cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13133/uniroma1/ig6lzl/nn0mqt
title: al-Fajr_1-16_1990_ANewTestimonyRegardingtheTorture_OCR.pdf

description: :unav
DOI: 10.5061/dryad.sf7m0cg4m
title: Land use impacts on parasitic infection: A cross-sectional epidemiological study on the role of irrigated agriculture in schistosome infection in a dammed landscape

description: Background: Water resources development promotes agricultural expansion
 and food security. But are these benefits offset by increased infectious
 disease risk? Dam construction on the Senegal River in 1986 was followed
 by agricultural expansion and increased transmission of human
 schistosomes. Yet the mechanisms linking these  processes at the
 individual and household levels remain unclear. We investigated the
 association between household land use and schistosome infection in
 children. Methods: We analyzed cross-sectional household survey data (n =
 655) collected in 16 rural villages in August 2016 across demographic,
 socio-economic and land use dimensions, which were matched to S.
 haematobium (n = 1232) and S. mansoni (n = 1222) infection data collected
 from school-aged children. Mixed effects regression determined the
 relationship between irrigated area and schistosome infection presence and
 intensity. Results: Controlling for socio-economic and demographic risk
 factors, irrigated area cultivated by a household was associated with an
 increase in the presence of S. haematobium infection (odds ratio [OR] =
 1.14; 95% confidence interval [95% CI]: 1.03, 1.28) but not S. mansoni
 infection (OR = 1.02; 95% CI: 0.93, 1.11). Associations between infection
 intensity and irrigated area were positive but imprecise (S. haematobium:
 rate ratio [RR] = 1.05; 95% CI: 0.98, 1.13, S. mansoni: RR = 1.09; 95% CI:
 0.89, 1.32). Conclusion: Household engagement in irrigated agriculture
 increases individual risk of S. haematobium but not S. mansoni infection.
 Increased contact with irrigated landscapes likely drives exposure, with
 greater impacts on households relying on agricultural livelihoods.
DOI: 10.5061/dryad.ffbg79css
title: Code and scripts used to generate results for: Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency

description: The danger posed by infectious agents necessitates the development of new
 tools to both predict and manage emerging diseases. One promising approach
 is the development of recombinant viral vaccines that are themselves
 infectious. Transmissible vaccines have been shown to greatly reduce the
 effort required to control the spread of zoonotic pathogens in their
 animal reservoirs, thereby limiting the chances of human infection. While
 this approach can be immensely useful in combating emerging diseases, the
 ability to self-replicate exposes vaccines to evolutionary change. As a
 recombinant transmissible vaccine mutates, selection is expected to favor
 variants with reduced efficacy against the pathogen and increased
 transmission rates. This creates a trade-off in vaccine design priorities
 between efficacy, reduction in transmission, and evolutionary stability.
 Here we ask how such trade-offs influence the overall performance of
 transmissible vaccines. We find that evolutionary instability can
 dramatically reduce performance, even for vaccine candidates with ideal
 efficacy and transmission dynamics. One method to increase functional
 stability is through the inclusion of multiple redundant antigens. We show
 that the inclusion of a second antigen can increase functional stability
 in the face of evolutionary pressures. However, the benefit of genetic
 redundancy plus any gain in efficacy must outweigh the reduction in
 transmission for dual-gene designs to be effective. Our results suggest
 that the successful application of recombinant transmissible vaccines will
 require consideration of evolutionary dynamics and epistatic effects, as
 well as basic measurements of epidemiological features.
description: The data in this study was generated using a combination of
 custom c++ code and Mathematica notebooks. Data were analyzed and plotted
 using R scripts.
description: Uploaded data includes all files and scripts as well as the
 folder structure used to generate results zipped into a single archive.
 All effort was made to utilize relative path structures to document code
 in as much detail as possible to ease replication of results.
DOI: 10.5061/dryad.rjdfn2z8q
title: Inter- and intraspecific selection in alien plants: how population growth, functional traits and climate responses change with residence time

