Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

data set regarding to project Optimal assessment of nutritional status in older subjects with the chronic obstructive pulmonary disease – a comparison of three screening tools used in the GLIM diagnostic algorithm

data set regarding to project Optimal assessment of nutritional status in older subjects with the chronic obstructive pulmonary disease – a comparison of three screening tools used in the GLIM diagnostic algorithm

opencc-zeroJan 2022View details →

Spatial targeting of Screening + Eave tubes (SET), a house-based malaria control intervention, in Côte d'Ivoire: A geostatistical modelling study

New malaria control tools and tailoring interventions to local contexts are needed to reduce the malaria burden and meet global goals. The housing modification, screening plus a targeted house-based insecticide delivery system called the In2Care® Eave Tubes, has been shown to reduce clinical malaria in a large cluster randomised controlled trial. However, the widescale suitability of this approach is unknown. We aimed to predict household suitability and define the most appropriate locations for ground-truthing where Screening + Eave Tubes (SET) could be implemented across Côte d'Ivoire. We classified DHS sampled households into suitable for SET based on the walls and roof materials. We fitted a Bayesian beta-binomial logistic model using the integrated nested Laplace approximation (INLA) to predict suitability of SET and to define priority locations for ground-truthing and to calculate the potential population coverage and costs. Based on currently available data on house type and malaria infection rate, 31% of the total population and 17.5% of the population in areas of high malaria transmission live in areas suitable for SET. The estimated cost of implementing SET in suitable high malaria transmission areas would be $46m ($13m –$108m). Ground-truthing and more studies should be conducted to evaluate the efficacy and feasibility of SET in these settings. The study provides an example of implementing strategies to reflect local socio-economic and epidemiological factors, and move beyond blanket, one-size-fits-all strategies.

opencc-by-4.0Oct 2021View details →

High-Throughput Screening of Tribological Properties of Monolayer Films using Molecular Dynamics and Machine Learning: Supplemental Repository

Supplemental repository for the "High-Throughput Screening of Tribological Properties of Monolayer Films using Molecular Dynamics and Machine Learning" article. Contains calculated tribological properties of dual-monolayer systems from Molecular Dynamics (MD) simulation and Machine Learning (ML).

opencc-by-4.0Mar 2022View details →

Metabolomics-based phenotypic screens for evaluation of drug synergy via DIMS

Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent drug resistance. While conventional high-throughput screens relied on univariate data are incredibly valuable to identify promising drug candidates, phenotypic screening methodologies could be beneficial to provide deep insight into the molecular response of drug combination with a likelihood of improved clinical outcomes. We developed a high-content metabolomics drug screening platform using stable isotope tracer direct infusion mass spectrometry that informs a novel algorithm to determine synergy from multivariate phenomics data. Using a cancer drug library, we validated the drug screening integrating isotope enriched metabolomics data and computational data mining on a panel of prostate cell lines and verified the synergy between CB-839 and docetaxel both in vitro (three-dimensional model) and in vivo. The proposed unbiased metabolomics screening platform can be used to rapidly generate phenotype-informed datasets and quantify synergy for combinatorial drug discovery. Drugs used in combination can synergize to increase efficacy, decrease toxicity, and prevent drug resistance. While conventional high-throughput screens relied on univariate data are incredibly valuable to identify promising drug candidates, phenotypic screening methodologies could be beneficial to provide deep insight into the molecular response of drug combination with a likelihood of improved clinical outcomes. We developed a high-content metabolomics drug screening platform using stable isotope tracer direct infusion mass spectrometry that informs a novel algorithm to determine synergy from multivariate phenomics data. Using a cancer drug library, we validated the drug screening integrating isotope enriched metabolomics data and computational data mining on a panel of prostate cell lines and verified the synergy between CB-839 and docetaxel both in vitro (three-dimensional model) and in vivo. The proposed unbiased metabolomics screening platform can be used to rapidly generate phenotype-informed datasets and quantify synergy for combinatorial drug discovery.

opencc-zeroMay 2022View details →

Differences in neurotoxic outcomes of organophosphorus pesticides revealed via multi-dimensional screening in adult and regenerating planarians

