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Raw data for the article: Investigating the Differential Circulating microRNA Expression in Adolescent Females with Severe Idiopathic Scoliosis: A Proof-of-Concept Observational Clinical Study
<p>Adolescent Idiopathic Scoliosis (AIS) is the most common form of three-dimensional spinal disorder in adolescents between the ages of 10 and 18 years of age, most commonly diagnosed in young women when severe disease occurs. Patients with AIS are characterized by abnormal skeletal growth and reduced bone mineral density. The etiology of AIS is thought to be multifactorial, involving both environmental and genetic factors, but to date, it is still unknown. Therefore, it is crucial to further investigate the molecular pathogenesis of AIS and to identify biomarkers useful for predicting curve progression. In this perspective, the relative abundance of a panel of microRNAs (miRNAs) was analyzed in the plasma of 20 AIS patients and 10 healthy controls (HC). The data revealed a significant group of circulating miRNAs dysregulated in AIS patients compared to HC. Further bioinformatic analyses evidenced a more restricted expression of some miRNAs exclusively in severe AIS females. These include some members of the miR-30 family, which are considered promising regulators for treating bone diseases. We demonstrated circulating extracellular vesicles (EVs) from severe AIS females contained miR-30 family members and decreased the osteogenic differentiation of mesenchymal stem cells. Proteomic analysis of EVs highlighted the expression of proteins associated with orthopedic disease. This study provides preliminary evidence of a miRNAs signature potentially associated with severe female AIS and suggests the corresponding vesicular component may affect cellular mechanisms crucial in AIS, opening the scenario for in-depth studies on prognostic differences related to gender and grade.</p>
Climate change signal in the ocean circulation of the Tyrrhenian Sea
<p> ROM model data for climate change signal in the ocean circulation of the Tyrrhenian Sea.</p>
Figure 3 from: Gómez-Sánchez EF, Ochoa-Díaz-López H, Espinoza-Medinilla EE, Velázquez-Ramírez DD, Santos-Hernandez NG, Ruiz-Castillejos C, Vidal-López DG, Moreno-Rodríguez A, Flores-Villegas AL, López-Argueta E, De Fuentes-Vicente JA (2022) Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico. ZooKeys 1084: 139-150. https://doi.org/10.3897/zookeys.1084.78664
Figure 3 PCR products of the mini-exon gene in blood of smalls mammals from the "El Zapotal" Ecological Reserve. Amplification resulted in a PCR product of 350 bp and this confirms that these parasites belong to the TCI group. L: ladder; samples: Q positive control (Qro. strain); 1–6 D. marsupialis; 7–10 P. mexicanus; 11 H. desmarestianus; 12 D. mexicana.
Figure 1 from: Gómez-Sánchez EF, Ochoa-Díaz-López H, Espinoza-Medinilla EE, Velázquez-Ramírez DD, Santos-Hernandez NG, Ruiz-Castillejos C, Vidal-López DG, Moreno-Rodríguez A, Flores-Villegas AL, López-Argueta E, De Fuentes-Vicente JA (2022) Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico. ZooKeys 1084: 139-150. https://doi.org/10.3897/zookeys.1084.78664
Figure 1 Location of the "El Zapotal" Ecological Reserve in southeastern Mexico, note the border of the reserve with the urban area.
Figure 2 from: Gómez-Sánchez EF, Ochoa-Díaz-López H, Espinoza-Medinilla EE, Velázquez-Ramírez DD, Santos-Hernandez NG, Ruiz-Castillejos C, Vidal-López DG, Moreno-Rodríguez A, Flores-Villegas AL, López-Argueta E, De Fuentes-Vicente JA (2022) Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico. ZooKeys 1084: 139-150. https://doi.org/10.3897/zookeys.1084.78664
Figure 2 PCR products of the mini-exon gene in blood of bats from the "El Zapotal" Ecological Reserve. Amplification resulted in a PCR product of 350 bp and this confirms that these parasites belong to the TCI group. L: Ladder; Samples: 1 positive control (Qro. strain); 2–11 A. jamaicensis; 12–14 A. lituratus; 15–16 C. perspicillata; 17–18 S. lilium; 19 G. soricina.
