cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/x8kbx5hmxs.1
title: Eukaryotic clathrin adapter protein and mediator of cholesterol homeostasis, PICALM, affects trafficking to the chlamydial inclusion

description: The obligate intracellular pathogen Chlamydia trachomatis has unique metabolic requirements as it proceeds through its biphasic developmental cycle from within the inclusion within the host cell. In our previous study, we identified a host protein, PICALM, which localizes to the chlamydial inclusion. PICALM functions in many host pathways including the recycling of receptors, specific SNARE proteins, and molecules like transferrin, and maintaining cholesterol homeostasis. Hence, we hypothesized that PICALM functions to maintain the cholesterol content and to moderate trafficking from the endosomal recycling pathway to the inclusion, which controls chlamydial access to this pathway. In uninfected cells, siRNA knockdown of PICALM resulted in increased cholesterol within the Golgi and transferrin receptor (TfR) positive vesicles (recycling endosomes). PICALM knockdown in cells infected with C. trachomatis resulted in increased levels of Golgi-derived lipid and protein, TfR, transferrin, and Rab11-FIP1 localized to inclusions and a decrease of Golgi fragmentation at and Rab11 trafficking to the inclusion. Interestingly, chlamydial infection alone also increases cholesterol in TfR and Rab11-associated vesicles, and PICALM knockdown reverses this effect. Our data suggest that PICALM functions to balance or limit chlamydial access to multiple subcellular trafficking pathways to maintain the health of the host cell during chlamydial infection.
DOI: 10.17632/stbtg4hnv9.1
title: Scripts for calculating groundwater recharge via a stochastic vadose zone water budget

description: This archive contains code related to the Open Source scientific computation software GNU Octave for a stochastic vadose zone water budget. A range of groundwater recharge estimates is generated using a Monte Carlo approach based on stochastic spatiotemporal rainfall variability and empirically-derived temporal evapotranspiration variability. This project is useful for calculating the uncertainty in recharge rates due to spatiotemporal variability in rainfall and annual variability in actual evapotranspiration. Including the spatial/temporal variability in rainfall reduces the uncertainty in precipitation and therefore uncertainty in recharge for a multi-decade water budget.
DOI: 10.17632/c7z6r8ksrk.1
title: LDHU3_10.0510

description: Pteridine transporter; Leishmania donovani (HU3 strain)
DOI: 10.17632/gdrt6mbmgw.1
title: LDHU3_10.0530

description: Folate/biopterin transporter | AdoMetT1; Leishmania donovani (HU3 strain)
DOI: 10.17632/xc3wxyf73c.1
title: LDHU3_10.0620

description: Hypothetical protein; Leishmania donovani (HU3 strain)
DOI: 10.15468/dl.x3g4fs
title: Occurrence Download

description: A dataset containing 354999 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lyrurus tetrix (Linnaeus, 1758)"
 ]
}

 The dataset includes 354999 records from 349 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004325-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/63jsfp4gkm.1
title: LDHU3_10.0600

description: Folate/biopterin transporter | FT5; Leishmania donovani (HU3 strain)
DOI: 10.17632/hbkrn2gk3w.1
title: LDHU3_10.0540

description: Folate/biopterin transporter; Leishmania donovani (HU3 strain)
DOI: 10.17632/wk8nd5zjyf.1
title: Acoustic Camera for UAVs

description: This data was collected with an acoustic camera that was designed for use on UAVs, for airborne acoustic surveillance. The dataset contains a video of camera operation in an indoor setting.
DOI: 10.17632/zpmrt2tmvx.1
title: Wrinkle nanostructures generate a novel form of blue structural color in great argus flight feathers

description: Code and data necessary to run optical simulations and generate figures in the paper.
DOI: 10.17632/y626cpvg24.1
title: System dynamics models to assess shortage and wastage levels in demand-driven blood supply chains

description: The files 2_proposedDonorModule.mdl, 4_proposedBcModule.mdl, and 6_proposedHospitalModule.mdl contain the independently proposed donor, blood center, and hospital modules.

The files 1_Clay-et-al-(2016)_donorModule.mdl, 3_Clay-et-al-(2016)_bcModule.mdl, 5_Clay-et-al-(2016)_hospitalModule.mdl present the donor, blood center, and hospital modules proposed by Clay et al. (2016).

