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7,518 results for “screenings”
Extended data for: Screening for antifolate and artemisinin resistance in Plasmodium falciparum clinical isolates from three hospitals of Eritrea
<p><i>Background</i>: Antimalarial drug resistance is a major challenge hampering malaria control and elimination. <i>Plasmodium falciparum</i>, the leading causative parasite species, has developed resistance to basically all antimalarials. Continued surveillance of drug resistance using genetic markers provides important molecular data for treatment policies. This study sought to verify the genetic mechanism of resistance to sulfadoxine-pyrimethamine and assess the occurrence of point mutations associated with artemisinin resistance in <i>P. falciparum</i> clinical isolates from Eritrea.</p> <p><i>Methods</i>: Nineteen dried blood spot samples were collected from patients visiting Adi Quala, Keren and Gash Barka Hospitals, Eritrea. The patients were followed up after receiving treatment with first line artesunate-amodiaquine. Nested polymerase chain reaction and Sanger sequencing techniques were employed to genotype point mutations in the <i>P. falciparum</i> bifunctional dihydrofolate reductase-thymidylate synthase (<i>Pfdhfr</i>, PF3D7_0417200), dihydropteorate synthase (<i>Pfdhps</i>, PF3D7_0810800) and kelch 13 (<i>PfK13</i>, PF3D7_1343700) genes.</p> <p><i>Results</i>: Eight of nineteen (42%) of the dried blood spot samples were successful for PCR-amplification. Data analyses of the PCR-positive isolates revealed the following point mutations: <i>Pfdhfr </i>N51I in four isolates, C59R in one isolate, S108N in four isolates, a rare non-synonymous substitution V45A in four isolates and <i>Pfdhps</i> K540E in four isolates. No <i>PfK13</i> point mutations were reported.</p> <p><i>Conclusions</i>: <i>Pfdhfr</i> C59R and <i>Pfdhps</i> K540E point mutations are reliable markers for the sulfadoxine-pyrimethamine quintuple mutant haplotype combination. These findings highlight first reports in Eritrea, which verify the underlying genetic mechanism of antifolate resistance. Continuous monitoring of the <i>PfK13</i> marker is recommended.</p>
Data from: A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and blasticidin S
Fighting antibiotic resistance requires a deeper understanding of the genetic factors that determine the antibiotic susceptibility of bacteria. Here we describe a chemical-genomic screen in Escherichia coli K-12 that was designed to discover new aspects of antibiotic resistance by focusing on a set of 26 antibiotics and other stresses with poorly characterized mode-of-action and determinants of resistance. We show that the screen identifies new resistance determinants for these antibiotics including a common signature from two antimicrobials, kasugamycin and blasticidin S, used to treat crop diseases like rice blast and fire blight. Following this signature, we further investigated the mechanistic basis for susceptibility to kasugamycin and blasticidin S in E. coli using both genetic and biochemical approaches. We provide evidence that these compounds hijack an overlapping set of peptide ABC-importers to enter the bacterial cell. Loss of uptake may be an underappreciated mechanism for the development of kasugamycin resistance in bacterial plant pathogens.
Data from: RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells
The Golgi apparatus has many important physiological functions, including sorting of secretory cargo and biosynthesis of complex glycans. These functions depend on the intricate and compartmentalized organization of the Golgi apparatus. To investigate the mechanisms that regulate Golgi architecture, we developed a quantitative morphological assay using three different Golgi compartment markers and quantitative image analysis, and performed a kinome- and phosphatome-wide RNAi screen in HeLa cells. Depletion of 159 signaling genes, nearly 20% of genes assayed, induced strong and varied perturbations in Golgi morphology. Using bioinformatics data, a large regulatory network could be constructed. Specific subnetworks are involved in phosphoinositides regulation, acto-myosin dynamics and mitogen activated protein kinase signaling. Most gene depletion also affected Golgi functions, in particular glycan biosynthesis, suggesting that signaling cascades can control glycosylation directly at the Golgi level. Our results provide a genetic overview of the signaling pathways that control the Golgi apparatus in human cells.
