cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15916642
title: Filtered-Connectivity-Matrices-Mullus-barbatus-Northwestern-Mediterranean

description: This repository contains the filtered connectivity matrices used in the article "Early-life dispersal and adult natural markers reveal between- and within-stock connectivity: challenging the stock unit paradigm in Mediterranean fisheries" (DOI: XXXX). It includes four .zip files:

main: Contains the connectivity matrices from the simulation set where all three filters were applied.

B200_Tf_Nf, Sf_Nf, B200_Nf: Contain matrices from the corresponding sensitivity analyses, where one or two filters were removed.

Each .zip file includes 910 filtered daily connectivity matrices ("T") representing larval dispersal patterns during the red mullet spawning season—spanning from May 1st (day 1) to July 30th (day 91), for each year between 2009 and 2018. July 31st was excluded, as no larval release was assumed for that day.

In addition to the matrices, the four .zip files also contain the 910 daily calculated connectivity indices ("ConnectInd") corresponding to each simulation.
DOI: 10.5061/dryad.v5n28fn
title: Data from: Effect of polygenic load on striatal dopaminergic deterioration in Parkinson's disease

description: Objective: To investigate the effect of polygenic load on the progression
 of striatal dopaminergic dysfunction in patients with Parkinson's
 disease (PD). Methods: Using data from 335 PD patients in the
 Parkinson's Progression Markers Initiative (PPMI) database, we
 investigated the longitudinal association of PD-associated polygenic load
 with changes in striatal dopaminergic activity as measured by
 123I-N-3-fluoropropyl-2-beta-carboxymethoxy-3beta-(4-iodophenyl)
 nortropane (123I-FP-CIT) single photon emission computed tomography
 (SPECT) over 4 years. PD-associated polygenic load was estimated by
 calculating weighted genetic risk scores (GRS) using: i) all available 27
 PD-risk single nucleotide polymorphisms (SNPs) in the PPMI database
 (GRS1); and ii) 23 SNPs with minor allele frequency &gt; 0.05 (GRS2).
 Results: GRS1 and GRS2 were correlated with younger age-at-onset in PD
 patients (GRS1, Spearman's rho = -0.128, p = 0.019; GRS2,
 Spearman's rho = -0.109, p = 0.047). Although GRS1 did not show an
 association with changes in striatal 123I-FP-CIT availability, GRS2 was
 associated with a slower decline of striatal dopaminergic activity
 (interactions with disease duration in linear mixed model; caudate
 nucleus, estimate = 0.399, SE = 0.165, p = 0.028; putamen, estimate =
 0.396, SE = 0.137, p = 0.016). Conclusions: Our results suggest that
 genetic factors for PD risk may have heterogeneous effects on the striatal
 dopaminergic degeneration, and some factors may be associated with a
 slower decline of dopaminergic activity. Composition of PD-progression
 specific GRS may be useful in predicting disease progression in patients.
description: R2_SupplementsSupplementary material; appendix e-1; table e-1~4
DOI: 10.5061/dryad.gp8730r
title: Data from: Diatraea saccharalis history of colonization in the Americas. The case for human-mediated dispersal

