cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t4b8gtj25
title: Parallel generation of extensive vascular networks with application to an archetypal human kidney model

description: Given the relevance of the inextricable coupling between microcirculation
 and physiology, and the relation to organ function and disease
 progression, the construction of synthetic vascular networks for
 mathematical modelling and computer simulation is becoming an increasingly
 broad field of research. Building vascular networks that mimic in-vivo
 morphometry is feasible through algorithms such as constrained
 constructive optimisation (CCO) and variations. Nevertheless, these
 methods are limited by the maximum number of vessels to be generated due
 to the whole network update required at each vessel addition. In this
 work, we propose a CCO-based approach endowed with a domain decomposition
 strategy to concurrently create vascular networks. The performance of this
 approach is evaluated by analysing the agreement with the sequentially
 generated networks and studying the scalability when building vascular
 networks up to 200,000 vascular segments. Finally, we apply our
 method to vascularise a highly complex geometry corresponding to the
 cortex of a prototypical human kidney. The technique presented in this
 work enables the automatic generation of extensive vascular networks,
 removing the limitation from previous works. Thus, we can extent vascular
 networks (e.g., obtained from medical images) to pre-arteriolar level,
 yielding patient-specific whole-organ vascular models with an
 unprecedented level of detail.
description: This dataset was generated by the DCCO and PDCCO vascularization
 algorithms implemented in the VItA library.<br> The .vtk geometry
 files were manually crafted using Blender and converting the resulting
 .stl files through VTK. The resulting .vtp files were visualized using
 ParaView. These .vtp files were also converted to .csv and analysed
 through plots created using the matplotlib library for Python.
description: To run the source code contained in this dataset we need a
 working installation of the VTK 8.1.2 and VItA libraries.<br> To
 analyse the results ParaView and Python with matplotlib are
 required.<br> These are described in detail in README.txt.
DOI: 10.26036/cnp0008694
title: Five Kinds of Kiwifruit Transcriptome Studies

description: In this study, the flesh tissues of two Actinidia arguta genotypes and three Actinidia chinensis genotypes were selected for transcriptome analysis.
DOI: 10.7272/q6c24tpk
title: Data from: Scholarly influence of surgical hip randomized controlled trials

description: Background: Randomized control trials (RCTs) are considered the highest
 level of evidence for therapeutic research. Surgical RCTs, however, have
 drawbacks, leading some to question their role in filling the information
 gap in orthopaedic surgery. Pragmatism in study design was introduced to
 increase the clinical applicability of study results. However, there is a
 paucity of studies examining the effects of pragmatism on surgical RCTs.
  The purpose of this study was to examine how pragmatism affects
 the scholarly influence of surgical RCTs. Hip fracture surgical RCTs were
 used as an example. We hypothesized that a more pragmatic design would
 result in increased scholarly influence. Methods: A search for surgical
 hip fracture-related RCTs published between 1995-2015 was done in both
 PubMed and EMBASE. Journal impact factor, citation number, research
 question, significance and type of outcome, number of centers involved,
 and the PRECIS-2 level of pragmatism score were recorded for each study. A
 study was estimated to have scholarly influence if it was incorporated
 into clinical practice guidelines, professional societies’ recommended
 readings, or included professional textbooks’ references. A secondary
 estimate for scholarly influence was the study’s average yearly citation
 rate. Results: 160 RCTs were included in the final analysis. The number of
 yearly surgical hip fracture RCTs increased over the study period and the
 most common research question examined the best surgical implant. A
 multivariate logistic regression identified high study sample size as the
 only predictor of an RCT being used in clinical guidance texts. Large
 sample size and multi-center RCTs were predictors of high average yearly
 citation rates. The level of pragmatism in study design did not
 independently predict scholarly influence. Conclusions: Pragmatic design,
 as measured by the PRECIS2 score, is not independently associated with
 increased scholarly influence. However, since high study sample size was
 the most important study characteristic affecting scholarly influence, a
 pragmatic design with broad inclusion criteria may increase scholarly
 influence by increasing enrollment numbers.
DOI: 10.7280/d1vt3g
title: The effects of adaptation to urea on feeding rates and growth in Drosophila larvae

