cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12416360
title: 02_N250_T20_ICC0.Rdata

description: example data file<br>
DOI: 10.6084/m9.figshare.12416363.v1
title: Raw data.dta

description: The dependent variable of interest was self-medication of children. Independent variables included 15 measures of characteristics at the children, primary caregivers and household levels.
DOI: 10.6084/m9.figshare.12416366.v1
title: 03_N250_T20_ICC050.Rdata

description: example data file<br>
DOI: 10.6084/m9.figshare.12416369
title: Supplementary Material for: Prediction of Neurodevelopmental Impairment in Congenital Cytomegalovirus Infection by Early Postnatal Magnetic Resonance Imaging

description: <b><i>Introduction:</i></b> Congenital cytomegalovirus infection (CCMVI) may result in neurodevelopmental impairments (NDIs) such as hearing loss, developmental delay, epilepsy, and cerebral palsy. We aimed to investigate the potential for brain magnetic resonance imaging (MRI) to predict NDI in patients with CCMVI. <b><i>Methods:</i></b> We studied infants with CCMVI who were referred to our hospital from April 2010 to October 2018 and underwent a brain MRI within 3 months since birth. We screened for 6 classic presentations of CCMVI including ventriculomegaly, periventricular cysts, hippocampal dysplasia, cerebellar hypoplasia, migration disorders, and white matter abnormalities. Images were interpreted by a blinded pediatric radiologist. NDI was defined as having a developmental quotient &lt;80, hearing dysfunction, blindness, or epilepsy requiring anti-epileptic drugs at approximately 18 months of corrected age. <b><i>Results:</i></b> The study involved 42 infants with CCMVI (median gestational age 38 weeks, birthweight 2,516 g). At least one abnormal finding was detected in 28 (67%) infants. Abnormal findings consisted of 3 cerebellar hypoplasia (7%), 7 migration disorders (17%), 26 white matter abnormalities (62%), 12 periventricular cysts (28%), 1 hippocampal dysplasia (2%), and 20 ventriculomegaly (48%). Abnormal findings were significantly more prevalent in infants with clinical symptoms (21/24, 91%) than in those without (7/19, 37%, <i>p</i> &lt; 0.01). For NDI prediction, having ≥2 of ventriculomegaly, periventricular cysts, and white matter abnormality produced the highest Youden index values (0.78). <b><i>Conclusion:</i></b> Infants with CCMVI with at least 2 of the abovementioned specific brain image abnormalities may be at high risk of developing NDI.
DOI: 10.6084/m9.figshare.12416351
title: 01_N1_T250.Rdata

description: example data set<br>
DOI: 10.6084/m9.figshare.12416360.v1
title: 02_N250_T20_ICC0.Rdata

description: example data file<br>
DOI: 10.6084/m9.figshare.12416339
title: Supplementary Material for: How Much Liver Tissue Is Required for Sufficient Histological Staging in Patients with Primary Biliary Cholangitis?

