cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7272/q6h41pb7
title: Progression of white matter degeneration in amyotrophic lateral sclerosis: A diffusion tensor imaging study

description: Whether longitudinal diffusion tensor MRI imaging (DTI) can capture
 disease progression in patients with amyotrophic lateral sclerosis (ALS)
 is unclear. The primary goal of this study was to determine if DTI detects
 progression of the corticospinal tracts (CST) degeneration in ALS.
 Seventeen ALS patients and 19 ageand gender-matched healthy controls were
 scanned with DTI at baseline for cross-sectional analyses. For
 longitudinal analyses, the ALS patients had repeat DTI scans after eight
 months. Tractography of the CST was used to guide regions-of-interest
 (ROI) analysis and complemented by a voxelwise analysis. Cross-sectional
 study found that baseline FA of the right superior CST was markedly
 reduced in ALS patients compared to controls. The FA reductions in this
 region correlated with the disease severity in ALS patients. Longitudinal
 study found that FA change rate of the right superior CST significantly
 declined over time. In conclusion, longitudinal DTI study captures
 progression of upper motor fiber degeneration in ALS. DTI can be useful
 for monitoring ALS progression and efficacy of treatment interventions.
description: The dataset available here consists of Fractional Anisotropy (FA), and
 Mean Diffusivity (MD) images as well as subject-study-specific
 normalization images (B0, see methods in paper) in Analyze format. There
 are B0, FA, and MD images for 53 subjects, and a spreadsheet describing
 each subject's age (at time of scan), gender, and diagnosis (ALS or
 Control). For ALS subjects, there are two timepoints (duration between
 timepoints is indicated) as well as additional info including ALS subtype,
 side at onset, and scores on the Amyotrophic Lateral Sclerosis Functional
 Rating Scale–revised (ALSFRSr).
DOI: 10.5281/zenodo.18393134
title: HYGIENIC INDICATORS OF DRINKING WATER QUALITY AND HEALTH RISKS IN RURAL SETTLEMENTS USING WELL WATER: A CASE STUDY OF FERGANA DISTRICT

description: Access to safe drinking water remains a major public health challenge in rural areas where centralized water supply systems are absent. This study aimed to assess the hygienic quality of drinking water from wells used in rural settlements of Fergana District and to evaluate potential health risks associated with physicochemical and microbiological contamination. Water samples were collected from selected household and public wells and analyzed according to standard hygienic methods. Key indicators included organoleptic properties, physicochemical parameters (pH, total hardness, nitrates, nitrites, and heavy metals), and microbiological indicators (total coliforms and Escherichia coli). The results revealed that a significant proportion of samples exceeded recommended hygienic standards, particularly for nitrates and microbiological contamination. Identified health risks included gastrointestinal infections and chronic toxic effects, especially among vulnerable population groups such as children. The findings emphasize the need for systematic hygienic monitoring, improvement of well protection measures, and implementation of local water treatment solutions in rural areas.
DOI: 10.5061/dryad.6b6150p
title: Is Cyclocardia (Conrad) a wastebasket taxon? Exploring the phylogeny of the most diverse genus of the Carditidae (Archiheterodonta, Bivalvia)

description: The carditid genus Cyclocardia is currently the most diverse genus of the
 family, including nearly 180 nominal species from a wide stratigraphical
 (Cretaceous–Recent) and geographical range (Antarctica, South and North
 America, Europe, Africa, Alaska, Russia, Japan, and New Zealand). Due to
 the lack of autapomorphies in the diagnosis of the genus and its large
 account of species, we re-evaluated the systematic and phylogenetic status
 of Cyclocardia. We carried out three approaches: bibliographic revision,
 phylogenetic analysis, and morphological disparity exploration. We used a
 shell-character matrix including 65 taxa (two outgroups, 29
 non-Cyclocardia carditids, and 28 species of Cyclocardia) for phylogenetic
 and disparity analyses. The morphological disparity analysis was conducted
 using Maximum Observable Rescaled Distances for calculate distance matrix,
 and comparing Cyclocardia species and other carditid groups. According to
 our results, Cyclocardia is a ‘wastebasket taxon‘, chiefly because its
 diagnosis was based mainly on plesiomorphic characters. Also, Cyclocardia
 represents a non-monophyletic taxon. The European species C. kickxi and C.
 chameformis are placed within Scalaricardita, and the previously proposed
 genus Crassicardia is monophyletic (including C. crassidens, C.
 crebricostata, C. isaotakii, and C. rjabininae). Three new genera are
 proposed for new groups identified by the phylogenetic analysis: South
 American Oesterheldia nov. gen. (including O. cannada and O. dalek),
 Western North American Coanicardita nov. gen. (including C. ventricosa and
 C. occidentalis), and North Pacific Hippocampocardia nov. gen. (including
 H. barbarensis, H. hamiltonensis, and H. yakatagensis). The newly defined
 monophyletic Cyclocardia is restricted to the Atlantic Ocean species C.
 borealis, C. novangliae, and C. compressa.
description: Appendix
 1Bibliographic catalogue
 of species assigned to Cyclocardia in the bibliography.Appendix
 2Table with material
 included for phylogenetic and morphological disparity
 analyses.Appendix
 3List
 of morphological characters used for build the data-matrix of Cyclocardia
 species.Appendix
 4Data-matrix in TNT
 format for phylogenetic analysis, including constraint
 model.Appendix
 5Results of phylogenetic
 analysis, including tree topology, index, and length.Appendix
 6List
 of common synapomorphies of clades obtained.
DOI: 10.5281/zenodo.18393133
title: HYGIENIC INDICATORS OF DRINKING WATER QUALITY AND HEALTH RISKS IN RURAL SETTLEMENTS USING WELL WATER: A CASE STUDY OF FERGANA DISTRICT

