cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/mh4k929nbw
title: Evolutionary relationships of the Phytophthora 1a subclade species based on complete mitogenomes, and novel markers for their differentiation

description: Phytophthora is a genus of oomycetes that includes many aggressive pathogens capable of devastating farmlands and forests worldwide. Among the oldest and most well-known species, P. cactorum exhibits morphological and genetic similarities to other homothallic species within subclade 1a, which complicates the understanding of their evolutionary relationships. This study primarily compared seven P. cactorum strains from diverse origins with three closely related species in subclade 1a, utilizing mitogenome sequences for analysis. The circular mitogenomes of the four species were nearly identical in size and comprised 38 protein-coding genes (PCGs), 25 transfer ribonucleic acid genes, and 2 ribosomal RNA genes. The mitochondrial genomes exhibited a higher percentage of A/T compared to G/C content. The majority of AT-skew and GC-skew values among the 38 PCGs were positive, with the AT-skew demonstrating a more pronounced bias than the GC-skew. The Ka/Ks ratios revealed that 35 PCGs underwent significant purifying selection. Although the AliGROOVE analysis indicated notable similarities among the subclade 1a species, four PCGs exhibited significantly higher paring frequency compared to the complete mitogenome. The results from the phylogenetic analysis aligned with the pairwise genetic distances, indicating that P. cactorum is more closely related to P. pseudotsugae than to P. hedraiandra. Furthermore, we found that the nad9 gene is informative to differentiate closely related Phytophthora species within subclade 1a, akin to the cox1 gene.
DOI: 10.17632/s2k87sfc3t
title: Data for: Systematic peak-load pricing during holiday periods: Evidence from the U.S. airline industry

description: The present repository is for the article: "Systematic peak-load pricing during holiday periods:
Evidence from the U.S. airline industry" Alberto A. Gaggero and Alexander Luttmann, published on "Economics of Transportation".

For any query, please contact Alberto A. Gaggero (a.gaggero@univda.it)
DOI: 10.17632/tx62fvtjhz
title: The effectiveness of social network interventions for psychiatric patients: Dataset of a systematic review and meta-analysis

description: Datasets of a systematic review and meta-analysis examining the effectiveness of social network interventions for psychiatric patients. 
&gt; 'Datafile complete dd 17-1-2023' contains all data extracted from included studies. 
&gt; 'Datafile R Mendeley dd 2-2-2022' contains all data used in the final analysis. 

More information about this study can be found in the article (Swinkels, Hoeve, ter Harmsel, Schoonmade, Dekker, Popma & van der Pol, 2023; accepted in Clinical Psychology Review).
DOI: 10.17632/wrmdw82nzr
title: fNIRS data

description: For the data collection, subjects first performed a baseline Stroop test, followed by three different sessions in randomized order: a) control (resting in a seated position); b) Tai Chi (24 simplified Yang style or 28 simplified Chen style moves), and c) brisk walking (Figure 1). In the control session, subjects rested for 11 minutes. In the exercise sessions, subjects performed brisk walking (5.6 km/h) on the treadmill or Tai Chi for about 6 min, followed by a 5-minute rest. The heart rate (HR) was monitored during exercise and rest. Raw data are fNIRS data collected during stroop tests. Each subject has 4 files，named as baseline, control, TC (Tai Chi), and BW (brisk walking).
DOI: 10.6084/m9.figshare.20186825.v1
title: Synthetic Printed Words and Test Protocols Data for Bangla OCR

description: Synthetic Printed word image data and test protocols word image Data repository for the paper <strong>"A Multifaceted Evaluation of Representation of Graphemes for Practically Effective Bangla OCR."</strong> In this paper, we have utilized the popular Convolutional Recurrent Neural Network (CRNN) architecture and implemented our grapheme representation strategies to design the final labels of the model. Due to the absence of a large-scale Bangla word-level printed dataset, we created a synthetically generated Bangla corpus containing 2 million samples that are representative and sufficiently varied in terms of fonts, domain, and vocabulary size to train our Bangla OCR model. To test the various aspects of our model, we have also created 6 test protocols. Finally, to establish the generalizability of our grapheme representation methods, we have performed training and testing on external handwriting datasets. Updates: 10 June 2023: The paper has been accepted for publication in International Journal on Document Analysis and Recognition (IJDAR).
DOI: 10.6084/m9.figshare.24934785.v1
title: Supplemental tables for The Impact of Physical Activity on Thyroid Health: Insights from Representative Data in Korea