Autism Spectrum Disorder and screen time during lockdown
<p><span>Abstract: this dataset contain data from a research conducted during the Italian lockdown due to COVID-19 (March-May 2020). </span>Lockdown due to Covid-19 pandemic brought deep changes to the daily lives of children with Autism Spectrum Disorder (ASD), greatly increasing their amount of time spent at home. Parents of children with ASD filled an online survey. A cohort of 243 parents of children with ASD (2-15 years old) completed an original online survey regarding the child's screen time and the modification of the ASD symptomatology during lockdown to investigate the relationship between them. This data investigated the relation between ASD symptoms modification during lockdown and the amount of time spent with the screen by the children.</p> <p><span>Methods:</span> The data were analyzed with Pycharm (Python language). Descriptive and Spearman correlation statistics were computed on the original survey data. The variables expressed on a Likert scale were transformed into dichotomous variable in order to depict and highlight the effect of any improvements or worsen of child's symptomatology, weakening the negative impact of a relatively low sample size on model accuracy; the time spent in the screen time activity done during lockdown were reparametrized as a percentage of time spent in a specific screen time activity over the total time spent in all screetime.</p>
Moderate-severe OSA screening based on support vector machine of the Chinese population facio-cervical measurements dataset: A cross-sectional study
<p><strong>Objectives</strong> Obstructive sleep apnea (OSA) has received much attention as a risk factor for perioperative complications and 68.5% of OSA patients remain undiagnosed before surgery. Facio-cervical characteristics may screen OSA for Asians due to smaller upper airways compared to Caucasians. Thus, our study aimed to explore a machine-learning model to screen moderate-severe OSA based on facio-cervical and anthropometric measurements.</p> <p><strong>Design </strong>A cross-sectional study.</p> <p><strong>Setting</strong> Data were collected from the Shanghai Jiao Tong University School of Medicine affiliated Ruijin Hospital between February 2019 and August 2020.</p> <p><strong>Participants</strong> A total of 481 Chinese participants were included in the study.</p> <p><strong>Primary and secondary outcome</strong> (1) Identification of moderate-severe OSA with apnea-hypopnea index (AHI)15 events·h<sup>−1</sup>. (2) Verification of the machine learning model.</p> <p><strong>Results</strong> The SABIHC2 model (Sex-Age-Body mass index-maximum Interincisal distance-ratio of Height to thyro-sternum distance-neck Circumference-waist Circumference) was set up. The SABIHC2 model could screen moderate-severe OSA with an area under the curve (AUC)=0.832, the sensitivity of 0.916, and specificity of 0.749, and performed better than the STOP-BANG questionnaire, which showed AUC=0.631, the sensitivity of 0.487, and specificity of 0.772. Especially for asymptomatic patients (ESS < 10), the SABIHC2 model demonstrated better predictive ability compared to the STOP-BANG questionnaire, with AUC (0.824 vs. 0.530), sensitivity (0.892 vs. 0.348), and specificity (0.755 vs. 0.809).</p> <p><strong>Conclusion</strong> The SABIHC2 machine learning model provides a simple and accurate assessment of moderate-severe OSA in the Chinese population, especially for those without significant daytime sleepiness.</p>
Dataset for the paper "Three indexes to characterize crushing and screening of reclaimed asphalt pavement"
<p>The dataset includes Reclaimed Asphalt Pavement (RAP) grading curve testing results from seven different materials that were produced using four different full-scale aggregate crushing machines. Samples of the same material before and immediately after crushing were obtained. The grading curves include white RAP (aggregates without bitumen) and black RAP (reclaimed asphalt together with bitumen). The data was used to develop and validate three indexes – chunk, breakdown, and filler increase indexes. These indexes can be used to quantitatively characterize crushing equipment and to optimize the crushing parameters.</p> <p>When using, please cite the paper: <a href="https://doi.org/10.1080/10298436.2021.1990287">Zaumanis M., et al. (2021). Three indexes to characterize processing of reclaimed asphalt pavement, International Journal of Pavement Engineering. DOI: https://doi.org/10.1080/10298436.2021.1990287</a></p>
Therapeutic genome screen in AsPC1
<p>Pancreatic adenocarcinoma generally does not respond to our current therapeutic approaches of surgical resection, radiation and chemotherapy with an overall five-year survival of only 8%. In an effort to identify potential new therapeutic approaches for pancreatic cancer, we carried out a targeted synthetic lethal CRISPR screens in the pancreatic cell line AsPC1. A custom CRISPR knockout library, termed the Therapeutic Genome (RxG) Library, which targets genes for which a current drug already exists was utilized in the screens. We used the RxG library to identify genes and corresponding gene products which modulate the sensititive and resistance to three chemotherapeutics, Gemcitabine, 5-fluorouracil, and Niraparib in the AsPC1 cell line. This screen identified multiple gene products which potentiate sensitivity to these three chemotherapeutics, and in particular, BCL2L1 which encodes BCL-xL, was identified as a common genetic factor that when mutant, enhances sensitivity to all three drugs. A novel drug, DT2216, in Phase I clinical trials which targets BCL-xL for degradation was shown to enhance the effectiveness of Gemcitabine in additional pancreatic cancer cell lines as well as patient-derived xenograft models without enhanced systemic toxicity. This work supports a possible utility of combined Gemcitabine/DT2216 as a novel therapy for pancreatic cancer.</p>
Figures 16-17 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figures 16-17 - Female genitalia. 16 Caryocolum amaurella, Finland, slide GU 14/1372 P.Huemer 17 Caryocolum amaurella, Finland, slide GU 14/1371 P.Huemer.