description: Access to safe drinking water remains a major public health challenge in rural areas where centralized water supply systems are absent. This study aimed to assess the hygienic quality of drinking water from wells used in rural settlements of Fergana District and to evaluate potential health risks associated with physicochemical and microbiological contamination. Water samples were collected from selected household and public wells and analyzed according to standard hygienic methods. Key indicators included organoleptic properties, physicochemical parameters (pH, total hardness, nitrates, nitrites, and heavy metals), and microbiological indicators (total coliforms and Escherichia coli). The results revealed that a significant proportion of samples exceeded recommended hygienic standards, particularly for nitrates and microbiological contamination. Identified health risks included gastrointestinal infections and chronic toxic effects, especially among vulnerable population groups such as children. The findings emphasize the need for systematic hygienic monitoring, improvement of well protection measures, and implementation of local water treatment solutions in rural areas.
DOI: 10.7272/q6sf2t3q
title: Protocol for the Training and Calibration of Dental Examiners

description: OBJECTIVES: To summarize diagnostic criteria and examiner training and
 calibration of the National Institute of Dental and Craniofacial
 Research-funded Early Childhood Caries Collaborating Centers (EC4) and
 report examiner calibration results from 2010 to 2014. The EC4 at Boston
 University, University of Colorado, and University of California San
 Francisco are performing randomized controlled early childhood caries
 (ECC) prevention trials with caries as the main outcome measure. METHODS:
 The EC4 with University of Iowa consultants developed standardized tooth
 and tooth surface status examination criteria for use in field conditions,
 examiner training materials, and examiner calibration and re-calibration
 methodologies. Calibration and re-calibration were performed with 1- to
 5-year-old children in the San Francisco Mission District in which
 assessments from each examiner to be calibrated were compared with those
 from a single gold standard examiner from 2010 to 2014. Cohen's kappa
 statistic was used to determine inter-examiner agreement. RESULTS: A total
 of seven examiners were successfully (re)calibrated during that period,
 examining a total of 231 children. Overall unweighted Cohen's kappas
 for 10 surface conditions exceeded the criterion of 0.70. However,
 separate agreement for assessment of noncavitated lesions, as in other
 studies, was lower. CONCLUSIONS: An experienced multidisciplinary and
 multi-institutional team was able to develop criteria and training
 materials to anticipate situations and field conditions the main trials
 would encounter. Examiners were successfully trained and (re)calibrated.
description: Please cite NIH grant numbers in any publications using this
 dataset.
DOI: 10.7280/d1nk5z
title: Crystal Cove Marine Conservation Area Citizen Science Monitoring

description: Crystal Cove Alliance operates the Crystal Cove Marine Protected Are
 Citizen Science Cruise in partnership with Newport Landing Sportfishing.
 Under the supervision of trained Crystal Cove Alliance staff, junior high
 school and high school students collect data on fish and plankton
 biodiversity and nearshore water quality in the Crystal Cove Marine
 Conservation Area, following protocols designed in partnership with UCI
 and other researchers. Data made available in the OC Data Portal in
 partnership with UCI Libraries. See README file for more detailed
 information.
description: Contact Crystal Cove Alliance for detailed protocols.
 
 Fish biodiversity: Used an underwater camera to perform a vertical
 transect within the kelp forest or rocky reef to look for presence or
 absence of 6 key fish species. Videos available upon request.
 
 Plankton biodiversity: Used 3 plankton nets to perform a surface
 horizontal tow and identified presence or absence of 9 key species using a
 microscope. 
 
