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7,518 results for “screenings”
Row data from: Screening and response profile of Iraqi barley accessions under PEG- induced drought conditions
<p><span>Among the abiotic stresses, drought influences plant growth and productivity, and plant stress responses depend on stress intensity and genotype. The effects of simulated drought stress on germination parameters were tested for tolerance and sensitivity in 59 barley accessions from all regions of Iraq and phenotypic, physiological and biochemical responses associated with drought stress were investigated. Stress treatments with polyethylene glycol (PEG) reduced the germination rate and dramatically delayed the development of the seedlings. Significant changes in the physiological and biochemical profiles in barley accessions were observed. A smaller reduction in water absorption of seeds was observed across all accessions, while all biochemical characteristics except total flavonoid content were increased with the increase in water deficiency in most accessions. Among the 59 barley accessions, ABN was the most tolerant accession, while Black-Garmiyan was the most drought-prone. Significant relationships were found between most trait pairs, with 32 significant associations under no stress, 39 significant correlations under the 10.25% PEG treatment, and 81 significant correlations under the 20.50% PEG treatment. According to the key importance analysis, seed water uptake, total phenol content, soluble sugar content and catalase are classified as relative significance traits for germination percentage, root and shoot length under stress conditions.</span></p>
Figure 2 from: Shkondrov A, Krasteva I (2021) Liquid chromatography – high resolution mass spectrometry screening of Astragalus hamosus and Astragalus corniculatus. Pharmacia 68(1): 135-139. https://doi.org/10.3897/pharmacia.68.e60621
Figure 2 A base peak chromatogram of the extract of A. corniculatus with identification of 4 (m/z 737 [M-H]-) and MS2 spectrum displaying kaempferol fragment (m/z 284).
Figure 1 from: Shkondrov A, Krasteva I (2021) Liquid chromatography – high resolution mass spectrometry screening of Astragalus hamosus and Astragalus corniculatus. Pharmacia 68(1): 135-139. https://doi.org/10.3897/pharmacia.68.e60621
Figure 1 A base peak chromatogram of the extract of A. hamosus with identification of 3 (m/z 753 [M-H]-) and MS2 spectrum displaying quercetin fragment (m/z 301).
Data from: High-throughput screening of inorganic compounds for dielectric and optical properties to enable the discovery of novel materials
Dielectrics are an important class of materials that are ubiquitous in modern electronic applications. Even though their properties are important for the performance of devices, the number of compounds with known dielectric constant is on the order of a few hundred. Here, we use Density Functional Perturbation Theory as a way to screen for the dielectric constant and refractive index of materials in a fast and computationally efficient way. Our results form the largest database to date, containing the full dielectric tensor for 1,056 compounds. Details regarding the computational methodology and technical validation are presented along with the format of our publicly available data. In addition, we integrate our dataset with the Materials Project allowing users easy access to material properties. Finally, we explain how our dataset and calculation methodology can be used in the search for novel dielectric compounds.
Data from: Forward genetic screening for regulators involved in cholesterol synthesis using validation-based insertional mutagenesis
Somatic cell genetics is a powerful approach for unraveling the regulatory mechanism of cholesterol metabolism. However, it is difficult to identify the mutant gene(s) due to cells are usually mutagenized chemically or physically. To identify important genes controlling cholesterol biosynthesis, an unbiased forward genetics approach named validation-based insertional mutagenesis (VBIM) system was used to isolate and characterize the 25-hydroxycholesterol (25-HC)-resistant and SR-12813-resisitant mutants. Here we report that five mutant cell lines were isolated. Among which, four sterol-resistant mutants either contain a truncated NH2-terminal domain of sterol regulatory element-binding protein (SREBP)-2 terminating at amino acids (aa) 400, or harbor an overexpressed SREBP cleavage-activating protein (SCAP). Besides, one SR-12813 resistant mutant was identified to contain a truncated COOH-terminal catalytic domain of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase). This study demonstrates that the VBIM system can be a powerful tool to screen novel regulatory genes in cholesterol biosynthesis.
