cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6086/d1p07x
title: #BLKTwitterstorians January 2018 Chat

description: The first #BLKTwitterstorians chat of 2018.
description: The tweet ids were collected using the Documenting the Now
 prototype tweet collecting tool: http://app.docnow.io/ This dataset
 contains a text file of the tweet ids.
description: Because of restrictions in the Twitter terms of service, only
 tweet ids can be shared at scale for research. You can download and use
 the DocNow Hydrator to recreate the original tweets from the
 ids https://github.com/DocNow/hydrator
DOI: 10.15146/r32x0g
title: Data for Cold adaptation does not alter ATP homeostasis during cold exposure in Drosophila melanogaster

description: Data and analysis scripts for Williams et al. 2018 Integrative
 Zoology:
DOI: 10.25338/b8v308
title: A Strawberry Database: Geometric Properties, Images and 3D Scans

description: 1611 strawberries from different places and varieties are used to collect
 images, 3D scans as well as physical properties such as shape, width,
 height, and weight.
description: The database described in this paper was made using 1611
 strawberries divided into 20 groups, representing 15 varieties and
 harvested at 3 locations: Oxnard, Santa Maria and Watsonville (California,
 USA). A description of each group is given in table \ref{tab:straw}. The
 strawberries were harvested between June and September 2014. They were
 shipped overnight and delivered at the University of California, Davis the
 next day, where they were stored in a temperature-controlled chamber set
 at two degrees Celsius. They were processed within one up to four days
 after being picked. The first step consisted in
 collecting 22 images for each berry with a NIKON DS 2000 camera. To do so,
 each strawberry was placed on a robotic arm and rotated between each
 picture. For images 1 to 11, the robot rotates around vector x by 18
 degrees. For images 12 to 22, the rotation is around vector z by 18
 degrees. In order to obtain a uniform set of images, the lighting
 environment was controlled and the white balance was held constant over
 time.  The second step of the data collection consisted
 in identifying the shape of each strawberry, measure its dimension, and
 weigh it with and without the calyx. First, the shape classification was
 manually done. Next, the maximal height and width were manually measured
 with a caliper. Finally, each fruit was weighed with and without the calyx
 thanks to a Scout Pro SP602 scale. The calyx was manually removed while
 trying to minimize the amount of removed flesh. The
 final step consisted of scanning the flesh of the strawberries. The
 scanning was performed using a Solutionix Rexcan DS2 scanner. The fruits
 were spray-coated with a white titanium solution to minimize light
 reflection. Each berry was then pinned on a mobile platform within the
 scanner. Finally, 10 different views were used to create the 3D
 model.  For each fruit, the scanning process provides a
 point cloud, which was then manually processed using the Meshlab software.
 First, the close vertices were merged to reduce the point cloud size.
 Next, the points corresponding to the surface of the pin were removed, and
 finally, a Poisson surface reconstruction filter was applied to the point
 cloud using a tree depth of 4, 6 and 8.
DOI: 10.5061/dryad.57qv82g
title: Data from: Generic and specific facets of vulnerability for analyzing trade-offs and synergies in natural resource management

description: 1. The concept of vulnerability as the combination of exposure,
 sensitivity and adaptive capacity to a stressor is gaining traction
 outside of the climate realm, opening new avenues to address contemporary
 sustainability issues more holistically. Yet, critical notions that
 underpin vulnerability have yet to be integrated into its application to
 natural resource management and non-climatic stressors. In particular, the
 way generic and stressor-specific facets of vulnerability interact and can
 inform decision-makers about how interventions combine and/or trade-off
 remains unexplored. 2. Here, we investigate the salience of the
 generic/specific framing in the context of Chilean artisanal fishing
 communities engaged in rights-based co-management and experiencing
 pressures from two stressors: poaching and market volatility.
 Specifically, we draw on market data combined with socioeconomic surveys
 conducted with 446 members and leaders from 42 fisher unions to
 quantitatively investigate potential trade-offs and synergies between
 facets of vulnerability to poaching and markets. 3. Generic adaptive
 capacity (i.e. flexibility, assets, learning, organization and agency)
 likely facilitated stressor-specific adaptive capacities to both
 stressors. High levels of specific adaptive capacity to one stressor
 neither increased exposure nor undermined specific adaptive capacity to
 the other stressor. However, adaptive capacity did not translate into
 exposure reduction as expected, suggesting that adaptation barriers may
 prevent fishers from mobilizing adaptive capacity into effective adaptive
 action. 4. This study illustrates how breaking down vulnerability into
 generic and specific facets can help us better anticipate important
 trade-offs and synergies in management interventions. More generally, it
 highlights the potential of the climate adaptation and vulnerability
 literatures in informing place-based management of natural resources.
description: See paper.
DOI: 10.25338/b8qc7f
title: Caltrans PEMS highway sensor average flows by occupancy