Organophosphorus pesticides (OPs) are a chemically diverse class of commonly used insecticides. Epidemiological studies suggest that low dose chronic prenatal and infant exposures can lead to life-long neurological damage and behavioral disorders. While inhibition of acetylcholinesterase (AChE) is the shared mechanism of acute OP neurotoxicity, OP-induced developmental neurotoxicity (DNT) can occur independently and/or in the absence of significant AChE inhibition, suggesting alternative targets. Moreover, different OPs can cause different adverse outcomes, suggesting that different OPs act through different mechanisms, emphasizing the importance of comparative studies of OP toxicity. Freshwater planarians are an invertebrate system that uniquely allows for automated, rapid and inexpensive testing of adult and developing organisms in parallel to differentiate neurotoxicity from DNT. Effects found only in regenerating planarians would be indicative of DNT, whereas shared effects may represent general neurotoxicity. We leverage this feature to investigate potential differential effects of these OPs on the adult and developing brain by performing a comparative high-throughput screen to test 7 OPs (acephate, chlorpyrifos, dichlorvos, diazinon, malathion, parathion and profenofos) across 10 concentrations in quarter-log steps. Neurotoxicity was evaluated using a wide range of quantitative morphological and behavioral readouts. AChE activity was measured using an Ellman assay. The toxicological profiles of the 7 OPs differed across the OPs and between adult and regenerating planarians. Toxicological profiles were not correlated with levels of AChE inhibition. Twenty-two "mechanistic control compounds" known to target pathways suggested in the literature to be affected by OPs (cholinergic neurotransmission, serotonin neurotransmission, endocannabinoid system, cytoskeleton, adenyl cyclase and oxidative stress) and 2 negative controls were also screened. When compared with the mechanistic control compounds, the phenotypic profiles of the different OPs separated into distinct clusters. The phenotypic profiles of adult vs regenerating planarians exposed to the OPs clustered differently, suggesting some developmental-specific mechanisms. These results further support findings in other systems that OPs cause different adverse outcomes in the (developing) brain and build the foundation for future comparative studies focused on delineating the mechanisms of OP neurotoxicity in planarians.

opencc-by-4.0Dec 2021View details →

Mendelian gene identification through mouse embryo viability screening

Supplementary files to support a manuscript entitled "Mendelian gene identification through mouse embryo viability screening"

Covalent Data Screen of TBXTA-C006

Uploaded data set contains the mass spec labelling data covalent inhibitor campaign against TBXTA-C006. The data was collected at Oxford and it contains the Structure IDs we use, the SMILE strings, and the %-labelling of protein by mass spec at 5 uM (10 minutes or 60 minutes) or 50 uM (60 minutes). A more detailed protocol is given below. Protocol: Protein is TBXTA-C006 (13 mg/ml 130x final concentration 0.1 mg/ml or 5 uM) Buffer is 10 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM TCEP (freshly prepared) Compounds are in stock plates at 100 mM, Initial 1:40 dilution into buffer (50 uM) and further 1:10 dilution for Low conc (5uM) 1 ul of compound is added to 50 ul of protein for final 50 uM and 5 uM conc. At 1hr (or less) 5ul is removed and added to 50 ul of MS buffer.

Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"

Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores.  For the details please see the original publication or the bioarxiv preprint:  https://doi.org/10.1101/2021.04.05.438521 The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment.  For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)

IN SILICO SCREENING OF TWO-PHOTON ABSORPTION PROPERTIES OF A LARGE SET OF BIS-BF2-DYES

This data set is a part of Supporting Info for our work entitled “IN SILICO SCREENING OF TWO-PHOTON ABSORPTION PROPERTIES OF A LARGE SET OF BIS-BF2-DYES” which is published in ChemPhotoChem peer-reviewed scientific journal (<a href="https://doi.org/10.1002/cptc.202200137">doi.org/10.1002/cptc.202200137</a>). In this data set, we provide the XYZ coordinates for the 280 compounds studied in this work.

opencc-by-4.0Jul 2022View details →

Screening Rafflesia and Sapria Metabolites Using a Bioinformatics Approach to Assess Their Potential as Drugs

This dataset contains molecular docking results read using LigPlus, referred in the text: Wicaksono et al. (2022) Screening Rafflesia and Sapria Metabolites Using a Bioinformatics Approach to  Assess Their Potential as Drugs. Philippine Journal of Science. As Appendix II.

