cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/p8yzkdccg7
title: Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model: VESSEL COLLAPSE

description: Data and results for `VESSEL COLLAPSE` simulations. Simulations of cancerous cells in tissue context with realistic vasculature (single root with two arteries and two veins). Different variations of the vasculature are produced using random seeds 0 - 9 and assigned letters from A - J, respectively. Each condition is run for 22 days (31680 ticks) with 10 replicates (random seeds 0 - 9) for each of the 10 vasculature variations, for 100 total simulations per parameter value. Cancerous cells (max_height x 1.5, meta_pref x 1.5, migra_threshold x 0.5) are introduced to the center of the environment after a 1 day delay. Snapshots are taken every 0.5 days (720 ticks). Parameters (degradation rate and stabilization fraction) are varied from 0.0 to 1.0 (increments of 0.1). For stabilization fraction simulations, stabilization step is set to day 8 (11520 ticks). Note that simulations with stabilization fraction use modified code. The data folder contains .tar.xz compressed replicate sets. The data.graph folder contains .tar.xz compressed replicate sets for .GRAPH output. The results folder contains compressed .csv files with parsed metrics for each simulation and .csv files with all simulation metrics consolidated into a single file. Simulations are labeled as: [parameter]_[value]_[graph] - [parameter] - degradation = degradation rate - stabilized = stabilization fraction - [value] - ### = parameter value (###/100) - [graph] - A = single root graph with two arteries and two veins, seed 0 - B = single root graph with two arteries and two veins, seed 1 - ... - J = single root graph with two arteries and two veins, seed 9
DOI: 10.17632/rgyg4dwsx6
title: Attitudes, Barriers, Motivators and Utilization of Clinical Research: A cross-sectional survey of hospital pharmacists

description: The attached data was gathered from Jordanian hospital pharmacists to evaluate their attitudes, barriers and motivators toward clinical research practice and extent of its’ utilization in practice settings.
DOI: 10.17632/xsc759fvyp
title: Flow cytometry data SBCW without Eurobitum for: Water-soluble bitumen degradation products can fuel nitrate reduction from non-radioactive bituminized waste

description: Flow Cytometry data files of anoxic batch experiments performed in synthetic Boom Clay pore water supplemented with 15 mM sodium acetate, 15 mM sodium formate, 15 mM sodium oxalate, a combination of 5 mM sodium acetate, 5 mM sodium formate and 5 mM sodium oxalate or without additional organic additive. The microbial community of Boom Clay pore water obtained from piezometer TD-11D-23 was used as inoculum to study ongoing microbial reactions.
DOI: 10.17632/yv7mkjgrdf
title: BMP2

description: The protein encoded by this gene belongs to the transforming growth factor-beta (TGFB) superfamily. The encoded protein acts as a disulfide-linked homodimer and induces bone and cartilage formation.
DOI: 10.17632/2ps8zp2c8c
title: Data for: Geochronology and geochemistry of Late Paleozoic volcanic rocks from eastern Inner Mongolia, NE China: Implication for petrogenesis, tectonic setting and tectonic evolution of the south-eastern Central Asian Orogenic Belt

description: LA-ICP-MS zircon U–Pb data,Major and trace element data and In situ zircon Hf isotopic data for the volcanic rocks in the Dashizhai Formation from Dashizhai Town
DOI: 10.17632/6mpxrdgh79
title: Collaboration networks and word cloud

description: A total of 296 articles on COVID-19 in the field of Dentistry published from February to September 6, 2020, is presented through collaboration networks and word cloud. The scientific collaboration network where nodes are authors and links are co-authorships is given in Appendix Network file 1, revealing regular study groups and pivotal authors of the Covid-19 research in the field of Dentistry. The collaboration network among the 250 most productive institutions can be explored through Appendix Network file 2, where colours are used to make distinctions between different clusters, and the size of the nodes representing institutions indicates the total number of identified COVID-19 articles. The social structure represented on a macro level using the collaboration network among countries is given in Appendix network file 3. The overview of the authors' keywords revealing COVID-19 interests of dental researchers and the frequency of their occurrence is shown in Appendix Word Cloud 1. Bibliometric networks were graphically presented using R packages bibliometrix version 3.0.2 and wordcloud2 version 0.2.1.
DOI: 10.17632/f6w9bbzhdz
title: Synthesis, Study and Characterization of Tin Oxide Thin Films

