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8,819 results for “new data”
New York City Multi-scalar Street Segment Data
<p>This dataset compiles a comprehensive database containing 90,327 street segments in New York City, covering their street design features, streetscape design, Vision Zero treatments, and neighborhood land use. It has two scales-street and street segment group (aggregation of same type of street at neighborhood). This dataset is derived based on all publicly available data, most from NYC Open Data. The detailed methods can be found in the published paper, <a href="https://journals.sagepub.com/doi/10.1177/03611981241263570" target="_blank" rel="noopener">Pedestrian and Car Occupant Crash Casualties Over a 9-Year Span of Vision Zero in New York City</a>. To use it, please refer to the metadata file for more information and cite our work. A full list of raw data source can be found below:</p> <ul> <li>Motor Vehicle Collisions – NYC Open Data: <a href="https://data.cityofnewyork.us/Public-Safety/Motor-Vehicle-Collisions-Crashes/h9gi-nx95">https://data.cityofnewyork.us/Public-Safety/Motor-Vehicle-Collisions-Crashes/h9gi-nx95</a></li> <li>Citywide Street Centerline (CSCL) – NYC Open Data: <a href="https://data.cityofnewyork.us/City-Government/NYC-Street-Centerline-CSCL-/exjm-f27b">https://data.cityofnewyork.us/City-Government/NYC-Street-Centerline-CSCL-/exjm-f27b</a></li> <li>NYC Building Footprints – NYC Open Data: <a href="https://data.cityofnewyork.us/Housing-Development/Building-Footprints/nqwf-w8eh">https://data.cityofnewyork.us/Housing-Development/Building-Footprints/nqwf-w8eh</a></li> <li>Practical Canopy for New York City: https://zenodo.org/record/6547492</li> <li>New York City Bike Routes – NYC Open Data: <a href="https://data.cityofnewyork.us/Transportation/New-York-City-Bike-Routes/7vsa-caz7">https://data.cityofnewyork.us/Transportation/New-York-City-Bike-Routes/7vsa-caz7</a></li> <li>Sidewalk Widths NYC (originally from Sidewalk – NYC Open Data): <a href="https://www.sidewalkwidths.nyc/">https://www.sidewalkwidths.nyc/</a></li> <li>LION Single Line Street Base Map - The NYC Department of City Planning (DCP): <a href="https://www.nyc.gov/site/planning/data-maps/open-data/dwn-lion.page">https://www.nyc.gov/site/planning/data-maps/open-data/dwn-lion.page</a></li> <li>NYC Planimetric Database Median – NYC Open Data: <a href="https://data.cityofnewyork.us/Transportation/NYC-Planimetrics/wt4d-p43d">https://data.cityofnewyork.us/Transportation/NYC-Planimetrics/wt4d-p43d</a></li> <li>NYC Vision Zero Open Data (including multiple datasets including all the implementations): <a href="https://www.nyc.gov/content/visionzero/pages/open-data">https://www.nyc.gov/content/visionzero/pages/open-data</a></li> <li> NYS Traffic Data - New York State Department of Transportation Open Data: <a href="https://data.ny.gov/Transportation/NYS-Traffic-Data-Viewer/7wmy-q6mb">https://data.ny.gov/Transportation/NYS-Traffic-Data-Viewer/7wmy-q6mb</a></li> <li> Smart Location Database - US Environmental Protection Agency: <a href="https://www.epa.gov/smartgrowth/smart-location-mapping">https://www.epa.gov/smartgrowth/smart-location-mapping</a></li> <li> Race and ethnicity in area - American Community Survey (ACS): https://www.census.gov/programs-surveys/acs</li> </ul> <p> </p>
Data from: Phylogeny and systematics of the "Pronophila clade", with two new genera to resolve the formerly polyphyletic genus Pseudomaniola (Lepidoptera: Nymphalidae, Satyrinae)
<p>Analysis of a target enrichment molecular dataset confirms the monophyly of the Neotropical montane butterfly group known as the <em>Pronophila</em> Westwood clade, one of two major lineages of the satyrine subtribe Pronophilina. The <em>Pronophila </em>clade comprises 18-20 recognized genera and some 125 species. Within this group, the genus <em>Pseudomaniola</em>Röber appears as paraphyletic, and is split here into three genera, <em>Pseudomaniola </em>sensu novum<em> </em>with six species, including four previously considered as subspecies of <em>P. phaselis </em>(Hewitson), the monobasic <em>Fahraeusia </em>Pyrcz n. gen. for <em>Catargynnis asuba </em>Thieme, n. comb., and <em>Boyeriana </em>Pyrcz, Espeland & Willmott<strong> </strong>n. gen., with nine species. The adults of all three genera can be recognized by their wing colour patterns, but the strongest synapomorphies are found in the genitalia, especially those of the male, supporting the above systematic decisions. Notable differences are also found in scale organization and morphology. A divergence time analysis suggests that <em>Fahraeusia </em>diverged<em> </em>from <em>Pseudomaniola </em>+<em>Boyeriana </em>in the mid-Miocene, around 12 Mya, and the subsequent separation of the last two genera occurred at the start of the Pliocene at around 5 Mya.</p>