description: A collection of forty populations were used to study the phenotypic
 adaptation of Drosophila melanogaster larvae to urea laced food. A
 long-term goal of this research is to map genes responsible for these
 phenotypes. This mapping requires large numbers of populations. Thus, we
 studied fifteen populations subjected to direct selection for urea
 tolerance and five controls. In addition, we studied another twenty
 populations which had not been exposed to urea but were subjected to
 stress or demographic selection. In this study we describe the
 differentiation in these population for six phenotypes: (1) larval feeding
 rates, (2) larval viability in urea laced food, (3) larval development
 time in urea laced food, (4) adult starvation times, (5) adult desiccation
 times and (6) larval growth rates. No significant differences were
 observed for desiccation resistance. The demographically/stress selected
 populations had longer times to starvation than urea selected populations.
 The urea adapted populations showed elevated survival and reduced
 development time in urea laced food relative the control and non-adapted
 populations. The urea adapted populations also showed reduced larval
 feeding rates relative to controls. We show that there is a strong linear
 relationship between feeding rates and growth rates at the same larval
 ages feeding rates were measured. This suggests that feeding rates are
 correlated with food intake and growth. This relationship between larval
 feeding rates, food consumption, and efficiency has been postulated to
 involve important trade-offs that govern larval evolution in stressful
 environments. Our results support the idea that energy allocation is a
 central organizing theme in adaptive evolution.
description: Multiple phenotypes on Drosophila larvae and adults were
 collected. These included, larval feeding rates, asult desiccation
 resistance, adult starvation resistance, egg-to-adult viability in control
 food and urea laced food, egg-to-adult development time in control food
 and urea laced food and larval growth rates.
DOI: 10.26036/cnp0008920
title: Chinese pine PtARN DAP-seq

description: This project employs DNA affinity purification sequencing (DAP-seq) to identify the genome-wide binding sites of the PtARN transcription factor in Chinese pine (Pinus tabuliformis). The DAP-seq assay was performed using genomic DNA isolated from two-year-old shoot tissues. This dataset elucidates the direct DNA-binding landscape of PtARN.
DOI: 10.5061/dryad.pg4f4qrpn
title: Age matters: Demographic senescence in the moss Polytrichastrum formosum

description: It is known that many animal species senesce demographically, showing a
 decrease in survival and/or fertility with age. Though there is mounting
 evidence for and against senescence in various flowering plant species,
 the question of whether senescence also occurs in other plant taxa, such
 as mosses and other bryophytes, remains unanswered. We used GAMMs
 (generalized additive mixed models) and GLMMs (generalized linear mixed
 models) to assess effects of age on survival, size and the monocarpic
 female ramets’ sexual reproduction in Polytrichastrum formosum using
 demographic, ramet-level data collected over 25 years in Solhomfjell
 nature reserve, Norway. Survival was found to be negatively correlated
 with ramet age, with one-year survival decreasing from 83% in 1-year-old
 to 43% in ten-year-old plants. Stem growth was positively correlated with
 survival but accounting for it in our models did not change the
 relationship between age and survival qualitatively. Annual growth
 decreased during the first years of the ramets’ life but then stabilised.
 Sexual reproduction in the monocarpic females peaked at ramet age 2–4
 years but was observed at ages up to 13 years. The longest-living
 (non-reproducing) ramet died at age 14. Synthesis: Our findings indicate
 that Polytrichastrum formosum ramets experience constant actuarial
 senescence, at least in terms of survival. This finding improves our
 understanding of age-dependent demography in mosses, as well as in plants
 in general. This new knowledge about moss demography may also aid in
 management decisions for threatened species, as it can improve the
 precision of predictions of population longevity.
DOI: 10.5061/dryad.dfn2z351t
title: Chironomid assemblages and inferred summer temperature from the Last Glacial Period (ca. 98–46 ka), from Füramoos, Southern Germany

