cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12093456
title: Dataset for: Spatial variability of heavy metals in native oysters from an anthropogenically impacted estuary in Northeastern Brazil

description: Dataset 1 Native oysters:This dataset compares the bioconcentration of heavy metals (Cd, Cr, Cu, Pb, Ni, and Zn) in the soft tissues of native oysters (<i>Crassostrea rhizophorae</i>) from two estuarine areas in the Potengi estuary, northeastern coast of Brazil. The purpose was to test the hypotheses of relevant differences in bioaccumulation while the environmental conditions change upward the stream.<br>A - Class: overall sample ordination.B - Collection Site: categorical information which divides the dataset into 2 groups: oysters collected in Naval Base (NB), and oysters collected in Quartel (Qt).C - D sampling date (dd/mm/aa); and time (hh: mm): recording of the moment of samplingE - Ebb tide hour (hh: mm): lower tide occurrence on the sampling dateF -Tide level: tide height at the time of collection in meters (m)G - Tare (g): weight of the recipient (grams)H - Total weight (g): soft tissue + recipient weight after dehydration processI - Dry weight (g) = soft tissue after dehydration process (H – G)J - Shell length: length of the longer shaft (cm)K - Shell (g = ml): volume of the shells. Calculated through volumetric methodology (i.e., water column displacement in a graduated Becker)L - Condition Index - CI = (dehydrated soft tissue weight /shell volume) * 100. Results are expressed in (g/ cm³)M - FALCON #: polypropylene tube identificationN-S Metals in parts per billion (ppb)T-Y Metals in milligrams per kilograms (mg/kg)
DOI: 10.6084/m9.figshare.12093438
title: Matlab workspaces for Zaydman et al

description: This zip file contains all .mat workspaces needed to run supplemental code for Zaydman et al.
DOI: 10.6084/m9.figshare.12093438.v1
title: Matlab workspaces for Zaydman et al

description: This zip file contains all .mat workspaces needed to run supplemental code for Zaydman et al.
DOI: 10.6084/m9.figshare.12093360
title: datasetHealthcareAccIndex.xlsx

description: Healthcare accessibility index published at municipality-level (Continental Portugal only)
DOI: 10.6084/m9.figshare.12093360.v1
title: datasetHealthcareAccIndex.xlsx

description: Healthcare accessibility index published at municipality-level (Continental Portugal only)
DOI: 10.6084/m9.figshare.12092139
title: P6.zip

description: PNAS
DOI: 10.6084/m9.figshare.12092139.v1
title: P6.zip

description: PNAS
DOI: 10.6084/m9.figshare.12091971
title: Supplementary Material for: Expanding Primary Care to Pharmaceutical Patient Care in Diabetes Mellitus Type 2 through the European Union’s Community Pharmacies, between 2008 and 2018: A Systematic Review

description: <b><i>Background:</i></b> The analysis of the European Union (EU28) health systems’ intervention for type 2 diabetes mellitus (T2DM) reports an insufficient combination of legal support, prevention, and early diagnosis. This fact compromises the patient’s health outcomes. The inclusion of pharmacy services oriented to T2DM (PS-T2DM) in strategic primary care network’s programs could be a solution. However, the different regulatory frameworks that include good pharmaceutical practices and clinical guidelines for T2DM in each EU28 country may be a limitation. Health systems need to know the evolution of these community services and to analyze their operational and regulatory base, both in time and space. <b><i>Methods:</i></b> A systematic review was carried out on a qualitative and quantitative approach to the expansion and upgrading of PS-T2DM provided in EU28 pharmacies between 2008 and 2018. <b><i>Results:</i></b> The implementation of PS-T2DM in EU28 has increased sharply since 2009 and 2010. Diabetes mellitus (DM) is regulated in 5 countries (Bulgaria, Spain, Italy, Lithuania, and Portugal) and T2DM in 3 (Austria, Latvia, and Romania). Also, in 3 countries (Latvia, Poland, and Spain), pharmacists are involved in implementing guidelines for DM and T2DM, but there is no evidence on the regulation of PS-T2DM. Twenty-two countries showed detailed studies for the PS-T2DM’s provision. The type of PS-T2DM implemented in the highest number of EU28 countries was “promoting the rational use of medicines,” and the specific subtype T2DM-related more commonly reported was the “glucose measurement.” <b><i>Discussion/Conclusion:</i></b> Pharmacy disease-oriented services contributed to improving the accessibility, proximity, and equity of primary care for T2DM provided in community pharmacies across the EU28 in recent decades. This promising strategy for improving health outcome sets may be a call to the action of health systems due to its impact consistent with some objectives of universal health coverage for the eradication of DM and T2DM.
DOI: 10.6084/m9.figshare.12091947
title: cq_covid-19.json

