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Health-promoting lifestyle behavior and its associated factors among pregnant women attending antenatal care service in public health institutions of Debre Markos town, Ethiopia
<p>Here is the dataset for the manuscripit entitled "Health-promoting lifestyle and related factors among pregnant women at public health institutions in Debre Markos, Ethiopia"</p>
Code & Data for "Adoption of Transparency and Openness Promotion (TOP) guidelines across journals"
<p>This entry contains code and data that was used in the publication: "Adoption of Transparency and Openness Promotion (TOP) guidelines across journals" submitted in Publications journal.</p> <p>*It was version 2 when we added Fig_3_Tab2_Defining_science_disciplines_plus_plot.R script to version 1.</p> <p>*It was version 3 because we added script that calculates median and mean values of the stringency levels to version 2 data.</p> <p>*Latest version is version 4: we added supplementary data.</p> <p>#IDEA:</p> <p>This project was about analyzing policies of two thousand journals within the framework of eight TOP standards: <br> data citation, transparency of data, material, code and design and analysis, replication, plan and study pre-registration, <br> and two effective interventions: “Registered reports” and “Open science badges”. </p> <p># MATERIALS & METHODS<br> We downloaded the TOP Factor (v33, 2022-08-29 3:12 PM) metric from the https://osf.io/kgnva/files/osfstorage/5e13502257341901c3805317 <br> website and analyzed its content with an in-house R script (in this repo):<br> 1) SCRIPT: fig1_Analyzing_journals_policies_and_TOP_guidelines.R<br> 2) SCRIPT: Figure2a_b_TOP_impl_journal_statistist_0_1_piechart_barplot.R<br> In order to get statistics about implementation of the TOP guidelines across discipline-specific journals, <br> we extracted information about journal’s disciplines from the Scopus content database. <br> We downloaded SCOPUS content coverage from the https://www.elsevier.com/solutions/scopus/how-scopus-works/content?dgcid=RN_AGCM_Sourced_300005030 (existJuly2022.xlsx)<br> and used the first Sheet.<br> We identified match between those 2 tables: <br> 3) SCRIPT: Rscript_overlapping_TOP_dataframe_and_SCOPUS_db.R<br> And resulted in Overlap_SCOPUS_TOP.rds file<br> And performed visualization and statistics:<br> 4) SCRIPT: Fig_3_Tab2_Defining_science_disciplines_plus_plot.R</p> <p> </p> <p>#RESULTS Submitted to Publications 30.9.2022.</p> <p>Reviewed 2.11.2022.</p> <p>Latest version: 25.11.2022.</p>
Supplementary files for the article entitled: PIEZO2 promotes cell proliferation and metastasis in colon carcinoma through the SLIT2/ROBO1/VEGFC pathway
<p>All results were analyzed using the Statistical Package for the Social Sciences version 20.0 (IBM Corporation, Armonk, NY, USA). The results of Schoenfeld residuals method were analyzed using the R 4.2.2 software and survminer package.</p>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
Tea seed meal application promoted microbial community diversity in the soil of peach orchard
<p><span>Soil microbes are indispensable in agricultural production, and they respond differently to different fertilization regimes. However, there is limited understating of microbial composition and function responses to an organic fertilizer tea seed meal (TSM) and conventional fertilizer. Here we first reported the change rules and functions of soil microbial community in peach orchard soil after application of compound fertilizer plus urea (CFU) and different amounts (1.25, 2.50, 3.75 and 5.00 kg) of TSM. Compared to CFU, the application of 1.25, 2.50 and 3.75 kg TSM significantly decreased the Chao1 index of bacterial community in peach orchard soil. The Shannon index of bacterial and fungal communities in 2.50 kg TSM treatment was significantly higher than that in CFU. Beta diversity analysis of bacteria and fungi (based on Bray-Curtis matrix and OTUs level) revealed significant structural differences among all five experimental groups (ANOSIM, bacteria: R= 0.665, p = 0.001; fungi: R= 0.996, p = 0.001). The TSM treatments significantly decreased the relative abundances of potentially unfriendly bacteria (<em>Acidothermus</em>, <em>Acidicaldus</em>, </span><span><em>Sphingomonas</em>,</span><span> <em>Candidatus</em> <em>Koribacter</em> and <em>Candidatus</em> <em>Solibacter</em>) and fungi (<em>Fusarium</em>), and significantly increased the relative abundances of potentially beneficial fungi (<em>Trechispora</em>, <em>Sagenomella</em>, <em>Penicillium</em>, <em>Acaulium</em> <em>caviariforme</em>, <em>Leucoagaricus</em> and <em>Chlorophyllum</em>) compared with CFU. These changes were more obvious when the application amount of TSM was 2.50 kg. This study provides insights into the potential of application of TSM as an organic fertilizer in agricultural production.</span></p>
Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution
<p>The archives uploaded here include the code used to perform the evolutionary simulations as described in <em>Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution </em>authors: Martin,R. Tate, A. as well as the data that was used in the generation of the figures for that paper. Code requires the Julia programming language and necessary packages to run.</p>
Salt-inducible kinase 3 protects tumor cells from cytotoxic T-cell attack by promoting TNF-induced NF-κB activation
<p>WHAT IS ALREADY KNOWN ON THIS TOPIC</p> <ul> <li> <p>Tumor-intrinsic resistance to T cell (TC)-released cytokines, such as tumor necrosis factor (TNF)-α, has recently emerged as a major mechanism of tumor immune evasion. Yet, a deeper characterization of the genes that are responsible for this effect is needed.</p> </li> </ul> <p>WHAT THIS STUDY ADDS</p> <ul> <li> <p>Salt-inducible kinase 3 (SIK3) is a novel regulator of tumor-intrinsic resistance to cytotoxic TC attack.</p> </li> <li> <p>SIK3 confers tumor cell protection from TC-released TNF by sustaining the expression of pro-survival and anti-apoptotic genes under the control of nuclear factor kappa B (NF-κB).</p> </li> <li> <p>A TNF/SIK3/NF-κB-mediated gene signature correlated with significantly reduced patient survival in pancreatic cancer.</p> </li> </ul> <p>HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE AND/OR POLICY</p> <ul> <li> <p>Pharmacological inhibition of SIK3 might be an effective strategy to sensitize cancer cells to TC-based immunotherapies by rewiring tumor cell responses to TC-secreted TNF.</p> </li> </ul>
Supplemental data of the comment on "Sexual selection promotes giraffoid head-neck evolution and ecological adaptation"
<p>This dataset is the supplemental data of the comment paper on "Sexual selection promotes giraffoid head-neck evolution and ecological adaptation" (Hou et al., 2023, Science 379, eadd9559). 333 codings are rescored and the statements of 10 characters are modified, with notes and explanations in the Microsoft Excel file. </p>
Data for: Low protease activity in B cell follicles promotes retention of intact antigens after immunization
<p>The structural integrity of vaccine antigens is critical to the generation of protective antibody responses, but the impact of protease activity on vaccination in vivo is poorly understood. We characterized protease activity in lymph nodes and found that antigens were rapidly degraded in the subcapsular sinus, paracortex, and interfollicular regions, whereas low protease activity and antigen degradation rates were detected in the vicinity of follicular dendritic cells (FDCs). Correlated with these findings, immunization regimens designed to target antigen to FDCs led to germinal centers dominantly targeting intact antigen, whereas traditional immunizations led to much weaker responses that equally targeted the intact immunogen and antigen breakdown products. Thus, spatially compartmentalized antigen proteolysis affects humoral immunity and can be exploited.</p>
A Study on the Promotion of Cooperative Behavior in Local Communities through Recalling Place Memory
<p>Items for "Emotional Valence" = q4 and q8</p> <p>Items for "Place Attachment" = q11, q12, q13, q14, q15 and q16</p> <p>Items for "Willingness to follow local garbage disposal rules" = q22 and q23</p> <p>Items for "Perceived self-interest in following local garbage disposal rules" = q24 and q25</p> <p>Items for "Willingness to participate in local pro-environmental events" = q17, q19 and q20</p> <p>Items for "Perceived self-interest in local pro-environmental events" = q18 and q21</p>
Deciphering the structural dynamics in molten salt-promoted MgO-based CO2 sorbents and their role in the CO2 uptake. Open data access
<p><strong>Open data for publication "Deciphering the structural dynamics in molten salt-promoted MgO-based CO<sub>2</sub> sorbents and their role in the CO<sub>2</sub> uptake" </strong></p>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