description: <b><i>Introduction:</i></b> Histological alterations in primary biliary cholangitis (PBC) are heterogeneously distributed throughout the liver. Thus, the quality of histological staging is probably dependent on the available amount of liver tissue. The goals of this study were to test this hypothesis and to define biopsy conditions for obtaining sufficient tissue. <b><i>Methods:</i></b> In this retrospective analysis, we investigated 34 patient cases who fulfilled the criteria of the European Association for the Study of the Liver (EASL) for PBC and underwent a mini-laparoscopic liver biopsy between 2011 and 2018 using 16 or 18G needles. For histological assessment of fibrosis, we used the Ishak score, and the amount of tissue was measured by the number of portal fields. Histological staging was compared with the macroscopic mini-laparoscopic fibrosis score (MLFS), and non-invasive liver stiffness measurements using acoustic radiation force impulse (ARFI) imaging and the FIB-4 score. <b><i>Results:</i></b> Biopsy was successful in 33 of 34 patients (97%). Fibrosis assessment by MLFS and ARFI correlated strongly with each other (<i>r</i> = 0.7088, <i>p</i> = 0.000017). However, the correlation of both methods with the histological staging was weaker (MLFS vs. histology: <i>r</i> = 0.4231, <i>p</i> = 0.0142; ARFI vs. histology: <i>r</i> = 0.3564, <i>p</i> = 0.0577). The correlation of ARFI and MLFS with the histological staging was better in the subgroup of biopsies with at least 10 portal fields (= SG<sub>≥10PF</sub>) (MLFS vs. histology: <i>r</i> = 0.6369, <i>p</i> = 0.006; ARFI vs. histology: <i>r</i> = 0.7538, <i>p</i> = 0.0012). FIB-4 correlated weakly with the histological staging, which was statistically not significant (all samples: <i>r</i> = 0.2693, <i>p</i> = 0.1296; SG<sub>≥10PF</sub>: <i>r</i> = 0.2244, <i>p</i> = 0.3866). The number of portal fields correlated well with the length of the samples (<i>r</i> = 0.6436, <i>p</i> = 0.00012). The probability to attain at least 10 portal fields depended on the needle diameter and number of samples (1 × 16G or 18G [<i>n</i> = 10]: 30.0%; 2 × 18G [<i>n</i> = 15]: 53.3%; 2 × 16G [<i>n</i> = 5]: 100%; <i>p</i> = 0.0414). <b><i>Conclusion:</i></b> ARFI and MLFS are probably well suited for the assessment of liver fibrosis in patients with PBC. A minimum of 10 portal fields could improve the histological assessment in PBC and can probably be achieved by obtaining two 16G biopsies.
DOI: 10.6084/m9.figshare.12416264
title: Supplementary Material for: Physical Activity and Outcomes in Colorectal Surgery: A Pilot Prospective Cohort Study

description: <b><i>Background:</i></b> Mobilization after surgery is recommended to reduce the risk of adverse effects and to improve recovery. The aim of this study was to examine the associations between perioperative physical activity and postoperative outcomes in colorectal surgery. <b><i>Methods:</i></b> The daily number of footsteps was recorded from preoperative day 5 to postoperative day 3 in a prospective cohort of patients using wrist accelerometers. Timed Up and Go Test (TUGT), 6 Min Walking Test (6MWT), and peak expiratory flow (PEF) were assessed preoperatively. ROC curves were used to assess the performance of physical activity as a diagnostic test of complications and prolonged length of stay (LOS) of more than 5 days. <b><i>Results:</i></b> A total of 50 patients were included. Patients with complications were significantly older (67 years) than those without complications (53 years, <i>p</i> = 0.020). PEF was significantly lower in the group with complications (mean flow 294.3 vs. 363.6 L/min, <i>p</i> = 0.038) while there was no difference between groups for the other two tests (TUGT and 6MWT). The tests had no capacity to discriminate the occurrence of complications and prolonged LOS, except the 6MWT for LOS (AUC = 0.746, <i>p</i> = 0.004, 95% CI: 0.604–0.889). There was no difference in the mean number of preoperative footsteps, but patients with complications walked significantly less postoperatively (mean daily footsteps 1,101 vs. 1,243, <i>p</i> = 0.018). <b><i>Conclusions:</i></b><i></i>Colorectal surgery patients with complications were elderly, had decreased PEF, and walked less postoperatively. The 6MWT could be used preoperatively to discriminate patients with potentially increased LOS and foster mobilisation strategies.
DOI: 10.6084/m9.figshare.12416339.v1
title: Supplementary Material for: How Much Liver Tissue Is Required for Sufficient Histological Staging in Patients with Primary Biliary Cholangitis?

