cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jsxksn06c
title: Data from: Curation: heat stress responses and population genetics of the kelp Laminaria digitata (Phaeophyceae) across latitudes reveal differentiation among North Atlantic populations

description: We aim to understand the thermal plasticity of a coastal foundation
 species across its latitudinal distribution by assessing physiological
 responses to high temperature stress in the kelp Laminaria digitata in
 combination with population genetic characteristics. We hypothesize that
 Arctic and cold-temperate populations are less heat resilient than
 warm-temperate populations. Using meristems of natural L. digitata
 populations from six locations ranging between Kongsfjorden, Spitsbergen
 (79°N), and Quiberon, France (47°N), we performed a common-garden heat
 stress experiment applying 15°C to 23°C over eight days. We assessed
 growth, quantum yield, carbon and nitrogen storage, and xanthophyll
 pigment contents as response traits. Population connectivity and genetic
 diversity were analysed with microsatellite markers to relate heat
 resilience to genetic features and phylogeography. Microsatellite
 genotyping revealed all sampled populations to be genetically distinct,
 underlying strong hierarchical structuring between and within southern and
 northern clades. Genetic diversity was lowest in the isolated population
 of the North Sea island of Helgoland and highest in Roscoff in the English
 Channel. Results from the heat stress experiment suggest that the upper
 temperature limit of L. digitata is nearly identical across its
 distribution range, but subtle differences were revealed for the two
 populations currently at their warm limits. They respectively show a
 significant advantage in growth at 19°C and 21°C (Quiberon) and a lack of
 stress responses in photosynthetic quantum yield and xanthophyll pigments
 at 23°C (Helgoland). In addition, quantum yield indicated the highest heat
 sensitivity in L. digitata from the northernmost population in
 Spitsbergen. All together, these results support the hypothesis of
 moderate local differentiation across L. digitata’s European distribution,
 whereas effects are likely too weak to ameliorate the species’ capacity to
 withstand ocean warming and marine heatwaves at the southern range edge.
description: Genotype data The samples were collected
 during 2018/beginning of 2019 in all locations. At least 30 individuals
 were collected and genotyped for 12 markers. The
 acquisition of the genotype data are explained in the M&M section
 of the manuscript.
description: We encountered some problems for genotyping the population of
 Helgoland. Therefore the samples collected in 2016 were used for the
 genotypic comparison instead. The data is presented as
 for GenAlex. The missing data are shown as "0". GenAlex can then
 be used to export the data file for other programs (GENEPOP, STRUCTURE
 etc.)
DOI: 10.5061/dryad.mpg4f4qwd
title: Hierarchy of the factors influencing the broad-scale waterbirds functional diversity gradients in temperate China

description: Geographical gradients in species diversity have long fascinated
 biogeographers and ecologists. However, the extent and generality of the
 positive/negative effects of the important factors governing functional
 diversity (FD) patterns are still debated, especially for the freshwater
 domain. We examined lake productivity and functional richness (FRic) of
 waterbirds sampled from 35 lakes and reservoirs in northern China with a
 geographic coverage of over 5 million km2. We used structural equation
 modelling (SEM) to explore the causal relationships between geographic
 position, climate, lake productivity and waterbirds FRic. We found
 unambiguous altitudinal and longitudinal gradients in lake productivity
 and waterbirds FD, which were strongly mediated by local environmental
 factors. Specifically, we found 1) lake productivity increased northeast
 but decreased with altitude, and the observed gradients were driven by
 climate and nutrient availability, with 93% of variation explained in the
 individual SEM; 2) waterbirds FD showed similar geographic and elevational
 gradients.; the environmental factors which had direct and/or indirect
 effects on these geographic and elevational gradients included climate,
 lake productivity and morphology, which collectively explained more than
 56% of the variation in waterbirds FD; and 3) a significant (P = 0.029)
 causality between lake productivity and waterbirds FD was confirmed.
 Nevertheless, the causality link was relatively weak in comparison with
 climate and lake area (standardized path coefficient was 0.65, 0.21, and
 0.17 for climate, area, and productivity, respectively). Through
 articulating the dominant causality paths, our results could contribute to
 the mechanistic explanations underlying the observed broad–scale
 biodiversity gradients.
DOI: 10.5061/dryad.jwstqjq6c
title: Data from: The protected flora of long-established cemeteries in Hungary: using historical maps in biodiversity conservation

