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opencc-zeroNov 2021View details →

Screening of 6000 compounds for uncoupling activity: input parameters, the predicted uncoupling activity, as well as the results in respect to structural alerts

Protonophoric uncoupling of phosphorylation is an important factor when assessing chemicals for their toxicity, and has recently moved into focus in pharmaceutical research with respect to the treatment of diseases such as cancer, diabetes or obesity. Reliably identifying uncoupling activity is thus a valuable goal. To that end, we screened more than 6000 anionic compounds for in-vitro uncoupling activity, using a biophysical model based on ab-initio COSMO-RS input parameters with the molecular structure as the only external input. We combined these results with a model for baseline toxicity (narcosis). Our model identified more than 1250 possible uncouplers in the screening dataset, and identified possible new uncoupler classes such as thiophosphoric acids. When tested against 423 known uncouplers and 612 known inactive compounds in the dataset, the model reached a sensitivity of 83% and a specificity of 96%. In a direct comparison, it showed a similar specificity than the structural alert profiler Mitotox (97%), but much higher sensitivity than Mitotox (47%). The biophysical model thus allows for a more accurate screening for uncoupling activity than existing structural alert profilers. We propose to use our model as a complementary tool to screen large datasets for protonophoric uncoupling activity in drug development and toxicity assessment.

opencc-by-4.0Nov 2021View details →

Virtual Screening and Testing of GSK-3 Kinase Inhibitors Using human SH-SY5Y Neuronal cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Neuron Culture Under Tau Cytotoxicity

Supplementary Figure S1. for IJMS

opencc-by-4.0Dec 2020View details →

Health care professionals' experiences of screening immigrant mothers for postpartum depression – a systematic review

This is the dataset and supplementary material to a study looking at the health care professionals’ experiences of postpartum depression in immigrant mothers. Postpartum depression is considered a major public health problem, which immigrant mothers are at particular risk of being affected by, but it can also have long-lasting traumatic effects on the partner’s health and the child’s health and development. Previous studies have suggested that identifying signs of postpartum depression and performing screening on immigrant mothers is challenging for HCPs, and a meta-synthesis was therefore undertaken to describe their experiences.  Methods The databases CINAHL, PubMed, PsycINFO, SocINDEX, Embase, and Cochrane were searched for papers published January 2000–December 2020, reporting qualitative data on immigrants, postpartum depression, and the Edinburgh Postnatal Depression Scale. Eight papers representing eight studies from four countries were included and the Critical Appraisal Skills Program was used to assess their quality. The synthesis of studies was guided by Noblit & Hare’s seven-step method based on meta-ethnography. The dataset is the information from the quality appraisal and grid of concepts from the analysis.  Findings The synthesis resulted in two final themes: “I do my best, but I doubt that it’s enough” and “I can find no way forward”. The themes convey the fear and frustration that health care professionals experienced; fear of missing mothers with signs of postpartum depression, related to feeling uncomfortable in the cross-cultural setting and frustration in handling difficulties associated with communication, translated versions of the Edinburgh Postnatal Depression Scale and cultural implications of postpartum depression.  Conclusions and clinical implication By supporting HCPs’ self-efficacy in handling cultural implications of postpartum depression and by developing evidence-based clinical guidelines for the use of interpreters and translated versions of the Edinburgh Postnatal Depression Scale the screening of immigrant mothers may be facilitated.

Virtual screening of the Janssen compound collection against SARS-CoV-2 Mpro

This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Mpro and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Virtual screening of the Enamine REAL database against SARS-CoV-2 RdRP

This short report describes the most relevant results of virtually screening the Enamine REAL database for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Virtual screening of 2629 Janssen compounds against SARS-CoV-2 RdRP

This short report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 RdRP and confirmation of potential hits in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Screening of 67 compounds with predicted biosignature profile similar to remdesivir for anti-SARS-CoV-2 activity

This short report describes the most relevant results of screening compounds with a similar predicted biosignature as remdesivir in a VeroE6 cell-based anti-SARS-CoV-2 assay.