description: <b><i>Introduction:</i></b> Histological alterations in primary biliary cholangitis (PBC) are heterogeneously distributed throughout the liver. Thus, the quality of histological staging is probably dependent on the available amount of liver tissue. The goals of this study were to test this hypothesis and to define biopsy conditions for obtaining sufficient tissue. <b><i>Methods:</i></b> In this retrospective analysis, we investigated 34 patient cases who fulfilled the criteria of the European Association for the Study of the Liver (EASL) for PBC and underwent a mini-laparoscopic liver biopsy between 2011 and 2018 using 16 or 18G needles. For histological assessment of fibrosis, we used the Ishak score, and the amount of tissue was measured by the number of portal fields. Histological staging was compared with the macroscopic mini-laparoscopic fibrosis score (MLFS), and non-invasive liver stiffness measurements using acoustic radiation force impulse (ARFI) imaging and the FIB-4 score. <b><i>Results:</i></b> Biopsy was successful in 33 of 34 patients (97%). Fibrosis assessment by MLFS and ARFI correlated strongly with each other (<i>r</i> = 0.7088, <i>p</i> = 0.000017). However, the correlation of both methods with the histological staging was weaker (MLFS vs. histology: <i>r</i> = 0.4231, <i>p</i> = 0.0142; ARFI vs. histology: <i>r</i> = 0.3564, <i>p</i> = 0.0577). The correlation of ARFI and MLFS with the histological staging was better in the subgroup of biopsies with at least 10 portal fields (= SG<sub>≥10PF</sub>) (MLFS vs. histology: <i>r</i> = 0.6369, <i>p</i> = 0.006; ARFI vs. histology: <i>r</i> = 0.7538, <i>p</i> = 0.0012). FIB-4 correlated weakly with the histological staging, which was statistically not significant (all samples: <i>r</i> = 0.2693, <i>p</i> = 0.1296; SG<sub>≥10PF</sub>: <i>r</i> = 0.2244, <i>p</i> = 0.3866). The number of portal fields correlated well with the length of the samples (<i>r</i> = 0.6436, <i>p</i> = 0.00012). The probability to attain at least 10 portal fields depended on the needle diameter and number of samples (1 × 16G or 18G [<i>n</i> = 10]: 30.0%; 2 × 18G [<i>n</i> = 15]: 53.3%; 2 × 16G [<i>n</i> = 5]: 100%; <i>p</i> = 0.0414). <b><i>Conclusion:</i></b> ARFI and MLFS are probably well suited for the assessment of liver fibrosis in patients with PBC. A minimum of 10 portal fields could improve the histological assessment in PBC and can probably be achieved by obtaining two 16G biopsies.
DOI: 10.21954/ou.rd.12416222
title: iNaturalist participation data for young volunteers

description: This dataset includes anonymised data of contribution and participation metrics for iNaturalist young volunteers
DOI: 10.6084/m9.figshare.12416225
title: Supplementary Material for: Low Back Pain and Sacroiliitis on Cross-Sectional Abdominal Imaging for Axial Spondyloarthritis Diagnosis in Inflammatory Bowel Diseases

description: <b><i>Background:</i></b> Joint damage is the most frequent extraintestinal manifestation in inflammatory bowel disease (IBD). <b><i>Aims:</i></b> The aim of the study was to assess the value of low back pain (LBP) associated with sacroiliitis on abdominal imaging for the diagnosis of spondyloarthritis (SpA) in IBD. <b><i>Methods:</i></b> We used a questionnaire assessing rheumatological symptoms for all patients with abdominal computed tomography (CT) and magnetic resonance enterography (MRE). Sacroiliitis was assessed on available CT and MRE. Patients were classified as axial SpA according to the Assessment of SpondyloArthritis International Society criteria. <b><i>Results:</i></b> Fifty-one patients completed the questionnaire and performed both exams. LBP was present in 27 patients (52.9%), and 10 (19.6%) had an inflammatory component. Sacroiliitis was reported in 12 patients (23.5%), and 6 of them suffered from LBP. Among the 20 patients referred to the rheumatologist, 11 patients suffered from LBP. One patient was HLA-B27 positive and presented sacroiliitis. For the last 10 patients, none of them had a sacroiliitis, and 2 patients were negative for HLA-B27. <b><i>Conclusion:</i></b> An axial SpA has been diagnosed in 11.8% of IBD patients undergoing cross-sectional imaging, whereas one-fifth had inflammatory LBP, and sacroiliitis was observed in one-quarter of them. To optimize the diagnosis of axial SpA, HLA-B27 testing might be required for patients with both IBD and LBP, but this will require further investigation before its implementation in routine practice.
DOI: 10.6084/m9.figshare.12416246
title: Supplementary Material for: Predictive Value of Endobronchial Ultrasound Strain Elastography in Mediastinal Lymph Node Staging: The E-Predict Multicenter Study Results