PanDDA files from a ligand screen against the NSP3 macrodomain of SARS-CoV-2 - ligands from fragment merging/linking and virtual screening

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 Gahbauer et al. 2022 (doi: https://doi.org/10.1101/2022.06.27.497816). 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.  mac1_ligand-bound_states.zip contains the ligand-bound states extracted from the multi-state PDB files.

opencc-zeroSep 2022View details →

Reduction of chickens use to perform in vitro pre-screening of novel anticoccidials by miniaturisation and increased throughput of the current Eimeria tenella compound-screening model

In vitro models have supported important advances in biomedical sciences and have significantly contributed to reduce the use of experimental animals in different disciplines. We have developed an in vitro model for the evaluation of potential anticoccidial properties of novel compounds aimed to control chicken coccidiosis, a costly disease for the poultry industry. This disease is caused by protozoan parasites of the genus Eimeria (Apicomplexa), and it is mainly controlled by chemoprophylaxis with ionophors and chemical anticoccidials; however, there is an overall agreement about the limitation of these classical drugs and the need to improve current methods of control. Anticoccidial activities of novel compounds is currently evaluated by expensive experiments that involve large numbers of chickens. The use of our in vitro model for the pre-screening of essential oils led to a reduction of 67% of the chickens used in the vivo trials for validation. In this study, we describe how further optimisation of this in vitro model by miniaturisation can have an additional impact on the number of chickens used for the generation of parasite stocks for provision of the in vitro model (which cannot be done in vitro). We have estimated that the use of one chicken could support the evaluation of ten compounds with a 96-well plate format vs. only two with a 24-well plate format, which means an 80% of chicken use reduction. In this study, we have proved that the miniaturisation into a 96-well plate format has perfectly mimicked the invasion and replication observed before in the 24-well plate format. In addition, this format has allowed the simultaneous pre-screening of higher numbers of anticoccidial drugs at different concentrations following streamlined protocols in a more cost-effective way, factors that are beneficial for a wider uptake of the model by other researchers investigating anticoccidial compounds.

openother-openSep 2022View details →

evanradith/datasetEPB7: Dataset Survei Analisa Screen Time dan Pengeluaran Belanja Online

Dataset dari hasil survei yang dilakukan untuk menyusun paper berjudul "Analisis Hubungan Screen Time pada Aplikasi Belanja Online di Ponsel dan Bidang Studi dengan Jumlah Pengeluaran pada Masa New Normal Setelah Pandemi (Studi Kasus: Mahasiswa ITS)". Responden dataset merupakan mahasiswa ITS yang telah mengisi kuesioner yang telah disebarkan.

opencc-zeroOct 2022View details →

Data reported in development and cross-validation of a veterans mental health risk factor screen

Background. VA primary care patients are routinely screened for current symptoms of PTSD, depression, and alcohol disorders, but many who screen positive do not engage in care. In addition to stigma about mental disorders and a high value on autonomy, some veterans may not seek care because of uncertainty about whether they need treatment to recover. A screen for mental health risk could provide an alternative motivation for patients to engage in care. Results. Twelve items assessing dissociation, emotional lability, life stress, and moral injury correctly classified 86% of those who later had elevated PTSD and/or depression symptoms (sensitivity) and 75% of those whose later symptoms were not elevated (specificity). Performance was also very good for 110 veterans who identified as members of ethnic/racial minorities. Conclusions. Mental health status was prospectively predicted in VA primary care patients with high accuracy using a screen that is brief, easy to administer, score, and interpret, and fits well into VA's integrated primary care. When care is readily accessible, appealing to veterans, and not perceived as stigmatizing, information about mental health risk may result in higher rates of engagement than information about current mental disorder status.