description: This data summarizes average vehicle flow as a function of occupancy for
 traffic sensor data available from CalTrans Performance Management System
 (PEMS). It's useful because it shows the behavior of traffic in
 congested regimes, without requiring the preprocessing of several hundred
 GB of the raw data. Open the pdf files to see what this data looks like.
description: First open the pdf files to see what this data looks
 like. Traffic engineers model the flow of traffic
 (vehicles per hour) as a function of traffic density (vehicles
 per<br> mile). This model dictates how traffic will flow in a given
 stretch of road, so it is known as the fundamental<br> diagram
 Daganzo (1997). Flow is the number of
 vehicles<br> that pass over the detector in a 30 second period, and
 occupancy is the fraction of time that a vehicle is<br> over the
 detector.<br> We downloaded 10 months of 30 second loop detector
 data in 2016 from the CalTrans Performance Measurement<br> System
 (PEMS) http://pems.dot.ca.gov/ website. We chose Caltrans district 3, the
 San Francisco Bay Area,<br> because this area contains many
 observations of high traffic activity and it’s large enough to motivate
 the<br> computational techniques. We used a
 nonparametric method based on dynamically binning the data using the
 values of<br> the occupancy and then computing the mean flow in each
 bin. We started out with a fixed minimum bin<br> width of w = 0.01,
 which means that there will be no more than 1/w = 100 bins in total. We
 chose 0.01<br> because it provides sufficient resolution for the
 fundamental diagram in areas of low density. Furthermore,<br> we
 required that each bin has at least k observations in each bin. Some
 experimentation for a few different<br> stations showed that
 choosing k = 200 provided a visually smooth fundamental diagram.
    
description: First open the pdf files to see what this data looks
 like. The following R command will load the
 data: <br>     fd_shape =
 read.table("fd_shape.tsv"<br>         , col.names =
 c("station", "right_end_occ", "mean_flow",
 "sd_flow", "number_observed")<br>         ,
 colClasses = c("integer", "numeric",
 "numeric", "numeric", "integer")<br>  
       , na.strings = "NULL"<br>         )
 The columns are as follows: 
 station: station ID from PEMS
 right_end_occ: right end of the occupancy bin where the means
 are observed. Ranges from 0 to 1 sd_flow: standard
 deviation of vehicle flow in bin mean_flow: mean
 vehicle flow in bin number_observed: the number of
 vehicles in bin
DOI: 10.6086/d1cm12
title: #GifHistory

description: This data set contains 31,929 tweets ids for tweets containing the hashtag
 #GifHistory. This hashtag was used by Twitter user @MatthewACherry on
 February 9th, 2018 to start a conversation about the history of popular
 gifs on Twitter. Here is a link to the original tweet using the
 hashtag https://twitter.com/MatthewACherry/status/962011241815277568 
description: The tweet ids in this dataset we're collected using the
 DocNow prototype Twitter data collection
 tool. http://app.docnow.io/  You can recreate the
 original tweets by using the DocNow
 Hydrator https://github.com/DocNow/hydrator
DOI: 10.15146/r3h09m
title: Data set for "Planar Hall torque"

description: This is the data set used to generate the figures and to support
 the findings of "Planar Hall torque"
  (arXiv:1712.07335). The data set includes magnetoresistance,
 spin torque ferromagnetic resonance, ferromagnetic resonance, and
 microwave emmision data.
DOI: 10.13144/lil-0088
title: Emploi du temps (EDT) - 1985-1986