description: Aim: When alien species are introduced to new ranges, climate or trait
 mismatches may initially constrain their population growth. However,
 inter- and intraspecific selection in the new environment should cause
 population growth rates to increase with residence time. Using a
 species-for-time approach, we test whether with increasing residence time
 (a) negative effects of climatic mismatches between the species’ new and
 native range on population growth weaken, and (b) functional traits
 converge towards values that maximize population growth in the new range.
 Location: Germany. Time period: 12,000 years BP to present. Major taxa
 studied: 46 plant species of the Asteraceae family. Methods: We set up a
 common-garden mesocosm-experiment using annual plant species with a wide
 range of residence times (7-12,000 years) and followed their population
 dynamics over two years. We calculated climatic distance between the
 common garden and the species’ native range. We also measured key
 functional traits of each species to analyse trait-demography
 relationships and test trait convergence with increasing residence time.
 Results: We found no support for the hypothesis that negative effects of
 climatic mismatches on population growth weaken with residence time.
 However, seed mass had a clear negative effect on population growth. As
 expected under such strong directional selection between or within
 species, increasing residence time led seed mass to converge to low values
 that increase population growth. Accordingly, population growth tended to
 increase with residence time. Main conclusions: We identify trait but not
 climatic mismatches as important constraints on population growth of
 invaders. Understanding how inter- and intraspecific selection shapes
 functional traits of alien species should improve the predictability of
 future invasions and help understanding limits to the population growth
 and spread of invaders already present. In a broader context, this study
 contributes to the conceptual integration of invasion biology with
 community, functional, and population ecology.
DOI: 10.5061/dryad.6m905qfz6
title: Data generated and analyzed in the work entitled: Signs of the plastid: Enzymes involved in plastid-localized metabolic pathways in a eugregarine species

description: The data were generated and analyzed in the manuscript entitled
 "Signs of the plastid: Enzymes involved in plastid-localized
 metabolic pathways in a eugregarine species". This work is currently
 accepted to be published in Parasitology International. As of April 17,
 2021, we have no detail about the manuscript (e.g., issue, volume, page
 number, DOI number). We generated the transcriptome data from the
 apicomplexan parasites/symbionts isolated from three terrestrial
 arthropods, namely the centipede Scolopocryptops rubiginosus and
 two millipedes Parafontaria laminata armigera and Orthomorpha sp.
 Based on the phylogenetic analyses based on 73 nucleus-encoded genes
 identified in the transcriptome data generated in this study, we resolved
 the phylogenetic positions of the three apicomplexans as eugregarines. As
 apicomplexans were most likely derived from the ancestral cell
 bearing a non-photosynthetic (cryptic) plastid, we then searched for the
 transcripts encoding potent enzymes localized in the cryptic plastid in
 the transcriptome data of the three eugregarine species. As the results,
 the transcripts encoding four enzymes involved in plastid-localized
 metabolic pathways were identified from the data of the eugregarine
 species isolated from the centipede, albeit none in those of the other two
 eugregarine species examined here. We concluded that the eugregarine
 species isolated from the centipede possesses the cryptic plastid while
 the eugregarine species in the millipedes lost their plastids secondarily.
 We here provide the contigs reconstructed from the transcriptome data of
 the three eugregarine species and phylogenetic alignments used in this
 study.
description: Please refer to the article for the details of the methods.
description: This entry includes the following items:
 73-gene alignment; GLP_51taxa_73genes.fasta
 Individual single-gene alignments comprising 73-gene alignment;
 Single_gene_alignments.tar.gz Alignments of four
 plastid-localized proteins (i.e. DXS, DXR, IspF & PBGD);
 4plastid_protein_alignments.tar.gz Putative DXS, DXR,
 IspF & PBGD amino acid sequences of Eugregarine sp. ex
 <em>Scolopocryptops rubiginosus</em>;
 GLP_plastid_protein_aa.fasta Assemble data of the
 transcriptomes from the eugregarine species isolated
 from <em>Scolopocryptos rubiginosus</em>;
 GLP_Srubi_Tsukuba_Trinity.fasta Assemble data of the
 transcriptomes from the eugregarine species isolated
 from <em>Parafontaria laminata
 armigera</em>; GLP_Plami_Nagano_Trinity.fasta
 Assemble data of the transcriptomes from the eugregarine species
 isolated from <em>Orthomorpha
 </em>sp.; GLP_Orthomorpha_Palau_Trinity.fasta We
 also provide the three assemble data mentioned above after the exclusion
 of the potential sequences that originated from the hosts, namely
 GLP_Orthomorpha_Palau_exHOST_Trinity.fasta, GLP_Plami_Nagano_exHOST_Trinity.fasta, and GLP_Srubi_Tsukuba_exHOST_Trinity.fasta
DOI: 10.5061/dryad.kkwh70s3g
title: Data from: Are human natal sex ratio differences across the world adaptive? A test of Fisher’s principle