description: The data herein presents a new chironomid record and associated
 chironomid-based temperature reconstruction covering the time interval ca.
 98–46 ka from the palaeolake Füramoos, Southern
 Germany. These data also include non-chironomid invertebrate
 remains, including Ceratopogonidae, Daphnia and Ephemeroptera as well as
 Characean oospores.
description: <strong>Sample processing</strong>: Sediment samples
 between depths 9.6-6.0 m required no chemical treatment. Samples betweend
 depths of 13-9.6 m were heated in 10% KOH for 15  minutes at 85°C due to
 the dificulty of processing those samples. Sediment samples were then
 sieved through 100 and 200 micrometer sieves. Chironomids were picked from
 those samples using a Bogorov tray under a stereomicroscope (30 – 50 x
 magnification). Samples were dried and then mounted on microscope slides
 using Euparal and identified under at 40 – 100 x magnification  with a
 compound microscope. Next to chironomids the remains of Sialidae,
 Ceratopogonidae, <em>Daphnia</em>, Ephemeroptera, oribatid
 mites, Trichoptera, Plecoptera, Sciaridae and Tipulidae as well as
 Characeae oogonia and <em>Plumatella</em> statoblasts were
 mounted and identified. The chironmoid based temperature reconstruciton
 was produced using a two-component weighted averaging partial least
 squares model.  For post identification data processing
 and temperature reconstruction analysis please see the associated
 publication in Quaternary Science Reviews where the results are discussed in detail. The manuscript is fully open access: https://doi.org/10.1016/j.quascirev.2021.107008.
description: We outline which parts of the temperature reconstruciton are
 considered more reliable in the manuscript. For a discussion please see
 the associated publication in Quaternary Science Reviews which is fully open access: https://doi.org/10.1016/j.quascirev.2021.107008. There are two samples in the dataset presented with no temperature reconstruction as there were no chironomids present in that section.
DOI: 10.5061/dryad.v15dv41w5
title: Genomic, karyological, and morphological changes of South American garlics (Ipheion) provide insights into mechanisms of speciation in the Pampean region

description: Speciation proceeds through mechanisms that promote reproductive isolation
 and shape the extent of genetic variation in natural populations, and
 thus, its study is essential to understand the evolutionary processes
 leading to increased biodiversity. Chromosomal rearrangements are known to
 facilitate reproductive isolation by hybrid sterility and favor speciation
 events. The genus Ipheion (Amaryllidaceae, Allioideae) is unique as its
 species exhibits a remarkable karyological variability but lack
 population-level genetic data. To unveil diversification processes acting
 upon the formation of new lineages within Ipheion in the Pampas of South
 America, we combined morphology and karyology approaches with
 genotyping-by-sequencing. Our phylogenomic and population genomics results
 supported the taxonomic division of Ipheion into three morphological and
 genetically well-differentiated groups. The origin of I. uniflorum was
 traced back to its current southern distribution area in the southern
 Pampean region (in Argentina), from where it had expanded to the North
 reaching Uruguay. Our results further suggested that chromosome
 rearrangements and ploidy shifts had triggered speciation events, first
 during the origin of I. uniflorum and later during its subsequent
 diversification into I. recurvifolium and I. tweedieanum, in both cases
 reinforced by extrinsic factors and biogeographical settings. The current
 study illustrates the analytical power of multidisciplinary approaches
 integrating phylo- and population genomics with classic analyses to
 disclose evolutionary processes in plants. 
description: Methods are described in the manuscript
description: All Data And Scripts This archive contains
 all the scripts and data used in the analyses for the paper
DOI: 10.5061/dryad.sj3tx9652
title: Prevalence and polymorphism of a mussel transmissible cancer in Europe__GenotypeKASPdatasetMytilus

