cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f4qrfj6x8
title: Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

description: Dusky Salamanders (genus Desmognathus) currently comprise only 22
 described, extant species. However, recent mitochondrial and nuclear
 estimates indicate the presence of up to 49 candidate species based on
 ecogeographic sampling. Previous studies also suggest a complex history of
 hybridization between these lineages. Studies in other groups suggest that
 disregarding admixture may affect both phylogenetic inference and
 clustering-based species-delimitation. With a dataset comprising 233
 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus
 specimens from all 49 candidate species, we test three hypotheses
 regarding i) species-level diversity, ii) hybridization and admixture, and
 iii) misleading phylogenetic inference. Using phylogenetic and
 population-clustering analyses considering gene flow, we find support for
 at least 47 candidate species in the phylogenomic dataset, some of which
 are newly characterized here while others represent combinations of
 previously named lineages that are collapsed in the current dataset.
 Within these, we observe significant phylogeographic structure, with up to
 64 total geographic genetic lineages, many of which hybridize either
 narrowly at contact zones or extensively across ecological gradients. We
 find strong support for both recent admixture between terminal lineages
 and ancient hybridization across internal branches. This signal appears to
 distort concatenated phylogenetic inference, wherein more heavily admixed
 terminal specimens occupy apparently artifactual early diverging
 topological positions, occasionally to the extent of forming false clades
 of intermediate hybrids. Additional geographic and genetic sampling and
 more robust computational approaches will be needed to clarify taxonomy,
 and to reconstruct a network topology to display evolutionary
 relationships in a manner that is consistent with their complex history of
 reticulation. --
description: Anchored Hybrid Enrichment
description: All raw data and output files from the sequencing runs and
 analyses described in the article are included here.
DOI: 10.15468/dl.rejw5e
title: Occurrence Download

description: A dataset containing 16142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vannella",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 16142 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003016-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28450102
title: Epidemiology, resource use, and treatment patterns of locally advanced or metastatic urothelial carcinoma in France

description: Describe real-world epidemiology, treatment patterns, health care resource utilization, and costs of locally advanced or metastatic urothelial carcinoma (la/mUC) in France. Retrospective study including all adults with la/mUC diagnosis during January 2017 to December 2020 in the PMSI database. Annual prevalence and incidence ranged from 36.4 to 38.9 and 16.4 to 18.5 cases per 100,000 people, respectively. Of the 25,314 patients with incident la/mUC, 37.6% did not receive first-line systemic treatment. Of the 14,656 patients who started first-line systemic treatment, 66.6%, 22.5%, and 10.9% received 1, 2, and 3 lines of therapy, respectively. Annual per-patient costs in second-/third-line setting ranged from €8803 to €16,012. The substantial disease burden of la/mUC in France highlights the unmet need for new therapies. <b>What is this article about?</b> Urothelial carcinoma (UC) is a type of cancer affecting the urinary system. It can spread to other parts of the body, described as locally advanced or metastatic (la/m). We used information from a French database recording hospitalizations in France to find out how many people have la/mUC, how many new cases develop each year, what treatments they receive, how many die in the hospital, and how much their care costs. <b>What were the results?</b> Based on database information, 37 to 39 of every 100,000 people have la/mUC and 17 to 19 of every 100,000 people are identified with a new case yearly. Slightly more than one-third of patients with la/mUC did not receive recommended treatment (chemotherapy) when first diagnosed. Chemotherapy was the most common treatment type for the first, second, or third treatment; checkpoint inhibitors (a unique treatment) became more commonly used as a second treatment over time. Yearly in-hospital death rates were high, ranging from 47.8% of patients who died within 1 year from diagnosis to 62.9% dying within 3 years. Yearly cost of care was high (costing €8803 to €16,012) in patients starting a second or third treatment. <b>What do the results of the study mean?</b> The study shows many patients may not be fit enough or choose not to receive treatment. Even those receiving treatment are at high risk for poor outcomes. The burden of la/mUC in France is high, underscoring the need for more therapies and better supportive care early in disease management.
DOI: 10.6084/m9.figshare.28450102.v1
title: Epidemiology, resource use, and treatment patterns of locally advanced or metastatic urothelial carcinoma in France