 Water Quality: Used Van Dorn bottles to collect water from the surface to
 14 meters in two meter intervals. Tested for temperature, salinity and pH.
DOI: 10.7280/d1x30q
title: UCI Campus Tree Inventory

description: GIS data collected as part of a campus-wide tree inventory, done in part
 to determine scope and effect of Polyphagous Shot Hole Borer (PSHB)
 infestation.
description: Includes DBF spreadsheet of data on individual trees as well as
 SHP/SHX/PRJ files for GIS representation.
DOI: 10.5061/dryad.kg87554
title: Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination

description: Wolbachia are widespread intracellular bacteria that mediate many
 important biological processes in arthropod species. In this study, we
 identified 210 conserved single-copy genes in 33 genome-sequenced
 Wolbachia strains in the A, B, C, D, E and F supergroups. Phylogenomic
 analysis with these core genes indicate that all 33 Wolbachia strains
 maintain the supergroup relationship classified previously based on the
 multilocus sequence typing (MLST) genes. Using an interclade recombination
 screening method, 14 inter-supergroup recombination events were discovered
 in six genes (2.9%) among 210 single copy orthologs. This finding suggests
 a relatively low frequency of intergroup recombination. Interestingly,
 they have occurred not only between A and B supergroups (9 events), but
 also between A and E supergroups (5 events). Maintenance of such transfers
 suggests possible roles in Wolbachia infection related functions.
 Comparisons of strain divergence using the five genes of the MLST system
 show a high correlation (Pearson correlation coefficient r = 0.98) between
 MLST and whole genome divergences, indicating that MLST is a reliable
 method for identifying related strains when whole genome data are not
 available. The phylogenomic analysis and the identified core gene set in
 our study will serve as a valuable foundation for strain identification
 and the investigation of recombination and genome evolution in Wolbachia.
description: <b>Data S1. List of
 210 orthogroups identified in 34 <i>Wolbachia</i>
 strains.</b> <b>Data S2. Nucleotide
 </b><b>sequence
 alignments for 210 core ortholog genes among 33
 <i>Wolbachia</i> strains. </b>
 <b>Data S3.
 RAxML phylogenetic trees constructed with concatenated nucleotide sequence
 alignment and six individual gene alignments with inter-supergroup
 recombination events.</b> <b>Data S4.
 </b><b>Protein
 sequence alignments for 210 core ortholog genes among 33
 <i>Wolbachia</i>
 strains.</b> <b>Data S5. RAxML
 phylogenetic trees constructed with concatenated protein sequence
 alignment and six individual protein alignments with inter-supergroup
 recombination events.</b> <b>Data S6. Estimates
 of Evolutionary Divergence between multiple <i>Wolbachia</i>
 strains with 210 core gene set and five MLST
 genes.</b>
DOI: 10.7280/d15k5m
title: Simulation input and out and data analysis for calculating partition coefficients of small molecules in octanol/water and cyclohexane/water

description: Below are summaries for each archived file. There are READMEs in each
 sub-directory detailing the contents. RunFiles.tar These are a set of
 GROMACS molecular dynamics parameter files and an example run
 scriptData.tar.gz This directory contains all data produced by the project
 including input files created by Solvation Toolkit, output files from the
 GROMACS simulations, Alchemical Analysis, average density convergence
 plots, and dictionaries and text files with all calculated and
 experimental data.pythonScripts.tar These are python scripts that were
 used for the project as a whole. ErythromycinConformations.tar This
 directory contains all the python scripts and analysis related to repeated
 erythromycin calculations with different initial conformations.
 Density_followup.tar This directory includes python scripts and data
 analysis for the example density convergence plots that are referenced in
 the text.
description: Associated article is still in review, but we will link it to
 this database if it is accepted.
DOI: 10.7280/d1988w
title: Analysis Scripts and Data for SAMPL5 Distribution Coefficients Submission Analysis and Reference Calculations,

description: This is the supporting information associated with the analysis of the
 distribution coefficient part of the SAMPL5 challenge. Below are the list
 of the files included here. (1) SubmissionResults.tar: this is the
 complete set of distribution coefficient predictions submitted for SAMPL5.
 (2) 282_data_36253.tar.gz: This is the set of files provided to SAMPL5
 participants before the challenge. It is also available on the Drug Design
 Data Resource webpage (https://drugdesigndata.org/about/sampl5). (3)
 SAMPL5_SI.tar.gz: This directory includes all analysis scripts and data
 files for the analysis of the SAMPL5 prediction submissions. It also
 contains all of the input, parameter, output, and results files associated
 with our reference distribution coefficient calculations. (4)
 allSolvents.mpg: This is a video created in VMD to visualize a simulation
 with water, cyclohexane, DMSO, and Acetonitrile at approximately
 experimental concentrations(5) wetCyclohexane_SAMPL5_074.mpg: This is a
 video created with VMD to visualize a simulation with water present in
 cyclohexane while calculating the solvation free energy of molecule
 SAMPL5_074There are README files in all the sub-directories detailing the
 contents and its organization.
DOI: 10.7280/d1pk58
title: DATA set for PLOS One Hsieh et al. 2016