description: <b><i>Background:</i></b> Systematic assessment of lymph node status by endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is indicated in (suspected) lung cancer. Sampling is herein guided by nodal size and FDG-PET characteristics. Ultrasound strain elastography (SE) might further improve risk stratification. By imaging tissue deformation over time, SE computes relative tissue strain. In several tissues, a lower strain (deformation) has been associated with a higher likelihood of malignancy. <b><i>Objectives:</i></b> To assess if EBUS-SE can independently help predict malignancy, and when combined with size and FDG uptake information. <b><i>Methods:</i></b> This multicenter (<i>n</i> = 5 centers) prospective trial included patients with suspected or proven lung cancer using a standardized measurement protocol. Cytopathology combined with surgery or follow-up imaging (&gt;6 months) were used as reference standard. <b><i>Results:</i></b> Between June 2016 and July 2018, 327 patients and 525 lymph nodes were included (mean size 12.3 mm, malignancy prevalence 0.48). EBUS-SE had an overall AUC of 0.77. A mean strain &lt;115 (range 0–255) showed 90% sensitivity, 43% specificity, 60% positive predictive value, and 82% negative predictive value. Combining EBUS-SE (&lt;115) with size (&lt;8 mm) and FDG-PET information into a risk stratification algorithm increased the accuracy. Combining size and SE showed that the 48% a priori chance of malignancy changed to 11 and 70% in double negative or positive nodes, respectively. In the subset where FDG-PET was available (<i>n</i> = 370), triple negative and positive nodes went from a 42% a priori chance of malignancy to 9 and 73%, respectively. <b><i>Conclusions:</i></b> EBUS-SE can help predict lymph node malignancy and may be useful for risk stratification when combined with size and PET information.
DOI: 10.21954/ou.rd.12416222.v1
title: iNaturalist participation data for young volunteers

description: This dataset includes anonymised data of contribution and participation metrics for iNaturalist young volunteers
DOI: 10.6084/m9.figshare.12416084
title: Supplementary Material for: Acute Kidney Injury Caused by TAFRO Syndrome in a Chinese Patient: Efficacy of Long-Term Corticosteroids Combined with Bortezomib and Cyclophosphamide

description: <b><i>Introduction:</i></b> Thrombocytopenia, ascites, myelofibrosis, renal dysfunction, and organomegaly (TAFRO) syndrome is a newly recognized and rare clinical subtype of Castleman disease. Renal involvement in TAFRO syndrome usually presents with mild proteinuria, microscopic hematuria, and acute renal injury requiring temporary renal replacement. There is no standard therapy available and treatment failures are common, leading to a poor prognosis. We report a case of acute renal failure caused by TAFRO syndrome, successfully managed by long-term corticosteroids combined with bortezomib and cyclophosphamide. <b><i>Case Presentation:</i></b> The patient was a 52-year-old female who presented with fever, anasarca, oliguria, and abdominal distension at first. She progressed rapidly to anuric renal failure requiring hemodialysis. She also demonstrated thrombocytopenia, anemia, coagulopathy, and a hyperinflammatory status. Her CT scan showed severe polyserositis, splenomegaly, and lymphadenopathy. Her serum vascular epithelial growth factor level was significantly elevated. Axillary lymph node biopsy showed hyaline-vascular type Castleman disease, supporting the diagnosis of TAFRO syndrome. Her renal function recovered after high-dose steroids and supportive treatment. A weekly dosing regimen of bortezomib, cyclophosphamide, and dexamethasone combined with medium dose prednisone in between were deployed. Her blood cell count and renal function remained stable after 6 months. The inflammation was suppressed and the polyserositis resolved completely. <b><i>Conclusion:</i></b> TAFRO syndrome is rare and has a poor prognosis due to the lack of standard treatment. Our patient might be the first TAFRO case successfully treated by bortezomib, cyclophosphamide, and corticosteroids.
DOI: 10.6084/m9.figshare.12416096
title: genes.gtf

