cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11317760.v5
title: TGD POInT datasets and models

description: Datasets for analysis of the teleost-specific genome duplication (TGD) using POInT (Polyploidy Orthology Inference Tool; https://github.com/gconant0/POInT). Eight genome order files are included (*POInT_gene_orders.txt) corresponding to the eight genomes studied. An optimized ancestral genome order (TGD_OptOrder.txt), WGD gene loss model (WGD_fix_biasconverg_singlerate_model.txt) and assumed phylogeny (TGD_Topo.tre) are also included. All of these files are POInT inputs. POInT's optimal orthology inferences for each duplicated locus is also provided (Optimal_orthology_inferences.txt).Additionally, I provide the conditional probabilities of all possible state transitions along each branch at every duplicated locus (TGD_WGDbcnbnf_OptOrder_condprobs.xlsx). Finally, I provide a list of all inferred ohnolog pairs in zebrafish (AllDrerio_WGD_duplpairs_wtandem_merged.txt), a list which includes a number of ohnolog pairs omitted from the main dataset because homologs of the pair were lacking in at least one other teleost genome. The corresponding list of single-copy genes is AllDrerio_WGD_singls_WTANDEMS.txt.All four supplemental figures (Supplemental Figure 1-4) from the manuscript are included as fully scalable PDF files. Finally, the underlying data for Figure 2-4 are provided as MS Excel files. (Figure 1 can be constructed from the posterior probability file provided).
DOI: 10.6084/m9.figshare.11317625
title: Metadata record for: The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies

description: This dataset contains key characteristics about the data described in the Data Descriptor The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11317760.v4
title: TGD POInT datasets and models

description: Datasets for analysis of the teleost-specific genome duplication (TGD) using POInT (Polyploidy Orthology Inference Tool; https://github.com/gconant0/POInT). Eight genome order files are included (*POInT_gene_orders.txt) corresponding to the eight genomes studied. An optimized ancestral genome order (TGD_OptOrder.txt), WGD gene loss model (WGD_fix_biasconverg_singlerate_model.txt) and assumed phylogeny (TGD_Topo.tre) are also included. All of these files are POInT inputs. POInT's optimal orthology inferences for each duplicated locus is also provided (Optimal_orthology_inferences.txt).Additionally, I provide the conditional probabilities of all possible state transitions along each branch at every duplicated locus (TGD_WGDbcnbnf_OptOrder_condprobs.xlsx). Finally, I provide a list of all inferred ohnolog pairs in zebrafish (AllDrerio_WGD_duplpairs_wtandem_merged.txt), a list which includes a number of ohnolog pairs omitted from the main dataset because homologs of the pair were lacking in at least one other teleost genome. The corresponding list of single-copy genes is AllDrerio_WGD_singls_WTANDEMS.txt.Finally, all four supplemental figures (Supplemental Figure 1-4) from the manuscript are included as fully scalable PDF files.
DOI: 10.6084/m9.figshare.11317601
title: Database process evaluation

description: Database of the process evaluation questionnaire
DOI: 10.6084/m9.figshare.11317475
title: Supplementary Material for: Management of Gastroesophageal Reflux Disease in Asian Countries: Results of a Questionnaire Survey

description: <b><i>Introduction:</i></b> The Asia-Pacific consensus on the management of gastroesophageal reflux disease (GERD) and the GERD treatment guidelines of 2015 drawn up by the Japanese Society of Gastroenterology were proposed, and GERD management in Asian regions was assumed to be performed based on these consensuses. In this environment, the current status of GERD management in clinical practice among Asian regions is less well-known. <b><i>Objective:</i></b> This questionnaire-based consensus survey was performed to clarify the current status of management of GERD in clinical practice in Asian regions. <b><i>Methods:</i></b> A questionnaire related to management of GERD was distributed to members of the International Gastroenterology Consensus Symposium Study Group. We analyzed the questionnaire responses and compared the results among groups. <b><i>Results:</i></b> The frequencies of erosive GERD (ERD), non-ERD, uninvestigated GERD, and Barrett’s esophagus varied significantly among Asian countries. The most important factor in diagnosing GERD was the presence of symptoms in all countries. A proton pump inhibitor was the most commonly prescribed drug to treat GERD in all countries. Endoscopic surveillance for GERD was performed regularly. <b><i>Conclusion:</i></b> This questionnaire survey revealed the current status of management of GERD in clinical practice in various Asian countries.
DOI: 10.6084/m9.figshare.11317625.v2
title: Metadata record for: The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies

description: This dataset contains key characteristics about the data described in the Data Descriptor The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11317625.v1
title: Metadata record for: The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies

description: This dataset contains key characteristics about the data described in the Data Descriptor The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11317250
title: table S1.pdf

description: Here we present surface seawater iodine isotopes data from the central English Channel in December 2010 as part of the 2010/2011 Antarctica two-ship expedition
DOI: 10.6084/m9.figshare.11317601.v1
title: Untitled Item

description: Database of the process evaluation questionnaire
DOI: 10.6084/m9.figshare.11317175
title: bacteria_clean_data

description: including cleandata of bacteria and metadata
DOI: 10.6084/m9.figshare.11317169
title: EASE2020-Evaluation Results

description: It presents the project list and evluation results of study "Take care of the assumptions of machine learning methods: a framework towards predictive CI/CD".
DOI: 10.6084/m9.figshare.11317172
title: Quantification_of_U__Th_and_Specific_Radionuclides.xlsx

description: Data for ICP-MS and Gamma Spectroscopy for U, Th and specific radionuclides in coal samples from 3 South African provinces
DOI: 10.6084/m9.figshare.11317169.v1
title: EASE2020-Evaluation Results

description: It presents the project list and evluation results of study "Take care of the assumptions of machine learning methods: a framework towards predictive CI/CD".
DOI: 10.6084/m9.figshare.11317175.v1
title: bacteria_clean_data

description: including cleandata of bacteria and metadata
DOI: 10.6084/m9.figshare.11317172.v1
title: Quantification_of_U__Th_and_Specific_Radionuclides.xlsx

description: Data for ICP-MS and Gamma Spectroscopy for U, Th and specific radionuclides in coal samples from 3 South African provinces
DOI: 10.6084/m9.figshare.11317097
title: Supplementary Material for: Computer-Aided Diagnosis Systems in Diagnosing Malignant Thyroid Nodules on Ultrasonography: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Computer-aided diagnosis (CAD) systems are being applied to the ultrasonographic diagnosis of malignant thyroid nodules, but it remains controversial whether the systems add any accuracy for radiologists. <b><i>Objective:</i></b> To determine the accuracy of CAD systems in diagnosing malignant thyroid nodules. <b><i>Methods:</i></b> PubMed, EMBASE, and the Cochrane Library were searched for studies on the diagnostic performance of CAD systems. The diagnostic performance was assessed by pooled sensitivity and specificity, and their accuracy was compared with that of radiologists. The present systematic review was registered in PROSPERO (CRD42019134460). <b><i>Results:</i></b> Nineteen studies with 4,781 thyroid nodules were included. Both the classic machine learning- and the deep learning-based CAD system had good performance in diagnosing malignant thyroid nodules (classic machine learning: sensitivity 0.86 [95% CI 0.79–0.92], specificity 0.85 [95% CI 0.77–0.91], diagnostic odds ratio (DOR) 37.41 [95% CI 24.91–56.20]; deep learning: sensitivity 0.89 [95% CI 0.81–0.93], specificity 0.84 [95% CI 0.75–0.90], DOR 40.87 [95% CI 18.13–92.13]). The diagnostic performance of the deep learning-based CAD system was comparable to that of the radiologists (sensitivity 0.87 [95% CI 0.78–0.93] vs. 0.87 [95% CI 0.85–0.89], specificity 0.85 [95% CI 0.76–0.91] vs. 0.87 [95% CI 0.81–0.91], DOR 40.12 [95% CI 15.58–103.33] vs. DOR 44.88 [95% CI 30.71–65.57]). <b><i>Conclusions:</i></b> The CAD systems demonstrated good performance in diagnosing malignant thyroid nodules. However, experienced radiologists may still have an advantage over CAD systems during real-time diagnosis.
DOI: 10.6084/m9.figshare.11317118
title: Supplementary Material for: Chemotherapy in Resected Neuroendocrine Carcinomas of the Digestive Tract: A National Study from the French Group of Endocrine Tumours