description: Citations that all together suggest that chloroquine is prone to adverse effects in COVID-19 due to aggravation of oxidative stress.
DOI: 10.6084/m9.figshare.12091935
title: Albrich_et_al_2020_GCB

description: This contains the necessary data and code to perform the Analyses presented in <b>"Climate change causes critical transitions and irreversible alterations of mountain forests" published in Global Change Biology" (</b><b>https://doi.org/10.1111/gcb.15118)</b>
DOI: 10.6084/m9.figshare.12091947.v1
title: cq_covid-19.json

description: Citations that all together suggest that chloroquine is prone to adverse effects in COVID-19 due to aggravation of oxidative stress.
DOI: 10.6084/m9.figshare.12091935.v1
title: Albrich_et_al_2020_GCB

description: This contains the necessary data and code to perform the Analyses presented in <b>"Climate change causes critical transitions and irreversible alterations of mountain forests" published in Global Change Biology" (</b><b>https://doi.org/10.1111/gcb.15118)</b>
DOI: 10.6084/m9.figshare.12091860
title: Banco CIQ Stroke.xlsx

description: This is the research database PREDICTORS OF COMMUNITY INTEGRATION IN INDIVIDUALS AFTER STROKE IN A RESIDENTIAL SETTING: A LONGITUDINAL STUDY in Excel Windows format
DOI: 10.6084/m9.figshare.12091749
title: A freshwater radiation of diplonemids

description: Diplonemids are considered marine protists and have been recently reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. Here, we performed 18S rRNA amplicon sequencing, shotgun metagenomics and CARD-FISH analyses in seven freshwater lakes in Japan, Czech Republic, and Switzerland in order to uncover the diversity and abundance of diplonemids in deep freshwater environments. We detected diplonemids in all lakes we examined. Phylogenetic analyses of the assembled long 18S rRNA sequences from deep-sequenced metagenomes showed that freshwater diplonemids form a distinct clade with a much lower diversity than their marine counterparts. The abundance estimations based on CARD-FISH quantification were similar to those observed from sequencing approaches and showed that in contrast to the marine counterparts, freshwater diplonemids display low abundances associated with a reduced diversity. The microscopy data showed that the freshwater diplonemids range in size between 5 and 10 μm and that they appear to contain intra-cytoplasmatic bacteria. The reduced diversity of the freshwater diplonemids clade, together with the group monophyly and its position inside a diversified marine group indicate a recent habitat transition from marine to freshwater environments. Overall, our study shows the widespread presence of diplonemids in freshwater ecosystems and suggests their presence through a recent habitat transition from marine environments.
DOI: 10.6084/m9.figshare.12091746
title: Electronic journal subscription contracts negotiated by IReL, broken down by publisher name, agreement commencement and end-date.

description: Data received subject to the following Freedom of Information Request (March 2020):<br>"All records related to the commencement and the end-date of electronic journal subscription contracts negotiated by IReL, broken down by publisher name."<br><br>Total national spend (Ireland) on electronic journal subscriptions per year (euro):<br>2016: 14,268,9392017: 13,889,9232018: 12,800,4422019: Not yet available
DOI: 10.6084/m9.figshare.12091746.v1
title: Electronic journal subscription contracts negotiated by IReL, broken down by publisher name, agreement commencement and end-date.

