cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7564634
title: CNN-SVM-based parasite egg counting

description: 1. trained weights for a CNN network to identify parasite eggs in McMaster fecal floatation microscope images. <br>2. MATLAB code to take CNN-processed images and extract morphometric parameters, which are then used in conjunction with an SVM classifier to count and type eggs.3. 3000+ test images for code validation and utilization by interested parties.<br>
DOI: 10.6084/m9.figshare.7564646
title: Adjuvant radiotherapy and chemotherapy in early-stage diffuse large B cell lymphoma of head and neck with extranodal involvement

description: <b>Objectives:</b> Diffuse large B cell lymphoma (DLBCL) is a heterogeneous lymphoma with a variety of presentations and treatment modalities. With the introduction of immunotherapy as an addition to chemotherapy (CT), there is ongoing debate about the role of radiotherapy (RT) in treatment and a need to clarify differences by specific anatomic locations. <b>Methods:</b> We identified a cohort of 1929 individuals with limited stage (stage I and II) head and neck DLBCL with extranodal involvement from the National Cancer Data Base. Overall survival (OS) was evaluated by Kaplan-Meier analysis, multivariable Cox proportional hazard regression, and propensity score-matched analysis. <b>Results:</b> Multi-agent CT plus RT was associated with longer OS (HR, 0.763; 95% CI, 0.614 to 0.948; <i>p</i> = 0.015) when compared with multi-agent CT alone on multivariate analysis. After propensity score matching to account for confounding variables, multi-agent CT plus RT was associated with longer OS than those who received multi-agent CT alone (HR = 0.769; 95% CI, 0.609–0.971; <i>p</i> = 0.027). The survival benefit persisted in patients over the age of 60 years and those who received RT within 180 days of CT. However, there was no significant difference in OS between the two groups in subgroup analysis of patients who received immunotherapy. <b>Conclusion:</b> The addition of RT to CT resulted in longer OS in patients with limited stage head and neck DLBCL with extranodal involvement.
DOI: 10.6084/m9.figshare.7564646.v1
title: Adjuvant radiotherapy and chemotherapy in early-stage diffuse large B cell lymphoma of head and neck with extranodal involvement

description: <b>Objectives:</b> Diffuse large B cell lymphoma (DLBCL) is a heterogeneous lymphoma with a variety of presentations and treatment modalities. With the introduction of immunotherapy as an addition to chemotherapy (CT), there is ongoing debate about the role of radiotherapy (RT) in treatment and a need to clarify differences by specific anatomic locations. <b>Methods:</b> We identified a cohort of 1929 individuals with limited stage (stage I and II) head and neck DLBCL with extranodal involvement from the National Cancer Data Base. Overall survival (OS) was evaluated by Kaplan-Meier analysis, multivariable Cox proportional hazard regression, and propensity score-matched analysis. <b>Results:</b> Multi-agent CT plus RT was associated with longer OS (HR, 0.763; 95% CI, 0.614 to 0.948; <i>p</i> = 0.015) when compared with multi-agent CT alone on multivariate analysis. After propensity score matching to account for confounding variables, multi-agent CT plus RT was associated with longer OS than those who received multi-agent CT alone (HR = 0.769; 95% CI, 0.609–0.971; <i>p</i> = 0.027). The survival benefit persisted in patients over the age of 60 years and those who received RT within 180 days of CT. However, there was no significant difference in OS between the two groups in subgroup analysis of patients who received immunotherapy. <b>Conclusion:</b> The addition of RT to CT resulted in longer OS in patients with limited stage head and neck DLBCL with extranodal involvement.
DOI: 10.6084/m9.figshare.23812674
title: Additional file 7 of Identification of a novel immune-related transcriptional regulatory network in sarcopenia

description: Additional file 7. Results of DEIGSs.
DOI: 10.6084/m9.figshare.11758959
title: Additional file 1 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 1: Table S1. The quality of RNA extration.
DOI: 10.6084/m9.figshare.11758965
title: Additional file 20 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 20: Table S10. The primers of qRT-PCR used for validation of expression trend in Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11758971
title: Additional file 2 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 2: Table S2. Overview of the sequencing data of Zanthoxylum armatum transcriptome.
DOI: 10.6084/m9.figshare.7564676
title: Supplementary tables

