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12,455 results for “promoters”
Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma
<p>These are whole-slide digital pathology images of esophageal adenocarcinoma (EAC) patient-derived xenograft models. EAC biopsy specimens were cultured <em>in vitro</em> before implanting into immuno-deficient mice. Mice were then divided into the following treatment groups and treated with combinations of chemotherapy and PDE5 inhibitors as follows:</p> <ol> <li>Untreated</li> <li>Epirubicin + Cisplatin + Capecitabine (ECX)</li> <li>ECX + Vardenafil</li> <li>ECX + Tadalafil</li> </ol> <p>All whole slide images are in Olympus .vsi format and can be opened using the BioFormats library in QuPath. We have also included classifiers and scripts for performing the digital pathology analysis in QuPath, and information to link each mouse with treatment groups and corresponding whole slide images.</p> <p>File metadata:</p> <p>classifiers.zip - Folder containing pixel classifiers used for segmentation of IHC stains. These classifiers are to be important into QuPath for the respective analysis of Periostin (POSTN) and alpha Smooth Muscle Actin (SMA) staining using the included Groovy scripts in the scripts folder.</p> <p>SMA.zip - Folder containing whole slide images of mouse patient-derived xenograft tumours in .vsi format (Olympus VS110). Immunohistochemistry with anti-alpha Smooth Muscle Actin antibody.<br> POSTN.zip - Folder containing whole slide images of mouse patient-derived xenograft tumours in .vsi format (Olympus VS110). Immunohistochemistry with anti-Periostin antibody.</p> <p>scripts.zip - Folder containing all groovy scripts used in QuPath for tissue detection (Whole Section Tissue Detection.groovy), and segmentation of POSTN (POSTN Quantification Mice.groovy) and SMA staining tissue areas (SMA Quantification Mice.groovy).</p> <p>POSTN.xlsx - Data on the mice for which anti-POSTN IHC is available. Column names as follows:<br> Image: file name (corresponding to .vsi file).<br> Mouse_ID: Mouse identifier.<br> Treatment: Treatment administered. ECX - Epirubicin, Cisplatin and Capecitabine.<br> POSTN_Area: Total measured area of POSTN+ tissue in the tissue section (in um^2).<br> Total_Area: Total area of the tissue section (in um^2).<br> percentage_POSTN: Percentage of total tissue area that is stained with POSTN (%).</p> <p>SMA.xlsx - Data on the mice for which anti-SMA IHC is available. Column names as follows:<br> Image: file name (corresponding to .vsi file).<br> Mouse_ID: Mouse identifier.<br> Treatment: Treatment administered. ECX - Epirubicin, Cisplatin and Capecitabine.<br> SMA_Area: Total measured area of SMA+ tissue in the tissue section (in um^2).<br> Total_Area: Total area of the tissue section (in um^2).<br> percentage_SMA: Percentage of total tissue area that is stained with SMA (%).</p>
Datasets and Software for publication "Distinct RPA domains promote recruitment and the helicase-nuclease activities of Dna2"
<p>- Magnetic tweezers and mass photometry datasets for the publication "Distinct RPA domains promote recruitment and the helicase-nuclease activities of Dna2, Nature Communications 2021"</p> <p>- costum written Matlab Software for Helicase Analysis</p>
Cooperative action of separate interaction domains promotes high-affinity DNA binding of Arabidopsis thaliana ARF transcription factors
<p>The repository contains the smFRET and SAXS data presented in the preprint https://doi.org/10.1101/2022.11.16.516730 (BioRxiv)</p>
Predator discrimination of prey promotes the predator-mediated coexistence of prey species
<p><span>The predator discrimination of prey can affect predation intensity and the prey density-dependence of predators, which has the potential to alter the coexistence of prey species. We used a predator–prey population dynamics model accounting for the predator's adaptive diet choice and predator discrimination of prey to investigate how the latter influences prey coexistence. The model revealed that: (1) prey species that are perceived as belonging to the same species by a predator are attacked in the same manner, and it is more difficult for them to coexist than those that are recognised as different prey species; and (2) prey species that are not discriminated by a predator—and therefore cannot coexist—may coexist in the presence of an alternative predator that does discriminate between them. These results suggest that prey diversity, which favours the predator discrimination of prey, and the different capabilities of predators to identify prey species both enhance prey coexistence.</span></p>
