "id": 40943, - "strid": "1b7bebe0-19b2-4b12-8ac6-669c276a503e", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 6, - "category_name": "Caption", + "id": 313, + "strid": "0423a96b-2663-4356-8988-3b402dec4102", + "image_id": 13, + "image_name": "10595.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2552.476, - 1767.96, - 1274.0729999999999, - 45.50299999999993 + 36.623, + 2080.201, + 1005.7249999999999, + 1257.257 ], "priority": 8, "parents": [ - 40941 + 312 ], "children": [], - "area": 4512675.46896, + "area": 76183.201223, "iscrowd": 0, - "segmentation": [], - "text": "Table 1. Brief description of the sample groups with different habitat types." + "segmentation": [] }, { - "id": 40944, - "strid": "2f71e461-dfce-4ec3-ad28-f117dc068eb6", - "image_id": 202109, - "image_name": "118146.png", + "id": 314, + "strid": "ce938ebb-5163-4fc1-9397-701be24abda7", + "image_id": 13, + "image_name": "10595.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1826.934, - 1792.878, - 281.9440000000002, - 81.85500000000002 + 65.438, + 3432.593, + 544.354, + 47.585000000000036 ], "priority": 9, "parents": [ - 40957 + 305 ], "children": [ - 40946, - 40953, - 40950, - 40947, - 40954 + 315 ], - "area": 3275469.776052, + "area": 224622.020734, "iscrowd": 0, "segmentation": [], - "text": "Results" + "text": "Material and Methods" }, { - "id": 40950, - "strid": "8efa5b5e-afb7-4dcb-956f-86e04b52f7c1", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 2, - "category_name": "Figure", + "id": 315, + "strid": "ff67f399-a39f-41dd-b422-23cf68a72355", + "image_id": 13, + "image_name": "10595.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 27.728, - 1831.749, - 1984.411, - 1074.197 + 64.564, + 3538.017, + 963.5770000000001, + 1069.9840000000004 ], "priority": 10, "parents": [ - 40944 + 314 ], - "children": [ - 40952, - 40951 - ], - "area": 50790.736272, + "children": [], + "area": 228428.52958799998, "iscrowd": 0, "segmentation": [] }, { - "id": 40951, - "strid": "dbed359b-cd8d-4f46-9ef2-2406f1412348", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 6, - "category_name": "Caption", + "id": 316, + "strid": "dd1e12da-02f8-4868-9f1d-d923aef01969", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 40.04, - 2915.647, - 957.073, - 368.47299999999996 + 1090.678, + 712.731, + 1014.2480000000003, + 59.053999999999974 ], "priority": 11, "parents": [ - 40950 + 305 ], - "children": [], - "area": 116742.50588, + "children": [ + 317 + ], + "area": 777360.0216180001, "iscrowd": 0, "segmentation": [], - "text": "Figure 1 Pearson correlation resulting from Mantel\ncorrelogram between the pairwise matrix of OTU niche\ndistances and phylogenetic distances (with Jukes-Cantor\nmodel) for each sample group with 9,999 permutations.\nSignificant correlations (P < 0.05, solid circles) indicate\nphylogenetic signal in species ecological niches, and were\nconsistently found across short phylogenetic distances for all\nsample groups." + "text": "PTMs present at GP conserved residues" }, { - "id": 40952, - "strid": "8b3b609e-bc5e-43eb-9cdc-e210d111d935", - "image_id": 202109, - "image_name": "118146.png", + "id": 317, + "strid": "db6e8146-398e-4c81-81fc-1c269f818487", + "image_id": 13, + "image_name": "10595.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 1126.254, + 805.959, + 987.0299999999997, + 560.6240000000001 + ], + "priority": 12, + "parents": [ + 316 + ], + "children": [ + 318 + ], + "area": 907714.5475859998, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 318, + "strid": "a260c563-3c03-46bb-9953-540cb46e3732", + "image_id": 13, + "image_name": "10595.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1037.048, - 2915.963, - 1104.869, - 413.94299999999976 + 1092.412, + 1413.085, + 1042.331, + 88.64100000000008 ], - "priority": 12, + "priority": 13, "parents": [ - 40950 + 317 ], "children": [], - "area": 3023993.5972240004, + "area": 1543671.01102, "iscrowd": 0, "segmentation": [], - "text": "Figure 3. The relationships between unweighted Unifrac and spatial\nchange for different sample groups. (A-D) Lake surface sediments; (E,\nF) lake subsurface sediments; (G) soils; (H) stream biofilm and (I) Lake\nwater. The regression slopes of the linear relationships based on\nGaussian generalized model are shown with solid (statistically\nsignificant, ranked Mantel test, 9,999 permutations, P< 0.05) or J\ndashed (statistically non-significant, P > 0.05) lines. The significant\nslope (unweighted Unifrac per 10? km) is shown at the corner of each\nsample group panel." + "text": "Figure: The ConSurf diagram (Celinker et al 2013) of GP protein two types of structural views\n(left: space-filled; right: ribbon) with different PTMs sites at cons. residues. (Abbreviation: P=-\nphosphorylation, GPI=GPl-anchor, O=o-linked glycosylation, M=Methylation)" }, { - "id": 40953, - "strid": "cdf5201c-40f8-4282-b8cd-419d76789bfa", - "image_id": 202109, - "image_name": "118146.png", + "id": 319, + "strid": "07ccb1df-3aee-4a11-beb2-943acd2615b9", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 2166.43, + 711.767, + 1127.0170000000003, + 60.650999999999954 + ], + "priority": 14, + "parents": [ + 305 + ], + "children": [ + 320 + ], + "area": 1541993.38181, + "iscrowd": 0, + "segmentation": [], + "text": "PTMs present at conserved interface residue" + }, + { + "id": 320, + "strid": "5922aa3f-e848-4167-abef-256715348163", + "image_id": 13, + "image_name": "10595.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 15.831, - 3367.098, - 1153.268, - 774.6610000000001 + 2264.972, + 784.971, + 886.0210000000002, + 571.5630000000001 ], - "priority": 13, + "priority": 15, "parents": [ - 40944 + 319 ], "children": [ - 40956 + 321 ], - "area": 53304.528438, + "area": 1777937.335812, "iscrowd": 0, "segmentation": [] }, { - "id": 40956, - "strid": "6debec17-783a-4eea-9b5e-7b76fd0a108e", - "image_id": 202109, - "image_name": "118146.png", + "id": 321, + "strid": "0eca03be-e154-4cf0-8a3e-9f94e8b71eb8", + "image_id": 13, + "image_name": "10595.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 19.212, - 4225.948, - 1059.414, - 188.6790000000001 + 2250.769, + 1408.234, + 963.748, + 59.013999999999896 ], - "priority": 14, + "priority": 16, "parents": [ - 40953 + 320 ], "children": [], - "area": 81188.912976, + "area": 3169609.4319459996, "iscrowd": 0, "segmentation": [], - "text": "Figure 2. Non-metric multidimensional scaling plots (A and C), or\nboxplots (B and D) of community dissimilarities within habitat\ngroups using unweighted Unifrac and betaMNTD, respectively. The\nsamples are colored by habitat groups." + "text": "Figure: The PTMs position at interface of two complexes between virus molecules, (A)\nVP35 and RNA (B) NP and VP35; whereas PTM positions are shown in red." }, { - "id": 40954, - "strid": "eebb1c80-04bd-42a5-8e7a-bebc0a089e1a", - "image_id": 202109, - "image_name": "118146.png", + "id": 322, + "strid": "c7e51a64-217f-4a45-a7da-3bbf66fb9911", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 1139.121, + 1570.698, + 730.394, + 60.03099999999995 + ], + "priority": 17, + "parents": [ + 305 + ], + "children": [ + 323 + ], + "area": 1789215.0764580003, + "iscrowd": 0, + "segmentation": [], + "text": "EBOV proteins Conservation" + }, + { + "id": 323, + "strid": "2cb6228c-c295-4548-b3ec-a80ffbf279d4", + "image_id": 13, + "image_name": "10595.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1209.873, - 3361.148, - 861.038, - 846.1109999999999 + 1243.699, + 1695.806, + 1775.7649999999999, + 1150.6690000000003 ], - "priority": 15, + "priority": 18, "parents": [ - 40944 + 322 ], "children": [ - 40955 + 324 ], - "area": 4066562.2142040003, + "area": 2109072.226394, "iscrowd": 0, "segmentation": [] }, { - "id": 40955, - "strid": "9c221c8e-3589-4f73-b45a-b85513325e96", - "image_id": 202109, - "image_name": "118146.png", + "id": 324, + "strid": "208e894b-61de-449b-8fcf-90284d313a6a", + "image_id": 13, + "image_name": "10595.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1115.951, - 4223.788, - 996.6889999999999, - 191.89999999999964 + 1137.13, + 2921.008, + 1882.625, + 29.73700000000008 ], - "priority": 16, + "priority": 19, "parents": [ - 40954 + 323 ], "children": [], - "area": 4713540.442388, + "area": 3321565.82704, "iscrowd": 0, "segmentation": [], - "text": "Figure 4. Non-metric multidimensional scaling plots (A & C), or\nboxplots (B & D) of community dissimilarities within habitat\ngroups using unweighted Unifrac and betaMNTD, respectively.\nThe samples are colored by habitat groups." + "text": "Figure: The ConSurf diagrams of EBOV proteins shows conserved residues in respective secondary structures. (red is the most conserved one and blue is most variable)" }, { - "id": 40946, - "strid": "05cee974-ffe8-40ed-8520-18f3fefa52b6", - "image_id": 202109, - "image_name": "118146.png", - "category_id": 7, - "category_name": "Table", + "id": 325, + "strid": "ac4059e0-9c04-447d-b21e-527caa820e24", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2188.777, - 2093.931, - 1692.179, - 674.7089999999998 + 1104.717, + 3035.746, + 765.117, + 51.733000000000175 ], - "priority": 17, + "priority": 20, "parents": [ - 40944 + 305 ], "children": [ - 40945 + 326 ], - "area": 4583148.012387, + "area": 3353640.213882, + "iscrowd": 0, + "segmentation": [], + "text": "ATM “Junction Kinase’”in EVD" + }, + { + "id": 326, + "strid": "a112c5c2-cc20-4713-98ca-64d282da80dd", + "image_id": 13, + "image_name": "10595.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 1094.968, + 3202.571, + 1094.6379999999997, + 665.7049999999999 + ], + "priority": 21, + "parents": [ + 325 + ], + "children": [ + 327 + ], + "area": 3506712.762728, "iscrowd": 0, "segmentation": [] }, { - "id": 40945, - "strid": "bf79be8e-0578-4691-96da-119a957884d8", - "image_id": 202109, - "image_name": "118146.png", + "id": 327, + "strid": "ca2e02d6-81c8-4794-a1ef-98deead76405", + "image_id": 13, + "image_name": "10595.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 2178.012, - 1891.36, - 1700.5750000000003, - 161.41099999999983 + 1109.784, + 3921.323, + 1030.424, + 118.61799999999994 ], - "priority": 18, + "priority": 22, "parents": [ - 40946 + 326 ], "children": [], - "area": 4119404.77632, + "area": 4351821.524232, "iscrowd": 0, "segmentation": [], - "text": "Table 1 Mantel and partial Mantel tests for the correlation between ses.betaMNTD and the\nexplanatory distances (elevational, geographic and environmental distance) using Spearman’s\nrho for different habitat types and spatial scales." + "text": "Figure: The role of ATM kinase in different EVD related pathways. The functions of DNA\ndamage response element, ATM, elucidated in four closely related and virus exploited path-\nways under stress.The blue arrows show the published interactions, black arrows normal cell\nsignaling and green shows the predicted phosphorylation on VP40 by ATM in out analysis." }, { - "id": 40947, - "strid": "f78a7863-dd08-4135-8126-a904b568ae48", - "image_id": 202109, - "image_name": "118146.png", + "id": 328, + "strid": "f0f89f94-2747-448e-9d0d-a7aa33a81852", + "image_id": 13, + "image_name": "10595.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 2240.21, + 3039.606, + 293.2159999999999, + 49.23100000000022 + ], + "priority": 23, + "parents": [ + 305 + ], + "children": [ + 329 + ], + "area": 6809355.75726, + "iscrowd": 0, + "segmentation": [], + "text": "Conclusion" + }, + { + "id": 329, + "strid": "9e94f303-6d8c-44dd-a58e-5a96dd9378f5", + "image_id": 13, + "image_name": "10595.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2201.149, - 2804.498, - 1645.5989999999997, - 169.76200000000017 + 2241.186, + 3143.959, + 960.1300000000001, + 185.13799999999992 ], - "priority": 19, + "priority": 24, "parents": [ - 40944 + 328 ], "children": [], - "area": 6173117.968202, + "area": 7046196.895374, "iscrowd": 0, "segmentation": [], - "text": "The significances are tested based on 10,000 permutations. °** P < 0.001; ** P < 0.01; * P< 0.05. For the HX\ngroup, both the geographic and environmental distances were not significantly related to bacterial phylogenetic\n\nturnover (P > 0.05). For ZJ and NJ groups, the Mantel analyses are not conducted due to their lower sample\nnumbers (7 and 5, respectively)." + "text": "Based on our results and current understanding of EVD\ndependent activated pathways, an association is\n\nanticipated of ATM kinase with these pathways and\nkinases through which Ebola pathology is achieved." }, { - "id": 40948, - "strid": "175d38da-dcf9-47c6-9011-7c4a29ef921a", - "image_id": 202109, - "image_name": "118146.png", + "id": 330, + "strid": "f27a602a-6217-44bf-93b1-ce397e2ea106", + "image_id": 13, + "image_name": "10595.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2812.593, - 3001.095, - 455.797, - 72.42300000000023 + 2238.766, + 3432.566, + 450.38099999999986, + 53.934999999999945 ], - "priority": 20, + "priority": 25, "parents": [ - 40957 + 305 ], "children": [ - 40949 + 331 ], - "area": 8440858.789335, + "area": 7684712.053556, "iscrowd": 0, "segmentation": [], - "text": "Conclusions" + "text": "Acknowledgements" }, { - "id": 40949, - "strid": "a8d3b0df-e515-40c1-a39a-d944cdb4f06a", - "image_id": 202109, - "image_name": "118146.png", + "id": 331, + "strid": "cc19bc7a-06e0-4e12-b5d0-9af6f8de0e8e", + "image_id": 13, + "image_name": "10595.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 2240.484, + 3525.099, + 941.634, + 116.46399999999994 + ], + "priority": 26, + "parents": [ + 330 + ], + "children": [], + "area": 7897927.907916, + "iscrowd": 0, + "segmentation": [], + "text": "| would like to thank to the people at Harvard and MIT, who pro-\nvided the genomic sequences of EBOV. Also, | would like to\nthanks CMPG/CSB group for their guidance and support." + }, + { + "id": 332, + "strid": "5b340f6c-8f3d-4c4f-beec-1672c220acca", + "image_id": 13, + "image_name": "10595.png", "category_id": 4, "category_name": "List", "bbox": [ - 2124.399, - 3116.194, - 1754.995, - 1285.4569999999999 + 2242.398, + 3801.605, + 542.857, + 268.14699999999993 ], - "priority": 21, + "priority": 27, "parents": [ - 40948 + 305 ], "children": [], - "area": 6620039.417405999, + "area": 8524711.44879, "iscrowd": 0, "segmentation": [] }, { - "id": 89437, - "strid": "2f957cb9-b5b1-4a97-a8a9-89fafd5438f0", - "image_id": 203972, - "image_name": "121247.png", + "id": 333, + "strid": "aa1e22b0-c59d-4d6a-8b43-db8ac23ef499", + "image_id": 14, + "image_name": "10631.png", "category_id": 9, "category_name": "Root", "bbox": [ - 25.27, - 37.72, - 103.48, - 147.84 + 33.12, + 34.15, + 122.24000000000001, + 130.4 ], "priority": -1, "parents": [], "children": [ - 89410, - 89408, - 89426, - 89415, - 89409, - 89411, - 89434, - 89431, - 89435 + 335, + 336, + 338, + 371, + 342, + 334, + 369, + 364, + 373 ], - "area": 953.1844, + "area": 1131.0479999999998, "iscrowd": 0, "segmentation": [] }, { - "id": 89408, - "strid": "b3e8418b-6188-40b8-a4ea-9dc120f85cb2", - "image_id": 203972, - "image_name": "121247.png", + "id": 334, + "strid": "077d64a4-e311-4cee-95b3-3f02a1c88545", + "image_id": 14, + "image_name": "10631.png", "category_id": 1, "category_name": "Title", "bbox": [ - 164.987, - 35.536, - 2392.408, - 180.581 + 204.649, + 159.346, + 2934.202, + 308.913 ], "priority": 1, "parents": [ - 89437 + 333 ], "children": [], - "area": 5862.978032, + "area": 32609.999554, "iscrowd": 0, "segmentation": [], - "text": "Interactome-regulome-transcriptome integrative approach:\na mean to disclose cancer stem cells regulatory circuits" + "text": "Comparison of Mortality in Fizi Health Zone,\nDemocratic Republic of Congo, 2014 and 2016" }, { - "id": 89409, - "strid": "42598880-6247-4fe5-abc0-f906ab1db102", - "image_id": 203972, - "image_name": "121247.png", + "id": 335, + "strid": "5c540e1a-f934-4a65-b6a0-b6cf86911794", + "image_id": 14, + "image_name": "10631.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 75.198, - 245.72, - 2606.576, - 152.816 + 640.418, + 540.447, + 2007.315, + 364.68500000000006 ], "priority": 2, "parents": [ - 89437 + 333 ], "children": [], - "area": 18477.65256, + "area": 346111.986846, "iscrowd": 0, "segmentation": [], - "text": "ie >A Tol 0T-] (=) a bane R El-Helou??:4, Q Da Costa!?:?4, E Charafe-Jauffret?:?:37, Centre de Recherche en Cancérologie de Marseille\nC Ginestier?*34 and G Bidaut 1234 a eee\nRey or letoil maak\n\ncontact: claire.rioualen@inserm.fr www.iti.sourceforge.net Pea erseiet ato Orda eracc" + "text": "Yalda Jafari', Colette Badjo', Marit de Wit?, Harriet Roggeveen?,\nIdriss Ait-Bouziad*, Bhargavi Rao?, Ruby Siddiqui®\n\n'MSF, Bukavu, Democratic Republic of Congo; 7MSF, Amsterdam,\nNetherlands; 3MSF, London, UK" }, { - "id": 89410, - "strid": "bd18aef6-fa3b-4767-9e9e-98b7f06ae900", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 336, + "strid": "8b2835bf-fd42-462e-8c1c-12d3dd5e74a4", + "image_id": 14, + "image_name": "10631.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 115.912, - 466.936, - 1264.458, - 152.57200000000006 + 92.256, + 1112.49, + 108.15099999999998, + 48.94699999999989 ], "priority": 3, "parents": [ - 89437 + 333 ], - "children": [], - "area": 54123.485632, + "children": [ + 337 + ], + "area": 102633.87744, "iscrowd": 0, "segmentation": [], - "text": "Breast cancer is the deadliest cancer in women worldwide’. One rising\nhypothesis is»that» cancer stem cells (CSC) could ‘explain relapses, by\nresisting to ‘conventional “treatments and/being able to generate\nmetastases thanks to self-renewal and differentiation properties’." + "text": "Aim" }, { - "id": 89435, - "strid": "55ea631d-b9f3-43af-9254-6d171ed99425", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 337, + "strid": "f1ba018b-eb7b-4a16-9beb-ebda74cad7c7", + "image_id": 14, + "image_name": "10631.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1490.239, - 463.113, - 1190.618, - 156.06400000000002 + 94.855, + 1243.654, + 676.9, + 267.9390000000001 ], "priority": 4, "parents": [ - 89437 + 336 ], "children": [], - "area": 690149.054007, + "area": 117966.80017, "iscrowd": 0, - "segmentation": [], - "text": "An miRNA screening revealed miR-600 could be a potential regulator of\nCSCs. We decided to,nvestigate the effect of miR-600 knock up and kock\ndown on CSCs, and>to»incorporate a network-based approach in order\nto identify key signaling pathways." + "segmentation": [] }, { - "id": 89411, - "strid": "0892b792-8d93-4f2a-af99-437213b2bbd0", - "image_id": 203972, - "image_name": "121247.png", + "id": 338, + "strid": "577ccd93-df1d-4dc8-b875-7cb0cdbbf9ff", + "image_id": 14, + "image_name": "10631.png", "category_id": 5, "category_name": "Section", "bbox": [ - 32.569, - 655.021, - 531.121, - 83.70299999999997 + 90.629, + 1664.827, + 196.99399999999997, + 50.298 ], "priority": 5, "parents": [ - 89437 + 333 ], "children": [ - 89418, - 89412, - 89416, - 89419, - 89417, - 89413, - 89414, - 89436 + 340, + 339 ], - "area": 21333.378949, + "area": 150881.606183, "iscrowd": 0, "segmentation": [], - "text": "Input ‘data" + "text": "" }, { - "id": 89436, - "strid": "5f81f402-f400-449a-bbf8-a1d290af6e5e", - "image_id": 203972, - "image_name": "121247.png", + "id": 339, + "strid": "8e05c98f-41b2-47e3-80ad-9bd8241318ac", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 74.506, - 805.153, - 324.125, - 42.04399999999998 + 87.446, + 1781.909, + 713.367, + 1138.2440000000001 ], "priority": 6, "parents": [ - 89411 + 338 ], "children": [], - "area": 59988.729418, + "area": 155820.814414, "iscrowd": 0, "segmentation": [], - "text": "Networks building" + "text": "In 2014, a mortality survey was\nperformed in Fizi HZ to estimate\nmortality rates during the recall period\nDecember 2013 to May 2014\".\n\nIn 2016, two retrospective mortality\nsurveys were carried out in Fizi HZ, one\nin Presque’lle and the other in the rest of\nFizi, with a recall period of one year.\n\nThe 2016 mortality surveys were\ncombined and the recall period restricted\nto the same time period utilised in the\n2014 mortality survey, in order to be\ncomparable.\n\nReasons that may have contributed to\nchanges in outcomes were explored.\n\nAnalysis was completed using STATA\n14.2 (StataCorp, TX, USA, 2017) and\nresults are presented with 95%\nconfidence intervals." }, { - "id": 89412, - "strid": "d156d2db-7f30-4833-87d0-b6a940569eff", - "image_id": 203972, - "image_name": "121247.png", + "id": 340, + "strid": "ce79f9fa-a8ee-461c-a0e0-eca62ad4297c", + "image_id": 14, + "image_name": "10631.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 117.543, - 859.092, - 577.087, - 516.87 + 74.707, + 3007.562, + 742.042, + 1047.2110000000002 ], "priority": 7, "parents": [ - 89411 + 338 ], - "children": [], - "area": 100980.250956, + "children": [ + 341 + ], + "area": 224685.93433399996, "iscrowd": 0, "segmentation": [] }, { - "id": 89413, - "strid": "b00baac4-4a0b-46a4-b98a-97a5ebca7062", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 2, - "category_name": "Figure", + "id": 341, + "strid": "976c7c42-66da-42ba-b7b0-7d7870597768", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 815.066, - 855.747, - 562.0330000000001, - 516.87 + 74.416, + 4080.036, + 709.3330000000001, + 64.29899999999998 ], "priority": 8, "parents": [ - 89411 + 340 ], "children": [], - "area": 697490.284302, + "area": 303619.95897599997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig 1-Map of Fizi Health Zone, iCCM and PSH posts, and\nsurvey areas" }, { - "id": 89414, - "strid": "55a97f66-67c7-47e6-b9dc-72719d9d394c", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 342, + "strid": "0f7a5fc7-4aa7-43f5-9adb-8c928f3cf6d0", + "image_id": 14, + "image_name": "10631.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 113.002, - 1388.388, - 1265.291, - 97.97299999999996 + 927.433, + 1113.94, + 199.48299999999995, + 47.97499999999991 ], "priority": 9, "parents": [ - 89411 + 333 ], - "children": [], - "area": 156890.620776, + "children": [ + 351, + 361, + 344, + 355, + 346, + 347, + 358, + 353, + 356, + 343, + 349, + 362, + 360 + ], + "area": 1033104.71602, "iscrowd": 0, "segmentation": [], - "text": "Public databases were parsed, and two bignetworks were built: the interactome, made of\nprotein-protein interactions, andthe regulome, made of TFAarget relationships. Above are\nsubsets of these networks. &" + "text": "" }, { - "id": 89417, - "strid": "48539a14-b021-4e65-9164-05aa3fc60fd6", - "image_id": 203972, - "image_name": "121247.png", + "id": 343, + "strid": "443fc0bb-f14e-46cd-ac0e-8a824495d0ea", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1454.851, - 804.862, - 1011.0070000000001, - 220.0970000000001 + 926.847, + 1177.545, + 185.31799999999998, + 45.48900000000003 ], "priority": 10, "parents": [ - 89411 + 342 ], "children": [], - "area": 1170954.285562, + "area": 1091404.050615, "iscrowd": 0, "segmentation": [], - "text": "Transcriptome data\n\nAfter a genome-wide miRNA screening, miR-600 was identified as a\npotential \"switcher\" for CSCs: its activation by MIMIC and its\ninhibition by LNA could have a mirror effect on CSC» pathways, by\nfavoring their differentiation and preventing their self-renewal at the\nsame time." + "text": "Mortality:" }, { - "id": 89418, - "strid": "aa54ee17-d18a-4a33-97a7-4bc587a11068", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 2, - "category_name": "Figure", + "id": 344, + "strid": "db292781-1f77-48a2-9c25-2316943d7a41", + "image_id": 14, + "image_name": "10631.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2488.484, - 791.492, - 210.8409999999999, - 271.52199999999993 + 930.4, + 1273.307, + 776.6819999999999, + 188.19299999999998 ], "priority": 11, "parents": [ - 89411 + 342 ], - "children": [], - "area": 1969615.1781279999, + "children": [ + 345 + ], + "area": 1184684.8328, "iscrowd": 0, "segmentation": [] }, { - "id": 89416, - "strid": "1e1b3208-214b-49ee-b0eb-72497ad8c167", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 345, + "strid": "f5aac883-dfd5-4c7b-976a-ca0c8c06d151", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1493.933, - 1035.244, - 1014.0920000000001, - 64.79500000000007 + 936.005, + 1467.265, + 262.65199999999993, + 30.304000000000087 ], "priority": 12, "parents": [ - 89411 + 344 ], "children": [], - "area": 1546585.174652, + "area": 1373367.376325, "iscrowd": 0, "segmentation": [], - "text": "Transcriptome data was generated by measuring. gene expression in\nmiR-600 overexpression and knock-down, by adding either LNA or MIMIC." + "text": "Table 1-Demographics" }, { - "id": 89419, - "strid": "ae4e4404-9b56-446b-9033-32128227a77c", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 2, - "category_name": "Figure", + "id": 346, + "strid": "a2769b0c-cabc-4d14-93aa-f86cbe0ed77e", + "image_id": 14, + "image_name": "10631.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1538.158, - 1126.972, - 1085.241, - 351.5519999999999 + 1768.908, + 1294.022, + 585.2040000000002, + 157.75900000000001 ], "priority": 13, "parents": [ - 89411 + 342 ], "children": [], - "area": 1733460.997576, + "area": 2289005.8679759996, "iscrowd": 0, "segmentation": [] }, { - "id": 89415, - "strid": "bc202445-fec2-475b-982e-261abca2e53a", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 5, - "category_name": "Section", + "id": 347, + "strid": "9f2badf6-315f-4229-abc9-3f6f3a698e8f", + "image_id": 14, + "image_name": "10631.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 31.06, - 1549.593, - 1962.544, - 94.82500000000005 + 913.837, + 1566.152, + 734.598, + 486.05999999999995 ], "priority": 14, "parents": [ - 89437 + 342 ], "children": [ - 89422, - 89424, - 89428, - 89423, - 89429, - 89421, - 89425, - 89427, - 89420 + 348 ], - "area": 48130.35858, + "area": 1431207.645224, "iscrowd": 0, - "segmentation": [], - "text": "Data -tntegration & Networks analysis" + "segmentation": [] }, { - "id": 89420, - "strid": "d60a26f3-90e8-42ea-aa54-94a7925c4ca0", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 348, + "strid": "0e7833b9-2962-4d86-9e35-8700f6d9199b", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 75.781, - 1710.741, - 1306.244, - 465.98799999999983 + 927.222, + 2059.43, + 516.0420000000001, + 30.972999999999956 ], "priority": 15, "parents": [ - 89415 + 347 ], "children": [], - "area": 129641.663721, + "area": 1909548.8034599999, "iscrowd": 0, "segmentation": [], - "text": "Subnetworks detection algorithm\n\nA subnetwork is recursively*aggregated around a \"seed\", a gene from the\nnetwork, by using the I?Palgorithm*®. Its score is calculated by averaging\ncorrelations between .genes expressions (LNA vs control, MIMIC vs\ncontrol).\n\nNeighbouring nodes,are added if they improve the score of the subnetwork.\nThis procedure isepeated for each gene of the two networks (interactome and\nregulome).\n\nResulting (‘subnetworks are _ statistically validated by/ randomizing\ninteraction\\data, expression data and subnetworks interactions.\n\nThe procedure is repeated separately in the interactome andthe regulome." + "text": "Figure 2-Crude and under five mortality rates" }, { - "id": 89421, - "strid": "26350161-bf49-4401-9779-be679d5a5a89", - "image_id": 203972, - "image_name": "121247.png", + "id": 349, + "strid": "9e684b1d-2382-449a-8fe4-2b327ead7d30", + "image_id": 14, + "image_name": "10631.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 145.175, - 2208.456, - 1186.013, - 301.73099999999977 + 1672.524, + 1566.462, + 734.0129999999999, + 486.56399999999985 ], "priority": 16, "parents": [ - 89415 + 342 ], - "children": [], - "area": 320612.5998, + "children": [ + 350 + ], + "area": 2619945.290088, "iscrowd": 0, "segmentation": [] }, { - "id": 89423, - "strid": "aece182b-b9cf-4a8a-9f6d-40909c6b457f", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 350, + "strid": "adc4fe32-cdf5-4de8-adcf-e89a8da3e94d", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1450.685, - 1709.553, - 1229.3309999999997, - 268.8689999999999 + 1681.513, + 2060.022, + 342.6590000000001, + 29.134000000000015 ], "priority": 17, "parents": [ - 89415 + 349 ], "children": [], - "area": 2480022.893805, + "area": 3463953.773286, "iscrowd": 0, "segmentation": [], - "text": "Switchers identification\n\n42 subetworks are found ine the 4 different conditions (LNA-\ninteractome, LNA-regulome, MIMIC-interactome;MIMIC-regulome).\n\n35 genes were found to act like switchers in the subnetworks (double\necircles): they were both being strongly over-expressed in MIMIC and\nunder-expressed in LNA, confirming:the-biological experiments." + "text": "Figure 3-Mortality rate by sex" }, { - "id": 89422, - "strid": "9779a2a4-796b-4bad-b246-7626ad937560", - "image_id": 203972, - "image_name": "121247.png", + "id": 351, + "strid": "ca39c860-24df-4bad-9de5-007a5a17988b", + "image_id": 14, + "image_name": "10631.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1498.484, - 2009.791, - 1177.0499999999997, - 439.153 + 915.51, + 2127.031, + 732.511, + 484.24299999999994 ], "priority": 18, "parents": [ - 89415 + 342 ], - "children": [], - "area": 3011639.656844, + "children": [ + 352 + ], + "area": 1947318.15081, "iscrowd": 0, "segmentation": [] }, { - "id": 89428, - "strid": "49720abc-025e-4f92-8d18-afa3485db9ec", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 352, + "strid": "88fd0b1e-5fc2-4142-a500-dcb61add2a32", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 76.525, - 2623.069, - 682.568, - 533.8980000000001 + 926.598, + 2618.292, + 483.615, + 30.213000000000193 ], "priority": 19, "parents": [ - 89415 + 351 ], "children": [], - "area": 200730.355225, + "area": 2426104.130616, "iscrowd": 0, "segmentation": [], - "text": "Subnetworks integration\n\nIn order to visualize pathways of\nregulation that involve several levels\nof regulation, . we “integrated the\ninteractome subnetworks (groups of\ninteracting proteins) with regulome\nsubnetworks (transcription factors and\ntargets):\n\nMost subnetworks interact with each\nother»showing a possible implication in\ncommon pathways regulating cancer\nstem cells." + "text": "Figure 4 — Main cause of death in all ages" }, { - "id": 89429, - "strid": "4792ac1a-8ee8-4419-8e5b-06bd0e921d3b", - "image_id": 203972, - "image_name": "121247.png", + "id": 353, + "strid": "95b5dc6c-0f3b-448a-8f09-752317fa0a08", + "image_id": 14, + "image_name": "10631.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 793.49, - 2699.002, - 587.1290000000001, - 451.6880000000001 + 1673.193, + 2126.062, + 732.905, + 483.74699999999984 ], "priority": 20, "parents": [ - 89415 + 342 ], - "children": [], - "area": 2141631.09698, + "children": [ + 354 + ], + "area": 3557312.0559659996, "iscrowd": 0, "segmentation": [] }, { - "id": 89427, - "strid": "b7bda5a3-abb6-4704-b1e1-d8634f9dddbf", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 354, + "strid": "cf7cd4f0-4ead-4717-aaa4-dda8366499f6", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 112.313, - 3183.854, - 1269.661, - 159.82799999999997 + 1681.445, + 2618.85, + 705.5380000000002, + 30.126999999999953 ], "priority": 21, "parents": [ - 89415 + 353 ], "children": [], - "area": 357588.194302, + "area": 4403452.2382499995, "iscrowd": 0, "segmentation": [], - "text": "The integration sheds light on potential pathways that are connecting\nswitching genes, thus regulating CSC «differentiation and proliferation. It\ncould also enable the discovery of new*switchers, whose expression is only\nslightly affected by miR-600 overexpression or knock-down." - }, - { - "id": 89424, - "strid": "f1e7c829-7dbb-4ab1-80f9-3b37fe082e32", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1498.484, - 2634.165, - 1159.1259999999997, - 492.92700000000013 - ], - "priority": 22, - "parents": [ - 89415 - ], - "children": [], - "area": 3947254.1058599995, - "iscrowd": 0, - "segmentation": [] + "text": "Figure 5 - Main cause of death in all children under five years" }, { - "id": 89425, - "strid": "b3ce30c3-d97c-44b8-9102-39405f207b15", - "image_id": 203972, - "image_name": "121247.png", + "id": 355, + "strid": "2c4ce3f1-fb68-46f8-b706-17f48556c3cb", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1492.509, - 3183.854, - 1187.5060000000003, - 161.32200000000012 + 953.103, + 2749.752, + 411.611, + 435.34400000000005 ], - "priority": 23, + "priority": 22, "parents": [ - 89415 + 342 ], "children": [], - "area": 4751930.749686, + "area": 2620796.8804559996, "iscrowd": 0, "segmentation": [], - "text": "Targeting a\\pathway, rather than several genes separately, could™prove to\nbe more efficient and less money-consuming.\n\nA GenesOntology enrichment search revealed the presence\\of several\nterms-related to cell proliferation." + "text": "Violence\n\nIn 2016, 4.6% (95% Cl: 4.0,\n5.2) had experienced an\nepisode of violence during\nthe recall period, compared\nto 3.0% (95% Cl: 2.3-3.8) in\n2014\". In both years, the\nleading nature of violence\nexperienced was being\n\nbeaten." }, { - "id": 89426, - "strid": "5d8d8eae-839e-4056-8358-805d2098d831", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 5, - "category_name": "Section", + "id": 356, + "strid": "32dd6028-2223-40f6-92e7-8d125544ce90", + "image_id": 14, + "image_name": "10631.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 36.134, - 3407.912, - 1672.965, - 82.154 + 1487.901, + 2708.989, + 924.1800000000001, + 536.3009999999999 ], - "priority": 24, + "priority": 23, "parents": [ - 89437 + 342 ], "children": [ - 89430, - 89432, - 89433 + 357 ], - "area": 123141.492208, + "area": 4030707.4420890003, "iscrowd": 0, - "segmentation": [], - "text": "Online database of subnetworks" + "segmentation": [] }, { - "id": 89430, - "strid": "33723ade-2365-4ec7-b5a1-d25ad4f6de42", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 3, - "category_name": "Text", + "id": 357, + "strid": "8e871ced-c6e4-4998-b056-83b32299902f", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 109.693, - 3565.698, - 1082.219, - 471.462 + 1492.656, + 3247.689, + 455.807, + 29.96199999999999 ], - "priority": 25, + "priority": 24, "parents": [ - 89426 + 356 ], "children": [], - "area": 391132.11071399995, + "area": 4847682.471984, "iscrowd": 0, "segmentation": [], - "text": "Our pipeline includes the possibility of generating full HTML\nreports.\n\nDetected subnetworks are stored and can be investigated gene by.\ngene (a). .This_visualization also includes all the information on\nGene Ontology terms enriched in the subnetworks (b).. Each\nsubnetwork has its own page, compiling all the related information\n(c).\n\nAll the data can be downloaded from the site in flat format, and\nsubnetwork files are formatted in *.nnf format, thus.enabling their\nanalysis in Cytoscape." + "text": "Figure 6-Nature of violence experienced" }, { - "id": 89432, - "strid": "1828ec01-0897-4a53-a125-9f827697ab66", - "image_id": 203972, - "image_name": "121247.png", + "id": 358, + "strid": "8bb6836f-161d-4bab-b46c-f663a396a304", + "image_id": 14, + "image_name": "10631.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1227.701, - 3571.405, - 826.5360000000001, - 571.4169999999999 + 920.348, + 3306.512, + 899.79, + 504.6419999999998 ], - "priority": 26, + "priority": 25, "parents": [ - 89426 + 342 ], - "children": [], - "area": 4384617.489905001, + "children": [ + 359 + ], + "area": 3043141.706176, "iscrowd": 0, "segmentation": [] }, { - "id": 89433, - "strid": "1e12f6cf-889b-457b-9312-02d2058677db", - "image_id": 203972, - "image_name": "121247.png", - "category_id": 2, - "category_name": "Figure", + "id": 359, + "strid": "8426511a-bfb8-4ebc-8f26-5e8263d1d5ac", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2103.7, - 3495.91, - 609.1639999999998, - 648.2129999999997 + 919.203, + 3814.597, + 869.3490000000002, + 30.646000000000186 ], - "priority": 27, + "priority": 26, "parents": [ - 89426 + 358 ], "children": [], - "area": 7354345.866999999, + "area": 3506389.006191, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 7-Main symptoms in those ill in the previous two weeks, under 5 years" }, { - "id": 89431, - "strid": "5b100668-ace3-4666-b88f-fef60418c9d6", - "image_id": 203972, - "image_name": "121247.png", + "id": 360, + "strid": "0146b909-52fb-4fd0-8e2f-0f361a15389e", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 111.224, - 4102.981, - 1268.966, - 385.741 + 1862.213, + 3393.256, + 510.49599999999987, + 305.80700000000024 ], - "priority": 28, + "priority": 27, "parents": [ - 89437 + 342 ], "children": [], - "area": 456349.958744, + "area": 6318965.435528, "iscrowd": 0, "segmentation": [], - "text": "We developed a new multi-level integrative approach mixing interactome,\nregulome, transcriptome data and\\,post-translational information with a\ncandidate approach.\n\nThe integrative analysis confirmed\\the potential implication of miR-600 in CSC\ndifferentiation or self-renewal>Using a pathway approach to explore the\nbiology of cancer stem cells is‘a good way to develop new targets in breast\ncancer treatment.\n\nUltimately, elaborating a new drug targeting CSCs could greatly improve\nbreast cancer clinical outcome." + "text": "Morbidity\n\nIn both 2014\" and 2016\nFever/Malaria, Diarrhoea, and\nRespiratory symptoms were the\nleading causes of morbidity in\nchildren aged less than five years." }, { - "id": 89434, - "strid": "c22a33fd-d859-4d52-baba-8cab679ca423", - "image_id": 203972, - "image_name": "121247.png", + "id": 361, + "strid": "e7b54ed6-f514-4600-a53d-f32b0f8c58f4", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1493.606, - 4406.309, - 1174.258, - 82.7470000000003 + 945.125, + 3925.061, + 423.30899999999997, + 558.3700000000003 ], - "priority": 29, + "priority": 28, "parents": [ - 89437 + 342 ], "children": [], - "area": 6581289.560254, + "area": 3709673.277625, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgments\nSupport to this project is coming from the Institut National’du Cancer grant Number INCA_5911 to CG.\nAdditional support for QDC obtained from Plan Cancer 2013-2016 Action 3.6 to GB." + "text": "In 2016, 60.0% (95% Cl:\n55.5, 64.3) of sick\nindividuals sought care ata\nhealth structure compared to\n62.7% (95% Cl: 58.4-67.0)\nin 2014\". In 2016, the\nleading reason for not\nseeking healthcare was\nbecause individuals bought\nmedication at the\nmarket/pharmacy. In 2014\",\nthe leading reason was\nbecause the cost of the\nconsultation was prohibitive." }, { - "id": 192991, - "strid": "4c11d755-af98-4ada-84a2-3e9d2529bca0", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 9, - "category_name": "Root", + "id": 362, + "strid": "71ef48f8-8e6e-4df4-b16c-65bdaeeb8889", + "image_id": 14, + "image_name": "10631.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 12.98, - 43.79, - 110.88, - 170.01000000000002 + 1454.785, + 3898.026, + 952.7589999999998, + 577.6930000000002 + ], + "priority": 29, + "parents": [ + 342 ], - "priority": -1, - "parents": [], "children": [ - 192960, - 192961, - 192964, - 192963, - 192962 + 363 ], - "area": 568.3942, + "area": 5670789.7544100005, "iscrowd": 0, "segmentation": [] }, { - "id": 192960, - "strid": "ff9b5d90-36e0-4d1e-baab-4c3c52d29f9b", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 1, - "category_name": "Title", - "bbox": [ - 154.79, - 132.104, - 2966.367, - 216.131 - ], - "priority": 1, - "parents": [ - 192991 - ], - "children": [], - "area": 20448.37816, - "iscrowd": 0, - "segmentation": [], - "text": "IL-12 therapy suppresses TC-1 tumor growth accelerated by\nadmixture of the docetaxel-treated senescent tumor cells" - }, - { - "id": 192961, - "strid": "3de928e9-a77d-4e57-ac74-c8146cdede3c", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 0, - "category_name": "Author Info", + "id": 363, + "strid": "df8b9764-22af-4e9c-a711-61ffcb71125d", + "image_id": 14, + "image_name": "10631.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 462.365, - 369.924, - 2475.0690000000004, - 211.91499999999996 + 1452.373, + 4481.849, + 501.80600000000004, + 31.548999999999978 ], - "priority": 2, + "priority": 30, "parents": [ - 192991 + 362 ], "children": [], - "area": 171039.91026, + "area": 6509316.477677001, "iscrowd": 0, "segmentation": [], - "text": "O. Sapega, J. Simova, T. Imrichova, |. Stepanek, L. Kyjacova, R. Mikyskova, M. Indrova, J. Bieblova,\nJ. Bartek, Z. Hodny, M. Reinis\n\nInstitute of Molecular Genetics CAS, Prague" + "text": "Figure 8-Reasons for not seeking healthcare" }, { - "id": 192962, - "strid": "41ec0913-f41c-413e-89c4-770fd83a47c4", - "image_id": 208040, - "image_name": "9264.png", + "id": 364, + "strid": "a457f580-0eb0-4012-b9e1-6f88ffc6ca9e", + "image_id": 14, + "image_name": "10631.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1479.35, - 608.667, - 290.24800000000005, - 53.72500000000002 + 2527.851, + 1113.161, + 298.2359999999999, + 49.71199999999999 ], - "priority": 3, + "priority": 31, "parents": [ - 192991 + 333 ], "children": [ - 192965 + 365, + 367, + 368, + 366 ], - "area": 900431.52645, + "area": 2813905.147011, "iscrowd": 0, "segmentation": [], - "text": "Background" + "text": "Discussion" }, { - "id": 192965, - "strid": "90a051c2-1d14-4142-b64b-3b2120accc28", - "image_id": 208040, - "image_name": "9264.png", + "id": 365, + "strid": "2e50b11d-5d34-4ab7-b266-a83760045396", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 102.377, - 701.546, - 3093.2, - 199.043 + 2528.242, + 1177.101, + 600.0520000000001, + 135.95800000000008 ], - "priority": 4, + "priority": 32, "parents": [ - 192962 + 364 ], "children": [], - "area": 71822.17484200001, + "area": 2975996.1864420003, "iscrowd": 0, "segmentation": [], - "text": "Cellular senescence is considered to be a principal barrier against tumorigenesis that inhibits acquisition of an immortal phenotype. However, senescent cells can survive in the\norganism for protracted periods of time and they can promote tumor development. Elimination of such potentially cancer-promoting senescent cells could offer a therapeutic benefit.\nIn this study, we have documented significant acceleration of tumor growth, when proliferating tumor cells were co-administered into syngeneic mice together with syngeneic tumor\ncells that had been subjected to the senescence-inducing treatment with docetaxel (DTX). We have also documented that IL-12 therapy can be a suitable candidate for senescent\ncells detrimental effects elimination." + "text": "Reduction in mortality rate can be\nattributed to improved security and\nimproved access to healthcare." }, { - "id": 192963, - "strid": "a3cfcc4a-e2c0-4e9f-9904-c0f699f6af7a", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 5, - "category_name": "Section", + "id": 366, + "strid": "edab5563-a72f-41aa-8f80-a50d83554839", + "image_id": 14, + "image_name": "10631.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1503.823, - 944.645, - 271.9870000000001, - 44.754999999999995 + 2527.529, + 1363.738, + 744.3719999999998, + 371.7070000000001 ], - "priority": 5, + "priority": 33, "parents": [ - 192991 - ], - "children": [ - 192966 + 364 ], - "area": 1420578.8778350002, + "children": [], + "area": 3446887.343402, "iscrowd": 0, - "segmentation": [], - "text": "Conclusion" + "segmentation": [] }, { - "id": 192966, - "strid": "34f3c70a-2f01-4a4f-9ae4-14594d382015", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 367, + "strid": "8a9074d9-c522-47a7-8266-fa488c3a5465", + "image_id": 14, + "image_name": "10631.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 97.56, - 1051.159, - 3065.984, - 229.22199999999998 + 2526.617, + 1783.678, + 741.3589999999999, + 1238.9999999999998 ], - "priority": 6, + "priority": 34, "parents": [ - 192963 + 364 ], "children": [], - "area": 102551.07204000001, + "area": 4506671.157326001, "iscrowd": 0, - "segmentation": [], - "text": "We have demonstrated that two tumorigenic cell lines TC-1 and TRAMP-C2 treated with DTX in vitro in sub-apoptotic doses, induced persistent DNA damage response, cell cycle\narrest and development of senescence-like phenotype accompanied by complex alteration of cytokine expression. In vivo, we demonstrated that senescent cells co-injected with\nproliferating tumor cells can ensure tumor growth-promoting microenvironment, similarly as admixture of proliferating or lethally irradiated tumor cells. We also show that\n\nimmunotherapy with irradiated IL-12-producing cells injected into the vicinity of growing tumors inhibited tumor growth both in proliferating tumor cells only-injected mice and in\nmice co-administered with proliferating and senescent cells to similar levels." + "segmentation": [] }, { - "id": 192964, - "strid": "eab9af7e-64d4-4cd8-81b1-b121ed14ec7a", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 5, - "category_name": "Section", + "id": 368, + "strid": "32e73241-1c06-4c36-8929-359e3ce2a456", + "image_id": 14, + "image_name": "10631.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1537.632, - 1329.326, - 226.67000000000007, - 45.96499999999992 - ], - "priority": 7, + 2526.844, + 3042.074, + 735.6680000000001, + 590.027 + ], + "priority": 35, "parents": [ - 192991 - ], - "children": [ - 192987, - 192969, - 192975, - 192978, - 192980, - 192971, - 192982, - 192983, - 192981, - 192974, - 192967, - 192970, - 192972, - 192973, - 192976, - 192984, - 192990, - 192979, - 192989, - 192986, - 192988, - 192968, - 192977, - 192985 + 364 ], - "area": 2044014.196032, + "children": [], + "area": 7686846.434456, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 192970, - "strid": "8e841ed8-7fed-4f6e-82b9-1fb18b45b6be", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 369, + "strid": "da9506b4-8d19-4b7a-a84b-0cbb742c034b", + "image_id": 14, + "image_name": "10631.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 115.582, - 1325.736, - 1146.3380000000002, - 209.25 + 2527.73, + 3765.847, + 303.4369999999999, + 51.43100000000004 ], - "priority": 8, + "priority": 36, "parents": [ - 192964 + 333 ], - "children": [], - "area": 153231.218352, + "children": [ + 370 + ], + "area": 9519044.43731, "iscrowd": 0, "segmentation": [], - "text": "TC-1 cell line was obtained by in vitro co-transfection of\nmurine lung C57BL/6 cells with HPV16 E6/E7 and\nactivated human H-Ras (G12V) oncogenes (Lin KY et al,.\nCancer Res. 1996)." + "text": "Conclusion" }, { - "id": 192971, - "strid": "e63802b1-1a10-46f7-be73-a8f8fbc97fb0", - "image_id": 208040, - "image_name": "9264.png", + "id": 370, + "strid": "ee5a3fa7-79cf-4907-bfa5-a5140a95c7ba", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 269.029, - 1643.533, - 566.383, - 95.21900000000005 + 2526.59, + 3849.991, + 739.194, + 649.8850000000002 ], - "priority": 9, + "priority": 37, "parents": [ - 192964 + 369 ], "children": [], - "area": 442158.039457, + "area": 9727348.76069, "iscrowd": 0, "segmentation": [], - "text": "Cell morphology after DTX\ntreatment" + "text": "A dramatic decrease in both crude and\nunder-five mortality was observed in Fizi\nHZ between 2014 and 2016. This can be\nattributed to multiple factors including\nimproved security, increased health\nservice coverage, and improved water and\nsanitation. Despite this decrease, mortality\nrates continue to lie above emergency\nthresholds and the main causes of death\nand morbidity continue to be fever\n/malaria, diarrhoea and respiratory\ninfections. The MSF iCCM/PSH\nprogramme is targeting these morbidities\nin an effort to reduce mortality in Fizi HZ." }, { - "id": 192984, - "strid": "67556c2d-940f-4cf4-958b-f48af1636ec9", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 2, - "category_name": "Figure", + "id": 371, + "strid": "1707bf20-98c7-402d-821e-c0a99a430be7", + "image_id": 14, + "image_name": "10631.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 8.688, - 1812.038, - 1155.278, - 564.8250000000003 + 93.418, + 4252.617, + 421.15199999999993, + 48.789999999999964 ], - "priority": 10, + "priority": 38, "parents": [ - 192964 - ], - "children": [], - "area": 15742.986144, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 192977, - "strid": "6eed7a2c-e0fd-45d3-bfe6-2eb04aed3775", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 64.213, - 2405.737, - 1054.255, - 78.54899999999998 + 333 ], - "priority": 11, - "parents": [ - 192964 + "children": [ + 372 ], - "children": [], - "area": 154479.589981, + "area": 397270.974906, "iscrowd": 0, "segmentation": [], - "text": "Senescence-associated B-galactosidase activity in TC-1 and TRAMP-C2 cells treated with DTX for 4 days\n(A). Phase contrast microscopic images of control and DTX-treated (7.5 uM) TC-1 and TRAMP-C2 cells at\nday 4 after the treatment (B)." + "text": "Acknowledgements" }, { - "id": 192972, - "strid": "07f6bb43-d942-4b97-83b2-984947bfaa95", - "image_id": 208040, - "image_name": "9264.png", + "id": 372, + "strid": "cd5055d5-686d-4186-b060-d41eb1f07f0f", + "image_id": 14, + "image_name": "10631.png", "category_id": 3, "category_name": "Text", "bbox": [ - 117.538, - 2642.105, - 912.7369999999999, - 95.3409999999999 + 93.892, + 4304.709, + 677.0989999999999, + 197.85599999999977 ], - "priority": 12, + "priority": 39, "parents": [ - 192964 + 371 ], "children": [], - "area": 310547.73748999997, + "area": 404177.73742799996, "iscrowd": 0, "segmentation": [], - "text": "Docetaxel-induced senescence in TC-1 and\nTRAMP-C2 cell lines in vitro and in vivo" + "text": "A Lenglet, AJ Willis, K Bil, and J Mandelkow\nperformed the 2014 mortality survey. We also\nacknowledge the Ministry of Health, South\nKivu; the survey teams; the South Kivu\nMission; and the people of Fizi Health Zone." }, { - "id": 192986, - "strid": "c531ceeb-b894-4fb3-892a-0b5c4a7fd2a3", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 2, - "category_name": "Figure", + "id": 373, + "strid": "55c7058f-3a0b-4317-8acd-071e542df74f", + "image_id": 14, + "image_name": "10631.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 17.483, - 2866.252, - 1152.154, - 1240.199 + 64.637, + 4547.841, + 2632.451, + 98.05299999999988 ], - "priority": 13, + "priority": 40, "parents": [ - 192964 + 333 ], "children": [], - "area": 50110.683716, + "area": 293958.798717, "iscrowd": 0, "segmentation": [] }, { - "id": 192979, - "strid": "b90c905b-d4d1-4f43-b709-6ddd04169e71", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 374, + "strid": "87c2fa82-30a1-449a-b861-a9ba348e81af", + "image_id": 15, + "image_name": "10632.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 32.771, - 4166.695, - 1020.28, - 181.17500000000018 + 90.17, + 42.3, + 154.83999999999997, + 154.85000000000002 ], - "priority": 14, - "parents": [ - 192964 + "priority": -1, + "parents": [], + "children": [ + 405, + 403, + 400, + 377, + 382, + 376, + 380, + 375, + 390 ], - "children": [], - "area": 136546.761845, + "area": 3814.191, "iscrowd": 0, - "segmentation": [], - "text": "Cell proliferation was determined by counting cell number every 24 h and plotted as log* ratio of total\nnumber of cells to seeding cell number to compensate for different seeding capacity of control and\nDTX-treated cells (A). To detect DNA damage, control and DTX-treated cells were stained with\nphosphoSer139 H2AX (yH2AX) antibody and mounted with Mowiol containing DAPI (B). Mice were\ntransplanted s.c. on day 0 with TC-1 cells (3 x 10*) or with senescent DTX-treated cells at the doses 3\nx 104 [TC-1/DTX(a)] or 5 x 105 [TC-1/DTX(b)] tumor cells, respectively, and the tumor growth was\nmonitored." + "segmentation": [] }, { - "id": 192969, - "strid": "fc3acd76-399f-4731-b427-25ba74ea3776", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 375, + "strid": "c71d368d-faba-410d-9e12-6d8c5009ba14", + "image_id": 15, + "image_name": "10632.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 1391.464, - 1472.959, - 483.4390000000001, - 95.71000000000004 + 733.826, + 146.169, + 2003.183, + 619.334 ], - "priority": 15, + "priority": 1, "parents": [ - 192964 + 374 ], "children": [], - "area": 2049569.421976, + "area": 107262.612594, "iscrowd": 0, "segmentation": [], - "text": "Expression of selected\nsenescence markers" + "text": "Strengthening malaria control\nthrough seasonal malaria\nchemoprevention campaign in\nGuinea-Bissau" }, { - "id": 192985, - "strid": "208031f3-2ecb-40ab-a99f-ecb45a2e7096", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 2, - "category_name": "Figure", + "id": 376, + "strid": "e6412abc-29ee-430a-bc89-1897d593ef75", + "image_id": 15, + "image_name": "10632.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1196.817, - 1649.334, - 938.2370000000001, - 428.42100000000005 + 528.337, + 891.802, + 2348.461, + 175.2399999999999 ], - "priority": 16, + "priority": 2, "parents": [ - 192964 + 374 ], "children": [], - "area": 1973950.969878, + "area": 471171.993274, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Rocaspana Merce’, Houedakor Dakitche Lawoe’, Villen Susana?\nMSF\", Barcelona, Spain. MSF?, Bissau, Guinea-Bissau" }, { - "id": 192978, - "strid": "b7be8488-2bb2-4d73-9262-d0196bdd0ddb", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 377, + "strid": "dcb2e625-11b7-43ff-af96-c446aa4ebf54", + "image_id": 15, + "image_name": "10632.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1201.468, - 2113.102, - 924.595, - 106.19900000000007 + 125.48, + 1220.357, + 317.629, + 46.60200000000009 ], - "priority": 17, + "priority": 3, "parents": [ - 192964 + 374 ], - "children": [], - "area": 2538824.433736, + "children": [ + 378, + 379 + ], + "area": 153130.39636, "iscrowd": 0, "segmentation": [], - "text": "Immunoblotting detection of mouse pi6INK4A (p16) and p21waft/cip1 (p21) in control and\nDTX-treated TC-1 and TRAMP-C2 cells. GAPDH was used as a loading control (C). qRT-\nPCR quantification of p16 and p21 in control and DTX-treated TC-1 and TRAMP-C2 cells.\n*p<0.05, **p<0.005 (D)." + "text": "Introduction" }, { - "id": 192973, - "strid": "054ad714-4708-4424-9e9a-cd8d6a3b6b71", - "image_id": 208040, - "image_name": "9264.png", + "id": 378, + "strid": "660908b0-e2da-4b17-b7a7-a2634269599b", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1330.799, - 2336.141, - 648.527, - 48.48799999999983 + 122.745, + 1365.513, + 677.96, + 879.3499999999999 ], - "priority": 18, + "priority": 4, "parents": [ - 192964 + 377 ], "children": [], - "area": 3108934.1066590003, + "area": 167609.893185, "iscrowd": 0, "segmentation": [], - "text": "Explanted tumor cells analysis" + "text": "In Guinea-Bissau, West African\ncountry malaria is the leading morbidity\nand cause of mortality due to diseases\nin children under 5years old.\n(http:/Awww.who.int/countries/gnb/en/).\n\nMSF OCBA in Guinea-Bissau since\n2014 in collaboration with the MoH is\ncarrying out several health programs\namong which the seasonal malaria\nchemoprevention strategy.\n\nBased on the WHO recommendation\nand considering the opportunity of its\ninterventions, MSF designed the\nSeasonal Malaria Chemoprevention\n(SMC) strategy aiming to reduce\nmainly the burden of malaria in\nchildren under five years old in Bafata\nregion." }, { - "id": 192987, - "strid": "928b1fc0-3163-4cd1-ad1b-087ad51a6b8e", - "image_id": 208040, - "image_name": "9264.png", + "id": 379, + "strid": "9182f5e5-dc5a-468c-b27b-daa66789a3a5", + "image_id": 15, + "image_name": "10632.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1197.071, - 2457.357, - 1094.92, - 1029.234 + 82.74, + 2293.675, + 758.486, + 571.3600000000001 ], - "priority": 19, + "priority": 5, "parents": [ - 192964 + 377 ], "children": [], - "area": 2941630.8013469996, + "area": 189778.6695, "iscrowd": 0, "segmentation": [] }, { - "id": 192980, - "strid": "67fbb614-0ef7-4871-ad2b-4516da5b4786", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 380, + "strid": "29c84e38-9d86-4328-aa87-dd8f3b43b7e3", + "image_id": 15, + "image_name": "10632.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1135.22, - 3551.416, - 983.758, - 158.85500000000002 + 124.653, + 3108.336, + 103.23, + 44.496000000000095 ], - "priority": 20, + "priority": 6, "parents": [ - 192964 + 374 ], - "children": [], - "area": 4031638.47152, + "children": [ + 381 + ], + "area": 387463.40740799997, "iscrowd": 0, "segmentation": [], - "text": "Explanted tumor cells were cultured for seven days and analyzed for the proportion of TC-1\n(CD80+) and TRAMP-C2 (CD80-) cells by flow cytometry using CD80 as a marker. To exclude\nleukocytes from the analysis, CD45+ cells were gated out. For comparison, explanted cells were\ncultured in the culture medium optimized either for TC-1 cells (TC-1 medium) or for TRAMP-C2\n\ncells (TRAMP-C2 medium) (A). Flow cytometry analysis of the CD80 cell surface expression on\ncultured TC-1 and TRAMP-C2 cells, as well as their mixed culture (B)." + "text": "Aim" }, { - "id": 192975, - "strid": "6368bb80-41e2-433a-911f-9f80bf757fec", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 381, + "strid": "c6b91c56-e693-4b74-b836-ff7e3e13f3a8", + "image_id": 15, + "image_name": "10632.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1233.59, - 3816.993, - 838.4420000000002, - 102.69399999999996 + 125.753, + 3178.215, + 676.73, + 1143.0730000000003 ], - "priority": 21, + "priority": 7, "parents": [ - 192964 + 380 ], "children": [], - "area": 4708604.39487, + "area": 399670.070895, "iscrowd": 0, - "segmentation": [], - "text": "IL12-based immunotherapy suppresses\nsenescence-accelerated tumor growth" + "segmentation": [] }, { - "id": 192990, - "strid": "3667431c-1412-4472-bfe7-afc1d1cab1e3", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 2, - "category_name": "Figure", + "id": 382, + "strid": "efc2798f-482f-4995-bc1b-2df8879480c0", + "image_id": 15, + "image_name": "10632.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1337.21, - 3997.76, - 593.2950000000001, - 400.79299999999967 + 944.429, + 1221.906, + 191.54000000000008, + 44.16100000000006 ], - "priority": 22, + "priority": 8, "parents": [ - 192964 + 374 ], - "children": [], - "area": 5345844.6496, + "children": [ + 384, + 386, + 388, + 385, + 389, + 383, + 387 + ], + "area": 1154003.461674, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 192981, - "strid": "d9a0e7c3-d695-4cb2-9cb7-cc7e76e7d069", - "image_id": 208040, - "image_name": "9264.png", + "id": 383, + "strid": "eab181a5-75bf-4d10-81d3-a0534ed01bb7", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1247.242, - 4509.14, - 898.836, - 104.48099999999977 + 941.188, + 1368.288, + 673.7579999999999, + 321.71900000000005 ], - "priority": 23, + "priority": 9, "parents": [ - 192964 + 382 ], "children": [], - "area": 5623988.79188, + "area": 1287816.246144, "iscrowd": 0, "segmentation": [], - "text": "Mice were transplanted on day O s.c. with TC-1 cells (3 x 10%), docetaxel-induced\nsenescent TC-1/DTX (3 x 105) or TC-1 cells (3 x 10*) admixed with TC-1/DTX. IL-12\nproducing TC-1/IL-12 cells were administered on day 3 in the vicinity of transplanted\ncontrol TC-1 cells and TC-1 cells admixture with TC-1/DTX senescent cells. p < 0.05." + "text": "The SMC campaign was organized\nwithin the 7 health areas currently\ncovered by MSF in the Bafata region\nand the SMC team did one\ndistribution round per month for 4\nmonths (August, September,\nOctober and November)" }, { - "id": 192967, - "strid": "7af4604f-f488-41c8-aa1e-baa2592933dd", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 384, + "strid": "25345e58-4bd8-48fd-8cdc-dbd114fd34eb", + "image_id": 15, + "image_name": "10632.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2040.122, - 1326.725, - 1064.077, - 211.22000000000003 + 971.791, + 1742.739, + 548.949, + 604.4009999999998 ], - "priority": 24, + "priority": 10, "parents": [ - 192964 + 382 ], "children": [], - "area": 2706680.86045, + "area": 1693578.0755490002, "iscrowd": 0, - "segmentation": [], - "text": "TRAMP-C2 tumor cells, MHC class I-deficient, were\nestablished from a heterogeneous, 32-week tumor of\nthe TRAMP model (Foster BA et al., Cancer res.\n1997)." + "segmentation": [] }, { - "id": 192968, - "strid": "3418da25-f129-427c-8cfd-096ea889e3cb", - "image_id": 208040, - "image_name": "9264.png", + "id": 385, + "strid": "c7a3fea2-5119-40ef-aeea-0099c46f093a", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2320.117, - 1633.693, - 851.808, - 102.71199999999999 + 941.474, + 2375.88, + 644.8570000000001, + 135.22699999999986 ], - "priority": 25, + "priority": 11, "parents": [ - 192964 + 382 ], "children": [], - "area": 3790358.902081, + "area": 2236829.2471200004, "iscrowd": 0, "segmentation": [], - "text": "The analysis of TC-1 and TRAMP-C2 cell\nproliferation by EdU incorporation" + "text": "A combination of 3 molecules was\nused: Sulfadoxine / Pyrimethamine\nand Amodiaquine (SP+AQ)." }, { - "id": 192988, - "strid": "15e06cd4-386a-4e21-a893-2fafa4d700d7", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 2, - "category_name": "Figure", + "id": 386, + "strid": "3342b76d-11c1-4f75-b817-112a7d68f5e5", + "image_id": 15, + "image_name": "10632.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2251.53, - 1823.677, - 1016.2269999999999, - 1089.9620000000002 + 941.829, + 2534.639, + 584.479, + 296.5479999999998 ], - "priority": 26, + "priority": 12, "parents": [ - 192964 + 382 ], "children": [], - "area": 4106063.47581, + "area": 2387196.514731, "iscrowd": 0, "segmentation": [] }, { - "id": 192982, - "strid": "573c8bce-57fc-4dc4-a05d-fbe4869310a8", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 387, + "strid": "2718bf8d-abeb-4788-9a63-d9cfe14dc93f", + "image_id": 15, + "image_name": "10632.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2364.483, - 3010.268, - 911.4740000000002, - 158.5590000000002 + 941.659, + 2920.967, + 675.571, + 241.67300000000023 ], - "priority": 27, + "priority": 13, "parents": [ - 192964 + 382 ], "children": [], - "area": 7117727.5114440005, + "area": 2750554.864253, "iscrowd": 0, - "segmentation": [], - "text": "The cells were driven to senescence by 4-day treatment with 7.5 yM docetaxel (DTX),\nincubated with 10 uM ethynyl deoxyuridine (EdU) for 6 h. Click-iT reaction was performed on\nfixed cells and FACS analysis was carried out to determine the fraction of proliferating cells\nin DTX-treated and control samples (A). Control and DTX-treated TC-1 and TRAMP-C2 cells\nwere incubated with 10 uM Edu for 6 h. Following fixation, Click-iT reaction was performed\nand the cover slides were mounted with Mowiol containing DAPI (B)." + "segmentation": [] }, { - "id": 192974, - "strid": "8eef66a4-ec9a-40e6-8977-64ecb6ae00d3", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 388, + "strid": "862ca221-867d-4df6-a750-bb35b1df9418", + "image_id": 15, + "image_name": "10632.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2323.703, - 3339.681, - 930.6640000000002, - 156.46399999999994 + 941.475, + 3258.541, + 678.68, + 672.7359999999999 ], - "priority": 28, + "priority": 14, "parents": [ - 192964 + 382 ], "children": [], - "area": 7760426.758743, + "area": 3067834.8879750003, "iscrowd": 0, - "segmentation": [], - "text": "Co-administration of DTX-treated senescent\ncells and TC-1 tumor cells resulted in\naccelerated tumor growth" + "segmentation": [] }, { - "id": 192989, - "strid": "8dd9e87f-709f-4237-a73c-d6da501358c2", - "image_id": 208040, - "image_name": "9264.png", + "id": 389, + "strid": "a6dae55a-ed58-441c-9367-8ff525051b06", + "image_id": 15, + "image_name": "10632.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2148.689, - 3619.349, - 1121.149, - 776.598 + 968.855, + 4003.48, + 610.836, + 457.61900000000014 ], - "priority": 29, + "priority": 15, "parents": [ - 192964 + 382 ], "children": [], - "area": 7776855.3834609995, + "area": 3878791.6154, "iscrowd": 0, "segmentation": [] }, { - "id": 192983, - "strid": "8a616047-823b-4976-abca-4e53c130cdb3", - "image_id": 208040, - "image_name": "9264.png", - "category_id": 3, - "category_name": "Text", + "id": 390, + "strid": "1968263b-325f-41c1-b77c-03a3b5dab5b9", + "image_id": 15, + "image_name": "10632.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2213.128, - 4508.97, - 1052.0149999999999, - 77.58200000000033 + 1757.799, + 1220.65, + 195.69299999999998, + 47.12799999999993 ], - "priority": 30, + "priority": 16, "parents": [ - 192964 + 374 ], - "children": [], - "area": 9978927.75816, + "children": [ + 392, + 396, + 398, + 399, + 394, + 391, + 397, + 393, + 395 + ], + "area": 2145657.3493500003, "iscrowd": 0, "segmentation": [], - "text": "Mice were transplanted s.c. on day 0 with TC-1 cells (3 x 10*), or (A) TC-1 cells admixed with TC-1/DTX\n(3 x 105), or (B) TC-1 cells admixed with TRAMP-C2/DTX cells (3 x 105), or (C) irradiated TC-1 cells (150\nGy; 3 x 105), or (D) TRAMP-C2 cells (3 x 105), p < 0.05." + "text": "" }, { - "id": 192976, - "strid": "c9c5243a-5848-49f9-8dc8-46adcb5bfdd8", - "image_id": 208040, - "image_name": "9264.png", + "id": 391, + "strid": "1b25726c-85e1-46db-b98b-4ad55d6092ab", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 62.859, - 4447.77, - 861.711, - 158.33600000000024 + 1754.121, + 1302.267, + 505.6399999999999, + 42.919000000000096 ], - "priority": 31, + "priority": 17, "parents": [ - 192964 + 390 ], "children": [], - "area": 279582.37443, + "area": 2284333.8923070002, "iscrowd": 0, "segmentation": [], - "text": "This work was supported by research grants Nos. 15-24769S from the Czech Science\n\nFoundation and NT14461 from the Grant Agency of the Ministry of Health of the Czech\nRepublic\n\nO.S. is a Ph.D. student supported in part by the Faculty of Science, Charles University,\n\nPrague.\n\nolena.sapega @img.cas.cz" + "text": "Results from implementation:" }, { - "id": 165173, - "strid": "131401c9-f763-4c12-804d-7bb7bdee0f54", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 9, - "category_name": "Root", + "id": 392, + "strid": "94480b1d-d8e8-47ec-8750-ebfed8e4bf1c", + "image_id": 15, + "image_name": "10632.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 234.4, - 79.89, - 185.83, - 109.60000000000001 + 1742.649, + 1370.537, + 708.384, + 416.096 ], - "priority": -1, - "parents": [], - "children": [ - 165160, - 165159, - 165163, - 165158, - 165162, - 165161, - 165164, - 165165 + "priority": 18, + "parents": [ + 390 ], - "area": 18726.216, + "children": [], + "area": 2388364.932513, "iscrowd": 0, "segmentation": [] }, { - "id": 165158, - "strid": "6e943f15-2693-4401-bc11-899658ccc42d", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 1, - "category_name": "Title", + "id": 393, + "strid": "af38da7f-01c6-4011-b7b2-932ae014302a", + "image_id": 15, + "image_name": "10632.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 507.562, - 125.443, - 3648.898, - 295.257 + 1744.346, + 1833.65, + 700.9169999999999, + 431.53600000000006 ], - "priority": 1, + "priority": 19, "parents": [ - 165173 + 390 ], "children": [], - "area": 63670.099966, + "area": 3198520.0429000002, "iscrowd": 0, - "segmentation": [], - "text": "Lack of Evidence for Central Sensitization in Idiopathic,\ni Non-Traumatic Neck Pain — A Systematic Review" + "segmentation": [] }, { - "id": 165159, - "strid": "7d4e2bc2-e18c-4af1-8959-0ddb94c3b595", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 0, - "category_name": "Author Info", + "id": 394, + "strid": "0a6a6245-b2eb-4d36-93a9-0de958c7abaa", + "image_id": 15, + "image_name": "10632.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 118.421, - 462.215, - 4438.833, - 252.84599999999995 + 1742.805, + 2289.477, + 692.6090000000002, + 471.672 ], - "priority": 2, + "priority": 20, "parents": [ - 165173 + 390 ], "children": [], - "area": 54735.962515, + "area": 3990111.962985, "iscrowd": 0, - "segmentation": [], - "text": "Anneleen Malfliet'!:23,msc; Jeroen Kregel'*,msc; Barbara Cagnie'?,PhD; Mandy Kuipers?,BSc; Mieke Dolphens',Php; Nathalie Roussel'*,PhD; Mira Meeus'*:4,PhD;\nLieven Danneels'?,PhD ; Bramer Wichor5,BSc & JO Nijs':25,PhD\n\n1 Pain in Motion Research Group; ? Dept of Human Physiology and Physiotherapy, Faculty of Physical Education & Physiotherapy, Vrije Universiteit Brussel, Brussels, Belgium; * Dept of Rehabilitation Sciences and Physiotherapy, Faculty of Medicine & Health\nSciences, Ghent University, Ghent, Belgium; + Dept of Rehabilitation Sciences and Physiotherapy, Faculty of Medicine & Health Sciences, University of Antwerp, Antwerp, Belgium; 5° Medical Library, Erasmus MC - University MC Rotterdam, the Netherlands" + "segmentation": [] }, { - "id": 165163, - "strid": "f94bb4d0-0e64-4549-b06d-a4502f887636", - "image_id": 206942, - "image_name": "6691.png", + "id": 395, + "strid": "72a284a0-efe2-4538-8fe2-ef07a5a64de8", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 260.974, - 784.006, - 1192.67, - 324.15099999999995 + 1754.505, + 2792.741, + 542.1570000000002, + 87.11700000000019 ], - "priority": 3, + "priority": 21, "parents": [ - 165173 + 390 ], "children": [], - "area": 204605.18184399998, + "area": 4899878.048205, "iscrowd": 0, "segmentation": [], - "text": "Chronic Neck Pain\nCommon but poorly understood\nRX = age # symptoms" + "text": "Coverage Data from Post-SMC\nCoverage survey" }, { - "id": 165165, - "strid": "3f224331-397d-41e5-9f51-8efc078d501c", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 2, - "category_name": "Figure", + "id": 396, + "strid": "a8bc98b9-57a7-4356-b382-93cdd7329b64", + "image_id": 15, + "image_name": "10632.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 34.423, - 1160.201, - 1637.704, - 1135.7730000000001 + 1754.741, + 2898.603, + 678.1199999999999, + 416.42599999999993 ], - "priority": 4, + "priority": 22, "parents": [ - 165173 + 390 ], "children": [], - "area": 39937.599023, + "area": 5086297.526823, "iscrowd": 0, "segmentation": [] }, { - "id": 165164, - "strid": "34b96660-bc0f-4a53-a374-bf8889f18826", - "image_id": 206942, - "image_name": "6691.png", + "id": 397, + "strid": "a29f0f13-c609-4615-91ed-faea4699ae90", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 117.918, - 2322.605, - 1478.714, - 443.04399999999987 + 1756.586, + 3315.561, + 673.4129999999998, + 84.2159999999999 ], - "priority": 5, + "priority": 23, "parents": [ - 165173 + 390 ], "children": [], - "area": 273876.93639, + "area": 5824068.034746001, "iscrowd": 0, "segmentation": [], - "text": "Aim\nTo review the existing literature on the\nrole of central sensitization in chronic\nidiopathic, non-traumatic NP." + "text": "The data are the means (average) of Tantan Cosse HA,\nContuboel HA, Fanjonquito HA, Cambaju HA, Tendinto HA\nand Sare Bacar HA" }, { - "id": 165160, - "strid": "ab36a19b-0654-416e-8fd8-e27817932e27", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 5, - "category_name": "Section", + "id": 398, + "strid": "f29e0027-9e5d-48f6-a673-78bada2e449d", + "image_id": 15, + "image_name": "10632.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2285.447, - 773.237, - 417.2069999999999, - 81.173 + 1742.452, + 3450.776, + 1497.9309999999998, + 581.6109999999999 ], - 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"priority": 11, + "priority": 29, "parents": [ - 165161 - ], - "children": [], - "area": 6709105.887302999, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 165170, - "strid": "666a6a92-b9f8-4de6-b653-371cf18eceb7", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 4041.017, - 2276.744, - 504.10300000000007, - 348.9340000000002 + 374 ], - "priority": 12, - "parents": [ - 165161 + "children": [ + 404 ], - "children": [], - "area": 9200361.208648, + "area": 6438825.235722, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Conclusion" }, { - "id": 165171, - "strid": "c8cd97cf-0c99-4708-ba4c-476b2f3c833a", - "image_id": 206942, - "image_name": "6691.png", - "category_id": 2, - "category_name": "Figure", + "id": 404, + "strid": "eb0031a5-d24b-461e-8d20-ef7c31e72d9e", + "image_id": 15, + "image_name": "10632.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3299.25, - 2703.56, - 1281.2749999999996, - 111.1909999999998 + 2565.865, + 2587.43, + 699.288, + 622.9859999999999 ], - "priority": 13, + "priority": 30, "parents": [ - 165161 + 403 ], "children": [], - "area": 8919720.33, + "area": 6638996.076949999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The malaria control in the African\nsubsaharian countries demands\ninvestments. SMC as part of the malaria\ncontrol tools contributes where indicated\nto mitigate the burden of this lethal\ndisease.\n\nThis SMC implementation, first\nexperience in Guinea-Bissau with its\ngood outcomes, has triggered\nenthusiastically the MoH whom staffs\nhave been trained in Gabu region by\nMSF in order to extend it to other\nregions." }, { - "id": 165162, - "strid": "4d96be54-f0e9-4f30-ad29-14175196935f", - "image_id": 206942, - "image_name": "6691.png", + "id": 405, + "strid": "3bae7041-a637-4047-952c-e663545c0c23", + "image_id": 15, + "image_name": "10632.png", "category_id": 5, "category_name": "Section", "bbox": [ - 89.833, - 2865.709, - 510.477, - 84.34299999999985 + 123.849, + 4629.36, + 523.608, + 59.34900000000016 ], - "priority": 14, + "priority": 31, "parents": [ - 165173 + 374 ], "children": [ - 165172 + 406 ], - "area": 257435.23659699998, + "area": 573341.60664, "iscrowd": 0, "segmentation": [], - "text": "Conclusion" + "text": "Acknowledgements" }, { - "id": 165172, - "strid": "1f6d5d14-9e37-4a84-b186-74d8e979ad4b", - "image_id": 206942, - "image_name": "6691.png", + "id": 406, + "strid": "9f980d90-fccd-4ca4-991c-f62c9ea0ca26", + "image_id": 15, + "image_name": "10632.png", "category_id": 3, "category_name": "Text", "bbox": [ - 84.668, - 2997.19, - 4427.064, - 192.3739999999998 + 123.927, + 4714.121, + 3070.621, + 39.80799999999999 ], - "priority": 15, + "priority": 32, "parents": [ - 165162 + 405 ], "children": [], - "area": 253766.08292000002, + "area": 584206.873167, "iscrowd": 0, "segmentation": [], - "text": "CS is not a major characteristic feature of Chronic Idiopathic Non-Traumatic NP, but can be present in some individuals.\nLiterature on this subject is rare and inconclusive." + "text": "We kindly appreciate the collaboration of Ministry of Health of Guinea Bissau and the job done by all the community members and health care workers to make this SMC possible." }, { - "id": 146914, - "strid": "6aa78d34-1bcd-4346-afd4-d9e205b5678f", - "image_id": 206203, - "image_name": "18835.png", + "id": 407, + "strid": "7c81efa8-e894-41fa-955e-35352e85b695", + "image_id": 16, + "image_name": "10739.png", "category_id": 9, "category_name": "Root", "bbox": [ - 613.29, - 133.82, - 291.56000000000006, - 216.90000000000003 + 857.59, + 69.54, + 227.95999999999992, + 227.96999999999997 ], "priority": -1, "parents": [], "children": [ - 146899, - 146897, - 146898, - 146900, - 146893, - 146896, - 146901, - 146894, - 146895 + 409, + 410, + 415, + 412, + 420, + 408 ], - "area": 82070.46779999998, + "area": 59636.80860000001, "iscrowd": 0, "segmentation": [] }, { - "id": 146893, - "strid": "b886e2a7-f301-4736-be66-e1a76f67e276", - "image_id": 206203, - "image_name": "18835.png", + "id": 408, + "strid": "29a4e5cd-0cee-45cf-8050-9153fb0157eb", + "image_id": 16, + "image_name": "10739.png", "category_id": 1, "category_name": "Title", "bbox": [ - 1132.19, - 29.747, - 1621.4389999999999, - 171.85199999999998 + 254.086, + 605.746, + 2685.4749999999995, + 180.524 ], "priority": 1, "parents": [ - 146914 + 407 ], "children": [], - "area": 33679.25593, + "area": 153911.578156, "iscrowd": 0, "segmentation": [], - "text": "DRUG REPOSITIONING FOR\nMUCOPOLYSACCHARIDOSES BASED ON SYSTEMS\nBIOLOGY DATA" + "text": "Modeling of adjustment for misclassification and incompleteness in mortality\ndata-Isfahan 2014" }, { - "id": 146894, - "strid": "6593deed-e12e-4a8b-819f-b198c288b6f4", - "image_id": 206203, - "image_name": "18835.png", + "id": 409, + "strid": "8cb9c28b-ea22-49c7-8972-8f121a458ecf", + "image_id": 16, + "image_name": "10739.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 912.965, - 227.968, - 2077.636, - 101.631 + 123.452, + 860.253, + 2463.3239999999996, + 270.99799999999993 ], "priority": 2, "parents": [ - 146914 + 407 ], "children": [], - "area": 208126.80512, + "area": 106199.953356, "iscrowd": 0, "segmentation": [], - "text": "Gerda Cristal Villalba Silva, Ursula Matte\n\nUniversidade Federal do Rio Grande do Sul | Bioinformatics Core | HCPA" + "text": "Shams-Beyranvand M(Presenter) +, Maracy MR}, Farzadfar F*, Mohammadi Y?, Mansouri A2\n'Epidemiology & Biostatistics Dept, Isfahan Uni of Medical Sciences, Isfahan, Iran\n\n2Non-communicable Diseases Research Center, Tehran Uni of Medical Sciences, Tehran, Iran\n\nEpidemiology & Biostatistics Dept, Hamadan Uni of Medical Sciences, Hamadan, Iran" }, { - "id": 146895, - "strid": "841f4afc-cd24-428c-8933-6eea2a63bf30", - "image_id": 206203, - "image_name": "18835.png", + "id": 410, + "strid": "cbc1c6fb-5a89-4407-808f-661c18768a7d", + "image_id": 16, + "image_name": "10739.png", "category_id": 5, "category_name": "Section", "bbox": [ - 45.792, - 398.419, - 577.735, - 37.144000000000005 + 151.549, + 1264.72, + 484.871, + 40.68599999999992 ], "priority": 3, "parents": [ - 146914 + 407 ], "children": [ - 146902 + 411 ], - "area": 18244.402848, + "area": 191667.05128, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Introduction and background:" }, { - "id": 146902, - "strid": "75a026d3-c038-41b9-94bc-b732303be447", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 3, - "category_name": "Text", + "id": 411, + "strid": "faba18b9-4727-42ac-b3c2-e5caa1e25ded", + "image_id": 16, + "image_name": "10739.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 44.289, - 542.248, - 684.874, - 275.558 + 150.609, + 1318.15, + 2822.311, + 89.83699999999999 ], "priority": 4, "parents": [ - 146895 + 410 ], "children": [], - "area": 24015.621672, + "area": 198525.25335, "iscrowd": 0, - "segmentation": [], - "text": "accharidoses\nmal storage\n\non\n\nIn MPS, secondary cell\ndisturbance affects\npathways common to\ncancer." + "segmentation": [] }, { - "id": 146896, - "strid": "307a1f69-c61f-4aa9-8ae1-66eb0c63ff8f", - "image_id": 206203, - "image_name": "18835.png", + "id": 412, + "strid": "47a552fb-2f55-4115-91c4-ce650d1cc98f", + "image_id": 16, + "image_name": "10739.png", "category_id": 5, "category_name": "Section", "bbox": [ - 43.894, - 914.381, - 174.134, - 34.827 + 146.181, + 1519.414, + 158.169, + 34.547000000000025 ], "priority": 5, "parents": [ - 146914 + 407 ], "children": [ - 146908 + 413 ], - "area": 40135.839614, + "area": 222109.457934, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Methods:" }, { - "id": 146908, - "strid": "1a1924e2-5d0a-4851-a245-cef283e0da26", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 4, - "category_name": "List", + "id": 413, + "strid": "6fe105c7-1a62-4259-a8bd-864810ccacea", + "image_id": 16, + "image_name": "10739.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 41.199, - 1018.445, - 707.663, - 214.4430000000001 + 437.899, + 1634.326, + 2394.931, + 1126.589 ], "priority": 6, "parents": [ - 146896 + 412 ], - "children": [], - "area": 41958.915555, + "children": [ + 414 + ], + "area": 715669.721074, "iscrowd": 0, "segmentation": [] }, { - "id": 146897, - "strid": "02a1ec92-a7ca-4327-8c82-e0451247dc26", - "image_id": 206203, - "image_name": "18835.png", + "id": 414, + "strid": "48e0428b-f1ed-46f3-8f18-50cca063581c", + "image_id": 16, + "image_name": "10739.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 960.291, + 2834.055, + 1175.2619999999997, + 28.84400000000005 + ], + "priority": 7, + "parents": [ + 413 + ], + "children": [], + "area": 2721517.510005, + "iscrowd": 0, + "segmentation": [], + "text": "Fig 1. Scientific scheme of processes in modeling of adjustment for misclassification and incompleteness in mortality data" + }, + { + "id": 415, + "strid": "235e46e7-f0fc-4576-a62d-f26d4d614565", + "image_id": 16, + "image_name": "10739.png", "category_id": 5, "category_name": "Section", "bbox": [ - 46.372, - 1303.352, - 346.239, - 34.835000000000036 + 137.364, + 2966.303, + 131.564, + 35.61000000000013 ], - "priority": 7, + "priority": 8, "parents": [ - 146914 + 407 ], "children": [ - 146910 + 416, + 418 ], - "area": 60439.03894400001, + "area": 407463.245292, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Results:" }, { - "id": 146910, - "strid": "974dbfdc-7d17-4fb4-8680-b4803c81cff8", - "image_id": 206203, - "image_name": "18835.png", + "id": 416, + "strid": "a5ed7b45-1592-49df-8f1a-1051af6baf67", + "image_id": 16, + "image_name": "10739.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 24.119, - 1401.292, - 748.975, - 567.1979999999999 + 193.241, + 3049.057, + 953.202, + 485.60199999999986 ], - "priority": 8, + "priority": 9, "parents": [ - 146897 + 415 ], - "children": [], - "area": 33797.761748, + "children": [ + 417 + ], + "area": 589202.823737, "iscrowd": 0, "segmentation": [] }, { - "id": 146898, - "strid": "6a851528-9ead-4f45-ac2f-0f0e19d13e9a", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 1686.509, - 380.671, - 326.69000000000005, - 34.976999999999975 - ], - "priority": 9, - "parents": [ - 146914 - ], - "children": [ - 146912, - 146911, - 146909, - 146913 - ], - "area": 642005.067539, - "iscrowd": 0, - "segmentation": [], - "text": "" - }, - { - "id": 146911, - "strid": "73384e7a-7d0a-4cdd-a472-c6bafc497199", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 808.517, - 494.902, - 2226.925, - 693.45 - ], - "priority": 10, - "parents": [ - 146898 - ], - "children": [ - 146905 - ], - "area": 400136.68033400003, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 146905, - "strid": "47482102-c0a9-4f06-80e9-03d967ed9452", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 6, - "category_name": "Caption", - "bbox": [ - 899.601, - 1215.398, - 650.6079999999998, - 106.57600000000002 - ], - "priority": 11, - "parents": [ - 146911 - ], - "children": [], - "area": 1093373.256198, - "iscrowd": 0, - "segmentation": [], - "text": "Figures 1 and 2: Top\ngenes down and up\nand target compounds" - }, - { - "id": 146913, - "strid": "dcf2e963-1939-42a4-a283-da05e314d0ce", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 802.008, - 1223.674, - 724.1310000000001, - 878.337 - ], - "priority": 12, - "parents": [ - 146898 - ], - "children": [ - 146906 - ], - "area": 981396.337392, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 146906, - "strid": "9cbfdfe0-8a10-49a0-a004-1dc33d28021a", - "image_id": 206203, - "image_name": "18835.png", + "id": 417, + "strid": "698af2ac-192c-4d62-b71f-aa717c42ff2c", + "image_id": 16, + "image_name": "10739.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 821.52, - 2110.372, - 630.531, - 106.04100000000017 + 414.363, + 3599.815, + 400.242, + 26.79399999999987 ], - "priority": 13, + "priority": 10, "parents": [ - 146913 + 416 ], "children": [], - "area": 1733712.8054399998, + "area": 1491630.142845, "iscrowd": 0, "segmentation": [], - "text": "Figure 3: Network by\ncytoscape nodes: 244\nedges: 1824." + "text": "Fig 2. Misclassification correction results" }, { - "id": 146912, - "strid": "fce020eb-c3d1-4cbb-aa84-194b2d368362", - "image_id": 206203, - "image_name": "18835.png", + "id": 418, + "strid": "1afb26f1-9ea4-4f1c-ae9a-c0f9bafb9b73", + "image_id": 16, + "image_name": "10739.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1589.207, - 1207.606, - 1442.314, - 657.511 - ], - "priority": 14, - "parents": [ - 146898 - ], - "children": [], - "area": 1919135.9084420002, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 146909, - "strid": "5f2085c9-8a73-40b6-933a-815cdfe006c5", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 7, - "category_name": "Table", - "bbox": [ - 1735.219, - 1888.408, - 900.877, - 314.2739999999999 + 1947.141, + 3133.643, + 925.7150000000001, + 305.297 ], - "priority": 15, + "priority": 11, "parents": [ - 146898 + 415 ], "children": [ - 146907 + 419 ], - "area": 3276801.441352, + "area": 6101644.764663001, "iscrowd": 0, "segmentation": [] }, { - "id": 146907, - "strid": "18f42b32-6bd9-472e-840c-b1105142311f", - "image_id": 206203, - "image_name": "18835.png", + "id": 419, + "strid": "02dd462c-d0a9-418c-afe0-61c25f3b279b", + "image_id": 16, + "image_name": "10739.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 2695.406, - 1992.808, - 312.87300000000005, - 139.6329999999998 - ], - "priority": 16, - "parents": [ - 146909 - ], - "children": [], - "area": 5371426.640048, - "iscrowd": 0, - "segmentation": [], - "text": "Table 1:\nGenes with\nunique\ncompounds" - }, - { - "id": 146899, - "strid": "0b5d99f3-6c2f-4fef-b061-4ab48fb2d436", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 3220.74, - 407.323, - 463.40099999999984, - 34.803999999999974 - ], - "priority": 17, - "parents": [ - 146914 - ], - "children": [ - 146904 - ], - "area": 1311881.4790199997, - "iscrowd": 0, - "segmentation": [], - "text": "S CUS SION" - }, - { - "id": 146904, - "strid": "3808d2e8-1053-4cc5-b9ca-e19cd7d57a1b", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 3101.949, - 528.37, - 855.6089999999999, - 731.8470000000001 + 2226.403, + 3599.278, + 389.5720000000001, + 27.916999999999916 ], - "priority": 18, + "priority": 12, "parents": [ - 146899 + 418 ], "children": [], - "area": 1638976.7931300001, + "area": 8013443.337033999, "iscrowd": 0, "segmentation": [], - "text": "he 51 genes down -\nlated ° the network\nc i several\ngulation of\nation and\n\nadhesion,\na resp e to Low -\ny lipoprotein particle\nus, and\n\n\"5 -O 9050\n\nAs>TOOPH—xVO\n3\n\n44 genes up-regulated\nipate in kinase and\n\nr\ne pathways,\nother metabolic\nignaling pathways.\n\na\n\n\"XO \"OF TYNAA*TTTO *\n—s x3\n\na7\n\nA .\n\n=\n\nRo\n\nQqa-\n\nDespite the compounds, mo\no f them are Antineoplasti\nand Immunomodula\nAgents, inhibitors\nproteasome targets.\n\no3 ry\n-Q 0 &" + "text": "Fig 3. Incompleteness estimation results" }, { - "id": 146900, - "strid": "678111e0-8f41-4b6e-b875-e0d36701090b", - "image_id": 206203, - "image_name": "18835.png", + "id": 420, + "strid": "f1b8a5a1-dc9e-460a-bd13-c03452c34af5", + "image_id": 16, + "image_name": "10739.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3219.809, - 1363.872, - 540.741, - 34.769000000000005 + 131.224, + 3699.424, + 431.18800000000005, + 36.4340000000002 ], - "priority": 19, + "priority": 13, "parents": [ - 146914 + 407 ], "children": [ - 146903 - ], - "area": 4391407.3404480005, - "iscrowd": 0, - "segmentation": [], - "text": "" - }, - { - "id": 146903, - "strid": "f7b6cb62-8d7c-416f-94aa-0ffde622ce5a", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 3102.666, - 1491.639, - 869.1880000000001, - 401.163 - ], - "priority": 20, - "parents": [ - 146900 + 421 ], - "children": [], - "area": 4628057.609574, + "area": 485453.21497599996, "iscrowd": 0, "segmentation": [], - "text": "studies.\n\niological" + "text": "Discussion and conclusion:" }, { - "id": 146901, - "strid": "c85da70e-fca0-4017-ac40-7a3c5668df3d", - "image_id": 206203, - "image_name": "18835.png", - "category_id": 5, - "category_name": "Section", + "id": 421, + "strid": "baf1057a-8071-4f0d-a0e4-5c75de30f9aa", + "image_id": 16, + "image_name": "10739.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 3138.539, - 1941.604, - 796.5520000000001, - 34.39200000000005 + 132.04, + 3743.898, + 2866.63, + 79.2159999999999 ], - "priority": 21, + "priority": 14, "parents": [ - 146914 + 420 ], "children": [], - "area": 6093799.876556001, + "area": 494344.29192, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 4423, - "strid": "248b38ec-f107-4c32-91d3-05c920b289f9", - "image_id": 200683, - "image_name": "10595.png", + "id": 422, + "strid": "1c984ab4-f10f-4673-9664-5336e8139920", + "image_id": 17, + "image_name": "10746.png", "category_id": 9, "category_name": "Root", "bbox": [ - 345.98, - 316.05, - 185.17999999999995, - 172.40999999999997 + 1060.2, + 27.46, + 116.69000000000005, + 121.00999999999999 ], "priority": -1, "parents": [], "children": [ - 4406, - 4399, - 4412, - 4397, - 4401, - 4400, - 4402, - 4405, - 4403, - 4404, - 4407, - 4396, - 4398 + 432, + 444, + 424, + 429, + 446, + 425, + 427, + 423 ], - "area": 109346.979, + "area": 29113.092, "iscrowd": 0, "segmentation": [] }, { - "id": 4396, - "strid": "77d06594-b552-40e7-a1b3-34ad9b80276e", - "image_id": 200683, - "image_name": "10595.png", + "id": 423, + "strid": "0063223d-12c3-407c-bcaf-a29cebaa945a", + "image_id": 17, + "image_name": "10746.png", "category_id": 1, "category_name": "Title", "bbox": [ - 715.473, - 97.569, - 2560.519, - 273.629 + 1677.27, + 28.925, + 1442.75, + 151.75 ], "priority": 1, "parents": [ - 4423 + 422 ], "children": [], - "area": 69807.985137, + "area": 48515.03475, "iscrowd": 0, "segmentation": [], - "text": "Evolutionary conservation of Ebola virus proteins\npredicts important functions at residue level" + "text": "Association of Hyponatremia with Infectious Outcomes\nFollowing Liver Transplantation" }, { - "id": 4397, - "strid": "5df094cf-188a-473e-8377-64f92173df35", - "image_id": 200683, - "image_name": "10595.png", + "id": 424, + "strid": "e8a7a95b-42ca-428e-8c98-963cae93fdc5", + "image_id": 17, + "image_name": "10746.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 735.091, - 409.722, - 1844.0790000000002, - 167.17200000000003 + 760.221, + 194.804, + 3277.584, + 98.51599999999999 ], "priority": 2, "parents": [ - 4423 + 422 ], "children": [], - "area": 301182.954702, + "area": 148094.091684, "iscrowd": 0, "segmentation": [], - "text": "A. Arslan* and V. van Noort\nCentre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S),\nKU Leuven, Kasteelpark Arenberg 22 —box 2460, 3001 Leuven, Belgium. *presenting author, ahmed.arslan@biw.kuleuven.be" + "text": "Christos A Koutentis!, Gebhard Wagener’, Jianfang Liu* Elaine Larson!\nMailman School of Public Health, Columbia University, New York, NY, 7Department of Anesthesiology, Columbia University, New York, NY, *School of Nursing, Columbia University, New York, NY" }, { - "id": 4398, - "strid": "5da104e9-9c23-49e5-88a5-0690bb3ba23c", - "image_id": 200683, - "image_name": "10595.png", + "id": 425, + "strid": "09752857-a41b-4dde-8803-c82fb0414020", + "image_id": 17, + "image_name": "10746.png", "category_id": 5, "category_name": "Section", "bbox": [ - 63.212, - 710.796, - 316.784, - 61.48299999999995 + 57.345, + 330.87, + 242.52400000000003, + 34.21300000000002 ], "priority": 3, "parents": [ - 4423 + 422 ], "children": [ - 4408 + 426 ], - "area": 44930.836752, + "area": 18973.74015, "iscrowd": 0, "segmentation": [], - "text": "Background" + "text": "Introduction" }, { - "id": 4408, - "strid": "45637b19-2a01-4a62-be5b-4c51b5102390", - "image_id": 200683, - "image_name": "10595.png", + "id": 426, + "strid": "57de249c-6134-438a-8d60-edea662d0a9e", + "image_id": 17, + "image_name": "10746.png", "category_id": 3, "category_name": "Text", "bbox": [ - 65.541, - 857.114, - 979.988, - 599.635 + 58.383, + 421.777, + 1069.151, + 146.209 ], "priority": 4, "parents": [ - 4398 + 425 ], "children": [], - "area": 56176.108674, + "area": 24624.606591, "iscrowd": 0, "segmentation": [], - "text": "Ebola Virus (EBOV), a member of Filoviridae family,\ncauses severe hemorrhagic fever known as Ebola Virus\nDisease (EVD) with a mortality rate of up to 90%.\n\nThe recent outbreak of EVD resulted in a large number of\nhuman deaths; moreover there is no suitable medicine\ncommercially available to date for EVD. Due to this dev-\nastation and lack of medication, EBOV has attracted re-\nnewed interest as model for virus evolution.\n\nRecent literature on EBOV has improved our under-\nstanding of the underlying genetics and its scope with ref-\nerence to the 2014 outbreak. But no study yet, has fo-\ncused on the conservation patterns of EBOV proteins\nthat can contribute to the virus fitness and onset of EVD." + "text": "Hyponatremia (hNa) and its rapid correction are associated with increased hospital length of stay (LOS),\nmortality, renal dysfunction and inflammatory processes after liver transplantation. It is generally assumed\nthat these adverse outcomes are due to neurological complications, however, electrolyte and osmolality\nderangements may contribute to other complications as well. The independent effect of hyponatremia on\ninfectious outcomes after liver transplants has not been previously described." }, { - "id": 4399, - "strid": "f13423cf-c298-45c7-ab85-a3d6962b38c3", - "image_id": 200683, - "image_name": "10595.png", + "id": 427, + "strid": "69fc9898-0616-41dc-92f3-bc4682deae92", + "image_id": 17, + "image_name": "10746.png", "category_id": 5, "category_name": "Section", "bbox": [ - 77.118, - 1566.558, - 108.95999999999998, - 49.317999999999984 + 58.055, + 739.909, + 166.579, + 33.888000000000034 ], "priority": 5, "parents": [ - 4423 + 422 ], "children": [ - 4409 + 428 ], - "area": 120809.819844, + "area": 42955.416995, "iscrowd": 0, "segmentation": [], - "text": "Aim" + "text": "" }, { - "id": 4409, - "strid": "fe0e58c9-8c09-43e4-b05f-bac521498269", - "image_id": 200683, - "image_name": "10595.png", + "id": 428, + "strid": "314adb0d-b9f4-439a-a32f-e84ac53e04cf", + "image_id": 17, + "image_name": "10746.png", "category_id": 3, "category_name": "Text", "bbox": [ - 59.573, - 1670.902, - 989.4130000000001, - 184.76 + 56.465, + 826.693, + 1107.884, + 326.1099999999999 ], "priority": 6, "parents": [ - 4399 + 427 ], "children": [], - "area": 99540.64484600001, + "area": 46679.220245000004, "iscrowd": 0, "segmentation": [], - "text": "The aim is to understand the molecular biology of\nEVD by discovering most conserved regions of EBOV\nproteins and predicting their functional annotations\nwith computational tools." + "text": "This is a retrospective, single center study of 277 adult patients undergoing liver transplantation between\nJanuary 2006 and May 2009, that had been matched with an independent infectious disease database. The\noutcomes of interest were bloodstream, surgical site, urinary tract infections and pneumonia, - associated with\nS. aureus, K. pneumoniae, P. aeruginosa, enterococci, St. pneumoniae, or A. baumannii. hNa was defined as\nminimum Na<130mEq/L pre- day of transplantation (“preopNamin” on adjacent posters), and compared with\nperioperative increases (ANa) between 2 and 10mEq/L/24h to max Na on postoperative day 1. Covariates and\noutcomes were compared using two sample t-tests, y2-tests, Fisher's exact, and Kruskall-Wallis tests.\nUnivariate and multivariate logistic models were used to analyze associations of the infections with hNa,\ncontrolling for age, Donor Risk Index (DRI), Model for End Stage Liver Disease score (MELD),\nhepatocellular carcinoma (HCC), and BMI. We also investigated whether ANa influenced the effect of\npreoperative hyponatremia on the study infections, adjusted for diabetes, dialysis, or %A creatinine at 48h." }, { - "id": 4400, - "strid": "8c16303b-be12-47f9-abae-eaeb478b1a55", - "image_id": 200683, - "image_name": "10595.png", + "id": 429, + "strid": "94e60bbd-79b4-42e4-89dc-9117813f4064", + "image_id": 17, + "image_name": "10746.png", "category_id": 5, "category_name": "Section", "bbox": [ - 39.288, - 1975.632, - 194.72899999999998, - 48.39499999999998 + 57.52, + 1291.632, + 139.864, + 33.47199999999998 ], "priority": 7, "parents": [ - 4423 + 422 ], "children": [ - 4410 + 431, + 430 ], - "area": 77618.630016, + "area": 74294.67264, "iscrowd": 0, "segmentation": [], - "text": "Results" + "text": "" }, { - "id": 4410, - "strid": "86fa7151-2fe6-4a6a-970b-ddb4c4d18ce2", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 4, - "category_name": "List", + "id": 430, + "strid": "bd8395e2-eca3-4bf3-9d55-c51bfbd4975f", + "image_id": 17, + "image_name": "10746.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 36.623, - 2080.201, - 1005.7249999999999, - 1257.257 + 55.597, + 1382.964, + 1113.465, + 662.73 ], "priority": 8, "parents": [ - 4400 + 429 ], "children": [], - "area": 76183.201223, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 4404, - "strid": "fed58e1f-2ec4-4185-8bd1-33333c8c0bcb", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 65.438, - 3432.593, - 544.354, - 47.585000000000036 - ], - "priority": 9, - "parents": [ - 4423 - ], - "children": [ - 4411 - ], - "area": 224622.020734, + "area": 76888.649508, "iscrowd": 0, "segmentation": [], - "text": "Material and Methods" + "text": "Of 277 patients in the sample, 54 patients (19%) had preoperative hyponatremia hNa, and 68 (24%)\nexperienced a ANa>10mEq/24h. hNa patients had higher mean MELD scores than other patients (able 1: 27\nvs 20, p<0.0001), a higher prevalence of renal failure (p=0.01), and higher mean preoperative serum creatinine\n(n=258; 1.4 versus 1.1mg/dL, p=0.006). 