cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12471977.v1
title: Supplementary Material for: Severe Leukoaraiosis Is Associated with Poor Outcome after Successful Recanalization of M1 Middle Cerebral Artery Occlusion Strokes

description: <b><i>Background:</i></b> Severe leukoaraiosis (LA) is an established risk factor for poor outcome after mechanical thrombectomy (MT) for large vessel occlusion stroke. There is uncertainty whether this association also applies to successfully recanalized patients with M1 segment middle cerebral artery (MCA) occlusions. <b><i>Methods:</i></b> A retrospective single-centre study of patients with successful reperfusion (thrombolysis in cerebral infarction, TICI 2b or 3) after MT for an M1 MCA occlusion was performed over a 7-year period. LA score (LAS) was assessed using the age-related white matter change scale on pre-interventional brain imaging. <b><i>Results:</i></b> A total of 209 patients (median age 75.0 years) were included. LAS was assessed on pre-interventional imaging by computed tomography in 177 (84.7%) patients and magnetic resonance imaging in 32 (15.3%) patients. The median LAS was 1 (IQR 0–8), and severe LA consisted of the top 25 percentile, ranging from 9 to 24. Multivariable analysis demonstrated an association of severe LA (OR 0.32, 95% CI 0.12–0.88, <i>p</i> = 0.023), higher NIHSS on admission (OR 0.89, 95% CI 0.84–0.94, <i>p</i> &lt; 0.001), advanced age (OR 0.97, 95% CI 0.95–1.00, <i>p</i> = 0.039), good leptomeningeal collaterals (OR 3.65, 95% CI 1.46–8.15, <i>p</i> = 0.001), and TICI 3 score (OR 3.26, 95% CI 10.52–7.01) with good clinical outcome after 3 months as measured with the modified Rankin scale. <b><i>Conclusion:</i></b> Severe LA is associated with poor clinical outcome at 3 months in acute stroke patients undergoing MT due to emergent M1 MCA occlusion.
DOI: 10.6084/m9.figshare.12471776
title: Supplementary Material for: Coronavirus Disease 2019 in Pregnancy: A Clinical Management Protocol and Considerations for Practice

description: The coronavirus disease 2019 (COVID-19) pandemic has represented a major impact to health systems and societies worldwide. The generation of knowledge about the disease has occurred almost as fast as its global expansion. The mother and fetus do not seem to be at particularly high risk. Nevertheless, obstetrics and maternal-fetal medicine practice have suffered profound changes to adapt to the pandemic. In addition, there are aspects specific to COVID-19 and gestation that should be known by specialists in order to correctly diagnose the disease, classify the severity, distinguish specific signs of COVID-19 from those of obstetric complications, and take the most appropriate management decisions. In this review we present in a highly concise manner an evidence-based protocol for the management of COVID-19 in pregnancy. We briefly contemplate all relevant aspects that we believe a specialist in obstetrics and maternal medicine should know, ranging from basic concepts about the disease and protection measures in the obstetric setting to more specific aspects related to maternal-fetal management and childbirth.
DOI: 10.6084/m9.figshare.12471755
title: Supplementary Material for: Activation, Deficiency, and Reduced IFN-γ Production of Mucosal-Associated Invariant T Cells in Patients with Inflammatory Bowel Disease

description: Mucosal-associated invariant T (MAIT) cells are innate-like T cells that can activate either in response to T-cell receptor (TCR) engagement or through activating cytokines and play an important role in autoimmune disorders. The study examined the level and function of MAIT cells in patients with inflammatory bowel disease (IBD). Circulating MAIT cell levels were significantly reduced in IBD patients. This MAIT cell deficiency was correlated with IBD disease activity grades, hemoglobin, and CRP. IFN-γ production of circulating MAIT cells in response to both MHC class 1b-like related protein (MR1)-dependent and -independent stimulations was decreased in IBD patients, which was partially associated with reduced activation of nuclear factor of activated T cells 1 (NFAT1) transcription factor, a main regulator of IFN-γ production. Expression levels of CD69, programmed death-1 (PD-1), and annexin V in MAIT cells were elevated in IBD patients. CCL20, CXCL10, CXCL16, and CCL25 were expressed higher in inflamed intestinal tissues than in noninflamed tissues. This study demonstrates that circulating MAIT cells are activated and numerically and functionally deficient in IBD patients. Furthermore, activated MAIT cells have the potential to migrate to inflamed tissues. These findings suggest an important role of MAIT cells in mucosal immunity in IBD.
DOI: 10.6084/m9.figshare.12471755.v1
title: Supplementary Material for: Activation, Deficiency, and Reduced IFN-γ Production of Mucosal-Associated Invariant T Cells in Patients with Inflammatory Bowel Disease

