cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ffbg79cst
title: Different genes are recruited during convergent evolution of pregnancy and the placenta

description: The repeated evolution of the same traits in distantly related groups
 (convergent evolution) raises a key question in evolutionary biology: do
 the same genes underpin convergent phenotypes? Here, we explore one such
 trait, viviparity (live birth), which, qualitative studies suggest, may
 indeed have evolved via genetic convergence. There are 150 independent
 origins of live birth in vertebrates, providing a uniquely powerful system
 to test the mechanisms underpinning convergence in morphology, physiology,
 and/or gene recruitment during pregnancy. We compared transcriptomic data
 from eight vertebrates (lizards, mammals, sharks) that gestate embryos
 within the uterus. Since many previous studies detected qualitative
 similarities in gene use during independent origins of pregnancy, we
 expected to find significant overlap in gene use in viviparous taxa.
 However, we found no more overlap in uterine gene expression associated
 with viviparity than we would expect by chance alone. Each viviparous
 lineage exhibits the same core set of uterine physiological functions.
 Yet, contrary to prevailing assumptions about this trait, we find that
 none of the same genes are differentially expressed in all viviparous
 lineages, or even in all viviparous amniote lineages. Therefore, across
 distantly related vertebrates, different genes have been recruited to
 support the morphological and physiological changes required for
 successful pregnancy. We conclude that redundancies in gene function have
 enabled the repeated evolution of viviparity through recruitment of
 different genes from genomic “toolboxes”, which are uniquely constrained
 by the ancestries of each lineage.
description: These files are the Supplementary Materials for our manuscript
 submission: "Different genes are recruited during convergent
 evolution of pregnancy and the placenta". Briefly, transcriptomes
 (both <em>de novo </em>and pre-existing) from eight
 vertebrates (lizards, mammals, shark) were compared to determine
 gene-expression changes during pregnancy. We found that, despite broad
 physiological and morphological convergence, there was next to no
 convergence in gene recruitment during pregnancy. A more in-depth
 explanation of methods can be found within the Supplementary
 Methods.
description: This upload to Dryad contains all files supplementary to our
 submission to PNAS. There are: 3
 supplementary figures (.pdf) 13 supplementary tables
 (.pdf; .xlsx) A "Supplementary Materials"
 document (.docx) with supplementary figure captions 
 This upload also contains: All de
 novo transcriptome assemblies The raw counts for each
 sample from each species The code necessary to
 replicate the DE and GO analysis results (and associated accessory
 metadata files) The code for overlap analyses, and
 associated metadata files
DOI: 10.5061/dryad.wdbrv15mq
title: Human Responses to Visually Evoked Threat

description: Vision is the primary sense humans use to evaluate and respond to threats.
 Understanding the biological underpinnings of the human threat response
 has been hindered by lack of realistic in-lab threat paradigms. We
 established an immersive Virtual Reality (VR) platform to simultaneously
 measure behavior, physiological state and neural activity from the human
 brain using chronically implanted electrodes. Subjects with high anxiety
 showed increased visual scanning in response to threats as compared to
 healthy controls. In both healthy and anxious subjects, the amount of
 scanning behavior correlated with the magnitude of physiological arousal,
 suggesting that visual scanning behavior is directly linked to internal
 state. Intracranial electroencephalography (iEEG) recordings from three
 subjects suggested that high frequency gamma activity in the insula
 positively correlates with physiological arousal induced by visual threats
 and that low frequency theta activity in the orbitofrontal cortex (OFC)
 negatively correlates with physiological arousal induced by visual
 threats. These findings reveal a key role of eye movements and suggest
 that distinct insula and OFC activation dynamics may be important for
 detecting and adjusting human stress in response to visually perceived
 threats.  
description: This dataset contains gaze, peripheral physiology and iEEG neural
 recordings from healthy and anxious adult human subjects who experienced a
 simulated heights stimulus in Virtual Reality. The experimental design,
 including explanation of metrics of interest, is detailed in Yilmaz Balban
 et al. (2020) <i>Current Biology</i>.
 Please see the "Read me for STARS" file on the attached
 link for a complete description of the data set and the analysis
 scripts.
DOI: 10.57760/sciencedb.psych.00980
title: CSPTP-GA Data
title: 大学生时间贫困感量表简化研究数据集

