cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7851488
title: C-Stock Endline Datasets

description: Endline data collected in November 2018 as part of the project entitled "Replicating C-Stock: Making Essential Health Commodities Available at the Community Level". Data collected from CHVs, CHAs and facilities in two sub-counties in Kenya.
DOI: 10.1184/r1/7851515.v2
title: Reorganized language network connectivity after left arcuate fasciculus resection: A case study

description: Dataset supporting a paper of the same title: Reorganized language network connectivity after left arcuate fasciculus resection: A case study<br><br>This dataset contains raw MRI data for the patient (DTI, fMRI, Anatomy) and 52 healthy control subjects (DTI, Anatomy). It also contains scripts used to produce the results of the paper including a BASH script to run tractography, and R scripts to run ANOVA on the functional connectivity data. Lastly, it includes summary level data in CSV files that were used as inputs to the scripts to produce the results.<br>ABSTRACT:Understanding the neural mechanisms that support spontaneous recovery of cognitive abilities can place important constraints on mechanistic theories of brain organization and function, and holds potential to inform clinical interventions. Connectivity-based MRI measures have emerged as a way to study how recovery from brain injury is modulated by changes in intra- and interhemispheric connectivity. Here we report a detailed and multi-modal case study of a 26 year-old male who presented with a left inferior parietal glioma infiltrating the left arcuate fasciculus. The patient underwent pre- and post-operative functional MRI and Diffusion Tensor Imaging, as well as behavioral assessments of language, motor, vision and praxis. The surgery for removal of the tumor was carried out with the patient awake, and direct electrical stimulation mapping was used to evaluate cortical language centers. The patient developed a specific difficulty with repeating sentences toward the end of the surgery, after resection of the tumor and partial transection of the arcuate fasciculus. The patient recovered from the sentence repetition impairments over several months after the operation. Coincident with the patient’s cognitive recovery, we document a pattern whereby intra-hemispheric functional connectivity was reduced in the left hemisphere, while inter-hemispheric connectivity increased between classic left hemisphere language regions and their right hemisphere homologues. These findings suggest that increased synchrony between the two hemispheres, in the setting of focal transection of the left arcuate fasciculus, may facilitate functional recovery.<br>
DOI: 10.6084/m9.figshare.7851488.v1
title: C-Stock Endline Datasets

description: Endline data collected in November 2018 as part of the project entitled "Replicating C-Stock: Making Essential Health Commodities Available at the Community Level". Data collected from CHVs, CHAs and facilities in two sub-counties in Kenya.
DOI: 10.1184/r1/7851515.v1
title: Reorganized language network connectivity after left arcuate fasciculus resection: A case study

description: Dataset supporting a paper of the same title: Reorganized language network connectivity after left arcuate fasciculus resection: A case study<br><br>This dataset contains raw MRI data for the patient (DTI, fMRI, Anatomy) and 52 healthy control subjects (DTI, Anatomy). It also contains scripts used to produce the results of the paper including a BASH script to run tractography, and R scripts to run ANOVA on the functional connectivity data. Lastly, it includes summary level data in CSV files that were used as inputs to the scripts to produce the results.<br>ABSTRACT:Understanding the neural mechanisms that support spontaneous recovery of cognitive abilities can place important constraints on mechanistic theories of brain organization and function, and holds potential to inform clinical interventions. Connectivity-based MRI measures have emerged as a way to study how recovery from brain injury is modulated by changes in intra- and interhemispheric connectivity. Here we report a detailed and multi-modal case study of a 26 year-old male who presented with a left inferior parietal glioma infiltrating the left arcuate fasciculus. The patient underwent pre- and post-operative functional MRI and Diffusion Tensor Imaging, as well as behavioral assessments of language, motor, vision and praxis. The surgery for removal of the tumor was carried out with the patient awake, and direct electrical stimulation mapping was used to evaluate cortical language centers. The patient developed a specific difficulty with repeating sentences toward the end of the surgery, after resection of the tumor and partial transection of the arcuate fasciculus. The patient recovered from the sentence repetition impairments over several months after the operation. Coincident with the patient’s cognitive recovery, we document a pattern whereby intra-hemispheric functional connectivity was reduced in the left hemisphere, while inter-hemispheric connectivity increased between classic left hemisphere language regions and their right hemisphere homologues. These findings suggest that increased synchrony between the two hemispheres, in the setting of focal transection of the left arcuate fasciculus, may facilitate functional recovery.<br>
DOI: 10.6084/m9.figshare.7851464
title: Reduced exploration capacity despite brain volume increase in warm acclimated common minnow