description: Mucosal-associated invariant T (MAIT) cells are innate-like T cells that can activate either in response to T-cell receptor (TCR) engagement or through activating cytokines and play an important role in autoimmune disorders. The study examined the level and function of MAIT cells in patients with inflammatory bowel disease (IBD). Circulating MAIT cell levels were significantly reduced in IBD patients. This MAIT cell deficiency was correlated with IBD disease activity grades, hemoglobin, and CRP. IFN-γ production of circulating MAIT cells in response to both MHC class 1b-like related protein (MR1)-dependent and -independent stimulations was decreased in IBD patients, which was partially associated with reduced activation of nuclear factor of activated T cells 1 (NFAT1) transcription factor, a main regulator of IFN-γ production. Expression levels of CD69, programmed death-1 (PD-1), and annexin V in MAIT cells were elevated in IBD patients. CCL20, CXCL10, CXCL16, and CCL25 were expressed higher in inflamed intestinal tissues than in noninflamed tissues. This study demonstrates that circulating MAIT cells are activated and numerically and functionally deficient in IBD patients. Furthermore, activated MAIT cells have the potential to migrate to inflamed tissues. These findings suggest an important role of MAIT cells in mucosal immunity in IBD.
DOI: 10.6084/m9.figshare.12471749
title: FAL18505_fccbc80b8b81a4540fc5188e93969fe2aa7fee18_10.fast5

description: Sample data for testing Deeplexicon direct RNA demultiplexing software
DOI: 10.6084/m9.figshare.12471764
title: Body mass and early life mortality in rhesus macaques

description: Uploaded are 3 datasets used for the analyses presented in the article 'Higher early life mortality with lower infant body mass in a free-ranging primate'. <br>The data was collected from in a population of free-ranging rhesus macaques on Cayo Santiago.<br> All 3 datasets contain information on: 'mab' = maternal age at birth (years; standardized); 'wt' = infant body mass measured prior to weaning (standardized within age-sex category; see the paper for specific method); 'rank' = maternal rank (low/middle/high as 0/1/2); 'fchild' = whether a child was a first-born offspring (1) or not (0); 'centbd' = birth date centered at the peak birth date of a birth season; 'bs' = birth season number; 'newid' = maternal ID.<br><br>1) weight_time_to_death.csvThe data contains 2 additional variables: 'ttd' = time to death (days), assessed up to the first 4 years of life; 'ttd_observed' = whether the time to death was censored or not.<br>2) weight_birthskipping.csvThe data contains 1 additional variable: 'skipped' = whether a mother failed (1) or not (0) to reproduce again in the consequent year. 3) weight_lastsuckle.csvThe data contains 1 additional variable: 'lastsuck' = postpartum week at which the offspring was observed to suckle for the last time (see the paper for detailed method for assessing the last week of suckling). Note that this dataset does not contain information on maternal ID and birth season, because there is no repeated observation within each categories.
DOI: 10.6084/m9.figshare.12471668
title: OBSdata

description: OBS data in SCS
DOI: 10.6084/m9.figshare.12471572
title: Supplementary Material for: Comparison of Platinum/S-1 and Platinum/5-Fluorouracil as First-Line Chemotherapy for Advanced Gastric or Gastroesophageal Junction Cancer: A Meta-Analysis Based on Randomized Controlled Trials

description: <b><i>Background:</i></b> Platinum/S-1 (PS) and platinum/5-fluorouracil (PF) as first-line chemotherapies are extensively used for the treatment of advanced gastric or gastroesophageal junction cancer (AGC); however, there is no definite consensus on which regimen is best. In our meta-analysis, we compared PS with PF in terms of their efficacy and safety in AGC patients. <b><i>Methods:</i></b> PubMed, ScienceDirect, Web of Science, Scopus, Ovid MEDLINE, EMBASE, The Cochrane Library, Google Scholar, and CNKI were systematically searched for pertinent literature. We analyzed overall survival (OS), progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), and adverse effects (AEs) as major end points. <b><i>Results:</i></b> A total of 3,225 studies were identified, among which 6 randomized controlled trials, including 1,736 participants, were ultimately included in our analysis. Our results showed that PS and PF were comparable in terms of OS (<i>p</i> = 0.33, 95% confidence interval [CI]: 0.84–1.06), PFS (<i>p</i> = 0.63, 95% CI: 0.87–1.09), ORR (<i>p</i> = 0.38, 95% CI: 0.91–1.28), DCR (<i>p</i> = 0.41, 95% CI: 0.86–1.43), total AEs (<i>p</i> = 0.41, 95% CI: 0.98–1.01), and grade ≥3 AEs (<i>p</i> = 0.58, 95% CI: 0.82–1.41). However, those who received PF had a shorter time to failure (TTF) (<i>p</i> = 0.01, 95% CI: 0.77–0.97), and a significantly higher rate and more severe cases of stomatitis, nausea, and hypokalemia were reported in the PF group. <b><i>Conclusions:</i></b> PF and PS show similar antitumor efficacy (OS, PFS, ORR, and DCR), but patients receiving PS exhibit longer TTF and fewer AEs (stomatitis, nausea, and hypokalemia) than those receiving PF.
DOI: 10.25375/uct.12471569
title: Compensatory breeding in years following drought in a desert-dwelling cooperative breeder

