cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1hm2w
title: Data: Researcher Perspectives on the Use and Sharing of Software

description: We are interested in learning about perceptions, values, and behaviors
 around the computer software generated as part of the research process.
  To understand researchers' prespectives on software usage
 and sharing, we conducted an online survey sent to researchers at academic
 institutions throughout the United States. We used the Qualtrics platform
 to distribute our survey. This data set contains the responses of the
 survey participants after excluding any personally identifying data. All
 study materials and procedures were approved by the University of
 California Berkeley Committee for Protection of Human Subjects and Office
 for the Protection of Human Subjects (protocol ID 2016-11-9358).
description: Survey data was collected via the Qualtrics platform. All survey
 questions, consent materials, and instructions are included in the file
 "Alnoamany_Borghi_2018_survey.pdf". Code used for data analysis
 can be found at https://doi.org/10.5281/zenodo.1195605.
description: A description of the uploaded materials can be found in the
 readme file. Note that the "Alnoamany_Borghi_2018_data.csv" does
 not contain all of the responses from the survey questions. Responses that
 provided potentially identifying information were removed as were
 responses that will be the subject of future analysis. All variable names
 are listed alongside the corresponding survey question in the data
 dictionary.
DOI: 10.7291/d1q94r
title: Chemical shift-based methods in NMR structure determination

description: Chemical shifts are highly sensitive probes that can be harnessed by NMR
 spectroscopists and structural biologists as conformational parameters to
 characterize a range of biological molecules. Traditionally, assignment of
 chemical shifts has been a labor-intensive process requiring numerous
 samples and a suite of multidimensional experiments. Over the past two
 decades, the development of complementary automated and computational
 approaches has bolstered the analysis, interpretation and utilization of
 chemical shifts for elucidation of high-resolution protein and nucleic
 acid structures. Here, we review the development and application of
 chemical shift-based methods for structure determination with a focus on
 ab initio fragment assembly, comparative modeling, oligomeric systems, and
 automated assignment methods. Throughout our discussion, we point out
 practical uses, as well as advantages and caveats, of using chemical
 shifts in structure modeling. We additionally highlight (i) hybrid methods
 that employ chemical shifts with other types of NMR restraints (residual
 dipolar couplings, paramagnetic relaxation enhancements and pseudocontact
 shifts) that allow for improved accuracy and resolution of generated 3D
 structures, (ii) the utilization of chemical shifts to model the
 structures of sparsely populated excited states, and (iii) conformational
 modeling of protein sidechains. Finally, we briefly discuss the advantages
 of contemporary methods that employ sparse NMR data recorded using
 site-specific isotope labeling schemes for chemical shift-driven structure
 determination of larger molecules. With this review, we hope to emphasize
 the accessibility and versatility of chemical shifts for structure
 determination of challenging biological systems and point out emerging
 areas of development that lead us towards the next generation of tools.
description: The NMR dataset consisting of chemical shifts and NOEs used for
 structure calculations of Abl kinase regulatory module were obtained from
 BMRB ID: 30332. The protein structures deposited here were computed using
 RASREC-Rosetta.
description: This dataset consists of three files:
 abl2_final.pdb : Ensemble of 10 lowest-energy
 structures. abl2_final.str : NMR STAR file consisting
 of NMR chemical shifts and NOE restraints used for structure
 calculation. abl2.nef : NMR exchange format file
 consisting of NMR chemical shifts and NOE restraints used for structure
 calculation (This file has the same data as that of abl2_final.str file
 but in NEF format). All the datasets are compatible
 with wwPDB. To extract information from .str or .nef
 files, please refer to the CSRosetta website
 (https://csrosetta.chemistry.ucsc.edu/).
DOI: 10.5061/dryad.9n2k1vk
title: Data from: Modelling of dysregulated glucagon secretion in type 2 diabetes by considering mitochondrial alterations in pancreatic alpha cells