Data from: The CD73 immune checkpoint promotes tumor cell metabolic fitness
<p>CD73 is an ectonucleotidase overexpressed on tumor cells that suppresses anti-tumor immunity. Accordingly, several CD73 inhibitors are currently being evaluated in the clinic, including in large randomized clinical trials. Yet, the tumor cell-intrinsic impact of CD73 remains largely uncharacterized. Using metabolomics, we discovered that CD73 significantly enhances tumor cell mitochondrial respiration and aspartate biosynthesis. Importantly, rescuing aspartate biosynthesis was sufficient to restore proliferation of CD73-deficient tumors in immune-deficient mice. Seahorse analysis of a large panel of mouse and human tumor cells demonstrated that CD73 enhanced oxidative phosphorylation (OXPHOS) and glycolytic reserve. Targeting CD73 decreased tumor cell metabolic fitness, increased genomic instability and suppressed poly ADP ribose polymerase (PARP) activity. Our study thus uncovered an important immune-independent function for CD73 in promoting tumor cell metabolism and provides the rationale for previously unforeseen combination therapies incorporating CD73 inhibition.</p>
Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing
<p><strong>Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing.</strong></p> <p>Zhang, Annie, Massachusetts Institute of Technology, ORCID: 0000-0003-3939-2585</p> <p>DOI: 10.5281/zenodo.7814499</p> <p>Primary publication DOI: <a href="https://doi.org/10.1073/pnas.2305556120">https://doi.org/10.1073/pnas.2305556120</a></p> <p> </p> <p><strong>Folder Structure</strong></p> <p> </p> <p>Source data are organized based on the parent figures from the main text (Figs 1-6). Source data from supplementary figures associated are placed within the associated parent figure folder. All figures, their associated parent figures, and the experiment names from which these figures are derived are summarized in the 'Summary.xlsx' file.</p> <p> </p> <p><strong>File Formats</strong></p> <p><strong> </strong></p> <p>1. Integrated trace files are saved as .dat files.</p> <p> </p> <p>- These trace files are obtained by integrating the fluorescence intensity contained within each DNA spot, or Area of Interest (AOI), over the range of the experimental time frame. They can be read and viewed in Matlab or the Matlab program imscroll, which is publicly available: <a href="https://github.com/gelles-brandeis/CoSMoS_Analysis">https://github.com/gelles-brandeis/CoSMoS_Analysis</a>.</p> <p> </p> <p>- Naming of files:</p> <p>The experiment name is specified at the beginning of the file name.</p> <p>The excitation and emission fields are specified using the following abbreviations.</p> <p>Gex: Green excited (Donor excited)</p> <p>Rex: Red excited (Acceptor excited)</p> <p>GexRex: Green and red excited (Donor and acceptor excited)</p> <p>Gem: Green emission (Donor emission)</p> <p>Rem: Red emission (Acceptor emission)</p> <p> </p> <p> </p> <p>To read the .dat integrated trace files in Matlab the user may type: </p> <p>>>[fn fp] = uigetfile</p> <p>% use the dialog box to mouse click on the appropriate *.dat file, then type:</p> <p>>>eval(['load ' [fp fn] ' -mat'])</p> <p>% This loads an aoifits structure array into the Matlab command environment</p> <p> </p> <p>The integrated trace data is stored in the aoifits.data matrix. A description of the columns is in the aoifits.dataDescription.</p> <p> </p> <p>The first five columns within aoifits.data are the most relevant to view fluorescence emission intensities at individual AOIs over time.</p> <p>Column 1: aoinumber</p> <p>Column 2: framenumber</p> <p>Column 3: amplitude (of fluorescence emission)</p> <p>Column 4: xcenter of the aoi</p> <p>Column 5: ycenter of the aoi</p> <p> </p> <p> </p> <p>2. Time Intervals are stored as excel spreadsheet (.xlsx) files.</p> <p> </p> <p>These files contain the AOI numbers used for analysis and frame numbers that correspond to specific events, such as protein arrival and departure events.</p> <p> </p> <p> </p> <p>3. For experiments with <em>E</em><sub>FRET</sub> analysis performed, <em>E</em><sub>FRET</sub> values are stored as .mat matrix files.</p> <p> </p> <p>Column 1: Time in seconds after protein colocalization with DNA</p> <p>Column 2: <em>E</em><sub>FRET </sub>values</p> <p>Column 3: AOI number</p> <p>Column 4: Frame number</p>
