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3,223 results for “Human Study”
California Current Ecosystem site, station San Diego County, CA (FIPS 6073), study of human population (total) in units of number on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from California Current Ecosystem (CCE) contains human population (total) measurements in number units and were aggregated to a yearly timescale.
California Current Ecosystem site, station Ventura County, CA (FIPS 6111), study of human population density in units of numberPerKilometerSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from California Current Ecosystem (CCE) contains human population density measurements in numberPerKilometerSquared units and were aggregated to a yearly timescale.
Survey 200 long term study of multiple sites in central Arizona-Phoenix: human activity related measurements
The Ecological Survey of Central Arizona (ESCA) is an extensive field survey and integrated inventory designed to capture key ecological indicators of the CAP LTER study area consisting of the urbanized, suburbanized, and agricultural areas of metropolitan Phoenix, and the surrounding Sonoran desert. The survey is conducted every five years at approximately 200 sample plots (30m x 30m) that were located randomly using a tessellation-stratified dual-density sampling design. Study plots cover habitats throughout the CAP LTER study area ranging from native Sonoran desert sites to residential yards to an airport tarmac. Measurements include an inventory of all plants (identified to the lowest possible taxonomic unit, typically species), plant biovolume, soil coring for physicochemical properties, arthropod sweep-net sampling, photo documentation, and a visual survey of site and area characteristics. The objectives of the survey are to (1) characterize patches in terms of key biotic, physical, and chemical variables, and (2) examine relationships among land use, general plant diversity, native plant diversity, plant biovolume, soil nutrient status, and social-economic indices along an indirect urban gradient. Survey 200 was the original name of the project, and it was renamed to ESCA following the survey conducted in 2015. The data set here includes a subset of information from the Survey200/ESCA focusing exclusively on buildings and indicators of human activity in the survey plots. Investigators interested in more recent survey data, or other variables measured as part of ESCA should search the data catalog for 'ecological survey of central arizona' or 'survey 200'.
Data from: Prevalence characteristics of cervical human papillomavirus (HPV) genotypes in the Taizhou area, China: a cross-sectional study of 37 967 women from the general population
Objectives: High-risk human papillomaviruses (hrHPVs) are highly prevalent worldwide, and HPV genotypes differ between geographical regions; however, sexually transmitted HPV may lead to cervical carcinogenesis. The objective of this cross-sectional study was to estimate the prevalence characteristics of cervical HPV genotypes in Taizhou, Southeast China. Setting and participants: A population-based sample of 37 967 eligible women (median age: 41.6; range: 15–90 years) visiting the Taizhou ENZE Medical Center in Taizhou (2012–2016) was analysed. HPV genotyping was performed on the collected specimens using a GP5+/bioGP6+-PCR/MPG assay by Luminex 200, which simultaneously identifies 27 different HPV genotypes and the β-globin gene (internal control). Results: The overall HPV infection rate was 22.8% in the Taizhou-based population, and the prevalence of high-risk HPV, low-risk HPV and mixed high-risk and low-risk HPV infection was 14.2%, 5.7% and 3.0%, respectively. The most prevalent genotypes were HPV52 (19.7%), 16 (11.9%), 58 (11.5%), 39 (7.2%), 18 (6.6%) and 56 (5.6%). The rate of multiple-type HPV infection was 5.7% in the whole population, and the HPV52+58, HPV16+52 and HPV16+18 mixed genotypes were most common in women with multiple infections. The age-specific HPV prevalence showed a bimodal curve, with a first peak below the age of 21 years (41.6%), followed by a second peak in the age group of 56–60 years (28.5%). Moreover, the HPV infection rate differed significantly between the outpatient and physical examination groups (24.0% vs 19.5%, p<0.0001). Further data comparisons showed that the distribution of HPV genotypes varied markedly between the two groups. Conclusions: Data from this study could be valuable for HPV-based cervical cancer screening efforts in certain areas, support the local vaccination programme in the Taizhou region and facilitate future diagnosis and treatment of HPV diseases.