description: Transmissible cancers are parasitic malignant cell lineages that acquired
 the ability to infect new hosts from the same species, or sometimes
 related species. First described in dogs and Tasmanian devils,
 transmissible cancers were later discovered in some marine bivalves
 affected by a leukemia-like disease. In Mytilus mussels,
 two lineages of Bivalve Transmissible Neoplasia (BTN), both
 emerged in a M. trossulus founder
 individual, have been described to date
 (MtrBTN1 and MtrBTN2). Here, we performed an extensive
 screening of genetic chimerism, a hallmark of transmissible cancer, by
 genotyping 106 SNPs of 5907
 European Mytilus mussels. The genetic analysis allowed
 us to simultaneously obtain the genotype of hosts -M. edulis, M.
 galloprovincialis or hybrids- and the genotype of tumors of
 heavily infected individuals. In addition, a subset of 222 individuals
 were systematically genotyped and analysed by histology in order to screen
 for possible non-transmissible cancers. We detected MtrBTN2 at low
 prevalence in M. edulis, and also in M.
 galloprovincialis and hybrids although at a much lower
 prevalence. No MtrBTN1 or new BTN were found but
 8 individuals with non-transmissible neoplasia were
 observed at a single polluted site on the same sampling
 date. We observed a diversity of MtrBTN2 genotypes that appeared more
 introgressed or more ancestral than MtrBTN1 and reference
 healthy M. trossulus individuals. The observed
 polymorphism is most likely due to somatic null alleles caused by
 structural variations or point mutations in primer-binding sites leading
 to enhanced detection of the host alleles. Despite low prevalence, two
 divergent sublineages with 10% somatic null alleles and one
 non-synonymous mtCOI substitution, are co-spreading in the same geographic
 area, suggesting a complex diversification of MtrBTN2 since its emergence
 and host species shift.
description: 5907 Mytilus mussels have been sampled in two tissues (n=1749,
 hemolymph and mantle) or one tissue (n=4158; hemolymph for 197 or gill for
 3988). Then, genotyping have been perform by
 KASP<sup>TM</sup> method on 74 bi-allelic SNPs (subcontracted
 to LGC genomics (Hoddensdon, UK)).  Quickly, this
 method puts two “allele specific” primers with two different fluorochromes
 in competition during a PCR amplification and gives two values of
 fluorescence level, one for allele X and the other for allele Y.
description: This dataset gives the fluorescence values for each alleles (X
 and Y) and the calling performed by two LGC genomics expert (for more
 information see the 'Material and method' section of the article
 and the README file).
DOI: 10.5061/dryad.zgmsbccbm
title: Behavioral data file following treatment of laboratory rats with paracetamol

description: Based on several lines of evidence, numerous investigators have suggested
 that acetaminophen exposure during early development can induce
 neurological disorders. We had previously postulated that acetaminophen
 exposure early in life, if combined with antioxidants that prevent
 accumulation of NAPQI, the toxic metabolite of acetaminophen, might be
 innocuous. In this study, we administered acetaminophen at or below the
 currently recommended therapeutic dose to male laboratory rat pups aged
 4-10 days. The antioxidants cysteine and mannitol were included to prevent
 accumulation of NAPQI. In addition, animals were exposed to a cassette of
 common stress factors: an inflammatory diet, psychological stress,
 antibiotics, and mock infections using killed bacteria. At age 37-49 days,
 observation during introduction to a novel conspecific revealed increased
 rearing behavior, an asocial activity, in animals treated with
 acetaminophen plus antioxidants, regardless of their exposure to oxidative
 stress factors (2-way ANOVA; P &lt; 0.0001). This observation would
 suggest that the initial hypothesis is incorrect, and that oxidative
 stress mediators do not entirely eliminate the effects of acetaminophen on
 neurodevelopment. This study provides additional cause for caution when
 considering the use of acetaminophen in the pediatric population, and
 provides evidence that the effects of acetaminophen on neurodevelopment
 need to be considered both in the presence and in the absence of oxidative
 stress.
description: Social play behavior was assessed in rats between postnatal days
 37 through 49 days in accordance with Veenema and colleagues (citations in
 manuscript). Briefly, all subjects and stimulus animals will be handled
 for 5 consecutive days prior to the beginning of behavior testing. All
 experimental subject animals were isolated for 24 hours prior to
 behavioral testing to potentiate their motivation to engage in social
 interactions. All testing took place during the last two hours of the
 light phase. Animals were placed together with an unfamiliar animal
 belonging to the same experimental group. Clean cages with bedding were
 used, and activity was video recorded for 10 min. All behavioral videos
 were subsequently scored by an observer blind to the treatment condition
 of each animal using Solomon coder software (version beta 19.08.02; https://solomon.andraspeter.com/). Behavioral bins were as follows: exploration, play, investigation, chasing, rearing, auto grooming, and allogrooming. Play activity was further assigned to the following bins: nape attacks, boxing, pinning, and supine. Rearing was assessed for all animals (2 per cage), and all other behaviors were assessed for only one animal per cage. All videos had a total of 600.2 seconds of graded behavior.
description: See attached ReadMe file.
DOI: 10.5061/dryad.8931zcrr2
title: Data and code from: Mixed infection, risk projection and misdirection: Interactions among pathogens alter links between host resources and disease