description: Data accompanying the following publication:<br>Bourne AR, Cunningham SJ, Spottiswoode CN and Ridley AR(2020) Compensatory Breeding in Years Following Drought in aDesert-Dwelling Cooperative Breeder. Front. Ecol. Evol. 8:190.https://www.frontiersin.org/articles/10.3389/fevo.2020.00190/abstract<br><br>Variation in weather patterns can influence reproductive effort and success not only within but also between breeding seasons. Where environmental conditions can be highly variable between years, the weather, and particularly extreme weather events such as heat waves and droughts, may exert a strong influence on reproductive effort (number of breeding attempts) and success (number of surviving young) from one breeding season to the next. <br><br>We used a 15-year dataset for a cooperatively breeding bird, the southern pied babbler Turdoides bicolor, to determine the impact of high temperatures and drought on reproductive effort and success. We tested the influence on reproductive effort and success of mean daily maximum air temperature and drought both within a breeding season, to determine the relative importance of current conditions, and during the previous breeding season, to determine the relative importance of compensatory effects in response to prior conditions. Reproductive effort and success were lower during breeding seasons characterized by drought, and higher in the breeding seasons that followed droughts, but were not predicted by mean daily maximum temperatures measured over the full length of the breeding season.<br>We provide evidence of compensatory breeding following drought in a bird species endemic to a semi-arid ecosystem and suggest that compensatory mechanisms may be an important part of both long-term population persistence and post-drought population recovery.
DOI: 10.6084/m9.figshare.12471572.v1
title: Supplementary Material for: Comparison of Platinum/S-1 and Platinum/5-Fluorouracil as First-Line Chemotherapy for Advanced Gastric or Gastroesophageal Junction Cancer: A Meta-Analysis Based on Randomized Controlled Trials

description: <b><i>Background:</i></b> Platinum/S-1 (PS) and platinum/5-fluorouracil (PF) as first-line chemotherapies are extensively used for the treatment of advanced gastric or gastroesophageal junction cancer (AGC); however, there is no definite consensus on which regimen is best. In our meta-analysis, we compared PS with PF in terms of their efficacy and safety in AGC patients. <b><i>Methods:</i></b> PubMed, ScienceDirect, Web of Science, Scopus, Ovid MEDLINE, EMBASE, The Cochrane Library, Google Scholar, and CNKI were systematically searched for pertinent literature. We analyzed overall survival (OS), progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), and adverse effects (AEs) as major end points. <b><i>Results:</i></b> A total of 3,225 studies were identified, among which 6 randomized controlled trials, including 1,736 participants, were ultimately included in our analysis. Our results showed that PS and PF were comparable in terms of OS (<i>p</i> = 0.33, 95% confidence interval [CI]: 0.84–1.06), PFS (<i>p</i> = 0.63, 95% CI: 0.87–1.09), ORR (<i>p</i> = 0.38, 95% CI: 0.91–1.28), DCR (<i>p</i> = 0.41, 95% CI: 0.86–1.43), total AEs (<i>p</i> = 0.41, 95% CI: 0.98–1.01), and grade ≥3 AEs (<i>p</i> = 0.58, 95% CI: 0.82–1.41). However, those who received PF had a shorter time to failure (TTF) (<i>p</i> = 0.01, 95% CI: 0.77–0.97), and a significantly higher rate and more severe cases of stomatitis, nausea, and hypokalemia were reported in the PF group. <b><i>Conclusions:</i></b> PF and PS show similar antitumor efficacy (OS, PFS, ORR, and DCR), but patients receiving PS exhibit longer TTF and fewer AEs (stomatitis, nausea, and hypokalemia) than those receiving PF.
DOI: 10.25375/uct.12471569.v1
title: Compensatory breeding in years following drought in a desert-dwelling cooperative breeder