description: Describe real-world epidemiology, treatment patterns, health care resource utilization, and costs of locally advanced or metastatic urothelial carcinoma (la/mUC) in France. Retrospective study including all adults with la/mUC diagnosis during January 2017 to December 2020 in the PMSI database. Annual prevalence and incidence ranged from 36.4 to 38.9 and 16.4 to 18.5 cases per 100,000 people, respectively. Of the 25,314 patients with incident la/mUC, 37.6% did not receive first-line systemic treatment. Of the 14,656 patients who started first-line systemic treatment, 66.6%, 22.5%, and 10.9% received 1, 2, and 3 lines of therapy, respectively. Annual per-patient costs in second-/third-line setting ranged from €8803 to €16,012. The substantial disease burden of la/mUC in France highlights the unmet need for new therapies. <b>What is this article about?</b> Urothelial carcinoma (UC) is a type of cancer affecting the urinary system. It can spread to other parts of the body, described as locally advanced or metastatic (la/m). We used information from a French database recording hospitalizations in France to find out how many people have la/mUC, how many new cases develop each year, what treatments they receive, how many die in the hospital, and how much their care costs. <b>What were the results?</b> Based on database information, 37 to 39 of every 100,000 people have la/mUC and 17 to 19 of every 100,000 people are identified with a new case yearly. Slightly more than one-third of patients with la/mUC did not receive recommended treatment (chemotherapy) when first diagnosed. Chemotherapy was the most common treatment type for the first, second, or third treatment; checkpoint inhibitors (a unique treatment) became more commonly used as a second treatment over time. Yearly in-hospital death rates were high, ranging from 47.8% of patients who died within 1 year from diagnosis to 62.9% dying within 3 years. Yearly cost of care was high (costing €8803 to €16,012) in patients starting a second or third treatment. <b>What do the results of the study mean?</b> The study shows many patients may not be fit enough or choose not to receive treatment. Even those receiving treatment are at high risk for poor outcomes. The burden of la/mUC in France is high, underscoring the need for more therapies and better supportive care early in disease management.
DOI: 10.5061/dryad.n2z34tmz5
title: Histological and life history data for small-bodied mammals from: Multituberculate mammals show evidence of a life history strategy similar to that of placentals, not marsupials

description: The remarkable evolutionary success of placental mammals has been partly
 attributed to their reproductive strategy of prolonged gestation and
 birthing of relatively precocial, quickly weaned neonates. Although this
 strategy was conventionally considered derived relative to that of
 marsupials with highly altricial neonates and long lactation periods,
 mounting evidence has challenged this view. Until now, the fossil record
 has been relatively silent on this debate, but here we find that
 proportions of different bone tissue microstructures in the femoral
 cortices of small extant marsupials and placentals correlate with length
 of lactation period, allowing us to apply this histological correlate of
 reproductive strategies to Late Cretaceous and Paleocene members of
 Multituberculata, an extinct mammalian clade that is phylogenetically
 stemward of Theria. Multituberculate bone histology closely resembles that
 of placentals, suggesting that they had similar life history strategies.
 That a stem-therian clade exhibits evidence of placental-like life
 histories supports the hypothesis that intense maternal-fetal contact
 characteristic of placentals is ancestral for therians. Alternatively,
 multituberculates and placentals may have independently evolved prolonged
 gestation and abbreviated lactation periods. Our results challenge the
 hypothesis that the rise of placental mammals was driven by unique life
 history innovations, and shed new light on early mammalian
 diversification.
DOI: 10.15151/esrf-es-2286885247
title: Italian CryoEM Bag II (ICB-II)

description: This BAG application builds on the development of single particle cryoEM in the Italian Structural Biology community, as in Italy there is no top-end instrument isopen to rhe structural biology community.
The groups in this application have acquired know-how in cryoEM through international collaborations or by acquiring medium-level in-house equipment. Access tothe CM01 beamline at the ESRF since August 2020 has allowed the development of projects from groups that do not have in-house equipment that resulted inpaper in publication on Nucleic Acid Research NAR.
We now have six screening microscopes in Italy and two more are being funded, making the access to CM01 more demanded and relevant for high-resolution
data and, consequently high profile publications
DOI: 10.5061/dryad.4xgxd25bf
title: Datafiles and code for Covas et al: The oxidative cost of helping and its minimisation in a cooperative breeder