description: These are theoretical and experimental data for the characterization of Tin Oxide thin films doped with F, Ni, and Co. These samples were synthesized through the spray pyrolysis technique. There are results for XRD, XPS, SEM, EDS, Optical Spectroscopy, magnetic moment, and other related data. In addition, there are some DFT-based theoretical results for DOS and dielectric function.
DOI: 10.17632/g7fbjvf6yw
title: LDHU3_06.1230

description: protein disulfide isomerase | PDI15 | PDI-1
Leishmania donovani (HU3 strain)
DOI: 10.17632/g8zxvgp2yt
title: Supplemental figures: regulation of Cyp19a1 by Klf4

description: Kruppel-like factor 4 (GKLF) is rapidly and transiently increased by luteinizing hormone (LH) surge in the ovary. KLF4 inhibited Cyp19a1 expression most likely through interaction to the SF1 binding motif of Cyp19a1 promoter in periovulatory granulosa cells.
DOI: 10.17632/j35vdt7hkf
title: LINF_290021100

description: protein of unknown function - conserved
Leishmania infantum (strain JPCM5)
DOI: 10.17632/j7k2y8zdzy
title: Data and Appendix for Sustainability spillover effects of social, environment and economy: mapping global sustainable development in a systematic analysis

description: The uploaded files are organized as follows:

1 - Appendix Tables
They show the coefficients and statistics of the estimated simultaneous equation system of life expectancy, per capita CO2 emissions and per capita GDP of various regions of the world including 1. North America, 2. Latin America and Caribbean, 3. European Union, 4. Sub-Saharan Africa, 5. North Africa and Middle East (MENA), and finally 6. Pacific and East Asia. 

2- Appendix Figures
They represent the impulse functions of VAR model for the mentioned variables.

3- Data
It is the data which employed in the research

4- EView-WorkFile
It is the software file for running the mentioned models.

5- Methodology in Details
It describes the methodology of the research in details.

6- Results in Summary (Table A-1 to A-6)
It represents all the estimated coefficients and statistics summarily.
DOI: 10.17632/jfhc6z4nyn
title: Supplementary Materials: Estimation of worker population size-density by nest counting in the Asian weaver ant, Oecophylla smaragdina (Formicidae: Formicinae) and it’s dynamic in oil palm plantations industry

description: Supplementary material supporting the research article.
DOI: 10.17632/jr3mvd29vm
title: Media Trial and Justice

description: Media has the potential to take the lead to ensure administration of justice in a community or country. Though it has controversial role in criminal justice throughout the world but in Bangladesh currently its positive side outweighs the dark one it belongs and acts as a pioneer to ensure justice for the oppressed and helpless one. There is nothing to deny the fact that media is sometimes engaged in making news rather covering but the data presented here collected from various case references, national & international newspapers, journals and news and programs covered by television make it lucid and understandable that what a strong and effective role it can play to ensure justice for everyone irrespective of belief, color and political affiliation. Now in Bangladesh, the power of media in administrating proper justice is tested and the power is positively proved in this regard. This data can be a helpful tool in the hand of the government to strengthen and regulate the media properly so that it can carry on its duty as watchdog to protect the interest of mass people against all kind of malpractice.
DOI: 10.17632/mzp2943cyw
title: Comparison of doses received from non-contrast enhanced brain CT examinations between two CT scanners

description: Supplementary data
DOI: 10.17632/nkjcstp2cp
title: Supplementary_Data_IJEAC

description: Hypothesis: To estimate the variation in the profile of the metal in aerosol due to nationwide lockdown. Data: Variation in metal profile and their contribution percentages in normal, pre-lockdown, lockdown, and post-lockdown sampling phase. Analysis method: Source apportionment analysis using PMF version 5. Interpretation: The source apportionment of metals can be identified through their respective contribution percentages.
DOI: 10.17632/px5wfcvwwb
title: Intestinal microbiota modulates adrenomedullary response through Nod1 sensing in chromaffin cells

description: Original western blot images for Figures 2E, 3F, 4B and S1A.
DOI: 10.17632/r7mdjt7gh9
title: Additional material to article: Optimizing functionals using Differential Evolution

description: The file includes the additional material to article: Optimizing functionals using Differential Evolution
DOI: 10.17632/sggzrtf5dz
title: Complexity-functioning relationships differ across different environmental conditions

