cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gs7fv
title: Data from: Epithelial magnesium transport by TRPM6 is essential for prenatal development and adult survival

description: Mg2+ regulates many physiological processes and signalling pathways.
 However, little is known about the mechanisms underlying the organismal
 balance of Mg2+. Capitalizing on a set of newly generated mouse models, we
 provide an integrated mechanistic model of the regulation of organismal
 Mg2+ balance during prenatal development and in adult mice by the ion
 channel TRPM6. We show that TRPM6 activity in the placenta and yolk sac is
 essential for embryonic development. In adult mice, TRPM6 is required in
 the intestine to maintain organismal Mg2+ balance, but is dispensable in
 the kidney. Trpm6 inactivation in adult mice leads to shortened lifespan,
 growth deficit and metabolic alterations indicative of impaired energy
 balance. Dietary Mg2+ supplementation not only rescues all phenotypes
 displayed by Trpm6-deficient adult mice, but also may extend the lifespan
 of wildtype mice. Hence, maintenance of organismal Mg2+ balance by TRPM6
 is crucial for prenatal development and survival to adulthood.
description: Whole genome profiling
 of hepatic transcripts altered in Trpm6-deficient miceExcel file contains two
 worksheets: (1) Genome-wide analysis of hepatic transcriptome in control
 vs Trpm6-deficient mice. (2) Up- and down-regulated transcripts in the
 liver of Trpm6-deficient mice with the false discovery rate (FDR)
 P≤0.1.Table
 S2.xlsIngenuity Pathway
 Analysis (IPA) analysis of hepatic transcripts altered in Trpm6-deficient
 miceExcel file contains two
 worksheets: (1) IPA Canonical Pathways representing differentially
 expressed genes in the liver of Trpm6-deficient mice. (2) IPA Causal
 Networks for differentially expressed genes in the liver of
 Trpm6-deficient mice.Table
 S3.xlsMetabolic profiling of
 the serum, liver and gastrocnemius muscle of Trpm6-deficient
 miceExcel file contains
 seven worksheets: (1) Statistical analysis of metabolite measurements in
 serum samples. (2) Statistical analysis of metabolite measurements in
 gastrocnemius muscle samples. (3) Statistical analysis of metabolite
 measurements in liver samples. (4) Metabolites significantly changed in
 serum samples of Trpm6-deficient mice (FDR P≤0.05). (5) Metabolites
 significantly changed in gastrocnemius muscle samples of Trpm6-deficient
 mice (FDR P≤0.05). (6) Metabolites significantly changed in liver samples
 of Trpm6-deficient mice (FDR P≤0.05). (7) Abbreviations of
 metabolites.Table
 S4.xlsxMATLAB
 codeMATLAB code used for
 statistical analysis of survival distributions of control and dietary
 treated miceMATLAB
 Code.docx
DOI: 10.5061/dryad.4812p
title: Data from: Phylogenomics using target-restricted assembly resolves intra-generic relationships of parasitic lice (Phthiraptera: Columbicola)

description: Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove
 and pigeon hosts are a well-recognized model system for coevolutionary
 studies at the intersection of micro- and macroevolution. Selection on
 lice in microevolutionary time occurs as pigeons and doves defend
 themselves against lice by preening. In turn, behavioral and morphological
 adaptations of the lice improve their ability to evade host defense. Over
 macroevolutionary time wing lice tend to cospeciate with their hosts; yet,
 some species of Columbicola have switched to new host species.
 Understanding the ecological and evolutionary factors that influence
 coadaptation and codiversification in this system will substantially
 improve our understanding of coevolution in general. However, further work
 is hampered by the lack of a robust phylogenetic framework for Columbicola
 spp. and their hosts. Previous attempts to resolve the phylogeny of
 Columbicola based on sequences from a few genes provided limited support.
 Here we apply a new approach, target restricted assembly, to assemble 977
 orthologous gene sequences from whole-genome sequence data generated from
 very small, ethanol-preserved specimens, representing up to 61 species of
 wing lice. Both concatenation and coalescent methods were used to estimate
 the species tree. These two approaches yielded consistent and
 well-supported trees with 90% of all relationships receiving 100% support,
 which is a substantial improvement over previous studies. We used this new
 phylogeny to show that biogeographic ranges are generally conserved within
 clades of Columbicola wing lice. Limited inconsistencies are probably
 attributable to intercontinental dispersal of hosts, and host switching by
 some of the lice.
description: Table
 S1.Collection,
 identification, and sequencing data.Columbicola_MS_TableS1_Sarah.xlsxSupplementary Text and Fig S1This file includes additional details on DNA extraction methods, commands used in phylogenetic analysis, and figure S1.Boyd_Syst_Biol_Supplementary_Materials_VS6.pdfTrees, Alignment Matrix, PartitionsThis file contains all of the phylogenetic data associated with this Systematic Biology submission. This includes, taxon list, phylogenetic trees (RAxML, ASTRAL, and ASTRID), DNA alignment matrix, Data partitions (sets for RAxML analysis and ordering of genes in the matrix).Boyd.SystBiol.Trees.Matrix.Sets.tgz
DOI: 10.5061/dryad.1257
title: Data from: Climatic stability and genetic divergence in the tropical insular lizard Anolis krugi, the Puerto Rican "Lagartijo Jardinero de la Montaña"