description: Information about gene structureThis file is a copy downloaded from UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/<br>
DOI: 10.6084/m9.figshare.12416096.v1
title: genes.gtf

description: Information about gene structureThis file is a copy downloaded from UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/<br>
DOI: 10.6084/m9.figshare.12416015
title: Supplementary Material for: Prior Therapeutic Experiences, Not Expectation Ratings, Predict Placebo Effects: An Experimental Study in Chronic Pain and Healthy Participants

description: <b><i>Introduction:</i></b> Many clinical trials fail because of placebo responses. Prior therapeutic experiences and patients’ expectations may affect the capacity to respond to placebos in chronic disorders. <b><i>Objective:</i></b> The scope of this study in 763 chronic orofacial pain and healthy study participants was to compare the magnitude and prevalence of placebo effects and determine the putative role of prior therapeutic experiences vs. expectations. <b><i>Methods:</i></b> We tested placebo propensity in a laboratory setting by using 2 distinct levels of individually tailored painful stimulations (high pain and low pain) to reinforce expectations and provide a hypoalgesic experience (conditioning phase). Afterwards, both levels of pain were surreptitiously set at a moderate pain level to test for placebo effects (testing phase). Pain and expectation ratings were assessed as primary outcomes using visual analog scales. <b><i>Results:</i></b> In both chronic pain and healthy participants, placebo effects were similar in magnitude, with the larger prevalence of responders in the healthy participants. Although chronic pain participants reported higher pain relief expectations, expectations did not account for the occurrence of placebo effects. Rather, prior experience via conditioning strength mediated placebo effects in both pain and healthy participants. <b><i>Conclusions:</i></b> These findings indicate that participants with chronic pain conditions display robust placebo effects that are not mediated by expectations but are instead directly linked to prior therapeutic experiences. This confirms the importance of assessing the therapeutic history while raising questions about the utility of expectation ratings. Future research is needed to enhance prediction of responses to placebos, which will ultimately improve clinical trial designs.
DOI: 10.6084/m9.figshare.12416015.v1
title: Supplementary Material for: Prior Therapeutic Experiences, Not Expectation Ratings, Predict Placebo Effects: An Experimental Study in Chronic Pain and Healthy Participants

description: <b><i>Introduction:</i></b> Many clinical trials fail because of placebo responses. Prior therapeutic experiences and patients’ expectations may affect the capacity to respond to placebos in chronic disorders. <b><i>Objective:</i></b> The scope of this study in 763 chronic orofacial pain and healthy study participants was to compare the magnitude and prevalence of placebo effects and determine the putative role of prior therapeutic experiences vs. expectations. <b><i>Methods:</i></b> We tested placebo propensity in a laboratory setting by using 2 distinct levels of individually tailored painful stimulations (high pain and low pain) to reinforce expectations and provide a hypoalgesic experience (conditioning phase). Afterwards, both levels of pain were surreptitiously set at a moderate pain level to test for placebo effects (testing phase). Pain and expectation ratings were assessed as primary outcomes using visual analog scales. <b><i>Results:</i></b> In both chronic pain and healthy participants, placebo effects were similar in magnitude, with the larger prevalence of responders in the healthy participants. Although chronic pain participants reported higher pain relief expectations, expectations did not account for the occurrence of placebo effects. Rather, prior experience via conditioning strength mediated placebo effects in both pain and healthy participants. <b><i>Conclusions:</i></b> These findings indicate that participants with chronic pain conditions display robust placebo effects that are not mediated by expectations but are instead directly linked to prior therapeutic experiences. This confirms the importance of assessing the therapeutic history while raising questions about the utility of expectation ratings. Future research is needed to enhance prediction of responses to placebos, which will ultimately improve clinical trial designs.
DOI: 10.6084/m9.figshare.12415928
title: Tetracentron sinense genome