description: Fisher’s principle states that natural selection favours an equal number
 of male and female births at the population level, unless there are sex
 differences in rearing costs or sex differences in mortality before the
 end of the period of parental investment. Sex differences in rearing costs
 should be more pronounced in low- than in high-resource settings. We,
 therefore, examined whether human development index and sex differences in
 child mortality contribute to the natural variation in human sex ratio at
 birth across the globe. As predicted by Fisher’s principle, the proportion
 of male births increased with both increasing male-biased childhood
 mortality and level of development of each country. However, these
 relationships were absent after accounting for spatial autocorrelation in
 the residuals, which our inference is conditioned on. This work shows how
 the failure to account for residual spatial autocorrelation can lead to
 incorrect conclusions regarding support for predictions from sex
 allocation theory.
description: The txt files included here allow to replicate all study findings
 reported in the article. Analysis code (R script) is available in an R
 Markdown document (Supplement.Rmd). This document allows to generate the
 electronic supplementary file.
DOI: 10.5061/dryad.12jm63xwh
title: Phylotranscriptomics reveal the complex evolutionary and biogeographic history of the genus Tsuga with an East Asian-North American disjunct distribution

description: The disjunct distribution between East Asia and North America is one of
 the best established biogeographic patterns. A robust phylogeny is
 fundamental for understanding the biogeographic histories of taxa with
 this distribution pattern. Tsuga (hemlock) is a genus of Pinaceae with a
 typical intercontinental disjunct distribution in East Asia and eastern
 and western North America, and its phylogeny has not been completely
 reconstructed in previous studies. In this study, we reconstructed a
 highly resolved phylogeny of Tsuga using 881 nuclear genes, 60 chloroplast
 genes and 23 mitochondrial genes and explored its biogeographic and
 reticulate evolutionary history. The results of phylogenetic analysis,
 molecular dating and ancestral area reconstruction indicate that Tsuga
 very likely originated from North America in the late Oligocene and
 dispersed from America to East Asia via the Bering Land Bridge during the
 middle Miocene. In particular, we found complex reticulate evolutionary
 pattern among the East Asian hemlock species. Tsuga sieboldii possibly
 originated from hybridization with the ancestor of Tsuga chinensis from
 mainland China and Tsuga forrestii as the paternal donor and the ancestor
 of Tsuga diversifolia and Tsuga ulleungensis as the maternal donor. T.
 chinensis (Taiwan) could have originated by hybridization together with T.
 sieboldii and then evolved independently after dispersal to the Taiwan
 Island, subsequently experiencing mitochondrial DNA introgression with T.
 chinensis from mainland China. Moreover, our study found that T. chinensis
 from western China is more closely related to T. forrestii than to T.
 chinensis from eastern China. The nonmonophyletic T. chinensis needs
 taxonomic reconsideration.
DOI: 10.5061/dryad.8cz8w9gns
title: Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data

description: Analysis of population genetic data often includes the search for genomic
 regions with signs of recent positive selection. One of the approaches
 involves the concept of Extended Haplotype Homozygosity (EHH) and its
 associated statistics. These statistics typically need phased haplotypes
 and, some of them, polarized variants. Here, we unify and extend
 previously proposed modifications to loosen these requirements. We compare
 the modified versions with the original ones by measuring the False
 Discovery Rate in simulated whole-genome scans and quantifying the overlap
 of inferred candidate regions in empirical data. We find that phasing
 information is indispensable for the accurate estimation of
 within-population statistics for all but very large samples and of
 cross-population statistics for small samples. Ancestry information, in
 contrast, is of lesser importance for both. Our publicly available R
 package rehh incorporates the modified statistics presented here.
description: This data set contains three statistics aimed at detecting
 positive selection. They were calculated on publicly available SNP data
 from the 1000 Genomes Project using R package "rehh". The
 purpose of the study was to compare versions of the statistics that
 neglect haplotype phase or variant polarization. More detailed information
 can be found in a README file.
description: Results are stored as compressed tables in ASCII format.
DOI: 10.5061/dryad.95x69p8j9
title: Dental molds from: Three-dimensional dental topography and feeding ecology in the extinct cave bear