description: The supplementary tables of paper "A
new method for real-time evaluation of urban traffic congestion: a case study
in Xi’an, China"
DOI: 10.6084/m9.figshare.25218122
title: Alignments of KaiA3, KaiA, and NarL orthologs

description: Alignments of KaiA3, KaiA, and NarL orthologs
DOI: 10.6084/m9.figshare.24866232
title: Innovative insight into the mechanism of enantioselective skin permeation for chiral drugs

description: A profound comprehension of the molecular mechanisms underpinning the enantioselective transdermal permeation of chiral drugs is critical in the design and assessment of transdermal preparations. The primary objective of this study is to investigate the distinct skin permeation behaviors exhibited by enantiomers of non-steroidal anti-inflammatory drugs (NSAIDs) and elucidate the intricate molecular mechanism at play. <i>In vitro</i> and <i>in vivo</i> transdermal permeation studies of chiral NSAIDs were performed using transdermal patch and solution system. Chiral interaction between NSAIDs enantiomers and synthesized chiral ceramide present in the skin was characterized to clarify the different transdermal behaviors. The S-enantiomers of NSAIDs exhibited higher permeability through the skin than R-enantiomer <i>in vitro</i> (1.5-fold) and <i>in vivo</i> (2.0-fold), which was attributed to a stronger interaction between S-enantiomer and ceramide caused by more favorable spatial conformations. S-enantiomer required lower activation energy (24.4 kJ/mol) and Gibbs energy (43.3 kJ/mol), which was favorable in forming the H-bond with ceramide in the skin, resulting in more permeation. This research furnished an innovative comprehension of the molecular underpinnings governing the enantioselective permeation of drug enantiomers through the skin, fostering the minimization of undesired enantiomer ingestion (distomers) and amplifying therapeutic efficiency.
DOI: 10.6084/m9.figshare.24866232.v1
title: Innovative insight into the mechanism of enantioselective skin permeation for chiral drugs

description: A profound comprehension of the molecular mechanisms underpinning the enantioselective transdermal permeation of chiral drugs is critical in the design and assessment of transdermal preparations. The primary objective of this study is to investigate the distinct skin permeation behaviors exhibited by enantiomers of non-steroidal anti-inflammatory drugs (NSAIDs) and elucidate the intricate molecular mechanism at play. <i>In vitro</i> and <i>in vivo</i> transdermal permeation studies of chiral NSAIDs were performed using transdermal patch and solution system. Chiral interaction between NSAIDs enantiomers and synthesized chiral ceramide present in the skin was characterized to clarify the different transdermal behaviors. The S-enantiomers of NSAIDs exhibited higher permeability through the skin than R-enantiomer <i>in vitro</i> (1.5-fold) and <i>in vivo</i> (2.0-fold), which was attributed to a stronger interaction between S-enantiomer and ceramide caused by more favorable spatial conformations. S-enantiomer required lower activation energy (24.4 kJ/mol) and Gibbs energy (43.3 kJ/mol), which was favorable in forming the H-bond with ceramide in the skin, resulting in more permeation. This research furnished an innovative comprehension of the molecular underpinnings governing the enantioselective permeation of drug enantiomers through the skin, fostering the minimization of undesired enantiomer ingestion (distomers) and amplifying therapeutic efficiency.
DOI: 10.6084/m9.figshare.19094137.v1
title: Additional file 2 of Seek COVER: using a disease proxy to rapidly develop and validate a personalized risk calculator for COVID-19 outcomes in an international network

description: Additional file 2.
DOI: 10.6084/m9.figshare.19094137
title: Additional file 2 of Seek COVER: using a disease proxy to rapidly develop and validate a personalized risk calculator for COVID-19 outcomes in an international network

description: Additional file 2.
DOI: 10.6084/m9.figshare.23812680
title: Additional file 9 of Identification of a novel immune-related transcriptional regulatory network in sarcopenia

description: Additional file 9. Results of C-Map database.
DOI: 10.6084/m9.figshare.7964345
title: Origin of Late Permian amphibole syenite from the Panxi area, SW China: high degree fractional crystallization of basaltic magma in the inner zone of the Emeishan mantle plume