description: Data accompanying the following publication:<br>Bourne AR, Cunningham SJ, Spottiswoode CN and Ridley AR(2020) Compensatory Breeding in Years Following Drought in aDesert-Dwelling Cooperative Breeder. Front. Ecol. Evol. 8:190.https://www.frontiersin.org/articles/10.3389/fevo.2020.00190/abstract<br><br>Variation in weather patterns can influence reproductive effort and success not only within but also between breeding seasons. Where environmental conditions can be highly variable between years, the weather, and particularly extreme weather events such as heat waves and droughts, may exert a strong influence on reproductive effort (number of breeding attempts) and success (number of surviving young) from one breeding season to the next. <br><br>We used a 15-year dataset for a cooperatively breeding bird, the southern pied babbler Turdoides bicolor, to determine the impact of high temperatures and drought on reproductive effort and success. We tested the influence on reproductive effort and success of mean daily maximum air temperature and drought both within a breeding season, to determine the relative importance of current conditions, and during the previous breeding season, to determine the relative importance of compensatory effects in response to prior conditions. Reproductive effort and success were lower during breeding seasons characterized by drought, and higher in the breeding seasons that followed droughts, but were not predicted by mean daily maximum temperatures measured over the full length of the breeding season.<br>We provide evidence of compensatory breeding following drought in a bird species endemic to a semi-arid ecosystem and suggest that compensatory mechanisms may be an important part of both long-term population persistence and post-drought population recovery.
DOI: 10.6084/m9.figshare.12471464
title: Supporting Data for "Towards more equitable and inclusive conservation and ecology conferences" (Tulloch 2020, Nature Ecology and Evolution)

description: Supporting data for:Tulloch, Ayesha I.T. (2020) Towards more equitable and inclusive conservation and ecology conferences”, Perspective in Nature Ecology and Evolution.<br>4 worksheets:1. Conference Initiatives: Results of review supporting Table 1 and Table S2 in main text of paper. Indicates which of 30 conference events for 10 international conference and ecology conferences implemented different initiatives.<br>To evaluate how ecology and conservation conferences support these principles, the actions and policies of 10 international conferences held by nine academic societies for ecology and conservation were reviewed. Data were collated for the past three events that had been held by each conference targeting an international audience: the biannual International Congress for Conservation Biology (ICCB), International Marine Conservation Congress (IMCC), European Ecological Federation (EEF) Conference and the Society for Ecological Restoration (SER) World Conference on Ecological Restoration, the annual conferences of the Ecological Society of America (ESA), Ecological Society of Australia (ESAus), British Ecological Society (BES) and Association for Tropical Biology and Conservation (ATBC), the conference of the International Association for Ecology (INTECOL), held once every 5 years, and the IUCN World Conservation Congress (WCC) held once every 4 years. Data came from conferences between 2009 and 2020. Data were sourced from conference websites, conference programs and marketing material. Initiatives of interest were those targeted on improving equity and diversity in sex, gender identity and sexual orientation, and associated diversity types and lifestyle choices ̶ marital status, family or carer responsibilities, pregnancy and breastfeeding and physical appearance are categorised according to three broad groups:<br>(a) Minimising discrimination, harassment and implicit bias<br>(b) Minimising barriers to attendance<br>(c) Maximising opportunities for participation & education.<br>2. Conference Affordability: Data on conference registration fees and discounts for students and developing countries.<br>3. Conference Attendance: Data on conference attendee diversity provided by individual conferences and societies on websites and marketing material.<br>4. Conference_equity_forR_200505: Input data (csv file) for GLMM code in R, provided in S3. Code for Statistical Models.<br><br>
DOI: 10.6084/m9.figshare.12471464.v1
title: Supporting Data for "Towards more equitable and inclusive conservation and ecology conferences" (Tulloch 2020, Nature Ecology and Evolution)

