cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.79cnp5hs7
title: Statistical data from: Cholinergic modulation of hippocampally mediated attention and perception

description: Attention to the relations between visual features modulates hippocampal
 representations. Moreover, hippocampal damage impairs discrimination of
 spatial relations. We explore a mechanism by which this might occur:
 modulation by the acetylcholine system. Acetylcholine enhances afferent
 input to the hippocampus and suppresses recurrent connections within it.
 This biases hippocampal processing toward environmental input, and should
 improve externally-oriented, hippocampally mediated attention and
 perception. We examined cholinergic modulation on an attention task that
 recruits the hippocampus. On each trial, participants viewed two images
 (rooms with paintings). On “similar room” trials, they judged whether the
 rooms had the same spatial layout from a different perspective. On
 “similar art” trials, they judged whether the paintings could have been
 painted by the same artist. On “identical” trials, participants simply had
 to detect identical paintings or rooms. We predicted that cholinergic
 modulation would improve performance on the similar room task, given past
 findings that hippocampal representations predicted, and hippocampal
 damage impaired, behavior on this task. To test this, nicotine cigarette
 smokers took part in two sessions: one before which they abstained from
 nicotine for 12 hours, and one before which they ingested nicotine in the
 past hour. Individual differences in expired breath carbon monoxide levels
 — a measure of how recently or how much someone smoked — predicted
 performance improvements on the similar room task. This finding provides
 novel support for computational models that propose that acetylcholine
 enhances externally oriented attentional states in the hippocampus.
description: All .rda R binary data files uploaded here were produced from our
 final run of the analysis code posted in this
 GitHub repository. The raw data (uploaded to the GitHub
 repository, not uploaded here) come from 50 participants completing two
 sessions of our attention task, one after not smoking cigarettes for the
 previous 12 hours, and one after smoking cigarettes within the last
 hour. These intermediate R data files include model outputs from Bayesian
 multilevel regression analyses using the rstanarm package, and
 bootstrap-resampled datasets for nonparametric analyses.
description: Please see the GitHub repository for the raw data, the data
 dictionary describing the raw data, and the R analysis code that produces
 these intermediate files. Note that the code was run
 without setting a random seed, so subsequent runs of the GitHub code on
 your local machine to reproduce our analyses from scratch should return
 values near, but not identical to, those in the files here.
DOI: 10.5061/dryad.hdr7sqvfd
title: Association of Angiotensin-II stimulating antihypertensive use and dementia risk: Post hoc analysis of the preDIVA trial

description: Objective: To assess whether angiotensin-II stimulating antihypertensives
 (thiazides, dihydropyridine calcium channel blockers, and angiotensin-1
 receptor blockers) convey a lower risk of incident dementia compared to
 angiotensin-II inhibiting antihypertensives (angiotensin-converting enzyme
 inhibitors, beta blockers, and non-dihydropyridine calcium channel
 blockers), in accordance with the ‘angiotensin hypothesis’. Methods: Cox
 regression analyses of incident dementia (and/or mortality as competing
 risk) during 6-8 years of follow-up, in a population sample of 1909
 non-demented community-dwelling individuals (54% women), aged 70-78 (mean:
 74.5 ±2.5) years. Results: After a median of 6.7 years of follow-up,
 dementia status was available for 1870 (98%) and mortality for 1904
 (&gt;99%) participants. Dementia incidence was 5.6% (27/480) in
 angiotensin-II stimulating, 8.2% (59/721) in angiotensin-II inhibiting,
 and 6.9% (46/669) in both antihypertensive type users. Adjusted for
 dementia risk factors including blood pressure and medical history,
 angiotensin-II stimulating antihypertensive users had a 45% lower incident
 dementia rate (HR=0.55, 95%CI=0.34-0.89) without excess mortality
 (HR=0.86, 95%CI=0.64-1.16), and individuals using both types had a
 non-significant 20% lower dementia rate (HR=0.80, 95%CI=0.53-1.20) without
 excess mortality (HR=0.97, 95%CI=0.76-1.24), compared to angiotensin-II
 inhibiting antihypertensive users. Results were consistent for subgroups
 based on diabetes and stroke history, but may be specific for individuals
 without a history of cardiovascular disease. Conclusions: Users of
 angiotensin-II stimulating antihypertensives had lower dementia rates
 compared to angiotensin-II inhibiting antihypertensive users, supporting
 the ‘angiotensin hypothesis’. Confounding by indication must be examined
 further, although sub-analyses suggest this did not influence results. If
 replicated, dementia prevention could become a compelling indication for
 older individuals receiving antihypertensive treatment.
DOI: 10.5061/dryad.59zw3r24j
title: Phylogenetic relationships and divergence dating of Mantodea using mitochondrial phylogenomics

