cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wm37pvmr3
title: Lung microbiome in children with hematological malignancies and lower respiratory tract infections

description: Background: Respiratory infectious complications remain a major cause of
 morbidity and mortality in children with hematological malignancies.
 Knowledge regarding the lung microbiome in the aforementioned children is
 limited. Methods: A prospective cohort was conducted, enrolling 16
 children with hematological malignancies complicated
 with moderate to severe lower respiratory tract
 infections(LRTIs), versus 21 LRTIs children with age, gender,
 weight, infection severity matched, with no underlying
 malignancies, to evaluate the lung
 microbiome from bronchoalveolar lavage fluid samples in different
 groups. Results: Lung microbiome from children with hematological
 malignancies and LRTIs showed obviously decreased α and β diversity,
 increased microbial function in infectious disease:bacteria/parasite, drug
 resistance:antimicrobial and human pathogenesis than the control group,
 and significantly reduced proportion of Firmicutes, Bacteroidota,
 Actinobacteriota , increased Proteobacteria at the phylum level,
 distinctly elevated Parabacteroides, Klebsiella, Grimontia,
 Escherichia_Shigella, unclassified_Enterobacteriaceae at the genus level
 than the control group. Besides, it was revealed that α diversity
 (Shannon), β diversity (Bray Curtis dissimilarity), Proteobacteria at the
 phylum level, and unclassified_Enterobacteriaceae and Escherichia_Shigella
 at the genus level were significantly negatively associated with
 hospitalization course, whereas Firmicutes at the phylum level was
 established positively correlated with hospitalization course.
 Conclusions: Children with hematological malignancies and LRTIs showed
 obviously decreased α and β diversity, significantly increased function in
 infectious disease pathogenesis, antimicrobial drug resistance, and
 unfavorable environment tolerance. Besides, α diversity (Shannon), β
 diversity (Bray Curtis dissimilarity), Proteobacteria may be used as
 negatively correlated predictors for hospitalization course in these
 children whereas Firmicutes is a positively correlated
 predictor. 
description: <strong>Amplicon generation</strong>
 The diluted genomic DNA was used as a template; specific primers
 with Barcode were used according to the selection of the sequencing
 region; Phusion® High-Fidelity PCR Master Mix with GC Buffer was used. The
 PCR was performed using efficient and high fidelity enzymes to ensure
 amplification efficiency and accuracy. Primer corresponding area: 16S
 V3+V4 338F 5'- ACTCCTACGGGAGGCAGCA-3', 806R 5'-
 GGACTACHVGGGTWTCTAAT-3'.
DOI: 10.5061/dryad.r7sqv9sg9
title: Bitter taste receptor genes of primates

description: Bitter taste perception plays a critical role in deterring animals from
 consuming harmful and toxic substances. To characterize the evolution of
 primate Tas2rs and test whether dietary preference has shaped the Tas2rs
 repertoire of primates, we identified Tas2r genes of 35 genomes including
 16 Cercopithecidae species, 6 Hominidae species, 4 Cebidae species, 3
 Lemuridae species, and other 6 species. The results showed that the total
 numbers of primates' Tas2rs ranged from 27 to 51, which concentrated
 on 2–4 scaffolds of each species and the closely related genes tandemly
 duplicated in the same scaffold. Phylogenetic construction revealed that
 the Tas2r genes can be divided into 21 clades, among which,
 anthropoid-specific clades, Prosimii-specific clade, clades with multiple
 gene copies, or even Cercopithecidea-specific Tas2rs were detected. In
 addition, phylogenetically independent contrast (PIC) analysis revealed
 that the number of intact Tas2rs was significantly correlated with feeding
 preferences. Altogether, our data supported diet as a driving force of
 primate Tas2rs evolution, and Cercopithecidae species have developed some
 specific Tas2rs during the evolutionary process. These results are
 probably because most Cercopithecidae species feed on plants containing
 many toxins, and it is necessary to develop specialized Tas2rs to protect
 them from poisoning.
DOI: 10.5061/dryad.n2z34tn0k
title: When ancestors transmit their stress: Prenatal maternal stress transmission across generations in a precocial bird