description: <b><i>Background:</i></b> Neuroendocrine carcinomas (NECs) of the digestive tract are rare and aggressive tumours. In localised disease the treatment is surgery. Based on expert consensus, international guidelines recommend the administration of adjuvant chemotherapy combining etoposide and platinum derivatives, justified by the high risk of metastatic relapse. However, no clinical study has proven the benefit of neoadjuvant or adjuvant chemotherapy. <b><i>Objectives:</i></b> We aimed to evaluate the effect of neoadjuvant +/– adjuvant and adjuvant therapy in this indication. <b><i>Methods:</i></b> We performed a retrospective observational French study to evaluate overall survival (OS) and disease-free survival (DFS), prognostic factors for survival, and chemotherapy toxicity. <b><i>Results:</i></b> Seventy-three patients had surgical resection of a localised digestive NEC between January 1, 2000 and December 31, 2016. The majority of patients presented colorectal (35%) tumours and the median Ki-67 value was 70%. Forty-three patients received chemotherapy, either perioperative (neoadjuvant +/– adjuvant) or adjuvant. The median OS and DFS for the whole population was 24 and 9 months, respectively. The median OS and DFS for patients receiving chemotherapy was 62 and 13 months, respectively. Positive postoperative node status and Ki-67 ≥80% had a negative prognostic impact on OS and DFS. Administration of chemotherapy had a positive prognostic impact on OS and DFS. Sixteen grade 3/4 toxicities were reported without toxic death. <b><i>Conclusions:</i></b> Our results suggest a positive effect on survival of chemotherapy in resected digestive NECs, but further studies are needed to confirm these results.
DOI: 10.6084/m9.figshare.11317097.v1
title: Supplementary Material for: Computer-Aided Diagnosis Systems in Diagnosing Malignant Thyroid Nodules on Ultrasonography: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Computer-aided diagnosis (CAD) systems are being applied to the ultrasonographic diagnosis of malignant thyroid nodules, but it remains controversial whether the systems add any accuracy for radiologists. <b><i>Objective:</i></b> To determine the accuracy of CAD systems in diagnosing malignant thyroid nodules. <b><i>Methods:</i></b> PubMed, EMBASE, and the Cochrane Library were searched for studies on the diagnostic performance of CAD systems. The diagnostic performance was assessed by pooled sensitivity and specificity, and their accuracy was compared with that of radiologists. The present systematic review was registered in PROSPERO (CRD42019134460). <b><i>Results:</i></b> Nineteen studies with 4,781 thyroid nodules were included. Both the classic machine learning- and the deep learning-based CAD system had good performance in diagnosing malignant thyroid nodules (classic machine learning: sensitivity 0.86 [95% CI 0.79–0.92], specificity 0.85 [95% CI 0.77–0.91], diagnostic odds ratio (DOR) 37.41 [95% CI 24.91–56.20]; deep learning: sensitivity 0.89 [95% CI 0.81–0.93], specificity 0.84 [95% CI 0.75–0.90], DOR 40.87 [95% CI 18.13–92.13]). The diagnostic performance of the deep learning-based CAD system was comparable to that of the radiologists (sensitivity 0.87 [95% CI 0.78–0.93] vs. 0.87 [95% CI 0.85–0.89], specificity 0.85 [95% CI 0.76–0.91] vs. 0.87 [95% CI 0.81–0.91], DOR 40.12 [95% CI 15.58–103.33] vs. DOR 44.88 [95% CI 30.71–65.57]). <b><i>Conclusions:</i></b> The CAD systems demonstrated good performance in diagnosing malignant thyroid nodules. However, experienced radiologists may still have an advantage over CAD systems during real-time diagnosis.
DOI: 10.6084/m9.figshare.11317118.v1
title: Supplementary Material for: Chemotherapy in Resected Neuroendocrine Carcinomas of the Digestive Tract: A National Study from the French Group of Endocrine Tumours