description: This dataset is for review and use by reviewers. The open use of this dataset will be unlocked after the author's paper is officially published; The dataset includes all the raw data, data processing procedures, and R code of the paper; The dataset is divided into three parts: the training set for genetic algorithms, the validation set, and the empirical dataset; The research subjects of the three datasets are Chinese young people aged 18-35, with educational backgrounds ranging from college, undergraduate, and graduate. The survey period is from 2024 to 2025; The content of the scale includes the College Students' Time Poverty Perception Scale (CSPTP), State Anxiety Inventory (SSAI), and the Simplified Scale for College Students' Time Poverty Perception (CSPTP-GA) developed through research; All data have good reliability and validity, and have passed the CMB test. 
description: This dataset is for review and use by reviewers. The open use of this dataset will be unlocked after the author's paper is officially published; The dataset includes all the raw data, data processing procedures, and R code of the paper; The dataset is divided into three parts: the training set for genetic algorithms, the validation set, and the empirical dataset; The research subjects of the three datasets are Chinese young people aged 18-35, with educational backgrounds ranging from college, undergraduate, and graduate. The survey period is from 2024 to 2025; The content of the scale includes the College Students' Time Poverty Perception Scale (CSPTP), State Anxiety Inventory (SSAI), and the Simplified Scale for College Students' Time Poverty Perception (CSPTP-GA) developed through research; All data have good reliability and validity, and have passed the CMB test.
DOI: 10.5061/dryad.bcc2fqzb8
title: cGAS suppresses genomic instability as a decelerator of replication forks

description: The cyclic GMP-AMP synthase (cGAS), a sensor of cytosolic DNA, is critical
 for the innate immune response. Here, we show that loss of cGAS in
 untransformed and cancer cells results in uncontrolled DNA replication,
 hyperproliferation, and genomic instability. While the majority of cGAS is
 cytoplasmic, a fraction of cGAS associates with chromatin. cGAS interacts
 with replication fork proteins in a DNA binding–dependent manner,
 suggesting that cGAS encounters replication forks in DNA. Independent of
 cGAMP and STING, cGAS slows replication forks by binding to DNA in the
 nucleus. In the absence of cGAS, replication forks are accelerated, but
 fork stability is compromised. Consequently, cGAS-deficient cells are
 exposed to replication stress and become increasingly sensitive to
 radiation and chemotherapy. Thus, by acting as a decelerator of DNA
 replication forks, cGAS controls replication dynamics and suppresses
 replication-associated DNA damage, suggesting that cGAS is an attractive
 target for exploiting the genomic instability of cancer cells.
description:  BJ WT and cGAS KO cells were harvested by trypsinization,
 centrifuged, and rinsed once with ice-cold PBS. To- tal RNA was extracted
 using the PureLink RNA Mini Kit (Invitrogen), according to the
 manufacturer's instructions. RNAs isolated from all fibroblast lines
 (1 ug per sample) were reverse-transcribed to generate sequencing
 libraries using the TruSeq Stranded Total RNA Library Prep Kit (Illumina)
 and sequenced by HiSeq2000 (Illumina) (Novogene Corporation, 8801 Folsom
 Blvd., Suite 290, Sacramento, CA). Approximately 27 million to 39 million
 sequencing reads were generated for each fibroblast mRNA preparation, and
 81 to 94% of fragments were mapped by both ends to the human genome (hg19)
 using TopHat (version 2.0.7) and bowtie2 (version 2.1.0).
 GFP-U2OS cells treated with or without
 H<sub>2</sub>O<sub>2</sub> for 24h were collected.
 Lysates were cleared by centrifugation at 13,000 rpm for 15 min and
 incubated with G-Sepharose protein beads (GE Healthcare Bio-Sciences)
 attached with and without GFP antibody overnight at<br> 4°C on a
 rocking platform. Beads were then collected by centrifugation at 8200 rpm
 for 5 s at 4°C, extensively washed in lysis buffer, and resuspended in SDS
 gel loading buffer. The proteins were separated on a 10%
 SDS–polyacrylamide gel then for the sequence.
DOI: 10.5061/dryad.xksn02vdz
title: The phylogeny and function of gut microbiota associated with host geographic/genetic distance and biological characteristics (data S1)