Aurora A and cortical flows promote polarization and cytokinesis by inducing asymmetric ECT-2 accumulation - Data Archive
<p>This archive contains all the images and raw data generated for: Katrina M Longhini & Michael Glotzer, “Aurora A and cortical flows promote polarization and cytokinesis by inducing asymmetric ECT-2 accumulation”</p> <p>The data is organized by figure then experiment. Each embryo folder contains formatted embryos, which are rotated, cropped, and photobleach corrected. Each recording starts at time 0 on the respective graph.</p> <p>The “AccumulationDataNew” files contain all the data generated from the “3pixel_membranefinder_w_dir.ijm” and “membrane_ROI_TimeSeries_max_scaled_dirs.ijm” scripts organized in a Tidy format generated in R using the first portion of the script “Edited_Membrane_Accumulation_Line_Script.Rmd”. These Fiji and R Markdown scripts are located in the “Analysis Scripts“ folder.</p> <p>All data visualization scripts are included in the “Analysis Scripts” folder.</p> <p>Sequences of plasmids generated for this paper are located in the “Plasmid Sequences” folder.</p>
Benzaldehyde-Promoted (Auto)Photocatalysis under Visible Light: Pitfalls and Opportunities in Photocatalytic H2O2 Production
<p>Data to our study "Benzaldehyde-Promoted (Auto)Photocatalysis under Visible Light: Pitfalls and Opportunities in Photocatalytic H<sub>2</sub>O<sub>2</sub> Production"</p>
Data and Code for "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility"
<p>This snapshot contains code and data for the preprint "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility".</p> <p>Instructions on re-using the data and running the code can be found in the README.md.</p> <p>Changes:</p> <ul> <li>Added survey instrument and informed consent.</li> </ul>
Data for: Higher floral richness promotes rarer bee communities across remnant and reconstructed tallgrass prairies, though remnants contain higher abundances of a threatened bumble bee (Bombus Latreille)
<p>Managing and restoring tallgrass prairie ecosystem is an important form of pollinator conservation in the Midwestern United States. Prairie reconstruction has been found to enhance native bee diversity and abundance, but it is less clear if prairie reconstruction conserves species thought to be at-risk. We reanalyze a previously published dataset on the bee communities of reconstructed and remnant prairie in the US state of Minnesota to investigate how the abundance of at-risk species respond to local factors, such as floral diversity and prairie type (reconstructed or remnant), and landscape factors, in the form of surrounding agricultural production. We defined at-risk species in two ways. For bumble bees, we used the IUCN red list of bumble bees for North America. As other species in the bee community have not been systematically evaluated, we used an independent data set to calculate a community-level measure of rarity as a proxy for at-risk species. We calculated community rarity metrics using a Species Weighted Mean (SWM) approach, with species-level rarity (relative abundance and site occurrence) derived from a regional dataset comprised of over 30,000 specimens from across the US state of Minnesota. We found that the declining bumble bee <em>Bombus</em> <em>fervidus</em> had higher abundances in remnant rather than reconstructed prairies. Floral richness was associated with rarer bee communities (lower SWM values) across remnant and reconstructed prairies. We show that planting and managing prairies for floral diversity promotes bee communities with rarer species, but that remnants better support some at-risk species such as <em>Bombus</em> <em>fervidus</em>. </p>
