cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27020455.v6
title: <b>Assessment of computational methods in predicting TCR-epitope binding recognition</b>

description: T-cell receptors (TCRs) are critical for the immune system's ability to recognize specific epitopes. Accurate prediction of TCR-epitope interactions is fundamental for understanding and enhancing immune responses. Despite significant advances in computational methods for TCR-epitope binding prediction, a thorough evaluation of these tools remains lacking. Here, we assessed 50 state-of-the-art TCR-epitope prediction models using 21 datasets covering 762 epitopes and over 105,909 bound TCR sequences. Our analysis revealed that while the ratio of positive to negative samples subtly influences performance, the source of negative TCR samples significantly impacts model accuracy. External negative data may introduce uncontrolled confounders, compromising evaluation reliability. A positive correlation between the number of TCRs per epitope and model performance highlights the importance of large, diverse datasets. Multi-feature models generally outperform single CDR3β models, but generalization to unseen epitopes remains a challenge across all evaluated models. Using independently sourced test sets, which offer practical predictions for real-world applications, for both seen and unseen epitopes is crucial for objective performance assessment. These insights would guide the development of more accurate and robust computational tools for TCR-epitope interaction prediction, accelerating advancements in this evolving field.
DOI: 10.6084/m9.figshare.28302875.v1
title: Human bone marrow mononuclear cells

description: The gene expression portion of the NeurIPS 2021 challenge 10x multiome dataset (Luecken et al., NeurIPS datasets and benchmarks track 2021), originally obtained from GEO. Contains single-cell gene expression of 69,249 cells for 13,431 genes. The <code>adata.X</code> field contains normalized data and <code>adata.layers['counts']</code> contains raw expression values. We computed a latent space using scANVI (Xu et al., MSB 2021), following their tutorial.
DOI: 10.6084/m9.figshare.7420265.v1
title: Combination of fixative agents and fixation times to visually differentiate the cortical from the medullary layer in bovine adrenal glands

description: Abstract Chronic stress exposure commonly increases adrenals weight and changes their morphology. This study aimed to compare four methods to delimitate the cortical and medullary layers of adrenals glands in Nelore bulls. Fresh adrenals did not present differentiation between layers. Then, frozen adrenals were distributed in plastics bags with fixative Bouin (G1), 96ºGL ethylic alcohol (G2), 10% formaldehyde (G3), or 2.5% glutaraldehyde (G4). After 12 hours of fixation, the G1 adrenal glands did not show the entire cortical layer marked by Bouin’s solution. For G2 and G3 there was a poor contrast, while for G4 there was a reasonable contrast. After 24 hours of fixation, G1 had an excellent contrast between layers, while G2 and G4 had a reasonable contrast and G3 a very bad contrast. After 48 hours it was difficult to differentiate cortical and medullar layers for G1; for Group 2 we get a reasonable contrast; and for G3 the contrast was bad. For G4 the contrast was not as sharp due to the medulla became dark. It was concluded that fixation of adrenals must be done in Bouin’s solution for 24 hours to obtain an effective evaluation of the adrenals’ morphometry.
DOI: 10.17632/5t8p3rwhxb
title: Data for: Numerical study of the effect of vascular bed on heat transfer during high intensity focused ultrasound (HIFU) ablation of the liver tumor

description: This is a sample file of simulations in Comsol Multiphysics 5.3 and is related to the case of a tumor embedded in the vascular bed with a density of 0.2.
DOI: 10.17632/7n2sgxrtm5
title: Data for: Trade Policy toward Supply Chains after the Great Recession

description: How does trade policy treat intermediate inputs relative to other imported products? Slow economic and trade growth during the recovery from the Great Recession, as well as recent political developments in the United Kingdom and the United States, pose a threat to cross-border supply chains and have thus brought this question to the forefront of policy circles. By examining new and detailed data on the Group of 20 (G-20) countries, this paper investigates trade policy use through 2016, with special emphasis on changes in policymaking behavior since 2010. First, there is no evidence that the G-20 economies made significant changes to their applied import tariffs during this period. However, there has been a modest increase in import protection arising through other policy instruments of note such as the temporary trade barriers (TTBs) of antidumping, countervailing duties, and safeguards. More importantly, there is evidence of changes in how countries have applied their TTBs. TTBs were increasingly imposed on imports not only from China but also from other countries, reversing a post-2001 trend. Furthermore, TTB protection has moved away from imports of final goods and toward imports of intermediate inputs. These shifts in policy have several potential contributing causes as well as economic consequences, including for cross-border supply chains.
DOI: 10.17632/bzhmmfymsb
title: Fire Extinguisher

