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Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer
<p>Colorectal Cancer (CRC) is a highly heterogeneous group of diseases, with distinctive genetic and epigenetic alterations. CRC tumors bearing KRAS or BRAF mutations still remain resistant to new therapies. Thus, this augments the necessity to reveal new therapeutic targets in mutKRAS/BRAF, which may account for up to 50% of the total CRC patients. To this end, we investigated primary untreated CRC tumors (WES & RNA-Seq) from 28 Greek patients for their systematic molecular characterization and stratification into diverse groups based on their microsatellite instability (MSI) status and KRAS/BRAF genetic variations, in order to unravel novel targets and putative personalized treatment interventions. The raw data of this project (WES & RNA-Seq) have been uploaded in the EGA European Genome-Phenome Archive (EGAD00001011262 and EGAD00001011263).</p>
atmosphere profile data
Open the record for dataset details and reuse information.
Seawater temperature and salinity depth profiles (CTD) - SAMS IMTA Lab
<p>Dataset contains depth profiles (0m to 20m below the surface) of seawater temperture and salinity, recorded using a handheld CTD (SonTek CastAway-CTD).</p> <p>Data range spans over 4 years (Oct 2020-2024; ASTRAL H2020 project lifespan) containing 53 sampling occassions i.e. on average montghly CTD casts.</p> <p>Hnadheld CTD was frequently cross-calibrated agianst SAMS in-house Seabird CTD and resulting offests appliced to the raw data recordings.</p>
BERT-assisted behavioral profiling of polysemy: contrastive analysis of HONG in Chinese and RED in English
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Multiplexed spatial profiling of Hodgkin Reed-Sternberg cell neighborhoods in classic Hodgkin lymphoma
<p>Single-cell data from multiplexed imaging (Leica Cell DIVE) of 29 proteins in 587 fields of view across 30 classic Hodgkin lymphoma patients.</p> <p>Bulk RNA sequencing (NanoString IO360 panel) raw and normalized data for 32 classic Hodgkin lymphoma patients.</p> <p>Meta data containing information about patients, cell type and state information, and statistical comparisons.</p>
Impacts of a high fat diet on the metabolic profile and the phenotype of atrial myocardium in mice
<p>Aims: Obesity, diabetes and metabolic syndromes are risk factors of atrial fibrillation (AF). We tested the hypothesis that metabolic disorders have a direct impact on the atria favoring the formation of the substrate of AF.</p> <p>Methods & Results: Untargeted metabolomic and lipidomic analysis was used to investigate the consequences of a prolonged high fat diet (HFD) on mouse atria. Atrial properties were characterized by measuring mitochondria respiration in saponin-permeabilized trabeculae, by recording action potential with glass microelectrodes in trabeculae and ionic currents in myocytes using the perforated configuration of patch clamp technique and by several immuno-histological and biochemical approaches. After 16 weeks of HFD, obesogenic mice showed a vulnerability to AF. The atrial myocardium acquired an adipogenic and inflammatory phenotypes. Metabolomic and lipidomic analysis revealed a profound transformation of atrial energy metabolism with a predominance of long-chain lipid accumulation and beta-oxidation activation in the obese mice. Mitochondria respiration showed an increased use of palmitoyl-CoA as energy substrate. Action potentials were short duration and sensitive to the K-ATPdependent channel inhibitor, whereas K-ATP current was enhanced in isolated atrial myocytes of obese mouse.</p> <p>Conclusion:<em><strong> </strong></em>HFD transforms energy metabolism, causes fat accumulation, and induces electrical remodeling of the atrial myocardium of mice that become vulnerable to AF.</p> <p>Translational perspective: Understanding the link between metabolic diseases and atrial fibrillation is of major importance. One hypothesis claims that, in addition to shared co-morbidities, metabolic disorders favor the substrate of atrial fibrillation. Here we show that after prolonged high fat diet, the atrial myocardium becomes adipogenic, inflamed and vulnerable to atrial fibrillation. This tissue remodeling appears to result from an unbalance between uptake and oxidation of fatty acid resulting in long-chain lipid storage, activation metabolic-sensitive potassium channel and action potential shortening. Therefore, diet appears to be an important link between metabolic disorders and atrial fibrillation.</p>
Wind profile in the wave boundary layer and its application in a coupled atmosphere-wave model
<p>The simulation data for the study</p>
Stable isotope profile of autumnal migratory bird feathers on Italian Alps
<p>In the study of migration of birds, there are many aspects to be deepened to comprehend both ecology of the species and their geographical connectivity between breeding and wintering grounds. In the last decades, stable isotopes of light elements such as hydrogen, oxygen, nitrogen, carbon and sulphur measured in cheratinous tissues such feathers are increasingly used in order to delineate origin of migrants and to define ecological aspects of birds. Here we present a complete isotopic profile of several passerine species migrating through Italian Alps during post-breeding season. Stable isotope ratios of hydrogen, oxygen, carbon, nitrogen and sulphur were measured in juvenile feathers of 807 individuals of 48 different specie ringed in central Italian Alps during post-breeding migration in the years 2010, 2011, 2012, and 2013. Birds were ringed in two ringing and monitoring stations of Progetto Alpi (<a href="http://progetto-alpi.muse.it/">http://progetto-alpi.muse.it/</a>). No birds were mistreated, and the sampling took place in compliance with the national and international laws in force at the time of the study.</p>
Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiomes identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis
<p>Supplemental files associated with patient ulcerative colitis metaproteomics study including protein fasta files, protein group (CD-HIT cluster) files, label free quantification output, de novo-database peptide comparison output tables, ComPIL database search output PSM files, 16S amplicon sequencing data, and Interproscan annotations.</p>