description: Data from study testing effect of warm acclimation on metabolism, brain morphology, behavior and cognitive capacity of common minnow.
DOI: 10.6084/m9.figshare.7851521.v1
title: Combination of novel transcripts from de novo assembly and genes from reference annotations for 11 species

description: Details about the creation of these assemblies can be found at doi.org/10.1101/575837
DOI: 10.6084/m9.figshare.7851452
title: C-Stock Baseline Datasets

description: Baseline data collected in October/November 2017 as part of the project entitled "Replicating C-Stock: Making Essential Health Commodities Available at the Community Level". Data collected from CHVs, CHAs and facilities in two sub-counties in Kenya.
DOI: 10.6084/m9.figshare.7851464.v1
title: Reduced exploration capacity despite brain volume increase in warm acclimated common minnow

description: Data from study testing effect of warm acclimation on metabolism, brain morphology, behavior and cognitive capacity of common minnow.
DOI: 10.6084/m9.figshare.7851467.v2
title: Metabolic pathways phylogenies / Photosynthesis phylogenies

description: Phylogenetic reconstructions of 30 enzymes for plastid metabolic pathways (isoprenoid, heme, iron-sulfur cluster and fatty acid biosynthesis) and 8 photosynthetic complex subunits as pdf figure (*.tre.pdf) and in newick format (*.tre). Trees were inferred using IQ-TREE, using the best model identified for each alignment separately, node support was calculated using 1000 ultrafast bootstrap (UFBoot) replicates. In the pdf figures: groups are indicated by colored taxon names: green, Viridiplantae; red, rhodophytes; grey, glaucophytes; turquoise, cryptophytes; pink, stramenopiles; dark blue, haptophytes; yellow, dinoflagellates; light green, RSD; orange, chrompodellids/Apicomplexa; brown, Opisthokonta/Amoebozoa/Apusozoa/Ancyromonadida/ciliates; black, prokaryotes. Selected clades are collapsed for increased clarity, see corresponding newick files for full trees. Filenames contain, in that order, the pathway/photosynthetic complex, the query ID, the name of the gene, the e-value used for parsing the BLASTP result (if deviating from the default of ≤1e-25 = 1E25) and the model used for tree reconstruction. See Fig. 2 and Table S2 in the manuscript for overview of the enzymes/subunits.
DOI: 10.6084/m9.figshare.7851467
title: Metabolic pathways phylogenies / Photosynthesis phylogenies

description: Phylogenetic reconstructions of 30 enzymes for plastid metabolic pathways (isoprenoid, heme, iron-sulfur cluster and fatty acid biosynthesis) and 8 photosynthetic complex subunits as pdf figure (*.tre.pdf) and in newick format (*.tre). Trees were inferred using IQ-TREE, using the best model identified for each alignment separately, node support was calculated using 1000 ultrafast bootstrap (UFBoot) replicates. In the pdf figures: groups are indicated by colored taxon names: green, Viridiplantae; red, rhodophytes; grey, glaucophytes; turquoise, cryptophytes; pink, stramenopiles; dark blue, haptophytes; yellow, dinoflagellates; light green, RSD; orange, chrompodellids/Apicomplexa; brown, Opisthokonta/Amoebozoa/Apusozoa/Ancyromonadida/ciliates; black, prokaryotes. Selected clades are collapsed for increased clarity, see corresponding newick files for full trees. Filenames contain, in that order, the pathway/photosynthetic complex, the query ID, the name of the gene, the e-value used for parsing the BLASTP result (if deviating from the default of ≤1e-25 = 1E25) and the model used for tree reconstruction. See Fig. 2 and Table S2 in the manuscript for overview of the enzymes/subunits.
DOI: 10.6084/m9.figshare.7851332
title: Undergraduate Data files

description: Male fish Brightness Data over Varying Predator Concentrations and Environments. <br>
DOI: 10.6084/m9.figshare.7851332.v1
title: Undergraduate Data files - SimBio Guppy

description: Male Guppy Brightness Data over Varying Predator Concentrations and Environments. <br>
DOI: 10.6084/m9.figshare.7851296
title: Mannose-binding lectin has a direct deleterious effect on ischemic brain microvascular endothelial cells