Data from: The latest freshwater giants: a new Peltocephalus (Pleurodira: Podocnemididae) turtle from the Late Pleistocene of the Brazilian Amazon
<p>Overkill of large mammals is recognised as a key driver of Pleistocene megafaunal extinctions in the Americas and Australia. While this phenomenon primarily affected mega-mammals, its impact on large Quaternary reptiles has been debated. Freshwater turtles, due to the scarcity of giant forms in the Quaternary record, have been largely neglected in such discussions. Here we present a new giant podocnemidid turtle, <em>Peltocephalus maturin</em> sp. nov., from the Late Pleistocene Rio Madeira Formation in the Brazilian Amazon, that challenges this assumption. Morphological and phylogenetic analyses of the holotype, a massive partial lower jaw, reveal close affinities to extant Amazonian species and suggests an omnivorous diet. Body size regressions indicate <em>Pe. maturin</em> possibly reached about 180 cm in carapace length and is amongst the largest freshwater turtles ever found. This finding presents the latest known occurrence of giant freshwater turtles, hinting at coexistence with early human inhabitants in the Amazon.</p>
Detrended and corrected GNSS data from Lake Taupō, New Zealand, 2014–2021
<p>If using this data please cite the following publication:</p> <p>Schuler, J., Hreinsdóttir, S., Illsley-Kemp, F., Holden, C., Townend, J., Villamor, P. The response of Taupō Volcano to the M7.8 Kaikōura Earthquake. <em>Journal of Geophysical Research - Solid</em> <em>Earth. </em>2024.</p> <p>Also refer to this publication for full details on the methods used to derive the dataset. </p>
Data for: A new threshold selection method for species distribution models with presence-only data: extracting the mutation point of the P/E curve by threshold regression
<p>Selecting thresholds to convert continuous predictions of species distribution models proves critical for many real-world applications and model assessments. Prevalent threshold selection methods for presence-only data require unproven pseudo-absence data or subjective researchers' decisions. This study proposes a new method, Boyce-Threshold Quantile Regression (BTQR), to determine thresholds objectively without pseudo-absence data. We summarize that the mutation point is a typical shape feature of the predicted-to-expected (P/E) curve after reviewing relevant articles. Analysis based on source-sink theory suggests that this mutation point may represent a transition in habitat types and serve as an appropriate threshold. Threshold regression is introduced to accurately locate the mutation point.</p> <p>To validate the effectiveness of BTQR, we used four virtual species of varying prevalence and a real species with reliable distribution data. Six different species distribution models were employed to generate continuous suitability predictions. BTQR and nine other traditional methods transformed these continuous outputs into binary results. Comparative experiments show that BTQR has advantages in terms of accuracy, applicability, and consistency over the existing methods.</p>
Data for: Viral receptor-binding protein evolves new function through mutations that cause trimer instability and functional heterogeneity
<p>When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However, recent work has revealed that non-native, often unstable protein conformations play an important role in mediating evolutionary transitions, raising the question of whether instability can itself potentiate the evolution of new activity. We explored this question in a bacteriophage receptor binding protein (RBP) during host-range evolution. We studied the properties of the RBP of bacteriophage before and after host-range evolution and demonstrated that the evolved protein is relatively unstable and may exist in multiple conformations with unique receptor preferences. Through a combination of structural modeling and in vitro oligomeric state analysis, we found that the instability arises from mutations that interfere with trimer formation. This study raises the intriguing possibility that protein instability might play a previously unrecognized role in mediating host-range expansions in viruses.</p>
Fig. 4 in New data on distribution of Miramiola pusilla (Miram, 1927) (Orthoptera: Tettigoniidae
Fig. 4. Reliability test for the Miramiola pusilla. Maxent distribution model (bioclimatic
Fig. 2 in New data on distribution of Miramiola pusilla (Miram, 1927) (Orthoptera: Tettigoniidae
Fig. 2. Miramiola pusilla known localities in the Asian part of its range.