File 7_proposedSingleProduct.mdl incudes the proposed model for the single-product system simulations. File 8_proposedMultipleProduct.mdl contains the proposed model for the multi-product system simulations and sensitivity analysis.

References
Clay, N.M., Abbasi, B., Eberhard, A., Hearne, J., 2016. On the volatility of blood inventories. International Transactions in Operational Research 25, 215–242. doi:10.1111/itor.12326.
DOI: 10.17632/xxkkkbx3hg.1
title: Modeling pH and temperature effects as climatic hazards in Vibrio vulnificus and Vibrio parahaemolyticus planktonic growth and biofilm formation

description: This study aimed to better understand the potential effects of temperature and pH on V. vulnificus and V. parahaemolyticus planktonic and biofilm growth. Vibrio strains were grown in triplicate at 25°C, 30ºC, and 37ºC in 96 well plates containing Modified Seawater Yeast Extract modified with CaCl2 at pH’s ranging from 5 to 9.6. AMiGA software was used to model growth curves using Gaussian process regression. The effects of temperature and pH were evaluated using randomized complete block analysis of variance, and V. parahaemolyticus and V. vulnificus growth rates were modeled using the interpolation fit on the MatLab Curve Fitting Toolbox. Different optimal conditions involving temperature and pH were observed for planktonic and biofilm Vibrio growth within- and between-species. This study showed that temperature and pH factors significantly affect Vibrio planktonic growth rates and Vibrio parahaemolyticus biofilm formation.

Vv_Planktonic_SPSS_All: All V. vulnificus strains for planktonic growth rates and statistics
Vv_Biofilm_SPSS_All: All V. vulnificus strains for biofilm growth rates and statistics
Vp_Planktonic_SPSS_All: All V. parahaemolyticus strains for planktonic growth rates and statistics
Vp_Biofilm_SPSS_All: All V. parahaemolyticus strains for biofilm growth rates and statistics
DOI: 10.17632/9fkyf68mzc.1
title: Regional variations in non-communicable comorbid diseases and its management in the patient of medical retinal diseases in India.

description: This supplementary data provides a comprehensive overview of a multi-center study on medical retinal diseases (MRDs) and non-communicable comorbid diseases (NCCDs) across different regions of India. The data is presented in five tables:

Table 1: Distribution of patients according to demographic characteristics

Presents age and gender distribution across six centers in different regions of India
Includes mean, median, and range of body weight and BMI for each center


Table 2: Distribution of patients according to retinal disease characteristics

Shows the prevalence of various retinal diseases (DR, BRVO, CRVO, ARMD) across centers
Includes both single and multiple retinal disease occurrences


Table 3: Distribution of patients according to multiple retinal diseases

Provides a detailed breakdown of patients with multiple retinal diseases
Highlights regional variations in the co-occurrence of different retinal conditions


Table 4: Zone-wise distribution of Non-communicable comorbid diseases and addiction history

Presents the prevalence of various NCCDs (e.g., DM, HTN, CAD, CKD) across centers
Includes data on addiction history (alcohol and tobacco use)


Table 5: Zone-wise distribution of Non-communicable comorbid diseases and their management

Offers insights into the management strategies for various NCCDs across centers
Provides data on medication types and interventions for conditions like DM, HTN, CAD, and CKD



Key observations:

Significant regional variations in the prevalence of both MRDs and NCCDs
High prevalence of diabetes and hypertension across all centers
Varying patterns of multiple comorbidities and retinal disease co-occurrences
Differences in management strategies for NCCDs across regions

This data provides valuable insights into the complex interplay between retinal diseases and systemic comorbidities across different regions of India, highlighting the need for tailored healthcare strategies.
DOI: 10.17632/skyxsvkm2p.1
title: LDHU3_10.0780

description: GP63 | Leishmanolysin; Leishmania donovani (HU3 strain)
DOI: 10.17632/5gyt2hc656.1
title: LDHU3_10.0740

description: GP63 | Leishmanolysin; Leishmania donovani (HU3 strain)
DOI: 10.17632/d73mpc529b.1
title: AIWR Dataset