description: This dataset contains 668 images of fire extinguishers captured in diverse environments and lighting conditions. It is designed for object detection and classification tasks, helping in the development of safety monitoring systems, robotics, and computer vision models that require accurate identification of fire safety equipment. The dataset includes varying angles, backgrounds, and distances to ensure robustness in real-world applications.
DOI: 10.17632/dmtv7gvvf7
title: Population Dynamics and Nesting Ecology of Black-headed Ibis (Threskiornis melanocephalus Latham, 1790) in Anand District, Central Gujarat, India

description: Black-headed Ibis (Threskiornis melanocephalus Latham, 1790), also known as Oriental White Ibis, Indian White Ibis, and Black-necked Ibis, is a species of wading bird of ibis family Threskiornithidae, breeds in South and Southeast Asia from India to west and as far east as Japan. It is the only native ibis species in its range that has an overall white plumage with a black neck and head. The down-curved beak and legs are also black. Though often referred to as a wetland species, the black-headed ibis also forages in natural and man-made habitats. This species of ibis nests only during the rainy season. To understand population trend, nesting ecology, and potential habitats of this species, nine months (March-September, 2023) field study was undertaken in eight Talukas of Anand District, Central Gujarat, India. Among physical, phytological and ornithological parameters, following findings were observed and recorded [Refer Data File: 2024 Mendeley Data Elsevier Black-headed Ibis Population Dynamics Nesting Ecology Hiren B Soni.pdf (Attached)]. Plant Height (m) (Min. 3.10-March, Max. 6.90-April, Mean: 5.51), Plants (N=129) (Min. 4.00-September, Max. 35.00-August, Mean: 18.43), Plants (N=129) (Min. 4.00-September, Max. 35.00-August, Mean: 18.43), Nests (N=1518): Min. 64.00-September, Max. 404.00-April, Mean: 216.86, Individuals (N=2742): Min. 108.00-September, Max. 780.00-April, Mean: 391.71), Nest Height (m): Min. 2.20-March, Max. 6.20-April, Mean: 4.73), Outer Canopy (N): Min. 57.00-September, Max. 376.00-April, Mean: 202.71), Inner Canopy (N): Min. 7.00-March & September, Max. 42.00-September, Mean: 14.14), Upper Canopy (N): Min. 36.00- September, Max. 248.00-April, Mean: 138.14), Middle Canopy (N): Min. 16.00- August, Max. 154.00-March, Mean: 65.57), Lower Canopy (N): Min. 2.00- May, Max. 56.00-March, Mean: 14.57), Birds (N=1528): Min. 64.00- September, Max. 404.00-April, Mean: 218.29), Nest Position: North (Min. 11.00-June, Max. 122.00-April, Mean: 63.57), East (Min. 22.00-September, Max. 187.00-March, Mean: 90.14), South (Min. 6.00-June, Max. 75.00-April, Mean: 20.00), West (Min. 20.00-September, Max. 100.00-March, Mean: 42.29), Nesting Birds (N=1512): Min. 64.00-September, Max. 404.00-April, Mean: 216.00). This ‘Near Threatened’ species is undergoing a population reduction, which is suspected to be moderately rapid, and faces threats like hunting and disturbance at breeding colonies to drainage and conversion of foraging habitats to agriculture. It is vulnerable to drainage, disturbance, pollution, agricultural conversion, destruction of roosting and nesting sites, hunting, and collection of eggs and nestlings from colonies. Regular monitoring the population across its range, colonies at agricultural land, assessing effects of threats on population levels, and conducting local education programmes to discourage hunting and disturbance to encourage the protection of nesting areas in Anand District, Central Gujarat, India is warranted.
DOI: 10.17632/tngf9w3pgd
title: C. elegans AWA Olfactory Neurons Fire Calcium-Mediated All-or-None Action Potentials

description: Raw electrophysiological recording traces and calcium imaging movies shown in this paper and accompanying analyzed data.
DOI: 10.6084/m9.figshare.10264805.v2
title: Raw Data: Production and characteristics of fish protein hydrolysate from parrotfish (Chlorurus sordidus) head