Data from: Fencing solves human‐wildlife conflict locally but shifts problems elsewhere: a case study using functional connectivity modelling of the African elephant
1. Fencing is one of the commonest methods for mitigating human-wildlife conflicts. At the same time, fencing is considered to be of one of the most pressing emerging threats to conservation globally. Although fences act as barriers and eventually can cause population isolation and fragmentation, it is challenging to quantitatively predict the possible consequences fences have for wildlife. 2. Here, we model how fencing designed to mitigate human-elephant conflict (HEC) on the Borderlands between Kenya and Tanzania will affect functional connectivity and movement corridors for African elephants. Specifically, we (1) model functional landscape connectivity integrating natural and anthropogenic factors; (2) predict seasonal movement corridors used by elephants in non-protected areas; and (3) evaluate whether fencing in one area can potentially intensify human-wildlife conflicts elsewhere. 3. We used GPS movement and remote sensing data to develop monthly step-selection functions to model functional connectivity. For future scenarios, we used a currently ongoing fencing project designed for human-elephant conflict mitigation within the study area. We modelled movement corridors using least-cost path and circuit theory methods, evaluated their predictive power and quantified connectivity changes resulting from the planned fencing. 4. Our results suggest that fencing will not cause landscape fragmentation and will not change functional landscape connectivity dramatically. However, fencing will lead to a loss of connectivity locally and will increase the potential for HEC in new areas. We estimated that wetlands important for movement corridors will be more intensively used by the elephants, which may also cause problems of overgrazing. Seasonal analysis highlighted an increasing usage of non-protected lands in the dry season and equal importance of the pinch point wetlands for preserving overall function connectivity. 5. Synthesis and applications. Fencing is a solution to small-scale HEC problems, but will not solve the issue at a broader scale. Moreover, our results highlight that it may intensify the conflicts and overuse of habitat patches in other areas, thereby negating any conservation benefits. If fencing is employed on a broader scale, then it is imperative that corridors are integrated within the protected area network to ensure local connectivity of affected species.
Data from: Toward a mechanistic understanding of human-induced rapid environmental change: a case study linking energy development, nest predation, and predators
1. Demographic consequences of human-induced rapid environmental change (HIREC) have been widely documented for many populations. The mechanisms underlying such patterns, however, are rarely investigated and yet are critical to understand for effective conservation and management. 2. We investigated the mechanisms underlying reduced avian nest survival with intensification of natural gas development, an increasing source of HIREC globally. We tested the hypothesis that energy development increased the local activity of important nest predator species thereby elevating nest predation rates. During 2011–2012, we surveyed predators and monitored 668 nests of Brewer's sparrows Spizella breweri, sagebrush sparrows Artemisiospiza nevadensis and sage thrashers Oreoscoptes montanus breeding at twelve sites spanning a gradient of habitat loss from energy development in western Wyoming, USA. 3. Nine species, representing four mammalian and three avian families, were video-recorded depredating eggs and nestlings. Important nest predator species differed across songbird species, despite similar nesting habitats. Approximately 75% of depredation events were by rodents. 4. Consistent with our predictions, detections of most rodent nest predators increased with surrounding habitat loss due to natural gas development, which was associated with increased probability of nest predation for our three focal bird species. 5. An altered nest predator assemblage was therefore at least partly responsible for elevated avian nest predation risk in areas with more surrounding energy development. 6. Synthesis and applications. We demonstrate one mechanism, i.e. the local augmentation of predators, by which human-induced rapid environmental change (HIREC) can influence the demography of local populations. Given the accelerating trajectory of global energy demands, an important next step will be to understand why the activity and/or abundance of rodent predators increased with surrounding habitat loss from energy development activities.
Data from: Combining human acceptance and habitat suitability in a unified socio-ecological suitability model: a case study of the wolf in Switzerland
Habitat suitability models (HSMs) are commonly used in conservation practise to assess the potential of an area to be occupied and colonised. A major limitation of these models, however, is the omission of spatially explicit understanding of human acceptance towards the focal species. As wildlife is more and more subject to human-dominated landscapes, ignoring the sociological component will result in misrepresentation of the observed processes and inappropriate management. We distributed 10 000 questionnaires across Switzerland and identified key socio-demographical factors correlated with human acceptance of the wolf. We then created a spatially explicit acceptance model based on geo-referenced socio-demographical, social and geographical information. Finally, we combined our acceptance model with a HSM to obtain a unified socio-ecological suitability model, which included human and ecological components. We showed that the key factors associated with human acceptance were perception of how harmful the wolf is, interest in wolf-related issues, need for livestock protection, and fear of the wolf. Perceived harmfulness was in turn correlated with direct and indirect experience with the wolf, and level of education. Our acceptance map predicted decreasing acceptance with increasing altitude of residency and proximity to locations of confirmed wolf presence. This resulted in the overall opposition to the wolf for the Alpine region, albeit substantial regional differences. We found little spatial overlap (6% of Switzerland) between areas where the wolf was accepted and areas of suitable habitat. These areas of socio-ecological suitability were concentrated in the Jura Mountains and in the eastern and southern Alps, and were absent in the western and central Alps. Particularly in the Jura region, which is yet to be colonised, management of human acceptance will be a crucial conservation target. Synthesis and applications. We developed an integrative, socio-ecological approach that allowed us to accurately reproduce recent wolf recolonisation. We anticipate our framework to be a powerful tool to reliably evaluate overall suitable habitats and predict short to medium-term range expansion for species whose distribution is also dependent on human attitudes. Because our approach is sensitive to both the ecological and human component, it is ideally suited to identify key regions where proactive and targeted socio-ecological management plans are needed.
