cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125162.v1
title: Supplementary Material for: High Proportions of CD4+ T Cells among Residual Bone Marrow T Cells in Childhood Acute Lymphoblastic Leukemia Are Associated with Favorable Early Responses

description: Residual nonmalignant T cells in the bone marrow of patients with acute leukemias may be involved in active immune responses to leukemic cells. Here, we investigated the phenotypic signature of T cells present at diagnosis in 39 pediatric patients with acute lymphoblastic leukemia (ALL) treated within standardized ALL-BFM study protocols. Previously described age associations of lymphocyte subpopulations in the peripheral blood of healthy children were reproduced in leukemic bone marrow. Analysis of individual lymphocyte parameters and risk-associated variables using univariate linear regression models revealed a correlation of higher CD4/CD8 ratios at diagnosis with a favorable bone marrow response on day 15. Separate analysis of CD4+ cells with the CD4+CD25<sup>hi</sup>FoxP3+ T<sub>reg</sub> cell phenotype showed that the association was caused by non-T<sub>reg</sub> CD4+ cells. The association of higher CD4/CD8 ratios with a favorable bone marrow response on day 15 of treatment persisted in a cohort extended to 69 patients. We conclude that CD4+ non-T<sub>reg</sub> cells in leukemic bone marrow at diagnosis may have a role in early response to treatment. Prospective analysis of the CD4/CD8 ratio in a large cohort of pediatric patients is now needed. Moreover, future experiments will establish the functional role of the individual T cell subsets in immune control in pediatric ALL.
DOI: 10.17632/4gpbv5vpcr
title: Reprogramming liver metastasis-associated macrophages towards an anti-tumoral phenotype through enforced miR-342 expression

description: Upon metastatic seeding in the liver, liver macrophages, including Kupffer cells, acquire a transcriptional profile typical of tumor-associated macrophages (TAMs), which support tumor progression. MicroRNAs (miRNAs) fine-tune TAM pro-tumoral functions, making their modulation a promising strategy for macrophage reprogramming into an anti-tumoral phenotype. Here, we analyze the transcriptomic profiles of liver and splenic macrophages, identifying miR-342-3p as a key regulator of liver macrophage function. miR-342-3p is highly active in healthy liver macrophages but significantly downregulated in colorectal cancer liver metastases (CRLMs). Lentiviral vector-engineered liver macrophages enforcing miR-342-3p expression acquire a pro-inflammatory phenotype and reduce CRLM growth. We identify Slc7a11, a cysteine-glutamate antiporter linked to pro-tumoral activity, as a direct miR-342-3p target, which may be at least partially responsible for TAM phenotypic reprogramming. Our findings highlight the potential of in vivo miRNA modulation as a therapeutic strategy for TAM reprogramming, offering an approach to enhance cancer immunotherapy.

Data and code availability: Next-generation sequencing data are deposited at the Gene Expression Omnibus (GEO) with the following accession numbers: GEO: GSE274043 (scRNA-seq), GSE274044 (RNA-seq on iKCs), GSE274045 (small RNA-seq on splenic and hepatic cell populations), and GSE274046 (bulk RNA-seq on splenic and hepatic cell populations). The code is available at GitLab: http://www.bioinfotiget.it/gitlab/custom/Bresesti_Cell_Reports_2025.
DOI: 10.6084/m9.figshare.17030054.v1
title: Genome sequences of Jasminum sambac cultivars provide insights into the evolution of aroma compound biosynthesis

description: The Jasminum sambac genome sequence, CDS sequence, protein sequence, gene and repeat gff files
DOI: 10.6084/m9.figshare.22583749.v2
title: Supplemental Table 1: Summary of Quality Control of Sequence

description: Summary of quality control metrics of raw sequencing data obtained from FastQC application. Alias: sample names; Seq.length: sequence length; GC(%): percentage of GC content; Dup(%): percentage of duplicate reads; Total Reads: Total number of reads obtained; Total Read pairs: Total number of read pairs; Mapped Read Pairs: Number of reads that mapped to either the genome or junction reference database; Mapped Read pairs (Junction): Mapped Junction Reads and percentage (Mapped Junction Reads/Total number of reads); Gene counts: Number of reads mapped to a gene; Exon counts: Number of reads mapped to an exon. Analysis provided by Mellowes Center for Genomic Sciences and Precisions Medicine at the Medical College of Wisconsin.
DOI: 10.6084/m9.figshare.28684610.v4
title: Figure 6 source images