description: Type 2 diabetes mellitus (T2DM) has been associated with insulin
 resistance and the failure of β-cells to produce and secrete enough
 insulin as the disease progresses. However, clinical treatments based
 solely on insulin secretion and action have had limited success. The focus
 is therefore shifting towards α-cells, in particular to the dysregulated
 secretion of glucagon. Our qualitative electron-microscopy-based
 observations gave an indication that mitochondria in α-cells are altered
 in Western-diet-induced T2DM. In particular, α-cells extracted from mouse
 pancreatic tissue showed a lower density of mitochondria, a less expressed
 matrix, and a lower number of cristae. These deformities in mitochondrial
 ultrastructure imply a decreased efficiency in mitochondrial ATP
 production, which prompted us to theoretically explore and clarify one of
 the most challenging problems associated with T2DM, namely the lack of
 glucagon secretion in hypoglycemia and its oversecretion at high blood
 glucose concentrations. To this purpose, we constructed a novel
 computational model that links α-cell metabolism with their electrical
 activity and glucagon secretion. Our results show that defective
 mitochondrial metabolism in α-cells can account for dysregulated glucagon
 secretion in T2DM, thus improving our understanding of T2DM
 pathophysiology and indicating possibilities for new clinical treatments.
description: Computational α-cell A computational α-cell
 model to simulate and explore several interconnected steps in the
 glucose-dependent signaling cascade form the initial metabolic processes
 to exocytosis. We combined a mathematical model for glycolysis and glucose
 driven mitochondrial activity [1] with a model for simulating α-cell
 electrical and Ca2+ activity and finally with glucagon secretion [2]. This
 unique coupling of the α-cell metabolism with the electrical activity
 enables us to study the interplay between processes related to glucagon
 secretion and ATP production in mitochondria. Most importantly, we
 adjusted the model and the parameters in order to fit several aspects of
 model predictions with experimental findings. In addition, we
 interconnected glucose and free fatty acid metabolism with a mechanism
 that enables the α-cell to regulate its energetics in a
 stimulation-dependent manner. We have also included an interaction between
 cytosolic ATP concentration and the activity ATP-ases. Fig. 1 features the
 scheme of the computational model with highlighted the crucial processes
 that are involved in ATP production and regulation of glucagon secretion.
 The whole mathematical model has been written in Berkeley Madonna software
 (University of California at Berkeley, California, USA) and C++.
 Alfa_cell.rar
DOI: 10.6086/d1337p
title: #twitterandnews

description: 364 tweet ids and referenced urls collected from the #twitterandnews
 Twitter chat hosted by the Knight Foundation on Thursday, March 8th,
 2018. 
description: Collected using the DocNow Twittter collection demo application
 on March 8th, 2018.
description: Use the DocNow Hydrator tool to turn the tweet ids back into the
 original tweets. Download and run DocNow Hydrator
 here: https://github.com/DocNow/hydrator
DOI: 10.15146/r3s962
title: Sewage loading and microbial risk in urban waters of the Great Lakes

description: Theis dataset contains untreated sewage (wastewater treatment plant
 influent) samples from Milwaukee, WI, USA collected over a two year
 peroid.  These were analyzed by qPCR for human associated
 indicators human Bacteroides (HB assay) and human Lachnospiraceae (Lachno2
 assay), and by qPCR for E. coli and enterococci. Water samples were also
 collected at the estuary using a Telodyne ISCO sampler to perform
 automated, high frequnency sampling of 15 minute subsamples. Hourly
 samples were analyzed by culture for E. coli and enterococci. 
 Composites of 1, 2, or 4 hours were analyzed by qPCR for These samples
 were analyzed by qCRP for HB, Lachno2, E. coli, and
 enterococci.  
description: BLD is below the limit of detection BLQ is
 below the limit of quantification, whihc is 225 CN/100 ml for all qPCR
 assays
DOI: 10.7280/d1nw9k
title: Southeast Greenland Bed Elevation - v2