description: Two factors that can lead to geographic structuring in conspecific
 populations are barriers to dispersal and climatic stability. Populations
 that occur in different physiographic regions may be restricted to those
 areas by physical and/or ecological barriers, which may facilitate the
 formation of phylogeographic clades. Long-term climatic stability can also
 promote genetic diversification, because new clades are likely to evolve
 in areas that experience lesser climatic shifts. We conducted a
 phylogeographic study of the Puerto Rican lizard Anolis krugi to assess
 whether populations of this anole show genetic discontinuities across the
 species' range, and if they do, whether these breaks coincide with
 the boundaries of the five physiographic regions of Puerto Rico. We also
 assessed whether interpopulation genetic distances in A. krugi are
 positively correlated with relative climatic stability in the island.
 Anolis krugi exhibits genetic structuring, but the phylogroups do not
 correspond to the physiographic regions of Puerto Rico. We used climatic
 reconstructions of two environmental extremes of the Quaternary period,
 the present conditions and those during the last glacial maximum, to
 quantify the degree of climatic stability between sampling locations. We
 documented positive correlations between genetic distances and relative
 climatic stability, although these associations were not significant when
 corrected for autocorrelation. The approach that we employed to assess the
 relationship between climatic stability and the genetic architecture of A.
 krugi can also be used to investigate the impact of factors such as the
 spatial distribution of food sources, parasites, predators or competitors
 on the genetic landscape of a species.
description: Genetic diversity of
 Anolis krugiAnolis_krugi_cytB.sqnAnolis_krugi_ND2.sqn
DOI: 10.5061/dryad.533gf
title: Data from: Using collision cones to assess biological deconfliction methods

description: Biological systems consistently outperform autonomous systems governed by
 engineered algorithms in their ability to reactively avoid collisions. To
 better understand this discrepancy, a collision avoidance algorithm was
 applied to frames of digitized video trajectory data from bats, swallows
 and fish (Myotis velifer, Petrochelidon pyrrhonota and Danio
 aequipinnatus). Information available from visual cues, specifically
 relative position and velocity, was provided to the algorithm which used
 this information to define collision cones that allowed the algorithm to
 find a safe velocity requiring minimal deviation from the original
 velocity. The subset of obstacles provided to the algorithm was determined
 by the animal's sensing range in terms of metric and topological
 distance. The algorithmic calculated velocities showed good agreement with
 observed biological velocities, indicating that the algorithm was an
 informative basis for comparison with the three species and could
 potentially be improved for engineered applications with further study.
description: Bat Trajectory
 Data3D position data for
 Myotis velifer. The columns represent the trial number, the index number
 (to differentiate individual animals within a trial -- note they are not
 consistent between trials), the frame (used for synchronizing the data),
 and the XYZ position coordinates with respect to a global reference frame.
 Information about how the data was collected is in the ReadMe
 file.bat_trajectories.csvBird Trajectory Data3D position data for Petrochelidon pyrrhonota. The columns represent the trial number, the index number (to differentiate individual animals within a trial -- note they are not consistent between trials), the frame (used for synchronizing the data), and the XYZ position coordinates with respect to a global reference frame. Information about how the data was collected is in the ReadMe file.bird_trajectories.csvFish Trajectory Data3D position data for Danio aequipinnatus. The columns represent the trial number, the index number (to differentiate individual animals within a trial -- note they are not consistent between trials), the frame (used for synchronizing the data), and the XYZ position coordinates with respect to a global reference frame. Information about how the data was collected is in the ReadMe file.fish_trajectories.csv
DOI: 10.5061/dryad.f26dt
title: Data from: Reconstructing the past: methods and techniques for the digital restoration of fossils