Data from: Shifting niches of marine predators due to human exploitation: the diet of the South American sea lion (Otaria flavescens) since the late Holocene as a case study
Stable isotope ratios of carbon and nitrogen in archaeological and modern bone samples have been used to reconstruct the dietary changes of the South American sea lion Otaria flavescens from the late Holocene to the present in the southwestern Atlantic. We sampled bones from archaeological sites in northern-central and southern Patagonia, Argentina, and bones housed in modern scientific collections. Additionally, we analyzed the stable isotope ratios in ancient and modern shells of intertidal molluscs to explore changes in the isotope baseline and allow comparison between bone samples from different periods after correction for baseline shifts. Results confirmed the trophic plasticity of the South American sea lion, demonstrated the much larger impact of modern exploitation of marine resources as compared with that of hunter-gatherers, and underscored the dissimilarity between the past and modern niches of exploited species. These conclusions are supported by the rather stable diet of South American sea lions during several millennia of aboriginal exploitation, in both northern-central and southern Patagonia, and the dramatic increase in trophic level observed during the twentieth century. The recent increase in trophic level might be related to the smaller population size resulting from modern sealing and the resulting reduced intraspecific competition. These results demonstrate how much can be learned about the ecology of modern species thanks to retrospective studies beyond the current, anthropogenically modified setting where ecosystem structure is totally different from that in the pristine environments where current species evolved.
Datasets for the study "A Pan-Cancer Single Cell Panorama of Human Natural Killer Cells"
<p>File "comb_CD56_CD16_NK.h5ad" contains processed expression data and raw count data used in most part of the paper and annotations such as "meta_tissue_in_paper" and "cellType".</p><p>File "comb_CD56_CD16_NK_blood.h5ad" contains processed expression data used in the analysis of circulating NK cells and annotations such as "meta_tissue" and "cellType".</p><p>File "Integrated_CD16_NK cells.h5ad" contains processed expression data of CD56dimCD16hi NK cells used in most part of the paper and annotations such as "meta_tissue_in_paper" and "cellType".</p><p>File "Integrated_CD56_NK cells.h5ad" contains processed expression data of CD56brightCD16lo NK cells used in most part of the paper and annotations such as "meta_tissue_in_paper" and "cellType".</p>
Polymerase Chain Reaction Study of Human Bocavirus in Children with Acute Gastroenteritis
<p>Human bocavirus (HBoV) in stool samples from young children below 5 years complaining of acute gastroenteritis (GE) in addition to detection of rotavirus, norovirus and astrovirus.</p>
Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages. in Suidae
Distribution. Sulawesi and adjacent Is (Buton, Kabaena, Muna, Peleng, Lembeh, and on some of the Togian Is); thought to be extinct on Selayar I. Pigs have been widely domesticated through the Indonesian archipelago and beyond. This primarily involved the Eurasian Wild Pig (S. scrofa), but also S. celebensis, the only other species of pig successfully domesticated. Mitochondrial DNA studies of the dispersion of these domesticated forms agree on three major dispersal events, two involving S. scrofa and one S. celebensis. Evidence supports an early human-mediated translocation of S. celebensis to Flores and Timor and two later, separate human-mediated dispersals of domestic pig through islands of SE Asia into Oceania. In addition to Flores and Timor, S. celebensis is also thought to occur in its domesticated form on Halmahera, Lendu, Roti, and Savur Is, and even on Simeulue and Nias Is to the W of Sumatra and far from its island of origin, Sulawesi. In the Moluccas, and possibly elsewhere in this region, introduced S. celebensis are thought to have hybridized with other introduced pigs of S. scrofa derivation, and apparent hybrids between these species are now reported to survive on a number of islands, including Salawatti, Great Kei, Dobu, Seram, Ambon, Bacan, Ternate, Morotai, and New Guinea. It is also reported that in the 19" century the sows of domestic pigs in Sulawesi frequently mated with wild animals, after which they returned to their villages.
