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53 results for “Manuscript Studies”
Data for manuscript titled 'Impact of urbanization and drought on river water quality, case study of nutrient levels in Cuenca and Giron (Azuay, Ecuador)'
<p>The uploaded zip-file entails the data obtained through four field campaigns performed in the province of Azuay (Ecuador) in the period July 2023 - May 2024, which is used as a basis for the manuscript titled 'Impact of urbanization and drought on river water quality, case study of nutrient levels in Cuenca and Giron (Azuay, Ecuador)' that was submitted to a Special Issue in the journal Water in 2024. The study aimed at illustrating the impact of urbanisation and drought on the abiotic water conditions of the rivers passing through the studied urban areas.</p> <p>The data includes a subfolder with data obtained from an external website (https://generacioncsr.celec.gob.ec/graficasproduccion/) and aligns with the folder structure of the GitHub-repository that contains the analysis scripts (to be added when the manuscript is accepted). The data file only contains the baseline data, while results can be obtained through running the R-scripts in the GitHub-repository. Additional comments on the analyses are also provided in the analysis scripts.</p> <p><strong>DATA COLLECTION</strong></p> <p>Information on the locations was collected prior to the first field campaign (July 2023) and confirmed in the field (and corrected when necessary). The following variables were registered: Date & Time, Coordinates (latitude and longitude, in WGS84 format), Altitude (in meters above mean sea level), Distance (to a fixed location downstream; being the province border), and Category (River or Stream).</p> <p>Information on the physicochemical conditions was collected directly in the field with a <strong>Horiba U-52</strong> multiprobe. The following variables were registered: Temperature, pH, Electrical conductivity (reference at 25 °C), Oxygen level (as concentration), and Turbidity (in NTU).</p> <p>At each site, a bucket was rinsed thrice with prevailing surface water and subsequently filled with a water sample of the top of the water column. The multiprobe was rinsed with this sample water and then submerged in the bucket, followed by continuous stirring (to avoid a decrease of the oxygen levels) until the readings stabilised. After stabilisation, readings were recorded on a separate data sheet prior to being digitalised.</p> <p>Information on the nutrient levels was obtained through the collection of water samples in the field and the subsequent analysis in the laboratory. The following nutrients were selected: ammonium, nitrate, nitrite, and orthophosphate. For the analyses, <strong>Merck test kits</strong> (equivalent to USEPA analyses) were used in combination with a Genesys UV-VIS spectrophotometer (Thermofisher).</p> <p><strong>In the field</strong>, a bucket was rinsed thrice with prevailing surface water and subsequently filled with a water sample of the top of the water column. A polyethylene syringe was rinsed thrice with sample water and subsequently filled prior to being fitted with a 0.45 µm PES filter. About 100 mL of sampled water was filtered and collected in a 250 mL polyethylene bottle that was rinsed with the first 5 mL of filtered water. The bottle was stored in a cooling box and transported to the laboratory.</p> <p><strong>In the laboratory</strong>, the 250 mL bottle was stored at 4 °C until analysis. Within 36 hours, concentrations of ammonium, nitrate, nitrite, and orthophosphate were determined <strong>in triplicate</strong>. More specifically, the following test kits were used to determine said nitrogen and phosphorus concentrations (with quantification range between brackets):</p> <ul> <li>Ammonium: 1.14752.0001 (0.05-3.00 mgN/L)</li> <li>Nitrate: 1.14773.0001 (2-20 mgN/L)</li> <li>Nitrite: 1.14776.0001 (0.02-1.00 mgN/L)</li> <li>Orthophosphate: 1.14848.0001 (0.05-5.00 mgP/L)</li> </ul> <p>Regarding the <strong>spectrophotometric determination</strong>, all analyses were complemented with a blank and a standard with a known concentration of each individual nutrient component. For each nutrient, a specific wavelength was used and the resulting absorbance was converted to the associated nutrient concentration through known factors (similar to the use of calibration curves), after setting the absorbance of the blank as reference absorbance (i.e. a concentration of 0 mg/L). All of the analyses were performed with plastic 1-cm cuvettes during the first campaign, while 5-cm cuvettes were used in the remaining three campaigns due to low nutrient levels (except for nitrate, for which an analysis through 5-cm cuvettes is not supported by the used test kits).</p>