description: During fossilization, the remains of extinct organisms are subjected to
 taphonomic and diagenetic processes. As a result, fossils show a variety
 of preservational artefacts, which can range from small breaks and cracks,
 disarticulation and fragmentation, to the loss and deformation of skeletal
 structures and other hard parts. Such artefacts can present a considerable
 problem, as the preserved morphology of fossils often forms the basis for
 palaeontological research. Phylogenetic and taxonomic studies, inferences
 on appearance, ecology and behaviour and functional analyses of fossil
 organisms strongly rely on morphological information. As a consequence,
 the restoration of fossil morphology is often a necessary prerequisite for
 further analyses. Facilitated by recent computational advances, virtual
 reconstruction and restoration techniques offer versatile tools to restore
 the original morphology of fossils. Different methodological steps and
 approaches, as well as software are outlined and reviewed here, and
 advantages and disadvantages are discussed. Although the complexity of the
 restorative processes can introduce a degree of interpretation, digitally
 restored fossils can provide useful morphological information and can be
 used to obtain functional estimates. Additionally, the digital nature of
 the restored models can open up possibilities for education and outreach
 and further research.
description: Erlikosaurus skull
 modelDigital model of the
 skull of the Cretaceous therizinosaur dinosaur Erlikosaurus andrewsi.
 Model derived from CT scanning of the original specimen. Model depicted in
 figures 1, 3-5. (.stl)Therizinosaurus claw
 modelDigital model of the
 manual ungual of the Cretaceous therizinosaur dinosaur Therizinosaurus
 cheloniformes. Model derived from photogrammetry of the original specimen.
 Model depicted in figure 2. (.stl)Dysalotosaurus braincase
 modelDigital model of the
 braincase of the Jurassic ornithopod dinosaur Dysalotosaurus
 lettowvorbecki. Model derived from CT scanning of the original specimen.
 Model depicted in figures 6. (.stl)Dysalotosaurus_braincase_model.stl
DOI: 10.5061/dryad.hj1t4
title: Data from: Rich do not rise early: spatio-temporal patterns in the mobility networks of different socio-economic classes

description: We analyse the urban mobility in the cities of Medellín and Manizales
 (Colombia). Each city is represented by six mobility networks, each one
 encoding the origin-destination trips performed by a subset of the
 population corresponding to a particular socio-economic status. The nodes
 of each network are the different urban locations whereas links account
 for the existence of a trip between two different areas of the city. We
 study the main structural properties of these mobility networks by
 focusing on their spatio-temporal patterns. Our goal is to relate these
 patterns with the partition into six socio-economic compartments of these
 two societies. Our results show that spatial and temporal patterns vary
 across these socio-economic groups. In particular, the two datasets show
 that as wealth increases the early-morning activity is delayed, the midday
 peak becomes smoother and the spatial distribution of trips becomes more
 localized.
description: Medellín Origin
 Destination Survey 2005Medellin
 Origin-destination survey (dated back to 2005-2006). Data gathered by
 Universidad Nacional de Colombia for Area Metropolitana del Valle de
 Aburrá (cite as: AREA Metropolitana del Valle de Aburrá 2006. Chapter 2:
 Diagnóstico. Formulación del Plan Maestro de Movilidad para la Región
 Metropolitana del Valle de Aburrá. Informe Final pp. 102-108 and
 Universidad Nacional de Colombia and AREA Metropolitana del Valle de
 Aburrá 2006. Encuesta origen destino de viajes 2005 del Valle de Aburrá,
 estudios de tránsito complementarios y validación. Technical Report).
 Column description: ORIG describes the id of the origin zone of the trip
 (from 1 to 413). DEST the id of the destination zone (from 1 to 413). EST
 indicates the "estrato" or socioeconomic class/status of the
 household of the traveler (1 the lowest income householders and 6 the
 richest). HSAL indicates the departure hour (decimal) of the trip, HLLEG
 the arrival hour (decimal) of the trip, MOT indicates the purpose of trip
 (1 work, 2 study, 3 shopping, 4 health, 5 recreation, 6 return home, 7
 others), HMV describes the mean hour of trip, FEV is the expansion factor
 of the survey.OD_DB_Med2005.xlsxManizales Origin Destination Survey 2005Manizales Origin-destination survey (dated back to 2005). Data gathered by Universidad Nacional de Colombia for Alcaldía de Manizales (cite as: Alcaldía de Manizales 2005. Plan de movilidad para el municipio de Manizales. Informe del estudio origen-destino. Technical Report). Column description: ORIG describes the id of the origin zone of the trip (from 1 to 57). DEST the id of the destination zone (from 1 to 57). EST indicates the "estrato" or socioeconomic class/status of the household of the traveler (1 the lowest income householders and 6 the richest). HSAL indicates the departure hour (decimal) of the trip, HLLEG the arrival hour (decimal) of the trip, HMV describes the mean hour of trip, FEV is the expansion factor of the survey.OD_DB_Man2005.xlsx
DOI: 10.13120/awym8v
title: Dolphins validated sightings reported by avvistAPP users

