cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3vm2818
title: Data from: Effects of a titin mutation on force enhancement and force depression in mouse soleus muscles

description: The force produced by muscles varies with muscle length. Compared to
 isometric contractions at the same final length, force increases after
 lengthening, known as force enhancement, and decreases after shortening,
 known as force depression. The mechanisms of force enhancement remain
 unexplained by the sliding-filament and cross-bridge theories of muscle
 contraction. Although cross-bridge mechanisms have been proposed to
 account for force depression, so too have other mechanisms. In addition to
 cross bridges, titin has been suggested to contribute to both force
 enhancement and depression. Although titin is too compliant in passive
 muscles to contribute to active stiffness, recent evidence suggests that
 calcium activation increases titin stiffness. To test the hypothesis that
 titin plays a role in force enhancement and depression, we investigated
 muscle force in active and passive wild type and mdm soleus muscles after
 isovelocity stretching and shortening at three activation levels. Muscles
 from mdm mice (muscular dystrophy with myositis) have a predicted 83 amino
 acid deletion in the N2A region of titin and show no increase in stiffness
 when activated. We found that: 1) force enhancement and depression were
 reduced in mdm soleus compared to wild type muscles; 2) force enhancement
 increased with the amplitude of stretch across all activation levels in
 wild type and mdm muscles, while force depression increased with amplitude
 in wild type but not in mdm muscles; and 3) maximal shortening velocity of
 wild type and mdm muscles was similar, although active stress was reduced
 in mdm compared to wild type muscles. The results of this study suggest a
 role for titin in force enhancement and depression, which contribute
 importantly to regulation of muscle force during natural movements.
description: All data reported in the
 paper are included in this excel file.The excel file has five
 sheets: 1) animal data and statistics; 2) force enhancement and depression
 data and statistics relative to isometric force at final length;
 force-length data and statistics; Hill equation parameters and statistics;
 and 5) force enhancement and depression data and statistics relative to
 passive force after stretch to final length.FEFD9
 (1).xlsx
DOI: 10.5061/dryad.8th871g
title: Exploring variability in the diet of depredating sperm whales in the Gulf of Alaska through stable isotope analysis

description: Sperm whales interact with commercially important groundfish fisheries
 offshore in the Gulf of Alaska (GOA). This study aims to use stable
 isotope analysis to better understand the trophic variability of sperm
 whales and their potential prey, and to use dietary mixing models to
 estimate the importance of prey species to sperm whale diets. We analyzed
 tissue samples from sperm whales and seven potential prey (five groundfish
 and two squid species). Samples were analyzed for stable carbon and
 nitrogen isotope ratios, and diet composition was estimated using Bayesian
 isotopic mixing models. Mixing model results suggest that an isotopically
 combined sablefish/dogfish group, skates, and rockfish make up the largest
 proportion of sperm whale diets (35%, 28% and 12%) in the GOA. The top
 prey items of whales that interact more frequently with fishing vessels
 consisted of skates (49%) and the sablefish/dogfish group (24%). This is
 the first known study to provide an isotopic baseline of adult male sperm
 whales and these adult groundfish and offshore squid species, and to
 assign contributions of prey to whale diets in the GOA. This study
 provides information to commercial fishermen and fisheries managers to
 better understand trophic connections of important commercial species.
description: Sperm whale diet in the
 Gulf of Alaska analysis repositoryThis repository contains
 r-scripts/r-project and downloadable .csv data files used to reproduce all
 analysis done in this manuscript.Sperm Whale Diet
 DataAll diet data used in
 this analysis is available through GitHub at
 https://github.com/LaurenWild/UAF_SpermWhale_Diet.git. This includes all
 r-script files and raw data files,
 downloadable.Sperm Whale Diet
 AnalysisR project file (and
 associated csv files) for analysis done on this manuscript. This includes
 isotope analysis, including dietary mixing models, of sperm whales and
 their major groundfish and squid prey in the Gulf of
 Alaska.UAF_SpermWhale_Diet_Isotopes.RprojBiopsy_DetailsBiopsy Data for Creating MapsSperm whale isotope datasperm whale isotope data used in analysisPmIsotopes2_forR.csvStable Isotope Mixing Model Data - Sperm whalesSperm whale table for stable isotope mixing modelsPmSIMMData2.csvTEF data for Stable Isotope Mixing ModelsTrophic Enrichment Factor Data for Stable Isotope Mixing ModelsPmSourceTEFsd-AfSaComb.csvSource isotope data for mixing modelsStable isotope data of sperm whale prey for isotope mixing modelsPmSources_SaAf_Comb.csvPrey Isotope DataStable isotope data from sperm whale prey used in this analysisPrey.LE.final.Isotopes.forR5.csvPrey Data 2Isotope data of sperm whale prey - outliers removedPrey-outliers-removed-Sep2018.csv
DOI: 10.7272/q61z429d
title: Pooled metagenomic sequence from human stool