description: Symbiotic microbiomes play important roles in hosts’ adaptation and
 evolution. Here, the gut bacterial communities in Cephalcia chuxiongica, a
 key pest of pines in China, were studied for the first time by using 16S
 rRNA amplicon sequencing. The composition of gut bacterial communities
 differed in different C. chuxiongica geographic populations, while the
 various microbes performed similar functions, suggesting some kinds of
 functional complementation. The predicted functional profiles of microbes
 indicated that most of identified KEGG Pathways were shared by different
 populations, in which metabolism was the most dominant functional pathway.
 Moreover, the function of major microbes associated with host dietary
 specialization (pine needles), such as cellulose degradation. All samples
 contained abundant Wolbachia, which may play important roles on the
 parthenogenesis of C. chuxiongica. The high abundances of Serratia and
 Sphingomonas in samples suggest that gut microbiota may crucial for the
 long-term larval diapause in C. chuxiongica. Interestingly, this study
 found that the phylogeny and diversity of gut microbiota correlated to
 host geographic/genetic distance, i.e., the microbiota was more similar as
 the geographic/genetic distance decreased, and vice versa. Therefore, the
 synergy of environmental and host factors appears to be the main force
 shaping the structure and variability of gut microbiota and likewise, gut
 microbiota may exert a significant effect on its host by shaping host
 biological characters, suggesting some kinds of extraordinary symbiosis
 and coevolution. These results demonstrate the important contribution of
 gut microbiota and provide a sound foundation for developing control
 strategies for this pest.
DOI: 10.15468/dl.55brfj
title: Occurrence Download

description: A dataset containing 873 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acestrorhynchus falcirostris"
 ]
}

 The dataset includes 873 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002646-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dncjsxkxq
title: A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus)

description: A high-quality genome assembly of a mature female individual of striped
 catfish was generated by integration of short reads from an Illumina Hiseq
 Xten platform, long reads from a Nanopore platform, and Hi-C sequencing
 data. The Illumina short reads were sequenced at 60 X coverage, while the
 Nanopore long reads covered 85 X of the genome. This assembled genome is
 742.6 Mb in length, with a contig N50 of 3.5 Mb and a scaffold N50 of 29.5
 Mb, of which a total of 731.7 Mb reads (98.5%) were anchored on 30
 pseudo-chromosomes. Among the totally searched 4,584 BUSCO groups in the
 popular actinopterygii_odb9 database, 4,279 (93.3%) BUSCO core genes were
 completely identified.
DOI: 10.5061/dryad.f7m0cfxtp
title: Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages

description: Insects and other terrestrial invertebrates are declining in species
 richness and abundance. This includes the invertebrates associated with
 herbivore dung, which have been negatively affected by grazing abandonment
 and the progressive loss of large herbivores since the Late Pleistocene.
 Importantly, traditional monitoring of these invertebrates is
 time-consuming and requires considerable taxonomic expertise, which is
 becoming increasingly scarce. In this study, we investigated the potential
 of environmental DNA (eDNA) metabarcoding of cow dung samples for
 biomonitoring of dung-associated invertebrates. From eight cow pats we
 recovered eDNA from 12 orders, 29 families, and at least 54 species of
 invertebrates (mostly insects), representing several functional groups.
 Furthermore, species compositions differed between the three sampled
 habitats of dry grassland, meadow, and forest. These differences were in
 accordance with the species’ ecology; for instance, several species known
 to be associated with humid conditions or lower temperatures were found
 only in the forest habitat. We discuss potential caveats of the method, as
 well as directions for future study and perspectives for implementation in
 research and monitoring.
DOI: 10.5061/dryad.6t1g1jwxg
title: Supplemental Data to: Mediterranean Diet, Alzheimer Disease Biomarkers, and Brain Atrophy in Old Age