Public attitudes to a human challenge study with SARS-CoV-2: a mixed-methods study
<p>Human challenge studies involve the deliberate exposure of healthy volunteers to an infectious micro-organism in a highly controlled and monitored way. They are used to understand infectious diseases and have contributed to the development of vaccines. In early 2020, the UK started exploring the feasibility of establishing a human challenge study with SARS-CoV-2. Given the significant public interest and the complexity of the potential risks and benefits, it is vital that public views are considered in the design and approval of any such study and that investigators and ethics boards remain accountable to the public.</p> <p>We conducted a mixed methods study comprising online surveys conducted with 2,441 UK adults and in-depth virtual focus groups with 57 UK adults during October 2020 to explore the public’s attitudes to a human challenge study with SARS-CoV-2 taking place in the UK.</p> <p>This depositary includes:</p> <ul> <li>Documentation relating to the online surveys; <ul> <li>Survey</li> <li>Animation that survey participants were asked to view</li> <li>Survey wrappers (invitations, participant information sheet and consent, end of survey messages)</li> <li>Survey data (demographic information not included)</li> </ul> </li> <li>Documentation relating to focus groups: <ul> <li>Participant Information Sheet</li> <li>Focus Group Discussion guide</li> </ul> </li> </ul>
Supplemental table 1. Results of systematic literature search for human studies of obesity-related hypothalamic inflammation and gliosis
<p>Supplemental table 1 for the manuscript entitled " The significance of hypothalamic inflammation and gliosis for the pathogenesis of obesity in humans".</p> <p> </p>
Adhesive Antibacterial Moisturizing Nanostructured Skin Patch for Sustainable Development of Atopic Dermatitis Treatment in Humans [Swelling studies]
<p>Adhesive Antibacterial Moisturizing Nanostructured Skin Patch [Swelling studies]</p>
Dataset related to the following study: Humanoid attitudes influence humans in video and live interactions
Open the record for dataset details and reuse information.
Prevalence, Prevention and Willingness to Vaccinate against Human Papillomavirus (HPV) among Women with Adolescent Daughters in Rivers State, Nigeria: A Cross-Sectional Study
<p>Human papillomavirus (HPV) is a significant public health concern due to its association with cervical cancer. Understanding the prevalence of HPV vaccination, prevention practices, and the willingness to vaccinate among women with adolescent daughters is important for improving vaccination coverage. This study aims to assess the prevalence of HPV vaccination, knowledge of HPV prevention, and the willingness to vaccinate daughters among women attending outpatient clinics in Rivers State, Nigeria. A hospital-based descriptive, multi-centre, cross-sectional study was conducted from March to May 2021 at the University of Port Harcourt Teaching Hospital (UPTH) and Rivers State University Teaching Hospital (RSUTH). The study included 304 women with adolescent daughters, recruited through purposive sampling. Data were collected using a pretested self-administered questionnaire. Data analysis was performed using SPSS version 23, with results presented in frequencies and percentages. Of the 304 participants, 40% were aged 30-39 years, and 73.4% had tertiary education. Only 2.3% had previously vaccinated their daughters against HPV. The primary reasons for not vaccinating included insufficient information (54.2%) and lack of access to the vaccine (26.9%). Despite this, 70.4% of the respondents expressed willingness to vaccinate their daughters if provided with adequate information and access. The study highlights a low prevalence of HPV vaccination among adolescent girls in Rivers State, with significant barriers including lack of information and access. However, there is a high willingness to vaccinate, indicating the potential for increased vaccination rates through targeted educational and accessibility interventions.</p>
Humanoid facial expressions as a tool to study human behaviour
<p>Dataset and MATLAB codes relative to the kinematic study titled <em>Humanoid facial expressions as a tool to study human behaviour (Lombardi G., Sciutti A., Rea F., Vannucci F., Di Cesare G, Scientific Reports 2024, DOI: https://doi.org/10.1038/s41598-023-45825-6) </em></p> <p><strong>analysis.m</strong> is the main matlab code for data organization and peak values extraction</p> <p><strong>VelocityCurves.m</strong>, <strong>AccelerationCurves.m</strong> and <strong>HeightCurves.m</strong> are codes to extract and plot mean velocity, acceleration and trajectory curves respectively and visualize comparison between congruent and incongruent conditions.</p> <p><strong>order.mat</strong> contains the order of experimental conditions</p> <p><strong>subject_kinamatic_data</strong> contains the kinematic dataset. Each subject folder contains different runs saved in .csv and .excel format (these are loaded in code analysis.m) </p> <p><strong>For additional information contact Dr. Alessandra Sciutti, alessandra.sciutti@iit.it</strong></p> <p> </p>
Dataset of the study on field evidence for manipulation of mosquito host selection by the human malaria parasite
<p>This repository contains the dataset from host preferences assays to determine odour-mediated mosquito host preference as well as mosquito host selection determination through identification of the blood meal origin from indoor-resting blood-fed mosquito females in Burkina Faso.</p>
Supplemental Material for "Urban blue spaces and human health: A systematic review and meta-analysis of quantitative studies"
Open the record for dataset details and reuse information.