description: Tsi.chr.fa.gz--------Tetracentron sinense chromosome assemblyTsi.chr.cds.gz-------Tetracentron sinense CDS sequenceTsi.chr.gff.gz-------Tetracentron sinense gene structure gff fileTsi.chr.pep.gz-------Tetracentron sinense protein sequence<br>
DOI: 10.6084/m9.figshare.12415916
title: Supporting information for Nguyen et al. (2020)

description: Supporting information for Nguyen et al. (2020, in revision)<br>
DOI: 10.6084/m9.figshare.12415916.v1
title: Supporting information for Nguyen et al. (2020)

description: Supporting information for Nguyen et al. (2020, in revision)<br>
DOI: 10.6084/m9.figshare.12415877
title: Contrasting effects of commercial and native arbuscular mycorrhizal fungal inoculants on plant biomass allocation, nutrients and phenolics

description: Data associated with this publication are separated into two files:<br>- data (contains plant biomass, nutrient and phenolic response data)<br>- Colonisation (contains arbuscular mycorrhizal fungal colonisation data)<br>
DOI: 10.6084/m9.figshare.12415877.v1
title: Contrasting effects of commercial and native arbuscular mycorrhizal fungal inoculants on plant biomass allocation, nutrients and phenolics

description: Data associated with this publication are separated into two files:<br>- data (contains plant biomass, nutrient and phenolic response data)<br>- Colonisation (contains arbuscular mycorrhizal fungal colonisation data)<br>
DOI: 10.6084/m9.figshare.12415679
title: table_physical_function.xlsx

description: test<br>
DOI: 10.6084/m9.figshare.12415679.v1
title: table_physical_function.xlsx

description: 333 PLHIV in West Africa. Socio-demographics, medical and physical function data.<br>
DOI: 10.6084/m9.figshare.12415643.v1
title: RNA editing impact phylogenetic reconstruction

description: this folder included alignment and trees used for evaluation of RNA editing on mitochondrial phylogenetic reconstruction
DOI: 10.6084/m9.figshare.12415622
title: FSE2020 - Boosting Fuzzer Efficiency An Information-Theoretic Perspective

description: Entropic is an information-theoretic power schedule implemented into LibFuzzer. It boosts performance by changing how weights are assigned to the seeds in the corpus. Seeds revealing more ‘‘information’’ about globally rare features are assigned a higher weight.
DOI: 10.6084/m9.figshare.12415679.v3
title: table_physical_function.xlsx

description: test<br>
DOI: 10.6084/m9.figshare.12415643.v2
title: RNA editing impact phylogenetic reconstruction

description: this folder included alignment and trees used for evaluation of RNA editing on mitochondrial phylogenetic reconstruction
DOI: 10.6084/m9.figshare.12415679.v2
title: table_physical_function.xlsx

description: 333 PLHIV in West Africa. Socio-demographics, medical and physical function data.<br>
DOI: 10.6084/m9.figshare.12415415
title: tcr_beta_synrep_set1_08.txt.bz2

description: Synthetic T cell receptor beta chain repertoire generated using IGoR software. <br><br>Record format: V-gene D-gene J-gene amino-acid-CDR3<br>Where CDR3 contains anchor residues (V-gene Cys, J-gene Phe/Val)