cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12801206
title: Targeted PCR Rickettsia screen

description: A targeted PCR <i>Rickettsia </i>screen of 1,612 individuals from 169 species was undertaken to increase our understanding of <i>Rickettsia</i> ecology. Within this, we included a range of both aquatic and terrestrial taxa, to investigate if the previous work highlighting particular aquatic taxa as hotspots for <i>Rickettsia </i>symbiosis (water beetles, biting midges, damselflies) reflects a wider higher incidence in species from this habitat. <br>mtDNA <i>COI </i>amplification was conducted as a control for DNA quality. To investigate symbiont infection status, rickettsial-specific primers based on<i> gltA</i> and <i>16S rRNA </i>genes were used for conventional PCR screening, with Sanger sequences obtained from at least one specimen per <i>Rickettsia </i>positive species to identify any misamplification false positives. <br>
DOI: 10.6084/m9.figshare.12801134
title: Patterson BrownMcLean Reyes COVID 19 Field Faculty Survey Results 2020.pdf

description: Dataset includes survey data collected from the COVID-19 social work field faculty and staff study conducted in June 2020. The survey questions were adapted from the ITHAKA S+R COVID Faculty Survey (Wolff-Eisenberg, 2020). Data includes brief demographic questions and Likert-scale responses to faculty's perceptions of ease or difficulty with managing field, teaching, and seminar tasks once field faculty and staff transitioned to remote teaching.
DOI: 10.6084/m9.figshare.12801134.v1
title: Patterson BrownMcLean Reyes COVID 19 Field Faculty Survey Results 2020.pdf

description: Dataset includes survey data collected from the COVID-19 social work field faculty and staff study conducted in June 2020. The survey questions were adapted from the ITHAKA S+R COVID Faculty Survey (Wolff-Eisenberg, 2020). Data includes brief demographic questions and Likert-scale responses to faculty's perceptions of ease or difficulty with managing field, teaching, and seminar tasks once field faculty and staff transitioned to remote teaching.
DOI: 10.6084/m9.figshare.12800909
title: Raw_data_Rendueles&Velicer.xlsx

description: <b>BACKGROUND: Evolution in a selective environment often latently generates phenotypic change manifested only later in different environments, but the complexity of behaviour important to fitness in the original environment might influence the character of such latent evolution. Using <i>Myxococcus xanthus, </i>a bacterium possessing two motility systems differing in effectiveness on hard vs. soft surfaces,<i></i>here we test i) whether and how evolution while swarming on one surface – the selective surface – latently alters motility on the alternative surface type and ii) whether patterns of such latent phenotype evolution depend on the complexity of ancestral motility, specific ancestral motility genotypes and/or the selective surface of evolution. We analyse an experiment in which populations<i></i>established from three ancestral</b><b>genotypes – one with both motility systems intact and two others with one system debilitated – </b><b>evolved </b><b>while swarming across either hard or soft agar in six evolutionary treatments. We then compare motility-phenotype patterns across selective vs alternative surface types. </b><b>RESULTS: Latent motility evolution was pervasive but varied in character as a function of the presence of one vs two functional motility systems and, for some individual-treatment comparisons, the specific ancestral genotype and/or selective surface. Swarming rates on alternative vs selective surfaces were positively correlated generally among populations with one functional motility system but not among those with two. This suggests that opportunities for pleiotropy and epistasis generated by increased genetic complexity underlying behavior can alter the character of latent phenotype evolution. No tradeoff between motility performance across surface types was detected in the dual-system treatments, even after adaptation on a surface on which one motility system dominates strongly over the other in driving movement, but latent phenotype evolution was instead idiosyncratic in these treatments. We further find that the magnitude of stochastic diversification at alternative-surface swarming among replicate populations greatly exceeded diversification of selective-surface swarming within some treatments and varied across treatments. </b><b>CONCLUSION: Collectively, our results suggest that increases in the genetic and mechanistic complexity of behavior can increase the complexity of latent evolution outcomes and illustrate that diversification manifested during evolution in one environment can be augmented greatly by diversification of latent phenotypes manifested later.</b>
DOI: 10.6084/m9.figshare.12801107.v2
title: BOLD contaminant pool dataset