38 (70%) hNa patients experienced a ANa>10mEq/24h (p<0.0001).\n\nThe incidence of infections was strongly associated with MELD, renal failure, preoperative and peak\ncreatinine at 48h and with ANa >6mEq/24h.\n\nInfections were also associated with increased hospital (HR 0.24 (0.17, 0.33)), intensive care unit LOS (HR\n0.29 (0.21 0.4)), and with mortality (HR 3.23 (1.99, 5.24)) all at p<0.0001.\n\nBoth hNa and ANa were associated with UTI (Zable 2: p=0.01, p=0.02), pneumonia (p=0.03, p=0.003), and\nwith Enterococcus (p=0.001, p=0.02). In logistic regression (Zable 3:), the crude odd ratios (OR) for the\nassociations of infections with hNa and ANa were statistically significant, but the adjusted ORs were not -\nalthough the association of infection with MELD was statistically significant. Model 2 includes both Na<130\nand ANa>10 without an interaction term; neither these nor the interaction p value in Table 3a is significantly\nassociated with infection, although the interaction effect size estimate of 0.77 is noteworthy. The Relative\nExcess Risk due to Interaction using the values in Figure I further suggests that there is positive interaction\non an additive and multiplicative scale.\n\nModel 3 controls for diabetes and age: This suggests that the true effect sizes are higher, and that neither\ndiabetes nor age contribute to infections.\n\nModel 4 adjusts for AKI estimates by 48h. These were calculated from the raw Creatinine values listed in\nTable 1." }, { - "id": 4411, - "strid": "566b0827-5fa7-4ff1-a014-57774f09a706", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 4, - "category_name": "List", + "id": 431, + "strid": "e4207cb4-6894-402b-ba82-3e1d18f13efd", + "image_id": 17, + "image_name": "10746.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 64.564, - 3538.017, - 963.5770000000001, - 1069.9840000000004 + 57.603, + 2068.912, + 1036.743, + 55.422000000000025 ], - "priority": 10, + "priority": 9, "parents": [ - 4404 + 429 ], "children": [], - "area": 228428.52958799998, + "area": 119175.537936, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Table 4: ANa=2 when adjusted for dialysis becomes significant. Adjusting for AKI at 48h when ANa=8&\nbecomes more significant" }, { - "id": 4402, - "strid": "a8a3220b-1ada-4a17-8855-ba2ae86f8532", - "image_id": 200683, - "image_name": "10595.png", + "id": 432, + "strid": "acb8b3bd-7f7b-48d2-8e64-58b647b3fb60", + "image_id": 17, + "image_name": "10746.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1090.678, - 712.731, - 1014.2480000000003, - 59.053999999999974 + 2931.562, + 331.177, + 140.16600000000017, + 34.47800000000001 ], - "priority": 11, + "priority": 10, "parents": [ - 4423 + 422 ], "children": [ - 4419 + 438, + 440, + 437, + 435, + 433, + 442 ], - "area": 777360.0216180001, + "area": 970865.908474, "iscrowd": 0, "segmentation": [], - "text": "PTMs present at GP conserved residues" + "text": "" }, { - "id": 4419, - "strid": "d1967840-af65-4c53-bd6e-ff8809346785", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 2, - "category_name": "Figure", + "id": 433, + "strid": "6536ff64-774f-45d2-a346-40c4056ddc70", + "image_id": 17, + "image_name": "10746.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1126.254, - 805.959, - 987.0299999999997, - 560.6240000000001 + 1297.013, + 550.015, + 1070.018, + 833.985 ], - "priority": 12, + "priority": 11, "parents": [ - 4402 + 432 ], "children": [ - 4421 + 434 ], - "area": 907714.5475859998, + "area": 713376.605195, "iscrowd": 0, "segmentation": [] }, { - "id": 4421, - "strid": "839551ee-07b1-4e16-b8d2-834fb462752d", - "image_id": 200683, - "image_name": "10595.png", + "id": 434, + "strid": "84f74a07-ec6e-4301-b12c-7da20a1c96c6", + "image_id": 17, + "image_name": "10746.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1092.412, - 1413.085, - 1042.331, - 88.64100000000008 + 1303.17, + 451.29, + 1048.411, + 76.15799999999996 ], - "priority": 13, + "priority": 12, "parents": [ - 4419 + 433 ], "children": [], - "area": 1543671.01102, + "area": 588107.5893000001, "iscrowd": 0, "segmentation": [], - "text": "Figure: The ConSurf diagram (Celinker et al 2013) of GP protein two types of structural views\n(left: space-filled; right: ribbon) with different PTMs sites at cons. residues. (Abbreviation: P=-\nphosphorylation, GPI=GPl-anchor, O=o-linked glycosylation, M=Methylation)" + "text": "Table 1, 1096:\nDistribution of demographic, intraoperative and AKI related variables across categories of min Na pre- day of\ntransplantation and ANa of 10mEq/24h to max Na on day 1" }, { - "id": 4403, - "strid": "254ec75c-7eeb-40f9-b378-538edb99f9e0", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 5, - "category_name": "Section", + "id": 435, + "strid": "ff58d6d1-7121-4a89-be5e-bf3e1d43fd01", + "image_id": 17, + "image_name": "10746.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2166.43, - 711.767, - 1127.0170000000003, - 60.650999999999954 + 1296.982, + 1634.005, + 1045.031, + 569.9920000000002 ], - "priority": 14, + "priority": 13, "parents": [ - 4423 + 432 ], "children": [ - 4420 + 436 ], - "area": 1541993.38181, + "area": 2119275.07291, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 436, + "strid": "a40d9a47-d314-422a-817c-2d27e8880751", + "image_id": 17, + "image_name": "10746.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 1303.217, + 1547.014, + 913.56, + 75.83200000000011 + ], + "priority": 14, + "parents": [ + 435 + ], + "children": [], + "area": 2016094.944038, "iscrowd": 0, "segmentation": [], - "text": "PTMs present at conserved interface residue" + "text": "Table 2, 1096:\nComparison of Infectious outcomes across preoperative hyponatremia <130mEq/DL, and ANa >\n10mEq/L/24h" }, { - "id": 4420, - "strid": "68a1c5df-6501-4e24-8878-fec826c3f613", - "image_id": 200683, - "image_name": "10595.png", + "id": 437, + "strid": "dead8de9-a367-4a84-8024-1fc2818b9cb5", + "image_id": 17, + "image_name": "10746.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2264.972, - 784.971, - 886.0210000000002, - 571.5630000000001 + 2450.501, + 433.524, + 973.509, + 1021.7479999999999 ], "priority": 15, "parents": [ - 4403 + 432 ], - "children": [ - 4422 - ], - "area": 1777937.335812, + "children": [], + "area": 1062350.9955240001, "iscrowd": 0, "segmentation": [] }, { - "id": 4422, - "strid": "9303b83a-fb29-4043-be99-37452a86ef06", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 6, - "category_name": "Caption", + "id": 438, + "strid": "d1440f70-0d0d-42ef-ae28-092186b2251b", + "image_id": 17, + "image_name": "10746.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2250.769, - 1408.234, - 963.748, - 59.013999999999896 + 2388.037, + 1542.621, + 1098.6460000000002, + 478.6869999999999 ], "priority": 16, "parents": [ - 4420 + 432 ], - "children": [], - "area": 3169609.4319459996, + "children": [ + 439 + ], + "area": 3683836.024977, "iscrowd": 0, - "segmentation": [], - "text": "Figure: The PTMs position at interface of two complexes between virus molecules, (A)\nVP35 and RNA (B) NP and VP35; whereas PTM positions are shown in red." + "segmentation": [] }, { - "id": 4401, - "strid": "89bc8248-4ae0-4be0-90a3-c63488dbeca4", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 5, - "category_name": "Section", + "id": 439, + "strid": "74cdeed8-6596-40c7-825b-e30084d7328c", + "image_id": 17, + "image_name": "10746.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1139.121, - 1570.698, - 730.394, - 60.03099999999995 + 2398.436, + 1492.638, + 851.1959999999999, + 48.54899999999998 ], "priority": 17, "parents": [ - 4423 - ], - "children": [ - 4418 + 438 ], - "area": 1789215.0764580003, + "children": [], + "area": 3579996.714168, "iscrowd": 0, "segmentation": [], - "text": "EBOV proteins Conservation" + "text": "Table 3, 1096:\nInfection with organism of interest: ORs (CI 95%) in Univariate and Multivariate models" }, { - "id": 4418, - "strid": "c96a4070-a077-490e-bf4f-94ca00ff6d5e", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 2, - "category_name": "Figure", + "id": 440, + "strid": "587f8b96-7a21-4703-bf29-805479b84fd0", + "image_id": 17, + "image_name": "10746.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1243.699, - 1695.806, - 1775.7649999999999, - 1150.6690000000003 + 2388.991, + 2168.008, + 638.0259999999998, + 201.9920000000002 ], "priority": 18, "parents": [ - 4401 + 432 ], "children": [ - 4415 + 441 ], - "area": 2109072.226394, + "area": 5179351.599927999, "iscrowd": 0, "segmentation": [] }, { - "id": 4415, - "strid": "b82b8305-8ff9-4b5d-bd89-580933c0f3cf", - "image_id": 200683, - "image_name": "10595.png", + "id": 441, + "strid": "b9139bba-5072-4365-a574-08b91b3f02cb", + "image_id": 17, + "image_name": "10746.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1137.13, - 2921.008, - 1882.625, - 29.73700000000008 + 2395.48, + 2110.646, + 573.038, + 38.48000000000002 ], "priority": 19, "parents": [ - 4418 + 440 ], "children": [], - "area": 3321565.82704, + "area": 5056010.280080001, "iscrowd": 0, "segmentation": [], - "text": "Figure: The ConSurf diagrams of EBOV proteins shows conserved residues in respective secondary structures. (red is the most conserved one and blue is most variable)" + "text": "Table 3a, 1096:\nAnalysis of Maximum Likelihood Estimates between ANa>10 and preop Na<130" }, { - "id": 4405, - "strid": "3d705c32-3d11-4fd0-ad34-52524d791b7b", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 5, - "category_name": "Section", + "id": 442, + "strid": "c242da52-ef85-4ca9-8264-398b871e984e", + "image_id": 17, + "image_name": "10746.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1104.717, - 3035.746, - 765.117, - 51.733000000000175 + 3569.011, + 566.023, + 1182.0120000000002, + 495.977 ], "priority": 20, "parents": [ - 4423 - ], - "children": [ - 4417 - ], - "area": 3353640.213882, - "iscrowd": 0, - "segmentation": [], - "text": "ATM “Junction Kinase’”in EVD" - }, - { - "id": 4417, - "strid": "6faed6b4-8fd9-4f81-9de3-5667581a782d", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1094.968, - 3202.571, - 1094.6379999999997, - 665.7049999999999 - ], - "priority": 21, - "parents": [ - 4405 + 432 ], "children": [ - 4416 + 443 ], - "area": 3506712.762728, + "area": 2020142.3132530001, "iscrowd": 0, "segmentation": [] }, { - "id": 4416, - "strid": "a23f012b-d7e2-4feb-b463-051c3032d8ea", - "image_id": 200683, - "image_name": "10595.png", + "id": 443, + "strid": "b22c2c10-bd22-4d6d-b263-a980e159bdcd", + "image_id": 17, + "image_name": "10746.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 1109.784, - 3921.323, - 1030.424, - 118.61799999999994 + 3578.508, + 466.947, + 1066.1660000000002, + 73.51800000000003 ], - "priority": 22, + "priority": 21, "parents": [ - 4417 + 442 ], "children": [], - "area": 4351821.524232, + "area": 1670973.5750759998, "iscrowd": 0, "segmentation": [], - "text": "Figure: The role of ATM kinase in different EVD related pathways. The functions of DNA\ndamage response element, ATM, elucidated in four closely related and virus exploited path-\nways under stress.The blue arrows show the published interactions, black arrows normal cell\nsignaling and green shows the predicted phosphorylation on VP40 by ATM in out analysis." + "text": "Table 4, 1096:\nInfection with organism of interest: ORs (95%CTI) in Comparison of severity of ANa, controlling for Dialysis as a\ncovariate, or %A Creatinine levels" }, { - "id": 4406, - "strid": "64f546f0-5da3-4191-bf3c-4f612f4849e8", - "image_id": 200683, - "image_name": "10595.png", + "id": 444, + "strid": "2c8f4f1e-72ab-4a5c-b227-8501db121f13", + "image_id": 17, + "image_name": "10746.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2240.21, - 3039.606, - 293.2159999999999, - 49.23100000000022 + 3614.395, + 1411.733, + 230.40200000000004, + 34.94900000000007 ], - "priority": 23, + "priority": 22, "parents": [ - 4423 + 422 ], "children": [ - 4413 + 445 ], - "area": 6809355.75726, + "area": 5102560.696535, "iscrowd": 0, "segmentation": [], - "text": "Conclusion" + "text": "Conclusions" }, { - "id": 4413, - "strid": "422d3953-cf24-491f-bb46-9f77af29ea43", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 3, - "category_name": "Text", + "id": 445, + "strid": "8978efdb-738b-4fab-85c9-1cf1901b8606", + "image_id": 17, + "image_name": "10746.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2241.186, - 3143.959, - 960.1300000000001, - 185.13799999999992 + 3647.556, + 1514.166, + 1023.4959999999996, + 323.5640000000001 ], - "priority": 24, + "priority": 23, "parents": [ - 4406 + 444 ], "children": [], - "area": 7046196.895374, + "area": 5523005.278295999, "iscrowd": 0, - "segmentation": [], - "text": "Based on our results and current understanding of EVD\ndependent activated pathways, an association is\n\nanticipated of ATM kinase with these pathways and\nkinases through which Ebola pathology is achieved." + "segmentation": [] }, { - "id": 4407, - "strid": "dc4a1541-a4a8-4236-8f7e-9b9c10c5c32d", - "image_id": 200683, - "image_name": "10595.png", + "id": 446, + "strid": "54a7fdaa-e0ad-429b-ab44-b5251089c99a", + "image_id": 17, + "image_name": "10746.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2238.766, - 3432.566, - 450.38099999999986, - 53.934999999999945 + 3608.538, + 1987.938, + 371.817, + 43.909000000000106 ], - "priority": 25, + "priority": 24, "parents": [ - 4423 + 422 ], "children": [ - 4414 + 447 ], - "area": 7684712.053556, + "area": 7173549.8146440005, "iscrowd": 0, "segmentation": [], "text": "Acknowledgements" }, { - "id": 4414, - "strid": "8f06ac8d-c723-4652-af68-caf5e47f9cdc", - "image_id": 200683, - "image_name": "10595.png", + "id": 447, + "strid": "50bb3e31-bffa-4e7d-9c56-14edbba076d3", + "image_id": 17, + "image_name": "10746.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2240.484, - 3525.099, - 941.634, - 116.46399999999994 + 3632.357, + 2090.262, + 1132.862, + 209.14300000000003 ], - "priority": 26, + "priority": 25, "parents": [ - 4407 + 446 ], "children": [], - "area": 7897927.907916, + "area": 7592577.807534001, "iscrowd": 0, "segmentation": [], - "text": "| would like to thank to the people at Harvard and MIT, who pro-\nvided the genomic sequences of EBOV. Also, | would like to\nthanks CMPG/CSB group for their guidance and support." - }, - { - "id": 4412, - "strid": "623d6be0-66b3-4a83-97dc-ce757d5c72bd", - "image_id": 200683, - "image_name": "10595.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 2242.398, - 3801.605, - 542.857, - 268.14699999999993 - ], - "priority": 27, - "parents": [ - 4423 - ], - "children": [], - "area": 8524711.44879, - "iscrowd": 0, - "segmentation": [] + "text": "Funding provided in part by NIH, ROINRO10822\n\nJianfang Liu and Elaine Larson for sharing their infectious disease dataset and invaluable guidance. Jianfang Liu\nfor her highly imaginative and original approach with SAS code in merging the databases.\n\nGebhard Wagener for sharing the Anesthesia dataset, and guidance.\nKim Love for Statistical guidance\nChris Reich for assistance in preparing posters." }, { - "id": 74751, - "strid": "bb7bdac0-965f-4ed5-8685-74064243a5f6", - "image_id": 203414, - "image_name": "120189.png", + "id": 448, + "strid": "8fe0a95c-8b97-4690-9dd1-52346a6f24b5", + "image_id": 18, + "image_name": "10784.png", "category_id": 9, "category_name": "Root", "bbox": [ - 80.42, - 149.17, - 399.33, - 325.99 + 3892.51, + 389.85, + 125.78999999999996, + 143.76 ], "priority": -1, "parents": [], "children": [ - 74742, - 74734, - 74733, - 74749, - 74737, - 74735 + 457, + 450, + 449, + 453, + 451, + 464 ], - "area": 11996.2514, + "area": 1517495.0235000001, "iscrowd": 0, "segmentation": [] }, { - "id": 74733, - "strid": "f6e553e3-fd04-4b1d-bb3b-797fa42b610b", - "image_id": 203414, - "image_name": "120189.png", + "id": 449, + "strid": "2dabca0d-434a-4495-9c04-c4e11f4b87d0", + "image_id": 18, + "image_name": "10784.png", "category_id": 1, "category_name": "Title", "bbox": [ - 510.605, - 47.843, - 2596.155, - 220.745 + 60.802, + 101.418, + 3015.8, + 123.91 ], "priority": 1, "parents": [ - 74751 + 448 ], "children": [], - "area": 24428.875015, + "area": 6166.417236, "iscrowd": 0, "segmentation": [], - "text": "Estimation of Cortical Thickness from T1- weighted MR Images\nusing Tissue Fractions\n\n \n\ni" + "text": "Genomic signatures to guide gastric cancer chemotherapy" }, { - "id": 74734, - "strid": "96ba31fa-1607-44da-8c20-e2319dd06c23", - "image_id": 203414, - "image_name": "120189.png", + "id": 450, + "strid": "1c36acf6-4d95-4b5a-858b-85df7a19365f", + "image_id": 18, + "image_name": "10784.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 630.575, - 270.987, - 2349.017, - 249.53800000000007 + 122.874, + 290.029, + 2036.0159999999998, + 267.972 ], "priority": 2, "parents": [ - 74751 + 448 ], "children": [], - "area": 170877.62752500002, + "area": 35637.023346, "iscrowd": 0, "segmentation": [], - "text": "Anand A. Joshi2, Chitresh Bhushan?, Ronald Salloum?, David W. Shattuck?, Richard M. Leahy?\n\n1Signal and Image Processing Institute, University of Southern California, Los Angeles, USA\n2Brain and Creativity Institute, University of Southern California, Los Angeles, USA\n3Ahmanson-Lovelace Brain Mapping Center, University of California, Los Angeles, USA" + "text": "Zhengdeng Lei*, Hong Hu, George Chlipala, Pinal Kanabar,\nMorris Chukhman and Mark Maienschein-Cline\n\n*Correspondence: zlei2@uic.edu Center for Research Informatics, University of Illinois at Chicago" }, { - "id": 74735, - "strid": "f65e0594-f39b-4abb-81b0-a4908879207e", - "image_id": 203414, - "image_name": "120189.png", + "id": 451, + "strid": "30c8fe4c-00af-4e17-9cab-81a0cb87aa35", + "image_id": 18, + "image_name": "10784.png", "category_id": 5, "category_name": "Section", "bbox": [ - 840.821, - 599.926, - 214.2510000000001, - 48.898000000000025 + 577.975, + 624.26, + 289.5, + 63.648000000000025 ], "priority": 3, "parents": [ - 74751 + 448 ], "children": [ - 74736 + 452 ], - "area": 504430.379246, + "area": 360806.67350000003, "iscrowd": 0, "segmentation": [], "text": "Abstract" }, { - "id": 74736, - "strid": "6b2dcc06-2a45-4e42-b9bb-b443483ac438", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 4, - "category_name": "List", + "id": 452, + "strid": "e10ffb36-3d2e-4e47-91b3-64ef8d7e677f", + "image_id": 18, + "image_name": "10784.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 35.615, - 690.234, - 1705.479, - 1085.502 + 72.985, + 729.572, + 1271.766, + 696.917 ], "priority": 4, "parents": [ - 74735 + 451 ], "children": [], - "area": 24582.683910000003, + "area": 53247.81242, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "In the past years, scientists have been searching for genomic signatures\nto guide the use of chemotherapeutics. We have witnessed the Duke\nUniversity’s scandal [1], but also the successfully story of Oncotype Dx\ntest [2]. In the present study, we are going to use machine learning\ntechnology to investigate if the genomic signatures derived from gastric\ntumors can guide the chemotherapy. We validate the results in multiple\npatient cohorts. Previously, We have identified three subtypes of gastric\ncancer based on gene expression of gastric tumors [8]. The three\nidentified subtypes are termed as: \"Mesenchymal (Angiogenic)\",\n\"Proliferative\", and \"Metabolic\". In the current study, we re-confirmed that\nmetabolic subtype patients benefited from 5-fluorouracil (5-FU)\nchemotherapy, and proposed that proliferative subtype patients would\npotentially benefit from taxane (paclitaxel), and mesenchymal subtype\npatients might benefit from angiogenesis inhibitors or PISK/ATK/mTOR\ninhibitors." }, { - "id": 74737, - "strid": "f904c668-ce1e-442f-a998-980995d6cf42", - "image_id": 203414, - "image_name": "120189.png", + "id": 453, + "strid": "a79a1e88-4f1b-40ea-8efc-3e902673b3e7", + "image_id": 18, + "image_name": "10784.png", "category_id": 5, "category_name": "Section", "bbox": [ - 821.677, - 1799.962, - 228.438, - 49.152000000000044 + 492.822, + 1570.344, + 424.76200000000006, + 66.25199999999995 ], "priority": 5, "parents": [ - 74751 + 448 ], "children": [ - 74738, - 74739, - 74741 + 456, + 455, + 454 ], - "area": 1478987.376274, + "area": 773900.070768, "iscrowd": 0, "segmentation": [], - "text": "Methods" + "text": "Introduction" }, { - "id": 74738, - "strid": "acae79bd-8184-4879-a4c6-fc9d625ba12a", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 4, - "category_name": "List", + "id": 454, + "strid": "2e377212-c59c-4d51-a630-1a2dfa6115a5", + "image_id": 18, + "image_name": "10784.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 58.191, - 1885.465, - 1645.371, - 380.52600000000007 + 70.555, + 1659.3, + 1276.192, + 380.289 ], "priority": 6, "parents": [ - 74737 + 453 ], "children": [], - "area": 109717.093815, + "area": 117071.9115, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Gastric cancer remains one of most commonly diagnosed cancers and\none of most deadly cancers worldwide. Gene expression profiling of\ngastric tumors has been proved useful in identification of molecular\nsubtypes of gastric cancer. Previously, we have identified three subtypes\nof gastric cancer termed: “Mesenchymal (Angiogenic)”, “Proliferative”,\nand “Metabolic”. These subtypes show distinct biological properties and\nresponses to chemotherapy and targeted agents.\n\nGastric cancer patients" }, { - "id": 74739, - "strid": "f1bed759-82dc-4883-a4a6-7e437cffc5f3", - "image_id": 203414, - "image_name": "120189.png", + "id": 455, + "strid": "78e5d91f-a464-4e00-9c1d-b6c3371ac17b", + "image_id": 18, + "image_name": "10784.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 176.101, - 2276.71, - 1461.3609999999999, - 398.3910000000001 + 187.29, + 2049.69, + 888.279, + 865.904 ], "priority": 7, "parents": [ - 74737 - ], - "children": [ - 74740 + 453 ], - "area": 400930.90771, + "children": [], + "area": 383886.4401, "iscrowd": 0, "segmentation": [] }, { - "id": 74740, - "strid": "229f5a6f-2596-4436-96b4-d2b62605f20d", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 6, - "category_name": "Caption", + "id": 456, + "strid": "e7f91ac0-5213-479b-a0b9-33d49696b511", + "image_id": 18, + "image_name": "10784.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 127.419, - 2682.502, - 1561.93, - 209.79100000000017 + 319.301, + 2946.918, + 675.7180000000001, + 590.694 ], "priority": 8, "parents": [ - 74739 + 453 ], "children": [], - "area": 341801.72233799996, + "area": 940953.864318, "iscrowd": 0, - "segmentation": [], - "text": "Figure 1: Thickness estimation procedure. (a) Gray-matter fraction estimated using a\npartial volume model; (b) Temperature map obtained using the proposed ALE\nmethod; and (c) Thickness estimate using the ALE method shown on the estimated\nmid-cortical surface." + "segmentation": [] }, { - "id": 74741, - "strid": "628fa42b-d035-4c80-96a1-da4198f43208", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 4, - "category_name": "List", + "id": 457, + "strid": "33f0fd6f-9882-4073-a5fe-44145693e678", + "image_id": 18, + "image_name": "10784.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 34.316, - 2913.779, - 1693.083, - 1741.6700000000005 + 1973.628, + 638.054, + 254.07100000000014, + 65.52599999999995 ], "priority": 9, "parents": [ - 74737 + 448 ], - "children": [], - "area": 99989.240164, + "children": [ + 463, + 458, + 462, + 460, + 461, + 459 + ], + "area": 1259281.2399119998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Results" }, { - "id": 74742, - "strid": "de546dd4-6cc0-4757-a8a4-47901bddf99e", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 5, - "category_name": "Section", + "id": 458, + "strid": "06efd0fd-d3ab-437d-af69-b5c66cad47c0", + "image_id": 18, + "image_name": "10784.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2637.61, - 601.698, - 180.82999999999993, - 46.572 + 1443.231, + 749.357, + 1326.914, + 1208.507 ], "priority": 10, "parents": [ - 74751 - ], - "children": [ - 74746, - 74743, - 74744, - 74747 + 457 ], - "area": 1587044.66178, + "children": [], + "area": 1081495.252467, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 74743, - "strid": "e310b309-2d39-419a-95fd-9af271edc352", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 4, - "category_name": "List", + "id": 459, + "strid": "5031c9fc-3793-44c6-9954-d6044d32c32e", + "image_id": 18, + "image_name": "10784.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1871.619, - 698.605, - 1685.1379999999997, - 772.1770000000001 + 1444.752, + 2047.452, + 1277.6, + 1391.711 ], "priority": 11, "parents": [ - 74742 + 457 ], "children": [], - "area": 1307522.3914949999, + "area": 2958060.3719039997, "iscrowd": 0, "segmentation": [] }, { - "id": 74744, - "strid": "c9a8f370-308b-44d2-963f-efd73eb8e3bf", - "image_id": 203414, - "image_name": "120189.png", + "id": 460, + "strid": "45c89a96-0f2a-4db7-a383-e502c6bd4854", + "image_id": 18, + "image_name": "10784.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1935.611, - 1481.447, - 1497.4260000000002, - 991.885 + 2854.364, + 646.791, + 1259.7000000000003, + 570.5569999999999 ], "priority": 12, "parents": [ - 74742 - ], - "children": [ - 74745 + 457 ], - "area": 2867505.109117, + "children": [], + "area": 1846176.945924, "iscrowd": 0, "segmentation": [] }, { - "id": 74745, - "strid": "85949c67-0d83-4b39-a049-a6057863a593", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 6, - "category_name": "Caption", + "id": 461, + "strid": "71024f5a-4e59-4532-8000-da2c5aa035a0", + "image_id": 18, + "image_name": "10784.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1938.269, - 2473.638, - 1562.5199999999998, - 204.48099999999977 + 2854.979, + 1233.147, + 1225.8290000000002, + 419.93499999999995 ], "priority": 13, "parents": [ - 74744 + 457 ], "children": [], - "area": 4794575.852622, + "area": 3520608.7889129994, "iscrowd": 0, - "segmentation": [], - "text": "Figure 2: Average,cortical thickness map estimated using (row 1) histological findings\nfrom literature. [4]*; (row 2) proposed Anisotropic Laplace Equation*(ALE) method;\n(row 3) Isotropic Laplace Equation (LE) method; and (row.4)-Linked Distance (LD)\nmethod," + "segmentation": [] }, { - "id": 74746, - "strid": "038bf9d2-6433-4e7d-bf86-535e72ab0e79", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 4, - "category_name": "List", + "id": 462, + "strid": "38590e77-3781-4e7e-921e-9f0ed6ecd39b", + "image_id": 18, + "image_name": "10784.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1868.999, - 2709.26, - 1679.907, - 635.4259999999999 + 2856.601, + 1662.606, + 1217.188, + 577.269 ], "priority": 14, "parents": [ - 74742 + 457 ], "children": [], - "area": 5063604.2307400005, + "area": 4749401.962206, "iscrowd": 0, "segmentation": [] }, { - "id": 74747, - "strid": "9ff72d1c-eb63-4b1b-b4aa-67b29db9fe25", - "image_id": 203414, - "image_name": "120189.png", + "id": 463, + "strid": "4091af19-f82a-4b4d-bcfe-29e98a18117a", + "image_id": 18, + "image_name": "10784.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1896.799, - 3394.329, - 762.511, - 691.0259999999998 + 2961.763, + 2300.287, + 1038.19, + 510.145 ], "priority": 15, "parents": [ - 74742 - ], - "children": [ - 74748 - ], - "area": 6438359.852871, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 74748, - "strid": "b274fa1f-fa94-4f9b-8c61-1f10c601ff0d", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 6, - "category_name": "Caption", - "bbox": [ - 2649.166, - 3598.04, - 885.2840000000001, - 157.82700000000023 - ], - "priority": 16, - "parents": [ - 74747 + 457 ], "children": [], - "area": 9531805.23464, + "area": 6812904.925980999, "iscrowd": 0, - "segmentation": [], - "text": "Figure 3: The p-valuexmap of significant left-to-\nright cortical thickness differences estimated\nusing the three different methods (LD, LE, ALE)." + "segmentation": [] }, { - "id": 74749, - "strid": "9116f1fd-2ec5-4a80-bbae-b5a080218a09", - "image_id": 203414, - "image_name": "120189.png", + "id": 464, + "strid": "37122e11-9cf4-4dec-b977-65a8972d31b3", + "image_id": 18, + "image_name": "10784.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2402.294, - 4156.703, - 664.1480000000001, - 50.904999999999745 + 3302.119, + 2904.469, + 371.2130000000002, + 65.60500000000002 ], - "priority": 17, + "priority": 16, "parents": [ - 74751 + 448 ], "children": [ - 74750 + 465 ], - "area": 9985622.676682001, + "area": 9590902.269811, "iscrowd": 0, "segmentation": [], - "text": "Discussion and Conclusion" + "text": "Conclusion" }, { - "id": 74750, - "strid": "5737b6c2-1fb7-4561-8887-c81c83c9cc4c", - "image_id": 203414, - "image_name": "120189.png", - "category_id": 4, - "category_name": "List", + "id": 465, + "strid": "a23c8cd2-0b5c-4fc4-bb45-fa2970e664eb", + "image_id": 18, + "image_name": "10784.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1838.641, - 4256.608, - 1703.629, - 574.0129999999999 + 2836.904, + 3012.599, + 1288.5880000000002, + 245.34000000000015 ], - "priority": 18, + "priority": 17, "parents": [ - 74749 + 464 ], "children": [], - "area": 7826373.989728001, + "area": 8546454.153496, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "We confirmed metabolic subtype gastric cancer patients benefited from\n5-FU chemotherapy. We had other evidence to show that proliferative\nsubtype patients would potentially benefit from taxane (paclitaxel), and\nmesenchymal subtype patients might benefit from angiogenesis inhibitors\nor PI3K/ATK/mTOR inhibitors." }, { - "id": 98154, - "strid": "a2dc1a3e-bd9a-4ca1-8727-ba056298fbaa", - "image_id": 204299, - "image_name": "12180.png", + "id": 466, + "strid": "149f76a8-9db1-4bd5-87a4-7bdbd7ec8b24", + "image_id": 19, + "image_name": "10967.png", "category_id": 9, "category_name": "Root", "bbox": [ - 7.23, - 1.74, - 19.8, - 45.54 + 45.63, + 62.46, + 208.5, + 167.95999999999998 ], "priority": -1, "parents": [], "children": [ - 98133, - 98131, - 98129, - 98147, - 98127, - 98151, - 98149, - 98141, - 98128, - 98135, - 98139, - 98153 + 469, + 493, + 485, + 477, + 495, + 467, + 483, + 468, + 489 ], - "area": 12.580200000000001, + "area": 2850.0498000000002, "iscrowd": 0, "segmentation": [] }, { - "id": 98127, - "strid": "792b9c1d-f2a5-41b9-be19-2239e9037cd6", - "image_id": 204299, - "image_name": "12180.png", + "id": 467, + "strid": "675711dc-79df-4a2d-9d9a-0ce524d1b0e3", + "image_id": 19, + "image_name": "10967.png", "category_id": 1, "category_name": "Title", "bbox": [ - 37.627, - 11.87, - 282.497, - 14.806 + 786.626, + 216.944, + 3222.897, + 303.8860000000001 ], "priority": 1, "parents": [ - 98154 + 466 ], "children": [], - "area": 446.63249, + "area": 170653.79094399998, "iscrowd": 0, "segmentation": [], - "text": "ide Memoire for Medical Ward rounds" + "text": "Transformational Apparent Motion is Driven By Figural\nParsing, Not Low-Level Motion Signals" }, { - "id": 98128, - "strid": "27368ba2-4d16-4ced-897c-a69d68fac7bb", - "image_id": 204299, - "image_name": "12180.png", + "id": 468, + "strid": "61d8bf6d-bba8-433f-b573-0562932f95ee", + "image_id": 19, + "image_name": "10967.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 660.649, - 42.309, - 171.33299999999997, - 115.827 + 1822.367, + 597.399, + 1159.657, + 116.399 ], "priority": 2, "parents": [ - 98154 + 466 ], "children": [], - "area": 27951.398541, + "area": 1088680.223433, "iscrowd": 0, "segmentation": [], - "text": "Doncaster and Bassetlaw\n\nTeaching Hospitals\nNHS Foundation Trust\n\nBy\nDr Aiyappa B Nanjappa\nCore Medical Trainee" + "text": "Kevin C. Hartstein & Peter U. Tse\nPsychological & Brain Sciences, Dartmouth College" }, { - "id": 98129, - "strid": "3ad075c6-26f5-4d85-a488-8b0d61de7c9d", - "image_id": 204299, - "image_name": "12180.png", + "id": 469, + "strid": "4cce5b4d-6e5f-4846-8841-8a81676c5b15", + "image_id": 19, + "image_name": "10967.png", "category_id": 5, "category_name": "Section", "bbox": [ - 7.771, - 62.222, - 101.988, - 15.131999999999998 + 58.322, + 815.698, + 400.223, + 61.94200000000001 ], "priority": 3, "parents": [ - 98154 + 466 ], "children": [ - 98130 + 474, + 471, + 470, + 475, + 472, + 476, + 473 ], - "area": 483.52716200000003, + "area": 47573.138756, "iscrowd": 0, "segmentation": [], - "text": "introduction:" + "text": "Introduction" }, { - "id": 98130, - "strid": "f08b8ab3-7d2a-4503-8a5c-c086d997196e", - "image_id": 204299, - "image_name": "12180.png", - "category_id": 3, - "category_name": "Text", + "id": 470, + "strid": "3e187474-06a8-4d83-8d37-030909c4fe5b", + "image_id": 19, + "image_name": "10967.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 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"children": [], - "area": 7510.4159, + "children": [ + 484 + ], + "area": 1341823.837488, "iscrowd": 0, "segmentation": [], - "text": "cic) osm eRe meL ict\nPeruri cmucraars\nPeer eaeaccn\neee iene aks etsy\nmeeCRe emus Ronse!\nBree eee an ecu\nDeen eye en\ncannulas )being reviewed and\nPeete Ree uiecccs\nERLE a ee tel" + "text": "Stimuli" }, { - "id": 98145, - "strid": "9b45599e-fe21-45f2-b511-19cfe8b3a03f", - "image_id": 204299, - "image_name": "12180.png", - "category_id": 6, - "category_name": "Caption", + "id": 484, + "strid": "2ef0d9cf-a0c5-4c9c-9fbb-190c54a52036", + "image_id": 19, + "image_name": "10967.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 12.304, - 781.849, - 777.947, - 40.55600000000004 + 1604.452, + 888.65, + 1507.354, + 1354.4719999999998 ], "priority": 18, "parents": [ - 98142 + 483 ], "children": [], - "area": 9619.870096, + "area": 1425796.2698, "iscrowd": 0, - "segmentation": [], - "text": "Investigations showed a 33% improvement, diagnosis 29% ,Medications 28%, Early warning score 36%\nce otuenecnneoec eee" + "segmentation": [] }, { - "id": 98143, - "strid": "d49c5389-a4a4-433f-9855-debf5705e66e", - "image_id": 204299, - "image_name": "12180.png", - "category_id": 2, - "category_name": "Figure", + "id": 485, + "strid": "ebf6af3d-7fc5-4552-a3b2-07c3be9bc3fc", + "image_id": 19, + "image_name": "10967.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 22.262, - 883.084, - 773.5830000000001, - 194.476 + 1635.592, + 2366.58, + 739.1289999999999, + 72.11799999999994 ], "priority": 19, "parents": [ - 98141 + 466 ], "children": [ - 98146 + 488, + 487, + 486 ], - "area": 19659.216008, + "area": 3870759.31536, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Results - Experiment 1" }, { - "id": 98146, - "strid": "393a9f2b-9eff-4973-9de8-7f795d7b5047", - "image_id": 204299, - "image_name": "12180.png", - "category_id": 6, - "category_name": "Caption", + "id": 486, + "strid": "31af07d7-7a13-4ea4-93af-8c96dd70720f", + "image_id": 19, + "image_name": "10967.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 13.042, - 823.212, - 665.863, - 38.275999999999954 + 1647.94, + 2497.755, + 672.2730000000001, + 505.8739999999998 ], "priority": 20, "parents": [ - 98143 + 485 ], "children": [], - "area": 10736.330904, + "area": 4116150.3747000005, "iscrowd": 0, - "segmentation": [], - "text": "Graph 2:The below line graph displays the compliance of the 7 parameters across the 89\nETO aA COCR RCI Cn niacin)" + "segmentation": [] }, { - "id": 98147, - "strid": "a41d285b-fd98-4dd5-b19a-8ffed85537ac", - "image_id": 204299, - "image_name": "12180.png", - "category_id": 5, - "category_name": "Section", + "id": 487, + "strid": "b354c917-cd73-467a-a8cc-8477c3ba3d92", + "image_id": 19, + "image_name": "10967.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 20.991, - 1112.65, - 104.327, - 14.805000000000064 + 2395.339, + 2495.608, + 675.8409999999999, + 508.77599999999984 ], "priority": 21, "parents": [ - 98154 - ], - "children": [ - 98148 + 485 ], - "area": 23355.636150000002, + "children": [], + "area": 5977827.171112, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 98148, - "strid": "40c14b0c-2ad0-4743-8c07-3a2301bf888c", - "image_id": 204299, - "image_name": "12180.png", + "id": 488, + "strid": "ed411eac-b6ad-4193-8c34-6c0720c166fe", + "image_id": 19, + "image_name": "10967.png", "category_id": 4, "category_name": "List", "bbox": [ - 14.637, - 1129.914, - 449.853, - 97.81500000000005 + 1658.889, + 3062.934, + 1349.6430000000003, + 345.34500000000025 ], "priority": 22, "parents": [ - 98147 + 485 ], "children": [], - "area": 16538.551218, + "area": 5081067.520326, "iscrowd": 0, "segmentation": [] }, { - "id": 98149, - "strid": "5dbd03e5-aad9-428e-8e81-5cf86eaddc20", - "image_id": 204299, - "image_name": "12180.png", + "id": 489, + "strid": "7bdeb7ec-9aad-44fd-b0a9-26181e362718", + "image_id": 19, + "image_name": "10967.png", "category_id": 5, "category_name": "Section", "bbox": [ - 506.481, - 1112.562, - 107.793, - 15.506000000000085 + 3259.569, + 814.151, + 740.7739999999999, + 72.92499999999995 ], "priority": 23, "parents": [ - 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425.148, - 1279.672, - 378.804, - 98.22299999999996 + 3307.01, + 1514.042, + 1378.7029999999995, + 346.23 ], - "priority": 25, + "priority": 26, "parents": [ - 98154 + 489 ], "children": [], - "area": 544049.991456, + "area": 5006952.03442, "iscrowd": 0, "segmentation": [] }, { - "id": 98151, - "strid": "2082dc46-527c-41ca-8ea0-e37046d8eb22", - "image_id": 204299, - "image_name": "12180.png", + "id": 493, + "strid": "a9f0305f-c86d-4ac8-bf2d-ac65f610fa45", + "image_id": 19, + "image_name": "10967.png", "category_id": 5, "category_name": "Section", "bbox": [ - 21.546, - 1265.396, - 95.71000000000001, - 14.902000000000044 + 3260.389, + 2065.993, + 401.55499999999984, + 62.585000000000036 ], - "priority": 26, + "priority": 27, "parents": [ - 98154 + 466 ], "children": [ - 98152 + 494 ], - "area": 27264.222216, + "area": 6735940.851277, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Conclusions" }, { - "id": 98152, - "strid": "8097b97e-f349-4973-8757-6cf8264c0d17", - "image_id": 204299, - "image_name": "12180.png", + "id": 494, + "strid": "37c2f1cb-c6fe-479d-bbb6-b18d1385502f", + "image_id": 19, + "image_name": "10967.png", "category_id": 4, "category_name": "List", "bbox": [ - 13.738, - 1283.698, - 375.584, - 97.82099999999991 + 3307.02, + 2212.304, + 1366.0480000000002, + 536.9499999999998 ], - "priority": 27, + "priority": 28, "parents": [ - 98151 + 493 ], "children": [], - "area": 17635.443124, + "area": 7316133.574080001, "iscrowd": 0, "segmentation": [] }, { - "id": 122229, - "strid": "dacb5c1b-0c91-465d-b7c7-37545ea451f7", - "image_id": 205257, - "image_name": "14528.png", + "id": 495, + "strid": "98e25265-5733-41e9-b50c-3121a42eedcb", + "image_id": 19, + "image_name": "10967.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 3259.012, + 3014.401, + 1092.395, + 75.46900000000005 + ], + "priority": 29, + "parents": [ + 466 + ], + "children": [ + 496 + ], + "area": 9823969.031812, + "iscrowd": 0, + "segmentation": [], + "text": "Acknowledgements & References" + }, + { + "id": 496, + "strid": "4ba3d034-608f-44c6-813d-9be3f584e04e", + "image_id": 19, + "image_name": "10967.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 3279.713, + 3141.784, + 1359.1640000000002, + 322.7330000000002 + ], + "priority": 30, + "parents": [ + 495 + ], + "children": [], + "area": 10304149.827992002, + "iscrowd": 0, + "segmentation": [], + "text": "Thanks to Nikita Shaiva for help with data collection!\n\nHikosaka, O., Miyauchi, S., & Shimojo, S. (1993). Focal visual attention produces illusory temporal order and motion\nsensation. Vision Research, 33(9), 1219-1240.\n\nNakayama, K., & Mackeben, M. (1989). Sustained and transient components of focal visual attention. Vision Research,\n29(11), 1631-1647.\n\nTse, P. U., & Logothetis, N. K. (2002). The duration of 3-D form analysis in transformational apparent motion. Perception &\nPsychophysics, 64(2), 244-265.\n\nTse, P. U. (2006). Neural correlates of transformational apparent motion. Neurolmage, 31, 766-773." + }, + { + "id": 497, + "strid": "951dbd15-4ab7-4d3f-8b75-80346700f91f", + "image_id": 20, + "image_name": "11016.png", "category_id": 9, "category_name": "Root", "bbox": [ - 195.6, - 348.25, - 288.28999999999996, - 251.33000000000004 + 93.28, + 53.15, + 196.41, + 108.37 ], "priority": -1, "parents": [], "children": [ - 122189, - 122190, - 122188, - 122186, - 122183, - 122185, - 122184, - 122187 + 504, + 511, + 499, + 498, + 500 ], - "area": 68117.7, + "area": 4957.832, "iscrowd": 0, "segmentation": [] }, { - "id": 122183, - "strid": "67dd1479-f31b-418d-8f62-64f242cdb7ae", - "image_id": 205257, - "image_name": "14528.png", + "id": 498, + "strid": "b4d35968-dd36-4ecf-a5fe-98f3299084f8", + "image_id": 20, + "image_name": "11016.png", "category_id": 1, "category_name": "Title", "bbox": [ - 134.368, - 39.357, - 3013.503, - 195.19 + 392.488, + 68.358, + 2461.935, + 134.874 ], "priority": 1, "parents": [ - 122229 + 497 ], "children": [], - "area": 5288.321376, + "area": 26829.694704, "iscrowd": 0, "segmentation": [], - "text": "Improving the resolution of the dental calculus dietary record: insights from\n\nchimpanzee faecal material —" + "text": "Trends in PhD Career Outcomes Tracking" }, { - "id": 122184, - "strid": "c25b4e68-8b69-4041-b4ab-267bf4561b03", - "image_id": 205257, - "image_name": "14528.png", + "id": 499, + "strid": "812cd26e-c9b8-4292-93b0-f8ccc03a03cb", + "image_id": 20, + "image_name": "11016.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 594.46, - 266.415, - 2115.228, - 233.034 + 65.818, + 210.323, + 3060.632, + 153.297 ], "priority": 2, "parents": [ - 122229 + 497 ], "children": [], - "area": 158373.0609, + "area": 13843.039214, "iscrowd": 0, "segmentation": [], - "text": "Robert C Power a, b, Ellen Schulz-Kornas c\na Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische StraBe 10, 07745 Jena, Germany\nb Research Group on Plant Foods in Hominin Dietary Ecology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany\nc Max Planck Weizmann Center for Integrative Archaeology and Anthropology, Max Planck Institute of Evolutionary Anthropology" + "text": "Authors: Jacquelyn Brinkman & Jens Locher - University of British Columbia; Adriana Bankston\n- Future of Research; Shilpa Gadwal - ASM; Melanie Sinche & Heather Morgan - Co-Chairs" }, { - "id": 122185, - "strid": "b6bb2719-4568-46e8-92ab-dac4ca5aacfd", - "image_id": 205257, - "image_name": "14528.png", + "id": 500, + "strid": "e9e0b5db-270a-427a-8527-e1f787ba4550", + "image_id": 20, + "image_name": "11016.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1495.017, - 551.276, - 257.17599999999993, - 41.462999999999965 + 176.266, + 488.368, + 881.937, + 166.00500000000005 ], "priority": 3, "parents": [ - 122229 + 497 ], "children": [ - 122193, - 122216, - 122191, - 122214, - 122192, - 122213, - 122215 + 502, + 501, + 503 ], - "area": 824166.991692, + "area": 86082.67388799999, "iscrowd": 0, "segmentation": [], - "text": "Introduction" + "text": "PhD Outcomes from GCC\nMembership Survey" }, { - "id": 122191, - "strid": "efa69c28-f6c6-4c97-bca3-49dab648be55", - "image_id": 205257, - "image_name": "14528.png", + "id": 501, + "strid": "32449beb-c73b-4419-aeb0-f7d6f380a69b", + "image_id": 20, + "image_name": "11016.png", "category_id": 3, "category_name": "Text", "bbox": [ - 181.721, - 650.73, - 2913.278, - 76.12599999999998 + 66.857, + 679.318, + 1110.403, + 274.9649999999999 ], "priority": 4, "parents": [ - 122185 + 500 ], "children": [], - "area": 118251.30633, + "area": 45417.163526, "iscrowd": 0, "segmentation": [], - "text": "Researchers have performed phytolith analysis on reference populations to measure the reliability of dietary studies based on phytoliths in dental calculus. However, these studies are challenged by\nincomplete knowledge of phytoliths in the diet of these reference populations. To cross validate published this data, this study describes egested phytoliths of a group used as a reference population." + "text": "Responses: universities (91.2%), independent research\ninstitute/hospital (4.7%), professional society (2.8%),\ngovernment agency (0.5%), other (0.93%) - 215 total\n\nPopulation data: Responses (%) - 66 of 215 (31%)." }, { - "id": 122213, - "strid": "319faf0a-0119-46e7-92a2-2e1ef85670e8", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 4, - "category_name": "List", + "id": 502, + "strid": "65856cf5-c9ba-4ca7-bbeb-467a6e419402", + "image_id": 20, + "image_name": "11016.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 197.456, - 841.648, - 998.5659999999999, - 521.5769999999999 + 101.793, + 963.774, + 1039.0929999999998, + 588.389 ], "priority": 5, "parents": [ - 122185 + 500 ], "children": [], - "area": 166188.447488, + "area": 98105.446782, "iscrowd": 0, "segmentation": [] }, { - "id": 122214, - "strid": "f6e004c9-a7c9-4229-bf5a-4cae2c5659d9", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 503, + "strid": "244ebf8a-5f7d-4a85-ad95-895ba5938693", + "image_id": 20, + "image_name": "11016.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1425.892, - 805.572, - 915.876, - 447.81799999999987 + 71.785, + 1565.524, + 1090.44, + 743.7469999999998 ], "priority": 6, "parents": [ - 122185 + 500 ], "children": [], - "area": 1148658.670224, + "area": 112381.14033999998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Methods: LinkedIn/alumni databases (83.3%), direct\nsurveys (80.3%), reports from academic departments\n(51.5%), training grant data (24.2%), other (10.6%).\nData sources: graduate school (60.6%), career center\n(53%), individual programs (40.9%), postdoc office\n(25.8%), Dean’s office (25.8%), institutional research\noffice (19.7%), other (13.6%).\n\nTiming of data collection: graduation/end of postdoc\n(86.4%), 1 year out (37.9%), 5 years out (33.3%), 10\nyears out (21.2%), other (21.2%).\n\n_ Note: Some responses included multiple options." }, { - "id": 122193, - "strid": "b38b3771-51dd-4397-a5f0-edb7e3f23201", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 504, + "strid": "1cb56b7e-ad61-4934-95c5-012404ba0d66", + "image_id": 20, + "image_name": "11016.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1510.674, - 1335.059, - 1061.663, - 94.48700000000008 + 1388.949, + 486.42, + 832.9900000000002, + 67.87200000000001 ], "priority": 7, "parents": [ - 122185 + 497 ], - "children": [], - "area": 2016838.919766, + "children": [ + 509, + 508, + 505, + 507, + 510, + 506 + ], + "area": 675612.57258, "iscrowd": 0, "segmentation": [], - "text": "Discrepancy between diet and dental calculus. Colours represent different foods. Outermost\nring = minutes spent consuming each genus averaged in feeding records, innermost\nring = phytolith counts" + "text": "National PhD Outcomes" }, { - "id": 122192, - "strid": "c706cd6e-409c-4a04-a949-b508dcf11462", - "image_id": 205257, - "image_name": "14528.png", + "id": 505, + "strid": "7216b237-49e8-4565-9a8a-cc9d61e96a24", + "image_id": 20, + "image_name": "11016.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2460.173, - 884.549, - 338.451, - 274.0799999999999 + 1284.707, + 601.104, + 1034.7, + 276.898 ], "priority": 8, "parents": [ - 122185 + 504 ], "children": [], - "area": 2176143.566977, + "area": 772242.5165280001, "iscrowd": 0, "segmentation": [], - "text": "Previous research has\nbuilt a quantitative\ndataset of diet and\nphytoliths from\nchimpanzees from the\nTai National Park in\nCéte d'Ivoire" + "text": "Sample organizations that track outcomes: NSF,\nCGS, MLA, AHA, Legion Project.\n\nChallenges: What “should” a PhD outcome be -\nABD, postdoc, tenure-track, alt-a? When is it\nachieved - first destination or later?" }, { - "id": 122215, - "strid": "7d025b2c-ba8b-4808-9593-9dde9104c972", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 506, + "strid": "395e4f7d-5867-4e2c-91ee-27a2533b6e43", + "image_id": 20, + "image_name": "11016.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2590.955, - 1264.348, - 192.70400000000018, - 191.78199999999993 + 1270.774, + 904.891, + 1058.3849999999998, + 684.023 ], "priority": 9, "parents": [ - 122185 + 504 ], "children": [], - "area": 3275868.7723399997, + "area": 1149911.9556339998, "iscrowd": 0, "segmentation": [] }, { - "id": 122216, - "strid": "78fc010c-edc9-431c-963f-01e6a1f79038", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 507, + "strid": "cb80e5cf-59b8-4ff0-965a-b3ae9ae4385f", + "image_id": 20, + "image_name": "11016.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2841.761, - 859.371, - 221.67700000000013, - 416.131 + 1398.694, + 1596.966, + 804.7829999999999, + 43.68599999999992 ], "priority": 10, "parents": [ - 122185 + 504 ], "children": [], - "area": 2442126.992331, + "area": 2233666.762404, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Career Outcomes of History PhDs (2004-2013)" }, { - "id": 122186, - "strid": "58dbfc9a-3f6e-4274-8efd-853a7c297990", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 5, - "category_name": "Section", + "id": 508, + "strid": "0f957634-8180-44ae-84c6-ff77412ed0f5", + "image_id": 20, + "image_name": "11016.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1561.788, - 1545.535, - 186.6010000000001, - 43.90599999999995 + 1434.848, + 1641.165, + 791.4189999999999, + 91.07500000000005 ], "priority": 11, "parents": [ - 122229 - ], - "children": [ - 122219, - 122207, - 122198, - 122218, - 122204, - 122203, - 122220, - 122206, - 122228, - 122200, - 122205, - 122202, - 122221, - 122201, - 122222, - 122196, - 122217, - 122199, - 122197 + 504 ], - "area": 2413798.01658, + "children": [], + "area": 2354822.31792, "iscrowd": 0, - "segmentation": [], - "text": "Methods" + "segmentation": [] }, { - "id": 122221, - "strid": "8009844c-ba4b-46d8-ab70-b709775739cd", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 509, + "strid": "732a6872-1cca-4799-b693-277e9f29013c", + "image_id": 20, + "image_name": "11016.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 173.255, - 1705.141, - 272.044, - 247.52999999999997 + 1404.086, + 1733.127, + 809.97, + 44.817999999999984 ], "priority": 12, "parents": [ - 122186 + 504 ], "children": [], - "area": 295424.20395500003, + "area": 2433459.356922, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "From the AHA at https://www.historians.org; Page titled: Where Historians Work an Interactive\nDatabase of History PhD Career Outcomes" }, { - "id": 122207, - "strid": "565cc3de-f8d9-446a-a185-1cac00a12f4b", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 510, + "strid": "54fe367d-7bf6-48e8-a645-1b4183643b90", + "image_id": 20, + "image_name": "11016.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 487.428, - 1658.264, - 611.9509999999999, - 182.95399999999995 + 1425.948, + 1811.171, + 763.4300000000001, + 514.97 ], "priority": 13, "parents": [ - 122186 + 504 ], "children": [], - "area": 808284.304992, + "area": 2582635.6651080004, "iscrowd": 0, - "segmentation": [], - "text": "Sample treatment\n\nFaeces of wild chimpanzees were\ncollected in the Tai Forest during January\nand February 2015." + "segmentation": [] }, { - "id": 122222, - "strid": "3ed12eaf-d1d3-40c1-aa03-fed363945e87", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 511, + "strid": "136b8e12-cbe9-4a40-98ae-4b64a2d2b154", + "image_id": 20, + "image_name": "11016.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 162.298, - 2130.805, - 222.736, - 245.73500000000013 + 2445.986, + 480.806, + 1041.7640000000001, + 81.92699999999996 ], "priority": 14, "parents": [ - 122186 + 497 ], - "children": [], - "area": 345825.38989, + "children": [ + 517, + 512, + 516, + 514, + 513, + 515 + ], + "area": 1176044.7447159998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Example: UBC PhD Outcomes" }, { - "id": 122206, - "strid": "37fe17d6-069f-4a31-b5ac-c895797e213a", - "image_id": 205257, - "image_name": "14528.png", + "id": 512, + "strid": "31f66cbe-8bcc-4cec-9c64-bfd091d5a8d8", + "image_id": 20, + "image_name": "11016.png", "category_id": 3, "category_name": "Text", "bbox": [ - 400.47, - 2172.989, - 324.957, - 191.9079999999999 + 2445.127, + 602.521, + 1045.734, + 343.336 ], "priority": 15, "parents": [ - 122186 + 511 ], "children": [], - "area": 870216.9048300001, + "area": 1473240.3651669999, "iscrowd": 0, "segmentation": [], - "text": "Then 20 40, 63um\nfractions were burned\nfor 4 hours at 500°C\nand then treated with\n10% HCI." + "text": "Why: Quality assurance, program design,\ntransparency, enrollment management\n\nDesign: 1) Survey 2) Manual research\n\nTiming: PhD graduates from 2005-2013\n\nResults: Outcomes for 91% of 3805 alumni; shared\nwithin & beyond UBC" }, { - "id": 122220, - "strid": "b7e55788-6bd0-4e08-83fd-ab8af6bf99a6", - "image_id": 205257, - "image_name": "14528.png", + "id": 513, + "strid": "662bd315-aa58-4ca3-8dd7-90a289cf6b17", + "image_id": 20, + "image_name": "11016.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 747.722, - 1865.729, - 183.09500000000003, - 279.36800000000017 + 2444.398, + 998.676, + 524.7110000000002, + 611.5080000000002 ], "priority": 16, "parents": [ - 122186 + 511 ], "children": [], - "area": 1395046.619338, + "area": 2441161.6170480005, "iscrowd": 0, "segmentation": [] }, { - "id": 122205, - "strid": "db0e8f51-58ab-48a1-949f-1d53562c11f9", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 514, + "strid": "daa3f441-8954-4b6a-86a3-f160bb7c05ce", + "image_id": 20, + "image_name": "11016.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 960.819, - 1923.636, - 339.30500000000006, - 120.66300000000001 + 2992.269, + 1007.655, + 537.433, + 642.9550000000002 ], "priority": 17, "parents": [ - 122186 + 511 ], "children": [], - "area": 1848266.017884, + "area": 3015174.8191949995, "iscrowd": 0, - "segmentation": [], - "text": "Each sample sieved to\nquantify size fractions\n(Fritz et al. 2012)." + "segmentation": [] }, { - "id": 122219, - "strid": "734e98a8-c530-46e5-bc49-31aebb2363d5", - "image_id": 205257, - "image_name": "14528.png", + "id": 515, + "strid": "9ea4d069-30b7-41ef-8da9-141ed53595df", + "image_id": 20, + "image_name": "11016.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 761.782, - 2221.07, - 246.99300000000005, - 304.36500000000024 + 2436.959, + 1672.683, + 544.2649999999999, + 601.5430000000001 ], "priority": 18, "parents": [ - 122186 + 511 ], "children": [], - "area": 1691971.1467400002, + "area": 4076259.8909969996, "iscrowd": 0, "segmentation": [] }, { - "id": 122204, - "strid": "3b981c41-18b0-46f4-911d-30a7b189365f", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 516, + "strid": "0493507b-63c8-476c-a3bb-8f459b604b7d", + "image_id": 20, + "image_name": "11016.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1041.8, - 2303.636, - 314.3910000000001, - 201.05000000000018 + 3030.961, + 1683.884, + 481.74900000000025, + 288.5999999999999 ], "priority": 19, "parents": [ - 122186 + 511 ], "children": [], - "area": 2399927.9847999997, + "area": 5103786.732524, "iscrowd": 0, - "segmentation": [], - "text": "Samples were\nmounted and\nphytoliths counted at\n400x with an optical\nmicroscope." + "segmentation": [] }, { - "id": 122200, - "strid": "df2e3533-f84e-476b-bc5b-7531236747c3", - "image_id": 205257, - "image_name": "14528.png", + "id": 517, + "strid": "0b84239b-92b8-4f3d-bd63-4300a2f9149c", + "image_id": 20, + "image_name": "11016.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1707.038, - 1655.299, - 504.57000000000016, - 35.162000000000035 + 3038.59, + 2009.941, + 461.89400000000023, + 286.44600000000014 ], "priority": 20, "parents": [ - 122186 + 511 ], "children": [], - "area": 2825658.294362, + "area": 6107386.623190001, "iscrowd": 0, "segmentation": [], - "text": "Dental calculus reference dataset" + "text": "Methodology, findings\n& interactive data\npublished at:\n\noutcomes. grad.ubc.ca" }, { - "id": 122218, - "strid": "4c62f008-b4e8-4fb6-8274-b124955c506f", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 518, + "strid": "4e4c8753-5409-43b0-8319-0517f40b5899", + "image_id": 21, + "image_name": "11024.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 1635.334, - 1717.734, - 235.45299999999997, - 288.4839999999999 + 114.6, + 338.75, + 319.27, + 127.69999999999999 ], - "priority": 21, - "parents": [ - 122186 + "priority": -1, + "parents": [], + "children": [ + 519, + 520, + 521, + 535, + 527 ], - "children": [], - "area": 2809068.813156, + "area": 38820.75, "iscrowd": 0, "segmentation": [] }, { - "id": 122201, - "strid": "59b6355f-f08c-4252-90cf-67bfb538037f", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 519, + "strid": "4e2d0d33-87fe-47b3-9391-b55dd542c111", + "image_id": 21, + "image_name": "11024.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 1907.46, - 1783.639, - 322.6089999999999, - 117.79199999999992 + 1159.168, + 159.269, + 989.425, + 127.041 ], - "priority": 22, + "priority": 1, "parents": [ - 122186 + 518 ], "children": [], - "area": 3402220.04694, + "area": 184619.528192, "iscrowd": 0, "segmentation": [], - "text": "Calculus deposits\nwere identified on Tai\nChimpanzee teeth." + "text": "Galaxy@Pasteur" }, { - "id": 122228, - "strid": "06201725-de0c-4ce2-879f-791f9fb38574", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 520, + "strid": "28de10e3-6b26-424d-9667-e51bf207529c", + "image_id": 21, + "image_name": "11024.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1635.744, - 2049.103, - 231.40499999999997, - 242.3040000000001 + 559.833, + 375.986, + 2185.106, + 76.22500000000002 ], - "priority": 23, + "priority": 2, "parents": [ - 122186 + 518 ], "children": [], - "area": 3351807.937632, + "area": 210489.37033799998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fabien Mareuil, Olivia Doppelt-Azeroual and Hervé Ménager\nCentre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS), Institut Pasteur, F-75724, Paris, France" }, { - "id": 122202, - "strid": "176e3bf0-2b0c-4b3d-90e4-8424a56a42ca", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 1911.881, - 2061.181, - 366.38800000000015, - 193.4090000000001 - ], - "priority": 24, - "parents": [ - 122186 - ], - "children": [], - "area": 3940732.791461, - "iscrowd": 0, - "segmentation": [], - "text": "Calculus samples were\nremoved with a dental\nscaler. Samples were\n\ntreated with 10% HCL to\n\nremove carbonites." - }, - { - "id": 122203, - "strid": "95f62a0a-9fe5-4e88-bef2-12927aa94623", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 521, + "strid": "62557e88-4ae6-46a4-ac03-a79bd14b2f30", + "image_id": 21, + "image_name": "11024.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1607.215, - 2464.869, - 687.8689999999999, - 76.59999999999991 + 52.228, + 550.753, + 850.245, + 83.88099999999997 ], - "priority": 25, + "priority": 3, "parents": [ - 122186 - ], - "children": [], - "area": 3961574.429835, - "iscrowd": 0, - "segmentation": [], - "text": "How do assemblages compare with the dental\ncalculus reference dataset?" - }, - { - "id": 122199, - "strid": "13221261-5784-4da7-9d91-88a47a7b5c04", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 2670.502, - 1656.435, - 350.81500000000005, - 39.94399999999996 + 518 ], - "priority": 26, - "parents": [ - 122186 + "children": [ + 525, + 524, + 523, + 526, + 522 ], - "children": [], - "area": 4423512.98037, + "area": 28764.727684, "iscrowd": 0, "segmentation": [], - "text": "Reference feeding data" + "text": "Galaxy@Pasteur today" }, { - "id": 122217, - "strid": "fdd89b22-b2e2-44eb-90c8-c5acb685aa5a", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 522, + "strid": "c53155eb-eae6-4afc-a27f-5ecd16e1ec2e", + "image_id": 21, + "image_name": "11024.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2514.86, - 1860.577, - 298.91499999999996, - 240.87500000000023 + 58.107, + 747.609, + 1003.221, + 398.17399999999986 ], - "priority": 27, + "priority": 4, "parents": [ - 122186 - ], - "children": [ - 122212 + 521 ], - "area": 4679090.67422, + "children": [], + "area": 43441.316163, "iscrowd": 0, "segmentation": [] }, { - "id": 122212, - "strid": "30db06eb-2917-48a2-9202-4aad319e0d4f", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 6, - "category_name": "Caption", + "id": 523, + "strid": "7293931e-3f06-4348-bf49-4daeaf71bedf", + "image_id": 21, + "image_name": "11024.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2510.295, - 2117.305, - 346.06899999999996, - 28.577000000000226 + 71.353, + 1348.168, + 1155.105, + 572.126 ], - "priority": 28, + "priority": 5, "parents": [ - 122217 + 521 ], "children": [], - "area": 5315060.154975, + "area": 96195.83130399999, "iscrowd": 0, - "segmentation": [], - "text": "Picture by Adam van Carsteren" + "segmentation": [] }, { - "id": 122198, - "strid": "53c2759c-d5fa-4412-adec-b61492ede1df", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 524, + "strid": "47672f72-cd09-4b87-bb79-ba0645f18554", + "image_id": 21, + "image_name": "11024.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2837.226, - 1851.815, - 292.63499999999976, - 243.13900000000012 + 1143.257, + 544.94, + 1439.442, + 752.6379999999999 ], - "priority": 29, + "priority": 6, "parents": [ - 122186 + 521 ], "children": [], - "area": 5254017.66519, + "area": 623006.4695800002, "iscrowd": 0, - "segmentation": [], - "text": "Comprehensive\nbehavioural data\nwas collected from\n1992 onwards from\nabout 128\nchimpanzees." + "segmentation": [] }, { - "id": 122197, - "strid": "ee58be1e-864a-4d66-9b25-6baa1c6a351c", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 525, + "strid": "53565d69-379d-4625-843b-06c4e6e7e445", + "image_id": 21, + "image_name": "11024.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2503.944, - 2233.081, - 556.7089999999998, - 81.48999999999978 + 1445.735, + 1302.916, + 1168.9909999999998, + 638.7639999999999 ], - "priority": 30, + "priority": 7, "parents": [ - 122186 + 521 ], "children": [], - "area": 5591509.771464, + "area": 1883671.2632599997, "iscrowd": 0, - "segmentation": [], - "text": "Feeding information was subsampled\nfrom data and trends plotted." + "segmentation": [] }, { - "id": 122196, - "strid": "b72bfcc3-7703-495a-9878-ce160340d37c", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 526, + "strid": "6c4a115e-dc3d-4ce8-9448-5b2ce13e6275", + "image_id": 21, + "image_name": "11024.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2479.926, - 2462.112, - 649.3499999999999, - 79.77500000000009 + 2634.512, + 553.66, + 616.4990000000003, + 1299.4470000000001 ], - "priority": 31, + "priority": 8, "parents": [ - 122186 + 521 ], "children": [], - "area": 6105855.563712, + "area": 1458623.91392, "iscrowd": 0, - "segmentation": [], - "text": "How do assemblages compare with feeding\nrecords?" + "segmentation": [] }, { - "id": 122187, - "strid": "d34f28a4-053e-4974-87ef-3773c1aeb8b4", - "image_id": 205257, - "image_name": "14528.png", + "id": 527, + "strid": "774484e4-8ad7-47be-a02f-b22d40f657af", + "image_id": 21, + "image_name": "11024.png", "category_id": 5, "category_name": "Section", "bbox": [ - 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"id": 122194, - "strid": "9fa68dec-d40d-464e-9628-914cc573c96f", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 968.613, - 2680.6, - 276.51199999999994, - 150.94999999999982 - ], - "priority": 34, - "parents": [ - 122187 - ], - "children": [], - "area": 2596464.0078000003, - "iscrowd": 0, - "segmentation": [], - "text": "A selection of phytolith\nmorphotypes in faecal\nsamples. A) short-cell,\nB) Multicellular tracheid,\nC) Spheroid echinate." - }, - { - "id": 122225, - "strid": "0a76f7da-2fa7-4c63-8cee-42882ff4f1f7", - "image_id": 205257, - "image_name": "14528.png", + "id": 529, + "strid": "c9517ce4-c8df-4360-bdab-b4352696ff02", + "image_id": 21, + "image_name": "11024.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1573.13, - 2669.118, - 888.5610000000001, - 305.12400000000025 + 53.154, + 2834.834, + 785.318, + 1010.4670000000001 ], - "priority": 35, + "priority": 11, "parents": [ - 122187 + 527 ], "children": [], - "area": 4198869.59934, + "area": 150682.766436, "iscrowd": 0, "segmentation": [] }, { - "id": 122195, - "strid": "6f8918e7-3d3a-4ae6-983d-aefaf5053f44", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 530, + "strid": "e8d28fe7-9e80-4a0a-b6a9-3c4347ab9429", + "image_id": 21, + "image_name": "11024.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2490.159, - 2700.911, - 628.598, - 160.31399999999985 + 1133.867, + 2876.261, + 738.4869999999999, + 327.8159999999998 ], - "priority": 36, + "priority": 12, "parents": [ - 122187 + 527 ], "children": [], - "area": 6725697.834849, + "area": 3261297.431287, "iscrowd": 0, - "segmentation": [], - "text": "Remaining residue percent following\nphytolith extraction. Phytoliths and other\nparticles were a relatively small portion of\neach sample." + "segmentation": [] }, { - "id": 122224, - "strid": "fd62e2c3-c52d-4225-aec9-aeba523f57e0", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 2, - "category_name": "Figure", + "id": 531, + "strid": "513ae3a1-6753-4c83-a164-09a0f156db44", + "image_id": 21, + "image_name": "11024.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 83.952, - 2969.003, - 883.931, - 1085.6330000000003 + 883.373, + 3519.257, + 780.777, + 322.5430000000001 ], - "priority": 37, + "priority": 13, "parents": [ - 122187 + 527 ], "children": [], - "area": 249253.739856, + "area": 3108816.613861, "iscrowd": 0, "segmentation": [] }, { - "id": 122226, - "strid": "eab561e5-9eec-4e15-98a8-b09d7fed6e3b", - "image_id": 205257, - "image_name": "14528.png", + "id": 532, + "strid": "a6ff4717-b6f1-40f9-8a87-5f5543e1e2b5", + "image_id": 21, + "image_name": "11024.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1055.957, - 2985.772, - 982.8320000000001, - 1071.4899999999998 + 1575.158, + 2036.908, + 1675.105, + 688.0540000000001 ], - "priority": 38, + "priority": 14, "parents": [ - 122187 + 527 ], "children": [], - "area": 3152846.8438040004, + "area": 3208451.9314639997, "iscrowd": 0, "segmentation": [] }, { - "id": 122227, - "strid": "6e4300a6-44c7-4535-b3e9-caece897db8c", - "image_id": 205257, - "image_name": "14528.png", + "id": 533, + "strid": "6d8132bd-c51f-4785-a936-4a3a6f6b7055", + "image_id": 21, + "image_name": "11024.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2127.447, - 2990.838, - 1058.824, - 1066.424 + 2182.159, + 2775.395, + 1030.2800000000002, + 760.1010000000001 ], - "priority": 39, + "priority": 15, "parents": [ - 122187 + 527 ], "children": [], - "area": 6362849.330586, + "area": 6056353.177805, "iscrowd": 0, "segmentation": [] }, { - "id": 122208, - "strid": "85371832-06cb-43c7-ab66-1e50aa9cd1f9", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 534, + "strid": "645a38e8-39a1-4b29-8903-f40d9991a09f", + "image_id": 21, + "image_name": "11024.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 102.091, - 4153.584, - 1409.141, - 80.21500000000015 + 1757.577, + 3574.868, + 1101.0959999999998, + 235.78999999999996 ], - "priority": 40, + "priority": 16, "parents": [ - 122187 + 527 ], "children": [], - "area": 424043.544144, + "area": 6283105.774836, "iscrowd": 0, - "segmentation": [], - "text": "Phytolith assemblages in faecal samples are relatively diverse, but are dominated by dicot-type\nphytoliths including some relatively rare types." + "segmentation": [] }, { - "id": 122188, - "strid": "6b75172f-4dc7-4ac5-a460-7a16c0d083ea", - "image_id": 205257, - "image_name": "14528.png", + "id": 535, + "strid": "149951bc-0f5f-458c-b979-bc614795a03b", + "image_id": 21, + "image_name": "11024.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2314.607, - 4081.037, - 236.471, - 42.06600000000026 + 52.648, + 4036.311, + 411.038, + 66.42200000000003 ], - "priority": 41, + "priority": 17, "parents": [ - 122229 + 518 ], "children": [ - 122211 + 536 ], - "area": 9445996.807458999, + "area": 212503.70152800003, "iscrowd": 0, "segmentation": [], - "text": "Discussion" + "text": "Conclusion" }, { - "id": 122211, - "strid": "9f071801-ca8c-4e15-8199-a9bc27f57131", - "image_id": 205257, - "image_name": "14528.png", + "id": 536, + "strid": "138075fa-67e4-4297-b5b6-da84e3739324", + "image_id": 21, + "image_name": "11024.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1686.62, - 4168.49, - 1445.274, - 203.66300000000047 + 67.607, + 4167.094, + 2683.801, + 297.1750000000002 ], - "priority": 42, + "priority": 18, "parents": [ - 122188 + 535 ], "children": [], - "area": 7030658.603799999, + "area": 281724.724058, "iscrowd": 0, "segmentation": [], - "text": "Phytoliths from dental calculus differ from faecal samples. Unlike dental calculus, faecal samples\nshow a relative diverse assemblage that is not shewed to any particular morphotype. Dental\ncalculus overrepresents spheroid echinates, potentially due to tapbhonomic robustness (Cabanes\nand Shahack-Gross, 2015). Further interpretation of faecal samples requires a larger sample size\nand coverage of faecal samples from additional seasons." + "text": "The scientists of the Institut Pasteur have access since 2013 to our Galaxy instance. This server is now public, and provides a wide range of tools\nto the scientific community, including tools that have been created at the Institut Pasteur i.e. TXSScan (https://10.1038/srep23080), alienTrimmer\n(https://10.1016/j.ygeno.2013.07.011), PhageTerm (doi:https://doi.org/10.1101/108100),\n\nSARTools Deseq2 (https://10.1371/journal.pone.0157022)...\n\nThe use of Galaxy as an execution hub for dedicated web interfaces simplifies their development, and facilitates their monitoring, while enabling\na high degree of customization." }, { - "id": 122189, - "strid": "17577216-a656-404b-9ba4-017065e510ba", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 5, - "category_name": "Section", + "id": 537, + "strid": "c09826d6-2334-46ab-a7a7-0a21529c7a3d", + "image_id": 22, + "image_name": "11076.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 2225.858, - 4401.058, - 396.21399999999994, - 49.71100000000024 - ], - "priority": 43, - "parents": [ - 122229 + 685.99, + 90.75, + 301.16999999999996, + 144.8 ], + "priority": -1, + "parents": [], "children": [ - 122210 + 549, + 538, + 540, + 545, + 539, + 553, + 542 ], - "area": 9796130.157764, + "area": 62253.5925, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 538, + "strid": "e8e3ecd8-17f3-4cca-9e00-3a6bb9310345", + "image_id": 22, + "image_name": "11076.png", + "category_id": 1, + "category_name": "Title", + "bbox": [ + 1797.637, + 55.901, + 1995.771, + 73.868 + ], + "priority": 1, + "parents": [ + 537 + ], + "children": [], + "area": 100489.705937, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgments" + "text": "The effects of acute stress on the attentional network" }, { - "id": 122210, - "strid": "572745a6-77fb-40b7-82c3-feb87640f4be", - "image_id": 205257, - "image_name": "14528.png", - "category_id": 3, - "category_name": "Text", + "id": 539, + "strid": "ceb70464-86cb-4654-91a7-b23e709f1de5", + "image_id": 22, + "image_name": "11076.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1703.796, - 4465.397, - 1468.584, - 94.47000000000025 + 1655.812, + 156.649, + 2279.565, + 160.88400000000001 ], - "priority": 44, + "priority": 2, "parents": [ - 122189 + 537 ], "children": [], - "area": 7608125.547012, + "area": 259381.293988, "iscrowd": 0, "segmentation": [], - "text": "We thank Amanda Henry for access to research facilities. | also thank Adam van Carsteren for his picture. We thank Roman Wittig, and field assistants at Tai National Park\nfor collection of samples. We also wish to acknowledge the Ministére de la Recherche Scientifique and the Ministére de I'Environnement et des Eaux et Foréts of Céte\nd'Ivoire, the Office Ilvorien des Parcs et Reserves, the Director of the Tai National Park for permission to conduct this research. We are grateful for support by the Centre\nSuisse de Recherches Scientifiques at Abidjan, Céte d'Ivoire" + "text": "Stuart M. Pugh” Tamaryn Menneer?, Dominic Taunton” Anne P. Hillstrom*, Nick Donnelly?\n1Centre for Vision and Cognition, Psychology, University of Southampton\n2Southampton Marine and Maritime Institute, Engineering and the Environment, University of Southampton" }, { - "id": 122190, - "strid": "ec6abe79-552f-460c-9fe3-2f893646f4e6", - "image_id": 205257, - "image_name": "14528.png", + "id": 540, + "strid": "36640941-0ee9-4ede-8ef5-3f83939616d7", + "image_id": 22, + "image_name": "11076.png", "category_id": 5, "category_name": "Section", "bbox": [ - 704.137, - 4308.365, - 273.087, - 50.07800000000043 + 720.851, + 415.797, + 434.523, + 82.57900000000001 ], - "priority": 45, + "priority": 3, "parents": [ - 122229 + 537 ], "children": [ - 122209 + 541 ], - "area": 3033679.2060049996, + "area": 299727.68324700004, "iscrowd": 0, "segmentation": [], - "text": "Bibliography" + "text": "Background" }, { - "id": 122209, - "strid": "df6f0e15-7ef6-4851-ba98-0bb61b5ccd5a", - "image_id": 205257, - "image_name": "14528.png", + "id": 541, + "strid": "ee2c02e5-2fac-4c42-b59f-61f2cbb9727b", + "image_id": 22, + "image_name": "11076.png", "category_id": 3, "category_name": "Text", "bbox": [ - 123.723, - 4377.312, - 1437.492, - 189.35800000000017 + 57.467, + 536.061, + 1693.658, + 455.284 ], - "priority": 46, + "priority": 4, "parents": [ - 122190 + 540 ], "children": [], - "area": 541574.172576, + "area": 30805.817487, "iscrowd": 0, "segmentation": [], - "text": "Cabanes, D., Shahack-Gross, R., 2015. Understanding fossil phytolith preservation: The role of partial dissolution in paleoecology and archaeology. PLoS ONE. 10,\n\n0125532.\n\nFritz J, Streich WJ, Schwarm A, Clauss M. 2012. Condensing results of wet sieving analyses into a single data: a comparison of methods for particle size description. J\nAnim Physiol Anim Nutr 96:783-797.\n\nLeonard, C., Vashro, L., O'Connell, J.F., Henry, A.G., 2015. Plant microremains in dental calculus as a record of plant consumption: A test with Twe forager-\nhorticulturalists. Journal of Archaeological Science: Reports. 2, 449-457.\n\nPower, R.C., Salazar-Garcia, D.C., Wittig, R.M., Freiberg, M., Henry, A.G., 2015. Dental calculus evidence of Tai Forest Chimpanzee plant consumption and life history\n\ntransitions. Scientific Reports. 5, 15161." + "text": "Stress impacts on cognition and attention but there is little consensus on\nhow. Here we explore if some of the differences can be accounted for by\nwhen the effect of stress is tested. Our hypothesis is based on the fact that\ntesting in the immediate aftermath of a stressor (0-15 minutes) measures\ntask performance during peak activation the Sympathetic Nervous System\n(SNS) while testing 20-45 minutes after the stressor tests task performance\nduring peak Hypothalamic Pituitary Adrenal (HPA) Axis activation." }, { - "id": 159252, - "strid": "5533e026-1d19-475b-abf5-faabfae06dc3", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 9, - "category_name": "Root", + "id": 542, + "strid": "b5213fec-4087-40b9-a78a-a32fac817cd3", + "image_id": 22, + "image_name": "11076.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 296.95, - 130.49, - 556.5, - 201.14 + 600.033, + 1041.263, + 675.7310000000001, + 84.5909999999999 + ], + "priority": 5, + "parents": [ + 537 ], - "priority": -1, - "parents": [], "children": [ - 159242, - 159245, - 159250, - 159241, - 159244, - 159243, - 159249, - 159240, - 159247, - 159251, - 159248, - 159246 + 543 ], - "area": 38749.0055, + "area": 624792.161679, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The Present Study" }, { - "id": 159240, - "strid": "e697cc93-00e3-4280-9620-3da1bedf2141", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 1, - "category_name": "Title", + "id": 543, + "strid": "49962279-5403-42e5-af85-f18d0d90825b", + "image_id": 22, + "image_name": "11076.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1136.914, - 27.903, - 1174.8500000000001, - 345.802 + 45.662, + 1158.706, + 1749.279, + 2869.651 ], - "priority": 1, + "priority": 6, "parents": [ - 159252 + 542 ], - "children": [], - "area": 31723.311341999997, + "children": [ + 544 + ], + "area": 52908.833371999994, "iscrowd": 0, - "segmentation": [], - "text": "Jpred 4:\n\nIncorporating Jnet" + "segmentation": [] }, { - "id": 159241, - "strid": "aa356ce8-0f56-46b3-be09-f6ae992393ff", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 0, - "category_name": "Author Info", + "id": 544, + "strid": "b8a7f8b8-f42f-4359-9c5b-b4d8296aa3a5", + "image_id": 22, + "image_name": "11076.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2271.278, - 8.605, - 528.1759999999999, - 237.65 + 44.91, + 4036.177, + 1717.871, + 86.60200000000032 ], - "priority": 2, + "priority": 7, "parents": [ - 159252 + 543 ], "children": [], - "area": 19544.34719, + "area": 181264.70906999998, "iscrowd": 0, "segmentation": [], - "text": "Alexey Drozdetskiy\n\nChris Cole\n\nJim Procter\n\nGeoff Barton\njpred@compbio.dundee.ac.uk\nwww.compbio. dundee.ac.uk/jpred" + "text": "Figure 1 — Schematic representation of the order of tasks conducted in the experiment (a), the ANT-R (b) and\ndifference score calculations from the ANT-R (c)" }, { - "id": 159242, - "strid": "078a20b4-2583-41c1-9e8b-bd860d42d6bf", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 545, + "strid": "be1677ef-f1b6-469c-9b1c-0cd77f555186", + "image_id": 22, + "image_name": "11076.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 56.021, - 371.421, - 3306.619, - 515.5129999999999 + 2573.469, + 416.271, + 446.78600000000006, + 84.98599999999999 ], - "priority": 3, + "priority": 8, "parents": [ - 159252 + 537 ], - "children": [], - "area": 20807.375841, + "children": [ + 547, + 546 + ], + "area": 1071260.514099, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Key Result 1" }, { - "id": 159243, - "strid": "7de031a3-c6d7-4959-89fe-b6e64a5dc8bb", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 546, + "strid": "5542d5e2-b768-4ff8-89ec-0ec0a91af6cc", + "image_id": 22, + "image_name": "11076.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 57.56, - 929.779, - 3138.386, - 601.808 + 1916.235, + 537.195, + 1659.1990000000003, + 292.91999999999996 ], - "priority": 4, + "priority": 9, "parents": [ - 159252 + 545 ], "children": [], - "area": 53518.07924, + "area": 1029391.8608250001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Did the SECPT lead to a differential stress response over time? YES\n\nThe SECPT generated a stress response evidenced by both self-report and\nCortisol measures. In addition, Alpha Amylase increased amongst all\nparticipants indicating anticipatory stress (See Figure 2)." }, { - "id": 159244, - "strid": "a75f01c1-457e-4eb9-9829-5af1d2c5f208", - "image_id": 206721, - "image_name": "6321.png", + "id": 547, + "strid": "1a79f542-bf3f-4001-996a-f5518a73ff23", + "image_id": 22, + "image_name": "11076.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 10.153, - 1641.733, - 703.322, - 787.05 + 1906.318, + 848.488, + 1777.8949999999998, + 2234.7649999999994 ], - "priority": 5, + "priority": 10, "parents": [ - 159252 + 545 ], - "children": [], - "area": 16668.515149, + "children": [ + 548 + ], + "area": 1617487.9471840002, "iscrowd": 0, "segmentation": [] }, { - "id": 159245, - "strid": "7d8d9405-1967-4c64-ba8f-0aed161eaee6", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 548, + "strid": "595f5fa9-7ab9-4980-bc93-1bcae6e7c635", + "image_id": 22, + "image_name": "11076.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 706.776, - 1805.841, - 743.5109999999999, - 587.7759999999998 + 1907.668, + 3107.348, + 1727.646, + 94.4369999999999 ], - "priority": 6, + "priority": 11, "parents": [ - 159252 + 547 ], "children": [], - "area": 1276325.0786159998, + "area": 5927788.344463999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 2 — Physiological (a) and selective self-report data (b) demonstrating stress levels across time-points, in\n\ncontrol and stress conditions." }, { - "id": 159246, - "strid": "35d4227e-e778-4495-87a3-bb19372c5466", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 549, + "strid": "29ca496d-1eb1-4982-a0e5-7679e1a1cfb2", + "image_id": 22, + "image_name": "11076.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1444.794, - 1570.663, - 1097.0449999999998, - 1295.2909999999997 + 4427.882, + 413.59, + 445.46500000000015, + 84.23899999999998 ], - "priority": 7, + "priority": 12, "parents": [ - 159252 + 537 ], - "children": [], - "area": 2269284.478422, + "children": [ + 551, + 550 + ], + "area": 1831327.7163799996, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Key Result 2" }, { - "id": 159247, - "strid": "0fa23b91-c7c3-4794-9e25-d351f56c7297", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 550, + "strid": "617b6bb8-b930-4e47-9b42-0c5d8d694603", + "image_id": 22, + "image_name": "11076.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2577.922, - 1400.568, - 947.7620000000002, - 1456.2839999999999 + 3774.129, + 537.195, + 1747.2799999999997, + 426.0659999999999 ], - "priority": 8, + "priority": 13, "parents": [ - 159252 + 549 ], "children": [], - "area": 3610555.059696, + "area": 2027443.2281550001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Did performance on the ANT-R change over time between groups? YES\n\nControl performance on the ANT-R changed over time points. Control and\nstress groups differed on (1) accuracy with respect to the Inhibition of Return\nmeasure during the SNS period, and (2) RT with respect to the flanker conflict\nmeasure in HPA-Axis period. Females also differed between condition on\nlocation congruency RT during the HPA-Axis period." }, { - "id": 159248, - "strid": "6f323d0e-4329-476d-a6a6-12d4dadac498", - "image_id": 206721, - "image_name": "6321.png", + "id": 551, + "strid": "76bc20b1-7f9a-4b3c-baaa-8a9c0c539d28", + "image_id": 22, + "image_name": "11076.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 40.293, - 2496.868, - 1471.872, - 740.5529999999999 + 3862.156, + 983.721, + 1573.7489999999998, + 2089.517 ], - "priority": 9, + "priority": 14, "parents": [ - 159252 + 549 ], - "children": [], - "area": 100606.30232399999, + "children": [ + 552 + ], + "area": 3799283.962476, "iscrowd": 0, "segmentation": [] }, { - "id": 159251, - "strid": "089f902c-db92-4afa-9ade-6cb3b036a712", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 3, - "category_name": "Text", + "id": 552, + "strid": "66db90fb-2143-4472-8eb7-a4b75161c607", + "image_id": 22, + "image_name": "11076.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1565.16, - 2915.624, - 1927.088, - 283.0479999999998 + 3757.527, + 3109.2, + 1707.277, + 96.28900000000021 ], - "priority": 10, + "priority": 15, "parents": [ - 159252 + 551 ], "children": [], - "area": 4563418.05984, + "area": 11682902.9484, "iscrowd": 0, "segmentation": [], - "text": "...simple one-liners > Shell, Perl, Python, JS, Java, etc.\n\nPLUS: ready mass submission and results retrieval scripts.\n\nE.g.: Input: UniProt proteome collection in FASTA > “Push of a button” > Output (a few\ndays later): collection of, say, 50,000 results on your computer.\n\n... ALL AUTOMATED" + "text": "Figure 3 — ANT-R measures indicating significant differences in loR Accuracy (a) Flanker x Location RT (b) and\n\nfemale Validity x Location RT (c)" }, { - "id": 159249, - "strid": "8cdf9118-3f7b-4d9b-9c75-abed70bff2db", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 553, + "strid": "d7af4433-965e-43f0-af32-a6b6d086c5f3", + "image_id": 22, + "image_name": "11076.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 50.744, - 3241.612, - 3315.049, - 656.4880000000003 + 3120.215, + 3297.917, + 1210.1220000000003, + 67.16199999999981 ], - "priority": 11, + "priority": 16, "parents": [ - 159252 + 537 ], - "children": [], - "area": 164492.359328, + "children": [ + 554 + ], + "area": 10290210.092155, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Discussion and Future Directions" }, { - "id": 159250, - "strid": "3988cf90-e0d4-4552-b1bd-f69b52ecc063", - "image_id": 206721, - "image_name": "6321.png", - "category_id": 2, - "category_name": "Figure", + "id": 554, + "strid": "e1dad778-e0ae-473a-b018-0671e7b4b4cf", + "image_id": 22, + "image_name": "11076.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 50.695, - 3899.898, - 3417.646, - 644.0100000000002 + 1920.145, + 3447.341, + 3288.1520000000005, + 459.15599999999995 ], - "priority": 12, + "priority": 17, "parents": [ - 159252 + 553 ], "children": [], - "area": 197705.32911000002, + "area": 6619394.584445, "iscrowd": 0, "segmentation": [] }, { - "id": 124801, - "strid": "3d2e6f71-ffa9-47ce-bdd6-521ddd80a27a", - "image_id": 205358, - "image_name": "14866.png", + "id": 555, + "strid": "5bfd2993-6a3d-4910-8a36-639b46c57c65", + "image_id": 23, + "image_name": "11139.png", "category_id": 9, "category_name": "Root", "bbox": [ - 69.11, - 196.09, - 119.47000000000001, - 141.86999999999998 + 140.88, + 368.93, + 299.5, + 248.16000000000003 ], "priority": -1, "parents": [], "children": [ - 124772, - 124778, - 124791, - 124786, - 124773, - 124794, - 124796, - 124775, - 124799, - 124784, - 124788, - 124798, - 124782, - 124771, - 124780, - 124800, - 124790 + 556, + 557, + 558, + 578, + 564, + 560 ], - "area": 13551.7799, + "area": 51974.8584, "iscrowd": 0, "segmentation": [] }, { - "id": 124771, - "strid": "4d68f9f5-e506-4fbc-8468-e6822799f35d", - "image_id": 205358, - "image_name": "14866.png", + "id": 556, + "strid": "77bd094e-5e01-4b81-91c8-3d9de6dc1c28", + "image_id": 23, + "image_name": "11139.png", "category_id": 1, "category_name": "Title", "bbox": [ - 182.336, - 72.564, - 1277.68, - 232.14700000000002 + 475.042, + 464.089, + 2313.504, + 259.191 ], "priority": 1, "parents": [ - 124801 + 555 ], "children": [], - "area": 13231.029504, + "area": 220461.76673799998, "iscrowd": 0, "segmentation": [], - "text": "Tackle your Tics\n\na unique and innovative cooperation between researchers,\ntherapists and patient representatives" + "text": "Independent Component Analysis Helps\nClassifying Melanoma Patients" }, { - "id": 124772, - "strid": "2a0307f4-febb-43f5-bb86-fc3eba9c97ee", - "image_id": 205358, - "image_name": "14866.png", + "id": 557, + "strid": "2302563a-f20a-40f4-9465-551480f91779", + "image_id": 23, + "image_name": "11139.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 96.476, - 313.143, - 1462.7149999999997, - 75.98500000000001 + 319.182, + 760.584, + 2477.9890000000005, + 214.79200000000003 ], "priority": 2, "parents": [ - 124801 + 555 ], "children": [], - "area": 30210.784067999997, + "area": 242764.722288, "iscrowd": 0, "segmentation": [], - "text": "L. Beljaars (1,3,10), A. Heijerman (1,2), C. Verdellen (3,4), J. van de Griendt (4), M. Bus (5), I. Vlaanderen (1), E. Carper (1), D. Cath (6,7,8), P. Hoekstra (7,8), C. Huyser (5), E. Utens (5,9)\n\n1 Dutch Tourette Association , 2 Dutch Knowledge Centre for Child- and Adolescent Psychiatry, 3 PsyQ Nijmegen / Parnassia Group, 4 TicXperts, 5 De Bascule, Academic Centre for Child and Adolescent Psychiatry\nAmsterdam, 6 GGZ Drenthe, 7 University of Groningen (RUG), 8 University Medical Centre Groningen (UMCG), 9 University of Amsterdam (UvA), 10 TicTalk & more" + "text": "Petr V. Nazarov!, Anke Wienecke-Baldacchino2, Gunnar Dittmar!, Stephanie Kreis?, Francisco Azuaje!\n\n1 Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, petr.nazarov@lih.lu\n\n2 Signal Transduction Group, Life Science Research Unit, Faculty of Science, Technology and Communication (FSTC), University of Luxembourg" }, { - "id": 124773, - "strid": "9bfbf382-4e34-4e3a-9448-9f2c48d2c099", - "image_id": 205358, - "image_name": "14866.png", + "id": 558, + "strid": "0fad43c3-b97e-4958-8b21-35e8dc90fb5f", + "image_id": 23, + "image_name": "11139.png", "category_id": 5, "category_name": "Section", "bbox": [ - 85.7, - 460.597, - 191.83100000000002, - 17.593999999999994 + 131.379, + 1132.518, + 328.13, + 56.9670000000001 ], "priority": 3, "parents": [ - 124801 + 555 ], "children": [ - 124774 + 559 ], - "area": 39473.1629, + "area": 148789.082322, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Background" }, { - "id": 124774, - "strid": "ee118472-8ebe-4d6b-b65b-4942d6dfc01f", - "image_id": 205358, - "image_name": "14866.png", + "id": 559, + "strid": "fa7c3610-6393-4b7b-96ba-138f70b0f785", + "image_id": 23, + "image_name": "11139.png", "category_id": 3, "category_name": "Text", "bbox": [ - 56.508, - 505.685, - 471.829, - 45.60600000000005 + 92.029, + 1219.414, + 1509.735, + 409.5719999999999 ], "priority": 4, "parents": [ - 124773 + 558 ], "children": [], - "area": 28575.24798, + "area": 112221.45100599999, "iscrowd": 0, "segmentation": [], - "text": "Academically educated researchers: conducting research\nPatients: undergoing research, research subjects" + "text": "Cancer samples investigated by high-throughput transcriptomics are often\nhighly heterogeneous. This, in conjunction with sample composition variability,\nlimits diagnostics of patients based on bulk sample transcriptome. Here we\ninvestigated the independent component analysis (ICA) as a feature\nextraction method for sample classification and patient diagnostics (Fig.1).\nIndependent component analysis allows data-driven separation of mixed\nsignals into statistically independent sources that can represent various cell\nsubtypes or biological processes [1]." }, { - "id": 124775, - "strid": "6829a541-799f-4ddb-b325-a13fedc7c717", - "image_id": 205358, - "image_name": "14866.png", + "id": 560, + "strid": "e1d00688-2050-4948-8bf0-3dc4faf78ff8", + "image_id": 23, + "image_name": "11139.png", "category_id": 5, "category_name": "Section", "bbox": [ - 86.3, - 616.73, - 196.255, - 15.519999999999982 + 116.243, + 1675.419, + 510.04400000000004, + 46.13499999999999 ], "priority": 5, "parents": [ - 124801 + 555 ], "children": [ - 124776, - 124777 + 561, + 563 ], - "area": 53223.799, + "area": 194755.730817, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 124776, - "strid": "549324c8-2fc8-49e5-b704-919cf1d12aae", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 3, - "category_name": "Text", + "id": 561, + "strid": "3a686a2d-3120-47dc-bf04-e4a7b37cd1d3", + "image_id": 23, + "image_name": "11139.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 59.101, - 654.147, - 383.89, - 46.98900000000003 + 86.441, + 1770.441, + 1542.23, + 755.095 ], "priority": 6, "parents": [ - 124775 + 560 ], - "children": [], - "area": 38660.741847000005, + "children": [ + 562 + ], + "area": 153038.690481, "iscrowd": 0, - "segmentation": [], - "text": "Involving patient representatives or ‘experts by\nexperience’ as part of the research team" + "segmentation": [] }, { - "id": 124777, - "strid": "6ca7955a-dee3-4447-8413-8afd222bb6b8", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 3, - "category_name": "Text", + "id": 562, + "strid": "77563460-bf28-4d89-9886-9cd18825438a", + "image_id": 23, + "image_name": "11139.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 57.771, - 719.311, - 485.40399999999994, - 45.41300000000001 + 118.156, + 2563.356, + 1471.962, + 119.72200000000021 ], "priority": 7, "parents": [ - 124775 + 561 ], "children": [], - "area": 41555.315781000005, + "area": 302875.89153600007, "iscrowd": 0, "segmentation": [], - "text": "Goal: to better attune research to patients’ and parents’\nneeds, and therefore strive for more effective research" + "text": "Figure 1. General scheme of ICA-based analysis (A) of the gene expression data: ICA followed by\na classifier are trained on the large data set and then applied to the new data set. The detailed\nsteps of ICA analysis are shown in (B)." }, { - "id": 124778, - "strid": "acccd7a1-bc90-4ed8-b3f1-7f5a66931ad5", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", + "id": 563, + "strid": "858f2229-bc34-4f49-b8df-a58c2558a48b", + "image_id": 23, + "image_name": "11139.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 632.473, - 461.441, - 214.84899999999993, - 20.208000000000027 + 91.594, + 2693.605, + 1512.276, + 644.2019999999998 ], "priority": 8, "parents": [ - 124801 - ], - "children": [ - 124779 + 560 ], - "area": 291848.973593, + "children": [], + "area": 246718.05636999998, "iscrowd": 0, "segmentation": [], - "text": "About Tackle your Tics" + "text": "Processed and normalized RNA-seq data from melanoma patients were\ndownloaded from TCGA Research Network [2]. Genes, lowly expressed in all\nsamples were removed from the consideration.\n\nICA from /fastICA package of R was used to estimate independent components\n(signals, $S) and their weights (mixture matrices, M). Genes with strong\ninvolvement in the components were used to identify their biological basis.\nFunctional annotation was performed by topGO package independently for\npositive and negative genes of each component. The stability of ICA\ndeconvolution was improved by performing multiple runs and building a\nconsensus signal and weight matrices. To classify the samples based on the\ncomponent weights we used support vector machine (SVM) approach\nimplemented in e1071 package." }, { - "id": 124779, - "strid": "515764dd-4e47-4bd7-9dd1-920cf12648cb", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 564, + "strid": "46082eb8-ba80-43ed-b3aa-876c7d5a04f1", + "image_id": 23, + "image_name": "11139.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 603.432, - 501.336, - 458.077, - 270.1700000000001 + 117.631, + 3387.32, + 567.15, + 45.89399999999978 ], "priority": 9, "parents": [ - 124778 + 555 ], - "children": [], - "area": 302522.185152, + "children": [ + 565, + 575, + 573, + 569, + 570, + 566, + 572, + 568, + 576 + ], + "area": 398453.83892, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 124780, - "strid": "86ee8b30-b0ea-41e1-a282-345c7c8ec4cc", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", + "id": 565, + "strid": "4a776d5a-c6f2-4c9b-b11a-916680280cdf", + "image_id": 23, + "image_name": "11139.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1171.117, - 461.729, - 147.26700000000005, - 20.286999999999978 + 95.004, + 3477.906, + 675.46, + 891.6570000000002 ], "priority": 10, "parents": [ - 124801 + 564 ], - "children": [ - 124781 - ], - "area": 540738.681293, + "children": [], + "area": 330414.981624, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Several gene expression metrics\nwere investigated and FPKM,\nwhich showed the most promising\nresults, was chosen for the\nsubsequent analysis.\n\nWe optimized the number of\nindependent components by\nminimizing the correlation\nbetween component weights. As\nan additional condition we set a\ngood separation of male and\nfemale patients with at least one\ncomponent. Thus, 39 components\nwere chosen for further analysis\n(Fig. 2). We performed 200 runs\nof ICA to identify the consensus\ndeconvolution." }, { - "id": 124781, - "strid": "32084a8b-54a6-4cff-bd6d-596fd5243f39", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 566, + "strid": "2ed14d25-b798-4f5e-9075-0a2f736c5072", + "image_id": 23, + "image_name": "11139.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1142.86, - 524.865, - 375.94600000000014, - 177.45500000000004 + 851.951, + 3469.67, + 762.883, + 678.4660000000003 ], "priority": 11, "parents": [ - 124780 + 564 ], - "children": [], - "area": 599847.2139, + "children": [ + 567 + ], + "area": 2955988.8261700002, "iscrowd": 0, "segmentation": [] }, { - "id": 124782, - "strid": "cf3b16ee-95f3-4d5e-9c12-3ad8d5f721cf", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", + "id": 567, + "strid": "ebb5fd95-994e-4a90-a82e-922596e5cf10", + "image_id": 23, + "image_name": "11139.