cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9761663
title: Surveying nocturnal ants, with a novel modification for collecting nocturnal arboreal ants

description: These datasets contain presence/absence data of ant species collected from Mt. Isarog, Philippines. Ants were collected using three techniques: leaf litter sampling, pitfall sampling and beating. Ants were collected during the day and during the night.
DOI: 10.6084/m9.figshare.9761663.v1
title: Surveying nocturnal ants, with a novel modification for collecting nocturnal arboreal ants

description: These datasets contain presence/absence data of ant species collected from Mt. Isarog, Philippines. Ants were collected using three techniques: leaf litter sampling, pitfall sampling and beating. Ants were collected during the day and during the night.
DOI: 10.6084/m9.figshare.12869276
title: Changes in antibiosis growth stage data.xlsx

description: Dataset of:<i>Rhopalosiphum padi </i>(bird cherry-oat aphid) mean relative growth rate (mRGR), % survival (after 7 days), number of days to produce 1st nymph, and nymph production on <i>Triticum aestivum </i>var. Solstice, <i>Triticum monococcum </i>MDR037, MDR045 and MDR049 at four different growth stages; Zadocks growth stage 11, 12-13, 37-41, 51-55 at the start of experimentation.
DOI: 10.6084/m9.figshare.12869276.v1
title: Changes in antibiosis growth stage data.xlsx

description: Dataset of:<i>Rhopalosiphum padi </i>(bird cherry-oat aphid) mean relative growth rate (mRGR), % survival (after 7 days), number of days to produce 1st nymph, and nymph production on <i>Triticum aestivum </i>var. Solstice, <i>Triticum monococcum </i>MDR037, MDR045 and MDR049 at four different growth stages; Zadocks growth stage 11, 12-13, 37-41, 51-55 at the start of experimentation.
DOI: 10.6084/m9.figshare.9761558
title: Supplementary Material for: Outcomes of Prophylactic Pantoprazole in Adult Intensive Care Unit Patients Receiving Dialysis: Results of a Randomized Trial

description: <b><i>Background:</i></b> Intensive care unit (ICU) patients with acute kidney injury requiring renal replacement therapy (RRT) are considered at high risk of gastrointestinal (GI) bleeding and stress ulcer prophylaxis (SUP) is often prescribed. We aimed to assess the incidence of GI bleeding and effects of SUP in these patients. <b><i>Methods:</i></b> We assessed GI bleeding in ICU patients receiving RRT at baseline (and at any time in the ICU) and effects of prophylactic pantoprazole versus placebo in the international SUP in the ICU (SUP-ICU) trial. All analyses were conducted according to a published protocol and statistical analysis plan. <b><i>Results:</i></b> Data of 3,291 acutely admitted adult ICU patients with one or more risk factors for GI bleeding randomized to pantoprazole or placebo intravenously once daily during ICU stay (until ICU discharge, death, or a maximum of 90 days) were analyzed. Some 20 out of 258 (7.8%, 95% CI 4.5–11.1%) and 52 out of 568 (9.2%, 95% CI 6.8–11.6%) of the patients receiving RRT at baseline and at any time in ICU, respectively, developed clinically important GI bleeding in the ICU. We did not observe statistically significant differences in the intervention effect (pantoprazole vs. placebo) in the proportion of patients with clinically important GI bleeding, clinically important events, infectious adverse events, use of interventions to stop GI bleeding, or 90-day mortality in patients with versus without RRT at baseline. <b><i>Conclusions:</i></b> In adult ICU patients receiving RRT at baseline, we observed high incidences of clinically important GI bleeding, but did not observe effects of pantoprazole versus placebo in this subgroup.
DOI: 10.6084/m9.figshare.9761612.v2
title: data and core codes

description: In this study, we proposed a method for building navigation networks of indoor spaces based on a quantitative visibility analysis.
DOI: 10.6084/m9.figshare.9761612.v3
title: Generation of navigation networks for corridor spaces based on indoor visibility map()data and core codes

description: In this study, we proposed a method for building navigation networks of indoor spaces based on a quantitative visibility analysis. we share data and core codes in the figshare repository.
DOI: 10.6084/m9.figshare.9761528
title: LSK109_R10_NBD_EcoliK12MG1655_ZymoMock.tar.gz