description: The c.a. 259–260 Ma Emeishan mantle plume caused extensive flood basalts and associated peralkaline rocks; petrogenesis of these peralkaline rocks can provide detailed information about the melting process in the mantle. In this paper, we present detailed petrology, chronology, major and trace element geochemistry, Sr-Nd isotope and <i>in situ</i> zircon Hf isotope for an amphibole syenite from Panxi area, inner zone of the Emeishan large Igneous province (ELIP). The amphibole syenite has a zircon U-Pb ages of 260 ± 2 Ma (MSWD = 1.2, n = 22), which is synchronous with Emeishan mantle plume. It displays moderate SiO<sub>2</sub> (64.89–65.67 wt.%), high Na<sub>2</sub>O (7.35–7.71 wt.%) and K<sub>2</sub>O (4.78–4.96 wt.%) contents, with A/CNK values of 0.86 to 0.90, with high Rittman index of 6.6 to 7.1, showing peralkaline affinity. It displays significantly negative Sr anomalies (133 to 200 ppm) and slightly negative Eu anomalies (Eu/Eu* = 0.78–1.04). The rock displays high ε<sub>Nd</sub>(t) values of +2.4 to +2.5. Zircons from the amphibole syenite display positive ε<sub>Hf</sub>(t) values from +8.9 to +11.0, with single-stage Hf model ages ranging from 0.47 to 0.55 Ga, combined with the well-developed correlation of TFe<sub>2</sub>O<sub>3</sub>, CaO/Al<sub>2</sub>O<sub>3</sub>, TiO<sub>2</sub>, Ni and Cr with MgO, suggesting the amphibole syenite was derived from the mantle source, and the fractional crystallization played a significant role in the generation of the magma. The MELTS model results show that Houzishan amphibole syenite can be formed by the high degree (~80%) fractional crystallization of ~24% clinopyroxene, ~4% orthopyroxene, ~35% plagioclase and ~5% oxide from parental magma resembling high-Ti basalts. These results indicate that Houzishan amphibole syenite represents the juvenile mantle-derived peralkaline melts addition to the continental lower crust in the inner zone of the ELIP and assimilating with minor crust material.
DOI: 10.6084/m9.figshare.7964345.v1
title: Origin of Late Permian amphibole syenite from the Panxi area, SW China: high degree fractional crystallization of basaltic magma in the inner zone of the Emeishan mantle plume

description: The c.a. 259–260 Ma Emeishan mantle plume caused extensive flood basalts and associated peralkaline rocks; petrogenesis of these peralkaline rocks can provide detailed information about the melting process in the mantle. In this paper, we present detailed petrology, chronology, major and trace element geochemistry, Sr-Nd isotope and <i>in situ</i> zircon Hf isotope for an amphibole syenite from Panxi area, inner zone of the Emeishan large Igneous province (ELIP). The amphibole syenite has a zircon U-Pb ages of 260 ± 2 Ma (MSWD = 1.2, n = 22), which is synchronous with Emeishan mantle plume. It displays moderate SiO<sub>2</sub> (64.89–65.67 wt.%), high Na<sub>2</sub>O (7.35–7.71 wt.%) and K<sub>2</sub>O (4.78–4.96 wt.%) contents, with A/CNK values of 0.86 to 0.90, with high Rittman index of 6.6 to 7.1, showing peralkaline affinity. It displays significantly negative Sr anomalies (133 to 200 ppm) and slightly negative Eu anomalies (Eu/Eu* = 0.78–1.04). The rock displays high ε<sub>Nd</sub>(t) values of +2.4 to +2.5. Zircons from the amphibole syenite display positive ε<sub>Hf</sub>(t) values from +8.9 to +11.0, with single-stage Hf model ages ranging from 0.47 to 0.55 Ga, combined with the well-developed correlation of TFe<sub>2</sub>O<sub>3</sub>, CaO/Al<sub>2</sub>O<sub>3</sub>, TiO<sub>2</sub>, Ni and Cr with MgO, suggesting the amphibole syenite was derived from the mantle source, and the fractional crystallization played a significant role in the generation of the magma. The MELTS model results show that Houzishan amphibole syenite can be formed by the high degree (~80%) fractional crystallization of ~24% clinopyroxene, ~4% orthopyroxene, ~35% plagioclase and ~5% oxide from parental magma resembling high-Ti basalts. These results indicate that Houzishan amphibole syenite represents the juvenile mantle-derived peralkaline melts addition to the continental lower crust in the inner zone of the ELIP and assimilating with minor crust material.
DOI: 10.6084/m9.figshare.7040492
title: Additional file 1: of Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5 in flowering