description: ABSTRACT

Habitat complexity is widely considered an important determinant of biodiversity, and enhancing complexity can play a key role in restoring degraded habitats. However, the effects of habitat complexity on ecosystem functioning – as opposed to biodiversity and community structure – are relatively poorly understood for artificial habitats, which dominate many coastlines. With Greening of Grey Infrastructure (GGI) approaches, or eco-engineering, increasingly being applied around the globe, it is important to understand the effects that modifying habitat complexity has on both biodiversity and ecological functioning in these highly modified habitats. We assessed how manipulating physical (primary substrate) and/or biogenic habitat (bivalves) complexity on intertidal artificial substrata affected filtration rates, net and gross primary productivity (NPP and GPP, respectively) and community respiration (CR) – as well as abundance of filter feeders and macro-algae and habitat use by cryptobenthic fish across six locations in three continents. We manipulated both physical and biogenic complexity using 1) flat or ridged (2.5 cm or 5 cm) settlement tiles that were either 2) unseeded or seeded with oysters or mussels. Across all locations, increasing physical and biogenic complexity (5 cm seeded tiles) had a significant effect on most ecological functioning variables, increasing overall filtration rates of the assemblages on tiles but decreasing productivity (both GPP and NPP) across all locations. There were no overall effects of increasing either type of habitat complexity on cryptobenthic fish MaxN, total time in frame or macro-algal cover. Within each location, there were marked differences in the effects of habitat complexity. In Hobart, Australia, we found higher GPP on flat tiles than on 5 cm tiles. In Sydney, Australia, we found higher filtration rates and biomass of filter feeders on seeded than unseeded tiles and greater abundance (MaxN) of cryptobenthic fish on 5 cm tiles than on flat tiles, whereas in Dublin, Ireland, there were higher filtration rates on 5 cm complex tiles than on flat tiles. Our findings suggest that GGI solutions via increased habitat complexity are likely to have trade-offs among potentially desired functions, such as productivity and filtration rates, and variable effects on cryptobenthic fish communities. Importantly, our results show that the effects of GGI practices can vary markedly according to the environmental context and therefore should not be blindly and uniformly applied across the globe.
DOI: 10.17632/sxvvyzzd6t
title: DataCOVID

description: DATABASE - This was a longitudinal retrospective cohort study of patients ≥20 years-old who were hospitalised due to COVID-19 in 52 hospitals comprising a private Brazilian healthcare network (Rede D’Or São Luiz). Participating institutions were tertiary hospitals distributed across four (Northeast, Central-West, Southeast, and South) of Brazil’s five macro-regions. Data were extracted from the institutional central database comprised of COVID-19 diagnoses and related deaths (both of which are of compulsory notification to the BMH). Participating hospitals utilized a standardized data collection model including weekly reporting to the BMH. The study period included the first 13 months of the pandemic, i.e., from March 1st, 2020 to March 31st, 2021. All patients hospitalised due to COVID-19 (as the primary diagnosis upon admission) who were either discharged or died were included
DOI: 10.17632/sztb9ydr86
title: Применение окрашивания для идентификации гусениц и имаго чешуекрылых (Lepidoptera)

description: Материалы конференции "Защита и карантин растений" (25 – 28 октября 2023, Быково, Московская область)
DOI: 10.17632/59gdmr7ztf
title: LINF_180014400

description: protein of unknown function
Leishmania infantum (strain JPCM5)
DOI: 10.17632/5d96cps5m4
title: The State of Inclusive and Human-Centred Design in Oral Healthcare

description: Full list of coded projects included in a review of the state of inclusive and human-centred design in oral healthcare.
DOI: 10.17632/67r72zcfxx
title: Genome-wide convergent analyses and transgenic evidence reveal a single origin of laryngeal echolocation in bats

description: We hypothesized that if the echolocation of bats originated in the ancestor of all bats, more convergent sites in hearing-related genes will be observed between dolphin and the ancestral lineage of all bats and these substitutions might affect the function of hearing-related genes. We used comparative genomics and functional experiments to test these hypotheses!
DOI: 10.17632/dcy22r53ns
title: Dataset for "Hepatic glycogen participates in the regulation of hypothalamic pAkt/Akt ratio in high-sugar/high-fat diet-induced obesity."

description: This data was used in the production of the article entitled "Hepatic glycogen participates in the regulation of hypothalamic pAkt/Akt ratio in high-sugar/high-fat diet-induced obesity." published in 2022 at Metabolic Brain Disease (ISSN: 0885-7490) (DOI : 10.1007/s11011-022-00944-3)