description: Raw data from the ms by Neglia et al.
DOI: 10.6084/m9.figshare.7851218
title: vSNP dependencies

description: minimal dependencies folder for vSNP pipeline
DOI: 10.6084/m9.figshare.7851218.v2
title: vSNP dependencies

description: minimal dependencies folder for vSNP pipeline
DOI: 10.6084/m9.figshare.7851218.v1
title: vSNP dependencies

description: minimal dependencies folder for vSNP pipeline
DOI: 10.6084/m9.figshare.7851047
title: Coder A

description: The standard biomedical terminologies ICD-10, ICD-O, TNM, MeSH, NCIt, MedDRA, and SNOMED CT were used in a case study where two dimensions of cancer (anatomy and histology) had already been coded in a dataset using a custom terminology (ROCHE).
DOI: 10.6084/m9.figshare.7851047.v1
title: Coder A

description: The standard biomedical terminologies ICD-10, ICD-O, TNM, MeSH, NCIt, MedDRA, and SNOMED CT were used in a case study where two dimensions of cancer (anatomy and histology) had already been coded in a dataset using a custom terminology (ROCHE).
DOI: 10.6084/m9.figshare.7851005
title: GRCh37/hg19 RepeatMasker

description: We used RepeatMasker with Dfam2.0 and RepBaseRepeat MaskerEdition 20170127 libraries on GRCh37/hg19 human genome reference and here are the results.<br><br>If you are using this data, please cite RepeatMasker, Dfam and Repbase.<br>
DOI: 10.6084/m9.figshare.7851005.v1
title: GRCh37/hg19 RepeatMasker

description: We used RepeatMasker with Dfam2.0 and RepBaseRepeat MaskerEdition 20170127 libraries on GRCh37/hg19 human genome reference and here are the results.<br><br>If you are using this data, please cite RepeatMasker, Dfam and Repbase.<br>
DOI: 10.6084/m9.figshare.7850987
title: Predictors of pediatric attrition from HIV care in Kenya

description: The minimal data set contains deidentified records for pediatric care and treatment data collected in Kenya.
DOI: 10.6084/m9.figshare.7850987.v1
title: Predictors of pediatric attrition from HIV care in Kenya

description: The minimal data set contains deidentified records for pediatric care and treatment data collected in Kenya.
DOI: 10.6084/m9.figshare.7850978
title: Supplementary Material for: Effects of an Oral CRTh2 Antagonist (AZD1981) on Eosinophil Activity and Symptoms in Chronic Spontaneous Urticaria

description: <b><i>Background:</i></b> Approximately 50% of patients with chronic spontaneous urticaria (CSU) experience symptoms that are not fully controlled by antihistamines, indicating an unmet clinical need. <b><i>Objective:</i></b> To evaluate the effects of the selective CRTh2 antagonist AZD1981 on symptoms and targeted leukocytes in adults with persistent CSU despite treatment with H<sub>1</sub>-antihistamines. <b><i>Methods:</i></b> We performed a single-center, randomized, placebo-controlled study involving adult CSU subjects with symptoms despite daily antihistamines. The subjects underwent a 2-week placebo run-in and 4 weeks of double-blinded therapy with either AZD1981 40 mg TID or placebo, followed by a 2-week placebo washout. The primary objective was to assess the effect of AZD1981 on CSU signs and symptoms. Secondary objectives included the effects of AZD1981 on prostaglandin D<sub>2</sub> (PGD<sub>2</sub>)-induced eosinophil shape change, circulating leukocyte subsets, CRTh2 expression on blood leukocytes, and total blood leukocyte histamine content. <b><i>Results:</i></b> Twenty-eight subjects were randomized to AZD1981 or placebo, with 26 subjects completing the study. The urticaria activity scores declined during the treatment phase in both groups, and they were significantly reduced in the AZD1981 group at the end of washout. AZD1981 treatment increased circulating eosinophils and significantly impaired PGD<sub>2</sub>-mediated eosinophil shape change. CRTh2 surface expression rose significantly on blood basophils during active treatment. No serious adverse events were observed. <b><i>Conclusions:</i></b> This is the first study to examine the efficacy of a CRTh2 antagonist in antihistamine-refractory CSU. AZD1981 treatment was well tolerated, effectively inhibited PGD<sub>2</sub>-mediated eosinophil shape change, shifted numbers of circulating eosinophils, and reduced weekly itch scores more than hives during treatment and into washout. Further studies are needed to determine whether inhibition of the PGD<sub>2</sub>/CRTh2 pathway will be an ­effective treatment for CSU.
DOI: 10.6084/m9.figshare.7850981
title: REPORT_GWAS.xlsx