Data from: Preschool children's vision screening in New Zealand: a retrospective evaluation of referral accuracy
Objectives: To assess the accuracy of preschool vision screening in a large, ethnically diverse, urban population in South Auckland, New Zealand. Design: Retrospective longitudinal study. Methods: B4 School Check vision screening records (n=5572) were compared with hospital eye department data for children referred from screening due to impaired acuity in one or both eyes who attended a referral appointment (n=556). False positive screens were identified by comparing screening data from the eyes that failed screening with hospital data. Estimation of false negative screening rates relied on data from eyes that passed screening. Data were analysed using logistic regression modelling accounting for the high correlation between results for the two eyes of each child. Primary outcome measure: Positive predictive value of the preschool vision screening programme. Results: Screening produced high numbers of false positive referrals, resulting in poor positive predictive value (PPV=31%, 95% CI 26% to 38%). High estimated negative predictive value (NPV=92%, 95% CI 88% to 95%) suggested most children with a vision disorder were identified at screening. Relaxing the referral criteria for acuity from worse than 6/9 to worse than 6/12 improved PPV without adversely affecting NPV. Conclusions: The B4 School Check generated numerous false positive referrals and consequently had a low PPV. There is scope for reducing costs by altering the visual acuity criterion for referral.
Data from: Perfusion index in newborns during critical congenital heart disease screening at 24 hours in healthy newborns: retrospective observational study from the United States
Objective: To describe the distribution of Perfusion Index (PI) in asymptomatic newborns at 24 hours of life when screening for Critical Congenital Heart Disease (CCHD) using an automated data selection method. Design: This is a retrospective observational study. Setting: Newborn nursery in a California public hospital with 3500 to 4000 deliveries annually. Methods: We developed an automated program to select the PI values from CCHD screens. Included were term and late preterm infants who were screened for CCHD from November 2013 to January 2014 and from May 2015 to July 2015. PI measurements were downloaded every 2 seconds from the pulse oximeter and median PI were calculated for each oxygen saturation screen in our cohort. Results: We included data from 2768 oxygen saturation screens. Each screen had a median of 29 data points (interquartile range 17 to 49). The median PI in our study cohort was 1.8 (95% confidence interval 1.8 to 1.9) with interquartile range 1.2 to 2.7. The median pre-ductal PI was significantly higher than the median post-ductal (1.9 vs. 1.8, p = 0.03) although this difference may not be clinically significant. Conclusion: Using an automated data selection method, the median PI in asymptomatic newborns at 24 hours of life is 1.8 with a narrow interquartile range of 1.2 to 2.7. This automated data selection method may improve accuracy and precision compared to manual data collection method. Further studies are needed to establish external validity of this automated data selection method and its clinical application for CCHD screening.
Data from: Screening of cytotoxic or cytostatic flavonoids with quantitative FUCCI-based cell cycle assay
The Fluorescence-Ubiquitin Cell Cycle Indicator (FUCCI) system can be used not only to study gene expression at a specific cell cycle stage, but also to monitor cell cycle transitions in real time. In this study, we used a single clone of FUCCI-expressing HeLa cells (FUCCI-HeLa cells) and monitored the cell cycle in individual live cells over time by determining the ratios between red fluorescence (RF) of RFP-Cdt1 and green fluorescence (GF) of GFP-Geminin. Cytotoxic and cytostatic compounds, the latter of which induced G2 or mitotic arrest, were identified based on periodic cycling of the RF/GF and GF/RF ratios in FUCCI-HeLa cells treated with anticancer drugs. With this cell cycle monitoring system, ten flavonoids were screened. Of these, apigenin and luteolin, which have a flavone backbone, were cytotoxic, whereas kaempferol, which has a flavonol backbone, was cytostatic and induced G2 arrest. In summary, we developed a system to quantitatively monitor the cell cycle in real time. This system can be used to identify novel compounds that modulate the cell cycle and to investigate structure–activity relationships.
Data from: Effectiveness of diagnostic screening tests in mass screening for COPD using a cooperative regional system in a region with heavy air pollution: a cross-sectional study
Objective: This research aimed to evaluate the effectiveness of a cooperative health care model for early detection and diagnosis of chronic obstructive pulmonary disease (COPD), in Omuta Japan. Methods: This was a cross-sectional observational study. We performed diagnosis of COPD at four public health centres in Omuta, Japan from March 2015 to March 2016, by adding screening for COPD at the time of routine medical evaluations. All patients over 50 years were eligible to participate. Of a total of 397 eligible patients, 293 agreed to take part in the study. Results: The estimated prevalence of COPD in Omuta was 10% among subjects over 40 years and was 17% among smokers. Out of those who were screened, over half had questionnaire scores over the cut-off of 17 points and decreased FEV1/FVC%, indicating COPD (p>0.05). Thirty subjects with suspected COPD were given a referral for further investigation at a local central hospital, but only six underwent further medical examinations. Conclusion: The combination of COPD questionnaire and medical exam was effective as a COPD screening tool. Future research should investigate behavioural interventions for smoking cessation that can be offered in a cooperative model, as well as for improving participation in COPD screening and for encouraging early presentation for treatment in those suspected of having COPD.