description: The sugarcane borer moth, Diatraea saccharalis, is one of the most
 important pests of sugarcane and maize crops in the Western Hemisphere.
 The pest is widespread throughout South and Central America, the Caribbean
 region and the southern United States. One of the most intriguing features
 of D. saccharalis population dynamics is the high rate of range expansion
 reported in recent years. To shed light on the history of colonization of
 D. saccharalis, we investigated the genetic structure and diversity in
 American populations using single nucleotide polymorphism (SNPs) markers
 throughout the genome and sequences of the mitochondrial gene cytochrome
 oxidase (COI). Our primary goal was to propose possible dispersal routes
 from the putative center of origin that can explain the spatial pattern of
 genetic diversity. Our findings showed a clear correspondence between
 genetic structure and the geographical distributions of this pest insect
 on the American continents. The clustering analyses indicated three
 distinct groups: one composed of Brazilian populations, a second group
 composed of populations from El Salvador, Mexico, Texas and Louisiana and
 a third group composed of the Florida population. The predicted time of
 divergence predates the agriculture expansion period, but the pattern of
 distribution of haplotype diversity suggests that human-mediated movement
 was most likely the factor responsible for the widespread distribution in
 the Americas. The study of the early history of D. saccharalis promotes a
 better understanding of range expansion, the history of invasion, and
 demographic patterns of pest populations in the Americas.
description: 17IL004_S1_L002_R1_001_part1.fq17IL004_S1_L002_R1_001_part2.fq17IL004_S1_L002_R1_001_part3.fq17IL004_S1_L002_R1_001_part4.fq17IL004_S1_L002_R1_001_part5.fq17IL004_S1_L002_R1_001_part6.fq17IL004_S1_L002_R1_001_part7.fq17IL004_S1_L002_R1_001_part8.fq17IL004_S1_L002_R1_001_part9.fq17IL004_S1_L002_R1_001_part10.fq17IL004_S1_L002_R1_001_part11.fq17IL004_S1_L002_R1_001_part12.fq17IL004_S1_L002_R1_001_part13.fq17IL004_S1_L002_R1_001_part14.fq17IL004_S1_L002_R1_001_part15.fq17IL004_S1_L002_R1_001_part16.fq17IL004_S1_L002_R1_001_part17.fq17IL004_S1_L002_R1_001_part18.fq17IL004_S1_L002_R1_001_part19.fq17IL004_S1_L002_R1_001_part20.fq17IL004_S1_L002_R1_001_part21.fq17IL004_S1_L002_R1_001_part22.fq17IL004_S1_L002_R1_001_part23.fq17IL004_S1_L002_R1_001_part24.fq17IL004_S1_L002_R1_001_part25.fq17IL004_S1_L002_R1_001_part26.fq17IL004_S1_L002_R1_001_part27.fq17IL004_S1_L002_R1_001_part28.fq17IL004_S1_L002_R1_001_part29.fq17IL004_S1_L002_R1_001_part30.fq17IL004_S1_L002_R1_001_part31.fq17IL004_S1_L002_R1_001_part32.fq17IL004_S1_L002_R1_001_part33.fq17IL004_S1_L002_R1_001_part34.fq17IL004_S1_L002_R1_001_part35.fq17IL004_S1_L002_R1_001_part36.fq17IL004_S1_L002_R1_001_part37.fq17IL004_S1_L002_R1_001_part38.fq17IL004_S1_L002_R1_001_part39.fq17IL004_S1_L002_R1_001_part40.fq17IL004_S1_L002_R1_001_part41.fq
DOI: 10.5061/dryad.6vm72sm
title: Data from: A general and efficient algorithm for the likelihood of diversification and discrete-trait evolutionary models

description: As the size of phylogenetic trees and comparative data continue to grow
 and more complex models are developed to investigate the processes that
 gave rise to them, macroevolutionary analyses are becoming increasingly
 limited by computational requirements. Here we introduce a novel
 algorithm, based on the "flow" of the differential equations
 that describe likelihoods along tree edges in backward time, to reduce
 redundancy in calculations and efficiently compute the likelihood of
 various macroevolutionary models. Our algorithm applies to several
 diversification models, including birth-death models and models that
 account for state- or time-dependent rates, as well as many commonly used
 models of discrete-trait evolution, and provides an alternative way to
 describe macroevolutionary model likelihoods. As a demonstration of our
 algorithm's utility, we implemented it for a popular class of
 state-dependent diversification models - BiSSE, MuSSE, and their
 extensions to hidden-states. Our implementation is available through the R
 package castor. We show that, for these models, our algorithm is one or
 more orders of magnitude faster than existing implementations when applied
 to large phylogenies. Our algorithm thus enables the fitting of
 state-dependent diversification models to modern massive phylogenies with
 millions of tips, and may lead to potentially similar computational
 improvements for many other macroevolutionary models.
description: Supplemental
 InformationSupplemental text and
 Supplemental Figures.supplement.pdfSupplemental Code 1R code demonstrating the use of the flow algorithm for fitting dSSE models to large phylogenetic trees. This example fits a BiSSE model to a dated angiosperm tree and woodiness trait data.Supplemental_code_example.R
DOI: 10.5061/dryad.7d837c6
title: Data from: High-dose methylprednisolone for acute traumatic spinal cord injury: A meta-analysis