description: This dataset corresponds to the data presented in "The complete
 genome of klassevirus – a novel picornavirus in pediatric stool" by
 Greninger et al (http://www.ncbi.nlm.nih.gov/pubmed/19538752).
description: 141 diarrhea samples were prepared, pooled, and pyrosequenced on the Roche
 Genome Sequence FLX as described in "The complete genome of
 klassevirus – a novel picornavirus in pediatric stool" by Greninger
 et al (http://www.ncbi.nlm.nih.gov/pubmed/19538752). A novel member of the
 Picornaviridae viral family, Human klassevirus 1, was discovered in the
 540,412 unique reads with an average length of 240 nt. The reads were
 stripped of sequences mapping with 90% or greater identity to known
 diarrhea-causing viruses: 6,959 reads mapped to the Adenoviridae and
 Caliciviridae viral families by translated BLAST. Of the remaining 533,453
 unique reads, 483 derived from Human klassevirus 1. The data are provided
 in FASTA format.
description: The complete genome of klassevirus a novel picornavirus in
 pediatric stool. Greninger AL, Runckel C, Chiu CY, Haggerty T, Parsonnet
 J, Ganem D, DeRisi JL. Virol J. 2009 Jun 18;6:82. doi:
 10.1186/1743-422X-6-82. PMID: 19538752
DOI: 10.7272/q6x63jt1
title: Tobacco-free retailers project

description: This dataset contains the transcripts of 15 focus groups conducted in
 California, New York state, and Ohio from 2009-2013 concerning retailers
 that had voluntarily discontinued tobacco sales. Transcripts are grouped
 by state: FG1-8 are the California groups, FG9-13 are the New York groups,
 and FG14-15 are the Ohio groups.
description: Focus groups with one moderator, and, in California, one
 note-taker who occasionally asked questions. All but one of the focus
 groups in California were conducted by the same person. All of the New
 York and Ohio focus groups were conducted by the same person.
description: McDaniel PA, Malone RE. Why California retailers stop selling
 tobacco products, and what their customers and employees think about it
 when they do: case studies. BMC Public Health. 2011 Nov
 8;11(1):848.
description: McDaniel PA, Malone RE. “People over Profits”: Retailers Who
 Voluntarily Ended Tobacco Sales. PLoS ONE 2014 9(1): e85751.
DOI: 10.7272/q65q4t1r
title: C. elegans RNA Sequence for viral discovery

description: Nucleic acid from two nematode species, C. elegans JU1580 (isolated from a
 rotting apple in Orsay, France) and C. briggsae JU1264 (isolated from a
 snail on a rotting grape in Santeuil, France) were prepared and
 pyrosequenced on the Roche Titanium Genome Sequencer. Raw sequence reads
 were filtered for quality and repetitive sequences as described in
 "Natural and experimental infection of Caenorhabditis nematodes by
 novel viruses related to nodaviruses" by F?©lix et al
 (http://www.ncbi.nlm.nih.gov/pubmed/21283608). Two novel members of the
 Nodaviridae viral family, Orsay nodavirus and Santeuil nodavirus, were
 discovered in the the 15933 and 20,787 reads, respectively. 1046 Orsay
 nodavirus reads were found in the C. elegans samples while 2492 Santeuil
 nodavirus reads were identified in in the C. briggsae sample. The data are
 provided in FASTA format.
description: This is a 454 dataset corresponding to the raw reads from Felix
 et al., 2011
description: Félix M-A, Ashe A, Piffaretti J, Wu G, Nuez I, et al. (2011)
 Natural and Experimental Infection of Caenorhabditis Nematodes by Novel
 Viruses Related to Nodaviruses. PLoS Biol 9: e1000586.
 doi:10.1371/journal.pbio.1000586. PMC3026760
DOI: 10.5061/dryad.gq60sj7
title: Data from: The role of glycine betaine in range expansions; protecting mangroves against extreme freeze events