Data from: Automated morphological feature assessment for zebrafish embryo developmental toxicity screens
Detection of developmental phenotypes in zebrafish embryos typically involves a visual assessment and scoring of morphological features by an individual researcher. Subjective scoring could impact results and be of particular concern when phenotypic effect patterns are also used as a diagnostic tool to classify compounds. Here we introduce a quantitative morphometric approach based on image analysis of zebrafish embryos. A software called FishInspector was developed to detect morphological features from images collected using an automated system to position zebrafish embryos. The analysis was verified and compared with visual assessments of three participating laboratories using three known developmental toxicants (methotrexate, dexamethasone and topiramate) and two negative compounds (loratadine and glibenclamide). The quantitative approach exhibited higher sensitivity and made it possible to compare patterns of effects with the potential to establish a grouping and classification of developmental toxicants. Our approach improves the robustness of phenotype scoring and reliability of assay performance and, hence, is anticipated to improve the predictivity of developmental toxicity screening using the zebrafish embryo.
Data from: Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae
Microsatellites are often the marker of choice for population genetic studies at intermediate spatial and temporal scales. Developing large numbers of markers has traditionally been technically difficult and this has limited our ability to investigate evolutionary phenomena that emerge across short temporal scales. Moreover, few markers tend to successfully amplify across species boundaries. As rapid advancements in high-throughput sequencing make microsatellite development cost and time-effective, new avenues for evolutionary, population genetic, and chromosome linkage mapping research are emerging. We used a published PERL script and second-generation sequencing to rapidly and affordably develop microsatellite loci for a widespread phyllostomid bat, Artibeus lituratus, for which no markers were previously available. We used Roche FLX (Titanium) Genome Sequencing to randomly sequence ~101 Mb (255,065 unique reads) of genomic DNA for A. lituratus, within which we discovered 30100 microsatellite loci. We designed primers for 19395 loci that contained suitable flanking regions. We ordered primers for 96 loci, 90 of which produced a single PCR product in A. lituratus. We genotyped 52 loci, and 45 were polymorphic in A. lituratus. We tested cross-species amplification for 96 loci in six additional phyllostomid species: A. planirostris, A. fimbriatus, A. phaeotis, Enchisthenes hartii, Sturnira lilium, and Carollia perspicillata. Cross-species amplification was successful for at least one species for 87 loci (A. fimbriatus), and in all species at least 66 loci amplified. These markers will facilitate future work on these seven species, but also illustrate the utility of this high-throughput method for development of primers across many species simultaneously.
Data from: Membrane-assisted extraction of monoterpenes: from in-silico solvent screening towards biotechnological process application
This work focuses on the process development of membrane-assisted solvent extraction of hydrophobic compounds such as monoterpenes. Beginning with the choice of suitable solvents, quantum chemical calculations with the simulation tool COSMO-RS were carried out to predict the partition coefficient (logP) of (S)-(+)-carvone and terpinen-4-ol in various solvent-water systems and validated afterwards with experimental data. COSMO-RS results show good prediction accuracy for nonpolar solvents like n-hexane, ethyl acetate and n-heptane even in the presence of salts and glycerol in aqueous medium. Based on the high logP value, n-heptane was chosen for the extraction of (S)-(+)-carvone in a lab-scale hollow-fiber membrane contactor. Two operation modes are investigated where experimental and theoretical mass transfer values, based on their related partition coefficients were compared. In addition, the process is evaluated in terms of extraction efficiency and overall product recovery, and its biotechnological application potential discussed. Our work demonstrates that the combination of in-silico prediction by COSMO-RS with membrane-assisted extraction is a promising approach for the recovery of hydrophobic compounds from aqueous solutions.