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 70.887, - 837.642, - 88.31, - 16.436000000000035 + 841.72, + 4161.889, + 763.202, + 191.5039999999999 ], "priority": 12, "parents": [ - 124801 + 566 ], - "children": [ - 124783 - ], - "area": 59377.928454, + "children": [], + "area": 3503145.2090800004, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "FIGURE 2. Average correlation between detected\nIC mixing coefficients and _ original mixing\nproportions (mean for 20 tries). Three metrics of\nRNA-seq gene expression were considered: FPKM,\ncounts and RSEM." }, { - "id": 124783, - "strid": "785a9cb1-dcf8-428b-ba4d-70f9b71d2387", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 568, + "strid": "383df526-509a-40c4-9fee-8d1d6294d84d", + "image_id": 23, + "image_name": "11139.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 37.953, - 895.401, - 530.075, - 267.746 + 1702.251, + 1117.29, + 1505.1589999999999, + 147.72199999999998 ], "priority": 13, "parents": [ - 124782 + 564 ], "children": [], - "area": 33983.154153, + "area": 1901908.0197899998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Biological knowledge. ICA method resulted in both gene signatures and\nclinical predictors (weights). Using them and clinical annotation, each\ncomponent was associated to a biological, technical or clinical factor." }, { - "id": 124784, - "strid": "c6bd4215-c4e6-42b2-99a8-17899dd537b7", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", + "id": 569, + "strid": "c6bddbd1-71ee-4748-9037-da0b411e51e3", + "image_id": 23, + "image_name": "11139.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 71.37, - 1205.349, - 77.83499999999998, - 17.767000000000053 + 1698.151, + 1298.655, + 1003.4729999999997, + 607.857 ], "priority": 14, "parents": [ - 124801 + 564 ], - "children": [ - 124785 - ], - "area": 86025.75813, + "children": [], + "area": 2205312.286905, "iscrowd": 0, "segmentation": [], - "text": "Defence" + "text": "The majority of the components (32/39) were linked\nto biological processes, with the largest groups\nbeing: cell cycle & DNA replication, epidermis\ndevelopment & keratinization, immune response &\nleukocyte activity and developmental processes\n(including neuron development). One component\nwas specifically linked to melanin metabolic\nprocess. In addition, three components (#11, 13,\n26) were linked to patient survival (e.g. in Fig. 3).\nThe same component #13 was negatively linked to\nthe immune response. Thus, high immune response\ncould be linked to better survival." }, { - "id": 124785, - "strid": "e01b3c77-c855-4ac1-9b07-090811563834", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 570, + "strid": "25f16e1c-114e-4ffe-af84-1805000651d3", + "image_id": 23, + "image_name": "11139.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 45.519, - 1269.709, - 428.497, - 202.106 + 2789.21, + 1275.752, + 408.77800000000025, + 515.982 ], "priority": 15, "parents": [ - 124784 + 564 ], - "children": [], - "area": 57795.883971, + "children": [ + 571 + ], + "area": 3558340.23592, "iscrowd": 0, "segmentation": [] }, { - "id": 124790, - "strid": "6e929d32-131a-44f7-b25b-eef180292d1d", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 2, - "category_name": "Figure", + "id": 571, + "strid": "2bb84b67-cf01-4a01-b5a4-434c5ee1199f", + "image_id": 23, + "image_name": "11139.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 576.969, - 818.748, - 503.31999999999994, - 726.309 + 2754.85, + 1794.767, + 463.16499999999996, + 156.06600000000003 ], "priority": 16, "parents": [ - 124801 + 570 ], "children": [], - "area": 472392.21481200005, + "area": 4944313.86995, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "FIGURE 3. Kaplan-Meier plot\nshowing the survival linked to\nthe weight of independent\ncomponent #13" }, { - "id": 124791, - "strid": "99a96064-a76f-4e36-a4f3-33189d839643", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", + "id": 572, + "strid": "743687ae-bff1-4ea4-85cb-104a44b3d9a3", + "image_id": 23, + "image_name": "11139.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1134.238, - 837.373, - 103.654, - 20.434999999999945 - ], + 1699.289, + 1969.636, + 1509.4199999999998, + 245.21900000000005 + ], "priority": 17, "parents": [ - 124801 - ], - "children": [ - 124792, - 124793 + 564 ], - "area": 949780.2767740001, + "children": [], + "area": 3346980.788804, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Diagnostics. The data processing scheme, used for the validation of\ndiagnostics ability, is showed in Fig. 4A. We addressed accuracy of the\nmethod (Fig. 4B) using leave-one-out cross-validation (LOOCV) and applied it\nthen to classify a new patient (coded as P6) with an aggressive form of\nmelanoma." }, { - "id": 124792, - "strid": "f0c991e4-d1bc-49e6-9541-ea1ba9c16594", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 573, + "strid": "89de1730-150b-435f-a7bd-46375b3f7797", + "image_id": 23, + "image_name": "11139.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1118.838, - 896.209, - 485.1980000000001, - 128.8270000000001 + 1703.414, + 2221.991, + 1515.0690000000002, + 508.9499999999998 ], "priority": 18, "parents": [ - 124791 + 564 ], - "children": [], - "area": 1002712.6851419999, + "children": [ + 574 + ], + "area": 3784970.577274, "iscrowd": 0, "segmentation": [] }, { - "id": 124793, - "strid": "54c119fa-5fde-4232-b2a0-a201655ddf94", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 574, + "strid": "c80c45ee-0ffd-405c-9cea-86437dc680cf", + "image_id": 23, + "image_name": "11139.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1107.486, - 1048.728, - 454.595, - 104.14699999999993 + 1691.01, + 2752.156, + 1470.419, + 80.49699999999984 ], "priority": 19, "parents": [ - 124791 + 573 ], "children": [], - "area": 1161451.5778080001, + "area": 4653923.31756, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "FiGuRE 4. Training and validation scheme used for patient diagnostics (A) and confusion matrixes\nobserved on TCGA data (B). Note that ICA is re-run for each new sample to be classified." }, { - "id": 124794, - "strid": "07e035f8-3e74-48ef-9403-d3aa8372ed11", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", + "id": 575, + "strid": "227e7352-4a36-4144-9513-2c3b18b2e353", + "image_id": 23, + "image_name": "11139.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1155.7, - 1205.144, - 106.29999999999995, - 18.125999999999976 + 1691.795, + 2864.06, + 1505.312, + 459.46000000000004 ], "priority": 20, "parents": [ - 124801 + 564 ], - "children": [ - 124795 - ], - "area": 1392784.9208, + "children": [], + "area": 4845402.3877, "iscrowd": 0, "segmentation": [], - "text": "Number 10" + "text": "Fig. 5 demonstrate the position of the patient P6 in the space of independent\ncomponents. Based on the classification, we concluded that this male patient\nprovided primary melanoma sample of keratin subtype (though, the later\nconclusion cannot be validated). Interestingly, the SVM classified this tumour\nas “metastatic”, despite distribution of the values for IC#2 in Fig. 5B. This,\nperhaps is linked to the fact, that the tumour of P6 was very aggressive and\nalready metastasise at the time of treatment. From the high weight of\ncomponent #13 we can conclude that this patient had a poor prognosis, which\nwas true, as the patient died soon after diagnosis." }, { - "id": 124795, - "strid": "6652f350-7ac2-45fa-8976-5d3a3745d4f3", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 576, + "strid": "2a4bfef2-c05e-4a86-bbd6-5c09369c0303", + "image_id": 23, + "image_name": "11139.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1122.725, - 1263.824, - 385.567, - 195.5999999999999 + 1671.761, + 3349.395, + 1478.9389999999999, + 396.1109999999999 ], "priority": 21, "parents": [ - 124794 - ], - "children": [], - "area": 1418926.8004, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 124786, - "strid": "79329f45-025b-44d3-8165-e105ce58a55a", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 86.142, - 1598.976, - 193.04199999999997, - 20.7829999999999 - ], - "priority": 22, - "parents": [ - 124801 + 564 ], "children": [ - 124787 - ], - "area": 137738.99059200002, - "iscrowd": 0, - "segmentation": [], - "text": "Impact on the study" - }, - { - "id": 124787, - "strid": "f8861ae8-e3b2-4536-b23e-f6c208cb1d60", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 58.431, - 1636.678, - 441.638, - 280.4370000000001 - ], - "priority": 23, - "parents": [ - 124786 + 577 ], - "children": [], - "area": 95632.732218, + "area": 5599387.934595, "iscrowd": 0, "segmentation": [] }, { - "id": 124788, - "strid": "970c19b4-e5b2-4b02-bb45-bf25bfd3609d", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 639.532, - 1599.509, - 90.78999999999996, - 19.66300000000001 - ], - "priority": 24, - "parents": [ - 124801 - ], - "children": [ - 124789 - ], - "area": 1022937.1897880001, - "iscrowd": 0, - "segmentation": [], - "text": "Response" - }, - { - "id": 124789, - "strid": "b38bac94-14bb-4b4a-861a-f4b959b0baf6", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 4, - "category_name": "List", + "id": 577, + "strid": "b94461ae-9dd8-4fa2-950f-cedeadd5b664", + "image_id": 23, + "image_name": "11139.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 598.749, - 1661.331, - 453.818, - 227.2460000000001 + 1691.963, + 3790.583, + 1514.4199999999998, + 75.96099999999979 ], - "priority": 25, + "priority": 22, "parents": [ - 124788 + 576 ], "children": [], - "area": 994720.274919, + "area": 6413526.184429, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "FIGURE 5. The results of classification for the new patient: (A) the new patient (P6) in the space of\nindependent components and his weight coefficients compared to the values from the training cohort." }, { - "id": 124796, - "strid": "5244092d-5f89-4918-8b5c-f8b21c09ce85", - "image_id": 205358, - "image_name": "14866.png", + "id": 578, + "strid": "f61ee05d-2dc5-4deb-a991-a6651215788b", + "image_id": 23, + "image_name": "11139.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1171.391, - 1598.197, - 114.0150000000001, - 15.517000000000053 + 1723.05, + 3904.189, + 334.95000000000005, + 45.79100000000017 ], - "priority": 26, + "priority": 23, "parents": [ - 124801 + 555 ], "children": [ - 124797 + 579 ], - "area": 1872113.582027, + "area": 6727112.85645, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Conclusions" }, { - "id": 124797, - "strid": "b6d8357a-8d2a-4623-97fc-f1d0e16efdbf", - "image_id": 205358, - "image_name": "14866.png", + "id": 579, + "strid": "59fb79db-6720-44a8-9a3b-2b7f15ff8aa9", + "image_id": 23, + "image_name": "11139.png", "category_id": 4, "category_name": "List", "bbox": [ - 1141.884, - 1646.281, - 441.51700000000005, - 244.683 + 1703.541, + 3996.664, + 1507.943, + 317.18899999999985 ], - "priority": 27, + "priority": 24, "parents": [ - 124796 + 578 ], "children": [], - "area": 1879861.933404, + "area": 6808480.9872240005, "iscrowd": 0, "segmentation": [] }, { - "id": 124798, - "strid": "f2b938a3-5654-491c-9184-c4101057d4c1", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 70.447, - 1965.693, - 485.914, - 23.261999999999944 - ], - "priority": 28, - "parents": [ - 124801 - ], - "children": [], - "area": 138477.174771, - "iscrowd": 0, - "segmentation": [], - "text": "“Most adults don’t get me, but you do.” - boy (11)" - }, - { - "id": 124799, - "strid": "fb5bc014-239c-43bd-9577-5c8202bc5e03", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 645.936, - 1967.064, - 922.0690000000001, - 21.60200000000009 - ], - "priority": 29, - "parents": [ - 124801 - ], - "children": [], - "area": 1270597.451904, - "iscrowd": 0, - "segmentation": [], - "text": "it doesn’t matter to me whether he has tics, it matters that he’s happy.” - mother of a boy (10)" - }, - { - "id": 124800, - "strid": "b373daac-ce63-46ac-918f-5595e6552372", - "image_id": 205358, - "image_name": "14866.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 72.339, - 2051.443, - 1446.584, - 21.108999999999924 - ], - "priority": 30, - "parents": [ - 124801 - ], - "children": [], - "area": 148399.335177, - "iscrowd": 0, - "segmentation": [], - "text": "iked the explanation about the content of the therapy. The contacts with other parents were also nice (sharing experiences).” - mother of a girl (13)" - }, - { - "id": 159514, - "strid": "b280896a-8adb-4a22-8797-1b31dad78b9c", - "image_id": 206731, - "image_name": "6334.png", + "id": 580, + "strid": "0151148a-05d8-498e-bc74-cbbb51ce3d99", + "image_id": 24, + "image_name": "11159.png", "category_id": 9, "category_name": "Root", "bbox": [ - 56.67, - 527.33, - 154.83999999999997, - 154.83999999999992 + 165.64, + 106.82, + 86.48000000000002, + 196.55 ], "priority": -1, "parents": [], "children": [ - 159489, - 159490, - 159483, - 159484, - 159486, - 159487, - 159491, - 159488, - 159485 + 585, + 582, + 583, + 601, + 587, + 581, + 598, + 600, + 589 ], - "area": 29883.791100000002, + "area": 17693.6648, "iscrowd": 0, "segmentation": [] }, { - "id": 159484, - "strid": "446f19b8-ddae-49a5-9408-3956bf4838ec", - "image_id": 206731, - "image_name": "6334.png", + "id": 581, + "strid": "653a372c-030f-4c10-9a54-9ffe3a3b59f8", + "image_id": 24, + "image_name": "11159.png", "category_id": 1, "category_name": "Title", "bbox": [ - 248.45, - 617.068, - 2794.676, - 203.19900000000007 + 335.525, + 58.498, + 2284.849, + 304.075 ], "priority": 1, "parents": [ - 159514 + 580 ], "children": [], - "area": 153310.5446, + "area": 19627.541449999997, "iscrowd": 0, "segmentation": [], - "text": "A systems approach to unravel host response processes and host-\nparasite interactions in trypanosome infections" + "text": "Transmission analysis of aMDR\nM.tuberculosis outbreak in Bulgaria" }, { - "id": 159483, - "strid": "c3e8564c-e0ba-47b7-9eea-017a8a4d9169", - "image_id": 206731, - "image_name": "6334.png", + "id": 582, + "strid": "28edf506-4a60-44e0-b294-7d3854a13cce", + "image_id": 24, + "image_name": "11159.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 1806.695, - 64.698, - 1480.907, - 377.101 + 89.267, + 368.998, + 2766.659, + 396.15500000000003 ], "priority": 2, "parents": [ - 159514 + 580 ], "children": [], - "area": 116889.55310999998, + "area": 32939.344465999995, "iscrowd": 0, "segmentation": [], - "text": "Siddharth Jayaraman’, Sofie Demeyer’, Darren Creek?, Christiane\nHertz-Fowler?, Michael P. Barrett’, Liam J. Morrison? & Tom Michoel*\n\n1Roslin Institute, University of Edinburgh, Bush Estate, Midlothian EH25 9RG, 2 Biochemistry\nand Molecular Biology, University of Melbourne, Parkville 3010, Victoria, Australia and\n3Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool,\nCrown Street, Liverpool L69 7ZB , 4 Wellcome Trust Centre for Molecular Parasitology,\nInstitute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA" + "text": "S. Panaiotov', E. Bachiyska’, S. Yordanova!, D.M. Cirillo 7, E. Tigliani ,\nA. Trovato 2, M.R. de Filippo 7, G. Refregier 3, C. Sola\n1. National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; 2. Emerging\nBacterial Pathogens Unit, IRCCS S. Rafaelle Scientific Institute, 20132 Milano, Italy; 3. Institute\nfor Integrative Biology of the Cell, CEA, CNRS, University Paris-Sud, 91198 Paris, France" }, { - "id": 159485, - "strid": "5de5da18-452b-4e07-bfaf-a5c0aa7888ca", - "image_id": 206731, - "image_name": "6334.png", + "id": 583, + "strid": "1051e4fc-e6df-4231-a345-34e80e8b321d", + "image_id": 24, + "image_name": "11159.png", "category_id": 5, "category_name": "Section", "bbox": [ - 96.33, - 868.153, - 328.648, - 45.71799999999996 + 236.304, + 929.753, + 576.145, + 103.26799999999992 ], "priority": 3, "parents": [ - 159514 + 580 ], "children": [ - 159492, - 159508 + 584 ], - "area": 83629.17849, + "area": 219704.352912, "iscrowd": 0, "segmentation": [], - "text": "1 Introduction" + "text": "Background" }, { - "id": 159492, - "strid": "c3d412ec-1ec0-4de9-a691-3b02a9e16daf", - "image_id": 206731, - "image_name": "6334.png", + "id": 584, + "strid": "53ec5203-6c20-4c0f-a455-a28f6946b405", + "image_id": 24, + "image_name": "11159.png", "category_id": 3, "category_name": "Text", "bbox": [ - 131.789, - 921.267, - 1469.299, - 417.49599999999987 + 127.853, + 1114.489, + 780.618, + 1025.4810000000002 ], "priority": 4, "parents": [ - 159485 + 583 ], "children": [], - "area": 121412.856663, + "area": 142490.762117, "iscrowd": 0, "segmentation": [], - "text": "The relative resistance or susceptibility to parasite infections depends on a complex\ninterplay between host and parasite genotypes (1,2). A host-parasite genotype infection\nmatrix using severe and mildly virulent trypanosome strains (3,4) with susceptible and\nresistant mice (5)(Fig. 1A) will enable investigation of the relative contribution of host or\nparasite genotype to disease phenotypes. In order to identify key host response processes\nand host-parasite interactions at the molecular, pathway and whole-system level, we have\ngenerated mouse RNAseq gene expression profiles during disease progression and used\ndata mining algorithms to link those data to mouse metabolome profiles derived from the\nsame samples. byo 3 6 1» 2" + "text": "An outbreak of = multidrug-resistant\ntuberculosis was detected in Bulgaria in\n2008 when spoligo and MIRU-VNTR\ngenotyping was introduced. Molecular\ntyping confirmed strong association\nbetween MDR and SIT41 (TUR) MTB\nsublineage. The MDR TB cases of SIT41\ngenotype in Bulgaria are >40% The drug\nsensitive MTB strains of SIT41 genotype\nrepresented only 2%. SIT41 genotype is\nconsidered as a marker for MDR\ntuberculosis in Bulgaria. SIT41 (TUR) is\nendemic M. tuberculosis genotype for\nBulgaria and Turkey. SIT41 is a low copy\nnumber of the 1S6110 element as identified\nby RFLP-IS6110 typing.\n\nSpoligo- and MIRU-VNTR strain typing\nlacks sufficent discriminatory power to\nresolve large outbreaks and the potential of\nNGS technique _ for identification of\noutbreak-related transmission chains should\nbe applied." }, { - "id": 159508, - "strid": "2fea4f48-fb00-4098-8dad-ee64ad8533fd", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 2, - "category_name": "Figure", + "id": 585, + "strid": "296938d7-0027-4873-9015-825db5b84a04", + "image_id": 24, + "image_name": "11159.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 104.783, - 1311.959, - 1513.487, - 383.28300000000013 + 275.699, + 2206.712, + 483.877, + 102.15299999999979 ], "priority": 5, "parents": [ - 159485 + 580 ], "children": [ - 159498 + 586 ], - "area": 137470.999897, + "area": 608388.291688, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Objectives" }, { - "id": 159498, - "strid": "fb73baf4-9fac-4d66-85b0-374edcdefe87", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 6, - "category_name": "Caption", + "id": 586, + "strid": "be2763e9-8ef1-49a6-8c60-466dd3a2f19e", + "image_id": 24, + "image_name": "11159.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 117.509, - 1715.965, - 1485.516, - 160.55600000000004 + 132.991, + 2371.839, + 760.613, + 274.5329999999999 ], "priority": 6, "parents": [ - 159508 + 585 ], "children": [], - "area": 201641.331185, + "area": 315433.24044900003, "iscrowd": 0, "segmentation": [], - "text": "Figure 1: A) Our experimental models; C57BI/6 mice are tolerant to trypanosome infections, BALB/c mice are\nsusceptible, Trypanosoma brucei TREU927 are virulent pathogens, Trypanosoma brucei STIB247 are less\nvirulent. B) experimental time series setup and C) shows the biological replicates and total number of\nsamples used for this analysis." + "text": "Our study intended to apply core genome\nMultilocus Sequencing Typing (cgMLST)\nanalysis to reconstruct the transmission\ndynamics of a MDR endemie in Bulgaria at\nhigher resolution than 24 MIRU-VNTR\nanalysis." }, { - "id": 159486, - "strid": "0180cd56-99b7-4b8d-a29f-81d6721cd90d", - "image_id": 206731, - "image_name": "6334.png", + "id": 587, + "strid": "c4d340b1-9b7c-4706-9745-a5a0ef005c20", + "image_id": 24, + "image_name": "11159.png", "category_id": 5, "category_name": "Section", "bbox": [ - 97.197, - 1920.269, - 597.801, - 55.011999999999944 + 288.4, + 2732.634, + 510.04200000000003, + 195.80099999999993 ], "priority": 7, "parents": [ - 159514 + 580 ], "children": [ - 159504, - 159509 + 588 ], - "area": 186644.385993, + "area": 788091.6455999999, "iscrowd": 0, "segmentation": [], - "text": "2 Methods and objectives" + "text": "Materials &\nMethods" }, { - "id": 159509, - "strid": "0fa34e0d-0505-40d6-ab08-6e73739ee9ea", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 2, - "category_name": "Figure", + "id": 588, + "strid": "9af2e290-c271-4f68-b8b8-720a6863a266", + "image_id": 24, + "image_name": "11159.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 131.965, - 2116.312, - 1484.009, - 688.1459999999997 + 134.368, + 3007.936, + 794.1400000000001, + 604.0769999999998 ], "priority": 8, "parents": [ - 159486 - ], - "children": [ - 159499 + 587 ], - "area": 279279.11308, + "children": [], + "area": 404170.344448, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "In total, 185 MDR/XDR TB strains of SIT41\n(TUR) have been characterized by\nspoligotyping and 24 loci MIRU-VNTR\nanalysis. These represent about 75%\ncoverage of the MDR/XDR TB cases of\nSIT41 (TUR) in the country for the period\n2007-2016. A core genome Multilocus\nSequence Typing (cgMLST) V2 scheme\n(2891 genes) using the Ridom SeqSphere+\nsoftware, which transfers the genome-wide\nSNP diversity into a standardized allele\nnumbering system was_ applied for\nsequencing analysis of 34 SIT41 strains." }, { - "id": 159499, - "strid": "a4a77b20-ba13-4ea3-a0d5-a59eee8075ee", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 6, - "category_name": "Caption", + "id": 589, + "strid": "a0b0641d-8617-478e-bb91-f92a7a054483", + "image_id": 24, + "image_name": "11159.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 118.47, - 1979.381, - 1488.004, - 117.68000000000006 + 1276.957, + 934.394, + 346.7650000000001, + 88.03899999999999 ], "priority": 9, "parents": [ - 159509 + 580 ], - "children": [], - "area": 234497.26707, + "children": [ + 595, + 597, + 590, + 591, + 593 + ], + "area": 1193180.959058, "iscrowd": 0, "segmentation": [], - "text": "Figure 2: The experimental workflow consisting of extracting the RNA from spleens, which underwent RNA-\nSeq for transcriptome analysis, and the blood plasma from each of the sampled mice was subjected to LC-MS\nfor metabalome analysis." + "text": "Results" }, { - "id": 159504, - "strid": "714f8e77-bed3-4b3e-a983-0539e4b09800", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 4, - "category_name": "List", + "id": 590, + "strid": "7a58fab2-fd6a-4153-8e78-a9436730ae4a", + "image_id": 24, + "image_name": "11159.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 115.5, - 2797.768, - 1499.974, - 368.94000000000005 + 1029.982, + 1108.966, + 824.598, + 846.874 ], "priority": 10, "parents": [ - 159486 + 589 ], "children": [], - "area": 323142.204, + "area": 1142215.018612, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "In total, 1385 MDR strains of SIT41 (TUR)\ngenotype were identified between 2007 —\n2016. The percentage of the MDR-TB cases\nwith SIT41 genotype significantly increased in\nBulgaria, from 40% in the period 2007-2011 to\n60% in 2012 - 2013. MIRU-VNTR analysis\nidentified three clusters including 17, 26 and 67\nstrains. Five other clusters include between 3\nand 9 strains. The largest cluster’s MIRU-\nVNTR_ profile 244124132134425113333b32\nwas identified all over the country, suggesting\na common ancestor. This genotype was not\nfound in other countries. MIRU-VNTR analysis\nshowed that SIT41 strains from Bulgaria differ\nfrom those from Albania, Greece and Turkey\n(Fig. 2). The highest number of MIRU-VNTR\nclustered strains was in the North-West part of\nthe country. (Fig.1)" }, { - "id": 159487, - "strid": "1a989a15-d917-4ce8-a180-6e5cb582d4e6", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 5, - "category_name": "Section", + "id": 591, + "strid": "6255b99b-5e89-410e-8ebb-897d812e9a6c", + "image_id": 24, + "image_name": "11159.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 94.98, - 3217.008, - 1192.861, - 129.962 + 1039.733, + 1994.458, + 787.671, + 527.3969999999999 ], "priority": 11, "parents": [ - 159514 + 589 ], "children": [ - 159511, - 159493, - 159494, - 159510 + 592 ], - "area": 305551.41984, + "area": 2073703.799714, "iscrowd": 0, - "segmentation": [], - "text": "3 Results\n3.1 Exploration of relationships between conditions" + "segmentation": [] }, { - "id": 159493, - "strid": "48b74f19-7b85-4a2e-b65d-0bb1d147243c", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 3, - "category_name": "Text", + "id": 592, + "strid": "5edb1b44-8607-4eb3-9bf2-ba8ade6289f0", + "image_id": 24, + "image_name": "11159.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 112.197, - 3345.415, - 1456.437, - 116.54399999999987 + 1059.749, + 2549.287, + 765.105, + 52.38299999999981 ], "priority": 12, "parents": [ - 159487 + 591 ], "children": [], - "area": 375345.526755, + "area": 2701604.348963, "iscrowd": 0, "segmentation": [], - "text": "The first step of analysis was to examine sample variability (the data for each sample encompassing gene\nexpression for all genes in a given sample), the similarities and differences between treatments, and outline\ngeneral trends.\n\nOO" + "text": "Fig. 1 Distribution of 185 MDR SIT41 strains" }, { - "id": 159510, - "strid": "fe15e9f8-e538-4fae-afcb-64e4006556a7", - "image_id": 206731, - "image_name": "6334.png", + "id": 593, + "strid": "8db35031-f1e2-48fe-b787-d34c447ebe3b", + "image_id": 24, + "image_name": "11159.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 123.118, - 3469.166, - 661.1870000000001, - 703.2789999999995 + 1051.106, + 2644.164, + 769.7279999999998, + 704.0660000000003 ], "priority": 13, "parents": [ - 159487 + 589 ], "children": [ - 159500 + 594 ], - "area": 427116.779588, + "area": 2779296.645384, "iscrowd": 0, "segmentation": [] }, { - "id": 159500, - "strid": "fffd7a85-843c-45df-a4bd-e1f6b4bf129e", - "image_id": 206731, - "image_name": "6334.png", + "id": 594, + "strid": "debe73b8-de60-45eb-aa56-75db64dcccb5", + "image_id": 24, + "image_name": "11159.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 124.669, - 4186.37, - 606.991, - 72.80100000000039 + 1053.04, + 3381.327, + 836.1869999999999, + 84.05499999999984 ], "priority": 14, "parents": [ - 159510 + 593 ], "children": [], - "area": 521910.56152999995, + "area": 3560672.58408, "iscrowd": 0, "segmentation": [], - "text": "Figure 3: Dendrogram showing the distances\nbetween different conditions" + "text": "Fig. 2 Comparison between Albanian, Bulgarian\nand Turkish MDR SIT41 M. tuberculosis strains." }, { - "id": 159511, - "strid": "e0bb8973-bd8b-4c9b-850e-b3bf4e08f177", - "image_id": 206731, - "image_name": "6334.png", + "id": 595, + "strid": "23182014-04fb-42e0-abb3-d88529aec587", + "image_id": 24, + "image_name": "11159.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 808.859, - 3451.628, - 789.216, - 722.5710000000004 + 1942.031, + 1090.556, + 933.8820000000001, + 510.68499999999995 ], "priority": 15, "parents": [ - 159487 + 589 ], "children": [ - 159501 + 596 ], - "area": 2791880.372452, + "area": 2117893.559236, "iscrowd": 0, "segmentation": [] }, { - "id": 159501, - "strid": "30fef6a9-e27a-4126-a184-e934d605bd57", - "image_id": 206731, - "image_name": "6334.png", + "id": 596, + "strid": "f0cf68f1-b61a-4f58-92fd-3b9166228d2e", + "image_id": 24, + "image_name": "11159.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 853.22, - 4191.232, - 718.556, - 113.45600000000013 + 1971.674, + 1651.32, + 910.8310000000001, + 47.999000000000024 ], "priority": 16, "parents": [ - 159511 + 595 ], "children": [], - "area": 3576042.96704, + "area": 3255864.70968, "iscrowd": 0, "segmentation": [], - "text": "Figure 4: Individual replicate level MDS plot for gene-\nlevel features showing a separation between the\nmouse genotype along the second dimension" + "text": "Fig. 3. cgMLST analysis of 34 SIT41 MDR TB strains" }, { - "id": 159494, - "strid": "fbfa1227-af20-4f19-b47a-af18dc39c01a", - "image_id": 206731, - "image_name": "6334.png", + "id": 597, + "strid": "dfe7ff23-e340-4449-9774-60fede2816b6", + "image_id": 24, + "image_name": "11159.png", "category_id": 3, "category_name": "Text", "bbox": [ - 100.587, - 4321.861, - 1519.353, - 90.70799999999963 + 1984.656, + 1780.765, + 882.9969999999998, + 322.81600000000003 ], "priority": 17, "parents": [ - 159487 + 589 ], "children": [], - "area": 434723.032407, + "area": 3534205.94184, "iscrowd": 0, "segmentation": [], - "text": "The data showed a strong time-dependent effect (early vs late) and the second level of variation\nis due to a mouse genotype effect." + "text": "Few MIRU-VNTR clustered strains originated from\ngeographically distant regions >350 km.\nEpidemiological links were difficult to establish\nbased on patients interview. cgMLST analysis of\n34 SIT41 strains demonstrated allelic differences\nbetween 1 and 54 alleles. Several clustered strains\nwith identical cgMLST profile were identified." }, { - "id": 159488, - "strid": "7fea39b8-03d9-4971-b039-cbebbd8cb062", - "image_id": 206731, - "image_name": "6334.png", + "id": 598, + "strid": "a37ccd43-3152-4239-8fc1-2fcf159928bf", + "image_id": 24, + "image_name": "11159.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1671.352, - 864.433, - 1282.6580000000001, - 115.74000000000001 + 2106.437, + 2237.733, + 574.4299999999998, + 84.4340000000002 ], "priority": 18, "parents": [ - 159514 + 580 ], "children": [ - 159496, - 159513, - 159495 + 599 ], - "area": 1444771.823416, + "area": 4713643.587321, "iscrowd": 0, "segmentation": [], - "text": "3.2 Summary of differentially expressed genes between\nconditions" + "text": "Conclusions" }, { - "id": 159495, - "strid": "80bbbc39-4bd8-4e9f-a835-b225d3c7ad7c", - "image_id": 206731, - "image_name": "6334.png", + "id": 599, + "strid": "a815cf09-75b6-4445-89cf-926f10353c9a", + "image_id": 24, + "image_name": "11159.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1672.597, - 984.449, - 1455.314, - 38.798 + 1989.94, + 2401.663, + 853.9969999999998, + 653.9900000000002 ], "priority": 19, "parents": [ - 159488 + 598 ], "children": [], - "area": 1646586.4440529998, + "area": 4779165.27022, "iscrowd": 0, "segmentation": [], - "text": "The next level of analysis is to examine genes that are differentially expressed between treatments." + "text": "The endemic SIT41 MDR genotype, spreading in\nBulgaria, was not found in other countries,\nsuggesting local evolution.\n\nMain characteristics of the Bulgarian SIT41\nstrains is the 11 VNTR copy number of QUB-\n26(4052) marker.\n\nContact tracing analysis could not explain how\npatients living at a distance of >350 km have\nidentical MIRU-VNTR and cgMLST profiles.\nApplying WGS we hope to date the start of this\nongoing MDR_ endemy, to identify true\ntransmissions across the country. The clonal\nexpansion of SIT41 among the MDR-TB patients\nin Bulgaria remains to be further analyzed." }, { - "id": 159513, - "strid": "344f8b83-8b07-4c12-b290-fac8df399ed4", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 2, - "category_name": "Figure", + "id": 600, + "strid": "0dcedd02-ada0-42e2-a616-1a1692627913", + "image_id": 24, + "image_name": "11159.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1727.973, - 1054.9, - 1452.8559999999998, - 358.6779999999999 + 2008.807, + 3105.857, + 774.3810000000001, + 112.22899999999981 ], "priority": 20, "parents": [ - 159488 + 580 + ], + "children": [], + "area": 6239067.282599, + "iscrowd": 0, + "segmentation": [], + "text": "References:\nKohl, T. Et al. J. Clin. Microbiol., 52(7):2479-2486 (2014)\nPanaiotov, S. et al. Med. Pregled. 52(3):47-54 (2016) (in Bulg.)" + }, + { + "id": 601, + "strid": "03b2e640-c4eb-49b4-8a9d-29372bf993b8", + "image_id": 24, + "image_name": "11159.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 1383.599, + 3522.807, + 1473.0090000000002, + 122.34000000000015 + ], + "priority": 21, + "parents": [ + 580 + ], + "children": [], + "area": 4874152.242392999, + "iscrowd": 0, + "segmentation": [], + "text": "Acknowledgements: S.P. has received funding from the European Union’s Horizon 2020\nresearch and innovation programme under the Marie Sklodowska-Curie grant agreement\nNo 660150 and with the support of Marie Curie Alumni Association" + }, + { + "id": 602, + "strid": "49d327f0-3da4-47b0-bedb-6d948bb9d932", + "image_id": 25, + "image_name": "11175.png", + "category_id": 9, + "category_name": "Root", + "bbox": [ + 33.09, + 412.09, + 178.79, + 191.56 ], + "priority": -1, + "parents": [], "children": [ - 159502 + 604, + 607, + 605, + 603, + 612, + 610 ], - "area": 1822838.7177000002, + "area": 13636.0581, "iscrowd": 0, "segmentation": [] }, { - "id": 159502, - "strid": "92fbaf82-6bf5-4859-8844-2c8eaf2dd8d4", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 6, - "category_name": "Caption", + "id": 603, + "strid": "de30a166-29de-4a30-b9bd-8e214cc9c62d", + "image_id": 25, + "image_name": "11175.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 1699.933, - 1418.3, - 1478.73, - 121.23399999999992 + 17.818, + 46.068, + 3284.426, + 298.231 ], - "priority": 21, + "priority": 1, "parents": [ - 159513 + 602 ], "children": [], - "area": 2411014.9739, + "area": 820.8396240000001, "iscrowd": 0, "segmentation": [], - "text": "Figure 5: A) Venn diagram showing the overlap between the differentially expressed genes relative to\nrespective uninfected mice for both genotypes, B) shows the differences in the genes differentially\nexpressed (relative to uninfected) between the mouse-parasite genotype pairs at early time point (day 3)." + "text": "EDAM - The ontology of bioinformatics operations, types of\ndata, topics, and data formats" }, { - "id": 159496, - "strid": "76feecaf-3a3a-4cb3-acc5-b57409c16cfd", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 3, - "category_name": "Text", + "id": 604, + "strid": "9fd988e2-dd51-4faf-bc71-c9a1ed485448", + "image_id": 25, + "image_name": "11175.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1668.214, - 1552.491, - 1538.9279999999999, - 231.3520000000001 + 337.517, + 367.512, + 2656.181, + 308.82 ], - "priority": 22, + "priority": 2, "parents": [ - 159488 + 602 ], "children": [], - "area": 2589887.221074, + "area": 124041.547704, "iscrowd": 0, "segmentation": [], - "text": "Genes differentially expressed between infected and uninfected mice show both significant time\ndependent and host and pathogen genotype effects. More perturbation is seen in the\ntranscriptome from mice infected with 927 at early time points, but the differentially expressed\ngenes between the different genotype combinations (Fig. 5B) only partially overlap, suggesting a\nhost-parasite genotype effect." + "text": "MatuS Kalas, Herve Méenager, Veit Schwammle, Jon Ison and EDAM Contributors\n1 : Bioinformatics and Biostatistics Hub of the C3BI, Institut Pasteur, Paris - France\n2 : Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Denmark\n3 : Computational Biology Unit (CBU), University of Bergen, Bergen, Norway\n\n4: Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark" }, { - "id": 159489, - "strid": "7413f7c2-69fb-4909-b1c9-243e16abdf09", - "image_id": 206731, - "image_name": "6334.png", + "id": 605, + "strid": "3dbc5b1b-9e97-4a6a-88eb-9b0b6fbf7ddb", + "image_id": 25, + "image_name": "11175.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1675.583, - 1830.78, - 1469.3470000000002, - 58.350999999999885 + 264.918, + 731.582, + 519.163, + 64.24900000000002 ], - "priority": 23, + "priority": 3, "parents": [ - 159514 + 602 ], "children": [ - 159512, - 159507, - 159497 + 606 ], - "area": 3067623.84474, + "area": 193809.240276, "iscrowd": 0, "segmentation": [], - "text": "3.3 Gene-metabolite correlation — Trypanosomes and Glycolysis" + "text": "" }, { - "id": 159512, - "strid": "97150d12-878e-4b0d-befd-a9b7ad71098c", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 2, - "category_name": "Figure", + "id": 606, + "strid": "62fbb1c5-484c-4c1e-b4ef-2a98d67b7163", + "image_id": 25, + "image_name": "11175.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1690.274, - 1903.626, - 1501.085, - 898.135 + 116.939, + 846.61, + 3074.376, + 461.544 ], - "priority": 24, + "priority": 4, "parents": [ - 159489 - ], - "children": [ - 159503 + 605 ], - "area": 3217649.5335239996, + "children": [], + "area": 99001.72679, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and\ndata identifiers, data formats, operations, and topics. EDAM has a simple structure, and comprises a set of concepts with terms,\nsynonyms, definitions, relations, links, and some additional information (especially for data formats).\n\n3 consecutive stable versions of EDAM have been released since May 2016 (version 1.15), with version 1.18 being the current one.\nEDAM is developed in a participatory and transparent fashion, with a growing community of contributors. EDAM is used by\nmultiple bioinformatics projects, including ELIXIR bio.tools, Debian Med and the Common Workflow Language." }, { - "id": 159503, - "strid": "8d9ac236-a453-48c2-8b16-913ed767bf54", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 6, - "category_name": "Caption", + "id": 607, + "strid": "57f44182-0fe6-403c-96ee-ac33eda698e6", + "image_id": 25, + "image_name": "11175.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1700.899, - 2819.963, - 1474.455, - 119.36700000000019 + 202.141, + 1393.002, + 403.163, + 65.85899999999992 ], - "priority": 25, + "priority": 5, "parents": [ - 159512 + 602 ], - "children": [], - "area": 4796472.246737, + "children": [ + 609, + 608 + ], + "area": 281582.817282, "iscrowd": 0, "segmentation": [], - "text": "Figure 6: A) Aerobic glycolysis in bloodstream form T. brucei, B) Host gene expression plot over time and\ngenotype for hexokinase and pyruvate kinase, compared to plasma metabolite levels over time and\ngenotype for glucose and pyruvate." + "text": "Architecture" }, { - "id": 159497, - "strid": "bc235d14-0510-4e0d-97b9-ec9b59501406", - "image_id": 206731, - "image_name": "6334.png", + "id": 608, + "strid": "7f47822e-b893-4914-992d-14e482ea2991", + "image_id": 25, + "image_name": "11175.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1678.185, - 2959.218, - 1502.6, - 231.84000000000015 + 87.969, + 1524.875, + 1441.171, + 655.8490000000002 ], - "priority": 26, + "priority": 6, "parents": [ - 159489 + 607 ], "children": [], - "area": 4966115.25933, + "area": 134141.728875, "iscrowd": 0, "segmentation": [], - "text": "Study objectives: Applying integrated omics approach to study the impact of trypanosome\nglucose consumption in vivo, upon the host response and infection phenotype along with\nsignatures of parasite glucose consumption. Trypanosomes in mammals rely entirely on\nglucose consumption for energy but lack functional Krebs cycle or oxidative phosphorylation\nproducing pyruvate as the major end product of glucose catabolism." + "text": "Concepts - All concepts have a name (term or label) and a definition.\nFurther, a concept may have relations (see below) to other EDAM\nconcepts, as well intrinsic properties, e.g. an identifier may have a\nregular expression defining its syntax.\n\nHierarchy - Every concept (excluding top-level concepts) is related to\none or more other concepts within the same branch by an is a\n(specialisation) relation. Hence EDAM has 4 primary hierarchies (for\nData, Format, Operation, and Topic).\n\nRelations - Concepts are related by defined relation types (see figure),\nwhich reflect well established or self-evident principles, and are used\nprimarily to define internal consistency of EDAM." }, { - "id": 159507, - "strid": "0b21bc06-4189-41f3-92d8-5810a275f268", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 4, - "category_name": "List", + "id": 609, + "strid": "93489952-c0fc-48e0-90c2-26b71b07933e", + "image_id": 25, + "image_name": "11175.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1679.313, - 3216.146, - 1504.1390000000001, - 228.89100000000008 + 450.397, + 2203.437, + 789.588, + 624.8119999999999 ], - "priority": 27, + "priority": 7, "parents": [ - 159489 + 607 ], "children": [], - "area": 5400915.787698001, + "area": 992421.414489, "iscrowd": 0, "segmentation": [] }, { - "id": 159490, - "strid": "f5f7b125-de60-43a0-beed-f12b15b11657", - "image_id": 206731, - "image_name": "6334.png", + "id": 610, + "strid": "292edaec-9957-4b13-ad01-305a5557cf16", + "image_id": 25, + "image_name": "11175.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1670.947, - 3504.168, - 327.66200000000003, - 47.53099999999995 + 1874.58, + 1397.543, + 304.25300000000016, + 61.28800000000001 ], - "priority": 28, + "priority": 8, "parents": [ - 159514 + 602 ], "children": [ - 159506 + 611 ], - "area": 5855279.007096, + "area": 2619806.1569399997, "iscrowd": 0, "segmentation": [], - "text": "4 Future work" + "text": "Overview" }, { - "id": 159506, - "strid": "4e7cd102-a127-4128-9353-23956e7e7b85", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 4, - "category_name": "List", + "id": 611, + "strid": "5c0c27df-f620-4656-8432-99d5a233f823", + "image_id": 25, + "image_name": "11175.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1687.488, - 3590.137, - 1489.834, - 369.904 + 1695.762, + 1650.22, + 1539.035, + 1135.0019999999997 ], - "priority": 29, + "priority": 9, "parents": [ - 159490 + 610 ], "children": [], - "area": 6058313.105856, + "area": 2798380.36764, "iscrowd": 0, "segmentation": [] }, { - "id": 159491, - "strid": "23f76c81-df66-4c2e-9f15-707dc6e06384", - "image_id": 206731, - "image_name": "6334.png", + "id": 612, + "strid": "5fbe90e9-6bed-4609-a5ee-62daf4b36139", + "image_id": 25, + "image_name": "11175.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1673.702, - 4009.704, - 269.54099999999994, - 42.05600000000004 + 226.969, + 2926.757, + 678.7139999999999, + 79.47499999999991 ], - "priority": 30, + "priority": 10, "parents": [ - 159514 + 602 ], "children": [ - 159505 + 617, + 616, + 614, + 615, + 613 ], - "area": 6711049.604208, + "area": 664283.109533, "iscrowd": 0, "segmentation": [], - "text": "5 Reference" + "text": "Latest developments" }, { - "id": 159505, - "strid": "bc349b6e-4cc7-4bfa-8bc8-9d5653e2f116", - "image_id": 206731, - "image_name": "6334.png", - "category_id": 4, - "category_name": "List", + "id": 613, + "strid": "6bf040f0-e9bb-4ca1-acf0-c888f50de3d0", + "image_id": 25, + "image_name": "11175.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1669.726, - 4074.516, - 1528.533, - 334.547 + 104.841, + 3052.078, + 2990.162, + 131.34799999999996 ], - "priority": 31, + "priority": 11, "parents": [ - 159491 + 612 ], "children": [], - "area": 6803325.302616, + "area": 319982.909598, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Contents evolution: Over the last year, 3 new versions have been published, introducing, correcting or deprecating terms: 74\nnew terms have been created, 44 terms were deprecated, and 109 have been modified (mostly for restructuration purposes)." }, { - "id": 199909, - "strid": "f9116181-f70e-4e5d-ac5c-388a23a41921", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 9, - "category_name": "Root", + "id": 614, + "strid": "59bca374-4dcb-4e75-8773-8ba76cb54ff4", + "image_id": 25, + "image_name": "11175.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3038.98, - 115.42, - 163.0, - 209.56 + 104.494, + 3260.708, + 3000.084, + 200.41699999999992 ], - "priority": -1, - "parents": [], - "children": [ - 199908, - 199890, - 199893, - 199904, - 199907, - 199900, - 199889, - 199899, - 199898, - 199901, - 199905, - 199897, - 199892, - 199906, - 199891, - 199896, - 199903, - 199902 + "priority": 12, + "parents": [ + 612 ], - "area": 350759.0716, + "children": [], + "area": 340724.421752, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Continuous Integration: The EDAM release process now includes automatic controls that check the EDAM ontology at every\nmodification for a number of potential errors. This continuous integration process has eliminated the need for many tedious\nmanual controls, and thus enabled a more frequent pace for the releases of EDAM." }, { - "id": 199889, - "strid": "8aeae012-bc8e-4d02-be84-79f7874ba1f0", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 1, - "category_name": "Title", + "id": 615, + "strid": "ba0474fa-c627-4d2c-966c-42042b217f06", + "image_id": 25, + "image_name": "11175.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1713.42, - 41.584, - 1209.1040000000003, - 395.092 + 103.672, + 3537.894, + 3018.616, + 193.17000000000007 ], - "priority": 1, + "priority": 13, "parents": [ - 199909 + 612 ], "children": [], - "area": 71250.85728000001, + "area": 366780.54676799994, "iscrowd": 0, "segmentation": [], - "text": "Web-based Tools for\nIntegrative Analysis of\nPancreatic Cancer Data" + "text": "New release formats, new interfaces: Starting in version 1.18, EDAM is now available in TSV and CSV formats, to facilitate its\nbrowsing with spreadsheet applications. It can be browsed online using WebProtégé as well as OLS at EBI and BioPortal at\nNCBO." }, { - "id": 199890, - "strid": "ec4a242e-87ab-413e-8779-fdde346bb7c9", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 0, - "category_name": "Author Info", + "id": 616, + "strid": "8de39143-8fc6-4e05-b65f-67960d16990f", + "image_id": 25, + "image_name": "11175.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 73.739, - 545.037, - 3158.039, - 132.139 + 102.806, + 3819.299, + 3061.32, + 130.33600000000024 ], - "priority": 2, + "priority": 14, "parents": [ - 199909 + 612 ], "children": [], - "area": 40190.48334300001, + "area": 392646.852994, "iscrowd": 0, "segmentation": [], - "text": "Derek W. Wright, Rosanna Upstill-Goddard, Kamna Ramakrishnan, Craig Nourse, Andrew V. Biankin, Peter Bailey\n\nWolfson Wohl Cancer Research Centre, University of Glasgow" + "text": "Integration in resource registries, catalogues, and repositories: EDAM is used in a large number of registries, including ELIXIR\nbio.tools, the IFB RAINBio registry of bioinformatics cloud appliances, SEQanswer’s SEOwiki," }, { - "id": 199893, - "strid": "f01220ce-6c52-453e-8d07-03642bf945ec", - "image_id": 208326, - "image_name": "9947.png", + "id": 617, + "strid": "2d2e79ec-d9d3-4a63-b4c6-d877b3520ab6", + "image_id": 25, + "image_name": "11175.png", "category_id": 3, "category_name": "Text", "bbox": [ - 113.795, - 711.666, - 3079.718, - 115.39800000000002 + 104.018, + 4029.577, + 2810.573, + 129.89800000000014 ], - "priority": 3, + "priority": 15, "parents": [ - 199909 + 612 ], "children": [], - "area": 80984.03247, + "area": 419148.540386, "iscrowd": 0, "segmentation": [], - "text": "We present a suite of web applications, developed for the PRECISION-Panc initiative, to provide integrative analyses of genomic and\ntranscriptomic data from patient primary samples, cell lines and xenografts, as well as clinical data on patient survival." + "text": "Integration with Galaxy: Galaxy datatypes and tools can now be annotated respectively with EDAM data/format and\ntopic/operationsterms,toallowaneasierintegration. with service registries such_as_bio.tools." }, { - "id": 199899, - "strid": "ad8e6c5a-51a0-4192-b012-ea7f504d1752", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", + "id": 618, + "strid": "591b892e-c4bb-4d9f-9e95-bfa941d90859", + "image_id": 26, + "image_name": "11231.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 384.44, - 874.723, - 652.364, - 353.07899999999995 + 13.57, + 159.72, + 285.24, + 260.78999999999996 ], - "priority": 4, - "parents": [ - 199909 + "priority": -1, + "parents": [], + "children": [ + 619, + 621, + 620, + 626, + 642, + 624, + 644, + 640 ], - "children": [], - "area": 336278.51012, + "area": 2167.4004, "iscrowd": 0, "segmentation": [] }, { - "id": 199896, - "strid": "94b2a3ef-307f-470b-bf26-94727b05a20f", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 4, - "category_name": "List", + "id": 619, + "strid": "0d875d4e-c720-4e9f-ae7b-3062e2fc9ab3", + "image_id": 26, + "image_name": "11231.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 74.291, - 1245.615, - 978.5070000000001, - 422.73900000000003 + 365.403, + 70.783, + 2921.142, + 189.11 ], - "priority": 5, + "priority": 1, "parents": [ - 199909 + 618 ], "children": [], - "area": 92537.98396499999, + "area": 25864.320549000004, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Evaluation of Physiological Noise Cleaning Methods at High-Resolution\nsoo Across Cortical Depth" }, { - "id": 199907, - "strid": "908b03f9-fcc8-4eee-a56b-1c8e589e5611", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", + "id": 620, + "strid": "d686a667-8dcc-4cc7-a035-1d9e64019db3", + "image_id": 26, + "image_name": "11231.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 36.504, - 1694.029, - 1052.611, - 594.7930000000001 + 530.371, + 296.106, + 2540.911, + 297.74700000000007 ], - "priority": 6, + "priority": 2, "parents": [ - 199909 + 618 ], "children": [], - "area": 61838.83461599999, + "area": 157046.03532599998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "; Andrew Hall’, Laurentius Huber’, Daniel A Handwerker’,\nJavier Gonzalez-Castillo’, Natasha Topolski’, David Jangraw’, Peter A Bandettini*\n\n1. Section on Functional Imaging Methods, NIH/NIMH, Bethesda, MD, United States\n2. Section on Functional Imaging Methods, NIH/NIMH 3. NIH/NIMH" }, { - "id": 199908, - "strid": "ce535556-d5f5-488c-8c16-c20ee314964f", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", + "id": 621, + "strid": "61c6c064-0639-4ae1-a5f1-a660de183721", + "image_id": 26, + "image_name": "11231.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 25.821, - 2290.735, - 1071.526, - 2151.123 + 1192.255, + 692.431, + 820.817, + 82.48400000000004 ], - "priority": 7, + "priority": 3, "parents": [ - 199909 + 618 ], - "children": [], - "area": 59149.06843500001, + "children": [ + 623, + 622 + ], + "area": 825554.3219050001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 199900, - "strid": "19bd1da1-a575-4854-950d-994fe1ac35e8", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", + "id": 622, + "strid": "3047f97f-a558-4c03-ae1c-b0019e2b2b92", + "image_id": 26, + "image_name": "11231.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1410.156, - 881.456, - 776.2359999999999, - 371.48400000000004 + 36.117, + 823.772, + 1640.351, + 673.814 ], - "priority": 8, + "priority": 4, "parents": [ - 199909 + 621 ], "children": [], - "area": 1242990.467136, + "area": 29752.173324, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Resting-state {MRI has proven a valuable tool in the mapping of functional\nbrain connectivity (Bandettini 2014). Sub-millimeter, layer-dependent {MRI\nresting-state can provide additional information about directional connectivity\ne.g. feed-forward vs feed-back (Polimeni 2010) connectivity or afferent vs. effer-\nent connectiviy (Huber 2016).\n\nHere we seek to characterize respiratory and cardiac induced signal fluctuations\nacross cortical depths and their impact on layer-dependent resting state {MRI\nstudies. Furthermore, it was the goal of this experiment to determine whether\ntraditional methods (Glover 2000) of physiological noise cleaning are able to im-\nprove our ability to discern layer-dependent and/or layer-scale directional activ-\n\nity." }, { - "id": 199897, - "strid": "d3d15192-06f4-43a6-a00f-8a80baf2ab86", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 4, - "category_name": "List", + "id": 623, + "strid": "f9f517b7-b7af-4040-8ab2-f7a01ea82b1f", + "image_id": 26, + "image_name": "11231.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1264.949, - 1311.932, - 781.2829999999999, - 359.11300000000006 - ], - "priority": 9, - "parents": [ - 199909 - ], - "children": [], - "area": 1659527.071468, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199905, - "strid": "31e933f1-8eff-4fe1-8ac4-0c179c665726", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1225.009, - 1728.955, - 854.462, - 842.221 - ], - "priority": 10, - "parents": [ - 199909 - ], - "children": [], - "area": 2117985.435595, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199906, - "strid": "f6ef432b-b84b-4c71-b62d-53c4141a85eb", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1133.63, - 2622.786, - 1036.4560000000001, - 496.0079999999998 - ], - "priority": 11, - "parents": [ - 199909 - ], - "children": [], - "area": 2973268.89318, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199901, - "strid": "c32be843-7bd8-4f25-8afd-d85e94543445", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 2568.055, - 891.092, - 361.68200000000024, - 266.649 - ], - "priority": 12, - "parents": [ - 199909 - ], - "children": [], - "area": 2288373.26606, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199898, - "strid": "4d532f3b-ecad-4d2a-af09-5b1656d182df", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 2270.228, - 1209.693, - 957.0050000000001, - 597.645 - ], - "priority": 13, - "parents": [ - 199909 - ], - "children": [], - "area": 2746278.920004, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199902, - "strid": "8de1f269-3ed2-440f-a6b7-9d82e3e4b587", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 2394.642, - 1843.648, - 707.9740000000002, - 749.5469999999998 - ], - "priority": 14, - "parents": [ - 199909 - ], - "children": [], - "area": 4414876.934016, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199903, - "strid": "46d34344-1305-419a-8b29-88e2d3e3f3a7", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 2234.896, - 2613.519, - 1027.4940000000001, - 756.837 - ], - "priority": 15, - "parents": [ - 199909 - ], - "children": [], - "area": 5840943.159024, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 199904, - "strid": "2d5f13c2-c75c-4403-9fa0-601932911759", - "image_id": 208326, - "image_name": "9947.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 2269.468, - 3399.922, - 959.0810000000001, - 934.9869999999996 + 1720.587, + 820.419, + 1846.8049999999998, + 687.089 ], - "priority": 16, + "priority": 5, "parents": [ - 199909 + 621 ], "children": [], - "area": 7716014.181496, + "area": 1411602.265953, "iscrowd": 0, "segmentation": [] }, { - "id": 199891, - "strid": "2715599d-4222-4752-a9b0-a16904428d3e", - "image_id": 208326, - "image_name": "9947.png", + "id": 624, + "strid": "91ebc17a-0523-4291-bf1e-8e287f03d43a", + "image_id": 26, + "image_name": "11231.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1529.85, - 3230.631, - 248.81899999999996, - 53.63799999999992 + 528.404, + 1582.011, + 544.9859999999999, + 75.75999999999999 ], - "priority": 17, + "priority": 6, "parents": [ - 199909 + 618 ], "children": [ - 199894 + 625 ], - "area": 4942380.835349999, + "area": 835940.940444, "iscrowd": 0, "segmentation": [], - "text": "Availability" + "text": "" }, { - "id": 199894, - "strid": "860d98bd-c2d4-499a-96b4-56ac34b209f9", - "image_id": 208326, - "image_name": "9947.png", + "id": 625, + "strid": "0e3f06e5-c070-46f3-92b9-2606adc611f6", + "image_id": 26, + "image_name": "11231.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1121.746, - 3291.587, - 1064.437, - 446.80099999999993 + 45.322, + 1712.986, + 1513.321, + 990.47 ], - "priority": 18, + "priority": 7, "parents": [ - 199891 + 624 ], "children": [], - "area": 3692324.550902, + "area": 77635.95149200001, "iscrowd": 0, "segmentation": [], - "text": "Apps available on University of Glasgow’s network at\n\nshiny.tcrc.qla.ac.uk\nNB Pathway Analysis is currently restricted to IP\naddresses within Wolfson Wohl Cancer Research\nCentre and The Beatson Institute.\nWe intend to make our apps widely available in due\ncourse, as well as the underlying code to enable you\nto host your own datasets." + "text": "14 healthy volunteers were scanned on a 7T Siemens scanner, with a 32\nchannel NOVA Medical head coil at 0.71-0.78 mm‘# resolution in plane, and\n0.78-1.8 mm slices aligned perpendicular to cortical surface (Huber 2016)\nwith a 3D-EPI reaout (Poser 2010). Here, we present examples from the first\nparticipants. Physiological signals were concurrently acquired with a\nrespiratory belt and pulse oximeter. Physiological noise regressors were\ngenerated from Biopac® traces. Voxel maps of the effects of respiratory and\ncardiac regressors were generated with AFNI/FSL.\n\nThe effect of cardiac and respiratory induced signal fluctuations was\ninvestigated in the sensory-motor system. Beta values corresponding to the\npremotor seed region are mapped. Finally, profiles of these Beta values are\ngenerated across cortical layers in M1. To test the effect of different\nphysiological noise correction methods, a resting-state analysis is conducted\nwith a seed in the premotor region, which is believed to have afferent\nfunctional connectivity to the upper layers in M1 (Weiler 2008).\n\nDetails of the analysis pipeline may be found at the following site:\n\nhttps://github.com/andrew-r-hall/OHBM2017" }, { - "id": 199892, - "strid": "5caa1095-273c-4ae1-85cc-ab21cd63198f", - "image_id": 208326, - "image_name": "9947.png", + "id": 626, + "strid": "0e03d804-0640-4ace-adec-8ce0058628f2", + "image_id": 26, + "image_name": "11231.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1479.886, - 3786.096, - 345.82500000000005, - 49.01899999999978 + 2400.508, + 1549.241, + 440.3699999999999, + 77.94200000000001 ], - "priority": 19, + "priority": 8, "parents": [ - 199909 + 618 ], "children": [ - 199895 + 632, + 638, + 637, + 635, + 628, + 629, + 634, + 639, + 630, + 636, + 627, + 631, + 633 ], - "area": 5602990.465056, + "area": 3718965.414428, "iscrowd": 0, "segmentation": [], - "text": "Implementation" + "text": "" }, { - "id": 199895, - "strid": "3b7fbfd6-bed2-49f2-b586-359e73aa9d92", - "image_id": 208326, - "image_name": "9947.png", + "id": 627, + "strid": "9e749726-e2bf-4ffd-96b6-c70b6b2d0f45", + "image_id": 26, + "image_name": "11231.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1118.883, - 3841.324, - 1067.1029999999998, - 160.88200000000006 + 1829.581, + 1718.24, + 147.7639999999999, + 34.611000000000104 ], - "priority": 20, + "priority": 9, "parents": [ - 199892 + 626 ], "children": [], - "area": 4297992.121092, + "area": 3143659.25744, "iscrowd": 0, "segmentation": [], - "text": "These apps have been implemented using the R\nstatistical programming language and Shiny web\napplication framework." + "text": "cardiac" }, { - "id": 166178, - "strid": "d251ce68-cae2-42a4-97a5-d6a595e62dd5", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 9, - "category_name": "Root", + "id": 628, + "strid": "2648f8fc-98a6-4924-b633-aa3043fd8ca4", + "image_id": 26, + "image_name": "11231.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 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"text": "Population code modelling of grating detectability\nalong the apparent motion path" + "text": "respiration" }, { - "id": 166160, - "strid": "9d43276d-72ac-40f8-9611-bd0ee61d1485", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 0, - "category_name": "Author Info", + "id": 630, + "strid": "893e8754-efe4-4826-8fef-41e0d1fcef58", + "image_id": 26, + "image_name": "11231.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 506.401, - 443.52, - 2279.945, - 217.23800000000006 + 2174.233, + 1770.461, + 465.0210000000002, + 480.28700000000003 ], - "priority": 2, + "priority": 12, "parents": [ - 166178 + 626 ], "children": [], - "area": 224598.97152, + "area": 3849394.7314130003, "iscrowd": 0, - "segmentation": [], - "text": "Nathalie Van Humbeeck, Tom Putzeys, & Johan Wagemans\nLaboratory of Experimental Psychology, University of Leuven (KU Leuven), Belgium" + "segmentation": [] }, { - "id": 166161, - "strid": "213c1c0e-653d-40a7-ae36-92ee89234d27", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 5, - "category_name": "Section", + "id": 631, + "strid": "6df72fb9-6f58-498f-a4da-41132198d89c", + "image_id": 26, + "image_name": "11231.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 121.514, - 806.668, - 598.769, - 72.35900000000004 + 2672.369, + 1676.753, + 909.1390000000001, + 616.5049999999999 ], - "priority": 3, + "priority": 13, "parents": [ - 166178 - ], - "children": [ - 166167, - 166169, - 166168 + 626 ], - "area": 98021.455352, + "children": [], + "area": 4480902.737857, "iscrowd": 0, - "segmentation": [], - "text": "The present study" + "segmentation": [] }, { - "id": 166169, - "strid": "c67eb8df-3415-454f-bb56-56bc4d5b7db4", - "image_id": 206984, - "image_name": "6742.png", + "id": 632, + "strid": "a105277f-fbe9-4446-ad20-6437c0cc751f", + "image_id": 26, + "image_name": "11231.png", "category_id": 3, "category_name": "Text", "bbox": [ - 100.164, - 946.414, - 1407.79, - 110.36500000000001 + 1641.881, + 2303.97, + 1786.4749999999997, + 216.98599999999988 ], - "priority": 4, + "priority": 14, "parents": [ - 166161 + 626 ], "children": [], - "area": 94796.611896, + "area": 3782844.56757, "iscrowd": 0, "segmentation": [], - "text": "Contrast detection impaired when but not when perceiving\nperceiving apparent motion (AM)... _ flicker (= control condition)" + "text": "Cardiac and respiratory signal fluctuations have local effects on the {MRI time courses.\nThe largest effect occurs at the cortical surface.\n\nsignal and noise charateristics in M1" }, { - "id": 166167, - "strid": "d28850f7-30dd-47a4-b59b-8f1360a71416", - "image_id": 206984, - "image_name": "6742.png", + "id": 633, + "strid": "273317eb-6774-4aa4-a37b-38c57ce24448", + "image_id": 26, + "image_name": "11231.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 151.185, - 1080.441, - 1338.376, - 375.35699999999997 + 1653.08, + 2541.504, + 1890.616, + 430.73099999999977 ], - "priority": 5, + "priority": 15, "parents": [ - 166161 + 626 ], "children": [], - "area": 163346.472585, + "area": 4201309.43232, "iscrowd": 0, "segmentation": [] }, { - "id": 166168, - "strid": "d2a5045e-74ed-4bfc-b8bb-ee981f321d3d", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 4, - "category_name": "List", + "id": 634, + "strid": "d83338d7-bd1e-4ea5-9275-a808857ca795", + "image_id": 26, + "image_name": "11231.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 123.19, - 1505.612, - 1418.953, - 233.64200000000005 + 1667.28, + 3092.681, + 864.3770000000002, + 50.31899999999996 ], - "priority": 6, + "priority": 16, "parents": [ - 166161 + 626 ], "children": [], - "area": 185476.34228, + "area": 5156365.17768, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "directional connectivity from premotor to M1" }, { - "id": 166163, - "strid": "4c2880a4-5d2e-4c63-bfe1-5feabec5dba7", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 5, - "category_name": "Section", + "id": 635, + "strid": "f95819f1-b6f5-4845-b5f1-c84b92bc5684", + "image_id": 26, + "image_name": "11231.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 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"image_id": 206984, - "image_name": "6742.png", - "category_id": 5, - "category_name": "Section", + "id": 637, + "strid": "31ec0fc2-d875-45d4-a71e-59cd43119d5c", + "image_id": 26, + "image_name": "11231.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 121.345, - 2300.681, - 1262.188, - 81.41499999999996 + 2056.418, + 3155.301, + 620.607, + 50.31899999999996 ], - "priority": 9, + "priority": 19, "parents": [ - 166178 + 626 ], - "children": [ - 166172, - 166171 - ], - "area": 279176.135945, + "children": [], + "area": 6488617.771818, "iscrowd": 0, "segmentation": [], - "text": "Gain control model of AM masking" + "text": "correlations with pre-motor area" }, { - "id": 166171, - "strid": "e9be301b-03e7-42a0-929c-a74d15c49c29", - "image_id": 206984, - "image_name": "6742.png", + "id": 638, + "strid": "dbdb58fb-60ac-4f8f-bf8b-2dcb85196c32", + "image_id": 26, + "image_name": "11231.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 105.019, - 2456.945, - 1441.165, - 1245.1780000000003 + 2134.842, + 3210.552, + 469.5300000000002, + 494.3879999999999 ], - "priority": 10, + "priority": 20, "parents": [ - 166165 + 626 ], "children": [], - "area": 258025.90695500004, + "area": 6854021.252784001, "iscrowd": 0, "segmentation": [] }, { - "id": 166172, - "strid": "dcef3609-960b-47d5-bc94-479f62a90dd0", - "image_id": 206984, - "image_name": "6742.png", + "id": 639, + "strid": "02735bda-bc62-4124-a243-7fc79866068b", + "image_id": 26, + "image_name": "11231.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 143.306, - 3784.366, - 1403.641, - 500.3909999999996 + 2742.47, + 3106.979, + 832.7260000000001, + 591.056 ], - "priority": 11, + "priority": 21, "parents": [ - 166165 + 626 ], "children": [], - "area": 542322.353996, + "area": 8520796.698129999, "iscrowd": 0, "segmentation": [] }, { - "id": 166162, - "strid": "0087258e-fe2c-439d-90ef-69c997ab6135", - "image_id": 206984, - "image_name": "6742.png", + "id": 640, + "strid": "2b2c8f6b-d691-46b5-a667-7ff2e670c25e", + "image_id": 26, + "image_name": "11231.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1740.03, - 810.565, - 761.9469999999999, - 57.902000000000044 + 2234.762, + 3766.87, + 763.5210000000002, + 78.27700000000004 ], - "priority": 12, + "priority": 22, "parents": [ - 166178 + 618 ], "children": [ - 166173 + 641 ], - "area": 1410407.41695, + "area": 8418057.934940001, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 166173, - "strid": "fcf7579f-7181-4cde-8c80-1dba7ec2f147", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 2, - "category_name": "Figure", + "id": 641, + "strid": "1bcfbe7a-f006-4846-9d5b-dac94fbeea15", + "image_id": 26, + "image_name": "11231.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1725.299, - 940.164, - 1462.7910000000002, - 982.6870000000001 + 1621.237, + 3901.962, + 1896.2529999999997, + 405.0250000000001 ], - "priority": 13, + "priority": 23, "parents": [ - 166162 + 640 ], "children": [], - "area": 1622064.009036, + "area": 6326005.166994, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Here, we characterize the effect of cardiac and respiratory induced physiological noise in\nlayer-dependent resting-state {MRI. The results presented here show that there is only\nsignificant physiological noise in few local areas. In those areas, the effect of physiological\nnoise is strongest in superficial laminae.\n\nCorrecting for physiologocal noise has a limited effect on layer-dependent resting-state\nconnectivity results in the image noise dominated regime.\n\nOnly if big draining veins are present in seed and target regions, they may cause a significant\nbias across cortical depth." }, { - "id": 166164, - "strid": "96f423e1-0003-4f66-9824-35d31262f778", - "image_id": 206984, - "image_name": "6742.png", + "id": 642, + "strid": "e211ba08-ddaf-4ebd-9d00-b234828bb859", + "image_id": 26, + "image_name": "11231.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1736.861, - 2084.951, - 1137.7480000000003, - 72.9380000000001 + 400.58, + 2957.139, + 799.6220000000001, + 52.13000000000011 ], - "priority": 14, + "priority": 24, "parents": [ - 166178 + 618 ], "children": [ - 166174, - 166175 + 643 ], - "area": 3621270.078811, + "area": 1184570.74062, "iscrowd": 0, "segmentation": [], - "text": "AM masking is due to suppression" - }, - { - "id": 166175, - "strid": "97ec7bbd-252b-42f3-bcfb-2520d51eb387", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 1754.165, - 2211.167, - 1441.257, - 289.59900000000016 - ], - "priority": 15, - "parents": [ - 166164 - ], - "children": [], - "area": 3878751.7605549996, - "iscrowd": 0, - "segmentation": [] + "text": "ACKNOWLEDGEMENTS" }, { - "id": 166174, - "strid": "6641d82d-f750-41d0-9dd7-849385d3534d", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 2, - "category_name": "Figure", + "id": 643, + "strid": "06cd4e1b-a526-4b96-bb04-b81c2cc99be9", + "image_id": 26, + "image_name": "11231.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1754.136, - 2537.501, - 1354.411, - 1269.6019999999999 + 32.434, + 3032.999, + 1507.797, + 456.57400000000007 ], - "priority": 16, + "priority": 25, "parents": [ - 166164 + 642 ], "children": [], - "area": 4451121.854136, + "area": 98372.28956599999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "We thank Benedikt Poser and Dimo Ivanov for rthe 3D-EPI sequence used\nhere. We acknowledge Rick Reynolds for help with best applicability of\nRETROICOR in afni_proc.py. We thank Chatie Chang for helpful\ndiscussions. The work was supported by the NIMH Intramural Research\nProgram. We thank the two amazing volunteers who participated in this study.\nThe research was supported by the NIMH Intramural Research Program\n(#ZIA-MH002783). The study was approved under NIH Combined\nNeuroscience Institutional Review Board protocol #93-M- 0170\nClinical Trials.gov identifier: NCT00001360)." }, { - "id": 166166, - "strid": "4e801e4d-c2af-4192-a648-67d696f6103b", - "image_id": 206984, - "image_name": "6742.png", + "id": 644, + "strid": "aa4bd18c-8773-40aa-8001-8d22d1de4614", + "image_id": 26, + "image_name": "11231.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1728.44, - 3969.086, - 364.88599999999997, - 58.141999999999825 + 571.653, + 3767.183, + 459.99599999999987, + 53.23999999999978 ], - "priority": 17, + "priority": 26, "parents": [ - 166178 + 618 ], "children": [ - 166176 + 645 ], - "area": 6860327.00584, + "area": 2153521.4634990003, "iscrowd": 0, "segmentation": [], - "text": "Conclusion" - }, - { - "id": 166176, - "strid": "28d83c49-aca2-416f-9411-3c7eae389225", - "image_id": 206984, - "image_name": "6742.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 1706.821, - 4104.401, - 1398.368, - 159.2479999999996 - ], - "priority": 18, - "parents": [ - 166166 - ], - "children": [], - "area": 7005477.819220999, - "iscrowd": 0, - "segmentation": [] + "text": "" }, { - "id": 166177, - "strid": "b11b567c-b151-4665-b89d-bcff3d0115eb", - "image_id": 206984, - "image_name": "6742.png", + "id": 645, + "strid": "f6e04b80-4b8e-434b-8a53-c2ea6d3d384f", + "image_id": 26, + "image_name": "11231.png", "category_id": 3, "category_name": "Text", "bbox": [ - 102.763, - 4450.995, - 2276.737, - 85.57800000000043 - ], - "priority": 19, - "parents": [ - 166178 - ], - "children": [], - "area": 457397.599185, - "iscrowd": 0, - "segmentation": [], - "text": "Supported by the Research Foundation - Flanders (FWO) and the Methusalem program by the Flemish Government (METH/08/02)\nContact: nathalie.vanhumbeeck@ppw.kuleuven.be — website: http:/Awww.gestaltrevision.be" - }, - { - "id": 155232, - "strid": "5c2fc7e1-e8e9-43bf-a194-20b5dc9bcf33", - "image_id": 206556, - "image_name": "22727.png", - "category_id": 9, - "category_name": "Root", - "bbox": [ - 95.23, - 47.42, - 113.58, - 63.81999999999999 - ], - "priority": -1, - "parents": [], - "children": [ - 155231, - 155230 - ], - "area": 4515.806600000001, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 155230, - "strid": "12d5b22b-71a6-41d7-b728-b7328c602b07", - "image_id": 206556, - "image_name": "22727.png", - "category_id": 1, - "category_name": "Title", - "bbox": [ - 336.739, - 43.721, - 877.2819999999999, - 317.758 - ], - "priority": 1, - "parents": [ - 155232 - ], - "children": [], - "area": 14722.565818999998, - "iscrowd": 0, - "segmentation": [], - "text": "Unusual Properties of a Fie\nby Low-Level Laser Radiation Used in\nTherapy of Infection Pathology\nIncluding Hepatitis C Virus and a New\nCoronavirus Infection" - }, - { - "id": 155231, - "strid": "a3f69a70-71e4-4f03-acd8-4b0b4399176f", - "image_id": 206556, - "image_name": "22727.png", - "category_id": 0, - "category_name": "Author Info", - "bbox": [ - 338.584, - 438.227, - 646.665, - 227.75599999999997 + 37.958, + 3832.003, + 1285.034, + 447.36799999999994 ], - "priority": 2, + "priority": 27, "parents": [ - 155232 + 644 ], "children": [], - "area": 148376.65056799998, + "area": 145455.169874, "iscrowd": 0, "segmentation": [], - "text": "Naylya Djumaeva, M.D., Ph.D.\nNeurologist,\n\nExpert in “Medicament testing”\nScientific-Research Institute of Virology,\nUzbekistan" + "text": "Bandettini Brain Connect. 2014, 4:487-498;\n\nDuvernoy et al., Brain Research, 1981, 7: 519- 579;\n\nGlover et al. , Magnetic Resonance i in Medicine, 2000, 99:45 12:\nHuber et al., Neurolmage, 2015, 107:23-33;\n\nHuber et al., NeuroImage, 2017, 10.1016/j.neuroimage.2016.11.039;\nMao et al., Neuron, 2011, 72: 111-123;\n\nPolimeni et al., ISMRM, 2010, #353;\n\nPolimeni et al., ISMRM, 2015, #355;\n\nPoser et al., Neurolmage, 2010, 51:261-266;\n\nWeiler et al., Nat Neurosci, 2008, 1 1:360-366" }, { - "id": 26235, - "strid": "ba9a2867-f6b1-4e2c-9e89-0f21d2acbed2", - "image_id": 201541, - "image_name": "117271.png", + "id": 646, + "strid": "bab7373e-a3de-4ecd-a02f-1d8c80a9421c", + "image_id": 27, + "image_name": "11272.png", "category_id": 9, "category_name": "Root", "bbox": [ - 152.16, - 27.12, - 78.99000000000001, - 81.91 + 23.07, + 47.48, + 51.74, + 295.68 ], "priority": -1, "parents": [], "children": [ - 26219, - 26218, - 26215, - 26217, - 26216 + 649, + 674, + 647, + 670, + 664, + 648, + 658 ], - "area": 4126.5792, + "area": 1095.3636, "iscrowd": 0, "segmentation": [] }, { - "id": 26215, - "strid": "c5af7d79-00e2-4110-9b3a-934586730ca9", - "image_id": 201541, - "image_name": "117271.png", + "id": 647, + "strid": "99ac1975-a362-4efd-9438-18e792f9a0ab", + "image_id": 27, + "image_name": "11272.png", "category_id": 1, "category_name": "Title", "bbox": [ - 214.541, - 136.013, - 847.316, - 49.768 + 116.706, + 130.04, + 2319.215, + 279.31000000000006 ], "priority": 1, "parents": [ - 26235 + 646 ], "children": [], - "area": 29180.365033000002, + "area": 15176.44824, "iscrowd": 0, "segmentation": [], - "text": "Visual Search during Motion Perception" + "text": "Convolutional architecture for prediction\nof peptide-MHC binding affinities" }, { - "id": 26216, - "strid": "a05f48a0-200f-4622-a74a-9263cac911fe", - "image_id": 201541, - "image_name": "117271.png", + "id": 648, + "strid": "04479725-bde2-4c43-823f-212b45aa214a", + "image_id": 27, + "image_name": "11272.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 288.971, - 198.466, - 689.198, - 102.96800000000002 + 116.801, + 445.123, + 2321.425, + 249.23200000000003 ], "priority": 2, "parents": [ - 26235 + 646 ], "children": [], - "area": 57350.918486, + "area": 51990.811523, "iscrowd": 0, "segmentation": [], - "text": "Benassi M’, Baroni G’, Lugli L?, Bolzani R', Nicoletti R?\n1Department of Psychology, University of Bologna\n2Department of Communication Studies, University of Bologna" + "text": "Rudolph Layko, Vadim Nazarov’', Mikhail Shugay®?*”\n\nNational Research University — Higher School of Economics, Moscow, Russia; 2Institute of Bioorganic Chemistry of Russian Academy of Science, Moscow, Russia;°Pirogov\nRussian National Research Medical University, Moscow, Russia; “Central European Institute of Technology, Masaryk University, Brno, Czech Republic;’Nizhny Novgorod\n\nState Medical Academy, Nizhny Novgorod, Russia\n*Author for correspondence : layko.ds@gmail.com" }, { - "id": 26217, - "strid": "b4778852-991f-447d-a27d-bbf1c667b95c", - "image_id": 201541, - "image_name": "117271.png", + "id": 649, + "strid": "e1c6fbde-4550-46ae-98c1-2360659c261b", + "image_id": 27, + "image_name": "11272.png", "category_id": 5, "category_name": "Section", "bbox": [ - 666.788, - 403.247, - 72.51300000000003, - 27.52600000000001 + 209.443, + 761.294, + 403.472, + 61.365999999999985 ], "priority": 3, "parents": [ - 26235 + 646 ], "children": [ - 26220, - 26223 + 652, + 654, + 650, + 655, + 653, + 651, + 656 ], - "area": 268880.260636, + "area": 159447.699242, "iscrowd": 0, "segmentation": [], - "text": "AIM" + "text": "Introduction" }, { - "id": 26223, - "strid": "a259117a-b908-4de7-bb5f-57cba4e31c35", - "image_id": 201541, - "image_name": "117271.png", + "id": 650, + "strid": "2e667858-305e-4522-b7ff-34f32be3cbc4", + "image_id": 27, + "image_name": "11272.png", "category_id": 3, "category_name": "Text", "bbox": [ - 397.824, - 442.164, - 608.9389999999999, - 105.56899999999996 + 128.285, + 871.324, + 1485.128, + 147.591 ], "priority": 4, "parents": [ - 26217 + 649 ], "children": [], - "area": 175903.451136, + "area": 111777.79934, "iscrowd": 0, "segmentation": [], - "text": "Analysis of the gaze movement pattern during the\nearly phase of the coherent motion perception in\ncomparison with visual search using steady stimuli and\nBrownian motion stimulus." + "text": "One of the problem with high importance in immunoinformatics is prediction of binding\naffinities among MHC molecules (Fig.1) and their peptide ligands given input amino acids\nsequences of each. Primary reason of such problem significance is:" }, { - "id": 26220, - "strid": "c06edf14-035e-49fb-a66b-4d048bcdc5fc", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 2, - "category_name": "Figure", + "id": 651, + "strid": "80739124-8ad0-4640-a421-2f2ef6da12a9", + "image_id": 27, + "image_name": "11272.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 97.204, - 397.091, - 186.976, - 216.68200000000002 + 137.823, + 1033.462, + 1476.267, + 220.212 ], "priority": 5, "parents": [ - 26217 + 649 ], "children": [], - "area": 38598.833564, + "area": 142434.83322600002, "iscrowd": 0, "segmentation": [] }, { - "id": 26218, - "strid": "458839d6-a913-4675-9fd4-553f5612db1a", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 5, - "category_name": "Section", + "id": 652, + "strid": "7b2eb2e8-1810-41ad-bc81-78792d479a13", + "image_id": 27, + "image_name": "11272.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 448.44, - 604.189, - 171.90899999999993, - 27.57299999999998 + 130.708, + 1271.898, + 1481.302, + 97.89499999999998 ], "priority": 6, "parents": [ - 26235 - ], - "children": [ - 26226, - 26221, - 26227, - 26231, - 26230, - 26229, - 26234, - 26224, - 26228, - 26225, - 26232 + 649 ], - "area": 270942.51516, + "children": [], + "area": 166247.243784, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Detailed overview of current state-of-the-art packages, including pan-allele NetMHCPan[1]\nand MHCflurry[2] showed that they share same problems and constraints:" }, { - "id": 26226, - "strid": "9f941892-c6c9-401c-9d87-655ba15bbdff", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 653, + "strid": "7ac4dd52-4e10-4c66-9fb1-8f575570483d", + "image_id": 27, + "image_name": "11272.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 58.394, - 696.49, - 263.647, - 43.98199999999997 + 138.218, + 1391.253, + 1466.224, + 104.62400000000002 ], "priority": 7, "parents": [ - 26218 + 649 ], "children": [], - "area": 40670.83706, + "area": 192296.20715399997, "iscrowd": 0, - "segmentation": [], - "text": "Participants:\n\n36 students (mean age: 20.7; SD 3.0 years)" + "segmentation": [] }, { - "id": 26225, - "strid": "1846302b-394d-49c7-8388-6ceef910d2b1", - "image_id": 201541, - "image_name": "117271.png", + "id": 654, + "strid": "f931d318-4c1d-4894-a1e5-ad23d5700ff6", + "image_id": 27, + "image_name": "11272.png", "category_id": 3, "category_name": "Text", "bbox": [ - 138.603, - 820.826, - 110.799, - 29.08699999999999 + 130.303, + 1518.587, + 1483.319, + 92.19399999999996 ], "priority": 8, "parents": [ - 26218 + 649 ], "children": [], - "area": 113768.94607800001, + "area": 197876.441861, "iscrowd": 0, "segmentation": [], - "text": "Stimuli" + "text": "With the goal to overcome this constraints and surpass existing solutions in performance we\npropose following approaches and methods:" }, { - "id": 26234, - "strid": "52417985-40e5-4283-8814-c6313d3cf1cd", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 655, + "strid": "71ae93ae-61c4-4dc9-9aeb-575daa69ac7f", + "image_id": 27, + "image_name": "11272.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 31.056, - 901.241, - 320.536, - 24.601 + 138.539, + 1634.827, + 1476.009, + 208.25700000000006 ], "priority": 9, "parents": [ - 26218 + 649 ], "children": [], - "area": 27988.940496, + "area": 226487.297753, "iscrowd": 0, - "segmentation": [], - "text": "100 witfe giSts {0.05\"} presented on a black background wafhin\n‘a chculor fame (7° of diameter)," + "segmentation": [] }, { - "id": 26228, - "strid": "d289f79f-9e15-47cc-a4bb-125567c1237d", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 656, + "strid": "4b38daa0-31d9-4b09-8857-b7aca3e42a6f", + "image_id": 27, + "image_name": "11272.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 33.542, - 963.298, - 314.83799999999997, - 63.215999999999894 + 224.425, + 1932.649, + 1204.729, + 490.241 ], "priority": 10, "parents": [ - 26218 + 649 ], - "children": [], - "area": 32310.941516000003, + "children": [ + 657 + ], + "area": 433734.751825, "iscrowd": 0, - "segmentation": [], - "text": "Motion coherence task Each dot has a limitedilifetime of 200\n\nmsec to avoid tracking. The coherence level isheld constant\n\nat 4 decibel [le., 36% of dots move coherently in one of eight\n\npossible direction, cardinal or oblique, while the rest move in\nnaniet rae" + "segmentation": [] }, { - "id": 26229, - "strid": "c3fb6339-0b86-4d5a-a201-2e532e7f4d50", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 657, + "strid": "fbd35c75-6ad2-4602-b99f-507ae6f8e0c6", + "image_id": 27, + "image_name": "11272.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 28.376, - 1056.407, - 322.311, - 13.097999999999956 + 130.258, + 2468.8, + 1480.891, + 78.73199999999997 ], "priority": 11, "parents": [ - 26218 + 656 ], "children": [], - "area": 29976.605032, + "area": 321580.95040000003, "iscrowd": 0, "segmentation": [], - "text": "‘Steady visual search task 97 white dots and 3 blue target dots." + "text": "Figure 1: MHC Class I. In case of homo sapiens MHC refers to HLA (Human Leukocyte Antigen). It is located\non the surface of any cell in living organism." }, { - "id": 26230, - "strid": "d62bd2d1-5d8f-41fb-9396-08c40a600223", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 658, + "strid": "e291ad4d-c653-4ad6-937c-e89a7614e3e9", + "image_id": 27, + "image_name": "11272.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 32.645, - 1106.506, - 318.287, - 24.14300000000003 + 212.361, + 2625.628, + 801.952, + 71.53600000000006 ], "priority": 12, "parents": [ - 26218 + 646 ], - "children": [], - "area": 36121.88837000001, + "children": [ + 661, + 660, + 663, + 659 + ], + "area": 557580.987708, "iscrowd": 0, "segmentation": [], - "text": "Pee eee ere OP Seer mere: mt aner a mor Freee mane\nTid Commie Maleate" + "text": "From proteins to vectors" }, { - "id": 26231, - "strid": "2ae46f3d-0a76-4560-8a85-2d83d5bb779b", - "image_id": 201541, - "image_name": "117271.png", + "id": 659, + "strid": "2cbfa30e-1d17-424c-b8ea-88db27934c66", + "image_id": 27, + "image_name": "11272.png", "category_id": 3, "category_name": "Text", "bbox": [ - 33.251, - 1154.69, - 312.756, - 35.958000000000084 + 130.621, + 2740.145, + 1482.163, + 144.05200000000013 ], "priority": 13, "parents": [ - 26218 + 658 ], "children": [], - "area": 38394.59719, + "area": 357920.48004500003, "iscrowd": 0, "segmentation": [], - "text": "Procedae'e? motion tasks he subject is osked fo Giscrimiggig\nthe direction of coherent moving dots, while in steady visual\n3Purch task the subject has fo detect the blue doi" + "text": "Essential part of any kind of problem where sequences appear is preprocessing and appropriate\nrepresentation of input, which can be fed to algorithms and machine learning models. In\norder to retrieve such representation for our task we produce following procedure:" }, { - "id": 26224, - "strid": "33237247-9566-4ed0-8da6-b7789bf8e993", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 660, + "strid": "81493644-d498-4d14-a882-53a6b2bddbe1", + "image_id": 27, + "image_name": "11272.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 373.707, - 685.321, - 397.20500000000004, - 34.36699999999996 + 137.947, + 2906.355, + 1475.902, + 269.81799999999976 ], "priority": 14, "parents": [ - 26218 + 658 ], "children": [], - "area": 256109.254947, + "area": 400922.953185, "iscrowd": 0, - "segmentation": [], - "text": "Eye movements parameters" + "segmentation": [] }, { - "id": 26227, - "strid": "4249307f-424b-4d25-8016-d756523024c3", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 3, - "category_name": "Text", + "id": 661, + "strid": "77be64dd-2f5f-4ff1-aa36-ca15f97af87c", + "image_id": 27, + "image_name": "11272.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 395.442, - 747.135, - 339.779, - 83.755 + 512.706, + 3269.292, + 724.859, + 459.0129999999999 ], "priority": 15, "parents": [ - 26218 + 658 ], - "children": [], - "area": 295448.55867, + "children": [ + 662 + ], + "area": 1676185.624152, "iscrowd": 0, - "segmentation": [], - "text": "Eye positions were recorded by SMI 500 at 120Hz\nsampling rate.\n\nHorizontal and vertical components of gaze were\nrepresented on a XY graph." + "segmentation": [] }, { - "id": 26232, - "strid": "e44b66a5-4f7c-433a-a0dc-73fe1ef78127", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 4, - "category_name": "List", + "id": 662, + "strid": "ec297d01-03fd-4161-a0fa-1b220cc4e37e", + "image_id": 27, + "image_name": "11272.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 395.488, - 848.697, - 353.598, - 407.19899999999996 + 130.697, + 3780.265, + 1483.466, + 77.36499999999978 ], "priority": 16, "parents": [ - 26218 + 661 ], "children": [], - "area": 335649.479136, + "area": 494069.294705, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 2: t-SNE visualization of retrieved vectors for amino acids. Each point corresponds to particular amino\nacid. It is clearly seen that they clustered well by hydropathy physiochemical property." }, { - "id": 26221, - "strid": "348ba3bd-bd98-46d5-bb29-154c25a8e9df", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 2, - "category_name": "Figure", + "id": 663, + "strid": "665a07c6-e4ce-465e-84da-80f172c2934f", + "image_id": 27, + "image_name": "11272.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 780.192, - 677.165, - 298.9749999999999, - 318.91599999999994 + 128.445, + 3927.111, + 1485.794, + 352.65099999999984 ], "priority": 17, "parents": [ - 26218 + 658 ], "children": [], - "area": 528318.71568, + "area": 504417.772395, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "In order to validate that learned embeddings in high-dimensional space are capturing biolog-\nical properties and patterns we visualized retrieved 20-dimensional vectors of amino acids in\nterms of two t-SNE components where color refers to value of hydropathy property(Fig.2)\n\nWhile solving this particular encoding problem we implemented effective distributed repre-\nsentation of amino acid sequences, which could be applied in range of tasks where feature\nextraction from proteins occurs(e.g. family classification and structural class prediction and\n\netc.)" }, { - "id": 26219, - "strid": "ad823b7f-73bd-4e9a-84a5-77290fd511b2", - "image_id": 201541, - "image_name": "117271.png", + "id": 664, + "strid": "ffd0a770-7050-4293-82f1-ef1217d4e335", + "image_id": 27, + "image_name": "11272.png", "category_id": 5, "category_name": "Section", "bbox": [ - 330.02, - 1320.145, - 174.462, - 28.47499999999991 + 1779.235, + 760.864, + 719.6769999999999, + 73.15499999999997 ], "priority": 18, "parents": [ - 26235 + 646 ], "children": [ - 26222, - 26233 + 667, + 666, + 669, + 665 ], - "area": 435674.25289999996, + "area": 1353755.85904, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Proposed architecture" }, { - "id": 26233, - "strid": "9082a3e7-1ee9-4bcc-935f-58b3211a6807", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 4, - "category_name": "List", + "id": 665, + "strid": "7ea6c52e-48e3-4129-85f2-727e4f451c86", + "image_id": 27, + "image_name": "11272.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 28.691, - 1383.428, - 761.75, - 206.3889999999999 + 1696.611, + 874.043, + 1484.5619999999997, + 189.678 ], "priority": 19, "parents": [ - 26219 + 664 ], "children": [], - "area": 39691.932748, + "area": 1482910.968273, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Throughout the experiments great diversity of neural network architectures were implemented\nand accurately evaluated on test dataset. In general, seeking the most successful solution\nrequired approximately 200 of experiments. Several of them are shown by learning curves on\n\n3:" }, { - "id": 26222, - "strid": "f9be8274-bfdb-4754-9afc-335c6c8d8634", - "image_id": 201541, - "image_name": "117271.png", - "category_id": 2, - "category_name": "Figure", + "id": 666, + "strid": "2de1ede7-ffe7-46ab-86a0-7aa7b4305e19", + "image_id": 27, + "image_name": "11272.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 799.905, - 1059.737, - 279.44499999999994, - 536.184 + 1706.617, + 1084.717, + 1477.6560000000002, + 218.106 ], "priority": 20, "parents": [ - 26219 + 664 ], "children": [], - "area": 847688.924985, + "area": 1851196.4723890002, "iscrowd": 0, "segmentation": [] }, { - "id": 111999, - "strid": "8a0ce5d6-5db4-4864-a41c-2f0922a40dd3", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 9, - "category_name": "Root", + "id": 667, + "strid": "6ebb3ff5-164c-4d55-bb7e-b8697ef5983b", + "image_id": 27, + "image_name": "11272.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 158.82, - 419.1, - 236.54000000000002, - 221.76 + 1705.664, + 1384.134, + 1471.983, + 608.856 + ], + "priority": 21, + "parents": [ + 664 ], - "priority": -1, - "parents": [], "children": [ - 111974, - 111973, - 111977, - 111978, - 111976, - 111975, - 111979 + 668 ], - "area": 66561.462, + "area": 2360867.534976, "iscrowd": 0, "segmentation": [] }, { - "id": 111973, - "strid": "c640d2a3-8eda-4c38-b7a0-53765acfd33c", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 1, - "category_name": "Title", + "id": 668, + "strid": "153de6ef-1535-437e-a1e3-c06cb4e6760e", + "image_id": 27, + "image_name": "11272.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 564.691, - 190.265, - 2549.3940000000002, - 73.406 + 1696.745, + 2042.672, + 1485.0150000000003, + 119.10800000000017 ], - "priority": 1, + "priority": 22, "parents": [ - 111999 + 667 ], "children": [], - "area": 107440.93311499999, + "area": 3465893.5026399996, "iscrowd": 0, "segmentation": [], - "text": "Lab-tokens: A case-based approach to integrate basic and clinical sciences" + "text": "Figure 3: (a) Final model architecture. Taking in consideration significant length of pseudosequence comparing\nto peptide experiments showed that number of blocks should be greater as well.(b, c) Models was evaluated\nin terms of F1-score which comes as trade-off between precision and recall metrics." }, { - "id": 111974, - "strid": "9225bc90-3301-46f3-86fd-3837e5fec343", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 0, - "category_name": "Author Info", + "id": 669, + "strid": "b0645b83-5822-4f05-a6ea-89899c98b22c", + "image_id": 27, + "image_name": "11272.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 631.302, - 300.413, - 2415.885, - 403.72399999999993 + 1696.843, + 2183.903, + 1486.162, + 607.7539999999999 ], - "priority": 2, + "priority": 23, "parents": [ - 111999 + 664 ], "children": [], - "area": 189651.32772600002, + "area": 3705740.518229, "iscrowd": 0, "segmentation": [], - "text": "E. Buxbaum’, A. Blanchetot?, N. Larsen”, G. Meisenberg?, A. Yin3, D.B. Averill4 & B.E.\nWright?\n(1) Address for Correspondence: Department of Biochemistry, Ross University School of Medicine Portsmouth\nCampus, P.O. Box 266, Roseau, Commonwealth of Dominica, West Indies, ebuxbaum@rossmed.edu.dm\n(2) Dept. of Biochemistry, RUSM, (3) Dept. of Anatomy, RUSM\n(4) Department of Basic Sciences, The Commonwealth Medical College (5) Dept. of Physiology, RUSM" + "text": "Final solution(learning curve \"cnnSmall\" on Fig.3(c)) was implemented in terms of resid-\nual blocks approach. We would like to make neural network extract high-order correlation\nand learn binding \"motifs\" between MHC and peptide ligands. Training of the model was\nproceeded with following procedure: after getting embeddings for MHC and peptides, we\nput them in separate branches, which consists of two residual blocks for peptide and three\nblocks for MHC as shown on Fig.3(a). Each of block consists of 2-dim. convolutional filters\nof size 1. Sequence of blocks ends up with concatenation of output flattened vectors from\nconvolutional filters that follows up with fully-connected layers for prediction of the binding\naffinity between input MHC and peptide. Final model consists of nearly 260.000 learning\nparameters. Input is following: each MHC was presented in terms of pseudosequence, which\nis 34 exact positions where peptide binds to MHC[1], which leads to 34*20 dim. vector for\nMHC branch and 9*20 dim. vector for peptide ligand branch." }, { - "id": 111975, - "strid": "ea29c658-fdec-4135-85c5-2db0c6a22564", - "image_id": 204847, - "image_name": "13273.png", + "id": 670, + "strid": "08d559aa-737e-4683-a38b-3630d9423826", + "image_id": 27, + "image_name": "11272.png", "category_id": 5, "category_name": "Section", "bbox": [ - 594.188, - 837.447, - 144.43200000000002, - 27.851 + 1778.738, + 2925.056, + 780.2430000000002, + 59.5949999999998 ], - "priority": 3, + "priority": 24, "parents": [ - 111999 + 646 ], "children": [ - 111980 + 671, + 672 ], - "area": 497600.95803599997, + "area": 5202908.259328, "iscrowd": 0, "segmentation": [], - "text": "Abstract" + "text": "Results and future work" }, { - "id": 111980, - "strid": "085cc06e-3ce2-41d5-9514-d24d661ad3af", - "image_id": 204847, - "image_name": "13273.png", + "id": 671, + "strid": "0c56d990-0ffa-4b73-9042-bb61740a86e5", + "image_id": 27, + "image_name": "11272.png", "category_id": 3, "category_name": "Text", "bbox": [ - 194.941, - 905.566, - 946.6689999999999, - 492.2850000000001 + 1697.624, + 3039.304, + 1484.1299999999999, + 401.404 ], - "priority": 4, + "priority": 25, "parents": [ - 111975 + 670 ], "children": [], - "area": 176531.941606, + "area": 5159595.413696, "iscrowd": 0, "segmentation": [], - "text": "N order to help students integrate basic science and clinical\n\nconcepts, we use an approach where students solve a clin-\nical case and then answer questions relating to the case. In\norder to arrive at the correct diagnosis, students have to or-\nder exams and lab tests, and pay for them from a restricted\nbudget, represented by “tokens”. To order tests in a proper se-\nquence (search to confirmatory) students need a good under-\nstanding of the science behind the disease, how tests work,\nand how they are interpreted.\nBoth students and faculty enjoy this new format, which is very\nflexible and can be easily adjusted for different learning ob-\njectives." + "text": "Proposed approach in amino acid sequences representation and sophisticated neural network\narchitecture let us achieve competitive results comparing to state-of-the-art methods : F1-\nScore on all alleles: 0.82. One of the most great advantage of our solution is that our\nmodel generalizable on any pair of MHC and peptide, due to the fact that it is global(for\nall alleles), while existing best solutions are local(pan-allele). In further study, apart from\nimproving architecture by decreasing learning parameters, we also would like to explore what\nexactly our neural network learned by looking inside activations on different residual blocks\nand layers as shown on Fig.4." }, { - "id": 111976, - "strid": "c3fd30ff-fbd0-49fa-843d-e624ceb52be5", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 5, - "category_name": "Section", + "id": 672, + "strid": "29f61377-c26f-4b8a-84ef-804e80e83a6c", + "image_id": 27, + "image_name": "11272.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 550.471, - 1460.666, - 234.53499999999997, - 29.76800000000003 + 1995.257, + 3524.688, + 965.279, + 331.62699999999995 ], - "priority": 5, + "priority": 26, "parents": [ - 111999 + 670 ], "children": [ - 111981 + 673 ], - "area": 804054.273686, + "area": 7032658.404816001, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 673, + "strid": "d2df0e71-4d85-4a71-8db7-d085c6b7e590", + "image_id": 27, + "image_name": "11272.