description: Objective Due to the continuing debates on the utility of high-dose
 methylprednisolone (MP) early after acute spinal cord injury (ASCI), we
 aim to evaluate the therapeutic and adverse effects of high-dose MP
 according to NASCIS-2 dosing protocol in comparison to no steroids on
 patients with ASCI, by performing a meta-analysis on the basis of the
 current available clinical trials. Methods We searched PubMed and Cochrane
 Library (to May 22 2018) for studies comparing neurological recoveries,
 adverse events and in-hospital costs between ASCI patients who underwent
 high-dose MP treatment or not. Data were synthesized with corresponding
 statistical models according to the degree of heterogeneity. Results We
 enrolled 16 studies (1863 participants) including 3 RCTs and 13
 observational studies. Pooled results indicated that MP was not associated
 with an increase in motor score improvement (RCTs: p = 0.84; Observational
 studies: p = 0.44) and incidence of recovery by at least one grade on the
 ASIA Impairment Scale (AIS) or Frankel (p=0.53). Meanwhile, MP did not
 lead to better sensory recovery (p=0.07). However, MP was associated with
 a significant higher incidence of gastrointestinal hemorrhage (p=0.04) and
 respiratory tract infection (p=0.01). The difference in the overall
 in-hospital costs between MP and control groups was not statistically
 significant (p=0.78). Conclusions Based on the current evidence, high-dose
 MP treatment, in comparison to controls, does not contribute to better
 neurological recoveries but may increase the risk of adverse events in
 patients with ASCI. Therefore, we recommend against routine use of
 high-dose MP early after ASCI.
description: Figures e-1, e-2,
 e-3Figure e-1 describes the
 quality of the included RCTs, with non-numerical data. Figure e-2 and e-3
 compare the adverse events and in-hospital costs between MP and no-steroid
 groups. All the numerical data is shown in the forest
 plots.Supplemental figures and
 legends (updated).pdfPRISMA
 ChecklistMoher D, Liberati A,
 Tetzlaff J, Altman DG. Preferred reporting items for systematic reviews
 and meta-analyses: the PRISMA statement. International journal of surgery
 (London, England) 2010;8:336-341.
DOI: 10.5061/dryad.8t15p7t
title: Data from: Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon.

description: In vitro experimental evolution has taught us many lessons on the
 molecular bases of adaptation. To move towards more natural settings,
 evolution in the mice gut has been successfully performed. Yet, these
 experiments suffered from the use of laboratory strains as well as the use
 of axenic or streptomycin treated mice to maintain the inoculated strains.
 To circumvent these limitations, we conducted a one-year experimental
 evolution in vivo using a natural isolate of E. coli, strain 536, in
 conditions mimicking as much as possible natural environment with mother
 to offspring microbiota transmission. Mice were then distributed in 24
 independent cages and separated in two different diets: a regular one
 (Chow diet, CD) and high-fat high-sugar one (Western diet, WD). Genome
 sequences revealed an early and rapid selection during the breast-feeding
 period that selected the constitutive expression of the well-characterized
 lactose operon. E. coli was lost significantly more in CD than WD,
 however, we could not detect any genomic signature of selection, nor any
 diet specificities during the later part of the experiments. The
 apparently neutral evolution presumably due to low population size
 maintained nevertheless at high frequency the early selected mutations
 affecting lactose regulation. The rapid loss of lactose operon regulation
 challenges the idea that plastic gene expression is both optimal and
 stable in the wild.
description: Mothers_fastq_files_E.colifastq files corresponding to the sequences of Escherichia coli 536 strains extracted from 13 mothers at day 16. Please see README file ' Mothers_fastq_files_E.coli-README.txt ' for additional information.CD_offsprings_fastq_files_E.colifastq files corresponding to the sequences of Escherichia coli 536 strains extracted from offsprings fed with a regular diet. Please see README file 'CD_offsprings_fastq_files_E.coli-README.txt' for additional information.WD_offsprings_fastq_files_E.colifastq files corresponding to the sequences of Escherichia coli 536 strains extracted from offsprings fed with a high fat high sugar diet. Please see README file 'WD_offsprings_fastq_files_E.coli-README.txt' for additional information.E. coli 536 reference (gbk file)gbk file of the reference of E. coli 536 used for the analysis of the mutations by the software breseqE_coli_536_ref_breseq.gbkMothers_fastq_files_E.coli_day_1fastq files corresponding to the sequences of Escherichia coli 536 population extracted from 4 mothers (Mo4, Mo5, Mo11 and Mo12) at day 1. Please see README file ' Mothers_fastq_files_E.coli_day1_README.txt ' for additional information.Mothers_fastq_files_E.coli_lacI_instability_after_maternally_microbiota_transmission_day_1.tar.gz
DOI: 10.5061/dryad.33h8n22
title: Data from: Repeatable glucocorticoid expression is associated with behavioural syndromes in males but not females in a wild primate