Dataset for the manuscript Marmet, Wicki, Gmel, Gachoud, Daeppen, Bertholet, Studer (2021). The psychological impact of the COVID-19 crisis is higher among young Swiss men with a lower socioeconomic status: evidence from a cohort study. Plos One. DOI:10.1371/journal.pone.0255050
<p>Dataset for the manuscript Marmet, Wicki, Gmel, Gachoud, Daeppen, Bertholet, Studer (2021). The psychological impact of the COVID-19 crisis is higher among young Swiss men with a lower socioeconomic status: evidence from a cohort study. Plos One DOI:10.1371/journal.pone.0255050</p> <p>The dataset contains all data needed to reproduce the results in the above cited manuscript. Variable description and labels can be found in the codebook. For further information on the instruments used please refer to the manuscript.</p> <p> </p>
A Corpus of Biblical Names in the Greek New Testament to Study the Additions, Omissions, and Variations across Different Manuscripts
<p>The analysis of textual variants of verses in the Ancient Greek New Testament across different manuscripts has mainly been done by close reading with manual effort. With the increasing number of transcriptions of the different manuscripts, quantitative analyses (so-called distant reading) can be used to search for patterns of omission, addition, or other variations, to formulate novel hypotheses to be investigated by close reading. In this work, we present a corpus of biblical names including spelling variation and inflections and their mentions in the transcriptions of the Ancient Greek New Testament.</p>
Case studies related to the manuscript Tuning Trains Speed in Railway Scheduling
<p>This dataset is dedicated to the case studies related to the manuscript <strong>Tuning Trains Speed in Railway Scheduling</strong> by Étienne André, published in the proceedings of the 25th International Conference on Formal Engineering Methods (ICFEM 2024).</p> <p>See README.md for more information.</p>
Data for the study of Posidonia microbial nitrogen metabolism manuscript
<p>These are data related to the study of the seagrass microbiome and function. <em>Posidonia oceanica</em>, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we test whether microbial metabolisms associated with <em>P. oceanica</em> and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we show that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that microbial ammonification was reduced at lower pH. The presence of <em>P. oceanica</em> enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6 to 17.4 with the greatest effect at CO<sub>2</sub> vent sites. Seagrass and its microbial associates thus enhanced water column productivity and were a locus for nutrient cycling.</p>
Supplementary Material no. 2 to the manuscript: Reemission of inorganic pollution from permafrost? – a freshwater hydrochemistry study in the lower Kolyma basin (North-East Siberia)
<p>A dataset on the inorganic chemistry of permafrost-related creeks and ice, thermokarst lakes and the Kolyma river and its tributaries in late July 2021.<br> Companion dataset to the manuscript: "Reemission of inorganic pollution from permafrost? – a freshwater hydrochemistry study in the lower Kolyma basin (North-East Siberia)".<br> Current abstract of the manuscript (prior to peer review):</p> <p>Permafrost regions are under particular pressure from climate change resulting in widespread landscape changes, which impact also freshwater chemistry. We investigated a snapshot of hydrochemistry in various freshwater environments in the lower Kolyma river basin (North-East Siberia, continuous permafrost zone) to explore the mobility of metals, metalloids and non-metals resulting from permafrost thaw. Particular attention was focused on heavy metals as contaminants potentially released from the secondary source in the permafrozen Yedoma complex. Permafrost creeks represented the Mg-Ca-Na-HCO<sub>3</sub>-Cl-SO<sub>4</sub> ionic water type (with mineralisation in the range 600-800 mg/L), while permafrost ice and thermokarst lake waters were the HCO<sub>3</sub>-Ca-Mg type. Multiple heavy metals (As, Cu, Co, Mn and Ni) showed much higher dissolved phase concentrations in permafrost creeks and ice than in Kolyma and its tributaries, and only in the permafrost samples and one Kolyma tributary have we detected dissolved Ti or Hg. In thermokarst lakes, several metal and metalloid dissolved concentrations increased with water depth (Fe, Mn, Ni and Zn - in both lakes; Al, Cu, K, Sb, Sr and Pb in either lake), reaching 1370 µg/L Cu, 4610 µg/L Mn, and 687 µg/L Zn in the bottom water layers. Permafrost-related waters were also enriched in dissolved phosphorus (up to 512 µg/L in Yedoma-fed creeks). The impact of permafrost thaw on river and lake water chemistry is a complex problem which needs to be considered both in the context of legacy permafrost shrinkage and the interference of the deepening active layer with newly deposited antropogenic contaminants.</p>