description: The role of anthropogenically influenced habitats in conserving elements
 of the original wildlife has increased worldwide simultaneously with the
 disappearance of natural sites. Burial places are able to conserve
 original elements of the wildlife and this fact has been known for at
 least a century. To this day little is known about long-time changes, and
 the effect of long-time management methods in cemeteries on the flora they
 harbour. The utility of historical maps in research focused on natural
 values, as well as in answering questions related to conservation was
 recently demonstrated, but the use of digitized historical maps in
 biodiversity research of the Carpathian Basin is very limited. In the
 present paper, we aimed to predict the conservation potential of
 long-established and newly established cemeteries of Hungarian settlements
 with various population sizes based on the digitized maps of the 2nd
 Military Survey of the Austrian Empire (1819–1869), by categorizing
 cemeteries into 3 distinct (anthropogenic habitat, cemetery, or natural
 habitat) types. To build our models we used records of the protected flora
 from Hungarian cemeteries, based on data of thematic botanical surveys of
 991 cemeteries. Out of the surveyed cemeteries 553 (56%) harboured
 protected plants, totalling 306.617 estimated individuals of 92 protected
 species, belonging to 28 plant families. These species represent 12% of
 the entire protected flora of Hungary. Hungarian cemeteries play a key
 role mainly in preserving steppe and dry grassland plant
 species.Long-established and large cemeteries harbour more protected plant
 species than small and newly established ones.Human population size of the
 settlements correlated negatively with the number of protected species and
 individuals. Moreover, woodland cover and proportion of grassland, also
 significantly positively affected the number of protected plant species in
 cemeteries.
description: We surveyed burial grounds between 2014 and 2017, regardless of
 their religious affiliation, spatial dimension or geographic location
 within Hungary. Surveyed cemeteries were selected without any previous
 knowledge on their history or flora. A total of 991 by a  cemeteries were
 surveyed, including cemeteries from every county of Hungary. All protected
 plant taxa were identified and recorded. Taxa were identified based on the
 Plant List, the nomenclature used in this paper also follows this work.
 Protected plant species were chosen based to the Decree No. 13/2001.
 (V.9.) of the Ministry of Environmental Protection.
DOI: 10.5061/dryad.h9w0vt4ft
title: Data from: Studded leather collars are very effective in protecting cattle from leopard (Panthera pardus) attacks

description: Human-wildlife conflicts are widespread, particularly with big cats which
 can kill domestic livestock and create a counteraction between
 conservation and local livelihoods, especially near protected areas.
 Minimization of livestock losses caused by big cats and other predators is
 essential to mitigate conflicts and promote socially acceptable
 conservation. As big cats usually kill by throat bites, protective collars
 represent a potentially effective non-lethal intervention to prevent
 livestock depredation, yet the application and effectiveness estimation of
 these tools are very limited. In this study, for the first time we
 measured the effectiveness of studded leather collars in protecting cattle
 from leopard (Panthera pardus) attacks. We conducted a randomized
 controlled experiment during 14 months to collar 202 heads and leave
 uncollared 258 heads grazing in forests and belonging to 27 owners from
 eight villages near three protected areas in Mazandaran Province, northern
 Iran. Our results show that none of collared cattle and nine uncollared
 cattle were lost to leopard depredation, meaning that collars caused a
 zero relative risk of damage and a perfect 100% damage reduction. Most
 losses occurred in summer and autumn due to lush vegetation attracting
 more cattle, long daytime allowing movements deep into leopard habitats,
 and dense cover favoring leopard hunts from ambush. Losses were recorded
 in only six owners and four villages, suggesting local rarity and patchy
 distribution of leopards. We suggest that collars can be successfully
 applied to cattle freely grazing in habitats of leopards or other felids
 for a long time and thus remaining persistently exposed to depredation. As
 grazing cattle are usually not supervised by shepherds or dogs, collars
 can be the only practical protection tool. Production and sales of collars
 can become a sustainable small-scale business for farmers to further boost
 conservation and rural livelihoods.
DOI: 10.5061/dryad.73n5tb2ts
title: Heat stress responses of the kelp Laminaria digitata (Phaeophyceae) across Northeast Atlantic populations: growth, biochemistry, chlorophyll fluorescence, pigments

