cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dfn2z34wd
title: Unvalidated R source code

description: Univalidated R source code implmenting a performance comparison of
 adaptive sample size recalculation rules including in particular
 the new performance score by Herrmann et al. (2019)
DOI: 10.5061/dryad.qz612jm95
title: Data from: Insect herbivory reshapes a native leaf microbiome

description: Publication abstract: Insect herbivory is pervasive in plant communities,
 but its impact on microbial plant colonizers is not well-studied in
 natural systems. By calibrating sequencing-based bacterial detection to
 absolute bacterial load, we find that the within-host abundance of most
 leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified
 within leaves impacted by insect herbivory. Herbivore-associated bacterial
 amplification reflects community-wide compositional shifts towards lower
 ecological diversity, but the extent and direction of such compositional
 shifts can be interpreted only by quantifying absolute abundance.
 Experimentally eliciting anti-herbivore defenses reshaped within-host
 fitness ranks among Pseudomonas spp. field isolates and amplified a subset
 of putative P. syringae phytopathogens in a manner causally consistent
 with observed field-scale patterns. Herbivore damage was inversely
 correlated with plant reproductive success and was highly clustered across
 plants, which predicts tight co-clustering with putative phytopathogens
 across hosts. Insect herbivory may thus drive the epidemiology of
 plant-infecting bacteria as well as the structure of a native plant
 microbiome by generating variation in within-host bacterial fitness at
 multiple phylogenetic and spatial scales. This study emphasizes that
 'non-focal' biotic interactions between hosts and other
 organisms in their ecological settings can be crucial drivers of the
 population and community dynamics of host-associated microbiomes.
description: This repository contains R data objects (.rds) and text summaries
 from each of the Bayesian regression models we ran to evaluate the
 relationship between insect herbivory and the abundance of various
 bacterial taxonomic groups from our field studies. Please refer to the
 main text and supplemental information of our manuscript for detailed
 information on model structure, assumptions, and interpretation. Each
 model object can be loaded in R and used to, among other things:
 output summaries of coefficient posterior
 estimates generate samples from the joint posterior
 of model coefficients generate samples from the
 posterior predicted response variable calculate
 additional information criteria (e.g., WAIC) and compare amongst
 models
description: A full description of our analysis workflow, as well as when and
 how these models were used, can be found in our github repository for this
 project: https://www.github.com/phumph/coinfection
DOI: 10.5061/dryad.tdz08kpw1
title: New active substances approved by EMA or FDA initially in 2014-2016, with approval date tracked until 2017

description: Objective: To compare review outcome alignment between European Medicines
 Agency (EMA) and US Food and Drug Administration (FDA) for medicines
 approved by both agencies in the time period 2014 to 2016. Design: Using
 publicly available information from FDA and EMA websites, new active
 substances (NASs) approved by each agency from 2014-2016 were identified
 and their characteristics assessed. Divergences in regulatory outcomes for
 simultaneous (within 91 days) submissions to both agencies were identified
 and then examined for use of facilitated regulatory pathways and orphan
 designations; submitted versus approved indications; and approval times.
 Results: In 2014-2016, 115 NASs were approved by EMA or FDA or both;
 74/115 were new chemical entities and 41 new biological/biotechnology
 entities; 82/115 were approved by both agencies, 24 only by FDA and 9 only
 by EMA. Simultaneous submission occurred for 52/115; 13/52 received
 expedited review by both agencies and 18 only by FDA; 8/52 received
 conditional approval from both agencies, 2/52 only from FDA and 1/52 only
 from EMA; 17/52 were designated as orphans by both agencies and 10/52 by
 FDA only; 31/52 indications were approved as submitted and 21 changed by
 EMA and 29/46 were approved as submitted (6 not assessed) and 17/46
 changed by FDA. Median FDA review timelines were 319 days compared with
 409 days for EMA. Conclusions: There was general agreement in EMA/ FDA
 conditional approvals. FDA used expedited pathways and orphan designation
 more often than EMA, suggesting stricter EMA criteria or definitions for
 these designations or less flexible processes. Despite consistency in
 submitted indications, there was lack of concordance in approved
 indications, which should be further investigated. FDA review times are
 faster because of a wider range of expedited pathways and the two-step EMA
 process; this may change with recent revisions to EMA accelerated
 assessment guidelines and the launch of PRIME.
DOI: 10.3886/e244689v2-198149
title: Kibritçi kız