description: Validated sightings reported from 2019 onwards by avvistAPP users. avvistAPP is a free citizen science tool that allows everyone to actively contribute to the monitoring of marine animals. Available both in Google and Apple app stores. App description: https://doi.org/10.13120/h127-9v54
DOI: 10.5061/dryad.vs27p
title: Data from: Type 2 porcine reproductive and respiratory syndrome virus infection increases apoptosis at the maternal-fetal interface in late gestation pregnant gilts

description: The pathogenesis of fetal death associated with porcine reproductive and
 respiratory syndrome (PRRS) is hypothesized to be a consequence of PRRS
 virus-induced apoptosis at the maternal-fetal interface (MFI). The
 objectives of this study were to evaluate distribution and degree of
 apoptosis in the uterine and fetal placental tissues during the
 experimental type 2 PRRS virus (PRRSV) infection and determine
 associations between apoptosis at the MFI, PRRSV RNA concentration and
 antigen staining intensity, PRRSV-induced microscopic lesions, and fetal
 preservation status. A total of 114 naÃ¯ve, high-health pregnant gilts
 were inoculated with type 2 PRRSV on gestation day 85Â±1 with euthanasia
 21 days later; 19 sham-inoculated gilts served as controls. Two hundred
 and fifty samples of uterine tissue with fetal placenta were selected
 based on negative, low PRRSV RNA, and high PRRSV RNA concentration (0,
 &lt; or &gt; 2.7 log10 copies/mg, respectively). TUNEL assay was
 used to detect apoptosis in the endometrium and at the MFI. PRRSV RNA
 concentration and numbers of PRRSV immunopositive cells in uterine and
 placental tissue were positively associated with the severity of apoptosis
 in the endometrium and the MFI (P&lt;0.001, P&lt;0.05 and
 P&lt;0.001, respectively). The number of TUNEL positive cells at the
 MFI was also positively associated with the severity (P&lt;0.001) of
 vasculitis, but not total numbers of inflammatory cells in the
 endometrium. Increased numbers of TUNEL positive cells at the MFI were
 associated with PRRSV load in the fetal thymus, and greater odds of
 meconium staining of the fetus at 21 days post infection (P&lt;0.001
 for both). These findings suggest an important role of apoptosis in the
 pathogenesis of uterine epithelial and trophoblastic cell death at the
 MFI. Moreover, apoptosis at the MFI is significantly associated with fetal
 demise during in utero type 2 PRRSV infection.
description: Apoptosis at
 maternal-fetal interface during type 2 PRRSV infectionFile contains data from
 our study of the apoptosis at maternal-fetal placental interface (MFI) in
 late gestation pregnant gilts experimentally challenged with type 2 PRRS
 virus: counts of TUNEL (apoptotic) positive cells at MFI, uterine
 endometrium, area size tissue measurements used for counting of TUNEL
 positive cells, RT-qPCR results of concentration of PRRS virus in uterus
 and fetal thymus, fetal preservation status and
 microscopy.PRRS apoptosis paper PloS
 One.xlsx
DOI: 10.5061/dryad.871pc
title: Data from: Pyrodiversity promotes avian diversity over the decade following forest fire