Abstract (DOI : 10.1007/s11011-022-00944-3)
The hypothalamus is a major integrating centre that controls energy homeostasis and plays a major role in hepatic glycogen (HGlyc) turnover. Not only do hypothalamic and hepatic Akt levels influence glucose homeostasis and glycogen synthesis, but exposure to high-sugar/high-fat diets (HSHF) can also lead to hypothalamic inflammation and HGlyc accumulation. HSHF withdrawal overall restores energy and glucose homeostasis, but the actual relationship between hypothalamic inflammation and HGlyc after short-term HSHF withdrawal has not yet been fully elucidated. Here we investigated the short-term effects of HSHF withdrawal preceded by a 30-day HSHF intake on the liver-hypothalamus crosstalk and glucose homeostasis. Sixty-day old male Wistar rats were fed for 30 days a control chow (n=10) (Ct), or an HSHF diet (n=20). On the 30th day of dietary intervention, a random HSHF subset (n=10) had their diets switched to control chow for 48 h (Hw) whilst the remaining HSHF rats remained in the HSHF diet (n=10) (Hd). All rats were anaesthetized and euthanized at the end of the protocol. We quantified HGlyc, Akt phosphorylation, inflammation and glucose homeostasis biomarkers. We also assessed the effect of propensity to obesity on those biomarkers, as detailed previously. Hd rats showed impaired glucose homeostasis, higher HGlyc and hypothalamic inflammation, and lower pAkt/Akt. Increased HGlyc was significantly associated with HSHF intake on pAkt/Akt lowered levels. We also found that HGlyc breakdown may have prevented a further pAkt/Akt drop after HSHF withdrawal. Propensity to obesity showed no apparent effect on hypothalamic inflammation or glucose homeostasis. Our findings suggest a comprehensive role of HGlyc as a structural and functional modulator of energy metabolism, and such roles may come into play relatively rapidly.

It contains the .csv file with the data used in the publication.

Researcher in charge: Debora Estadella
Researcher in charge of data collection: Breno Picin Casagrande
Date of data collection: 01/04/2018 - 1/12/2019
Financial support: CAPES - Brazil, FAPESP (2017/25420-3), CNPq
DOI: 10.17632/dpt7htfhwg
title: Distinct silencer states generate epigenetic states of heterochromatin

description: Raw image data for microscopy and western blots.
DOI: 10.17632/dyrwyv3jty
title: Virtual Lab for the SP

description: Raw Data and analyses on Likert scale data, testimonial videos of expert and student participants
DOI: 10.17632/dz6dnzbtpv
title: metabolic reprogramming in PMOP

description: 1.Morphological data
Micro-CT and morphological data in SHAM, OVX and OVX+ICA group as well as in OVX, OVX+low-dosage DCA and OVX+low-dosage DCA group.

2. The Rat Glucose Metabolism RT² Profiler PCR Array
84 glucose metabolism related genes were detected in SHAM, OVX and OVX+ICA groups.

3. Immunoblotting raw pictures
For detections in SHAM, OVX and OVX+ICA groups, the sequences in the band is SHAM, OVX and ICA+OVX from left to right.For detections in cells, the sequences in the band is siCON, siPDK1, DCA and ICA from left to right. For detections in DCA-interventioned OVX group, the sequences in the band is OVX, low-dosage DCA and high-dosage DCA from left to right. For PDK1 enzymatic activity detection, the sequences in the band was phosphorylated PDHA Ser232 at 0, 5, 10 minutes.

4. Immunofluorescence pictures
Immunofluorescences of PDHA and PDHA pSer232 were performed on paraffin cuts in SHAM, OVX and OVX+ICA group, reconfirming the upregulation  of PDHA pSer232 in OVX group.
The co-labelled PDHA pSer232 with osteoclast marker and osteoblast marker respectively indicated the the upregulation of PDHA pSer232 mainly existed in osteoclasts.

5.qPCR raw data
Osteoclast marker genes (Nfatc1, Tracp, Oscar, Mmp9 and Cathepsin K ) significantly decreased after PDK1 knockdown, DCA and ICA administration, indicating that DCA and ICA both hindered osteoclast differentiation. 

6.TRAP staining pictures
The numbers of TRAP positive osteoclasts dramatically diminished after PDK1 knockdown, DCA and ICA administration.
DOI: 10.17632/jtzcv2m4rm
title: data on financial inclusion and health outcomes

description: This are the dataset use for the paper on financial inclusion and health outcomes
DOI: 10.17632/k4rt99sfbt
title: COVID-19 Android apps data set

description: This data set consist of Android apps which are developed during the current time when the whole world face the pandemic situation. Cybercriminals are developing malware-infected apps on a regular basis and upload them to different repositories.
DOI: 10.17632/kmt8tx7gh6
title: NeoMHCI Training and Evaluation Data

description: All training and evaluation data used in the NeoMHCI study.