Healthy and cancer individuals from Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer
<p>Oxford Nanopore sequencing data from 61 samples described in manuscript "Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer"<br><br></p> <p>All data are aligned to UCSC analysisSet hg38 (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/), and use 0-based coordinates.</p> <p><strong>Level 2:</strong> In order to provide combined fragmentation and methylation information, Biscuit was used to create “epiBED” files (see Methods). epiBED files contain each read on a separate line, with each DNA methylation call on the read. epiBED files can be used for combined methylation/fragmentomic analysis, and are compatible with the CelFiE-ISH software that was used for cell of origin deconvolution.</p> <p>Creation of Biscuit EpiBED files:<br>Biscuit (https://huishenlab.github.io/biscuit/) v. 1.4.1-dev was used with the command “biscuit epiread -M -b 0 -m 0 -a 0 -5 0 -3 0 -y 0.9 -L 1000000 hg38.analysisSet.fa”, where the reference is the same UCSC reference genome used for alignment. Files are available in the Zenodo repository listed in Data Availability.</p> <p><strong>Level 3</strong>: DNA methylation BED files. BED files created by modkit (see Methods) provide one line for each CpG covered, and can be used for basic DNA methylation analysis.<br><br>Creation of modkit BED files:<br>BED files were created using modkit (https://github.com/nanoporetech/modkit) v. 0.1.5 with the command “modkit pileup --cpg --combine-strands --ignore h --filter-threshold 0.9 --bedgraph". </p> <p> </p>
CTMM Data for: 'Sex-specific differences in cytokine signaling pathways in circulating monocytes of cardiovascular disease patients'
<p><span>Data from the publication 'Sex-specific differences in cytokine signaling pathways in circulating monocytes of cardiovascular disease patients' <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.atherosclerosis.2023.04.005" target="_blank" rel="noreferrer noopener"><span>https://doi.org/10.1016/j.atherosclerosis.2023.04.005</span></a> </span></p> <p><span>We generated sex-biased gene expression signatures by comparing male versus female monocytes of coronary artery disease (CAD) patients (n = 450) from the Center for Translational Molecular Medicine-Circulating Cells Cohort. </span></p> <p><span>the data includes 3 dataframes : </span></p> <p><span>clin_cvd: patient info</span></p> <p><span>geneexprs_hgnc: gene expression after batch correction</span></p> <p><span>GES_cvdmf_HGNC: limma results (male vs female)</span></p>
Analysis of Circulating Biomarkers for Minimally Invasive Early Detection of Breast Cancer
<p>A nested case–control study was conducted on plasma samples of 65 cases and 66 controls (discovery set) and 32 cases and 127 controls (validation set). 10 circulating microRNAs have been analyzed by RT-qPCR and 7 microRNA ratios (as the difference between their threshold cycles) have been included in a model to predict the presence of breast cancer. Together with the women identifier (andromeda_id) and the seven microRNA ratios, menopause staus (menopause), body mass index (bmi_di), the interaction term between menopause and BMI (bmi_men), the life-style score according to the World Cancer Research Fund (score_wcrf), the breast density classification (tabar), the cancer diagnosis (status) and the type of control (class2 - only for the validation cohort where there were two types of controls: mammography negatives (N) and mammography false-positives(N2)) are reported in the first sheet (validation set) and in the third sheet (discovery set). The second sheet contains the time intervals between enrollment with blood sampling and breast cancer diagnosis. This information was used only for the validation set, where these intervals were much higher than in the discovery set.</p> <p>Raw threshold cycles (Ct) are available upon request.</p>
Geothermal heating affecting ocean stratification and circulation after the Last Glacial Maximum
<p>Data generated in this study is archived here.</p>
The data for "Climatology of the Residual Mean Circulation of the Martian Atmosphere and Contributions of Resolved and Unresolved Waves Based on a Reanalysis Dataset" by A. Asumi, K. Sato, M. Kohma, and Y. Hayashi in JGR, Planet
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Single Basin Simulations for "A Framework for Constraining Ocean Mixing Rates and Overturning Circulation from Age Tracers"
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Data and codes for Toda et al. 2024 Walker circulation strengthening driven by sea surface temperature changes outside the tropics
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DALROMS-NWA12 v1.0, a coupled circulation-sea ice-biogeochemistry model for the northwest North Atlantic: input files (3 of 3)