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 1696.771, + 3912.985, + 1484.736, + 77.59400000000005 + ], + "priority": 27, + "parents": [ + 672 + ], + "children": [], + "area": 6639439.471435, "iscrowd": 0, "segmentation": [], - "text": "1. Introduction" + "text": "Figure 4: Convolution filters visualization on both weak and strong peptide ligand of HLA:A0101. It is seen\nthat activations patterns are widely divergent." }, { - "id": 111981, - "strid": "cf5cd4fa-ab08-4a29-a4a1-0ac6a7743c82", - "image_id": 204847, - "image_name": "13273.png", + "id": 674, + "strid": "8e38d03a-fe6f-4333-b42a-b09fcc074bf7", + "image_id": 27, + "image_name": "11272.png", "category_id": 3, "category_name": "Text", "bbox": [ - 192.429, - 1532.228, - 947.783, - 653.4940000000001 + 1697.527, + 4093.864, + 1302.063, + 93.20800000000008 ], - "priority": 6, + "priority": 28, "parents": [ - 111976 + 646 ], "children": [], - "area": 294845.10181200004, + "area": 6949444.674328, "iscrowd": 0, "segmentation": [], - "text": "EDICAL students have to integrate basic science with clin-\nM ical knowledge. In order to use medical tests success-\nfully, students have to understand the working principle, and\nbe able to interpret its results in the context of the patient’s\nsituation. Clinical cases that simulate aspects of the work of\na physician are used to achieve this. Often, such sessions are\noffered in team-based learning (TBL) format to also improve\nsocial competencies of students.\nThe decision to order procedures, laboratory tests, or physi-\ncal exams depends upon cost (see for example [4]), complex-\nity, risk and availability. Physicians should not simply order\nevery available test. This concept can be made more con-\ncrete by incorporating \"tokens\" as tangible assets, with which\nstudents pay for test results. This should prepare students\nfor the budget restrictions they will encounter later in their\ncareer." + "text": "Acknowledgments\nThis work was supported by the Russian Science Foundation grant 17-15-01495." }, { - "id": 111977, - "strid": "e6306130-9f31-4c5f-a91e-c3b67304b476", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 5, - "category_name": "Section", + "id": 675, + "strid": "c518dabf-31c7-49b9-9fb7-53038c8e92b7", + "image_id": 28, + "image_name": "11274.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 578.373, - 2247.82, - 179.29499999999996, - 28.447999999999865 - ], - "priority": 7, - "parents": [ - 111999 + 23.63, + 21.91, + 81.09, + 86.88000000000001 ], + "priority": -1, + "parents": [], "children": [ - 111993, - 111983, - 111982, - 111992 + 701, + 677, + 676, + 685, + 689, + 678, + 679, + 699, + 694, + 681, + 680 ], - "area": 1300078.3968600002, + "area": 517.7333, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 676, + "strid": "353ea8eb-3972-414e-be84-8a652879e166", + "image_id": 28, + "image_name": "11274.png", + "category_id": 1, + "category_name": "Title", + "bbox": [ + 666.202, + 24.401, + 2868.031, + 65.001 + ], + "priority": 1, + "parents": [ + 675 + ], + "children": [], + "area": 16255.995002, "iscrowd": 0, "segmentation": [], - "text": "2. Methods" + "text": "" }, { - "id": 111992, - "strid": "68d7b037-dca2-49bf-b5ce-7c672b381b3f", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 4, - "category_name": "List", + "id": 677, + "strid": "605dae2e-c968-4932-a6b2-4e15fe678ee3", + "image_id": 28, + "image_name": "11274.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 193.126, - 2318.194, - 945.3500000000001, - 797.1210000000001 + 337.889, + 107.705, + 3522.07, + 250.60900000000004 ], - "priority": 8, + "priority": 2, "parents": [ - 111977 + 675 ], "children": [], - "area": 447703.534444, + "area": 36392.334745, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Timothy J. Griffin’, Matthew C. Chambers?, James E. Johnson?, Thomas McGowan2, Thomas G. Doak?, Jeremy Fischer’, Praveen Kumar?®, and Pratik Jagtap?*\n, ‘University of Minnesota, Minneapolis, MN; ?Minnesota Supercomputing Institute, Minneapolis, MN; ?National Center for Genome Analysis Support, Indiana\nUniversity, Bloomington, IN; *UITS Research Technologies, Indiana University, Bloomington, IN; °Biomedical Informatics and Computational Biology, University of\nMinnesota, Minneapolis, MN" }, { - "id": 111982, - "strid": "e79e1ac3-0381-4f33-9ef6-ad127c4fc83e", - "image_id": 204847, - "image_name": "13273.png", + "id": 678, + "strid": "b1f6271c-ed78-4a70-a497-ff11d37605da", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 194.797, - 3130.546, - 947.299, - 325.49400000000014 + 24.885, + 399.591, + 1770.043, + 587.576 ], - "priority": 9, + "priority": 3, "parents": [ - 111977 + 675 ], "children": [], - "area": 609820.969162, + "area": 9943.822035000001, "iscrowd": 0, "segmentation": [], - "text": "Exam results can be given to the students on paper slips, or by\naccess to an electronic database. The entire session can even\nbe applied electronically, using web-shop software to handle\nthe selling of test results. Multiple choice questions can be\nanswered by simple show of hands, web survey (e.g., Survey-\nMonkey) or by an audience response system.\n\nWe have tested this format in first year students with four\ncases:" + "text": "Introduction. The Galaxy platform (Nucleic Acids Res. 44(W1):W3-W10) has proven a\npowerful solution to meet the multi-faceted requirements of multi-omic informatics. The\ncollaborative Galaxy for proteomics project (Galaxy-P, galaxyp.org) has demonstrated Galaxy’s\nvalue in integrating genomic and MS-based proteomic software for next generation\napplications such as proteogenomic and metaproteomic analysis (see\nz.umn.edu/galaxypreferences). To date, the tools and workflows developed have been most\nreadily available to other users of Galaxy who are operating local instances of the platform. To\nincrease accessibility, the Galaxy-P team has partnered with Jetstream, a cloud-based\ncyberinfrastructure aimed at supporting research computing needs. Here we describe the\nprocess of utilizing the Jetstream resource, as well as details on the multi-omic tools that are\nbeing made available on this scalable and extensible infrastructure." }, { - "id": 111993, - "strid": "208276ab-1669-4361-ae44-83f779869570", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 4, - "category_name": "List", + "id": 679, + "strid": "1141ed1c-dc37-49a5-8c7c-29e26b61364f", + "image_id": 28, + "image_name": "11274.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 209.741, - 3474.763, - 928.655, - 495.2829999999999 + 35.974, + 1006.554, + 1748.029, + 589.3350000000002 ], - "priority": 10, + "priority": 4, "parents": [ - 111977 + 675 ], "children": [], - "area": 728800.2663830001, + "area": 36209.773596, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Results. Working with the Jetstream team (see below for more information), initial work has\nfocused on two main multi-omic applications, proteogenomics and metaproteomics. For both\nof these research areas, we have developed “gateway” Galaxy instances supported by cloud-\nbased, cyberinfrastructure maintained by the Jetstream resource. The proteogenomics\nresource (see top right) offers workflows for carrying out core operations required for\nintegrative analysis of RNA-Seq and mass spectrometry (MS)-based proteomics data. The\nmetaproteomics resource (see middle right) offers tools for integrating metagenomics-guided\ndata on bacterial community composition with MS-based proteomics data, as well as\ntaxonomic and functional annotation tools, to better understand the functional dynamics of\ncomplex communities. We have also generated an educational gateway (see lower right),\nwhich serves as an instance for training researchers via workshops and other venues." }, { - "id": 111983, - "strid": "7475c8f2-0281-42c9-8d28-f2f00560ddbf", - "image_id": 204847, - "image_name": "13273.png", + "id": 680, + "strid": "4ea338bd-6080-4d0a-87f8-a5d56166eaba", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 193.788, - 3988.0, - 946.8409999999999, - 206.75900000000001 + 27.65, + 1612.537, + 1749.694, + 322.96900000000005 ], - "priority": 11, + "priority": 5, "parents": [ - 111977 + 675 ], "children": [], - "area": 772826.544, + "area": 44586.648049999996, "iscrowd": 0, "segmentation": [], - "text": "Students reception of this teaching strategy was assessed\nafter IRB approval and Informed Consent by an anonymous\nquestionnaire using SurveyMonkey. A LIKERT-scale [3] was\nused to assess how much students agreed with the state-\nments given." + "text": "Conclusions. Jetstream provides a powerful cyberinfrastructure resource, accessible to all\nresearchers, and supporting Galaxy-based multi-omic platforms such as those being developed\nby the Galaxy-P project. The resource provides scalable infrastructure needed to support big\ndata applications in multi-omics. In addition to those gateways described here we anticipate\nJetstream to provide access for more application areas in the future (e.g. metabolomics, data-\nindependent acquisition)." }, { - "id": 111978, - "strid": "fc08d22d-0a53-4a85-951b-c59e0aa94c90", - "image_id": 204847, - "image_name": "13273.png", + "id": 681, + "strid": "71ece291-4ae0-47be-bb5c-7b2d9d2dbfa9", + "image_id": 28, + "image_name": "11274.png", "category_id": 5, "category_name": "Section", "bbox": [ - 459.507, - 4257.016, - 413.56800000000004, - 33.935999999999694 + 682.432, + 2152.202, + 439.99, + 50.26099999999997 ], - "priority": 12, + "priority": 6, "parents": [ - 111999 + 675 ], "children": [ - 111996, - 111984, - 111989, - 111997, - 111988, - 111986, - 111987, - 111995, - 111998, - 111985 + 684, + 683, + 682 ], - "area": 1956128.6511119998, + "area": 1468731.5152640003, "iscrowd": 0, "segmentation": [], - "text": "3. Results and Discussion" + "text": "What is Jetstream?" }, { - "id": 111984, - "strid": "7f2016a7-7433-402d-8275-2b0bf09f03d8", - "image_id": 204847, - "image_name": "13273.png", + "id": 682, + "strid": "c98a11a4-b785-4de8-840f-82d9808e3512", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 194.731, - 4346.926, - 944.316, - 146.2569999999996 + 35.989, + 2224.514, + 1741.858, + 428.68600000000015 ], - "priority": 13, + "priority": 7, "parents": [ - 111978 + 681 ], "children": [], - "area": 846481.2469060001, + "area": 80058.034346, "iscrowd": 0, "segmentation": [], - "text": "3.1 Case presentation\n\nWW: have originally developed this format for use with first\nyear Progressive Academic Education (PAcE)-students" + "text": "Background. Jetstream (Proceedings of the 2015 XSEDE Conference: Scientific Advancements\nEnabled by Enhanced Cyberinfrastructure. ACM: 2792774. 1-8.) is a cloud-based\ncyberinfrastructure resource, supported primarily through a grant from the National Science\nFoundation (ACI-1445604). Development and maintenance of the resource is led by the\nIndiana University Pervasive Technology Institute. The resource offers the opportunity for\nresearchers to create remote virtual machines, accessible via the web from their own computer\nworkstation, but with orders of magnitude more computing power. More information on\nJetstream is available at jetstream-cloud.org" }, { - "id": 111997, - "strid": "3fb69264-6849-4786-90bd-1467090edbd9", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 2, - "category_name": "Figure", + "id": 683, + "strid": "5aeb0c9d-b82c-4484-899c-18670c702ca9", + "image_id": 28, + "image_name": "11274.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1222.033, - 1216.694, - 851.049, - 592.3969999999999 + 32.188, + 2668.674, + 1742.701, + 341.0 ], - "priority": 14, + "priority": 8, + "parents": [ + 681 + ], + "children": [], + "area": 85899.278712, + "iscrowd": 0, + "segmentation": [], + "text": "Accessing Jetstream. Resources are accessed through a web interface, based on the\nAtmosphere cloud computing environment customized to support science and engineering\napplications. The operating software environment is based on OpenStack.\n\nJetstream is supported by the Extreme Science and Engineering Discovery Environment (XSEDE)\ndigital resource (www.xsede.org). U.S.-based researchers and collaborators can request an\nallocation, free of charge, on Jetstream through XSEDE." + }, + { + "id": 684, + "strid": "c3fa1913-5a72-4848-8ab5-5ffdc7b9d572", + "image_id": 28, + "image_name": "11274.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 31.617, + 3022.148, + 1748.939, + 503.72699999999986 + ], + "priority": 9, "parents": [ - 111978 + 681 + ], + "children": [], + "area": 95551.253316, + "iscrowd": 0, + "segmentation": [], + "text": "Services and capabilities. Jetstream offers pre-configured images with many popular software\npackages used in science and engineering. The popular Galaxy bioinformatics platform is one\nfeatured image. The resource also offers science “gateways” which include pre-configured\nvirtual machines of workflow engines such as Galaxy, which can be deployed as persistently\naccessible web services and made publically available to any researcher through a URL.\n\nVirtual machines can be configured to meet compute and storage needs of different\napplications. For the gateways described here, the VMs are utilizing the large capacity\nconfigurations (e.g. 44 CPUs, 120GB RAM and 4 TB storage). Extra volumes of storage can be\nadded if additional storage is required." + }, + { + "id": 685, + "strid": "e0f1bdfe-520f-4007-8cb2-c4a5ffc38191", + "image_id": 28, + "image_name": "11274.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 2669.403, + 391.279, + 1359.4469999999997, + 57.764999999999986 + ], + "priority": 10, + "parents": [ + 675 ], "children": [ - 111990 + 687, + 688, + 686 ], - "area": 1486840.2189019998, + "area": 1044481.336437, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Proteogenomics gateway (tiny.cc/galaxyp-proteogenomics)" }, { - "id": 111990, - "strid": "d6b26418-fe71-4cc2-9143-7d43b77010ae", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 6, - "category_name": "Caption", + "id": 686, + "strid": "ca1dc42e-c277-4499-88ea-188e380d02f6", + "image_id": 28, + "image_name": "11274.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1179.92, - 813.038, - 945.2110000000002, - 207.28300000000002 + 2563.473, + 465.215, + 1566.7849999999999, + 322.99899999999997 ], - "priority": 15, + "priority": 11, "parents": [ - 111997 + 685 ], "children": [], - "area": 959319.7969600001, + "area": 1192566.091695, "iscrowd": 0, "segmentation": [], - "text": "Fig. 1: Tokens used for a paper-based lesson. Exam- and lab-\ntokens have different color. All tokens of a group are num-\nbered, the group number is added by hand. Students are\nasked to use the tokens in sequence, we are thus able to fol-\nlow their thinking later." + "text": "We have established a Galaxy-based gateway on Jetstream which offers tools and\nworkflows (see below) for the core operations of proteogenomics: 1) Generation of\nprotein sequence database from RNA-Seq data (reference proteins and selected\nvariants); 2) Matching MS/MS spectra to sequences and confirming novelty of\nputative variants. This gateway provides instructions on how to use this resource,\nemphasizing cancer research applications of proteogenomics." }, { - "id": 111998, - "strid": "9a61c9fa-0bb2-45d6-9808-f17c6919bc5f", - "image_id": 204847, - "image_name": "13273.png", + "id": 687, + "strid": "ea2ceabc-b571-4225-9a97-3c8175832b9a", + "image_id": 28, + "image_name": "11274.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1220.615, - 2377.39, - 854.923, - 2099.89 + 1836.674, + 385.019, + 668.7690000000002, + 417.256 ], - "priority": 16, + "priority": 12, "parents": [ - 111978 + 685 ], - "children": [ - 111991 - ], - "area": 2901877.89485, + "children": [], + "area": 707154.386806, "iscrowd": 0, "segmentation": [] }, { - "id": 111991, - "strid": "a383f835-737b-476f-b4e0-91f09accd65f", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 6, - "category_name": "Caption", + "id": 688, + "strid": "9d2d0137-6cc9-43c9-a853-b3c11f6a9aa7", + "image_id": 28, + "image_name": "11274.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1180.673, - 2025.736, - 942.278, - 163.3610000000001 + 2115.745, + 794.256, + 1820.274, + 500.95400000000006 ], - "priority": 17, + "priority": 13, "parents": [ - 111998 + 685 ], "children": [], - "area": 2391731.800328, + "area": 1680443.1607199998, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 689, + "strid": "e448fcb7-0174-4b8a-ae36-8b91564d326e", + "image_id": 28, + "image_name": "11274.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 2246.104, + 1331.376, + 1471.158, + 55.31700000000001 + ], + "priority": 14, + "parents": [ + 675 + ], + "children": [ + 690, + 692, + 691, + 693 + ], + "area": 2990408.9591039997, "iscrowd": 0, "segmentation": [], - "text": "Fig. 2: Lab results for a paper-based presentation. The two\nsides are printed onto the same sheet of paper, one sheet is\nneeded per group. The individual strips are cut with a guillo-\ntine and folded, so that the result is covered." + "text": "Metaproteomics gateway (z.umn.edu/metaproteomicsgateway)" }, { - "id": 111985, - "strid": "95a05f82-85af-456d-8186-90d7c6153482", - "image_id": 204847, - "image_name": "13273.png", + "id": 690, + "strid": "03a1abce-3322-4cc9-9cd4-746652fc19f4", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2162.638, - 808.628, - 947.1590000000001, - 1294.6169999999997 + 1857.349, + 1406.85, + 1078.847, + 371.01199999999994 ], - "priority": 18, + "priority": 15, "parents": [ - 111978 + 689 ], "children": [], - "area": 1748769.640664, + "area": 2613011.44065, "iscrowd": 0, "segmentation": [], - "text": "(a scholar program), to help them integrate basic and clini-\ncal sciences. The lab-token approach is, however, extremely\nflexible. We have also used it for large classes. Other de-\npartments have modified this approach for teaching in sec-\nond year, with emphasis more on clinical procedure rather\nthan basic knowledge. Academic Success is now using this\napproach to develop the critical thinking ability of weak stu-\ndents.\n\nBy numbering the tokens, one can check that students order\ntests in proper sequence. For example, for a patient with pale\nmucus membranes a CBC should be ordered to check for the\npresence of anemia and to identify its type. If it is megaloblas-\ntic, blood levels of cobalamin and folate should be checked. If\ncobalamin is low in a child, one might do a SCHILLING-test. In\nan elderly patient, a search for anti-intrinsic factor autoanti-\nbodies would be more appropriate. To get this right, students\nneed a good understanding of how a test works and what the\nresult means. They also need to understand the role of vita-\nmin B,, and its uptake. This can be aided by keeping the re-\nport brief (e. g., “SCHILLING-test positive both with and without\nintrinsic factor”). Students work on level 5 (synthesis) and 6\n(evaluation) of BLOOM’s taxonomy [2]. We allow students one\nworking computer per group to search for information.\nStudents who get to the right diagnosis in a minimum number\nof steps receive commendation in front of their peers or even\na fruit basket. If they get it very wrong, students may receive\na letter from the insurance company that a certain test will\nnot be paid for.\n\nIt is possible to ask some basic science questions after an ini-\ntial case presentation, then have the case progress further\nand ask more questions." + "text": "Metaproteomics utilizes metagenomics data (e.g. 16sRNA,\nwhole genome sequencing) coupled with MS-based\nproteomics from the same sample, to characterize proteins\nexpressed by the community. Metaproteomics analysis can\nbe used to capture the functional signature from bacterial\ncommunities contained in a host sample (e.g. humans) or\nfrom environmental samples. Our Galaxy-based gateway" }, { - "id": 111986, - "strid": "ba19a8f1-83cf-4b13-b72b-4e8e9b8278ad", - "image_id": 204847, - "image_name": "13273.png", + "id": 691, + "strid": "19918b1b-efa1-4bad-8ad7-b57c6c379dcd", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2166.784, - 2115.385, - 938.886, - 136.94000000000005 + 1861.99, + 1781.829, + 402.28300000000013, + 257.10300000000007 ], - "priority": 19, + "priority": 16, "parents": [ - 111978 + 689 ], "children": [], - "area": 4583582.371840001, + "area": 3317747.77971, "iscrowd": 0, "segmentation": [], - "text": "3.2 Student responses\n\n23 out of 33 attending students answered the question-\nnaire after the second presentation of the Floppy Girl case." + "text": "provides instructions\non using our\nmetaproteomics\nworkflows and how to\nvisualize the results." }, { - "id": 111995, - "strid": "0f7b64cc-f523-4dac-9151-160606f60b17", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 7, - "category_name": "Table", + "id": 692, + "strid": "af7eff14-aca4-4a6d-8be5-f72de9a38b12", + "image_id": 28, + "image_name": "11274.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2164.669, - 2265.104, - 928.1329999999998, - 270.81899999999996 + 2281.781, + 1781.668, + 662.4949999999999, + 420.2259999999999 ], - "priority": 20, + "priority": 17, "parents": [ - 111978 + 689 ], "children": [], - "area": 4903200.410575999, + "area": 4065376.1907079997, "iscrowd": 0, "segmentation": [] }, { - "id": 111989, - "strid": "6bdc0fa0-b116-43a4-8634-e71c035b4c47", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 3, - "category_name": "Text", + "id": 693, + "strid": "604083d2-57bb-446f-84cd-eb478dc8d096", + "image_id": 28, + "image_name": "11274.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2164.459, - 2536.393, - 943.6909999999998, - 113.16400000000021 + 2976.315, + 1415.131, + 1187.1460000000002, + 769.6719999999998 ], - "priority": 21, + "priority": 18, "parents": [ - 111978 + 689 ], "children": [], - "area": 5489918.656386999, + "area": 4211875.622265, "iscrowd": 0, - "segmentation": [], - "text": "When asked, how many of the 4 practice sessions of a\nsemester should contain tokens, the following results were\nobtained:" + "segmentation": [] }, { - "id": 111996, - "strid": "09935e38-327f-4742-b921-780411eeebf5", - "image_id": 204847, - "image_name": "13273.png", - "category_id": 7, - "category_name": "Table", + "id": 694, + "strid": "8f6d4038-92af-430a-84f4-a004d39324f6", + "image_id": 28, + "image_name": "11274.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2164.796, - 2648.394, - 307.43600000000015, - 332.5430000000001 + 2794.573, + 2247.654, + 472.8380000000002, + 56.085999999999785 ], - "priority": 22, + "priority": 19, "parents": [ - 111978 + 675 ], - "children": [], - "area": 5733232.737623999, + "children": [ + 695, + 698, + 697, + 696 + ], + "area": 6281233.181741999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Educational gateway" }, { - "id": 111987, - "strid": "d1204dea-cc8c-4b38-8025-5ff9d8454c3a", - "image_id": 204847, - "image_name": "13273.png", + "id": 695, + "strid": "883379c3-6cce-47fc-aafa-ba82f865eb4a", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2164.803, - 2991.635, - 944.7159999999999, - 328.3580000000002 + 2499.885, + 2330.344, + 1063.306, + 366.828 ], - "priority": 23, + "priority": 20, "parents": [ - 111978 + 694 ], "children": [], - "area": 6476300.422905, + "area": 5825592.01044, "iscrowd": 0, "segmentation": [], - "text": "These results can be affected negatively when too little time\n(only one hour) is available. Students then wish for fewer\ncases (median 2 rather than 3), and are less sure about the\nvalue of the token format. More students feel that getting the\nright diagnosis is the primary objective of the presentation.\nTwo hours are normally required to do a meaningful presenta-\ntion of such a token-based case and to ask some 5-6 multiple\nchoice questions relating to it." + "text": "Jetstream also allows for special allocations focusing on\neducational activities. Since its inception, the Galaxy-P\nteam has been active in conducting hands-on, training\nworkshops for researchers interested in using\nbioinformatics tools for multi-omic applications.\nJetstream offers an ideal resource for such training\nworkshops, providing required computing power to" }, { - "id": 111988, - "strid": "89241599-e469-4061-8df0-95ffd8b91c18", - "image_id": 204847, - "image_name": "13273.png", + "id": 696, + "strid": "165f8b5c-9776-42ea-bf67-057c376853af", + "image_id": 28, + "image_name": "11274.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2164.682, - 3335.097, - 945.203, - 263.6909999999998 + 2956.527, + 2698.917, + 607.04, + 416.65700000000015 ], - "priority": 24, + "priority": 21, "parents": [ - 111978 + 694 ], "children": [], - "area": 7219424.444154, + "area": 7979420.981259, "iscrowd": 0, "segmentation": [], - "text": "3.3 Faculty responses\n\nFaculty enjoy this format. It has been easier to enlist faculty\nfrom various departments for these cases than for those in\nother formats, even though they are more laborious to set up\nand administer. This may have to do with the more active role\nfaculty have, or it may simply be the novelty of the format." + "text": "enable simultaneous use of a\nsingle Galaxy instance by dozens\nof researchers. This provides the\nnecessary infrastructure for\ninteractive and hands-on training\nactivities for researchers seeking\nto learn about the use of these\ntools." }, { - "id": 111979, - "strid": "e76300e6-da3a-47b7-b7c6-89a381da18a2", - "image_id": 204847, - "image_name": "13273.png", + "id": 697, + "strid": "4bf27551-83cd-4038-808d-99e3791f80c6", + "image_id": 28, + "image_name": "11274.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 1831.613, + 2249.565, + 664.5109999999997, + 416.8220000000001 + ], + "priority": 22, + "parents": [ + 694 + ], + "children": [], + "area": 4120332.498345, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 698, + "strid": "82c5fd35-5972-4025-a15d-52f9f5eb9a10", + "image_id": 28, + "image_name": "11274.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 1834.807, + 2697.72, + 1116.4750000000001, + 435.451 + ], + "priority": 23, + "parents": [ + 694 + ], + "children": [], + "area": 4949795.540039999, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 699, + "strid": "b4613b6c-966a-4f64-8b36-011cae6b36d5", + "image_id": 28, + "image_name": "11274.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2545.106, - 3659.8, - 183.90999999999985, - 29.572000000000116 + 2563.529, + 3171.905, + 285.74000000000024, + 41.034999999999854 ], - "priority": 25, + "priority": 24, "parents": [ - 111999 + 675 ], "children": [ - 111994 + 700 ], - "area": 9314578.938800002, + "area": 8131270.452745001, "iscrowd": 0, "segmentation": [], - "text": "References" + "text": "" }, { - "id": 111994, - "strid": "1d2c05a7-fecd-4f9c-b041-416442daf3cb", - "image_id": 204847, - "image_name": "13273.png", + "id": 700, + "strid": "412cc9a3-4441-40bd-aef8-7a4edcd3aef9", + "image_id": 28, + "image_name": "11274.png", "category_id": 4, "category_name": "List", "bbox": [ - 2193.465, - 3740.71, - 917.3139999999999, - 503.5510000000004 + 1835.7, + 3234.617, + 1743.4369999999997, + 330.2080000000001 ], - "priority": 26, + "priority": 25, "parents": [ - 111979 + 699 ], "children": [], - "area": 8205116.460150001, + "area": 5937786.4269, "iscrowd": 0, "segmentation": [] }, { - "id": 119308, - "strid": "4a7d1280-ece3-4040-a9e6-90c7f04d40f4", - "image_id": 205141, - "image_name": "14344.png", + "id": 701, + "strid": "f1bc8b54-ee0f-4985-b41b-1052cdc85515", + "image_id": 28, + "image_name": "11274.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 3717.222, + 2248.447, + 343.172, + 38.38000000000011 + ], + "priority": 26, + "parents": [ + 675 + ], + "children": [ + 702 + ], + "area": 8357976.6542340005, + "iscrowd": 0, + "segmentation": [], + "text": "Acknowledgements" + }, + { + "id": 702, + "strid": "dc3d78d2-cc70-415d-b03f-8ee92c6a0308", + "image_id": 28, + "image_name": "11274.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 3625.583, + 2294.424, + 527.4990000000003, + 836.319 + ], + "priority": 27, + "parents": [ + 701 + ], + "children": [], + "area": 8318624.649192, + "iscrowd": 0, + "segmentation": [], + "text": "We thank Subina Mehta for\nhelp in testing and\ndocumenting the Jetstream\ngateways. We thank the\n\nGalaxy development\ncommunity and core Galaxy\nteam for continued\n\ninnovation and improvement\nof the framework. We also\nacknowledge NSF — grant\n1458524, and NIH grant\n1U24CA199347 for funding\nsupport to the Galaxy-P team\nat the University of\nMinnesota, and NSF grant\nACI-1445604 to the Jetstream\nteam." + }, + { + "id": 703, + "strid": "7243178c-7117-4e50-9719-e972ec96aa77", + "image_id": 29, + "image_name": "11275.png", "category_id": 9, "category_name": "Root", "bbox": [ - 1043.16, - 64.85, - 506.53999999999996, - 228.19000000000003 + 51.26, + 431.27, + 77.62, + 178.51999999999998 ], "priority": -1, "parents": [], "children": [ - 119271, - 119287, - 119261, - 119289, - 119282, - 119264, - 119300, - 119257, - 119293, - 119266, - 119277, - 119281, - 119292, - 119305, - 119284, - 119258, - 119259, - 119307, - 119304, - 119301, - 119267, - 119306, - 119303, - 119254, - 119265, - 119302, - 119270, - 119268, - 119255, - 119269, - 119295, - 119288, - 119283, - 119260, - 119256, - 119298, - 119291, - 119273, - 119275, - 119253, - 119297, - 119276, - 119278, - 119272, - 119299, - 119252, - 119280, - 119296, - 119285, - 119263, - 119286, - 119274, - 119294, - 119262, - 119279, - 119290 + 737, + 735, + 705, + 733, + 704, + 712, + 710, + 706, + 708 ], - "area": 67648.92599999999, + "area": 22106.900199999996, "iscrowd": 0, "segmentation": [] }, { - "id": 119252, - "strid": "a25b4e53-48d5-4f64-a130-5a314e3e328a", - "image_id": 205141, - "image_name": "14344.png", + "id": 704, + "strid": "2ab76f41-9512-4f63-9c9f-ca2d7ac593e8", + "image_id": 29, + "image_name": "11275.png", "category_id": 1, "category_name": "Title", "bbox": [ - 508.048, - 483.321, - 2527.7160000000003, - 119.20799999999997 + 58.799, + 49.337, + 3472.935, + 225.716 ], "priority": 1, "parents": [ - 119308 + 703 ], "children": [], - "area": 245550.267408, + "area": 2900.9662630000003, "iscrowd": 0, "segmentation": [], - "text": "UNCOVERING THE GENETIC HEREDITABLE COMPONENT OF LATE ONSET ALZHEIMER’S DISEASE\nTHROUGH THE ANALYSIS OF GWA DATA" + "text": "New binding site of the quorum sensing molecule N-3-oxododecanoyl homoserine lactone\nwith the transcriptional regulator LasR of Pseudomonas aeruginosa Same" }, { - "id": 119253, - "strid": "789b99a8-7b5a-40ac-a64d-cc55f1f88ba2", - "image_id": 205141, - "image_name": "14344.png", + "id": 705, + "strid": "d2f26776-eea0-4715-9096-52e58caf5991", + "image_id": 29, + "image_name": "11275.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 958.361, - 673.445, - 1726.661, - 150.10299999999995 + 533.912, + 276.363, + 2609.8359999999993, + 318.1720000000001 ], "priority": 2, "parents": [ - 119308 + 703 ], "children": [], - "area": 645403.4236450001, + "area": 147553.52205600002, "iscrowd": 0, "segmentation": [], - "text": "Margherita Squillario*, Federico Tomasi*, Veronica Tozzo*, Annalisa Barla*, Daniela Uberti**\n(*) DIBRIS, University of Genoa, Via Dodecaneso 35, 16146, Genova, Italy\n(**) DMMT, University of Brescia, Viale Europa 11, 25123 Brescia, Italy" + "text": "Hovakim Grabski, Lernik Hunanyan, Susanna Tiratsuyan, Hrachik Vardapetyan\n\nDepartment of Medical Biochemistry and Biotechnology\nInstitute of Mathematics and High Technologies\nRussian-Armenian University, Yerevan, Armenia\n\nE-mail: hovakim.grabski@rau.am; lernik.hunanyan@rau.am; susanna.tiratsuyan@rau.am; hrachik.vardapetyan@rau.am" }, { - "id": 119254, - "strid": "67aedc14-3106-4019-be4f-20537f0bacdb", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 706, + "strid": "04436b34-5c71-4d2e-b6d3-bb4e58233585", + "image_id": 29, + "image_name": "11275.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 129.125, - 949.165, - 1777.012, - 139.8019999999999 + 97.953, + 697.417, + 366.706, + 53.111999999999966 ], "priority": 3, "parents": [ - 119308 + 703 ], - "children": [], - "area": 122560.930625, + "children": [ + 707 + ], + "area": 68314.08740100001, "iscrowd": 0, "segmentation": [], - "text": "Background: The late onset form of Alzheimer's Disease is the most widespread and APOE represents the only strong associated gene.\nFrom the literature is coming out the idea that multiple low penetrance genetic variants could be responsible. Therefore the genetic\npredisposition of the patients and their relatives should be unveiled from the analysis of their genetic profiles. The main purpose of this\nwork is to uncover the signatures of genetic variants, genes and pathways that characterize the patients." + "text": "Introduction" }, { - "id": 119255, - "strid": "6be53aa7-c184-440b-90b9-2b86473ed4a2", - "image_id": 205141, - "image_name": "14344.png", + "id": 707, + "strid": "3bd3b24a-8cdd-4ff4-ba65-d8b98a7cf583", + "image_id": 29, + "image_name": "11275.png", "category_id": 3, "category_name": "Text", "bbox": [ - 127.234, - 1109.229, - 1800.355, - 140.5530000000001 + 97.302, + 785.188, + 1004.2609999999999, + 732.0479999999999 ], "priority": 4, "parents": [ - 119308 + 706 ], "children": [], - "area": 141131.642586, + "area": 76400.36277600001, "iscrowd": 0, "segmentation": [], - "text": "Methods: We analysed two public GWA data derived from the Alzheimer’s Disease Neuroimaging initiative (ADNI) using a 3-fold kernel\napproach, based on SNPs, Genes and Pathways, and two binary classification tasks : AD vs. cognitively healthy subjects (CN) and\nsubjects at risk vs. subjects not at risk of developing AD, according with APOE status (1 or 2 alleles (High risk) vs. 0 allele (Low risk)\nof APOEé4)." + "text": "In 2017 World Health Organization announced the list of the\nmost dangerous superbugs and among them is Pseudomonas\naeruginosa, which is an antibiotic-resistant opportunistic\nhuman pathogen. This organism attacks human patients\nsuffering from such diseases as AIDS, cancer, cystic fibrosis,\netc. Current therapies lack efficacy because P. aeruginosa\ncreates and inhabits surface-associated biofilms conferring\nincreased resistance to antibiotics and host immune\nresponses. Biofilm formation is controlled through cell-cell\ncommunication system called quorum sensing. The main\nquorum sensing system of P. aeruginosa includes receptor\nprotein LasR. The transcriptional regulator LasR acts as a\ndimer with the help of its native autoinducer ligand and binds\nto the promoter DNA. However, there remains a need for the\nunderstanding of the LasR protein, because till date there is\nno molecular detail information." }, { - "id": 119256, - "strid": "65fa3864-e1ce-491a-864e-fefb015fc870", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 708, + "strid": "e15f933a-2cd7-41f2-8649-ff38de125c87", + "image_id": 29, + "image_name": "11275.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 127.569, - 1272.821, - 1819.188, - 182.60300000000007 + 96.461, + 1612.414, + 280.882, + 70.70700000000011 ], "priority": 5, "parents": [ - 119308 + 703 ], - "children": [], - "area": 162372.50214899998, + "children": [ + 709 + ], + "area": 155535.066854, "iscrowd": 0, "segmentation": [], - "text": "Results: Among the results, we identified 4 statistically robust SNPs signatures and the comparisons of these lists showed: 1) the new and\nstrong involvement of GRM7 in AD which is active within the shared KEGG pathway “Neuroactive ligand-receptor interaction” 2) the\nconfirmation of the involvement of TOMM40 in AD; 3) the involvement of many identified genes, with their SNPs, in many neurological\ndiseases or disorders (e.g., Bipolar and Mood disorders, Schizophrenia) common to both datasets. Phenopedia have been utilized to\n\nperform an accurate comparison of these signatures with the literature." + "text": "Objective" }, { - "id": 119257, - "strid": "fe256cac-39ed-4714-b0c1-5ea0e0724380", - "image_id": 205141, - "image_name": "14344.png", + "id": 709, + "strid": "4288d453-5e90-4f45-b5bd-660129ae089a", + "image_id": 29, + "image_name": "11275.png", "category_id": 3, "category_name": "Text", "bbox": [ - 127.263, - 1477.316, - 1786.351, - 69.2360000000001 + 97.285, + 1695.212, + 1002.964, + 183.41200000000003 ], "priority": 6, "parents": [ - 119308 + 708 ], "children": [], - "area": 188007.666108, + "area": 164918.69942, "iscrowd": 0, "segmentation": [], - "text": "Conclusions: This new approach allowed us to confirm the involvement of specific genes, SNPs and pathways in AD but also to uncover\nnew knowledge that we mostly validated using in silico procedures." + "text": "In the present study, we tried to analyze the molecular\nproperties of the receptor protein LasR monomer as well as\nthe mode of its interactions with signal molecule N-3-\noxododecanoyl homoserine lactone (3-O-C12-HSL)." }, { - "id": 119267, - "strid": "800b0a11-e93c-4d78-bd4e-6e7ac359a663", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 710, + "strid": "43914f59-4b86-49ee-9864-2ce7146a93a3", + "image_id": 29, + "image_name": "11275.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2092.852, - 937.538, - 162.29599999999982, - 31.639999999999986 + 99.202, + 1906.873, + 253.90999999999997, + 54.5630000000001 ], "priority": 7, "parents": [ - 119308 + 703 ], - "children": [], - "area": 1962128.278376, + "children": [ + 711 + ], + "area": 189165.615346, "iscrowd": 0, "segmentation": [], - "text": "Workflow" + "text": "Methods" }, { - "id": 119261, - "strid": "aebd24d1-69ab-4c7b-b464-407740fac401", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 2, - "category_name": "Figure", + "id": 711, + "strid": "f2e67357-8968-4e89-9df1-163119696c98", + "image_id": 29, + "image_name": "11275.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2135.111, - 960.555, - 1225.6999999999998, - 566.41 + 94.748, + 1991.706, + 1006.625, + 1016.0539999999999 ], "priority": 8, "parents": [ - 119308 + 710 ], "children": [], - "area": 2050891.5466049998, + "area": 188710.160088, "iscrowd": 0, "segmentation": [] }, { - "id": 119273, - "strid": "b22bc05f-47f8-409e-972c-128f029abda7", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 712, + "strid": "b89fe0ad-24c2-48f7-8a47-dd6cc440e9fe", + "image_id": 29, + "image_name": "11275.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 136.238, - 1651.142, - 241.33499999999998, - 35.4369999999999 + 97.803, + 3043.177, + 213.899, + 56.71900000000005 ], "priority": 9, "parents": [ - 119308 + 703 ], - "children": [], - "area": 224948.283796, + "children": [ + 730, + 727, + 719, + 731, + 726, + 723, + 721, + 715, + 717, + 713, + 724, + 714, + 720, + 728 + ], + "area": 297631.84013100003, "iscrowd": 0, "segmentation": [], - "text": "ADNI datasets" + "text": "Results" }, { - "id": 119265, - "strid": "aeacb94c-c922-46bc-aa7b-272168cd1415", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 2, - "category_name": "Figure", + "id": 713, + "strid": "0bf8de63-c1c4-4345-9803-db2abf37ae19", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 293.213, - 1656.091, - 1040.623, - 558.9919999999997 + 97.913, + 3117.993, + 801.269, + 50.309999999999945 ], "priority": 10, "parents": [ - 119308 + 712 ], "children": [], - "area": 485587.410383, + "area": 305292.048609, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Part 1:Reconstruction of LasR Structure" }, { - "id": 119266, - "strid": "3592dede-f190-462c-9d84-4bf20dd58459", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 4, - "category_name": "List", + "id": 714, + "strid": "7f1507f1-484f-4eea-9f65-94bf8c79e9ef", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 126.639, - 2232.827, - 1203.088, - 154.3789999999999 + 96.013, + 3180.765, + 1008.7979999999999, + 461.14300000000003 ], "priority": 11, "parents": [ - 119308 + 712 ], "children": [], - "area": 282762.978453, + "area": 305394.789945, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "LasR is a 239 residue long protein. The crystal structure of\nthe N-terminal ligand binding domain (LBD) of LasR\ncontains residues | to 169 (see Fig.1a). However, in order to\nfind the mode of interactions between the LasR and 3-O-\nC12-HSL, the structure of the entire LasR protein was\nneeded. The homology modeling of LasR, including DNA\nbinding domain(DBD), was done with HHPred web server\nusing the following templates (see Table 1 and Fig. 1b). We\nperformed MD simulation run of 100 ns for the assessment of\nconformational changes of LasR (see Fig. Ic)." }, { - "id": 119272, - "strid": "625f76de-44c1-4c77-8362-e3472bf6de3c", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 715, + "strid": "6e0d9a00-6134-40c1-80c0-babde3bb1ee0", + "image_id": 29, + "image_name": "11275.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 146.875, - 2483.34, - 311.791, - 34.98100000000022 + 77.491, + 3678.668, + 1017.6280000000002, + 424.36299999999983 ], "priority": 12, "parents": [ - 119308 + 712 ], - "children": [], - "area": 364740.5625, + "children": [ + 716 + ], + "area": 285063.66198800004, "iscrowd": 0, - "segmentation": [], - "text": "SNP-based results" + "segmentation": [] }, { - "id": 119296, - "strid": "4c60e529-d5a9-4380-9a92-c71fe288c84a", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 716, + "strid": "8b277c27-f92b-4140-8cea-0a81dba086a2", + "image_id": 29, + "image_name": "11275.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 210.095, - 2543.208, - 534.088, - 363.5540000000001 + 101.817, + 3645.19, + 927.0129999999999, + 29.666000000000167 ], "priority": 13, "parents": [ - 119308 + 715 ], "children": [], - "area": 534315.2847600001, + "area": 371142.31023, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Table 1 List of similar structures to LasR obtained from BLAST search." }, { - "id": 119295, - "strid": "f7b6dd81-ebd8-443e-abfa-d80e1531c478", - "image_id": 205141, - "image_name": "14344.png", + "id": 717, + "strid": "333c54dd-beda-498e-a75c-607d71a92d8f", + "image_id": 29, + "image_name": "11275.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 764.412, - 2541.33, - 399.74599999999987, - 350.3000000000002 + 72.92, + 4108.689, + 1018.7330000000001, + 532.8620000000001 ], "priority": 14, "parents": [ - 119308 + 712 ], - "children": [], - "area": 1942623.14796, + "children": [ + 718 + ], + "area": 299605.60188000003, "iscrowd": 0, "segmentation": [] }, { - "id": 119293, - "strid": "7d6cc13a-f57c-4a8f-801c-2e55beca0219", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 2, - "category_name": "Figure", + "id": 718, + "strid": "e70cd08e-e2fc-4e62-9f27-9117bf8a17b7", + "image_id": 29, + "image_name": "11275.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 207.903, - 2921.863, - 1034.398, - 275.08899999999994 + 125.264, + 4660.026, + 950.314, + 108.21900000000005 ], "priority": 15, "parents": [ - 119308 + 717 ], "children": [], - "area": 607464.083289, + "area": 583733.496864, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 1 3D LasR structures: a) Crystal structure of the LBD of LasR (PDB\nid: 3I1X3) b) Reconstructed structure with DBD c) Representative\nstructure after 100ns MD run." }, { - "id": 119298, - "strid": "c33b60c4-61e0-4f68-81d2-a67213c777ce", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 719, + "strid": "493a5d2a-cc53-4409-9ae2-2f5330d57937", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 145.592, - 3238.319, - 591.382, - 700.3359999999998 + 1237.572, + 662.819, + 803.519, + 99.04899999999998 ], "priority": 16, "parents": [ - 119308 + 712 ], "children": [], - "area": 471473.33984800003, + "area": 820286.2354679998, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Part 2: Docking analysis of 3-O-C12-HSL\nwith LasR monomer" }, { - "id": 119294, - "strid": "fd59dbf3-318f-4cd0-aaef-1233e9a8e1d1", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 2, - "category_name": "Figure", + "id": 720, + "strid": "a53726dd-1f56-4da6-b05c-582a948c78a5", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 749.812, - 3246.136, - 553.6350000000001, - 450.25599999999986 + 1229.383, + 784.055, + 1158.0849999999998, + 280.63199999999995 ], "priority": 17, "parents": [ - 119308 + 712 ], "children": [], - "area": 2433991.726432, + "area": 963903.888065, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Molecular docking approach was used to inspect the possible binding\nmodes of 3-O-C12-HSL in LasR. PCA and cluster analysis were\nperformed on docking data. The results show three binding sites (see\nFig. 2). An optimal number of clusters were chosen for docking results,\nsimultaneously accounting for a low Davies-Bouldin Index, high\nDunn, high Silhoeutte and high pSF values (see Fig. 2)." }, { - "id": 119297, - "strid": "84da7a1e-b273-4e91-98d0-8ae8895e8b2f", - "image_id": 205141, - "image_name": "14344.png", + "id": 721, + "strid": "18a6ba65-ab4f-4cec-b0a0-4b4f7d7d4163", + "image_id": 29, + "image_name": "11275.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 754.13, - 3722.764, - 507.91600000000005, - 219.44700000000012 + 1253.226, + 1083.078, + 1120.8979999999997, + 886.0230000000001 ], "priority": 18, "parents": [ - 119308 + 712 ], - "children": [], - "area": 2807448.0153200002, + "children": [ + 722 + ], + "area": 1357341.5096280002, "iscrowd": 0, "segmentation": [] }, { - "id": 119258, - "strid": "ec387884-3faa-4d54-a6d1-7c5eb41a5717", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 4, - "category_name": "List", + "id": 722, + "strid": "74071f69-d619-4ae8-ae2f-3f6ceda53777", + "image_id": 29, + "image_name": "11275.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 109.748, - 4014.5, - 1272.689, - 618.7430000000004 + 1260.747, + 1998.054, + 1051.6960000000001, + 76.4409999999998 ], "priority": 19, "parents": [ - 119308 + 721 ], "children": [], - "area": 440583.346, + "area": 2519040.5863380004, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 2 Silhouette plot and clustering results on the docking data using k-means\nalgorithm formed by first two PCs." }, { - "id": 119268, - "strid": "0b07140b-9dfd-43a3-b442-338bc6dc6d9e", - "image_id": 205141, - "image_name": "14344.png", + "id": 723, + "strid": "65a23e9a-1b75-4812-9afb-2997c7232fb0", + "image_id": 29, + "image_name": "11275.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1477.284, - 1666.043, - 327.47399999999993, - 36.39599999999996 + 1228.576, + 2122.754, + 1158.48, + 735.9049999999997 ], "priority": 20, "parents": [ - 119308 + 712 ], "children": [], - "area": 2461218.667212, + "area": 2607964.618304, "iscrowd": 0, "segmentation": [], - "text": "Gene-based results" + "text": "We generated 2000 docked poses and performed representative\nstructure extraction for use in MD simulations of the LasR 3-O-C12-\nHSL binding sites. The results show three binding sites, cluster 2\ncorresponds to experimental data, while cluster | and cluster 3 do not\n(see Fig 3).\n\nRepresentative structures from each cluster were extracted. These\ncluster representative structures were produced by finding the centroid\nconformations. The binding energy for the centroid conformation of\ncluster 1 is -5.4 kcal/mol. Cluster 1 contains 839 docked poses from\n2000 (41.95%). For cluster 2 the binding affinity is -5.1 kcal/mol and\nthis one corresponds to the experimental binding site data. Cluster 2\ncontains 864 docked poses from 2000 (43.2%). For cluster 3, the\nrepresentative structure features the highest binding affinity -5.7\nkcal/mol. Cluster 3 contains 297 docked poses from 2000 (14.85%),\nwhich is arather unstudied area." }, { - "id": 119276, - "strid": "175edf2a-4eda-43bc-8ecf-8a98834a6f52", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 724, + "strid": "bc216c6d-6cdc-412d-99c2-8d5c7466b69d", + "image_id": 29, + "image_name": "11275.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1917.605, - 1724.569, - 92.80899999999997, - 27.615999999999985 + 1284.194, + 2956.405, + 1015.5210000000002, + 1541.2809999999995 ], "priority": 21, "parents": [ - 119308 + 712 ], - "children": [], - "area": 3307042.137245, + "children": [ + 725 + ], + "area": 3796597.56257, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 119277, - "strid": "2f8577ad-3ed3-474a-8980-b1e21e7c90f4", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 725, + "strid": "1d54009c-050a-469b-89f8-f17f1fbc2557", + "image_id": 29, + "image_name": "11275.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1473.481, - 1755.807, - 240.39699999999993, - 24.44699999999989 + 1260.54, + 4588.576, + 1112.6, + 108.06700000000001 ], "priority": 22, "parents": [ - 119308 + 724 ], "children": [], - "area": 2587148.254167, + "area": 5784083.59104, "iscrowd": 0, "segmentation": [], - "text": "Cases & Controls Label" + "text": "Fig. 3 3D visualization of the analyzed docking data with their representative\n\nstructures and clusters. Mean bin\nkcal/mol, cluster 2 - AG = -5.5934\n\nding affinities: cluster 1 - AG = -5.257 4\n\n+0.233\n\n \n\n \n\n+0.386 kcal/mol, cluster 3 - AG = -5.267 4\n\n+0).233" }, { - "id": 119279, - "strid": "6a1e4fa6-19d3-4d59-9f36-47ab8566390f", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 726, + "strid": "f3beae32-fc42-414d-a910-919d23afcef4", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1468.612, - 1814.149, - 300.79600000000005, - 242.18499999999995 + 2552.252, + 663.943, + 491.9250000000002, + 97.73000000000002 ], "priority": 23, "parents": [ - 119308 + 712 ], "children": [], - "area": 2664280.991188, + "area": 1694549.8496359999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Part 3: Binding Modes of\n3-O-C12-HSL" }, { - "id": 119280, - "strid": "b6792d94-e581-46e0-bf32-c2ff1ba20044", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 727, + "strid": "0aa938c5-b3ff-4a39-bf3b-3f482638feb7", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1778.962, - 1814.32, - 300.10199999999986, - 241.8900000000001 + 2514.366, + 774.99, + 1039.3109999999997, + 417.87300000000005 ], "priority": 24, "parents": [ - 119308 + 712 ], "children": [], - "area": 3227606.33584, + "area": 1948608.50634, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "We performed three 300 ns simulations using standard MD\nprotocol. The representative structures were taken from\ndocking results (see Fig. 3) and used as starting points for MD\nsimulation with LasR. The overall stability was assessed using\nthe RMSD of the backbone atoms (see Fig. 4). In simulation 1,\nwhich corresponds to cluster 1, the molecule of 3-O-C12-HSL\ndid not fixate and reach equilibrium, so further research was\nnot performed. Simulation 2 and 3 correspond to clusters 2 and\n3 of docking data." }, { - "id": 119281, - "strid": "ba9c89dc-4282-4048-91fc-9485c9143b73", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 728, + "strid": "cbd261e9-725c-490a-abc1-b4fd1425f715", + "image_id": 29, + "image_name": "11275.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2087.857, - 1813.756, - 301.02999999999975, - 278.26300000000015 + 2558.847, + 1199.953, + 911.5929999999998, + 723.9670000000001 ], "priority": 25, "parents": [ - 119308 + 712 ], - "children": [], - "area": 3786863.160892, + "children": [ + 729 + ], + "area": 3070496.1341910004, "iscrowd": 0, "segmentation": [] }, { - "id": 119278, - "strid": "f10b051c-f6ab-47cc-902d-1a1f4ff5771d", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 729, + "strid": "fba06d8d-d948-4c2b-89b9-8fff6a9cb3c0", + "image_id": 29, + "image_name": "11275.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1472.165, - 2072.513, - 135.65599999999995, - 22.45699999999988 + 2553.146, + 1941.863, + 911.2139999999999, + 114.22199999999998 ], "priority": 26, "parents": [ - 119308 + 728 ], "children": [], - "area": 3051081.1006449996, + "area": 4957859.750998001, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Fig. 4 RMSD evolution during 300 ns of simulation for 3 independent\nruns using representative structures of 3-O-C12-HSL docking poses\nas starting points." }, { - "id": 119282, - "strid": "6668bd2b-0f75-42d3-ab46-052955c1196c", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 730, + "strid": "be0aa716-a81c-490d-9387-0c6e383de481", + "image_id": 29, + "image_name": "11275.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1466.288, - 2111.473, - 303.05899999999997, - 241.03099999999995 + 2516.068, + 2071.931, + 1034.87, + 464.1700000000001 ], "priority": 27, "parents": [ - 119308 + 712 ], "children": [], - "area": 3096027.522224, + "area": 5213119.287308001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Over the course of simulation 3, 3-O-C12-HSL establishes\nhydrogen bonds and a large number of hydrophobic contacts\nwith amino acid side chains in the beta turns of the short linker\nregion (SLR) of LasR. SLR connects LBD and DBD together.\n3-O-C12-HSL forms 2 hydrogen bonds: O21 of C20 with\nLys182 and O11 of C10 with Leu1l77 of the beta turns in the\nSLR of LasR. During the 300 ns trajectory, it was observed that\nthe interaction between 3-O-C12-HSL and the Leu177 residue\nin LasR persisted for more than 93.64% of this simulation\n(from the period of 0-300ns)." }, { - "id": 119299, - "strid": "59be3dcd-f9ed-420c-b539-9fcda0267048", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 731, + "strid": "bfc4ec88-c7f5-4b2e-9419-987f9dea877b", + "image_id": 29, + "image_name": "11275.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1583.773, - 2357.852, - 66.93000000000006, - 19.40599999999995 + 2575.845, + 2556.635, + 794.4740000000002, + 1100.0119999999997 ], "priority": 28, "parents": [ - 119308 + 712 ], - "children": [], - "area": 3734302.3355959994, + "children": [ + 732 + ], + "area": 6585495.481575, "iscrowd": 0, - "segmentation": [], - "text": "Burden" + "segmentation": [] }, { - "id": 119283, - "strid": "16ceb2a7-2f86-42f9-b5d3-c54dda90eda6", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 732, + "strid": "ed15f5c7-5476-439b-bdf1-e00e73f10977", + "image_id": 29, + "image_name": "11275.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1778.32, - 2111.272, - 301.3259999999998, - 241.087 + 2551.392, + 3667.573, + 750.5430000000001, + 37.42900000000009 ], "priority": 29, "parents": [ - 119308 + 731 ], "children": [], - "area": 3754517.2230399996, + "area": 9357416.411616, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 5 Interaction of 3-O-C12-HSL with the SLR of LasR." }, { - "id": 119300, - "strid": "47ed2e5e-6476-49f0-844d-f7e43826a0b6", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 733, + "strid": "7ecfa810-5310-443c-9954-afa34d9c55ef", + "image_id": 29, + "image_name": "11275.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1902.919, - 2356.815, - 53.121000000000095, - 20.04599999999982 + 2586.746, + 3738.72, + 285.192, + 66.40099999999984 ], "priority": 30, "parents": [ - 119308 + 703 ], - "children": [], - "area": 4484828.042985001, + "children": [ + 734 + ], + "area": 9671119.00512, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 119284, - "strid": "75a4f9ad-6d73-4d79-9740-0c155edb2202", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 734, + "strid": "73776203-cbbc-49d4-b7d5-7dc5f1756afe", + "image_id": 29, + "image_name": "11275.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2091.847, - 2110.918, - 299.94399999999996, - 241.39699999999993 + 2552.281, + 3821.622, + 996.3559999999998, + 507.5989999999997 ], "priority": 31, "parents": [ - 119308 + 733 ], "children": [], - "area": 4415717.485546, + "area": 9753853.219781999, "iscrowd": 0, "segmentation": [] }, { - "id": 119301, - "strid": "945f3d6b-0c9e-470b-aff3-ace2c402852e", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 735, + "strid": "17be7ce3-d0a6-464e-bc6a-0630d95fe7e4", + "image_id": 29, + "image_name": "11275.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2208.05, - 2357.497, - 66.13700000000017, - 19.43199999999979 + 2552.145, + 4348.968, + 418.99900000000025, + 54.3149999999996 ], "priority": 32, "parents": [ - 119308 + 703 ], - "children": [], - "area": 5205471.25085, + "children": [ + 736 + ], + "area": 11099196.93636, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Acknowledgements" }, { - "id": 119291, - "strid": "d90aab97-7441-4105-a979-bdfbd42f345d", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 736, + "strid": "714cb20d-7cb2-43d9-9182-c39a48484b05", + "image_id": 29, + "image_name": "11275.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1573.561, - 2412.496, - 711.633, - 24.02500000000009 + 2521.892, + 4417.602, + 1025.6819999999998, + 150.0020000000004 ], "priority": 33, "parents": [ - 119308 + 735 ], "children": [], - "area": 3796209.618256, + "area": 11140715.142984, "iscrowd": 0, - "segmentation": [], - "text": "0.05/36.000 =1.37*10*-6 conservative threshold for genome-wide significance" + "segmentation": [] }, { - "id": 119274, - "strid": "3300e055-8415-42d4-b9d9-7feb35d86b34", - "image_id": 205141, - "image_name": "14344.png", + "id": 737, + "strid": "99a0ee78-0be3-4615-9b04-6e6e6ab5ec1d", + "image_id": 29, + "image_name": "11275.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2881.765, - 1724.461, - 99.38200000000006, - 31.057000000000016 + 2587.6, + 4607.473, + 963.259, + 150.5590000000002 ], "priority": 34, "parents": [ - 119308 + 703 ], "children": [], - "area": 4969491.353665, + "area": 11922297.1348, "iscrowd": 0, "segmentation": [], - "text": "ADNI-2" + "text": "Further reading:\n\nGrabski, H., Hunanyan, L., Tiratsuyan, S., Vardapetyan, H. 2017. Interaction of N-3-\noxododecanoyl homoserine lactone with transcriptional regulator LasR of\nPseudomonas aeruginosa: Insights from molecular docking and dynamics simulations.\nbioRxiv doi:10.1101/121681" }, { - "id": 119275, - "strid": "0d97779a-a2e1-4960-b0cb-cfd02534a5a6", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 738, + "strid": "b7a2b205-aa1e-4668-85d7-46ccc0dae7f6", + "image_id": 30, + "image_name": "11282.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 2453.179, - 1765.278, - 252.0050000000001, - 27.508000000000038 + 34.04, + 39.29, + 312.76, + 121.63 ], - "priority": 35, - "parents": [ - 119308 + "priority": -1, + "parents": [], + "children": [ + 759, + 743, + 764, + 757, + 741, + 740, + 739, + 745, + 748 ], - "children": [], - "area": 4330542.918762, + "area": 1337.4316, "iscrowd": 0, - "segmentation": [], - "text": "Cases & Controls Label" + "segmentation": [] }, { - "id": 119285, - "strid": "2c5ceb73-3d70-420f-8dd9-b9303c6a84ac", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 739, + "strid": "ee706947-545f-485b-aab6-c491993f4b6d", + "image_id": 30, + "image_name": "11282.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 2454.731, - 1807.699, - 311.47699999999986, - 250.66100000000006 + 624.427, + 125.346, + 3558.3489999999997, + 283.786 ], - "priority": 36, + "priority": 1, "parents": [ - 119308 + 738 ], "children": [], - "area": 4437414.773969, + "area": 78269.42674200001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Impact of temperature shifts on the independent and\njoint evolution of seed dormancy and seed size" }, { - "id": 119286, - "strid": "7d58c0aa-948f-4722-836a-7c2f41c84e82", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 740, + "strid": "7c6d2dab-64c4-4d95-a180-404cd3481ded", + "image_id": 30, + "image_name": "11282.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 2780.819, - 1807.637, - 310.4200000000001, - 249.36199999999985 + 213.93, + 447.905, + 3994.707, + 168.57299999999998 ], - "priority": 37, + "priority": 2, "parents": [ - 119308 + 738 ], "children": [], - "area": 5026711.314703, + "area": 95820.31665, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "HY Yang LIU? (yliu2011@interchange.ubc.ca), Sebastien BAROT?, Yousry EL-KASSABY’, Nicolas LOEUILLE? taat so\n\n1Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, BC, Canada ? Sorbonne Universités, Institute of Ecology and Environmental Sciences (UMR 7618, UPMC, CNRS, INRA, IRD), Paris, France" }, { - "id": 119287, - "strid": "75a336f7-6cd7-4e76-887e-69246e4e0c96", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 741, + "strid": "15424537-7965-4474-b5ad-c25b2e85b35a", + "image_id": 30, + "image_name": "11282.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 3104.473, - 1807.912, - 310.3649999999998, - 250.2700000000002 + 650.757, + 678.14, + 353.342, + 57.68100000000004 ], - "priority": 38, + "priority": 3, "parents": [ - 119308 + 738 ], - "children": [], - "area": 5612613.990376, + "children": [ + 742 + ], + "area": 441304.35198, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Background" }, { - "id": 119302, - "strid": "79d04b6d-9268-43e8-9109-177607f9ed9c", - "image_id": 205141, - "image_name": "14344.png", + "id": 742, + "strid": "656d6e4d-927f-4068-9097-cfac14d89751", + "image_id": 30, + "image_name": "11282.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2463.816, - 2075.923, - 142.42599999999993, - 23.965999999999894 + 113.118, + 793.923, + 1451.14, + 330.124 ], - "priority": 39, + "priority": 4, "parents": [ - 119308 + 741 ], "children": [], - "area": 5114692.302167999, + "area": 89806.98191399999, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Seed dormancy is an adaptation for survival during bad seasons and exerts\ncascading selective pressures on subsequent life stages. Seed size links the ecology\nof reproduction and seedling establishment with that of vegetative growth.\n\nThe two traits exhibit co-varying phenotypes and evolve under similar agents of\n\nselection. (— independent vs. joint evolution)" }, { - "id": 119290, - "strid": "4d41576b-efa7-4cbc-a5aa-77f279a47707", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 743, + "strid": "f6fc898a-b8b2-4b0e-bcfd-a46746bba215", + "image_id": 30, + "image_name": "11282.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2460.57, - 2111.178, - 310.73, - 251.0050000000001 + 542.237, + 1178.668, + 569.909, + 57.250999999999976 ], - "priority": 40, + "priority": 5, + "parents": [ + 738 + ], + "children": [ + 744 + ], + "area": 639117.4003159999, + "iscrowd": 0, + "segmentation": [], + "text": "Research Questions" + }, + { + "id": 744, + "strid": "5edf512e-573c-45f2-96b9-b5795214d2f6", + "image_id": 30, + "image_name": "11282.png", + "category_id": 4, + "category_name": "List", + "bbox": [ + 122.306, + 1299.861, + 1437.816, + 257.4660000000001 + ], + "priority": 6, "parents": [ - 119308 + 743 ], "children": [], - "area": 5194701.25146, + "area": 158980.799466, "iscrowd": 0, "segmentation": [] }, { - "id": 119303, - "strid": "c5e17301-ce57-4b60-8edf-bd659e363b87", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 745, + "strid": "787cdcac-5d95-44d5-b5dc-0f5907bc3648", + "image_id": 30, + "image_name": "11282.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2557.723, - 2375.021, - 69.56500000000005, - 18.815000000000055 + 471.158, + 1613.328, + 708.7670000000002, + 58.33200000000011 ], - "priority": 41, + "priority": 7, "parents": [ - 119308 + 738 ], - "children": [], - "area": 6074645.8371830005, + "children": [ + 747, + 746 + ], + "area": 760132.393824, "iscrowd": 0, "segmentation": [], - "text": "Burden" + "text": "The Model (eco-evo dynamics)" }, { - "id": 119289, - "strid": "9ec3fa1e-403d-4e7f-b09c-0642be666adb", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 746, + "strid": "e79f36f7-ca73-458a-aa6f-849696f8dedf", + "image_id": 30, + "image_name": "11282.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2779.638, - 2111.598, - 311.08600000000024, - 250.86299999999983 + 131.695, + 1713.545, + 1407.945, + 542.7269999999999 ], - "priority": 42, + "priority": 8, "parents": [ - 119308 + 745 ], "children": [], - "area": 5869478.041524, + "area": 225665.308775, "iscrowd": 0, "segmentation": [] }, { - "id": 119304, - "strid": "11a7f8d8-8924-431a-a63a-753de5137ffa", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 747, + "strid": "72fa1b7f-226f-473e-af8b-e59907e18e8c", + "image_id": 30, + "image_name": "11282.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2889.89, - 2374.137, - 54.81700000000001, - 19.746000000000095 + 119.82, + 2328.012, + 1367.083, + 117.70299999999997 ], - "priority": 43, + "priority": 9, "parents": [ - 119308 + 745 ], "children": [], - "area": 6860994.77493, + "area": 278942.39784, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 748, + "strid": "64558044-785d-4351-9a3a-63ea220829d6", + "image_id": 30, + "image_name": "11282.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 719.461, + 2501.95, + 214.14599999999996, + 47.22400000000016 + ], + "priority": 10, + "parents": [ + 738 + ], + "children": [ + 749, + 751, + 756, + 752, + 755, + 754, + 753, + 750 + ], + "area": 1800055.4489499999, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Results" }, { - "id": 119288, - "strid": "018ed83d-e23e-4ec0-b399-c1e14fcc6949", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 7, - "category_name": "Table", + "id": 749, + "strid": "8d0550ca-b32f-4a08-a862-e188319aa77a", + "image_id": 30, + "image_name": "11282.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 3097.525, - 2110.905, - 310.3960000000002, - 250.76499999999987 + 107.07, + 2609.804, + 1458.426, + 689.2660000000001 ], - "priority": 44, + "priority": 11, "parents": [ - 119308 + 748 ], "children": [], - "area": 6538581.010125001, + "area": 279431.71428, "iscrowd": 0, "segmentation": [] }, { - "id": 119305, - "strid": "a1d771ff-da3d-43c9-8801-959da58f829d", - "image_id": 205141, - "image_name": "14344.png", + "id": 750, + "strid": "ced0edbc-841e-4378-a959-2c9a4fda4bf5", + "image_id": 30, + "image_name": "11282.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3207.295, - 2374.387, - 68.95400000000018, - 18.722999999999956 + 104.709, + 3359.305, + 1452.344, + 144.98700000000008 ], - "priority": 45, + "priority": 12, "parents": [ - 119308 + 748 ], "children": [], - "area": 7615359.553165001, + "area": 351749.467245, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Ecological equilibria (curves in black and green for seeds and adults,\nrespectively)\nEvolutionary directions (red arrows) & equilibria (red dots)" }, { - "id": 119292, - "strid": "fe942c8d-1dc9-481a-a4b4-fb3b812d2c43", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 751, + "strid": "ec70113f-ed64-4200-bccd-3b88f702ef52", + "image_id": 30, + "image_name": "11282.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2548.282, - 2420.842, - 739.5430000000001, - 25.92599999999993 + 1616.101, + 671.212, + 1565.2580000000003, + 770.8299999999999 ], - "priority": 46, + "priority": 13, "parents": [ - 119308 + 748 ], "children": [], - "area": 6168988.093444001, + "area": 1084746.384412, "iscrowd": 0, - "segmentation": [], - "text": "0.05/29.484 =1.70*104-6 conservative threshold for genome-wide significance" + "segmentation": [] }, { - "id": 119269, - "strid": "0c9cd0a4-b6b2-462c-939d-061b588b4a92", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 752, + "strid": "f3feadd7-60e9-4172-a0a0-12854a620133", + "image_id": 30, + "image_name": "11282.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1630.552, - 2579.947, - 475.8059999999998, - 41.61299999999983 + 1687.266, + 1514.323, + 1458.0819999999999, + 143.13300000000004 ], - "priority": 47, + "priority": 14, "parents": [ - 119308 + 748 ], "children": [], - "area": 4206737.740744, + "area": 2555065.7109180004, "iscrowd": 0, - "segmentation": [], - "text": "Pathways-analysis workflow" + "segmentation": [] }, { - "id": 119262, - "strid": "cfb9fa41-05ab-45f0-8f2f-30c348e41919", - "image_id": 205141, - "image_name": "14344.png", + "id": 753, + "strid": "59245f04-a971-4bf8-96dd-b3d6945363f0", + "image_id": 30, + "image_name": "11282.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1493.973, - 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"priority": 51, + "priority": 18, "parents": [ - 119308 + 748 ], "children": [], - "area": 5237165.147112, + "area": 4840541.227200001, "iscrowd": 0, - "segmentation": [], - "text": "SNP signatures: in silico functional and literature characterization" + "segmentation": [] }, { - "id": 119306, - "strid": "e816858c-4875-4c4e-9707-b54856168176", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 3, - "category_name": "Text", + "id": 757, + "strid": "5aab2936-2a2d-48cb-b55c-e80d26299a3f", + "image_id": 30, + "image_name": "11282.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1833.608, - 3680.319, - 160.91599999999994, - 36.3090000000002 + 3815.74, + 676.464, + 324.7629999999999, + 49.668000000000006 ], - "priority": 52, + "priority": 19, "parents": [ - 119308 + 738 ], - "children": [], - "area": 6748262.360952, + "children": [ + 758 + ], + "area": 2581210.74336, "iscrowd": 0, "segmentation": [], - "text": "Functional" + "text": "Conclusion" }, { - "id": 119264, - "strid": "a28a735a-1da9-4e5a-a572-9626ac9fc7c7", - "image_id": 205141, - "image_name": "14344.png", - "category_id": 2, - "category_name": "Figure", + "id": 758, + "strid": "3b6aa4eb-6449-437b-82ec-15a710f799ad", + "image_id": 30, + "image_name": "11282.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1516.193, - 3815.206, - 923.28, - 725.7560000000003 + 3267.33, + 784.862, + 1384.3490000000002, + 187.202 ], - "priority": 53, + "priority": 20, "parents": [ - 119308 + 757 ], "children": [], - "area": 5784588.630758001, + "area": 2564403.15846, "iscrowd": 0, "segmentation": [] }, { - "id": 119307, - "strid": "95da1060-6735-4a99-995d-85e3a9538856", - "image_id": 205141, - "image_name": "14344.png", + "id": 759, + "strid": "eaa17cc0-411f-4169-b989-846a69607bf6", + "image_id": 30, + "image_name": "11282.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 3810.52, + 1023.618, + 333.74000000000024, + 57.73899999999992 + ], + "priority": 21, + "parents": [ + 738 + ], + "children": [ + 761, + 762, + 763, + 760 + ], + "area": 3900516.86136, + "iscrowd": 0, + "segmentation": [], + "text": "Perspective" + }, + { + "id": 760, + "strid": "24d6cf40-7532-4de5-9a26-fbc394647607", + "image_id": 30, + "image_name": "11282.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2867.597, - 3700.124, - 154.31500000000005, - 35.483999999999924 + 3246.248, + 1130.322, + 1450.734, + 635.895 ], - "priority": 54, + "priority": 22, "parents": [ - 119308 + 759 ], "children": [], - "area": 10610464.482028, + "area": 3669305.5318559995, "iscrowd": 0, "segmentation": [], - "text": "Literature" + "text": "> Temporal & Spatial Dispersal <\n\n§ Essential messages from literature (dispersal syndrome):\n\n@ a potent force in maintaining diversity; ®@ conducive to sustaining sink\npopulations (=> ¢ alpha diversity) but homogenizing composition across patches\n(=> | beta diversity); ©@ tradeoff between “competition ability” (local selective\nadvantages) and “colonization ability” (dispersability) => species coexistence.\n\n§ Primary selective forces:\n\n@ parent-offspring conflicts or kin competition; @ temporal heterogeneity of the\n\nenvironment (e.g. local population extinction); ® inbreeding depression." }, { - "id": 119263, - "strid": "ed6204a4-1240-4037-8d4d-01a8ef0bef83", - "image_id": 205141, - "image_name": "14344.png", + "id": 761, + "strid": "6b2f8b33-635b-4b4a-8bd2-9befd0427f6e", + "image_id": 30, + "image_name": "11282.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2532.134, - 3770.579, - 809.9490000000001, - 423.87000000000035 + 3267.58, + 1821.144, + 1025.317, + 1282.564 ], - "priority": 55, + "priority": 23, "parents": [ - 119308 + 759 ], "children": [], - "area": 9547611.285586001, + "area": 5950733.711519999, "iscrowd": 0, "segmentation": [] }, { - "id": 119259, - "strid": "dd149b8c-22a8-4d8e-a66d-0705c8d04041", - "image_id": 205141, - "image_name": "14344.png", + "id": 762, + "strid": "359d34b8-b109-452a-90a1-fc0dce2ec828", + "image_id": 30, + "image_name": "11282.png", "category_id": 4, "category_name": "List", "bbox": [ - 2501.101, - 4326.288, - 912.8560000000002, - 252.71399999999994 + 4188.08, + 1954.651, + 492.83899999999994, + 612.595 ], - "priority": 56, + "priority": 24, "parents": [ - 119308 + 759 ], "children": [], - 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"id": 80730, - "strid": "d1ffbd4e-db31-4c7d-8532-40930a50c127", - "image_id": 203646, - "image_name": "120653.png", + "id": 767, + "strid": "c0d2db7e-9dab-411c-b970-24a57106577e", + "image_id": 31, + "image_name": "11293.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 726.629, - 267.434, - 1839.243, - 129.548 + 853.266, + 447.329, + 3093.962, + 151.935 ], "priority": 2, "parents": [ - 80757 + 765 ], "children": [], - "area": 194325.29998600003, + "area": 381690.626514, "iscrowd": 0, "segmentation": [], - "text": "DeniS‘Yavna, Vitaly Babenko y»\nSouthern Federal University, Rostov-on=Don, Russia" + "text": "a John J. Fraser, PT, MS, OCS?!”, Jay Hertel PhD, ATC, FACSM?! a\n1. Exercise and Sport Injury Laboratory, University of Virginia, 2. US Navy Medicine Professional Development Center" }, { - "id": 80736, - "strid": "e62051f2-9e38-4abb-a0ff-ed3d56ce1ee8", - "image_id": 203646, - "image_name": "120653.png", - "category_id": 3, - "category_name": "Text", + "id": 768, + "strid": "ac5579b8-491c-45f6-84a1-3d01c1d320d4", + "image_id": 31, + "image_name": "11293.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 76.059, - 433.925, - 1236.691, - 488.415 + 311.573, + 603.386, + 575.112, + 89.25400000000002 ], "priority": 3, "parents": [ - 80757 + 765 ], - "children": [], - "area": 33003.901574999996, + "children": [ + 769 + ], + "area": 187998.78617799998, "iscrowd": 0, "segmentation": [], - "text": "The s@cond-order visual filters (SOVFs) are considered assa texture\nsegmentation mechanism. The segmentation becomes possible due to\nthevintegration of a distributed visual information. However, a spatial\nbinding is also necessary for the image formation. We investigated\nwhether the information taken out by the SOFVs is» sufficient for the\nrecognition.\n\nBasing on the psychophysical data, we implemented a software model\nof the SOFV, following the scheme -filtering-rectification-filtering”\n(FRF). This model was used to/demonstrate the role of spatial\nmodulations of the local features in the image recognition." + "text": "Introduction" }, { - "id": 80733, - "strid": "90c147d2-612d-41fb-be9a-c6a422d0b186", - "image_id": 203646, - "image_name": "120653.png", - "category_id": 5, - "category_name": "Section", + "id": 769, + "strid": "2f223ee8-d148-4532-a515-9fba53cc66ec", + "image_id": 31, + "image_name": "11293.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 596.26, - 951.435, - 192.966, - 55.472999999999956 + 30.64, + 727.151, + 1124.861, + 602.9599999999999 ], "priority": 4, "parents": [ - 80757 - ], - "children": [ - 80753, - 80739, - 80751, - 80752, - 80741, - 80743, - 80740 + 768 ], - "area": 567302.6331, + "children": [], + "area": 22279.906639999997, "iscrowd": 0, - "segmentation": [], - "text": "Model" + "segmentation": [] }, { - "id": 80739, - "strid": "d04bcb16-1a2d-4da8-b8b8-d4a363d494db", - "image_id": 203646, - "image_name": "120653.png", - "category_id": 3, - "category_name": "Text", + "id": 770, + "strid": "bf940381-5890-44a4-b61d-759ce34749a9", + "image_id": 31, + "image_name": "11293.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 70.579, - 1034.502, - 1234.986, - 421.423 + 404.252, + 1361.928, + 376.098, + 108.43000000000006 ], "priority": 5, "parents": [ - 80733 + 765 ], - "children": [], - "area": 73014.11665799998, + "children": [ + 771 + ], + "area": 550562.1178560001, "iscrowd": 0, "segmentation": [], - "text": "The first level of the model was a set of bandpass linear filters with a\nGabor kernel. The parameters of the filter were being changed to\nachieve a relatively complete coverage of the spatial frequencies and an\norientation of the(luminance gradients in the image: we used 6 peak\nspatial frequencies (from 0.5 to 16 cycles per picture, increasing by\noctave on each step) and 6 preferred orientations (from 0 to 150-witha\n30 degrees0.05" + "segmentation": [] }, { - "id": 16777, - "strid": "fc87dbe9-089f-4292-ad5c-7b1d6e1ed0e2", - "image_id": 201162, - "image_name": "116691.png", - "category_id": 5, - "category_name": "Section", + "id": 844, + "strid": "6372edf9-4166-45c0-b3bc-c597d78ec13c", + "image_id": 33, + "image_name": "11333.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1837.329, - 784.398, - 275.93299999999977, - 50.86099999999999 + 124.094, + 3031.181, + 1690.593, + 171.17700000000013 ], "priority": 12, "parents": [ - 16762 - ], - "children": [ - 16768, - 16772, - 16767 + 832 ], - "area": 1441197.192942, + "children": [], + "area": 376151.375014, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Purple Node: Reference media. Annotations: 50. Links: 168\nBlue Nodes: Related media\nLinks: Common annotations (the thickness represents the number of shared annotations)" }, { - "id": 16767, - "strid": "a16dc2f9-b432-4ae4-a095-7c67bd8123ce", - "image_id": 201162, - "image_name": "116691.png", - "category_id": 7, - "category_name": "Table", + "id": 845, + "strid": "72f7b167-872d-45b1-b9c7-2d49f4582656", + "image_id": 33, + "image_name": "11333.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1333.141, - 899.37, - 1131.857, - 548.878 + 1783.579, + 1242.103, + 1461.303, + 173.2840000000001 ], "priority": 13, "parents": [ - 16777 + 832 ], "children": [], - "area": 1198987.02117, + "area": 2215388.826637, "iscrowd": 0, "segmentation": [] }, { - "id": 16768, - "strid": "da38759b-a430-47bc-8f50-4b8f69f56b77", - "image_id": 201162, - "image_name": "116691.png", + "id": 846, + "strid": "a3e1dffd-2b61-46ea-b040-de26ff726d9c", + "image_id": 33, + "image_name": "11333.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1327.075, - 1462.008, - 1133.5290000000002, - 599.0330000000001 + 2193.289, + 1444.0, + 976.8579999999997, + 660.6089999999999 ], "priority": 14, "parents": [ - 16777 + 832 ], "children": [], - "area": 1940194.2666000002, + "area": 3167109.316, "iscrowd": 0, "segmentation": [] }, { - "id": 16772, - "strid": "ee5b6856-fd25-4a92-a5ed-7ee5542e36d0", - "image_id": 201162, - "image_name": "116691.png", + "id": 847, + "strid": "9ca49d5e-0cec-4118-8093-57fca4ae96ca", + "image_id": 33, + "image_name": "11333.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1328.73, - 2079.243, - 1138.493, - 651.9859999999999 + 2359.611, + 2129.303, + 642.9189999999999, + 387.93100000000004 ], "priority": 15, "parents": [ - 16777 + 832 ], "children": [], - "area": 2762752.55139, + "area": 5024326.781133, "iscrowd": 0, "segmentation": [] }, { - "id": 16778, - "strid": "d64c959b-e3af-4f78-891c-6c31a1538828", - "image_id": 201162, - "image_name": "116691.png", - "category_id": 5, - "category_name": "Section", + "id": 848, + "strid": "e479001c-4d8d-447d-8cec-52d81c62b73a", + "image_id": 33, + "image_name": "11333.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3068.05, - 908.004, - 320.2339999999999, - 55.039999999999964 + 2129.723, + 2540.45, + 1104.3559999999998, + 160.0949999999998 ], "priority": 16, "parents": [ - 16762 + 832 ], - "children": [ - 16779 - ], - "area": 2785801.6722000004, + "children": [], + "area": 5410454.795349999, "iscrowd": 0, "segmentation": [], - "text": "Discussion" + "text": "Purple Node: Reference media. Annotations: 5. Links: 15\nGreen Node: Selected media. Annotations: 2. Links: 15\nBlue Nodes: Related media. Links: Common annotations" }, { - "id": 16779, - "strid": "accbd6f4-dd5c-4f40-8f61-9e510e51d162", - "image_id": 201162, - "image_name": "116691.png", + "id": 849, + "strid": "54fa858b-6443-4809-acc5-4243e884c56f", + "image_id": 33, + "image_name": "11333.png", "category_id": 4, "category_name": "List", "bbox": [ - 2585.39, - 993.422, - 1278.888, - 419.837 + 1981.776, + 2783.978, + 1248.6810000000003, + 334.1970000000001 ], "priority": 17, "parents": [ - 16778 + 832 ], "children": [], - "area": 2568383.3045799998, + "area": 5517220.7849280005, "iscrowd": 0, "segmentation": [] }, { - "id": 16780, - "strid": "c71e5a55-d0e6-4fef-97bc-432d2835a187", - "image_id": 201162, - "image_name": "116691.png", - "category_id": 5, - "category_name": "Section", + "id": 850, + "strid": "b764c546-52c9-4cea-a0f0-64d1da058648", + "image_id": 33, + "image_name": "11333.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 3039.429, - 1431.576, - 404.69399999999996, - 49.95499999999993 + 2363.969, + 3144.898, + 503.43899999999985, + 501.259 ], "priority": 18, "parents": [ - 16762 - ], - "children": [ - 16781 - ], - "area": 4351173.610104, - "iscrowd": 0, - "segmentation": [], - "text": "" - }, - { - "id": 16781, - "strid": "21e7f4af-3b39-4c27-96de-f429c1f1391c", - "image_id": 201162, - "image_name": "116691.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 2579.354, - 1533.171, - 1322.163, - 522.3170000000002 - ], - "priority": 19, - "parents": [ - 16780 + 832 ], "children": [], - "area": 3954590.751534, + "area": 7434441.380162001, "iscrowd": 0, "segmentation": [] }, { - "id": 16782, - "strid": "0ba76ac4-f443-4986-b538-8887fe5e8354", - "image_id": 201162, - "image_name": "116691.png", - "category_id": 5, - "category_name": "Section", + "id": 851, + "strid": "ca2b58d5-c8b6-4633-97af-1488f616e498", + "image_id": 33, + "image_name": "11333.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3021.892, - 2130.603, - 415.83500000000004, - 51.64800000000014 + 1991.155, + 3669.743, + 1249.0309999999997, + 216.53600000000006 ], - "priority": 20, + "priority": 19, "parents": [ - 16762 - ], - "children": [ - 16783 + 832 ], - "area": 6438452.160875999, + "children": [], + "area": 7307027.123165, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Black Node: Previous reference media. Annotations: 5. Links: 25\nPurple Node: Reference media. Annotations: 119. Links: 60\nGreen Node: Selected media. Annotations: 13. Links: 33\n\nBlue Nodes: Related media. Links: Common annotations" }, { - "id": 16783, - "strid": "e5b833dc-0f89-4e98-aed6-43e8bfdce9d3", - "image_id": 201162, - "image_name": "116691.png", + "id": 852, + "strid": "fc4d5439-caaf-4603-8aa3-9d6ab3d153ed", + "image_id": 33, + "image_name": "11333.png", "category_id": 4, "category_name": "List", "bbox": [ - 2567.03, - 2231.142, - 1357.0170000000003, - 500.7669999999998 + 565.263, + 3274.361, + 1163.851, + 228.63700000000017 ], - "priority": 21, + "priority": 20, "parents": [ - 16782 + 832 ], "children": [], - "area": 5727408.44826, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 111463, - "strid": "d944eacb-aaa0-4769-9244-e498f527d794", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 9, - "category_name": "Root", - "bbox": [ - 250.5, - 231.88, - 293.73, - 229.88 - ], - "priority": -1, - "parents": [], - "children": [ - 111442, - 111445, - 111440, - 111439, - 111441, - 111446, - 111447, - 111444, - 111443 - ], - "area": 58085.94, + "area": 1850875.121943, "iscrowd": 0, "segmentation": [] }, { - "id": 111439, - "strid": "fa3290fc-6f3e-43c4-b7a6-379fb44da9f2", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 1, - "category_name": "Title", + "id": 853, + "strid": "57cdb0dc-a9a2-445b-89f3-1b48d626a898", + "image_id": 33, + "image_name": "11333.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 822.14, - 73.426, - 1749.5100000000002, - 233.26800000000003 + 71.253, + 3351.94, + 1179.049, + 664.7130000000002 ], - "priority": 1, + "priority": 21, "parents": [ - 111463 + 832 ], "children": [], - "area": 60366.45164, + "area": 238835.78082, "iscrowd": 0, - "segmentation": [], - "text": "Ethics & Governance for the\nCanadian Open Neuroscience Platform" + "segmentation": [] }, { - "id": 111440, - "strid": "262e36d6-003e-4867-b42d-2ae6ecce7def", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 0, - "category_name": "Author Info", + "id": 854, + "strid": "4c326d01-f469-4d1c-9cd4-f373565c570c", + "image_id": 33, + "image_name": "11333.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 918.708, - 363.679, - 1560.085, - 164.995 + 1273.944, + 3565.977, + 601.3409999999999, + 271.7399999999998 ], - "priority": 2, + "priority": 22, "parents": [ - 111463 + 832 ], "children": [], - "area": 334114.80673199997, - "iscrowd": 0, - "segmentation": [], - "text": "Stephanie O. M. Dyke?, Bartha M. Knoppers?, Alan C. Evanst\n\n1. Montreal Neurological Institute, Department of Neurology & Neurosurgery, McGill University\n2. Centre of Genomics and Policy, Department of Human Genetics, McGill University" - }, - { - "id": 111441, - "strid": "663346f6-766f-4663-b36c-138069a076f0", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 427.595, - 626.142, - 143.31999999999994, - 47.773000000000025 - ], - "priority": 3, - "parents": [ - 111463 - ], - "children": [ - 111451 - ], - "area": 267735.18849000003, + "area": 4542855.003288, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Black Node: Previous reference\nPurple Node: Reference media\nGreen Node: Selected media\nBlue Nodes: Related media\nLinks: Common annotations" }, { - "id": 111451, - "strid": "608efbab-f8ce-43eb-856c-26244c874a7d", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 855, + "strid": "78321599-5e0c-4f08-b2b7-3d7134f57585", + "image_id": 33, + "image_name": "11333.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 163.61, - 737.681, - 2687.419, - 134.37099999999998 + 165.881, + 4043.766, + 983.2600000000001, + 409.82699999999977 ], - "priority": 4, + "priority": 23, "parents": [ - 111441 + 832 ], "children": [], - "area": 120691.98841000002, + "area": 670783.947846, "iscrowd": 0, "segmentation": [] }, { - "id": 111442, - "strid": "8c8aa26d-621b-49f9-9c11-c68b30b30419", - "image_id": 204827, - "image_name": "13211.png", + "id": 856, + "strid": "e375f092-5f64-403e-a49e-a492d2e78ff3", + "image_id": 33, + "image_name": "11333.png", "category_id": 5, "category_name": "Section", "bbox": [ - 449.251, - 980.589, - 310.03999999999996, - 56.444000000000074 + 1378.905, + 3939.647, + 414.46299999999997, + 57.853999999999814 ], - "priority": 5, + "priority": 24, "parents": [ - 111463 + 832 ], "children": [ - 111452, - 111460, - 111462, - 111450, - 111453, - 111454 + 857 ], - "area": 440530.588839, + "area": 5432398.946535, "iscrowd": 0, "segmentation": [], - "text": "Policy Survey" + "text": "Media Highlighted" }, { - "id": 111452, - "strid": "58eb1009-7590-467e-95b6-472788c57b28", - "image_id": 204827, - "image_name": "13211.png", + "id": 857, + "strid": "ca14aebf-e9f6-44eb-8c8c-990bf808a25b", + "image_id": 33, + "image_name": "11333.png", "category_id": 4, "category_name": "List", "bbox": [ - 165.449, - 1090.821, - 1428.108, - 95.61799999999994 + 1382.281, + 4057.528, + 1857.159, + 474.93100000000004 ], - "priority": 6, + "priority": 25, "parents": [ - 111442 + 856 ], "children": [], - "area": 180475.243629, + "area": 5608643.861368, "iscrowd": 0, "segmentation": [] }, { - "id": 111460, - "strid": "587ac33f-d29a-43d5-88e2-7e0a12242ff6", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 2, - "category_name": "Figure", + "id": 858, + "strid": "b85075fe-8a25-46d0-9af2-7adfb5534de9", + "image_id": 34, + "image_name": "11367.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 133.469, - 1227.44, - 857.277, - 839.1709999999998 + 2140.39, + 91.34, + 475.49000000000024, + 297.17999999999995 ], - "priority": 7, - "parents": [ - 111442 + "priority": -1, + "parents": [], + "children": [ + 860, + 865, + 859, + 863, + 861, + 868, + 872 ], - "children": [], - "area": 163825.18936, + "area": 195503.2226, "iscrowd": 0, "segmentation": [] }, { - "id": 111453, - "strid": "0797b910-9483-4095-96fd-72106f1d0ab0", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 859, + "strid": "314fc1a6-a871-4a03-a533-7ff86611eeea", + "image_id": 34, + "image_name": "11367.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 1004.424, - 1249.671, - 593.76, - 98.70299999999997 + 74.589, + 368.479, + 1975.9360000000001, + 223.65699999999998 ], - "priority": 8, + "priority": 1, "parents": [ - 111442 + 858 ], "children": [], - "area": 1255199.544504, + "area": 27484.480130999997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "A Self-training Approach for Functional\nAnnotation of UniProtKB Proteins" }, { - "id": 111462, - "strid": "3d0fb949-9749-4c95-a323-f0bb0f402cdc", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 2, - "category_name": "Figure", + "id": 860, + "strid": "24ca6711-b87c-41e0-ae79-f73357b5233a", + "image_id": 34, + "image_name": "11367.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1064.193, - 1384.414, - 164.35500000000002, - 322.8689999999999 + 75.489, + 103.651, + 1969.152, + 167.445 ], - "priority": 9, + "priority": 2, "parents": [ - 111442 + 858 ], "children": [], - "area": 1473283.687902, + "area": 7824.510339, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Maryam Abdollahyan '2, Rabie Saidi *, Fabrizio Smeraldi ', Maria J. Martin ¢\n\n1 Queen Mary University of London, London, UK\n2 EMBL-European Bioinformatics Institute, Cambridge, UK" }, { - "id": 111454, - "strid": "65cbe73a-7c22-4efb-86b5-eb600534786d", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 861, + "strid": "6afc582f-1fc2-4722-b40f-6f00500a1d18", + "image_id": 34, + "image_name": "11367.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 985.534, - 1883.725, - 607.64, - 215.29899999999998 + 163.958, + 770.58, + 962.4130000000001, + 74.64700000000005 ], - "priority": 10, + "priority": 3, "parents": [ - 111442 + 858 ], - "children": [], - "area": 1856475.03415, + "children": [ + 862 + ], + "area": 126342.75564, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The UniProt Knowledgebase" }, { - "id": 111450, - "strid": "37ad9583-36c8-4bbd-9f1f-473a309f6f12", - "image_id": 204827, - "image_name": "13211.png", + "id": 862, + "strid": "e1474f3e-8a0b-48e1-b430-bec5efeccfb9", + "image_id": 34, + "image_name": "11367.png", "category_id": 3, "category_name": "Text", "bbox": [ - 200.413, - 2142.705, - 1396.778, - 765.2750000000001 + 162.286, + 885.846, + 1437.66, + 354.491 ], - "priority": 11, + "priority": 4, "parents": [ - 111442 + 861 ], "children": [], - "area": 429425.937165, + "area": 143760.403956, "iscrowd": 0, "segmentation": [], - "text": "> Wishlist:\n\nSimplicity & awareness\n- “An easy way to navigate the data access working with ethics requirements”\n- “Information sessions across Canada to provide information on the platform,\nadvantages, sharing plan, ethical obligations, what are the steps, contact\npersons, etc.”\n\nCultural change\n- “Most places do not want to allow access to data as it’s seen as “giving away”\nproperty - a loss to science and society.”\n\nPolicy engagement\n- “Engagement of institutional REB and clinical health research oversight\norganizations to identify clear pathways for pursuing open science.”\n- “If lam dreaming, legislation allowing broad sharing of data sets that were not\noriginally consented for sharing outside of their research teams without spending\nmonths/years jumping through legal and bureaucratic hurdles.”" + "text": "The UniProt Knowledgebase (UniProtKB) [1] is a large resource of\nprotein sequences and associated functional information,\nconsisting of two sections: UniProtKB/Swiss-Prot contains over\nhalf a million entries that are manually annotated by expert\ncurators, while UniProtKB/TrEMBL hosts over 80 million entries\nthat are annotated by rule-based automatic annotation systems." }, { - "id": 111445, - "strid": "132e9ef7-d480-4e04-8e99-2558018613bb", - "image_id": 204827, - "image_name": "13211.png", + "id": 863, + "strid": "347f2bd6-343a-4d39-98dc-8e8d905bd950", + "image_id": 34, + "image_name": "11367.png", "category_id": 5, "category_name": "Section", "bbox": [ - 572.75, - 3023.2, - 605.6990000000001, - 54.66899999999987 + 1714.063, + 770.083, + 1038.801, + 77.93899999999996 ], - "priority": 12, + "priority": 5, "parents": [ - 111463 + 858 ], "children": [ - 111458 + 864 ], - "area": 1731537.7999999998, + "area": 1319970.777229, "iscrowd": 0, "segmentation": [], - "text": "Moving to Open Science..." + "text": "The Challenge of Data Scarcity" }, { - "id": 111458, - "strid": "ba7bed4c-abac-455d-b445-1acc7df23c74", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 864, + "strid": "4bc8d2cf-e2a7-49bd-a6c9-9d6338edf6ec", + "image_id": 34, + "image_name": "11367.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 153.871, - 3127.053, - 1452.456, - 400.16600000000017 + 1714.827, + 882.564, + 1431.095, + 356.62800000000004 ], - "priority": 13, + "priority": 6, "parents": [ - 111445 + 863 ], "children": [], - "area": 481162.772163, + "area": 1513444.576428, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Rule-based automatic annotation systems use rules that are\nderived from manually annotated UniProtKB/Swiss-Prot entries\nto annotate UniProtKB/TrEMBL entries. However, manual\ncuration is time consuming and labour intensive. As a result,\nmanually annotated data (excluding HAMAP [3] entries) are\nscarce and currently constitute less than 1% of UniProtKB." }, { - "id": 111443, - "strid": "59084699-f0e1-4816-8a0f-06a091b20866", - "image_id": 204827, - "image_name": "13211.png", + "id": 865, + "strid": "740cb4ca-af1a-4721-98d6-8039589d512d", + "image_id": 34, + "image_name": "11367.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2119.464, - 983.085, - 760.7380000000003, - 51.64499999999998 + 163.962, + 1370.654, + 1018.97, + 75.93900000000008 ], - "priority": 14, + "priority": 7, "parents": [ - 111463 + 858 ], "children": [ - 111448, - 111456, - 111455 + 867, + 866 ], - "area": 2083613.26644, + "area": 224735.171148, "iscrowd": 0, "segmentation": [], - "text": "Ethics & Governance Committee" - }, - { - "id": 111455, - "strid": "065d131d-4ce6-4a2a-a4fe-74563b311a0e", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 1770.078, - 1092.469, - 1469.614, - 93.70800000000008 - ], - "priority": 15, - "parents": [ - 111443 - ], - "children": [], - "area": 1933755.342582, - "iscrowd": 0, - "segmentation": [] + "text": "A Self-training Based Solution" }, { - "id": 111448, - "strid": "0192f7eb-e38c-440c-8bed-51a552d1ca45", - "image_id": 204827, - "image_name": "13211.png", + "id": 866, + "strid": "65bbad56-5f6c-4e0a-ab95-a0b5f355df73", + "image_id": 34, + "image_name": "11367.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1769.281, - 1198.69, - 1468.0410000000002, - 166.9380000000001 + 164.042, + 1483.165, + 2983.742, + 170.85799999999995 ], - "priority": 16, + "priority": 8, "parents": [ - 111443 + 865 ], "children": [], - "area": 2120819.44189, + "area": 243301.35293, "iscrowd": 0, "segmentation": [], - "text": "Terms of Reference\n\nThe Ethics and Governance Committee will work to facilitate the sharing of rich imaging, genomic, clinical and phenotypic\ndatasets in a manner that: respects the privacy and expectations of participants; complies with regulatory requirements; and\naligns with international best practices for open science data governance, such as those of the Global Alliance for Genomics\nand Health (GA4GH). In particular, the Committee will:" + "text": "The Association Rule Based Annotator (ARBA) [2] is a system developed for automatic classification and annotation of UniProtKB\nentries. ARBA can be combined with self-training and used to annotate UniProtKB/TrEMBL entries when manually annotated data are\nscarce." }, { - "id": 111456, - "strid": "9639d5fe-f51b-41c3-b4ee-ac4a619b2013", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 867, + "strid": "26c34151-810e-4c30-9dd8-7beb9ae330c8", + "image_id": 34, + "image_name": "11367.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1769.679, - 1368.813, - 1467.714, - 365.3029999999999 + 177.061, + 1678.295, + 2959.006, + 1164.444 ], - "priority": 17, + "priority": 9, "parents": [ - 111443 + 865 ], "children": [], - "area": 2422359.6210270002, + "area": 297160.59099500004, "iscrowd": 0, "segmentation": [] }, { - "id": 111444, - "strid": "f5d6aba9-8cfd-4a5d-b814-c8016bf6ca9e", - "image_id": 204827, - "image_name": "13211.png", + "id": 868, + "strid": "13c605ee-f59d-4586-8b92-dd256b6fbc0a", + "image_id": 34, + "image_name": "11367.