Screening of ~7000 coronavirus-specific compounds for anti-SARS-CoV-2 activity

This short report describes the most relevant results of screening selected compounds with potential activity against SARS-CoV-2 in a VeroE6 cell-based anti-SARS-CoV-2 assay.

opencc-zeroJan 2022View details →

Mitochondrial and ER membrane protein trafficking CRISPR screens

The trafficking of specific protein cohorts to the correct subcellular location at the correct time is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or FACS. To broadly empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identify genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. We show that loss of the SUMO E1 component SAE1 results in the mislocalization and destabilization of mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.

opencc-zeroJan 2022View details →

ESM of determination of transdermal rate of metallic microneedle array through impedance measurements-based numerical check screening algorithm

Microneedle systems have been widely used in health monitoring, painless drug delivery, and medical cosmetology. Although many studies on microneedle materials, structures, and applications have been conducted, the applications of microneedles often suffered from issues of inconsistent penetration rates due to the complication of skin-microneedle interface. In this study, we demonstrated a methodology of determination of transdermal rate of metallic microneedle array through impedance measurements-based numerical check screening algorithm. Metallic sheet microneedle array sensors with different sizes were fabricated to evaluate different transdermal rates. In vitro sensing of hydrogen peroxide confirmed the effect of transdermal rate on the sensing outcomes. A FEM simulation model of a microneedle array revealed the monotonous relation between the transdermal state and test current. Accordingly, two methods were first derived to calculate the transdermal rate from the test current. First, an exact logic method provided the number of unpenetrated tips per sheet, but it required more rigorous testing results. Second, a fuzzy logic method provided an approximate transdermal rate on adjacent areas, being more applicable and robust to errors. Real-time transdermal rate estimation may be essential for improving the performance of microneedle systems, and this study provides various fundaments toward that goal.

opencc-zeroFeb 2022View details →

Screening coffee genotypes for brown eye spot resistance in Brazil

Several researchers have attempted to develop coffee plants that are resistant to brown eye spot (BES); however, no coffee cultivars are resistant to the disease. In the present study, a blend of strains from Cercospora coffeicola was inoculated into 19 Brazilian commercial cultivars and 41 accessions from the Germplasm Collection of Minas Gerais to evaluate the genetic resistance ability within the population and select superior genotypes for the breeding program. After predicting the genotypic values of the studied material, the evaluations number necessary for selecting genotypes with accuracy and efficiency was determined based on the data of severity to BES. The action of defense mechanisms plant was also investigated by assessing the levels of total soluble phenolic compounds and soluble lignin in contrasting genotypes for disease susceptibility. Based on the results, the accession MG 1207 Sumatra, had an intrinsic genetic capacity to maintain low levels of severity to BES. The genotype MG 1207 Sumatra can substantially contribute to the development of new cultivars, which may lead to the reduced use of pesticides. According to the accuracy and efficiency results obtained, four evaluations BES severity are sufficient to achieve accuracy, providing expressive genetic gains. Finally, the levels of lignin and phenolic compounds were not found to be associated with the resistance of coffee genotypes to BES.

opencc-by-4.0Mar 2022View details →

Dataset of the study "Factor Structure, Validity, and Reliability of the STarT Back Screening Tool in Italian Obese and Non-obese Patients With Low Back Pain"

Dataset of the study "Factor Structure, Validity, and Reliability of the STarT Back Screening Tool in Italian Obese and Non-obese Patients With Low Back Pain" published in Frontiers in Psychology 20 October 2021 12:740851, doi: 10.3389/fpsyg.2021.740851

opencc-by-4.0Oct 2021View details →

Processed data from Repair-seq screens of prime editing of point mutations

Processed data from Repair-seq screens of prime editing of point mutations.

opencc-zeroMar 2022View details →

Chemical screening in an estrogen receptor transactivation assay with metabolic competence