Data for: Seasonal differences in observed versus modeled new particle formation at two European boreal stations
<p>Model dataset variables produced from the IFS and TM5 modules in EC-Earth3 version 3.4.0 which contains the control case and four experiments with the NPF lookup table. This paper is under review.</p> <p>The files contain:</p> <ul> <li>NetCDF files from TM5 general output for each simulation at the two location grid points.</li> </ul> <p>File-name description of the EC-Earth3 experiments: "Hyyt" = Hyytiälä, "Mossa" = Hyltemossa.</p> <p>"ricc2" = CLUST-HIGH case</p> <p>"dlpno" = CLUST-Low case</p> <p>"bono" = CLUST-Low+Riccobono case</p> <p>"ctrl" = Model control run case</p> <p>"nonpf" = No NPF case</p> <ul> <li>Compressed tar file of NetCDF data from IFS output for all four simulations. All IFS data have been averaged to monthly means from 3-hourly grib datasets.</li> </ul> <p> </p> <ul> <li>ADCHEM base-case particle number size distributions from Hyytiälä and Hyltemossa.</li> </ul>
Transcriptomic Analysis Data for MSTN Mutations and Mechanisms of Muscle Hypertrophy in a New Guinea Pig Breed
<p>This dataset contains raw RNA-seq data from six guinea pig muscle samples, split into two groups:</p> <ul> <li><strong>Native guinea pigs (B1 to B3):</strong> Control group with no selective breeding.</li> <li><strong>Kuri breed guinea pigs (B4 to B6):</strong> Synthetic hybrid group selectively bred for increased muscle mass.<br>Each sample has paired-end FASTQ files (e.g., B1_1.fq.gz and B1_2.fq.gz).</li> </ul>
File data and Code for submitted manuscript to New Phytologist
<p>Original data from submitted manuscript: Nutrient resorption of leaves and roots coordinates with root nutrient-acquisition strategies in a temperate forest by Wang, Freschet, McCormack, Lambers, and Gu, submitted for publication in <em>New phytologist</em>.</p> <p> </p> <p>The data includes the leaf and root resorption traits (NRE_L, PRE_L, N_Ls, P_Ls, NRE_R, PRE_R, N_Rs, P_Rs), and root economic traits (RN, RP, RD, SRL, RTD) of 34 woody species in temperate forest.</p> <p> </p> <p>Abbreviations of the data:</p> <p>NRE_L, Nitrogen resorption efficiency of leaf (%)</p> <p>PRE_L, Phosphorus resorption efficiency of leaf (%)</p> <p>N_Ls, Nitrogen concentration of senesced leaf (mg g<sup>-1</sup>)</p> <p>P_Ls, Phosphorus concentration of senesced leaf (mg g<sup>-1</sup>)</p> <p>NRE_R, Nitrogen resorption efficiency of root (%)</p> <p>PRE_R, Phosphorus resorption efficiency of root (%)</p> <p>N_Rs, Nitrogen concentration of senesced root (mg g<sup>-1</sup>)</p> <p>P_Rs, Phosphorus concentration of senesced root (mg g<sup>-1</sup>)</p> <p>RN, root nitrogen concentration (mg g<sup>-1</sup>);</p> <p>RP, root phosphorus concentration (mg g<sup>-1</sup>);</p> <p>RD, root diameter (mm);</p> <p>SRL, specific root length (m g<sup>-1</sup>);</p> <p>RTD, root tissue density (g cm<sup>-3</sup>);</p> <p> </p> <p>The R files used to generate the results are provided respectively.</p>
Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
<p>Modern phylogenetic comparative methods allow estimating evolutionary rates of phenotypic change, how these rates differ across clades, and assessing whether the rate remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, hence they do not allow us to determine rate variations among different parts of a single, complex phenotype, or charting of realized rate variation directly onto the phenotype. Herein, we present a new method which allows the mapping of evolutionary rate variation directly on three-dimensional phenotypes, informing on the direction and magnitude of trait change automatically.