description: Mantodea is a predatory insect group, its members occupying a diverse
 array of widely distributed habitats. Praying mantis species utilize
 hunting strategies including remarkable mimicry and unique camouflage for
 hiding from natural enemies while catching their prey. The emergence of a
 “cyclopean ear” in mantises is thought to be a morphological innovation of
 the group, and an “arms race” with echolocating bats is one of the
 hypotheses put forward to account for the emergence of the mantis ear from
 a coevolutionary perspective. However, this hypothesis has not been
 rigorously tested because of a lack of robust higher‐level phylogeny and a
 detailed chronogram of Mantodea. Previous phylogenetic studies found an
 incongruence between traditional classification and molecular
 phylogenetics due to the convergent evolution of various ecomorphic
 strategies of the lineage. Here, we performed a comprehensive phylogenetic
 analysis of Mantodea based on data from 61 mitogenomes. Our analyses
 showed that the monophyly of Acanthopidae, Haaniidae, Nanomantidae,
 Miomantidae and Mantidea was supported. The newly updated Gonypetidae were
 paraphyletic, whereas Eremiaphilidae, Deroplatyidae and Toxoderidae were
 polyphyletic. Our molecular dating analyses inferred that Spinomantodea
 originated at ca. 149 Ma (Late Jurassic), whereas the origin of hearing
 mantises (Cernomantodea) was inferred as Early Cretaceous (119 Ma, 95% CI:
 110–129 Ma). The molecular dating results indicated that the hearing organ
 in mantises did not arise in response to bat predation. Our study provides
 a robust framework for further evolutionary comparative studies of
 mantises.
description: This dataset contains nucleotide matrices, phylogenetic trees and
 chronogram of the research "Phylogenetic relationships and divergence
 dating of Mantodea using mitochondrial phylogenomics". The phylip
 format protein-coding sequence file (cd12,.phy, cdsrna.phy, and
 cdsrna_mcmc.phy), phylogenetic topology for ML and BI analyses
 (cdsrna_ML.tre & rnacds_BI.nex.con.tre), constrained tree file for
 molecular dating (analysis1-4_mcmc.tre) and ctl file in PAML mcmctree
 analysis (analysis1_mcmctree.ctl) are provided in the data set.
DOI: 10.5061/dryad.bcc2fqz94
title: C porosus genotype data

description: We collected 714 tissue samples of non-captive saltwater crocodiles
 Crocodylus porosus from Australia and its neighbouring countries and got
 them genotyped by Diversity Arrays Technology (Canberra,
 Australia) between 2016 and 2019. The folder contains two files
 named 'Report_DCroc19-4196_4_moreOrders_SNP_mapping_2.csv' and
 'IDpop_sample_data_.csv'. The former contains the
 single-nucleotide polymorphism (SNP) data and latter has attributes
 (population ID, GPS coordinates, species, country) of each sample.
description: DNA extraction and genotyping were conducted at Diversity Arrays
 Technology (Canberra, Australia) using the DArTseq approach (Kilian et
 al., 2012). DArTseq uses genome complexity reduction and NGS approaches
 conceptually similar to RADseq, in this case based around a
 <i>SphI</i> enzyme digestion of genomic DNA and Illumina HiSeq
 2500 sequencing. We ran 30% of samples twice as technical replicates to
 assess the repeatability of single-nucleotide polymorphism (SNP) calls.
 These are pre-filtering data for analyses.
 Reference Kilian, A., Wenzl, P., Huttner, E.,
 Carling, J., Xia, L., Blois, H., … Uszynski, G. (2012). Diversity Arrays
 Technology: a generic genome profiling technology on open platforms. In
 <i>Methods in Molecular Biology</i>. <i>Data Production
 and Analysis in Population Genomics</i> (pp. 67–89). doi:
 10.1007/978-1-61779-870-2_5
DOI: 10.5061/dryad.6wwpzgmvp
title: Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity

description: Adaptation to different environments can directly and indirectly generate
 reproductive isolation between species. Bluefin killifish (Lucania goodei)
 and rainwater killifish (L. parva) are sister species that have diverged
 across a salinity gradient and are reproductively isolated by habitat,
 behavioral, extrinsic, and intrinsic postzygotic ­­isolation. We asked if
 salinity adaptation contributes indirectly to other forms of reproductive
 isolation via linked selection and hypothesized that low recombination
 regions, such as sex chromosomes or chromosomal rearrangements, might
 facilitate this process. We conducted QTL mapping in backcrosses between
 L. parva and L. goodei to explore the genetic architecture of salinity
 tolerance, behavioral isolation, and intrinsic isolation. We mapped traits
 relative to a chromosome that has undergone a centric fusion in L. parva
 (relative to L. goodei). We found that the sex locus appears to be male
 determining (XX-XY), was located on the fused chromosome, and was
 implicated in intrinsic isolation. QTL associated with salinity tolerance
 were spread across the genome and did not overly co-localize with regions
 associated with behavioral or intrinsic isolation. This preliminary
 analysis of the genetic architecture of reproductive isolation between
 Lucania species does not support the hypothesis that divergent natural
 selection for salinity tolerance led to behavioral and intrinsic isolation
 as a byproduct. Combined with previous studies in this system, our work
 suggests that adaptation as a function of salinity contributes to habitat
 isolation and that reinforcement may have contributed to the evolution of
 behavioral isolation instead, possibly facilitated by linkage between
 behavioral isolation and intrinsic isolation loci on the fused chromosome.
description: This dataset include the R markdown files used for QTL mapping
 and statistical analyses of genotype frequencies along with all data files
 necessary for those analyses.
DOI: 10.5061/dryad.fj6q573r9
title: The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)

description: Vision is a crucial sense for the evolutionary success of many animal
 groups. In this work, we explore the diversity of opsins in over 100
 amphipod (Crustacea: Amphipoda) species with sequenced transcriptomes and
 concluded that it is generally restricted to middle wavelength-sensitive
 (MWS) and long wavelength-sensitive (LWS) opsins. We found that multiple
 lineages of amphipods, including two lineages from the deep and ancient
 Lake Baikal in Eastern Siberia, lost the expression of MWS opsins. We
 provide reassembled transcriptomes and list of opsin sequences.
description: Raw sequencing reads were downloaded from the sequence read
 archive (SRA) NCBI database with the fastq-dump command from NCBI SRA
 toolkit v2.9.2 (http://ncbi.github.io/sra-tools/). Data quality control
 was performed with<br> FastQC
 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) v0.11.8 and
 summarized with MultiQC v1.2. Read trimming was performed with trimmomatic
 v0.36 in the pair-end mode. Transcriptome reassemblies were obtained with
 Trinity v2.8.5 or rnaSPAdes v3.13.1. Assembly completeness was estimated
 with BUSCO v3.0.2.
DOI: 10.5061/dryad.2bvq83bn0
title: Inferring individual fate from aquatic acoustic telemetry data