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1876.846, - 1844.637, - 658.377, - 49.39599999999996 + 165.213, + 2989.806, + 384.20500000000004, + 61.34400000000005 ], - "priority": 18, + "priority": 10, "parents": [ - 111463 + 858 ], "children": [ - 111457, - 111461 + 871, + 870, + 869 ], - "area": 3462099.574902, + "area": 493954.818678, "iscrowd": 0, "segmentation": [], - "text": "Ethics & Governance Toolkit" + "text": "" }, { - "id": 111457, - "strid": "330ca9cf-89c0-4bc1-acfd-16ed1d39e7a3", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 869, + "strid": "2b13dd30-fe9d-4921-b8ff-893c3627b5cb", + "image_id": 34, + "image_name": "11367.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1772.741, - 1949.942, - 1469.505, - 406.4949999999999 + 285.596, + 3133.279, + 1242.683, + 313.5920000000001 ], - "priority": 19, + "priority": 11, "parents": [ - 111444 + 868 ], "children": [], - "area": 3456742.1310219998, + "area": 894851.949284, "iscrowd": 0, "segmentation": [] }, { - "id": 111461, - "strid": "7b5192be-712d-4312-998a-1613f8e89e03", - "image_id": 204827, - "image_name": "13211.png", + "id": 870, + "strid": "d9c0a374-38a1-4132-998f-bd007288bc4d", + "image_id": 34, + "image_name": "11367.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1988.158, - 2359.796, - 1250.536, - 1167.7909999999997 + 1668.519, + 3045.629, + 1429.8949999999998, + 450.43600000000015 ], - "priority": 20, + "priority": 12, "parents": [ - 111444 + 868 ], "children": [], - "area": 4691647.295767999, + "area": 5081689.853451, "iscrowd": 0, "segmentation": [] }, { - "id": 111446, - "strid": "c389c470-f00c-4ff4-bf88-4f07751e8618", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 1558.144, - 3649.036, - 287.345, - 57.253000000000156 - ], - "priority": 21, - "parents": [ - 111463 - ], - "children": [ - 111459 - ], - "area": 5685723.549184, - "iscrowd": 0, - "segmentation": [], - "text": "In Summary" - }, - { - "id": 111459, - "strid": "0233b0e7-43a6-4929-bf70-0db18367ce1f", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 4, - "category_name": "List", + "id": 871, + "strid": "38d77fd5-e858-4398-88ab-b1e23cf27679", + "image_id": 34, + "image_name": "11367.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1119.82, - 3739.388, - 2106.4800000000005, - 90.01999999999998 + 158.213, + 3562.175, + 2988.729, + 338.53999999999996 ], - "priority": 22, + "priority": 13, "parents": [ - 111446 + 868 ], "children": [], - "area": 4187441.4701599996, + "area": 563582.393275, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The performance of ARBA, with and without self-training, was evaluated in a task of metabolic pathway prediction. The evaluation\nmetrics shown are averaged over two 2-fold cross-validation runs.\n\nBoth the original and the self-trained models were used to predict metabolic pathways in UniProtKB/TrEMBL bacterial data which are\n\npoorly covered at present (only 35%). Using the original model, annotation coverage would increase to 74%. In comparison, with self-\ntraining, annotation coverage would increase to 72.7%." }, { - "id": 111447, - "strid": "71352f76-26f3-471a-9c8b-23e1c65012fa", - "image_id": 204827, - "image_name": "13211.png", + "id": 872, + "strid": "1a1943d1-e537-4ee5-9ada-ff51d83014bb", + "image_id": 34, + "image_name": "11367.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2702.992, - 3905.028, - 287.442, - 40.90299999999979 + 161.859, + 4025.948, + 375.89699999999993, + 75.17899999999963 ], - "priority": 23, + "priority": 14, "parents": [ - 111463 + 858 ], "children": [ - 111449 + 873 ], - "area": 10555259.443776, + "area": 651635.917332, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgment" + "text": "References" }, { - "id": 111449, - "strid": "b357d918-ba1b-4d32-ba8f-31a4973c389e", - "image_id": 204827, - "image_name": "13211.png", - "category_id": 3, - "category_name": "Text", + "id": 873, + "strid": "7d94d386-1022-45bf-a776-e9c026f48a7e", + "image_id": 34, + "image_name": "11367.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1072.244, - 3974.974, - 2206.053, - 35.891000000000076 + 159.637, + 4123.595, + 2978.166, + 209.85999999999967 ], - "priority": 24, + "priority": 15, "parents": [ - 111447 + 872 ], "children": [], - "area": 4262142.021656, + "area": 658278.3350150001, "iscrowd": 0, - "segmentation": [], - "text": "This project has been made possible in part by the Brain Canada Foundation through the Canada Brain Research Fund, with the financial support of Health Canada." + "segmentation": [] }, { - "id": 113476, - "strid": "486460bc-bee5-4c86-8b73-52f9aba4b8b2", - "image_id": 204902, - "image_name": "13474.png", + "id": 874, + "strid": "d8d09d12-8b0f-4cb5-b1aa-d6ecbed4b5d8", + "image_id": 35, + "image_name": "11383.png", "category_id": 9, "category_name": "Root", "bbox": [ - 31.16, - 131.72, - 306.51, - 153.26000000000002 + 132.25, + 36.38, + 242.02999999999997, + 168.55 ], "priority": -1, "parents": [], "children": [ - 113456, - 113449, - 113442, - 113441, - 113443, - 113453, - 113463, - 113472, - 113468, - 113457 + 889, + 914, + 899, + 877, + 893, + 876, + 911, + 920, + 883, + 918, + 901, + 875, + 922 ], - "area": 4104.3952, + "area": 4811.255, "iscrowd": 0, "segmentation": [] }, { - "id": 113441, - "strid": "1dd837d7-f6b0-4ccf-b6dc-c806399f0e38", - "image_id": 204902, - "image_name": "13474.png", + "id": 875, + "strid": "d3991019-8221-4075-90af-01005357d134", + "image_id": 35, + "image_name": "11383.png", "category_id": 1, "category_name": "Title", "bbox": [ - 429.193, - 16.888, - 1883.599, - 241.797 + 913.589, + 29.66, + 2476.111, + 122.99200000000002 ], "priority": 1, "parents": [ - 113476 + 874 ], "children": [], - "area": 7248.211384, + "area": 27097.049740000002, "iscrowd": 0, "segmentation": [], - "text": "Porcine subcutaneous fat tissue transcriptome analysis,\ndifferential gene expression, and target analysis on backfat\nthickness divergent samples" + "text": "Qualitative differences between professional forensic face examiners and untrained people\nin person recognition revealed by item analysis" }, { - "id": 113442, - "strid": "0717c6c0-981a-4afd-a78b-183482b01294", - "image_id": 204902, - "image_name": "13474.png", + "id": 876, + "strid": "5089f3f0-b664-4151-9548-1ad46628555a", + "image_id": 35, + "image_name": "11383.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 728.811, - 263.702, - 1159.078, - 96.18899999999996 + 1250.069, + 160.219, + 2002.4900000000002, + 104.58499999999998 ], "priority": 2, "parents": [ - 113476 + 874 ], "children": [], - "area": 192188.918322, + "area": 200284.805111, "iscrowd": 0, "segmentation": [], - "text": "Paolo Zambonelli', Martina Zappaterra', Roberta Davoli'\n\nCorresponding author: paolo.zambonelli@unibo. it" + "text": "Ying Hu’, Kelsey M. Jackson’, Amy Yates’, David White’, P. Jonathon Phillips? & Alice J. O’Toole?\n1The University of Texas at Dallas, USA; *National Institute of Standards & Technology, USA; ?University of New South Wales, Australia" }, { - "id": 113443, - "strid": "54ef4967-bc0b-4a0f-a53a-bf831d50e088", - "image_id": 204902, - "image_name": "13474.png", + "id": 877, + "strid": "a28d5dad-4ae1-4e1f-b872-72859882f37d", + "image_id": 35, + "image_name": "11383.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1217.079, - 389.012, - 259.394, - 42.44599999999997 + 395.323, + 275.832, + 181.274, + 35.004999999999995 ], "priority": 3, "parents": [ - 113476 + 874 ], "children": [ - 113445, - 113444 + 882, + 878, + 879, + 881, + 880 ], - "area": 473458.33594799996, + "area": 109042.733736, "iscrowd": 0, "segmentation": [], "text": "Introduction" }, { - "id": 113444, - "strid": "14545da0-e137-4009-86ba-1582fb263f92", - "image_id": 204902, - "image_name": "13474.png", - "category_id": 3, - "category_name": "Text", + "id": 878, + "strid": "aa31baf3-2e7d-44a1-8467-e0e01567306b", + "image_id": 35, + "image_name": "11383.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 60.927, - 440.743, - 2555.025, - 141.825 + 105.285, + 303.336, + 762.601, + 68.75900000000001 ], "priority": 4, "parents": [ - 113443 + 877 ], "children": [], - "area": 26853.148761, + "area": 31936.73076, "iscrowd": 0, - "segmentation": [], - "text": "The identification of the molecular mechanisms regulating pathways associated to fat deposition aptitude in pigs is essential to detect key genes _ influencing fat traits and genetic markers for genetic\nimprovement of porcine carcass and meat fat content. Short noncoding RNAs (sRNAs) modulate the expression of messenger RNAs (mRNAs). In particular, microRNAs (miRNAs) interactions with target\n\nmRNAs regulate gene expression and modulate pathways activation. In pigs, miRNA discovery is far from saturation and the knowledge of miRNA expression in backfat tissue is still fragmentary. Moreover, as\ngene expression can change between breeds, developmental stages and farming condition. the identification of the porcine backfat mRNAs transcription profile is still incomplete." + "segmentation": [] }, { - "id": 113445, - "strid": "e9556066-f48c-4dd7-86cf-ba374c6490f9", - "image_id": 204902, - "image_name": "13474.png", + "id": 879, + "strid": "f0fff5d6-5039-4d2e-a665-04b97fdfded6", + "image_id": 35, + "image_name": "11383.png", "category_id": 4, "category_name": "List", "bbox": [ - 61.413, - 586.573, - 2173.387, - 126.01200000000006 + 106.535, + 375.846, + 687.591, + 113.76499999999999 ], "priority": 5, "parents": [ - 113443 + 877 ], "children": [], - "area": 36023.207648999996, + "area": 40040.75361, "iscrowd": 0, "segmentation": [] }, { - "id": 113449, - "strid": "4c45389a-4760-48c6-8381-6bf1a92b0228", - "image_id": 204902, - "image_name": "13474.png", - "category_id": 5, - "category_name": "Section", + "id": 880, + "strid": "5d46fcc2-a9e7-4951-adef-4a699dc7fbd7", + "image_id": 35, + "image_name": "11383.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 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"segmentation": [], - "text": "The bioinformatics analyses to filter the raw reads, to map the genes onto the pig genome and to detect the differentially expressed (DE) genes were carried out\nusing publicly available software and a custom made pipeline developed to this aim." + "segmentation": [] }, { - "id": 113455, - "strid": "394a56d7-4cd2-4880-a956-8afc52cfc8bd", - "image_id": 204902, - "image_name": "13474.png", + "id": 891, + "strid": "8f404aaa-4a23-4dca-bab7-9943f2d3df65", + "image_id": 35, + "image_name": "11383.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 29.662, - 1285.58, - 2586.617, - 337.29099999999994 + 176.325, + 1699.065, + 211.85399999999998, + 170.8499999999999 ], - "priority": 15, + "priority": 17, "parents": [ - 113453 + 889 ], "children": [], - "area": 38132.87396, + "area": 299587.636125, "iscrowd": 0, "segmentation": [] }, { - "id": 113456, - "strid": "c354119f-a7f6-4298-915f-816246b7c72d", - "image_id": 204902, - "image_name": "13474.png", + "id": 892, + "strid": "599d588d-8252-40c1-bb84-3c12c4517687", + "image_id": 35, + "image_name": "11383.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 508.154, + 1704.38, + 212.61300000000006, + 165.53500000000008 + ], + "priority": 18, + "parents": [ + 889 + ], + "children": [], + "area": 866087.5145200001, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 893, + "strid": "d734df19-c8dd-4135-8921-081a6df51134", + "image_id": 35, + "image_name": "11383.png", "category_id": 5, "category_name": "Section", "bbox": [ - 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"segmentation": [], - "text": "325 mature types of sRNAs of which 99 are currently to be considered as novel in\npigs were detected." + "segmentation": [] }, { - "id": 113460, - "strid": "da194dfe-0189-46c1-ad56-e96a73c4de0f", - "image_id": 204902, - "image_name": "13474.png", - "category_id": 7, - "category_name": "Table", + "id": 895, + "strid": "95e0b5c4-700b-4e65-9843-c0328a1c7380", + "image_id": 35, + "image_name": "11383.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 84.168, - 1810.955, - 459.9889999999999, - 198.0229999999999 + 970.718, + 403.263, + 825.996, + 136.53799999999995 ], - "priority": 18, + "priority": 21, "parents": [ - 113456 + 893 ], "children": [], - "area": 152424.46044, + "area": 391454.65283399995, "iscrowd": 0, "segmentation": [] }, { - "id": 113462, - "strid": "e3e8a7c2-f923-4fe3-a2d3-27fd09687b21", - "image_id": 204902, - "image_name": "13474.png", - "category_id": 3, - "category_name": "Text", + "id": 896, + "strid": "1883d8d9-fb24-4975-a770-02744a746b28", + "image_id": 35, + "image_name": "11383.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 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"text": "The transcription profile of the sRNAs\nshows that only 17 miRNAs are\nexpressed at least at 1% of the\ncumulative expression (CE)." + "segmentation": [] }, { - "id": 113461, - "strid": "502f8955-46e9-4a5e-8616-011c4d052f33", - "image_id": 204902, - "image_name": "13474.png", - "category_id": 2, - "category_name": "Figure", + "id": 898, + "strid": "08dc423a-3674-495b-a81b-47465020f844", + "image_id": 35, + "image_name": "11383.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 676.928, - 2004.1, - 567.823, - 146.75599999999986 + 983.762, + 1156.549, + 823.694, + 69.19399999999996 ], - "priority": 21, + "priority": 24, "parents": [ - 113456 + 893 ], "children": [], - "area": 1356631.4048, + "area": 1137768.957338, "iscrowd": 0, "segmentation": [] }, { - "id": 113457, - "strid": "af986165-24e9-4460-9c9f-070ca4786fe3", - "image_id": 204902, - "image_name": "13474.png", + "id": 899, + "strid": "a03a91bf-89a2-4b91-92c6-9b17c53c306c", + "image_id": 35, + "image_name": "11383.png", "category_id": 5, "category_name": "Section", "bbox": [ - 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"text": "The transcription profile of long RNAs is characterized by the expression of 23483" + "text": "PICT: Fusion" }, { - "id": 113474, - "strid": "449b61b4-dc02-426d-99c3-572a9ef4041a", - "image_id": 204902, - "image_name": "13474.png", + "id": 902, + "strid": "a04381d5-8915-4fd0-873d-f9fe63ef0295", + "image_id": 35, + "image_name": "11383.png", "category_id": 4, "category_name": "List", "bbox": [ - 1346.291, - 1758.036, - 752.8619999999999, - 389.41100000000006 + 1911.561, + 316.375, + 1066.3479999999997, + 20.31099999999998 ], - "priority": 24, + "priority": 28, "parents": [ - 113457 + 901 ], "children": [], - "area": 2366828.044476, + "area": 604770.111375, "iscrowd": 0, "segmentation": [] }, { - "id": 113475, - "strid": "35c44cc6-1a7e-41d6-989c-bd62c66fc6c8", - "image_id": 204902, - "image_name": "13474.png", + "id": 903, + "strid": "e3d559fd-1297-437e-9b6a-d47dea19d48b", + "image_id": 35, + "image_name": "11383.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2126.48, - 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908.235, - 3422.993, - 298.8639999999999, - 52.97600000000011 + 3679.074, + 1184.566, + 203.4760000000001, + 32.519000000000005 ], - "priority": 34, + "priority": 44, "parents": [ - 113476 + 874 ], "children": [ - 113467 + 919 ], - "area": 3108882.047355, + "area": 4358105.971884, "iscrowd": 0, "segmentation": [], "text": "Conclusions" }, { - "id": 113467, - "strid": "c34dcdad-4c29-4cb7-9212-71dbe4aae74e", - "image_id": 204902, - "image_name": "13474.png", + "id": 919, + "strid": "bec7a46a-0e5f-474d-9772-dd71eea5c57c", + "image_id": 35, + "image_name": "11383.png", "category_id": 4, "category_name": "List", "bbox": [ - 45.044, - 3490.813, - 2016.8999999999999, - 314.81899999999996 + 3246.106, + 1236.596, + 1013.6650000000004, + 126.3599999999999 ], - "priority": 35, + "priority": 45, "parents": [ - 113468 + 918 ], "children": [], - "area": 157240.180772, + "area": 4014121.6951760002, "iscrowd": 0, "segmentation": [] }, { - "id": 157406, - "strid": "467f0bc6-c9df-4af3-ad38-62dffeb2548f", - "image_id": 206647, - "image_name": "6180.png", + "id": 920, + "strid": "2538efca-53bf-4ba5-ac1f-1ecdfd456d77", + "image_id": 35, + "image_name": "11383.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 3691.153, + 1369.46, + 181.17799999999988, + 31.589999999999918 + ], + "priority": 46, + "parents": [ + 874 + ], + "children": [ + 921 + ], + "area": 5054886.38738, + "iscrowd": 0, + "segmentation": [], + "text": "Discussion" + }, + { + "id": 921, + "strid": "f2699515-89ce-40f0-89da-730cde5c115e", + "image_id": 35, + "image_name": "11383.png", + "category_id": 4, + "category_name": "List", + "bbox": [ + 3250.752, + 1410.134, + 986.721, + 207.19299999999998 + ], + "priority": 47, + "parents": [ + 920 + ], + "children": [], + "area": 4583995.920768, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 922, + "strid": "54cc7b09-c5cd-42bd-a117-64cad73db348", + "image_id": 35, + "image_name": "11383.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 3505.33, + 1642.207, + 524.0209999999997, + 39.02299999999991 + ], + "priority": 48, + "parents": [ + 874 + ], + "children": [ + 923 + ], + "area": 5756477.4633100005, + "iscrowd": 0, + "segmentation": [], + "text": "References & Acknowledgement" + }, + { + "id": 923, + "strid": "f3a6a4b6-4e85-4177-b13a-e7973f10e0c8", + "image_id": 35, + "image_name": "11383.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 3259.114, + 1684.946, + 1072.199, + 212.76700000000005 + ], + "priority": 49, + "parents": [ + 922 + ], + "children": [], + "area": 5491431.097844, + "iscrowd": 0, + "segmentation": [], + "text": "White, D., Phillips, P. J., Hahn, C. A., Hill, M., & O'Toole, A. J. (2015). Perceptual expertise in forensic facial image comparison. Proceedings\nof the Royal Society B: Biological Sciences,,282, 1814-1822.\n\nRice, A., Phillips, P. J., & O'Toole, A. (2013). The role of the face and body in unfamiliar person identification. Applied Cognitive Psychology,\n27(6), 761-768. doi:10.1002/acp.2969\n\nPhillips, P. J., Beveridge, J. R., Draper, B. A., Givens, G., O'Toole, A. J., Bolme, D..,...Weimer, S. (2012). The good, the bad, and the ugly\nface challenge problem. Image and Vision Computing, 30 (3), 177-185. doi:10.1016/j.imavis.2012.01.004\n\nHu, Y., Jackson, K., Yates, A., White, D., Phillips, P. J., & O'Toole, A. J. (2017). Person recognition: Qualitative differences in how forensic\nface examiners and untrained people rely on the face versus the body for identification. Visual Cognition, 1-15.\n\n \n\nAcknowledgement\nFunded by the National Institute of Justice (NIJ) and National Institute of Standards and Technology (NIST)" + }, + { + "id": 924, + "strid": "9b786fbe-a006-40d9-bd76-37e0ddb6f643", + "image_id": 36, + "image_name": "11430.png", "category_id": 9, "category_name": "Root", "bbox": [ - 86.41, - 107.7, - 61.43000000000001, - 104.43999999999998 + 120.07, + 461.77, + 308.42, + 227.97000000000003 ], "priority": -1, "parents": [], "children": [ - 157383, - 157388, - 157384, - 157387, - 157386, - 157391, - 157390, - 157385, - 157389 + 927, + 933, + 947, + 939, + 929, + 926, + 931, + 949, + 925, + 945 ], - "area": 9306.357, + "area": 55444.7239, "iscrowd": 0, "segmentation": [] }, { - "id": 157383, - "strid": "c26d4d53-4e94-49c9-be70-fc60215b5962", - "image_id": 206647, - "image_name": "6180.png", + "id": 925, + "strid": "33c2a24b-c056-4977-a464-e507e5c83563", + "image_id": 36, + "image_name": "11430.png", "category_id": 1, "category_name": "Title", "bbox": [ - 26.971, - 19.699, - 1483.567, - 113.992 + 459.13, + 51.495, + 2221.305, + 273.573 ], "priority": 1, "parents": [ - 157406 + 924 ], "children": [], - "area": 531.301729, + "area": 23642.89935, "iscrowd": 0, "segmentation": [], - "text": "Solving the Problem of Overfitting in Neuroimaging? = *ws%\nCross-Validated Bayesian Model Selection for Methodological Control in fMRI Data Analysis" + "text": "Niosome, a novel drug delivery system, for improving\n\ntherapeutic efficacy of curcumin (review)" }, { - "id": 157384, - "strid": "86f50252-e4bc-4ecb-818e-1f02715ac7f3", - "image_id": 206647, - "image_name": "6180.png", + "id": 926, + "strid": "c9f364d9-c6d2-4462-b52b-6d388cb2669b", + "image_id": 36, + "image_name": "11430.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 283.817, - 143.814, - 999.5230000000001, - 134.06199999999998 + 526.182, + 424.756, + 2093.768, + 199.19899999999996 ], "priority": 2, "parents": [ - 157406 + 924 ], "children": [], - "area": 40816.858038, + "area": 223498.96159199998, "iscrowd": 0, "segmentation": [], - "text": "Joram Soch'®*, Carsten Allefeld':2, John-Dylan Haynes? 2.3:4.5.6\n\n1 Bernstein Center for Computational Neuroscience, Berlin, Germany ? Berlin Center of Advanced Neuroimaging, Berlin, Germany\n3 Berlin School of Mind and Brain, Berlin, Germany ¢ Excellence Cluster NeuroCure, Charité-Universitatsmedizin Berlin, Germany\n5 Department of Neurology, Charité-Universitatsmedizin Berlin, Germany ® Department of Psychology, Humboldt-Universitat zu Berlin, Germany\n© Bernstein Center for Computational Neuroscience, PhilippstraBe 13, Haus 6, 10115 Berlin, Germany / joram.soch @bccn-berlin.de" + "text": "Zaynab Sadeghi Ghadi* !, Pedram Ebrahimnejad !\n\n' Pharmacy school, Mazandaran University of Medical Sciences, Sari, Iran." }, { - "id": 157385, - "strid": "a1a5d65f-86f5-4ee1-8fcf-927c24e0c009", - "image_id": 206647, - "image_name": "6180.png", + "id": 927, + "strid": "a30483f3-e85a-41aa-be8b-905be81e5cad", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 22.343, - 304.468, - 195.327, - 35.059000000000026 + 70.664, + 774.397, + 284.451, + 50.870000000000005 ], "priority": 3, "parents": [ - 157406 + 924 ], "children": [ - 157392 + 928 ], - "area": 6802.728524, + "area": 54721.989608, "iscrowd": 0, "segmentation": [], - "text": "Introduction" + "text": "1. Objective:" }, { - "id": 157392, - "strid": "997bf1e6-5dd7-449a-b37d-2a4e02d235d6", - "image_id": 206647, - "image_name": "6180.png", + "id": 928, + "strid": "de4703fb-eb60-4e30-b646-0754f8b9d5af", + "image_id": 36, + "image_name": "11430.png", "category_id": 3, "category_name": "Text", "bbox": [ - 17.488, - 354.88, - 462.038, - 409.20799999999997 + 66.336, + 860.319, + 874.173, + 140.22000000000003 ], "priority": 4, "parents": [ - 157385 + 927 ], "children": [], - "area": 6206.141439999999, + "area": 57070.121183999996, "iscrowd": 0, "segmentation": [], - "text": "EMU ols SCO Co\nAtari eur en Rome aan RU Ry\nCore M ene Set ae eMac Oem\neee ce Me MC\nperformed for general linear models (GLMs) [1] used to\nPrN mee On eon lee eae eel}\n(NOM CMR ce Mere ie ee eum Ciuc)\nCCR CME NSM eo roo C= SUE\nCeO oe SUR ong mot\nCee Cae an aC Rea mse Mead\nee Rome eR UC Nea rua\neee ROM SC Mu Recent Re Une col cy\nroe M OMReaeS (Mee CM ONTO\neRe Rm ORC eae Ren LS\nCRS CN Ma eam UCR miu aed\nReece MCT TeR (ot\nRca niccCh mute icccelen hace cecal" + "text": "Review trials that studied niosome as a\n\ncarrier to improve delivery of curcumin." }, { - "id": 157386, - "strid": "589a81d9-a2de-46e6-ac24-8695dab01ea7", - "image_id": 206647, - "image_name": "6180.png", + "id": 929, + "strid": "43fd0d73-f597-4cb7-918e-7a44fe380365", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 21.042, - 802.841, - 319.41099999999994, - 40.56000000000006 + 40.736, + 1232.697, + 750.08, + 51.64200000000005 ], "priority": 5, "parents": [ - 157406 + 924 ], "children": [ - 157393 + 930 ], - "area": 16893.380322, + "area": 50215.144991999994, "iscrowd": 0, "segmentation": [], - "text": "First-Level Analysis" + "text": "2. Introduction and Background:" }, { - "id": 157393, - "strid": "2fdb0c8a-b60d-4b29-ad51-23f111409c5c", - "image_id": 206647, - "image_name": "6180.png", + "id": 930, + "strid": "60bd2f7e-9f0a-4172-8260-f75cf2e0ecba", + "image_id": 36, + "image_name": "11430.png", "category_id": 3, "category_name": "Text", "bbox": [ - 19.45, - 856.36, - 464.767, - 602.188 + 39.849, + 1407.209, + 1008.728, + 926.941 ], "priority": 6, "parents": [ - 157386 + 929 ], "children": [], - "area": 16656.202, + "area": 56075.871440999996, "iscrowd": 0, "segmentation": [], - "text": "Be REUE NEM Seen eae ae\nmodel (GLM) [1] in which fMRI data (y) are modelled as a\nECO Som CCRC Cream ca\nCONTRO RUE OR re Sctu ROM mun\neure Rte Ona m OM eae Name e une\nRute ten MMe Man CICInceod cad\n\ny=XBt+e e~N(0,0°V)\n\nUsing normal-gamma priors p(B,tlm) on the unknown\nparameters B and t = 1/0? [3], the Bayesian model evidence\n(ME), also called marginal likelihood [4], is given as:\n\ner ee cd eo\n\nem Re eae Mme eM Mme Ute\nMeme merecca ee ein aces mom ure ued\neS Ree ec CMe me ot\nRe Re Can un mut cme on)\nProce eee eevee mae\n\nEy\noan oe eal PACA DCO te spk\n\nSCRA Reet Re eVect\nRiese rte unica oe" + "text": "Curcumin is a natural hydrophobic compound\nthat is known as a health promoting agent and\nhas outstanding benefits in the prevention and\ntreatment of wide variety of human diseases\n(1). On the other hand its poor water solubility\nand instability caused some troubles including\npoor bioavailability and insufficient clinical\nefficacies (2). To overcome these deficiencies\nmany novel delivery systems were used. One\nof these promising approaches is\n\nencapsulating curcumin in noisome (3)." }, { - "id": 157387, - "strid": "78e2cb43-c147-4698-9e24-ed558286840b", - "image_id": 206647, - "image_name": "6180.png", + "id": 931, + "strid": "435281bd-1f6b-4a89-bf65-b2b32b13a8b9", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 19.858, - 1496.15, - 367.693, - 39.82400000000007 + 65.389, + 2623.676, + 271.495, + 42.759000000000015 ], "priority": 7, "parents": [ - 157406 + 924 ], "children": [ - 157394 + 932 ], - "area": 29710.546700000003, + "area": 171559.54996399998, "iscrowd": 0, "segmentation": [], - "text": "Second-Level Analysis" + "text": "" }, { - "id": 157394, - "strid": "040e46a0-aa1d-4577-a3e9-a04565b499bc", - "image_id": 206647, - "image_name": "6180.png", + "id": 932, + "strid": "d7c5afa7-e1d7-4275-80fe-2bd31c39012d", + "image_id": 36, + "image_name": "11430.png", "category_id": 3, "category_name": "Text", "bbox": [ - 14.195, - 1551.149, - 470.18, - 630.7599999999998 + 65.519, + 2798.398, + 999.81, + 393.5830000000001 ], "priority": 8, "parents": [ - 157387 + 931 ], "children": [], - "area": 22018.560054999998, + "area": 183348.238562, "iscrowd": 0, "segmentation": [], - "text": "Second-level analysis is performed using group-level,\nee ee ece seamen gaa) eR\nCeo ys enmereser oumule CRW Mey\nused for model inference in dynamic causal modelling (DCM).\neee om UeR CRORE eeu Ne eck en ines\nmR Monee enue See noe)\nPeel ont cme much.\n\nN M\n= al al pole)\n\nrion\n\n \n\nN\nOoms erie\nfoe\n\nBU Toes eel oR OM UTA SLere ce)\n\nN N M\np(m|r) = al Mult(m;; 1, r) = atc\nfoe\n\nil\nmre cs Pou aoe Pte me le a\n\nGear eee sta\ni) vit\n\n \n\n \n\nrear ean Mer Rta Te nc)\neee Rca ae ciom suet ub casa Koad\nmodel frequencies [6] to make quantitative statements about\nOe tUe Meet Caine eum aR atic?\nTenn aa ace URC RuCl eee-Unecy\neech keusunosssecehuc enue sacks" + "text": "The following databases were searched:\nMedline and Embase (2010 to December\n2016). Additionally, references lists in review\narticles, guidelines, and in the retrieved trials\n\nwere checked." }, { - "id": 157390, - "strid": "a954cc65-3436-496f-880d-86a09e09fe8a", - "image_id": 206647, - "image_name": "6180.png", + "id": 933, + "strid": "be47d4b7-4810-4b05-a7f0-a59e66336e40", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 508.805, - 303.518, - 350.64899999999994, - 33.653999999999996 + 48.47, + 3523.592, + 245.15, + 42.58699999999999 ], "priority": 9, "parents": [ - 157406 + 924 ], "children": [ - 157404, - 157397, - 157403, - 157401, - 157405 + 937, + 934, + 935 ], - "area": 154431.47598999998, + "area": 170788.50424, "iscrowd": 0, "segmentation": [], - "text": "Empirical Validation I:" + "text": "4. Results:" }, { - "id": 157397, - "strid": "1f3d126e-0d3b-4670-9642-7b7b9fcf48f5", - "image_id": 206647, - "image_name": "6180.png", + "id": 934, + "strid": "8e5c4dd7-3be3-4193-acb5-2467086c93b5", + "image_id": 36, + "image_name": "11430.png", "category_id": 3, "category_name": "Text", "bbox": [ - 508.608, - 341.056, - 411.367, - 33.84300000000002 + 45.709, + 3611.669, + 1019.4579999999999, + 1004.54 ], "priority": 10, "parents": [ - 157390 + 933 ], "children": [], - "area": 173463.81004799998, + "area": 165085.77832100002, "iscrowd": 0, "segmentation": [], - "text": "orientation pop-out processing [8]" + "text": "Nine trials were included in this review. One of\nthem was a comparative study that used\ntween 20 to prepare niosomes and micelles\nfrom curcumin, its evidences showed that\nniosomes suppress curcumin degradation\nbetter than micelles. (reference 4 - figure 1,2).\nTwo trials showed that skin permeation and\nhalf-life of the curcumin enhanced when\nformulated in niosome system, this conclusion\nsupported by three similar trials that co-\nencapsulated curcumin with other antioxidants\n\nin niosomes and solutions." }, { - "id": 157401, - "strid": "44793612-042a-4771-bde7-6ef8df8887d6", - "image_id": 206647, - "image_name": "6180.png", + "id": 935, + "strid": "9dddd712-62f7-4be7-a3c8-691262ad1d35", + "image_id": 36, + "image_name": "11430.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 539.5, - 396.374, - 438.36, - 341.409 + 1216.996, + 2949.983, + 748.002, + 547.0129999999999 ], "priority": 11, "parents": [ - 157390 + 933 ], - "children": [], - "area": 213843.77300000002, + "children": [ + 936 + ], + "area": 3590117.5110680005, "iscrowd": 0, "segmentation": [] }, { - "id": 157403, - "strid": "b4e9634e-2e75-45dc-a029-d5e16b209d22", - "image_id": 206647, - "image_name": "6180.png", - "category_id": 2, - "category_name": "Figure", + "id": 936, + "strid": "20d71a00-b308-463c-a8d3-41410f953e34", + "image_id": 36, + "image_name": "11430.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 528.125, - 773.827, - 462.97299999999996, - 341.31600000000003 + 1224.914, + 3511.728, + 729.6099999999999, + 133.66499999999996 ], "priority": 12, "parents": [ - 157390 + 935 ], "children": [], - "area": 408677.384375, + "area": 4301564.791392, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig.1.Fluorescence decays of curcumin in\nTween-20 micelles and TW-20/cholesterol\nniosomes (reference 4)." }, { - "id": 157404, - "strid": "99d2f6e6-8c38-47d1-b56a-72389bb82975", - "image_id": 206647, - "image_name": "6180.png", + "id": 937, + "strid": "f49c397c-c86f-4f0f-b933-7ab6554bed46", + "image_id": 36, + "image_name": "11430.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 523.768, - 1142.976, - 468.346, - 178.17499999999995 + 1214.803, + 4011.157, + 702.1789999999999, + 490.91299999999956 ], "priority": 13, "parents": [ - 157390 + 933 ], - "children": [], - "area": 598654.253568, + "children": [ + 938 + ], + "area": 4872765.557071, "iscrowd": 0, "segmentation": [] }, { - "id": 157405, - "strid": "e9cb5f1e-649b-4dff-949c-862dbbb99e3d", - "image_id": 206647, - "image_name": "6180.png", - "category_id": 2, - "category_name": "Figure", + "id": 938, + "strid": "d2dac81f-87e5-4fa4-a6ef-0f43646749a2", + "image_id": 36, + "image_name": "11430.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 528.38, - 1356.696, - 466.649, - 322.932 + 1227.155, + 4512.734, + 688.4280000000001, + 173.3109999999997 ], "priority": 14, "parents": [ - 157390 + 937 ], "children": [], - "area": 716851.0324799999, + "area": 5537824.091770001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 2. Arrhenius plots of In(knr) of\ncurcumin in TW-20 micelles\nand niosomes versus 1/T(reference 4)." }, { - "id": 157391, - "strid": "3a14c630-98d6-478a-805b-36f9286e8b5f", - "image_id": 206647, - "image_name": "6180.png", + "id": 939, + "strid": "8b0605ba-9ed3-4e4a-bcad-9b29a40faee1", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1032.447, - 302.894, - 357.1870000000001, - 35.740999999999985 + 2042.735, + 914.082, + 244.57399999999984, + 39.22199999999998 ], "priority": 15, "parents": [ - 157406 + 924 ], "children": [ - 157402, - 157399, - 157400, - 157398 + 943, + 940, + 941 ], - "area": 312722.001618, + "area": 1867227.29427, "iscrowd": 0, "segmentation": [], - "text": "Empirical Validation Il:" + "text": "" }, { - "id": 157398, - "strid": "03264e7f-13cc-470f-9ab0-49716d64d615", - "image_id": 206647, - "image_name": "6180.png", + "id": 940, + "strid": "603cd60b-1aa1-45cb-ab10-c784c9d19236", + "image_id": 36, + "image_name": "11430.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1034.924, - 342.223, - 380.44100000000003, - 36.17700000000002 + 2041.447, + 1086.44, + 1008.6409999999998, + 577.1089999999999 ], "priority": 16, "parents": [ - 157391 + 939 ], "children": [], - "area": 354174.796052, + "area": 2217909.67868, "iscrowd": 0, "segmentation": [], - "text": "conflict adaptation paradigm [9]" + "text": "the anti-aging property of curcumin was\nstudied by preparing niosomes and liposomes,\naccording to this trial, niosomes of curcumin\nhad better efficacy (reference 5 - figure 3).\n\nIN the field of the cancer therapy, two trials\nsupported delivery enhancement of curcumin\n\nby preparing noisomes(reference 6,7-figure 4)." }, { - "id": 157402, - "strid": "2a259d40-5157-4b63-8de7-b7752f669b82", - "image_id": 206647, - "image_name": "6180.png", + "id": 941, + "strid": "5be50b89-75bf-4dca-87da-28aad7a96c02", + "image_id": 36, + "image_name": "11430.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1054.729, - 415.365, - 452.903, - 299.5640000000001 + 1069.988, + 779.965, + 877.0510000000002, + 714.275 ], "priority": 17, "parents": [ - 157391 + 939 ], - "children": [], - "area": 438097.511085, + "children": [ + 942 + ], + "area": 834553.1904200001, "iscrowd": 0, "segmentation": [] }, { - "id": 157400, - "strid": "fd5312e3-75ca-46e9-beb8-a00f2e76ea22", - "image_id": 206647, - "image_name": "6180.png", - "category_id": 7, - "category_name": "Table", + "id": 942, + "strid": "9a9faa3c-fe32-4187-85f0-5e8d160bfaf0", + "image_id": 36, + "image_name": "11430.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1046.928, - 764.862, - 467.37099999999987, - 283.48699999999997 + 1124.876, + 1503.446, + 760.021, + 184.125 ], "priority": 18, "parents": [ - 157391 + 941 ], "children": [], - "area": 800755.443936, + "area": 1691190.3226959999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 3. Photomicrograph of mice skin\nexposed to UV and treated with gel\ncontaining niosomes (A), liposomes (B),\ncurcumin (C) (reference 5)." }, { - "id": 157399, - "strid": "6155404e-8581-4d9e-8243-5bb04ea982d3", - "image_id": 206647, - "image_name": "6180.png", + "id": 943, + "strid": "575b6aa1-6dcf-46b2-8aba-6aae79c37c52", + "image_id": 36, + "image_name": "11430.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1059.001, - 1079.235, - 450.183, - 600.5829999999999 + 1134.023, + 1930.984, + 780.617, + 462.11400000000003 ], "priority": 19, "parents": [ - 157391 + 939 ], - "children": [], - "area": 1142910.9442349998, + "children": [ + 944 + ], + "area": 2189780.268632, "iscrowd": 0, "segmentation": [] }, { - "id": 157388, - "strid": "f6b90eb5-c7b6-44d5-a886-7f248e29a115", - "image_id": 206647, - "image_name": "6180.png", + "id": 944, + "strid": "1470a658-8541-43f2-854c-704595617462", + "image_id": 36, + "image_name": "11430.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 1151.115, + 2417.415, + 762.769, + 229.23799999999983 + ], + "priority": 20, + "parents": [ + 943 + ], + "children": [], + "area": 2782722.667725, + "iscrowd": 0, + "segmentation": [], + "text": "Fig. 4. Microscopy of DMBA treated mice\nskin showing tumor cells with keratinous\npearl (left), niosome treated mice skin\nshowing intact epithelial layer with\nhyperkeratosis (right)(reference 6)." + }, + { + "id": 945, + "strid": "03009ce0-783d-41c1-8d6f-80eb8a488078", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 510.703, - 1730.997, - 205.64699999999993, - 38.465999999999894 + 2043.029, + 1989.034, + 732.7440000000001, + 44.565000000000055 ], - "priority": 20, + "priority": 21, "parents": [ - 157406 + 924 ], "children": [ - 157395 + 946 ], - "area": 884025.360891, + "area": 4063654.143986, "iscrowd": 0, "segmentation": [], - "text": "Conclusions" + "text": "5. Discussion and Conclusions:" }, { - "id": 157395, - "strid": "f75307cf-dca6-443a-ab97-ee9721e4264f", - "image_id": 206647, - "image_name": "6180.png", + "id": 946, + "strid": "4d73be14-af79-49d2-8a2b-87176d662b53", + "image_id": 36, + "image_name": "11430.png", "category_id": 3, "category_name": "Text", "bbox": [ - 503.891, - 1782.623, - 1031.741, - 158.13400000000001 + 2040.432, + 2162.928, + 1011.3410000000001, + 577.6199999999999 ], - "priority": 21, + "priority": 22, "parents": [ - 157388 + 945 ], "children": [], - "area": 898247.6860930001, + "area": 4413307.504896, "iscrowd": 0, "segmentation": [], - "text": "In this work, we have introduced a method of model selection for GLMs for fMRI. Using simple, but reasonable assumptions on model\nRaat Cmt Re eeu Ne Mute aon ee eee mute Ree Uceu Ome Weenie seer U Net cece\nPee MOC ieee CUP ee OR meer ie Recut cen ue RCC\nReese en CRON aC eeu meee mse CUR Mine he en aR ramon ae nme m IS\nPecoraro eee Mie at Reem cee OMe CU RUC me CMS Cu tne mi\nOy RMN ne ee eee eC SCM CR CR Reece Reem cea\nCOEUR rae INRIRe MME ONCE URC ye Mele Regie RSC" + "text": "Niosome seems to be a potential delivery\nsystem to improve water solubility of\ncurcumin, half-life and clinical efficacy. This\ndelivery system also seems to suppress the\nlevel of degradation of curcumin. Noisome\ncan also promote skin permeation of the\n\ncurcumin and enhanced its bioavailability." }, { - "id": 157389, - "strid": "7dba75d5-40f2-46fc-9b07-89f6f4a99524", - "image_id": 206647, - "image_name": "6180.png", + "id": 947, + "strid": "1118a79f-6448-427a-a242-e11e73ec432e", + "image_id": 36, + "image_name": "11430.png", "category_id": 5, "category_name": "Section", "bbox": [ - 512.182, - 1972.151, - 180.49599999999998, - 35.50700000000006 + 2071.769, + 2880.255, + 314.99800000000005, + 49.5920000000001 ], - "priority": 22, + "priority": 23, "parents": [ - 157406 + 924 ], "children": [ - 157396 + 948 ], - "area": 1010100.2434820001, + "area": 5967223.021094999, "iscrowd": 0, "segmentation": [], - "text": "References" + "text": "6. Key words:" }, { - "id": 157396, - "strid": "1aec189d-494a-4601-aff1-2df22485fd94", - "image_id": 206647, - "image_name": "6180.png", + "id": 948, + "strid": "ef4f2800-f5a1-415a-9443-ba2842c0926d", + "image_id": 36, + "image_name": "11430.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 2072.138, + 3015.105, + 941.8490000000002, + 138.19000000000005 + ], + "priority": 24, + "parents": [ + 947 + ], + "children": [], + "area": 6247713.64449, + "iscrowd": 0, + "segmentation": [], + "text": "Noisome, Curcumin, Anti-aging property,\n\nSkin permeation." + }, + { + "id": 949, + "strid": "25978ef8-d10e-4024-a782-c052eff51168", + "image_id": 36, + "image_name": "11430.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 2009.222, + 3255.608, + 334.99, + 42.57400000000007 + ], + "priority": 25, + "parents": [ + 924 + ], + "children": [ + 950 + ], + "area": 6541239.216976, + "iscrowd": 0, + "segmentation": [], + "text": "7. References:" + }, + { + "id": 950, + "strid": "8f322665-bef1-4b27-8b8d-e72ce4c7031f", + "image_id": 36, + "image_name": "11430.png", "category_id": 4, "category_name": "List", "bbox": [ - 508.694, - 2020.965, - 1003.827, - 158.93900000000008 + 2009.213, + 3333.63, + 1102.4000000000003, + 1233.2510000000002 ], - "priority": 23, + "priority": 26, "parents": [ - 157389 + 949 ], "children": [], - "area": 1028052.76971, + "area": 6697972.73319, "iscrowd": 0, "segmentation": [] }, { - "id": 51818, - "strid": "f7b2144a-4118-4be6-94dc-deb554b80892", - "image_id": 202538, - "image_name": "118839.png", + "id": 951, + "strid": "bdcfebe1-8e6c-4342-9e80-fd46a963de1b", + "image_id": 37, + "image_name": "11524.png", "category_id": 9, "category_name": "Root", "bbox": [ - 2387.43, - 229.21, - 293.74000000000024, - 146.86999999999998 + 38.25, + 73.01, + 167.61, + 435.8 ], "priority": -1, "parents": [], "children": [ - 51798, - 51796, - 51817, - 51794, - 51812, - 51804, - 51808, - 51810, - 51800, - 51795, - 51815, - 51799, - 51807, - 51811, - 51816, - 51802, - 51809, - 51805, - 51806, - 51801, - 51814, - 51803, - 51813 + 968, + 956, + 952, + 954, + 953, + 966 ], - "area": 547222.8303, + "area": 2792.6325, "iscrowd": 0, "segmentation": [] }, { - "id": 51794, - "strid": "5ee4d0c6-19c5-4b60-b671-fbde200ac323", - "image_id": 202538, - "image_name": "118839.png", + "id": 952, + "strid": "16ad1cb2-c6c4-4045-9de4-56f9622c90a8", + "image_id": 37, + "image_name": "11524.png", "category_id": 1, "category_name": "Title", "bbox": [ - 115.401, - 71.938, - 3664.748, - 95.43600000000002 + 270.028, + 115.967, + 1928.41, + 305.794 ], "priority": 1, "parents": [ - 51818 + 951 ], "children": [], - "area": 8301.717138, + "area": 31314.337076000003, "iscrowd": 0, "segmentation": [], - "text": "System Wide Analyses have Underestimated Protein Abundances and Transcriptional Importance" + "text": "Getting neuron morphologies\nregistered to a brain atlas" }, { - "id": 51795, - "strid": "09df74fe-895b-474a-a0b0-e4015d2f4d2f", - "image_id": 202538, - "image_name": "118839.png", + "id": 953, + "strid": "7229772a-49cf-4b39-9ba0-469b7c222aac", + "image_id": 37, + "image_name": "11524.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 117.738, - 184.562, - 1713.955, - 198.41899999999998 + 264.095, + 446.983, + 2130.9929999999995, + 182.78699999999998 ], "priority": 2, "parents": [ - 51818 + 951 ], "children": [], - "area": 21729.960756, + "area": 118045.97538500001, "iscrowd": 0, "segmentation": [], - "text": "Jingyi Jessica Li'?, Peter J. Bickel? and Mark D. Biggin?\n\n‘Department of Statistics, University of California, Los Angeles CA 90095, USA\n2Department of Statistics, University of California, Berkeley CA 94720, USA\n\n3Genomics Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA." + "text": "Rembrandt Bakker! *, Marfa Garcia-Amado?, Marian Evangelio’, Francisco Clascé?, Paul Tiesinga!\n\n' Neuroinformatics department, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands\n? Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jiilich Research Centre, Jiilich, Germany.\n3 Departamento de Anatom{ia, Histologia y Neurociencia, Facultad de Medicina, Universidad Aut6noma de Madrid, Madrid, Spain" }, { - "id": 51796, - "strid": "9c1a96b4-3565-4d72-8437-01ed91535aa1", - "image_id": 202538, - "image_name": "118839.png", + "id": 954, + "strid": "26c472f3-8552-42b4-a4b4-d9a792817521", + "image_id": 37, + "image_name": "11524.png", "category_id": 5, "category_name": "Section", "bbox": [ - 124.641, - 430.566, - 218.325, - 30.420000000000016 + 270.253, + 726.873, + 265.33599999999996, + 47.74000000000001 ], "priority": 3, "parents": [ - 51818 + 951 ], "children": [ - 51797 + 955 ], - "area": 53666.176805999996, + "area": 196439.608869, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Motivation" }, { - "id": 51797, - "strid": "7c4f6023-9a1e-430a-9414-54d4b3c7c0e8", - "image_id": 202538, - "image_name": "118839.png", + "id": 955, + "strid": "85b0c789-9353-4e1d-bf78-e80b6f9aaf43", + "image_id": 37, + "image_name": "11524.png", "category_id": 3, "category_name": "Text", "bbox": [ - 121.764, - 466.431, - 1136.623, - 900.7429999999999 + 268.131, + 806.563, + 959.948, + 1101.4539999999997 ], "priority": 4, "parents": [ - 51796 + 954 ], "children": [], - "area": 56794.504283999995, + "area": 216264.54375299998, "iscrowd": 0, "segmentation": [], - "text": "System wide surveys in mammalian tissue culture cells suggest that the protein expressed\nat the median abundance is present at 8,000 - 16,000 molecules per cell and that\ndifferences in mRNA expression between genes explain only 10-40% of the differences in\nprotein levels. We find, however, that these surveys have significantly underestimated\nprotein abundances. Using individual measurements for 61 housekeeping proteins to\nrescale whole proteome data from Schwanhausser et al., we find that the median protein\ndetected is expressed at 170,000 molecules per cell and that our corrected protein\nabundance estimates show a higher correlation with mRNA abundances than do the\nuncorrected protein data.\n\nTo estimate the degree to which mRNA expression levels determine protein levels, it is\ncritical to measure the error in protein and mRNA abundance data and to consider all\ngenes, not only those whose protein expression is readily detected. By taking direct\nmeasurements of experimental error into account, we estimate that MRNA levels explain at\nleast 56% of the differences in protein abundance for the 4,212 genes detected by\nSchwanhausser et al. By in addition modeling all genes’ expression, we show that under\nreasonable assumptions MRNA levels can explain at least 65% of protein levels for genes\nthat are expressed and 100% for genes that are not expressed. Separately, we employ a\nsecond strategy to determine the contribution of mRNA levels to protein expression. This\nshows that the variance in translation rates directly measured by Ingolia et al. is 4.6 fold less\nthan the variance inferred by Schwanhausser et al. and that based on this mRNA levels are\nexpected to explain ~75% of the variance in protein levels for the 4,212 detected genes and\n~82% for all expressed genes. While the magnitude of our differently derived estimates\nvary, all suggest that the previous studies have significantly underestimated the importance\nof transcription.\n\nA preprint describing this work is publicly available at http://arxiv.org/abs/1212.0587." + "text": "A key aim of the Human Brain Project is to build a\ntissue simulator that covers multiple brain areas. The\nfirst step of this simulator is the tissue builder. It\ngenerates neuronal tissue —in silico— by placing neuron\nmorphologies in a reference brain.\n\nA large public resource of neuron morphologies is the\nNeuroMorpho.Org data base. It collects reconstructed\naxonal and dendritic trees from experimental groups\naround the world.\n\nTo use NeuroMorpho.Org morphologies in the tissue\nbuilder, their position in a reference atlas must be\nknown. However, the only positional information\nprovided is the name of the brain region where the\nsoma resides. Especially for projection neurons, which\nextend beyond a single brain region, this is grossly\ninsufficient.\n\nTo help experimenters with providing atlas coordinates\nfor their data, we present a procedure to register\nreconstructed neurons to a brain atlas. The result is\nstored within the morphology file. The reward for the\nexperimenter is that he can interactively view the\nneuron in 3d together with sections from the atlas." }, { - "id": 51808, - "strid": "4a19f8ed-2448-453c-8052-abcc717c6e5d", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 956, + "strid": "0b6ae8d5-987f-46d6-a1c8-c5237a75c9e7", + "image_id": 37, + "image_name": "11524.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 220.39, - 1467.475, - 922.7119999999999, - 419.9680000000001 + 272.054, + 1978.901, + 529.08, + 57.628999999999905 ], "priority": 5, "parents": [ - 51818 + 951 ], - "children": [], - "area": 323416.81525, + "children": [ + 963, + 962, + 961, + 957, + 959, + 960, + 958, + 964, + 965 + ], + "area": 538367.932654, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Registration pipeline" }, { - "id": 51798, - "strid": "37a28a16-b0a1-47c6-9dee-cd31bf8cecd1", - "image_id": 202538, - "image_name": "118839.png", + "id": 957, + "strid": "9f64df9d-da67-4a4a-a683-556b4db93bb9", + "image_id": 37, + "image_name": "11524.png", "category_id": 3, "category_name": "Text", "bbox": [ - 119.349, - 1906.797, - 1140.392, - 175.03200000000015 + 267.676, + 2081.011, + 960.1500000000001, + 462.0830000000001 ], "priority": 6, "parents": [ - 51818 + 956 ], "children": [], - "area": 227574.315153, + "area": 557036.700436, "iscrowd": 0, "segmentation": [], - "text": "2. Four steps determine protein expression levels. The steady state\nconcentration of a protein in a cell is determined by the combined effects of the rates of\ngene transcription, RNA degradation, translation and protein degradation. The differences in\nprotein levels between highly expressed, poorly expressed and not expressed genes is\ntherefore determined by the differences between each gene in the rates of these four steps." + "text": "Step 1. Inspect the reconstructed neuron\n\nFor this purpose we have created a web-based\ninteractive 3d morphology viewer.\n\nThe viewer accepts files in the Neurolucida™ format,\nas well as in the open SWC format.\n\nIt contains a searcheable interface to NeuroMorpho.Org\nand several other morphology resources.\n\nIt can save files to SWC, and the code to convert\nNeurolucida to SWC is released as a Node.js package." }, { - "id": 51809, - "strid": "e120a148-6657-46ba-9b89-9aefce6db6fa", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 958, + "strid": "a637ae2a-42f7-4c2f-a016-6961a9f51cae", + "image_id": 37, + "image_name": "11524.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 132.581, - 2193.141, - 1096.061, - 496.68499999999995 + 274.636, + 2599.651, + 1060.043, + 52.28600000000006 ], "priority": 7, "parents": [ - 51818 + 956 ], "children": [], - "area": 290768.82692099997, + "area": 713957.752036, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "https://neuroinformatics .nl/HBP/morphology-viewer" }, { - "id": 51799, - "strid": "2a0b9b75-041a-4cb0-b6e6-6d175ed4f2b0", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 959, + "strid": "f053b4e0-328a-4d31-be35-4d339082b6b4", + "image_id": 37, + "image_name": "11524.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 120.038, - 2718.29, - 1140.646, - 438.1410000000001 + 264.531, + 2658.041, + 2028.0120000000002, + 1063.4859999999999 ], "priority": 8, "parents": [ - 51818 + 956 ], "children": [], - "area": 326298.09502, + "area": 703134.2437710001, "iscrowd": 0, - "segmentation": [], - "text": "3. Published work suggest that translation is the most important step.\nIn the most detailed paper to quantitate the relative importance of the four steps,\nSchwanhausser et al claimed to have measured that translation is the most important,\nfollowed by transcription. Their evidence for this is largely that measured levels of mRNA for\n4,212 genes in mouse NIH3T3 cells only correlate poorly with mass spectrometry\nmeasurements of protein abundance for the same genes in the same cells. Schwanhausser\net al—and also a number of other groups who have used a similar approach to come to\nsimilar conclusions—argue that the vertical displacement of data points about the line of\nbest fit (above, right) measures the combined influences of differences in translation and\nprotein degradation rates between each gene. Since Schwanhausser et al separately\nquantitated the degradation rates of proteins and mRNAs, they were able to calculate the\nfraction of the total variance in protein expression levels that is explained the variance in\neach of the four steps (above, left)." + "segmentation": [] }, { - "id": 51800, - "strid": "27c58eb2-62dc-437f-b207-6d08ff4470a6", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 960, + "strid": "4021daf3-2206-4bce-b7ac-d67145b52b48", + "image_id": 37, + "image_name": "11524.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 116.509, - 3273.468, - 637.345, - 479.799 + 1313.799, + 760.738, + 959.8090000000002, + 452.126 ], "priority": 9, "parents": [ - 51818 + 956 ], "children": [], - "area": 381388.483212, + "area": 999456.823662, "iscrowd": 0, - "segmentation": [], - "text": "4. A non-linear bias in the published\nprotein abundances. We first noticed that for\nhousekeeping proteins that are expressed below\none million molecules per cell, Schwanhausser et\nal.'s protein abundance estimates are lower than\nindividual measurements in the literature. The\nliterature data are mostly western blot and SILAC\nMS/MS measurements, both of which diverge to a\nsimilar degree from Schwanhausser et al.’s\nestimates. We have also shown that the\ndisagreement between the western and SILAC\ndata and Schwanhausser et al.’s results is not due\nto differences in expression levels between cell\nlines (see our preprint)." + "segmentation": [] }, { - "id": 51810, - "strid": "2d82aa83-1d83-4d80-8542-975036d28485", - "image_id": 202538, - "image_name": "118839.png", + "id": 961, + "strid": "fca3a944-54f1-4c31-b854-205e9404be10", + "image_id": 37, + "image_name": "11524.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 783.877, - 3264.123, - 490.69100000000003, - 493.39699999999993 + 1329.227, + 1199.999, + 741.2650000000001, + 789.116 ], "priority": 10, "parents": [ - 51818 + 956 ], "children": [], - "area": 2558670.944871, + "area": 1595071.0707730001, "iscrowd": 0, "segmentation": [] }, { - "id": 51815, - "strid": "b30720b5-9614-467e-ab4b-9df8783f6cef", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 962, + "strid": "bce9e9fe-a22f-4228-9ca1-7f4e8fc7ca94", + "image_id": 37, + "image_name": "11524.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1465.504, - 413.24, - 958.328, - 918.048 + 1345.932, + 2082.9, + 754.55, + 500.2950000000001 ], "priority": 11, "parents": [ - 51818 + 956 ], "children": [], - "area": 605604.87296, + "area": 2803441.7628, "iscrowd": 0, "segmentation": [] }, { - "id": 51801, - "strid": "a2665db5-b016-4e5a-a61b-e02da12fd618", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 963, + "strid": "427752d8-e056-4635-9c59-d3378fc82083", + "image_id": 37, + "image_name": "11524.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1375.418, - 1359.383, - 1141.651, - 212.1579999999999 + 2104.932, + 1696.163, + 256.2919999999999, + 879.4079999999999 ], "priority": 12, "parents": [ - 51818 + 956 ], "children": [], - "area": 1869719.8470939999, + "area": 3570307.775916, "iscrowd": 0, - "segmentation": [], - "text": "5. Correcting protein abundances increases the correlation between\nprotein and mRNA levels. We rescaled Schwanhausser et al.’s whole proteome data\nusing the individual abundance estimates for 61 house keeping proteins from the literature.\nThis correction removes the non-linear bias (compare panels A and C) and increases the\ncorrelation between protein and mRNA levels (compare panel B and D). This result\nsuggests that translation rates vary less that Schwanhausser et al. estimated." + "segmentation": [] }, { - "id": 51814, - "strid": "bf998e57-479a-43a8-8e7d-6a6a947138ae", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 964, + "strid": "e0d66002-d2b8-424c-a6cd-d95840729452", + "image_id": 37, + "image_name": "11524.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1475.351, - 1659.863, - 949.7539999999999, - 484.3509999999999 + 2370.138, + 761.047, + 839.2660000000001, + 411.9069999999999 ], "priority": 13, "parents": [ - 51818 + 956 ], "children": [], - "area": 2448880.536913, + "area": 1803786.414486, "iscrowd": 0, "segmentation": [] }, { - "id": 51802, - "strid": "50724054-a480-4383-90fd-4377f5098789", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 965, + "strid": "bfdad377-3bb1-41fd-a734-c1c84a0f44a0", + "image_id": 37, + "image_name": "11524.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1375.293, - 2161.684, - 1141.622, - 374.9659999999999 + 2399.962, + 1218.831, + 793.8380000000002, + 3240.6679999999997 ], "priority": 14, "parents": [ - 51818 + 956 ], "children": [], - "area": 2972948.873412, + "area": 2925148.0844219998, "iscrowd": 0, - "segmentation": [], - "text": "6. Estimating two other sources of measurement error. A second source of\nerror in Schwanhausser et al.’s data is due to the stochastic error between replica protein\nabundance experiments, which can be estimated from the variance about the line of best fit\nfor the plot on the left. The third source of error is due to the well known GC content bias in\nmRNA Seq data. The plot on the right compares Schwanhausser et al.’s mMRNA-seq data to\nNanoString data for 78 genes. NanoString is more accurate method than mRNA-seq, giving\na better correlation with known standards than does mRNA-seq (R? 0.99 vs R? 0.77). Thus,\nthe bulk of the variance about the line of best fit (right panel) should be due to error in the\nmRNA-seq data. Note there is a final source of error that for technical reasons we are not\nable to estimate: the tendency of label free mass spectrometry to reproducibly\nunderestimate some proteins’ abundances and overestimate others." + "segmentation": [] }, { - "id": 51811, - "strid": "6e89bb21-3b29-412d-88c2-40924de9ceb6", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 966, + "strid": "e89cde60-238a-40e1-a99d-a5e63df5d213", + "image_id": 37, + "image_name": "11524.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1384.767, - 2619.296, - 1115.0020000000002, - 816.279 + 288.81, + 3826.988, + 686.685, + 60.3130000000001 ], "priority": 15, "parents": [ - 51818 + 951 ], - "children": [], - "area": 3627114.664032, + "children": [ + 967 + ], + "area": 1105272.40428, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Use case: projection neuron" }, { - "id": 51803, - "strid": "d751929d-5b3c-4377-a43d-643d05b2cc7e", - "image_id": 202538, - "image_name": "118839.png", + "id": 967, + "strid": "2ed924d9-f79a-4cb4-93f3-85954ce21914", + "image_id": 37, + "image_name": "11524.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1375.589, - 3448.127, - 1142.4359999999997, - 309.741 + 284.392, + 3932.073, + 915.691, + 460.8979999999997 ], "priority": 16, "parents": [ - 51818 + 966 ], "children": [], - "area": 4743205.571803, + "area": 1118250.1046159999, "iscrowd": 0, "segmentation": [], - "text": "7. Using ANOVA to estimate the impact of error. We have the relationship\nbetween measured mRNA levels and our correction to measured protein levels (green\nellipses). Given that we now have estimates for variance due to the measurement errors\ndetermined in Section 6 (green circles), it is possible to use Analysis of Variance (ANOVA)\nto determine the lower variances expected in true protein and true MRNA levels as well as\nthe variance in true protein levels due to the combined effect of translation and protein\nturnover (green arrow). By also using Schwanhausser et al.’s data for protein and mRNA\ndegradation rates, we can then formally calculate the reduced role that translation is\nexpected to play (see Section 11)." + "text": "Our use-case is a thalamocortical projection neuron that\nspans multiple brain areas, in this case from the lateral\nposterior thalamic nucleus to visual area V1.\n\nThe neuron was transfected in-vivo by direct\nelectroporation with an adeno-associated virus type 2\nDNA construct, which releases GFP throughout the\naxonal and dendritic trees. After sectioning and\ncounterstaining, the neuron was manually traced using\nNeurolucida (Microbrighfield Inc.) and saved in .DAT\nfile format." }, { - "id": 51807, - "strid": "334d3732-89c6-4d22-8cc9-ccbb62f8c153", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 968, + "strid": "002abd16-7fe4-413b-af5a-b42a6604bcbb", + "image_id": 37, + "image_name": "11524.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2631.222, - 425.499, - 553.3040000000001, - 374.4169999999999 + 1326.696, + 3812.334, + 439.3989999999999, + 55.01099999999997 ], "priority": 17, "parents": [ - 51818 + 951 ], - "children": [], - "area": 1119582.3297780002, + "children": [ + 969 + ], + "area": 5057808.268463999, "iscrowd": 0, "segmentation": [], - "text": "8. The variance in measured\n\ntranslation rates. Ingolia et al. (2012,\nCell 147, p 337) have directly measured the\ndistribution of translation rates for\nthousands of genes by ribosome profiling in\nmouse ES cells (grey line). The variance in\nthese measured translation rates is 4.6 fold\nless than that. inferred indirectly by\nSchwanhausser et al. in NIH3T3 cells (black\nline). The 2.5 and 97.5 percentiles of each\ndistribution are shown as dashed lines." + "text": "SWC+ file format" }, { - "id": 51816, - "strid": "a4334bab-9a13-4ac9-8ccc-bf27bbd5da05", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 969, + "strid": "831fea35-4345-4143-b941-97a7fb027792", + "image_id": 37, + "image_name": "11524.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3217.397, - 430.66, - 562.48, - 508.95200000000006 + 1320.7, + 3928.147, + 963.2169999999999, + 521.9830000000002 ], "priority": 18, "parents": [ - 51818 + 968 ], "children": [], - "area": 1385604.19202, + "area": 5187903.7429, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Closed-source morphology formats (Neurolucida) are\nnot suitable for storing additional metadata like anchor\npoints and transformation results. The open SWC\nformat used by NeuroMorpho.Org on the other hand has\nno structured way to store metadata.\n\nWe present SWC+, an extension of SWC in which the\nplain text header is replaced by XML. User-defined\nproperties can be assigned to SWC points or objects\n(defined as connected points of the same type).\nhttps://neuroinformatics .nl/swcPlus" }, { - "id": 51817, - "strid": "035137f4-a01d-4255-953b-ae3c8af6c2e3", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 970, + "strid": "bd8d88c3-cb1d-4e47-910b-a74b46b79e76", + "image_id": 38, + "image_name": "11536.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 2664.975, - 1041.619, - 1056.107, - 791.5840000000001 + 596.4, + 57.42, + 370.6700000000001, + 382.26 ], - "priority": 19, - "parents": [ - 51818 + "priority": -1, + "parents": [], + "children": [ + 995, + 976, + 971, + 978, + 991, + 972, + 985, + 982, + 980, + 993, + 988, + 973 ], - "children": [], - "area": 2775888.5945249996, + "area": 34245.288, "iscrowd": 0, "segmentation": [] }, { - "id": 51806, - "strid": "e5e8ee4f-51dd-4a8a-ae0e-3b6e8a0db258", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 971, + "strid": "4b1a5b5e-473c-46fd-827c-0a388878581c", + "image_id": 38, + "image_name": "11536.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 2630.868, - 1846.722, - 1140.078, - 278.5350000000001 + 1242.412, + 85.187, + 3505.437, + 238.781 ], - "priority": 20, + "priority": 1, "parents": [ - 51818 + 970 ], "children": [], - "area": 4858481.814696, + "area": 105837.351044, "iscrowd": 0, "segmentation": [], - "text": "9. Using directly measured translation rates. The availability of measured\ntranslation rates opens up a second strategy. By using direct experimental data for the\nvariances of the terms circled, we can infer the variance in true protein and true RNA levels\nand at the same time capture all protein errors (arrowed) as the unexplained term. In this\ncase, we are not relying on our rescaling of Schwanhausser et al.’s protein abundance\nestimates, but use their published estimates. This “measured translation” calculation is thus\nsignificantly independent from the “measured error” strategy described earlier and leads to a\nsignificantly higher estimate of the importance of transcription (Section 11)." + "text": "Attentional blink as a product of attentional control signals:\nA computational investigation" }, { - "id": 51805, - "strid": "e3583d90-eaa5-4d84-ac68-000cf0e88579", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 972, + "strid": "bad28982-c76e-4282-93ed-812a9a3fabc5", + "image_id": 38, + "image_name": "11536.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 2631.507, - 2204.776, - 582.0219999999999, - 607.2870000000003 + 1381.428, + 337.565, + 3229.3560000000007, + 179.15699999999998 ], - "priority": 21, + "priority": 2, "parents": [ - 51818 + 970 ], "children": [], - "area": 5801883.4774319995, + "area": 466321.74282000004, "iscrowd": 0, "segmentation": [], - "text": "10. Estimates for all. genes.\nSchwanhausser et al. considered only the\n4,212 genes whose expression they detected.\nTo determine the relationship between protein\nand mRNA levels for all genes we used deep\nmRNA-seq data and insights from Hebenstreit\net al. (2011, 2012) to model protein expression\nlevels. Since 8,763 genes express no MRNA\nin a given cell, these genes are assumed to\nhave the same rate of translation as each\nother, i.e. zero (Section 11). The 12,546\nexpressed genes are assumed to have the\nsame variances in rates of translation and\nprotein degradation as the 4,212 detected\ngenes. Because the total variance in protein\nlevels is now higher, this leads to translation\nand protein degradation contributing less as a\npercent of the total variance (Section 11)." + "text": "Rakesh Sengupta!?, Omar Abid!, Asheer Bachoo!, and John K. Tsotsos!?\n\n1. Department of Electrical Engineering and Computer Science, 2. Centre for Vision Research, York University, Toronto, ON, Canada" }, { - "id": 51813, - "strid": "3dfa766b-f999-4af7-80cf-38eef2015e66", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 2, - "category_name": "Figure", + "id": 973, + "strid": "b13dbbe4-60e4-4e62-b902-c1a361c083be", + "image_id": 38, + "image_name": "11536.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 3245.721, - 2247.334, - 536.5320000000002, - 486.41600000000017 + 850.953, + 707.787, + 383.78600000000006, + 52.47199999999998 ], - "priority": 22, + "priority": 3, "parents": [ - 51818 + 970 ], - "children": [], - "area": 7294219.157814, + "children": [ + 974 + ], + "area": 602293.471011, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Introduction" }, { - "id": 51812, - "strid": "7fa8648e-7c39-475e-b5ff-e7188b047ca0", - "image_id": 202538, - "image_name": "118839.png", + "id": 974, + "strid": "c41593fb-d5c7-4b73-b570-7446f2a0933b", + "image_id": 38, + "image_name": "11536.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2626.133, - 2920.503, - 1163.29, - 551.0419999999999 + 612.748, + 867.948, + 997.1010000000001, + 984.4689999999999 ], - "priority": 23, + "priority": 4, "parents": [ - 51818 + 973 ], - "children": [], - "area": 7669629.304899, + "children": [ + 975 + ], + "area": 531833.401104, "iscrowd": 0, "segmentation": [] }, { - "id": 51804, - "strid": "1a7c38f6-28a9-4d45-8e35-6d8a81640491", - "image_id": 202538, - "image_name": "118839.png", - "category_id": 3, - "category_name": "Text", + "id": 975, + "strid": "20346a21-ceee-432a-9eeb-3043e1250a5d", + "image_id": 38, + "image_name": "11536.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2632.943, - 3509.458, - 1137.7330000000002, - 248.36500000000024 + 116.55, + 1911.77, + 1771.889, + 151.96500000000015 ], - "priority": 24, + "priority": 5, "parents": [ - 51818 + 974 ], "children": [], - "area": 9240202.874894, + "area": 222816.7935, "iscrowd": 0, "segmentation": [], - "text": "11. Transcription is the predominant step determining protein\n\nexpression levels. Shown are the variance in protein expression levels determined by\nthe variance in the rates of the four steps in gene expression for different senarios. We\nbelieve that the estimates using measured rates of translation are likely more accurate than\nthose using only measurements of error as we are unable to estimate an important class of\nprotein error for the latter strategy. We assume that the absence of transcrption is the\npredominant reason why ~40% of genes are not expressed." - }, - { - "id": 132708, - "strid": "7958c61e-c367-431d-b02f-d52ab7a58099", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 9, - "category_name": "Root", - "bbox": [ - 59.13, - 28.96, - 268.19, - 280.96000000000004 - ], - "priority": -1, - "parents": [], - "children": [ - 132683, - 132685, - 132684, - 132688, - 132689, - 132687, - 132682, - 132686 - ], - "area": 1712.4048, - "iscrowd": 0, - "segmentation": [] + "text": "Figure: Attentional blink (AB) tasks generally demand subjects identify a target (here white letter) in the\nstream based on a feature and report if a pre-specified probe, here X was present in the RSVP stream\n(Raymond et al., 1992)." }, { - "id": 132682, - "strid": "ad2ec3d4-a26e-43f3-85ae-859be3c830f3", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 1, - "category_name": "Title", + "id": 976, + "strid": "7e7f60be-6f45-45f6-a4e6-ac08ccdcc099", + "image_id": 38, + "image_name": "11536.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 473.066, - 469.539, - 2368.022, - 257.256 + 562.256, + 2204.794, + 963.3729999999999, + 64.59400000000005 ], - "priority": 1, + "priority": 6, "parents": [ - 132708 + 970 ], - "children": [], - "area": 222122.936574, + "children": [ + 977 + ], + "area": 1239658.655264, "iscrowd": 0, "segmentation": [], - "text": "OpenRiskNet Part III:\nModelling Services in Chemical/Nano-safety, Environmental Science\nand Pharmacokinetics" + "text": "Current theories and challenges" }, { - "id": 132683, - "strid": "4566ce1e-1106-4078-97ef-e741238259ae", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 0, - "category_name": "Author Info", + "id": 977, + "strid": "690ca7eb-2d2c-4068-a08b-361a436da780", + "image_id": 38, + "image_name": "11536.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 147.28, - 777.932, - 3027.681, - 45.889999999999986 + 117.299, + 2361.945, + 1847.655, + 693.9859999999999 ], - "priority": 2, + "priority": 7, "parents": [ - 132708 + 976 ], "children": [], - "area": 114573.82496, + "area": 277053.78655500006, "iscrowd": 0, - "segmentation": [], - "text": "Stefan Kramer?, Philip Doganis®, Denis Gebele?, Atif Raza?, Pantelis Karatzas®, Haralambos Sarimveis®, Jonathan Alvarsson®, Ola Spjuth®, Staffan Arvidsson®, Thomas Exner’, Lucian Farcal', Barry Hardy’" + "segmentation": [] }, { - "id": 132684, - "strid": "a12213ef-5313-40db-9f5c-0edc04357549", - "image_id": 205650, - "image_name": "15506.png", + "id": 978, + "strid": "b524abdb-6983-40a9-90e1-20ed5e722694", + "image_id": 38, + "image_name": "11536.png", "category_id": 5, "category_name": "Section", "bbox": [ - 670.625, - 927.758, - 320.471, - 47.35299999999995 + 872.828, + 3171.809, + 342.14699999999993, + 64.42099999999982 ], - "priority": 3, + "priority": 8, "parents": [ - 132708 + 970 ], "children": [ - 132690 + 979 ], - "area": 622177.70875, + "area": 2768443.705852, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Hypothesis" }, { - "id": 132690, - "strid": "998dbed9-2f4f-4932-86cd-8c58955e4f9b", - "image_id": 205650, - "image_name": "15506.png", + "id": 979, + "strid": "39c772a0-f86c-4b10-85f2-ee5ad41d28f9", + "image_id": 38, + "image_name": "11536.png", "category_id": 3, "category_name": "Text", "bbox": [ - 33.403, - 1039.561, - 1592.691, - 509.5629999999999 + 144.987, + 3284.291, + 1800.094, + 241.04100000000017 ], - "priority": 4, + "priority": 9, "parents": [ - 132684 + 978 ], "children": [], - "area": 34724.456083, + "area": 476179.49921700003, "iscrowd": 0, "segmentation": [], - "text": "The OpenRiskNet project has the main objective of developing an open e-infrastructure\nproviding data, software resources and services to a variety of industries requiring risk\nassessment (e.g. chemicals, cosmetic ingredients, pharma or nanotechnologies).\nCentral to risk assessment decisions is the ability to generate predictions that provide\ninsights into the relationships among material composition, functionality and adverse\neffects.\n\nThe concept of case studies was followed in OpenRiskNet in order to test and evaluate\nproposed solutions, as described in:\nhttps://openrisknet.org/e-infrastructure/development/case-studies/.\n\nModelling within risk assessment is the focus of two case studies, namely ModelRX and\nRevK." + "text": "Identifying the target requires memory consolidation that can be disrupted by incoming\nstimuli in the stream. Thus a top down inhibitory signal (to the visual processing hierar-\nchy) following target feature detection during memory consolidation phase is responsible\nfor AB." }, { - "id": 132686, - "strid": "61ff53d9-f816-4683-a060-ca8f1f597e64", - "image_id": 205650, - "image_name": "15506.png", + "id": 980, + "strid": "cdf4e630-16c4-4464-ad3d-5c4ddacf84db", + "image_id": 38, + "image_name": "11536.png", "category_id": 5, "category_name": "Section", "bbox": [ - 134.576, - 1598.796, - 1388.794, - 134.79500000000007 + 802.456, + 3632.107, + 485.54499999999996, + 64.67700000000013 ], - "priority": 5, + "priority": 10, "parents": [ - 132708 + 970 ], "children": [ - 132693, - 132698, - 132692, - 132703, - 132691 + 981 ], - "area": 215159.570496, - "iscrowd": 0, - "segmentation": [], - "text": "Modelling for Reverse dosimetry and PBPK prediction\n(RevK Case Study)" - }, - { - "id": 132691, - "strid": "a1d2bd30-ba07-4935-a822-4aed1ad71fee", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 38.326, - 1789.135, - 1585.306, - 135.39100000000008 - ], - "priority": 6, - "parents": [ - 132686 - ], - "children": [], - "area": 68570.38801, + "area": 2914606.054792, "iscrowd": 0, "segmentation": [], - "text": "Modelling within the RevK - Reverse dosimetry and PBPK prediction case study is\ncentered on physiologically based pharmacokinetic (PBPK) models for the purpose of\nrisk assessment-relevant scenarios." + "text": "Implementation" }, { - "id": 132698, - "strid": "24548020-50ce-4107-ac74-274e5c53b4c3", - "image_id": 205650, - "image_name": "15506.png", + "id": 981, + "strid": "f42bca8c-66cf-4231-9d89-f7df795eb2f5", + "image_id": 38, + "image_name": "11536.png", "category_id": 4, "category_name": "List", "bbox": [ - 36.275, - 1975.811, - 1567.254, - 285.14200000000005 + 117.476, + 3788.672, + 1789.217, + 332.7199999999998 ], - "priority": 7, + "priority": 11, "parents": [ - 132686 + 980 ], "children": [], - "area": 71672.544025, + "area": 445078.031872, "iscrowd": 0, "segmentation": [] }, { - "id": 132692, - "strid": "1139ecce-afeb-4372-80aa-249f493c307c", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 3, - "category_name": "Text", + "id": 982, + "strid": "6affa20f-1b36-4b3d-a0f6-921c449032f9", + "image_id": 38, + "image_name": "11536.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 37.095, - 2301.16, - 1582.844, - 376.6329999999998 + 2423.451, + 708.915, + 1177.2730000000001, + 65.22299999999996 ], - "priority": 8, + "priority": 12, "parents": [ - 132686 + 970 ], - "children": [], - "area": 85361.5302, + "children": [ + 983 + ], + "area": 1718020.7656649998, "iscrowd": 0, "segmentation": [], - "text": "Development of PBPK models is supported through the integration of the PKSim open-\nsource software (developed by Bayer AG), the httk R package and additionally it is\npossible to develop and integrate custom-made PBPK models.\n\nFor each of these three modelling services, simulations have been performed for a\nreferenced chemical: Imazalil for the httk model, Theophylline for the PKSim model,\nand Diazepam for the user-defined model.\n\nPBPK models aew exposed as a web service using the Jaqpot modelling platform,\nallowing the user to consume services both over UI and API." + "text": "Attention and Visual working memory" }, { - "id": 132703, - "strid": "03c19815-4fc2-4625-8af2-4601863dd6f3", - "image_id": 205650, - "image_name": "15506.png", + "id": 983, + "strid": "864b63b6-25c9-4828-8666-a87fc7e94150", + "image_id": 38, + "image_name": "11536.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 30.166, - 2759.238, - 1566.976, - 1101.156 + 2132.119, + 919.143, + 1796.297, + 1430.844 ], - "priority": 9, + "priority": 13, "parents": [ - 132686 + 982 ], - "children": [], - "area": 83235.17350799999, + "children": [ + 984 + ], + "area": 1959722.254017, "iscrowd": 0, "segmentation": [] }, { - "id": 132693, - "strid": "8137527f-cfc5-464c-93d1-644c23799875", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 3, - "category_name": "Text", + "id": 984, + "strid": "d90046a9-b004-4e77-88d1-930352536e95", + "image_id": 38, + "image_name": "11536.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 36.275, - 3877.44, - 1554.946, - 102.56899999999996 + 2345.388, + 2425.783, + 1328.4279999999999, + 47.99499999999989 ], - "priority": 10, + "priority": 14, "parents": [ - 132686 + 983 ], "children": [], - "area": 140654.136, + "area": 5689402.338803999, "iscrowd": 0, "segmentation": [], - "text": "Users can edit the PBPK model description, perform predictions using their own\ndatasets, validate the model, discuss its performance or share it within user groups." + "text": "Figure: Visual working memory operation alongside Visual processing hierarchy." }, { - "id": 132687, - "strid": "eff7a6da-5abe-4de8-96d6-d5ccfc9b9222", - "image_id": 205650, - "image_name": "15506.png", + "id": 985, + "strid": "68e9c1a0-add0-4688-bce5-ead1d8f691e2", + "image_id": 38, + "image_name": "11536.png", "category_id": 5, "category_name": "Section", "bbox": [ - 524.253, - 4043.392, - 580.9989999999999, - 61.95100000000002 + 2453.079, + 2612.837, + 1120.9429999999998, + 66.51699999999983 ], - "priority": 11, + "priority": 15, "parents": [ - 132708 + 970 ], "children": [ - 132699, - 132704 + 986 ], - "area": 2119760.386176, + "area": 6409495.575123001, "iscrowd": 0, "segmentation": [], - "text": "OpenRiskNet partners" + "text": "Control signals and attentional blink" }, { - "id": 132704, - "strid": "dd8ba311-2bc9-4404-8f57-ee96e042bf39", - "image_id": 205650, - "image_name": "15506.png", + "id": 986, + "strid": "d7614c66-68e1-4633-b10e-9afb827d447b", + "image_id": 38, + "image_name": "11536.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 48.104, - 4160.074, - 612.784, - 455.89999999999964 + 2370.645, + 2771.354, + 1281.085, + 1021.2199999999998 ], - "priority": 12, + "priority": 16, "parents": [ - 132687 + 985 ], - "children": [], - "area": 200116.19969599997, + "children": [ + 987 + ], + "area": 6569896.50333, "iscrowd": 0, "segmentation": [] }, { - "id": 132699, - "strid": "747a5583-6a41-4aec-b472-a8757c53181f", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 4, - "category_name": "List", + "id": 987, + "strid": "cab69639-e32e-4007-9bc4-407fba878136", + "image_id": 38, + "image_name": "11536.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 682.295, - 4139.987, - 919.651, - 499.5119999999997 + 2085.858, + 3810.742, + 1852.877, + 101.36900000000014 ], - "priority": 13, + "priority": 17, "parents": [ - 132687 + 986 ], "children": [], - "area": 2824692.430165, + "area": 7948666.686636001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure: Memory consolidation signal is issued from attentional executive system to suppress the inputs coming\nfrom visual processing hierarchy in a top-down fashion for a finite amount of time." }, { - "id": 132685, - "strid": "cb611e11-eaaf-444e-bbe4-984b5347662b", - "image_id": 205650, - "image_name": "15506.png", + "id": 988, + "strid": "e54b51eb-ebb6-4840-ac1d-d5a0f2c2dd38", + "image_id": 38, + "image_name": "11536.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1963.03, - 928.076, - 1026.7809999999997, - 129.14499999999998 + 4864.935, + 708.277, + 227.4939999999997, + 52.40300000000002 ], - "priority": 14, + "priority": 18, "parents": [ - 132708 + 970 ], "children": [ - 132696, - 132697, - 132701, - 132707, - 132700, - 132695, - 132702 - ], - "area": 1821841.03028, - "iscrowd": 0, - "segmentation": [], - "text": "Modelling for Prediction or Read Across\n(ModelRX Case Study)" - }, - { - "id": 132697, - "strid": "e6a92521-2f30-4b70-ba34-fe3924e4dbdf", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 1679.43, - 1093.718, - 660.5440000000001, - 287.193 - ], - "priority": 15, - "parents": [ - 132685 + 989 ], - "children": [], - "area": 1836822.82074, + "area": 3445721.5669950005, "iscrowd": 0, "segmentation": [], - "text": "The ModelRX - Modelling for\nPrediction or Read Across case\nstudy provides computational\nmethods for predictive modelling\nand support of existing data\nsuitability assessment." - }, - { - "id": 132701, - "strid": "6d7ffbb9-ddf1-4b33-9323-867e4811fd50", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 1680.947, - 1424.183, - 643.2029999999997, - 372.3800000000001 - ], - "priority": 16, - "parents": [ - 132685 - ], - "children": [], - "area": 2393976.141301, - "iscrowd": 0, - "segmentation": [] + "text": "Results" }, { - "id": 132702, - "strid": "629a3321-ffa5-4dee-9139-5c0046efa1a6", - "image_id": 205650, - "image_name": "15506.png", + "id": 989, + "strid": "86d2f9a5-9c00-4077-83ce-98e4ca4f2a78", + "image_id": 38, + "image_name": "11536.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2372.285, - 1088.816, - 897.8600000000001, - 796.6319999999998 + 4467.941, + 913.163, + 1024.4210000000003, + 1641.25 ], - "priority": 17, + "priority": 19, "parents": [ - 132685 + 988 ], - "children": [], - "area": 2582981.86456, + "children": [ + 990 + ], + "area": 4079958.407383, "iscrowd": 0, "segmentation": [] }, { - "id": 132696, - "strid": "3f8ac1c6-6c62-4ab4-8147-921b89f888f0", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 3, - "category_name": "Text", + "id": 990, + "strid": "1ed2ff12-bbaf-431b-863e-daabceb57ac4", + "image_id": 38, + "image_name": "11536.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1684.863, - 1895.992, - 1537.204, - 274.70000000000005 + 4766.03, + 2568.636, + 430.16499999999996, + 45.128000000000156 ], - "priority": 18, + "priority": 20, "parents": [ - 132685 + 989 ], "children": [], - "area": 3194486.769096, + "area": 12242196.23508, "iscrowd": 0, "segmentation": [], - "text": "The ModelRX case study suggests a workflow that produces semantically annotated\npredictive models that can be shared, tested, validated and eventually applied for\npredicting adverse effect of substances in a safe by design and/or risk assessment\nregulatory framework.\n\nThe following tools are available in the area of modelling for prediction or read\nacross:" + "text": "Figure: Simulation results" }, { - "id": 132707, - "strid": "88f7cb00-6fbb-4916-b1db-607888d219a8", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 7, - "category_name": "Table", + "id": 991, + "strid": "c67086a5-3582-4218-9b56-9146f99519f6", + "image_id": 38, + "image_name": "11536.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1686.663, - 2179.589, - 1591.629, - 914.482 + 4819.705, + 2756.455, + 319.3770000000004, + 53.14899999999989 ], - "priority": 19, + "priority": 21, "parents": [ - 132685 + 970 ], - "children": [], - "area": 3676232.1215069997, + "children": [ + 992 + ], + "area": 13285299.945775, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Discussion" }, { - "id": 132700, - "strid": "fe75ff87-ed06-4d39-b75c-bc1b8d7adbe1", - "image_id": 205650, - "image_name": "15506.png", + "id": 992, + "strid": "c86833a3-ad24-40df-aafd-a0759f9bcae1", + "image_id": 38, + "image_name": "11536.png", "category_id": 4, "category_name": "List", "bbox": [ - 1679.084, - 3141.542, - 1590.9459999999997, - 336.06500000000005 + 4052.905, + 2913.666, + 1846.9389999999999, + 588.1509999999998 ], - "priority": 20, + "priority": 22, "parents": [ - 132685 + 991 ], "children": [], - "area": 5274912.907528, + "area": 11808811.499730002, "iscrowd": 0, "segmentation": [] }, { - "id": 132695, - "strid": "c3506c87-f92e-48d4-a1ab-399fb0ae422f", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 3, - "category_name": "Text", - "bbox": [ - 1681.535, - 3518.764, - 1591.736, - 284.826 - ], - "priority": 21, - "parents": [ - 132685 - ], - "children": [], - "area": 5916924.822740001, - "iscrowd": 0, - "segmentation": [], - "text": "The produced models contain all the necessary metadata and ontological information\nto make them easily searchable and define systematically and rigorously their domain\nof applicability.\n\nMost importantly, the produced resources are not just a static representation of the\nmodels, but actual web applications where the users can supply the necessary\ninformation for query substances and receive the predictions for their adverse effects." - }, - { - "id": 132688, - "strid": "3967a770-04b3-4d79-9c87-1ceca3a1aa29", - "image_id": 205650, - "image_name": "15506.png", + "id": 993, + "strid": "a79cac50-c00a-49a6-88e9-523c1beb6df0", + "image_id": 38, + "image_name": "11536.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2271.09, - 3873.912, - 422.1289999999999, - 52.41600000000017 + 4816.279, + 3603.156, + 326.491, + 49.57499999999982 ], - "priority": 22, + "priority": 23, "parents": [ - 132708 + 970 ], "children": [ - 132706 + 994 ], - "area": 8798002.80408, + "area": 17353804.576524, "iscrowd": 0, "segmentation": [], - "text": "Other resources" + "text": "References" }, { - "id": 132706, - "strid": "5543964e-dd88-4b98-89f4-53ab91d58626", - "image_id": 205650, - "image_name": "15506.png", + "id": 994, + "strid": "a7364146-d793-4174-9c44-ec0f32e667e2", + "image_id": 38, + "image_name": "11536.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1679.959, - 3964.305, - 1550.061, - 327.1749999999997 + 4054.042, + 3748.135, + 1854.65, + 177.14499999999998 ], - "priority": 23, + "priority": 24, "parents": [ - 132688 + 993 ], "children": [], - "area": 6659869.863495, + "area": 15195096.71167, "iscrowd": 0, "segmentation": [], - "text": "RevK Case Study\n\nDescription, Technical Implementation, Outcomes, Service catalog, Tutorial and report are available\nhere:\n\nhttps://openrisknet.org/e-infrastructure/development/case-studies/case-study-revk/\n\nModelRX Case Study\n\nDescription, Technical Implementation, Outcomes, Service catalog, Webinar recording and\npresentation are available here:\nhttps://openrisknet.org/e-infrastructure/development/case-studies/case-study-modelrx/" + "text": "Dux, P. E. and Marois, R. (2009). The attentional blink: A review of data and theory. Attention, Perception, & Psychophysics, 71(8):1683-1700.\n\nPotter, M. C., Wyble, B., Hagmann, C. E., and McCourt, E. S. (2014). Detecting meaning in rsvp at 13 ms per picture. Attention, Perception, & Psychophysics, 76(2):270-279.\n\nRaymond, J. E., Shapiro, K. L., and Arnell, K. M. (1992). Temporary suppression of visual processing in an rsvp task: An attentional blink? Journal of experimental psychology: Human\nperception and performance, 18(3):849.\n\nTsotsos, J. K. and Kruijne, W. (2014). Cognitive programs: Software for attention’s executive. Frontiers in Psychology, 5(1260)." }, { - "id": 132689, - "strid": "782ad6fe-132b-47e6-a3d2-70c0c0be294a", - "image_id": 205650, - "image_name": "15506.png", + "id": 995, + "strid": "cc127192-a741-4efe-a531-8b3fe5f2bd4a", + "image_id": 38, + "image_name": "11536.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2223.507, - 4325.855, - 511.7040000000002, - 63.051000000000386 + 4691.485, + 4000.283, + 576.1999999999998, + 64.96399999999994 ], - "priority": 24, + "priority": 25, "parents": [ - 132708 + 970 ], "children": [ - 132694, - 132705 + 996 ], - "area": 9618568.873484999, + "area": 18767267.690254997, "iscrowd": 0, "segmentation": [], "text": "Acknowledgements" }, { - "id": 132694, - "strid": "c4c31e1b-9d68-462a-ae43-60d57ffaa9f8", - "image_id": 205650, - "image_name": "15506.png", + "id": 996, + "strid": "0d9f14dd-30f2-4ba6-8b00-b7a827ff5f33", + "image_id": 38, + "image_name": "11536.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1747.49, - 4465.345, - 1047.89, - 160.84900000000016 - ], - "priority": 25, - "parents": [ - 132689 - ], - "children": [], - "area": 7803145.73405, - "iscrowd": 0, - "segmentation": [], - "text": "OpenRiskNet (Project no. 731075) is funded by the\nEuropean Commission within the\nHorizon 2020 Programme" - }, - { - "id": 132705, - "strid": "493ba4b0-11a5-475a-9a6c-117656b4a266", - "image_id": 205650, - "image_name": "15506.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 2842.505, - 4426.909, - 341.9250000000002, - 227.94999999999982 + 4053.692, + 4134.397, + 1684.3670000000002, + 26.765000000000327 ], "priority": 26, "parents": [ - 132689 + 995 ], "children": [], - "area": 12583510.967045, + "area": 16759572.043724, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "This research was supported by the Air Force Office for Scientific Research (USA) grant no. FA9550-14-1-0393 and the Canada Research Chairs Program awarded to JT." }, { - "id": 152701, - "strid": "82e1d3ce-edd8-430a-9570-d50ffe795650", - "image_id": 206444, - "image_name": "21463.png", + "id": 997, + "strid": "da91d603-23ec-4f94-aa28-1aa72469f27a", + "image_id": 39, + "image_name": "116600.png", "category_id": 9, "category_name": "Root", "bbox": [ - 77.77, - 24.78, - 543.08, - 53.629999999999995 + 11.28, + 15.72, + 59.14, + 421.34 ], "priority": -1, "parents": [], "children": [ - 152676, - 152677, - 152679, - 152675, - 152680, - 152678 + 1002, + 998, + 1016, + 1006, + 1045, + 999, + 1047, + 1049, + 1035, + 1028, + 1000 ], - "area": 1927.1406, + "area": 177.3216, "iscrowd": 0, "segmentation": [] }, { - "id": 152675, - "strid": "5949232f-2c3c-406d-a6d9-e47b654cf184", - "image_id": 206444, - "image_name": "21463.png", + "id": 998, + "strid": "561a0142-f9e4-4966-9e77-c857efe1105f", + "image_id": 39, + "image_name": "116600.png", "category_id": 1, "category_name": "Title", "bbox": [ - 96.018, - 125.079, - 3156.709, - 232.822 + 740.79, + 90.889, + 1827.286, + 209.19599999999997 ], "priority": 1, "parents": [ - 152701 + 997 ], "children": [], - "area": 12009.835422, + "area": 67329.66231, "iscrowd": 0, "segmentation": [], - "text": "Structure-activity relationships generated for peptaibols produced\nby Trichoderma: via accelerated MD simulations" + "text": "Aligning fundus images via the automatic\nextraction of retinal surface vessels" }, { - "id": 152676, - "strid": "af133ab6-de3f-4125-8531-576b401acc6b", - "image_id": 206444, - "image_name": "21463.png", + "id": 999, + "strid": "165d3350-077b-4373-a25e-a71355cac8eb", + "image_id": 39, + "image_name": "116600.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 327.951, - 415.01, - 2687.843, - 214.24900000000002 + 794.039, + 327.295, + 1722.6990000000003, + 113.35200000000003 ], "priority": 2, "parents": [ - 152701 + 997 ], "children": [], - "area": 136102.94451, + "area": 259884.994505, "iscrowd": 0, "segmentation": [], - "text": "Dora Balazs, Tamas Marik, Andras Szekeres, Csaba Vagvolgyi, Laszlo Kredics, Chetna Tyagi\n\nDepartment of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary\ndora.balazs91@gmail.com" + "text": "Sven Holm and Dr Niall McLoughlin\n\nFaculty of Life Sciences, Carys Bannister Building, University of Manchester, Manchester, M13 9PL, UK" }, { - "id": 152677, - "strid": "175b94e6-8206-448a-bd02-1ffdda5614ef", - "image_id": 206444, - "image_name": "21463.png", + "id": 1000, + "strid": "83dcb140-d3e6-406b-bad4-a7ee75dc4f6f", + "image_id": 39, + "image_name": "116600.png", "category_id": 5, "category_name": "Section", "bbox": [ - 184.4, - 692.279, - 428.611, - 54.68100000000004 + 424.577, + 578.514, + 254.322, + 35.884000000000015 ], "priority": 3, "parents": [ - 152701 + 997 ], "children": [ - 152681, - 152682 + 1001 ], - "area": 127656.2476, + "area": 245623.738578, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 152681, - "strid": "2f116e03-4e43-4a83-b221-82e91a13ee0f", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 4, - "category_name": "List", + "id": 1001, + "strid": "c87b4380-c82d-4d32-80be-2e8229d8ff5d", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 123.612, - 825.644, - 840.204, - 897.856 + 85.558, + 742.536, + 928.109, + 1159.9969999999998 ], "priority": 4, "parents": [ - 152677 + 1000 ], "children": [], - "area": 102059.506128, + "area": 63529.895088, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Extraction of retinal surface vessels allows for fast reg-\nistration of human fundus images. Two unsupervised,\nautomatic blood vessel extraction algorithms were im-\nplemented. The first approach enhanced the surface\nvessels by applying Gabor filters (Oloumi et al, 2007).\nThe second approach combines multiple preprocessing\nsteps to reduce the influence of noise within the images\n(such as the central light reflex) (Marin et al, 2011). Both\napproaches resulted in similar accuracy (~94%) when\napplied to the DRIVE database of fundus images (Staal\net al, 2004).\n\nSpectroscopic fundus images were then aligned using\nthe outputs of each approach. In particular, the auto-\nmatically generated vessel masks for each fundus im-\nage were shifted. both vertically and horizontally rela-\ntive to a reference vessel mask. For each possible shift,\nthe absolute difference between the two masks was\ncomputed. The translation that generates the minimal\ndifference between the two masks was used to align the\nraw images. Thus, translations, resulting from minor\neye tremors and movements, were corrected. Spectro-\nscopic fundus images can then be used to calculate the\nrelative oxygenation of different retinal compartments." }, { - "id": 152682, - "strid": "e19a7438-3154-488a-9f12-3fd8eb8b4a37", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 2, - "category_name": "Figure", + "id": 1002, + "strid": "9d301c06-01e0-4226-add5-da05b0a0a16f", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1006.728, - 846.072, - 307.2199999999999, - 829.493 + 298.965, + 2027.114, + 502.84599999999995, + 96.57999999999993 ], "priority": 5, "parents": [ - 152677 + 997 ], "children": [ - 152683 + 1003, + 1005 ], - "area": 851764.372416, + "area": 606036.13701, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "VESSEL EXTRACTION:\nDRIVE DATABASE" }, { - "id": 152683, - "strid": "36d74d98-a665-43fa-930d-edeae7667f26", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1003, + "strid": "1c92c4b0-473b-4dcb-bb80-eaa5d95fc9c1", + "image_id": 39, + "image_name": "116600.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 854.747, - 1748.821, - 459.4409999999999, - 42.309999999999945 + 297.975, + 2158.977, + 507.06499999999994, + 523.0630000000001 ], "priority": 6, "parents": [ - 152682 + 1002 ], - "children": [], - "area": 1494799.5032869999, + "children": [ + 1004 + ], + "area": 643321.171575, "iscrowd": 0, - "segmentation": [], - "text": "Figure 1. Peptaibol sequence" + "segmentation": [] }, { - "id": 152678, - "strid": "db6a694e-f378-4f19-9f43-a5e99f230f0e", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 5, - "category_name": "Section", + "id": 1004, + "strid": "aabdaee9-b126-4770-a05d-5bcf97376f10", + "image_id": 39, + "image_name": "116600.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1501.158, - 693.888, - 740.1219999999998, - 52.299999999999955 + 85.531, + 2716.321, + 489.08, + 35.4050000000002 ], "priority": 7, "parents": [ - 152701 + 1003 ], - "children": [ - 152688, - 152689, - 152684, - 152685 - ], - "area": 1041635.522304, + "children": [], + "area": 232329.651451, "iscrowd": 0, "segmentation": [], - "text": "METHODS AND MATERIAL" + "text": "" }, { - "id": 152684, - "strid": "3911157f-5e44-4a39-9e46-0b770f75edc1", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 4, - "category_name": "List", + "id": 1005, + "strid": "ff3f35ca-c6ae-4a4b-b005-d4e015e524e9", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1452.362, - 814.452, - 911.8130000000001, - 399.9179999999999 + 85.432, + 2763.784, + 924.112, + 237.17500000000018 ], "priority": 8, "parents": [ - 152678 + 1002 ], "children": [], - "area": 1182879.135624, + "area": 236115.594688, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The DRIVE database (Staal et al, 2004) consists of 40\nRGB retinal fundus images (45° field-of-view, 768 x 584\npixels), 20 of which were grouped into a test set. Both\nvessel extraction algorithms were applied to the test set\nimages." }, { - "id": 152685, - "strid": "c82982ba-53d4-41d4-9f26-4187408fa9ed", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 2, - "category_name": "Figure", + "id": 1006, + "strid": "903fa212-e51b-41f6-892b-c6f5e815ba74", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1538.972, - 1237.108, - 769.7279999999998, - 391.76700000000005 + 219.018, + 3068.16, + 666.091, + 98.61400000000003 ], "priority": 9, "parents": [ - 152678 + 997 ], "children": [ - 152686 + 1009, + 1012, + 1008, + 1011, + 1007, + 1015, + 1010, + 1013, + 1014 ], - "area": 1903874.572976, + "area": 671982.26688, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "VESSEL EXETRACTION:\nNOISE REMOVAL APPROACH" }, { - "id": 152686, - "strid": "d8e201f0-c4b6-4a4e-9a5a-9059cc47e37f", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1007, + "strid": "173faa1a-5e42-4607-9e03-3444a0877012", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1464.936, - 1658.847, - 878.5179999999998, - 137.82500000000005 + 365.877, + 3256.484, + 370.55, + 42.26800000000003 ], "priority": 10, "parents": [ - 152685 + 1006 ], "children": [], - "area": 2430104.688792, + "area": 1191472.596468, "iscrowd": 0, "segmentation": [], - "text": "Figure 2. T. reesei SZMC 22616 against Gram-positive C.