</p> <p>This new method, implemented by the function rate.map embedded in the R package 'RRphylo', is based on phylogenetic ridge regression rate estimates. Since the latter represent ridge regression slopes, they possess sign and magnitude. In 'RRphylo', different rates are calculated for different districts of the phenotype, which can then be visualized directly onto the phenotype itself. We present the application of rate.map to the evolution of facial skeleton in Hominoidea (the clade including living and fossil apes), the primate clade inclusive of Homo and the greater apes. We found that the highly derived, unique shape of the face in modern humans evolved through rapid phenotypic changes affecting the nasal bones, the brow ridge and the maxillary region. The canine fossa, a facial feature unique to Homo sapiens, did not belong to a region of rapid phenotypic change, and could be seen as the by-product of midface evolution as suggested by previous studies.</p>
Data for the Scotogenic and EW-ino results presented in "Constraining new physics with SModelS version 2" (arxiv: 2112.00769 )
<p>Data used for the results presented in "Constraining new physics with SModelS version 2" (arXiv: <a href="https://arxiv.org/abs/2112.00769">2112.00769</a>).</p> <p>The following data files are available:</p> <ol> <li>EWinoData.tar.gz: contains the SLHA files for the random scan over the electroweak-ino parameter space. The tarball also contains the SModelS and Micromegas results for the corresponding points.</li> <li>ScotoScalarDMData.tar.gz: contains the SLHA files for the scan over the scotogenic model with a scalar DM candidate (neutral CP-even Higgs). The tarball also contains the SModelS results for the corresponding points.</li> <li>ScotoFermionDMData.tar.gz: contains the SLHA files for the scan over the scotogenic model with a fermionic DM candidate (lightest right-handed neutrino). The tarball contains 2 folders containing the SLHA files and the SModelS output. Each folder has the following structure: <ul> <li>mhc_<electronic/muonic/mixed>_decays: scenario with the charged Higgs decaying with a 100% BR to electron+N<sub>1</sub> muon +N<sub>1 </sub>or 50% BR to each (electron/muon) flavor <ul> <li>deltam_<5/50>: scenario with a 5 (50) GeV mass difference between the scalars. </li> </ul> </li> </ul> </li> </ol> <p> </p> <p>More details about the scans can be found in arXiv:<a href="https://arxiv.org/abs/2112.00769">2112.00769</a> .</p>
Seafloor pressure data from 2019 deployment at the Hikurangi subduction zone, New Zealand
<p>We include here hourly seafloor pressure time series (and locations) from a 2019 deployment at the Hikurangi subduction zone, used in "Using seafloor geodesy to detect vertical deformation at the Hikurangi subduction zone: insights from self-calibrating pressure sensors and ocean general circulation models", a paper submitted to JGR: Solid Earth in January 2022.</p> <p><strong>APG_hikurangi_2019.json/.mat: </strong>Seafloor pressure time series data (JSON and MATLAB format) from a deployment at the Hikurangi subduction zone in 2019. The files contain the hourly time series in datetime (UTC) and pressure in hectopascals, with the convention that a decrease in pressure is equivalent to a reduction in the height of the water column (seafloor uplift).</p> <p>The only processing that has been applied to the data is filtering using a 2-day corner lowpass filter for all sites, and the A-0-A correction for the POBS sensors (which are therefore drift corrected). All APGs not equipped with A-0-A still contain sensor drift. Each time series has been adjusted using the mean of the absolute data, which is why the time series for the sites plot about zero - amplitude has been preserved.</p> <p><strong>locations_APG_hikurangi_2019.csv: </strong>Locations of the seafloor pressure sites from a deployment at the Hikurangi subduction zone in 2019. Indicated for each site are the sensor’s institute (UTIG - University of Texas Institute for Geophysics, Austin, USA; GNS Science - GNS Science, New Zealand; LDEO - Lamont-Doherty Earth Observatory, Columbia University, USA; KU - Kyoto University and Tohoku University, Japan), A-0-A drift correction capability, deployment longitude, latitude, and depth, and whether there are usable data. The sensors without usable data either contained data logger issues or were not recovered, and are not included in APG_hikurangi_2019.json/.mat.</p>