Dataset to manuscript entitled "Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies" submitted to Scientifc Reports
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to</strong><strong> </strong><strong><em>Scientifc Reports, </em>and entitled</strong><strong>:</strong></p> <p><strong><em>Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies</em></strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p><strong>Niusha Bagheri <sup>1</sup>, Hongjian Chen <sup>1</sup>, Mihailo Rabasovic <sup>2</sup>, Jerker Widengren <sup>1,*</sup></strong></p> <p><sup>1 </sup>Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center 106 91 Stockholm, Sweden</p> <p><sup>2 </sup>Laboratory for Biophysics, Institute of Physics Belgrade, Pregrevica 118<br>11080 Zemun-Belgrade, Serbia</p> <p>* Corresponding author (jwideng@kth.se)</p> <p><strong> </strong></p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Like most fluorescent organic molecules, these amino acids also tend to undergo transitions into dark meta-stable states, such as triplet and photo-radical states. While this may be perceived as a problem, these transitions are also highly environment-sensitive and can be used as an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, we applied the transient state monitoring (TRAST) technique, analyzing the average intensity of tyrosine emission under different excitation modulations, to characterize the photo physics of tyrosine for such readout purposes. By investigating how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), which upon calcium binding takes a more folded conformation. From these TRAST experiments, performed with 280nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.</p>
STATA code to reproduce results in the manuscript "Low birth weight risk during COVID-19: Evidence from a nationwide study in India"
<p>This STATA code will reproduce results in the manuscript "Low birth weight risk during COVID-19: Evidence from a nationwide study in India" The users will have to register and access the data from www.dhsprogram.com to run the analysis code. </p>
Data files for manuscript "Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study"
<p>#2021-09-19<br> #Summary<br> This ZIP-file contains the Excel files used for all analyses for the manuscript "Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study".</p> <p><br> #File structure<br> README.txt This README file.<br> File S1 ("FileS1_GCKD-ADTKD.cohort.xlsx") Cohort characteristics, sequencing quality parameters and fingerprinting results.<br> File S2 ("FileS2_GCKD-ADTKD.content.xlsx") Sequencing panel design/ content with information on gene domains used for Figure 2.<br> File S3 ("FileS3_GCKD-ADTKD.variants.xlsx") Information on small variants, CNVs and MUC1 analyses (SNaPshot and adVNTR).<br> File S4 ("FileS4_GCKD-ADTKD.simulation.xlsx") Curated variant and individual data from the Groopman study with results of the simulation for Figure 4.</p> <p><br> #Files and checksums<br> 2D6184BC145987D3EE2E0DC6873DDDDB ./README.txt<br> 10EE4C3C9D9ED6417647F26A09583820 ./FileS1_GCKD-ADTKD.cohort.xlsx<br> 9F95661845215FB7875EB053F887AB36 ./FileS2_GCKD-ADTKD.content.xlsx<br> 2AC19FBC6103CB48905F64716428AE5B ./FileS3_GCKD-ADTKD.variants.xlsx<br> 2D6184BC145987D3EE2E0DC6873DDDDB ./FileS4_GCKD-ADTKD.simulation.xlsx</p>
Datasets of the manuscript "Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons"
<p><strong>DATASETS</strong></p> <p>Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons</p> <p>Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber<sup>*</sup></p> <p>* Correspondence: <a href="mailto:argruber@usp.br">argruber@usp.br</a> (AG); Tel. +55 11 3091 7274</p> <p> </p> <p>Here we provide different data of <em>Microviridae</em>, <em>Flavivirus</em> and casposons used throughout the work:</p> <ul> <li>Microviridae folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Microviridae</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Microviridae</em></li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Microviridae_113-seq_training_set.fasta - 113 VP1 sequences covering diversity of the <em>Microviridae</em> family</li> <li>Microviridae_113-seq.aln – multiple sequence alignment of the 113-protein dataset</li> <li>Microviridae_1836-seq_testset.fasta - 1,836 sequence dataset covering 1,836 sequences of the major capsid protein (VP1) comprising 501 <em>Alpavirinae</em> sequences, 1,040 <em>Gokushovirinae</em> sequences and 295 <em>Pichovirinae</em> sequences</li> <li>Microviridae_1866-seq.aln - multiple sequence alignment of the 1,866-protein <em>Microviridae</em> dataset used in the experiment of Figure 4</li> </ul> </li> </ul> </li> <li>Flavivirus folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Flavivirus</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Flavivirus</em> <ul> <li>full-length – models constructed from full-length protein sequences</li> <li>short - models constructed from selected short alignment blocks of the protein sequences</li> </ul> </li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Flavivirus_127-seq_training_set.fasta - 127 polyprotein sequences covering species diversity of the genus <em>Flavivirus</em></li> <li>Flavivirus_127-seq.aln – multiple sequence alignment of the 127-protein dataset</li> <li>Flavivirus_6364-seq_testset.fasta - 6,364 sequence dataset covering species diversity of <em>Flavivirus</em>, including 3,919 of dengue virus (DENV), 327 of Zika virus (ZIKV), 63 of yellow fever virus (YFV), and the remaining 2,055 sequences covering other available flaviviruses</li> <li>Flavivirus_6364-seq.aln - multiple sequence alignment of the 6,364-protein <em>Flavivirus</em> dataset</li> </ul> </li> </ul> </li> <li>Casposons folder <ul> <li>casposon_generic_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the generic detection of all casposons and discrimination from CRISPRs.</li> <li>casposon_family_discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the specific discrimination among casposon families and from CRISPRs.</li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>casposons_crisprs.fasta – 106 Cas1 <em>bona fide</em> sequences derived from 52 CRISPRs and 54 casposons</li> <li>casposon_family_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for the discrimination of each casposon family.</li> <li>casposons_crisprs_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for discrimination of CRISPRs and casposons.</li> </ul> </li> </ul> </li> </ul>
Supplementary materials of the manuscript "Establishing a new workflow in the study of core reduction intensity and distribution".
<p>This repository hosts the R code scripts and datasets that allow reproducibility and replicability of the statistical analyses implemented in the paper: Lombao et al. (2022). Establishing a new workflow in the study of core reduction distribution. Journal of Lithic Studies.</p> <p> </p> <p>The analytical and statistical protocols applied for this study were implemented in in R (version 3.6.3) (R Core Team, 2021).</p> <p>Contents:<br> 1. Script.txt: The R- Script with all the packages and functions used and all the steps followed in the statistical analyses.<br> 2. vrm_experiment_database.xlsx: the database with the data used in this manuscript. The data comes from an experiment presented in Lombao et al., 2020. A new approach to measure reduction intensity on cores and tools on cobbles: the Volumetric Reconstruction Method. Archaeological and Anthropological Sciences 12(9)<br> DOI: 10.1007/s12520-020-01154-7<br> 3. Supplementary_table_S1.docx<br> 4. Supplementary_table_S2.docx<br> 5. Supplementary_table_s3.xlsx This database is used in the R-script. </p>
Data set for the manuscript "Development of Hydropower and the Environmental Impacts of Hydroelectric Dam Construction: A Case Study of the Three Gorges Dam"
<p>This document provides the data set supplementary to the manuscript "Development of Hydropower and the Environmental Impacts of Hydroelectric Dam Construction: A Case Study of the Three Gorges Dam"</p> <p>Data content: Tables 1-3</p> <ul> <li>Table 1. The global annual data of GDP, surface temperature anomalies, carbon dioxide emissions and different kinds of renewable energy during 2000-2020. The renewable energy includes hydropower, wind, solar, geothermal, biomass and others (unit: TWh).</li> <li>Table 2. The annual mean temperature, CO2 emissions, and renewable energy data in China from 2000 to 2020. The renewable energy data include hydro, solar, and wind electricity generation (unit: kWh).</li> <li>Table 3. Annual variation of precipitation and biodiversity in the TGD area. Annual mean precipitation data over China and the TGD are provided. Biodiversity data include the number of Yangtze Finless Porpoise, Carp Egg and Larvae, and the number of spawners in spawning ground for Acipenser_sinensis.</li> </ul> <p> </p>
