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7,518 results for “screenings”
OpenAthens Guest Login Screen Capture
<p>This is what openathens login looks like for multiple types of users.</p>
Figure 3 in The shell-eyes of the chiton Acanthopleura granulata (Mollusca, Polyplacophora) use pheomelanin as a screening pigment
Figure 3. High-performance liquid chromatography (HPLC) elution profile of the degradation products of the pigment that we extracted from the valves of the chiton Acanthopleura granulata (where absorption was set at 280 nm). The solid line represents the digestion product of the extracted pigment. For reference, the dashed line represents the same digestion reaction minus the pigment. The inset shows an elution profile for the degradation products of synthetic pheomelanin (DOPA-cysteine melanin) from Panzella et al. (2007), a paper whose methods we replicated. We hypothesize that the distinct peak that we see at 30 min in our elution profile represents BTCA, a diagnostic degradation product of pheomelanin.
Figure 2 in The shell-eyes of the chiton Acanthopleura granulata (Mollusca, Polyplacophora) use pheomelanin as a screening pigment
Figure 2. Absorption spectra of the pigment that we extracted from the valves of the chiton Acanthopleura granulata. The black line represents freshly extracted pigment. The grey line represents the same sample of pigment after it had been digested in alkaline hydrogen peroxide for 14 h. Note that digestion by hydrogen peroxide causes: (1) the absorption peak in the visible wavelengths to drop and shift towards shorter wavelengths; and (2) the appearance of degradation products that absorb strongly in the UV wavelengths. Both of these observations are consistent with the degradation of pheomelanin by hydrogen peroxide.
Figure 1 in The shell-eyes of the chiton Acanthopleura granulata (Mollusca, Polyplacophora) use pheomelanin as a screening pigment
Figure 1. The results of using sodium hydroxide to extract pigment from the decalcified shell plates of the eyed chiton Acanthopleura granulata. (A) An image taken before bleaching, where the dark spots are the rings of screening pigment associated with the shell-eyes (the arrow points to a single eye). The same red-brown pigment is expressed around the shell-eyes and, more broadly, in the proteinaceous extra-cellular matrix that surrounds the eyes and aesthetes. (B) The same valve after 48 h in 1 M sodium hydroxide at room temperature. The scale bar represents 1 mm.
Figure 1 in Preliminary health screening and possible pathogen determination in a Bufo bufo (Linnaeus, 1758) (Amphibia: Bufonidae) population
Figure 1. Inverse measure of the degree of aggregation (k-value) and frequency distribution of parasites of each identified helminth species in the sampled common toads. In our study, all the parasite species showed high degree of aggregation, since their k-values are all lower than one. Please note x-axes are different among panels, in order to show more clearly the distributions of the different parasite species among the common toad population.
Screening of anti-Acinetobacter baumannii plant-based compounds, based on potential inhibition of OmpA and OmpW functions
<p><span>Considering the adverse effect of antimicrobial resistance (AMR) crisis on human life, there is an immediate need for finding new alternatives for treatment of emerging infectious diseases. Therapeutic options, including last-line or combined antibiotic therapies for <i>Acinetobacter baumannii</i>, as an emergent multi-drug resistant (MDR) human pathogen responsible for severe nosocomial and several other infections, are apparently ineffective. The outer membrane protein A (OmpA) and outer membrane protein W (OmpW) are two porins known as virulence factors with different cellular functions. Identification of natural compounds with potentials to block these putative virulence factors can possibly attenuate the growth of the bacteria and control the relating diseases. The current work aimed to screen the therapeutic potential of a library of 371 phytochemicals, as multi-blockers of OmpA and OmpW in <em>A. baumannii</em>. Although the anti-virulence activities of these biomolecules are reported previously, no evaluation on <i>A. baumannii </i>has been performed so far. Moreover, there is no safety screening and early alerts of these compounds. In this study, hits were initially selected based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) drug-like properties. Afterwards, the selected ligands were subjected to standard docking calculations against predicted three-dimensional structure of OmpA and OmpW in <i>A. baumannii</i>. We identified five phytochemicals (Amorphigenin (PUBCHEM CID 92207), Bisdemethoxy-curcumin (PUBCHEM CID 5315472), Dalbinol (PUBCHEM CID 44257412), Epicatechin gallate (PUBCHEM CID 72276) and Nordihydroguaiaretic acid (PUBCHEM CID 4534)) bearing appreciable binding affinity towards the selected binding pocket of OmpA and OmpW. </span></p>
Data from: Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean
<p>Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon in British Columbia, Canada, using quantitative PCR to assess presence and load of 58 infective agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo salar). Our analysis reveals temporal trends, agent correlations within hosts, and agent-associated mortality signatures. Multiple agents, most notably Tenacibaculum maritimum, were elevated in dead and dying salmon. We also report detections of agents only recently shown to infect farmed salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2), detection in freshwater hatcheries of two marine agents (Kudoa thyrsites and Tenacibaculum maritimum), and detection in the ocean of a freshwater agent (Flavobacterium psychrophilum). Our results provide information for farm managers, regulators, and conservationists, and enable further work to explore patterns of multi-agent infection and farm/wild transmission risk.</p>
Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens
Millions of putative transcriptional regulatory elements (TREs) have been cataloged in the human genome, yet their functional relevance in specific pathophysiological settings remains to be determined. This is critical to understand how oncogenic transcription factors (TFs) engage specific TREs to impose transcriptional programs underlying malignant phenotypes. Here, we combine cutting edge CRISPR screens and epigenomic profiling to functionally survey ≈15,000 TREs engaged by estrogen receptor (ER). We show that ER exerts its oncogenic role in breast cancer by engaging TREs enriched in GATA3, TFAP2C, and H3K27Ac signal. These TREs control critical downstream TFs, among which TFAP2C plays an essential role in ER-driven cell proliferation. Together, our work reveals novel insights into a critical oncogenic transcription program and provides a framework to map regulatory networks, enabling to dissect the function of the noncoding genome of cancer cells.