description: 1. Due to a warming climate, mangrove populations within the Gulf of
 Mexico and along the Florida Atlantic coastline are expanding their range
 poleward. As mangroves expand their range limit, leading edge individuals
 are more likely to experience an increased incidence of freeze events.
 However, we still lack a clear understanding of the mechanisms used by
 mangroves to survive freezing conditions. 2. Here, we conducted common
 garden experiments at different locations experiencing variable winter
 freeze conditions to show glycine betaine, an organic osmolyte, increases
 significantly with freeze exposure, playing an important role in the
 freeze tolerance of Avicennia germinans, a widespread Neotropical
 mangrove. 3. We found glycine betaine accumulation was similar across all
 source populations and freeze exposure locations, suggesting glycine
 betaine is not a range limit adaptation and is instead used for freeze
 tolerance by A. germinans irrespective of source population. Plants
 sourced from populations that experience freezing conditions exhibited
 greater rates of survival, indicating range edge populations of A.
 germinans have other heritable adaptations in addition to glycine betaine
 for freeze tolerance. 4. Synthesis. Continued mangrove expansion poleward
 will result in a greater incidence of freeze events for individuals at the
 leading edge. Our findings suggest freeze tolerance in this species may be
 genetically based and that leading edge A. germinans have the potential to
 survive extreme freeze events and recover post-freeze, allowing for their
 continued expansion poleward. This process of selective survival may act
 to promote adaptation of freeze tolerance in range edge populations.
description: GB data Hayes et al
 2019Glycine betaine values
 for leaves collected from mangroves sourced from different locations
 across southern USA.
DOI: 10.7272/q6td9v7j
title: Re-analysis of microarray data from rapamycin resistant DLBCL cell lines

description: This dataset contains a re-analysis of the raw microarray data originally
 published by Petrich AM et al in 2012 (citation details are provided
 through the link to the GEO record). We were interested in re-analyzing
 the data because the list of differentially expressed genes that were
 identified when comparing rapamycin resistant DLBCL cell lines to
 rapamycin sensitive cell lines was not included in the original article or
 supplemental materials. We were interested in validating and expanding
 upon the findings from the original article by reevaluating the raw
 microarray data. Our reanalysis identified over 200 genes that were
 significantly differentially expressed between rapamycin resistant and
 sensitive cells. Importantly, our analysis highlighted a gene that was
 highly upregulated in rapamycin resistant cells, CD247, that was not the
 focus on the original publication, and is the target of a drug currently
 in clinical trials for refractory DLBCL. Our reanalysis also highlighted
 the role of SYK, a kinase upregulated in rapamycin resistant cell lines,
 that has a direct molecular relationship with CD247, and is a potential
 biomarker of drug response in DLBCL.
description: The methods used to generate the original microarray data are described in
 the GEO record where the data were originally published:
 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27255 We downloaded
 the raw Affymetrix data (CEL files) from GEO for renalysis. Statistical
 and quality analysis was performed using the data analysis pipeline in
 iReport (http://www.ingenuity.com/products/ireport) which utilizes
 packages such as RMA and Limma from Bioconductor, in the R programming
 language. A full description of the analysis packages used by this
 pipeline are included in the word document "GSE27255 stats and QC
 details" included in this DataShare record. Analysis of microarray
 data in iReport identified 229 differentially expressed genes (DEGs) with
 a p-value &lt;0.05, fold change &gt;1.5. These DEGs were then uploaded and
 analyzed in Ingenuity Pathway Analysis (www.ingenuity.com) for functional
 enrichment, pathway analysis, and drug target/biomarker analysis. Our
 novel findings with respect to the role of CD247 and SYK in rapamycin
 resistant DLBCL cell lines is depicted in the pathway image fine "Rap
 resist network with CD247" which is included in this DataShare
 record.
description: The original microarray data that was used for this reanalysis
 use case is described in the GEO record GSE27255.
description: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27255
DOI: 10.7272/q67p8w9z
title: Patterns of age-related water diffusion changes in human brain by concordance and discordance analysis.