description: Prenatal maternal stress (PMS) induces life-long effects in offspring.
 Accumulating evidence suggests that these effects can be transmitted
 across generations. Although multigenerational effects (F0 mother to F2
 grand-offspring) of PMS have been demonstrated in different species,
 transgenerational transmission (F0 mother to F3 great-grand-offspring) has
 been less explored. We showed previously in the Japanese quail that PMS
 increased F1 offspring’s emotional reactivity related to epigenetic marks
 levels in their brain and to modulation of testosterone concentrations in
 eggs from which they hatched. Here, we evaluated the multi- and
 transgenerational effects of PMS by analysing the emotional reactivity of
 the F2 and the F3 offspring. We also investigated the mechanisms
 potentially involved in the transmission of PMS across generations by
 analysing the hormonal composition of F1 and F2 eggs and by studying
 histone post-translational modifications in F3 brains. We showed that PMS
 increased the neophobia of F2 offspring and F3 females’ offspring. We also
 observed modulations of androgens levels in F1 and F2 eggs but no
 modifications of the level of histone post-translational modification in
 F3 brains. Although the mechanisms involved in PMS transmission still need
 to be explored, our results demonstrate a multi- and transgenerational
 behavioural effect of PMS in birds.
DOI: 10.5061/dryad.r4xgxd2gq
title: High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

description: Understanding patterns of genetic structure and adaptive variation in
 natural populations is crucial for informing conservation and management.
 Past genetic research using 11 microsatellite loci identified six genetic
 stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan,
 USA. However, ambiguity in genetic stock assignments suggested those
 neutral microsatellite markers did not provide adequate power for
 delineating lake whitefish stocks in this system, prompting calls for a
 genomics approach to investigate stock structure. Here, we generated a
 dense genomic dataset to characterize population structure and investigate
 patterns of neutral and adaptive genetic diversity among lake whitefish
 populations in Lake Michigan. Using Rapture sequencing, we genotyped 829
 individuals collected from 17 baseline populations at 197,588 SNP markers
 after quality filtering. Although the overall pattern of genetic structure
 was similar to the previous microsatellite study, our genomic data
 provided several novel insights. Our results indicated a large genetic
 break between the northwestern and eastern sides of Lake Michigan, and we
 found a much greater level of population structure on the eastern side
 compared to the northwestern side. Collectively, we observed five genomic
 islands of adaptive divergence on five different chromosomes. Each island
 displayed a different pattern of population structure, suggesting that
 combinations of genotypes at these adaptive regions are facilitating local
 adaptation to spatially heterogenous selection pressures. Additionally, we
 identified a large linkage disequilibrium block of ~8.5 Mb on chromosome
 20 that is suggestive of a putative inversion but with a low frequency of
 the minor haplotype. Our study provides a comprehensive assessment of
 population structure and adaptive variation that can help inform
 management of Lake Michigan's lake whitefish fishery and highlights
 the utility of incorporating adaptive loci into fisheries
 management.
DOI: 10.5061/dryad.ghx3ffbsb
title: Effects of global change on bird and beetle populations in boreal forest landscape: an assemblage dissimilarity analysis