\nmichiganensis (A), T. longibrachiatum f. bissettii SZMC\n12546 against Gram-negative R. radiobacter (B)" + "text": "Grey-scale conversion" }, { - "id": 152688, - "strid": "c33525bd-d24e-4c51-b9d3-470132bf8bba", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 7, - "category_name": "Table", + "id": 1008, + "strid": "d9bd0de1-2ff2-43fd-a44f-c2fd0a070496", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2383.825, - 924.87, - 852.031, - 382.3659999999999 + 782.745, + 3343.048, + 221.61, + 32.22699999999986 ], "priority": 11, "parents": [ - 152678 - ], - "children": [ - 152687 + 1006 ], - "area": 2204728.2277499996, + "children": [], + "area": 2616754.10676, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "CLR removal" }, { - "id": 152687, - "strid": "a357b438-f0cb-4d2f-9ecf-796c52e5224c", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1009, + "strid": "31422d03-e33f-4e34-a601-c03fd7bfcf54", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2388.145, - 823.329, - 819.1869999999999, - 83.93600000000004 + 362.222, + 3417.578, + 378.322, + 33.90299999999979 ], "priority": 12, "parents": [ - 152688 + 1006 ], "children": [], - "area": 1966229.0347049998, + "area": 1237921.938316, "iscrowd": 0, "segmentation": [], - "text": "Table 1. Peptaibol sequences from the Trichoderma\nstrains selected for aMD simulations" + "text": "Contrast enhancement" }, { - "id": 152689, - "strid": "a9ff2231-ab77-4ad9-82d4-7d886969135a", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 4, - "category_name": "List", + "id": 1010, + "strid": "0cd15ccc-6ecf-467d-83e6-37916677bc71", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2363.975, - 1347.254, - 863.1010000000001, - 456.57500000000005 + 349.684, + 3531.46, + 402.618, + 41.88000000000011 ], "priority": 13, "parents": [ - 152678 + 1006 ], "children": [], - "area": 3184874.7746499996, + "area": 1234895.0586400002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Background subtraction" }, { - "id": 152679, - "strid": "e6de1574-dec5-48a0-bca1-49d0c4ec71c4", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 5, - "category_name": "Section", + "id": 1011, + "strid": "eacecf8e-a32a-4832-9ad4-58e5855821d9", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 184.113, - 1919.521, - 229.11399999999998, - 54.27500000000009 + 379.322, + 3640.344, + 343.909, + 44.02399999999989 ], "priority": 14, "parents": [ - 152701 + 1006 ], - "children": [ - 152692, - 152699, - 152696, - 152693, - 152691, - 152694 - ], - "area": 353408.769873, + "children": [], + "area": 1380862.5667680001, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Gaussian smoothing" }, { - "id": 152691, - "strid": "11f896fa-41e3-4d87-bd4a-d834d0e1f501", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 7, - "category_name": "Table", + "id": 1012, + "strid": "3adebe59-eb05-4672-922a-92c90eb4e888", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 137.412, - 2182.968, - 1544.446, - 551.2579999999998 + 373.755, + 3753.704, + 355.12199999999996, + 32.0329999999999 ], "priority": 15, "parents": [ - 152679 - ], - "children": [ - 152690 + 1006 ], - "area": 299965.998816, + "children": [], + "area": 1402965.63852, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "H-maxima transform" }, { - "id": 152690, - "strid": "ac58987e-10be-4213-bcc4-37d73b229a9e", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1013, + "strid": "046425bc-3253-4a96-a359-97bee4011ad9", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 200.486, - 2070.701, - 1418.518, - 89.38999999999987 + 437.75, + 3862.731, + 226.17700000000002, + 43.465000000000146 ], "priority": 16, "parents": [ - 152691 + 1006 ], "children": [], - "area": 415146.560686, + "area": 1690910.4952500002, "iscrowd": 0, "segmentation": [], - "text": "Table 2. Minimum inhibitory concentration (MIC) values of the purified peptaibol extracts\nagainst Gram-positive and Gram-negative bacteria (n/a: no data)" + "text": "Thresholding" }, { - "id": 152692, - "strid": "f2651882-d923-4ae5-ac3d-b3b393b775dd", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 4, - "category_name": "List", + "id": 1014, + "strid": "16b0361b-21b3-4246-9625-e2f10f95253f", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1717.9, - 2104.976, - 1465.534, - 573.123 + 269.411, + 3975.416, + 562.675, + 41.903999999999996 ], "priority": 17, "parents": [ - 152679 + 1006 ], "children": [], - "area": 3616138.2704000003, + "area": 1071020.799976, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Post-processing for noise removal" }, { - "id": 152694, - "strid": "31a8a4ff-a092-4d13-a392-b6fceef9ba46", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 2, - "category_name": "Figure", + "id": 1015, + "strid": "a607aacd-deb8-46de-aa28-5fd6689c7c02", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 108.268, - 2749.521, - 867.125, - 1666.453 + 86.671, + 4075.625, + 925.176, + 282.15499999999975 ], "priority": 18, "parents": [ - 152679 + 1006 ], - "children": [ - 152695 - ], - "area": 297685.13962800003, + "children": [], + "area": 353238.494375, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Each image was processed twice, once with central\nlight reflex (CLR) removal (Marin et al, 2011) and once\nwithout. The two resulting images were combined after\nthe noise removal stage. Most of the remaining pre-\nand post-processing steps were based on (Saleh and\nEswaran, 2011)." }, { - "id": 152695, - "strid": "de759af3-f63c-47e8-bb7e-ecfe0f807136", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1016, + "strid": "b8e3aaa8-9239-4891-a04a-70acc33e1636", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 262.347, - 4427.451, - 620.379, - 88.51000000000022 + 1348.684, + 547.57, + 616.201, + 98.94500000000005 ], "priority": 19, "parents": [ - 152694 + 997 ], - "children": [], - "area": 1161528.487497, + "children": [ + 1019, + 1017, + 1018, + 1024, + 1020, + 1022, + 1023, + 1021, + 1027, + 1025 + ], + "area": 738498.8978800001, "iscrowd": 0, "segmentation": [], - "text": "Figure 4. The most produced peptaibol\n(Pept-B-XXVII) from group B" + "text": "VESSEL EXTRACTION:\nGABOR FILTER APPROACH" }, { - "id": 152693, - "strid": "bb8a6ea9-3b1f-498f-b880-da6fef92eb4a", - "image_id": 206444, - "image_name": "21463.png", + "id": 1017, + "strid": "97719d10-ba99-493b-a34f-f5cb3f80831a", + "image_id": 39, + "image_name": "116600.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1038.29, - 2793.297, - 1389.755, - 94.59799999999996 + 1472.308, + 690.242, + 370.001, + 38.210000000000036 ], "priority": 20, "parents": [ - 152679 + 1016 ], "children": [], - "area": 2900252.34213, + "area": 1016248.818536, "iscrowd": 0, "segmentation": [], - "text": "The most stable conformational states of sequences from group A and B were\ndetermined using the aMD simulation technique (Figure 3)." + "text": "Grey-scale conversion" }, { - "id": 152696, - "strid": "40090894-953a-4700-af7c-4dc582b6596a", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 2, - "category_name": "Figure", + "id": 1018, + "strid": "960a6f5b-b4dc-4a42-8f3e-f61ba1bd6f3b", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 975.506, - 2905.251, - 1473.1660000000002, - 473.9670000000001 + 1508.924, + 791.971, + 294.82500000000005, + 40.23599999999999 ], "priority": 21, "parents": [ - 152679 - ], - "children": [ - 152697 + 1016 ], - "area": 2834089.782006, + "children": [], + "area": 1195024.049204, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Invert grey-levels" }, { - "id": 152697, - "strid": "071c5a9d-6645-4d4d-9fdb-fe0b75752cba", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1019, + "strid": "e3f25786-1b72-4e92-a540-7bc844b12275", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1006.094, - 3394.808, - 1468.6390000000001, - 92.53600000000006 + 1454.571, + 901.296, + 403.4850000000001, + 41.60400000000004 ], "priority": 22, "parents": [ - 152696 + 1016 ], "children": [], - "area": 3415495.959952, + "area": 1310999.024016, "iscrowd": 0, "segmentation": [], - "text": "Figure 3. The three-dimensional representative models of the first three most-populated\nclusters in the case of Pept-B-XXVII (B) from the group B and Pept-A-lVa (A) from the group A" + "text": "Background subtraction" }, { - "id": 152699, - "strid": "46825e0d-eee5-4abc-9d0b-b6db52f24c52", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 2, - "category_name": "Figure", + "id": 1020, + "strid": "841c0d4d-24d2-47e1-bb97-596874396c57", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2530.902, - 2728.636, - 709.8040000000001, - 1679.8849999999998 + 1235.123, + 1013.06, + 842.5279999999998, + 42.31099999999992 ], "priority": 23, "parents": [ - 152679 - ], - "children": [ - 152700 + 1016 ], - "area": 6905910.309672, + "children": [], + "area": 1251253.7063799999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Assign non-ROI pixel mean intensity of ROI pixels" }, { - "id": 152700, - "strid": "b12031b5-4a17-4f90-b9c9-435982ffb529", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 6, - "category_name": "Caption", + "id": 1021, + "strid": "8b167e06-22be-4b62-887f-12633fdfdc9a", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2570.469, - 4432.495, - 619.3130000000001, - 90.3779999999997 + 1530.99, + 1124.386, + 249.48199999999997, + 41.708000000000084 ], "priority": 24, "parents": [ - 152699 + 1016 ], "children": [], - "area": 11393590.990155, + "area": 1721423.72214, "iscrowd": 0, "segmentation": [], - "text": "Figure 5. The most produced peptaibol\n(Pept-A-IVa) from group A" + "text": "Gabor filtering" }, { - "id": 152680, - "strid": "d43cf889-a0ff-4e24-9690-e0acee42f03b", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 5, - "category_name": "Section", + "id": 1022, + "strid": "89c1df1b-6ab7-4c8d-a519-8f37dacdbb7b", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1089.222, - 3608.895, - 420.60300000000007, - 57.76499999999987 + 1226.422, + 1235.507, + 861.7599999999998, + 33.815000000000055 ], "priority": 25, "parents": [ - 152701 - ], - "children": [ - 152698 + 1016 ], - "area": 3930887.82969, + "children": [], + "area": 1515252.9659540001, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Normalisation to unit mean and standard deviation" }, { - "id": 152698, - "strid": "c2121321-36b1-41cd-807e-1cbf9dca18d5", - "image_id": 206444, - "image_name": "21463.png", - "category_id": 4, - "category_name": "List", + "id": 1023, + "strid": "8116f494-feb2-44a2-be7e-adbd78c976b5", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1043.885, - 3727.807, - 1370.2609999999997, - 664.2280000000001 + 1248.881, + 1344.804, + 816.4959999999999, + 43.59899999999993 ], "priority": 26, "parents": [ - 152680 + 1016 ], "children": [], - "area": 3891401.810195, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 92366, - "strid": "f3323082-c86e-4a1f-80c7-bffe2ded1379", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 9, - "category_name": "Root", - "bbox": [ - 129.16, - 137.77, - 162.58, - 154.03 - ], - "priority": -1, - "parents": [], - "children": [ - 92313, - 92320, - 92319, - 92318, - 92314, - 92316, - 92317, - 92315 - ], - "area": 17794.3732, + "area": 1679500.1643240002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Thresholding and combination of different scales" }, { - "id": 92313, - "strid": "36b5448d-9471-4346-9647-e8d9865e1598", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 1, - "category_name": "Title", + "id": 1024, + "strid": "aadebaa0-28f0-4fec-b468-158df24c9890", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 424.376, - 94.537, - 1924.9960000000003, - 343.57899999999995 + 1191.042, + 1417.925, + 929.8240000000001, + 184.8209999999999 ], - "priority": 1, + "priority": 27, "parents": [ - 92366 + 1016 ], "children": [], - "area": 40119.233912, + "area": 1688808.22785, "iscrowd": 0, "segmentation": [], - "text": "Cross-presentation of the oncofetal tumor\nantigen 514 from irradiated prostate cancer\ng¢s cells —a key role for Hsp70" + "text": "Each image was filtered with differently oriented Gabor\nfilters. For each scale only the maximum response of\nthe differently oriented filters was kept. The Gabor fil-\nters were defined as in Oloumi et al (2007)." }, { - "id": 92314, - "strid": "ff975d35-6e5e-4a2b-858c-495f40e71ca1", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 0, - "category_name": "Author Info", + "id": 1025, + "strid": "f91c7b2a-ead7-46cc-93a9-3f7e42e48655", + "image_id": 39, + "image_name": "116600.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 62.599, - 510.953, - 2630.432, - 223.447 + 1189.996, + 1669.982, + 931.989, + 419.05600000000004 ], - "priority": 2, + "priority": 28, "parents": [ - 92366 + 1016 ], - "children": [], - "area": 31985.146846999996, + "children": [ + 1026 + ], + "area": 1987271.9000720002, "iscrowd": 0, - "segmentation": [], - "text": "J Salimu, L.K Spary, S Al-Taei and Z Tabi.\n\nInstitute of Cancer and Genetics, Cardiff University, Cardiff, United Kingdom." + "segmentation": [] }, { - "id": 92315, - "strid": "151a7bed-376b-4bf7-b773-cf40b1ac671c", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 5, - "category_name": "Section", + "id": 1026, + "strid": "75f1fc03-6eab-4b42-a578-46d8c8cb495d", + "image_id": 39, + "image_name": "116600.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 66.389, - 829.347, - 266.699, - 38.722999999999956 + 1191.036, + 2112.788, + 903.2089999999998, + 81.70699999999988 ], - "priority": 3, + "priority": 29, "parents": [ - 92366 - ], - "children": [ - 92339 + 1025 ], - "area": 55059.517983, + "children": [], + "area": 2516406.568368, "iscrowd": 0, "segmentation": [], - "text": "Introduction" + "text": "FIGURE 2: Two examples of differently oriented Ga-\nbor filters" }, { - "id": 92339, - "strid": "e60a446e-3ba4-4cd8-a0f0-551e7919da5d", - "image_id": 204078, - "image_name": "121417.png", + "id": 1027, + "strid": "a4c90545-38ab-4a98-8696-0a4b4eeaf989", + "image_id": 39, + "image_name": "116600.png", "category_id": 3, "category_name": "Text", "bbox": [ - 76.894, - 913.498, - 803.655, - 264.51 + 1191.346, + 2225.044, + 894.2739999999999, + 43.40599999999995 ], - "priority": 4, + "priority": 30, "parents": [ - 92315 + 1016 ], "children": [], - "area": 70242.51521200001, + "area": 2650797.2692239997, "iscrowd": 0, "segmentation": [], - "text": "Immune responses contribute to the success of radiation therapy\nof solid tumors; however, the mechanism of triggering CD8* T\ncell responses is poorly understood. Antigen cross-presentation\nfrom tumor cells by dendritic cells (DC) is a likely dominant\nmechanism to achieve CD8* T cell stimulation. We established a\ncross-presentation model in prostate cancer (PCa) in which DC\npresent a naturally expressed oncofetal tumor antigen (514)\nfrom irradiated DU145 tumor cells to 5T4-specific T cells." + "text": "Left: Filter oriented at 0°. Right: Filter oriented at 135°." }, { - "id": 92316, - "strid": "2b1d002c-3775-494a-b92f-019d518bd920", - "image_id": 204078, - "image_name": "121417.png", + "id": 1028, + "strid": "6c7a16eb-02c7-40d1-9a4f-a104341bb4d6", + "image_id": 39, + "image_name": "116600.png", "category_id": 5, "category_name": "Section", "bbox": [ - 63.642, - 1211.419, - 90.787, - 38.478000000000065 + 1403.524, + 2348.402, + 502.02, + 96.57600000000002 ], - "priority": 5, + "priority": 31, "parents": [ - 92366 + 997 ], "children": [ - 92340 + 1029, + 1031, + 1032, + 1034 ], - "area": 77097.12799800001, + "area": 3296038.568648, "iscrowd": 0, "segmentation": [], - "text": "Aim" - }, - { - "id": 92340, - "strid": "2a3d7c5f-96b6-4796-b6df-ca483a0fe687", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 104.362, - 1303.051, - 652.988, - 60.7829999999999 - ], - "priority": 6, - "parents": [ - 92316 - ], - "children": [], - "area": 135989.008462, - "iscrowd": 0, - "segmentation": [] + "text": "VESSEL EXTRACTION:\nRESULTS" }, { - "id": 92317, - "strid": "f426c218-de36-4043-b1c0-0309a89fcfa2", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 5, - "category_name": "Section", + "id": 1029, + "strid": "d2cfc7c3-2142-4254-9e2b-134fffac3da3", + "image_id": 39, + "image_name": "116600.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 67.283, - 1424.371, - 260.695, - 47.881000000000085 + 1195.982, + 2490.972, + 921.06, + 468.067 ], - "priority": 7, + "priority": 32, "parents": [ - 92366 + 1028 ], "children": [ - 92341 + 1030 ], - "area": 95835.953993, + "area": 2979157.674504, "iscrowd": 0, - "segmentation": [], - "text": "Key Players" + "segmentation": [] }, { - "id": 92341, - "strid": "cd5f7bb8-6c49-4557-8512-319442402cdf", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 2, - "category_name": "Figure", + "id": 1030, + "strid": "3af2612c-7b25-4baa-8d1d-4214294cc1af", + "image_id": 39, + "image_name": "116600.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 113.718, - 1497.009, - 690.923, - 245.26199999999994 + 1191.198, + 3003.699, + 666.6589999999999, + 32.39399999999978 ], - "priority": 8, + "priority": 33, "parents": [ - 92317 + 1029 ], "children": [], - "area": 170236.869462, + "area": 3578000.241402, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "FIGURE 3: Automatic vessel extraction" }, { - "id": 92318, - "strid": "2189d236-5f4d-4ec6-8bab-961896904dbc", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 5, - "category_name": "Section", + "id": 1031, + "strid": "46c8d034-5e1a-4a2d-beb6-06af228a6903", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 66.746, - 1783.755, - 461.94500000000005, - 42.47399999999993 + 1190.817, + 3049.62, + 920.5500000000002, + 189.89699999999993 ], - "priority": 9, + "priority": 34, "parents": [ - 92366 - ], - "children": [ - 92334, - 92326, - 92360, - 92330, - 92361, - 92332, - 92337, - 92329, - 92348, - 92362, - 92344, - 92323, - 92359, - 92336, - 92342, - 92325, - 92365, - 92328, - 92347, - 92358, - 92324, - 92349, - 92338, - 92364, - 92331, - 92333, - 92346, - 92335, - 92345, - 92327, - 92343, - 92363 + 1028 ], - "area": 119058.51123, + "children": [], + "area": 3631539.33954, "iscrowd": 0, "segmentation": [], - "text": "Methods and Results" + "text": "The automatic extraction for the fundus image shown\nin figure 1 using the noise removal (left) and Gabor fil-\nter (right) approaches. Green: True positives. Red: False\nnegatives. Blue: False positives." }, { - "id": 92343, - "strid": "06e98870-9451-4a06-b3cb-5c0c2e8a1c61", - "image_id": 204078, - "image_name": "121417.png", + "id": 1032, + "strid": "39e24a1f-3247-415e-9c5a-42d81e36eba4", + "image_id": 39, + "image_name": "116600.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 59.604, - 1968.938, - 838.548, - 275.9319999999998 + 1225.884, + 3365.749, + 866.779, + 544.2260000000001 ], - "priority": 10, + "priority": 35, "parents": [ - 92318 + 1028 ], "children": [ - 92355 + 1033 ], - "area": 117356.580552, + "area": 4126017.847116, "iscrowd": 0, "segmentation": [] }, { - "id": 92355, - "strid": "aad12aa5-070b-44b9-9753-8dd41b5ed38b", - "image_id": 204078, - "image_name": "121417.png", + "id": 1033, + "strid": "bae4fefb-4df9-4ded-bdd0-49241fa3237d", + "image_id": 39, + "image_name": "116600.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 63.4, - 1869.729, - 827.67, - 67.37400000000002 + 1190.693, + 3961.705, + 867.4489999999998, + 40.702000000000226 ], - "priority": 11, + "priority": 36, "parents": [ - 92343 + 1032 ], "children": [], - "area": 118540.8186, + "area": 4717174.411565, "iscrowd": 0, "segmentation": [], - "text": "Figure 1: Irradiation induces immunologically relevant cell\ndeath in PCa cells" + "text": "FIGURE 4: Accuracy of automatic vessel extraction" }, { - "id": 92361, - "strid": "9596cf47-b3ad-4623-9785-29881f8a598d", - "image_id": 204078, - "image_name": "121417.png", + "id": 1034, + "strid": "24f0507e-6bf4-456e-8bc5-1ddc18c43723", + "image_id": 39, + "image_name": "116600.png", "category_id": 3, "category_name": "Text", "bbox": [ - 93.636, - 2271.725, - 793.367, - 38.92399999999998 + 1190.267, + 4008.844, + 910.3219999999999, + 383.7659999999996 ], - "priority": 12, + "priority": 37, "parents": [ - 92318 + 1028 ], "children": [], - "area": 212715.24209999997, + "area": 4771594.721348001, "iscrowd": 0, "segmentation": [], - "text": "Representative dot plots showing different types of cell death and average percentages of DU145 cells labelled with\nAnnexin V and PI (Propidium Iodide), following 12Gy radiation and cultured up to 72 h." + "text": "Both approaches were of similar accuracy (noise re-\nmoval approach: 94.50%, Gabor filter approach:\n94.07%) when applied to the DRIVE database. The\nnoise removal approach extracted a greater proportion\nof the vessels (72.33%) than the Gabor filter approach\n(68.07%). In terms of segmentation noise, both ap-\nproaches performed similarly (percentage of correctly\nsegmented background pixels: ~98%)." }, { - "id": 92330, - "strid": "f0d2c830-b18f-4f58-b8ca-f391e39fe830", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1035, + "strid": "6b43896a-ee39-4fca-b0d7-c07f9f826363", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 98.366, - 2356.554, - 554.015, - 26.172000000000025 + 2494.566, + 579.507, + 529.4659999999999, + 34.936000000000035 ], - "priority": 13, + "priority": 38, "parents": [ - 92318 - ], - "children": [], - "area": 231804.790764, - "iscrowd": 0, - "segmentation": [], - "text": "What type of cell death is induced by irradiation?" - }, - { - "id": 92332, - "strid": "14d5c749-bfc9-4548-a3cd-da2f78e6018f", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 71.03, - 2412.682, - 812.993, - 52.48799999999983 + 997 ], - "priority": 14, - "parents": [ - 92318 + "children": [ + 1041, + 1042, + 1044, + 1036, + 1039, + 1038 ], - "children": [], - "area": 171372.80245999998, + "area": 1445618.4589619997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "IMAGE REGIST\n\nRATION." }, { - "id": 92346, - "strid": "18fd8f3d-b21b-4ed5-888b-39adf2a40fca", - "image_id": 204078, - "image_name": "121417.png", + "id": 1036, + "strid": "500bc263-7c2f-4474-8002-3e833022f7fa", + "image_id": 39, + "image_name": "116600.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 83.205, - 2621.407, - 793.66, - 295.08399999999983 + 2361.476, + 689.956, + 764.6839999999997, + 405.88 ], - "priority": 15, + "priority": 39, "parents": [ - 92318 + 1035 ], "children": [ - 92357 + 1037 ], - "area": 218114.16943500002, + "area": 1629314.535056, "iscrowd": 0, "segmentation": [] }, { - "id": 92357, - "strid": "2d2094b5-12ed-47f9-b614-5e0f5fe80eb8", - "image_id": 204078, - "image_name": "121417.png", + "id": 1037, + "strid": "fab80d7d-752c-4248-9b27-13622bd27904", + "image_id": 39, + "image_name": "116600.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 43.887, - 2502.709, - 867.2920000000001, - 67.40299999999979 + 2295.221, + 1107.846, + 877.431, + 90.2059999999999 ], - "priority": 16, + "priority": 40, "parents": [ - 92346 + 1036 ], "children": [], - "area": 109836.389883, + "area": 2542751.403966, "iscrowd": 0, "segmentation": [], - "text": "Figure 2: Radiation-induced expression of damage-associated\nmolecular patterns (DAMP) in tumor cells" + "text": "FIGURE 5: Schematic diagram of apparatus used to\nobtain spectroscopic fundus images" }, { - "id": 92363, - "strid": "1603c3ad-597a-43ed-8720-81ba223705c7", - "image_id": 204078, - "image_name": "121417.png", + "id": 1038, + "strid": "cbad1596-b1bf-4046-9c42-b6f5a7b48c2c", + "image_id": 39, + "image_name": "116600.png", "category_id": 3, "category_name": "Text", "bbox": [ - 103.191, - 2931.931, - 779.813, - 58.27599999999984 + 2294.378, + 1220.201, + 926.54, + 427.8430000000001 ], - "priority": 17, + "priority": 41, "parents": [ - 92318 + 1035 ], "children": [], - "area": 302548.891821, + "area": 2799602.3299780004, "iscrowd": 0, "segmentation": [], - "text": "(A) ELISA assay was used to detect the concentration of HMGBI passively released into the extracellular space.\n(B) Flow cytometry analysis was used to detect surface expression of Hsp70. The assays were carried out at\ndifferent times (x-axis) after 12Gy irradiation from triplicate cultures. Means+SEM shown." + "text": "A tungsten halogen light (Light Source) produced\nwhite light (black arrows), which were filtered by a\nVariSpec filter (Filter). The filtered light (red arrows)\nwas fed into the fundus camera via a fibre optic cable.\nThe light reflected back out of the subject’s eye (blue ar-\nrows) was captured by a CCD camera with 25° field-of-\nview. The images were then saved on a PC. The PC\nsynchronised the CCD camera (dotted double arrow)\nwith the filter (dotted arrow)." }, { - "id": 92328, - "strid": "6e04cc49-e8bb-4040-8067-e72eed890dfb", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1039, + "strid": "e6fe4b21-54b5-46cc-978a-e7305040011b", + "image_id": 39, + "image_name": "116600.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 75.57, - 3043.986, - 792.373, - 77.11599999999999 + 2297.941, + 1708.966, + 922.0590000000002, + 358.0749999999998 ], - "priority": 18, + "priority": 42, + "parents": [ + 1035 + ], + "children": [ + 1040 + ], + "area": 3927103.0390059995, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1040, + "strid": "8e40f4ff-d903-467a-8398-7f614ee09e4a", + "image_id": 39, + "image_name": "116600.png", + "category_id": 6, + "category_name": "Caption", + "bbox": [ + 2295.45, + 2092.186, + 892.1210000000001, + 90.43299999999999 + ], + "priority": 43, "parents": [ - 92318 + 1039 ], "children": [], - "area": 230034.02201999997, + "area": 4802508.3537, "iscrowd": 0, "segmentation": [], - "text": "Can irradiation induce the upregulation and/or release of danger\nSignals such as Hsp70 and HMGB1 required for efficient cross-\npresentation?" + "text": "FIGURE 6: Aligning fundus images using automati-\ncally extracted surface vessels" }, { - "id": 92327, - "strid": "2afa8fd4-27f0-4a75-83f2-9ceaeb7f8644", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", + "id": 1041, + "strid": "a26456b7-5f9e-4ef3-bb62-27f0cb45d4bc", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 51.929, - 3152.119, - 814.73, - 113.8739999999998 + 2293.904, + 2187.908, + 929.1210000000001, + 384.5819999999999 ], - "priority": 19, + "priority": 44, "parents": [ - 92318 + 1035 ], "children": [], - "area": 163686.38755100002, + "area": 5018850.912831999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The noise removal vessel extraction approach was ap-\nplied to spectroscopic images obtained with the appa-\nratus shown in figure 5 (yellow vessels: A = 605nm;\nblue vessels: A = 586nm). The alignment was obtained\nby shifting the yellow vessels relatively against the blue\nvessels. The shift resulting in the smallest difference\nwas considered to align the two images. Left: Una-\nligned images. Right: Aligned images." }, { - "id": 92349, - "strid": "808541ea-de69-4772-8818-06c4fe46f126", - "image_id": 204078, - "image_name": "121417.png", + "id": 1042, + "strid": "c17b0fb8-1487-4d0f-9f25-d9c4e39f4199", + "image_id": 39, + "image_name": "116600.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 73.625, - 3371.532, - 760.399, - 206.73399999999992 + 2378.912, + 2630.944, + 764.114, + 571.114 ], - "priority": 20, + "priority": 45, "parents": [ - 92318 + 1035 ], "children": [ - 92352 + 1043 ], - "area": 248229.0435, + "area": 6258784.252927999, "iscrowd": 0, "segmentation": [] }, { - "id": 92352, - "strid": "eea3f25c-ed7b-4796-94fc-27972b885549", - "image_id": 204078, - "image_name": "121417.png", + "id": 1043, + "strid": "3659fed1-27b6-4cf7-adf2-e137e22223c4", + "image_id": 39, + "image_name": "116600.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 61.991, - 3281.078, - 705.685, - 32.03200000000015 + 2294.715, + 3214.735, + 612.8670000000002, + 40.91800000000012 ], - "priority": 21, + "priority": 46, "parents": [ - 92349 + 1042 ], "children": [], - "area": 203397.306298, + "area": 7376900.6255250005, "iscrowd": 0, "segmentation": [], - "text": "Figure 3: Irradiated tumor cells are taken up by DC" + "text": "FIGURE 7: Aligning fundus images" }, { - "id": 92364, - "strid": "04b55b7f-a33b-4e8d-a679-44761ef1a75d", - "image_id": 204078, - "image_name": "121417.png", + "id": 1044, + "strid": "7c8ddd4c-d9e5-4d4d-824f-28b3e1c65343", + "image_id": 39, + "image_name": "116600.png", "category_id": 3, "category_name": "Text", "bbox": [ - 53.186, - 3589.663, - 848.941, - 38.73199999999997 + 2294.625, + 3260.652, + 903.4719999999998, + 190.10899999999992 ], - "priority": 22, + "priority": 47, "parents": [ - 92318 + 1035 ], "children": [], - "area": 190919.816318, + "area": 7481973.5955, "iscrowd": 0, "segmentation": [], - "text": "Phagocytosis of DU145 tumor cells by DCs at a 1:1 ratio HLA-DR and CFSE double positive population on dot plot\nrepresents phagocytosis." + "text": "The alignment of two spectroscopic fundus images (Ai\n= 586nm, A2 = 548nm). Each square is taken from one\nimage, while the 4 neighbouring squares belong to the\nalternate image." }, { - "id": 92325, - "strid": "66240aa3-4561-4346-a9ad-ff9c2c38a745", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1045, + "strid": "01005970-4b35-482c-b621-acb9bf1d6796", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 96.065, - 3667.803, - 666.1579999999999, - 25.94900000000007 + 2586.085, + 3550.405, + 346.84799999999996, + 37.715000000000146 ], - "priority": 23, + "priority": 48, "parents": [ - 92318 + 997 ], - "children": [], - "area": 352347.49519499997, + "children": [ + 1046 + ], + "area": 9181649.114425, "iscrowd": 0, "segmentation": [], - "text": "Are irradiated tumor cells taken up more efficiently by DC?" + "text": "" }, { - "id": 92326, - "strid": "8a038b06-743f-403a-b4d0-12fe3b060ff0", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", + "id": 1046, + "strid": "9282f989-0887-46a9-b5ac-b0e0eda9997c", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 71.305, - 3742.143, - 819.847, - 72.86200000000008 + 2294.393, + 3679.993, + 927.864, + 335.58399999999983 ], - "priority": 24, + "priority": 49, "parents": [ - 92318 + 1045 ], "children": [], - "area": 266833.506615, + "area": 8443350.179249, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Both automatic vessel extraction approaches resulted in\naccurate, binary masks of the surface vessels. The im-\nage registration algorithm was sufficiently robust to\ncorrect eye movements in spectroscopic datasets.\nAutomatic vessel extraction can also be used to select a\nspecific vessel segment for further processing, such as\nretinal oximetry measurements." }, { - "id": 92342, - "strid": "3197fd0c-8aed-40af-905c-cbec43840cce", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 2, - "category_name": "Figure", + "id": 1047, + "strid": "9b65c8cb-30bb-41cd-a0e8-b2c1ebe8f62c", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 955.668, - 947.162, - 850.484, - 565.9579999999999 - ], - "priority": 25, + 2486.648, + 4139.071, + 545.7129999999997, + 37.460000000000036 + ], + "priority": 50, "parents": [ - 92318 + 997 ], "children": [ - 92350 + 1048 ], - "area": 905172.414216, + "area": 10292412.624008, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "ACKNOWLEDGEMENTS" }, { - "id": 92350, - "strid": "95c68ed8-2358-4fab-aae0-88a39661ee64", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 6, - "category_name": "Caption", + "id": 1048, + "strid": "326e22bb-59ab-4026-a095-066f78cea713", + "image_id": 39, + "image_name": "116600.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 931.841, - 834.933, - 856.151, - 68.62300000000005 + 2294.801, + 4255.716, + 923.685, + 139.89000000000033 ], - "priority": 26, + "priority": 51, "parents": [ - 92342 + 1047 ], "children": [], - "area": 778024.801653, + "area": 9766021.332516, "iscrowd": 0, "segmentation": [], - "text": "Figure 4: DC activation and tumor antigen cross-presentation\nfollowing uptake of irradiated PCa cells" + "text": "We would like to thank the BBSRC for funding this\ndoctoral work and Prof D. Henson for providing the in-\nfrastructure and equipment used." }, { - "id": 92358, - "strid": "5fd72122-103a-44a6-9781-61ecf66759a5", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1049, + "strid": "612d50ec-ae83-43f8-9dd3-f6c7bfa4d02b", + "image_id": 39, + "image_name": "116600.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 960.796, - 1535.684, - 717.3970000000002, - 38.9670000000001 + 397.101, + 4495.553, + 296.87, + 37.797999999999774 ], - "priority": 27, + "priority": 52, "parents": [ - 92318 + 997 ], - "children": [], - "area": 1475479.044464, + "children": [ + 1050 + ], + "area": 1785188.591853, "iscrowd": 0, "segmentation": [], - "text": "(B) DC maturation by tumor cells at a 1:1 ratio. Mean and SD of MFIs for CD86 and HLA-DR are shown.\ni) Cross-presentation protocol. ii) Mean+SE of % IFNy+ CD8 T cells from triplicate cultures are shown." + "text": "" }, { - "id": 92337, - "strid": "f54e71c6-ac0a-4298-8f88-f3c9f611fd11", - "image_id": 204078, - "image_name": "121417.png", + "id": 1050, + "strid": "6dc3b412-8150-4744-967d-d99f7b595bfa", + "image_id": 39, + "image_name": "116600.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1003.459, - 1622.983, - 769.227, - 55.12200000000007 + 1029.769, + 4474.501, + 2196.295, + 90.04799999999977 ], - "priority": 28, + "priority": 53, "parents": [ - 92318 + 1049 ], "children": [], - "area": 1628596.898197, + "area": 4607702.420269, "iscrowd": 0, "segmentation": [], - "text": "Does the uptake of irradiated DU145 tumor cells by DC cause DC\nactivation and trigger antigen cross-presentation?" + "text": "Marin et al (2011), IEEE Trans Med Imaging, 30, 146-158 | Oloumi et al (2007), Conf Proc IEEE Eng Med Biol Soc., 6451-6454\nSaleh and Eswaran (2011), Comput Methods Biomech Biomed Engin., 1-9 | Staal et al (2004), IEEE Trans Med Imaging, 23, 501-509" }, { - "id": 92335, - "strid": "7036193e-f6ab-4f25-871b-caa2bad97a51", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", + "id": 1051, + "strid": "d6bbbf6c-f4d9-46cc-883d-faf392c4f5e2", + "image_id": 40, + "image_name": "11662.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 977.999, - 1712.042, - 794.152, - 147.51199999999994 + 47.81, + 51.21, + 166.78, + 195.37 ], - "priority": 29, - "parents": [ - 92318 + "priority": -1, + "parents": [], + "children": [ + 1058, + 1073, + 1053, + 1056, + 1054, + 1071, + 1052, + 1060 ], - "children": [], - "area": 1674375.363958, + "area": 2448.3501, "iscrowd": 0, "segmentation": [] }, { - "id": 92344, - "strid": "2a03226d-a4ec-4077-9d4a-4a1e04e3f634", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 2, - "category_name": "Figure", + "id": 1052, + "strid": "3eea14d1-acc7-4576-b107-86f9ee732819", + "image_id": 40, + "image_name": "11662.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 945.104, - 2050.992, - 852.81, - 390.4949999999999 + 429.226, + 27.571, + 779.102, + 87.768 ], - "priority": 30, + "priority": 1, "parents": [ - 92318 + 1051 ], - "children": [ - 92354 - ], - "area": 1938400.7431680004, + "children": [], + "area": 11834.190046000002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Connectome of Autistic Brains, Global versus\nLocal Characterization" }, { - "id": 92354, - "strid": "36f58165-45ba-4cfd-a07d-b5521aad17cb", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 6, - "category_name": "Caption", + "id": 1053, + "strid": "8962cc5d-9de4-4d51-bb69-1f93f9c1c179", + "image_id": 40, + "image_name": "11662.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 951.908, - 1914.356, - 853.0269999999999, - 67.42100000000005 + 367.688, + 122.34, + 905.3269999999999, + 186.69999999999996 ], - "priority": 31, + "priority": 2, "parents": [ - 92344 + 1051 ], "children": [], - "area": 1822290.791248, + "area": 44982.94992, "iscrowd": 0, "segmentation": [], - "text": "Figure 5: The effect of HMGB1/TLR4 pathway inhibitors on\nDC activation and antigen cross-presentation" + "text": "Saida S.Mohamed'*®, Nancy Duong Nguyen\", Eiko Yoneki* and Alessandro Crimi?\n\n‘African Institute for Mathematical Sciences of Tanzania, Tanzania\n2 African Institute for Mathematical Sciences of Ghana, Ghana\n3 School of Mathematics and Statistics, University College Dublin, Ireland\n4 Computer Laboratory, University of Cambridge, UK\n5 Faculty of Science, Cairo University, Egypt" }, { - "id": 92360, - "strid": "1b1daba8-fd70-40eb-9376-5aa0bf548ee9", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1054, + "strid": "38581dd9-a4f7-4af9-b345-9c9e9f168e89", + "image_id": 40, + "image_name": "11662.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 960.417, - 2466.669, - 829.417, - 78.74200000000019 + 349.364, + 325.703, + 136.12899999999996, + 29.523000000000025 ], - "priority": 32, + "priority": 3, "parents": [ - 92318 + 1051 ], - "children": [], - "area": 2369030.840973, + "children": [ + 1055 + ], + "area": 113788.90289199998, "iscrowd": 0, "segmentation": [], - "text": "(A) DC were cultured with OGy or 12Gy treated DU145 cells in the presence or absence of 504M HMGBI inhibitor\n(Glycyrrhizin) for 72h. CD86 upregulation on i) DC and ii) ST4 specific T cell stimulation were analyzed by flow\ncytometry. (B) DC cultured as in (A) but in the presence of 25yg/ml Myd88 and 25yg/ml TRIF inhibitory peptides\ntogether or of the same concentration of control peptide. Mean+SE of triplicate samples are shown" + "text": "TUT" }, { - "id": 92329, - "strid": "938d68a6-5e28-474d-9c59-f591f6b228ab", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1055, + "strid": "1c8cac14-9f63-482d-83fd-d67d985f0c10", + "image_id": 40, + "image_name": "11662.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 978.584, - 2627.108, - 808.899, - 73.18100000000004 + 50.721, + 376.196, + 741.618, + 268.12 ], - "priority": 33, + "priority": 4, "parents": [ - 92318 + 1054 ], "children": [], - "area": 2570845.855072, + "area": 19081.037316, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1056, + "strid": "867221c0-4b13-4522-9d5b-199c98a0a6d3", + "image_id": 40, + "image_name": "11662.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 1023.317, + 326.688, + 392.39200000000005, + 31.112000000000023 + ], + "priority": 5, + "parents": [ + 1051 + ], + "children": [ + 1057 + ], + "area": 334305.384096, "iscrowd": 0, "segmentation": [], - "text": "Does the inhibition of HMGB1 function or TLR4 signalling affect DC\nactivation and cross-presentation of antigen from irradiated tumor\ncells?" + "text": "1 — Dataset and parcellation" }, { - "id": 92333, - "strid": "a9a1678a-5ffd-4ccb-826b-2e36bfdd0917", - "image_id": 204078, - "image_name": "121417.png", + "id": 1057, + "strid": "2c6c46aa-89ef-48ad-b61c-58d3dfafbc91", + "image_id": 40, + "image_name": "11662.png", "category_id": 4, "category_name": "List", "bbox": [ - 952.823, - 2755.967, - 833.928, - 121.71300000000019 + 850.391, + 407.103, + 710.698, + 179.20099999999996 ], - "priority": 34, + "priority": 6, "parents": [ - 92318 + 1056 ], "children": [], - "area": 2625948.744841, + "area": 346196.727273, "iscrowd": 0, "segmentation": [] }, { - "id": 92348, - "strid": "56929ed1-a90a-41f6-946d-0f91c0f5e306", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 2, - "category_name": "Figure", + "id": 1058, + "strid": "0e0ae435-be76-40fc-b4e7-462ba6980e56", + "image_id": 40, + "image_name": "11662.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 983.99, - 3059.189, - 784.1490000000001, - 328.65200000000004 + 709.116, + 662.928, + 231.43200000000002, + 27.748000000000047 ], - "priority": 35, + "priority": 7, "parents": [ - 92318 + 1051 ], "children": [ - 92356 + 1059 ], - "area": 3010211.38411, + "area": 470092.851648, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "2 — Experiments" }, { - "id": 92356, - "strid": "d3893de2-c16f-4441-9fa7-1fde1367c8a9", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 6, - "category_name": "Caption", + "id": 1059, + "strid": "7a5892cf-c843-4919-a3d4-3c9138719dae", + "image_id": 40, + "image_name": "11662.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 938.314, - 2909.658, - 795.5660000000001, - 67.80699999999979 + 17.606, + 726.829, + 1615.012, + 245.06999999999994 ], - "priority": 36, + "priority": 8, "parents": [ - 92348 + 1058 ], "children": [], - "area": 2730172.8366119997, + "area": 12796.551374, "iscrowd": 0, - "segmentation": [], - "text": "Figure 6: TLR4 single nucleotide polymorphism does not\naffect cross-presentation" + "segmentation": [] }, { - "id": 92365, - "strid": "c3b3b5fe-842a-4d47-bd39-47e1fcea99ac", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1060, + "strid": "b993e698-d501-47a3-810e-6cf3e5602c8e", + "image_id": 40, + "image_name": "11662.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 960.401, - 3415.68, - 829.881, - 58.73500000000013 + 737.199, + 1029.146, + 157.98300000000006, + 25.450000000000045 ], - "priority": 37, + "priority": 9, "parents": [ - 92318 + 1051 ], - "children": [], - "area": 3280422.48768, + "children": [ + 1061, + 1065, + 1066, + 1067, + 1062, + 1068, + 1069, + 1063, + 1064, + 1070 + ], + "area": 758685.402054, "iscrowd": 0, "segmentation": [], - "text": "Stimulation of 5T4-specific T cells with DC, from 3 donors with the Asp299 TLR4 allele (299A) and 3 donors with Gly299\n(299G) allele, loaded with untreated, 12Gy irradiated or oxaliplatin-treated DU145 cells. Mean+SE of % IFNy+ CD8 T\ncells from triplicate cultures are shown." + "text": "" }, { - "id": 92324, - "strid": "deffb528-bf93-47dc-b9db-929626f5f48c", - "image_id": 204078, - "image_name": "121417.png", + "id": 1061, + "strid": "c2a3a364-dae5-42ca-97c3-9df73dbf421e", + "image_id": 40, + "image_name": "11662.png", "category_id": 3, "category_name": "Text", "bbox": [ - 991.194, - 3552.579, - 789.281, - 76.21399999999994 + 42.758, + 1079.543, + 738.423, + 60.20399999999995 ], - "priority": 38, + "priority": 10, "parents": [ - 92318 + 1060 ], "children": [], - "area": 3521294.989326, + "area": 46159.099594, "iscrowd": 0, "segmentation": [], - "text": "Does the TLR4 single nucleotide polymorphism (SNP) affect\nradiation-induced antigen cross-presentation, in a similar manner as\noxaliplatin-treated tumor cells?" + "text": "Several metrics [4] have been tested in separating the two groups.\nOnly those producing statistically significant results were kept:" }, { - "id": 92323, - "strid": "c30e6295-7d6c-4668-9975-466ac214af0d", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", + "id": 1062, + "strid": "f2867716-b662-41af-a639-ba9ab631b81e", + "image_id": 40, + "image_name": "11662.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 965.253, - 3659.179, - 813.2419999999998, - 77.69900000000007 + 18.634, + 1160.383, + 768.335, + 217.65499999999997 ], - "priority": 39, + "priority": 11, "parents": [ - 92318 + 1060 ], "children": [], - "area": 3532033.5072870003, + "area": 21622.576822000003, "iscrowd": 0, "segmentation": [] }, { - "id": 92345, - "strid": "812e412e-4400-4481-8401-e024bdb01219", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 2, - "category_name": "Figure", + "id": 1063, + "strid": "84805079-1f43-4f13-b1e3-d3043010aeef", + "image_id": 40, + "image_name": "11662.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1889.448, - 952.208, - 756.5829999999999, - 465.6940000000001 + 40.678, + 1403.624, + 751.608, + 213.7270000000001 ], - "priority": 40, + "priority": 12, "parents": [ - 92318 - ], - "children": [ - 92351 + 1060 ], - "area": 1799147.501184, + "children": [], + "area": 57096.617071999994, "iscrowd": 0, "segmentation": [] }, { - "id": 92351, - "strid": "643fa3f0-f77f-4cff-8250-57333b9d7052", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 6, - "category_name": "Caption", + "id": 1064, + "strid": "5616537f-666b-4cb3-9622-663258c40e5f", + "image_id": 40, + "image_name": "11662.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 1838.736, - 834.929, - 847.6020000000001, - 67.89499999999998 + 886.993, + 1092.108, + 731.0480000000001, + 132.93599999999992 ], - "priority": 41, + "priority": 13, "parents": [ - 92345 + 1060 ], "children": [], - "area": 1535214.009744, + "area": 968692.1512440001, "iscrowd": 0, - "segmentation": [], - "text": "Figure 7: Hsp70 inhibition prevents DC activation and blocks\nantigen cross-presentation" + "segmentation": [] }, { - "id": 92359, - "strid": "c57240a6-d9b4-4fce-81e3-4bd435484fc0", - "image_id": 204078, - "image_name": "121417.png", + "id": 1065, + "strid": "ba7c4305-1037-4512-86a3-5e72af62d7a2", + "image_id": 40, + "image_name": "11662.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1854.304, - 1438.75, - 828.9200000000001, - 58.74499999999989 + 894.875, + 1241.999, + 613.3009999999999, + 43.33600000000001 ], - "priority": 42, + "priority": 14, "parents": [ - 92318 + 1060 ], "children": [], - "area": 2667879.8800000004, + "area": 1111433.855125, "iscrowd": 0, "segmentation": [], - "text": "(A) CD86 expression following 48h co-culture of DU145 cells with or without Hsp70 inhibitor (VER155008) and DC (B)\nT cell stimulation with DC, loaded with 0Gy or 12Gy irradiated DUI4S5 that were treated with VER155008 (VER),\nPifithrin-1 (PFT) or left untreated. Mean+SE of % IFNy+ CD8 T cells from triplicate cultures are shown." + "text": "Mean value and standard deviation of the global metrics for both the ASD\nand TD population. The last column gives the one-tail p-values comparing the two." }, { - "id": 92338, - "strid": "d9502ec6-0124-40e1-a007-6dc762f64d41", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1066, + "strid": "e46a319e-9945-4a22-9953-3520810dc3bf", + "image_id": 40, + "image_name": "11662.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1885.958, - 1582.023, - 793.3339999999998, - 50.97399999999993 + 895.279, + 1298.699, + 703.069, + 283.7449999999999 ], - "priority": 43, + "priority": 15, "parents": [ - 92318 + 1060 ], "children": [], - "area": 2983628.933034, + "area": 1162697.942021, "iscrowd": 0, - "segmentation": [], - "text": "Does the inhibition of Hsp70 affect DC activation and cross-\npresentation of antigen?" + "segmentation": [] }, { - "id": 92336, - "strid": "f49033b0-9370-4a81-b135-bd4f7f0b0eae", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", + "id": 1067, + "strid": "576b3a62-1f5b-4a3e-acc6-4fc7be0e12ae", + "image_id": 40, + "image_name": "11662.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1846.111, - 1642.924, - 837.472, - 472.23900000000003 + 894.356, + 1591.779, + 332.4680000000001, + 75.02099999999996 ], - "priority": 44, + "priority": 16, "parents": [ - 92318 + 1060 ], "children": [], - "area": 3033020.068564, + "area": 1423617.099324, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Mean ROC and AUC for the classiffication task\nwith both features obtained averaging 100 times\nthe ROC with different Louvain modularity\ncomputed." }, { - "id": 92347, - "strid": "7b4ba2c1-4565-4d94-b395-e7f6cf214a80", - "image_id": 204078, - "image_name": "121417.png", + "id": 1068, + "strid": "5cb9ef39-dd5a-415f-a00e-d533f5f74327", + "image_id": 40, + "image_name": "11662.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1839.082, - 2300.581, - 860.6290000000001, - 401.35300000000007 - ], - "priority": 45, - "parents": [ - 92318 - ], - "children": [ - 92353 - ], - "area": 4230957.106642, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 92353, - "strid": "5fb38ef9-7a0f-41e5-8096-3d41a3d19ff2", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 6, - "category_name": "Caption", - "bbox": [ - 1870.787, - 2153.912, - 778.3549999999998, - 67.55200000000013 + 924.041, + 1669.499, + 223.98400000000004, + 275.797 ], - "priority": 46, + "priority": 17, "parents": [ - 92347 + 1060 ], "children": [], - "area": 4029510.5687439996, + "area": 1542685.5254590001, "iscrowd": 0, - "segmentation": [], - "text": "Figure 8: Irradiated tumor-derived Hsp70 signals mainly\nvia CD91 on DC" + "segmentation": [] }, { - "id": 92362, - "strid": "5d887fe6-8ddf-45ec-9cfe-3e995dd04cca", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 3, - "category_name": "Text", + "id": 1069, + "strid": "9e71ac01-acf0-4cdd-b886-484bdeff0346", + "image_id": 40, + "image_name": "11662.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1860.0, - 2730.203, - 829.906, - 59.33699999999999 + 1229.993, + 1597.339, + 391.538, + 265.105 ], - "priority": 47, + "priority": 18, "parents": [ - 92318 + 1060 ], "children": [], - "area": 5078177.58, + "area": 1964715.7886269998, "iscrowd": 0, - "segmentation": [], - "text": "(A) CD91 and SREC-I expression on day 5 DC. Mean+SEM of MFI for isotype and test from triplicate samples are shown.\n(B) Stimulation of 5T4-specific T cells in a cross-presentation experiment where DC were pre-treated either with\nneutralizing (N) or isotype (iso) antibodies, as indicate. Mean+SEM of IFNy*T cells from triplicate samples are shown." + "segmentation": [] }, { - "id": 92331, - "strid": "2b2a73c5-a430-4fb6-afe0-8ec0342b4139", - "image_id": 204078, - "image_name": "121417.png", + "id": 1070, + "strid": "42ad64cd-bf6d-4005-b68b-284818249f87", + "image_id": 40, + "image_name": "11662.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1884.142, - 2866.292, - 795.6409999999998, - 48.47499999999991 + 1163.364, + 1904.204, + 464.0609999999999, + 83.49500000000012 ], - "priority": 48, + "priority": 19, "parents": [ - 92318 + 1060 ], "children": [], - "area": 5400501.141464, + "area": 2215282.382256, "iscrowd": 0, "segmentation": [], - "text": "Which receptor is Hsp70 signalling via in the cross-presentation\nmodel?" - }, - { - "id": 92334, - "strid": "bfa70621-9472-43d5-9d26-e107745ce37a", - "image_id": 204078, - "image_name": "121417.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 1859.019, - 2965.579, - 818.8660000000002, - 172.23399999999992 - ], - "priority": 49, - "parents": [ - 92318 - ], - "children": [], - "area": 5513067.707001001, - "iscrowd": 0, - "segmentation": [] + "text": "Sagittal view of the statistical different connections between\nthe ASD and TD subjects. The used abbreviations are MOG =\nmiddle occipital gyrus,SOG = superior occipital gyrus, THA =\nthalamus, INS = insula, CAU = caudate,PHG = para" }, { - "id": 92319, - "strid": "bef5bf1c-72af-45b5-b0ca-4f3718df33ca", - "image_id": 204078, - "image_name": "121417.png", + "id": 1071, + "strid": "de8e8d8a-e548-4486-b1ad-538ef6add12e", + "image_id": 40, + "image_name": "11662.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1855.398, - 3188.769, - 250.58299999999986, - 39.284999999999854 + 314.134, + 1657.922, + 228.365, + 30.08699999999999 ], - "priority": 50, + "priority": 20, "parents": [ - 92366 + 1051 ], "children": [ - 92321 + 1072 ], - "area": 5916435.625061999, + "area": 520809.66954800003, "iscrowd": 0, "segmentation": [], - "text": "Conclusion" + "text": "4-Conclusions" }, { - "id": 92321, - "strid": "7e99ea08-31ca-41fa-af8b-fd17f9c90892", - "image_id": 204078, - "image_name": "121417.png", + "id": 1072, + "strid": "9d4b1f9a-7573-434f-90d4-91ea52d3706e", + "image_id": 40, + "image_name": "11662.png", "category_id": 4, "category_name": "List", "bbox": [ - 1871.979, - 3296.62, - 795.597, - 130.82799999999997 + 45.115, + 1718.571, + 738.17, + 266.58400000000006 ], - "priority": 51, + "priority": 21, "parents": [ - 92319 + 1071 ], "children": [], - "area": 6171203.41098, + "area": 77533.330665, "iscrowd": 0, "segmentation": [] }, { - "id": 92320, - "strid": "648f15d5-45fe-494f-85f7-356b72858bed", - "image_id": 204078, - "image_name": "121417.png", + "id": 1073, + "strid": "007ccc4b-ae22-4443-a800-2941d2684c63", + "image_id": 40, + "image_name": "11662.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1853.074, - 3484.695, - 433.8589999999999, - 48.91600000000017 + 743.429, + 1996.727, + 162.26599999999996, + 32.884000000000015 ], - "priority": 52, + "priority": 22, "parents": [ - 92366 + 1051 ], "children": [ - 92322 + 1074 ], - "area": 6457397.7024300005, + "area": 1484424.756883, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgements" + "text": "References" }, { - "id": 92322, - "strid": "1825fb26-5fcf-4c8c-b791-58a59202ebc6", - "image_id": 204078, - "image_name": "121417.png", + "id": 1074, + "strid": "cd0dcebf-e6ec-443f-b8bd-9d42bbdcf239", + "image_id": 40, + "image_name": "11662.png", "category_id": 4, "category_name": "List", "bbox": [ - 1865.579, - 3561.493, - 826.9950000000001, - 144.5050000000001 + 27.01, + 2038.396, + 1485.487, + 121.25099999999998 ], - "priority": 53, + "priority": 23, "parents": [ - 92320 + 1073 ], "children": [], - "area": 6644246.549447, + "area": 55057.07596, "iscrowd": 0, "segmentation": [] }, { - "id": 88505, - "strid": "c387f457-f3b6-4b46-ad84-8842a6586a26", - "image_id": 203936, - "image_name": "121201.png", + "id": 1075, + "strid": "a78dd320-01aa-483c-b4cc-2a8f1d2a5ea9", + "image_id": 41, + "image_name": "116691.png", "category_id": 9, "category_name": "Root", "bbox": [ - 95.15, - 92.07, - 242.59, - 188.69 + 839.5, + 10.68, + 94.09000000000003, + 176.41 ], "priority": -1, "parents": [], "children": [ - 88465, - 88464, - 88470, - 88473, - 88474, - 88463, - 88468, - 88469, - 88467, - 88466, - 88472, - 88471 + 1085, + 1077, + 1095, + 1093, + 1080, + 1082, + 1078, + 1076, + 1091 ], - "area": 8760.4605, + "area": 8965.86, "iscrowd": 0, "segmentation": [] }, { - "id": 88463, - "strid": "41780fde-4589-40d5-a58c-b686c6a9e667", - "image_id": 203936, - "image_name": "121201.png", + "id": 1076, + "strid": "0539b920-ab9c-495b-9315-2faa832e3244", + "image_id": 41, + "image_name": "116691.png", "category_id": 1, "category_name": "Title", "bbox": [ - 416.884, - 72.27, - 3104.026, - 201.327 + 977.699, + 2.851, + 2823.72, + 127.09100000000001 ], "priority": 1, "parents": [ - 88505 + 1075 ], "children": [], - "area": 30128.20668, + "area": 2787.419849, "iscrowd": 0, "segmentation": [], - "text": "Photophysical properties of porphyrins as a-selection criterion of porphyrins\n‘ for studyof their effectiveness“against microorganisms" + "text": "MMP-9 and HMGB-1 BIOMARKER(S) FOR PREDICTING SEVERITY OF CARDIAC DYSFUNCTION IN SEPTIC\nPATIENTS + tah." }, { - "id": 88464, - "strid": "08abdbc9-b1da-4f64-83b4-5938393e0951", - "image_id": 203936, - "image_name": "121201.png", + "id": 1077, + "strid": "8e8b6318-a447-4388-b978-28e2049e0635", + "image_id": 41, + "image_name": "116691.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 111.942, - 371.075, - 3711.311, - 407.454 + 1142.853, + 131.841, + 2227.028, + 170.80399999999997 ], "priority": 2, "parents": [ - 88505 + 1075 ], "children": [], - "area": 41538.877649999995, + "area": 150674.88237300003, "iscrowd": 0, "segmentation": [], - "text": "_ ' Anna G. Gyulkhandanyan, 2 Elena S. Tuchina, 3? Robert K. Ghazaryan, 4 Marina H. Paronyan, 5 Boris M. Dzagarov, Oat\n’ Grigor V. Gyulkhandanyan, ®”8 Valery V. Tuchin g\n‘Institute of Biochemistry NAS, Armenia; 2Biological Department,’/N.G. Chemyshevsky Saratov State University; 7Yerevan State Medical University,\n\nArmenia; Science and_Production Center \"Armbiotechnology\"\\NAS, Armenia; Institute of Physics: NAS, Belarus; ®Institute of Optics and-Biophotonics,\nN.G. Chemyshevsky Saratov State University; 7Institute of Precise Mechanics and Control RAS, Saratov, Russia; ®University of Oulu, Finland" + "text": "Florence Morriello, MD‘, Tao Rui, MD1,Ravi Taneja, MD‘, Claudio Martin, MD’, Raymond Kao, MD\"\n'Division of Critical Care Medicine, Department of Medicine, University of Western Ontario, Canada,\n2Division of Critical Care, Department of Medicine, University of Toronto,, Toronto, Ontario Canada" }, { - "id": 88465, - "strid": "75a338b6-7b7a-47e0-b28e-1fff0b1d0bac", - "image_id": 203936, - "image_name": "121201.png", + "id": 1078, + "strid": "bf66ce61-a437-48e9-86c1-262456c4f5ca", + "image_id": 41, + "image_name": "116691.png", "category_id": 5, "category_name": "Section", "bbox": [ - 911.478, - 1049.729, - 370.33900000000006, - 65.654 + 494.892, + 355.95, + 465.56199999999995, + 51.40500000000003 ], "priority": 3, "parents": [ - 88505 + 1075 ], "children": [ - 88483 + 1079 ], - "area": 956804.889462, + "area": 176156.8074, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 88483, - "strid": "f1a25192-9a87-4a18-9d0f-5874a21cba84", - "image_id": 203936, - "image_name": "121201.png", + "id": 1079, + "strid": "e8d1cd3e-dc39-432a-9b87-6c08a97ad2b4", + "image_id": 41, + "image_name": "116691.png", "category_id": 4, "category_name": "List", "bbox": [ - 82.573, - 1161.735, - 1821.351, - 853.5029999999999 + 62.085, + 437.081, + 1225.078, + 1292.688 ], "priority": 4, "parents": [ - 88465 + 1078 ], "children": [], - "area": 95927.94415499999, + "area": 27136.173885, "iscrowd": 0, "segmentation": [] }, { - "id": 88467, - "strid": "08b4ca1f-656a-476d-90cc-68d889861037", - "image_id": 203936, - "image_name": "121201.png", + "id": 1080, + "strid": "311fb7f0-6585-44a2-8062-02cab9842f0e", + "image_id": 41, + "image_name": "116691.png", "category_id": 5, "category_name": "Section", "bbox": [ - 214.104, - 2029.215, - 1568.214, - 152.93300000000022 + 494.822, + 1807.677, + 339.91600000000005, + 50.2829999999999 ], "priority": 5, "parents": [ - 88505 + 1075 ], "children": [ - 88484, - 88497, - 88504 + 1081 ], - "area": 434463.04836, + "area": 894478.3484939999, "iscrowd": 0, "segmentation": [], - "text": "JTOACTIVATION OF PORPHYRINS AND\n‘” PHOTODYNAMIC THERAPY OF TUMOR" + "text": "" }, { - "id": 88497, - "strid": "0de6972b-ce5f-4e44-9a9e-29ba7b1f712d", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 2, - "category_name": "Figure", + "id": 1081, + "strid": "22068c9a-73c8-4ddb-84c8-d6ab93ca900f", + "image_id": 41, + "image_name": "116691.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 80.989, - 2203.533, - 833.65, - 576.7860000000001 + 62.608, + 1905.059, + 1219.375, + 229.0690000000002 ], "priority": 6, "parents": [ - 88467 - ], - "children": [ - 88481 + 1080 ], - "area": 178461.934137, + "children": [], + "area": 119271.933872, "iscrowd": 0, "segmentation": [] }, { - "id": 88481, - "strid": "96b033b2-ea66-4897-b067-11901220682f", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 6, - "category_name": "Caption", + "id": 1082, + "strid": "b3d07338-036d-4246-b0d3-83bc59d3c6ed", + "image_id": 41, + "image_name": "116691.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 504.965, - 2781.512, - 142.69300000000004, - 58.233000000000175 + 506.367, + 2172.98, + 302.891, + 52.0300000000002 ], "priority": 7, "parents": [ - 88497 + 1075 ], - "children": [], - "area": 1404566.20708, + "children": [ + 1084, + 1083 + ], + "area": 1100325.36366, "iscrowd": 0, "segmentation": [], - "text": "Fig.1." + "text": "" }, { - "id": 88504, - "strid": "3e9d4863-e114-4a50-a182-1b869d30b1a3", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 2, - "category_name": "Figure", + "id": 1083, + "strid": "09b107e6-91dd-48ca-8a74-4c6077c56747", + "image_id": 41, + "image_name": "116691.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 957.233, - 2206.716, - 941.249, - 485.9180000000001 + 32.118, + 2247.21, + 1268.921, + 473.49800000000005 ], "priority": 8, "parents": [ - 88467 - ], - "children": [ - 88480 + 1082 ], - "area": 2112341.376828, + "children": [], + "area": 72175.89078, "iscrowd": 0, "segmentation": [] }, { - "id": 88480, - "strid": "bd16f242-81a1-48e1-9a07-c1a203e9a7bb", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 6, - "category_name": "Caption", + "id": 1084, + "strid": "ac66639e-d1b5-49a4-9150-28baba607dd1", + "image_id": 41, + "image_name": "116691.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1344.716, - 2780.708, - 164.57400000000007, - 57.583000000000084 + 1347.363, + 426.449, + 1174.6759999999997, + 297.982 ], "priority": 9, "parents": [ - 88504 + 1082 ], "children": [], - "area": 3739262.538928, + "area": 574581.6039870001, "iscrowd": 0, - "segmentation": [], - "text": "Fig. 2." + "segmentation": [] }, { - "id": 88484, - "strid": "8cd994f7-4cc1-435e-bbbf-912f1593fca8", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 4, - "category_name": "List", + "id": 1085, + "strid": "b6ca2cb9-8ea3-4938-80d8-0b102d1085a6", + "image_id": 41, + "image_name": "116691.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 85.34, - 2897.783, - 1827.967, - 242.5569999999998 + 1837.329, + 784.398, + 275.93299999999977, + 50.86099999999999 ], "priority": 10, "parents": [ - 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"image_id": 203936, - "image_name": "121201.png", + "id": 1087, + "strid": "25c29dc0-b5ae-4253-b478-b3816a88d560", + "image_id": 41, + "image_name": "116691.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 396.273, - 3260.799, - 1145.2669999999998, - 535.2139999999999 + 1327.075, + 1462.008, + 1133.5290000000002, + 599.0330000000001 ], "priority": 12, "parents": [ - 88468 + 1085 ], "children": [], - "area": 1292166.602127, + "area": 1940194.2666000002, "iscrowd": 0, "segmentation": [] }, { - "id": 88486, - "strid": "3feb3d2c-810b-4bbf-ba5c-535d9ea60a16", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 4, - "category_name": "List", + "id": 1088, + "strid": "d75db8b7-53e8-48a4-9592-0f36ab6cabdb", + "image_id": 41, + "image_name": "116691.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 106.03, - 3809.592, - 1772.206, - 240.32499999999982 + 1328.73, + 2079.243, + 1138.493, + 651.9859999999999 ], "priority": 13, "parents": [ - 88468 + 1085 ], "children": [], - "area": 403931.03976, + "area": 2762752.55139, "iscrowd": 0, "segmentation": [] }, { - "id": 88469, - "strid": "99a59372-dde9-4bd0-9244-ef4d93f30784", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 5, - "category_name": "Section", + "id": 1089, + "strid": "0949549f-7ddd-4615-82b9-fd61714dfbd4", + "image_id": 41, + "image_name": "116691.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 369.406, - 4066.22, - 1211.333, - 160.4090000000001 + 2570.78, + 332.578, + 1306.813, + 504.659 ], "priority": 14, "parents": [ - 88505 + 1085 ], - "children": [ - 88488, - 88493, - 88476 - ], - "area": 1502086.06532, + "children": [], + "area": 854984.87084, "iscrowd": 0, - "segmentation": [], - "text": "The quantum yieldsyof singlet oxygen\ngeneration.by porphyrins" + "segmentation": [] }, { - "id": 88476, - "strid": "6b238c0d-0ab6-4366-bfb3-da53b3a73763", - "image_id": 203936, - "image_name": "121201.png", + "id": 1090, + "strid": "05574efd-de89-49ff-bee4-8cd38983f032", + "image_id": 41, + "image_name": "116691.png", "category_id": 3, "category_name": "Text", "bbox": [ - 91.14, - 4240.989, - 1792.588, - 504.90700000000015 + 2633.73, + 836.769, + 1173.7329999999997, + 27.19799999999998 ], "priority": 15, "parents": [ - 88469 + 1085 ], "children": [], - "area": 386523.73746, + "area": 2203823.61837, "iscrowd": 0, "segmentation": [], - "text": "One of the most inportant criteria forthe effectiveness of the PS's is the quantunv yield\nof singlet oxygen generation ([@): LL of new porphyrins and metalloporphyrins were\ncompared with known cationic:porphyrins 5,10,15,20-tetra(N -methy!-2-pyri dyl)porphin\n(H5TM2PyP) (Ld=0.18) ~ and —5,10,15-+tri(N-rmethy|-4-pyridyl)20(N-C14H29)-4-\npyridyl )porphin (Ld=0.51) [1].\n\n[1]. Rapozzi V. et. al’Molecular Cancer, 13(1), 75-92 (2014).\n\nThe quantum yields (Ld) of singlet oxygen generation of new,frée-base porphyrins and\nzinc-porphyrin complexes in distilled\\water" + "text": "Comparison at each time point to baseline for MMP-9 and HMGB-1 are not statistically significant, P>0.05" }, { - "id": 88493, - "strid": "183ff7d8-413b-40f6-8dae-8620afee6096", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 7, - "category_name": "Table", + "id": 1091, + "strid": "366afb2a-3eb7-4372-b770-9cd1853d9845", + "image_id": 41, + "image_name": "116691.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 98.296, - 4766.062, - 1796.513, - 252.95499999999993 + 3068.05, + 908.004, + 320.2339999999999, + 55.039999999999964 ], "priority": 16, "parents": [ - 88469 + 1075 ], - "children": [], - "area": 468484.830352, + "children": [ + 1092 + ], + "area": 2785801.6722000004, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Discussion" }, { - "id": 88488, - "strid": "69e243ac-66bb-4dde-84a7-44740349bae1", - "image_id": 203936, - "image_name": "121201.png", + "id": 1092, + "strid": "77e007c9-0c96-4b69-8b7c-c5b5060f5ae1", + "image_id": 41, + "image_name": "116691.png", "category_id": 4, "category_name": "List", "bbox": [ - 84.854, - 5040.699, - 1814.333, - 123.85099999999966 + 2585.39, + 993.422, + 1278.888, + 419.837 ], "priority": 17, "parents": [ - 88469 + 1091 ], "children": [], - "area": 427723.47294599994, + "area": 2568383.3045799998, "iscrowd": 0, "segmentation": [] }, { - "id": 88466, - "strid": "60a1086a-719d-451b-859a-9f7fc0b49634", - "image_id": 203936, - "image_name": "121201.png", + "id": 1093, + "strid": "5493a46e-43d8-4390-b714-92b398f7d976", + "image_id": 41, + "image_name": "116691.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2190.971, - 993.157, - 1189.435, - 160.2399999999999 + 3039.429, + 1431.576, + 404.69399999999996, + 49.95499999999993 ], "priority": 18, "parents": [ - 88505 + 1075 ], "children": [ - 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"id": 88499, - "strid": "1e806478-3678-4fb4-88c4-e0e8d604e435", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 2, - "category_name": "Figure", + "id": 1097, + "strid": "2595a5c2-2eef-4761-8816-93fd48d4dc21", + "image_id": 42, + "image_name": "116696.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 2962.852, - 1493.635, - 257.76099999999997, - 230.67200000000003 - ], - "priority": 22, - "parents": [ - 88466 + 128.55, + 40.55, + 435.28000000000003, + 235.14999999999998 ], + "priority": -1, + "parents": [], "children": [ - 88479 + 1114, + 1104, + 1112, + 1116, + 1106, + 1098, + 1108, + 1110, + 1100, + 1102, + 1118, + 1099 ], - "area": 4425419.44702, + "area": 5212.7025, "iscrowd": 0, "segmentation": [] }, { - "id": 88479, - "strid": "2280e120-04de-4d4c-9f98-23d5a4f50fb4", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 6, - "category_name": "Caption", + "id": 1098, + "strid": "72b97398-ccc3-4a2d-b469-a090dc35716c", + "image_id": 42, + "image_name": "116696.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 3009.825, - 1742.487, - 195.46399999999994, - 78.13100000000009 + 597.924, + 14.767, + 3603.4219999999996, + 299.189 ], - "priority": 23, + "priority": 1, "parents": [ - 88499 + 1097 ], "children": [], - "area": 5244580.9347749995, + "area": 8829.543708, "iscrowd": 0, "segmentation": [], - "text": "Fig. 2" + "text": "Early Detection of Invasive Species — Surveillance Monitoring and\nRapid Response for Northeast Parks\n\nV4 Weve tee" }, { - "id": 88500, - "strid": "9900f088-9093-45c9-84ff-a1351bc48070", - "image_id": 203936, - "image_name": "121201.png", + "id": 1099, + "strid": "2c4a6b7b-44e6-4735-9b93-68d3f98cf18b", + "image_id": 42, + "image_name": "116696.png", + "category_id": 0, + "category_name": "Author Info", + "bbox": [ + 1068.148, + 322.526, + 2675.331, + 138.978 + ], + "priority": 2, + "parents": [ + 1097 + ], + "children": [], + "area": 344505.501848, + "iscrowd": 0, + "segmentation": [], + "text": "Jesse Wheeler and Kate Miller\nNortheast Temperate Network, National Park Service Inventory & Monitoring Program, Acadia National Park, Bar Harbor, ME 04609" + }, + { + "id": 1100, + "strid": "7452774f-501a-4d51-ae8f-b92354a8b156", + "image_id": 42, + "image_name": "116696.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 2971.126, - 1830.877, - 269.3620000000001, - 226.44799999999987 + 21.353, + 500.721, + 1217.843, + 1804.351 ], - "priority": 24, + "priority": 3, "parents": [ - 88466 + 1097 ], "children": [ - 88478 + 1101 ], - "area": 5439766.257502, + "area": 10691.895513000001, "iscrowd": 0, "segmentation": [] }, { - "id": 88478, - "strid": "1552ab6d-2757-4be0-bedf-f670ae5d7a83", - "image_id": 203936, - "image_name": "121201.png", + "id": 1101, + "strid": "13b5b5f5-be1c-4458-ba02-ada90efca218", + "image_id": 42, + "image_name": "116696.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 3004.315, - 2064.998, - 196.80600000000004, - 80.46399999999994 + 36.349, + 2310.159, + 1188.914, + 235.82900000000018 ], - "priority": 25, + "priority": 4, "parents": [ - 88500 + 1100 ], "children": [], - "area": 6203904.4663700005, + "area": 83971.969491, "iscrowd": 0, "segmentation": [], - "text": "Fig. 3" + "text": "Figure 1. Target ISED species vary among three northeast\nregional parks (Fredericksburg & Spotsylvania NMP (FRSP),\nMorristown NHP (MORR), Acadia NP (ACAD)), stretching\nfrom Virginia to,Maine. |" }, { - "id": 88502, - "strid": "823e5a87-d31e-4763-9455-87a9c09c80ef", - "image_id": 203936, - "image_name": "121201.png", + "id": 1102, + "strid": "a6083c8a-7049-439c-be40-99dce23371c6", + "image_id": 42, + "image_name": "116696.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3405.526, - 1199.149, - 293.3589999999999, - 257.778 + 32.742, + 2548.893, + 1184.62, + 913.681 ], - "priority": 26, + "priority": 5, "parents": [ - 88466 - ], - "children": [], - "area": 4083733.0973739997, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 88491, - "strid": "14845b3a-3bd0-4b5d-8262-bc7b0977b9b0", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 4, - "category_name": "List", - "bbox": [ - 3295.157, - 1459.331, - 527.1700000000001, - 161.4179999999999 + 1097 ], - "priority": 27, - "parents": [ - 88466 + "children": [ + 1103 ], - "children": [], - "area": 4808724.759967, + "area": 83455.854606, "iscrowd": 0, "segmentation": [] }, { - "id": 88503, - "strid": "62d296ab-10aa-423f-b840-6a1bfacec413", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 2, - "category_name": "Figure", + "id": 1103, + "strid": "02999b01-ea6d-4613-ba73-97533f6c0eec", + "image_id": 42, + "image_name": "116696.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 3401.592, - 1632.472, - 283.0039999999999, - 191.11899999999991 + 36.993, + 3479.774, + 1125.052, + 114.96099999999979 ], - "priority": 28, + "priority": 6, "parents": [ - 88466 + 1102 ], "children": [], - "area": 5553003.695424, + "area": 128727.279582, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 3. Locations of five ISED sightings at Morristown\nNational Historical Park in May 2011." }, { - "id": 88490, - "strid": "f6ec7816-4b59-4862-9a90-25d087273ecf", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 4, - "category_name": "List", + "id": 1104, + "strid": "7d93b40b-88f9-47e9-986a-f053801b2f6a", + "image_id": 42, + "image_name": "116696.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 3289.178, - 1824.901, - 493.4569999999999, - 75.21800000000007 + 966.204, + 526.355, + 263.74, + 63.149 ], - "priority": 29, + "priority": 7, "parents": [ - 88466 + 1097 ], - "children": [], - "area": 6002424.221378, + "children": [ + 1105 + ], + "area": 508566.30642, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Objective" }, { - "id": 88477, - "strid": "26f3c9ce-c5e9-45ba-a552-08527836dbf3", - "image_id": 203936, - "image_name": "121201.png", + "id": 1105, + "strid": "29b6ddd6-d487-4d7a-998a-8a7c2f42ebca", + "image_id": 42, + "image_name": "116696.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3280.484, - 1951.895, - 492.3899999999999, - 114.95699999999988 + 965.936, + 593.964, + 1367.8289999999997, + 358.4150000000001 ], - "priority": 30, + "priority": 8, "parents": [ - 88466 + 1104 ], "children": [], - "area": 6403160.31718, + "area": 573731.2103040001, "iscrowd": 0, "segmentation": [], - "text": "Microorganisms were grown on\ndense nutrient medium and [\nincubated at 37° C [/" + "text": "The overall goal of the Invasive Species Early Detection\n(ISED) protdcol is to utilize opportunistic sampling to\ndetect.invasive species in the early stages of\nestablishment while the costs of eradication-are still\nrelatively low." }, { - "id": 88472, - "strid": "a9b1d928-3e1b-4391-8064-3bc8d9243cca", - "image_id": 203936, - "image_name": "121201.png", + "id": 1106, + "strid": "e38a9b3c-103b-41a6-a306-5eff09bf4b03", + "image_id": 42, + "image_name": "116696.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2159.539, - 2219.488, - 1549.6370000000002, - 162.0540000000001 + 1258.981, + 987.52, + 793.6270000000002, + 61.61400000000003 ], - "priority": 31, + "priority": 9, "parents": [ - 88505 + 1097 ], "children": [ - 88485, - 88492 + 1107 ], - "area": 4793070.896032, + "area": 1243268.9171199999, "iscrowd": 0, "segmentation": [], - "text": "The inactivation of Gram (-) bacteria E. coli by\nporphyrins with-various peripheral groups. ~" + "text": "Creating the ISED species list" }, { - "id": 88492, - "strid": "e54520da-d52e-4bb7-9117-d4998b8c97d5", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 7, - "category_name": "Table", + "id": 1107, + "strid": "91932dab-0182-43c9-a0bc-7e13c187f307", + "image_id": 42, + "image_name": "116696.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2298.148, - 2387.311, - 1284.0789999999997, - 403.6089999999999 + 1251.011, + 1062.929, + 1293.591, + 588.5529999999999 ], - "priority": 32, + "priority": 10, "parents": [ - 88472 + 1106 ], "children": [], - "area": 5486394.000028, + "area": 1329735.871219, + "iscrowd": 0, + "segmentation": [], + "text": "The target list includes-species that are either 1)\npresent in the park.at low levels, and of\nmanagement concern if new populations are\ndetected, or 2) not present in the park, but that\nhave denjoenstrated impacts to ecosystem function\nin the-region. Target lists for terrestrial, riparian and\naquatic plants and priority pests are reviewed\nannually and updated as needed (Figures 1&2). §" + }, + { + "id": 1108, + "strid": "09217e6e-7509-44a9-a34e-74c61ad758e8", + "image_id": 42, + "image_name": "116696.png", + "category_id": 2, + "category_name": "Figure", + "bbox": [ + 2615.087, + 559.465, + 505.0279999999998, + 1067.2289999999998 + ], + "priority": 11, + "parents": [ + 1097 + ], + "children": [ + 1109 + ], + "area": 1463049.648455, "iscrowd": 0, "segmentation": [] }, { - "id": 88485, - "strid": "fe94d674-6aba-4229-86e8-17b76e7cb500", - "image_id": 203936, - "image_name": "121201.png", - "category_id": 4, - "category_name": "List", + "id": 1109, + "strid": "47ba1ab1-32ea-4fa2-a28c-554af543aa04", + "image_id": 42, + "image_name": "116696.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2075.968, - 2810.515, - 1731.2560000000003, - 243.76400000000012 + 3131.55, + 668.094, + 291.5819999999999, + 779.4589999999998 ], - "priority": 33, + "priority": 12, "parents": [ - 88472 + 1108 ], "children": [], - "area": 5834539.203519999, + "area": 2092169.7657000003, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "BTA\nAquatic plant\nlist for three\nNETN parks:\nVela ale\nBillings-\n\nNolo COSMIC: integrating and interpreting the world's knowledge of\nsomatic mutations 1n cancer" + "text": "Human Pheromones: Epigenetic effects of odors and their affects on behavior" }, { - "id": 122029, - "strid": "c5050df0-423f-4d6d-a6fb-d31f6908a462", - "image_id": 205250, - "image_name": "14511.png", + "id": 1122, + "strid": "99b29d9c-6397-4e49-8059-bdfb5b322c1b", + "image_id": 43, + "image_name": "116748.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 140.221, - 682.66, - 3058.644, - 79.84500000000003 + 1472.874, + 159.423, + 481.69499999999994, + 75.67700000000002 ], "priority": 2, "parents": [ - 122045 + 1120 ], "children": [], - "area": 95723.26785999999, + "area": 234809.991702, "iscrowd": 0, "segmentation": [], - "text": "Laura Ponting*, Sally Bamford, Charlotte G. Cole, Elisabeth Dawson, Raymund Stefancsik, Sari Ward, Nidhi Bindal, Harry Boutselakis, Peter Fish, Bhavana Harsha, Charlie Hathaway, Steve Jupe, Chai Yin Kok,\nKate Noble, Claire Rye, Zbyslaw Sondka, John Tate, Sam Thompson, Shicai Wang, Simon Forbes" + "text": "J.V. Kohl\n\nIndependent Researcher, Epworth, GA" }, { - "id": 122030, - "strid": "517a4811-8e44-481c-9356-9f62ac81848e", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 5, - "category_name": "Section", + "id": 1123, + "strid": "7506c218-2076-4df7-8f33-17e9caad75ca", + "image_id": 43, + "image_name": "116748.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 166.477, - 876.32, - 277.818, - 60.75400000000002 + 72.916, + 352.423, + 953.279, + 358.058 ], "priority": 3, "parents": [ - 122045 + 1120 ], - "children": [ - 122035 - ], - "area": 145887.12464000002, + "children": [], + "area": 25697.275468, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Background: A detailed model explains how chemical ecology\ndrives adaptive evolution via 1) ecological niche construction, 2)\nsocial niche construction, 3) neurogenic niche construction, and\n4) socio-cognitive niche construction (Kohl, 2012). That model is\nused to exemplify the effects of olfactory/pheromonal\nconditioning, which alters genetically predisposed, nutrient\nchemical-dependent, hormone-driven mammalian behavior and\nchoices for pheromones that control reproduction via their\neffects on luteinizing hormone (Kohl, 1992)." }, { - "id": 122035, - "strid": "b2bace87-f9e7-4d15-9c83-9c51e8ee4ea3", - "image_id": 205250, - "image_name": "14511.png", + "id": 1124, + "strid": "0499dedb-6f05-4440-a7b7-44b98b688c6c", + "image_id": 43, + "image_name": "116748.png", "category_id": 3, "category_name": "Text", "bbox": [ - 179.861, - 963.525, - 1639.078, - 78.30000000000007 + 74.099, + 751.093, + 958.839, + 599.0689999999998 ], "priority": 4, "parents": [ - 122030 + 1120 ], "children": [], - "area": 173300.570025, + "area": 55655.240207, "iscrowd": 0, "segmentation": [], - "text": "COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and\nmost comprehensive online resource for exploring the impact of somatic mutations in human cancer." + "text": "Model: In this diagrammatic representation of the model,\nnutrient chemicals are metabolized to pheromones that condition\nbehavior in precisely the same way that food odors condition\nbehavior associated with food preferences. The epigenetic\neffects of olfactory/pheromonal input calibrate and standardize\nmolecular mechanisms for genetically predisposed receptor-\nmediated changes in intracellular signaling and stochastic gene\nexpression in gonadotropin releasing hormone (GnRH)\nneurosecretory neurons of brain tissue. For example: glucose\n(Roland and Moenter, 2011) and pheromones alter the secretion\nof GnRH and luteinizing hormone (LH). Parenthetically, a form of\nGnRH that is also linked to sexual orientation appears to\ncontrol the feedback loops of developmental processes required\nfor nutrient chemical ingestion, movement, reproduction, and the\ndiversification of species from microbes to man." }, { - "id": 122031, - "strid": "a131d77f-3039-4740-ac82-b6e26eb652d6", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 5, - "category_name": "Section", + "id": 1125, + "strid": "0a9cd1a1-3285-427f-88e0-7bf558f1d79d", + "image_id": 43, + "image_name": "116748.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 171.011, - 1080.448, - 401.76800000000003, - 59.71100000000001 + 73.695, + 1393.439, + 961.777, + 671.5670000000002 ], "priority": 5, "parents": [ - 122045 - ], - "children": [ - 122036, - 122038 + 1120 ], - "area": 184768.49292800002, + "children": [], + "area": 102689.487105, "iscrowd": 0, "segmentation": [], - "text": "Data curation" + "text": "Additional Considerations (not shown): The honeybee is an\ninvertebrate model of adaptively evolved social behavior. The\nconcept that is extended is the epigenetic tweaking of immense\ngene networks in superorganisms that solve problems through\nthe exchange and the selective cancellation and modification of\nsignals. In the context of what has also been referred to as\n“biological embedding,” olfaction and odor receptors provide a\nclear evolutionary trail that can be followed from unicellular\norganisms to insects to humans.\n\nIt is now clearer how an environmental drive evolved from that of\nnutrient chemical ingestion in unicellular organisms to that of\nsocialization in insects. It is also clear that, in mammals, food\nodors and pheromones cause changes in hormones such as LH,\nwhich has developmental affects on sexual behavior in nutrient\nchemical-dependent reproductively fit individuals across species\nof vertebrates." }, { - "id": 122038, - "strid": "0cc8b54f-19dc-4eeb-b109-6a6a8c6ea24d", - "image_id": 205250, - "image_name": "14511.png", + "id": 1126, + "strid": "39d01683-9428-495b-a3fa-5982ac234d77", + "image_id": 43, + "image_name": "116748.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 169.821, - 1187.495, - 759.024, - 183.41800000000012 + 1135.999, + 346.397, + 1162.235, + 1299.456 ], "priority": 6, "parents": [ - 122031 + 1120 ], "children": [], - "area": 201661.58839499997, + "area": 393506.645603, "iscrowd": 0, "segmentation": [] }, { - "id": 122036, - "strid": "82a64c72-9a3c-480a-95bb-b122518b3b47", - "image_id": 205250, - "image_name": "14511.png", + "id": 1127, + "strid": "66047d53-2684-4da2-8d2d-fc501a6203b7", + "image_id": 43, + "image_name": "116748.png", "category_id": 3, "category_name": "Text", "bbox": [ - 985.045, - 1188.424, - 836.786, - 173.4079999999999 + 1153.442, + 1667.272, + 1123.2290000000003, + 105.40100000000007 ], "priority": 7, "parents": [ - 122031 + 1120 ], "children": [], - "area": 1170651.1190799999, + "area": 1923101.550224, "iscrowd": 0, "segmentation": [], - "text": "Expert manual curation allows the capture of very high detail across\nmutation positions, disease descriptions, and other patient and\nopulation data\n*perienced curators can identify inconsistencies or errors in\npublications, allowing the rejection of untrustworthy, incomplete or\nunspecific data sources" + "text": "Adaptive evolution and the prenatal migration of GnRH neurosecretory neurons allows nutrient chemicals and human\npheromones to alter GnRH pulsatility, which modulates the concurrent maturation of the neuroendocrine,\nreproductive, and central nervous systems, thus influencing the development of ingestive behavior, reproductive\nsexual behavior, and other behaviors." }, { - "id": 122032, - "strid": "24a5203c-5851-4a51-a69c-832ef876c14c", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 5, - "category_name": "Section", + "id": 1128, + "strid": "51ce2656-d16a-43ba-bd69-d56d2aa3d0df", + "image_id": 43, + "image_name": "116748.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 167.835, - 1519.327, - 950.0339999999999, - 74.529 + 1154.55, + 1788.476, + 1087.8099999999997, + 99.28099999999995 ], "priority": 8, "parents": [ - 122045 - ], - "children": [ - 122039 + 1120 ], - "area": 254996.24704500003, + "children": [], + "area": 2064884.9658000001, "iscrowd": 0, "segmentation": [], - "text": "Data integration and annotation" + "text": "AOS: accessory olfactory system; FSH: follicle stimulating hormone; GnRH: gonadotropin-releasing hormone;\nHPA: hypothalamic-pituitary-adrenal axis; HPG: hypothalamic-pituitary-gonadal axis; LH: luteinizing hormone;\nMOS: main olfactory system.\n\n‘Adapted from Kohl (1992) Luteinizing Hormoné: the lik between sex and the sense of smell?" }, { - "id": 122039, - "strid": "dedae7b7-482a-42e6-811d-199bf4422528", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 2, - "category_name": "Figure", + "id": 1129, + "strid": "fbd807d2-d910-448b-9317-3904c87a8887", + "image_id": 43, + "image_name": "116748.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 233.44, - 1715.487, - 1563.906, - 972.1579999999999 + 1114.72, + 1924.497, + 1142.698, + 165.90100000000007 ], "priority": 9, "parents": [ - 122032 + 1120 ], "children": [], - "area": 400463.28528, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 122034, - "strid": "760e09c3-3b28-470b-a9b4-7fcddfb7611b", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 168.717, - 2790.734, - 847.75, - 75.30600000000004 - ], - "priority": 10, - "parents": [ - 122045 - ], - "children": [ - 122040, - 122041 - ], - "area": 470844.268278, + "area": 2145275.2958400003, "iscrowd": 0, "segmentation": [], - "text": "Specialised projects and tools" + "text": "Proof of concept (unpublished): Kohl, J. V., Kelahan, L. C., & Hoffmann, H. (2012). Human\npheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic\nniches that affect behavior. Poster presented at Society for Social Neuroscience Annual\nMeeting. New Orleans, LA. Oct 11-12.\nhttp://posters.f1000.com/posters/browse/summary/1092668" }, { - "id": 122040, - "strid": "1625815b-4b76-46b0-9a51-c04fac51943b", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 2, - "category_name": "Figure", + "id": 1130, + "strid": "8aec21e7-3c7d-4f81-bd5d-ffc1461fab29", + "image_id": 43, + "image_name": "116748.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 161.835, - 2904.748, - 1704.39, - 570.5070000000001 + 2381.796, + 351.002, + 967.056, + 558.5920000000001 ], - "priority": 11, + "priority": 10, "parents": [ - 122034 + 1120 ], "children": [], - "area": 470089.89258000004, + "area": 836015.159592, "iscrowd": 0, "segmentation": [] }, { - "id": 122041, - "strid": "ab0868af-1df8-49c3-84bd-fc650c4a18a1", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 2, - "category_name": "Figure", + "id": 1131, + "strid": "0203d699-34e9-470e-8abc-956b87d90a8d", + "image_id": 43, + "image_name": "116748.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 162.502, - 3512.222, - 1700.97, - 882.3210000000004 + 2381.95, + 951.807, + 962.7359999999999, + 357.59400000000005 ], - "priority": 12, + "priority": 11, "parents": [ - 122034 + 1120 ], "children": [], - "area": 570743.099444, - "iscrowd": 0, - "segmentation": [] - }, - { - "id": 122033, - "strid": "0b5f59e6-f720-42d1-b1f9-ccd5e3e43fab", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 1959.584, - 864.396, - 193.00800000000004, - 62.83100000000002 - ], - "priority": 13, - "parents": [ - 122045 - ], - "children": [ - 122044, - 122037 - ], - "area": 1693856.571264, + "area": 2267156.68365, "iscrowd": 0, "segmentation": [], - "text": "Access" - }, - { - "id": 122044, - "strid": "da26e522-4d6d-4250-bfd2-473ebae68208", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1953.522, - 995.755, - 1193.5879999999997, - 1401.1689999999999 - ], - "priority": 14, - "parents": [ - 122033 - ], - "children": [], - "area": 1945229.29911, - "iscrowd": 0, - "segmentation": [] + "text": "Conclusions: Across species comparisons of epigenetic effects\non genetically predisposed nutrient-dependent and hormone-\ndriven invertebrate and vertebrate social and sexual behavior\nindicate that human pheromones also alter the development of\nthe brain and behavior via the same molecular mechanisms.\nThose molecular mechanisms must be conserved across all\nspecies for adaptive evolution of the human brain and human\nbehavior to occur (e.g., via properly timed reproductive sexual\nbehavior of mammals)." }, { - "id": 122037, - "strid": "4cece0b8-7747-4abb-8f99-09c252c47206", - "image_id": 205250, - "image_name": "14511.png", + "id": 1132, + "strid": "c8953a81-18cc-458a-8991-6363f175d819", + "image_id": 43, + "image_name": "116748.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2003.099, - 2449.301, - 762.0609999999999, - 66.23599999999988 + 2381.784, + 1351.355, + 958.326, + 317.8910000000001 ], - "priority": 15, + "priority": 12, "parents": [ - 122033 + 1120 ], "children": [], - "area": 4906192.383799, + "area": 3218635.7173200003, "iscrowd": 0, "segmentation": [], - "text": "The help pages contain a detailed description of key\nfeatures of COSMIC and how to use them" - }, - { - "id": 122043, - "strid": "8870d573-4ab4-4ddc-83a5-a9c059dd7caa", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 1925.605, - 2749.134, - 1245.5729999999999, - 751.7469999999998 - ], - "priority": 16, - "parents": [ - 122045 - ], - "children": [], - "area": 5293746.17607, - "iscrowd": 0, - "segmentation": [] + "text": "Note: In mammals, LH secretion is the measurable proxy for\ngenetically predisposed differences in hypothalamic GnRH pulse\nfrequency and amplitude and the downstream effects of GnRH\non the HPG axis and the HPA axis that provide feedback to the\nGnRH neuronal system. GnRH is the central regulator of\ngenetically predisposed nutrient chemical-dependent individual\nsurvival and pheromone-dependent species survival. In the\ncontext of adaptive evolution, there is no other model for that!" }, { - "id": 122042, - "strid": "d76990b0-15d9-4a0e-b281-35412b1c0bc0", - "image_id": 205250, - "image_name": "14511.png", - "category_id": 2, - "category_name": "Figure", + "id": 1133, + "strid": "f1d25722-4615-456f-a495-ec727984f65e", + "image_id": 43, + "image_name": "116748.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1956.996, - 3551.942, - 1178.413, - 850.8590000000004 + 2383.333, + 1707.885, + 961.0250000000001, + 368.376 ], - "priority": 17, + "priority": 13, "parents": [ - 122045 + 1120 ], "children": [], - "area": 6951136.286232, + "area": 4070458.680705, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "References:\n\nKohl, JV (1992). Unpublished. Luteinizing hormone: The link between sex and\nthe sense of smell? Annual Meeting of the Society for the Scientific Study of\nSex. San Diego, CA. Nov 12-15.\n\nKohl, J.V. (2012). Human pheromones and food odors: epigenetic influences\non the socioaffective nature of evolved behaviors. Socioaffective\nNeuroscience & Psychology, 2: 17338. DOI: 10.3402/snp.v2i0.17338\n\nRoland, A. V., & Moenter, S. M. (2011). Regulation of gonadotropin-releasing\nhormone neurons by glucose. Trends Endocrinol Metab, 22(11), 443-449." }, { - "id": 161983, - "strid": "4e303741-58ad-4242-b2b9-e6080624c149", - "image_id": 206822, - "image_name": "6495.png", + "id": 1134, + "strid": "6d8599f3-343a-48f3-a003-89adb03be7bd", + "image_id": 44, + "image_name": "116760.png", "category_id": 9, "category_name": "Root", "bbox": [ - 76.2, - 59.3, - 100.57000000000001, - 368.76 + 48.17, + 20.97, + 98.55, + 43.55 ], "priority": -1, "parents": [], "children": [ - 161962, - 161960, - 161959, - 161980, - 161964, - 161963, - 161965, - 161979, - 161961 + 1151, + 1137, + 1136, + 1135, + 1139 ], - "area": 4518.66, + "area": 1010.1249, "iscrowd": 0, "segmentation": [] }, { - "id": 161959, - "strid": "552c1f94-1e7e-4cf4-98ed-345e6d064d66", - "image_id": 206822, - "image_name": "6495.png", + "id": 1135, + "strid": "d4b64d0d-cebd-4024-ae73-32125e751eed", + "image_id": 44, + "image_name": "116760.png", "category_id": 1, "category_name": "Title", "bbox": [ - 239.035, - 175.405, - 2774.598, - 214.407 + 218.666, + 34.566, + 927.9590000000001, + 170.306 ], "priority": 1, "parents": [ - 161983 + 1134 ], "children": [], - "area": 41927.934175, + "area": 7558.408956, "iscrowd": 0, "segmentation": [], - "text": "CniP-Array 2: integrating multipie Omics data to construct gene\nregulatory networks" + "text": "IL-1 receptor antagonist (Anakinra) successful\ntreatment for malignancy associated hemophagocytie\nsyndrome (MAHS) in the immediate pre transplant\nperiod in a childwith JMML" }, { - "id": 161960, - "strid": "e673723c-99cb-473c-b591-877abcdb4f26", - "image_id": 206822, - "image_name": "6495.png", + "id": 1136, + "strid": "e4243c36-6d73-48ac-bb13-7064df056cdb", + "image_id": 44, + "image_name": "116760.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 234.842, - 427.37, - 2765.935, - 225.81600000000003 + 201.171, + 229.917, + 955.8499999999999, + 127.01000000000002 ], "priority": 2, "parents": [ - 161983 + 1134 ], "children": [], - "area": 100364.42554000001, + "area": 46252.632807, "iscrowd": 0, "segmentation": [], - "text": "Panwen Wang'## , Jing Qin'+#, Yiming Qin’, Yun Zhu', Lily Yan Wang'4, Mulin Jun Li‘, Michael Q. Zhang?*, Junwen Wang!\n\n‘Centre for Genomic Sciences and Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong; *Shenzhen Institute of Research and Innovation, The\nUniversity of Hong Kong; *Bioinformatics Division, TNLIST, Tsinghua University and “Department of Molecular and Cell Biology, Center for Systems Biology, The University of\nTexas at Dallas # The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint first authors." + "text": "L.M.Ball} C.L. Vermont, P.C.E,. Hissink Muller, R.G.M.:Bredius,\nW.J.WKollen, D Bresters, F.J>Smiers, R ten Cate, AC Lankester.\n\nDepartnient of Pediatric Stem Cell Transplantation, Leiden University Medical Centre, Leiden, The Netherlands." }, { - "id": 161961, - "strid": "5b0e43b6-c91d-44f4-af92-28efe7b13d23", - "image_id": 206822, - "image_name": "6495.png", + "id": 1137, + "strid": "2d21f50e-2419-465f-82cc-8ce22720b0f1", + "image_id": 44, + "image_name": "116760.png", "category_id": 5, "category_name": "Section", "bbox": [ - 804.649, - 820.963, - 254.77599999999995, - 39.028999999999996 + 16.459, + 406.029, + 162.782, + 23.896000000000015 ], "priority": 3, "parents": [ - 161983 + 1134 ], "children": [ - 161972 + 1138 ], - "area": 660587.0569869999, + "area": 6682.831311, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Introduction" }, { - "id": 161972, - "strid": "c64516ec-0baf-4e2f-9501-248076567f60", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 4, - "category_name": "List", + "id": 1138, + "strid": "25188d20-6d71-424d-b664-9f0cc47aa058", + "image_id": 44, + "image_name": "116760.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 153.208, - 908.771, - 1559.68, - 457.38200000000006 + 14.797, + 435.337, + 437.189, + 245.65300000000002 ], "priority": 4, "parents": [ - 161961 + 1137 ], "children": [], - "area": 139230.987368, + "area": 6441.681589, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Malignancy asscclated (pprophagocytosis (MAHS)inpalts the:\ntreatment of the underlying malignancy and is associated with a high\nfatality rate retard withthe histiocytic disorders namefp)\nacquired hemophagocytic Iymphohistiocytosis (HLH) (see figure 2)\nImmune dysregulation in cytotoxic T and natural killer cell Rea\nresul ation and proliferation of histiocytes with rolled\nhemiophagocytosis (see figure 4) and hypereytokiner a syndrome\neredltizelby eter Repetoeplensenseganetion Ion\ndysfunction, and hyperferritinemia (see figure\nTreatmentis aimed at controlling the MAHS as well as addressing the\nunderlying malignancy. 2\nMAHS has been described as a corhgliSstion of JMML.12" }, { - "id": 161962, - "strid": "9b40511d-de1c-430f-bcb0-581f73d25b40", - "image_id": 206822, - "image_name": "6495.png", + "id": 1139, + "strid": "3cba1a31-7523-4539-94af-dbd70fc55452", + "image_id": 44, + "image_name": "116760.png", "category_id": 5, "category_name": "Section", "bbox": [ - 650.081, - 1421.749, - 561.102, - 48.37200000000007 + 20.986, + 727.266, + 157.818, + 30.248000000000047 ], "priority": 5, "parents": [ - 161983 + 1134 ], "children": [ - 161970 + 1149, + 1145, + 1143, + 1141, + 1147, + 1140 ], - "area": 924252.011669, + "area": 15262.404276, "iscrowd": 0, "segmentation": [], - "text": "Workflow of ChiP-Array 2" + "text": "Case report" }, { - "id": 161970, - "strid": "7839bf31-b15f-47b9-bc03-8ad610735a69", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 2, - "category_name": "Figure", + "id": 1140, + "strid": "780b6138-672b-48d0-bfa7-683c2d09a3a0", + "image_id": 44, + "image_name": "116760.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 590.167, - 1516.655, - 659.8439999999999, - 942.8640000000003 + 25.409, + 768.714, + 419.789, + 536.4700000000001 ], "priority": 6, "parents": [ - 161962 + 1139 ], "children": [], - "area": 895079.731385, + "area": 19532.254026000002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "A'S month old boy with JMML (IKRAS mutation) was refereed for\n10/10 pee donor stem cell transplantation.