description: To understand the thermal plasticity of a coastal foundation species
 across its latitudinal distribution, we assess physiological responses to
 high temperature stress in the kelp Laminaria digitata in combination with
 population genetic characteristics and relate heat resilience to genetic
 features and phylogeography. We hypothesize that populations from Arctic
 and cold-temperate locations are less heat resilient than populations from
 warm distributional edges. Using meristems of natural L. digitata
 populations from six locations ranging between Kongsfjorden, Spitsbergen
 (79°N), and Quiberon, France (47°N), we performed a common-garden heat
 stress experiment applying 15°C to 23°C over eight days. We assessed
 growth, photosynthetic quantum yield, carbon and nitrogen storage, and
 xanthophyll pigment contents as response traits. Population connectivity
 and genetic diversity were analysed with microsatellite markers. Results
 from the heat stress experiment suggest that the upper temperature limit
 of L. digitata is nearly identical across its distribution range, but
 subtle differences in growth and stress responses were revealed for three
 populations from the species’ ecological range margins. Two populations at
 the species’ warm distribution limit showed higher temperature tolerance
 compared to other populations in growth at 19°C and recovery from 21°C
 (Quiberon, France), and photosynthetic quantum yield and xanthophyll
 pigment responses at 23°C (Helgoland, Germany). In L. digitata from the
 northernmost population (Spitsbergen, Norway), quantum yield indicated the
 highest heat sensitivity. Microsatellite genotyping revealed all sampled
 populations to be genetically distinct, with a strong hierarchical
 structure between southern and northern clades. Genetic diversity was
 lowest in the isolated population of the North Sea island of Helgoland and
 highest in Roscoff in the English Channel. All together, these results
 support the hypothesis of moderate local differentiation across L.
 digitata’s European distribution, whereas effects are likely too weak to
 ameliorate the species’ capacity to withstand ocean warming and marine
 heatwaves at the southern range edge.
description: We collected 30–35 fertile
 <i>L. digitata</i> sporophytes from the low intertidal zone,
 ensuring a distance of &gt;1 m between samples (for the samples
 collected by diving in Spitsbergen, this was not guaranteed), in each of
 the following locations during summer: Stuphallet, Kongsfjorden,
 Spitsbergen, Norway (SPT, 78.975 N, 11.633 E; 16 July 2019; approximate
 SST at time of sampling: 6.5°C); north of Tromsø, Norway (TRO, 69.790 N,
 19.054 E; 14 August 2018; 8.5°C); Bodø, Norway (67.284 N, 14.383 E; 12
 June 2018; 9°C); Helgoland, Germany (HLG, 54.178 N, 7.893 E; 13 August
 2018; 18°C); Roscoff, France (ROS, 48.727 N, 4.005 W; 11 September 2018;
 16.5°C) and Quiberon, France (QUI, 47.470 N, 3.091 W; 10 September 2018;
 16°C).
DOI: 10.5061/dryad.905qftthc
title: Implementation of a learning healthcare system for Sickle Cell disease: List of smart data elements contained in the Epic Smartform and their SmartData types

description: Objective: Using Sickle Cell Disease (SCD) as a model, the objective of
 this study was to create a comprehensive learning healthcare system to
 support disease management and research. A multidisciplinary team
 developed a SCD clinical data dictionary to standardize bedside data entry
 and inform a scalable environment capable of converting complex electronic
 healthcare records (EHR) into knowledge accessible in real-time. Materials
 and Methods: Clinicians expert in SCD care developed a data dictionary to
 describe important SCD associated health maintenance and adverse events.
 The SCD data dictionary was deployed in the EHR using Epic SmartForms, an
 efficient bedside data entry tool. Additional data elements were extracted
 from the EHR database (Clarity) using Pentaho Data Integration (PDI) and
 stored in a data analytics database (SQL). A custom application, the
 Sickle Cell Knowledgebase, was developed to improve data analysis and
 visualization. Utilization, accuracy and completeness of data entry were
 assessed. Results: The SCD Knowledgebase facilitates generation of
 patient-level and aggregate data visualization, driving the translation of
 data into knowledge that can impact care. A single patient can be selected
 to monitor health maintenance, comorbidities, adverse event frequency and
 severity, and medication dosing/adherence. Discussion: Disease-specific
 data dictionaries used at the bedside will ultimately increase the
 meaningful use of EHR datasets to drive consistent clinical data entry,
 improve data accuracy and support analytics that will facilitate quality
 improvement and research
description: The data were collected via Smartforms in Epic. The data were processed
 using standard extraction, load, and transfer processes as outlined in the
 manuscript. Customizable EHR-based SmartForms (ESFs, structured data
 capture) provide the utility for capturing granular data at the bedside
 that could then be mapped with high quality to a data dictionary.
description: The data dictionary was uploaded at this time. The raw electronic
 healthcare record data cannot be uploaded as per IRB / HIPPA compliance.
DOI: 10.5061/dryad.nzs7h44nz
title: Mating patterns influence vulnerability to the extinction vortex