<p>DALROMS-NWA12 v1.0 is a coupled circulation-sea ice-biogeochemistry modelling system based on ROMS, CICE, and MCT. The model domain covers the North Atlantic Ocean from ~81 deg W to ~39 deg W and ~33.5 deg N to 76 deg N. This record includes the files necessary for nudging the currents towards Copernicus GLORYS12V1 reanalysis values in a simulation from 1 September to 31 December 2013.</p> <p>The remaining input files for this period are available at <a href="https://doi.org/10.5281/zenodo.12752190" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12752190</a> and <a href="https://doi.org/10.5281/zenodo.12734049" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12734049</a>.</p> <p>Model codes, scripts for compiling the model, and sample CPP header files and runtime parameter files (namelists) for physics-only simulations are available at <a href="https://doi.org/10.5281/zenodo.12752091" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12752091</a>. CPP header and runtime parameter files for the biogeochemistry module are available upon request.</p> <p>Sample output files (from the physics and biogeochemistry modules) are available at <a href="https://doi.org/10.5281/zenodo.12744506" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12744506</a> and <a href="https://doi.org/10.5281/zenodo.12746262" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12746262</a>.</p>
DALROMS-NWA12 v1.0, a coupled circulation-sea ice-biogeochemistry model for the northwest North Atlantic: output files (1 of 2)
<p>DALROMS-NWA12 v1.0 is a coupled circulation-sea ice-biogeochemistry modelling system based on ROMS, CICE, and MCT. The model domain covers the North Atlantic Ocean from ~81 deg W to ~39 deg W and ~33.5 deg N to 76 deg N. This record includes daily-mean output of all (ocean circulation, sea ice, and biogeochemistry) modules for September 2013, when the simulation was initialized. Similar files for January 2015 are available at <a href="https://doi.org/10.5281/zenodo.12746262" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12746262</a>.</p> <p>Model codes, scripts for compiling the model, and sample CPP header files and runtime parameter files (namelists) for physics-only simulations are available at <a href="https://doi.org/10.5281/zenodo.12752091" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12752091</a>. CPP header and runtime parameter files for the biogeochemistry module are available upon request.</p> <p>Sample input files for physics-only simulations are available at <a href="https://doi.org/10.5281/zenodo.12752190" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12752190</a>, <a href="https://doi.org/10.5281/zenodo.12734049" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12734049</a>, and <a href="https://doi.org/10.5281/zenodo.12735153" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.12735153</a>. Input files for the biogeochemistry module are available upon request.</p>
Figure 1 in Density and diversity of Culicidae (Diptera), with analysis of viral circulation, in urban public establishments in Northern Paraná, Brazil
Figure 1 Geographical location of the study area, demonstrating the sample collection sites, carried out between January and September 2019, in the urban area of the municipality of Londrina, Paraná, Brazil.
Datasets accompanying Deep generative AI models analyzing circulating orphan non-coding RNAs enable accurate detection of early-stage non-small cell lung cancer
<p>These datasets accompany the manuscript "Deep generative AI models analyzing circulating orphan non-coding RNAs enable accurate detection of early-stage non-small cell lung cancer".</p> <p>The datasets include:</p> <ul> <li> <p><code>metadata.tsv.gz</code> Phenotype information of the samples</p> </li> <li> <p><code>mirna_counts.tsv.gz</code> MicroRNA count matrix (for data normalization)</p> </li> <li> <p><code>oncrna_counts.tsv.gz</code> oncRNA count matrix</p> </li> <li> <p><code>orion/</code> Ensemble of Orion models</p> </li> </ul>
Additional information and tables for: Association of circulating metabolites in plasma or serum and risk of stroke: Meta-analysis from seven prospective cohorts