description: Supplemental information
DOI: 10.6084/m9.figshare.26536351.v3
title: Example data

description: Dataset for the example code provided in the ShotgunCSP package. Available on GitHub: https://github.com/TsumiNa/ShotgunCSP.
DOI: 10.17632/27y943wbkw
title: Station-based peat moisture in Sumatra peatland 

description: Peat moisture is a key hydrological variable of peatland that has a practical value for a wide range of uses. In tropical peatland, the observation-based monitoring remains research challenge due to its remote and harsh environment.  The daily peat moisture from 21 observation-based monitoring stations is provided for period 2018-2019. The stations are in Sumatra peatland, Indonesia that were maintained by BRG. Information on peat moisture is of importance related to the assessment on the success of restoration projects.
DOI: 10.17632/759j7vhfgp
title: PIGLE - Particles Interacting in Generalized Langevin Equation simulator

description: We present a package using Simulink and MATLAB to perform molecular dynamics simulations of interacting particles obeying a Generalized Langevin Equation. The package, which accounts for three spatial dimensions and rigid-body like rotation, is tuned to explore surface diffusion of co-adsorbed species. The physical parameters are species specific, and include user-defined colored noise spectra and memory friction kernels acting independently on translational and rotational degrees of freedom. We benchmark the simulations using established analytical results for dynamical correlation functions, and we use the package to numerically verify novel analytical results concerning dissipative rotational motion and multi-exponential friction kernels. The package provides a straight-forward way to expand the modeling of ultra-fast surface diffusion problems at the atomic scale.
DOI: 10.17632/dh2ptbvfr6
title: Symmetrization of the product of Hermitian operators

description: The symmetrization process of the product of Hermitian operators is computerized. Indeed, we write a rather general code under Mathematica and Python which can be used for symmetrizing any kind of product of Hermitian operators including a linear combination of such operators with respect to some weight functions.
DOI: 10.17632/ffgc6shz36
title: Comprehensive split TEV based protein-protein interaction screening reveals TAOK2 as a key modulator of Hippo signalling to limit growth

description: Raw data for the focused split TEV protein-protein interaction screen on the Hippo pathway. For each interaction pair (bait/prey), six replicates (R1-R6) for fold change (FC) and control (Ctrl) conditions are provided. For data processing, resulting firefly values were divided by Renilla values to yield firefly/Renilla ratios for each well. Next, interaction data for each bait/prey interaction pair was normalized by calculating fold change values over a plate control (provided here as R1-R6). To compute fold changes, the averaged firefly/Renilla ratio of a bait/prey pair (bait-X-NTEV-tcs-GV::prey-Y-CTEV) was divided by the corresponding averaged firefly/Renilla ratio of the bait/RASSF1-noSARAH negative control (i.e., bait-X-NTEV-tcs-GV::R1-noSARAH-CTEV interaction) that was present on the same plate. Log2-transformed fold changes values were ranked and values above 1 (corresponds to a fold change of 2 and more) were considered as high-confidence hits. For the statistical analysis, each of the six replicates of firefly/Renilla ratios of a given bait/prey interaction pair were divided by the mean of the control bait/RASSF1-noSARAH negative control, yielding six normalized replicates per interaction. To compute statistical significance for each bait/prey pair, adjusted P values for multiple comparisons were calculated using the false discovery rate (FDR) correction method.
DOI: 10.6084/m9.figshare.28927931.v1
title: bigWig files

description: Just a homework item for my OMICs course
DOI: 10.6084/m9.figshare.28945952.v1
title: 265 Tomato Accessions across 27046 SNPs for Salt Tolerance

description: This is a SNP dataset for GWAS study of salt tolerance in tomato.
DOI: 10.6084/m9.figshare.13110656.v1
title: DataSet.csv