description: Aim  Despite an increasing number of studies highlighting the
 impacts of climate change on boreal species,  the main factors
 that will drive changes in species assemblages remain ambiguous. 
 We study how species community composition would change following
 anthropogenic and natural disturbances. We determine the main drivers of
 assemblage dissimilarity for bird and beetle communities. Location
 Côte-Nord, Québec, Canada. Methods We quantify two climate-induced
 pathways based on direct and indirect effects on species occurrence under
 different harvest management scenarios. The direct climate effects
 illustrate the impact of climate variables while the indirect effects are
 reflected through habitat-based climate change. We develop empirical
 models to predict the distribution of more than 100 species over the next
 century. We analyze the regional and the latitudinal species assemblage
 dissimilarity by decomposing it into 'balanced variation in species
 occupancy and occurrence' and 'occupancy and occurrence
 gradient'.   Results Both pathways increased
 dissimilarity in species assemblage.   At the regional
 scale, both effects have an impact on decreasing the number of winning
 species. Yet, responses are much larger in magnitude under mixed climate
 effects (a mixture of direct and indirect effects). Regional assemblage
 dissimilarity reached 0.77 and 0.69 under mixed effects versus 
 0.09 and 0.10 under indirect effects for beetles and birds, respectively,
 between RCP8.5 and baseline climate scenarios when considering harvesting.
 Latitudinally, assemblage dissimilarity increased following the climate
 conditions pattern.  Main conclusions The two pathways are
 complementary and alter biodiversity, mainly caused by species turnover.
 Yet, responses are much larger in magnitude under mixed climate effects.
 Therefore, the inclusion of climatic variables considers aspects other
 than just those related to forest landscapes, such as life cycles of
 animal species. Moreover, we expect differences in occupancy between the
 two studied taxa. This could indicate the potential range of change in
 boreal species concerning novel environmental conditions.
DOI: 10.5061/dryad.x69p8czn2
title: A field test of mechanisms underpinning animal diversity in recently burned landscapes

description: 1. Planned burning generates different types of pyrodiversity, however,
 experimental tests of how alternative spatial patterns of burning
 influence animal communities remain rare. Field tests are needed to
 understand the mechanisms through which spatial variation in planned fire
 affects fauna, and how fire can be applied to benefit biodiversity. 2. We
 tested five hypotheses of how fire-driven variation in habitat composition
 and configuration affects fauna at fine scales. Small mammal, reptile and
 invasive predator activity was monitored at 12 burnt and eight unburnt
 sites through the year following a large, planned burn in semi-arid
 ‘mallee’ woodlands of southern Australia. We explored measures of burnt or
 unburnt habitat (“habitat status”); amount of unburnt vegetation (“habitat
 amount”); interspersion of burnt and unburnt patches (“habitat
 complementation”); distance to external or internal unburnt vegetation
 (“habitat connectivity”); and unburnt patch size and local vegetation
 cover (“habitat refuge”). Generalized linear models were used to test the
 influence of each variable on capture rate of three small mammal and 11
 reptile species; activity of the introduced red fox (Vulpes vulpes); and
 species richness of native animals. 3. We found strong support for the
 habitat status hypothesis and moderate support for four hypotheses
 relating to spatial patterns of fire. Reptile assemblages varied between
 burnt and unburnt sites, and relationships were identified between
 abundance of one or more reptile species and each measure of spatial
 variation. Reptile species richness was higher at unburnt sites and at
 sites with more unburnt vegetation in the surrounding area. Sites that
 were less connected to unburnt vegetation had fewer reptile species.
 Mammals did not have clear relationships with fine-scale fire patterns. 4.
 Synthesis and applications: Application of planned fire to promote
 biodiversity is globally important. We show that retaining unburnt areas
 and well-connected habitat refuges is important for reptile diversity. We
 also found that several species of small mammals and reptiles appear
 resilient to the fine-scale patterns of planned fire experienced in this
 study, despite activity of introduced predators. The diversity of animals
 can remain relatively high in areas subject to planned fire, provided that
 internal and external habitat refuges are retained.
DOI: 10.5061/dryad.z34tmpghn
title: Data from: The evolution of sex similarities in social signals: Climatic seasonality is associated with lower sexual dimorphism and greater elaboration of female and male signals in antbirds (Thamnophilidae)