The U.S. EPA continues to utilize high-throughput screening data to evaluate potential biological effects of endocrine active substances without the use of animal testing. Determining the scope and need for in vitro metabolism in high-throughput assays requires the generation of larger data sets that assess the impact of xenobiotic transformations on toxicity-related endpoints. The objective of the current study was to screen a set of 768 ToxCast chemicals in the VM7Luc estrogen receptor transactivation assay (ERTA) using the Alginate Immobilization of Metabolic Enzymes (AIME) hepatic metabolism method. Chemicals were screened with or without metabolism to identify estrogenic effects and metabolism-dependent changes in bioactivity. Based on estrogenic hit calls, 85 chemicals were active in both assay modes, 16 chemicals were only active without metabolism, and 27 chemicals were only active with metabolism. Using a novel metabolism curve shift method that evaluates the shift in concentration-response curves, 29 of these estrogenic chemicals were identified as bioactivated and 59 were bioinactivated. Human biotransformation routes and associated metabolites were predicted in silico across the chemicals to mechanistically characterize possible transformation-related ERTA effects. Overall, the study profiled novel chemicals associated with metabolism-dependent changes in ERTA bioactivity, and suggested routes of biotransformation and putative metabolites responsible for the observed estrogenic effects. The data demonstrate a range of metabolism-dependent effects across a diverse chemical library and highlight the need to evaluate the role of intrinsic xenobiotic metabolism in endocrine and other toxicity-related health effects.

opencc-by-4.0Mar 2022View details →

Parameters for "Planning for the next pandemic: The Finnish colorectal cancer screening programme"

Parameters used in the pape "Planning for the next pandemic: The Finnish colorectal cancer screening programme"

opencc-zeroMar 2022View details →

Raw sequence of: Field investigation- and dietary metabarcoding-based screening of arthropods that prey on primary tea pests

Predatory natural enemies play key functional roles in biological control. Abundant predatory arthropod species have been recorded in tea plantation ecosystems. However, few studies have comprehensively evaluated the control effect of predatory arthropods on tea pests in the field. We performed a one-year field investigation and collected predatory arthropods and pests in the tea canopy. Total 7,931 predatory arthropod individuals were collected, and Coleosoma blandum (Araneae, Theridiidae) was the most abundant species in the studied tea plantation. The population dynamics between C. blandum and four main tea pest species (Aleurocanthus spiniferus, Empoasca onukii, Ectropis grisescens and Scopula subpunctaria) were established using the individual number of predators and pests in each month. The results showed that the occurrence of C. blandum showed high synchronism with the occurrence of A. spiniferus, Em. onukii and Ec. grisescens. The prey spectrum of C. blandum was further analyzed using DNA metabarcoding. Among prey species, A. spiniferus, Em. onukii and Ec. grisescens were included, and the relative abundance and positive rates of target DNA fragments of A. spiniferus were obviously greater than those of other two pests.

opencc-by-4.0Jul 2020View details →

AFM-Based High-Throughput Nanomechanical Screening of Single Extracellular Vesicles

I the present study, a novel AFM-based high throughput mechanical characterization for extracellular vesicles is presented. The method relies on the analysis of vesicles morphometry following their adsorption on surfaces. The deformation extent of the vesicle, which is representative of the vesicle stiffness, is evaluated by the calculation of the so-called vesicle contact angle. The method was applied to different etracellular vesicles (EVs) samples from different natural sources and was employed for spotting the presence of non-vesicular contaminants.

opencc-zeroMay 2022View details →

EHR screen, test, and refer to HFMH DPP

Objective: Determine if certified electronic health record technology (CEHRT) can be used to identify and refer patients with prediabetes to lifestyle change programs (LCPs) recognized by the National Diabetes Prevention Program (DPP). Materials and Methods: This pilot utilized a prediabetes registry, patient portal, and clinical decision support to increase referrals. Results: Data from 36 primary care providers showed 4,930 patients were eligible for DPP LCP, 293 referrals were generated, compared to 20 referrals in the baseline period, and 116 patients enrolled. Referral to enrollment conversion rates were 41% in the study period and 69% in the post-study 1-year period. Discussion: CEHRT functionalities can support systematic identification and management of prediabetes. The referral rate increased seven-fold compared to the baseline period, with high referral to enrollment conversion rates. Conclusions: CEHRT coupled with active provider engagement can serve as a tool to identify prediabetes patients and facilitate LCP referrals and enrollment.

opencc-by-4.0Jun 2022View details →

Virtual screening on SARS-CoV-2 Nsp14_testing of 5474 hits in a Nsp14 biochemical assay and an A549-hACE2 SARS-CoV-2 infected cells

This report describes the most relevant results of virtually screening the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 Nsp14 and confirmation of potential hits in a SARS-CoV-2 Nsp10/Nsp14 biochemical exonuclease assay and in a A549-hACE2 cell-based anti-SARS-CoV-2 assay.