cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xksn02vbk
title: Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management

description: Incorporating species' eco-evolutionary responses to human-caused
 disturbances remains a challenge in marine management efforts. A
 prerequisite is knowledge of geographic structure and scale of genetic
 diversity and connectivity - the so-called seascape genetic patterns. The
 Baltic Sea is an excellent model system for studies linking seascape
 genetics with effects of anthropogenic stress. However, seascape genetic
 patterns in this area are only described for a few species and are
 completely unknown for invertebrate herbivores, which constitute a
 critical part of the ecosystem. This information is crucial for
 sustainable management, particularly under future scenarios of rapid
 environmental change. Here, we investigate the population genetic
 structure among 31 locations throughout the Baltic Sea, of which 45 % were
 located in marine protected areas, in one of the most important herbivores
 of this region, the isopod crustacean Idotea balthica, using an array of
 33,774 genome-wide SNP markers derived from 2b-RAD sequencing. In
 addition, we generate a biophysical connectivity matrix for I. balthica
 from a combination of oceanographic current models and estimated life
 history traits. We find population structure on scales of hundreds of
 kilometers across the Baltic Sea, where genomic patterns in most cases
 closely match biophysical connectivity, indicating passive transport with
 oceanographic currents as an important mean of dispersal in this species.
 We also find a reduced genetic diversity in terms of heterozygosity along
 the main salinity gradient of the Baltic Sea, suggesting periods of low
 population size. Our results provide crucial information for management of
 a key ecosystem species under expected changes in temperature and salinity
 following global climate change in a marine coastal area.
DOI: 10.5061/dryad.rr4xgxd5h
title: Clinical and radiographic course of arrested cerebral adrenoleukodystrophy

description: Objective: To gain insight into the natural history of arrested cerebral
 adrenoleukodystrophy (CALD), we quantified the change in Neurologic
 Function Score (NFS) and Loes Score (LS) over time in patients whose
 cerebral lesions spontaneously stopped progressing. Methods: We
 retrospectively reviewed a series of 22 patients with arrested CALD
 followed longitudinally over a median time of 2.4 years (0.7 – 17.0).
 Primary outcomes were change in radiographic disease burden (measured by
 LS) and clinical symptoms (measured by NFS) between patients who never
 developed a contrast-enhancing lesion (GdE- subgroup), and those who did
 (GdE+ subgroup). Secondary analyses comparing patterns of neuroanatomical
 involvement and lesion number, and prevalence estimates, were performed.
 Results: Cerebral lesions were first detected at a median age of 23.3
 years old (8.0 – 67.6), with an initial LS of 4 (0.5 – 9).  NFS
 was 0.5 (0 – 6). Overall change in NFS or LS per year did not differ
 between subgroups. No patients who remained GdE- converted to a
 progressive CALD phenotype. The presence of contrast enhancement was
 associated with disease progression (rs = 0.559, p &lt;
 0.001). Four patients (18.2%) underwent step-wise progression, followed by
 spontaneous resolution of contrast enhancement, and re-arrest of
 disease.  Three patients (13.6%) converted to progressive
 CALD.  Nineteen patients (86.4%) have arrested CALD at most
 recent follow-up. The prevalence of arrested CALD is 12.4%. Conclusion:
 Arrested CALD lesions can begin in childhood, and patients are often
 asymptomatic early in disease. The majority of patients remain stable.
  However, clinical and MRI surveillance is recommended as a
 minority of patients undergo step-wise progression, or conversion to
 progressive CALD.
DOI: 10.5061/dryad.612jm6408
title: Calcareous defense structures of prey mediate the effects of predation and biotic resistance towards the tropics