description: Selection on signals that mediate social competition varies with resource
 availability. Climate regulates resource availability, which may affect
 the strength of competition and selection on signals. Traditionally, this
 meant that more seasonal, colder, or dryer – overall harsher –
 environments should favor the elaboration of male signals under stronger
 male-male competition, increasing sexual dimorphism. However, females also
 use signals to compete; thus, harsher environments could strengthen
 competition and favor elaboration of signals in both sexes, decreasing
 sexual dimorphism. Alternatively, harsher environments could decrease
 sexual dimorphism due to scarcer resources to invest in signal elaboration
 in both sexes. We evaluated these contrasting hypotheses in antbirds, a
 family of Neotropical passerines that varies in female and male signals
 and occurs across diverse climatic regimes. We tested the association of
 sexual dimorphism of plumage coloration and songs with temperature,
 precipitation and their seasonality. We found that greater seasonality is
 associated with lower sexual dimorphism in plumage coloration and greater
 elaboration of visual signals in both sexes, but not acoustic signals. Our
 results suggest that greater seasonality may be associated with convergent
 elaboration of female and male visual signals, highlighting the role of
 signals of both sexes in the evolution of sexual dimorphism.
description: Compressed folder “Macedo_et_al_2022_Evolution.rar” contains data
 and R code to replicate analyses of the paper: “The
 evolution of sex similarities in social signals: climatic seasonality is
 associated with lower sexual dimorphism and greater elaboration of female
 and male signals in antbirds (Thamnophilidae)”
 Description_of_Variables.xlsx describes variables of all
 datasets.  READ_ME.txt describes contents of all
 sub-directories.
DOI: 10.5281/zenodo.18401500
title: Dataset of the publication MCH11, a new monoacylglycerol lipase inhibitor, reduces ethanol consumption and motivation to drink in mice, with sex-dependent differences

description: Read the readme.txt
DOI: 10.5281/zenodo.18401501
title: Dataset of the publication MCH11, a new monoacylglycerol lipase inhibitor, reduces ethanol consumption and motivation to drink in mice, with sex-dependent differences

description: Read the readme.txt
DOI: 10.5061/dryad.98sf7m0mz
title: Data for: Spatial and temporal genetic stock composition of river herring bycatch in southern New England Atlantic herring and mackerel fisheries

description: Anadromous river herring (alewife and blueback herring) persist at
 historically low abundances and are caught as bycatch in commercial
 fisheries, potentially preventing recovery despite conservation efforts.
 We used newly established single-nucleotide polymorphism genetic baselines
 for alewife and blueback herring to define fine-scale reporting groups for
 each species. We then determined the occurrence of fish from these
 reporting groups in bycatch samples from a Northwest Atlantic fishery over
 four years.Within sampled bycatch events, the highest proportions of
 alewife were from the Block Island (34%) and Long Island Sound (22%)
 reporting groups, while for blueback herring the highest proportions were
 from the Mid-Atlantic (47%) and Northern New England (24%) reporting
 groups. We then quantified stock-specific mortality in a focal geographic
 area (~3500 km2 including Block Island Sound) of high bycatch incidence
 and sampling effort, where the most accurate estimates of mortality could
 be made. During this period, we estimate that bycatch took about 4.6
 million alewife and 1.2 million blueback herring, highlighting the need to
 reduce bycatch mortality for the most depleted river herring stocks.
description: The data uploaded for this project includes the SNP genotyped
 baselines for alewife and blueback herring as well as the genotyped
 bycatch of alewife and blueback herring. The methods are described in the
 manuscript.
description: We have provided the R-code for simulations to estimate the
 accuracy of RG for alewife and blueback herring and to estimate mixing
 proportion estimates for alewife and blueback herring bycatch.
DOI: 10.5061/dryad.hdr7sqvmf
title: Deep learning to estimate durable clinical benefit and prognosis from patients with non-small cell lung cancer treated with PD-1/PD-L1 blockade