description: This dataset describes 3,817 cytochrome c oxidase I gene sequences deemed to be contaminants by the Barcode of Life Data System (BOLD). These contaminants are from a barcoding project totalling 184,585 arthropods.<br>Contaminants are defined as sequences which do not match the initial arthropod taxa assigned morphologically. Contaminants include: spreadsheet 1, Rickettsia; spreadsheet 2, Bacteria; spreadsheet 3, all contaminants detected including bacteria, human and arthropod homologues.
DOI: 10.6084/m9.figshare.12801107.v1
title: BOLD contaminant pool dataset

description: This dataset describes 3,817 cytochrome c oxidase I gene sequences deemed to be contaminants by the Barcode of Life Data System (BOLD). These contaminants are from a barcoding project totalling 184,585 arthropods.<br>Contaminants are defined as sequences which do not match the initial arthropod taxa assigned morphologically. Contaminants include: spreadsheet 1, Rickettsia; spreadsheet 2, Wolbachia; spreadsheet 3, all contaminants detected including bacteria, human and arthropod homologues.
DOI: 10.6084/m9.figshare.12800822
title: JVASP-12892 to JVASP-14203

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800819
title: JVASP-10294 to JVASP-11212

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800810
title: JVASP-11213 to JVASP-12059

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800819.v1
title: JVASP-10294 to JVASP-11212

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800822.v1
title: JVASP-12892 to JVASP-14203

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800792
title: Early screening and risk factors of Autism Spectrum Disorder in a Large Cohort of Chinese Patients with Prader-Willi Syndrome

description: Raw scores of GARS-3 and ASQ-3 questionnaires, demographic, and other clinical features for the study on early screening and risk factors of Autism Spectrum Disorder in a large cohort of Chinese patients with Prader-Willi Syndrome.
DOI: 10.6084/m9.figshare.12800807
title: JVASP-12060 to JVASP-12891

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800810.v1
title: JVASP-11213 to JVASP-12059

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800783
title: Honeybees optimize their foraging behaviour in relation to spatio-temporal changes in nectar and pollen availability

description: See Material and Methods
DOI: 10.6084/m9.figshare.12800807.v1
title: JVASP-12060 to JVASP-12891

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.12800783.v1
title: Honeybees optimize their foraging behaviour in relation to spatio-temporal changes in nectar and pollen availability

description: See Material and Methods
DOI: 10.6084/m9.figshare.12800708
title: CYT UCSC hub hg19

description: Datasets used in the UCSC session that contains the results from the Nature Genetics article "The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes".
DOI: 10.6084/m9.figshare.12800792.v1
title: Early screening and risk factors of Autism Spectrum Disorder in a Large Cohort of Chinese Patients with Prader-Willi Syndrome

description: Raw scores of GARS-3 and ASQ-3 questionnaires, demographic, and other clinical features for the study on early screening and risk factors of Autism Spectrum Disorder in a large cohort of Chinese patients with Prader-Willi Syndrome.
DOI: 10.6084/m9.figshare.12800708.v1
title: CYT UCSC hub hg19

description: Datasets used in the UCSC session that contains the results from the Nature Genetics article "The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes".
DOI: 10.6084/m9.figshare.12800702
title: Supplementary Dataset from Symbionts shape host innate immunity in honeybees

description: Contains all data used for construction of all figures and supplementary figures. Survival assay data including censored points. Log2 fold-change values for qPCR gene expression experiments.
DOI: 10.6084/m9.figshare.12800702.v1
title: Supplementary Dataset from Symbionts shape host innate immunity in honeybees

description: Contains all data used for construction of all figures and supplementary figures. Survival assay data including censored points. Log2 fold-change values for qPCR gene expression experiments.
DOI: 10.17028/rd.lboro.12800645
title: Supplementary Information files for Invasive crayfish alter the long‐term functional biodiversity of lotic macroinvertebrate communities