description: <b>Figure </b><b>6</b><b>. </b><i>In vivo</i> spatiotemporal dynamics of mCCL2 during LPS-evoked systemic inflammation and laser-induced ablation injury.
DOI: 10.6084/m9.figshare.4649277.v1
title: The Drosophilidae (Diptera) of western Victoria, Australia

description: The Drosophilidae (Diptera) fauna of Australia is largely restricted to rainforests, moist temperate forests, and ecological niches that afford some relief from desiccation stress. Tropical Queensland has 255 described species in 35 genera, subtropical NSW 138 species in 21 genera, temperate Victoria 42 species in 8 genera, cold-temperate Tasmania 21 species in 5 genera, and dry-temperate South Australia 17 species in 4 genera. Western Victoria has 19 species in 5 genera (Table 1); only <i>Drosophila prodispar</i> (in the <i>D. setifemur</i> species group, subgenus <i>Sophophora</i>) is endemic to this region. About half of the species known from western Victoria are drawn to fruit baits (e.g., rotting-banana bait), the remainder, including <i>D. prodispar</i>, may only be collected using a sweep net or Malaise trap (Table 1). Table 2 gives the detailed results of collecting in western Victoria in February 2016. Voucher specimens are held in the Australian Museum, Sydney. <i>Drosophila prodispar</i> remains rare (only 11 specimens are known, all in AMS and ANIC, see Table 3), no further material was collected during the present survey. The author acknowledges the State Government of Victoria, Department of Environment, Land, Water & Planning for permission to collect and the Australian Museum Research Institute, Sydney.
DOI: 10.6084/m9.figshare.19312094.v1
title: Wine PDO map

description: The map of the 1177 wine PDO areas in Europe, defined based on the official EU geographical indication register e Ambrosia.
DOI: 10.17632/bt9sjgnkh3
title: slope stability analysis

description: A dataset comprising the soil properties and geometric characteristics for slope stability analysis.
DOI: 10.6084/m9.figshare.28771382.v1
title: Expanded Skin Microbial Genome Collection (eSMGC) genome database

description: Genome collection of skin microbiota derived from the study <i>'Geographic Variation and Host Genetics Shape the Human Skin Microbiome'</i>https://www.biorxiv.org/content/10.1101/2025.05.01.651599v1<br>
DOI: 10.17632/7n63b5r87v
title: Panel Data for DEA and Econometric Analyses

description: This study used two inputs variables; total hydropower installed capacity (megawatts per hour) and long-term average annual precipitation (in volume), and inputs costs; mean renewable energy feed-in tariffs (USD), and dam capacity per capita. One output variable which is hydroelectricity generation (terawatts per hour), was used to measure the cost-efficiency and its decompositions. Static panel regression analysis in the second stage with a partial log form of the variables in each of the three model estimated. where Cost Eﬃciency (CE) of country (i) in period (t) obtained from the DEA in the first stage, inflation rate based on consumer price index (INF), log of gross domestic product (GDP), log of labour input (numbers of labours), investment proxy for research & development (INV).
DOI: 10.17632/xfxnssythy
title: Dataset for the research article "Acquisition of L3 English past perfect, present progressive, and present perfect tenses by L1 Kirundi-L2 French bilinguals"

description: The present data were used to check through the LPM the effect of CLI in the acquisition of L3 English past perfect, present progressive, and present perfect tenses by L1 Kirundi-L2 French bilinguals.  The subtractive language groups design was used: One trilingual (L1 Kirundi-L2 French-L3 English learners) group was compared to two bilingual (L1 Kirundi-L2 English and L1 French-L2 English learners) groups in order to derive which previously acquired language was driving CLI among L3 learners. Each language group had 30 learners distributed in four proficiency groups, namely the pre-intermediate group (6 participants), lower-intermediate group (7 participants), upper-intermediate group (11 participants), and advanced group (6 participants). Therefore, there were two independent variables (language group and proficiency group) and three continuous dependent variables which were the participants' scores on the three target structures, namely the past perfect, present progressive, and present perfect tenses.

The following predictions were tested:

1. With regard to the past perfect tense (L1=L2=L3), learners of L3 English with a background knowledge in L1 Kirundi and L2 French are likely to have no difficulty in the acquisition of the said tense in English regardless of their English proficiency level; i.e. even lower proficiency learners will perform well on that tense. However, higher proficiency learners may make most correct use of this tense. 

2. With regard to the present progressive tense (L1≠L3≠L2), we can predict that all the three language groups, i.e. L1 Kirundi, L1 French and L3 groups, will face difficulties in their performance on this tense. In other words, none of the previously acquired languages (neither L1 Kirundi, nor L2 French) is expected to significantly affect the performance of L3ers on the said tense. Lower proficiency learners are predicted to face most difficulty on the tense.