description: In diffusion tensor imaging (DTI), interpreting changes in terms of
 fractional anisotropy (FA) and mean diffusivity or axial (D(||)) and
 radial (D(?)) diffusivity can be ambiguous. The main objective of this
 study was to gain insight into the heterogeneity of age-related diffusion
 changes in human brain white matter by analyzing relationships between the
 diffusion measures in terms of concordance and discordance instead of
 evaluating them separately, which is difficult to interpret. Fifty-one
 cognitively normal subjects (22-79 years old) were studied with DTI at 4
 Tesla. Age was associated with widespread concordant changes of decreased
 FA and increased MD but in some regions significant FA reductions occurred
 discordant to MD changes. Prominent age-related FA reductions were
 primarily related to greater radial (D(?)) than axial (D(||)) diffusivity
 changes, potentially reflecting processes of demyelination. In conclusion,
 concordant/discordant changes of DTI indices provide additional
 characterization of white matter alterations that accompany normal aging.
description: The dataset available here consists of Fractional Anisotropy (FA), Mean
 Diffusivity (MD), Axial Diffusivity (I1), and Radial Diffusivity (Dra)
 images as well as subject-study-specific normalization images (B0, see
 methods in paper) in Analyze format. There are B0, FA, MD, I1, and Dra
 images for 51 subjects, and a spreadsheet describing each subject's
 handedness (right, left or ambidextrous), age (at time of scan), gender,
 ApoE alleles, and Mini-Mental State Exam score. Data Acquisition Location:
 San Francisco VA Medical Center; Scanner Type: Siemens Bruker 4T, equipped
 with a birdcage transmit and 8 channel receive coil. DTI was based on a
 dual spin-echo echo-planar imaging (EPI) sequence, augmented by parallel
 imaging acceleration (GRAPPA) by a factor 2 to reduce susceptibility
 distortions. Other imaging parameters were: TR/TE = 6000/77 ms; field of
 view 256 cm × 224 cm; 128 × 112 matrix size, yielding 2 mm × 2 mm in-plane
 resolution; 40 continuous slices, each 3 mm thick. A diffusion reference
 image (no diffusion gradient b = 0) and six diffusion-weighted images (b =
 800 s/mm2 along 6 non-collinear directions) were acquired. Four DTI scans
 were acquired and averaged after motion correction to boost
 signal-to-noise.
DOI: 10.5061/dryad.1k84dt2
title: Auditory cortical representation of music favours the perceived beat

description: Previous research has shown that musical beat perception is a surprisingly
 complex phenomenon involving widespread neural coordination across
 higher-order sensory, motor, and cognitive areas. However, the question of
 how low-level auditory processing must necessarily shape these dynamics,
 and therefore perception, is not well understood. Here, we present
 evidence that the auditory cortical representation of music, even in the
 absence of motor or top-down activations, already favors the beat that
 will be perceived. Extracellular firing rates in the rat auditory cortex
 were recorded in response to twenty musical excerpts diverse in tempo and
 genre, for which musical beat perception had been characterised by the
 tapping behaviour of 40 human listeners. We found that firing rates in the
 rat auditory cortex were on average higher on the beat than off the beat.
 This “neural emphasis” distinguished the beat that was perceived from
 other possible interpretations of the beat, was predictive of the degree
 of tapping consensus across human listeners, and was accounted for by a
 spectrotemporal receptive field model. These findings strongly suggest
 that the “bottom-up” processing of music performed by the auditory system
 predisposes the timing and clarity of the perceived musical beat.
description: Code and data (rat electrophysiology + human tapping) from
 Auditory Cortical Representation of Music Favors the Perceived Beat. This
 .zip file contains raw and preprocessed data (spike data from the rat
 auditory cortex + human tapping data) and analysis code. See README for
 details.
DOI: 10.5061/dryad.4b6v2f0
title: Data from: Association between attitudes of stigma toward mental illness and attitudes toward adoption of evidence-based practice within health care providers in Bahrain

description: The health care system is one of the key areas where people with mental
 illnesses could experience stigma. Clinicians can hold stigma attitudes
 during their interactions with patients with mental illness. To improve
 the quality of mental health services and primary care, evidence-based
 practices should be disseminated and implemented. In this study, we
 evaluated the attitudes of health care providers in Bahrain toward people
 with mental illness and adoption of evidence-based practice using the
 Opening Minds Stigma Scale for Healthcare Providers (OMS-HC) and
 Evidence-Based Practice Attitude Scale (EBPAS). We conducted a
 cross-sectional study across 12 primary health care centers and a
 psychiatric hospital (the country’s main mental health care facility). A
 self-report questionnaire was distributed among all health care providers.
 A total of 547 health care providers participated, with 274 from mental
 health services and 273 from primary care services. Results of the OMS-HC
 indicated differences between both main groups and subgroups. Regression
 model analysis reported significant outcomes. There was no statistical
 difference found between both groups in EBPAS scores. A weak but
 statistically significant negative association was reported between both
 scales. Participants showed varying stigma attitudes across different
 working environments, with less stigma shown in mental health services
 than in primary care services. Providers who were more open to adopting
 evidence-based practices showed less stigma toward people with mental
 illness. Comparing our findings with previous research showed that health
 care providers in Bahrain hold more stigma attitudes than other groups
 studied. We hope that this study serves as an initial step toward future
 campaigns against the stigma of mental illness in Bahrain and across the
 region.
DOI: 10.5061/dryad.km27bv6
title: Data from: ­Phylogenomics in Cactaceae: a case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan/Sonoran Deserts