description: Supplementary Information files for Invasive crayfish alter the long‐term functional biodiversity of lotic macroinvertebrate communities. <br>1. Invasive species represent one of the primary threats to global biodiversity. Despite acknowledged implications for taxonomic properties of ecological communities following invasion, functional measures remain poorly understood.2. We examined the long-term implications of invasion by a crayfish species (Pacifastacus leniusculus) on functional alpha and beta diversity properties of lotic macroinvertebrate communities in three English regions. The dataset comprised 477 samples collected predominantly between 1990 and 2013. Unlike many invasion studies, we employed before and after invasion comparisons, in association with control rivers not invaded by crayfish.3. Functional richness and divergence metrics displayed the strongest responses to invasion, highlighting that P. leniusculus may alter the range of functional niches and extreme trait values (likely reflecting resistance and resilience mechanisms) displayed by macroinvertebrate communities. Interestingly, in one region, biodiversity gains seen in control rivers were not mirrored in invaded rivers, potentially suggesting that invasion inhibited4. Invasion by signal crayfish resulted in functional compositional changes in two of the three English regions studied, with these rivers yielding greater ecological differences between pre- and post-invasion periods relative to control rivers. This change was primarily driven by higher nestedness values in invaded rivers, with communities containing functional subsets relative to control rivers. The third region demonstrated no functional compositional changes or alterations in functional beta diversity associated with invasion.5. Our findings indicated that in most instances, the functional properties of macroinvertebrate communities responded to crayfish invasion and may therefore represent a complementary means to monitor the ecological condition of lotic ecosystems. Given their spatial transferability, functional traits could provide a platform to guide regional management practices in the face of biological invasions.
DOI: 10.6084/m9.figshare.12800627
title: Supplementary Material for: Genetic Variants in One-Carbon Metabolism Pathway Predict Survival Outcomes of Early-Stage Non-Small Cell Lung Cancer

description: <b><i>Background:</i></b> This study was conducted to investigate the association between genetic variants in one-carbon metabolism and survival outcomes of surgically resected non-small cell lung cancer (NSCLC). <b><i>Methods:</i></b> We genotyped 41 potentially functional variants of 19 key genes in the one-carbon metabolism pathway among 750 NSCLC patients who underwent curative surgery. The association between genetic variants and overall survival (OS)/disease-free survival (DFS) were analyzed. <b><i>Results:</i></b> Among the 41 single-nucleotide polymorphisms (SNPs) analyzed, 4 SNPs (<i>MTHFD1L</i> rs6919680T&gt;G and rs3849794T&gt;C, <i>MTR</i> rs2853523C&gt;A, and <i>MTHFR</i> rs4846049G&gt;T) were significantly associated with survival outcomes. <i>MTHFD1L</i> rs6919680T&gt;G and <i>MTR</i> rs2853523C&gt;A were significantly associated with better OS (adjusted hazard ratio [aHR] = 0.73, 95% confidence interval [CI] = 0.54–0.99, <i>p</i> = 0.04) and worse OS (aHR = 2.14, 95% CI = 1.13–4.07, <i>p</i> = 0.02), respectively. <i>MTHFD1L</i> rs3849794T&gt;C and <i>MTHFR</i> rs4846049G&gt;T were significantly associated with worse DFS (aHR = 1.41, 95% CI = 1.08–1.83, <i>p</i> = 0.01; and aHR = 1.97, 95% CI = 1.10–3.53, <i>p</i> = 0.02, respectively). When the patients were divided according to histology, the associations were significant only in squamous cell carcinoma (SCC), but not in adenocarcinoma (AC). In SCC, <i>MTHFD1L</i> rs6919680T&gt;G and <i>MTR</i> rs2853523C&gt;A were significantly associated with better OS (aHR = 0.64, 95% CI = 0.41–1.00, <i>p</i> = 0.05) and worse OS (aHR = 2.77, 95% CI = 1.11–6.91, <i>p</i> = 0.03), respectively, and <i>MTHFD1L</i> rs3849794T&gt;C and <i>MTHFR</i> rs4846049G&gt;T were significantly associated with worse DFS (aHR = 1.73, 95% CI = 1.17–2.56, <i>p</i> = 0.01; and aHR = 2.78, 95% CI = 1.12–6.88, <i>p</i> = 0.03, respectively). <b><i>Conclusions:</i></b> Our results suggest that the genetic variants in the one-carbon metabolism pathway could be used as biomarkers for predicting the clinical outcomes of patients with early-stage NSCLC.
DOI: 10.6084/m9.figshare.12800627.v1
title: Supplementary Material for: Genetic Variants in One-Carbon Metabolism Pathway Predict Survival Outcomes of Early-Stage Non-Small Cell Lung Cancer