description: The cave bear (Ursus spelaeus s.l.) is an iconic extinct bear that
 inhabited the Pleistocene of Eurasia whose extinction causes are
 controversial. To identify the actual causes of the cave bear extinction,
 it is crucial to understand their feeding preferences. Here, we quantify
 shape descriptor metrics (DNE, RFI and OPCR) in three dimensional (3D)
 models of cave bear upper teeth (P4-M2) to make inferences on its
 controversial feeding behaviour. We use a comparative sample including
 representatives of all living bear species with known diets as a template.
 Our topographic analyses evidence that the complexity of upper tooth rows
 in living bears is more associated with the mechanical properties of the
 items consumed than with the type of food. Cave bears exhibit intermediate
 values on topographic metrics between those exhibited by the bamboo-feeder
 giant panda (Ailuropoda melanoleuca) and those taken by specialists in
 hard-mast consumption (Ursus arctos and Ursus thibetanus). The crown
 topography of cave bear upper teeth suggests a high efficiency to chew on
 tough vegetal resources of lower-quality, and no living bear is currently
 exploiting it. Our results align with a climatic-driven hypothesis to
 explain demise in cave bear populations during the late Pleistocene.
description: A dual-phase technique was used to produce
 polyvinylsiloxane-based molds (Virtual<sup> </sup>Putty and
 Light Body compounds) from original tooth rows
 (P<sup>4</sup>-M<sup>2</sup>). High-resolution
 replicas were obtained from molds using non-reflective polyurethane
 (Feroca Composites, Spain). Dental replicas were scanned at 0.2 mm
 resolution with a Roland LPX-600 located at the Central Research Services
 (University of Málaga, Spain). Meshes were merged and processed in
 Geomagic Studio 2012 (Geomagic, Inc. USA) to obtain entire enamel caps
 (EEC) of each tooth row cropped at cervical margin, smoothed and
 downsampled to 10,000 polygons faces. The EEC method was used here to
 prevent planometric footprint area lost and produce metric values for
 whole tooth shape. Meshes (*.ply file format) were then aligned orthogonal
 to the occlusal surfaces using MeshLab to mitigate impact of topographic
 metrics.
DOI: 10.5061/dryad.qv9s4mwd1
title: Anthropogenic noise disrupts mate choice behaviors in female Gryllus bimaculatus

description: By assessing the sexual signals produced by conspecifics, individuals can
 make informed decisions on the best choice of mate, which can lead to
 reproductive fitness benefits. However, these communication systems are
 often vulnerable to disruption by conflicting with stimuli present in the
 environment. Anthropogenic noise may act as one such disruptive stimulus,
 leading to inefficient mate choice decisions, and thus reductions to an
 animal’s fitness. In this study, the mate choice behaviors of female
 Gryllus bimaculatus were tested when presented with artificial male
 courtship songs of differing ‘quality’ under different acoustic
 conditions. In ambient noise conditions, females significantly preferred
 mates paired with higher quality songs, indicated by increased mating
 rates and reduced latency to mate. However, this mate selection pattern
 was disrupted in both traffic and white noise conditions. Additionally,
 ‘high quality’ courtship songs had an increased mounting latency in
 traffic and white noise conditions, when compared to ambient noise
 conditions. Making non-optimal mating decisions, such as the ones seen
 here, can lead to deleterious fitness consequences, alter population
 dynamics and weaken sexual selection, unless individuals adapt to cope
 with anthropogenic interference.
description: Data collected from laboratory based phonotaxis experiments on
 Gryllus bimaculatus. Behavioural measurements and timings were analyzed
 using the software B.O.R.I.S.
description: Variable descirpitions are as follows: ID =
 Cricket ID<br> A_condition = Acoustic Condition<br>
 Q_condition = Quality Condition<br> Date = Date of trial<br>
 Time = Time of Trial<br> Temp = Temperature of testing
 room<br> M_size = Width of male pronotum (cm)<br> F_size
 = Width of female pronotum (cm)<br> M_age = Male age
 (post-ecolsion)<br> F_age = Female age (post-ecolsion)<br>
 M_trial = Ordinal measure of how many trials the male had been used in
 before<br> Duration = Duration of whole trial (s)<br>
 M_movement = Time until male first moved (s)<br> F_movement = Time
 until female first moved (s)<br> Contact = Time until male and
 female made contact (s)<br> Contact_to_court = Time between first
 contact and male courting behaviour (s)<br> Courted = Binary measure
 of wether male courted or not <br> Success = Binary measure of
 wether courtship was successful<br> Signal_to_mount = Time between
 start of courtship behaviour and female mounting (s)
DOI: 10.5061/dryad.8cz8w9gnt
title: Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