description: Table S1. List of primers used for PeMADS genes cloning. Table S2. List of primers used for qPCR in P. edulis. Table S3. List of repeat numbers in the PeMADS gene family identified by the Repeat Masker online software. Table S4. List of transposable elements in PeMADS1, − 2, − 6, and − 7. Table S5. The primers for Real-time quantitatively RT-PCR in Arabidopsis. Table S6. List of cis-elements in 1.5 kb upstream promoter regions of PeMADSs. Table S7. List of CArG box in PeMADSs promoter and intron region. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.7040492.v1
title: Additional file 1: of Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5 in flowering

description: Table S1. List of primers used for PeMADS genes cloning. Table S2. List of primers used for qPCR in P. edulis. Table S3. List of repeat numbers in the PeMADS gene family identified by the Repeat Masker online software. Table S4. List of transposable elements in PeMADS1, − 2, − 6, and − 7. Table S5. The primers for Real-time quantitatively RT-PCR in Arabidopsis. Table S6. List of cis-elements in 1.5 kb upstream promoter regions of PeMADSs. Table S7. List of CArG box in PeMADSs promoter and intron region. (XLSX 136 kb)
DOI: 10.6084/m9.figshare.25218134
title: Phylogeny of KaiA3, KaiA, and NarL orthologs

description: Phylogeny of KaiA3, KaiA, and NarL orthologs
DOI: 10.6084/m9.figshare.11759115
title: Additional file 4 of Identifying critical state of complex diseases by single-sample Kullback–Leibler divergence

description: Additional file 4. The common sKLD-signaling genes for LUSC, LUAD and STAD.
DOI: 10.18465/2a1da296-6aaf-4041-9ea4-d917e9464a0d
title: Protocole de calcul des MNB - Notre-Dame-de-Monts 2020

description: Exemple de suites de traitements des données LiDAR de l'approche classique à l'analyse des formes d'ondes. Notre Dame de Monts 2020. Le but de cette présentation dont les données originales sont téléchargeables est de montrer que l'analyse des formes d'ondes permet de caractériser directement la composition des surfaces pour interpréter correctement topographies et bathymétries. Les petits panaches de turbidité en bord de plage peuvent être vus comme des imperfections de détermination de la bathymétrie mais ce sont aussi des figures de diagnostique de la dynamique du littoral.
DOI: 10.6084/m9.figshare.23812673.v1
title: Additional file 2 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 2. Summary statistics of meQTL replication results for selected CpG sites using MeDIP-seq. TSV file with the following fields: (1) SNP: meQTL SNP ID in the format of chr:pos_A1_A2. (2) bin: MeDIP-seq bin ID in the format of chr.pos1.pos2. (3) CpG: CpG ID included within the bin. (4) type: type of association, can be cis or trans. (5) beta: association coefficient estimate. (6) t-stat: t-statistic value. (7) p-value: raw P-value of the association. (8) R2: coefficient of determination of the association.
DOI: 10.6084/m9.figshare.5986999
title: Cenozoic drainage evolution of the Rio Grande paleoriver recorded in detrital zircons in South Texas

description: Sediment provenance in the lower reach of rivers is important in reconstructing paleogeography and linking continental tectonic and climate changes with sedimentation in continental margins. This study presents 1300 new detrital zircon U–Pb ages from seven latest Eocene–Miocene sandstone and one modern river sand samples in south Texas and integrates these new data with published detrital zircon data to elucidate the evolution of the Rio Grande paleoriver during the Cenozoic. The new data contain a major population of the Cordillera magmatic province (22–280 Ma) and populations older than 280 Ma that were mostly recycled from sedimentary cover in the southern Rocky Mountains and southern Great Plains. The latest Eocene–Oligocene sandstones contain abundant air-fall zircons, and their detrital zircon maximum depositional ages constrain depositional ages. The changes in detrital zircon age distributions suggest that the paleoriver has changed its drainage extent three times, including a late Eocene drainage reduction by cutting off sediment supply from the west, a late Oligocene drainage reduction to the east of the southern Rocky Mountains and expansion to the East Mexico Arc in northeastern Mexico, and a latest Neogene drainage expansion to the west of the Rio Grande Rift and southern Colorado.
DOI: 10.6084/m9.figshare.25218137
title: Processed Data KaiA3