description: Earth’s biodiversity is undergoing mass extinction due to anthropogenic
 compounding of environmental, demographic and genetic stresses. These
 different stresses can trap populations within a reinforcing feedback loop
 known as the extinction vortex, in which synergistic pressures build upon
 one another through time, driving down population viability. Sexual
 selection, the widespread evolutionary force arising from competition,
 choice and reproductive variance within animal mating patterns, could have
 vital consequences for population viability and the extinction vortex: 1)
 if sexual selection reinforces natural selection to fix ‘good genes’ and
 purge ‘bad genes’, then mating patterns encouraging competition and choice
 may help protect populations from extinction; 2) by contrast, if mating
 patterns create load through evolutionary or ecological conflict, then
 population viability could be further reduced by sexual selection. We test
 between these opposing theories using replicate populations of the model
 insect Tribolium castaneum exposed to over ten years of experimental
 evolution under monogamous versus polyandrous mating patterns. After a
 95-generation history of divergence in sexual selection, we compared
 fitness and extinction of monogamous versus polyandrous populations
 through an experimental extinction vortex comprising 15 generations of
 cycling environmental and genetic stresses. Results showed that lineages
 from monogamous evolutionary backgrounds, with limited opportunities for
 sexual selection, showed rapid declines in fitness and complete extinction
 through the vortex. By contrast, fitness of populations from the history
 of polyandry, with stronger opportunities for sexual selection, declined
 slowly, with 60% of populations surviving by the study end. The three
 vortex stresses of i) nutritional deprivation, ii) thermal stress and iii)
 genetic bottlenecking had similar impacts on fitness declines and
 extinction risk, with an overall sigmoid decline in survival through time.
 We therefore reveal sexual selection as an important force behind lineages
 facing extinction threats, identifying the relevance of natural mating
 patterns for conservation management.
DOI: 10.5061/dryad.80gb5mknx
title: Untangling the importance of niche breadth and niche position as drivers of tree species abundance and occupancy across biogeographic regions

description: Aim: Ecological niches shape species commonness and rarity, yet the
 relative importance of different niche mechanisms within and across
 ecosystems remains unresolved. We tested the influence of niche breadth
 (range of environmental conditions where species occur) and niche position
 (marginality of a species’ environmental distribution relative to the mean
 environmental conditions of a region) on tree-species abundance and
 occupancy across three biogeographic regions. Location: Argentinian Andes;
 Bolivian Amazon; Missouri Ozarks. Time period: 2002–2010. Major taxa
 studied: Trees. Methods: We calculated abiotic-niche breadths and
 abiotic-niche positions using 16 climate, soil, and topographic variables.
 For each region, we used model selection to test the relative influence of
 niche breadth and niche position on local abundance and occupancy in
 regional-scale networks of 0.1-ha forest plots. To account for
 species-environment associations caused by other mechanisms (e.g.,
 dispersal), we used null models that randomized associations between
 species occurrences and environmental variables. Results: We found strong
 support for the niche-position hypothesis. In all regions, species with
 higher local abundance and occupancy occurred in non-marginal
 environments. Observed relationships between occupancy and niche position
 also differed from random species-environment associations in all regions.
 Surprisingly, we found little support for the niche-breadth hypothesis.
 Observed relationships between both local abundance and niche breadth, and
 occupancy and niche breadth, did not differ from random
 species-environment associations. Main conclusion: Niche position was more
 important than niche breadth in shaping species commonness and rarity
 across temperate, sub-tropical, and tropical forests. In all forests, tree
 species with widespread-geographic distributions were associated with
 environmental conditions commonly found throughout the region, suggesting
 that niche position has similar effects on species occupancy across
 contrasting biogeographic regions. Our findings imply that conservation
 efforts aimed at protecting populations of common and rare tree species
 should prioritize conservation of both common and rare habitats.
description: See ReadMe Files
description: See ReadMe Files
DOI: 10.5061/dryad.qbzkh18f6
title: Data from: A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface

description: The dynamics and organization of the actin cytoskeleton are crucial to
 many cellular events such as motility, polarization, cell shaping, and
 cell division. The intracellular and extracellular signaling associated
 with this cytoskeletal network is communicated through cell membranes.
 Hence the organization of membrane macromolecules and actin filament
 assembly are highly interdependent. Although the actin-membrane linkage is
 known to happen through many routes, the major class of interactions is
 through the direct interaction of actin-binding proteins with the lipid
 class containing poly-phosphatidylinositols (PPIs). Among the PPIs,
 phosphatidylinositol bisphosphate (PI(4,5)P2) acts as a significant factor
 controlling actin polymerization in the proximity of the membrane by
 binding to actin-associated proteins. The molecular interactions between
 these actin-binding proteins and the membrane lipids remain elusive. Here,
 using molecular modeling, analytical theory, and experimental methods, we
 investigate the binding of three different actin-binding proteins, mDia2,
 NWASP, and gelsolin, to membranes containing PI(4,5)P2 lipids. We perform
 molecular dynamics simulations on the protein-bilayer system and analyze
 the membrane binding in the form of hydrogen bonds and salt bridges at
 various PI(4,5)P2 and cholesterol concentrations. Our experimental study
 with PI(4,5)P2-containing large unilamellar vesicles mimics the
 computational experiments. Using the multivalencies of the proteins
 obtained in molecular simulations and the cooperative binding mechanisms
 of the proteins, we also propose a multivalent binding model that predicts
 the actin filament distributions at various PI(4,5)P2 and protein
 concentrations.
description: Molecular modeling, molecular dynamics, modeller, gromacs
description: Readme files are attached. The files are gromacs ready