description: In everyday life the perceptual system must processes concurrent multidimensional objects. Different theories suggest that this perceptual process involves the attention mechanism. Attention deficit\hyperactivity disorder (ADHD) has been related to several deficiencies in the attention mechanism. In the scoop of the present study, we attempted to investigate whether the attentional deficits in ADHD population impact perceptual process in the level of objects and its features when required to represent multidimensional concurrent objects. Fifty-two participants participated in this study, including 26 ADHD and 26 non-ADHD participants. For the purpose of this study, a behavioral paradigm was utilized, in which participants had to perceive a display contains only a small number of objects characterized by concurrent features on two dimensions: color and shape. The results of the current study pointed to impairment among ADHD participants in perceiving recurrent multidimensional objects when compared to control, reflected in slower RTs. In addition, positive correlation was found between the severity of the reported ADHD symptoms and mean RT. For the first time, our findings suggest that ADHD also manifests a perceptual malfunction at the level of representing multidimensional concurrent objects, and its implications where further discussed. <br><br>
DOI: 10.6084/m9.figshare.17089445.v1
title: Hi-VISTA

description: High speed visual insect swarm tracker
DOI: 10.15482/usda.adc/1239279
title: Dr. Duke's Phytochemical and Ethnobotanical Databases
DOI: 10.17632/y7vs4yby9y
title: Cardiorespiratory DB

description: The database is constituted by 50 datasets containing cardiorespiratory signals acquired from 50 healthy volunteer subjects (one dataset for each subject; 23 males and 27 females; age: 23±5 years) while performing normal breathing, deep breathing, and breath holding, and two spreadsheet files, namely the “SubjectsInfo.xlsx” and “DBInfo.xlsx” containing the metadata of subjects (including demographic data) and of acquired signals, respectively. 
Cardiorespiratory signals consisted in simultaneously recorded 12-lead electrocardiograms acquired by the clinical M12 Global Instrumentation® digital Holter ECG recorder, and single-lead electrocardiograms and respiration signals acquired by the wearable chest strap BioHarness 3.0 by Zephyr. 
The database may be useful to: (1) validate the use of wearable sensors in the acquisition of cardiorespiratory data during different respiration kinds, including apnea; (2) investigate the physiological association between cardiovascular and respiratory systems; (3) validate algorithms able to indirectly extract the respiration signal from the electrocardiogram; (4) study the fatigue level induced by a series of controlled respiration patterns; and (5) investigate the effect of COVID-19 infection on the cardiorespiratory system.
DOI: 10.6084/m9.figshare.11913750.v3
title: The magnifying effect of a thin shallow stiff layer on Love waves as revealed by multi-component analysis of surface waves

description: Enclosed files are the raw field multi-component seismic data presented in the article "The magnifying effect of a thin shallow stiff layer on Love waves as revealed by multi-component analysis of surface waves" (Dal Moro G., 2020, Scientific Reports - Nature Springer).<br><br>Data are saved according to the very classical SEGY format (https://en.wikipedia.org/wiki/SEG-Y)<br><br>Acquisition parameters and further details are reported in the paper.<br><br>geophone spacing: 1 m<br>minimum offset: 5 m<br>stack 10<br>sampling rate 1 ms (1000 Hz)<br><br>ZVF refers to the vertical [Z] component of Rayleigh waves [source: Vertical Force]<br>RVF refers to the radial [R] component of Rayleigh waves [source: Vertical Force]<br>THF refers to Love waves [transversal T component; source: Horizontal Force]<br><br>
DOI: 10.6084/m9.figshare.15171090.v1
title: NMDS species by site

description: Non-metric multidimensional scaling ordination of mosquito communities trapped in the Oklahoma City metro area in 2018-2020
DOI: 10.6084/m9.figshare.23047334.v1
title: Data for Population density and genetic diversity are positively correlated in wild felids globally

description: Data used for the analyses in "Population density and genetic diversity are positively correlated in wild felids globally". Article has been submitted to Global Ecology and Biogeography . <br> RDA and RDS datasets can only be opened using R software see the R script to read these datasets. Further details can be found in the R notebooks (.Rmd) which can be open using a browser (files with .html). <br>
DOI: 10.6084/m9.figshare.23537670.v2
title: Paeonia ludlowii genome annotation