3. With regard to the present perfect tense (L3=L2≠L1), we can predict that the L3 group will perform similarly as the L1 French group, while the two groups are likely to outperform the L1 Kirundi group. This implies that facilitative CLI is expected from L2 French in the L3 group.

4. Considering the present research scenarios for the past perfect (L1=L2=L3), present perfect (L1=L3≠L2), and present progressive (L1≠L2≠L3) tenses, we predict CLI where L3 learners are expected to acquire the past perfect earlier than the present perfect, and the present perfect earlier than the present progressive. In other words, their performance on the past perfect tense should be significantly higher than that on the present perfect while their score on the present perfect is expected to be significantly higher than that on the present progressive. 

Data were elicited through the grammaticality judgment task, and the raw data analyzed in the SPSS software using descriptive statistics, MANOVA, post-hoc comparisons, and independent samples t-tests.
DOI: 10.6084/m9.figshare.20001575.v2
title: TCGA.zip

description: Gene expression data from TCGA
DOI: 10.6084/m9.figshare.26506837.v3
title: Exploring Filipino Medical Students’ Attitudes and Perceptions of Artificial Intelligence in Medical Education: A Qualitative Mixed-Methods Study

description: The data shows the specific and summarized results of the quantitative and qualitative methods employed in the study entitled, "Exploring Filipino Medical Students’ Attitudes and Perceptions of Artificial Intelligence in Medical Education: A Qualitative Mixed-Methods Study". This includes the raw, anonymized survey results, transcript of the focus group discussions conducted, and diagrammatic summaries of the results.
DOI: 10.17632/5bfvmtfxgs
title: Interaction of 4-ethyl phenyl sulfate with bovine serum albumin: Experimental and molecular docking studies

description: 4-ethyl phenyl sulfate (EPS), a protein-bound uremic toxin found in serum of patients suffering from autism spectrum disorders (ASD) and chronic kidney disease (CKD). As per recent advances in the field, gut metabolites after their formation goes to blood stream crosses blood brain barrier and causes neuro related problems. Increased levels of 4-EPS in human body causes anxiety in patients and its role remains elusive. 4-EPS interacts with serum albumin in human body and thus, a model study of interaction of BSA with 4-EPS is presented in support of it. Absorption spectroscopy result demonstrated decrease in bovine serum albumin (BSA) absorption upon interaction with increasing concentration of EPS in a range from 2 µM to 100 µM. Moreover, this interaction was confirmed by the fluorescence quenching in presence of metabolite. The change in secondary structure was demonstrated by circular dichroism, synchronous fluorescence and Fourier transform infra-red spectroscopy. Docking studies reveals binding score of −5.28 Kcal mol−1, demarking that 4-EPS is involved in interaction with BSA via amino acid residues, forming the stable complex. This interaction study may be helpful in devising strategies for the treatment of chronic kidney disease and other neuro related diseases, by producing synthetic compound that competes with albumin binding sites to allow 4-EPS clearance from the body.
DOI: 10.17632/spcvbphfdn
title: Fatigue test data of S355 steel and 7075-T651 aluminum alloy subjected to in-phase multiaxial cyclic loading with superposed static components

description: The provided data set includes the applied nominal stress amplitudes and mean values of cyclic loading, and the number of cycles to failure defined as a 20% drop in specimen stiffness. The hourglass-shaped specimens were subjected to cyclic uniaxial plane bending, torsion, and their in-phase combination. The data were collected to verify the multiaxial fatigue life prediction models of parametric form (standard models) and the recently developed model based on the Gaussian process (Karolczuk, A.; Słoński, M. Application of the Gaussian process for fatigue life prediction under multiaxial loading. Mech. Syst. Signal Process. 2022, 167, 108599). The full description of experimental tests can be found in Kluger, K.; Karolczuk, A.; Derda, S. Application of life-dependent material parameters to fatigue life prediction under multiaxial and non - zero mean loading. Materials (Basel). 2020, 13.
DOI: 10.17632/w595yr9pmk
title: Anti-herbivore silicon defences in a model grass are greatest under Miocene levels of atmospheric CO2