description: Data received subject to the following Freedom of Information Request (March 2020):<br>"All records related to the commencement and the end-date of electronic journal subscription contracts negotiated by IReL, broken down by publisher name."<br><br>Total national spend (Ireland) on electronic journal subscriptions per year (euro):<br>2016: 14,268,9392017: 13,889,9232018: 12,800,4422019: Not yet available
DOI: 10.6084/m9.figshare.12091587
title: Supplementary Material for: High DHEAS Levels in Girls Is Associated with Earlier Pubertal Maturation and Mild Increase in Androgens throughout Puberty without Affecting Postmenarche Ovarian Morphology

description: <b><i>Objective:</i></b> To assess whether the presence of high DHEAS (HD) at 7 years determines different timing, sequence, and rate of pubertal events, and whether it is associated with adrenal and/or ovarian hyperandrogenism and changes in ovarian morphology throughout puberty. <b><i>Methods:</i></b> In a longitudinal study of 504 girls, clinical evaluation was performed every 6 months after 7 years of age to detect Tanner stages; hormonal and anthropometric measurements were conducted at thelarche (B2), breast Tanner 4 (B4), and 1 year after menarche; ultrasonographic evaluation was also performed after menarche. The girls were classified as HD if their DHEAS level was &gt;42.1 µg/dL (&gt;75th percentile) around 7 years. <b><i>Results:</i></b> HD around 7 years is associated with a younger age at thelarche, pubarche, and menarche. Girls with HD had higher androstenedione and total testosterone levels, and a higher free androgen index (FAI), and lower levels of antimüllerian hormone (AMH) at B2, and higher levels of androstenedione and FAI at B4 and after menarche. All these results were significant even after adjusting for body mass index, age at first DHEAS determination, and birth weight. One year after menarche, polycystic ovarian morphology was detected in 7.6 and 7.3% of the HD and the normal DHEAS group, respectively. Ovarian volume was correlated with AMH, testosterone, androstenedione, and LH but not with DHEAS around 7 years. <b><i>Conclusion:</i></b> Prepubertal HD in normal girls was associated with earlier thelarche, pubarche, and menarche, and a mild androgen increase throughout puberty. We believe continuous follow-up of this cohort is important to prospectively address the interrelationships between biochemical adrenarche and early growth as determinants of ovarian function.
DOI: 10.6084/m9.figshare.12091587.v1
title: Supplementary Material for: High DHEAS Levels in Girls Is Associated with Earlier Pubertal Maturation and Mild Increase in Androgens throughout Puberty without Affecting Postmenarche Ovarian Morphology

description: <b><i>Objective:</i></b> To assess whether the presence of high DHEAS (HD) at 7 years determines different timing, sequence, and rate of pubertal events, and whether it is associated with adrenal and/or ovarian hyperandrogenism and changes in ovarian morphology throughout puberty. <b><i>Methods:</i></b> In a longitudinal study of 504 girls, clinical evaluation was performed every 6 months after 7 years of age to detect Tanner stages; hormonal and anthropometric measurements were conducted at thelarche (B2), breast Tanner 4 (B4), and 1 year after menarche; ultrasonographic evaluation was also performed after menarche. The girls were classified as HD if their DHEAS level was &gt;42.1 µg/dL (&gt;75th percentile) around 7 years. <b><i>Results:</i></b> HD around 7 years is associated with a younger age at thelarche, pubarche, and menarche. Girls with HD had higher androstenedione and total testosterone levels, and a higher free androgen index (FAI), and lower levels of antimüllerian hormone (AMH) at B2, and higher levels of androstenedione and FAI at B4 and after menarche. All these results were significant even after adjusting for body mass index, age at first DHEAS determination, and birth weight. One year after menarche, polycystic ovarian morphology was detected in 7.6 and 7.3% of the HD and the normal DHEAS group, respectively. Ovarian volume was correlated with AMH, testosterone, androstenedione, and LH but not with DHEAS around 7 years. <b><i>Conclusion:</i></b> Prepubertal HD in normal girls was associated with earlier thelarche, pubarche, and menarche, and a mild androgen increase throughout puberty. We believe continuous follow-up of this cohort is important to prospectively address the interrelationships between biochemical adrenarche and early growth as determinants of ovarian function.
DOI: 10.6084/m9.figshare.12091530
title: Poplar_Isoform Expression_matrix_AND_Isoform_GTF