description: An emerging hypothesis in fire ecology is that pyrodiversity increases
 species diversity. We test whether pyrodiversity—defined as the standard
 deviation of fire severity—increases avian biodiversity at two spatial
 scales, and whether and how this relationship may change in the decade
 following fire. We use a dynamic Bayesian community model applied to a
 multi-year dataset of bird surveys at 1106 points sampled across 97 fires
 in montane California. Our results provide strong support for a positive
 relationship between pyrodiversity and bird diversity. This relationship
 interacts with time since fire, with pyrodiversity having a greater effect
 on biodiversity at 10 years post-fire than at 1 year post-fire.
 Immediately after fires, patches of differing burn severities hold similar
 bird communities, but over the ensuing decade, bird assemblages within
 patches of contrasting severities differentiate. When evaluated at the
 scale of individual fires, fires with a greater heterogeneity of burn
 severities hold substantially more species. High spatial heterogeneity in
 severity, sometimes called ‘mixed-severity fire', is a natural part
 of wildfire regimes in western North America, but may be jeopardized by
 climate change and a legacy of fire suppression. Forest management that
 encourages mixed-severity fire may be critical for sustaining biodiversity
 across fire-prone landscapes.
description: JAGS model
 codeCode, in JAGS language,
 for dynamic community occupancy modelJAGS_model.RCovariatesRelevant covariates and meta-data used in occupancy model fitting. Rdata file contains a list of objects.Z-matrix posteriorPosterior draw (300 thinned iterations) of the true occurrence matrix (Z-matrix). Object saved as a sparse matrix (package 'Matrix'). True dimensional attributes are: 1106 sites x 6 years x 124 species. Order of sites and species as included in the 'covariates' file.Z_posterior.Rdata
DOI: 10.34810/data2449
title: Partitura i enregistrament [score and recording] Sonata en Mi menor / E minor, de Carles Baguer (1768-1808)

description: &lt;p&gt;[CAT] Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical que estan desenvolupant la UB i el CSIC, juntament amb el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grup per a l’Estudi del Patrimoni Musical (GEPAM), el Grup de Recerca Patrimoni Musical Històric de la Institució Milà i Fontanals d’Investigació en Humanitats del CSIC, l’Arquebisbat de Barcelona, la Catedral de Barcelona, l’Arxiu de l’Església de Santa Maria del Pi i l'Oratori de Sant Felip Neri de Barcelona, i, en col·laboració amb el Museu de la Música de Barcelona, s'ha recuperat una peça musical de Carles Baguer (1768-1808) que es troba al manuscrit MS. 1378 del fons musical del CRAI Biblioteca de Fons Antic de la Universitat de Barcelona. Aquest dataset conté dos arxius:
&lt;p&gt;- Transcripció de la Sonata en Mi menor de Carles Baguer del manuscrit Ms. 1378.
&lt;p&gt;- Enregistrament sonor de la peça interpretada per: Dani Espasa, amb un piano Steinway, model D, cedit pel Museu de la Música de Barcelona.
description: &lt;p&gt;[ENG]The Study and Recovery of Musical Heritage project being developed by the UB and the CSIC, together with the CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, ​​the Grupo de Investigación Patrimonio Musical Histórico de la Institución Milá y Fontanals de Investigación en Humanidades of the CSIC, the Archdiocese of Barcelona, ​​the Barcelona Cathedral, the Arxiu de l’Església de Santa Maria del Pi, and the Oratory of Sant Felip Neri in Barcelona, and, in collaboration with the Barcelona Music Museum, has recovered musical heritage: a musical piece by Carles Baguer (1768-1808) which is found in the manuscript Ms.1378 of the music collection of theCRAI Biblioteca de Fons Antic de la Universitat de Barcelona. This dataset contains two files:
&lt;p&gt;- Transcription of the Sonata in E minor by Carles Baguer from the manuscript Ms. 1378.
&lt;p&gt;- Sound recording of the piece performed by: Dani Espasa, with a piano Steinway, model D, on loan from the Barcelona Music Museum.