description: Aims The importance of biotic interactions in creating and maintaining
 diversity is expected to increase toward low latitudes. However, the way
 in which predation affects diversity, can depend on how predators mediate
 competitive interactions and also on defensive traits of prey. Here we
 assessed the role of physical defences of prey to escape predation and how
 the importance of predation on community structure and diversity changes
 across latitude. Location Six sites, in three regions distributed across
 45 degrees of latitude in the Atlantic Ocean: a tropical region in Angola,
 a subtropical region in Brazil and a temperate region in Wales-UK. Methods
 We manipulated predation on marine sessile communities, using exclusion
 cages and assessed community parameters, including their susceptibility to
 biological invasion during early and advanced succession. Results
 Predation was more intense in the tropics and in advanced communities
 suggesting that predation effects increase through time. In the tropical
 region, predators reduced the number of co-occurring species and beta
 diversity, limited the occurrence of exotic species and promoted a change
 in the identity of the dominant organisms, replacing soft-bodied organisms
 with calcified animals. In the subtropical region, predation promoted a
 similar trait-mediated change in the identity of dominant prey, although
 it was not strong enough to affect diversity and did not prevent
 bioinvasion. In the temperate region other processes than predation seem
 to drive the community organization and resistance to invasion. Main
 conclusions Our results support both Biotic Interaction and Biotic
 Resistance Hypotheses, showing that the importance of predation to
 biodiversity increases toward the tropics. In addition, where predation is
 intense, morphological traits of prey drive the final structure and
 dominance in the community. Our results suggest that physical defences are
 the main traits preventing predation, perhaps explaining why calcified
 organisms are among the most common invasive species in coastal habitats.
description: Methods for data collection and processing can be obtained in
 https://doi.org/10.1111/ddi.13020
description: Dataset used to describe the effect of predation on sessile
 community diversity, considering the factors Region, Sites and Predation
 treatment on the total richness (number of species), exotic richness
 (number of exotic species), and coverage (percentage) of the main
 taxonomic/functional groups after 1 and 3 months of community
 development. Excel file includes tabs:
 - Diversity1m - Diversity3m
 - Coverage data for 1 month data - Coverage
 data for 3 month data
DOI: 10.5061/dryad.k6djh9w3g
title: Seasonal and directional dispersal behavior in an ongoing dove invasion

description: Range expansions require the dispersal of individual organisms, but
 dispersal behavior is notoriously difficult to study. Eurasian
 Collared-Doves have colonized both Europe and North America this century,
 with both initial invasions proceeding northwestward via "jump"
 dispersal. The European population has reached carrying capacity, but in
 the Americas, where exponential population growth continues, little is
 known about dispersal behavior. I queried citizen science field notes to
 investigate Eurasian Collared-Dove dispersal behavior in North America
 along the Pacific Ocean, a natural barrier to northwestward landbird
 dispersal. I examined coastal and pelagic records of Eurasian
 Collared-Doves to determine the seasonality and directionality of
 dispersal flights and to assess changes in the frequency of
 dispersal-related behavior across years. Most reports of Eurasian
 Collared-Doves flying in flocks along the coast and most pelagic sightings
 were in March-May, mirroring the spring natal dispersal documented during
 the European invasion. Almost all spring coastal flocks were flying north,
 consistent with the overall northwestward direction of the initial North
 American invasion and northward deflection of northwest-bound birds upon
 encountering the Pacific Ocean. Spring flying flock observations showed no
 significant change in frequency from 2010-2018 after controlling for
 overall increases in spring collared-dove reports. This refined
 understanding of Eurasian Collared-Dove dispersal behavior informs full
 life cycle management of this rapidly increasing invader in the Americas,
 raises new questions about evolutionary mechanisms driving this
 spectacular invasion, and illustrates the potential power of citizen
 science field notes for documenting dispersal behavior, a longstanding
 challenge in ecology.
DOI: 10.25349/d9cp4c
title: Data from: Dermal denticle assemblages in coral reef sediments correlate with conventional shark surveys