description: Kibritçi Kız
DOI: 10.6084/m9.figshare.30597743
title: <b>Smartphone-Based Gait Recognition Dataset: Naturalistic Walking Data from 390 Participants for Biometric Identification</b>

description: This dataset enables realistic biometric identification research with naturalistic gait data from 390 participants. Smartphone inertial sensors (triaxial accelerometer, gyroscope, and magnetometer at 30 Hz) captured 46.8 kilometers of walking across approximately 585 minutes, with participants holding devices in their dominant hand. Multiple sessions per participant on different days ensure robust representation of intra-subject variability. Comprehensive metadata and documentation support deep learning model development, gait-based authentication systems, and bench marking of recognition algorithms under real-world conditions.
DOI: 10.6084/m9.figshare.30597743.v1
title: <b>Smartphone-Based Gait Recognition Dataset: Naturalistic Walking Data from 390 Participants for Biometric Identification</b>

description: This dataset enables realistic biometric identification research with naturalistic gait data from 390 participants. Smartphone inertial sensors (triaxial accelerometer, gyroscope, and magnetometer at 30 Hz) captured 46.8 kilometers of walking across approximately 585 minutes, with participants holding devices in their dominant hand. Multiple sessions per participant on different days ensure robust representation of intra-subject variability. Comprehensive metadata and documentation support deep learning model development, gait-based authentication systems, and bench marking of recognition algorithms under real-world conditions.
DOI: 10.6084/m9.figshare.30597743.v2
title: <b>Smartphone-Based Gait Recognition Dataset: Naturalistic Walking Data from 390 Participants for Biometric Identification</b>

description: This dataset enables realistic biometric identification research with naturalistic gait data from 390 participants. Smartphone inertial sensors (triaxial accelerometer, gyroscope, and magnetometer at 30 Hz) captured 46.8 kilometers of walking across approximately 585 minutes, with participants holding devices in their dominant hand. Multiple sessions per participant on different days ensure robust representation of intra-subject variability. Comprehensive metadata and documentation support deep learning model development, gait-based authentication systems, and bench marking of recognition algorithms under real-world conditions.
DOI: 10.5061/dryad.pg4f4qrj9
title: Dityrosine formation via reactive oxygen consumption yields increasingly recalcitrant humic-like fluorescent organic matter in the ocean

description: Marine dissolved organic matter (DOM) is a massive elemental pool on Earth
 and is thought to consist of a chemically complex mixture of molecules.
  Part of marine DOM is fluorescent (FDOM) and includes humic-like
 compounds. The chemical composition of, and biochemical pathways that
 yield, autochthonous humic-like FDOM in the ocean is largely unknown.
  Inspired by medical and biochemical research detailing the
 formation of colored and fluorescent dityrosine via peroxidase mediated
 reactions, we used fluorometry and spectroscopy and found dityrosine
 exhibits humic-like fluorescence similar to that of marine FDOM.
  Investigating its recalcitrance, we conducted short-term
 nutrient-addition and light exposure experiments with dityrosine and found
 it is resistant to respiration or assimilation by marine microbial
 communities, yet readily photodegraded.  The formation and
 characteristics of dityrosine newly points to polymerization via reactive
 oxygen quenching, under aphotic and putatively photic conditions, as an
 explanation for autochthonous, humic-like, (semi-)recalcitrant DOM in the
 ocean.
DOI: 10.21223/p3/2wcuae
title: Dataset for: Parental value for tuber yield in potato clones with resistance to late blight and heat tolerance, under high temperatures conditions (SET 3)