description: This dataset is an excel file relating to the impact of atmospheric CO2 on grass (Brachypodium distachyon) silicon (Si) accumulation and the consequences for insect herbivore (Helicoverpa armigera). This study mainly focused on the hypothesis that reduced CO2 can increase Si in a grass and vice versa under elevated CO2. Moreover, we hypothesised that the variation in Si accumulation under extreme CO2 conditions can affect insect herbivore differently. In our present study, we found that reduced CO2 increased foliar Si accumulation, which was associated with decreased herbivore performance relative to elevated CO2.
DOI: 10.6084/m9.figshare.9923948.v1
title: Supplementary Material for: Clinical Significance of Galactose-Deficient IgA1 by KM55 in Patients with IgA Nephropathy

description: <b><i>Background:</i></b> Aberrant galactose-deficient IgA1 molecules (Gd-IgA1) are important causal factors in IgA nephropathy (IgAN); however, the detection of Gd-IgA1 in IgAN is complicated and instable. A monoclonal antibody, KM55, which specifically recognizes Gd-IgA1 has been developed. In the present study, we further explored the clinical significance of Gd-IgA1 using KM55. <b><i>Methods:</i></b> In this study, we enrolled 75 patients with IgAN and 80 healthy controls and detected the plasma Gd-IgA1 levels using the KM55 ELISA method. We also stained ­mesangial Gd-IgA1 deposition using KM55. <b><i>Results:</i></b> We observed that the levels of plasma Gd-IgA1 in IgAN patients were elevated compared to the corresponding levels of healthy controls. Patients were divided into 2 groups based on the median of Gd-IgA1. Patients with high Gd-IgA1 levels had significantly higher levels of uric acid (UA) and IgA. The other clinical manifestations demonstrated that there were no differences in age, sex, blood pressure, initial proteinuria, hematuria, estimated glomerular filtration rate and Oxford pathological classification between the 2 groups of patients. In addition, positive correlations were observed between Gd-IgA1 and Bb, C3a, C4d and MAC. Mesangial Gd-IgA1 was positive in IgAN but negative in the normal renal tissue adjacent to neoplasm. We next analyzed the correlation between plasma Gd-IgA1 and mesangial Gd-IgA1 deposition. The results showed that a high level of plasma Gd-IgA1 was related to the deposition of mesangial Gd-IgA1, although the difference was not significant. <b><i>Conclusion:</i></b> We verified the elevated level of plasma and ­mesangial Gd-IgA1 in patients with IgAN by KM55, which provided an alternative, easy, and reliable tool for diagnosis and activity assessment of IgAN. The level of plasma Gd-IgA1 positively correlated with levels of UA, total IgA levels, and complement activation products.
DOI: 10.17632/c2mjcst94p
title: Escala de evaluación de artículos con metodologías heterogéneas para revisiones integrativas

description: Recientemente ha sido publicada la escala de Evaluación de Artículos con Metodologías Heterogéneas para Revisiones Integrativas (EAMH), esta se generó en respuesta a la creciente necesidad de asegurar la calidad de los resultados en revisiones integrativas, la propuesta proporciona orientaciones sobre criterios básicos que cualquier artículo debe cumplir para ser incluidos en el análisis de los resultados.
DOI: 10.17632/dtpzbwwpm7
title: VegSeedsBD: A Comprehensive Image Dataset of Vegetable Seeds.

description: Type of data: 3456 x 4608 px images of vegetable seeds.
Data format: JEPG.

Dataset Contents: Original (raw) images of different varieties of vegetable seeds from single seed and bulk seeds perspectives.

Number of classes: Fifteen (15) varieties of common vegetable seeds – (1) Bitter Gourd, (2) Bottle Gourd, (3) Corn, (4) Cucumber, (5) Hyacinth Bean, (6) Malabar Spinach, (7) Okra, (8) Papaya, (9) Pea, (10) Pumpkin, (11) Ribbed Gourd, (12) Snake Gourd, (13) Sponge Gourd, (14) String Bean, and (15) Wax Gourd.

Total number of images: 4,500.

Distribution of instances: Number of images in VegSeedsBD dataset – 
(1) Bitter Gourd: Single Seed = 200 and Bulk Seeds = 100.
(2) Bottle Gourd: Single Seed = 200 and Bulk Seeds = 100.
(3) Corn: Single Seed = 200 and Bulk Seeds = 100.
(4) Cucumber: Single Seed = 200 and Bulk Seeds = 100.
(5) Hyacinth Bean: Single Seed = 200 and Bulk Seeds = 100.
(6) Malabar Spinach: Single Seed = 200 and Bulk Seeds = 100.
(7) Okra: Single Seed = 200 and Bulk Seeds = 100.
(8) Papaya: Single Seed = 200 and Bulk Seeds = 100.
(9) Pea: Single Seed = 200 and Bulk Seeds = 100.
(10) Pumpkin: Single Seed = 200 and Bulk Seeds = 100.
(11) Ribbed Gourd: Single Seed = 200 and Bulk Seeds = 100.
(12) Snake Gourd: Single Seed = 200 and Bulk Seeds = 100.
(13) Sponge Gourd: Single Seed = 200 and Bulk Seeds = 100.
(14) String Bean: Single Seed = 200 and Bulk Seeds = 100.
(15) Wax Gourd: Single Seed = 200 and Bulk Seeds = 100.