miR-126 promotes M1 to M2 macrophage phenotype switching via VEGFA and KLF4
<p><strong>Background. </strong>Macrophage polarization and microRNA play crucial roles in the development of atherosclerosis (AS). The M1 macrophage phenotype contributes to the formation of plaques, while the M2 macrophage phenotype resolves inflammation and promotes tissue repair. MiR-126 has been found to play a role in regulating macrophage polarization in the context of AS. However, the exact mechanism of miR-126 requires further research.</p> <p><strong>Methods.</strong> The foam cell model was established by stimulating THP-1 with oxidized low-density lipoprotein (ox-LDL). We transfected foam cells with miR-126 mimic and its negative control. The transfection of miR-126 was implemented by riboFECT CP transfection kit. The levels of miR-126 and M1/M2 associated genes in foam cells were quantified using reverse transcription-quantitative PCR (RT-qPCR). Additionally, the expressions of CD86<sup>+</sup> and CD206<sup>+</sup> cells in foam cells were determined by flow cytometry. Western blotting and RT-qPCR were used to determine the protein and mRNA levels of the vascular endothelial growth factor A (VEGFA) and the transcriptional regulator Krüppel-like factor 4 (KLF4), respectively. Additionally, we detected endothelial cell migration after co-culturing endothelial cells and macrophages. MG-132 was used to indirectly activate the expression of VEGFA, and the expression of KLF4 was also evaluated.</p> <p><strong>Results. </strong>The activation of apoptosis and production of foam cells were boosted by the addition of ox-LDL. We transfected foam cells with miR-126 mimic and its negative control and observed that miR-126 greatly suppressed foam cell development and inhibited phagocytosis. Moreover, it caused pro-inflammatory M1 macrophages to switch to the anti-inflammatory M2 phenotype. This was reflected by the increase in anti-inflammatory gene expression and the decrease in pro-inflammatory gene expression. Additionally, miR-126 dramatically decreased the expressions of VEGFA and KLF4. The protein-protein interaction network analysis showed a significantly high correlation between miR-126, VEGFA, and KLF4. MiR-126 may also promote EC migration by activating macrophage PPAR γ expression and effectively suppressing macrophage inflammation. MG-132 indirectly activated the expression of VEGFA, and the expression of KLF4 also significantly increased, which indicates a direct or indirect relationship between VEGFA and KLF4.</p> <p><strong>Conclusion.</strong> Our study shows that miR-126 can reverse ox-LDL-mediated phagocytosis and apoptosis in macrophages. Consequently, the potential role of miR-126 was manifested in regulating macrophage function and promoting vascular endothelial migration.</p>
Chlorine-Promoted Copper Catalysts for CO2 Electroreduction into Highly Reduced Products
<p>Datasets supporting the publication 'Chlorine-Promoted Copper Catalysts for CO<sub>2</sub> Electroreduction into Highly Reduced Products': catalyst evaluation data (Excel), XRD (2 column CSV), XPS (Excel), SEM images (TIFF)</p>
Multiple lines and levels of evidence for avian zoochory promoting fish colonization of artificial lakes
<p>Understanding how obligate freshwater organisms colonize seemingly isolated ecosystems has long fascinated ecologists. While recent investigations reveal that fish eggs can survive the digestive tract of birds and successfully hatch once deposited, evidence for avian zoochory in natura are still lacking. Here, we used a multiple lines and levels of evidence approach to demonstrate plausible bird-mediated colonization of lakes by the European perch (<em>Perca</em> <em>fluviatilis</em>). We studied a set of newly-formed artificial lakes that the public is either prohibited to access because of gravel extraction or allow to access (mainly for angling). The motivating observation is that a large proportion of prohibited-access lakes (>80%) were colonized by European perch while stocking by anglers and managers never occurred. Three supplementary lines of evidence supported avian zoochory. First, European perch spawning occurs when waterfowl abundance is very high. Second, European perch lays sticky eggs at shallow depths where they can be eaten by waterfowls or attached to their bodies. Third, genetic analyses suggested that European perch actually migrate among lakes, and that distance moved matches with daily flight range of foraging waterfowls. Together, multiple lines of evidence point to avian zoochory as a pathway for fish colonizing remote or newly-formed freshwater ecosystems.</p>