description: The data for Production and characteristics of fish protein hydrolysate from parrotfish (Chlorurus sordidus) head
DOI: 10.6084/m9.figshare.21511401.v1
title: Supplementary Material for: Local recurrence in choroidal melanomas following Robotic assisted Radiosurgery (CyberKnife)

description: Background: Tumor recurrence in choroidal melanoma has been associated with decreased overall survival due to metastatic spreading. To detect risk factors of local recurrence and side effects, we analyzed tumor planning and treatment parameters in patients with recurrence of choroidal melanoma after treatment with robotic-assisted radiosurgery (CyberKnife). Methods: 694 patients treated with CyberKnife between 2005 and 2019 were retrospectively reviewed. Age, gender, best-corrected visual acuity (BCVA), tumor height and diameter were recorded. Treatment planning and radiation doses were reviewed. Salvage therapy, overall survival, metastasis, and complications were recorded. Results: 74 patients showed local recurrence. Local recurrence occurred after 42.1 months post CyberKnife treatment (mean; range: 5 – 100 months). 14 out of 74 patients (18.9%) died during follow-up. Recurrence treatment included enucleation in 51 patients (68.9%) and radiosurgery in 19 patients (25.7%). Treatment planning without contrast medium MRI, radiation dose of less than 21 Gy and insufficient margin delineation were identified as risk factors incrementing local control. Discussion: Robotic assisted radiosurgery (CyberKnife) is a suitable treatment option for large choroidal melanoma up to 12mm. Patients with significantly better visual acuity received repeat Cyberknife treatment as salvage therapy and showed an eye retention rate of 81%.
DOI: 10.6084/m9.figshare.29094443.v2
title: Assemble sequence and RNA-seq of Malus micromalus

description: Assemble sequence and RNA-seq of Malus micromalus
DOI: 10.6084/m9.figshare.29137427.v1
title: Supplementary Material for: Towards Patient Involvement and Representation in the Governance of Genomic Data Archives: Deliberative forums with patients in Germany

description: Introduction: 
Although it is generally agreed that the perspectives of patients should be included in decision-making about genomic data, patients rarely have a significant role in the governance of genomic data archives (GDAs). Guidance on the successful implementation of patient involvement (PI) in the governance of GDAs is lacking. This study explores the perspectives of German patients on PI in the governance of GDAs and how these perspectives can be implemented to have an impact on governance.

Methods: 
We conducted two online deliberative forums with 26 members of the cancer and rare diseases (RD) communities in Germany. The forums were analyzed qualitatively. The findings were discussed in a follow-up dialogue event with 17 of the participants and members of a GDA (The German Human Genome-Phenome Archive, GHGA) (n=9). Two patient co-researchers were involved in all phases of the study.

Results: 
Five themes were identified: (a) motivations for PI; (b) concerns about PI; (c) areas of governance in which PI is required; (d) resources necessary for implementation of PI; and (e) the form PI should take. 

Conclusion:
For PI in GDAs to be meaningful, patient perspectives on the specific contextual aspects of GDAs should be actively sought. Patients’ views on representation affect what form of PI they prefer and whether they experience the representation as legitimate. We discuss how the suggestions from the participants of this study were taken up in the governance policy of the GHGA.
DOI: 10.17632/2r3sv6vtwz
title: Juvenile Idiopathic Epilepsy in Arabian horses is not a single-gene disorder

description: Juvenile Idiopathic Epilepsy is characterized by tonic-clonic seizures in young Egyptian Arabian foals.  The common signs include, disorientation and seizures which can sometimes lead to death and temporary blindness. Some foals grow out of the condition while others do not. Based on veterinary diagnosis, we included 180 horses (60 cases, 120 controls) for genotyping on the Affymetrix 670k genotyping array.  A GWAs was performed on a genetically matched 1:2 case/control set, totaling 180 individuals using a GRM. We also performed two separate GWAS for coat color to test the efficacy of the JIE GWAS. This dataset includes genotypes for horses that passed the minor allele frequency of 0.05 and genotyping rate above 95%.
DOI: 10.17632/2y538xxs2w
title: Good and Bad classification of Brassica Oleracea flower (Cauliflower)

description: For the project titled "Good and Bad Classification of Brassica oleracea Flower (Cauliflower)," a comprehensive dataset has been compiled containing 1,000 samples of Marsh Barbel Leaves, equally divided into 500 good samples and 500 bad samples. This dataset serves as the foundation for developing a classification model aimed at distinguishing between good and bad samples of cauliflower flowers based on their associated Marsh Barbel Leaves.