description: A matrix of isoform expression values(FPKM) for each replicate samples for an unstructured population of 268 Populus deltoides, and a GTF file describing the transcriptome. Isoforms were discovered as follows:Three transcript assembly platforms were used in order to maximize isoform detection: (i) Cufflinks version 2.2 with parameters “--library-type fr-firststrand –u -F 0.05 --max-intron-length 12000 --no-faux-reads -g”; (ii) StringTie version 1.3.3 with parameters “-f 0.05 -j 2 –rf” , and (iii) Trinity version 2.3.2 in genome guided mode with parameters “--genome_guided_bam --genome_guided_max_intron 12000 --full_cleanup --SS_lib_type RF --min_contig_length 50”. The collection of Cufflinks and Stringtie isoforms detected for each sample were merged with Stringtie merge using parameters “-F 1 -f 0.05”. PASA version 2.0.2-r20151207 was used to reconcile this merged assembly and the assembly from Trinity using parameters “-C –R -t --cufflinks_gtf -I 12000 --ALT_SPLICE --ALIGNER gmap,blat”. Additionally, the assemblies generated by PASA were filtered by requiring that (i) all splice junctions be supported by at least 2 reads, and (ii) retained introns be supported by a median read coverage of at least 2 (Python scripts stored in github.com/jdLikesPlants/poplar_AS). Requiring a minimum read support for retained introns minimizes the possibility of incorrect identification of intron retention events from the sequencing of pre-mRNA. Finally, the filtered PASA assemblies for each sample were merged with Cuffmerge (Cufflinks version 2.2.1) to generate a master transcriptome that represents all of the potential AS events and transcript isoforms for the population. The resulting assembly was then reformatted and annotated using gffcompare version 0.9.9c (https://github.com/gpertea/gffread). This transcriptome was subjected to a secondary expression-based filtering pipeline to remove artifacts generated during the merge. Cufflinks version 2.2 was used in quantification mode (parameters: --library-type fr-firststrand -G -u -F 0.05 --max-intron-length 12000) to measure the expression of the transcripts in the merged assembly in each sample. To minimize the presence of incorrectly assembled transcripts in the merged transcriptome assembly, each transcript was required to be expressed above FPKM (fragments per kilobase of exon model per million reads mapped) 3 in at least two of three biological replicates of a given individual, and in at least 3 individuals in the population. This final merged and filtered transcriptome was used in all downstream analyses. It is included here as 'Polpar_deltoides_gffcmp.annotated_3geno_filt_cleaned.gtf. Additionally, any individual that did not have at least 15 million reads generated during sequencing in at least two of three replicates, as well as individuals for which only one replicate was sequenced were removed from analysis, resulting in a final set of 268 individuals.Quantification of expression of each isoform is provided in Poplar_Isoform_Expression_matrix.zip file.
DOI: 10.6084/m9.figshare.12091530.v2
title: Poplar_Isoform Expression_matrix_AND_Isoform_GTF

description: A matrix of isoform expression values(FPKM) for each replicate samples for an unstructured population of 268 Populus deltoides, and a GTF file describing the transcriptome. Isoforms were discovered as follows:Three transcript assembly platforms were used in order to maximize isoform detection: (i) Cufflinks version 2.2 with parameters “--library-type fr-firststrand –u -F 0.05 --max-intron-length 12000 --no-faux-reads -g”; (ii) StringTie version 1.3.3 with parameters “-f 0.05 -j 2 –rf” , and (iii) Trinity version 2.3.2 in genome guided mode with parameters “--genome_guided_bam --genome_guided_max_intron 12000 --full_cleanup --SS_lib_type RF --min_contig_length 50”. The collection of Cufflinks and Stringtie isoforms detected for each sample were merged with Stringtie merge using parameters “-F 1 -f 0.05”. PASA version 2.0.2-r20151207 was used to reconcile this merged assembly and the assembly from Trinity using parameters “-C –R -t --cufflinks_gtf -I 12000 --ALT_SPLICE --ALIGNER gmap,blat”. Additionally, the assemblies generated by PASA were filtered by requiring that (i) all splice junctions be supported by at least 2 reads, and (ii) retained introns be supported by a median read coverage of at least 2 (Python scripts stored in github.com/jdLikesPlants/poplar_AS). Requiring a minimum read support for retained introns minimizes the possibility of incorrect identification of intron retention events from the sequencing of pre-mRNA. Finally, the filtered PASA assemblies for each sample were merged with Cuffmerge (Cufflinks version 2.2.1) to generate a master transcriptome that represents all of the potential AS events and transcript isoforms for the population. The resulting assembly was then reformatted and annotated using gffcompare version 0.9.9c (https://github.com/gpertea/gffread). This transcriptome was subjected to a secondary expression-based filtering pipeline to remove artifacts generated during the merge. Cufflinks version 2.2 was used in quantification mode (parameters: --library-type fr-firststrand -G -u -F 0.05 --max-intron-length 12000) to measure the expression of the transcripts in the merged assembly in each sample. To minimize the presence of incorrectly assembled transcripts in the merged transcriptome assembly, each transcript was required to be expressed above FPKM (fragments per kilobase of exon model per million reads mapped) 3 in at least two of three biological replicates of a given individual, and in at least 3 individuals in the population. This final merged and filtered transcriptome was used in all downstream analyses. It is included here as 'Polpar_deltoides_gffcmp.annotated_3geno_filt_cleaned.gtf. Additionally, any individual that did not have at least 15 million reads generated during sequencing in at least two of three replicates, as well as individuals for which only one replicate was sequenced were removed from analysis, resulting in a final set of 268 individuals.Quantification of expression of each isoform is provided in Poplar_Isoform_Expression_matrix.zip file.
DOI: 10.6084/m9.figshare.12091530.v1
title: Poplar_Isoform Expression_matrix.zip