description: The International Potato Center (CIP) has developed a population named LBHT, obtaining new clones that are more tolerant to high temperatures, resistant to late blight, virus and early maturity, and they are available for use by developing countries for the selection of varieties or as parents in their breeding programs. The potato is highly heterozygozus crop, the most important economical characters are governed by additive and non-aditive genes. Therefore, the parental value of a clone cannot be assessed from phenotypic value alone. It is very important to know its combining ability as an indicator of parental value. Combining ability analysis is a method very useful for choosing better parents, and in the formulation of a crossing plan for a plant breeding program. During 2013 and 2014, 9 advanced clones of LBHT population, were crossed using line x tester mating design, where the clones were used as female parents (lines) and as male parents (testers). The varieties, Katahdin (Solanum tuberosum spp tuberosum), Huagalina (Solanum tuberosum spp andigena) and clone CIP398098.204 were used. Therefore, during 2015 - 2016, 27 progenies were evaluated under field conditions in two locations in Peru: La Molina and Majes. All experiments were conducted using statistical design of randomized complete block with three replications of 40 plants per plot. At harvest, the number and weight of marketable and non- marketable tubers were recorded. Then, the average weight of tubers, weight of marketable and total tubers per hectare in tons were calculated The analysis of variance for line by tester mating desing and determination of the effects of general combining ability (GCA) for these characters were performed using statistical software, SAS V. 9.4 (SAS Institute Inc., Cary, NC, USA).
DOI: 10.5061/dryad.msbcc2ftm
title: Data from: Plasma neurofilament light levels are associated with risk of disability in multiple sclerosis

description: Objective: To investigate the association between plasma NfL (pNfL) levels
 and risk of developing sustained disability worsening. Methods:
 Concentrations of pNfL were determined in 4,385 persons with MS and 1,026
 randomly selected population-based sex- and age-matched controls using the
 highly sensitive Single Molecule Array (SimoaTM) NF-light® Advantage kit.
 We assessed the impact of age-stratified pNfL levels above 80th, 95th and
 99th of controls' percentiles on the risk of Expanded Disability
 Status Scale (EDSS) worsening within the following year and reaching
 sustained EDSS scores of 3.0, 4.0 and 6.0 and conversion to secondary
 progressive (SP) MS. Results: The median (interquartile range) pNfL was
 7.5 (4.1) pg/ml in controls and 11.4 (9.6) pg/ml in MS (P &lt;0.001).
 The median (interquartile range) duration of follow-up was 5 years (5.1).
 High pNfL was associated with increased adjusted rates of EDSS worsening
 ranging between 1.4 (95% confidence intervals (CI): 1.1-1.8) and 1.7
 (95%CI: 1.4-2.3). High pNfL was also associated with the risk of reaching
 a sustained EDSS score of 3.0 with adjusted rates ranging between 1.5
 (95%CI: 1.2-1.8) and 1.55 (95%CI: 1.3-1.8) over all percentile cut-offs
 (all P&lt;0.001). Similar increases were observed for risk of
 sustained EDSS score 4.0. In contrast, the risk for reaching sustained
 EDSS score 6.0 and conversion to SP MS was not consistently significant.
 Conclusions: Elevated pNfL levels at early stages of MS are associated
 with increased risk of reaching sustained disability worsening. Hence,
 pNfL may serve as a prognostic tool to assess the risk of developing
 permanent disability in MS.
DOI: 10.5061/dryad.1vhhmgqp5
title: Clinical and pathological features of cognitive-predominant corticobasal degeneration

description: OBJECTIVE: To describe clinical and pathological characteristics of CBD
 with cognitive predominant problem during the disease course. METHODS: In
 a series of autopsy-confirmed cases of CBD, we identified patients with
 cognitive rather than motor predominant features (CBD-Cog), including five
 patients thought to have Alzheimer disease (AD) (CBD-AD) and ten patients
 thought to have behavioral variant frontotemporal dementia (FTD)
 (CBD-FTD). We compare clinical and pathological features of CBD-Cog with
 those from a series of 31 patients with corticobasal syndrome (CBD-CBS).
 For pathological comparisons between CBD-Cog and CBD-CBS, we use
 semiquantitative scoring of neuronal and glial lesion types in multiple
 brain regions and quantitative assessments of tau burden from image
 analysis. RESULTS: Five of 15 CBD-Cog patients never had significant motor
 problems during their disease course. The most common cognitive
 abnormalities in CBD-Cog were executive and visuospatial dysfunction. The
 frequency of language problems did not differ between CBD-Cog and CBD-CBS.
 Argyrophilic grain disease, which is a medial temporal tauopathy
 associated with mild cognitive impairment, was more frequent in CBD-Cog.
 Apathy was also more frequent in CBD-Cog. Tau pathology in CBD-Cog was
 greater in the temporal and less in peri-Rolandic cortices than in
 CBD-CBS. CONCLUSION: A subset of patients with CBD has a cognitive
 predominant syndrome than can be mistaken for AD or FTD. Our findings
 suggest that distribution of tau cortical pathology (greater in temporal
 and less in peri-Rolandic cortices) may be the basis of this uncommon
 clinical variant of CBD.
DOI: 10.5061/dryad.dbrv15dx3
title: Natural variation in the contribution of microbial density to inducible immune dynamics