description: The auditory system encounters motion cues through an acoustic object’s
 movement or rotation of the listener’s head in a stationary sound field,
 generating a wide range of naturally occurring velocities from a few to
 several hundred degrees per second. The angular velocity of moving
 acoustic objects relative to a listener is typically slow and does not
 exceed tens of degrees per second, whereas head rotations in a stationary
 acoustic field may generate fast-changing spatial cues in the order of
 several hundred degrees per second. We hypothesized that these two types
 of systems (i.e., encoding slow movements of an object or fast head
 rotations) may engage functionally distinct substrates in processing
 spatially dynamic auditory cues, with the latter potentially involved in
 maintaining perceptual constancy in a stationary field during head
 rotations and therefore possibly involving corollary-discharge mechanisms
 in premotor cortex. Using fMRI, we examined cortical response patterns to
 sound sources moving at a wide range of velocities in 3D virtual auditory
 space. We found a significant categorical difference between fast and slow
 moving sounds, with stronger activations in response to higher velocities
 in the posterior superior temporal regions, the planum temporale, and
 notably the premotor ventral-rostral (PMVr) area implicated in planning
 neck and head motor functions
description: fMRI scanning of human cortex while listening to motion of an
 auditory source in 3D virtual space.
DOI: 10.7280/d1js3b
title: T4 Lysozyme (L99A) LigandFEP Homologous Ligand Series Data

description: Despite innovations in sampling techniques for molecular dynamics (MD),
 reliable prediction of protein-ligand binding free energies from MD
 remains a challenging problem, even in well studied model binding sites
 like the apolar cavity of T4 Lysozyme L99A. In this study, we model recent
 experimental results that show the progressive opening of the binding
 pocket in response to a series of homologous ligands. Even while using
 enhanced sampling techniques, we demonstrate that the predicted relative
 binding free energies (RBFE) are still highly sensitive to the initial
 protein conformational state. Particularly, we highlight the importance of
 sufficient sampling of protein conformational changes and possible
 techniques for addressing the issue.
description: free energy pertubation, molecular dynamics, replica exchange
 with solute tempering,
DOI: 10.5061/dryad.kr6409q
title: Data from: Small herbivores slow down species loss up to 22 years but only at early successional stage

description: The long-term influence of persistent small herbivores on successional
 plant community configuration is rarely studied. We used an herbivore
 exclusion experiment along the successional gradient in a salt-marsh
 system, to investigate the effects of hares and geese, and hares alone, on
 plant diversity at five successional stages (the earliest, two early, the
 intermediate and the late successional stages) in the short and long term,
 i.e. 7 and 22 years, respectively. Plant diversity declined over time at
 all successional stages except for the earliest one. Small herbivores
 slowed down species decline, but only at one early successional stage.
 Small herbivores slowed down species decline via decreasing dominance of
 preferred grass Festuca rubra in the short term, and less preferred
 Elytrigia atherica in the long term. The effects of hares and geese were
 more pronounced than hares alone, indicating an important additive role of
 geese, especially in the long term. Synthesis. Small herbivores can have a
 strong and long-lasting impact on plant diversity, but it highly depends
 on the abundance of small herbivores, which in turn depends on the quality
 and abundance of forage plants. A diverse herbivore community may have
 more positive effects on regulating plant communities.
description: Data for small
 herbivores slow down species loss up to 22 years but only at early
 successional stageThis excel file contains
 1) abundance data of plant species in 1995, 1997, 2001 and 2016; 2)
 dropping data in 2001 and 2016; 3) clay thickness, elevation and
 vegetation height in 2016.Data for small herbivores slow
 down species loss_QC.xlsx
DOI: 10.7280/d1t88j
title: Crystal Cove Marine Conservation Area Citizen Science Monitoring

description: Crystal Cove Alliance operates the Crystal Cove Marine Protected Area
 Citizen Science Cruise in partnership with Newport Landing Sportfishing.
 Under the supervision of trained Crystal Cove Alliance staff, junior high
 school and high school students collect data on fish and plankton
 biodiversity and nearshore water quality in the Crystal Cove Marine
 Conservation Area, following protocols designed in partnership with UCI
 and other researchers. Data made available in the OC Data Portal in
 partnership with UCI Libraries. See README file for more detailed
 information.
description: Contact Crystal Cove Alliance for detailed protocols. Fish
 biodiversity: Used an underwater camera to perform a vertical transect
 within the kelp forest or rocky reef to look for presence or absence of 6
 key fish species. Videos available upon request Plankton biodiversity:
 Used 3 plankton nets to perform a surface horizontal tow and identified
 presence or absence of 9 key species using a microscope. Water Quality:
 Used Van Dorn bottles to collect water from the surface to 16 meters in
 two meter intervals. Tested for temperature, salinity and pH.