description: Raw nanopore reads from EcoliK12MG1655 (demultiplex and look for barcode 13) related to the blogpost (https://albertsenlab.org/ar10e-we-there-yet/)
DOI: 10.6084/m9.figshare.9761495
title: Deciphering the BSE-type specific cell and tissue tropisms of atypical (H and L) and classical BSE

description: After the discovery of two atypical bovine spongiform encephalopathy (BSE) forms in France and Italy designated H- and L-BSE, the question arose whether these new forms differed from classical BSE (C-BSE) in their pathogenesis. Samples collected from cattle in the clinical stage of BSE during an intracranial challenge study with L- and H-BSE were analysed using biochemical and histological methods as well as in a transgenic mouse bioassay. Our results generally confirmed what had been described for C-BSE to be true also for both atypical BSE forms, namely the restriction of the pathological prion protein (PrP<sup>Sc</sup>) and BSE infectivity to the nervous system. However, analysis of samples collected under identical conditions from both atypical H- and L-BSE forms allowed us a more precise assessment of the grade of involvement of different tissues during the clinical end stage of disease as compared to C-BSE. One important feature is the involvement of the peripheral nervous and musculoskeletal tissues in both L-BSE and H-BSE affected cattle. We were, however, able to show that in H-BSE cases, the PrP<sup>Sc</sup> depositions in the central and peripheral nervous system are dominated by a glial pattern, whereas a neuronal deposition pattern dominates in L-BSE cases, indicating differences in the cellular and topical tropism of both atypical BSE forms. As a consequence of this cell tropism, H-BSE seems to spread more rapidly from the CNS into the periphery via the glial cell system such as Schwann cells, as opposed to L-BSE which is mostly propagated via neuronal cells.
DOI: 10.6084/m9.figshare.9761483
title: Final Table.xlsx

description: full result<br>
DOI: 10.6084/m9.figshare.9761483.v1
title: Final Table.xlsx

description: full result<br>
DOI: 10.6084/m9.figshare.9761393
title: Supplementary Material for: Reduced Cerebellar Size at Term-Equivalent Age Is Related to a 17% Lower Mental Developmental Index in Very Preterm Infants without Brain Injury

description: <b><i>Introduction:</i></b> Cerebellar injury is increasingly recognized as a relevant complication of premature birth. However, the prevalence of reduced cerebellar growth and its consequences for neurodevelopmental outcome in preterm infants without overt brain injury remain to be defined in detail. The aim of this study was to assess the transcerebellar diameter (TCD) at term-equivalent age (TEA) in very preterm infants without brain injury and to evaluate whether TCD is related to neurodevelopmental outcome in this population. <b><i>Methods:</i></b> Very preterm infants underwent magnetic resonance imaging at TEA. Infants with any grade of supra- or infratentorial brain injury were excluded. TCD was measured and categorized using existing cut-off values as normal TCD and mild or severe TCD reduction. Psychomotor Developmental index (PDI) and Mental Developmental index (MDI) were assessed using Bayley Scales of Infant Development II and III at a corrected age of 2 years. <b><i>Results:</i></b> A total of 166 infants with a mean gestational age of 29.9 ± 1.8 weeks and a mean birth weight of 1,317 ± 393 g were included. Mean TCD of girls was significantly lower compared to the mean TCD of boys (<i>p</i> = 0.004). TCD reduction was present in 8 infants (4.8%). Infants with a mild TCD reduction achieved lower mean MDI than infants with normal TCD (<i>p</i> = 0.021). <b><i>Discussion:</i></b> We found that reduced TCD was associated with a 17% lower mean MDI at a corrected age of 2 years. Thus, TCD at TEA may be used as an imaging marker for adverse cognitive outcome in the apparently low-risk group of preterm infants without brain injury.
DOI: 10.6084/m9.figshare.9761321
title: Supplementary Table

description: Supplementary files of our article.
DOI: 10.6084/m9.figshare.9761315
title: Paraquat and Parkinson’s disease: a systematic review and meta-analysis of observational studies