description: According to the standard of land use code by fundamental geographic data set: FGDS), Thailand [5] land use classification requires an analysis and transformation of satellite images data together with field survey data. In this article, researchers studied only land use in water bodies. The water bodies in this research can be divided into 2 levels: natural body of water (W1) artificial body of (W2) water. The aerial image data used in this research was 1:50 meters. Every aerial image had 650x650 pixels. Those images included water bodies type W1 and W2 as shown in Figure 3a. Ground truth of all aerial images was set for before sending it to be analyzed and interpreted by remote sensing experts. This assured that the water bodies groupings were correct. An example of ground truth, which has been checked by experts. Ground truth has been used in learning the algorithm in deep learning mode and also used in further evaluation. The aerial images used in this experiment consists of water body: types W1 (see, Figure 3, Column 1, 2, and 3) and W2 (see, Figure 3 Column 4). Aerial image water resources dataset, AIWR has 800 images. Data were chosen at random and divided into 3 sections: training, validation, and test set with ratio 8:1:1. Therefore, 640 aerial images were used for learning and creating the model, 80 images were used for validation, and the remaining 80 images were used for test.
DOI: 10.17632/d73mpc529b.2
title: AIWR Dataset

description: Aerial Image Water Resources (AIWR) Dataset According to the standard of land use code by fundamental geographic data set (FGDS), Thailand land use classification requires an analysis and transformation of satellite images data together with field survey data. In this article, researchers studied only land use in water bodies. The water bodies in this research can be divided into 2 levels: natural body of water (W1) artificial body of (W2) water. The aerial image data used in this research was 1:50 meters. Every aerial image had 650x650 pixels. Those images included water bodies type W1 and W2. Ground truth of all aerial images was set for before sending it to be analyzed and interpreted by remote sensing experts. This assured that the water bodies groupings were correct. An example of ground truth, which has been checked by experts. Ground truth has been used in learning the algorithm in deep learning mode and also used in further evaluation. The aerial images used in the experiment consists of water body: types W1 and W2. Aerial image water resources dataset, AIWR has 800 images. Data were chosen at random and divided into 3 sections: training, validation, and test set with ratio 8:1:1. Therefore, 640 aerial images were used for learning and creating the model, 80 images were used for validation, and the remaining 80 images were used for test.
DOI: 10.17632/d73mpc529b.3
title: AIWR: Aerial Image Water Resource Dataset

description: Aerial Image Water Resource (AIWR) Dataset

According to the land use code standards set by the Fundamental Geographic Data Set (FGDS), land use classification in Thailand requires the analysis and transformation of satellite imagery in conjunction with field survey data. In this study, researchers focused specifically on land use in water bodies. The water bodies are classified into two categories: natural bodies of water (W1) and artificial bodies of water (W2).

The aerial images used in this research were captured at a resolution of 1:50 meters, with each image measuring 650x650 pixels. These images included both types of water bodies, W1 and W2. Ground truth annotations were established for all aerial images prior to analysis by remote sensing experts to ensure accurate classification of the water bodies. An example of ground truth, validated by experts, was used to train the deep learning algorithm and further assess its performance.

The AIWR dataset, which contains 800 aerial images, consists of both W1 and W2 water bodies. The data were randomly divided into two sets: training and test sets, with a 9:1 ratio. Consequently, 720 aerial images were used for model training and development, while 80 images were reserved for testing.
DOI: 10.17632/p3pxsmby62.1
title: LDHU3_10.0720

description: GP63 | Leishmanolysin; Leishmania donovani (HU3 strain)
DOI: 10.17632/cy4zbzp63v.1
title: LDHU3_10.0840

description: Mitogen-activated protein kinase 3 | MPK3 | MAPK3; Leishmania donovani (HU3 strain)
DOI: 10.5281/zenodo.14686735
title: CASA cryo sperm PVP

description: This dataset contains raw data and processed results of CASA sperm motility data after cryopreservation.

 Contents: Raw data: raw measurements collected from experimental observations on 01/29/20.

 Processed data: results of statistical and computational analysis performed using Excel. 

Data structure: The dataset contains the following sheets: Sheet 1: raw sperm motility data.
DOI: 10.5281/zenodo.14686736
title: CASA cryo sperm PVP

description: This dataset contains raw data and processed results of CASA sperm motility data after cryopreservation.

 Contents: Raw data: raw measurements collected from experimental observations on 01/29/20.

 Processed data: results of statistical and computational analysis performed using Excel. 