\n\nTwo months after diagnosis he developed acute MAHS, requi\nadmission to the intensive care unit. He was stabilized wit\nmes ILH 2004 regimen (see fig) of weekly opote high\ndos\n\ndose steroids and 6MP.\nOn admission to our unit he was severely neut jc but without\nclinical or laboratory signs of MAHS. Despite continuing MAHS\ndirected treatment, he developed a wc of symptoms\nduring the second day of ATG infusion. He was severely unwell with\nsigns of raised intracranial pres: yaar by bulging\nfontanel and persistent few evident infection.\nLaboratory parameters were CRP >100, ferritine >2000 ugll, and\ndocumented severe thrombocytopenia with a normal fibrinogen. MRI\n\nof the brain revealed no acute intracranial bleed.\nIL 4 receptor antagonist Anakinra was administered at a dose of Q\n\n \n\n3mg/kg/d for 2 consecutive days with dramatic improvement in al\nparameters within 72 hours. oo\n\nHe pr led with standard conditioning (Busulphan,\n\\osphamide, Melphalan, ATG) with Cyclosporine-A an short\n.e Methotrexate for GVHD prophylaxis. His ppm\nperiod was relatively uncomplicated with grad oie no VOD\nor acute GVHD. At day + 20 hamattota@ aftment was\n\n \n \n\ndocumented\nHe remains clinically well with stable laboratory parameters and full\ndonor chimerism engraftment." }, { - "id": 161963, - "strid": "5398ba58-5e72-4ccb-ae32-db76eb272192", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 5, - "category_name": "Section", + "id": 1141, + "strid": "3b27d82d-ece9-4aa7-b8ad-5750f34bb92c", + "image_id": 44, + "image_name": "116760.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 838.48, - 2527.626, - 187.51, - 39.416999999999916 + 8.649, + 1317.337, + 447.078, + 234.1020000000001 ], "priority": 7, "parents": [ - 161983 + 1139 ], "children": [ - 161967, - 161973, - 161969, - 161966 + 1142 ], - "area": 2119363.84848, + "area": 11393.647712999998, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 161966, - "strid": "f712d4a8-7eac-40a2-9daa-75b9503332e3", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 4, - "category_name": "List", + "id": 1142, + "strid": "b03e3b55-cab6-4799-947d-6254519f8022", + "image_id": 44, + "image_name": "116760.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 149.147, - 2632.157, - 1566.309, - 910.134 + 19.235, + 1558.486, + 113.373, + 10.178000000000111 ], "priority": 8, "parents": [ - 161963 + 1141 ], "children": [], - "area": 392578.320079, + "area": 29977.47821, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig 1: HLH-2004 protocol" }, { - "id": 161967, - "strid": "462a12c7-931b-43c3-b33a-5063ff718c78", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 4, - "category_name": "List", + "id": 1143, + "strid": "cb383853-59e1-4ffd-9b3a-b79eb64d7506", + "image_id": 44, + "image_name": "116760.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 150.181, - 3587.036, - 1565.33, - 270.03200000000015 + 494.617, + 396.604, + 295.886, + 324.787 ], "priority": 9, "parents": [ - 161963 + 1139 ], - "children": [], - "area": 538704.653516, + "children": [ + 1144 + ], + "area": 196167.080668, "iscrowd": 0, "segmentation": [] }, { - "id": 161969, - "strid": "bf899c26-0be7-4318-98e8-366b73111fa6", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 7, - "category_name": "Table", + "id": 1144, + "strid": "0b72f670-dd5b-4cb2-bad7-3583bae68649", + "image_id": 44, + "image_name": "116760.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 133.0, - 3985.844, - 1594.368, - 640.3000000000002 + 491.485, + 738.491, + 69.22500000000002, + 26.49000000000001 ], "priority": 10, "parents": [ - 161963 - ], - "children": [ - 161968 + 1143 ], - "area": 530117.252, + "children": [], + "area": 362957.249135, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "igure 2:\nCauses of HLH" }, { - "id": 161968, - "strid": "5be6dedd-3efa-4fd8-a855-2e6b5a389dd8", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 6, - "category_name": "Caption", + "id": 1145, + "strid": "57813629-86d1-4ce4-a4ef-f0b45d8a3420", + "image_id": 44, + "image_name": "116760.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 458.593, - 3910.102, - 836.71, - 39.927999999999884 + 813.211, + 399.356, + 341.98900000000003, + 324.78700000000003 ], "priority": 11, "parents": [ - 161969 + 1139 ], - "children": [], - "area": 1793145.406486, + "children": [ + 1146 + ], + "area": 324760.692116, "iscrowd": 0, - "segmentation": [], - "text": "Table. New collection of PWMs in 7 species." + "segmentation": [] }, { - "id": 161973, - "strid": "bc213323-1a6a-45d7-9e26-b1ef053cb96a", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 4, - "category_name": "List", + "id": 1146, + "strid": "a491e1be-cdae-4b0e-8700-e8e165945316", + "image_id": 44, + "image_name": "116760.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1804.149, - 819.001, - 1564.6190000000001, - 228.03399999999988 + 828.723, + 737.772, + 239.34500000000003, + 28.982999999999947 ], "priority": 12, "parents": [ - 161963 + 1145 ], "children": [], - "area": 1477599.835149, + "area": 611408.625156, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 3:\n\nClinical findings at diagnosis of hemophagocytosis" }, { - "id": 161965, - "strid": "ec165c2a-3caa-43f3-84da-49cd91bf8d70", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 5, - "category_name": "Section", + "id": 1147, + "strid": "481ea4fb-e169-4683-8dba-da7e58e28aaf", + "image_id": 44, + "image_name": "116760.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2327.086, - 1077.154, - 520.5990000000002, - 48.79299999999989 + 860.522, + 802.84, + 95.14099999999996, + 87.769 ], "priority": 13, "parents": [ - 161983 + 1139 ], "children": [ - 161971, - 161974 + 1148 ], - "area": 2506629.993244, + "area": 690861.4824800001, "iscrowd": 0, - "segmentation": [], - "text": "Results of ChlP-Array 2" + "segmentation": [] }, { - "id": 161971, - "strid": "55149e07-ea9c-4042-baee-98df983e39c2", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 2, - "category_name": "Figure", + "id": 1148, + "strid": "85bd20cd-cd3d-4148-a350-cd733a2e1c8e", + "image_id": 44, + "image_name": "116760.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2146.902, - 1175.114, - 925.201, - 899.565 + 491.001, + 809.734, + 304.05099999999993, + 75.524 ], "priority": 14, "parents": [ - 161965 + 1147 ], "children": [], - "area": 2522854.596828, + "area": 397580.203734, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "ure 4: Bone marrow and hemaph\n\n \n \n\nPhagecyiosis by macrophages of enthe\n\nond their precursors in bone marrow and aher cue. Non-specific\nphenomenon found in several cond as hemolytic anemia,\nfophagc\n\nmalignant disease, infections, and | jocytic syndrome." }, { - "id": 161974, - "strid": "80838d28-9785-4420-95d0-487ce317bdcc", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 3, - "category_name": "Text", + "id": 1149, + "strid": "4cf9fcc4-e9ed-40bf-b94f-44173bc2c3de", + "image_id": 44, + "image_name": "116760.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1804.247, - 2101.048, - 1563.709, - 170.76699999999983 + 474.105, + 945.142, + 354.586, + 220.5920000000001 ], "priority": 15, "parents": [ - 161965 + 1139 ], - "children": [], - "area": 3790809.550856, + "children": [ + 1150 + ], + "area": 448096.54791, "iscrowd": 0, - "segmentation": [], - "text": "The events, including TF-binding, long-range chromatin interaction, open chromatin\nregion and histone modification, around a TSS, are intuitively displayed in JBrowse.\nFurthermore, enriched Gene Ontology (GO) and Pathways from the resulting GRN are\ndisplayed in the result page." + "segmentation": [] }, { - "id": 161964, - "strid": "2ef9a662-b484-41e6-9a49-9f660eafe844", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 5, - "category_name": "Section", + "id": 1150, + "strid": "be7981b7-2d31-4ace-8399-988f8fd724a5", + "image_id": 44, + "image_name": "116760.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2285.184, - 2322.97, - 606.1500000000001, - 48.38700000000017 + 837.138, + 952.341, + 319.7499999999999, + 208.49200000000008 ], "priority": 16, "parents": [ - 161983 + 1149 ], - "children": [ - 161975, - 161976, - 161978, - 161977 - ], - "area": 5308413.87648, + "children": [], + "area": 797240.8400580001, "iscrowd": 0, "segmentation": [], - "text": "Examples — mESC Library" + "text": "representation ofthe structure and function of Ankinra\n\n \n\n \n\ninra is an interleukin-1(IL-1) receptor antagonist Anakinra block :\nng yo ny igi corey ig\ntng as pn en, wich sein\ncet\n11s pod haere bry srl 24a\nie eg eee inc meee Fae\naap\nener oe\nny a ates pe pay rr ts\nmbna Re al fag\n\nmethionine residue at its amin therton," }, { - "id": 161975, - "strid": "581db630-4a8d-47eb-97ef-2f9687496a74", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 3, - "category_name": "Text", + "id": 1151, + "strid": "e6d972ef-45de-4b65-9b6f-ddb406469aab", + "image_id": 44, + "image_name": "116760.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1804.409, - 2426.979, - 1566.174, - 216.37699999999995 + 476.762, + 1209.354, + 152.29300000000006, + 25.1579999999999 ], "priority": 17, "parents": [ - 161964 + 1134 ], - "children": [], - "area": 4379262.750411, + "children": [ + 1152, + 1153 + ], + "area": 576574.0317480001, "iscrowd": 0, "segmentation": [], - "text": "We built a GRN library for mESC which is controlled by 18 TFs/ chromatin modifiers. This\nlibrary combines data from ChIP-seq of the TFs/chromatin modifiers, transcriptome\nprofiling under their perturbations, together with ChlIA-PET, DNase-seq and _ histone\nmodification ChlPseq. Integration of diverse omics data significantly improves the target\ndetection and our understanding of gene transcription regulation as shown below." + "text": "" }, { - "id": 161976, - "strid": "3bad7b54-9c6b-4632-8eae-bc822c59fca4", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 2, - "category_name": "Figure", + "id": 1152, + "strid": "f5a34251-2fae-4ad6-a919-40e8758b034b", + "image_id": 44, + "image_name": "116760.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1845.891, - 2685.481, - 1477.8759999999997, - 849.7939999999999 + 479.383, + 1258.438, + 414.37600000000003, + 250.827 ], "priority": 18, "parents": [ - 161964 + 1151 ], "children": [], - "area": 4957105.208571001, + "area": 603273.783754, "iscrowd": 0, "segmentation": [] }, { - "id": 161977, - "strid": "af3e6782-bc03-438c-90a3-7d85e1fd3f76", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 3, - "category_name": "Text", + "id": 1153, + "strid": "2643f228-81e0-41ca-b8bc-4a4f3e23d901", + "image_id": 44, + "image_name": "116760.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1806.406, - 3591.191, - 1342.589, - 37.71799999999985 + 914.447, + 1320.971, + 219.572, + 181.70100000000002 ], "priority": 19, "parents": [ - 161964 + 1151 ], "children": [], - "area": 6487148.969546, + "area": 1207957.968037, "iscrowd": 0, - "segmentation": [], - "text": "Example targets of Poudf1 identified by ChIP-Array 2 with multiple omics data." + "segmentation": [] }, { - "id": 161978, - "strid": "8b64eb32-6f0e-4d34-b9f0-0636d1f6074c", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 4, - "category_name": "List", + "id": 1154, + "strid": "28c715b5-59c3-412d-8061-071ba41b0f48", + "image_id": 45, + "image_name": "116774.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 1805.584, - 3636.565, - 1564.8510000000003, - 349.82699999999977 + 11.19, + 14.63, + 59.400000000000006, + 61.37 ], - "priority": 20, - "parents": [ - 161964 + "priority": -1, + "parents": [], + "children": [ + 1157, + 1161, + 1172, + 1159, + 1155, + 1163, + 1156 ], - "children": [], - "area": 6566123.578960001, + "area": 163.7097, "iscrowd": 0, "segmentation": [] }, { - "id": 161980, - "strid": "0e96681f-c64c-49de-82a5-d2cab6d140ee", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 5, - "category_name": "Section", + "id": 1155, + "strid": "fbf76f07-6b3c-4da2-9f9c-17aca147c39f", + "image_id": 45, + "image_name": "116774.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 2498.695, - 4336.797, - 177.4960000000001, - 50.100000000000364 + 98.184, + 22.085, + 690.258, + 86.886 ], - "priority": 21, + "priority": 1, "parents": [ - 161983 - ], - "children": [ - 161981 + 1154 ], - "area": 10836332.979915, + "children": [], + "area": 2168.3936400000002, "iscrowd": 0, "segmentation": [], - "text": "Funding" + "text": "Ss ‘stematic analysis of chemokines and chemokine receptorsin\ng lymphocyte infiltration in ovarian cancer we\n\nFrom microarray te ‘ein expression and serum leve" }, { - "id": 161981, - "strid": "40e6f305-e423-49ea-b467-d37763cf609e", - "image_id": 206822, - "image_name": "6495.png", - "category_id": 3, - "category_name": "Text", + "id": 1156, + "strid": "bb9116d0-51f3-425b-ba4f-f8992b881696", + "image_id": 45, + "image_name": "116774.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1802.881, - 4413.371, - 1568.1049999999998, - 217.71799999999985 + 172.396, + 135.087, + 551.534, + 71.85500000000002 ], - "priority": 22, + "priority": 2, "parents": [ - 161980 + 1154 ], "children": [], - "area": 7956782.721851001, + "area": 23288.458451999995, "iscrowd": 0, "segmentation": [], - "text": "Research Grants Council, Hong Kong SAR, China [781511M, 17121414M]. National\nNatural Science Foundation of China, China [91229105]. Small Project Funding, University\nGrants Committee, The University of Hong Kong, Hong Kong SAR, China\n[201409176183]. Funding for open access charge: Research Grants Council, Hong Kong\nSAR, China [17121414M]." + "text": "Marloes J.M. Gooden’, Ninke Leffers', Rudolf S.N. Fehrmann'*?, Klaske A. ten Hoor', Toos Daemen*,\nAte GJ. van der Zee\", Geertruida H. de Bock’, Annemiek ME. Walenkamp2, Hans W. Nijman*\n\nDepsrtmefts of Gynecological Oncology, Melcal Oncology, Genetics, Medial Microbiology\nEpidemiology®: University Medical Center Groningen, University of Groningen, Groningen, The Netherlands." }, { - "id": 161979, - "strid": "15a5605d-262a-427c-b6c0-cf38b2fe6946", - "image_id": 206822, - "image_name": "6495.png", + "id": 1157, + "strid": "3cf2c82b-27b5-42aa-9d58-4e966cb7f960", + "image_id": 45, + "image_name": "116774.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2461.566, - 4025.911, - 251.808, - 40.384000000000015 + 211.303, + 238.47, + 102.68600000000004, + 11.319999999999993 ], - "priority": 23, + "priority": 3, "parents": [ - 161983 + 1154 ], "children": [ - 161982 + 1158 ], - "area": 9910045.636626, + "area": 50389.42641, "iscrowd": 0, "segmentation": [], - "text": "References" + "text": "" }, { - "id": 161982, - "strid": "4212574c-72d9-4d79-b9e2-a22f3befc3a4", - "image_id": 206822, - "image_name": "6495.png", + "id": 1158, + "strid": "325329ae-3bde-4808-b4a5-9fc85ddde140", + "image_id": 45, + "image_name": "116774.png", "category_id": 4, "category_name": "List", "bbox": [ - 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"text": "by Constantin Ahlmann-Eltze & Wolfgang Huber, EMBL Heidelberg\n\nJ bioconductor. org/packages/glmGamPoi/ ©) github. com/const-ae/glmGamPoi" + "text": "To determine whether chemokines are involved in CTL\nrecruitment to ovarian cancer, using a microarray based approach" }, { - "id": 139388, - "strid": "700ad59d-142a-4cb4-b9fd-c27b273316ed", - "image_id": 205916, - "image_name": "16720.png", + "id": 1161, + "strid": "4c1cfd5e-1446-4303-b218-896dd5ef165c", + "image_id": 45, + "image_name": "116774.png", "category_id": 5, "category_name": "Section", "bbox": [ - 536.735, - 360.994, - 322.86199999999997, - 50.83800000000002 + 181.82, + 478.317, + 162.58999999999997, + 11.916999999999973 ], - "priority": 3, + "priority": 7, "parents": [ - 139399 + 1154 ], "children": [ - 139397, - 139393 + 1162 ], - "area": 193758.11459, + "area": 86967.59694, "iscrowd": 0, "segmentation": [], - "text": "~10x faster than edgeR and\nDESeq2" + "text": "MATERIALS & METHODS" }, { - "id": 139397, - "strid": "0d64787b-2f43-48a1-b06b-0983ff26a0be", - 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"id": 40486, - "strid": "e3c49190-c983-47b5-a970-6a4156a4e8cf", - "image_id": 202094, - "image_name": "118117.png", + "id": 1176, + "strid": "ab9f4aaf-1da9-4288-aea7-dbbd0d5d04fa", + "image_id": 46, + "image_name": "116793.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 1938.505, - 453.072, - 1786.272, - 137.99400000000003 + 479.255, + 309.085, + 2366.485, + 62.75400000000002 ], "priority": 2, "parents": [ - 40521 + 1174 ], "children": [], - "area": 878282.33736, + "area": 148130.53167499998, "iscrowd": 0, "segmentation": [], - "text": "Elisabetta Tomé, Massimo Tagliavini, Francesca Scandellari\n\nFree University of Bolzano-Bozen, Italy" + "text": "Haitze |. de Vries ', Michiel F. Reneman *, Joan W. Groothoff 2, Jan H.B. Geertzen *, Sandra Brouwer ”" }, { - "id": 40487, - "strid": "31ad5168-02d8-4ab6-b6ea-0df68973f940", - "image_id": 202094, - "image_name": "118117.png", + "id": 1177, + "strid": "c6984ead-684f-4f10-b3b5-5c85c9a831c1", + "image_id": 46, + "image_name": "116793.png", "category_id": 5, "category_name": "Section", "bbox": [ - 95.138, - 741.409, - 409.403, - 82.76200000000006 + 244.834, + 500.769, + 347.94300000000004, + 75.269 ], "priority": 3, "parents": [ - 40521 + 1174 ], "children": [ - 40495 + 1179, + 1178 ], - "area": 70536.169442, + "area": 122605.277346, "iscrowd": 0, "segmentation": [], - "text": "Background" + "text": "Backgtound" }, { - "id": 40495, - "strid": "80d0c5bb-4968-4990-b081-e1f3433dc070", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 3, - "category_name": "Text", + "id": 1178, + "strid": "a0902bbe-94dd-4193-87cb-379c6e7acfbc", + "image_id": 46, + "image_name": "116793.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 86.178, - 893.276, - 1489.3900000000003, - 353.533 + 240.488, + 637.833, + 1335.133, + 1049.788 ], "priority": 4, "parents": [ - 40487 + 1177 ], "children": [], - "area": 76980.73912799999, + "area": 153391.182504, "iscrowd": 0, - "segmentation": [], - "text": "Arbuscular mycorrhizal fungi (AMF) colonize plant roots and spread in\nthe surrounding soil, enhance plant nutrient uptake from the soil and\nstimulate the transfer of photosynthates from the plant to the soil (1).\nThe importance of this symbiotic association in agro-ecosystems has\ngained importance due to its role in the sustainability of fruit production\nas well as in carbon (C) budgets." + "segmentation": [] }, { - "id": 40489, - "strid": "83d02df9-0c79-4477-a91a-d95503ba115d", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 5, - "category_name": "Section", + "id": 1179, + "strid": "26165334-d01e-4a8a-8f54-0ff77773baf9", + "image_id": 46, + "image_name": "116793.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 98.376, - 1343.889, - 313.3430000000001, - 69.05999999999995 + 1708.486, + 705.849, + 1523.555, + 726.705 ], "priority": 5, "parents": [ - 40521 + 1177 ], "children": [ - 40497, - 40513, - 40514, - 40496, - 40515 + 1180 ], - "area": 132206.424264, + "area": 1205933.134614, "iscrowd": 0, - "segmentation": [], - "text": "Methods" + "segmentation": [] }, { - "id": 40496, - "strid": "03a50723-24a7-4260-8032-a467b06f8ece", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 3, - "category_name": "Text", + "id": 1180, + "strid": "2cb13d2b-fa8c-43fe-b228-a55b58a3741d", + "image_id": 46, + "image_name": "116793.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 91.026, - 1497.091, - 1486.388, - 290.6959999999999 + 1703.483, + 504.839, + 1392.9349999999997, + 142.084 ], "priority": 6, "parents": [ - 40489 + 1179 ], "children": [], - "area": 136274.20536599998, + "area": 859984.6542369999, "iscrowd": 0, "segmentation": [], - "text": "We studied 1, 2 and 5 years-old apple orchards grafted on M9 rootstock.\nIn each orchard, at planting, 4 plots of 20 trees each were either treated\nwith chemical fumigation (Basamid, 80 g m%), or inoculated with\nmycorrhizae (Micosat ,75 g tree). Untreated trees as control were also\npresent." + "text": "Table: Hierarchical multiple regression analysis with work\nability and work performance as dependent variables" }, { - "id": 40513, - "strid": "3ae77d2d-e89d-4198-b0ec-66c9b9172430", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 2, - "category_name": "Figure", + "id": 1181, + "strid": "48a1c1be-76de-4198-8ef7-ca581e754c9f", + "image_id": 46, + "image_name": "116793.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 138.517, - 1834.989, - 412.29299999999995, - 617.5430000000001 + 245.186, + 1867.07, + 266.99299999999994, + 58.19100000000003 ], "priority": 7, "parents": [ - 40489 + 1174 ], "children": [ - 40502 + 1183, + 1182 ], - "area": 254177.171313, + "area": 457779.42502, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Methods" }, { - "id": 40502, - "strid": "734537b9-eb11-4927-943e-ea8c2f2996e0", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 6, - "category_name": "Caption", + "id": 1182, + "strid": "14f3e098-6b1b-4e44-9c34-6015bbe401a7", + "image_id": 46, + "image_name": "116793.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 147.508, - 2456.867, - 392.43899999999996, - 79.47499999999991 + 244.011, + 1972.967, + 1324.565, + 915.9230000000002 ], "priority": 8, "parents": [ - 40513 + 1181 ], "children": [], - "area": 362407.5374360001, + "area": 481425.65063700004, "iscrowd": 0, - "segmentation": [], - "text": "Figure 1 : Soil respiration\nchamber" + "segmentation": [] }, { - "id": 40514, - "strid": "758113f6-54b8-414f-a485-8fea82997a6d", - "image_id": 202094, - "image_name": "118117.png", + "id": 1183, + "strid": "fcf57777-ec72-4f5b-a6e7-e8b7f6c4e509", + "image_id": 46, + "image_name": "116793.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 608.684, - 1833.282, - 404.39699999999993, - 615.6650000000002 + 1705.451, + 1891.447, + 1536.5150000000003, + 951.9709999999998 ], "priority": 9, "parents": [ - 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1069.518, - 1835.974, - 450.4200000000001, - 608.1209999999999 + 248.521, + 3051.979, + 208.65, + 56.43199999999979 ], "priority": 11, "parents": [ - 40489 + 1174 ], "children": [ - 40504 + 1186 ], - "area": 1963607.240532, + "area": 758480.8730589999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Results" }, { - "id": 40504, - "strid": "83415d8e-628e-47a4-be12-244a457f5073", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 6, - "category_name": "Caption", + "id": 1186, + "strid": "42d8abee-779a-4296-a300-d0e5bb4254e3", + "image_id": 46, + "image_name": "116793.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1072.539, - 2457.124, - 482.846, - 132.19000000000005 + 247.534, + 3160.143, + 1335.1329999999998, + 817.2849999999999 ], "priority": 12, "parents": [ - 40515 + 1185 ], "children": [], - "area": 2635361.3178359997, + "area": 782242.837362, "iscrowd": 0, - "segmentation": [], - "text": "Figure 3 : Apple roots after\nstaining procedure, visible in\ndark blue vesicles and hyphae" + "segmentation": [] }, { - "id": 40497, - "strid": "72cf1013-ee0e-4146-ba10-77259ddf8587", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 3, - "category_name": "Text", + "id": 1187, + "strid": "dbd7d291-fff3-41e8-ad27-c788f5fbea17", + "image_id": 46, + "image_name": "116793.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 91.457, - 2635.698, - 1487.138, - 413.0720000000001 + 1706.925, + 3042.984, + 352.568, + 58.164999999999964 ], "priority": 13, "parents": [ - 40489 + 1174 ], - "children": [], - "area": 241053.03198599996, + "children": [ + 1188 + ], + "area": 5194145.464199999, "iscrowd": 0, "segmentation": [], - "text": "We measured soil respiration (R,) in 60 positions per orchard (tot =180\nmeasurements) in September 2012 with a survey chamber coupled with\nan infrared gas analyser (LI-8100, Li-Cor) (Fig.1). At each position we\nsampled the soil (Fig.2) for the analysis of mycorrhizal root length\ncolonization (RLC) (Fig.3) (2), enzymatic activity (acid and alkaline\nphosphatase) (3), total soil C using an Elemental Analyzer Flash 2000\n(ThermoFisher Scientific), and microbial C concentrations (C,..) (4)." + "text": "Conclusions" }, { - "id": 40488, - "strid": "ba6ac0dc-2300-4b30-962a-851be65a31c9", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 5, - "category_name": "Section", + "id": 1188, + "strid": "1118e2e7-9325-4676-b2f7-828f9ffeef08", + "image_id": 46, + "image_name": "116793.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1687.543, - 741.356, - 365.4849999999999, - 79.673 + 1705.965, + 3149.575, + 1497.1809999999998, + 884.2179999999998 ], "priority": 14, "parents": [ - 40521 + 1187 ], + "children": [], + "area": 5373064.714875, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1189, + "strid": "ebc5065d-7a80-434d-b61b-f8ecdaaa2689", + "image_id": 47, + "image_name": "116809.png", + "category_id": 9, + "category_name": "Root", + "bbox": [ + 160.61, + 201.59, + 194.44, + 167.61999999999998 + ], + "priority": -1, + "parents": [], "children": [ - 40509 + 1191, + 1229, + 1192, + 1237, + 1202, + 1234, + 1190, + 1239, + 1215, + 1221 ], - "area": 1251070.1283079998, + "area": 32377.3699, "iscrowd": 0, - "segmentation": [], - "text": "Objectives" + "segmentation": [] }, { - "id": 40509, - "strid": "8b419f84-666e-4d75-98f4-bc8e3e712560", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 4, - "category_name": "List", + "id": 1190, + "strid": "f43abf56-7db4-48fa-a1fc-7cf803a9638a", + "image_id": 47, + "image_name": "116809.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 1680.45, - 892.699, - 1573.5600000000002, - 229.7399999999999 + 627.696, + 107.577, + 3573.1400000000003, + 127.03300000000002 ], - "priority": 15, + "priority": 1, "parents": [ - 40488 + 1189 ], "children": [], - "area": 1500136.03455, + "area": 67525.652592, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Controllability of Cancer Networks: a Bo1lean Perspective" }, { - "id": 40490, - "strid": "e3ac0f58-df11-418b-89ca-9e5379ebb7dd", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 5, - "category_name": "Section", + "id": 1191, + "strid": "b4dea473-95ea-409f-81fa-b3370434749a", + "image_id": 47, + "image_name": "116809.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1683.22, - 1240.654, - 249.60400000000004, - 66.30700000000002 + 1210.247, + 242.009, + 2368.9389999999994, + 184.50199999999998 ], - "priority": 16, + "priority": 2, "parents": [ - 40521 - ], - "children": [ - 40510, - 40518, - 40517, - 40516, - 40498, - 40499 + 1189 ], - "area": 2088293.62588, + "children": [], + "area": 292890.666223, "iscrowd": 0, "segmentation": [], - "text": "Results" + "text": "Sriganesh Srihari\nThe University of Queensland, Institute for Molecular Bioscience, St. Lucia, Brisbane, Queensland 4072, Australia.\n{ s.stihari | sriganesh.m.s } @ { uq.edu.au | gmail.com }" }, { - "id": 40516, - "strid": "3436c11c-d012-460f-aa9a-edd3bfaff3d5", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 2, - "category_name": "Figure", + "id": 1192, + "strid": "11ad2c4b-a2c2-46e4-9fb9-2c97c46f3da6", + "image_id": 47, + "image_name": "116809.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1718.739, - 1342.191, - 813.5720000000001, - 531.1000000000001 + 487.993, + 631.458, + 269.09100000000007, + 38.567999999999984 ], - "priority": 17, + "priority": 3, "parents": [ - 40490 + 1189 ], "children": [ - 40505 + 1194, + 1199, + 1200, + 1198, + 1197, + 1201, + 1195, + 1196, + 1193 ], - "area": 2306876.017149, + "area": 308147.083794, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 40505, - "strid": "c67e5d70-f983-42f8-b761-c6fd9c0822ac", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 6, - "category_name": "Caption", + "id": 1193, + "strid": "8d0cab38-0f09-4411-a739-60c0ab980e10", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1725.814, - 1881.974, - 786.7320000000002, - 88.53899999999999 + 294.44, + 710.935, + 655.175, + 48.90300000000002 ], - "priority": 18, + "priority": 4, "parents": [ - 40516 + 1192 ], "children": [], - "area": 3247937.076836, + "area": 209327.7014, "iscrowd": 0, "segmentation": [], - "text": "Figure 4 : Variation of RLC in the orchards (bars\nindicate standard errors)" + "text": "Controllability of a Dynamical System" }, { - "id": 40510, - "strid": "9a839c38-9faa-4a9a-a177-5445ec97fefa", - "image_id": 202094, - "image_name": "118117.png", + "id": 1194, + "strid": "568c14a3-e159-4697-a544-a72c633ee657", + "image_id": 47, + "image_name": "116809.png", "category_id": 4, "category_name": "List", "bbox": [ - 2557.977, - 1412.678, - 758.9180000000001, - 413.0240000000001 + 126.677, + 791.677, + 992.1919999999999, + 720.033 ], - "priority": 19, + "priority": 5, "parents": [ - 40490 + 1192 ], "children": [], - "area": 3613597.8324060002, + "area": 100287.26732900001, "iscrowd": 0, "segmentation": [] }, { - "id": 40498, - "strid": "d4726a7f-512e-492e-a349-476388291b7c", - "image_id": 202094, - "image_name": "118117.png", + "id": 1195, + "strid": "0b20a466-cb6e-4e16-83d8-081d5ab167f7", + "image_id": 47, + "image_name": "116809.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1724.839, - 2040.1, - 794.549, - 649.5219999999999 + 369.538, + 1559.579, + 648.272, + 100.827 ], - "priority": 20, + "priority": 6, "parents": [ - 40490 + 1192 ], "children": [], - "area": 3518844.0439, + "area": 576323.704502, "iscrowd": 0, "segmentation": [], - "text": "We observed a significant correlation\nof RLC with acid phosphatase\n(p<0.001) suggesting an active role of\nmycorrhizal symbiosis in the inorganic\nP uptake from soil. The two agronomic\ntreatments had neither a significative\neffect on the microbial biomass nor\naffected soil functionality. R, positively\ncorrelated with the total soil C\n(p<0.001), but not with microbial\ncarbon and RLC." + "text": "structural Controllability of Networks\n(Ching-Tai Lin, 1974)" }, { - "id": 40517, - "strid": "860f4400-da8d-4b7f-a3e9-54ba2802ab96", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 2, - "category_name": "Figure", + "id": 1196, + "strid": "e48a35ec-7967-4449-b5c4-876e356946ce", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2584.519, - 1944.353, - 740.569, - 740.569 + 123.018, + 1708.895, + 943.606, + 348.2840000000001 ], - "priority": 21, + "priority": 7, "parents": [ - 40490 + 1192 ], - "children": [ - 40506 + "children": [], + "area": 210224.84511, + "iscrowd": 0, + "segmentation": [], + "text": "A dynamical system,\ndx(t)\ndt\nx(t) = (x,(t),..., xN(t))’: state of N nodes at time t\nA (N XN): the system’s wiring and the interaction strengths,\nB(N XM): the M < Nnodes that are controlled,\nu(t): the signal applied to M nodes at time ¢,\n\n \n\n= Ax(t) + Bu(t), (1)" + }, + { + "id": 1197, + "strid": "8374a0eb-267e-4bf5-a858-9de91c2cf6aa", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", + "bbox": [ + 121.393, + 2108.875, + 731.923, + 92.48099999999977 ], - "area": 5025217.271207, + "priority": 8, + "parents": [ + 1192 + ], + "children": [], + "area": 256002.662875, "iscrowd": 0, "segmentation": [] }, { - "id": 40506, - "strid": "f7d296fa-c014-4b2a-8021-7513caa40da6", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 6, - "category_name": "Caption", + "id": 1198, + "strid": "1a289b34-9c0b-497b-83f1-e1ec1d40597b", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2597.799, - 2704.443, - 672.8699999999999, - 45.184999999999945 + 122.945, + 2252.693, + 978.0630000000001, + 143.48799999999983 ], - "priority": 22, + "priority": 9, "parents": [ - 40517 + 1192 ], "children": [], - "area": 7025599.320957, + "area": 276957.340885, "iscrowd": 0, "segmentation": [], - "text": "Figure 5 : PCA and Eigen values (small box)" + "text": "If we wish to control the network, we first need to identify the set of\nnodes that, if driven by different signals, can offer full control over\nthe network. This allows structural controllability of the network." }, { - "id": 40518, - "strid": "e453f0c2-50ae-4f43-a4b9-f06b4121800d", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 2, - "category_name": "Figure", + "id": 1199, + "strid": "a2ba4366-b5b5-4835-b878-de4ce9e3a795", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1712.668, - 2762.394, - 809.7140000000002, - 638.9670000000001 + 118.751, + 2492.012, + 969.733, + 298.5819999999999 ], - "priority": 23, + "priority": 10, "parents": [ - 40490 - ], - "children": [ - 40507 + 1192 ], - "area": 4731063.807192, + "children": [], + "area": 295928.91701200005, "iscrowd": 0, "segmentation": [] }, { - "id": 40507, - "strid": "53f8d197-6601-4c0b-b56f-b91a00a2f5b5", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 6, - "category_name": "Caption", + "id": 1200, + "strid": "eee0d098-6be1-4b90-bbca-c62db8075958", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1730.281, - 3416.851, - 777.4369999999999, - 82.66400000000021 + 320.883, + 2810.978, + 631.383, + 100.23900000000003 ], - "priority": 24, + "priority": 11, "parents": [ - 40518 + 1192 ], "children": [], - "area": 5912112.365131, + "area": 901995.053574, "iscrowd": 0, "segmentation": [], - "text": "Figure 6 : CO, soil fluxes in the orchards and\nbetween treatments" + "text": "Controllability of Complex Networks\n(Barabasi et al., 2011)" }, { - "id": 40499, - "strid": "1e613e67-7ba1-4194-adec-06c8043fd977", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 3, - "category_name": "Text", + "id": 1201, + "strid": "da64f886-e8c9-45f6-aa7e-23f1e7cf4a4c", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 2591.831, - 2882.422, - 721.8780000000002, - 529.1379999999999 + 126.677, + 2933.28, + 988.2289999999999, + 531.107 ], - "priority": 25, + "priority": 12, "parents": [ - 40490 + 1192 ], "children": [], - "area": 7470750.694682, + "area": 371579.11056000006, "iscrowd": 0, - "segmentation": [], - "text": "After one year from the\napplication of treatments, R, was\nhigher in fumigated plots\ncompared with the control and\ninoculated plots, probably due to a\npriming effect, whereas no\nsignificative difference was\ndetected after 3 and 5 years from\ntreatments." + "segmentation": [] }, { - "id": 40494, - "strid": "cf7a0cda-7eb8-4414-bb11-8f9e8318e28b", - "image_id": 202094, - "image_name": "118117.png", + "id": 1202, + "strid": "f965b833-02da-4094-bcd7-2849c5cdbeef", + "image_id": 47, + "image_name": "116809.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3489.039, - 735.843, - 373.2840000000001, - 81.45299999999997 + 1647.278, + 628.716, + 307.40800000000013, + 44.87699999999995 ], - "priority": 26, + "priority": 13, "parents": [ - 40521 + 1189 ], "children": [ - 40519, - 40520 + 1212, + 1208, + 1209, + 1206, + 1211, + 1210, + 1213, + 1207, + 1205, + 1204, + 1203, + 1214 ], - "area": 2567384.924877, + "area": 1035670.035048, "iscrowd": 0, "segmentation": [], - "text": "Study area" + "text": "2a. Our Approach" }, { - "id": 40519, - "strid": "23406442-07c7-4a2c-848c-123fbd1025a8", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 2, - "category_name": "Figure", + "id": 1203, + "strid": "38803cdf-c3e9-414f-b35f-bb303cc22c54", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3483.222, - 899.251, - 394.9960000000001, - 431.92599999999993 + 1502.272, + 707.989, + 599.7919999999999, + 48.31299999999999 ], - "priority": 27, + "priority": 14, "parents": [ - 40494 + 1202 ], "children": [], - "area": 3132290.8667220003, + "area": 1063592.051008, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Controllability of Cancer Networks" }, { - "id": 40520, - "strid": "dfac15fb-8592-426e-ac8e-3df146cd4120", - "image_id": 202094, - "image_name": "118117.png", + "id": 1204, + "strid": "3896e8e3-290e-4366-ad74-a097e244e7d6", + "image_id": 47, + "image_name": "116809.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3932.055, - 746.428, - 695.2000000000003, - 436.918 + 1279.778, + 784.183, + 1031.1160000000002, + 658.7089999999998 ], - "priority": 28, + "priority": 15, "parents": [ - 40494 - ], - "children": [ - 40508 + 1202 ], - "area": 2934995.94954, + "children": [], + "area": 1003580.151374, "iscrowd": 0, "segmentation": [] }, { - "id": 40508, - "strid": "622aa66a-a03b-4fbc-9acf-138d1497ee2f", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 6, - "category_name": "Caption", + "id": 1205, + "strid": "34493fd5-cb39-45e9-a04e-eb27a5fb012d", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 3942.514, - 1197.536, - 672.0889999999999, - 133.615 + 1306.016, + 1460.321, + 1013.9290000000001, + 222.54500000000007 ], - "priority": 29, + "priority": 16, "parents": [ - 40520 + 1202 ], "children": [], - "area": 4721302.445504, - "iscrowd": 0, - "segmentation": [], - "text": "Figure 7: The map shows the location of\napple orchards in the Alto Adige Region.\nThe red dot specify the study site" - }, - { - "id": 40491, - "strid": "385b58c1-7418-48f3-95ce-c9aa98b4c0b1", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 5, - "category_name": "Section", - "bbox": [ - 3482.845, - 1500.743, - 1211.1339999999996, - 82.09500000000003 - ], - "priority": 30, - "parents": [ - 40521 - ], - "children": [ - 40501, - 40511 - ], - "area": 5226855.253834999, + "area": 1907202.591136, "iscrowd": 0, - "segmentation": [], - "text": "Conclusions and future perspectives" + "segmentation": [] }, { - "id": 40511, - "strid": "ac1a374b-9770-4ab3-abc1-c505e6dced9a", - "image_id": 202094, - "image_name": "118117.png", + "id": 1206, + "strid": "50bc1e40-1d51-4961-af77-20b2668efcee", + "image_id": 47, + "image_name": "116809.png", "category_id": 4, "category_name": "List", "bbox": [ - 3482.127, - 1691.026, - 1219.3030000000003, - 643.8100000000002 + 1304.481, + 1741.212, + 960.693, + 190.29199999999992 ], - "priority": 31, + "priority": 17, "parents": [ - 40491 + 1202 ], "children": [], - "area": 5888367.292302, + "area": 2271377.970972, "iscrowd": 0, "segmentation": [] }, { - "id": 40501, - "strid": "53773428-7f96-4d9b-bf3f-43a81722421c", - "image_id": 202094, - "image_name": "118117.png", + "id": 1207, + "strid": "66b930f2-1f01-4d96-8296-db697e0e440b", + "image_id": 47, + "image_name": "116809.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3482.534, - 2408.879, - 1215.904, - 173.09299999999985 + 1338.827, + 1987.066, + 925.896, + 47.878999999999905 ], - "priority": 32, + "priority": 18, "parents": [ - 40491 + 1202 ], "children": [], - "area": 8389003.019385999, + "area": 2660337.611582, "iscrowd": 0, "segmentation": [], - "text": "Future work will be done to better understand the\ncontribution of the mycorrhizal fungi in R, and _ in the total\ncarbon budgets." + "text": "Boolean Model for Controllability of Cancer Networks" }, { - "id": 40492, - "strid": "7e946a52-18fa-4485-b567-738e25ce06e7", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 5, - "category_name": "Section", + "id": 1208, + "strid": "2785b758-82be-4266-ace6-a0c2bba8e864", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 3479.989, - 2688.074, - 685.6960000000004, - 79.96900000000005 + 1294.345, + 2060.668, + 1007.3570000000002, + 212.7539999999999 ], - "priority": 33, + "priority": 19, "parents": [ - 40521 - ], - "children": [ - 40500 + 1202 ], - "area": 9354467.951186, + "children": [], + "area": 2667215.3224600004, "iscrowd": 0, - "segmentation": [], - "text": "Acknowledgements" + "segmentation": [] }, { - "id": 40500, - "strid": "2d24ac6d-444a-4d33-823c-556149751662", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 3, - "category_name": "Text", + "id": 1209, + "strid": "a7f2aff2-fcab-461b-8807-f44351878e60", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 3477.952, - 2809.626, - 1218.531, - 345.96500000000015 + 1294.345, + 2326.61, + 809.9930000000002, + 163.68499999999995 ], - "priority": 34, + "priority": 20, "parents": [ - 40492 + 1202 ], "children": [], - "area": 9771744.365952002, + "area": 3011436.02045, "iscrowd": 0, - "segmentation": [], - "text": "This project is funded by the Free University of Bolzano\n(TN5051). We would like to thank Dr. Luciano Cavani and Dr.\nMartin Thalheimer for their support in the lab and in the\nfield. A big thank to Maddalena Bolognesi, Christian\nCeccon and Damiano Zanotelli for their support in field\nwork." + "segmentation": [] }, { - "id": 40493, - "strid": "d9c3c6b9-b298-4592-bb7d-b6e5976ab036", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 5, - "category_name": "Section", + "id": 1210, + "strid": "61dbcc39-9dc6-40a6-97cd-3a63f111384f", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 99.653, - 3128.61, - 246.012, - 43.583000000000084 + 1294.833, + 2534.614, + 686.2640000000001, + 279.0999999999999 ], - "priority": 35, + "priority": 21, "parents": [ - 40521 - ], - "children": [ - 40512 + 1202 ], - "area": 311775.37233000004, + "children": [], + "area": 3281901.849462, "iscrowd": 0, - "segmentation": [], - "text": "References:" + "segmentation": [] }, { - "id": 40512, - "strid": "8404aeea-af00-4e48-baf9-df7716bc83d0", - "image_id": 202094, - "image_name": "118117.png", - "category_id": 4, - "category_name": "List", + "id": 1211, + "strid": "e4902020-ceca-4e69-b287-7d8ddb3b76e4", + "image_id": 47, + "image_name": "116809.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 98.979, - 3222.569, - 1482.852, - 278.924 + 2013.131, + 2574.961, + 248.75699999999983, + 146.2159999999999 ], - "priority": 36, + "priority": 22, "parents": [ - 40493 + 1202 ], "children": [], - "area": 318966.657051, + "area": 5183733.812891, "iscrowd": 0, "segmentation": [] }, { - "id": 71717, - "strid": "59dcea7e-c73d-44ad-a92f-2bbde8e75b7c", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 9, - "category_name": "Root", + "id": 1212, + "strid": "7888c094-62b1-4fe7-bbfb-b63b4f070f5a", + "image_id": 47, + "image_name": "116809.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 387.53, - 273.05, - 242.59000000000003, - 224.62 + 1280.151, + 2834.965, + 1052.115, + 444.21500000000015 ], - "priority": -1, - "parents": [], - "children": [ - 71708, - 71709, - 71716, - 71707, - 71704, - 71710, - 71705, - 71706 + "priority": 23, + "parents": [ + 1202 ], - "area": 105815.0665, + "children": [], + "area": 3629183.279715, "iscrowd": 0, "segmentation": [] }, { - "id": 71704, - "strid": "5a557b51-ad4e-4fd7-ba64-bb179bf2189f", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 1, - "category_name": "Title", + "id": 1213, + "strid": "47085c22-4133-403a-bf03-5f6e3ba73388", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 287.94, - 89.93, - 5003.717, - 133.097 + 1285.552, + 3208.567, + 844.2610000000002, + 116.49699999999984 ], - "priority": 1, + "priority": 24, "parents": [ - 71717 + 1202 ], "children": [], - "area": 25894.4442, + "area": 4124779.723984, "iscrowd": 0, - "segmentation": [], - "text": "Local spatial synchronization {MRI indicates functional specialization of putamen in motorimagery" + "segmentation": [] }, { - "id": 71705, - "strid": "0a311785-09fd-46d7-8ba1-169dc4ba9419", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 0, - "category_name": "Author Info", + "id": 1214, + "strid": "868f4006-97c8-4221-997d-d02a2d206475", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 671.966, - 227.937, - 4234.493, - 167.608 + 1289.969, + 3369.748, + 978.3319999999999, + 122.45400000000018 ], - "priority": 2, + "priority": 25, "parents": [ - 71717 + 1202 ], "children": [], - "area": 153165.91414200002, + "area": 4346870.457812, "iscrowd": 0, "segmentation": [], - "text": "Henning U. Vosst, Santosh A: Helekar? & Nicholas D. Schiff?\n\nDepartment of Radiology, 7Department-of Neurology and Neuroscience, Weill Gornell Medical College, New York, NYs?Houston Methodist Research Institute, Houston, TX" + "text": "Our hypothesis\nThe nodes that are flipped between two SAT states of the network correspond to\nnodes controlling the transition." }, { - "id": 71706, - "strid": "daf3b725-e7c2-41e4-a0b8-5f22930ce3d8", - "image_id": 203296, - "image_name": "120011.png", + "id": 1215, + "strid": "97baa927-887f-4fc6-8e65-cae4daa074e2", + "image_id": 47, + "image_name": "116809.png", "category_id": 5, "category_name": "Section", "bbox": [ - 93.804, - 629.044, - 547.281, - 68.774 + 2827.225, + 630.96, + 309.01099999999997, + 45.19799999999998 ], - "priority": 3, + "priority": 26, "parents": [ - 71717 + 1189 ], "children": [ - 71712 + 1219, + 1216, + 1218, + 1217, + 1220 ], - "area": 59006.843376, + "area": 1783865.886, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "2b. Our Approach" }, { - "id": 71712, - "strid": "f942b335-406d-40c2-b00f-e2b8cd375842", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 4, - "category_name": "List", + "id": 1216, + "strid": "e914e38d-4f98-459e-9556-811faeb405fd", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 88.985, - 795.273, - 1648.633, - 659.139 + 2516.654, + 707.792, + 927.9679999999998, + 49.099000000000046 ], - "priority": 4, + "priority": 27, "parents": [ - 71706 + 1215 ], "children": [], - "area": 70767.367905, + "area": 1781267.567968, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Boolean Model for Controllability»of Cancer Networks" }, { - "id": 71707, - "strid": "b6ba8c76-bbb7-42c8-9768-6a466767e5ed", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 5, - "category_name": "Section", + "id": 1217, + "strid": "70ecd71b-296b-40d3-95fe-a4e32d6f2b36", + "image_id": 47, + "image_name": "116809.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 96.178, - 1539.873, - 354.062, - 64.14699999999993 + 2453.324, + 792.044, + 497.9340000000002, + 298.54200000000003 ], - "priority": 5, + "priority": 28, "parents": [ - 71717 - ], - "children": [ - 71713 + 1215 ], - "area": 148101.905394, + "children": [], + "area": 1943140.554256, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 71713, - "strid": "79f88f1a-6738-4cbc-9923-8dd22959a653", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 4, - "category_name": "List", + "id": 1218, + "strid": "f1cf968c-7896-4ff6-8e10-90c891f93ca3", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 83.777, - 1703.011, - 1653.533, - 1762.353 + 2484.908, + 1160.59, + 523.7490000000003, + 269.84899999999993 ], - "priority": 6, + "priority": 29, "parents": [ - 71707 + 1215 ], "children": [], - "area": 142673.152547, + "area": 2883959.37572, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "MIN VERTEX FLIP (Deduction):\nGiven a Boolean network H=(V,E),\na satisfying assignment B(H), and a\nset T of toggled edges,\n\nfind the minimum set of vertices in\nV that need to be flipped so that H\nremains SATISFIED." }, { - "id": 71716, - "strid": "c0cc42bf-a05a-41ce-b0b4-0eba39c34e38", - "image_id": 203296, - "image_name": "120011.png", + "id": 1219, + "strid": "79180e5a-7c72-4fe7-b194-98d7c9de84be", + "image_id": 47, + "image_name": "116809.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1796.433, - 617.428, - 2039.442, - 2501.461 + 3039.513, + 789.865, + 455.44000000000005, + 614.518 ], - "priority": 7, + "priority": 30, "parents": [ - 71717 - ], - "children": [ - 71711 + 1215 ], - "area": 1109168.034324, + "children": [], + "area": 2400804.935745, "iscrowd": 0, "segmentation": [] }, { - "id": 71711, - "strid": "54d75964-fbfc-4613-91de-3ed6c4950d84", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 6, - "category_name": "Caption", + "id": 1220, + "strid": "f43d2ab1-8006-4e63-8333-e213dafeaf41", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1799.514, - 3122.663, - 2023.0360000000003, - 306.759 + 2468.055, + 1493.737, + 957.6790000000001, + 220.37799999999993 ], - "priority": 8, + "priority": 31, "parents": [ - 71716 + 1215 ], "children": [], - "area": 5619275.785782, + "area": 3686625.071535, "iscrowd": 0, - "segmentation": [], - "text": "Figure 1: BOLD and local spatial synchronization fMRI (IssfMRI) for sports motor imagery\ntasks. Glass brains and SPMs for (a) BOLD response at an FDR controlled threshold of p-=\n0.05, (b) IssfMRI map with an exploratory(p « 0.005 (uncorr.), and (c) IssfMRI map masked.by\nthe BOLD response, FDR = 0.05; only,putaminal but not cortical synchronization withstands\nthe FDR controlled threshold." + "segmentation": [] }, { - "id": 71708, - "strid": "17a711d5-a7e2-4097-ae55-fd7ca88d139d", - "image_id": 203296, - "image_name": "120011.png", + "id": 1221, + "strid": "b2b4307d-ad7a-4fd8-baed-7980e73aa425", + "image_id": 47, + "image_name": "116809.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3900.152, - 632.014, - 293.6090000000004, - 64.70100000000002 + 2776.47, + 1758.212, + 413.7159999999999, + 45.444999999999936 ], - "priority": 9, + "priority": 32, "parents": [ - 71717 + 1189 ], "children": [ - 71714 + 1226, + 1228, + 1222, + 1224, + 1225, + 1227, + 1223 ], - "area": 2464950.6661280002, + "area": 4881622.87164, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Me elect)" }, { - "id": 71714, - "strid": "f6fd28f1-7024-48e6-8060-3d9355dac977", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 4, - "category_name": "List", + "id": 1222, + "strid": "e8601de7-15e2-4548-84f8-b0d16781d5e1", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3887.407, - 795.952, - 1603.013, - 951.74 + 2647.655, + 1838.116, + 672.6910000000003, + 39.94599999999991 ], - "priority": 10, + "priority": 33, "parents": [ - 71708 + 1221 ], "children": [], - "area": 3094189.376464, + "area": 4866697.01798, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Cancer Networks in Pancreatic Cancer" }, { - "id": 71709, - "strid": "ac553be5-a53b-44cc-a0aa-c2c3a617ca3c", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 5, - "category_name": "Section", + "id": 1223, + "strid": "5ec9148f-5158-45b9-8f1d-65755bef76e7", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 3895.232, - 1828.324, - 970.3490000000002, - 72.45800000000008 + 2482.045, + 1904.848, + 872.212, + 323.8409999999999 ], - "priority": 11, + "priority": 34, "parents": [ - 71717 - ], - "children": [ - 71715 + 1221 ], - "area": 7121746.151168, + "children": [], + "area": 4727918.45416, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 71715, - "strid": "b3b21c5e-4d38-4a08-933a-5dcf4bf5eb26", - "image_id": 203296, - "image_name": "120011.png", + "id": 1224, + "strid": "19d6d36c-9724-4b56-8f54-5cf0e3aa43e1", + "image_id": 47, + "image_name": "116809.png", "category_id": 4, "category_name": "List", "bbox": [ - 3895.394, - 1998.743, - 1594.3840000000005, - 1311.9069999999997 + 2483.484, + 2287.701, + 680.7860000000001, + 83.47899999999981 ], - "priority": 12, + "priority": 35, "parents": [ - 71709 + 1221 ], "children": [], - "area": 7785891.489742, + "area": 5681468.830283999, "iscrowd": 0, "segmentation": [] }, { - "id": 71710, - "strid": "83efb638-7152-49d6-9bed-383c1060df0f", - "image_id": 203296, - "image_name": "120011.png", - "category_id": 3, - "category_name": "Text", + "id": 1225, + "strid": "15fd6e1c-5846-40bc-9833-f6d21db1582f", + "image_id": 47, + "image_name": "116809.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 3894.882, - 3355.62, - 1588.8539999999998, - 119.55699999999979 + 2458.032, + 2389.503, + 1054.969, + 86.96099999999979 ], - "priority": 13, + "priority": 36, "parents": [ - 71717 + 1221 ], "children": [], - "area": 13069743.93684, + "area": 5873474.838096001, "iscrowd": 0, - "segmentation": [], - "text": "ACKNOWLEDGMENTS Funded by\\NIH, the James S. McDonnell Foundation\n(NDS), and the Nancy M and Samuel C Fleming Research Scholar Award (HUV)" + "segmentation": [] }, { - "id": 193783, - "strid": "26c3f74d-3e83-4478-957c-9ce981e6c407", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 9, - "category_name": "Root", + "id": 1226, + "strid": "366869c5-2995-4a86-b92c-726cb6fc98d1", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 211.22, - 293.04, - 281.32000000000005, - 137.89999999999998 + 2482.045, + 2507.913, + 921.1489999999999, + 130.9760000000001 ], - "priority": -1, - "parents": [], - "children": [ - 193740, - 193742, - 193778, - 193746, - 193744, - 193762, - 193777, - 193779, - 193747, - 193765, - 193745, - 193741, - 193743, - 193739, - 193764, - 193780, - 193763, - 193761 + "priority": 37, + "parents": [ + 1221 ], - "area": 61895.908800000005, + "children": [], + "area": 6224752.922085, "iscrowd": 0, "segmentation": [] }, { - "id": 193739, - "strid": "4be36e27-4341-4323-a81d-d1af0e077cae", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 1, - "category_name": "Title", + "id": 1227, + "strid": "6c94fa8b-6124-4313-a1ed-f584f9e3c357", + "image_id": 47, + "image_name": "116809.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 314.047, - 137.233, - 4973.994999999999, - 109.79000000000002 + 2477.483, + 2649.24, + 1033.2290000000003, + 259.73799999999983 ], - "priority": 1, + "priority": 38, "parents": [ - 193783 + 1221 ], "children": [], - "area": 43097.611951000006, + "area": 6563447.0629199995, "iscrowd": 0, - "segmentation": [], - "text": "Perceived chromatic diversity in dichromacy benefits trom the color distributions of natural scenes" + "segmentation": [] }, { - "id": 193740, - "strid": "f3a53997-1cd4-439c-9cb6-ecef79de9d10", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 0, - "category_name": "Author Info", + "id": 1228, + "strid": "572e33e3-cb1e-4171-9e30-bcec24ff17bb", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1159.065, - 293.586, - 3278.0749999999994, - 130.07299999999998 + 2469.865, + 2945.779, + 1015.692, + 563.1619999999998 ], - "priority": 2, + "priority": 39, "parents": [ - 193783 + 1221 ], "children": [], - "area": 340285.25709, + "area": 7275676.449835, "iscrowd": 0, - "segmentation": [], - "text": "Sérgio M.C. Nascimento+ (smcn@fisica.uminho.pt) , Jodo M.M. Linhares, Ruben C. Pastilha*, Jorge L. A. Santos* and Vasco M. N. de Almeida?\n1Centre of Physics, University of Minho, 4710-057 Braga, Portugal; 7Department of Physics, University of Beira Interior, 6201-001 Covilha, Portugal" + "segmentation": [] }, { - "id": 193741, - "strid": "99c1e2ec-74c3-4f36-8cfa-e104ccecb524", - "image_id": 208079, - "image_name": "9332.png", + "id": 1229, + "strid": "676d55d8-8fd4-4bc3-950f-05de47a6e0a0", + "image_id": 47, + "image_name": "116809.png", "category_id": 5, "category_name": "Section", "bbox": [ - 110.54, - 980.734, - 148.84299999999996, - 38.043000000000006 + 3929.25, + 630.194, + 465.866, + 46.250999999999976 ], - "priority": 3, + "priority": 40, "parents": [ - 193783 + 1189 ], "children": [ - 193748 + 1232, + 1233, + 1230, + 1231 ], - "area": 108410.33636000002, + "area": 2476189.7745, "iscrowd": 0, "segmentation": [], - "text": "Purpose" + "text": "4. Alterriative Perspectives" }, { - "id": 193748, - "strid": "71c02a68-5f07-4920-abfe-278c4b48bb88", - "image_id": 208079, - "image_name": "9332.png", + "id": 1230, + "strid": "7c81d0f9-4e40-4867-86fb-2af4bc60983b", + "image_id": 47, + "image_name": "116809.png", "category_id": 3, "category_name": "Text", "bbox": [ - 106.304, - 1077.704, - 1533.27, - 35.12799999999993 + 3665.472, + 722.778, + 935.2760000000003, + 79.62400000000002 ], - "priority": 4, + "priority": 41, "parents": [ - 193741 + 1229 ], "children": [], - "area": 114564.24601599999, + "area": 2649322.5212160004, "iscrowd": 0, "segmentation": [], - "text": "To estimate, empirically, how much dichromacy impairs discrimination of colors in natural scenes." + "text": "Cancer as attractor states in a Hopfield energy landscape\n(Si Huang et al. 2009; Koulakov and Lazebnik, 2012)" }, { - "id": 193742, - "strid": "79a29570-6271-4d05-abb3-23b3f63f0268", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 5, - "category_name": "Section", + "id": 1231, + "strid": "c354aacb-cccf-4cde-a533-9fb83bc7d5fa", + "image_id": 47, + "image_name": "116809.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 108.532, - 1229.877, - 273.494, - 32.460000000000036 + 3711.58, + 848.607, + 920.991, + 582.375 ], - "priority": 5, + "priority": 42, "parents": [ - 193783 + 1229 ], - "children": [ - 193749, - 193752, - 193750 + "children": [], + "area": 3149672.76906, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1232, + "strid": "5cd4ed28-63b3-4e42-83a2-4d11f6d092a3", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", + "bbox": [ + 3667.886, + 1465.095, + 970.7739999999999, + 221.34899999999993 ], - "area": 133481.010564, + "priority": 43, + "parents": [ + 1229 + ], + "children": [], + "area": 5373801.43917, "iscrowd": 0, - "segmentation": [], - "text": "1. Introduction" + "segmentation": [] }, { - "id": 193749, - "strid": "12e2f359-19ca-45ed-8a3c-01738717dbb0", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 3, - "category_name": "Text", + "id": 1233, + "strid": "a15c1df6-697e-4b55-953d-688c97ab2707", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 108.563, - 1328.8, - 1661.122, - 220.87400000000002 + 3667.642, + 1759.768, + 967.5420000000004, + 176.981 ], - "priority": 6, + "priority": 44, "parents": [ - 193742 + 1229 ], "children": [], - "area": 144258.5144, + "area": 6454199.027056, "iscrowd": 0, - "segmentation": [], - "text": "Inherited color vision deficiencies impair color discrimination and therefore impoverish the chromatic\ndiversity perceived in natural scenes.\n\nFor dichromacy, estimates based on Brettel’s perceptual model [1] and on the gamut of natural colors\npredict that dichromats see only a few percent of the colors that normal trichromats can see (Table 1)." + "segmentation": [] }, { - "id": 193750, - "strid": "452f0a53-a0d6-4df3-b1a4-0098f2342e0e", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 7, - "category_name": "Table", + "id": 1234, + "strid": "c42c20d7-c133-42b7-8abc-07e60bd4191b", + "image_id": 47, + "image_name": "116809.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 223.005, - 1629.227, - 1419.946, - 331.88599999999997 + 3883.828, + 1966.763, + 563.4900000000002, + 40.567999999999984 ], - "priority": 7, + "priority": 45, "parents": [ - 193742 + 1189 ], "children": [ - 193751 + 1235, + 1236 ], - "area": 363325.76713500003, + "area": 7638569.208764, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "5. Conclusions and Future Work" }, { - "id": 193751, - "strid": "bdc45479-ad55-4c4b-8461-9308796f394d", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1235, + "strid": "59b0c610-9b24-4760-8e7e-67f74604d3d6", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 230.746, - 1978.247, - 1394.906, - 26.899000000000115 + 3649.395, + 2046.276, + 1003.7680000000005, + 479.52600000000007 ], - "priority": 8, + "priority": 46, "parents": [ - 193750 + 1234 ], "children": [], - "area": 456472.582262, + "area": 7467669.40302, "iscrowd": 0, - "segmentation": [], - "text": "Table 1 — Theoretical predictions of the fraction of colors discriminated by dichromats. Predictions based on Brettel’s model." + "segmentation": [] }, { - "id": 193752, - "strid": "51b17242-6ca7-4a94-8c57-0189ae96139b", - "image_id": 208079, - "image_name": "9332.png", + "id": 1236, + "strid": "f6859bc3-58c6-4e3a-817d-bdc67781b6b9", + "image_id": 47, + "image_name": "116809.png", "category_id": 3, "category_name": "Text", "bbox": [ - 108.292, - 2074.962, - 1660.305, - 270.3119999999999 + 3727.371, + 2568.443, + 905.6239999999998, + 161.50700000000006 ], - "priority": 9, + "priority": 47, "parents": [ - 193742 + 1234 ], "children": [], - "area": 224701.784904, + "area": 9573539.953353, "iscrowd": 0, "segmentation": [], - "text": "These estimates, however, do not take into account how frequent the colors appear in the scenes. Pairs\nof colors confused by dichromats may be rare and thus have small impact on the overall perceived\nchromatic diversity.\n\nThe purpose of this work was to estimate with a psychophysical experiment how much dichromacy\nimpairs discrimination of pairs of colors in natural scenes." + "text": "MIN VERTEX FLIP (Prediction): Given H=(V,E) and a\nsatisfying assignment B(H), can we find a subset L < E on the\ntoggle of which H reaches a new SATISFIED state using the\nminimum number of vertex flips in V." }, { - "id": 193743, - "strid": "90e4b6a8-295d-4920-b68c-95bf41770083", - "image_id": 208079, - "image_name": "9332.png", + "id": 1237, + "strid": "9209bf76-6589-4b6e-a11b-cc5b5b9fa548", + "image_id": 47, + "image_name": "116809.png", "category_id": 5, "category_name": "Section", "bbox": [ - 105.104, - 2474.008, - 178.849, - 31.70699999999988 + 4062.445, + 2771.98, + 200.20199999999977, + 42.278999999999996 ], - "priority": 10, + "priority": 48, "parents": [ - 193783 + 1189 ], "children": [ - 193753, - 193754, - 193758 + 1238 ], - "area": 260028.136832, + "area": 11261016.291100001, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "CRASS" }, { - "id": 193753, - "strid": "c9932575-ec3c-4b7d-b314-64aabeddcda7", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1238, + "strid": "94fe02f1-9233-4f83-89aa-dc73807a704b", + "image_id": 47, + "image_name": "116809.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 105.938, - 2532.409, - 799.574, - 520.058 + 3664.753, + 2844.971, + 1019.1709999999998, + 452.55700000000024 ], - "priority": 11, + "priority": 49, "parents": [ - 193743 - ], - "children": [ - 193755 + 1237 ], - "area": 268278.34464200004, + "children": [], + "area": 10426116.007163001, "iscrowd": 0, "segmentation": [] }, { - "id": 193755, - "strid": "84de5fc3-a880-4c11-9d3e-22c06af5338c", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1239, + "strid": "828293f9-e796-45fb-b41b-fc52f55f2ef6", + "image_id": 47, + "image_name": "116809.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 112.57, - 3064.751, - 784.884, - 90.50700000000006 + 3773.604, + 3335.396, + 777.1200000000003, + 48.903999999999996 ], - "priority": 12, + "priority": 50, "parents": [ - 193753 + 1189 ], - "children": [], - "area": 344999.02007, + "children": [ + 1240 + ], + "area": 12586463.687184, "iscrowd": 0, "segmentation": [], - "text": "Figure 8 — Individual results expressed as d’ computed for a 1AFC.\nsame-different task using the differencing model [5, 6]. Data based\non 2640 trials for each observer." + "text": "Acknowledgements and Contact Information" }, { - "id": 193754, - "strid": "41b6be0a-8798-4483-b672-991446d8becb", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1240, + "strid": "bd227dd7-674f-44ac-8eef-121d015f3a4b", + "image_id": 47, + "image_name": "116809.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 954.637, - 2529.961, - 786.9089999999999, - 522.7629999999999 + 3665.862, + 3404.931, + 986.491, + 113.0909999999999 ], - "priority": 13, + "priority": 51, "parents": [ - 193743 - ], - "children": [ - 193756 + 1239 ], - "area": 2415194.3791569998, + "children": [], + "area": 12482007.165522, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.\nNHMRC project grant to Professor Mark Ragan and Dr Peter Simpson.\n\nContact: Dr Sriganesh Srihari — sriganesh.m.s@gmail.com" }, { - "id": 193756, - "strid": "ef9fe791-b964-485a-ae1f-d1d79a8b1613", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1241, + "strid": "b8df8f70-1b0b-4a22-b1f9-1c2ddeab5a9b", + "image_id": 48, + "image_name": "116872.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 965.12, - 3063.629, - 770.6849999999998, - 91.6289999999999 + 1048.8, + 1040.52, + 42.840000000000146, + 45.799999999999955 ], - "priority": 14, - "parents": [ - 193754 + "priority": -1, + "parents": [], + "children": [ + 1244, + 1253, + 1262, + 1259, + 1242, + 1246, + 1243 ], - "children": [], - "area": 2956769.62048, + "area": 1962.0720000000047, "iscrowd": 0, - "segmentation": [], - "text": "Figure 9 — Individual results expressed as % discrimination\ncomputed from d’ assuming that all observers have the same\ncriterion [5]. Data based on 2640 trials for each observer." + "segmentation": [] }, { - "id": 193758, - "strid": "a60035cc-e777-4ec0-99c1-9c723fd33c01", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1242, + "strid": "1cc8a091-ecfb-434b-af15-ffc6d81832ed", + "image_id": 48, + "image_name": "116872.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 531.181, - 3207.189, - 806.002, - 545.6669999999999 + 1016.418, + 170.25400000000002, + 28.813999999999965, + 761.377 ], - "priority": 15, + "priority": 1, "parents": [ - 193743 + 1241 ], - "children": [ - 193757 - ], - "area": 1703597.860209, + "children": [], + "area": 21938.316877999972, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 193757, - "strid": "0a9f92cc-65bd-46b8-8b5c-f632d53aa3a1", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1243, + "strid": "8fbebefc-2679-4b55-a5c3-771382ade568", + "image_id": 48, + "image_name": "116872.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 355.563, - 3762.118, - 1169.7999999999997, - 92.57900000000018 + 917.04, + 204.3100000000001, + 83.82000000000005, + 692.982 ], - "priority": 16, + "priority": 2, "parents": [ - 193758 + 1241 ], "children": [], - "area": 1337669.9624339999, + "area": 58085.751240000034, "iscrowd": 0, "segmentation": [], - "text": "Figure 10 — Average of group results expressed as % discrimination computed from a” assuming that all\nobservers have the same criterion [5]. Data based on 4 normal trichromats, 2 deuteranope, two\nprotanope and 2640 trials for each observer." + "text": "" }, { - "id": 193744, - "strid": "75324c82-ec4f-4059-9e0e-f476964d0538", - "image_id": 208079, - "image_name": "9332.png", + "id": 1244, + "strid": "b0d9f713-1cfd-4ff3-bdc4-9bd73dffb297", + "image_id": 48, + "image_name": "116872.png", "category_id": 5, "category_name": "Section", "bbox": [ - 1891.059, - 981.736, - 212.21800000000007, - 33.50800000000004 + 873.465, + 55.74000000000001, + 18.900999999999954, + 72.79200000000003 ], - "priority": 17, + "priority": 3, "parents": [ - 193783 + 1241 ], "children": [ - 193766, - 193759, - 193773, - 193760, - 193774 + 1245 ], - "area": 1856520.698424, + "area": 1375.8415919999973, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 193766, - "strid": "70b2ab02-b860-4688-8526-8d14df61a845", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 4, - "category_name": "List", + "id": 1245, + "strid": "b77e5156-acd0-4478-bfd3-bd57bfa8cf80", + "image_id": 48, + "image_name": "116872.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1890.098, - 1082.471, - 1176.7179999999998, - 358.1590000000001 + 765.89, + 55.8900000000001, + 99.96500000000003, + 471.36299999999994 ], - "priority": 18, + "priority": 4, "parents": [ - 193744 + 1244 ], "children": [], - "area": 2045976.272158, + "area": 47119.80229500001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "orm the\n“VO," }, { - "id": 193759, - "strid": "e563d8c9-1780-41fa-bec3-64e871839b07", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1246, + "strid": "7c449cd6-af1e-4c2a-9003-e58cb1740b91", + "image_id": 48, + "image_name": "116872.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1909.067, - 1457.419, - 518.549, - 349.31600000000003 + 741.794, + 54.337999999999965, + 17.552999999999997, + 77.36200000000008 ], - "priority": 19, + "priority": 5, "parents": [ - 193744 + 1241 ], "children": [ - 193767 + 1250, + 1248, + 1251, + 1247, + 1252 ], - "area": 2782310.518073, + "area": 1357.9351860000013, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 193767, - "strid": "1739bd62-407b-4b0b-8180-23b8971d5742", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1247, + "strid": "057617a0-6ce9-4044-9af0-ff7db7ef1efb", + "image_id": 48, + "image_name": "116872.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1920.39, - 1830.074, - 497.95399999999995, - 193.85500000000002 + 591.252, + 55.63499999999999, + 134.65700000000004, + 479.62699999999995 ], - "priority": 20, + "priority": 6, "parents": [ - 193759 + 1246 ], "children": [], - "area": 3514455.80886, + "area": 64585.13293900001, "iscrowd": 0, "segmentation": [], - "text": "Figure 1 — Stimuli were 3D objects painted\nwith a matte white paint. The scene\nsubtended 10 deg and was set inside a light\nbooth illuminated by a spectrally tunable\nlight source based on the Digital Light\nProcessor technology." + "text": "table 1. Values are genei\ncercise intensity ( C58% um" }, { - "id": 193760, - "strid": "c7d8f198-8d3d-4b4a-aecc-80c02ec57837", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1248, + "strid": "13208ffe-5167-4f0e-9c26-6ae917e5187d", + "image_id": 48, + "image_name": "116872.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 2485.784, - 1459.998, - 522.8089999999997, - 351.403 + 419.70900000000006, + 49.134000000000015, + 140.79599999999994, + 488.14599999999996 ], - "priority": 21, + "priority": 7, "parents": [ - 193744 + 1246 ], "children": [ - 193768 + 1249 ], - "area": 3629239.668432, + "area": 68729.00421599996, "iscrowd": 0, "segmentation": [] }, { - "id": 193768, - "strid": "4752be16-f77e-4ea0-a595-392a7f586468", - "image_id": 208079, - "image_name": "9332.png", + "id": 1249, + "strid": "2d1cad1f-33a3-4de1-9aec-c044c94c5db7", + "image_id": 48, + "image_name": "116872.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 2494.535, - 1824.737, - 501.85599999999977, - 154.5920000000001 + 563.029, + 56.406999999999925, + 12.236999999999966, + 417.1460000000001 ], - "priority": 22, + "priority": 8, "parents": [ - 193760 + 1248 ], "children": [], - "area": 4551870.312295, + "area": 5104.615601999987, "iscrowd": 0, "segmentation": [], - "text": "Figure 2 — OL 490 Agile Light Source, Gooch\n& Housego. The spectral composition of the\nlight source could be tuned very fast with a\nspectral resolution of 20 nm using in-house\nsoftware." + "text": "" }, { - "id": 193773, - "strid": "5002b772-1c4e-4b21-96ef-59e9d009d4af", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 4, - "category_name": "List", + "id": 1250, + "strid": "857bd107-022f-4d8e-aea5-376d4cd2787b", + "image_id": 48, + "image_name": "116872.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1892.773, - 2081.327, - 691.2639999999999, - 265.00700000000006 + 298.015, + 48.91599999999994, + 116.25099999999998, + 152.3420000000001 ], - "priority": 23, + "priority": 9, "parents": [ - 193744 + 1246 ], "children": [], - "area": 3939479.549771, + "area": 17709.90984200001, "iscrowd": 0, "segmentation": [] }, { - "id": 193774, - "strid": "62c381db-fe2d-4356-9e2b-80d8bb17e0d9", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 3, - "category_name": "Text", + "id": 1251, + "strid": "e644bc49-df27-4075-9fab-5e58ab99f7ba", + "image_id": 48, + "image_name": "116872.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1890.127, - 2431.042, - 1174.009, - 212.7260000000001 + 298.462, + 217.01199999999992, + 116.17499999999995, + 153.94100000000006 ], - "priority": 24, + "priority": 10, "parents": [ - 193744 + 1246 ], "children": [], - "area": 4594978.122334, + "area": 17884.095675, "iscrowd": 0, - "segmentation": [], - "text": "Design and procedure\n\nA 1AFC sequential same-different procedure (Fig. 7) was used. A large\nadapting field illuminated by the adapting illuminant was seen at all times\nduring the experimental sessions (Fig. 3 and 4)." + "segmentation": [] }, { - "id": 193745, - "strid": "58902555-4a57-40e8-8f85-302f8fa285cd", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 5, - "category_name": "Section", + "id": 1252, + "strid": "609cb103-e46d-46a3-a0e5-0b7f7eae0fcd", + "image_id": 48, + "image_name": "116872.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1888.776, - 2773.387, - 265.59600000000023, - 32.728999999999814 + 298.55899999999997, + 382.93499999999995, + 115.774, + 153.55600000000004 ], - "priority": 25, + "priority": 11, "parents": [ - 193783 - ], - "children": [ - 193775 + 1246 ], - "area": 5238306.804312, + "children": [], + "area": 17777.792344000005, "iscrowd": 0, - "segmentation": [], - "text": "4. Conclusions" + "segmentation": [] }, { - "id": 193775, - "strid": "39a5af45-e5ac-4d48-8207-8ca76d225341", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 4, - "category_name": "List", + "id": 1253, + "strid": "7686e6e8-facb-4fb3-b7ce-665c0b078dba", + "image_id": 48, + "image_name": "116872.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1888.512, - 2870.226, - 1171.974, - 450.85699999999997 + 876.53, + 570.134, + 16.632000000000062, + 64.61099999999999 ], - "priority": 26, + "priority": 12, "parents": [ - 193745 + 1241 ], - "children": [], - "area": 5420456.243712, + "children": [ + 1257, + 1254, + 1255 + ], + "area": 1074.6101520000038, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 193777, - "strid": "f13f9cc5-0e6c-4470-91c2-e12484a3f93e", - "image_id": 208079, - "image_name": "9332.png", + "id": 1254, + "strid": "316560c3-c257-4d1d-9c0f-f9b57709f994", + "image_id": 48, + "image_name": "116872.png", "category_id": 3, "category_name": "Text", "bbox": [ - 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"priority": 30, + "priority": 16, "parents": [ - 193783 + 1253 ], "children": [ - 193770 + 1258 ], - "area": 4219845.626787, + "area": 36191.330622, "iscrowd": 0, "segmentation": [] }, { - "id": 193770, - "strid": "eeeae125-3859-4128-823a-2cd9ee1e9607", - "image_id": 208079, - "image_name": "9332.png", + "id": 1258, + "strid": "a46f6446-ecd6-4965-97ce-e633fe26b89c", + "image_id": 48, + "image_name": "116872.png", "category_id": 6, "category_name": "Caption", "bbox": [ - 3736.412, - 1665.08, - 332.82299999999987, - 92.12300000000005 + 576.581, + 803.6189999999999, + 46.69399999999996, + 238.57400000000007 ], - "priority": 31, + "priority": 17, "parents": [ - 193762 + 1257 ], "children": [], - "area": 6221424.89296, + "area": 11139.974355999993, "iscrowd": 0, "segmentation": [], - "text": "Figure 4 — Large adapting\nfield illuminated by the\nadapting illuminant." + "text": "" }, { - "id": 193778, - "strid": "a3e7ddcd-2ba5-4a8d-8e96-b805712b1ce7", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 3, - "category_name": "Text", + "id": 1259, + "strid": "91229529-7f08-49c8-9fbf-ec000fc8642f", + "image_id": 48, + "image_name": "116872.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 4658.264, - 1021.656, - 400.6880000000001, - 39.156999999999925 + 553.957, + 573.5889999999999, + 15.720000000000027, + 97.53600000000006 ], - "priority": 32, + "priority": 18, "parents": [ - 193783 + 1241 ], - "children": [], - "area": 4759143.365184, + "children": [ + 1260, + 1261 + ], + "area": 1533.2659200000037, "iscrowd": 0, "segmentation": [], "text": "" }, { - "id": 193763, - "strid": "5f97dc8f-6b86-4cea-9e25-3826e48d9111", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1260, + "strid": "c52d56ac-6359-4021-8ab0-f922900a4c92", + "image_id": 48, + "image_name": "116872.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 4181.611, - 1123.694, - 762.8180000000002, - 510.0709999999999 + 392.3799999999999, + 566.667, + 150.63200000000006, + 329.82899999999995 ], - "priority": 33, + "priority": 19, "parents": [ - 193783 - ], - "children": [ - 193771 + 1259 ], - "area": 4698851.191033999, + "children": [], + "area": 49682.801928000015, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "gen\nrate\n20\n\n \n\n \n\n \n\n \n\n| ye\n\nFigure Metabole equivaler\ncalelated fr the handeyeling\nresting metabolic rate of 3.5\ncompared toeveling (Ainswort\n\nConclus.or" }, { - "id": 193771, - "strid": "5f6d4c8d-f1d7-4364-b864-7eaa53daa621", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1261, + "strid": "91a5a92c-ebfe-4fb5-a196-3c1356654b2a", + "image_id": 48, + "image_name": "116872.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 4190.819, - 1660.749, - 743.0339999999997, - 55.54299999999989 + 389.491, + 899.941, + 153.53300000000002, + 151.3219999999999 ], - "priority": 34, + "priority": 20, "parents": [ - 193763 + 1259 ], "children": [], - "area": 6959898.463431001, + "area": 23232.920625999985, "iscrowd": 0, - "segmentation": [], - "text": "Figure 5 — In each trial the spectra were Boece from random\nlocations of one of 4 natural scenes. \\" + "segmentation": [] }, { - "id": 193764, - "strid": "925d2e09-bb58-46eb-b385-bd71173060ba", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 2, - "category_name": "Figure", + "id": 1262, + "strid": "d0778049-5b2e-40d9-ab5a-dcccfb355525", + "image_id": 48, + "image_name": "116872.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 4973.611, - 1115.984, - 520.8310000000001, - 530.613 + 374.673, + 569.381, + 7.357999999999947, + 33.944000000000074 ], - "priority": 35, + "priority": 21, "parents": [ - 193783 + 1241 ], "children": [ - 193772 + 1263 ], - "area": 5550470.298223999, + "area": 249.75995199999875, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "" }, { - "id": 193772, - "strid": "b7819e7b-31bd-4255-89dd-e61ebe49b94c", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1263, + "strid": "8df60960-b8a9-4e5b-9b0a-d9fbfe7daa84", + "image_id": 48, + "image_name": "116872.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 4991.377, - 1659.782, - 494.7359999999999, - 59.548 + 300.557, + 566.387, + 71.60900000000004, + 361.82000000000005 ], - "priority": 36, + "priority": 22, "parents": [ - 193764 + 1262 ], "children": [], - "area": 8284597.699814, + "area": 25909.56838000002, "iscrowd": 0, - "segmentation": [], - "text": "Figure 6. Gamut of the 4 natural scenes\nunder the adapting illuminant." + "segmentation": [] }, { - "id": 193779, - "strid": "119282d2-7788-4fdd-8167-4ad907fcabc0", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 3, - "category_name": "Text", + "id": 1264, + "strid": "c5fa536c-2942-4646-8070-3f9c8363871f", + "image_id": 49, + "image_name": "116882.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 3986.787, - 1947.291, - 281.43799999999965, - 39.577 + 316.03, + 26.46, + 85.52000000000004, + 87.22999999999999 ], - "priority": 37, + "priority": -1, + "parents": [], + "children": [ + 1266, + 1265, + 1273, + 1267, + 1271, + 1272, + 1269, + 1268, + 1270 + ], + "area": 8362.1538, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1265, + "strid": "9f75141f-9704-4186-9d82-f096f901feee", + "image_id": 49, + "image_name": "116882.png", + "category_id": 1, + "category_name": "Title", + "bbox": [ + 418.081, + 64.335, + 876.736, + 106.057 + ], + "priority": 1, "parents": [ - 193783 + 1264 ], "children": [], - "area": 7763434.444017, + "area": 26897.241135, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Growth, reproduction and plant damage of\nCirsium arvense in its native and invasive range" }, { - "id": 193780, - "strid": "60e01e95-5867-48ca-bec2-b0abd9f82c68", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 3, - "category_name": "Text", + "id": 1266, + "strid": "687de28b-1db9-451d-b3c8-adb96c3a26ea", + "image_id": 49, + "image_name": "116882.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 5214.154, - 1948.332, - 113.22299999999996, - 37.85400000000004 + 716.218, + 215.171, + 569.1719999999999, + 73.06099999999998 ], - "priority": 38, + "priority": 2, "parents": [ - 193783 + 1264 ], "children": [], - "area": 10158903.091128001, + "area": 154109.343278, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "Presenter: Inés Abela Hofbauerova (Charles\nUniversity, Prague, Czech Republic)" }, { - "id": 193765, - "strid": "bdf4edf6-2902-47fe-8f5e-1e05ce44255d", - "image_id": 208079, - "image_name": "9332.png", + "id": 1267, + "strid": "01baf116-ba64-4e2e-9364-6d9de3b392ce", + "image_id": 49, + "image_name": "116882.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3221.667, - 2047.095, - 2244.4160000000006, - 502.9979999999998 + 16.243, + 209.279, + 275.22, + 156.10900000000004 ], - "priority": 39, + "priority": 3, "parents": [ - 193783 - ], - "children": [ - 193781 + 1264 ], - "area": 6595058.407365, + "children": [], + "area": 3399.3187969999994, "iscrowd": 0, "segmentation": [] }, { - "id": 193781, - "strid": "69d60c7d-0b45-4f01-9f57-bf0c253775f4", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 6, - "category_name": "Caption", + "id": 1268, + "strid": "5af9c933-294b-44b7-864d-64ff2f726672", + "image_id": 49, + "image_name": "116882.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 3770.78, - 2596.891, - 842.212, - 26.554000000000087 + 18.93, + 393.792, + 270.233, + 159.64500000000004 ], - "priority": 40, + "priority": 4, "parents": [ - 193765 + 1264 ], "children": [], - "area": 9792304.64498, + "area": 7454.4825599999995, "iscrowd": 0, - "segmentation": [], - "text": "Figure 7 — The procedure was a 1AFC sequential same-different procedure." + "segmentation": [] }, { - "id": 193746, - "strid": "fe9b0405-6f38-42ff-8262-97b03cb4a5f5", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 5, - "category_name": "Section", + "id": 1269, + "strid": "b4546838-5598-4b69-922f-1554c79bb5cd", + "image_id": 49, + "image_name": "116882.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1888.917, - 3541.251, - 342.33899999999994, - 41.63599999999997 + 18.099, + 583.37, + 271.064, + 158.81399999999996 ], - "priority": 41, + "priority": 5, "parents": [ - 193783 + 1264 ], - "children": [ - 193776 - ], - "area": 6689129.215167, + "children": [], + "area": 10558.413630000001, "iscrowd": 0, - "segmentation": [], - "text": "Acknowledgments" + "segmentation": [] }, { - "id": 193776, - "strid": "b1816b48-a1c8-407e-8381-f00840015767", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 3, - "category_name": "Text", + "id": 1270, + "strid": "51b12701-ddc1-4b4e-b79c-36928481b6d5", + "image_id": 49, + "image_name": "116882.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1887.779, - 3639.161, - 963.4230000000002, - 221.07200000000012 + 18.099, + 770.085, + 271.896, + 158.81399999999996 ], - "priority": 42, + "priority": 6, "parents": [ - 193746 + 1264 ], "children": [], - "area": 6869931.713419, + "area": 13937.768415, "iscrowd": 0, - "segmentation": [], - "text": "This work was supported by the Centro de Fisica of Minho\nUniversity, Braga, Portugal, by FEDER through the COMPETE\nProgram and by the Portuguese Foundation for Science and\nTechnology (FCT) in the framework of the project FCOMP-\n01-0124-FEDER-029564." + "segmentation": [] }, { - "id": 193747, - "strid": "7c7a8d2b-ade0-4994-8239-08d5e8017637", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 5, - "category_name": "Section", + "id": 1271, + "strid": "92bb4111-a535-4569-b7fc-23afd46c5112", + "image_id": 49, + "image_name": "116882.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 3191.492, - 2776.428, - 202.56500000000005, - 35.3090000000002 + 393.334, + 219.885, + 292.24499999999995, + 279.283 ], - "priority": 43, + "priority": 7, "parents": [ - 193783 + 1264 ], - "children": [ - 193782 + "children": [], + "area": 86488.24659, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1272, + "strid": "eabe1735-0410-4862-bdca-41b568c126b6", + "image_id": 49, + "image_name": "116882.png", + "category_id": 3, + "category_name": "Text", + "bbox": [ + 712.947, + 329.477, + 467.56499999999994, + 106.05200000000002 ], - "area": 8860947.750576, + "priority": 8, + "parents": [ + 1264 + ], + "children": [], + "area": 234899.63871899998, "iscrowd": 0, "segmentation": [], - "text": "References" + "text": "Date: Wednesday 23\" January\nTime: 12.30pm\nVenue: B4" }, { - "id": 193782, - "strid": "61f85621-d663-4df7-bdcd-ca552b642f6e", - "image_id": 208079, - "image_name": "9332.png", - "category_id": 4, - "category_name": "List", + "id": 1273, + "strid": "3e34fd6c-1279-43cb-afbf-cfed19148546", + "image_id": 49, + "image_name": "116882.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 3186.903, - 2875.951, - 2341.842, - 540.442 + 382.729, + 536.877, + 945.0839999999998, + 463.115 ], - "priority": 44, + "priority": 9, "parents": [ - 193747 + 1264 ], "children": [], - "area": 9165376.869753, + "area": 205478.39733299997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Observational studies in Cirsium arvense were done in Czech Republic (Europe) and Nebraska (USA),\nnative and invasive ranges, between 2005 and 2007, to test whether plants grow more in the invasive\nrange and suffer less damage than plants from populations in the native range, as the Enemy Release\nHypothesis states. To have more accurate results we afterwards experimentally tested (2008-2011) for\ndirect and indirect effects of non-overlapping herbivore insects on plant growth and reproduction. We\ncompared this effect between plants from the native (Spain and the Czech Republic, Europe) and\ninvasive range (Nebraska-and Illinois, North America). In a common garden experiment, herbivore\ninsects were added alone and in combinations to C. arvense which was planted in the Czech Republic in\nMarch 2008 and grew from seeds for two growing seasons. One underground insect (Cleonis pigra )\nand 3 aboveground insect species were used (Cassida rubiginosa, Rhinocyllus conicus, Urophora\ncardui). Results from observational studies indicate that in its native range, C. arvense experiences\nmore plant damage and grows less than in the invasive range. Results from the experimental study also\nshow that plants from the invasive range grew more than the ones from the native range. Plants. to\nwhich herbivores were not added were bigger than plants to which herbivores were added, showing a\nnegative effect of insects on plant growth. The effect of combined insect was bigger than the single\nadditions, suggesting a combination of more insects would be a better solution for biological control of\nC.arvense ." }, { - "id": 194848, - "strid": "b3e1b119-4590-4546-a013-67b7c7177301", - "image_id": 208124, - "image_name": "9417.png", + "id": 1274, + "strid": "fa38c15d-3742-40d5-b9cb-278cc502796b", + "image_id": 50, + "image_name": "11689.png", "category_id": 9, "category_name": "Root", "bbox": [ - 718.33, - 7.98, - 21.110000000000014, - 57.69 + 2552.5, + 63.09, + 209.55999999999995, + 194.04 ], "priority": -1, "parents": [], "children": [ - 194834, - 194833, - 194836, - 194831, - 194837, - 194830, - 194832, - 194835 + 1278, + 1287, + 1279, + 1276, + 1294, + 1277, + 1290, + 1292, + 1282, + 1275 ], - "area": 5732.273400000001, + "area": 161037.225, "iscrowd": 0, "segmentation": [] }, { - "id": 194830, - "strid": "38cd8a82-1898-4417-a2e6-347e868ef4b6", - "image_id": 208124, - "image_name": "9417.png", + "id": 1275, + "strid": "be5bce93-1227-4b53-99ad-2db2e1f8aa7a", + "image_id": 50, + "image_name": "11689.png", "category_id": 1, "category_name": "Title", "bbox": [ - 8.378, - 3.11, - 705.682, - 92.833 + 136.507, + 104.124, + 2377.109, + 360.42099999999994 ], "priority": 1, "parents": [ - 194848 + 1274 ], "children": [], - "area": 26.05558, + "area": 14213.654868, "iscrowd": 0, "segmentation": [], - "text": "EVALUATION OF THE QUALITY OF ASTHMA MANAGEMENT IN\nTHE ADULT EMERGENCY AND TRAUMA CENTRE AT QUEEN\nSOVAN eka Disy een eGR dV 4th" + "text": "How to analyze raw sequencing data from\nmicrobiota?\nUsing ASaiM!" }, { - "id": 194831, - "strid": "d566e9b1-dfe0-4cf1-a873-aad794af48d2", - "image_id": 208124, - "image_name": "9417.png", + "id": 1276, + "strid": "2a8f7828-ee7d-42ee-8ada-9b493708b992", + "image_id": 50, + "image_name": "11689.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 9.21, - 101.167, - 502.88000000000005, - 33.894000000000005 + 931.589, + 503.92, + 2311.804, + 140.71800000000002 ], "priority": 2, "parents": [ - 194848 + 1274 ], "children": [], - "area": 931.7480700000001, + "area": 469446.32888000004, "iscrowd": 0, "segmentation": [], - "text": "EUS ier mute)\nER Ten se rete tena eT ee Chen" + "text": "Bérénice Batut! (berenice.batut@gmail.com), Clamence Defois’, Kévin Gravouil,\nJean-Francois Brugére?, Eric Peyretaillade* and Pierre Peyret?" }, { - "id": 194832, - "strid": "87cc5429-9145-4668-8296-bd5ea7258f5c", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 5, - "category_name": "Section", + "id": 1277, + "strid": "4ccbc8f5-aa70-40ed-bb4c-ca7e29a411a0", + "image_id": 50, + "image_name": "11689.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 23.625, - 145.325, - 109.37799999999999, - 23.09899999999999 + 68.513, + 853.367, + 1362.561, + 610.7720000000002 ], "priority": 3, "parents": [ - 194848 - ], - "children": [ - 194839 + 1274 ], - "area": 3433.303125, + "children": [], + "area": 58466.733271000005, "iscrowd": 0, "segmentation": [], - "text": "Background" + "text": "New generation of sequencing platforms coupled to\nnumerous bioinformatics tools has led to rapid technological\nprogress in metagenomics, metatranscriptomics and\ncomplex microbial community studies. Nevertheless, a\ncombination of different bioinformatics tools remains\nnecessary for efficient extraction of useful information in\nmicrobiota studies. Modular, accessible, sharable and user-\nfriendly tools would greatly improve such studies.\n\nWe therefore developed ASaiM, an open-source Galaxy-\nbased framework dedicated to microbiota data analyses." }, { - "id": 194839, - "strid": "61df9646-d6c5-47e6-ae1e-5c7b8c8554ac", - "image_id": 208124, - "image_name": "9417.png", + "id": 1278, + "strid": "28d21af6-234c-460e-9da1-5eadb984de8a", + "image_id": 50, + "image_name": "11689.png", "category_id": 3, "category_name": "Text", "bbox": [ - 22.433, - 170.894, - 250.29500000000002, - 161.95600000000002 + 1530.204, + 742.541, + 1704.3259999999998, + 831.9130000000001 ], "priority": 4, "parents": [ - 194832 + 1274 ], "children": [], - "area": 3833.665102, + "area": 1136239.208364, "iscrowd": 0, "segmentation": [], - "text": "Evidence-based asthma management\nguidelines in everyday practice achieves\ngood clinical control for patients\npresenting with acute asthma and\nprevent further exacerbations.\n\nWe evaluated the quality of acute\nasthma management in adult patients\npresenting at the largest tertiary\nhospital in Malawi." + "text": "ASaiM provides an expertly selected collection of tools to explore\nand visualize taxonomic and functional information from raw amplicon,\nmetagenomic or metatranscriptomic sequences. To help the analyses,\nseveral (customizable) workflows are included. The available\nworkflows are supported by tutorials and Galaxy interactive tours to\nguide the users through the analyses. Furthermore, an effort on\ndocumentation of ASaiM, its tools and workflows has been made\n(http://asaim.readthedocs.io/). ASaiM is implemented as Galaxy Docker\nflavour and the associated source code is available under Apache 2\nlicense at http://github.com/ASaiM/framework.\n\nBased on the Galaxy framework, ASaiM offers sophisticated analyses to\nscientists without command-line knowledge. ASaiM provides a powerful\nframework to easily and quickly explore microbiota data in a reproducible\nand transparent environment." }, { - "id": 194834, - "strid": "345e6bba-a3c9-4d7f-9b89-6af0fa846724", - "image_id": 208124, - "image_name": "9417.png", + "id": 1279, + "strid": "6e753f8c-0c02-40e2-ac70-f64ca4366cce", + "image_id": 50, + "image_name": "11689.png", "category_id": 5, "category_name": "Section", "bbox": [ - 22.356, - 350.925, - 43.921, - 17.086000000000013 + 115.69, + 1751.334, + 1559.65, + 65.62999999999988 ], "priority": 5, "parents": [ - 194848 + 1274 ], "children": [ - 194840 + 1281, + 1280 ], - "area": 7845.279300000001, + "area": 202611.83046, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "A framework built on the shoulders of giants" }, { - "id": 194840, - "strid": "1257867e-aaf4-4f45-a338-2e141e6b0719", - "image_id": 208124, - "image_name": "9417.png", + "id": 1280, + "strid": "88832f5f-8419-4ebe-a3fc-aba28bfa0aba", + "image_id": 50, + "image_name": "11689.png", "category_id": 3, "category_name": "Text", "bbox": [ - 21.848, - 374.679, - 246.09699999999998, - 89.77300000000002 + 274.034, + 1829.487, + 2920.447, + 50.93100000000004 ], "priority": 6, "parents": [ - 194834 + 1279 ], "children": [], - "area": 8185.986791999999, + "area": 501341.640558, "iscrowd": 0, "segmentation": [], - "text": "To review the presentation of\nasthmatic patients and determine\nadherence to the departmental asthma\nmanagement protocols that are based\non national treatment guidelines." + "text": "To develop a modular, accessible, redistributable, sharable and user-friendly framework for scientists working with microbiota data" }, { - "id": 194835, - "strid": "8f505035-4ae1-41b6-a46b-c140c04b0cbc", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 5, - "category_name": "Section", + "id": 1281, + "strid": "44d120ad-2c95-4151-9f56-aa33331b9a80", + "image_id": 50, + "image_name": "11689.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 23.732, - 482.871, - 130.207, - 21.72800000000001 + 238.087, + 1928.915, + 2822.489, + 312.2249999999999 ], "priority": 7, "parents": [ - 194848 - ], - "children": [ - 194841 + 1279 ], - "area": 11459.494572, + "children": [], + "area": 459249.585605, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 194841, - "strid": "923cf618-5db2-433b-bbc8-455bf357bb23", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 3, - "category_name": "Text", + "id": 1282, + "strid": "c8369ea4-5599-4545-9ded-a3ddb55bd3cc", + "image_id": 50, + "image_name": "11689.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 21.228, - 506.961, - 249.13799999999998, - 237.70100000000002 + 282.486, + 2401.65, + 1100.243, + 141.35899999999992 ], "priority": 8, "parents": [ - 194835 + 1274 ], - "children": [], - "area": 10761.768108, + "children": [ + 1286, + 1283, + 1285, + 1284 + ], + "area": 678432.5019, "iscrowd": 0, "segmentation": [], - "text": "3n: Retrospective descriptive\nStudy setting: Short stay ward of the\nAdult Emergency and Trauma Centre\n(AETC) at Queen Elizabeth Central\nHospital\n\nStudy population: Asthmatic patients\nseen from January to April 2015\n\nData Collection: Case Record review of\npertinent history, examination,\ncategorization of the asthmatic\nexacerbation, treatment received,\noutcome and follow up plan.\n\nData Analysis done in STATA" + "text": "With a comprehensive set of\nmicrobiota related tools" }, { - "id": 194836, - "strid": "9ece6578-49eb-44b0-ae9a-678437cbdcdd", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 5, - "category_name": "Section", + "id": 1283, + "strid": "aae819a1-2fd5-4f24-a566-cbfd132b7d94", + "image_id": 50, + "image_name": "11689.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 23.254, - 767.249, - 101.09, - 17.389999999999986 + 98.546, + 2633.2, + 613.562, + 1545.478 ], "priority": 9, "parents": [ - 194848 - ], - "children": [ - 194842 + 1282 ], - "area": 17841.608246, + "children": [], + "area": 259491.3272, "iscrowd": 0, - "segmentation": [], - "text": "Conclusion" + "segmentation": [] }, { - "id": 194842, - "strid": "558ec067-411c-4945-8409-6df5d48ae43b", - "image_id": 208124, - "image_name": "9417.png", + "id": 1284, + "strid": "107a32cf-ca05-4873-8a16-2fbbf897f615", + "image_id": 50, + "image_name": "11689.png", "category_id": 3, "category_name": "Text", "bbox": [ - 22.054, - 791.248, - 243.431, - 127.28899999999999 + 586.749, + 2881.45, + 766.942, + 266.63200000000006 ], "priority": 10, "parents": [ - 194836 + 1282 ], "children": [], - "area": 17450.183392, + "area": 1690687.9060499999, "iscrowd": 0, "segmentation": [], - "text": "The quality of asthma management\nshowed that there was need for more\neffective training on the management\nof asthma.\n\nThere is need to identity factors that\naffect adherence to local acute asthma\nmanagement guidelines." + "text": "EBISearch, ENASearch, SRA Tools\nSee documentation for the full list\nSee documentation for the full list\nSAM Tools\n\nBIOM-Format tools" }, { - "id": 194833, - "strid": "beb5b590-e9d5-41eb-9f7a-7eea498797e9", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 5, - "category_name": "Section", + "id": 1285, + "strid": "6ce9c3d6-13a7-4c76-bd50-75ad3d59276d", + "image_id": 50, + "image_name": "11689.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 300.84, - 145.81, - 66.387, - 17.305000000000007 + 454.191, + 3232.765, + 1002.892, + 376.596 ], "priority": 11, "parents": [ - 194848 - ], - "children": [ - 194847, - 194845, - 194844, - 194846, - 194838 + 1282 ], - "area": 43865.4804, + "children": [], + "area": 1468292.7681149999, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "FastQ joiner, FastQ-join\n\nFastQC, PRINSEQ, Trim Galore!, Trimmomatic\nCD-Hit, Format CD-HIT outputs\n\nSortMeRNA, FragGeneScan\n\nNCBI Blast+, Diamond\n\nBWA, Bowtie\n\nHMMER3" }, { - "id": 194844, - "strid": "1b9d5875-2a51-491d-b9b0-9df8c6dd7b34", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 4, - "category_name": "List", + "id": 1286, + "strid": "74704b26-4e8b-4274-ac70-00f802a18b09", + "image_id": 50, + "image_name": "11689.