description: Supporting data for:Tulloch, Ayesha I.T. (2020) Towards more equitable and inclusive conservation and ecology conferences”, Perspective in Nature Ecology and Evolution.<br>4 worksheets:1. Conference Initiatives: Results of review supporting Table 1 and Table S2 in main text of paper. Indicates which of 30 conference events for 10 international conference and ecology conferences implemented different initiatives.<br>To evaluate how ecology and conservation conferences support these principles, the actions and policies of 10 international conferences held by nine academic societies for ecology and conservation were reviewed. Data were collated for the past three events that had been held by each conference targeting an international audience: the biannual International Congress for Conservation Biology (ICCB), International Marine Conservation Congress (IMCC), European Ecological Federation (EEF) Conference and the Society for Ecological Restoration (SER) World Conference on Ecological Restoration, the annual conferences of the Ecological Society of America (ESA), Ecological Society of Australia (ESAus), British Ecological Society (BES) and Association for Tropical Biology and Conservation (ATBC), the conference of the International Association for Ecology (INTECOL), held once every 5 years, and the IUCN World Conservation Congress (WCC) held once every 4 years. Data came from conferences between 2009 and 2020. Data were sourced from conference websites, conference programs and marketing material. Initiatives of interest were those targeted on improving equity and diversity in sex, gender identity and sexual orientation, and associated diversity types and lifestyle choices ̶ marital status, family or carer responsibilities, pregnancy and breastfeeding and physical appearance are categorised according to three broad groups:<br>(a) Minimising discrimination, harassment and implicit bias<br>(b) Minimising barriers to attendance<br>(c) Maximising opportunities for participation & education.<br>2. Conference Affordability: Data on conference registration fees and discounts for students and developing countries.<br>3. Conference Attendance: Data on conference attendee diversity provided by individual conferences and societies on websites and marketing material.<br>4. Conference_equity_forR_200505: Input data (csv file) for GLMM code in R, provided in S3. Code for Statistical Models.<br><br>
DOI: 10.6084/m9.figshare.12471338
title: Raw Data of binned NMR and Cytokines Quantification trial.xls

description: dfdfdfdf
DOI: 10.6084/m9.figshare.12470858
title: Table S1.docx

description: <b>Table S1. </b>Primer sequences for RT-qPCR.
DOI: 10.6084/m9.figshare.12470858.v1
title: Table S1.docx

description: <b>Table S1. </b>Primer sequences for RT-qPCR.
DOI: 10.6084/m9.figshare.12471338.v2
title: Raw Data of binned NMR and Cytokines Quantification trial.xls

description: dfdfdfdf
DOI: 10.6084/m9.figshare.12471338.v1
title: Raw Data of binned NMR and Cytokines Quantification trial.xls

description: dfdfdfdf
DOI: 10.6084/m9.figshare.12470804
title: Additional file 3 of Standardisation of lymphatic filariasis microfilaraemia prevalence estimates based on different diagnostic methods: a systematic review and meta-analysis

description: Additional file 3: Data S1. Predicted prevalence estimates for the various diagnostic techniques, with 95% confidence intervals, and relative risks, for transformation to mf prevalences as measured by TBS20 and vice versa.
DOI: 10.6084/m9.figshare.12471461.v3
title: Clostridioides difficile population structure

description: <b>Figure 1.</b> Species-wide phylogeny generated from 659 ST alleles sourced from PubMLST (dated 01-Jan-2020). Alleles were concatenated in frame (3501bp) and aligned with MAFFT v7.304. The final neighbour-joining tree was generated in MEGA v6.0 (evolutionary distances inferred using the Tajima-Nei model).<br><b>Table 1. </b>MLST allele profiles for 659 STs sourced from PubMLST (dated 01-Jan-2020).
DOI: 10.6084/m9.figshare.12470804.v1
title: Additional file 3 of Standardisation of lymphatic filariasis microfilaraemia prevalence estimates based on different diagnostic methods: a systematic review and meta-analysis

description: Additional file 3: Data S1. Predicted prevalence estimates for the various diagnostic techniques, with 95% confidence intervals, and relative risks, for transformation to mf prevalences as measured by TBS20 and vice versa.
DOI: 10.6084/m9.figshare.12471461.v4
title: Clostridioides difficile population structure (Knight et al, 2020)

description: <b>Figure 1.</b> Species-wide phylogeny generated from 659 ST alleles sourced from PubMLST (dated 01-Jan-2020). Alleles were concatenated in frame (3501bp) and aligned with MAFFT v7.304. The final neighbour-joining tree was generated in MEGA v6.0 (evolutionary distances inferred using the Tajima-Nei model).<br><b>Table 1. </b>MLST allele profiles for 659 STs sourced from PubMLST (dated 01-Jan-2020).<br><b>Table 2. </b>MLST data for 12098 genomes sourced from the NCBI Short Read Archive (dated 01-Jan-2020).
DOI: 10.6084/m9.figshare.12471461.v5
title: Clostridioides difficile population structure (Knight et al, unpublished)

description: <b>1. </b>Global MLST phylogeny (nwk file for manuscript figure 2)<b><br></b><b><br></b><b>2. </b>Supplementary Data<b><br></b>