Data and analysis scripts for: Lung adenocarcinoma promotion by air pollutants
<p>Code for "Lung adenocarcinoma promotion by air pollutants" manuscript</p> <p>egfrm_lc_incidence</p> <ul> <li>Epidemiological analyses of EGFRm lung cancer incidence and PM2.5 levels in England (NHS England), South Korea and Taiwan.</li> </ul> <p>ukbb</p> <ul> <li>Epidemiological analyses of lung cancer incidence and PM2.5 levels in England, using the UKBB data set.</li> </ul> <p>mouse_RNA_seq</p> <ul> <li>Analysis of RNA-seq data derived from lung tumour tissue of pollution-exposed mice.</li> </ul> <p>mouse_WGS</p> <ul> <li>Analysis of WGS data derived from lung tumour tissue of pollution-exposed mice.</li> </ul> <p>normal_lung</p> <ul> <li>Analysis of ddPCR for EGFRm from normal lung tissue from the TRACERx and PEACE cohorts.</li> <li>Analysis of Duplex-seq data from normal lung tissue from the PEACE and BDRE cohorts.</li> </ul>
Induction of Sis1 promotes fitness but not feedback in the heat shock response
<div class="page"> <div class="layoutArea"> <div class="column"> <p>The heat shock response (HSR) controls expression of molecular chaperones to maintain protein homeostasis. Previously, we proposed a feedback loop model of the HSR in which heat-denatured proteins sequester the chaperone Hsp70 to activate the HSR, and subsequent induction of Hsp70 deactivates the HSR. However, recent work has implicated newly synthesized proteins (NSPs) – rather than unfolded mature proteins – and the Hsp70 co-chaperone Sis1 in HSR regulation, yet their contributions to HSR dynamics have not been determined. Here we generate a new mathematical model that incorporates NSPs and Sis1 into the HSR activation mechanism, and we perform genetic decoupling and pulse-labeling experiments to demonstrate that Sis1 induction is dispensable for HSR deactivation. Rather than providing negative feedback to the HSR, transcriptional regulation of Sis1 by Hsf1 promotes fitness by coordinating stress granules and carbon metabolism. These results support an overall model in which NSPs signal the HSR by sequestering Sis1 and Hsp70, while induction of Hsp70 – but not Sis1 – attenuates the response.</p> </div> </div> </div>
Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"
<p><strong>Supplements for "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"</strong></p> <p>This supplement includes the following files:</p> <ul> <li>Main_v02.R --- Script in R language to process files (in "PDBs.zip") and produce the dataset ("Dataset_v02.csv")</li> <li>PDBs.zip --- PDB files include filtered structures processed by three programs</li> <li>Dataset_v02.csv --- final filtered version of dataset produced in R language (by "Main_v02.R"). </li> <li>Dataset key.txt --- key to column names in Dataset_v02.csv </li> </ul> <p>The article featuring this dataset is published in:</p> <p>Journal: Journal of Chemical Information and Modeling<br>Title: "Solvent Accessibility Promotes Rotamer Errors During Protein Modelling with Major Side-Chain Prediction Programs"<br>Author(s): Hameduh, Tareq; Mokry, Michal ; Miller, Andrew ; Heger, Zbynek; Haddad, Yazan</p> <p><a href="https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2F10.1021%2Facs.jcim.3c00134&data=05%7C01%7C%7C4876a5c33e5f4bd8daf008db7e55a28d%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C638242678496577396%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NE%2F0dYvc4m5%2B8T0YQtqxY21yk1pA9ZpiADqzx3vEJ4Q%3D&reserved=0">https://pubs.acs.org/doi/10.1021/acs.jcim.3c00134</a></p> <p> </p>
The locus coeruleus broadcasts prediction errors across the cortex to promote sensorimotor plasticity