description: <b><i>Background:</i></b> This study was conducted to investigate the association between genetic variants in one-carbon metabolism and survival outcomes of surgically resected non-small cell lung cancer (NSCLC). <b><i>Methods:</i></b> We genotyped 41 potentially functional variants of 19 key genes in the one-carbon metabolism pathway among 750 NSCLC patients who underwent curative surgery. The association between genetic variants and overall survival (OS)/disease-free survival (DFS) were analyzed. <b><i>Results:</i></b> Among the 41 single-nucleotide polymorphisms (SNPs) analyzed, 4 SNPs (<i>MTHFD1L</i> rs6919680T&gt;G and rs3849794T&gt;C, <i>MTR</i> rs2853523C&gt;A, and <i>MTHFR</i> rs4846049G&gt;T) were significantly associated with survival outcomes. <i>MTHFD1L</i> rs6919680T&gt;G and <i>MTR</i> rs2853523C&gt;A were significantly associated with better OS (adjusted hazard ratio [aHR] = 0.73, 95% confidence interval [CI] = 0.54–0.99, <i>p</i> = 0.04) and worse OS (aHR = 2.14, 95% CI = 1.13–4.07, <i>p</i> = 0.02), respectively. <i>MTHFD1L</i> rs3849794T&gt;C and <i>MTHFR</i> rs4846049G&gt;T were significantly associated with worse DFS (aHR = 1.41, 95% CI = 1.08–1.83, <i>p</i> = 0.01; and aHR = 1.97, 95% CI = 1.10–3.53, <i>p</i> = 0.02, respectively). When the patients were divided according to histology, the associations were significant only in squamous cell carcinoma (SCC), but not in adenocarcinoma (AC). In SCC, <i>MTHFD1L</i> rs6919680T&gt;G and <i>MTR</i> rs2853523C&gt;A were significantly associated with better OS (aHR = 0.64, 95% CI = 0.41–1.00, <i>p</i> = 0.05) and worse OS (aHR = 2.77, 95% CI = 1.11–6.91, <i>p</i> = 0.03), respectively, and <i>MTHFD1L</i> rs3849794T&gt;C and <i>MTHFR</i> rs4846049G&gt;T were significantly associated with worse DFS (aHR = 1.73, 95% CI = 1.17–2.56, <i>p</i> = 0.01; and aHR = 2.78, 95% CI = 1.12–6.88, <i>p</i> = 0.03, respectively). <b><i>Conclusions:</i></b> Our results suggest that the genetic variants in the one-carbon metabolism pathway could be used as biomarkers for predicting the clinical outcomes of patients with early-stage NSCLC.
DOI: 10.17028/rd.lboro.12800645.v1
title: Supplementary Information files for Invasive crayfish alter the long‐term functional biodiversity of lotic macroinvertebrate communities

description: Supplementary Information files for Invasive crayfish alter the long‐term functional biodiversity of lotic macroinvertebrate communities. <br>1. Invasive species represent one of the primary threats to global biodiversity. Despite acknowledged implications for taxonomic properties of ecological communities following invasion, functional measures remain poorly understood.2. We examined the long-term implications of invasion by a crayfish species (Pacifastacus leniusculus) on functional alpha and beta diversity properties of lotic macroinvertebrate communities in three English regions. The dataset comprised 477 samples collected predominantly between 1990 and 2013. Unlike many invasion studies, we employed before and after invasion comparisons, in association with control rivers not invaded by crayfish.3. Functional richness and divergence metrics displayed the strongest responses to invasion, highlighting that P. leniusculus may alter the range of functional niches and extreme trait values (likely reflecting resistance and resilience mechanisms) displayed by macroinvertebrate communities. Interestingly, in one region, biodiversity gains seen in control rivers were not mirrored in invaded rivers, potentially suggesting that invasion inhibited4. Invasion by signal crayfish resulted in functional compositional changes in two of the three English regions studied, with these rivers yielding greater ecological differences between pre- and post-invasion periods relative to control rivers. This change was primarily driven by higher nestedness values in invaded rivers, with communities containing functional subsets relative to control rivers. The third region demonstrated no functional compositional changes or alterations in functional beta diversity associated with invasion.5. Our findings indicated that in most instances, the functional properties of macroinvertebrate communities responded to crayfish invasion and may therefore represent a complementary means to monitor the ecological condition of lotic ecosystems. Given their spatial transferability, functional traits could provide a platform to guide regional management practices in the face of biological invasions.
DOI: 10.6084/m9.figshare.12800585
title: Supplementary Material for: Prediction of Radioresistant Prostate Cancer Based on Differentially Expressed Proteins