<p><b>Objective: </b>To conduct a comprehensive analysis of circulating metabolites and incident stroke in large prospective population-based settings.</p> <p><b>Methods: </b>We investigated the association of metabolites with risk of stroke in seven prospective cohort studies including 1,791 incident stroke events among 38,797 participants in whom circulating metabolites were measured by Nuclear Magnetic Resonance (<sup>1</sup>H-NMR) technology. The relationship between metabolites and stroke was assessed using Cox proportional hazards regression models. The analyses were performed considering all incident stroke events and ischemic and hemorrhagic events separately.</p> <p><b>Results: </b>The analyses revealed ten significant metabolite associations. Amino acid histidine (hazard ratio (HR) per standard deviation (SD) = 0.90, 95% confidence interval (CI): 0.85, 0.94; <i>P</i> = 4.45×10<sup>-5</sup>), glycolysis-related metabolite pyruvate (HR per SD = 1.09, 95% CI: 1.04, 1.14; <i>P</i> = 7.45×10<sup>-4</sup>), acute phase reaction marker glycoprotein acetyls (HR per SD = 1.09, 95% CI: 1.03, 1.15; <i>P</i> = 1.27×10<sup>-3</sup>), cholesterol in high-density lipoprotein (HDL) 2 and several other lipoprotein particles were associated with risk of stroke. When focusing on incident ischemic stroke, a significant association was observed with phenylalanine (HR per SD = 1.12, 95% CI: 1.05, 1.19; <i>P = </i>4.13×10<sup>-4</sup>) and total and free cholesterol in large HDL particles.</p> <p><b>Conclusions: </b>We found association of amino acids, glycolysis-related metabolites, acute phase reaction markers, and several lipoprotein subfractions with the risk of stroke. These findings support the potential of metabolomics to provide new insights into the metabolic changes preceding stroke.</p>
Body size and circulating levels of different molecules from tree swallows (Tachycineta bicolor) exposed to different doses of lipopolysaccharide (LPS)
<p class="CxSpFirst">The purpose of mounting an immune response is to destroy pathogens, but this response comes at a physiological cost, including the generation of oxidative damage. However, many studies on the effects of immune challenges employ a single high dose, meaning that the consequences of more mild immune challenges are poorly resolved. We tested whether the degree of immunological challenge in tree swallows (<i>Tachycineta bicolor</i>) affects oxidative physiology and body mass, and whether these metrics correlate with parasitic nest mite load. We injected 14-day-old nestlings with either 0, 0.01, 0.1, or 1 mg lipopolysaccharide (LPS) per kg body mass, then collected a blood sample 24-h later to quantify multiple physiological metrics, including oxidative damage (i.e., d-ROMs), circulating amounts of triglyceride and glycerol, and levels of the acute phase protein haptoglobin. After fledging, we identified and counted parasitic nest mites (<i>Dermanyssus</i> spp. and <i>Ornithonyssus</i> spp.). We found that only nestlings injected with 1 mg LPS/kg body mass, which is a common dosage in ecoimmunological studies, lost more body mass than individuals from other treatment groups. However, every dose of LPS resulted in a commensurate increase in oxidative damage. Parasitic mite abundance had no effect on oxidative damage across treatments. Amount of oxidative damage correlated with haptoglobin levels, suggesting compensatory mechanisms to limit self-damage during an immune response. We conclude that while only the highest-intensity immune challenges resulted in costs related to body mass, even low-intensity immune challenges result in detectable increases of oxidative damage.</p>
Supplemental methods for: Circulating plasma proteins differentiate epileptic from psychogenic non-epileptic seizures
<p><b>Objective:</b> To develop a diagnostic test that stratifies epileptic seizure (ES) from psychogenic non-epileptic seizure (PNES) by developing a multimodal algorithm that integrates plasma concentrations of selected immune response associated proteins and patient clinical risk factors for seizure.</p> <p><b>Methods: </b>Daily blood samples were collected from patients evaluated in the epilepsy monitoring unit (EMU) within 24 hours after EEG confirmed ES or PNES and plasma was isolated. Levels of 51 candidate plasma proteins were quantified using an automated, multiplexed, sandwich ELISA and then integrated and analyzed using our diagnostic algorithm.</p> <p><b>Results: </b>A 51 protein multiplexed ELISA panel was used to determine the plasma concentrations of ES patients, PNES patients, and healthy controls. A combination of protein concentrations, TRAIL, ICAM-1, MCP-2 and TNF-R1 were identified that provided a probability that a patient recently experienced a seizure. The diagnostic algorithm yielded an AUC of 0.94 ± 0.07, sensitivity of 82.6% (95% CI: 62.9-93.0) and specificity of 91.6% (95% CI: 74.2-97.7). Further, expanding the diagnostic algorithm to include previously identified PNES risk factors enhanced diagnostic performance with AUC of 0.97 ± 0.05, sensitivity of 91.3%; (95% CI: 73.2-97.6), and specificity of 95.8%; (95% CI: 79.8-99.3).</p> <p><b>Conclusions: </b>We have identified four plasma proteins that could provide a rapid, cost-effective, and accurate blood-based diagnostic test to confirm recent ES or PNES.</p> <p><b>Classification of Evidence</b>: This study provides Class III evidence that variable levels of four plasma proteins, when analyzed by a diagnostic algorithm, can distinguish PNES from ES with sensitivity of 82.6% and specificity of 91.6%.</p>