description: Paeonia ludlowii genome annotation dataset.
DOI: 10.6084/m9.figshare.25197074.v2
title: The epidemiology of tick infestation in dog breeds in the UK

description: ObjectivesThe study aimed to explore anonymised electronic patient records to report the prevalence and risk factors for tick infestation in dogs in the UK.MethodsClinical records of dogs under veterinary care in 2016 were followed over a 5-year period to identify cases of tick-infestation. Risk factor analysis used multivariable logistic regression modelling.ResultsThe study included 905,553 dogs. From a random sample, 1,903 tick infestation cases were identified. The estimated 5-year (2014-2018) period prevalence was 2.03% (95% CI: 2.00-2.06). Sixteen breeds showed increased odds compared with nondesigner-crossbreed dogs. Breeds with the highest odds included Cairn Terrier (OR 2.86, 95% CI 1.64-4.98), Standard Poodle (OR 2.80, 95% CI 1.25-6.29) and Goldendoodle (OR 2.63, 95% CI 1.17-5.91). Six breeds showed reduced odds, with lowest odds shown by Staffordshire Bull Terrier (OR 0.35, 95% CI 0.25-0.50), Rottweiler (OR 0.35, 95% CI 0.15-0.85) and Chihuahua (OR 0.38, 95% CI 0.26-0.55). Males had 1.24 (95% CI 1.13-1.36) times the odds of females. Compared with nondesigner-crossbred dogs, designer-crossbreed dogs had increased odds (OR 1.81, 95% CI 1.52-2.15). Compared with breeds with short coats, breeds with medium length coats (OR 2.20, 95% CI 1.96-2.48) showed increased odds. Breeds with V-shaped drop and pendulous ear carriage had higher odds compared with breeds with erect ear carriage.Clinical significanceThese findings provide an evidence base for veterinary professionals to raise awareness of tick-infestation as a preventable disorder in dogs in the UK and to support more effective prevention and therapeutic protocols based on targeted approaches.
DOI: 10.17632/3yn2f8d8rv
title: Data for: Spatial interactive effects on housing prices in Shanghai and Beijing

description: Code for simulations
DOI: 10.17870/bathspa.11283590.v1
title: Outliers - Installation images from Exhibition

description: <i>Outliers</i> is a research project articulated through a solo exhibition held at No 20 Arts in London. It contained a body of 26 works including paintings, drawings and photographs that were the culmination of a research trip to Greenland. This body of work aimed to explore how the medium of paint could be manipulated to not only represent the dramatic and transient nature of the icescapes of Greenland but to also emulate and explore the properties of snow and ice themselves. <br><br>This item contains installation images from the exhibition.<br>Photos courtesy of No. 20 Arts, London. Photos copyright of No. 20 Arts, London.<br><br>Used with permission. <br><b>The work is under copyright and may not be used without permission. Use of this repository acknowledges cooperation with its policies and relevant copyright law.</b><br>
DOI: 10.6084/m9.figshare.1007711.v8
title: DDR Experiments 2013

description: Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations, and the consequences of this relationship for ecosystem function, are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life-history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community types, which gave rise to transient diversity maxima when community types were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.
DOI: 10.6084/m9.figshare.27800211.v1
title: dataset

description: Zeolite dataset used in our experiment, the dataset is in deepmd format.
DOI: 10.6084/m9.figshare.7678190.v1
title: Porous media and images: an introduction

description: Abstract The research about porous media has a increasing demand in part of scientific community, and pursues the improvement in known techniques, as well the development of new methodologies. Image analysis is a very promising technique in this branch of applied science. In this paper we present some ideas behind the studies of porous materials via image analysis. We provide advanced references whenever necessary.
DOI: 10.60893/figshare.jcp.28454813.v1
title: Supplementary Information

description: Supporting analysis
DOI: 10.17632/jt287rs4n8
title: Data for: Insights into Features of Novel Type 1½ Inhibitors of p38αMitogen-Activated Protein Kinase Using QSAR, E-Pharmacophore Modeling, Quantum Mechanics, Bioisostere Replacement and ADMET Studies.