Uncovering the CO2 Capture Mechanism of NaNO3-Promoted MgO by 18O Isotope Labeling
<p>Raw data for the article "Uncovering the CO<sub>2</sub> Capture Mechanism of NaNO<sub>3</sub>-Promoted MgO by <sup>18</sup>O Isotope Labeling", already published in JACS Au</p> <p>All details concerning conditions and equipment for measurements can be found in the main text, supporting information of the article, and in text file contained in the folder.</p>
Functional matrices N, TEs vs promoters, weighted with L = 2.5e5kb, hg19
<p>Refers to the manuscript: "Statistical learning quantifies transposable element-mediated cis-regulation", by Pulver et al., 2023.</p> <p> </p> <p>TE subfamilies are split between so-called "functional" and complementary "non-functional" fractions. Functional integrants were defined as such based on overlapping epigenomics data (e.g. transcription factor binding by ChIP-seq, open chromatin by ATAC-seq).</p> <p> </p> <p>The "functional_weighted_mappability" only contain cis-regulatory weights for selected subfamilies, split between low and high mappability (median split over averages per integrants). They should be incorporated into N_functional_weighted matrices for the appropriate experiments, and not be used on their own.</p>
Matrices N, TEs vs promoters, weighted with L in [1e3kB, 1e10kB], hg19
<p>Related to "Statistical learning quantifies transposable element-mediated cis-regulation", Pulver et al. 2023</p> <p>Regulatory susceptibility matrices N, with rows as hg19 protein coding genes and columns as TE subfamilies. For any given gene, regulatory TEs are strictly out of any promoter and any exon belonging to that gene. The contribution of each single TE is weighted by a gaussian kernel centered on the closest promoter of that gene, with varying bandwiths spanning the range L = 1e3kB to 1e10kB.</p> <p>The "TAD_restricted" N matrices were built by bounding the distances until which TEs were considered as putative cis-regulatory elements for protein-coding genes to TAD boundaries. Pairs of genes - TEs that do not overlap TADs are weighted irrespective of TAD boundaries.</p> <p>The "weighted_mappability" N matrices only contain selected subfamilies and should be incorporated into N_weighted computed with L = 2.5e5kb before usage. Low vs high mappability fractions of subfamilies were separated using a median split on per-integrant average mappability scores.</p>
Fig. 5 in Constituents promoting osteogenesis from the fruits of Psoralea corylifolia and their structure-activity relationship study
Fig. 5. Effects of psoralidin (0.1 μM) and neobavaisoflavone (0.1 μM) on osteogenic differentiation and mineralisation in MC3T3-E1 cell without or with ICI (0.1 μM) treatment. (A1) Calcium nodules after induction for 16 days stained by 1% Alizarin Red S. (A2) Quantification assay of the calcium nodules. (B) ALP activity after induction for 7 days; *P <0.05, **P <0.01, ***P <0.001, vs Control group; ###P <0.001, vs corresponding group without ICI. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation
<p>During megakaryopoiesis, megakaryocytes (MK) undergo cellular morphological changes with strong modification of membrane composition and lipid signaling. Here we adopt a lipid-centric multiomics approach to create a quantitative map of the MK lipidome during maturation and proplatelet formation. Data reveal that MK differentiation is driven by an increased fatty acyl import and <em>de novo</em> lipid synthesis, resulting in an anionic membrane phenotype. Pharmacological perturbation of fatty acid import and phospholipid synthesis blocked membrane remodeling and directly reduced MK polyploidization and proplatelet formation resulting in thrombocytopenia. The anionic lipid shift during megakaryopoiesis was paralleled by lipid-dependent relocalization of the scaffold protein CKIP-1 and recruitment of the kinase CK2α to the plasma membrane, which seems to be essential for sufficient platelet biogenesis. Overall, this study provides a framework to understand how the MK lipidome is altered during maturation and the impact of MK membrane lipid remodeling on MK kinase signaling involved in thrombopoiesis.</p>
Effect of promoting computational thinking on 21st century skills: a systematic review of the literature
<p>Data extracted from primary studies of a systematic literature review investigating the effect of promoting computational thinking on 21st century skills.</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.