description: We employ NASA's Operation IceBridge (OIB) high‐resolution airborne
 gravity from 2016, NASA's Ocean Melting Greenland (OMG) bathymetry
 from 2015, ice thickness from Operation IceBridge (OIB) from 2010‐2015,
 and BedMachine v3 to analyze 20 major southeast Greenland glaciers. The
 results reveal glacial fjords several hundreds of meters deeper than
 previously thought; the full extent of the marine‐based portions of the
 glaciers; deep troughs enabling warm, salty Atlantic Water (AW) to reach
 the glacier fronts and melt them from below; and few shallow sills that
 limit the access of AW. The new oceanographic and topographic data help to
 fully resolve the complex pattern of historical ice front positions from
 the 1930s to 2017: glaciers exposed to AW and resting on retrograde beds
 have retreated rapidly, while glaciers perched on shallow sills or
 standing in colder waters or with major sills in the fjords have remained
 stable. Please cite the following paper when using this dataset: Millan
 R., E. Rignot, J. Mouginot, M. Wood, A.A Bjørk, and M. Morlighem (2018),
 Vulnerability of Southeast Greenland glaciers to warm Atlantic Water from
 Operation IceBridge and Ocean Melting Greenland data, Geophys.
 Res. Lett., 45, doi:10.1002/2017GL076561.   Projection
 informations can be found below:   Size is 2760, 4044 Coordinate
 System is: PROJCS["WGS 84 / NSIDC Sea Ice Polar Stereographic
 North",     GEOGCS["WGS 84",
        
 DATUM["WGS_1984",
             SPHEROID["WGS 84",6378137,298.257223563,     PROJECTION["Polar_Stereographic"],     PARAMETER["latitude_of_origin",70],     PARAMETER["central_meridian",-45],     PARAMETER["scale_factor",1],     PARAMETER["false_easting",0],     PARAMETER["false_northing",0],     AUTHORITY["EPSG","3413"]] Origin = (-109288.637000000002445,-2616698.799999999813735) Pixel Size = (150.000000000000000,-150.000000000000000) Metadata:   AREA_OR_POINT=Area Image Structure Metadata:   INTERLEAVE=BAND Corner Coordinates: Upper Left  ( -109288.637,-2616698.800) ( 47d23'29.82"W, 66d 9'34.51"N) Lower Left  ( -109288.637,-3223298.800) ( 46d56'30.90"W, 60d50'52.57"N) Upper Right (  304711.363,-2616698.800) ( 38d21'28.41"W, 66d 1'23.84"N) Lower Right (  304711.363,-3223298.800) ( 39d35'58.74"W, 60d44'22.03"N) Center      (   97711.363,-2919998.800) ( 43d 5' 0.37"W, 63d29'36.85"N)
DOI: 10.5061/dryad.7qj23gr
title: Data from: Differential requirements for the RAD51 paralogs in genome repair and maintenance in human cells

description: Deficiency in several of the classical human RAD51 paralogs [RAD51B,
 RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition
 and Fanconi anemia. To investigate their functions, isogenic disruption
 mutants for each were generated in non-transformed MCF10A mammary
 epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and
 HEK293 cells, viable ablated clones were readily isolated for each RAD51
 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are
 cell-essential in MCF10A cells. Underlining their importance for genomic
 stability, mutant cell lines display variable growth defects, impaired
 sister chromatid recombination, reduced levels of stable RAD51 nuclear
 foci, and hyper-sensitivity to mitomycin C and olaparib. Altogether these
 observations underscore the contributions of RAD51 paralogs in diverse DNA
 repair processes, and demonstrate essential differences in different cell
 types. Finally, this study will provide useful reagents to analyze
 patient-derived mutations and to investigate mechanisms of
 chemotherapeutic resistance deployed by cancers.
DOI: 10.15468/dl.6an8tt
title: Occurrence Download

description: A dataset containing 6641005 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-70 42,-71 42,-71 41,-70 41,-70 42))",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 6641005 records from 606 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001856-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7280/d1j37z
title: Jakobshavn Glacier Bed Elevation