Raw fMRI data from 12 rats used in the manuscript "Mapping of hemodynamic responses to the sensorymotor stimulation in a rodent model: a BOLD fMRI study" submitted to PlosOne for publication
<p>Raw data are from twelve male adult Wistar rats (Charles River Laboratories, Paris-France) weighing 300 ± 20g.</p> <p>Rats were initially anesthetized (induction) with 3% isoflurane and were maintained under 0,7-0.8% (sedation along with a muscle relaxation) during fMRI session. </p> <p>Each rat was submitted to two fMRI sessions: one with TE of 30 ms and and other with TE of 40 ms.</p> <p>For fMRI acquisition, electrodes were inserted subcutaneously in the palmar surface of the right hindpaw of each rat and electrical stimulation (current pulses with a 1.7 mA amplitude, 10 ms duration and 8 Hz frequency) was applied in a block-design starting with a resting period of 25s as a baseline followed by 25s stimulation, repeated 8 times.</p> <p>Ten 1-mm thick contiguous axial slices, from -6.36 mm to +2.64 mm to Bregma, were acquired with a two-shot gradient echo planar imaging (GE EPI) pulse sequence (2.56 cm2 FOV; 64x64 matrix size; a TR of 1000 ms; a flip angle of 50°) resulting in the pixel size of 0.4 mm.</p> <p>All imaging experiments were performed on a 4.7T Bruker (Biospec 47/40, Bruker, GmbH, Ettlingen,Germany) with a horizontal bore magnet equipped with a 12 cm gradient coil (Bruker BGA12, 400 mT/m) and interfaced to AVANCE III console. Two actively decoupled RF coils were used: a 7.2-cm diameter volume coil for transmission and a 2-cm diameter surface coil (Rapid Biomedical, Rimpar, Germany) positioned on the top of the animal's head for reception.</p>
Supplementary materials for the manuscript entitled: "Impacts of creatine on the health of elderly individuals: a bibliometric study"
<p>These images/figures complement what was presented in the results of the manuscript "Impacts of creatine on the health of elderly individuals: a bibliometric study.</p>
Data and codes for manuscript "A study on radiative efficiencies and warming effects of halocarbons"
<p>Data and codes for “A study on radiative efficiencies and warming effects of halocarbons”, including the 998-band radiative transfer model for calculating the radiative efficiency, scripts for plotting and corresponding data.</p>
Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"
<p><strong>Project files provided as supporting information to the manuscript "Membrane binding of pore-forming gamma-hemolysin components studied at different lipid compositions"</strong></p> <p>The dataset contains the following folders:</p> <p>- number_of_contacts: files with the number of contacts between the rim domains of LukF and Hlg2 and the membrane, for different bilayer compositions (Fig. 2).</p> <p>- binding_events: files with the duration of the time interavals in which LukF and Hlg2 are bound to the membrane, and the scripts used to compute for each system the number of binding/unbinding events and the average membrane residence time (Fig. 3).</p> <p>- electrostatic_potential: files of the surface electrostatic potential produced with the adaptive Poisson-Boltzmann solver and used for visualization with Chimera (Fig. 4).</p> <p>- angles: files with the angle values computed between the protein axis and the z-axis of the simulation box (Fig. 5).</p> <p>- contacts_per_residue: files with the number of frames in which each protein residue is in contact with the membrane, with respect to the total number of frames in which the rim domain interacts with the bilayer (Fig. 5).</p> <p>- distance_protein_membrane: files with the minimum distance between the protein and the membrane (Fig. 6).</p> <p>- binding_sites: file produced by PyLipid with relevant information on the main DOPC binding sites identified in LukF.</p> <p>- min_distance_per_residue: files with the minimum distance between each protein residue and the membrane, computed at the binding steps (Fig. S5).</p>
Data for "Why Study Gene Ratios" manuscript
<p>This upload includes the pre-processed data used for the "Why Study Gene Ratios" manuscript.</p>
Data set for the manuscript 'Studying the different coupling regimes for a plasmonic particle in a plasmonic trap'