Figures 10-13 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figures 10-13 - Details of male genitalia (vinculum-valva-complex). 10 Caryocolum crypticum sp. n., paratype, Italy, slide GU 86/041 P.Huemer 11 Caryocolum crypticum sp. n., paratype, Italy, slide GEL 1215 P.Huemer 12 Caryocolum amaurella, Finland, slide GU 14/1373 P.Huemer 13 Caryocolum amaurella, Finland, slide GU 14/1374 P.Huemer.
Figures 2-5 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figures 2-5 - Adults. 2 Caryocolum crypticum sp. n., holotype 3 Caryocolum crypticum sp. n., paratype, female, Greece 4 Caryocolum amaurella, male, Finland 5 Caryocolum amaurella, male, Austria.
Figure 1 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figure 1 - Neighbour-joining tree (Kimura 2 parameter, built with MEGA 5; cf. Tamura et al. 2011), with only sequences longer than 500 bp considered. The width of the triangles represents the sample size, and the depth the genetic variation within the cluster. Currently recognized conspecific taxa with maximum divergence greater than 3% are shown as separate clades. Source: DNA Barcode data from BOLD (Barcode of Life Database, cf. Ratnasingham and Hebert 2007).
Figures 8-9 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figures 8-9 - Male genitalia. 8 Caryocolum amaurella (Hering), Finland, slide GU 14/1373 P.Huemer; 9 Caryocolum amaurella, Finland, slide GU 14/1374 P.Huemer.
Figures 14-15 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figures 14-15 - Female genitalia. 14 Caryocolum crypticum sp. n., holotype, slide GEL 1234 P.Huemer 15 Caryocolum crypticum sp. n., paratype, Italy, slide GEL 1232 P.Huemer.
Figures 6-7 from: Huemer P, Karsholt O, Mutanen M (2014) DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae). ZooKeys 404: 91-111. https://doi.org/10.3897/zookeys.404.7234
Figures 6-7 - Male genitalia. 6 Caryocolum crypticum sp. n., paratype, Italy, slide GU 86/041 P.Huemer 7 Caryocolum crypticum sp. n., paratype, Italy, slide GEL 1215 P.Huemer.
Screening for novel carbon nanotubes binding-peptides
<p>This is the supplementary material section of the article "<strong>Screening for novel carbon nanotubes binding-peptides</strong>".</p> <p>Contents: Table S1-S9, contains all discovered peptides and intensities generated from the nanoLC-MS-MS experiment.</p>
Screening for Chagas disease using a deep neural network
<p>Pre-trained models accompanying the source code at https://github.com/carji475/ecg-chagas</p>
Cowpea drought stress application at early vegetative stage 2022 - screen 02 - day 02 - 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 02 after drought stress application. </p>
In Silico Screening of Coffee Plant Natural Products as Lead Compounds for Stroke Remedy (Supplementary material)
<p>Data set for ICSE 2023 conference proceeding</p>
Figure 3. Dioctophyma renale egg under a in Giant Red Kidney Worm (Dioctophyma Renale) Screening And Treatment Protocol And Aberrant Worm Migration In Dogs From Ontario And Manitoba, Canada
Figure 3. Dioctophyma renale egg under a light microscope. Color version available online.
Pooled CRISPR Screening of High-content Cellular Phenotypes by Ghost Cytometry_01
<p>Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry (NFkB NGS data, conventional flow cytometer data, Amnis data)</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.