description: Jakobshavn Isbræ, West Greenland, which holds a 0.6-m sea level volume
 equivalent, has been speeding up and retreating since the late 1990s.
 Interpretation of its retreat has been hindered by difficulties in
 measuring its ice thickness with airborne radar depth sounders. Here, we
 employ high-resolution, helicopter-borne gravity data from 2012 to
 reconstruct its bed elevation within 50 km of the ocean margin using a
 three-dimensional inversion constrained by fjord bathymetry data offshore
 and a mass conservation algorithm inland. We find the glacier trough to be
 asymmetric and several 100 m deeper than estimated previously in the lower
 part. From 1996-2016, the grounding line migrated at 0.6 km/yr from 700 m
 to 1,100 m depth. Upstream, the bed drops to 1,600 m over 10 km then
 slowly climbs to 1,200 m depth in 40 km. Jakobshavn Isbræ will continue to
 retreat along a retrograde slope for decades to come. An L., E.
 Rignot, S.H.P. Elieff, M. Morlighem, R.
 Millan, J. Mouginot, D.M. Holland, D. Holland,
 and J. Paden (2017), Bed elevation of
 Jakobshavn Isbræ, West Greenland, from high-resolution airborne gravity
 and other data, Geophys. Res.
 Lett., 44, doi:10.1002/2017GL073245.
DOI: 10.7280/d1dd39
title: Avannarleq and Kujalleq Glacial Stability

description: The evolution of Greenland glaciers in a warming climate depends on their
 depth below sea level, flow speed, surface melt, and ocean-induced
 undercutting at the calving front. We present an innovative mapping of bed
 topography in the frontal regions of Sermeq Avannarleq and Kujalleq, two
 major glaciers flowing into the ice-choked Torssukatak Fjord, central west
 Greenland. The mapping combines a mass conservation algorithm inland,
 multi-beam echo sounding data in the fjord, and high-resolution airborne
 gravity data at the ice-ocean transition where other approaches fail. We
 obtain a reliable, precision (± 40 m) solution for bed topography across
 the ice-ocean boundary. The results reveal a 700-m deep fjord that
 abruptly ends on a 100-300 m deep sill along the calving fronts. The
 shallow sills explain the presence of stranded icebergs, the resilience of
 the glaciers to ocean-induced undercutting, and their remarkable stability
 over the past century. An. L., E. Rignot, J. Mouginot, R. Milan, (2018), A
 century of stability of Avannarleq and Kujalleq glaciers, West Greenland,
 explained using high-resolution airborne gravity and other
 data, Geophys. Res. Lett., 10.1002/2018GL077204.
DOI: 10.7280/d18q1d
title: Bathymetry of the Amundsen Sea Embayment

description: We employ airborne gravity data from NASA's Operation IceBridge
 collected in 2009–2014 to infer the bathymetry of sub–ice shelf cavities
 in front of Pine Island, Thwaites, Smith, and Kohler glaciers, West
 Antarctica. We use a three‐dimensional inversion constrained by multibeam
 echo sounding data offshore and bed topography from a mass conservation
 reconstruction on land. The seamless bed elevation data refine details of
 the Pine Island sub–ice shelf cavity, a slightly thinner cavity beneath
 Thwaites, and previously unknown deep (&gt;1200 m) channels
 beneath the Crosson and Dotson ice shelves that shallow (500 m
 and 750 m, respectively) near the ice shelf fronts. These sub–ice
 shelf channels define the natural pathways for warm, circumpolar deep
 water to reach the glacier grounding lines, melt the ice shelves from
 below, and constrain the pattern of past and future glacial retreat.
 Millan, R., E. Rignot, V. Bernier, M.
 Morlighem, and P. Dutrieux (2017), Bathymetry of the
 Amundsen Sea Embayment sector of West Antarctica from Operation IceBridge
 gravity and other data, Geophys. Res. Lett., 44,
 1360–1368, doi:10.1002/2016GL072071.
DOI: 10.6078/d1bt11
title: Thermal and energetic ion dynamics in Ganymede's magnetosphere

description: This dataset accompanies the manuscript "Thermal and energetic
 dynamics in Ganymede's magnetosphere", JGR Space
 Physics, 2018. 
description: These datasets are the result of three-dimensional, plasma hybrid
 simulations and subsequent backwards Liouville particle tracing as
 described in Poppe et al., JGR Space Physics, 2018.
description: All files are in plain ASCII format.
DOI: 10.5061/dryad.50d300k
title: Data from: Does inbreeding affect personality traits?