Data from: A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus
<p>A new species of <i>Diasporus </i>is described from the lowlands of southwestern Colombia. The new species, along with <i>Diasporus citrinobapheus</i>, <i>D. gularis</i>, and <i>D. tigrillo </i>is the only species in this genus<i> </i>known to exhibit a yellowish coloration in life. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II–IV and toes II–IV. Further, the new species differs from all congeners by an uncorrected <i>p-distance</i> of >5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within <i>Diasporus</i>, which may be recognized as the <i>Diasporus diastema</i> species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in <i>Diasporus</i>, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of <i>Diasporus</i>. Regarding pointed disc covers (ungual flap) present in some species of <i>Diasporus</i>, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus <i>Diasporus</i>.</p>
letter to the New England Journal of Medicine: COVID-19 mortality data perplexity
<p>Una explicación para todos los públicos:</p> <p>Lo que he hecho es ver los muertos por COVID-19 declarados por los organismos gubernamentales antes y después de que comience la intervención farmacológica con los productos que se han dado en llamar vacunas por los medios de comunicación y los gobiernos. Primero he considerado el periodo completo de 2020 hasta la "vacunación" y el periodo desde el comienzo de la vacunación hasta el final de los datos (7 de enero 2022). El comienzo es un poco distinto para cada país. Reino Unido y USA comenzaron a principios de diciembre 2020 con gran aparato mediático. Otros no empezaron hasta marzo 2021. Para cada país he calculado el incremento relativo de mortalidad.</p> <p>El resultado es que una gran mayoría tiene incremento positivo: más muertos COVID-19 durante la intervención farmacéutica que antes (2020). En particular USA tiene un incremento considerable. Un test estadístico estándar confirma que la diferencia es significativa, o sea que no podemos afirmar que "no hay diferencia en la mortalidad COVID-19 antes y después del comienzo de la intervención farmacéutica". Por otro lado podemos decir que hay "razones de sobra" para afirmar que hay más muertos COVID-19 durante la "vacunación" que antes de que se comenzara a inocular a las personas.</p> <p>La revista ha comprobado los cálculos y no dicen en su respuesta que sean incorrectos. Ergo, no han falsificado lo que digo en la letter. </p> <p>En segundo lugar he considerado la pregunta ¿hay algún periodo de tiempo en el que la "vacunación" ha conseguido una disminución efectiva de la mortalidad COVID-19?</p> <p>Pudiera ser que al principio de la operación de intervención farmacéutica durante unos días se apreciara un efecto importante de la "vacunación" en forma de descenso de la mortalidad COVID-19, coincidiendo con la afirmación de las empresas de que los anticuerpos generados son fuertes al principio y se van debilitando, con la recomendación actual de "reforzar" con una nueva dosis al cabo de tres o cuatro meses. (curiosamente, el discurso oficial es que ahora han disminuido los casos graves gracias a unas inyecciones que se hicieron hace seis meses o más ¿no contradice lo anterior?)</p> <p>Para intentar responder a la pregunta, he considerado periodos de tiempo simétricos en torno al comienzo de la "vacunación" o sea, un día antes y un día después, dos días antes y después, y así hasta 300 días antes y después del comienzo de las inyecciones. Al hacer tests estadísticos, se encuentra que no hay efecto significativo desde el punto de vista estadístico (p-value < 0.01) hasta pasados más de 140 días, y para periodos mayores de 140 días la conclusión es que hay más muertos COVID-19 durante la "vacunación" que antes (estadísticamente significativo con p-value < 0.01). Hasta los 140 días, los resultados son que no se puede descartar que mortalidad COVID-19 antes y después tienen la misma mediana y que, por tanto, son indistinguibles estadísticamente.