Data structure: The dataset contains the following sheets: Sheet 1: raw sperm motility data.
DOI: 10.17632/sk3rfbh4n4.1
title: LDHU3_10.0800

description: GP63 | Leishmanolysin; Leishmania donovani (HU3 strain)
DOI: 10.17632/vs7yn8rcr9.1
title: LINF_340013000

description: Protein phosphatase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/k6n78cntzs.1
title: LINF_340014300

description: Serine/threonine-protein phosphatase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/wbycb9cd48.1
title: LINF_340014500

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/nyjjmc2htd.1
title: Dataset: Forest edge landscape context affects mosquito community composition and risk of pathogen emergence

description: Full dataset accompanying the manuscript "Forest edge landscape context affects mosquito community composition and risk of pathogen emergence", iScience, doi.org/10.1016/j.isci.2024.111576
DOI: 10.17632/zw32n2snj6.1
title: LINF_340013200

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/c4fgbzvzp5.1
title: LINF_340013100

description: NOC4; Leishmania infantum (strain JPCM5)
DOI: 10.17632/5r4f98rpj9.1
title: LDHU3_10.1000

description: FLA1-binding protein | FLA1BP; Leishmania donovani (HU3 strain)
DOI: 10.17632/3rjp6h7n8t.1
title: LDHU3_10.0990

description: Endonuclease G | EndoG; Leishmania donovani (HU3 strain)
DOI: 10.17632/zhf79592gn.1
title: LDHU3_10.0950

description: Chromatin assembly factor 1 subunit A; Leishmania donovani (HU3 strain)
DOI: 10.17632/3hd4rjhw36.1
title: The influence of catechols on the magnetization of iron oxide nanoparticles

description: The magnetization of maghemite nanoparticles should increase when catechols are adsorbed on the surface, either due to surface reconstruction or iron(III) reduction to iron (II). The magnetic measurements show an increase in magnetization. XPS measurements don't show the presence of iron(II) after the adsorption of catechols. The DFT calculation shows, that the adsorption doesn't influence the magnetic properties of nanoparticles. The average size of the particles and the size distribution from TEM images were determined. The size and size distribution of functionalized particles increased, which results in higher magnetizations.
DOI: 10.17632/jkxnx73mjf.1
title: The Intestinal Microbiome, Dietary Habits, and Physical and Psychological Resilience in Postpartum Women

description: This is the data sets of a research paper entitled "The Intestinal Microbiome, Dietary Habits, and Physical and Psychological Resilience in Postpartum Women".
DOI: 10.17632/z6285myxkm.1
title: Core-top carbon isotope measurements of dinoflagellate cysts

description: The here deposited data represents stable carbon isotope measurements of dinoflagellate cyst (dinocyst) taxa isolated from core-top sediments. Carbon isotope data were generated using laser-ablation / nano-combustion / gas chromatography isotope ratio mass spectrometry (LA-nC-GC/IRMS) and each measurement represents 3-7 individual, hand-picked, dinocysts. A more detailed description of sample and data processing can be found here: https://bg.copernicus.org/preprints/bg-2022-118/ (updated with final version once available). 

The data were used to test dependency of carbon isotope fractionation to environmental parameters, most notably CO2, in order to construct a pCO2 proxy based on dinocyst carbon isotope fractionation. Carbon isotope data for five species (Operculodinium centrocarpum, Spiniferites ramosus, Spiniferites elongatus, Spiniferites mirabilis and Impagidinium aculeatum are presented, from 19 localities in the Atlantic Ocean and Mediterranean sea (listed in the data files). 

Two data files (summary and raw measurements) are added. The summary file contains the data to calculate carbon isotope fractionation (ep) for each sample and species (average raw and corrected dinocyst d13C, d13C of dissolved inorganic carbon (DIC), temperature) and the environmental parameters (pCO2, NO3, PO4, Si, temperature, salinity, alkalinity) used to compare to the dinocyst carbon isotope data. The raw measurement data file contains the sample identifier which links to the summary file, the species and signal-size and d13C value for each of the 949 individual measurements. A signal-size dependent correction is applied based to eliminate small drift induced by background C (d13C adjusted). After this step, a disqualifier is given if the data is excluded based on too low signal intensity (below cut-off / BCO) or represents a statistical outlier within the d13C population of that specific sample and species (OUT). The adjusted d13C data without disqualifiers is included in the 'corrected d13C' and used in the summary file and statistical tests (see also https://bg.copernicus.org/preprints/bg-2022-118/). Species abbrevations: Operculodinium centrocarpum "Ocen", Spiniferites ramosus "Sram", S. elongatus, "Selon", S. mirabilis "Smira", Impagidinium aculeatum "Iacul".
DOI: 10.17632/ycjgjfr56d.1
title: data for gut microbiota in patients with LC-COPD