opencc-byMar 2021View details →

Martha's Screen, Rosedown

A 3D scan of Martha's Screen at Rosedown Plantation in St. Francisville, Louisiana, USA as part of a project to document the house, landscape, and artifacts. **Artifact:** Martha's Screen **Location:** Rosedown Plantation, St. Francisville, Louisiana, USA **Team:** Brendan Harmon & Nicholas Serrano **Camera:** Nikon 5600 **Software:** Agisoft Metashape Source: Objaverse 1.0 / Sketchfab

opencc-byJun 2021View details →

Westminster Abbey Choir Screen

The decorated screen in the nave, leading into the Quire of Westminster Abbey, London. It includes a monument to Sir Isaac Newton. the organ is located on top of the screen. https://www.westminster-abbey.org/about-the-abbey/history/nave 253 photos taken in June 2021 with a Sony a6000 and processed in Reality Capture. Above the screen is low quality because I could not photograph that area. Source: Objaverse 1.0 / Sketchfab

restrictedcc-by-4.0Oct 2022View details →

Adolescent screen time and unhealthy food consumption in the context of the digital development in New Caledonia

Data from self-report questionnaires on time spent in front of tablets, computers and mobile phones, as well as the consumption of unhealthy food and drinks. Participant characteristics: 11 to 15 years old students. Number of participants: 867. Year of the study: 2018 - 2019. Place of the study: New Caledonia.

opencc-by-4.0Dec 2021View details →

Fig. 1 Screening flow, testing 1600 FDA compounds against S in Assessment of FDA-approved drugs against StrongyloideS rAtti in vitro and in vivo to identify potentially active drugs against strongyloidiasis

Fig. 1 Screening flow, testing 1600 FDA compounds against S. ratti

opencc-by-4.0Apr 2024View details →

Dataset and Screening code for Reviewing Water Conflicts in a Changing Climate

A scoping review was performed to quantify concepts covered in the scientific literature relating to water conflict in a changing climate. The uploaded files consists of: <ul> <li>A list of all studies found using the search terms ("Included studies and categories")</li> <li>All meta categories and concept categories, with all search strings used, ("Included studies and categories") and </li> <li>The MATLAB code used to screen and remove irrelevant studies after the queries. ("Screening_review")</li> <li>An example Excel sheet on how to structure papers for screening using the MATLAB code. ("Example_screening")</li> </ul> All searches were using Scopus and performed 9 Jan 2024. Search terms used were: <ol> <li>(“climate change” OR “global warming” OR “environmental change”) AND (conflict OR dispute) AND (water OR hydrology)</li> <li>(conflict OR dispute) AND hydroclimat*</li> <li>(“water conflict” OR “water dispute”) AND (precipitation OR temperature OR drought)</li> <li>(conflict OR dispute) AND “climate change”</li> <li>hydropolitic*</li> <li>“water conflict” OR “water dispute”</li> </ol> The final publication selection for the scoping review was made based on four criteria, all of which needed to be fulfilled for each selected study: i) the study is considering water-related conflicts (conflicts directly or indirectly related to freshwater aspects, such as water scarcity or lack of access to water);  ii) the study considers the water-related conflict(s) in a climate change context (directly or indirectly related to climate change, including direct impact of climate change adaptation measures); iii) the study addresses factors relating to a previous or ongoing act of conflict (violent or non-violent) and not just potential conflicts or conflict mitigation measures, for example for future water resource decline.  Relevance based on these criteria was first evaluated by reading the abstracts and the full text was examined only when further clarification on the relevance of a study was needed. For our analysis, we created categories that bring together several similar words around the same broader concepts. For example, the category ‘governance’ includes the words policy, politic\w*, polici\w*, democra\w*, govern\w*, supreme court, minist\w*, and federal (for all concept categories, see the uploaded file). The different categories were further grouped together into category groups: political, livelihoods and industry, climate change, conflict, cooperation, and scale. Results will be found in the open-source article after publication and then the DOI and reference to that article will be added here.