description: Cooperative actions are beneficial to the group, but presumably costly to
 the individual co-operators. In cooperatively breeding species, helping to
 raise young is thought to involve important energetic costs, which could
 lead to elevated exposure to reactive oxygen species, resulting in
 oxidative stress. However, identifying such costs can be difficult if
 individuals adjust their investment in helping in relation to
 environmental conditions or their own physiological condition.
 Experimental approaches are therefore required to quantify the costs of
 helping but, to date, these have been infrequent. Here, we combined
 correlational and experimental data to investigate the oxidative cost of
 helping-at-the-nest and how this affects helping decisions in wild
 sociable weavers Philetairus socius, a colonial cooperatively breeding
 bird. At the correlational level, we found that the probability of helping
 was influenced by the interaction of an individual’s oxidative state and
 age: compared to younger birds, older individuals were more likely to help
 when they had higher oxidative damage, and the opposite trend was found
 for younger individuals. After experimentally increasing the energetic
 cost of flight, manipulated helpers in breeding colonies decreased
 nestling feeding rates and incurred an increase in oxidative damage, which
 was not present in manipulated helpers in non-breeding colonies. This
 indicates that individuals decreased their helping behaviour to minimise
 the associated costs. These results suggest that oxidative stress can
 influence helping decisions and underlie a trade-off between cooperation
 and self-maintenance, which is central to understanding when helping might
 take place in this and other species.
DOI: 10.5061/dryad.34tmpg4mq
title: Data for: Red foxes enhance long-term tree growth near the Arctic treeline

description: Recent climate warming is expected to increase tree growth and
 productivity, substantially altering ecological function and boundaries in
 northern ecosystems. Temperature and precipitation largely
 determine the range and growth of trees in any biome, yet variations in
 microsite conditions can also influence tree growth on a finer scale. By
 altering essential resources and habitat conditions, terrestrial organisms
 could modify Subarctic tree growth. Red foxes (Vulpes vulpes) are
 found in most terrestrial ecosystems and are considered ecosystem
 engineers by enriching soil nutrients and plant composition through
 denning. Added soil nutrients from prey remains, feces, and urine could
 benefit tree growth in Subarctic regions by alleviating soil nutrient
 limitations. We examined growth in white spruce (Picea glauca) trees
 growing on eight red fox dens and paired control sites near Churchill,
 Manitoba, Canada, at the Arctic treeline. Radial growth was 55% higher for
 trees on dens than on control sites between 1897 and 2017, despite
 similarities in tree ages, densities, and regional climate across all
 sites. By promoting tree growth near the treeline, red foxes may influence
 the position of the Arctic treeline. Although the impacts on tree growth
 largely depend on the spatial distribution of dens and predator activity
 in the boreal forest, predators can create distinct microhabitats across
 the landscape via ecosystem engineering processes, leading to increased
 vegetation productivity, persisting over many decades.
DOI: 10.5061/dryad.37pvmcvmm
title: Facile synthesis of Cu2O nanorods in the presence of NaCl by SILAR method and its characterizations