description: Acoustic telemetry has become a popular means of obtaining individual
 behavioural data from a wide array of species in marine and freshwater
 systems. Fate information is crucial to understand important aspects of
 population dynamics such as mortality, predation or dispersal rates. Here
 we present a method to infer individual fate from acoustic telemetry
 arrays of receivers with overlapping detection ranges. Our method depends
 exclusively on information on animal movements and the characteristics and
 configuration of the telemetry equipment. By answering a limited number of
 simple questions, our method identifies six different fates: tagging
 mortality, natural mortality, fishing mortality, predation, dispersal and
 survival. Applying the method to a cod telemetry dataset, we were able to
 determine fate for 97% of the individuals. We validate the results using
 several external sources of information, such as recaptures from fishers
 and control fish with known fate. The method is readily applicable to a
 wide array of species with minimal adjustments, expanding the range of
 hypotheses that can be tested using telemetry data.
description: There are three types of data: - Detection
 data: 1-3 files per fish - Fish information data:
 includes all the relevant information for each individual, e.g. when it
 was tagged, transmitter type, etc... - Receiver array
 information: includes the location of the receivers
description: <b>Metadata of the
 dataset:</b> Villegas Ríos, David et al.
 (2021), Inferring individual fate from aquatic acoustic telemetry data,
 Dryad, Dataset, https://doi.org/10.5061/dryad.2bvq83bn0   <b>Detections data (all files starting with 9002 or 9004):</b> Date and time: date and time of detection Receiver: name of the receiver Transmitter: ID of the transmitter Transmitter name: empty Transmitter serial: serial number of the transmitter Sensor value: depth measure Sensor units: units of the depth measure (meters) Station name: name of the station where the receiver is places Latitude: latitude of the station Longitude: longitude of the station <b>fishinformation.csv</b>: all the columns are self-explained except the following: MinDelaySec: minimum delay of the transmitter, in seconds. MaxDelaySec: maximum delay of the transmitter, in seconds. Release_lat_geo: release latitude, in geographic coordinates. Release_lon_geo: release longitude, in geographic coordinates. <b>array_information.csv</b>: all the columns are self-explained except the following: deploymentdatetime_timestamp: date of deployment of any particular receiver. recoverydatetime_timestamp: date of recovery of any particular receiver. lat_geo: latitude of the receiver location, in geographic coordinates. lon_geo: longitude of the receiver location, in geographic coordinates. lat_utm: latitude of the receiver location, in UTM. lon_utm: longitude of the receiver location, in UTM
DOI: 10.5061/dryad.prr4xgxj6
title: An investigation of ZZ/ZW and XX/XY sex determination systems in North African catfish (Clarias gariepinus)

description: Sex-specific loci are powerful tools for identifying sex determination
 systems. They offer a molecular biotechnological approach for producing
 all‐male or all-female fish for commercial breeding. The North African
 catfish has been widely adopted for aquaculture, because its superior
 growth and disease resistance render the species suitable for
 hybridization with other catfish, to improve the productivity and quality
 of fish meat. North African catfish have either a ZZ/ZW or XX/XY sex
 determination system. Here, we investigate and characterize these systems
 using high-throughput genome complexity reduction sequencing. This
 approach was effective for identifying sex-specific loci with both
 single-nucleotide polymorphisms (SNPs) and restriction fragment
 presence/absence (PA) markers in 30 phenotypic sex assignments of North
 African catfish. In total, 41 male-linked loci met the criteria of
 moderately sex-linked loci (70:30, male:female; 80:20, male:female). By
 contrast, only 25 female-linked loci were detected from moderately
 sex-linked loci, and no perfectly male- or female-specific sex-linked loci
 were observed. Several male-linked loci were partially homologous to
 transposable element and functional genes, and most also showed partial
 homology with several amniote sex chromosomal linkages. This suggests that
 an ancestral amniote super-sex chromosome with overlaps of partial sex
 chromosomal linkages was also found in teleosts, and that the male
 heterogametic XX/XY sex determination system should exist in North African
 catfish. The putative Y chromosome is young and the non-recombination
 region is highly cryptic. In addition, the ZW type of North African
 catfish exhibits heteromorphic sex chromosomes, whereas the two other
 groups of North African catfish have different sex determination systems.
 Thus, turnover of sex chromosome systems might have occurred
 stochastically in ancestral homomorphic sex chromosomes. The XY group has
 been introduced into Thailand for commercial breeding. This approach using
 sex-specific loci provides a solid baseline for revealing sex
 determination mechanisms and identify potential sex determination regions
 in catfish, allowing further investigation of genetic improvements in
 breeding programs.
description: Adult individuals, 15 male and 15 female African catfish, were
 sampled. The individuals were selected randomly from a large breeding
 stock (Kasetsart University, Bangkok, Thailand) to avoid the possibility
 of a high incidence of siblings in our genetic pool. The sex of each
 individual was determined based on external morphology and internal
 examination of gonadal morphology (Esmaeili et al., 2017; Ponjarat et al.,
 2019). The dorsal fins were then removed for DNA extraction. The following
 analyses were performed: total genomic DNA, DArT sequencing and
 genotyping, marker selection and DArT sequencing analysis, comparison of
 potential sex-linked loci, and homology searching
DOI: 10.5061/dryad.fqz612jq9
title: Data from: Experimental assessment of biotic and abiotic filters driving community composition