description: Troisième enquête réalisée par l'INSEE, l'enquête Emploi du temps de 1985-1986 s'intéresse à l'ensemble des activités quotidiennes des personnes vivant en France. Il s'agit principalement de mesurer les temps passés aux diverses activités qui composent la vie de tous les jours. Elle a pour but de faire progresser l'étude des comportements non monétaires dans le domaine des activités de la vie quotidienne et des emplois du temps en quantifiant la durée des activités quotidiennes et la répartition dans une journée des 4 temps fondamentaux du quotidien : travail professionnel, travail domestique, temps libre et temps physiologique. Le champ couvert par l'enquête est plus large que pour l'enquête précédente de 1974-75. Elle a été réalisée sur l'ensemble de la France et non plus seulement sur la France urbaine auprès d'un échantillon de 16 000 logements pour un échantillon final de 16 047 individus âgés de 15 ans et plus (10 373 Kish + 5674 conjoints) sous la forme de 8 vagues d'enquête permettant une couverture de l'ensemble des périodes d'une année. Les personnes interrogées décrivent pour une journée leurs activités par tranches de 5 mn. Pour chaque occupation l'enquêté indique s'il effectue une activité secondaire, le lieu, le but et en présence de qui s'est déroulée l'activité.
DOI: 10.5061/dryad.h3tj5mc
title: Data from: Factors determining species richness patterns of breeding birds along an elevational gradient in the Horn of Africa region

description: Aim: To document the species richness patterns of breeding birds along
 elevational gradients and explore its drivers in the Horn of Africa
 Region. Location: Horn of Africa Region Taxon: Breeding species of birds
 Methods: Distributional data for breeding birds were collected.
 Elevational distribution data were extracted, interpolated, and assembled
 for all birds, passerines and non-passerines. In order to tease apart how
 different environmental factors contributed to the variation in species
 richness, we found it necessary to divide the area into four subregions
 with different climatic regimes and topographic structure. Then, the
 species richness in each 100 m elevational band was counted along the
 elevational gradients of each subregion. Pearson’s correlation analyses
 and ordinary least squares (OLS) regressions were used to examine the
 relationships between species richness and factors Results: The variation
 in species richness followed hump-shaped patterns for all subregions,
 although with peak values at different elevations. The bird species groups
 on the western and eastern slopes showed low and high plateaus with
 mid-elevational peaks, respectively, but very low species diversities at
 the highest elevations. Species richness was significantly correlated with
 temperature range and productivity in each subregion. The temperature
 range, area and productivity explained 82% of the species richness
 variations for all birds on the western slope. Main conclusions: The
 separate analyses of four area subdivisions provide strong indications of
 how various factors interact. Productivity and temperature range were the
 best driving factors for shaping the richness patterns, but deviations
 from expected patterns suggest modifying roles of mist formation zones in
 the valleys that deeply intersect the large highlands in the west and rich
 riparian vegetation where water from cool and humid environments at high
 elevation reaches lower elevations in the arid east. Conservation is
 recommended in each subregion based on the elevational richness scenarios.
description: Breeding bird species
 elevation rangeBreeding birds elevation
 range data in the Horn of Africa.elevational_range.xlsx
DOI: 10.25338/b88593
title: Data deposition for Complex electrophysiological remodeling in postinfarction ischemic heart failure

description: Heart failure (HF) following myocardial infarction (MI) is associated with
 high incidence of cardiac arrhythmias. Development of therapeutic strategy
 requires detailed understanding of electrophysiological remodeling.
 However, changes of ionic currents in ischemic HF remain incompletely
 understood, especially in translational large animal models. Here, we
 systematically measure the major ionic currents in ventricular myocytes
 from the infarct border and remote zones in a porcine model of post-MI HF.
 We recorded eight ionic currents during the cell’s action potential (AP)
 under physiologically relevant conditions using selfAP-clamp Sequential
 Dissection. Compared to healthy controls, HF-remote zone myocytes
 exhibited increased late Na+ current, Ca2+-activated K+ current,
 Ca2+-activated Cl- current, decreased rapid delayed rectifier K+ current,
 and altered Na+/Ca2+ exchange current profile. In HF-border zone myocytes,
 the above changes also occurred but with additional decrease of L-type
 Ca2+ current, decrease of inward rectifier K+ current, and Ca2+
 release-dependent delayed afterdepolarizations. Our data reveal that the
 changes in any individual current are relatively small, but the integrated
 impacts shift the balance between the inward and outward currents to
 shorten AP in the border zone but prolong AP in the remote zone. This
 differential remodeling in post-MI HF increases the inhomogeneity of AP
 repolarization which may enhance the arrhythmogenic substrate. Our
 comprehensive findings provide a new mechanistic framework for
 understanding why single channel blockers may fail to suppress
 arrhythmias, and highlight the need to consider the rich tableau and
 integration of many ionic currents in designing therapeutic strategies for
 treating arrhythmias in HF.
description: Electrophysiology data were collected using pClamp10 (Molecular
 Devices) software, then Clampfit 10 (Molecular Devices), Excel 2016
 (Microsoft) and Origin 2016 (OriginLab) softwares were used for data
 processing and analysis. Calcium and contraction data
 were collected using IonWizard (IonOptix) software, then IonWizard, Excel
 and Origin softwares were used for data processing and analysis.
 Files are compressed to keep the folder structure and to ease the
 navigation between the uploaded documents.
DOI: 10.6078/d1xt19
title: Simulated antihydrogen orbits in an octupole-based Minimum-B trap