description: An association analysis was conducted for severe CAC using 550,779 SNPs at the Seoul National University Hospital Healthcare System Gangnam Center in Korea.
DOI: 10.6084/m9.figshare.7850981.v1
title: REPORT_GWAS.xlsx

description: An association analysis was conducted for severe CAC using 550,779 SNPs at the Seoul National University Hospital Healthcare System Gangnam Center in Korea.
DOI: 10.6084/m9.figshare.7850978.v1
title: Supplementary Material for: Effects of an Oral CRTh2 Antagonist (AZD1981) on Eosinophil Activity and Symptoms in Chronic Spontaneous Urticaria

description: <b><i>Background:</i></b> Approximately 50% of patients with chronic spontaneous urticaria (CSU) experience symptoms that are not fully controlled by antihistamines, indicating an unmet clinical need. <b><i>Objective:</i></b> To evaluate the effects of the selective CRTh2 antagonist AZD1981 on symptoms and targeted leukocytes in adults with persistent CSU despite treatment with H<sub>1</sub>-antihistamines. <b><i>Methods:</i></b> We performed a single-center, randomized, placebo-controlled study involving adult CSU subjects with symptoms despite daily antihistamines. The subjects underwent a 2-week placebo run-in and 4 weeks of double-blinded therapy with either AZD1981 40 mg TID or placebo, followed by a 2-week placebo washout. The primary objective was to assess the effect of AZD1981 on CSU signs and symptoms. Secondary objectives included the effects of AZD1981 on prostaglandin D<sub>2</sub> (PGD<sub>2</sub>)-induced eosinophil shape change, circulating leukocyte subsets, CRTh2 expression on blood leukocytes, and total blood leukocyte histamine content. <b><i>Results:</i></b> Twenty-eight subjects were randomized to AZD1981 or placebo, with 26 subjects completing the study. The urticaria activity scores declined during the treatment phase in both groups, and they were significantly reduced in the AZD1981 group at the end of washout. AZD1981 treatment increased circulating eosinophils and significantly impaired PGD<sub>2</sub>-mediated eosinophil shape change. CRTh2 surface expression rose significantly on blood basophils during active treatment. No serious adverse events were observed. <b><i>Conclusions:</i></b> This is the first study to examine the efficacy of a CRTh2 antagonist in antihistamine-refractory CSU. AZD1981 treatment was well tolerated, effectively inhibited PGD<sub>2</sub>-mediated eosinophil shape change, shifted numbers of circulating eosinophils, and reduced weekly itch scores more than hives during treatment and into washout. Further studies are needed to determine whether inhibition of the PGD<sub>2</sub>/CRTh2 pathway will be an ­effective treatment for CSU.
DOI: 10.6084/m9.figshare.7850954
title: Data for "What drives the future supply of regulating ecosystem services in a mountain forest landscape?"

description: Data used in the paper:<b>What drives the future supply of regulating ecosystem services </b><b>in a mountain forest landscape?</b>byRupert Seidl, Katharina Albrich, Karlheinz Erb, Herbert Formayer, David Leidinger, Georg Leitinger, Ulrike Tappeiner, Erich Tasser, and Werner Rammer<br><br><br>The data set contains landscape level aggregates for 9 regulating services for five points in time under 5 different climate scenarios and different assumptions regarding forest management and disturbance.<br>See about.txt for a detailed description.<br>
DOI: 10.6084/m9.figshare.7850948
title: Database of all genes in Escherichia coli K-12 MG1655 which are not susceptible to restriction enzyme digestion by NdeI and BamHI