description: The question of why variation is maintained in personality traits is an
 evolutionary puzzle. According to the condition-dependence hypothesis,
 such traits depend on condition, which limits the behavioural choices
 available to individuals. Because condition is affected by many genes, it
 can effectively be manipulated by inbreeding, which exposes the effects of
 deleterious recessive mutations. Here, I compared two personality traits,
 boldness and tendency to explore, of male guppies (Poecilia reticulata)
 from first-generation inbred and outbred treatments. Boldness in guppies
 is associated with increased sexual attractiveness, and is thus expected
 to affect fitness. Therefore, I hypothesised that the personality traits
 would be negatively affected by inbreeding. However, the results indicated
 that inbred guppies did not differ in either personality trait from their
 outbred counterparts. This finding suggests that mechanisms other than
 condition-dependence are maintaining personality variation in the guppy.
description: Behavioural data on
 inbred and outbred guppy malesThe file contains data
 from behavioural tests measuring courtship behaviour (number of sigmoids)
 and personality traits: boldness and exploration (latency to emerge from a
 shelter, swimming rate and time frozen in an open field test) of F1 guppy
 males from outbred and first-generation inbred matings. The experiment was
 performed in captivity.raw_data.xlsx
DOI: 10.25338/b8p88g
title: Heterotrophic N2-fixation contributes to nitrogen economy of a common wetland sedge, Schoenoplectus californicus

description: These data sets document environmental characteristics of sampling
 locations of Schoenoplectus californicus, california bulrush, throughout
 its range in the Americas. In addition, the data on nif gene in rhizomes
 and roots of Schoenoplectus are provided.
description: Soil samples from 52 locations of Schoenoplectus were collected
 as well as samples of plant tissue. Nitrogen fixation
 was measured using the acetylene reduction method, ARA.
 Copies of nifH gene were obtained using methods described in the
 publication
DOI: 10.6071/m3gt0p
title: A local and global sensitivity analysis of a mathematical model of coagulation and platelet deposition under flow

description: The hemostatic response involves blood coagulation and platelet
 aggregation to stop blood loss from an injured blood vessel. The
 complexity of these processes make it difficult to intuit the overall
 hemostatic response without quantitative methods. Mathematical models aim
 to address this challenge but are often accompanied by numerous parameters
 choices and thus need to be analyzed for sensitivity to such choices. Here
 we use local and global sensitivity analyses to study a model of
 coagulation and platelet deposition under flow. To relate with clinical
 assays, we measured the sensitivity of three specific thrombin metrics:
 lag time, maximum relative rate of generation, and final concentration
 after 20 minutes. In addition, we varied parameters of three different
 classes: plasma protein levels, kinetic rate constants, and platelet
 characteristics. In terms of an overall ranking of the model’s
 sensitivities, we found that the local and global methods provided similar
 information. Our local analysis, in agreement with previous findings,
 shows that varying parameters within 50-150% of baseline values, in a
 one-at-a-time (OAT) fashion, always leads to significant thrombin
 generation in 20 minutes. Our global analysis gave a different and novel
 result highlighting groups of parameters, still varying within the normal
 50-150%, that produced little or no thrombin in 20 minutes. Variations in
 either plasma levels or platelet characteristics, using either OAT or
 simultaneous variations, always led to strong thrombin production and
 overall, relatively low output variance. Simultaneous variation in
 kinetics rate constants or in a subset of all three parameter classes led
 to the highest overall output variance, incorporating instances with
 little to no thrombin production. The global analysis revealed multiple
 parameter interactions in the lag time and final concentration leading to
 relatively high variance; high variance was also observed in the thrombin
 generation rate, but parameters attributed to that variance acted
 independently and additively.
description: This data is being publicly furnished so that the methods and
 results seen in<br> the paper can be independently verified and to
 allow other researchers to gain<br> new insights into varied inputs
 for the KFHL coagulation model. The data is organized
 into two broad categories:<br>     1) local analysis, files starting
 with "LSA"<br>     2) global analysis, file starting with
 "GSA"
description: README file with data download provides documentaion on
 datasets.