description: <b><i>Introduction:</i></b> Although relapses after radiotherapy are common in prostate cancer (PCA) patients, those with a high risk for radioresistance cannot be identified prior to treatment yet. Therefore, this proof-of-concept study was performed to compare protein expression profiles of patients with radio-recurrent PCA to patients treated with primary radical prostatectomy separated by Gleason risk groups. We hypothesized that radio-recurrent PCA have a similar protein expression as high-risk Gleason PCA. <b><i>Methods:</i></b> Patient cohorts consisted of (i) 31 patients treated with salvage prostatectomy for locally recurrent PCA after primary radiotherapy and (ii) 94 patients treated with primary prostatectomy split into a Gleason high-risk (≥4 + 3; <i>n</i> = 42 [44.7%]) versus a low-risk group (≤3 + 4; <i>n</i> = 52 [55.3%]). Immunohistochemistry was performed using 15 antibodies with known association to radioresistance in PCA in vitro. ELISA was used for validation of selected markers in serum. <b><i>Results:</i></b> Androgen receptor (AR) was overexpressed in most radio-recurrent PCA (89.7%) and in most primary high-risk Gleason PCA (87.8%; <i>p</i> = 0.851), while only 67.3% of the low-risk group showed an expression (<i>p</i> = 0.017). Considering the highest Gleason pattern in primary PCA, aldo-keto reductase family 1 member C3 (AKR1C3) was most similarly expressed by patients with radio-recurrent PCA and patients with Gleason patterns 4 and 5 (<i>p</i> = 0.827 and <i>p</i> = 0.893) compared to Gleason pattern 3 (<i>p</i> = 0.20). These findings were supported by ELISA. <b><i>Conclusion:</i></b> This is the first study to evaluate protein markers in order to predict radioresistance in PCA. Our results point to AR and AKR1C3 as the most promising markers that might help stratify patients for radiotherapy.
DOI: 10.6084/m9.figshare.12800585.v1
title: Supplementary Material for: Prediction of Radioresistant Prostate Cancer Based on Differentially Expressed Proteins

description: <b><i>Introduction:</i></b> Although relapses after radiotherapy are common in prostate cancer (PCA) patients, those with a high risk for radioresistance cannot be identified prior to treatment yet. Therefore, this proof-of-concept study was performed to compare protein expression profiles of patients with radio-recurrent PCA to patients treated with primary radical prostatectomy separated by Gleason risk groups. We hypothesized that radio-recurrent PCA have a similar protein expression as high-risk Gleason PCA. <b><i>Methods:</i></b> Patient cohorts consisted of (i) 31 patients treated with salvage prostatectomy for locally recurrent PCA after primary radiotherapy and (ii) 94 patients treated with primary prostatectomy split into a Gleason high-risk (≥4 + 3; <i>n</i> = 42 [44.7%]) versus a low-risk group (≤3 + 4; <i>n</i> = 52 [55.3%]). Immunohistochemistry was performed using 15 antibodies with known association to radioresistance in PCA in vitro. ELISA was used for validation of selected markers in serum. <b><i>Results:</i></b> Androgen receptor (AR) was overexpressed in most radio-recurrent PCA (89.7%) and in most primary high-risk Gleason PCA (87.8%; <i>p</i> = 0.851), while only 67.3% of the low-risk group showed an expression (<i>p</i> = 0.017). Considering the highest Gleason pattern in primary PCA, aldo-keto reductase family 1 member C3 (AKR1C3) was most similarly expressed by patients with radio-recurrent PCA and patients with Gleason patterns 4 and 5 (<i>p</i> = 0.827 and <i>p</i> = 0.893) compared to Gleason pattern 3 (<i>p</i> = 0.20). These findings were supported by ELISA. <b><i>Conclusion:</i></b> This is the first study to evaluate protein markers in order to predict radioresistance in PCA. Our results point to AR and AKR1C3 as the most promising markers that might help stratify patients for radiotherapy.
DOI: 10.6084/m9.figshare.12800535
title: Supplementary Table S1 from Skeletal ageing in Virunga mountain gorillas

description: Study data
DOI: 10.6084/m9.figshare.12800535.v1
title: Supplementary Table S1 from Skeletal ageing in Virunga mountain gorillas

description: Study data