Dataset size: The total size of the dataset is 3.56 GB and the compressed ZIP file size is 3.36 GB.

Data acquisition process: Images of vegetable seeds are captured using a high-definition smartphone camera from different angles and the two perspectives of single seed and bulk seeds.
Data source location: Agro-industry grade seeds are collected from agricultural seed stores in Bangladesh.

Where applicable: Training and evaluating machine learning and deep learning models to distinguish varieties of common vegetable seeds in Bangladesh to support automated identification systems of various vegetable seeds.
DOI: 10.17632/cvbrftzfy5
title: BO: A unified tool for plasma waves and instabilities analysis

description: A unified numerically solvable framework for dispersion relations with an arbitrary number of species drifting at arbitrary directions and with Krook collision is derived for linear uniform/homogenous kinetic plasma, which greatly extended the standard one Stix (1992). The purpose of this work is to provide a kinetic plasma dispersion relation tool not only the physical model but also the numerical approach be as general/powerful as possible. As a very general application example, we give the final dispersion relations which assume further the equilibrium distribution function be bi-Maxwellian and including parallel drift, two directions of perpendicular drift (i.e., drift across magnetic field), ring beam and loss-cone. Both the electromagnetic and electrostatic versions are provided, with also the Darwin (a.k.a., magnetoinductive or magnetostatic) version. The species can be treated either magnetized or unmagnetized. Later, the equations are transformed to the matrix form be solvable by using the powerful matrix algorithm (Xie and Xiao, 2016), which is the first approach can give all the important solutions of a linear kinetic plasma system without requiring initial guess for root finding and thus can be extremely useful to the community. To the best of our knowledge, the present model is the most comprehensive one in literature for the distribution function constructed bases on Maxwellian, which thus can be applied widely for study waves and instabilities in space, astrophysics, fusion and laser plasma. We limit the present work to non-relativistic case.
DOI: 10.17632/fkbzpkm5pz
title: Customer Engagement Data

description: Customer Engagement Data from Social Media Users
DOI: 10.17632/j2mc3zzjx3
title: Raw data for manuscript "Recognition and combination of multiple cell-death features showed good predictive value in lung adenocarcinoma"

description: This dataste contains all the raw data and data analysis methods of our manuscript.
DOI: 10.17632/knj24fd366
title: The N-degron pathway mediates the autophagic degradation of cytosolic mitochondrial DNA during sterile innate immune responses. Jung et al.

description: The human body reacts to tissue damage by generating damage-associated molecular patterns (DAMPs) that activate sterile immune responses. To date, little is known about how DAMPs are removed to avoid excessive immune responses. Here, we show that proteasomal dysfunction induces the release of mitochondrial DNA (mtDNA) as a DAMP that activates the cGAS-STING pathway and is subsequently degraded through the N-degron pathway. In the resolution phase of sterile immune responses, DNA-PK senses cytosolic mtDNA and activates N-terminal (Nt-) arginylation by ATE1 R-transferases. The substrates of Nt-arginylation include the molecular chaperone BiP/GRP78 retrotranslocated from the endoplasmic reticulum (ER). R-BiP, the Nt-arginylated species of BiP, is associated with cytosolic mtDNA to accelerate its targeting to autophagic membranes for lysosomal degradation. Thus, cytosolic mtDNA activates the N-degron pathway to facilitate its own degradation to form a negative feedback loop, by which the cell can turn off sterile immune responses in a right time.
DOI: 10.17632/zm4pkcgbz8
title: Data for "Influence of Mental Health Curriculum Form on College Students’ Academic Adaptation: Chain Mediating Effect of Social Adaptation and Self-efficacy "

description: This is the dataset of the study "Influence of Mental Health Curriculum Form on College Students’ Academic Adaptation: Chain Mediating Effect of Social Adaptation and Self-efficacy", which includes the raw and analyzed data. Detailed information is available from the author (liujy2020@mail.tsinghua.edu.cn) on reasonable request.