description: In this dataset, we provide mechanistic insights into novel type 1 1/2 inhibitors developed by Walter et al., (2017) using: Combi-QSAR, E-pharmacophore modeling, Molecular docking, and Quantum mechanics (HOMO, LUMO, and MESP) methods. Finally, we generated 592 unique lead compounds using Bioisostere replacement methods. 474 were within the applicability domain (AD) of our QSAR model. The biological activities (pIC50) of the compounds (474) were predicted using our QSAR model and the binding free energy of the top compounds (pIC50 &gt; 3.0) was calculated by docking.
DOI: 10.17632/pxnddn22gn
title: Visibility Measurements During The 2018 Global Dust Storm Using Navcam and Mastcam onboard the Mars Science Laboratory Rover, Curiosity.

description: Raw visbility data supporting the paper "Visibility and Line-Of-Sight Extinction Estimates in Gale Crater during the 2018/MY34 Global Dust Storm" by Smith, Moores, Lemmon, Guzewich, Moore, Ellison, and Khayat, 2019. Data is in the format: Sol, LTST, Center Azimuth of image (degrees), Center Elevation of image (degrees), Feature Offset Azimuth (from image center, degrees), Feature Offset Elevation (from image center, degrees), Feature Distance (m) Filenames are of the form: Camera_ObservationType_BrightnessCorrected_RunNumber.dat. Camera = NCAM or MCAMR, MCAMG, MCAMB (Navcam or Mastcam red, green or blue filter) Observation type= "LOS", "CRE" or "DD360" (line of sight image, crater rim extinction image, or dust devil 360 frame). RunNumber can be 1, 2, or 3. Thresholds (1/signal-to-noise) for MCAM filters are provided in the files that end "_thresholds.dat" and are in the format: Sol, time (LTST), threshold.
DOI: 10.17632/rzhf2bjw4v
title: Database on ingestion of grit and arthropods by hummingbirds

description: This database contains data on the amount of grit particles and arthropods ingested by six hummingbird species sampled in a seasonal ecosystem in western Mexico. Data were collected from the stomach content analysis of the sampled hummingbirds over a one-year period. Data presented are: 1) the total number of grit particles per stomach, 2) the biomass of arthropods ingested (g dry weight/stomach), 3) the Orders of arthropods ingested, and 4) the average chitin content of arthropods ingested (percentage dry weight).
DOI: 10.17632/yjd5pbxdvm
title: Colorectal cancer and primary fibroblast, pericyte conditioned media

description: Proteomic profiling for 200 human cytokines of conditioned media samples as follows:
PM = pericyte-conditioned pericyte media
PCM = Caco2-conditioned pericyte media
PSM = SW480-conditioned pericyte media
PHM = HCT116-conditioned pericyte media
FM = fibroblast-conditioned fibroblast media
FCM = Caco2-conditioned fibroblast media
FSM = SW480-conditioned fibroblast media
FHM = HCT116-conditioned fibroblast media
DOI: 10.6084/m9.figshare.21213587.v2
title: Spatio-temporal variation in plant-pollinator interactions: a multilayer network approach

description: Despite the dynamic nature of communities, most research typically treated interaction networks as static entities, and only a few analysed the spatial and the temporal scales simultaneously. Here, we used spatial and temporal multilayer networks to explore the persistence of species and interactions in space and time, as well as the variation of species role (centrality) according to biotic factors. We further investigated, for the first time, the spatio-temporal variation in multilayer network structure. Species exhibited substantial turnover across time mainly due to differences in species phenology. In contrast, interaction turnover was more pronounced across habitats, which seems to be a common strategy of pollinators to adjust interactions spatially to different ecological scenarios. Plant species were comparatively more important to the cohesiveness of spatial than temporal networks whereas the centrality of pollinators correlated between scales. The importance of plant species fluctuated temporally due mainly to changes in flower density, whereas that of pollinators fluctuated in space and time according to their relative abundance. Module composition was highly unstable in time. Species were highly capable of changing partners and module affiliation across both scales. We conclude that plant-pollinator interactions are highly dynamic in space and time and that there are differences between plants and pollinators in their use of resources across habitats and subseasons with implications for the understanding of functional connectivity and multilayer structure.