All-atom molecular dynamics simulations for Targeting Human Prostaglandin Reductase 1 with Licochalcone A: Insights from Molecular Dynamics and Covalent Docking Studies
<p>The dataset comprises simulations of the PTGR1 protein under four different conditions: in its apo (unbound) form, bound to the cofactor NADH, and in complex with both covalently and non-covalently bound licochalcone A. Each simulation was conducted using the ff19SB force field and the OPC water model, with water molecules excluded from the trajectories.</p> <p>For the apo form, NADH-bound, and non-covalently bound licochalcone A conditions, each trajectory consists of 5000 snapshots, representing a total of 500 nanoseconds of simulation. However, the trajectory for the no covalently bound licochalcone A condition includes only 1000 frames, corresponding to 150 nanoseconds. This discrepancy in frame count and simulation length across conditions is important to consider when comparing dynamics and structural behavior within the dataset.</p> <p><strong>PTGR1-NADPH.tar.xz</strong> - PTGR1 dimer in complex with NADPH<br><strong>PTGR1-apo.tar.xz</strong> - PTGR1 apo dimer<br><strong>PTGR1-monomer_NADPH.tar.xz</strong> - PTGR1 monomer in complex with NADPH<br><strong>PTGR1-LicA_covalent.tar.xz </strong>- PTGR1 dimer with covalently bound licochalcone A<br><strong>PTGR1-LicA_NO_covalent.tar.xz</strong> - PTGR1 dimer with covalently bound licochalcone A</p> <p> </p> <p>All folders contain:</p> <p><em>*.parm7</em> - dry topology in amber format</p> <p><em>*.nc</em> - dry trajectories in netcdf format</p> <p> </p> <p><strong>Plain molecular dynamics simulations.</strong> Two structures of human PTGR1 have been deposited in the PDB: one bound to NADPH and the raloxifene inhibitor (PDB ID 2Y05, 2.2 Å resolution), and another in apo form (PDB ID 1ZSV, 2.3 Å resolution). In the first structure, it is reported as a monomer, whereas in the second as a dimer. However, the protomers exhibit highly similar conformations in both structures (backbone RMSD ~0.5 Å). Experimental evidence, akin to PTGR1 orthologs and many other MDR enzymes, indicates that the functional form of human PTGR1 is a homodimer (Mesa et al., 2015). Thus, to construct the dimeric form of the coenzyme complex, we duplicated the NADPH-bound protomer from 2Y05 and aligned the two subunits with the dimer from 1ZSV, deleting the raloxifene molecule. In the resulting structure, no steric clashes between the protomers were observed. This structure was used as the starting point for the simulations. Additionally, the apo dimer was generated by removing the NADPH from both subunits, and the monomeric form in complex with NADPH was derived from the initial structure. </p> <p>The pmemd.cuda module of AMBER 22 was used to perform the MD simulations, employing the force field FF19SB and the OPC water model (Case et al., 2022; Izadi, Anandakrishnan, & Onufriev, 2014; Salomon-Ferrer, Götz, Poole Duncan and Le Grand, & Walker, 2013; Tian et al., 2020). NADPH parameters were taken from (Cummins, Ramnarayan, Singh, & Gready, 1991). The system was protonated at pH 7.4 with PDBfixer (Eastman et al., 2017a) and placed in a truncated octahedral box, initially spanning 12 Å further from the solute in each direction using the AMBER tLeap module. The overall charge of the system was neutralized by the addition of four sodium ions. ParmEd (Eastman et al., 2017b) was used to implement the hydrogen mass repartitioning scheme (Hopkins, Le Grand, Walker, & Roitberg, 2015). Local clashes and solvent orientation were corrected using the steepest descent algorithm for 5,000 cycles. During the initial NVT equilibration, the velocities gradually increased through five steps of 200 ps each. The temperature progression started at 150 K and was raised to 200 K, 250 K, 300 K, and finally, 310 K. Position restraints were applied to heavy atoms of the protein, with the restraining forces progressively decreasing at each step. The spring constants were set at 4, 5, 3, and 1 kcal/mol Å2, respectively, to allow for the gradual