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 298.485, - 169.331, - 350.83000000000004, - 182.432 + 648.447, + 3742.695, + 813.9980000000002, + 415.73799999999983 ], "priority": 12, "parents": [ - 194833 + 1282 ], "children": [], - "area": 50542.763535, + "area": 2426939.344665, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "VSEARCH\nMothur, QIIME\nMetaPhlAn2, Kraken\n\nHUMANnN2, PICRUST, InterProScan\nCombine MetaPhlAn2 and HUMAnN2\n\nExport2graphlan, GraPhlAn, Krona" }, { - "id": 194845, - "strid": "ed91b063-09b0-4fdd-afe9-88ecb418bc1b", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 7, - "category_name": "Table", + "id": 1287, + "strid": "23a0deed-7f47-4311-8e0f-dee7f757dc42", + "image_id": 50, + "image_name": "11689.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 305.653, - 356.227, - 425.96299999999997, - 127.17700000000002 + 1736.296, + 2405.373, + 1333.4399999999998, + 72.67200000000003 ], "priority": 13, "parents": [ - 194833 + 1274 ], - "children": [], - "area": 108881.851231, + "children": [ + 1289, + 1288 + ], + "area": 4176439.518408, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "With predefined and tested workflows" }, { - "id": 194846, - "strid": "9cbd3ca3-399a-4233-b218-6f751cdfe877", - "image_id": 208124, - "image_name": "9417.png", + "id": 1288, + "strid": "46d6d5ea-d1c8-4752-9349-4854038a1a9e", + "image_id": 50, + "image_name": "11689.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 304.779, - 509.097, - 425.759, - 158.865 + 1586.063, + 2541.883, + 1592.71, + 656.819 ], "priority": 14, "parents": [ - 194833 + 1287 ], "children": [], - "area": 155162.074563, + "area": 4031586.576629, "iscrowd": 0, "segmentation": [] }, { - "id": 194838, - "strid": "fdaa8c0c-8078-4896-a144-62ef1f22a613", - "image_id": 208124, - "image_name": "9417.png", + "id": 1289, + "strid": "ddaa733e-e635-4794-8bcd-bb2896b273f1", + "image_id": 50, + "image_name": "11689.png", "category_id": 3, "category_name": "Text", "bbox": [ - 367.027, - 688.467, - 295.93799999999993, - 34.20799999999997 + 1721.733, + 3218.6, + 1315.7339999999997, + 57.14499999999998 ], "priority": 15, "parents": [ - 194833 + 1287 ], "children": [], - "area": 252685.977609, + "area": 5541569.8338, "iscrowd": 0, "segmentation": [], - "text": "Documentation of Pertinent history, assessment,\ntreatment, discharge and follow up plan" + "text": "Main workflow to analyze raw shotgun metagenomics data" }, { - "id": 194847, - "strid": "6dcb0f20-6693-41ad-b5a1-ff72a1e422e4", - "image_id": 208124, - "image_name": "9417.png", - "category_id": 2, - "category_name": "Figure", + "id": 1290, + "strid": "a76b9ebf-e265-4449-8c97-e491b6f0192f", + "image_id": 50, + "image_name": "11689.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 298.147, - 738.757, - 432.63499999999993, - 203.38800000000003 + 1735.753, + 3445.798, + 1153.267, + 68.15200000000004 ], "priority": 16, "parents": [ - 194833 + 1274 + ], + "children": [ + 1291 + ], + "area": 5981054.215894, + "iscrowd": 0, + "segmentation": [], + "text": "With documentation and training" + }, + { + "id": 1291, + "strid": "8a80b9a0-dd50-4338-9ba0-286c916585c6", + "image_id": 50, + "image_name": "11689.png", + "category_id": 4, + "category_name": "List", + "bbox": [ + 1574.495, + 3585.337, + 1530.333, + 613.8340000000003 + ], + "priority": 17, + "parents": [ + 1290 ], "children": [], - "area": 220258.183279, + "area": 5645095.179815, "iscrowd": 0, "segmentation": [] }, { - "id": 194837, - "strid": "749db3c5-8b12-4259-b633-99ae363bc590", - "image_id": 208124, - "image_name": "9417.png", + "id": 1292, + "strid": "5daa90d5-983e-4745-b80f-cb67c9f1c3df", + "image_id": 50, + "image_name": "11689.png", "category_id": 5, "category_name": "Section", "bbox": [ - 21.344, - 958.101, - 131.974, - 16.322000000000003 + 228.216, + 4369.567, + 643.067, + 58.77099999999973 ], - "priority": 17, + "priority": 18, "parents": [ - 194848 + 1274 ], "children": [ - 194843 + 1293 ], - "area": 20449.707744, + "area": 997205.102472, "iscrowd": 0, "segmentation": [], - "text": "Acknowledgement:" + "text": "Useful information" }, { - "id": 194843, - "strid": "d560eeba-c7dd-43af-a0a1-e77c6486e352", - "image_id": 208124, - "image_name": "9417.png", + "id": 1293, + "strid": "e691e78c-7718-431b-8fcb-68bf213a355b", + "image_id": 50, + "image_name": "11689.png", "category_id": 3, "category_name": "Text", "bbox": [ - 155.236, - 958.105, - 369.74699999999996, - 14.145999999999958 + 59.142, + 4468.401, + 978.3489999999999, + 107.76400000000012 ], - "priority": 18, + "priority": 19, "parents": [ - 194837 + 1292 ], "children": [], - "area": 148732.38778, + "area": 264270.171942, "iscrowd": 0, "segmentation": [], - "text": "Kenneth K ankhadze , Ivy Yelewa and all AETC staff at QECH" + "text": "GitHub: http://github.com/asaim/framework\nDoc: http://asaim.readthedocs.io" }, { - "id": 41490, - "strid": "e9c80eb3-b4ae-412e-8df9-5933a9e0c0f9", - "image_id": 202128, - "image_name": "118194.png", + "id": 1294, + "strid": "469be409-34fd-4e93-b4cf-3c51d2ff4888", + "image_id": 50, + "image_name": "11689.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 1501.969, + 4352.115, + 677.7979999999998, + 67.53300000000036 + ], + "priority": 20, + "parents": [ + 1274 + ], + "children": [], + "area": 6536741.814435, + "iscrowd": 0, + "segmentation": [], + "text": "Acknowledgements" + }, + { + "id": 1295, + "strid": "b4cd9229-b41e-4c39-a2a6-20e0820d6ae6", + "image_id": 51, + "image_name": "116909.png", "category_id": 9, "category_name": "Root", "bbox": [ - 15.36, - 5.29, - 100.57000000000001, - 268.19 + 87.68, + 72.09, + 225.08999999999997, + 279.41999999999996 ], "priority": -1, "parents": [], "children": [ - 41465, - 41459, - 41460, - 41461, - 41462, - 41463, - 41464 + 1297, + 1331, + 1321, + 1312, + 1300, + 1298, + 1296 ], - "area": 81.2544, + "area": 6320.851200000001, "iscrowd": 0, "segmentation": [] }, { - "id": 41459, - "strid": "86e0b2f2-4eab-4c3e-92d4-a4cb3e2ea42b", - "image_id": 202128, - "image_name": "118194.png", + "id": 1296, + "strid": "3b6dc97f-aeda-46de-81b2-93d1dc53d9eb", + "image_id": 51, + "image_name": "116909.png", "category_id": 1, "category_name": "Title", "bbox": [ - 662.988, - 104.365, - 2342.16, - 249.618 + 369.932, + 79.979, + 3054.6060000000007, + 202.04500000000002 ], "priority": 1, "parents": [ - 41490 + 1295 ], "children": [], - "area": 69192.74262, + "area": 29586.791428, "iscrowd": 0, "segmentation": [], - "text": "An activity-driven growth model to simulate\ncortical morphology" + "text": "High Field Magnetic Resonance Spectroscopy, Imaging and Elastography for\nCartilage Tissue Engineering" }, { - "id": 41460, - "strid": "07c15d92-fc8e-41f8-871a-7bd62e63c3fa", - "image_id": 202128, - "image_name": "118194.png", + "id": 1297, + "strid": "7698194e-b2db-4fce-b95d-d9a945794102", + "image_id": 51, + "image_name": "116909.png", "category_id": 0, "category_name": "Author Info", "bbox": [ - 755.046, - 385.849, - 1752.637, - 127.46499999999997 + 548.051, + 351.145, + 2679.759, + 295.092 ], "priority": 2, "parents": [ - 41490 + 1295 ], "children": [], - "area": 291333.744054, + "area": 192445.368395, "iscrowd": 0, "segmentation": [], - "text": "Andrew T. Reid*', John Lewis', Alan C. Evans’;\n\n1. McConnell Centre for Brain Imaging, Montreal Neurological Institute, McGill University, Montreal, QC Canada" + "text": "Mrignayani Kotecha\", Ziying Yin', Temel Kaya Yasar?, Dieter Klatt’,\nThomas J. Royston’, Richard L. Magin™\n\n1 Department of Bioengineering and *Department of Mechanical Engineering, University of Illinois at Chicago, IL\n60607, USA. “mkotecha@uic.edu ,rmagin @uic.edu" }, { - "id": 41461, - "strid": "69cc3cf2-03f1-47fb-9c67-56d68d595e60", - "image_id": 202128, - "image_name": "118194.png", + "id": 1298, + "strid": "c57144ef-1e70-4fca-9fe0-91683cff3dd8", + "image_id": 51, + "image_name": "116909.png", "category_id": 5, "category_name": "Section", "bbox": [ - 405.233, - 599.721, - 582.2080000000001, - 87.00700000000006 + 1685.885, + 680.798, + 435.99300000000017, + 61.14499999999998 ], "priority": 3, "parents": [ - 41490 + 1295 ], "children": [ - 41471, - 41470 + 1299 ], - "area": 243026.739993, + "area": 1147747.13623, "iscrowd": 0, "segmentation": [], - "text": "Introduction" + "text": "INTRODUCTION" }, { - "id": 41470, - "strid": "f07a92e5-cb6a-4e17-9ade-fc32724ae840", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1299, + "strid": "354ae68d-d8ef-42cc-87ee-1af6532a9db1", + "image_id": 51, + "image_name": "116909.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 431.459, - 734.65, - 892.912, - 641.2970000000001 + 82.898, + 793.186, + 3661.977, + 493.39 ], "priority": 4, "parents": [ - 41461 + 1298 ], "children": [], - "area": 316971.35435, + "area": 65753.533028, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Carti ge tissue engineering is a promisin echnology for cartilage restoration and regeneration therapies. Cartilage is cormposed of chondrocytes cells\n(~1%), tissue fluid (~75% of wet weigh an extra cellular matrix (~25%, -main!y proteoglycans and type II collagen). aa to mimic native cartilage,\ntissue engineers focus on producti the ECM components using a acd f approaches to assemble de novo ue from appropriate cell types,\nbiocompatible gels, biodegradable scaffolds and chondrogenic growth f cto . The success of engineered tissue is normally assessed using histology\nand biochemical assays. Unfo una ely, these techniques of visualizing growth can only be performed onc gnetic Resonance Imaging (MRI) i\nemerging as an alternative, non-invasive tracking tool for tissue engineering because it provides a means for the periodic acquisition of quantitative\ninformation (T,, T4,, To, ADC and stiffness) about the development engineered tissue, both pre and post-implantation [1, 2]. We present here recent\nresults for tracking cartilage tissue engineering at the early stages of growth in vitro and in vivo. eS 0 <" }, { - "id": 41471, - "strid": "ca8ac70b-7e50-49cf-8190-8271cc5abc26", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1300, + "strid": "cdef9cd2-f597-45d4-a13a-3c793530b855", + "image_id": 51, + "image_name": "116909.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 431.534, - 1425.233, - 890.0949999999999, - 506.62699999999995 + 207.764, + 1329.47, + 917.179, + 74.4380000000001 ], "priority": 5, "parents": [ - 41461 + 1295 ], - "children": [], - "area": 615036.4974219999, + "children": [ + 1302, + 1301, + 1306, + 1308, + 1310, + 1304, + 1303 + ], + "area": 276216.00508000003, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "MR Parametric Map Imaging (MRI)" }, { - "id": 41462, - "strid": "ff9c6d05-5c80-4c64-b8e5-751704be2fb9", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 5, - "category_name": "Section", + "id": 1301, + "strid": "2cf1fab4-ab18-44f5-84f2-4fe127bfc390", + "image_id": 51, + "image_name": "116909.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1433.595, - 599.309, - 400.0930000000001, - 85.36799999999994 + 76.032, + 1447.784, + 1194.571, + 430.22800000000007 ], "priority": 6, "parents": [ - 41490 - ], - "children": [ - 41473, - 41480, - 41479, - 41467, - 41472, - 41466, - 41469, - 41481, - 41482, - 41468, - 41474, - 41483, - 41475, - 41478 + 1300 ], - "area": 859166.385855, + "children": [], + "area": 110077.913088, "iscrowd": 0, "segmentation": [], - "text": "Methods" + "text": "A. High-Resolution T,, T;, ADC and T,, maps of articular\ncartilage at 11.7 T [3]\n\nHigh resolution multi-parametric MR imaging of articular cartilage (AC) is\nessential to monitcr early stage of proteoglycan (PG) loss resulting from aging\nor degenerative joint diseases. AC is a heterogeneous connective tissue\ncomposed of tiiree distinct zones: superficial zone (SZ), transitional zone {TZ}\nand radiai zone (RZ), each with a unique framework of chondrocytes, tissue\nfluid (water) and structural macromolecules (collagens, PGs and other proteins)\n[1]. Ditierences in the macromolecular composition of each layer provide the\nbasis for multi-parametric MR contrasts." }, { - "id": 41467, - "strid": "cc8c532c-258a-4c5c-9d89-9cfd9580f5b4", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 3, - "category_name": "Text", + "id": 1302, + "strid": "d09c5a31-9d86-44e4-b343-3ec7ab5a4381", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1453.499, - 735.493, - 672.3680000000002, - 237.18899999999996 + 81.917, + 1877.358, + 1176.917, + 793.4849999999999 ], "priority": 7, "parents": [ - 41462 + 1300 ], "children": [], - "area": 1069038.3400070001, + "area": 153787.535286, "iscrowd": 0, - "segmentation": [], - "text": "Dynamics (Wilson-Cowan)\nree =-E, +S (rer —Prely — Op + Pe + eat: + rer]\n\nna 1g = Te + SpE x = Ply — 81)" + "segmentation": [] }, { - "id": 41469, - "strid": "4573c48f-b43f-4b82-ade2-990f21dc57d4", - "image_id": 202128, - "image_name": "118194.png", + "id": 1303, + "strid": "06399d51-28f9-451e-9038-6070448f7f6e", + "image_id": 51, + "image_name": "116909.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1396.333, - 1007.982, - 372.318, - 481.211 + 81.917, + 2679.328, + 1189.76, + 247.52599999999984 ], "priority": 8, "parents": [ - 41462 + 1300 ], "children": [], - "area": 1407478.530006, + "area": 219482.511776, "iscrowd": 0, "segmentation": [], - "text": "Where:\n\nTe]\n\nEly\n\nSs\nPEE,ELIE,I\n\n%E1\n\nPre\n\nCue\nTe\n€\n\ntime constants\n\nmean firing rate of\nexcitatory and inhibitory\npools\n\nsigmoid fen: v = ae\nlocal connection weights\nfiring thresholds\nexternal input signal\n\ninterregional connection\nstrength\n\nGaussian white noise\n\npower of I’, in decibels" + "text": "B. Monitoring the formation of tissue-engineered cartilage\nusing magnetic resonance imaging [4]\n\nCartilage tissue engineering relies on the production of proteogivcans and\ncollagens as a biomarker. In this study, we used MRI to evaluate the scaffold-\nfree chondrocyte pellets over a 3-week period, and observed the distinct\nchanges in histograms of T,, T,, T,,, and apparent diffusion coefficient (ADC)." }, { - "id": 41479, - "strid": "a8c7367a-932d-411c-a958-9942c6a093f3", - "image_id": 202128, - "image_name": "118194.png", + "id": 1304, + "strid": "deff0b8a-ec41-4237-8d8e-439730db1c3a", + "image_id": 51, + "image_name": "116909.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 1813.777, - 997.566, - 341.46399999999994, - 510.40800000000013 + 88.533, + 2941.643, + 601.302, + 256.8670000000002 ], "priority": 9, "parents": [ - 41462 + 1300 ], - "children": [], - "area": 1809362.2667820002, + "children": [ + 1305 + ], + "area": 260432.479719, "iscrowd": 0, "segmentation": [] }, { - "id": 41478, - "strid": "e5144177-18ea-412f-83ec-0db303b0dba6", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1305, + "strid": "10a75e27-36d9-4e23-bf3c-4424c2dc207b", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1436.7, - 1522.913, - 729.2239999999999, - 209.34699999999998 + 705.403, + 2942.032, + 532.415, + 272.0450000000001 ], "priority": 10, "parents": [ - 41462 + 1304 ], "children": [], - "area": 2187969.1071, + "area": 2075318.1988960002, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "oints: 3, 7, 14 and 21 days\n\ndifferent +i\n\n(TE/TR = 50 ms s, in-plane resolution = 62\nyum, slice thickness = 0.5 mm). Red lines\nindicate ROIs selected. The MR parameters\n(T;, Typ, T;, and ADC) were calculated for\nLogie in ROls. At each time point, 3\n\npret were taken out of the incubator for\naging.\n\nFigure 2: ac s of pellets cultured at" }, { - "id": 41466, - "strid": "358b520c-91fa-405e-9c70-858aa89465cb", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 3, - "category_name": "Text", + "id": 1306, + "strid": "014457b6-6d4a-4b20-a297-ac04c24dfab3", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 1452.465, - 1746.302, - 668.662, - 207.385 + 106.047, + 3216.023, + 638.664, + 343.2669999999998 ], "priority": 11, "parents": [ - 41462 + 1300 ], - "children": [], - "area": 2536442.5344299995, + "children": [ + 1307 + ], + "area": 341049.591081, "iscrowd": 0, - "segmentation": [], - "text": "Simulated activity (blue) was wavelet transformed (W,,), and\nthe total broadband power BP,(t) (red) was obtained as:\n\nZ\nBP.(C) = |Wy, (Ol\nZ=1\n\nwhere scales z=[1:50] correspond to frequencies 16-800 Hz." + "segmentation": [] }, { - "id": 41480, - "strid": "7f1c8ad2-34e6-4a0b-bcf3-3974f79b3e4d", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1307, + "strid": "e7fb7db6-3d72-4b34-8ed5-2bfd1e5ed1ae", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2204.284, - 733.073, - 577.6460000000002, - 267.11299999999994 + 85.031, + 3565.129, + 1157.068, + 126.09799999999996 ], "priority": 12, "parents": [ - 41462 + 1306 ], "children": [], - "area": 1615901.084732, + "area": 303146.483999, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 3: nasear of T, Typ, T; and ADC during development. Acquisition parameters: T, 2\n= 5s, TE =5.5— 371 ms, 64 echoes), T,, (TE/TR = 7.5 ms/5 s, TSL = 10, 20, 40, 80, 120, 2\nspin-lock frequency = 500 Hz), T, (TE = 11.45 ms, TR = 104 ms — 10, 16 steps), and 20 2A EN R\n= 25) a, 8/A = 3/18 ms, b =0, 91, 234, 443, 717, 1057, 1463 s/mm2)." }, { - "id": 41473, - "strid": "39267bfa-b825-4d60-a5e9-5ef18574cf68", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1308, + "strid": "337cbe41-21c9-4e50-81d6-c94c5987a9b8", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2204.228, - 1010.747, - 560.8789999999999, - 472.3190000000001 + 841.62, + 3221.861, + 326.92099999999994, + 226.51000000000022 ], "priority": 13, "parents": [ - 41462 + 1300 ], - "children": [], - "area": 2227916.838316, + "children": [ + 1309 + ], + "area": 2711582.65482, "iscrowd": 0, "segmentation": [] }, { - "id": 41481, - "strid": "88392eca-d9e1-4052-8ae6-0bc0faba04d1", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1309, + "strid": "ed73f8e4-648d-4db7-aada-26f02ee85bab", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2204.832, - 1521.784, - 547.1089999999999, - 222.55299999999988 + 800.755, + 3456.544, + 409.8190000000001, + 88.73599999999988 ], "priority": 14, "parents": [ - 41462 + 1308 ], "children": [], - "area": 3355278.060288, + "area": 2767844.89072, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 4: Accumulation of\nproteoglycan (PG) and collagen\nin one pellet (n = 1) over 3 weeks." }, { - "id": 41472, - "strid": "eecbce1a-7975-473f-858b-9048d0d40892", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1310, + "strid": "18ef85ff-f150-40aa-a9e3-d0c20ef698bc", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2204.441, - 1777.492, - 561.9719999999998, - 167.9000000000001 + 86.198, + 3697.065, + 1150.063, + 220.67200000000003 ], "priority": 15, "parents": [ - 41462 + 1300 ], - "children": [], - "area": 3918376.2419719994, + "children": [ + 1311 + ], + "area": 318679.60887, "iscrowd": 0, "segmentation": [] }, { - "id": 41475, - "strid": "c484ef83-3aa3-43c6-9575-fda02d782667", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1311, + "strid": "79c6d581-8aef-40e3-ae50-9e782dc42bbb", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2837.325, - 735.827, - 564.3490000000002, - 248.11300000000006 + 86.198, + 3928.245, + 1131.381, + 65.38400000000001 ], "priority": 16, "parents": [ - 41462 + 1310 ], "children": [], - "area": 2087780.3427749998, + "area": 338606.86250999995, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 5: (a) Ts, (6) Typ, (c) T; and (d) ADC values of the pellets / center regions were averaged\nat each time point. The values represent mean + SD (n =3). »" }, { - "id": 41483, - "strid": "52929770-f442-4eb8-9fa2-194fc63aa69e", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1312, + "strid": "57b5f4ff-0bdc-4c54-81e5-11f92b592104", + "image_id": 51, + "image_name": "116909.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2820.758, - 1005.64, - 601.9189999999999, - 152.54100000000005 + 1364.208, + 1329.47, + 1087.3229999999999, + 74.4380000000001 ], "priority": 17, "parents": [ - 41462 + 1295 ], - "children": [], - "area": 2836667.0751199997, + "children": [ + 1317, + 1319, + 1313, + 1316, + 1314 + ], + "area": 1813673.6097600001, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Proton and Sodium Spectroscopy (MRS)" }, { - "id": 41468, - "strid": "f754c25f-bc09-437c-8c38-ebb8d14e06c2", - "image_id": 202128, - "image_name": "118194.png", + "id": 1313, + "strid": "f9e8d0b3-ed34-463d-bba8-1cebc95cf481", + "image_id": 51, + "image_name": "116909.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2859.933, - 1179.802, - 540.3600000000001, - 61.3420000000001 + 1311.611, + 1449.119, + 1191.2009999999998, + 342.567 ], "priority": 18, "parents": [ - 41462 + 1312 ], "children": [], - "area": 3374154.6732659996, + "area": 1900680.420709, "iscrowd": 0, "segmentation": [], - "text": "Two regional signals (blue and green) and the\ncorresponding WCo (red)." + "text": "C. Water suppressed proton NMR spectroscopy for cartilage\ntissue engineering [5]\n\nMagnetic Resonance Spectroscopy provides near unbiased tool to investigate\nbiochemical changes occurring at the molecular level. In order to mimic native\ncartilage, tissue engineers rely on a variety of approaches ior effective re-\ndifferentiation of chondrocytes and focus on the prociuction of major ECM\ncomponents. We used water suppressed proton spectroscopy to track\nchondrogenic differentiation in pellet culture." }, { - "id": 41474, - "strid": "7223479c-a38b-4c35-9bdc-30b3fdaf2057", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1314, + "strid": "467e8ec7-b54c-48b6-b217-764fab6db465", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2834.667, - 1293.32, - 565.576, - 360.836 + 1324.842, + 1799.975, + 1160.895, + 650.9410000000003 ], "priority": 19, "parents": [ - 41462 + 1312 ], - "children": [], - "area": 3666131.52444, + "children": [ + 1315 + ], + "area": 2384682.47895, "iscrowd": 0, "segmentation": [] }, { - "id": 41482, - "strid": "0b8f1ee6-66f2-4147-8b18-6fc941e373d2", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1315, + "strid": "5791dfe2-874a-40c7-a9b4-6c048897a8f9", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2834.921, - 1693.149, - 588.04, - 279.60400000000004 + 1325.5, + 2456.715, + 1166.6390000000001, + 64.05999999999995 ], "priority": 20, "parents": [ - 41462 + 1314 ], "children": [], - "area": 4799943.656229, + "area": 3256375.7325000004, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 6: Water suppressed 'H NMR spectra of chondrocyte pellets (top pa and HMSCs\ncea\n\nS in biomimetic scaffold (bottom panel). -" }, { - "id": 41463, - "strid": "011a56b4-a1e1-4f7b-a777-f5c254ec57bb", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 5, - "category_name": "Section", + "id": 1316, + "strid": "efaa9d91-e2c4-47e0-ba85-d57bc8ebefc2", + "image_id": 51, + "image_name": "116909.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 412.429, - 2031.775, - 330.505, - 79.34999999999991 + 1315.821, + 2527.698, + 1190.8670000000002, + 381.3119999999999 ], "priority": 21, "parents": [ - 41490 + 1312 ], - "children": [ - 41484, - 41488, - 41487, - 41486, - 41489, - 41485 - ], - "area": 837962.931475, + "children": [], + "area": 3325998.1100579994, "iscrowd": 0, "segmentation": [], - "text": "" + "text": "D. Sodium Relaxation and triple quantum coherence\nspectroscopy as a probe for early stage growth of engineered\ntissue [6]\n\nProteoglycans are negatively charged macromolecu!es, and sodium ions binds\ndirectly to them. This makes sodium spectroscopy and imaging as an attractive\ntool to track the cartilage growth progress. 'n tnis study we used sodium\nrelaxation and triple quantum coherence spectroscopy for characterization of\nbiomimetic scaffolds at the early growin stage for cartilage tissue\nregeneration." }, { - "id": 41484, - "strid": "7c8629f8-a1e2-487a-8ba4-fcf6932e2d0d", - "image_id": 202128, - "image_name": "118194.png", + "id": 1317, + "strid": "b981b379-2d05-4aba-b32a-e00a72dfff90", + "image_id": 51, + "image_name": "116909.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 430.259, - 2160.741, - 929.029, - 583.3159999999998 + 1318.641, + 2917.178, + 1164.2199999999998, + 376.23199999999997 ], "priority": 22, "parents": [ - 41463 + 1312 ], - "children": [], - "area": 929678.2619190001, - "iscrowd": 0, + "children": [ + 1318 + ], + "area": 3846710.515098, + "iscrowd": 0, "segmentation": [] }, { - "id": 41489, - "strid": "0d47dc3c-3d81-46da-922b-42329513c270", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1318, + "strid": "ea21c413-267e-4284-be6d-03aedb045ed5", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 429.268, - 2810.657, - 926.461, - 581.9409999999998 + 1320.256, + 3305.79, + 1157.7609999999997, + 96.88400000000001 ], "priority": 23, "parents": [ - 41463 + 1317 ], "children": [], - "area": 1206525.109076, + "area": 4364489.08224, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Figure 7: 28 ‘T, and T, relaxation times of biomimetic scaffolds at 9.4T. The smaller T, values\nas com arcd t T, values are indicative of sodium ions binding to proteoglycans. The ! ase\nin Tp paveta probably due to increased aggregation of proteoglycans molecules." }, { - "id": 41488, - "strid": "2aabb239-85dd-4de0-bf4a-c8e729d5693d", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1319, + "strid": "8d20cff1-dc77-4879-99fd-a73a35d0bca6", + "image_id": 51, + "image_name": "116909.png", + "category_id": 7, + "category_name": "Table", "bbox": [ - 429.01, - 3455.004, - 929.4739999999999, - 594.5059999999999 + 1322.157, + 3415.062, + 1169.492, + 387.491 ], "priority": 24, "parents": [ - 41463 + 1312 ], - "children": [], - "area": 1482231.26604, + "children": [ + 1320 + ], + "area": 4515248.128734, "iscrowd": 0, "segmentation": [] }, { - "id": 41485, - "strid": "9ab11831-a75b-49aa-8f90-47ddee1150f1", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1320, + "strid": "4a9c6c81-cac6-4bd8-a3a8-815cfc85c90a", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 1427.696, - 2161.073, - 917.6149999999998, - 582.078 + 1333.394, + 3812.295, + 1147.6589999999999, + 178.38200000000006 ], "priority": 25, "parents": [ - 41463 + 1319 ], "children": [], - "area": 3085355.2778079994, + "area": 5083291.27923, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "in ECM embedded scaffold seeded with HM Ils and chondrocytes embedded in alginate\n\nbeads as a function of growth time f eek period at 9.4T. For comparison, similar\n\nparameters from native human cartil BC thick, 3 mm diameter, from a 72 year old male\n( d\n\nTable 1: The fast and slow relaxation times MSC residual quadrupolar couplings for sodium ions\n\ndonor) explants at 9.4 T field are inclu in the table. The last column in each section gives\nestimated motional parameter Wotc." }, { - "id": 41486, - "strid": "1e2f50ef-a1e7-486a-aa91-16fbd3876a6a", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1321, + "strid": "f42c5a66-c820-4515-865f-5c054b11b0ce", + "image_id": 51, + "image_name": "116909.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 1428.393, - 2811.727, - 953.3739999999998, - 579.2429999999999 + 2829.584, + 1330.272, + 634.6680000000001, + 69.05500000000006 ], "priority": 26, "parents": [ - 41463 + 1295 ], - "children": [], - "area": 4016251.164711, + "children": [ + 1325, + 1323, + 1329, + 1322, + 1328, + 1326 + ], + "area": 3764116.3668479994, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "MR Elastography (MRE)" }, { - "id": 41487, - "strid": "d3671833-afe5-4cb4-ade6-5bccc9105971", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 2, - "category_name": "Figure", + "id": 1322, + "strid": "95a2ea14-0eb2-4772-9f98-28a7ea5fea02", + "image_id": 51, + "image_name": "116909.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1429.589, - 3455.835, - 951.6149999999998, - 579.2440000000001 + 2547.253, + 1449.305, + 1186.826, + 301.95399999999995 ], "priority": 27, "parents": [ - 41463 + 1321 ], "children": [], - "area": 4940423.701815, + "area": 3691746.509165, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "E. Geometric Focusing of high frequency shear waves for non-\ninvasive high resolution microscopic MR Elastography [7]\nMicroscopic Magnetic Resonance Elastograohy (uMRE) provides a non-\ninvasive method to assess the local mechanical properties of gel samples and\nengineered tissues /n vitro. In this stucy, we use UMRE to measure the shear\nstiffness of alginate hydrogel beads, a common scaffolds used in tissue\nengineering for providing mechanica! support for cell growth." }, { - "id": 41464, - "strid": "e1efaada-0323-48e8-b62b-9be513aab6b4", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 5, - "category_name": "Section", + "id": 1323, + "strid": "df0a46fc-0325-4f39-9631-6051afe3904a", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2467.476, - 2029.59, - 499.78099999999995, - 82.72500000000014 + 2586.007, + 1754.489, + 1099.6309999999999, + 424.674 ], "priority": 28, "parents": [ - 41490 + 1321 ], "children": [ - 41476, - 41477 + 1324 ], - "area": 5007964.61484, + "area": 4537120.835423, "iscrowd": 0, - "segmentation": [], - "text": "Discussion" + "segmentation": [] }, { - "id": 41476, - "strid": "f201ac8e-0be6-47bd-96a0-90726ade76ea", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1324, + "strid": "f53753a5-1db9-4a70-b655-e45a07bf9caa", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 2477.69, - 2185.904, - 957.5170000000003, - 965.7580000000003 + 2555.327, + 2200.154, + 1177.138, + 122.71900000000005 ], "priority": 29, "parents": [ - 41464 + 1323 ], "children": [], - "area": 5415992.48176, + "area": 5622112.920358, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "urc 8: Measured shear wave motion and calculated shear stiffness (~1043 a) at 5 kHz for\n\nthree alginate beads suspended in Agarose gel (0.7%). TE = 45 ms, FO 0x10 mm, slice\n\nickness -1 mm matrix size-128x128, 42 MSG cycles and 9 on ctuation cycles were\nused at 11.7T." }, { - "id": 41477, - "strid": "ff4bdfae-170a-4f03-9259-eb36332063f8", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 4, - "category_name": "List", + "id": 1325, + "strid": "6247b238-da99-404d-a4e1-a5213e2a6ad6", + "image_id": 51, + "image_name": "116909.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 2477.955, - 3175.388, - 952.1440000000002, - 597.027 + 2545.108, + 2328.461, + 1189.9939999999997, + 304.36400000000003 ], "priority": 30, "parents": [ - 41464 + 1321 ], "children": [], - "area": 7868468.57154, + "area": 5926184.718788, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "F. Measurement of In vitro local shear stiffness of alginate\nbeads using microscopic MR Elastography (8]\n\nIn this study, we monitored the change in shear stiffness of alginate beads\nembedded in agarose gel over a period of ~10 hours. During this time, a\ndecrease in bead stiffness couple with the increase in T2 was observed. We\nhypothesized that this change was duc to an osmotic pressure gradient\nbetween the alginate beads and the againse gel ." }, { - "id": 41465, - "strid": "c03710bb-3c68-471e-9aee-cec793dc09e7", - "image_id": 202128, - "image_name": "118194.png", - "category_id": 3, - "category_name": "Text", + "id": 1326, + "strid": "8d47dde3-5c90-4313-b217-739c6f31de54", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 2474.561, - 3862.791, - 494.875, - 174.37199999999984 + 2558.838, + 2655.709, + 796.3800000000001, + 350.1329999999998 ], "priority": 31, "parents": [ - 41490 - ], - "children": [], - "area": 9558711.959751, - "iscrowd": 0, - "segmentation": [], - "text": "Acknowledgements\nATR is supported by a CIHR\nPostdoctoral Fellowship" - }, - { - "id": 133413, - "strid": "e4a559e3-85a7-45e3-af7d-837965d7fc4b", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 9, - "category_name": "Root", - "bbox": [ - 235.99, - 126.92, - 260.63, - 220.08999999999997 + 1321 ], - "priority": -1, - "parents": [], "children": [ - 133393, - 133370, - 133392, - 133394, - 133369, - 133391, - 133390, - 133368, - 133371 + 1327 ], - "area": 29951.8508, + "area": 6795529.106142, "iscrowd": 0, "segmentation": [] }, { - "id": 133368, - "strid": "42d88765-100b-4091-a2b8-61082a58093f", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 1, - "category_name": "Title", + "id": 1327, + "strid": "5678e310-551d-4042-877c-6765d734d003", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 694.406, - 128.126, - 3103.766, - 289.67600000000004 + 3368.482, + 2682.89, + 326.9209999999998, + 305.9050000000002 ], - "priority": 1, + "priority": 32, "parents": [ - 133413 + 1326 ], "children": [], - "area": 88971.463156, + "area": 9037266.67298, "iscrowd": 0, "segmentation": [], - "text": "Determining a minimum flow regime\nto protect a winter warm-water refuge for manatees" + "text": "Figure 9: Calculated shear\nStiffness and T2 changes\nof the beads over time.\n\nThe experimental\nparameters were: FOV =\n1x1 cm2, in-plane\n\nresolution = 78x78 pm?,\nslice thickness = 0.5 mm,\nnumber of bipolar\ngradients = 23." }, { - "id": 133369, - "strid": "28607f87-8ca6-4a76-812d-b9c0bb056277", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 0, - "category_name": "Author Info", + "id": 1328, + "strid": "7822117b-85f4-4054-a696-4f958dde7e2c", + "image_id": 51, + "image_name": "116909.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1292.791, - 421.867, - 1913.519, - 126.73099999999994 + 2545.108, + 3042.457, + 1189.9939999999997, + 272.3249999999998 ], - "priority": 2, + "priority": 33, "parents": [ - 133413 + 1321 ], "children": [], - "area": 545385.860797, + "area": 7743381.650356, "iscrowd": 0, "segmentation": [], - "text": "Casey Harris (charris@sjrwmd.com), Joseph Stewart, Jian Di, and Andrew Sutherland\nSt. Johns River Water Management District, Palatka, FL" + "text": "G. In vivo Nude Mouse MR Elastography [9]\n\nIn this in vivo study at 9.4 T, we are monitoring shear stiffness of matrigel\nimpianted in a mouse model. Further, the sensitivity of vo!umeiric strain,\nmeasured as the divergence of the 3D displacement field induced by harmonic\nwaves, to the state of compression of poro-elastic cartilage is currently being\ninvestigated." }, { - "id": 133370, - "strid": "3c041833-5148-41ed-87c6-538c991b4fa1", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 5, - "category_name": "Section", + "id": 1329, + "strid": "32103a58-698c-4eef-9fd1-fcbdca156fa3", + "image_id": 51, + "image_name": "116909.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 97.261, - 629.793, - 906.777, - 57.750999999999976 + 2559.693, + 3345.614, + 1160.6390000000001, + 397.96500000000015 ], - "priority": 3, + "priority": 34, "parents": [ - 133413 + 1321 ], "children": [ - 133396 + 1330 ], - "area": 61254.296973, + "area": 8563744.736502001, "iscrowd": 0, - "segmentation": [], - "text": "Minimum flows -- Florida state laws" + "segmentation": [] }, { - "id": 133396, - "strid": "579549c6-2244-43f5-a1ef-b186b2838873", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1330, + "strid": "412e17d8-cf11-4496-b1a9-ba9efc46ad50", + "image_id": 51, + "image_name": "116909.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 98.632, - 690.337, - 1264.196, - 543.9389999999999 + 2554.151, + 3759.96, + 1162.8559999999998, + 243.87800000000016 ], - "priority": 4, + "priority": 35, "parents": [ - 133370 + 1329 ], "children": [], - "area": 68089.318984, + "area": 9603505.59396, "iscrowd": 0, "segmentation": [], - "text": "In Florida, water management districts are required to establish “minimum\nflows and levels” (here, minimum flows) for lakes, wetlands, rivers, and\naquifers.\n\nMinimum flows for a given water body are the limits at which further\ngroundwater or surface water withdrawals for human use would be\nsignificantly harmful to the water resources or ecology of the area (Section\n373.042, Florida Statutes).\n\nMinimum flows are expressed as multiple flows defining a minimum\nhydrologic regime, recognizing that water bodies experience variations and\nextremes that contribute to significant functions of the system." + "text": "Figure 10: : (a) Plastic actuator a n with conic tip pressing lower back of the mouse. After the tip\nof the actuator is positioned, whole mechanical setup is slid into the RF coil along with mouse.\n(b) Anatomical MR ima = mouse to locate/verify the position of actuator. FOV: 4cm x 4cm,\nread resolution: siz hase resolution: 156.25 um, slice thickness: 0.5 mm, TR: 300 msec,\nTE: 10 msec. (c) ropagation image obtained after post-processing of data acquired wit!\nMRE pulse se cre FOV: 4cm x 4cm, read resolution: 312.5 um, phase resolution: 156.25\nslice heres: mm, TR = 312.5 ms, TE = 11.186, frequency: 1kHz, # of motion encoding\n\ngradients = ime steps: 8." }, { - "id": 133371, - "strid": "34f09dc8-d9d4-49b2-8f71-3cfae2da53c0", - "image_id": 205677, - "image_name": "15572.png", + "id": 1331, + "strid": "cd8548cf-0111-45f4-9eb7-660604afd490", + "image_id": 51, + "image_name": "116909.png", "category_id": 5, "category_name": "Section", "bbox": [ - 97.168, - 1284.799, - 959.859, - 64.56799999999998 + 1368.714, + 4042.927, + 1091.88, + 57.06200000000035 ], - "priority": 5, + "priority": 36, "parents": [ - 133413 + 1295 ], "children": [ - 133403, - 133401, - 133400, - 133372, - 133395, - 133374, - 133373, - 133397, - 133404, - 133402, - 133398, - 133375, - 133399 + 1332 ], - "area": 124841.34923200001, + "area": 5533610.785878, "iscrowd": 0, "segmentation": [], - "text": "Spring Garden Run at De Leon Springs" + "text": "REFERENCES and ACKNOWLEDMENTS" }, { - "id": 133372, - "strid": "48e02844-c5d4-4ed0-a62f-a69d989c2965", - "image_id": 205677, - "image_name": "15572.png", + "id": 1332, + "strid": "809688ee-e967-4b3d-8157-ef0f2e43f8dc", + "image_id": 51, + "image_name": "116909.png", "category_id": 3, "category_name": "Text", "bbox": [ - 97.756, - 1361.605, - 315.84400000000005, - 447.8040000000001 + 71.892, + 4138.03, + 3675.584, + 449.8090000000002 ], - "priority": 6, + "priority": 37, "parents": [ - 133371 + 1331 ], "children": [], - "area": 133105.05838, + "area": 297491.25275999994, "iscrowd": 0, "segmentation": [], - "text": "De Leon Springs\nvents from the\nupper and lower\nFloridan aquifer at\na nearly-constant\n22°C (72°F) into\n\na large concrete\nswimming pool in\nDe Leon Springs\nState Park." + "text": "[1] W. Li, L. Hong, L. Hu, and R. L. Magi, Tissue Engineering Part C: Methods, vol. 16, pp. 1407-1415 (2010). [2] S. Ravindran, Q. Gao, M. Kotecha, R.L. Magin, S. Karol, A. Bedran-Russo, and A. George; Tissue engineering Part A, vol.\n18, pp. 295-309 (2012). [3]. Z. Yin, M. Kotecha, T. M. Schmid, and R. L. Magin, “High resolution T1p and T2 maps of articular cartilage at 11.7T”, The 11* iniernational conference on Magnetic Resonance Microscopy (!CMRM), Aug 14-\n18 (2011), beijing, China. [4] Z. Yin, T. M. Schmid, L. Madsen, M. Kotecha, and R. L. Magin, “Monitoring the formation of tissue-engineered carti!age in scaffold-free pellet culture using magnetic resonance imaging”, The 20!\nInternational society for magnetic resonance in medicine (ISMRM), May 5-11 (2012), Metbourne, Australia. [5] M. Kotecha, T. M. Schmid, R. L. Magin, “Proton NMR characterization of Chondrocytes re-differentiation in alginate beads\nand pellet culture”, submitted for Biomedical Engineering Society (BMES) annual meeiing, to be held at Atlanta, CA, Oct 24-27, 2012. [6] M. Kotecha, S. Ravindran, A. Vaidyanathan, A. George, R. L. Magin, “Characterization of ECM\nembedded biomimetic scaffolds for cartilage tissue engineering using sodium triple quantum coherencespectroscopy”, The 20\" International society for magnetic resonance in medicine (ISMRM), May 5-11 (2012), Melbourne,\nAustralia. [7] T. K. Yesai, T. J. Royston, and R. L. Magin, “Taking MR Elastography (MRE) to the microscopic (uMRE) level”, IEEE, 1618-1623 (2011). [8] Z. Yin, T. K. Yasar, and R. L. Magin, “measurement of in vitro local shear stiffness\nof alginate beads using microscopic MR Elastography”, submitted for Biomedical Engineering Society (BMES) annual meeting, to be held at Atlanta, CA, Oct 24-27, 2012. [9] T. K. Yasar, D. Klatt, T. J. Royston, and R. L. Magin, work\nin progress.\n\nThis study was supported by NIH/NIBIB grant EB007537. We acknowledge use of Research Resource Center (RRC)’s micro-imaging facility and the NMR facility (Chemistry department) at the University of Illinois at Chicago. We also\nacknowledge use of Lynn S. Florsheim MRIS lab at the University of Chicago for in vivo mouse MRI/MRE. We also wish to thank Articular Engineering( === = ~~~ —__) for providing human explants." }, { - "id": 133398, - "strid": "2849f1aa-dfb0-46d3-bc65-3085bfe8ba54", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1333, + "strid": "1c7ef227-1bd5-4e49-bded-2e1927e40c4d", + "image_id": 52, + "image_name": "116997.png", + "category_id": 9, + "category_name": "Root", "bbox": [ - 465.981, - 1352.067, - 900.8979999999999, - 507.27600000000007 + 238.77, + 114.1, + 213.92999999999998, + 188.26000000000002 ], - "priority": 7, - "parents": [ - 133371 + "priority": -1, + "parents": [], + "children": [ + 1337, + 1348, + 1347, + 1338, + 1334, + 1341, + 1343, + 1349, + 1345, + 1350, + 1339, + 1336, + 1340, + 1346, + 1335, + 1342, + 1344 ], - "children": [], - "area": 630037.532727, + "area": 27243.657, "iscrowd": 0, "segmentation": [] }, { - "id": 133399, - "strid": "07c1dcb8-b19a-476a-b14c-d306ae37b62c", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1334, + "strid": "26d11a93-aab1-4fcb-a935-f4fd30cd69df", + "image_id": 52, + "image_name": "116997.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 99.046, - 1857.976, - 901.639, - 506.7310000000002 + 536.583, + 441.402, + 2408.024, + 114.05299999999994 ], - "priority": 8, + "priority": 1, "parents": [ - 133371 + 1333 ], "children": [], - "area": 184025.090896, + "area": 236848.80936599997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Bearing Fruit under the APPLE scheme" }, { - "id": 133373, - "strid": "7dda7666-c2ec-4e38-83eb-37762a29b90d", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1335, + "strid": "c7be6697-d7e2-4e09-bdbc-c45b0dedb97a", + "image_id": 52, + "image_name": "116997.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 1013.308, - 1897.845, - 350.221, - 362.9950000000001 + 427.704, + 4157.947, + 2636.245, + 320.7960000000003 ], - "priority": 9, + "priority": 2, "parents": [ - 133371 + 1333 ], "children": [], - "area": 1923101.52126, + "area": 1778370.563688, "iscrowd": 0, "segmentation": [], - "text": "Water from the\n\npool flows over\n\na constructed\nwaterfall into a wide\nspring run (Spring\nGarden Run) used\nby manatees as a\nwarm-water refuge." + "text": "Author: Jenny Hopper, Occupational Therapy Practice Facilitator\nUniversity of Northampton\nJenny.hopper@northampton.ac.uk" }, { - "id": 133397, - "strid": "41b9ed17-5333-4ba5-acf4-8859b0be9486", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1336, + "strid": "e1ba638a-03a8-4a97-a21e-988a9c63a399", + "image_id": 52, + "image_name": "116997.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 965.867, - 2288.691, - 400.17499999999995, - 315.03099999999995 + 295.92, + 605.748, + 2889.704, + 420.98199999999997 ], - "priority": 10, + "priority": 3, "parents": [ - 133371 + 1333 ], "children": [], - "area": 2210571.110097, + "area": 179252.94816000003, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The College of Occupational Therapists recognises the skills, knowledge and expertise of Practice Placement Educators (PPEs) through the\n\nAccreditation of Practice Placement Educators’ (APPLE) scheme. By providing evidence for the 6 Learning Outcomes PPEs can apply for this\naccreditation. The 6 learning outcomes are illustrated here through the metaphor of a fruitful tree (1. the roles and attributes of an effective PPE ),\nembedded in nutritious soil (2. appropriate learning theories for adult and professional learners), supported by a network of\n\nestablished roots (3. planning, implementation and facilitation of learning), bearing a strong trunk (4. sound principles of judgement and\nassessment), giving rise to far reaching branches (5. evaluation of the learning experience) and evidence of new growth in the leaves\n\n(6. reflection on the learning experience and action plan for future practice)." }, { - "id": 133404, - "strid": "560915bf-782e-495c-bd2b-96cab5074891", - "image_id": 205677, - "image_name": "15572.png", + "id": 1337, + "strid": "92506fee-a174-4b77-bdc4-9b7e59241c0c", + "image_id": 52, + "image_name": "116997.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1076.403, - 2608.779, - 291.193, - 49.95400000000018 + 194.007, + 1112.586, + 1095.541, + 157.07400000000007 ], - "priority": 11, + "priority": 4, "parents": [ - 133371 + 1333 ], "children": [], - "area": 2808097.541937, + "area": 215849.472102, "iscrowd": 0, "segmentation": [], - "text": "Above: Same view, 1915\nSource: State Archives of Florida" + "text": "Role and attributes of the effective\nPractice Placement Educator (fruit)" }, { - "id": 133374, - "strid": "233c020c-2ad1-43d4-875b-473f901914c4", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1338, + "strid": "09d19522-7069-4a77-8fdf-fb33b7b42555", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 98.264, - 2455.835, - 816.181, - 226.17799999999988 + 193.984, + 1293.366, + 1093.09, + 358.923 ], - "priority": 12, + "priority": 5, "parents": [ - 133371 + 1333 ], "children": [], - "area": 241320.17044, + "area": 250892.31014400002, "iscrowd": 0, - "segmentation": [], - "text": "Manatees are susceptible to cold stress below\n20°C (68°F). Several warm-water sites, including\nSpring Garden Run at De Leon Springs, in the\nSt. Johns River basin provide manatees with a\nnetwork of warm-water refuges for resting and" + "segmentation": [] }, { - "id": 133375, - "strid": "d27e4016-bb5b-4ef5-86b6-d81d5b495dc7", - "image_id": 205677, - "image_name": "15572.png", + "id": 1339, + "strid": "7817dd5f-3e4c-4a22-ad18-d939071bf128", + "image_id": 52, + "image_name": "116997.png", "category_id": 3, "category_name": "Text", "bbox": [ - 98.213, - 2683.242, - 381.88300000000004, - 43.28699999999981 + 2361.292, + 1091.11, + 841.221, + 146.029 ], - "priority": 13, + "priority": 6, "parents": [ - 133371 + 1333 ], "children": [], - "area": 263529.246546, + "area": 2576429.3141199998, "iscrowd": 0, "segmentation": [], - "text": "foraging during winter." + "text": "Reflection on the learning\nexperience and action plan" }, { - "id": 133403, - "strid": "0731ae77-cdd8-44d3-9caa-bb3b3228d2b4", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1340, + "strid": "346a0a99-57ce-4d90-9c61-810110160390", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 244.776, - 2762.615, - 288.181, - 90.10500000000002 + 2363.617, + 1261.808, + 859.5299999999997, + 417.98299999999995 ], - "priority": 14, + "priority": 7, "parents": [ - 133371 + 1333 ], "children": [], - "area": 676221.84924, + "area": 2982430.839536, "iscrowd": 0, - "segmentation": [], - "text": "Right: A network of\nwarm-water refuges in\nthe St. Johns River basin" + "segmentation": [] }, { - "id": 133400, - "strid": "ad98de59-3a1c-4fc7-91d2-9288c8746bf3", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1341, + "strid": "3cb45b57-1095-4487-9cfa-52eae9f53b2d", + "image_id": 52, + "image_name": "116997.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 548.181, - 2710.446, - 817.2469999999998, - 829.335 + 276.251, + 2098.849, + 603.96, + 143.47800000000007 ], - "priority": 15, + "priority": 8, "parents": [ - 133371 + 1333 ], "children": [], - "area": 1485814.998726, + "area": 579809.135099, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Sound principles of\nassessment (trunk)" }, { - "id": 133401, - "strid": "b78fa07e-7882-4488-8bfc-ca1ec117c28a", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1342, + "strid": "678e90da-bcb9-46fb-ae01-ab9b58dc97bf", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 99.656, - 2901.853, - 701.0720000000001, - 979.9459999999999 + 272.838, + 2278.72, + 677.3720000000001, + 410.8409999999999 ], - "priority": 16, + "priority": 9, "parents": [ - 133371 + 1333 ], "children": [], - "area": 289187.06256800005, + "area": 621721.40736, "iscrowd": 0, "segmentation": [] }, { - "id": 133395, - "strid": "5d4d879c-b42f-40bd-ac9b-cf6597d439ce", - "image_id": 205677, - "image_name": "15572.png", + "id": 1343, + "strid": "f603ad4c-d8bc-4886-9db7-dc296a0cd5e0", + "image_id": 52, + "image_name": "116997.png", "category_id": 3, "category_name": "Text", "bbox": [ - 798.316, - 3613.266, - 349.24700000000007, - 115.84999999999991 + 278.987, + 3103.146, + 925.943, + 54.84299999999985 ], - "priority": 17, + "priority": 10, "parents": [ - 133371 + 1333 ], "children": [], - "area": 2884528.060056, + "area": 865737.3931020001, "iscrowd": 0, "segmentation": [], - "text": "Left: Manatee carcasses in the\nSt. Johns River basin since\n2005, in cases where mortality\nwas due to cold stress" + "text": "Learning Theories (soil) APPLE 2" }, { - "id": 133402, - "strid": "42af5c99-cc84-4012-b3f3-2539195b65a8", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1344, + "strid": "29c52b89-d222-4de7-8d4f-e59771ae8f8a", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 800.679, - 3759.939, - 326.08900000000006, - 45.090000000000146 + 275.15, + 3190.861, + 932.86, + 231.15999999999985 ], - "priority": 18, + "priority": 11, "parents": [ - 133371 + 1333 ], "children": [], - "area": 3010504.198581, + "area": 877965.4041499998, "iscrowd": 0, - "segmentation": [], - "text": "Data source: Florida Fish and Wildlife\nConservation Commission" + "segmentation": [] }, { - "id": 133394, - "strid": "b9011b14-de39-422d-897f-3c0886519b7f", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 5, - "category_name": "Section", + "id": 1345, + "strid": "d80c3e1e-89e9-478f-90f5-36723ea4251c", + "image_id": 52, + "image_name": "116997.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 96.165, - 3897.156, - 720.64, - 61.22699999999986 + 1329.755, + 1751.995, + 902.9139999999998, + 1219.88 ], - "priority": 19, + "priority": 12, "parents": [ - 133413 + 1333 ], - "children": [ - 133376 - ], - "area": 374770.00674000004, + "children": [], + "area": 2329724.111225, "iscrowd": 0, - "segmentation": [], - "text": "Water temperature modeling" + "segmentation": [] }, { - "id": 133376, - "strid": "5ce73e6a-465d-477a-91cd-796e120221ae", - "image_id": 205677, - "image_name": "15572.png", + "id": 1346, + "strid": "3c98ad84-1e38-47b3-a487-e5239979010c", + "image_id": 52, + "image_name": "116997.png", "category_id": 3, "category_name": "Text", "bbox": [ - 95.889, - 3958.035, - 1167.304, - 135.683 + 2483.619, + 1824.097, + 617.0329999999999, + 154.442 ], - "priority": 20, + "priority": 13, "parents": [ - 133394 + 1333 ], "children": [], - "area": 379532.018115, + "area": 4530361.967043, "iscrowd": 0, "segmentation": [], - "text": "Water temperatures in the spring run were modeled using the\nenvironmental fluid dynamics code (EFDC) to evaluate the sensitivity\nof water temperatures in the spring run to variations in spring flow." + "text": "Evaluation of\n\nlearning experience" }, { - "id": 133390, - "strid": "c6129d57-6223-4472-86d9-e979b619d382", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 5, - "category_name": "Section", + "id": 1347, + "strid": "aeacc755-19ba-4415-92d0-4510b8c472b6", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1710.419, - 633.591, - 907.1769999999999, - 60.995000000000005 + 2479.393, + 2001.017, + 804.895, + 363.7230000000002 ], - "priority": 21, + "priority": 14, "parents": [ - 133413 + 1333 ], - "children": [ - 133389, - 133388, - 133408, - 133412, - 133410, - 133407, - 133411 - ], - "area": 1083706.0846290002, + "children": [], + "area": 4961307.542681, "iscrowd": 0, - "segmentation": [], - "text": "Water temperature modeling results" + "segmentation": [] }, { - "id": 133388, - "strid": "e2b18bd6-caf6-46f4-82c4-01eb9c758996", - "image_id": 205677, - "image_name": "15572.png", + "id": 1348, + "strid": "1e9822da-25d3-4ffd-bd8f-598b9f492508", + "image_id": 52, + "image_name": "116997.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1714.141, - 692.961, - 1254.5430000000001, - 356.2180000000001 + 2341.15, + 2489.816, + 848.8789999999999, + 159.51800000000003 ], - "priority": 22, + "priority": 15, "parents": [ - 133390 + 1333 ], "children": [], - "area": 1187832.8615010001, + "area": 5829032.728399999, "iscrowd": 0, "segmentation": [], - "text": "Model results demonstrated the spring run is sensitive to variations\nin spring flow, and that reductions in flow result in lower winter water\ntemperatures in the spring run.\n\nResults were mapped for one of the coldest days of the model period,\nFebruary 21, 2015. Modeled 5% and 25% reductions in spring flow reduced\ntemperatures in the spring run, including in the two areas where manatees\nare seen most frequently (shown below)." + "text": "Planning and\n\nimplementation of learning" }, { - "id": 133412, - "strid": "f7393fbe-eb41-4704-aba8-77986fe927a3", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1349, + "strid": "a97aa821-f1b3-4ba2-a73d-6f19bfa0f337", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1799.972, - 1049.575, - 1100.3770000000002, - 851.203 + 2342.175, + 2667.351, + 958.748, + 693.2419999999997 ], - "priority": 23, + "priority": 16, "parents": [ - 133390 + 1333 ], "children": [], - "area": 1889205.6119000001, + "area": 6247402.828425, "iscrowd": 0, "segmentation": [] }, { - "id": 133407, - "strid": "4347ea85-74c7-4eb5-bbdd-2e70bb15092c", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1350, + "strid": "f65a4daa-5eaf-4464-864e-7ae8b489b356", + "image_id": 52, + "image_name": "116997.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 1702.45, - 2084.119, - 672.8370000000002, - 1362.9280000000003 + 903.746, + 3607.211, + 1693.199, + 387.94500000000016 ], - "priority": 24, + "priority": 17, "parents": [ - 133390 + 1333 + ], + "children": [], + "area": 3260002.512406, + "iscrowd": 0, + "segmentation": [] + }, + { + "id": 1351, + "strid": "5668610c-7b0d-4e9c-b185-b82273da4d21", + "image_id": 53, + "image_name": "117061.png", + "category_id": 9, + "category_name": "Root", + "bbox": [ + 215.27, + 61.49, + 203.73999999999998, + 195.59999999999997 ], + "priority": -1, + "parents": [], "children": [ - 133405 + 1388, + 1390, + 1356, + 1358, + 1352, + 1353, + 1371, + 1354, + 1392 ], - "area": 3548108.3915500003, + "area": 13236.9523, "iscrowd": 0, "segmentation": [] }, { - "id": 133405, - "strid": "ca1f4076-367b-4e8a-827e-6cd7c6e60194", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 6, - "category_name": "Caption", + "id": 1352, + "strid": "3ad6f99f-336a-4b8f-8c26-553d0a2cddf4", + "image_id": 53, + "image_name": "117061.png", + "category_id": 1, + "category_name": "Title", "bbox": [ - 2043.152, - 1960.211, - 287.25300000000016, - 87.9820000000002 + 684.421, + 19.455, + 2558.758, + 290.062 ], - "priority": 25, + "priority": 1, "parents": [ - 133407 + 1351 ], "children": [], - "area": 4005009.025072, + "area": 13315.410555, "iscrowd": 0, "segmentation": [], - "text": "Left side:\nTemperatures near water\ncolumn surface" + "text": "BUM Wee aD\nCompound ex vivo and in silico method to study stented arteries" }, { - "id": 133408, - "strid": "e28ec0d9-811e-457e-b4ae-3f9d5d385379", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1353, + "strid": "7fcf6a55-6d4a-4b00-a9bc-56c1089977f2", + "image_id": 53, + "image_name": "117061.png", + "category_id": 0, + "category_name": "Author Info", "bbox": [ - 2425.09, - 2054.503, - 453.759, - 1391.386 + 69.644, + 424.086, + 3625.7699999999995, + 480.96900000000005 ], - "priority": 26, + "priority": 2, "parents": [ - 133390 - ], - "children": [ - 133406 + 1351 ], - "area": 4982354.68027, + "children": [], + "area": 29535.045384000005, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "F Rikhtegar*, F. Pacheco, C. Wyss‘, K.S. Stok¢, H. Ges, R.J. Choo4, A. Ferrari?, D. Poulikakos?, R. Miuller4, V. Kurtcuoglu*©\n\n«Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Zurich, Switzerland\n‘Department of Bioengineering, Imperial College, London, United Kingdom\n‘Clinic of Cardiology, University Hospital Zurich, Zurich, Switzerland\ndInstitute for Biomechanics, Department Health Sciences and Technology, ETH Zurich, Zurich, Switzerland\n©The Interface Group, Institute of Physiology, University of Zurich, Zurich, Switzerland" }, { - "id": 133406, - "strid": "dec45c56-2c98-4f01-a26f-4731e158765e", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 6, - "category_name": "Caption", + "id": 1354, + "strid": "8a76553b-41de-43f8-b3a3-d7ceec5fe005", + "image_id": 53, + "image_name": "117061.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2506.369, - 1960.794, - 287.83500000000004, - 87.9820000000002 + 71.461, + 972.633, + 257.896, + 44.059999999999945 ], - "priority": 27, + "priority": 3, "parents": [ - 133408 + 1351 ], - "children": [], - "area": 4914473.296986001, + "children": [ + 1355 + ], + "area": 69505.326813, "iscrowd": 0, "segmentation": [], - "text": "Right side:\nTemperatures near water\ncolumn bottom" + "text": "Introduction" }, { - "id": 133389, - "strid": "daf1571c-a13a-4b65-89f1-a3936dd8e6fe", - "image_id": 205677, - "image_name": "15572.png", + "id": 1355, + "strid": "af145173-5021-4cef-a038-cacbb5c0dae0", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 1708.574, - 3479.331, - 1278.386, - 140.27199999999993 + 81.578, + 1096.168, + 1708.555, + 229.10400000000004 ], - "priority": 28, + "priority": 4, "parents": [ - 133390 + 1354 ], "children": [], - "area": 5944694.483994001, + "area": 89423.19310399999, "iscrowd": 0, "segmentation": [], - "text": "Decreases in water temperatures due to reductions in spring flow may even\nbe more severe than the modeled temperatures shown above, since the\nmodel did not fully capture the low-temperature extremes." + "text": "Cardiovascular diseases are the leading cause of death in the developed world, of these, coronary artery disease that can\nlead to heart attack is the most relevant. Hemodynamic factors such as low wall shear stress have been shown to influence\nendothelial healing and atherogenesis in stent-free vessels. However, in stented vessels, a reliable quantitative analysis of\n\nsuch relations has not been possible due to the lack of a suitable method for the accurate acquisition of blood flow." }, { - "id": 133411, - "strid": "e511d465-e40c-4159-8299-8f1beea9281e", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1356, + "strid": "b59e5203-197f-44bf-8f55-220cdfb8a3ed", + "image_id": 53, + "image_name": "117061.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2039.309, - 3635.315, - 704.7569999999998, - 27.210999999999785 + 69.649, + 1382.292, + 200.262, + 51.9079999999999 ], - "priority": 29, + "priority": 5, "parents": [ - 133390 + 1351 ], - "children": [], - "area": 7413530.597335, + "children": [ + 1357 + ], + "area": 96275.255508, "iscrowd": 0, "segmentation": [], - "text": "Comparison of modeled and observed temperatures at dock, winter 2014-2015" + "text": "Objective" }, { - "id": 133410, - "strid": "7b7b13fa-bb07-4c7a-81a7-b7acb7335e06", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1357, + "strid": "713c4d97-2bd7-47e2-a0c1-53bd37f4e922", + "image_id": 53, + "image_name": "117061.png", + "category_id": 3, + "category_name": "Text", "bbox": [ - 1601.492, - 3685.485, - 1443.3059999999998, - 416.56799999999976 + 87.07, + 1504.889, + 1703.439, + 95.03700000000003 ], - "priority": 30, + "priority": 6, "parents": [ - 133390 + 1356 ], "children": [], - "area": 5902274.74362, + "area": 131030.68522999997, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "The objective of this work is to develop a method for the precise reconstruction of hemodynamics and quantification of wall shear\n\nstress in stented vessels. To achieve this goal the geometry of implanted stent and the deformed artery are resolved accurately." }, { - "id": 133391, - "strid": "bf4c3f7e-27a1-4f37-8247-fe84e6a2f617", - "image_id": 205677, - "image_name": "15572.png", + "id": 1358, + "strid": "ade6434f-c668-4d29-9834-a114f4cff585", + "image_id": 53, + "image_name": "117061.png", "category_id": 5, "category_name": "Section", "bbox": [ - 3331.144, - 629.857, - 828.2149999999997, - 60.099000000000046 + 68.659, + 1663.413, + 487.842, + 43.58899999999994 ], - "priority": 31, + "priority": 7, "parents": [ - 133413 + 1351 ], "children": [ - 133379 + 1359, + 1368, + 1363, + 1366, + 1364, + 1361, + 1369, + 1360 ], - "area": 2098144.366408, + "area": 114208.273167, "iscrowd": 0, "segmentation": [], - "text": "Minimum flow recommendations" + "text": "Materials and Methods" }, { - "id": 133379, - "strid": "9bde81cf-424f-481d-9928-5c8dee2eb3a8", - "image_id": 205677, - "image_name": "15572.png", + "id": 1359, + "strid": "2beef0d6-fc59-42bd-926f-8f29f3db8c08", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3326.937, - 691.544, - 1278.7399999999998, - 272.5659999999999 + 81.271, + 1788.153, + 1677.561, + 96.20900000000006 ], - "priority": 32, + "priority": 8, "parents": [ - 133391 + 1358 ], "children": [], - "area": 2300723.320728, + "area": 145324.982463, "iscrowd": 0, "segmentation": [], - "text": "The loss of warm-water habitat has been identified by the U.S. Fish and\nWildlife Service and Florida Fish and Wildlife Conservation Commission\n\nas one of the most significant threats to manatee populations. To help\nachieve these agencies’ long-term goals of improving and enhancing warm-\nwater habitat, we recommend protecting existing manatee habitat at De\nLeon Springs by maintaining current water use impacts on spring flow." + "text": "This method consists of four major steps, namely ex vivo heart preparation and intervention, vascular corrosion casting, imaging,\n\nsegmentation and registration and finally grid generation and numerical simulation which is briefly illustrated as follows:" }, { - "id": 133392, - "strid": "798fb13b-34db-4091-b3e9-c19b707ad243", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 5, - "category_name": "Section", + "id": 1360, + "strid": "cab3d661-deb4-4de8-9510-75838ad95d53", + "image_id": 53, + "image_name": "117061.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 3330.546, - 1015.964, - 939.3809999999999, - 60.67999999999995 + 81.734, + 1930.326, + 1722.203, + 115.56400000000008 ], - "priority": 33, + "priority": 9, "parents": [ - 133413 + 1358 ], - "children": [ - 133384, - 133385, - 133382, - 133383, - 133386, - 133380, - 133381, - 133387 - ], - "area": 3383714.836344, + "children": [], + "area": 157773.265284, "iscrowd": 0, - "segmentation": [], - "text": "Calculating the minimum flow regime" + "segmentation": [] }, { - "id": 133380, - "strid": "7549a4f3-4d53-4ead-98eb-0018bb3c6c7f", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1361, + "strid": "4703e088-737c-460c-9e79-5727e22bf1d9", + "image_id": 53, + "image_name": "117061.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 3331.724, - 1077.293, - 717.223, - 537.326 + 134.482, + 2063.361, + 1581.619, + 443.8649999999998 ], - "priority": 34, + "priority": 10, "parents": [ - 133392 + 1358 ], - "children": [], - "area": 3589242.943132, + "children": [ + 1362 + ], + "area": 277484.914002, "iscrowd": 0, - "segmentation": [], - "text": "Flow data for De Leon Springs Is available\nfrom 1964 - present and water use data is\navailable 1950 - present. Total water use\nreached a maximum in the mid-1980s and\nhas since remained relatively stable.\n\nA rainfall/flow model was calibrated using\n1997 - 2016 flow data, considered\nrepresentative of current water use\nimpacts. The model was used along with\nrainfall data to estimate flows back to\n1910 as though current water use impacts" + "segmentation": [] }, { - "id": 133381, - "strid": "32a375ef-75be-46cf-8cc9-18d6d9c5ab5e", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1362, + "strid": "05434136-c16a-4268-bc1b-27626179a4a3", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 3331.238, - 1618.203, - 284.52700000000004, - 79.93000000000006 + 75.489, + 2525.363, + 1734.91, + 67.9090000000001 ], - "priority": 35, + "priority": 11, "parents": [ - 133392 + 1361 ], "children": [], - "area": 5390619.325313999, + "area": 190637.127507, "iscrowd": 0, "segmentation": [], - "text": "were present the\nwhole time." + "text": "Fig. 1. Heart preparation and stent implantation. A Porcine heart with stitched Cannula (left), Heart preserved for intervention inside saline (middle) and\nangiographic image of heart while stenting (right)" }, { - "id": 133382, - "strid": "5ba6627e-3639-45a2-bdda-86264534cc13", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 2, - "category_name": "Figure", + "id": 1363, + "strid": "54c75465-86fc-48e3-856e-90d3612657e0", + "image_id": 53, + "image_name": "117061.png", + "category_id": 4, + "category_name": "List", "bbox": [ - 4061.533, - 1078.992, - 532.9690000000005, - 517.3700000000001 + 80.856, + 2651.111, + 1639.161, + 97.6590000000001 ], - "priority": 36, + "priority": 12, "parents": [ - 133392 + 1358 ], "children": [], - "area": 4382361.614736, + "area": 214358.23101599998, "iscrowd": 0, "segmentation": [] }, { - "id": 133383, - "strid": "2dc4df8d-f5af-41f6-a4c4-b01c4ee6e832", - "image_id": 205677, - "image_name": "15572.png", + "id": 1364, + "strid": "8c9c904d-6a38-440a-84a9-901abe876bd8", + "image_id": 53, + "image_name": "117061.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3626.348, - 1626.393, - 677.2619999999997, - 482.5149999999999 + 475.97, + 2786.711, + 1244.185, + 507.62800000000016 ], - "priority": 37, + "priority": 13, "parents": [ - 133392 + 1358 ], - "children": [], - "area": 5897867.002764, + "children": [ + 1365 + ], + "area": 1326390.83467, "iscrowd": 0, "segmentation": [] }, { - "id": 133385, - "strid": "2890ac7f-4f6e-4a30-8f9d-9dd55278442b", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1365, + "strid": "2aed3c86-27ec-465b-b5b6-9e5d10ef96fa", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 3533.911, - 2129.287, - 922.9570000000003, - 32.65599999999995 + 77.443, + 2935.92, + 383.006, + 182.53899999999976 ], - "priority": 38, + "priority": 14, "parents": [ - 133392 + 1364 ], "children": [], - "area": 7524710.751456999, + "area": 227366.45256, "iscrowd": 0, "segmentation": [], - "text": "Model-estimated (black) and observed (blue) spring flow from 1910 - 2016" + "text": "Fig. 2. Vascular corrosion cast-\ning of stented artery. Left: Injec-\ntion of epoxy resin under physio-\nlogical pressure (90 mmHg). Right:\nMaceration of casted hearts with\nKOH 7.5 % for 12 hours at 55 °C" }, { - "id": 133384, - "strid": "772f1f48-f576-47ee-b5ca-a1d5d95c5e63", - "image_id": 205677, - "image_name": "15572.png", + "id": 1366, + "strid": "474aa831-7678-4a4d-bed3-4da5e5e856ff", + "image_id": 53, + "image_name": "117061.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3411.06, - 2163.079, - 1117.904, - 588.5039999999999 + 531.425, + 3297.553, + 1158.309, + 534.2739999999999 ], - "priority": 39, + "priority": 15, "parents": [ - 133392 + 1358 ], - "children": [], - "area": 7378392.253740001, + "children": [ + 1367 + ], + "area": 1752402.1030249998, "iscrowd": 0, "segmentation": [] }, { - "id": 133386, - "strid": "1554d2b7-f37b-4eb7-bd04-94a8c33fde13", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1367, + "strid": "bedb3807-c353-44e1-95b8-399db7d8f644", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 3328.248, - 2782.314, - 1259.364, - 183.8760000000002 + 72.092, + 3478.372, + 385.824, + 189.7489999999998 ], - "priority": 40, + "priority": 16, "parents": [ - 133392 + 1366 ], "children": [], - "area": 9260231.005872, + "area": 250762.79422399998, "iscrowd": 0, "segmentation": [], - "text": "The estimated flows from 1910 - 2016 were used to calculate the\nrecommended minimum flows, including the long-term mean and 10th,\n\n50th, and 90th percentiles of monthly mean flows to ensure variations and\nextremes of spring flow:" + "text": "Fig. 3. Final product of corro-\nsion casting. After maceration of\nthe heart tissue the cast is rinsed\nseveral times with water and a con-\nventional detergent. ‘The inset\nshows the stented segment." }, { - "id": 133387, - "strid": "89706b57-6474-4c6b-b89a-60d0a3987034", - "image_id": 205677, - "image_name": "15572.png", + "id": 1368, + "strid": "5aedd716-3e04-4e88-bf92-dc542139237c", + "image_id": 53, + "image_name": "117061.png", "category_id": 4, "category_name": "List", "bbox": [ - 3330.944, - 3008.711, - 1250.2490000000003, - 184.64699999999993 + 76.799, + 3888.318, + 1524.814, + 155.19700000000012 ], - "priority": 41, + "priority": 17, "parents": [ - 133392 + 1358 ], "children": [], - "area": 10021847.853184, + "area": 298618.93408200005, "iscrowd": 0, "segmentation": [] }, { - "id": 133393, - "strid": "063b93ff-06a5-476a-b4df-3a23f526a419", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 5, - "category_name": "Section", + "id": 1369, + "strid": "9be27b91-f668-4424-8572-e6f3b68b6c61", + "image_id": 53, + "image_name": "117061.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 3330.157, - 3241.459, - 430.9670000000001, - 55.690000000000055 + 98.713, + 4087.866, + 1660.946, + 544.3069999999998 ], - "priority": 42, + "priority": 18, "parents": [ - 133413 + 1358 ], "children": [ - 133409, - 133378, - 133377 + 1370 ], - "area": 10794567.379062999, + "area": 403525.516458, "iscrowd": 0, - "segmentation": [], - "text": "Future directions" + "segmentation": [] }, { - "id": 133377, - "strid": "34b0369e-cade-4fd9-9e5c-86874dcfe335", - "image_id": 205677, - "image_name": "15572.png", - "category_id": 3, - "category_name": "Text", + "id": 1370, + "strid": "8ed61739-8154-4f24-b51c-0251d7d81833", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 3326.97, - 3298.012, - 1273.2959999999998, - 269.4810000000002 + 76.277, + 4640.717, + 1711.951, + 98.97800000000007 ], - "priority": 43, + "priority": 19, "parents": [ - 133393 + 1369 ], "children": [], - "area": 10972386.98364, + "area": 353979.97060899995, "iscrowd": 0, "segmentation": [], - "text": "Based on the rainfall/flow model, current water use impacts at De Leon\nSprings cause a 10.4% average reduction in spring flow compared to less-\nsevere 1965 - 1977 water use impacts. Maintaining current water use\nimpacts should at least maintain existing manatee habitat, which will allow\nfor further improvement and enhancement of manatee habitat by other\nmeans." + "text": "Fig. 4. Imaging, segmentation and surface reconstruction. (A) High resolution image of stent and cast (top) together with the segmentation product of it\n(bottom) (B) Automatic image registration using Geomagic combining the high resolution stented part (green) with the low resolution arterial tree (red) (C)\nThe unstructured tetrahedral computational grid in a representative cross-section of domain. The whole domain consists of about 48 million elements." }, { - "id": 133378, - "strid": "fc9b9706-c44d-4d9d-95eb-7c8687f52f97", - "image_id": 205677, - "image_name": "15572.png", + "id": 1371, + "strid": "36264dfa-72c7-4bdc-bab0-0b49c4d45645", + "image_id": 53, + "image_name": "117061.png", + "category_id": 5, + "category_name": "Section", + "bbox": [ + 1946.136, + 976.59, + 148.60600000000022, + 39.85900000000004 + ], + "priority": 20, + "parents": [ + 1351 + ], + "children": [ + 1379, + 1383, + 1384, + 1386, + 1377, + 1381, + 1375, + 1373, + 1372 + ], + "area": 1900576.95624, + "iscrowd": 0, + "segmentation": [], + "text": "Results" + }, + { + "id": 1372, + "strid": "04d1cf02-c9c3-429b-a274-3b59b5798aaa", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 3326.97, - 3611.284, - 439.59000000000015, - 405.9050000000002 + 1953.607, + 1099.515, + 1723.464, + 77.53199999999993 ], - "priority": 44, + "priority": 21, "parents": [ - 133393 + 1371 ], "children": [], - "area": 12014633.52948, + "area": 2148020.2006050004, "iscrowd": 0, "segmentation": [], - "text": "This minimum flow\nregime will be used to set\nlong-term limits on local\nand regional water use,\nand similar methods for\ndetermining minimum\nflows may be applied to\nother springs used by\nmanatees." + "text": "It is shown in the following figures on ex vivo porcine hearts that the compound method presented in the methods part very well en-\nsures anatomic fidelity, capturing arterial tissue prolapse, radial and axial arterial deformation as well as stent malapposition" }, { - "id": 133409, - "strid": "79232a05-4303-436b-9df1-3f53fbcc3ab2", - "image_id": 205677, - "image_name": "15572.png", + "id": 1373, + "strid": "a978067f-17e1-4f4b-899c-f363efc948cf", + "image_id": 53, + "image_name": "117061.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 3771.689, - 3579.814, - 827.7959999999998, - 522.1129999999998 + 1975.82, + 1192.104, + 506.0669999999998, + 246.0809999999999 ], - "priority": 45, + "priority": 22, "parents": [ - 133393 + 1371 ], - "children": [], - "area": 13501945.085846, + "children": [ + 1374 + ], + "area": 2355382.92528, "iscrowd": 0, "segmentation": [] }, { - "id": 152242, - "strid": "4bc7962d-359c-4138-a177-262fc7922a3f", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 9, - "category_name": "Root", + "id": 1374, + "strid": "0e6fd441-c6a9-40c7-8fed-e81fa59c209d", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 445.29, - 70.75, - 75.30000000000001, - 127.41999999999999 + 2484.852, + 1250.339, + 442.00300000000016, + 124.66699999999992 ], - "priority": -1, - "parents": [], - "children": [ - 152223, - 152222, - 152226, - 152225, - 152224 + "priority": 23, + "parents": [ + 1373 ], - "area": 31504.2675, + "children": [], + "area": 3106907.364828, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 5. Final product of digitization\nof casted coronary artery. The stented\nand non-stented segments are registered\nand shown in different colors." }, { - "id": 152222, - "strid": "a77b9ea6-2b0f-4420-879d-6de9e317edd7", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 1, - "category_name": "Title", + "id": 1375, + "strid": "1a451987-7c13-4147-9833-1165deda8350", + "image_id": 53, + "image_name": "117061.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 616.414, - 128.971, - 2905.911, - 228.837 + 2023.171, + 1451.73, + 629.0229999999999, + 200.212 ], - "priority": 1, + "priority": 24, "parents": [ - 152242 + 1371 ], - "children": [], - "area": 79499.529994, + "children": [ + 1376 + ], + "area": 2937098.03583, "iscrowd": 0, - "segmentation": [], - "text": "Single cell-level analysis of responses to cancer immunotherapy\nusing a syngeneic murine model of lung cancer" + "segmentation": [] }, { - "id": 152223, - "strid": "b02a4d9f-4b86-4fb6-8354-b82aa1cecfaa", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 0, - "category_name": "Author Info", + "id": 1376, + "strid": "2449b308-ae03-4e66-a14f-60642905760b", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 924.515, - 384.677, - 2286.127, - 212.71500000000003 + 1955.919, + 1678.712, + 782.0409999999999, + 127.03999999999996 ], - "priority": 2, + "priority": 25, "parents": [ - 152242 + 1375 ], "children": [], - "area": 355639.656655, + "area": 3283424.696328, "iscrowd": 0, "segmentation": [], - "text": "Subin Cho’, Gyu jin Lee?, Jaesang Kim2*, Sanghyuk Lee™\n\n'EWHA Research Center for Systems Biology (ERCSB), Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Rep. of Korea\n2Ewha-JAX International Research Center for Cancer, Department of Life Science, Ewha Womans University, Seoul 03760, Rep. of Korea\nCorresponding author: sanghyuk@ewha.ac.kr, jkim1964@ewha.ac.kr" + "text": "Fig. 6. Radial wall deformation of stented artery. (A) Representative\nmicro-CT cross-section of a stented coronary artery corrosion cast.\nWith the dotted circle showing the nominal circular cross-section (B)\nRadial arterial enlargement caused by stenting." }, { - "id": 152224, - "strid": "731e69fb-2d8d-4869-8a65-9f068b6c9c9d", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 5, - "category_name": "Section", + "id": 1377, + "strid": "a025aa9b-adfe-495d-a555-f17805d98bd2", + "image_id": 53, + "image_name": "117061.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 200.522, - 607.361, - 242.502, - 52.68100000000004 + 2042.094, + 1845.927, + 677.1819999999998, + 629.3950000000002 ], - "priority": 3, + "priority": 26, "parents": [ - 152242 + 1371 ], "children": [ - 152227 + 1378 ], - "area": 121789.24244199999, + "area": 3769556.451138, "iscrowd": 0, - "segmentation": [], - "text": "Abstract" + "segmentation": [] }, { - "id": 152227, - "strid": "568d6036-01f3-4213-b49b-4bcf5d3721b0", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 3, - "category_name": "Text", + "id": 1378, + "strid": "638fa74f-6f66-45b1-a403-a3d2d04a4397", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 129.366, - 699.037, - 3865.007, - 280.289 + 1954.291, + 2490.966, + 779.4849999999999, + 281.2260000000001 ], - "priority": 4, + "priority": 27, "parents": [ - 152224 + 1377 ], "children": [], - "area": 90431.62054200002, + "area": 4868072.435106, "iscrowd": 0, "segmentation": [], - "text": "Immunotherapy is currently the most promising treatment modality for various types of cancers. It has been demonstrated that targeting immune checkpoints with PD-1 or CTLA-4 blockade (ICB) can lead to long-term survival or complete remission\nfrom cancers. However, immunotherapy is limited in efficacy as only a minority of patients benefit from such therapies. Clearly, closer scrutiny of responses from various cells found in tumor tissues during immunotherapy would significantly enhance\nour understanding of the interactions within the tumor microenvironment (TME) and possibly point to novel targets. Here, we report a longitudinal study using a Lewis lung carcinoma (LLC) syngeneic mouse model and anti-PD-1 antibody treatment.\nSpecifically, we performed single-cell RNA seq using tumor tissues isolated from multiple time points and attempted to reconstruct potentially significant cellular interactions in response to the immunotherapy. Interestingly, natural killer (NK) cells, in\nparticular, showed activation by anti-PD-1 antibody treatment and expressed elevated levels of Xcl-1, which has been implicated in recruiting conventional dendritic cells (cDCs). We present results from gene expression analysis suggesting enhanced\nantigen-presenting by cDCs and strategies for demonstrating the functionalities of altered cellular responses to immunotherapy." + "text": "Fig. 8. Stent malapposition and its effect on local hemodynamics.\n(A) Imprint of malapposed stent end section (arrow) in artery lumen\nnegative (top) and corresponding wall shear stress (WSS) distribution\n(bottom). Higher WSS can be observed in the vicinity of the malap-\nposed strut due to flow tunneling compared to (B), a similar fully ap-\nposed stent end. (C) Velocity contour in axial cross-section of the stent-\ned artery near a malapposed strut. (D) Velocity vector plot in the vicini-\nty of the malapposed strut demonstrates the presence of vortices.\nThese influence WSS distribution and may lead to thrombosis" }, { - "id": 152225, - "strid": "bec1689b-c9bf-4ea1-8f3d-9652e6fbc88e", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 5, - "category_name": "Section", + "id": 1379, + "strid": "e5dc3bc3-4f24-49b8-bbcc-3ed73ef47ea2", + "image_id": 53, + "image_name": "117061.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 216.693, - 1031.509, - 210.78, - 51.636999999999944 + 3056.119, + 1214.201, + 581.607, + 418.43100000000004 ], - "priority": 5, + "priority": 28, "parents": [ - 152242 + 1371 ], "children": [ - 152228, - 152231, - 152235, - 152232, - 152230, - 152233, - 152239, - 152236, - 152238, - 152240, - 152229, - 152234 + 1380 ], - "area": 223520.779737, + "area": 3710742.7459190004, "iscrowd": 0, - "segmentation": [], - "text": "" + "segmentation": [] }, { - "id": 152231, - "strid": "fb300695-abcf-4516-86b1-5b7ba7608a3f", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 3, - "category_name": "Text", + "id": 1380, + "strid": "cc28499c-84ba-4b8b-a8d6-c4ffd7447998", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 124.398, - 1128.607, - 1802.118, - 55.9380000000001 + 2902.345, + 1676.079, + 786.3130000000001, + 157.47399999999993 ], - "priority": 6, + "priority": 29, "parents": [ - 152225 + 1379 ], "children": [], - "area": 140396.453586, + "area": 4864559.505255, "iscrowd": 0, "segmentation": [], - "text": "Longitudinal study design using Lewis Lung Carcinoma syngeneic mouse model" + "text": "Fig. 7. Axial arterial deformation due to stenting. (A) The solid line\nshows the axis of the stent, while the dashed line approximates the cen-\nterline of the stent-free artery. (B) An extended area of low wall shear\nstress is seen immediately downstream of the stent at the outer artery\nwall due to the change in curvature." }, { - "id": 152228, - "strid": "2f0fb7f6-c56f-454e-aac1-0797be154b13", - "image_id": 206426, - "image_name": "21404.png", + "id": 1381, + "strid": "5579c298-13fb-4699-abb2-2b9e1e0923d6", + "image_id": 53, + "image_name": "117061.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 95.826, - 1218.186, - 1960.786, - 635.52 + 3061.947, + 1842.43, + 547.8069999999998, + 646.8779999999999 ], - "priority": 7, + "priority": 30, "parents": [ - 152225 + 1371 ], - "children": [], - "area": 116733.89163599999, + "children": [ + 1382 + ], + "area": 5641423.01121, "iscrowd": 0, "segmentation": [] }, { - "id": 152232, - "strid": "9a3b6442-565a-4e4e-b59c-ae4ec6026fa1", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 3, - "category_name": "Text", + "id": 1382, + "strid": "e7a239f8-a79e-412a-8f97-f3fcdb7ee73f", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 129.644, - 1908.969, - 1892.504, - 166.70499999999993 + 2897.397, + 2498.46, + 785.9859999999999, + 283.91399999999976 ], - "priority": 8, + "priority": 31, "parents": [ - 152225 + 1381 ], "children": [], - "area": 247486.37703600002, + "area": 7239030.5086199995, "iscrowd": 0, "segmentation": [], - "text": "(A) Outline of the longitudinal study. The top black arrow indicates the flow of days, and the day of LLC injection was set\nas day 0. On days marked with yellow boxes, pembrolizumab was administered, and control mice were simultaneously\nadministered with Ig. (B) Average tumor growth curve of the Ig-treated group and the anti-PD1-treated group. Statistically\nsignificant cases are marked with **** (p < 10 in two-way ANOVA test)." + "text": "Fig. 9. Arterial tissue prolapse between stent struts. (A) Recon-\nstructed surface of arterial lumen negative obtained by wCT of a corro-\nsion cast. The black arrows point to prolapsed regions. (B) Wall shear\nstress (WSS) distribution in the same region shown in B. Higher WSS is\nevident in prolapsed regions compared to regions without prolapse.\nBlood flow is from left to right. (C) Velocity contour plots in prolapsed\n(top) and prolapse-free inter-strut sections. Regions of low velocity are\nevident near stent struts in both cases, with larger low-velocity regions\nin the prolapse-free segment." }, { - "id": 152234, - "strid": "7e40abca-25f2-40bd-b986-408bced9ce23", - "image_id": 206426, - "image_name": "21404.png", + "id": 1383, + "strid": "dd91927d-9698-4c24-a208-5766b1e15f08", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 123.023, - 2110.422, - 1147.204, - 58.98700000000008 + 1957.922, + 2807.854, + 1723.5390000000002, + 180.69399999999996 ], - "priority": 9, + "priority": 32, "parents": [ - 152225 + 1371 ], "children": [], - "area": 259630.445706, + "area": 5497559.119388, "iscrowd": 0, "segmentation": [], - "text": "T cells were activated in response to anti-PD1" + "text": "Both the local geometry at the vessel wall, as well as the large scale arterial anatomy, influence WSS distribution and can be accounted\nfor with this method. In Fig. 10 regions of low, atheroprone shear stress are present at bifurcations and nearby individual stent struts.\nThe distribution of low (<0.5 Pa), intermediate (0.5 to 2.5 Pa) and high (>2.5 Pa) WSS is shown in Fig, 11 relative to the surface area\nof selected arterial sections in a vessel with two stents. In the stented sections, more than 40% of the wall surface area is exposed to\n\nlow shear stress. ey eee." }, { - "id": 152235, - "strid": "7cca18eb-ea9b-40ec-a4bf-7721339caa0f", - "image_id": 206426, - "image_name": "21404.png", + "id": 1384, + "strid": "f58c87df-7347-4dc5-88fa-d7c5e1322178", + "image_id": 53, + "image_name": "117061.png", "category_id": 2, "category_name": "Figure", "bbox": [ - 95.457, - 2184.814, - 1919.0700000000002, - 739.2130000000002 + 1979.803, + 3036.499, + 863.972, + 496.82400000000007 ], - "priority": 10, + "priority": 33, "parents": [ - 152225 + 1371 ], - "children": [], - "area": 208555.78999799996, + "children": [ + 1385 + ], + "area": 6011669.829697, "iscrowd": 0, "segmentation": [] }, { - "id": 152236, - "strid": "8610bd7c-9871-4fdc-b109-0be17b78556b", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 3, - "category_name": "Text", + "id": 1385, + "strid": "37609d1a-6f32-4b37-a6f0-692fc0727b6a", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 129.586, - 2962.227, - 1894.283, - 163.13500000000022 + 2018.19, + 3537.043, + 784.4410000000003, + 190.63099999999986 ], - "priority": 11, + "priority": 34, "parents": [ - 152225 + 1384 ], "children": [], - "area": 383863.14802200004, + "area": 7138424.812170001, "iscrowd": 0, "segmentation": [], - "text": "(A) UMAP plot of 124,786 cells in total, annotated into nine major cell types. (B) The T and NK clusters (2,123 cells) were\ndivided into four subgroups, representing CD8T, CD4T, and NK cells. (C) Differential display of //2rb expression (Ig vs. anti-\nPD1 treatment samples) by day in CD8T and CD4T cells. II2rb was used as a marker for T cell activation, differentiating\nCD8+ and CD4+ T cells into effector cells." + "text": "Fig. 10. Wall shear stress distribution in a porcine left coronary ar-\ntery with two stents. Wall shear stress (WSS) below 0.5 Pa is reported\nto correlate with sites of intimal thickening [51]. Such low WSS can be\nseen here to occur mainly in the vicinity of stent struts and at bifurca-\ntions. The left inset shows low and high wall shear stress regions occur-\nring, respectively, at the outer and inner walls of the bifurcation." }, { - "id": 152238, - "strid": "3d34bbf0-3910-4990-a728-28d4cbd134ee", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 3, - "category_name": "Text", + "id": 1386, + "strid": "cb0fe7ce-b4bc-49fe-9127-2a7b6082f68c", + "image_id": 53, + "image_name": "117061.png", + "category_id": 2, + "category_name": "Figure", "bbox": [ - 124.807, - 3161.522, - 1779.145, - 63.248999999999796 + 3014.178, + 2968.568, + 557.2649999999999, + 548.0540000000001 ], - "priority": 12, + "priority": 35, "parents": [ - 152225 + 1371 ], - "children": [], - "area": 394580.076254, + "children": [ + 1387 + ], + "area": 8947792.357104, "iscrowd": 0, - "segmentation": [], - "text": "NK cell activation and Xcl1 overexpression in anti-PD1 treated samples" + "segmentation": [] }, { - "id": 152239, - "strid": "d7e881e4-3a80-4039-baee-a0d2d5adcc79", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 2, - "category_name": "Figure", + "id": 1387, + "strid": "39f6bedc-3000-49c5-ac16-73fb65e5487b", + "image_id": 53, + "image_name": "117061.png", + "category_id": 6, + "category_name": "Caption", "bbox": [ - 142.157, - 3246.59, - 1882.316, - 603.7629999999999 + 2901.727, + 3537.409, + 784.0509999999999, + 187.09400000000005 ], - "priority": 13, + "priority": 36, "parents": [ - 152225 + 1386 ], "children": [], - "area": 461525.49463000003, + "area": 10264595.205343, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "Fig. 11. Distribution of relative vessel wall area exposed to differ-\nent levels of shear stress. Results are shown as percentage of the re-\nspective segment’s surface area in a porcine left coronary artery with two\nstents. Low wall shear stress: <0.5 Pa. Moderate: 0.52.5 Pa. Top: Corresponding reconstructed surface of the arterial\nlumen negative." }, { - "id": 152240, - "strid": "084cb724-57f4-45eb-8228-18e1e927958e", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 3, - "category_name": "Text", + "id": 1388, + "strid": "a5227298-a604-4f34-9d27-7c2356b2fea7", + "image_id": 53, + "image_name": "117061.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 132.31, - 3859.797, - 1891.489, - 166.46399999999994 + 1943.883, + 3776.516, + 248.09199999999987, + 39.914999999999964 ], - "priority": 14, + "priority": 37, "parents": [ - 152225 + 1351 ], - "children": [], - "area": 510689.74107, + "children": [ + 1389 + ], + "area": 7341105.251628, "iscrowd": 0, "segmentation": [], - "text": "(A) Violin plot shows that Prf1 and Xcl1 are overexpressed on anti-PD1 treatment in NK populations. (B) Cell-cell\ninteraction results predicted by CellPhoneDB. Xcl1 expression in NK cells are strongly correlated with Xcr1 expression in\ncDC1 cells. The size of the dot is proportional to the significance, and the color of the dot indicates the mean expression\nof the receptor-ligand complex." + "text": "Conclusions" }, { - "id": 152230, - "strid": "9b0f33cf-873a-4b15-9524-23cd7b422b41", - "image_id": 206426, - "image_name": "21404.png", + "id": 1389, + "strid": "449a8667-796a-4ffd-91ea-27a365b7cedf", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2107.118, - 1127.797, - 1507.9879999999998, - 58.03500000000008 + 1957.789, + 3877.297, + 1727.8060000000003, + 150.13700000000017 ], - "priority": 15, + "priority": 38, "parents": [ - 152225 + 1388 ], "children": [], - "area": 2376401.359046, + "area": 7590929.416333, "iscrowd": 0, "segmentation": [], - "text": "DCs, recruited by NK cells, overexpressed prosaposin (Psap)" + "text": "The method presented herein constitutes a unique tool for accessing WSS in stented arteries. It can be employed to study the effects\nof hemodynamics on vascular biology, to develop stenting strategies that optimize hemodynamics and to design new stents that mini-\n\nmize regions of NIH promoting WSS." }, { - "id": 152229, - "strid": "152bc171-7205-4d19-ada8-8541f1776dcc", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 2, - "category_name": "Figure", + "id": 1390, + "strid": "0c0c8bf5-037f-4a09-9c77-460ad7f593c8", + "image_id": 53, + "image_name": "117061.png", + "category_id": 5, + "category_name": "Section", "bbox": [ - 2113.032, - 1217.504, - 1909.83, - 992.8009999999999 + 1944.758, + 4081.769, + 230.72500000000014, + 41.14799999999968 ], - "priority": 16, + "priority": 39, "parents": [ - 152225 + 1351 ], - "children": [], - "area": 2572624.912128, + "children": [ + 1391 + ], + "area": 7938052.916902, "iscrowd": 0, - "segmentation": [] + "segmentation": [], + "text": "{ay ce) a2) aah" }, { - "id": 152233, - "strid": "dc1dca44-5062-4ad3-95d3-22c6005d2116", - "image_id": 206426, - "image_name": "21404.png", + "id": 1391, + "strid": "8e6580db-39fb-4a2c-9346-871faa70e4b2", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2103.86, - 2247.102, - 1889.864, - 210.29199999999992 + 1957.645, + 4214.618, + 1728.1780000000003, + 94.80199999999968 ], - "priority": 17, + "priority": 40, "parents": [ - 152225 + 1390 ], "children": [], - "area": 4727588.01372, + "area": 8250725.854610001, "iscrowd": 0, "segmentation": [], - "text": "(A) UMAP colored with the annotated DC subtypes. (B) A bar plot showing the proportions of dendritic cell types for each\nsample. The ratio of cDC1 increased substantially on anti-PD1 treatment at the initial days (D12 and D15). Colors for cell\ntypes are consistent with Fig. (A). (C) Expression of known marker genes for each DC subtype. (D) Violin plot shows\noverexpression of Psap on anti-PD1 treatment in cDC1 cells. Psap is an essential molecule for processing apoptotic body\nand presenting lipid antigens in DCs." + "text": "Rikhtegar F, Pacheco F, Wyss C, Stok KS, Ge H, et al. (2013) Compound Ex Vivo and In Silico Method for Hemodynamic Analysis\nof Stented Arteries. PLoS ONE 8(3): e58147. doi:10.1371/journal.pone.0058147" }, { - "id": 152226, - "strid": "48abda0f-f0aa-4fb0-833b-87cd73808ef6", - "image_id": 206426, - "image_name": "21404.png", + "id": 1392, + "strid": "b3cce14d-3dcc-42ab-a6d0-f5c65a56dda1", + "image_id": 53, + "image_name": "117061.png", "category_id": 5, "category_name": "Section", "bbox": [ - 2152.482, - 2548.528, - 314.672, - 53.3159999999998 + 1940.523, + 4362.333, + 799.1560000000002, + 51.29699999999957 ], - "priority": 18, + "priority": 41, "parents": [ - 152242 + 1351 ], "children": [ - 152237, - 152241 + 1393 ], - "area": 5485660.646496, + "area": 8465207.520158999, "iscrowd": 0, "segmentation": [], - "text": "Conclusion" - }, - { - "id": 152237, - "strid": "3730042a-2be1-44f3-97fc-4271512a6ab9", - "image_id": 206426, - "image_name": "21404.png", - "category_id": 2, - "category_name": "Figure", - "bbox": [ - 2165.381, - 2695.142, - 1760.1370000000002, - 1014.3360000000002 - ], - "priority": 19, - "parents": [ - 152226 - ], - "children": [], - "area": 5836009.2791019995, - "iscrowd": 0, - "segmentation": [] + "text": "Acknowledgments and ‘contact details" }, { - "id": 152241, - "strid": "651a0d99-b4b8-4ab8-8cf1-9ccb59474d06", - "image_id": 206426, - "image_name": "21404.png", + "id": 1393, + "strid": "2e137427-2ac6-406f-963a-57668c5673b3", + "image_id": 53, + "image_name": "117061.png", "category_id": 3, "category_name": "Text", "bbox": [ - 2099.914, - 3779.852, - 1894.004, - 196.67700000000013 + 1949.972, + 4466.277, + 1534.865, + 97.19499999999971 ], - "priority": 20, + "priority": 42, "parents": [ - 152226 + 1392 ], "children": [], - "area": 7937364.132728, + "area": 8709115.094244, "iscrowd": 0, "segmentation": [], - "text": "Summary overview of immune cell responses to anti-PD1 treatment.\n\nFrom the differentially expressed genes analysis of single-cell transcriptome data, we showed that T cells and NK were\nactivated on ICB treatment. Specifically, NK cells overexpressed Xcl1 and recruited cDC1. We hypothesize that the antigen-\npresenting ability of DC was enhanced via increased Psap expression. Validation experiments are currently in progress." + "text": "The authors thank the Swiss Federal Commission for Technology and Innovation (CTI) for partially funding this\n\nptoject through the EnOp project, grant 9921.1." }, { - "id": 77939, - "strid": "fbe0c255-59cf-41cc-a6b2-a18698e60dc8", - "image_id": 203540, - "image_name": "120439.png", + "id": 1394, + "strid": "5f8f2f12-75db-4334-ab53-5199910fdece", + "image_id": 54, + "image_name": "117074.png", "category_id": 9, "category_name": "Root", "bbox": [ - 542.23, - 202.8, - 287.17999999999995, - 325.98999999999995 + 357.3, + 16.13, + 160.91000000000003, + 127.39000000000001 ], "priority": -1, "parents": [], "children": [ - 77925, - 77927, - 77932, - 77938, - 77929, - 77923, - 77933, - 77924, - 77935 + 1406, + 1396, + 1395, + 1411, + 1413, + 1403, + 1397, + 1415 ], - "area": 109964.244, + "area": 5763.249, "iscrowd": 0, "segmentation": [] }, { - "id": 77923, - "strid": "a6f01d66-5d8b-4cfa-bc56-321a90c8a8fd", - "image_id": 203540, - "image_name": "120439.png", + "id": 1395, + "strid": "bee92592-5eb4-42ba-ae77-c3b6d7dee428", + "image_id": 54, + "image_name": "117074.png", "category_id": 1, "category_name": "Title", "bbox": [ - 1147.462, - 223.966, - 1970.498, - 363.644 + 563.288, + 144.154, + 2421.824, + 336.056 ], "priority": 1, "parents": [ - 77939 + 1394 ], "children": [], - "area": 256992.474292, + "area": 81200.218352, "iscrowd": 0, "segmentation": [], - "text": "QF Multiplexed protein\nMRM assay panel for high throughput\n\ntoxicological assessment in rat liver samples" + "text": "Using Weakly Conserved Motifs Hidden~tn\nSecretion Signals to