description: Species occurrence in a site can be limited by both the abiotic
 environment and biotic interactions. These two factors operate in concert,
 but their relative importance is often unclear. By experimentally
 introducing seeds or plants into competition-free gaps or into the intact
 vegetation, we can disentangle the biotic and abiotic effects on plant
 establishment. We established a seed sowing/transplant experiment in three
 different meadows. Species were introduced, as seeds and pre-grown
 transplants, into competition-free gaps and the intact vegetation. They
 included 12 resident plants from the locality and 18 species typical for
 different habitats. Last two years, gaps were overgrown with vegetation
 from surrounding plants and we observed the competitive exclusion of our
 focal plants. We compared plant survival with the expected occurrence in
 target locality (Beals index). Many of the species with habitat
 preferences different from our localities were able to successfully
 establish from seeds and grow in the focal habitat if competition was
 removed. They included species typical for much drier conditions. These
 species were thus not limited by the abiotic conditions, but by
 competition. Pre-grown transplants were less sensitive to competition,
 when compared to seedlings germinated from seeds. Beals index
 significantly predicted both species success in gaps and the ability to
 withstand competition. Survival in a community is dependent on the
 adaptation to both the abiotic environment and biotic interactions.
 Statistically significant correlation coefficients of the ratio of
 seedling survival in vegetation and gaps with Beals index suggest the
 importance of biotic interactions as a determinant of plant community
 composition. To disentangle the importance of abiotic and biotic effect on
 plant establishment, it is important to distinguish between species pool
 as a set of species typically found in given community type (determined by
 Beals index) and a set of species for which the abiotic conditions are
 suitable.
DOI: 10.5061/dryad.3ffbg79fs
title: Efficacy of high-intensity aerobic exercise on brain MRI measures in multiple sclerosis

description: Objective: To determine whether 24 weeks of high-intensity progressive
 aerobic exercise (PAE) affects brain MRI measures in people with multiple
 sclerosis (MS). Methods: We conducted a randomized, controlled, phase 2
 trial (with a crossover follow-up) including an exercise group (supervised
 PAE followed by self-guided physical activity) and a waitlist group
 (habitual lifestyle followed by supervised PAE). Mildly to severely
 impaired MS patients aged 18-65 years were randomized (1:1). The primary
 outcome was percentage brain volume change (PBVC) after 24 weeks, analyzed
 using the intention-to-treat principle. Results: Eighty-six participants
 were recruited. PBVC did not change over the intervention period (mean
 between-group change +0.12%, 95% CI -0.27;0.51, p=0.55). In contrast, gray
 matter parenchymal fraction (+1.13 percentage points, 0.00;2.26, p=0.05;
 did not remain after Bonferroni correction), cardiorespiratory fitness
 (+3.5 mL O2/min/kg, 2.0;5.1, p&lt;0.01), and annualized relapse rate
 (p&lt;0.01) improved in the exercise group. Conclusion: These findings
 do not support a neuroprotective effect of PAE in terms of total brain
 atrophy in people with MS. Oppositely, PAE-induced improvements in
 cardiorespiratory fitness was accompanied by a potential neuroprotective
 effect in terms of gray matter parenchymal fraction and a relapse rate of
 zero. While these exploratory findings cautiously support PAE as a
 potential adjunct disease-modifying treatment in MS, further
 investigations are warranted. ClinicalTrials.gov identifier: NCT02661555
 Level of evidence: This study provides level I evidence that 24 weeks of
 high-intensity PAE did not elicit disease-modifying effects in PBVC in
 people with MS. Exploratory analyses showed that PAE reduce relapse rate
 and may preserve gray matter brain volume.