description: It is challenging to assess long-term trends in mobile, long-lived, and
 relatively rare species such as sharks. Despite ongoing declines in many
 coastal shark populations, conventional surveys might be too fleeting and
 too recent to describe population trends over decades to millennia.
 Placing recent shark declines into historical context should improve
 management efforts as well as our understanding of past ecosystem
 dynamics. A new paleoecological approach for surveying shark abundance on
 coral reefs is to quantify dermal denticle assemblages preserved in
 sediments. This approach assumes that denticle accumulation rates
 correlate with shark abundances. Here, we test this assumption by
 comparing the denticle record in surface sediments to three conventional
 shark survey methods at Palmyra Atoll, Line Islands, central Pacific
 Ocean, where shark density is high and spatially heterogeneous. We
 generally found a significant positive correlation between denticle
 accumulation rates and shark abundances derived from underwater visual
 census, baited remote underwater video, and hook and line surveys.
 Denticle accumulation rates reflected shark abundances, suggesting that
 denticle assemblages can preserve a signal of time-averaged shark
 abundance in low-energy coral reef environments. We offer suggestions for
 applying this tool to measure shark abundance over long timescales in
 other contexts.
description: <b>DillonMEE_SupData_Palmyra_Sharks </b>
 This dataset includes relative shark abundance data from Palmyra
 Atoll, Line Islands, central Pacific collected using three conventional
 shark survey methods - underwater visual census, hook and line, and baited
 remote underwater video - as well as one new method - the shark dermal
 denticle record. Data were collected at low-energy sites in the lagoon and
 backreef between 2006 and 2016. Data were collected to compare shark
 dermal denticle assemblages preserved in surface sediments with
 conventional shark survey data to assess the ecological fidelity of the
 denticle record. Data provide an indication of relative shark abundance
 for the species observed at each site. This dataset
 contains six csv files: "denticle_accum",
 "sedimentation", "weathering", "uvc",
 "bruv", and "hook_line". Field attributes for each csv
 file are described in the accompanying Metadata ReadMe file.
DOI: 10.5061/dryad.8gtht76k2
title: A scalable realization of local U(1) gauge invariance in cold atomic mixtures

description: In the fundamental laws of physics, gauge fields mediate the interaction
 between charged particles. An example is quantum electrodynamics -- the
 theory of electrons interacting with the electromagnetic field -- based on
 U(1) gauge symmetry. Solving such gauge theories is in general a hard
 problem for classical computational techniques. While quantum computers
 suggest a way forward, it is difficult to build large-scale digital
 quantum devices required for complex simulations. Here, we propose a fully
 scalable analog quantum simulator of a U(1) gauge theory in one spatial
 dimension. To engineer the local gauge symmetry, we employ inter-species
 spin-changing collisions in an atomic mixture. We demonstrate the
 experimental realization of the elementary building block as a key step
 towards a platform for large-scale quantum simulations of continuous gauge
 theories.
DOI: 10.5061/dryad.ghx3ffbjv
title: Switchgrass v5 4-way (AP13 x DAC, WBC x VS16) genetic map

description: Here we present the genetic map construction methods for the switchgrass
 4-way mapping population. The map spans 750 recombinant 4-way (pseudo F2)
 progeny genotyped at 4700 markers. These data are formatted for simple
 input into R/qtl and most other QTL mapping programs.
DOI: 10.5061/dryad.9ghx3ffdd
title: Data from: A population-based screening for hepatitis C antibodies and active infection using a point-of-care test in a low prevalence area

