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307 results for “RAD”
Data from: Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling
Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
Major and ancillary features according to LI-RADS in the assessment of combined hepatocellular-cholangiocarcinoma
<p>We uploaded the Figures of the manuscript: Granata V, Fusco R, Venanzio Setola S, Sandomenico F, Luisa Barretta M, Belli A, Palaia R, Tatangelo F, Grassi R, Izzo F, Petrillo A. Major and ancillary features according to LI-RADS in the assessment of combined hepatocellular-cholangiocarcinoma. Radiol Oncol. 2020 May 28;54(2):149-158. doi: 10.2478/raon-2020-0029. PMID: 32463393; PMCID: PMC7276649.</p> <p><strong>Abstract</strong></p> <p>Background. The aim of the study was to investigate the performance of the Liver Imaging Reporting and Data<br> System (LI-RADS) v2018 for combined hepatocellular-cholangiocarcinoma (cHCC-CCA) identifying the features that<br> allow an accurate characterization.<br> Patients and methods. Sixty-two patients (median age, 63 years; range, 38–80 years), with pre-surgical biopsy<br> diagnosis of hepatocellular carcinoma (HCC) that underwent hepatic resection, comprised our retrospective study.<br> All patients were subject to multidetector computed tomography (MDCT); 23 patients underwent to magnetic<br> resonance (MR) study. The radiologist reported the presence of the HCC by using LIRADS v2018 assessing major and<br> ancillary features.<br> Results. Final histological diagnosis was HCC for 51 patients and cHCC-CCA for 11 patients. The median nodule size<br> was 46.0 mm (range 10–190 mm). For cHCC-CCA the median size was 33.5 mm (range 20–80 mm), for true HCC the<br> median size was 47.5 mm (range 10–190 mm). According to LIRADS categories: 54 (87.1%) nodules as defined as LR-5,<br> 1 (1.6%) as LR-3, and 7 (11.3%) as LR-M. Thirty-nine nodules (63%) showed hyper-enhancement in arterial phase; among<br> them 4 were cHCC-CCA (36.4% of cHCC-CCA) and 35 (68.6%) true HCC. Forty-three nodules (69.3%) showed washout<br> appearance; 6 cHCC-CCAs (54.5% of cHCC-CCA) and 37 true HCC (72.5%) had this feature. Only two cHCCCCA<br> patients (18.2% of cHCC-CCA) showed capsule appearance. Five cHCC-CCA (71.4% of cHCC-CCA) showed<br> hyperintensity on T2-W sequences while two (28.6%) showed inhomogeneous signal in T2-W. All cHCC-CCA showed<br> restricted diffusion. Seven cHCC-CCA patients showed a progressive contrast enhancement and satellite nodules.<br> Conclusions. The presence of satellite nodules, hyperintense signal on T2-W, restricted diffusion, the absence of<br> capsule appearance in nodule that shows peripheral and progressive contrast enhancement are suggestive features<br> of cHCC-CCA.</p>
Diagnostic performance of LI-RADS in adult patients with rare hepatic tumors.
<p>We uploadedthe images of the manuscript "Diagnostic performance of LI-RADS in adult patients with rare hepatic tumors" pubished on European Review for Medical and Pharmacological Sciences 2021.</p>
Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)
<p>Disjunct distribution is a key issue in biogeography and ecology, but it is often difficult to determine relative roles of dispersal vs. vicariance in disjunctions. We studied phylogeographic pattern of the monotypic <em>Conandron</em> <em>ramondioides</em> (Gesneriaceae), which shows Sino-Japanese disjunctions, with ddRAD sequencing based on a comprehensive sampling of 11 populations from mainland China, Taiwan Island, and Japan. We found a very high degree of genetic differentiation among these three regions, with very limited gene flow and a clear Isolation by Distance pattern. Mainland China and Japan clades diverged first from a widespread ancestral population in the middle Miocene, followed by a later divergence between mainland China and Taiwan Island clades in the early Pliocene. Three current groups have survived in various glacial refugia during the Last Glacial Maximum (LGM), and experienced contraction and/or bottlenecks since their divergence during Quaternary glacial cycles, with strong niche divergence between mainland China + Japan and Taiwan Island ranges. Thus, we verified a predominant role of vicariance in the current disjunction of the monotypic genus <em>Conandron</em>. The sharp phylogenetic separation, ecological niche divergences among these three groups and the great number of private alleles in all populations sampled indicate a considerable time of independent evolution and suggest the need for a taxonomic survey to detect potentially overlooked taxa.</p>
Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
<p>There are currently four radiation medical countermeasures that have been approved by the United States Food and Drug Administration to mitigate hematopoietic acute radiation syndrome, all of which are repurposed radiomitigators. The evaluation of additional candidate drugs that may also be helpful for use during a radiological/nuclear emergency is ongoing. A chlorobenzyl sulfone derivative (organosulfur compound) known as Ex-Rad, or ON01210, is one such candidate medical countermeasure, being a novel, small-molecule kinase inhibitor that has demonstrated efficacy in the murine model. In this study, nonhuman primates exposed to ionizing radiation were subsequently administered Ex-Rad as two treatment schedules (Ex-Rad I administered 24 and 36 h post-irradiation, and Ex-Rad II administered 48 and 60 h post-irradiation) and the proteomic profiles of serum using a global molecular profiling approach were assessed. We observed that administration of Ex-Rad post-irradiation is capable of mitigating radiation-induced perturbations in protein abundance, particularly in restoring protein homeostasis and immune response and mitigating hematopoietic damage, at least in part after acute exposure. Taken together, restoration of functionally significant pathway perturbations may serve to protect damage to vital organs and provide long-term survival benefits to the afflicted population.</p>
Abdominal Aortic Calcium and CAD-RADS 2.0
ClinicalTrials.gov study NCT06956924. IPD Sharing: UNDECIDED. Countries: 1. Publications: 31.
Trial of Rad-223 Activity in Asymptomatic Patients With mCRPC While on Abiraterone or Enzalutamide Besides AR-V7 Status
ClinicalTrials.gov study NCT03002220. IPD Sharing: NO. Countries: 1. Publications: 1.
Performance Evaluation of the Bio-Rad Geenius HIV1/2 Supplemental Assay
ClinicalTrials.gov study NCT02401555. IPD Sharing: Not stated. Countries: 1. Publications: 25.
Genome-wide RAD sequencing data suggest predominant role of vicariance in Sino-Japanese disjunction of the monotypic genus Conandron (Gesneriaceae)
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Data from: Finding stories in noise: mitochondrial portraits from RAD data
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Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
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Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
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Community Earth System Model (CESM) simulations disentangling CO2 effects - RAD (3 of 4)
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Data from: Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling
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Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird
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Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
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Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
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IIb-RAD-seq coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice (Lepeophtheirus salmonis)
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Data from: Substantial differences in bias between single-digest and double-digest RAD-seq libraries: a case study
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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)
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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.