description: Discovery of restriction enzymes that cuts DNA at specific sites ushered in the age of recombinant DNA technology. Although in use for more than 40 years, restriction enzymes remain an essential tool in genetic engineering workflow. Specifically, whether two or multiple fragment assembly, restriction enzymes are enabling tools for cutting DNA, and more crucially, generating the sticky ends that would enable DNA fragments to assemble in desired pattern and orientation. Through the decades, an expanding compendium of restriction enzymes capable of cutting single or double DNA strands as well as generating sticky or blunt ends has been discovered and catalogued. While characteristics of specific restriction enzyme can be obtained from product catalogues, key information concerning whether a gene contains the recognition site of a restriction enzyme remain inaccessible except with a bioinformatic search. Such information on the presence of a recognition site in a gene play a key role in restriction enzyme selection and success in gene cloning or DNA assembly as presence of a recognition sequence of a restriction enzyme would result in the digestion of the gene during the cloning process. Thus, the objective of this database is to provide information on whether the recognition site of two commonly used restriction enzymes, NdeI and BamHI are present in the genes of <i>Escherichia coli </i>K-12 MG1655 (Genbank accession number, NC_000913.3). An in-house MATLAB algorithm was used to parse gene identity and sequence information from the annotated genome sequence of <i>E. coli</i> K-12 MG1655. With the recognition sequence of the two restriction enzymes serving as inputs to the MATLAB programme, the algorithm was capable of cycling through all annotated genes in the<i> E. coli </i>genome and determine if each one contains the recognition sequence of NdeI or BamHI. In cases where the recognition sequence of the restriction enzyme is present in the gene sequence, a value of 1 will be output, otherwise, a value of 0 will be recorded. In short, the database catalogues whether genes in <i>E. coli</i> K-12 MG1655 contains recognition sequence of NdeI and BamHI restriction enzyme. Such information would find use in selecting appropriate restriction enzymes for cloning particular genes from <i>E. coli</i> K-12 MG1655.<br>
DOI: 10.6084/m9.figshare.7850948.v1
title: Database of all genes in Escherichia coli K-12 MG1655 which are not susceptible to restriction enzyme digestion by NdeI and BamHI

description: Discovery of restriction enzymes that cuts DNA at specific sites ushered in the age of recombinant DNA technology. Although in use for more than 40 years, restriction enzymes remain an essential tool in genetic engineering workflow. Specifically, whether two or multiple fragment assembly, restriction enzymes are enabling tools for cutting DNA, and more crucially, generating the sticky ends that would enable DNA fragments to assemble in desired pattern and orientation. Through the decades, an expanding compendium of restriction enzymes capable of cutting single or double DNA strands as well as generating sticky or blunt ends has been discovered and catalogued. While characteristics of specific restriction enzyme can be obtained from product catalogues, key information concerning whether a gene contains the recognition site of a restriction enzyme remain inaccessible except with a bioinformatic search. Such information on the presence of a recognition site in a gene play a key role in restriction enzyme selection and success in gene cloning or DNA assembly as presence of a recognition sequence of a restriction enzyme would result in the digestion of the gene during the cloning process. Thus, the objective of this database is to provide information on whether the recognition site of two commonly used restriction enzymes, NdeI and BamHI are present in the genes of <i>Escherichia coli </i>K-12 MG1655 (Genbank accession number, NC_000913.3). An in-house MATLAB algorithm was used to parse gene identity and sequence information from the annotated genome sequence of <i>E. coli</i> K-12 MG1655. With the recognition sequence of the two restriction enzymes serving as inputs to the MATLAB programme, the algorithm was capable of cycling through all annotated genes in the<i> E. coli </i>genome and determine if each one contains the recognition sequence of NdeI or BamHI. In cases where the recognition sequence of the restriction enzyme is present in the gene sequence, a value of 1 will be output, otherwise, a value of 0 will be recorded. In short, the database catalogues whether genes in <i>E. coli</i> K-12 MG1655 contains recognition sequence of NdeI and BamHI restriction enzyme. Such information would find use in selecting appropriate restriction enzymes for cloning particular genes from <i>E. coli</i> K-12 MG1655.<br>
DOI: 10.6084/m9.figshare.7850918
title: Dataset for testing the Discovery of Automatable Routines from User Interaction Logs

description: This is the set of user interaction logs used to evalution the approach proposed in the paper titled: "Discovery Automatable Routines From User Interaction Logs".<br>A. Bosco, A. Augusto, M. Dumas, M. La Rosa, G. Fortino
DOI: 10.6084/m9.figshare.7850882
title: Whole-genome Linkage Disequilibrium Maps for European and African Populations

description: These data are in Browser Extensible Data (BED) format, including the cumulative LDU position of every SNP marker within the generated maps. Additionally, these data are also made available as the kb/LDU ratio for each inter-SNP span providing a view of the regional 'intensity' of LD. These files are compatible with many commonly used genomic analysis tools.