description: This investigation aimed to conduct a systematic review of the literature and meta-analysis to determine whether exposure to the herbicide paraquat was associated with the development of Parkinson’s disease (PD). Observational studies that enrolled adults exposed to paraquat with PD as the outcome of interest were searched in the PubMed, Embase, LILACS, TOXNET, and Web of Science databases up to May 2019. Two authors independently selected relevant studies, extracted data, and assessed methodological quality. The evidence certainty was assessed by the GRADE approach, which served as basis for a tentative causality assessment, supplemented by the Bradford Hill criteria when necessary. Results from nine case–control studies indicated that PD occurrence was 25% higher in participants exposed to paraquat. The only cohort investigation included demonstrated a non-significant OR of 1.08. Results from subgroup analyses also indicated higher PD frequency in participants that were exposed to paraquat for longer periods or individuals co-exposed with paraquat and any other dithiocarbamate. Data indicate apositive association between exposure to paraquat and PD occurrence, but the weight-of-evidence does not enable one to assume an indisputable cause–effect relationship between these two conditions. Better designed studies are needed to increase confidence in results. <b>Systematic Review Registration</b>: PROSPERO CRD42017069994.
DOI: 10.6084/m9.figshare.9761231
title: Complete blood count evaluation of dogs: four chemotherapy protocols

description: This retrospective study aimed to evaluate potential hematological alterations in dogs treated with four different antineoplastic protocols.
DOI: 10.6084/m9.figshare.9761321.v2
title: Supplementary Table

description: Supplementary files of our article.
DOI: 10.6084/m9.figshare.9761321.v1
title: Supplementary Table

description: Supplementary files of our articles.
DOI: 10.6084/m9.figshare.9761231.v1
title: Complete blood count evaluation of dogs: four chemotherapy protocols

description: This retrospective study aimed to evaluate potential hematological alterations in dogs treated with four different antineoplastic protocols.
DOI: 10.6084/m9.figshare.9761222.v1
title: MEP_Olfactory_Data

description: Head-fixed mice were trained to perform an olfactory delayed non-match to sample task. For each trial, an olfactory stimulus (ethyl acetate, EA, or 2-pentanone, 2P) was presented as the sample, followed by a delay period (5 s) and then a testing olfactory stimulus, either matched or non-matched to the sample. Water-restricted mice were rewarded with water if they licked within a response time window in the non-match but not match trials. The mouse performed tasks continuously with a 10 s rest between neighboring trials. The experiment is designed to separate the working memory period and decision-making period.
DOI: 10.6084/m9.figshare.9761315.v3
title: Paraquat and Parkinson’s disease: a systematic review and meta-analysis of observational studies

description: This investigation aimed to conduct a systematic review of the literature and meta-analysis to determine whether exposure to the herbicide paraquat was associated with the development of Parkinson’s disease (PD). Observational studies that enrolled adults exposed to paraquat with PD as the outcome of interest were searched in the PubMed, Embase, LILACS, TOXNET, and Web of Science databases up to May 2019. Two authors independently selected relevant studies, extracted data, and assessed methodological quality. The evidence certainty was assessed by the GRADE approach, which served as basis for a tentative causality assessment, supplemented by the Bradford Hill criteria when necessary. Results from nine case–control studies indicated that PD occurrence was 25% higher in participants exposed to paraquat. The only cohort investigation included demonstrated a non-significant OR of 1.08. Results from subgroup analyses also indicated higher PD frequency in participants that were exposed to paraquat for longer periods or individuals co-exposed with paraquat and any other dithiocarbamate. Data indicate apositive association between exposure to paraquat and PD occurrence, but the weight-of-evidence does not enable one to assume an indisputable cause–effect relationship between these two conditions. Better designed studies are needed to increase confidence in results. <b>Systematic Review Registration</b>: PROSPERO CRD42017069994.
DOI: 10.6084/m9.figshare.9761315.v2
title: Paraquat and Parkinson’s disease: a systematic review and meta-analysis of observational studies