</p> <p>En palabras llanas, no se nota diferencia hasta más o menos 140 días y después la conclusión clara es que hay más muertos COVID-19 durante la "vacunación" que antes (en 2020). Otra vez, la revista no puede decir que los cálculos son incorrectos, por lo que simplemente indican que "no es de interés". No sé si esta calificación sería compartida por la población en general. Evidentemente, para los gobernantes estos datos y resultados son bastante "incómodos".</p> <p>La mayor limitación de este pequeño estudio es el conjunto de datos de base. Se puede argumentar sobre su inexactitud. De hecho una de las mayores inexactitudes es la declaración de comienzo de la "vacunación". Muchos países estaban vacunando antes de la fecha que aparece en OWID. De hecho, estaban vacunando a personas de riesgo o personal sanitario y auxiliar en sitios como residencias. Ajustando estas fechas, los resultados serían todavía más desfavorables para los productos sanitario. Otro ejemplo es China, cuya declaración de mortalidad es simplemente nula a partir de una fecha. No he intentado correcciones, simplemente he tomado los datos como lo he hecho con todos los demás países. Otra de las posibles inexactitudes son las primeras olas en países europeos y algunos estados de USA, en las que un estado de panico general y otras causas posibles pudieron influir en una fuerte sobre diagnosis de COVID-19, especialmente en las residencias de ancianos. Tampoco he hecho ningún intento de corrección, sino que he tomado los datos tal cual. Habrá otras limitaciones de las que no soy consciente.</p> <p>El test utilizado es el "Wilkinson rank sum" que no asume una distribución parametrizada de los datos, por lo que podemos estar bastante seguros de que no estoy introduciendo trucos estadísticos. </p> <p><strong>Importante</strong>: no estoy hablando de muertes producidas/declaradas por vacunas, aunque muchos muertos COVID-19 estaban "vacunados" durante 2021. No es hasta fechas recientes que los gobiernos han comenzado a precisar el estado "vacunal" de los muertos COVID-19, fundamentalmente como parte de la campaña de acoso a las personas "no vacunadas". Parece que las estadísticas recientes no son favorables a la estrategia gubernamental, por lo que los datos se van cubriendo de un velo de misterio.</p> <p><strong>En conclusión, la comparación de la mortalidad COVID-19 antes y después del comienzo de la "vacunación" más masiva de la historia de la humanidad (hasta ahora) no permite afirmar que las "vacunas" han disminuido la mortalidad COVID-19 hasta la fecha de los datos recogidos de OWID.</strong></p> <p> </p> <p>***** ******* **********</p> <p>Content:</p> <p>Data downloaded from Our World in Data at January 07, 2022</p> <p>Source code for the analysis and visualization </p> <p>submitted figure </p> <p>submitted letter</p> <p>response from the journal</p>
Cross-spectra used in "Detailed S-wave velocity structure of sediment and crust off Sanriku, Japan by a new analysis method for distributed acoustic sensing data using a seafloor cable and seismic interferometry"
<p>Cross-spectra used in "Detailed S-wave velocity structure of sediment and crust off Sanriku, Japan, derived from distributed acoustic sensing data collected using a seafloor cable with seismic interferometry", by Shun Fukushima, Masanao Shinohara, Kiwamu Nishida, Akiko Takeo, Tomoaki Yamada, and Kiyoshi Yomogida </p> <p>For more information, please contact Shun Fukushima (s-fuku@eri.u-tokyo.ac.jp)</p>
Supplementary data for "A new species of Rhagoletis (Diptera: Tephritidae) from Switzerland..."