A new look at the role of complement circulating in peripheral blood and expressed in hematopoietic stem cells in the regulation of hematopoiesis
<p>Hematopoietic transplantation is performed by intravenous infusion of donor-derived or autologous hematopoietic stem progenitor cells (HSPCs), which, in response to bone marrow (BM)-expressed chemoattractant navigate and home to BM hematopoietic niches. This process is followed by their engraftment and expansion to repopulate the recipient’s BM myeloablated before transplantation. The most important BM chemoattractant is the alpha-chemokine stromal-derived factor 1 (SDF-1). However, its homing role is supported by the bioactive phosphospingolipid sphingosine-1-phosphate (S1P) and by extracellular adenosine triphosphate (eATP). As we demonstrated in the past, the CXCR4 receptor for SDF-1 must be incorporated into cell surface membrane lipid rafts (MLRs) for optimal SDF-1 gradient sensing by HSPCs. Our previous research demonstrated that an important and for many years underestimated role in hematopoiesis plays an innate immunity soluble arm that is complement cascade (ComC). We provided an evidence that ComC becomes activated in BM during pharmacological mobilization in response to granulocyte colony-stimulating factor (G-CSF) or CXCR4 receptor antagonist AMD3100. In this proposal, we will focus on the role of ComC in a reverse phenomenon that is posttransplant homing/engraftment of HSPCs. It is known that the critical step before infusion of HSPCs is the myeloablative treatment of the recipient aimed to destroy pathological hematopoiesis and empty BM niches to provide space available for new transplanted HSPCs. Myeloablative treatment involves high-dose chemotherapy or myeloablative irradiation. In experimental animal transplant models, lethal irradiation is a standard procedure. The available literature indicates that both irradiation and chemotherapy induce in various organs and tissues similarly as during mobilization a state of sterile inflammation and extracellular ATP (eATP) released from damaged cells triggers this process. We postulate that the same occurs in the BM microenvironment, and in fact, our preliminary data shows that ComC becomes activated in mice after myeloablative conditioning for transplantation by lethal gamma-irradiation or exposure to myeloablative chemotherapy. It is known that ComC could be activated by i) classical-, ii) mannan-binding lectin, or iii) alternative-pathway. Activation of ComC leads to the release C3 and C5 complement components cleavage fragments - C3a and C5a anaphylatoxins that are processed by serum carboxypeptidase to desArgC3a and desArgC5a as well as leads to the formation of C5b-C9 or non-lytic or lytic membrane attack complex (MAC), which is the terminal product of ComC activation. On the other hand, both HSPCs and cells in the BM microenvironment express receptors for C3a and C5a (C3aR, C5aR1, and C5aR2). After myeloablative therapy, active ComC cleavage fragments circulate in PB. Therefore, HSPCs infused into the transplant recipient's bloodstream are exposed to these potent innate immunity mediators. This interaction of HSPCs with ComC meditators, as we propose, promotes better navigation of infused cells to the recipient BM niches and we hypothesize is a result of the promotion of MLRs formation on HSPCs. On the other hand, myeloablative conditioning for transplantation induces a state of sterile inflammation in transplant recipient BM to facilitate homing and engraftment of circulating in PB transplanted HSPCs. Finally, new intriguing evidence accumulated that in addition to the liver ComC synthesis occurs also inside some cells – e.g., in lymphocytes. Our recent data indicate that the same phenomenon occurs in HSPCs. Therefore, the intercellular expression of ComC elements known as complosome sheds new light on the underappreciated role of innate immunity in regulating hematopoiesis.</p> <p> </p> <p>This work was supported by the National Science Centre, Poland OPUS grant UMO-2022/45/B/NZ6/00475. </p> <p> </p> <p>The data included in the database were used in the following publications:</p> <p>1. <a href="https://www.nature.com/articles/s41375-024-02188-9" target="_blank" rel="noopener">https://www.nature.com/articles/s41375-024-02188-9</a></p> <p>2. <a href="https://link.springer.com/article/10.1007/s11302-023-09943-0" target="_blank" rel="noopener">https://link.springer.com/article/10.1007/s11302-023-09943-0</a></p> <p>3. <a href="https://www.nature.com/articles/s41375-023-01894-0" target="_blank" rel="noopener">https://www.nature.com/articles/s41375-023-01894-0</a></p>
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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.