description: The raw material included the alteration of gut microbiota, SCFA and inflammatory factors in patients with LC-COPD.
DOI: 10.17632/p3dhzyhvnk.2
title: List of PKL files for LC-MS/MS identification of Amaranthus seed proteins derived from 2-DE spots

description: List of PKL files for LC-MS/MS identification of Amaranthus seed proteins derived from 2-DE spots.
DOI: 10.17632/p3dhzyhvnk.3
title: List of PKL files for LC-MS/MS identification of Amaranthus seed proteins derived from 2-DE spots

description: List of PKL files for LC-MS/MS identification of Amaranthus seed proteins derived from 2-DE spots.
DOI: 10.17632/v7j5pvncyr.1
title: LINF_340017500

description: Amastin-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/jcyfv6mkcx.1
title: LINF_340014700

description: DNA-directed RNA polymerase III subunit | RPB6; Leishmania infantum (strain JPCM5)
DOI: 10.17632/jdfxdd66tt.1
title: LINF_340016500

description: Carnosine N-Methyltransferase; Leishmania infantum (strain JPCM5)
DOI: 10.17632/xrjrnjmydt.1
title: Comparison of oxygen induced retinopathy transcriptomes between Sprague Dawley rats from two vendors

description: To investigate variable susceptibilities to retinopathy of prematurity among infants, we performed RNA sequencing on whole retinal lysates from Sprague Dawley rat pups from Charles River Laboratories and Envigo that underwent the Penn 50/10 oxygen-induced retinopathy (OIR) model. Normoxia control and 50/10 OIR retinas underwent next-generation RNA sequencing, n=4/ group. Pairwise comparisons were performed to generate differentially expressed genes between OIR and control groups from the two vendors during the avascular phase of OIR (postnatal day 15) and the neovascular phase (postnatal day 20).
DOI: 10.17632/6p444yz4yb.1
title: ARTICLE SKIN HYPERPIGMENTATION INDUCED BY CLOFAZIMINE IN LEPROSY PATIENTS

description: Supplementary material from the appendices of the skin color measurement protocol with the colorimeter and the structured questionnaire on stigma caused by clofazimine-induced skin hyperpigmentation.
DOI: 10.17632/38z7h96km4.1
title: Untargeted metabolomics - TINMAN

description: Stool samples before and after prolonged (more than 2 weeks) antibiotic treatment were obtained from pediatric patients and analyzed via untargeted metabolomic profiling by third party laboratory "Metabolon". Further analyses of these results were performed to help determine the relationship between changes in metabolites after antibiotic treatment and the development of antibiotic-associated neutropenia.
DOI: 10.17632/ywrmpn7b4z.1
title: Neural-circuit basis of song preference learning in fruit flies

description: The dataset and code used for the publication of "Neural-circuit basis of song preference learning in fruit flies"
 (doi: 10.1016/j.isci.2024.110266).
DOI: 10.17632/v4w54r7snd.1
title: Lizard host abundances and climatic factors explain phylogenetic diversity and prevalence of blood parasites on an oceanic island

description: 1. Host abundance might favour the maintenance of a high phylogenetic diversity of some parasites via rapid transmission rates. Blood parasites of insular lizards represent a good model to test this hypothesis because these parasites can be particularly prevalent in islands and host lizards highly abundant.
2. We applied deep amplicon sequencing and analysed environmental predictors of blood parasite prevalence and phylogenetic diversity in the endemic lizard Gallotia galloti across 24 localities on Tenerife, an island in the Canary archipelago that has experienced increasing warming and drought in recent years.
3. Parasite prevalence assessed by microscopy was over 94% and a higher proportion of infected lizards was found in warmer and drier locations. A total of 33 different 18s rRNA parasite haplotype were identified and the phylogenetic analyses indicated that they belong to two genera of Adeleorina (Apicomplexa: Coccidia), with Karyolysus as the dominant genus. The most important predictor of between-locality variation in parasite phylogenetic diversity was the abundance of lizard hosts. 
4. A combination of climatic and host demographic factors associated with an insular syndrome may be favouring a rapid transmission of blood parasites among lizards on Tenerife, which may favour the maintenance of a high phylogenetic diversity of parasites.