description: Different biomarkers based on genomics variants have been used to predict
 the response of patients treated with PD-1/programmed death receptor 1
 ligand (PD-L1) blockade. We aimed to use deep-learning algorithm to
 estimate clinical benefit in patients with non-small-cell lung cancer
 (NSCLC) before immunotherapy. Peripheral blood samples or tumor tissues of
 915 patients from three independent centers were profiled by whole-exome
 sequencing or next-generation sequencing. Based on convolutional neural
 network (CNN) and three conventional machine learning (cML) methods, we
 used multi-panels to train the models for predicting the durable clinical
 benefit (DCB) and combined them to develop a nomogram model for predicting
 prognosis. In the three cohorts, the CNN achieved the highest
 area under the curve of predicting DCB among cML, PD-L1 expression, and
 tumor mutational burden (area under the curve [AUC] = 0.965, 95%
 confidence interval [CI]: 0.949–0.978, P &lt; 0.001; AUC =0.965, 95%
 CI: 0.940–0.989, P &lt; 0.001; AUC = 0.959, 95% CI:
 0.942–0.976, P &lt; 0.001, respectively). Patients with
 CNN-high had longer progression-free survival (PFS) and overall survival
 (OS) than patients with CNN-low in the three cohorts. Subgroup analysis
 confirmed the efficient predictive ability of CNN. Combining three cML
 methods (CNN, SVM, and RF) yielded a robust comprehensive nomogram for
 predicting PFS and OS in the three cohorts (each P &lt;
 0.001). The proposed deep-learning method based on mutational
 genes revealed the potential value of clinical benefit prediction in
 patients with NSCLC and provides novel insights for combined machine
 learning in PD-1/PD-L1 blockade.
DOI: 10.15468/dl.82yyhg
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Englerodendron gabunense",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 126 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003275-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/bdmxpk
title: Mayfly (Ephemeroptera) records from Britain and Ireland, via iRecord

description: This Mayfly dataset is part of the Ephemeroptera Recording Scheme. The dataset comprises records entered via iRecord and verified online.
DOI: 10.15468/ptw1tt
title: Stonefly (Plecoptera) records from Britain and Ireland, via iRecord

description: This Stonefly dataset is part of the Plecoptera Recording Scheme. The dataset comprises records entered via iRecord and verified online.
Additional_information
DOI: 10.5061/dryad.6q573n621
title: Focal vs. faecal: Seasonal variation in the diet of wild vervet monkeys from observational and DNA metabarcoding data

description: 1. Assessing the diet of wild animals reveals valuable information about
 their ecology and trophic relationships that may help elucidate dynamic
 interactions in ecosystems and forecast responses to environmental
 changes. 2. Advances in molecular biology provide valuable research tools
 in this field. However, comparative empirical research is still required
 to highlight strengths and potential biases of different approaches.
 Therefore, this study compares environmental DNA and observational methods
 for the same study population and sampling duration. 3. We employed DNA
 metabarcoding assays targeting plant and arthropod diet items in 823
 faecal samples collected over 12 months in a wild population of an
 omnivorous primate, the vervet monkey (Chlorocebus pygerythrus). DNA
 metabarcoding data were subsequently compared to direct observations. 4.
 We observed the same seasonal patterns of plant consumption with both
 methods, however, DNA metabarcoding showed considerably greater taxonomic
 coverage and resolution compared to observations, mostly due to the
 construction of a local plant DNA database. We found a strong effect of
 season on variation in plant consumption largely shaped by the dry and wet
 seasons. The seasonal effect on arthropod consumption was weaker but
 feeding on arthropods was more frequent in spring and summer, showing
 overall that vervets adapt their diet according to available resources.
 The DNA metabarcoding assay outperformed also direct observations of
 arthropod consumption in both taxonomic coverage and resolution. 5.
 Combining traditional techniques and DNA metabarcoding data can therefore
 not only provide enhanced assessments of complex diets or reveal trophic
 interactions to the benefit of wildlife conservationists and managers but
 also opens new perspectives for behavioural ecologists studying whether
 diet variation in social species is induced by environmental differences
 or might reflect selective foraging behaviours.