description: Behavioural syndromes are a well-established phenomenon in human and
 non-human animal behavioural ecology. However, the mechanisms that lead to
 correlations among behaviours and individual consistency in their
 expression at the apparent expense of behavioural plasticity remain
 unclear. The “state-dependent” hypothesis posits that inter-individual
 variation in behaviour arises from inter-individual variation in state and
 that the relative stability of these states within an individual leads to
 consistency of behaviour. The endocrine stress response, in part mediated
 by glucocorticoids (GCs), is a proposed behavioural syndrome-associated
 state as GC levels are linked to an individual’s behavioural responses to
 stressors. In this study, in wild Barbary macaques (Macaca sylvanus),
 consistent inter-individual differences were observed in both sexes for GC
 activity (faecal glucocorticoid [fGC] concentrations), but not GC
 variation (coefficient of variation in fGC concentrations). The expression
 of the behavioural syndrome “Excitability” (characterized by the
 frequencies of brief affiliation or aggressive interactions) was related
 to GC activity in males but not in females; more “excitable” males had
 lower GC activity. There was no relationship in females between any of the
 behavioural syndromes and GC activity, nor in either sex with GC
 variation. The negative relationship between GC activity and Excitability
 in males provides some support for GC expression as a behavioural
 syndrome-generating state under the state-dependent framework. The absence
 of this relationship in females highlights that state-behavioural syndrome
 associations may not be generalizable within a species and that broader
 sex differences in state need to be considered for understanding the
 emergence and maintenance of behavioural syndromes.
description: all_activityDataset for first model presented in manuscriptall_reactivityData for second model presented in manuscript
DOI: 10.5061/dryad.qm52585
title: Data from: Palaeoepidemiology in extinct vertebrate populations: factors influencing skeletal health in Jurassic marine reptiles

description: Palaeoepidemiological studies related to palaeoecology are rare, but have
 the potential to provide information regarding ecosystem-level
 characteristics by measuring individual health. In order to assess factors
 underlying the prevalence of pathologies in large marine vertebrates, we
 surveyed ichthyosaurs (Mesozoic marine reptiles) from the
 Posidonienschiefer Formation (Early Jurassic: Toarcian) of Southwestern
 Germany. This Formation provides a relatively large sample from a
 geologically and geographically restricted interval, making it ideal for
 generating baseline data for a palaeoepidemiological survey. We examined
 the influence of taxon, anatomical region, body size, ontogeny, and
 environmental change, as represented by the early Toarcian Oceanic Anoxic
 Event, on the prevalence of pathologies, based on a priori ideas of
 factors influencing population skeletal health. Our results show that the
 incidence of pathologies is dependent on taxon, with the small-bodied
 genus Stenopterygius exhibiting fewer skeletal pathologies than other
 genera. Within Stenopterygius, we detected more pathologies in large
 adults than in smaller size classes. Stratigraphic horizon, a proxy for
 palaeoenvironmental change, did not influence the incidence of pathologies
 in Stenopterygius. Quantification of the occurrence of pathologies within
 taxa and across guilds is critical to constructing more detailed
 hypotheses regarding changes in the prevalence of skeletal injury and
 disease through Earth history.
description: Specimen-level database
 of material examinedPardoPerez et
 al._ESM.xlsxCollated tables used in
 analyses and tabular results of logistic regressionTables 1-4 of logistic
 regression analysisPardo-Perez et
 al._Tables1-4_ESM_.doc
DOI: 10.15468/dl.6ags8n
title: Occurrence Download

description: A dataset containing 22893 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-91.75746 47.00702,-89.43424 48.11566,-91.78511 48.65245,-94.8391 49.00481,-99.62297 49.06081,-99.17711 40.65224,-91.15169 40.72737,-91.75746 47.00702))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Unionida"
 ]
}