description: Objective: To determine whether following a Mediterranean-like diet (MeDi)
 relates to cognitive functions and in vivo biomarkers for Alzheimer
 disease (AD), we analyzed cross-sectional data from the German
 DZNE-Longitudinal Cognitive Impairment and Dementia Study. Method: The
 sample (n = 512, mean age 69.5 ± 5.9 years) included 169 cognitively
 normal participants and individuals at higher AD risk (53 with relatives
 with AD, 209 with subjective cognitive decline, and 81 with mild cognitive
 impairment). We defined MeDi adherence according to the food frequency
 questionnaire. Brain volume outcomes were generated via voxel-based
 morphometry on T1-MRI, and cognitive performance was assessed with an
 extensive neuropsychological battery. AD-related biomarkers
 (β-amyloid42/40 [Aβ42/40] ratio, phosphorylated tau 181 [pTau181]) in CSF
 were assessed in n = 226 individuals. We analyzed the 
 associations between MeDi and outcomes with linear regression models
 controlling for several covariates. In addition, we applied
 hypothesis-driven mediation and moderation analysis. Results: Higher MeDi
 adherence related to larger mediotemporal gray matter volume (p &lt;
 0.05 familywise error corrected), better memory (β ±SE= 0.03±0.02; p =
 0.038), and less amyloid (Aβ42/40 ratio, β ± SE = 0.003 ± 0.001; p =
 0.008) and pTau181 (β ± SE = −1.96 ± 0.68; p = 0.004) pathology.
 Mediotemporal volume mediated the association between MeDi and memory (40%
 indirect mediation). Finally, MeDi favorably moderated the associations
 among Aβ42/40 ratio, pTau181, and mediotemporal atrophy. Results were
 consistent correcting for APOE-e4 status.   Conclusion: Our
 findings corroborate the view of MeDi as a protective factor against
 memory decline and mediotemporal atrophy. They suggest that these
 associations might be explained by a decrease of amyloidosis and tau
 pathology. Longitudinal and dietary intervention studies should further
 examine this conjecture and its treatment implications.
DOI: 10.5061/dryad.d51c5b01s
title: Data from: Cretaceous origins of the vibrotactile bill-tip organ in birds

description: Some probe-foraging birds locate their buried prey by detecting mechanical
 vibrations in the substrate using a specialised tactile bill-tip organ
 comprising mechanoreceptors embedded in densely clustered pits in the bone
 at the tip of their beak. This remarkable sensory modality is known as
 “remote-touch”, and the associated bill-tip organ is found in
 probe-foraging taxa belonging to both the paleognathous (in kiwi) and
 neognathous (in ibises and shorebirds) clades of modern birds.
 Intriguingly, a structurally similar bill-tip organ is also present in the
 beaks of extant, non-probing paleognathous birds (e.g. emu and ostriches)
 that do not use remote-touch. By comparison with our comprehensive sample
 representing all orders of extant modern birds (Neornithes), we provide
 evidence that the lithornithids (the most basal known paleognathous birds
 which evolved in the Cretaceous period) had the ability to use
 remote-touch. This finding suggests that the occurrence of the “vestigial”
 bony bill-tip organ in all modern non-probing paleognathous birds
 represents a plesiomorphic condition. Furthermore, our results show that
 remote-touch probe-foraging evolved very early among the Neornithes and it
 may even have predated the paleognathous-neognathous divergence. We
 postulate that the tactile bony bill-tip organ in Neornithes may have
 originated from other snout tactile specializations of their non-avian
 theropod ancestors.
DOI: 10.5061/dryad.wh70rxwm5
title: Body mass and hibernation microclimate may predict bat susceptibility to white-nose syndrome