description: These movies show simulations of the trajectories of antihydrogen atoms
 confined in a Minimum-B trap similar to the "flat" trap
 used by CERN's ALPHA collaboration.
description: See associated paper.
DOI: 10.25338/b8zp4k
title: INCREASING CORAL RESILIENCE TO BLEACHING THROUGH MICROBIOME MANIPULATION

description: Although the early coral reef-bleaching warning system (NOAA/USA) is
 established, there is no feasible treatment that can minimize temperature
 bleaching and/or disease impacts on corals in the field. Here, we present
 the first attempts to extrapolate the widespread and well-established use
 of bacterial consortia to protect or improve health in other organisms
 (e.g., humans and plants) to corals. Manipulation of the coral-associated
 microbiome was facilitated through addition of a consortium of native
 (isolated from Pocillopora damicornis and surrounding seawater) putatively
 beneficial microorganisms for corals (pBMCs), including five
 Pseudoalteromonas sp., a Halomonas taeanensis and a Cobetia marina-related
 species strains. The results from a controlled aquarium experiment in two
 temperature regimes (26 °C and 30 °C) and four treatments (pBMC; pBMC with
 pathogen challenge – Vibrio coralliilyticus, VC; pathogen challenge, VC;
 and control) revealed the ability of the pBMC consortium to partially
 mitigate coral bleaching. Significantly reduced coral-bleaching metrics
 were observed in pBMC-inoculated corals, in contrast to controls without
 pBMC addition, which displayed strong bleaching signs as indicated by
 significantly lower photopigment contents
 and Fv/Fm ratios. The structure of the coral microbiome
 community also differed between treatments and specific bioindicators were
 correlated with corals inoculated with pBMC (e.g., Cobetia sp.) or VC
 (e.g., Ruegeria sp.). Our results indicate that the microbiome in corals
 can be manipulated to lessen the effect of bleaching, thus helping to
 alleviate pathogen and temperature stresses, with the addition of BMCs
 representing a promising novel approach for minimizing coral mortality in
 the face of increasing environmental impacts.
DOI: 10.5061/dryad.f32p5g7
title: Data from: Bite marks and predation of fossil jawless fish during the rise of jawed vertebrates

description: Although modern vertebrate diversity is dominated by jawed vertebrates,
 early vertebrate assemblages were predominantly comprised of jawless
 fishes. Hypotheses for this faunal shift and the Devonian decline of
 jawless vertebrates include predation and competitive replacement. The
 nature and prevalence of ecological interactions between jawed and jawless
 vertebrates are highly relevant to both hypotheses, but direct evidence is
 limited. Here we use the occurrence and distribution of bite mark type
 traces in fossil jawless armoured heterostracans to infer predation
 interactions. A total of 41 predated specimens are recorded; their
 prevalence increases through time, reaching a maximum toward the end of
 the Devonian. The bite mark type traces significantly co-occur with jawed
 vertebrates and their distribution through time is correlated with jawed
 vertebrate diversity patterns, particularly placoderms and
 sarcopterygians. Environmental and ecological turnover in the Devonian,
 especially relating to the nektonic revolution, have been inferred as
 causes of the faunal shift from jawless to jawed vertebrates. Here we
 provide direct evidence of escalating predation from jawed vertebrates as
 a potential contributing factor to the demise and extinction of
 ostracoderms.
description: Supplementary
 DataBite mark occurrence
 data and jawed vertebrate diversity and occurrence dataPredation Data
 SI.xlsx
DOI: 10.7280/d1zd38
title: Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