Data from: The conditional nature of genetic interactions: the consequences of wild-type backgrounds on mutational interactions in a genome-wide modifier screen
The phenotypic outcome of a mutation cannot be simply mapped onto the underlying DNA variant. Instead, the phenotype is a function of the allele, the genetic background in which it occurs and the environment where the mutational effects are expressed. While the influence of genetic background on the expressivity of individual mutations is recognized, its consequences on the interactions between genes, or the genetic network they form, is largely unknown. The description of genetic networks is essential for much of biology; yet if, and how, the topologies of such networks are influenced by background is unknown. Furthermore, a comprehensive examination of the background dependent nature of genetic interactions may lead to identification of novel modifiers of biological processes. Previous work in Drosophila melanogaster demonstrated that wild-type genetic background influences the effects of an allele of scalloped (sd), with respect to both its principal consequence on wing development and its interactions with a mutation in optomotor blind. In this study we address whether the background dependence of mutational interactions is a general property of genetic systems by performing a genome wide dominant modifier screen of the sdE3 allele in two wild-type genetic backgrounds using molecularly defined deletions. We demonstrate that ~74% of all modifiers of the sdE3 phenotype are background-dependent due in part to differential sensitivity to genetic perturbation. These background dependent interactions include some with qualitative differences in the phenotypic outcome, as well as instances of sign epistasis. This suggests that genetic interactions are often contingent on genetic background, with flexibility in genetic networks due to segregating variation in populations. Such background dependent effects can substantially alter conclusions about how genes influence biological processes, the potential for genetic screens in alternative wild-type backgrounds identifying new loci that contribute to trait expression, and the inferences of the topology of genetic networks.
Data from: Silver nanoparticles as a medical device in healthcare settings: a five-step approach for candidate screening of coating agents
Silver nanoparticle-based antimicrobials can promote a long lasting bactericidal effect without detrimental toxic side effects. However, there is not a clear and complete protocol to define and relate the properties of the particles (size, shape, surface charge, ionic content) with their specific activity. In this paper, we propose an effective multi-step approach for the identification of a 'purpose-specific active applicability window' to maximize the antimicrobial activity of medical devices containing silver nanoparticles (Ag NPs) (such as surface coaters), minimizing any consequent risk for human health (safety by design strategy). The antimicrobial activity and the cellular toxicity of four types of Ag NPs, differing in their coating composition and concentration have been quantified. Through the implementation of flow-field flow fractionation, Ag NPs have been characterized in terms of metal release, size and shape. The particles are fractionated in the process while being left unmodified, allowing for the identification of biological particle-specific contribution. Toxicity and inflammatory response in vitro have been assessed on human skin models, while antimicrobial activity has been monitored with both non-pathogenic and pathogenic Escherichia coli. The main benefit associated with such approach is the comprehensive assessment of the maximal effectiveness of candidate nanomaterials, while simultaneously indexing their properties against their safety.
Data from: Screening of candidate substrates and coupling ions of transporters by thermostability shift assays
Substrates of most transport proteins have not been identified, limiting our understanding of their role in physiology and disease. Traditional identification methods use transport assays with radioactive compounds, but they are technically challenging and many compounds are unavailable in radioactive form or are prohibitively expensive, precluding large-scale trials. Here, we present a high-throughput screening method that can identify candidate substrates from libraries of unlabeled compounds. The assay is based on the principle that transport proteins recognize substrates through specific interactions, which lead to enhanced stabilization of the transporter population in thermostability shift assays. Representatives of three different transporter (super)families were tested, which differ in structure as well as transport and ion coupling mechanisms. In each case, the substrates were identified correctly from a large set of chemically related compounds, including stereo-isoforms. In some cases, stabilization by substrate binding was enhanced further by ions, providing testable hypotheses on energy coupling mechanisms.
Pulse Oximetry as a Tool for Neonatal Screening and Early Diagnosis of Critical Congenital Heart Disease
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Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening
<p>Deep screening datasets for experiments conducted in Porebski et al., (2023) Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening. <em>Nat. Biol. Eng., doi: 10.1038/s41551-023-01093-3</em>.</p> <p>Datasets are made available under a CC BY-NC-ND 4.0 licence.</p>
Dataset for the PLC-gamma-2 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the underlying data included in a study which characterized eleven commercially available antibodies for PLC-gamma-2. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.10108291">https://doi.org/10.5281/zenodo.10108291</a>).</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Supplementary material 1 from: Ruswanto R, Mardianingrum R, Septian AD, Yanuar A (2023) The design and virtual screening of thiourea derivatives as a Sirtuin-1 inhibitor. Pharmacia 70(4): 1335-1344. https://doi.org/10.3897/pharmacia.70.e108012
The structure and docking results of the 1-benzoyl-3-methylthioureas derivatives
Accurate Identification of Polyps in Screening Colonoscopies using Convolutional Neural Networks
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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.