Data Availability for "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"
<p><strong>The data support for this article "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"</strong></p>
All data support published article "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"
<p>There is a high level of conservation of tryptophans within the active site architecture of the cellulase family, whereas the function of the four tryptophans in the catalytic domain of Cel7A is unclear. By mutating four tryptophan residues in the catalytic domain of Cel7A from <em>Penicillium piceum</em> (PpCel7A), the binding affinity between PpCel7A and <em>p-</em>nitrophenol-D-cellobioside (<em>p</em>NPC) was reduced as determined by Michaelis–Menten constants, molecular dynamics simulations, and fluorescence spectroscopy. Furthermore, PpCel7A variants showed a reduced level of cellobiohydrolase activity against cellulose analogs or natural cellulose. Therefore, it could be concluded four tryptophan residues in Cel7A played a critical role in substrate binding. Mutagenesis results indicated that the W390 stacking interactions at the -2 site played an essential role in facilitating substrate distortion to the -1 site. As soon as the function was altered, the mutation would inevitably affect the catalytic activity against the natural substrate. Interestingly, no clear relationship was found between the cellobiohydrolase activity of PpCel7A variants against <em>p</em>NPC and Avicel. <em>p</em>NP contains many electrophilic groups that may result in overestimation of the binding constant between tryptophan residues and <em>p</em>NPC in comparison to the natural substrate. Consequently, screening improved cellulase using cellulose analogs would divert attention from the target direction for lignocellulose biorefinery. Clarifying mechanism of catalytic diversity on the natural cellulose or cellulose analogs may give better insight into cellulase screening and selecting strategy.</p>
C.Origami: Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
<p>This data repository includes dataset generated from IMR-90, GM12878 cell lines and C.Origami pre-trained model weights.</p> <p>GitHub page: https://github.com/tanjimin/C.Origami</p>
Fragment screening using biolayer interferometry reveals ligands targeting the SHP-motif binding site of the AAA+ ATPase p97
<p>Biosensor techniques have become increasingly important for fragment-based drug discovery during the last years. The AAA+ ATPase p97 is an essential protein with key roles in protein homeostasis and a possible target for cancer chemotherapy. Currently available p97 inhibitors address its ATPase activity and globally impair p97-mediated processes. In contrast, inhibition of cofactor binding to the N-domain by a protein-protein-interaction inhibitor would enable the selective targeting of specific p97 functions. Here, we describe a biolayer interferometry-based fragment screen targeting the N-domain of p97 and demonstrate that a region known as SHP-motif binding site can be targeted with small molecules. Guided by molecular dynamics simulations, the binding sites of selected screening hits were postulated and experimentally validated using protein- and ligand-based NMR techniques, as well as X-ray crystallography, ultimately resulting in the first structure of a small molecule in complex with the N-domain of p97. The identified fragments provide insights into how this region could be targeted and present first chemical starting points for the development of a protein-protein interaction inhibitor preventing the binding of selected cofactors to p97.</p> <p><br> Here we publish the primary data of the biolayer-interferometry (BLI), STD-NMR, HSQC-NMR and mixed-solvent MD simulation results.<br> For BLI, the sensorgrams of 10 binding fragments identified in the screening are given. Measurements were conducted with the N-domain and the ND1-construct of p97. Additionaly, the measurements with ADP as positive control (n=6) are provided.<br> Four of the 10 fragments were selected as most promising hits for further investigation: TROLL2, TROLL7, TROLL8 and TROLL12. For these fragemnts, the STD-NMR build-up data, the HSQC-NMR spectra and the representative poses from the mixed solvent MD simulations used for CORCEMA predictions are provided. For TROLL2 the anomalous map of the bromine atom of the crystal structure (PDB entry: 7PUX) is given.</p>
Data from: Dental health utilization in the Republic of Palau: A survey to determine feasibility of an oral cancer screening program