description: In multi-host disease systems, differences in mortality between species
 may reflect variation in host physiology, morphology, and behavior. In
 systems where the pathogen can persist in the environment, microclimate
 conditions, and the adaptation of the host to these conditions, may also
 impact mortality. White-nose syndrome is an emerging disease of
 hibernating bats caused by an environmentally persistent fungus,
 Pseudogymnoascus destructans. We assessed the effects of body mass, torpid
 metabolic rate, evaporative water loss, and hibernaculum temperature and
 water vapor deficit on predicted overwinter survival of bats infected by
 P. destructans. We used a hibernation energetics model in an
 individual-based model framework to predict the probability of survival of
 nine bat species at eight sampling sites across North America. The model
 predicts time until fat exhaustion as a function of species-specific host
 characteristics, hibernaculum microclimate, and fungal growth. We fit a
 linear model to determine relationships with each variable and predicted
 survival and semi-partial correlation coefficients to determine the major
 drivers in variation in bat survival. We found host body mass and
 hibernaculum water vapor deficit explained over half of the variation in
 survival with white-nose syndrome across species. As previous work on the
 interplay between host and pathogen physiology and the environment has
 focused on species with narrow microclimate preferences, our view on this
 relationship is limited. Our results highlight some key predictors of
 interspecific survival among western bat species and provide a framework
 to assess impacts of white-nose syndrome as the fungus continues to spread
 into western North America.
DOI: 10.3886/e240883v2
title: ECIN Relication Package for "Placebo Zones in Discontinuity-Based Designs: Estimation, Inference, and Implementation"

description: We propose a new model-selection algorithm for Regression Discontinuity Design and related estimators. The performance of candidate models is assessed within a `placebo zone' of the running variable. Candidate models can differ by bandwidth and other choice parameters. We outline (restrictive) sufficient conditions under which the approach is asymptotically optimal, and then show the approach also performs favorably under more general conditions in Monte Carlo simulations, including simulations calibrated to well-known real-world applications. We also propose a new randomization inference procedure which draws on the placebo estimates. Our Stata commands implement the procedure and compare its performance to other approaches.
DOI: 10.5061/dryad.tx95x69wj
title: Novel Asaia bogorensis signal sequences for Plasmodium inhibition in Anopheles stephensi

description: Mosquitoes vector many pathogens that cause human disease, such as malaria
 that is caused by parasites in the genus Plasmodium. Current strategies to
 control vector-transmitted diseases are hindered by mosquito and pathogen
 resistance, so research has turned to altering the microbiota of the
 vectors. In this strategy, called paratransgenesis, symbiotic bacteria are
 genetically modified to affect the mosquito’s phenotype by engineering
 them to deliver antiplasmodial effector molecules into the midgut to kill
 parasites. One paratransgenesis candidate is Asaia bogorensis, a
 Gram-negative, rod-shaped bacterium colonizing the midgut, ovaries, and
 salivary glands of Anopheles sp. mosquitoes. However, common secretion
 signals from E. coli and closely-related species do not function in Asaia.
 Here, we report evaluation of 20 native Asaia N-terminal signal sequences
 predicted from bioinformatics for their ability to mediate increased
 levels of antiplasmodial effector molecules directed to the periplasm and
 ultimately outside the cell. We tested the hypothesis that by increasing
 the amount of antiplasmodials released from the cell we would also
 increase parasite killing power. We scanned the Asaia bogorensis SF2.1
 genome to identify signal sequences from extra-cytoplasmic proteins and
 fused these to the reporter protein alkaline phosphatase. Six signals
 resulted in significant levels of protein released from the Asaia
 bacterium. Three signals were successfully used to drive the release of
 the antimicrobial peptide, scorpine.  Further testing in
 mosquitoes demonstrated that these three Asaia strains were able to
 suppress the number of oocysts formed after a blood meal containing P.
 berghei to a significantly greater degree than wild-type Asaia, although
 prevalence was not decreased beyond levels obtained with a previously
 isolated siderophore receptor signal sequence. We interpret these results
 to indicate that there is a maximum level of suppression that can be
 achieved when the effectors are constitutively driven due to stress on the
 symbionts. This suggests that simply increasing the amount of
 antiplasmodial effector molecules in the midgut is insufficient to create
 superior paratransgenic bacterial strains and that symbiont fitness must
 be considered as well.
DOI: 10.15468/dl.da8wvy
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Numenius madagascariensis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Korea, Republic of",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 169 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002648-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.