description: PREMISE OF THE STUDY: Although numerous phylogenetic studies have been
 conducted in Cactaceae, whole plastome datasets have not been employed. We
 used the chollas to develop a plastome dataset for phylogeny
 reconstruction to test species relationships, biogeography, clade age and
 morphological evolution. METHODS: We developed a plastome dataset for most
 known diploid members of the chollas, 42 taxa, as well as for other
 members of Cylindropuntieae. Paired-end, raw reads from genome skimming
 were referenced-mapped onto a de novo plastome assembly of one species of
 cholla, Cylindropuntia bigelovii, which were used to build our plastome
 dataset that was analyzed using various methods. KEY RESULTS: Our plastome
 dataset resolved the phylogeny of the chollas, including most inter- and
 intraspecific relationships. Tribe Cylindropuntieae arose during the early
 Miocene in southern South America, ca. 18 mya, and is supported as sister
 to the South American clade Tephrocacteae. The (Micropuntia
 (Cylindropuntia + Grusonia)) clade most likely originated in the
 Chihuahuan Desert region around 16 mya, and then migrated into other North
 American desert regions. Key morphological characters for recognizing
 traditional taxonomic series (e.g., spiny fruit) in Cylindropuntia are
 mostly homoplasious. CONCLUSIONS: This study provides the first
 comprehensive plastome phylogeny for any clade within Cactaceae. Although
 widespread throughout western North American deserts, the most recent
 common ancestor of the chollas s.l. likely arose in the Chihuahuan Desert
 region during the mid-Miocene, with much of their species diversity
 arising in the early to mid-Pliocene, showing a strikingly similar pattern
 to other western North American Desert groups.
description: Cylindropuntieae_align_25June2019_DryadAlignment of 67 taxa used in phylogenetic analysis of tribe Cylindropuntieae.Cylindropuntieae_67alignment_25June2019.nexCylindropuntieae_24June2019_RAxML_treeRAxML tree of tribe Cylindropuntieae.
DOI: 10.5061/dryad.g8q382h
title: Data from: The influence of infiltration rate on residual air distribution and water flow in heterogeneous porous sample: neutron imaging investigation

description: [Abstract not filled]
description: DE_part1We provide raw neutron imaging data of two infiltration experiments, which were conducted on a constructed sample under two different upper boundary conditions. The data set contains the radiograms for ponding infiltration (PE) and drip irrigation (DE) experiments, where each folder contains a series of radiograms that can be used to reconstruct one tomogram. Each TIF file in the PE folder represents and a 16-bit image of 1080 by 1280 matrix of pixel-wise measured neutron intensities, with 0.097 mm pixel size. Each radiogram took 16 s, 361 radiograms were collected over 180° of sample rotation. Each TIF file in the DE folder contain a 16-bit image of 512 by 512 matrix of pixel-wise measured neutron intensities, with 0.108 mm pixel size. Acquisition time for each radiogram was 0.25 s while count of radiograms for one tomogram was 461 over 360° angle. Datasets also contain a reference image of the dry image, the dark current image, and the open beam image.DE_part2see a description of DE_part 1DE_part3see a description of DE_part 1DE_part4see a description of DE_part 1DE_part5see a description of DE_part 1PE_part1PE_part2see a description of DE_part 1PE_part3see a description of DE_part 1PE_part4see a description of DE_part 1PE_part5see a description of DE_part 1PE_part6see a description of DE_part 1PE_part7see a description of DE_part 1PE_part8see a description of DE_part1PE_part9see a description of DE_part 1PE_part10see a description of DE_part 1PE_part11see a description of DE_part 1PE_part12see a description of DE_part 1PE_part13see a description of DE_part 1PE_part14see a description of DE_part 1PE_part15see a description of DE_part 1