description: Immune responses evolve to balance the benefits of microbial killing
 against the costs of autoimmunity and energetic resource use. Models that
 explore the evolution of optimal immune responses generally include a term
 for constitutive immunity, or the level of immunological investment prior
 to microbial exposure, and for inducible immunity, or investment in immune
 function after microbial challenge. However, studies rarely consider the
 functional form of inducible immune responses with respect to microbial
 density, despite the theoretical dependence of immune system evolution on
 microbe- versus immune-mediated damage to the host. In this study, we
 analyze antimicrobial peptide (AMP) gene expression from seven wild-caught
 flour beetle populations (Tribolium spp.) during acute infection with the
 virulent bacteria Bacillus thuringiensis (Bt) and Photorhabdus luminescens
 (P.lum) to demonstrate that inducible immune responses mediated by the
 humoral IMD pathway exhibit natural variation in both microbe
 density-dependent and independent temporal dynamics. Beetle populations
 that exhibited greater AMP expression sensitivity to Bt density were also
 more likely to die from infection, while populations that exhibited higher
 microbe density-independent AMP expression were more likely to survive P.
 luminescens infection. Reduction in pathway signaling efficiency through
 RNAi-mediated knockdown of the imd gene reduced the magnitude of both
 microbe-independent and dependent responses and reduced host resistance to
 Bt growth, but had no net effect on host survival. This study provides a
 framework for understanding natural variation in the flexibility of
 investment in inducible immune responses and should inform theory on the
 contribution of non-equilibrium host-microbe dynamics to immune system
 evolution.
DOI: 10.5061/dryad.ns1rn8pnq
title: Early angiogenic proteins associated with high risk for bronchopulmonary dysplasia and pulmonary hypertension in preterm infants

description: Introduction: Early pulmonary vascular disease in preterm infants
 is associated with the subsequent development of bronchopulmonary
 dysplasia (BPD) and pulmonary hypertension (PH), however, mechanisms that
 contribute to or identify infants with increased susceptibility for BPD
 and/or PH are incompletely understood. Therefore, we tested if changes in
 circulating angiogenic peptides during the first week of life are
 associated with the later development of BPD and/or PH. We further sought
 to determine alternate peptides and related signalling pathways with the
 risk for BPD or PH.  Methods: We prospectively enrolled
 infants with gestational age &lt;34 weeks gestation and collected
 blood samples during their first week of life.  BPD and
 PH were assessed at 36 weeks postmenstrual age. Samples were assayed for
 each of the 1121 peptides included in the SOMAscanTM technology,
 with subsequent pathway analysis.  Results: Of
 102 study infants, 82 had BPD and 13 had PH. Multiple
 angiogenic proteins  (PF-4, VEGF121, ANG-1,
 BMP10, HGF, ANG2) were associated with the subsequent diagnosis of BPD,
 and FGF-19,  PF-4, CTAP-III and PDGF-AA levels were
 associated with BPD severity. Early increases in BMP10 was strongly
 associated with the late risk for BPD and PH. Conclusion: We
 found that early alterations of circulating angiogenic peptides
 and others were associated with the subsequent development of BPD. We
 further identified  peptides that were associated with
 BPD severity and BPD-associated PH, including BMP10. We speculate that
 proteomic biomarkers during the first week of life may identify infants at
 risk for BPD and/or PH to enhance care and research. 
description: Supplemental tables and figures
DOI: 10.5061/dryad.nk98sf7pr
title: Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis

description: Studies assessing the predictability of evolution typically focus on
 short-term adaptation within populations or the repeatability of change
 among lineages. A missing consideration in speciation research is to
 determine whether natural selection predictably transforms standing
 genetic variation within populations into differences between species.
 Here, we test whether host-related selection on diapause timing
 anticipates genome-wide differentiation during ecological speciation by
 comparing ancestral hawthorn and newly formed apple-infesting host races
 of Rhagoletis pomonella to their sibling species R. mendax that attacks
 blueberries. The responses of 57,857 single nucleotide polymorphisms in a
 diapause study on the hawthorn race strongly predicted the direction and
 magnitude of genomic divergence among the three flies at a field site in
 Fennville, Michigan, USA. As anticipated, the apple race and R. mendax
 show parallel changes in the frequencies of putative inversions on three
 chromosomes associated with the earlier fruiting times of apples and
 blueberries compared to hawthorns. A diapause experiment on R. mendax
 revealed compensatory mutations throughout the genome accounting for the
 earlier eclosion of blueberry, but not apple flies. Thus, a degree of
 predictability, although not complete, exists in the genomics of diapause
 across the ecological speciation continuum in Rhagoletis. The generality
 of this result is placed in the context of other similar systems.
description: Filtered vcf file with genotype probabilities
 This is a vcf file generated using the GATK unified genotyper,
 then filtered as describe in the paper. The PL field provides the
 phred-scaled and normalized genotype probabilities produced using the GATK
 model. meyers.doellman.Rmendax.pops.e.l.vcf
 File mapping barcodes and ids to eclosion phenotypes
 column 1 = inline barcode (5' end of the forward read),
 column 2 = sample id (sample id in the vcf file), column 3 =
 population_phenotype: Blueberry_E = <em>R. mendax</em> early,
 Blueberry_L = <em>R. mendax</em> late
 meyers.doellman.Rmendax.e.l.barcode.map.txt
 140110_I481_FCC3KD2ACXX_L1_PJM_3_1.fq.gz
 Illumina forward reads, <em>R. mendax</em> early and
 late samples
 140110_I481_FCC3KD2ACXX_L1_PJM_3_2.fq.gz
 Illumina paired reads, <em>R. mendax</em> early and
 late samples File mapping barcodes to ids for
 population sample column 1 = inline barcode (5'
 end of the forward read), column 2 = sample id (sample id in the vcf
 file)
 meyers.doellman.Rmendax.pop.barcode.map.txt
 <b>150206_I1125_FCC638CACXX_L5_Rmendax_1_2_1.fq.gz</b> llumina forward reads, <em>R. mendax</em> population sample <b>150206_I1125_FCC638CACXX_L5_Rmendax_1_2_1.fq.gz</b> Illumina paired reads, <em>R. mendax</em> population sample
DOI: 10.5061/dryad.cfxpnvx2c
title: Data from: High ecosystem service delivery potential of small woodlands in agricultural landscapes

description: Global forest loss and fragmentation have strongly increased the frequency
 of forest patches smaller than a few hectares. Little is known about the
 biodiversity and ecosystem service supply potential of such small
 woodlands in comparison to larger forests. As it is widely recognized that
 high biodiversity levels increase ecosystem functionality and the delivery
 of multiple ecosystem services, small, isolated woodlands are expected to
 have a lower potential for ecosystem service delivery than large forests
 hosting more species. We collected data on the diversity of six taxonomic
 groups covering invertebrates, plants and fungi, and on the supply
 potential of five ecosystem services and one disservice within 224
 woodlands distributed across temperate Europe. We related their ability to
 simultaneously provide multiple ecosystem services (multiservice delivery
 potential) at different performance levels to biodiversity of all studied
 taxonomic groups (multidiversity), forest patch size and age, as well as
 habitat availability and connectivity within the landscape, while
 accounting for macroclimate, soil properties and forest structure.
 Unexpectedly, despite their lower multidiversity, smaller woodlands had
 the potential to deliver multiple services at higher performance levels
 per area than larger woodlands of similar age, probably due to positive
 edge effects on the supply potential of several ecosystem services.
 Biodiversity only affected multiservice delivery potential at a low
 performance level as well as some individual ecosystem services. The
 importance of other drivers of ecosystem service supply potential by small
 woodlands in agricultural landscapes also depended on the level of
 performance and varied with the individual ecosystem service considered.
 Synthesis and applications. Large, ancient woodlands host high levels of
 biodiversity and can therefore deliver a number of ecosystem services. In
 contrast, smaller woodlands in agricultural landscapes, especially ancient
 woodlands, have a higher potential to deliver multiple ecosystem services
 on a per area basis. Despite their important contribution to agricultural
 landscape multifunctionality, small woodlands are not currently considered
 by public policies. There is thus an urgent need for targeted policy
 instruments to ensure their adequate management and future conservation in
 order to either achieve multiservice delivery at high levels or to
 maximize the delivery of specific ecosystem services.