description: A growing body of literature links resources of hosts to their risk of
 infectious disease. Yet most hosts encounter multiple pathogens, and
 projections of disease risk based on resource availability could be
 fundamentally wrong if they do not account for interactions among
 pathogens within hosts. Here, we measured infection risk of grass hosts
 (Avena sativa) exposed to three naturally-co-occurring viruses either
 singly or jointly (barley and cereal yellow dwarf viruses [B/CYDVs]:
 CYDV-RPV, BYDV-PAV, and BYDV-SGV) along experimental gradients of nitrogen
 and phosphorus supply. We asked whether disease risk (i.e., infection
 prevalence) differed in single versus co-inoculations, and whether these
 differences varied with rates and ratios of nitrogen and phosphorus
 supply. In single inoculations, the viruses did not respond strongly to
 nitrogen or phosphorus. However, in co-inoculations, we detected
 illustrative cases of 1) resource-dependent antagonism (RPV with
 increasing N; possibly due to competition), 2) resource-dependent
 facilitation (SGV with decreasing N:P; possibly due to immunosuppression),
 and 3) weak or no interactions within hosts (for PAV). Together, these
 within-host interactions created emergent patterns for co-inoculated
 hosts, with both infection prevalence and viral richness increasing with
 the combination of low nitrogen and high phosphorus supply. We demonstrate
 that knowledge of multiple pathogens is essential for predicting disease
 risk from host resources, and that projections of risk that fail to
 acknowledge resource-dependent interactions within hosts could be
 qualitatively wrong. Expansions of theory from community ecology theory
 may help anticipate such relationships linking host resources to diverse
 pathogen communities.
DOI: 10.5061/dryad.fbg79cnv7
title: Challenging the established order: innovating clinical trials for amyotrophic lateral sclerosis

description: Development of effective treatment for amyotrophic lateral
 sclerosis (ALS) has been hampered by disease
 heterogeneity,a limited understanding of
 underlying pathophysiology and methodological design challenges.
 Here we have evaluated two major themes in the design of pivotal,
 phase 3 clinical trials for ALS: (1) patient selection and (2) analytical
 strategy, and discussed potential solutions with the European Medicines
 Agency (EMA). Several design considerations
 were assessed using data from five placebo-controlled
 clinical trials (N = 988), four population-based cohorts (N = 5,100), and
 2,436 placebo-allocated patients from the PRO-ACT database. The validity
 of each proposed design modification was confirmed by
 means of simulation and illustrated for a hypothetical
 setting. Compared to classical trial design, the proposed design
 modifications reduce the sample size by 30.5% and
 placebo exposure time by 35.4%. By making use of
 prognostic survival models, one creates a potential to
 include a larger proportion of the population and maximize
 generalizability. We propose a flexible design framework which naturally
 adapts the trial duration when inaccurate assumptions are
 made at the design stage such as the enrollment
 or survival rate. In case of futility, the follow-up time is shortened and
 patient exposure to ineffective treatments or
 placebo is minimized. For diseases such as ALS,
 optimizing the use of resources, widening eligibility criteria and
 minimizing the exposure to futile treatments and placebo is critical
 to the development of effective treatments. Our
 proposed design modifications could circumvent important pitfalls and may
 serve a blueprint for future clinical trials in this population.