description: Background. Data on the true prevalence of hepatitis C virus
 (HCV) infection in the general population is essential to health
 policies. We evaluated a program implementing free universal HCV screening
 using a non-invasive point-of-care test (POCT) (OraQuick-HCV rapid test)
 in oral fluid in an urban area in Valencia, South-Eastern Spain. 
 Methods. A cross-sectional study was performed during 2015-2017.
 Free HCV screening was offered by regular mail to 11,500 individuals aged
 18 and over, randomly selected from all census residents in the Health
 Department. All responding participants filled in a
 questionnaire about HCV infection risk factors and were tested in
 their tertiary Hospital. In those with a positive POCT, results were
 confirmed by enzyme-immunoassay and HCV-RNA. Results. 1,206
 persons agreed to participate (response rate: 11.16%). HCV antibodies were
 detected in 19 (1.60%) cases (age-sex standardized rate: 1.31%; 95%CI:
 0.82-2.07), but only 8 showed positive HCV-RNA (age-sex standardized rate:
 0.56%; 95%CI: 0.28-1.14). The majority (89%) of the cases were born before
 1965 and 74% had at least one known risk factor for HCV infection. All
 anti-HCV positive individuals were already aware of their infection, and
 no undiagnosed cases were detected. The performance of the POCT was
 excellent for detecting active infection. 
 Conclusions. These preliminary data suggest that HCV population
 screening with a POCT is feasible but, in our setting, mailing recruiting
 is not effective (11% response rate). The low prevalence of HCV antibodies
 and active infection in the participant population (with no new diagnoses
 made) suggests that, in our setting, underdiagnosis may be uncommon. Files
 uploaded include the study database (Stata  v.13) and
 the do.file of the study.
description: Data was collected from a cross-sectional universal screening
 study in the general adult population of a Healthcare Department in
 Valencia (Spain), from September 2015 to October 2017 using the OraQuick
 anti-HCV rapid test followed, if positive, by gold standard immunoassay
 (CIA) and characterized HCV positive cases including patient and virus
 characteristics. The target population was composed of
 all individuals aged 18 and over covered by the Valencia Public Healthcare
 System in a Healthcare Department. The analysis was
 made using STATA V.13 software.
description: Data are in STATA v12 format, anonymized, labeled with
 description of variables values. Include 1206 cases
 and there are some missing data in some variables
DOI: 10.5061/dryad.sn02v6x13
title: Longitudinal white-matter abnormalities in sports-related concussion: a diffusion MRI study of the NCAA-DoD CARE Consortium

description: Objective To study longitudinal recovery trajectories of white-matter
 after sports-related concussion (SRC), we performed diffusion tensor
 imaging (DTI) on collegiate athletes who sustained SRC.  Methods
 Collegiate athletes (n=219, 82 concussed athletes, 68 contact-sport
 controls, and 69 non-contact-sport controls) were included from the
 Concussion Assessment, Research and Education (CARE) Consortium. 
 The participants completed clinical assessments and DTI at four time
 points: 24-48-hours post-injury, asymptomatic state, seven days following
 return-to-play, and six-months post-injury.  Tract-based spatial
 statistics were used to investigate group differences in DTI metrics and
 identify white-matter areas with persistent abnormalities. 
 Generalized linear mixed models were used to study longitudinal changes
 and associations between outcome measures and DTI metrics.  Cox
 proportional hazards model was used to study effects of white-matter
 abnormalities on recovery time.  Results In the white matter of
 concussed athletes, DTI-derived mean diffusivity was significantly higher
 than the controls at 24-48 hours post-injury and beyond the point when the
 concussed athletes became asymptomatic.  While the extent of
 affected white matter decreased over time, part of the corpus callosum had
 persistent group-differences across all the time points.
  Furthermore, greater elevation of mean diffusivity at acute
 concussion was associated with worse clinical outcome measures (i.e.,
 Brief-Symptom-Inventory scores and symptom-severity scores) and prolonged
 recovery time.  No significant differences in DTI metrics were
 observed between the contact-sport and non-contact-sport
 controls.  Conclusions Changes in white matter were evident after
 SRC at six-months post-injury, but were not observed in contact-sport
 exposure.  Further, the persistent white-matter abnormalities
 were associated with clinical outcomes and delayed recovery time.
DOI: 10.5061/dryad.tqjq2bvv2
title: Testing whether ensemble modelling is advantageous for maximising predictive performance of species distribution models