### Data Description

The dataset comprises the following key features:

1. *Image Data*:
 - Each sample includes high-resolution images of Marsh Barbel Leaves.
 - Images are standardized in terms of resolution and format to ensure consistency.
 - Various angles and lighting conditions are considered to mimic real-world scenarios.

2. *Leaf Quality Label*:
 - Each image is annotated with a binary label indicating its quality:
 - 0 for bad samples.
 - 1 for good samples.
 - Labels are determined by expert agronomists to ensure accuracy.

3. *Visual Attributes*:
 - *Color*: Variations in leaf color, ranging from healthy green to diseased yellow or brown, are noted.
 - *Texture*: Differences in leaf surface texture, including signs of wilting or crispness.
 - *Shape*: Anomalies in leaf shape, such as irregular edges or deformities.
 - *Spots and Lesions*: Presence of spots, lesions, or other visible signs of disease or pest infestation.

4. *Metadata*:
 - *Capture Date and Time*: Timestamp for when each image was captured.
 - *Location*: Geographical data indicating where the leaf samples were collected.
 - *Weather Conditions*: Environmental factors at the time of capture, which might influence leaf quality.
 - *Growth Stage*: The developmental stage of the cauliflower plant, which can impact leaf appearance.

### Data Collection and Preprocessing

1. *Collection Method*:
 - Leaves were collected from various cauliflower fields to ensure diversity in the dataset.
 - Images were taken using high-resolution cameras under controlled conditions.

2. *Preprocessing Steps*:
 - *Image Normalization*: All images are resized to a uniform dimension to facilitate model training.
 - *Data Augmentation*: Techniques such as rotation, flipping, and scaling are applied to increase the dataset's variability and robustness.
 - *Label Encoding*: Quality labels are encoded as binary values to simplify the classification task.

### Dataset Utilization

This dataset is intended to train and evaluate machine learning models for the classification of Marsh Barbel Leaves quality, which indirectly assesses the health of Brassica oleracea flowers (cauliflower). The ultimate goal is to develop a reliable system that can aid farmers and agronomists in early detection of diseases or deficiencies in cauliflower crops, leading to timely interventions and improved crop yield.

### Potential Applications

- *Automated Crop Monitoring*: Integration of the model into automated systems for continuous mon
DOI: 10.17632/43b6p5czjr
title: Complementary and Alternative Medicine in Dermatomyositis: A Scoping Review: PRISMA DIAGRAM

description: Preferred Reporting Items for Systematic Reviews and Meta-analyses Flow Diagram (PRISMA)
DOI: 10.17632/byxw9bx73y
title: supplementary materials to https://doi.org/10.1016/j.jenvman.2020.111252

description: This data describes the supplementary materials (additional Figures, and Tables) for the article https://doi.org/10.1016/j.jenvman.2020.111252 
Thermoacidophilic effective microbes (tEM) were used to enhance the composting process of lignocellulosic waste. Composting with tEM slightly reduced NH3 emission during the composting process while CH4, and CO2 patterns positively correspond to the rate of composting, with higher emissions in tEM treatment during 60d – 90d composting. Compost microbial evolution based metagenomic DNA sequencing and culture-based microbial enumeration indicate higher abundance and diversity of microbes in tEM treated groups especially at thermophilic temperatures. Chemical analysis showed higher rate of mineralization in tEM treated compost compared to control group while the heavy metal content was below the international threshold levels in both treatment and control. Moreover, germination index (Gi) and global germination index (GI) were higher in tEM treated compost compared to control group. The data is important for evaluating composting efficiency and quality of the final compost product.
DOI: 10.17632/db7w3ztdj9
title: Periorificial dermatitis continues to be associated with corticosteroid use: A 15-year single center retrospective cohort study

description: Periorificial dermatitis (POD) has historically been associated with topical corticosteroid use. Despite greater awareness and education on safer corticosteroid use, patients continue to present with POD, prompting a reassessment of risk factors for POD and analysis of whether corticosteroid use continues to be associated with this condition. 
Objective: To identify trends in corticosteroid-related POD over time, other predisposing factors, and treatments used in subjects presenting with POD. 