description: <b><i>Background:</i></b> Neuroendocrine carcinomas (NECs) of the digestive tract are rare and aggressive tumours. In localised disease the treatment is surgery. Based on expert consensus, international guidelines recommend the administration of adjuvant chemotherapy combining etoposide and platinum derivatives, justified by the high risk of metastatic relapse. However, no clinical study has proven the benefit of neoadjuvant or adjuvant chemotherapy. <b><i>Objectives:</i></b> We aimed to evaluate the effect of neoadjuvant +/– adjuvant and adjuvant therapy in this indication. <b><i>Methods:</i></b> We performed a retrospective observational French study to evaluate overall survival (OS) and disease-free survival (DFS), prognostic factors for survival, and chemotherapy toxicity. <b><i>Results:</i></b> Seventy-three patients had surgical resection of a localised digestive NEC between January 1, 2000 and December 31, 2016. The majority of patients presented colorectal (35%) tumours and the median Ki-67 value was 70%. Forty-three patients received chemotherapy, either perioperative (neoadjuvant +/– adjuvant) or adjuvant. The median OS and DFS for the whole population was 24 and 9 months, respectively. The median OS and DFS for patients receiving chemotherapy was 62 and 13 months, respectively. Positive postoperative node status and Ki-67 ≥80% had a negative prognostic impact on OS and DFS. Administration of chemotherapy had a positive prognostic impact on OS and DFS. Sixteen grade 3/4 toxicities were reported without toxic death. <b><i>Conclusions:</i></b> Our results suggest a positive effect on survival of chemotherapy in resected digestive NECs, but further studies are needed to confirm these results.
DOI: 10.6084/m9.figshare.11317085
title: Supplementary Material for: Rapamycin Treatment Reduces Acute Myocarditis Induced by <b><i>Trypanosoma cruzi</i></b> Infection

description: Chagas disease affects millions of people mainly in Latin America and is a protozoan illness caused by the parasite <i>Trypanosoma cruzi</i>. Chagasic cardiomyopathy is the leading cause of mortality of infected patients, due to compromised electrical and mechanical cardiac function induced by tissue remodeling, especially fibrosis, and lymphocytic infiltration. Some cellular biochemical pathways can be protective to the heart, and we tested if the in vivo activation of the autophagic machinery by rapamycin could reduce parasite-induced myocarditis. Regarding the expression of LC3, an autophagy marker, we observed its upregulation in the cardiac tissue of infected untreated mice. However, after rapamycin treatment, an autophagy inducer, infected mice showed reduced electrical cardiac dysfunctions, myocarditis, cardiac damage, and reduced production of pro-inflammatory cytokines by the heart. On the other hand, the parasite’s life cycle was not affected, and we observed no modulations in cardiac tissue or blood parasitemia. Our data indicate that, at least partially, autophagy induction controls inflammation in the heart¸ illustrating the complexity of the pathways that concur to the development of the infection.
DOI: 10.6084/m9.figshare.11317094
title: fungi_CleanData.7z

description: including fungal community
DOI: 10.6084/m9.figshare.11317073
title: RAgrilus2019.xlsx

description: Second year of Agrilus spp. trapping data in course of the development of a new trap design.
DOI: 10.6084/m9.figshare.11317070
title: Supplementary Material for: Additive Value of Transrectal Systematic Ventral Biopsies in Combination with Magnet Resonance Imaging/Ultrasound Fusion-Guided Biopsy in Patients with 3 or More Negative Prostate Biopsies

description: <b><i>Introduction:</i></b> Patients with consistent suspicion for prostate cancer (PCa) and multiple negative prebiopsies prior to multiparametric magnetic resonance imaging (mpMRI) are still frequently evaluated for an image-guided biopsy and are reported with heterogeneous detection rates. The inclusion of a systematic biopsy (SB) is also still recommended with predominant sampling within the posterior/peripheral zone of the prostate. The aim of this study was (I) to evaluate PCa detection rates using a modified 10 core SB template including anterior biopsies in combination with mpMRI/ultrasound fusion-guided targeted biopsy (TB) in patients with 3 or more negative prebiopsies and (II) to compare mpMRI index lesion localization with histologically confirmed locali­zation from associated prostatectomy samples. <b><i>Methods:</i></b> Overall 1,337 consecutive patients underwent sensor-based registration TB of the prostate and a subsequent 10-core SB between January 2012 and December 2015 at our institution. For this study, 101 patients with ≥3 negative prebiopsies and prostate imaging – reporting data system lesions ≥3 were pooled prospectively and underwent TB and a modified SB including 2 ventral (anterior) biopsies. Detection rates were estimated for the modified SB, TB, and its combination. A subgroup analysis of 35 patients undergoing prostatectomy was performed by a head-to-head comparison of mpMRI index lesion and histologically confirmed PCa index lesion localization. <b><i>Results:</i></b> The overall detection rate for PCa was 54.5%. The combination of TB and SB detected 14 (25.4%) more cases missed by TB alone (<i>p</i> &lt; 0.001) and 7 (12.7%) more cases missed by SB alone (<i>p</i> = 0.016), respectively. A postoperative Gleason upgrade was seen in 12/35 (34.3%) cases within the TB group and in 14/35 (40.0%) in the SB group, respectively. The subgroup analysis showed a predominant location of PCa index lesions anteriorly at the level of the midgland. The MRI detection rate of the anteriorly located index lesions was 70.4% (15/21 cases) with a clinically significant Gleason score (≥3 + 4 = 7a [International Society of Urological Pathology grade 2]) in 80.9%. Interestingly a modified SB template detected 90.5% (19/21) of the anteriorly located index lesions. <b><i>Conclusion:</i></b> Our data suggest that in patients with multiple prebiopsies PCa seems to be predominantly located anteriorly. We suggest the general integration of anterior biopsies despite TB in repeat biopsy patients.
DOI: 10.6084/m9.figshare.11317073.v1
title: RAgrilus2019.xlsx