description: This investigation aimed to conduct a systematic review of the literature and meta-analysis to determine whether exposure to the herbicide paraquat was associated with the development of Parkinson’s disease (PD). Observational studies that enrolled adults exposed to paraquat with PD as the outcome of interest were searched in the PubMed, Embase, LILACS, TOXNET, and Web of Science databases up to May 2019. Two authors independently selected relevant studies, extracted data, and assessed methodological quality. The evidence certainty was assessed by the GRADE approach, which served as basis for a tentative causality assessment, supplemented by the Bradford Hill criteria when necessary. Results from nine case–control studies indicated that PD occurrence was 25% higher in participants exposed to paraquat. The only cohort investigation included demonstrated a non-significant OR of 1.08. Results from subgroup analyses also indicated higher PD frequency in participants that were exposed to paraquat for longer periods or individuals co-exposed with paraquat and any other dithiocarbamate. Data indicate apositive association between exposure to paraquat and PD occurrence, but the weight-of-evidence does not enable one to assume an indisputable cause–effect relationship between these two conditions. Better designed studies are needed to increase confidence in results. <b>Systematic Review Registration</b>: PROSPERO CRD42017069994.
DOI: 10.6084/m9.figshare.9761231.v2
title: Complete blood count evaluation of dogs: four chemotherapy protocols

description: This retrospective study aimed to evaluate potential hematological alterations in dogs treated with four different antineoplastic protocols.
DOI: 10.6084/m9.figshare.9761000
title: Additional file 6: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S6. Cluster Locator analyses of the FDRâ
DOI: 10.6084/m9.figshare.9760997
title: Additional file 5: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S5. MtDNA-sensitive genes are often under-enriched in housekeeping gene lists. Hypergeometric analyses of enrichment of mtDNA sensitive genes (FDR
DOI: 10.6084/m9.figshare.9761000.v1
title: Additional file 6: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S6. Cluster Locator analyses of the FDRâ
DOI: 10.6084/m9.figshare.9760991
title: Additional file 4: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S4. Gene ontologies of the five focal regions described in Fig. 7. GO Process, GO function and GO component terms are shown for each region, along with their metrics. (XLSX 137 kb)
DOI: 10.6084/m9.figshare.9760997.v1
title: Additional file 5: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S5. MtDNA-sensitive genes are often under-enriched in housekeeping gene lists. Hypergeometric analyses of enrichment of mtDNA sensitive genes (FDR
DOI: 10.6084/m9.figshare.9760982
title: Additional file 3: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S3. Gene rankings of sensitized PPI hubs in female and male data sets. (XLSX 836 kb)
DOI: 10.6084/m9.figshare.9760991.v1
title: Additional file 4: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S4. Gene ontologies of the five focal regions described in Fig. 7. GO Process, GO function and GO component terms are shown for each region, along with their metrics. (XLSX 137 kb)
DOI: 10.6084/m9.figshare.9760970
title: Additional file 2: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S2. Genes that are DE by ΔmtDNA ‘species’ (FDR
DOI: 10.6084/m9.figshare.9760982.v1
title: Additional file 3: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S3. Gene rankings of sensitized PPI hubs in female and male data sets. (XLSX 836 kb)
DOI: 10.6084/m9.figshare.9760970.v1
title: Additional file 2: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S2. Genes that are DE by ΔmtDNA ‘species’ (FDR
DOI: 10.6084/m9.figshare.9760958
title: Additional file 1: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S1. Genes that are DE by ΔmtDNA ‘haplotype’ (FDR
DOI: 10.6084/m9.figshare.9760958.v1
title: Additional file 1: of Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks

description: Table S1. Genes that are DE by ΔmtDNA ‘haplotype’ (FDR
DOI: 10.6084/m9.figshare.9760931
title: Additional file 1: of Sexual practices, sexual behavior and HIV risk profile of key populations in Nigeria

description: Data collection tool for sexual practices, sexual behavior and HIV risk profile of key populations in Nigeria (N = 488). (RTF 2339 kb)
DOI: 10.6084/m9.figshare.9760931.v1
title: Additional file 1: of Sexual practices, sexual behavior and HIV risk profile of key populations in Nigeria

description: Data collection tool for sexual practices, sexual behavior and HIV risk profile of key populations in Nigeria (N = 488). (RTF 2339 kb)
DOI: 10.6084/m9.figshare.9760823
title: Additional file 6 of SigsPack, a package for cancer mutational signatures

description: Tri-nucleotide frequency effect in 13 samples from 3 colon cancer patients. Exposure estimation for 13 samples from 3 colon cancer patients (4, 5 & 4 samples from patients 69, 80 & 99 resp.), after normalization of the mutational catalogue to the genome tri-nucleotides frequencies (Genome) and after normalization of the mutation signatures to the regions enriched by the Agilent SureSelect XT Human All Exon V4 kit (Exome). (TSV 14 kb)
DOI: 10.6084/m9.figshare.9760823.v1
title: Additional file 6 of SigsPack, a package for cancer mutational signatures