description: Processed Data KaiA3
DOI: 10.6084/m9.figshare.25218137.v1
title: Processed Data KaiA3

description: Processed Data KaiA3
DOI: 10.6084/m9.figshare.13324075
title: Additional file 7 of Identification of a quantitative trait loci (QTL) associated with ammonia tolerance in the Pacific white shrimp (Litopenaeus vannamei)

description: Additional file 7: Table S7. DEGs within the QTL interval and their expression levels and annotations
DOI: 10.6084/m9.figshare.21192009.v1
title: Additional file 3 of Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis

description: Additional file 3: Supplemental Table 2. Summary table of all significant MaAsLin results. All MaAsLin results from 16S rRNA gene sequencing with q-values for significant taxa which met our predetermined threshold for significance (q&lt;0.20). Mixed effects linear models using arcsine transform on relative abundances were used to determine significance. p-values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) method with FDR set at &lt;0.20. (XLS 224 kb)
DOI: 10.6084/m9.figshare.7035911
title: GADD45A inhibits autophagy by regulating the interaction between BECN1 and PIK3C3

description: GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, and DNA repair, and inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A<sub>1</sub> treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.
DOI: 10.6084/m9.figshare.7560548.v2
title: Table S3 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

description: Reference species used for the ortholog set and number of orthologs identified. Table S3.1: Official gene sets from whole genome projects of four reference species used for transcript orthology assessment, including the source, version and number of genes. Table S3.2: Orthograph statistics.
DOI: 10.6084/m9.figshare.23812676
title: Additional file 3 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 3: Tables S5–S25. Table S5. List of all the enrichment analyses, set of CpGs/SNPs of interest, and background set used in each. Tables S6–S17. Enrichment analyses on genomic annotations. Tables S18–S21. Enrichment analyses on specific transcription factor binding sites annotations. Tables S22–S25. Enrichment analyses on gene ontologies.
DOI: 10.6084/m9.figshare.23812682.v1
title: Additional file 4 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 4. Summary statistics of Summary-based Mendelian Randomisation with gene expression data. TSV file with the following fields: (1) SMRtest: type of SMR test, can be cis-meQTL, trans-meQTL or target_trans-meQTL. (2) CpG: CpG ID. (3) Gene: ENSEMBL gene ID. (4) SNP: SNP ID in the format of chr:pos, tested for co-localisation. (5–6) chr_cpg, pos_cpg: chromosome and position of CpG. (7) gene_cpg: gene annotated to the CpG. (8–9) chr_snp, pos_snp: chromosome and position of SNP. (10) A1: effect allele. (11) A2: alternative allele. (12) Freq: frequency of A1. (13–15) b_eQTL, se_eQTL, p_eQTL: coefficient estimate, standard error and p-value from the eQTL association. (16–18) b_meQTL, se_meQTL, p_meQTL: coefficient estimate, standard error and p-value from the meQTL association. (19–21) b_SMR, se_SMR, p_SMR: coefficient estimate, standard error and p-value from the SMR. (22) p_HEIDI: p-value from HEIDI. (23) nsnp_HEIDI: number of SNPs used in the HEIDI test.
DOI: 10.6084/m9.figshare.22769345
title: Supplementary material for "The presence and severity of NAFLD are associated with cognitive impairment and hippocampal damage"

description:  Supplementary material
DOI: 10.6084/m9.figshare.7560560.v2
title: Table S7 from An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

description: Results for approximately unbiased (AU) tests.
DOI: 10.6084/m9.figshare.25218143.v1
title: Raw Data KaiA3

description: Raw Data KaiA3
DOI: 10.6084/m9.figshare.25218143
title: Raw Data KaiA3

description: Raw Data KaiA3
DOI: 10.6084/m9.figshare.25131781.v1
title: Isotopic Data Sheets from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: Excel sheets organizing our isotopic data and corresponding to the SIBER, simple linear regression, and multivariable linear regressions conducted in this study.
DOI: 10.6084/m9.figshare.25218113
title: Current and suspended sediment concentration in the Bohai Strait during both ice-covered and ice-free conditions.

description: Current and suspended sediment concentration in the Bohai Strait during both ice-covered and ice-free conditions.