description: Second year of Agrilus spp. trapping data in course of the development of a new trap design.
DOI: 10.6084/m9.figshare.11316875
title: Spreadsheet of confusion matrices (Microsoft Excel)

description: Excel spreadsheet which only contains numeric data from a set of confusion matrices (one sheet per matrix).<br>It is the same quantitative data stored in a field of a table in the database. Only is provided as a complement to the database in order to access to the quantitative data in a more convenient format.<br><br>
DOI: 10.6084/m9.figshare.11316875.v1
title: Excel spreadsheet of confusion matrices

description: Excel spreadsheet which only contains numeric data from a set of confusion matrices (one sheet per matrix).<br>It is the same quantitative data stored in a field of a table in the database. Only is provided as a complement to the database in order to access to the quantitative data in a more convenient format.<br><br>
DOI: 10.6084/m9.figshare.11316815
title: Supplementary Material for: True Arterial Stiffness Does Not Change between Dialysis Sessions during 1 Week in Outpatients on Intermitted Hemodialysis

description: <b><i>Introduction:</i></b> End-stage renal disease (ESRD) is associated with exponentially elevated cardiovascular mortality. Arterial stiffness (AS) – usually expressed with pulse wave velocity (PWV) – is an established independent predictor of cardiovascular risk beyond the traditional risk factors. Higher PWV values are frequently observed in patients with ESRD. Due to the intrinsic physiologic relationship between PWV and prevailing arterial pressure, PWV can change without relevant changes in the arterial wall structure, and thus an individual pressure-independent expression of PWV is essential. <b><i>Methods:</i></b> The study is a single-center observational study. Repeated measurements of blood pressure (BP) and pulse wave analysis were performed during each dialysis session of 1 week. Aortic PWV was then adjusted to 120 mm Hg central systolic BP (PWV120) based on individually determined relationship. PWV120 values were compared between single sessions. Calculation of the PWV120 was performed retrospectively. <b><i>Results:</i></b> Fifty-four subjects were included, 61.1% of whom were male. The median age was 75.5 years, and median dialysis vintage was 33.1 months. Mean systolic/diastolic BP was 121.4/70.5 mm Hg, and the median heart rate was 64.6 beats/min. Mean PWV was 10.9 m/s, and mean PWV120 was 11.3 m/s. PWV120 did not change across single dialysis session during 1 week, while systolic, diastolic BP, PWV, and ultrafiltration volume differed significantly. <b><i>Discussion/Conclusions:</i></b> Our data suggest that true AS does not change in the short-term course in dialysis patients. The observed changes in PWV are rather associated with BP change due to intrinsic pressure dependence. Our analytical approach represents a novel method for this purpose, which is easy in performance and also applicable for large interventional trials and clinical practice.
DOI: 10.6084/m9.figshare.11316875.v2
title: Excel spreadsheet of confusion matrices

description: Excel spreadsheet which only contains numeric data from a set of confusion matrices (one sheet per matrix).<br>It is the same quantitative data stored in a field of a table in the database. Only is provided as a complement to the database in order to access to the quantitative data in a more convenient format.<br><br>
DOI: 10.6084/m9.figshare.11316758
title: MECP2 Rettbase genetic variant data in CSV

description: MECP2 genetic variant data from Rettbase in CSV format.<br>FAIR machine-readable metadata is available at:http://purl.org/biosemantics-lumc/rettbase/fdp<br>
DOI: 10.6084/m9.figshare.11316752
title: MECP2 MRD genetic variant data in CSV

description: MECP2 genetic variant data from the Maastricht Rett database (MRD) in CSV format.<br>FAIR machine-readable metadata is available at:http://purl.org/biosemantics-lumc/rettbase/fdp<br>