description: Tri-nucleotide frequency effect in 13 samples from 3 colon cancer patients. Exposure estimation for 13 samples from 3 colon cancer patients (4, 5 & 4 samples from patients 69, 80 & 99 resp.), after normalization of the mutational catalogue to the genome tri-nucleotides frequencies (Genome) and after normalization of the mutation signatures to the regions enriched by the Agilent SureSelect XT Human All Exon V4 kit (Exome). (TSV 14 kb)
DOI: 10.6084/m9.figshare.9760820
title: Additional file 5 of SigsPack, a package for cancer mutational signatures

description: Tri-nucleotide frequencies in the human genome & exome kit. Counts of tri-nucleotides in the human genome GRCh37 (Genome) and in the regions covered by the Agilent SureSelect XT Human All Exon V4 kit (Exome). The counts aggregate the tri-nucleotide sequence shown in the Cotext column and its reverse complement. (TSV 1 kb)
DOI: 10.6084/m9.figshare.9760811
title: Additional file 4 of SigsPack, a package for cancer mutational signatures

description: Exposure estimation for 13 samples from 3 colon cancer patients. Exposure estimation for 13 samples from 3 colon cancer patients (4, 5 & 4 samples from patients 69, 80 & 99 resp.). The mutational catalogues was resampled 1000 times, and for each signature, the minimum, first quartile, median, third quartile and maximum values of exposures computed from the re-sampled data are shown. (TSV 34 kb)
DOI: 10.6084/m9.figshare.9760811.v1
title: Additional file 4 of SigsPack, a package for cancer mutational signatures

description: Exposure estimation for 13 samples from 3 colon cancer patients. Exposure estimation for 13 samples from 3 colon cancer patients (4, 5 & 4 samples from patients 69, 80 & 99 resp.). The mutational catalogues was resampled 1000 times, and for each signature, the minimum, first quartile, median, third quartile and maximum values of exposures computed from the re-sampled data are shown. (TSV 34 kb)
DOI: 10.6084/m9.figshare.9760820.v1
title: Additional file 5 of SigsPack, a package for cancer mutational signatures

description: Tri-nucleotide frequencies in the human genome & exome kit. Counts of tri-nucleotides in the human genome GRCh37 (Genome) and in the regions covered by the Agilent SureSelect XT Human All Exon V4 kit (Exome). The counts aggregate the tri-nucleotide sequence shown in the Cotext column and its reverse complement. (TSV 1 kb)
DOI: 10.6084/m9.figshare.9760799
title: Additional file 3 of SigsPack, a package for cancer mutational signatures

description: Mutational catalogues of the 13 samples used to estimate exposure stability in presence of biological noise. There are 4 samples for patient 69, 5 for patient 80 and 4 for patient 99. All catalogues have been collected using the Agilent SureSelect XT Human All Exon V4 exome enrichment kit. (TSV 3 kb)
DOI: 10.6084/m9.figshare.9760799.v1
title: Additional file 3 of SigsPack, a package for cancer mutational signatures

description: Mutational catalogues of the 13 samples used to estimate exposure stability in presence of biological noise. There are 4 samples for patient 69, 5 for patient 80 and 4 for patient 99. All catalogues have been collected using the Agilent SureSelect XT Human All Exon V4 exome enrichment kit. (TSV 3 kb)
DOI: 10.6084/m9.figshare.9760784
title: Additional file 2 of SigsPack, a package for cancer mutational signatures

description: Exposure estimation for synthetic data example. Exposure estimation from synthetic data. 1000 mutations have been generated at random, using frequencies from set1 (signatures 7, 13, 21, 24 & 28), and set2 (signatures 3, 5, 8, 16, & 25). A perfect reconstruction would have original exposure values very close to 0.2 for these 5 signatures, and 0 for all the others. The mutational catalogues was resampled 1000 times, and for each signature, the minimum, first quartile, median, third quartile and maximum values of exposures computed from the re-sampled data are shown. (TSV 5 kb)