description: Cu2O nanorods have been deposited on soda-lime glass (SLG) substrates by
 the modified SILAR technique by varying the concentration of NaCl
 electrolyte into the pre-cursor complex solution. The structural,
 electrical, and optical properties of synthesized Cu2O nanorod films have
 been studied by a variety of characterization tools. Structural analyses
 by XRD confirmed the polycrystalline Cu2O phase with (111) preferential
 growth. Raman scattering spectroscopic measurements conducted at room
 temperature also showed characteristic peaks of the pure Cu2O phase. The
 surface resistivity of the Cu2O nanorod films decreased from 15,142 to 685
 Ω.cm with the addition of NaCl from 0 to 4 mmol, and then exhibited an
 opposite trend with further addition of NaCl. The optical bandgap of the
 synthesized Cu2O nanorod films was observed as 1.88~2.36 eV, while the
 temperature-dependent activation energies of the Cu2O films were measured
 as about 0.14~0.21 eV. SEM morphologies demonstrated Cu2O nanorod as well
 as closely packed spherical grains with the alteration of NaCl
 concentration. The Cu2O phase of nanorods was found stable up to
 230℃ corroborating the optical bandgap results of the same. The
 film fabricated in presence of 4 mmol of NaCl showed the lowest
 resistivity and activation energy as well comparatively uniform nanorod
 morphology. Our studies demonstrate that the nominal presence of NaCl
 electrolytes in the pre-cursor solutions has a significant impact on the
 physical properties of Cu2O nanorod films which could be beneficial in
 optoelectronic research.
description: The found data set from the XRD, Raman spectra, UV-Vis, SEM,
 etc. are used to calculate the properties or related properties used in
 the article by using OriginLab, N graph, Sigmaplot, excel, etc.
DOI: 10.5061/dryad.6t1g1jx0v
title: Digital research materials of spectral data for the article: [3+2]-Cycloaddition of azomethine ylides to 5-methylidene-3-aryl-2-сhalcogen-imidazolones: Access to dispiro indolinone-pyrrolidine-imidazolones

description: Digital research materials of NMR spectral data for the article
 "[3+2]-Cycloaddition of azomethine ylides to
 5-methylidene-3-aryl-2-сhalcogen-imidazolones: access to dispiro
 indolinone-pyrrolidine-imidazolones" submitted to the Royal
 Society Open Science. NMR spectra were recorded on Bruker Avance
 400 and Agilent MR-400 spectrometers in DMSO-d6 and C6D6. 
 Chemical shifts were measured relative to residual solvent signals and
 referenced in parts per million to TMS. Original fid files are
 presented, which can be opened, for example, using the ASD Labs software
 package.
description: <sup>1</sup>H (400 MHz), <sup>13</sup>C
 (101 MHz), and <sup>19</sup>F (376 MHz) NMR spectra were
 recorded on Bruker Avance 400 and Agilent MR-400 spectrometers.
description: Data can be opened and viewed using the TopSpin software by
 Bruker.
DOI: 10.5061/dryad.dncjsxm1b
title: Inflammatory cytokines and risk of gestational diabetes

description: Background: Over the last decade, an emerging role of novel cytokines in
 the pathogenesis of gestational diabetes mellitus (GDM) has been proposed
 by researches. The present study was performed to provide a more accurate
 estimate of the effect size of the association between leptin, tumor
 necrosis factor-α (TNF-α), and interleukin-6 (IL-6) and risk of GDM.
 Methods: Online databases were looked up to August 2021 using the search
 string: (leptin OR TNF-α OR IL-6) AND “gestational diabetes”.
 Observational studies investigating the association of the selected
 cytokines and risk of GDM were included. Odds ratios and their 95%
 confidence intervals (CIs) were used to estimate pooled effect. Results:
 19 studies were included in the meta-analysis (6792 women; 1405 diagnosed
 with GDM). A significant association was found between higher circulating
 leptin and risk of GDM and the pooled estimate was 1.15 (95%CI: 1.05,
 1.26). Higher circulating levels of IL-6 and TNF-α were associated with
 increased risk of GDM and the pooled estimates were 2.00 (95%CI: 1.20,
 3.31) and 1.29 (95%CI: 1.13, 1.46), respectively. Conclusions: The
 selected cytokines might be used as potential markers in predicting GDM
 and considered as contributing factors to the GDM pathogenesis.
description: This dataset has been collected by two independent reviewers (EH
 & ZM) using information obtained from the selected studies for
 performing the submitted systematic review and meta-analysis
 manuscript.
DOI: 10.5061/dryad.vdncjsxwh
title: Dataset of the bacterial fitness estimation values and mutation identifications from: Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment

description: Interactions between microbes can both constrain and enhance adaptation,
 but to date, most studies employ simplified communities and environments.
 We measured fitness of populations of the soil bacterium Pseudomonas
 fluorescens that have been evolved in both the presence and absence of a
 natural potting soil microbial community. Populations from both
 environments showed similar fitness increases with respect to the ancestor
 in the absence of the community, suggesting no significant cost of
 evolving with the community. By contrast, fitness in the presence of the
 community increased for community-evolved populations, but decreased
 considerably below the ancestral state for populations evolved in the
 absence of the community. This suggests some abiotic beneficial mutations
 are costly in the presence of the community, while others are not, with
 the former only selected against in the presence of the community. Most
 mutations underpinning fitness changes were clone specific, supporting the
 view that there are multiple genetic pathways to adaptation in this
 complex environment. Such extreme mutational effects have not been
 observed in comparable in vitro studies that employ much simpler abiotic
 and biotic environments, and suggest that a caution is need when
 extrapolating results from simplified in vitro systems to real-world
 contexts.
description: This research was experimentally preformed in the lab. On one
 hand, bacterial fitness was estimated according to the described procedure
 in the methodology. And in the other hand, whole-genome sequencing data
 was also following the describe procedure, having all sequences deposited
 in teh ENA database.
DOI: 10.5061/dryad.sqv9s4n5b
title: Flow cytometry changes in murine XBP1 KO fed high fat diet

description: Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes
 of liver diseases in the United States and can progress to cirrhosis,
 end-stage liver disease and need for liver transplantation. There are
 limited therapies for NAFLD, in part, due to incomplete understanding of
 the disease pathogenesis, which involves different cell populations in the
 liver.  Endoplasmic reticulum stress and its adaptative unfolded
 protein response (UPR) signaling pathway have been implicated in the
 progression from simple hepatic steatosis to nonalcoholic steatohepatitis
 (NASH). We have previously shown that mice lacking the UPR protein X-box
 binding protein 1 (XBP1) in the liver demonstrated enhanced liver injury
 and fibrosis in a high fat sugar (HFS) dietary model of NAFLD. In this
 study, to better understand the role of liver XBP1 in the pathobiology of
 NAFLD, we fed hepatocyte XBP1 deficient mice a HFS diet or chow and
 investigated UPR and other cell signaling pathways in hepatocytes, hepatic
 stellate cells and immune cells. We demonstrate that loss of XBP1 in
 hepatocytes increased inflammatory pathway expression and altered
 expression of the UPR signaling in hepatocytes and was associated with
 enhanced hepatic stellate cell activation after HFS feeding. We believe
 that a better understanding of liver cell-specific signaling in the
 pathogenesis of NASH may allow us to identify new therapeutic targets.
DOI: 10.5061/dryad.1g1jwstz9
title: Fine-scale ecological and anthropogenic variables predict the habitat use and detectability of sloth bears in the Churia habitat of east Nepal

description: Once widespread throughout the tropical forests of the Indian
 Subcontinent, the sloth bears have suffered a rapid range collapse and
 local extirpations in the recent decades. A significant portion of their
 current distribution range is situated outside of the protected areas
 (PAs). These unprotected sloth bear populations are under tremendous human
 pressures, but little is known about the patterns and determinants of
 their occurrence in most of these regions. The situation is more prevalent
 in Nepal where virtually no systematic information is available for sloth
 bears living outside of the PAs. We undertook a sign survey-based
 single-season occupancy study intending to overcome this information gap
 for the sloth bear populations residing in the Trijuga forest of southeast
 Nepal. Sloth bear sign detection histories and field-based covariates data
 were collected between 2nd October to 3rd December 2020 at the 74 randomly
 chosen 4-km^2 grid cells using a varying number of 400m long
 transects in each grid cell. From our results, the model-averaged estimate
 of site use probability (ψ ± SE) was estimated to be 0.432 ± 0.039, which
 is a 13% increase from the naïve estimate (0.297) not accounting for
 imperfect detections of sloth bear signs. The presence of termite mound
 and the distance to the nearest water source were the most important
 variables affecting the habitat use probability of sloth bears. The
 average site-level detectability (p ± SE) of sloth bear signs was
 estimated to be 0.195 ± 0.003 and was significantly determined by the
 index of human disturbances. We recommend considering the importance of
 fine-scale ecological and anthropogenic factors in predicting the sloth
 bear-habitat relationships across their range in the Churia habitat of
 Nepal, and more specifically in the unprotected areas.