A Single-center retrospective cohort study of all subjects diagnosed with periorificial dermatitis and treated by dermatologists at UMass Memorial Health from 2008-2023. Data on subject demographics, corticosteroid use, other common predisposing factors, treatment modalities, and frequency of resolution were collected.
DOI: 10.17632/hty66ngw5g
title: Linear response approach to collective electronic excitations of solids and surfaces

description: Abstract We have developed a parallel computer program for the study of dynamic response of periodic systems. It computes the linear response of an interacting many-electron system from its ground-state electronic structures, which are obtained from ab initio band structure calculations in the plane-wave and pseudopotential scheme. As test examples, we applied this program to calculate the linear response of bulk aluminum and a beryllium monolayer. The excitation spectra show prominent plasmon resonan... Title of program: Dresponse Catalogue Id: AECK_v1_0 Nature of problem The dynamic response of bulk and surface systems. It is usually dominated by collective electronic excitations (plasmons) at low-energy range. Versions of this program held in the CPC repository in Mendeley Data AECK_v1_0; Dresponse; 10.1016/j.cpc.2008.10.019 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.17632/nntck7ddgt
title: EVALUATING PATIENT READMISSION RISK: A DATA MINING APPROACH

description: Citation: Cite the attached article and this dataset. Structure: 55 attributes; 100,000 instances; Missing values = Yes Source: The data are submitted on behalf of the Center for Clinical and Translational Research, Virginia Commonwealth University, a recipient of NIH CTSA grant UL1 TR00058 and a recipient of the CERNER data. John Clore (jclore '@' vcu.edu), Krzysztof J. Cios (kcios '@' vcu.edu), Jon DeShazo (jpdeshazo '@' vcu.edu), and Beata Strack (strackb '@' vcu.edu). This data is a de-identified abstract of the Health Facts database (Cerner Corporation, Kansas City, MO). Data Set Information: The dataset represents 10 years (1999-2008) of clinical care at 130 US hospitals and integrated delivery networks. It includes over 50 features representing patient and hospital outcomes. Information was extracted from the database for encounters that satisfied the following criteria. (1) It is an inpatient encounter (a hospital admission). (2) It is a diabetic encounter, that is, one during which any kind of diabetes was entered to the system as a diagnosis. (3) The length of stay was at least 1 day and at most 14 days. (4) Laboratory tests were performed during the encounter. (5) Medications were administered during the encounter. The data contains such attributes as patient number, race, gender, age, admission type, time in hospital, medical specialty of admitting physician, number of lab test performed, HbA1c test result, diagnosis, number of medication, diabetic medications, number of outpatient, inpatient, and emergency visits in the year before the hospitalization, etc.
DOI: 10.17632/sc8xh8m8vh
title: PSQI data in HIV and healthy controls

description: Data used in manuscript, "Poor subjective sleep reported by people living with HIV is associated with impaired working memory".
DOI: 10.17632/ztpvzc6kkd
title: Hydrothermal Alteration of IOM and syn-IOM

description: Dataset from experiments conducted on syn-IOM and IOM samples with water (approximately 1:1 by weight) at high pressures and temperatures.
DOI: 10.6084/m9.figshare.12518354.v1
title: JVASP-17046 to JVASP-18015

description: JARVIS-DFT input/output files
DOI: 10.6084/m9.figshare.1460718.v1
title: Changes in the spatial patterns of human appropriation of net primary production (HANPP) in Europe 1990–2006

description: Changes in patterns of land use intesification (HANPP) in Europe between 1990 and 2006. Dataset used in Plutzar et al. (2015) Changes in the spatial patterns of human appropriation of net primary production (HANPP) in Europe 1990–2006. Regional Environmental Change. DOI 10.1007/s10113-015-0820-3 The global dataset is available here: https://www.uni-klu.ac.at/socec/inhalt/1191.htm
DOI: 10.6084/m9.figshare.16606850.v1
title: A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments

description: Training and validation set of papar "A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments"
DOI: 10.6084/m9.figshare.23431850.v1
title: 3-D P-wave Velocity Model of Central Sulawesi, Indonesia

description: P-wave seismic velocity (Vp) model of central Sulawesi, Indonesia, particularly along the rupture zone of 2018 Palu earthquake resulted from local earthquake tomography study.