All code is freely available at https://github.com/ZhuLab-Fudan/NeoMHCI.

------------------------------------------------------
Train Data:

1. EL_train.zip:
 Contains all eluted ligand data used for training the five-fold cross-validation model.
 - EL2020_A.txt: Corresponds to the EL2020_A dataset mentioned in the article.
 - EL2020_B.txt: Corresponds to the EL2020_B dataset mentioned in the article.
 Combining the data from these two files constitutes the EL2020_C dataset mentioned in the article.

2. NE_train.zip
 Contains all neoepitope data used during the fine-tuning process for the immunogenicity prediction task.
 - NE2023.txt: Corresponds to the NE2023 dataset mentioned in the article.
 - NE2023_list.json: A candidate pool constructed from all wild-type sequences in NE2023.
 - IN2023: Corresponds to the IN2023 dataset mentioned in the article, used as a validation set during the fine-tuning process.

------------------------------------------------------
Test Data:

3. EL_test.zip
 Contains the test set for ligand presentation prediction, along with the prediction scores of NeoMHCI and other comparison methods.
 - IM2020.csv: Corresponds to the IM2020 test set mentioned in the article.
 - IS2020.csv: Corresponds to the IS2020 test set mentioned in the article.

4. NE_test.zip
 Contains the neoepitope test set for immunogenicity prediction, along with the prediction scores of NeoMHCI and other comparison methods.
 - BM2023.csv: Corresponds to the BM2023 test set mentioned in the article.
 - COVID-19.txt: Corresponds to the COVID-19 test set mentioned in the article.
 - PM2018_data.txt: Corresponds to the PM2018 test set mentioned in the article. It includes `mutation_id` for mutation number, `patient_id` for patient number, `epitope` indicating whether the mutation is immunogenic, `tpm` for the gene expression level of the mutation, `cell_line` for the renamed multi-allele combination of the patient, with the specific correspondence in PM2018_allelelist. `pepseq` represents the specific sequence of the mutation. Each mutation is represented by all 8-11mer slices containing the mutation site, with the highest prediction value among all slices representing the prediction score for that mutation.
 - PM2018_records.csv: Records the prediction scores of each method for every mutation with TPM&gt;0.
 - PM2018_allelelist: Records the multi-allele combinations expressed by each patient in PM2018.
 - RV2023_data.txt, RV2023_records.txt, RV2023_allelelist: Same as PM2018

------------------------------------------------------
Common:

- allelelist: Records the specific MHC-I molecule combinations corresponding to the names of the multi-allele combinations (cell line) used in the MA data.
- MHC_pseudo.dat: Records the 34-mer pseudo sequences of MHC-I molecules.
- eval.py: Evaluation script used to compile various metrics from the records of each test set.
DOI: 10.17632/kzywcjt93m
title: Symptomatic upper urinary tract obstruction in a resource-poor region

description: This data is generated from retrospective review of medical records of patients who presented with symptomatic upper urinary tract obstruction at the University of Nigeria Teaching Hospital Enugu and Hansa Clinics and Diagnostic Centre Enugu, southeast Nigeria. Medical records from January 2011 to November 2017 were included in this dataset.
DOI: 10.17632/nn8hz7fztb
title: LINF_360042700

description: short chain dehydrogenase-like protein
Leishmania infantum (strain JPCM5)
DOI: 10.17632/pzjc2kxpwt
title: Thickness Gradient Pulloff Study - FEA Stress Results

description: Normal stresses in the direction of pulloff loading along the edge of a thin polymer coating near the polymer/epoxy interface. Produced from an FEM created in ANSYS. The study explored a range of average thicknesses, coating thickness gradient, and Poisson's ratio. Raw file contains columns with edge position and normal stress. Processed file contains the same data, normalized by epoxy stud radius in the case of the edge position and the applied stress in the case of the normal stress.
DOI: 10.17632/snvvrc8ymd
title: Life-long exposure to hypoxia affects metabolism and respiratory physiology across life stages in high-altitude deer mice (Peromyscus maniculatus) Supplemental Data

description: Supplemental data for the paper "Life-long exposure to hypoxia affects metabolism and respiratory physiology across life stages in high-altitude deer mice (Peromyscus maniculatus) " by Ivy, C.M. and Scott, G.R.