<p>Cancer is the second leading cause of death in the Western Pacific region. The prevalent tradition of chewing betel nut in Palau, an island nation in this region, is a risk factor in the development of oral cancer. Oral cancer is the fifth most common cancer in Palau, and prognosis can be improved with early detection. The purpose of this study is to assess the feasibility of oral cancer screening using existing dental health infrastructure in Palau.</p> <p>A mixed methods approach was used to explore topics related to dental health and use of these resources in Palau. Quantitative measures of dental health utilization and qualitative assessment of barriers and facilitators to accessing dental care were the primary measures of this study. Knowledge, attitudes, and beliefs about betel nut use and oral cancer were secondary measures of this study. Open-ended survey questions were coded to develop emergent themes based in grounded theory. These themes are interpreted in the context of the Three Delays model.</p> <p>There was a total of 223 completed surveys. Mean age was 43.7 years, 80% identified as female, and most (94.3%) reported ever having seen a dentist in Palau. Dental care was seen as important (mean score 82.3), and 57.9% reported it was easy to see a dentist. Themes regarding barriers to dental care addressed cost and availability of dentists/appointments. Themes regarding facilitators included multilevel resources and transportation. Approximately half of respondents were current users of betel nut, and the majority of these (64.1%) were daily users. Results suggest there are facilitators in place to promote seeking and obtaining dental care, however, existing infrastructure may not support an oral cancer screening program. These data provide important areas to address that can improve access and support the implementation of oral cancer screening through existing dental care in the future.</p>
PanDDA files from a ligand screen against the NSP3 macrodomain of SARS-CoV-2 - ligands from linking with FRESCO
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in McCorkindale et al. 2022 (https://doi.org/10.1101/2022.11.21.517375).</p> <p>mac1_pandda.zip contains the structure factor intensities, PanDDA input/ouput and refined models/maps. A description of the files can be found in the README file. </p> <p>mac1_ligand-bound_states.zip contains the ligand-bound states extracted from the multi-state PDB files. </p>
Cowpea drought stress application at early vegetative stage 2022 - screen 02 - day 08 - raw image data
<p>Cowpea (<em>Vigna unguiculata</em>) miniCore accessions were screened for responses to drought stress at early vegetative stress. The cowpea seedlings were exposed to drought stress at 17 days after germination using the weight of the pot and AAWEsmo device, developed in Julkowska Lab, Boyce Thompson Institute. The seedlings were kept at 60 and 10% of soil water holding capacity for 2 weeks and the data on cowpea shoot size, evapotranspiration and photosystem II efficiency was collected. </p> <p>This dataset represents the images collected for Screen number 02 and day 08 after drought stress application. </p>
Screening of key risk SNPs for glioma based on machine learning algorithms
<p>Glioma is a common primary malignant brain tumor and is the most aggressive and lethal solid tumor, accounting for approximately 80% of all intracranial malignancies. Our aim was to screen key SNP by LASSO regression and random forest (a machine learning algorithm) and construct a model based on these SNP to predict the risk of glioma in Chinese Han population.</p>
Anti-Riok2 virtual screening output results
<p>Various investigations have revealed the role of RIOK2 in the carcinogenesis and potential of RIOK2 inhibitors as anticancer medicine. In this study, an in-silico approach have been utilized to find potential RIOK2 inhibitors and the uplouded file is the output of docking based virtual screening.</p>
Screening for nucleoside inhibitors of the SARS-CoV-2 RdRP
<p>This report describes the most relevant results of screening compounds with a nucleoside analogue structure from the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 in a cell-based assay and nucleoside triphosphates in a radioactive filtering binding RdRP assay.</p>
Screening of 165,988 compounds reflecting biological and chemical diversity in the Janssen Library for anti-SARS-CoV-2 activity
<p>This report describes the most relevant results of screening a diversity set of the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 in a stable eGFP-expressing VeroE6 cell line infected with SARS-CoV-2.</p>
Figure 5 in Giant Red Kidney Worm (Dioctophyma Renale) Screening And Treatment Protocol And Aberrant Worm Migration In Dogs From Ontario And Manitoba, Canada
Figure 5. An incidental finding of Dioctophyma renale located around the testicle of a dog whose origin was from a northern community. Color version available online.
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.