description: Accurately predicting protein-ligand binding affinities and binding modes
 is a major goal in computational chemistry, but even the prediction of
 ligand binding modes in proteins poses major challenges. Here, we focus on
 solving the binding mode prediction problem for rigid fragments. That is,
 we focus on computing the dominant placement, conformation, and
 orientations of a relatively rigid, fragment-like ligand in a receptor,
 and the populations of the multiple binding modes which may be relevant.
 This problem is important in its own right, but is even more timely given
 the recent success of alchemical free energy calculations. Alchemical
 calculations are increasingly used to predict binding free energies of
 ligands to receptors. However, the accuracy of these calculations is
 dependent on proper sam- pling of the relevant ligand binding modes.
 Unfor- tunately, ligand binding modes may often be uncer- tain, hard to
 predict, and/or slow to interconvert on simulation timescales, so proper
 sampling with cur- rent techniques can require prohibitively long sim-
 ulations. We need new methods which dramatically improve sampling of
 ligand binding modes. Here, we develop and apply a nonequilibrium
 candidate Monte Carlo (NCMC) method to improve sampling of ligand binding
 modes. In this technique, the ligandis rotated and subsequently allowed to
 relax in its new position through alchemical perturbation before accepting
 or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo
 move. When applied to a T4 lysozyme model binding system, this NCMC method
 shows over two orders of magnitude improvement in binding mode sampling
 efficiency compared to a brute force molecular dynamics sim- ulation. This
 is a first step towards applying this methodology to
 pharmaceutically-relevant binding of fragments and, eventually, drug-like
 molecules. We are making this approach available via our new Binding Modes
 of Ligands using Enhanced Sampling (BLUES) package which is freely
 available on GitHub. This dataset acts as additional supporting info
 for 10.1021/acs.jpcb.7b11820 and includes the full trajectories
 as well as the assorted scripts used to produce the data found in the
 paper.
DOI: 10.5061/dryad.rd72rt2
title: Data from: Efficiency of using electric toothbrush as an alternative to tuning fork for artificial buzz pollination is independent of instrument buzzing frequency

description: Background: Breeding programs and research activities where artificial
 buzz pollinations are required have primarily relied upon using tuning
 forks, and bumble bees. However, these methods can be expensive,
 unreliable, and inefficient. To find an alternative, we tested the
 efficiency of pollen collection using electric toothbrushes and compared
 it with tuning forks at three vibration frequencies- low, medium, and high
 and two extraction times at 3 seconds and 16 seconds- from two buzz
 pollinated species (Solanum lycopersicum and Solanum elaeagnifolium).
 Results: Our results show that species, and extraction time significantly
 influenced pollen extraction, while there were no significant differences
 for the different vibration frequencies and more importantly, the use of a
 toothbrush over tuning fork. More pollen was extracted from Solanum
 elaeagnifolium when compared to Solanum lycopersicum, and at longer
 buzzing time of regardless of the instrument used. Conclusions: Our
 results suggest that electric toothbrush can be a viable and inexpensive
 alternative to tuning forks, and regardless of the instrument used and
 buzzing frequency, time of buzzing is also critical in pollen extraction
description: Tayal_ Raw Data for
 Dryad This data is collected
 in the lab from two plant species using electric toothbrush and tuning
 fork. Tabs in the Excel spreadsheet are: - Instrument
 -
 Time - Frequency
 - Species x
 instrument
DOI: 10.6078/d1n955
title: Sea Level Rise Impacts on Wastewater Treatment Systems along the U.S. Coasts

description: This dataset contains location data for wastewater treatment plants
 located with 2 km of the U.S. coastline, based on the U.S. Environmental
 Protection Agency's Facility Registry Service. Wastewater treatment
 plant locations were verified using imagery to improve accuracy. Also
 included is an interpolated depth-to-groundwater surface for the San
 Francisco Bay Area. All other datasets used in this manuscript are
 available at the links provided in the text, which can be accessed
 at https://doi.org/10.1002/2017EF000805.