<p>Raw data and code to generate the figures of the publication "The locus coeruleus broadcasts prediction errors across the cortex to promote sensorimotor plasticity" <a href="https://doi.org/10.7554/eLife.85111.2">https://doi.org/10.7554/eLife.85111</a>. </p>
Data from: Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)
<p>The upper and lower jaws of some wrasses (Eupercaria: Labridae) possess teeth that have been coalesced into a strong durable beak that they use to graze on hard coral skeletons, hard-shelled prey, and algae, allowing many of these species to function as important ecosystem engineers in their respective marine habitats. While the ecological impact of the beak is well-understood, questions remain about its evolutionary history and the effects of this innovation on the downstream patterns of morphological evolution. Here we analyze 3D cranial shape data in a phylogenetic comparative framework and use paleoclimate modeling to reconstruct the evolution of the labrid beak across 205 species. We find that wrasses evolved beaks three times independently, once within odacines, and twice within parrotfishes in the Pacific and Atlantic Oceans. We find an increase in the rate of shape evolution in the Scarus+Chlorurus+Hipposcarus (SCH) clade of parrotfishes likely driven by the evolution of the intramandibular joint. Paleoclimate modeling shows that the SCH clade of parrotfishes rapidly morphologically diversified during the middle Miocene. We hypothesize that possession of a beak in the SCH clade coupled with favorable environmental conditions allowed these species to rapidly morphologically diversify.</p>
Data used in the study "mRNA vaccination boosts spike-specific T cell memory and promotes expansion of CD45RAint TEMRA-like CD8+ T cells in COVID-19 recovered individuals"
<p>Data associated with an original research study examining T cell responses to mRNA vaccination in COVID-19 recovered individuals. 10X Cell Ranger outputs, bulk TCR sequencing data, and T cell functional (ICS) data in this study have been deposited. Authors KMB and HR contributed equally to this effort. Address correspondence to EWN.</p>
Fig. 1 in Infection with Toxoplasma gondii can promote chronic liver diseases in HIV-infected individuals
Fig. 1. Frequency of different liver pathologies in deceased patients from cohorts seropositive and seronegative to Toxoplasma gondii (Nicolle et Manceaux, 1908). * – difference between the indices for the entire cohort of seropositive patients and for the group of deceased patients from this cohort (p <0.05); ^ – difference between the indices for the entire cohort of seronegative patients and for the group of deceased patients from this cohort (p <0.05)
The promotional role of Mn in CO2 hydrogenation over Rh-based catalysts from a surface organometallic chemistry approach
<p>Rh-based catalysts modified by transition metals have been intensively studied for CO2 hydrogenation due<br> to their high activity. However, understanding the role of promoters at the molecular level remains<br> challenging due to the ill-defined structure of heterogeneous catalysts. Here, we constructed welldefined RhMn@SiO2 and Rh@SiO2 model catalysts via surface organometallic chemistry combined with thermolytic molecular precursor (SOMC/TMP) approach to rationalize the promotional effect of Mn in CO2 hydrogenation. We show that the addition of Mn shifts the products from almost pure CH4 to a mixture of methane and oxygenates (CO, CH3OH, and CH3CH2OH) upon going from Rh@SiO2 to RhMn@SiO2. In situ X-ray absorption spectroscopy (XAS) confirms that the MnII is atomically dispersed in the vicinity of metallic Rh nanoparticles and enables to induce the oxidation of Rh to form the Mn–O–Rh interface under reaction conditions. The formed interface is proposed to be key to maintaining Rh+ sites, which is related to suppressing the methanation reaction and stabilizing the formate species as evidenced by in situ DRIFTS to promote the formation of CO and alcohols<br> </p>
Supporting information for prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water
<p>Supporting information for prebiotic triose glycolysis promoted by co-catalytic proline and phosphate in neutral water</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.