 The dataset includes 22893 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001765-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v9s0hk5
title: Data from: Gregarious suspension feeding in a modular Ediacaran organism

description: Reconstructing Precambrian eukaryotic paleoecology is pivotal to
 understanding origins of the modern, animal-dominated biosphere. Here, we
 combine new fossil data from southern Namibia with computational fluid
 dynamics (CFD) testing between competing feeding models for the Ediacaran
 taxon Ernietta. In addition, we perform simulations for multiple
 individuals, allowing us to analyze hydrodynamics of living communities.
 We show Ernietta lived gregariously, forming shallow marine aggregations
 in the latest Ediacaran, 548-541 Ma. We demonstrate enhanced vertical
 mixing of the water column above aggregations, and preferential
 redirection of current into body cavities of downstream individuals. These
 results support reconstruction of Ernietta as a macroscopic Ediacaran
 suspension feeder, and moreover provide a convincing paleoecological
 advantage to feeding in aggregations analogous to those recognized in many
 extant marine metazoans. These results provide some of the oldest evidence
 of commensal facilitation by macroscopic eukaryotes yet recognized in the
 fossil record.
description: Ernietta_shallow-burial_single-individual_parallel-orientationCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_single-individual_parallel-orientationCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_deep-burial_single-individual_parallel-orientationCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_deep-burial_single-individual_perpendicular-orientationCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_single-individual_perpendicular-orientationCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_shallow-burial_single-individual_perpendicular-orientationCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_clumped_mixed-orientations_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_clumped_parallel-orientation_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_clumped_perpendicular-orientation_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_mixed-orientations_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_offset_mixed-orientations_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_parallel-orientation_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.Ernietta_moderate-burial_multiple-individuals_perpendicular-orientation_0.2msCOMSOL Multiphysics computational fluid dynamics simulation file.
DOI: 10.5061/dryad.qq1446k
title: Data from: Empirical targets for acute hemodynamic management of individuals with spinal cord injury

description: Objective: To determine the hemodynamic conditions associated with optimal
 neurological improvement in acute traumatic spinal cord injury (SCI)
 individuals who had lumbar intrathecal catheters placed to measure
 cerebrospinal fluid pressure (CSFP). Methods: Ninety-two acute SCI
 individuals were enrolled in this multi-center prospective observational
 clinical trial. We monitored mean arterial pressure (MAP) and CSFP during
 the first week post-injury, and assessed neurologic function at baseline
 and six-months post-injury. We used relative risk iterations to determine
 transition points at which the likelihood of either improving
 neurologically or remaining unchanged neurologically was equivalent. These
 transition points guided our analyses where we examined the linear
 relationships between time spent within target hemodynamic ranges (i.e.,
 clinical adherence) and neurological recovery. Results: Relative risk
 transition points for CSFP, MAP, and spinal cord perfusion pressure (SCPP)
 were linearly associated with neurological improvement and directed the
 identification of key hemodynamic target ranges. Clinical adherence to the
 target ranges was positively and linearly related to improved neurological
 outcomes. Adherence to SCPP targets, not MAP targets, was the best
 indicator of improved neurological recovery, which occurred with SCPP
 targets of 60-65 mmHg. Failing to maintain the SCPP within the target
 ranges was an important detrimental factor in neurologic recovery,
 particularly if the target range is set lower. Conclusion: We provide an
 empirical, data-driven approach to aid institutions in setting hemodynamic
 management targets that accept the real-life challenges of adherence to
 specific targets. Our results provide a framework to guide the development
 of widespread institutional management guidelines for acute traumatic SCI.
description: Supplemental
 TablesSupplementary Tables
 e1-4