description: Background: Studies on the airway microbiome have been performed using a
 wide range of laboratory protocols for high-throughput sequencing of the
 bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the
 impact of number of polymerase chain reaction (PCR) steps (1- or 2-steps)
 and choice of target marker gene region (V3 V4 and V4) on the presentation
 of the upper and lower airway microbiome. Our analyses included lllumina
 MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4
 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region).
 Samples included oral wash, protected specimen brushes and protected
 bronchoalveolar lavage (healthy and obstructive lung disease), and
 negative controls. Results: The number of sequences and amplicon sequence
 variants (ASV) decreased in order setup1&gt;setup2&gt;setup3. This
 trend appeared to be associated with an increased taxonomic resolution
 when sequencing the V3 V4 region (setup 1) and an increased number of
 small ASVs in setups 1 and 2. The latter was considered a result of
 contamination in the two-step PCR protocols as well as sequencing across
 multiple runs (setup 1). Although genera Streptococcus, Prevotella,
 Veillonella and Rothia dominated, differences in relative abundance were
 observed across all setups. Analyses of beta-diversity revealed that while
 oral wash samples (high biomass) clustered together regardless of number
 of PCR steps, samples from the lungs (low biomass) separated. The removal
 of contaminants identified using the Decontam package in R, did not
 resolve differences in results between sequencing setups. Conclusions:
 Differences in number of PCR steps will have an impact of final bacterial
 community descriptions, and more so for samples of low bacterial load. Our
 findings could not be explained by differences in contamination levels
 alone, and more research is needed to understand how variations in
 PCR-setups and reagents may be contributing to the observed protocol bias.
description: The data was collected as part of the larger Bergen COPD
 Microbiome Study ("MicroCOPD"). Data collection and analyses
 steps are described in the manuscript.
DOI: 10.6078/d1k70z
title: Dataset for: Fiber optic sensing of concrete cracking and rebar deformation using several types of cable

description: Distributed fiber optic sensing (DFOS) is increasingly being applied in
 civil engineering. One recently emerging type of DFOS, Optical Frequency
 Domain Reflectometry (OFDR), offers improved accuracy and resolution. This
 repository contains the data set and post processing for an
 experimental study conducted at University of California,
 Berkeley that investigates the ability of OFDR, implemented using
 several types of fiber optic cable, to detect concrete cracking and large
 strain steel deformation. More specifically, the experimental
 investigation involved six reinforced concrete specimens with different
 types of optical fiber embedded in both the concrete and rebar. OFDR
 successfully detected continuous rebar deformation and bond stress through
 the post yielding range, as well as strain localization indicative of
 concrete cracking. The type of optical fiber is shown to have a
 substantial influence on the measured strain response after the onset of
 nonlinear behavior (i.e. cracking, yielding) and into the large
 deformation regime where measurement survivability becomes an issue. The
 higher performing fibers reveal unprecedented detail regarding the
 interaction between concrete and rebar and demonstrate potential for
 application in RC structures. Please check our paper in Structural Control
 and Health Monitoring (https://doi.org/10.1002/stc.2664) for more detailed
 analysis. 
description: The fiber optic data is acquired based on the ODiSI 6000
 Series platform from Luna Innovations.