Hazelnut SSR database: genetic profiles of the accessions, list of synonyms, and true-to-type genotypes
<p>Hazelnut (<i>Corylus avellana</i> L.) is one of the most important tree nut crops in Europe. Germplasm accessions are conserved in <i>ex situ</i> repositories, located in countries where hazelnut production occurs. In this work, we used ten simple sequence repeat (SSR) markers as the basis to establish a core collection representative of the hazelnut genetic diversity conserved in different European collections. A total of 480 accessions were used: 430 from <i>ex situ</i> collections and 50 landraces maintained <i>on-farm</i>. SSR analysis identified 181 genotypes, that represented our whole hazelnut germplasm collection (WHGC). Four approaches (utilizing MSTRAT, Power Core, and Core Hunter's single- and multi-strategy) based on the maximization (M) strategy were used to determine the best sampling method. Core Hunter's multi-strategy, optimizing both allele coverage (Cv) and Cavalli-Sforza and Edwards (Dce) distance with equal weight, outperformed the others and was selected as the best approach. The final core collection (Cv-Dce30) comprised 30 entries (16.6% of genotypes). It recovered all SSR alleles and preserved parameter variations when compared to WHGC. Entries represented all six gene pools obtained from the population structure analysis of WHGC, further confirming the representativeness of Cv-Dce30. Our findings contribute towards improving the conservation and management of European hazelnut genetic resources and could be used to optimize future research by identifying a minimum number of accessions on which to focus.</p>
Targeted gene expression profiling of human myeloid cells from blood and lung compartments of patients with Tuberculosis and other lung diseases
<p>This dataset comprises expression profiles of 43 genes related to MSDC functioning and 5 reference genes in 8 blood samples and 8 brochio-alveolar lavage fluid (BALF) samples from TB patients. Also included are results from blood and BALF of 2 'other lung disease' patients each.</p>
Figure 6 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 6 Structures of amino acids from GP phenolic fraction "C", optimized at B3LYP/6-31+G(d,p) level.
Figure 3 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 3 Acyclovir triphosphate and its vicinity in the DNA polymerase pocket after docking procedure: a) 3D plane of view and b) 2D plane of view. The interactions of the ligand in the active site cavity are represented as follows: the proximity contour is depicted with a black dotted line; solvent accessibility, as blue clouds around atoms or blue shadows around amino acid residues; polar amino acids are displayed with pink, while the lipophilic ones are in green. Basic amino acids are outlined with blue and the acidic – with red. Hydrogen bond interactions are depicted with dotted arrows, while the ionic ones are depicted with dotted lines.
Figure 2 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 2 Phenolic (trans-ferulic) acid and its vicinity after docking procedure. The amino acid residues of HSV-1 DNA polymerase active site, mostly involved in interaction with ligands, are represented as follows: Lis928 is basic amino acid right from the ligand, Glu 927 is above it, basic amino acid on the left is Lis 939 and Asp 886 is in its right.
Supplementary material 1 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Tables S1–S3 and Figures S1–S4
Figure 8 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 8 Complex of acyclovir triphosphate and amino acids from DNA polymerase active site, optimized at B3LYP/6-31+G(d,p) level.
Figure 7 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 7 Complexes of phenolic acids from GP phenolic fraction "C" and amino acids from DNA polymerase active site, optimized at B3LYP/6-31+G(d,p) level.
Figure 5 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 5 Structures of hydroxybenzoic acids from GP phenolic fraction "C", optimized at B3LYP/6-31+G(d,p) level.
Genome-wide profiling of histone H3K4me3 and H3K27me3 modifications in individual bovine blastocysts by NTU-CAT
<p>BAM and corresponding BW files generated by NON-TiE-UP CUT&Tag (NTU-CAT).</p>
Association of gyrification pattern, white matter changes and phenotypic profile in patients with Parkinson's disease
<p><b>Objective:</b> To investigate the cortical gyrification changes as well as their relationships with white matter (WM) microstructural abnormalities in the akinetic-rigid (AR) and tremor-dominant (TD) subtypes of Parkinson's disease (PD).</p> <p><b>Methods:</b> Sixty-four patients with the AR subtype, 26 patients with the TD subtype and 56 healthy controls (HCs) were included in this study. High-resolution T1-weighted and diffusion-weighted images were acquired for each participant. We computed local gyrification index (LGI) and fractional anisotropy (FA) to identify the cortical gyrification and WM microstructural changes in the AR and TD subtypes.</p> <p><b>Results: </b>Compared with HCs, patients with the AR subtype showed decreased LGI in the precentral, postcentral, inferior and superior parietal, middle and superior frontal/temporal, anterior and posterior cingulate, orbitofrontal, supramarginal, precuneus, and some visual cortices, and decreased FA in the corticospinal tract, inferior and superior longitudinal fasciculus, inferior fronto-occipital fasciculus, forceps minor/major, and anterior thalamic radiation. Decreases in LGI and FA of the AR subtype were found to be tightly coupled. LGIs of the left inferior and middle frontal gyrus correlated with the mini-mental state examination and the Hoehn and Yahr scores of patients with the AR subtype. Patients with the TD subtype showed no significant change in the LGI and FA compared with patients with the AR subtype and HCs.</p> <p><b>Conclusions:</b> Our results suggest that cortical gyrification changes in PD are motor phenotype-specific and are possibly mediated by the microstructural abnormalities of the underlying WM tracts.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.