<p>Supplementary data file with the alignement of the seguences used in the paper by S. V. Korneyev et al. 2022. A new species of Rhagoletis (Diptera: Tephritidae) from Switzerland, with discussion of its relationships within the genus. <em>Zoodiversity</em>, 56(1)</p>
Data from: Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with description of a new species from montane California
<p>The spider genus <em>Hypochilus</em> is a relictual lineage of Nearctic species distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in <em>Hypochilus</em> has been challenging, with different data types recovering sometimes conflicting topologies. Furthermore, conserved morphology coupled with extreme genetic divergence and paraphyletic topologies at the species level has led to uncertain species limits in some complexes. Using a combination of ultraconserved elements (UCEs), mitochondrial CO1 by-catch, and studies of morphology, we have reconstructed <em>Hypochilus</em> interspecies relationships and have more critically evaluated the possibility of cryptic species in California and in southern Appalachia. Phylogenomic data from hundreds of nuclear loci strongly support the monophyly of regional clades, and furthermore support a ((California, Appalachia), southern Rocky Mountains)) topology. We hypothesize late Cenozoic age divergences in North America, but acknowledge that more research is needed to reliably date divergences in this genus. Within the southern Appalachian fauna, five species are resolved as four lineages (<em>H. thorelli</em> Marx, 1888 and <em>H. coylei</em> Platnick, 1987 are clearly sister taxa), but the interrelationships of these four lineages remain unresolved despite phylogenomic-scale data. The Appalachian species <em>H. pococki</em> Platnick, 1987 is recovered as monophyletic, which differs from prior mitochondrial evidence, but is clearly highly genetically structured at the nuclear level. Although algorithmic analyses of the nuclear data indicate many species (e.g., all populations as species), scanning electron microscopy (SEM) surveys of male morphology instead reveal striking morphological stasis, clearly illustrating the cryptic species problem. Within the California clade, nuclear and mitochondrial lineages of <em>H. petrunkevitchi</em> Gertsch, 1958 correspond directly to drainage basins of the southern Sierra Nevada, with <em>H. bernardino</em> Catley, 1994 nested within <em>H. petrunkevitchi</em> and sister to the southernmost basin populations. Again, algorithmic analyses of nuclear and mitochondrial data suggest many species, but we take a more conservative approach, allowing for population genetic structure within species. Combining nuclear, mitochondrial, geographic and morphological evidence we describe a new species from the Tule River and Cedar Creek drainages, <em>Hypochilus</em> <em>xomote</em> sp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.</p>
Raw Data for the article: Human Amnion-Derived Mesenchymal Stromal Cells: A New Potential Treatment for Carbapenem-Resistant Enterobacterales in Decompensated Cirrhosis
<p><strong>Background: </strong>Spontaneous bacterial peritonitis (SBP) is a severe and often fatal infection in patients with decompensated cirrhosis and ascites. The only cure for SBP is antibiotic therapy, but the emerging problem of bacterial resistance requires novel therapeutic strategies. Human amniotic mesenchymal stromal cells (hA-MSCs) possess immunomodulatory and anti-inflammatory properties that can be harnessed as a therapy in such a context.</p> <p><strong>Methods: </strong>An in vitro applications of hA-MSCs in ascitic fluid (AF) of cirrhotic patients, subsequently infected with carbapenem-resistant Enterobacterales, was performed. We evaluated the effects of hA-MSCs on bacterial load, innate immunity factors, and macrophage phenotypic expression.</p> <p><strong>Results: </strong>hA-MSCs added to AF significantly reduce the proliferation of both bacterial strains at 24 h and diversely affect M1 and M2 polarization, C3a complement protein, and ficolin 3 concentrations during the course of infection, in a bacterial strain-dependent fashion.</p> <p><strong>Conclusion: </strong>This study shows the potential usefulness of hA-MSC in treating ascites infected with carbapenem-resistant bacteria and lays the foundation to further investigate antibacterial and anti-inflammatory roles of hA-MSC in in vivo models.</p>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.