<p>This repository includes data set and Matlab scripts, which support the manuscript entitled 'Studying the different coupling regimes for a plasmonic particle in a plasmonic trap', published in Optics Express. We include the data set necessary to reproduce the results of the paper in the 'RawData.zip' file. We provide Matlab scripts and functions in the 'PostProcessing.zip' file to process the raw data. We also attach HTML documents explaining the data and how we process them. </p> <p><strong>Raw data visualization with python.html</strong>: This is the first HTML file containing all the information to understand and visualize the raw data. It is generated by Jupyter Notebook, and it includes python scripts to visualize the raw data.</p> <p><strong>Post-processing raw data using Matlab.html</strong>: This is the second HTML file, which gives you a guideline to the data processing routines with the explanations of the Matlab scripts and functions. </p> <p><strong>RawData.zip</strong>: the data set used to produce the results in the manuscript. </p> <p><strong>PostProcessing.zip</strong>: Matlab scripts and functions for data post-processing.</p> <p><strong>python.zip</strong>: python files</p> <p>Note: This version update includes the additional data set for the revision of the manuscript. </p>
Dataset for the manuscript "Assessing the Role of Hydrodynamics in Enhancing HAND-Derived Synthetic Rating Curves: A Comparative Study in the Wu River Basin, Taiwan"
<p>This is the dataset for developing the HAND-hd workflow mentione in the manuscript "Assessing the Role of Hydrodynamics in Enhancing HAND-Derived Synthetic Rating Curves: A Comparative Study in the Wu River Basin, Taiwan". In the manuscript, we used the topographical cross-sectional survey data to generate topographical synthetic rating curves (RCb) to validate the performance of the HAND method based synthetic rating curves (HAND-SRC) produced by the HAND-hd workflow. Due to regulatory restrictions under Taiwanese law, public sharing of 5-meter (or finer) DEM data is prohibited. However, researchers interested in accessing processed HAND raster data for research purposes may contact the corresponding author.</p>
Project files provided as supporting information to the manuscript "How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study"
<p>June 23, 2021</p> <p>Thomas Tarenzi, Marta Rigoli and Raffaello Potestio</p> <p>==================================</p> <p>The dataset contains the following folders:</p> <p>- contact_area_binding_site: files with the computed surface area, used for the calculation of the contact area between PD-1 and the antibody Fab (Fig. S41).</p> <p>- hbonds_ab-pd1: number of hydrogen bonds between the antigen and the antibody, for each holo cluster (Fig. S41).</p> <p>- mutual_information: matrices with the computed mutual information, for each pair of residues (Fig. S34, S35, S46). The folder contains also the generalized correlation coefficients (Fig. S43) and the correlation scores (Fig. 4, S44, S45), computed from the mutual informations.</p> <p>- networks: communities - for each cluster, each residue is assigned to a community within the interaction network (Fig. S32, S33). betweenness - the values of edge betweenness for each cluster (S30, S31).</p> <p>- output_clustering: each frame of the apo and holo simulations is assigned a cluster index, on the basis of the structural similarity (Fig. S4).</p> <p>- PAD: per-residue values of PAD parameter, for apo and holo systems (Fig. 3, S39).</p> <p>- PCA: principal component analysis for each conformational cluster (Section S2.1).</p> <p>- representative_structures: representative structures for each conformational cluster (Fig. 2).</p> <p>- r_gyr_antibody: radii of gyration of the antibody, for each cluster (Fig. 2).</p> <p>- r_gyr_hinge: radii of gyration of the sole hinge segment, for each cluster (Fig. S36).</p> <p>- RMSD_antibody: distributions of the root-mean-square deviation of the antibody, for each cluster (Fig. S5). </p> <p>- RMSD_antigen: root-mean-square deviation of the antigen PD-1, for each cluster (Fig. S42).</p> <p>- RMSD_binding_site: distributions of the root-mean-square deviation of the residues belonging to the paratope, for each cluster (Fig. S40, S47).</p> <p>- RMSD_matrix: root-mean-square deviation between structures belonging to different pairs of clusters (Fig. S9).</p> <p>- rmsf_antigen: root-mean-square fluctuation of the antigen PD-1, for each cluster (Fig. S42).</p> <p>- rmsf_hinge: difference between the total root-mean-square fluctuations of the two hinge segments, for each cluster (Fig. S38).</p> <p>- salt_bridge: distribution of distances between residues R979 and D1377 (Fig. 4).</p> <p>- sasa_domains: contact area between Fab and Fc antibody domains, for each cluster (Fig. S8).</p> <p>- sasa_hinge: solvent accessible surface area of each hinge segment, for each cluster (Fig. S37).</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.