relaxation of the protein. The system was further equilibrated for 1 ns in the NPT ensemble with no restraints. For treating long-range electrostatic interactions, periodic boundary conditions and Ewald sums were used with a 9 Å cutoff for direct interactions (Darden, York, & Pedersen, 1993; Simmonett & Brooks, 2021). The same cutoff was used for Lennard-Jones interactions. The Langevin thermostat (Sindhikara, Kim, Voter, & Roitberg, 2009) with a collision frequency of 4 ps-1 and the Monte Carlo barostat(Åqvist, Wennerström, Nervall, Bjelic, & Brandsdal, 2004) with a pressure relaxation time of 2 ps were used to control temperatures and pressures, respectively. The SHAKE algorithm was used to fix any bond involving hydrogen atoms (Ryckaert, Ciccotti, & Berendsen, 1977), and a 4-fs time step integration was used. This protocol was taken from (Cofas-Vargas et al., 2022; Medrano‐Cerano et al., 2024) Unless otherwise stated, no other constraints were used. Five replicas of 500 ns each per system were produced.</p> <p>The topology and parameter files for a LicA molecule and for this inhibitor covalently bound to the sulfur atom of a cysteine residue were generated with Antechamber suite (J. Wang, Wang, Kollman, & Case, 2006), using the general Amber force field (GAFF2) for organic molecules (He, Man, Yang, Lee, & Wang, 2020). Atomic charges were derived using the AM1-BB method (Jakalian, Jack, & Bayly, 2002). The parameters are documented in Supplementary Tables SI-1 and SI-2. Trajectories for PTGR1 covalently and noncovalently bound to LicA were run using the same conditions as described above. All molecular structure representations were created using UCSF ChimeraX v1.8 (Meng et al., 2023; Pettersen et al., 2021).</p> <p> </p> <p><strong>Solvent-site identification and guided docking.</strong> Determination of solvent sites (SS) for ethanol and water molecules was conducted by employing the MDmix method. After removing both NADPH molecules from the enzyme dimer, the system was protonated at pH 7.4 with PDBfixer (Eastman et al., 2017a) and placed in a truncated octahedral box of water/ethanol 80/20% v/v, extending12 Å beyond the solute in each direction using the AMBER tLeap module. Five 20 ns replicas were run, using the same conditions described above, but applying Cartesian restrictions of 0.01 kcal/mol A2 over all heavy atoms. After the alignment of trajectories, density maps for probe atoms were generated by constructing a static mesh with cubic grids (0.5 Å edge length) over the entire simulation box. The occurrence of probe atoms within each grid were tracked across the trajectories. These density distributions were then converted into binding free energy using the Boltzmann relationship, comparing observed probe atom distributions against the expected bulk solvent distribution at 1.0 M. Solvent sites were then filtered by applying an energy threshold of 1 kcal/mol, as previously described (Alvarez-Garcia & Barril, 2014; Avila-Barrientos et al., 2022).</p> <p><strong>LicA docking. </strong>For covalent docking, LicA, bound through its Cb atom to the sulfur atom of C239, was docked onto the NADPH-binding site of human PTGR1 employing the covalent docking module of AutoDock4 v4.2.6 (Bianco, Forli, Goodsell, & Olson, 2016; Morris et al., 2009). The flexible side-chain methodology was used. In a subsequent non-covalent docking, solvent sites previously identified for ethanol and water were used as pharmacophoric element for rDock (Ruiz-Carmona et al., 2014). This docking involved defining the receptor system and generating a binding cavity using the NADPH as a reference molecule. During the non-covalent docking, a penalty score proportional to the square of the distance from each ligand conformation to a solvent site (SS) was applied when the separation exceeded 2 Å. The docking run included 100 simulations, generating a set of potential binding modes for LicA within the NADPH site. </p>
ScienceDex guides
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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.