description: A matrix of isoform expression values(FPKM) for each replicate samples for an unstructured population of 268 Populus deltoides. Isoforms were discovered as follows:Three transcript assembly platforms were used in order to maximize isoform detection: (i) Cufflinks version 2.2 with parameters “--library-type fr-firststrand –u -F 0.05 --max-intron-length 12000 --no-faux-reads -g”; (ii) StringTie version 1.3.3 with parameters “-f 0.05 -j 2 –rf” , and (iii) Trinity version 2.3.2 in genome guided mode with parameters “--genome_guided_bam --genome_guided_max_intron 12000 --full_cleanup --SS_lib_type RF --min_contig_length 50”. The collection of Cufflinks and Stringtie isoforms detected for each sample were merged with Stringtie merge using parameters “-F 1 -f 0.05”. PASA version 2.0.2-r20151207 was used to reconcile this merged assembly and the assembly from Trinity using parameters “-C –R -t --cufflinks_gtf -I 12000 --ALT_SPLICE --ALIGNER gmap,blat”. Additionally, the assemblies generated by PASA were filtered by requiring that (i) all splice junctions be supported by at least 2 reads, and (ii) retained introns be supported by a median read coverage of at least 2 (Python scripts stored in github.com/jdLikesPlants/poplar_AS). Requiring a minimum read support for retained introns minimizes the possibility of incorrect identification of intron retention events from the sequencing of pre-mRNA. Finally, the filtered PASA assemblies for each sample were merged with Cuffmerge (Cufflinks version 2.2.1) to generate a master transcriptome that represents all of the potential AS events and transcript isoforms for the population. The resulting assembly was then reformatted and annotated using gffcompare version 0.9.9c (https://github.com/gpertea/gffread). This transcriptome was subjected to a secondary expression-based filtering pipeline to remove artifacts generated during the merge. Cufflinks version 2.2 was used in quantification mode (parameters: --library-type fr-firststrand -G -u -F 0.05 --max-intron-length 12000) to measure the expression of the transcripts in the merged assembly in each sample. To minimize the presence of incorrectly assembled transcripts in the merged transcriptome assembly, each transcript was required to be expressed above FPKM (fragments per kilobase of exon model per million reads mapped) 3 in at least two of three biological replicates of a given individual, and in at least 3 individuals in the population. This final merged and filtered transcriptome was used in all downstream analyses. An overview of this computational pipeline is depicted in Supplementary Figure 1. Additionally, any individual that did not have at least 15 million reads generated during sequencing in at least two of three replicates, as well as individuals for which only one replicate was sequenced were removed from analysis, resulting in a final set of 268 individuals.
DOI: 10.6084/m9.figshare.12091458
title: Metadata record for: A draft genome assembly of spotted hyena, Crocuta crocuta

description: This dataset contains key characteristics about the data described in the Data Descriptor A draft genome assembly of spotted hyena, Crocuta crocuta. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12091458.v1
title: Metadata record for: A draft genome assembly of spotted hyena, Crocuta crocuta

description: This dataset contains key characteristics about the data described in the Data Descriptor A draft genome assembly of spotted hyena, Crocuta crocuta. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format