description: Predictive performance is important to many applications of species
 distribution models (SDMs). The SDM ‘ensemble’ approach, which combines
 predictions across different modelling methods, is believed to improve
 predictive performance, and is used in many recent SDM studies. Here, we
 aim to compare the predictive performance of ensemble species distribution
 models to that of individual models, using a large presence-absence
 dataset of eucalypt tree species. To test model performance, we divided
 our dataset into calibration and evaluation folds using two spatial
 blocking strategies (checkerboard-pattern and latitudinal slicing). We
 calibrated and cross-validated all models within the calibration folds,
 using both repeated random division of data (a common approach) and
 spatial blocking. Ensembles were built using the software package
 ‘biomod2’, with standard (“untuned”) settings. Boosted regression tree
 (BRT) models were also fitted to the same data, tuned according to
 published procedures. We then used evaluation folds to compare ensembles
 against both their component untuned individual models, and against the
 BRTs. We used area under the receiver-operating characteristic curve (AUC)
 and log-likelihood for assessing model performance. In all our tests,
 ensemble models performed well, but not consistently better than their
 component untuned individual models or tuned BRTs across all tests.
 Moreover, choosing untuned individual models with best cross-validation
 performance also yielded good external performance, with blocked
 cross-validation proving better suited for this choice, in this study,
 than repeated random cross-validation. The latitudinal slice test was only
 possible for four species; this showed some individual models, and
 particularly the tuned one, performing better than ensembles. This study
 shows no particular benefit to using ensembles over individual tuned
 models. It also suggests that further robust testing of performance is
 required for situations where models are used to predict to distant places
 or environments.
description: The dataset has been compiled and used previously in Fithian, W.
 et al. 2015. Bias correction in species distribution models: pooling
 survey and collection data for multiple species. - Methods Ecol. Evol. 6:
 424–438., and made openly available with that paper. We do not re-host the
 data here, instead, we provide instructions for reusing the data in
 Fithian et a. 2015, and codes for reproducing our analyses.
 Details regarding the data can be found in Fithian et al. 2015,
 and in associated data publication:<br> Fithian, William and Elith,
 Jane and Hastie, Trevor and Keith, David. (2014). Code and data supplement
 for "Bias Correction in Species Distribution Models: Pooling Survey
 and Collection Data for Multiple Species". Stanford Digital
 Repository. Available at: http://purl.stanford.edu/vt558xk1600
description: See readme.txt file in the data package
DOI: 10.5061/dryad.np5hqbzph
title: Drought survival is positively associated with high turgor loss points in temperate perennial grassland species

description: 1. Turgor loss point (πtlp) has been suggested to be a key trait for
 drought resistance in woody species. In herbaceous grassland species the
 role of πtlp for species drought survival has not yet been tested,
 although grasslands are projected to experience more frequent and intense
 droughts with climate change. 2. To gain insights into the role of πtlp
 for drought resistance of temperate perennial grassland species, we
 assessed πtlp of 41 species common in Germany (20 forbs, 21 grasses). We
 directly related them to the species’ comparative whole-plant drought
 survival and midday leaf water potentials under drought (ΨMD) assessed in
 a common garden drought experiment, and to species moisture association.
 3. Species drought survival increased with increasing πtlp across all
 species as well as within forbs or grasses separately. ΨMD was positively
 related to πtlp and drought survival. Our results imply that high πtlp
 promotes drought survival of common perennial European temperate mesic
 grassland species by enabling them to maintain high leaf water potentials
 under drought, i.e., a desiccation avoidance strategy. However, πtlp was
 not related to species moisture association. 4. The positive relationship
 between πtlp and drought survival in herbaceous grassland species was
 opposite to the negative relationship previously established in woody
 plants, implying that mechanisms of drought resistance differ between
 woody and herbaceous species. Our results highlight the necessity of
 directly testing the relationship of functional traits to whole-plant
 drought survival in different plant life forms, before using trait
 assessments for predicting plant responses to drought.