cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8062559.v1
title: Additional file 1: of Evidence from genome wide association studies implicates reduced control of Epstein-Barr virus infection in multiple sclerosis susceptibility

description: Table S1. Genes dysregulated due to EBV infection. Table S2. LCLeQTL gene list. Table S3. Replication and combined p value for LCLeQTL gene list. Table S4. LCLeQTL* gene list. Table S5. Whole blood eQTLs gene list. Table S6. Whole blood eQTLs minus LCLeQTL*. Table S7. EBV Transcription Factor interactome gene list. Table S8. Intrinsic growth rate and genetic load of risk alleles. Table S9. Expression of EBV genes and genetic load of risk alleles. Table S10. EBV copy number in LCLs and genetic load of risk alleles. Table S11. LCLeQTL SNP sets and EBNA1 titres. (XLSX 730 kb)
DOI: 10.6084/m9.figshare.7538336.v1
title: Additional file 2: of Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model

description: Supplementary Tables. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.8062634
title: Additional file 3: of Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data

description: Transcription factors and Targets (XLSX 35 kb)
DOI: 10.6084/m9.figshare.8062649.v1
title: Additional file 5: of Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data

description: The correlation of gene expression and immune cell proportion in key lipidÂ metabolismÂ  pathways. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.12246755
title: Additional file 1 of Pre-transplant MRD negativity predicts favorable outcomes of CAR-T therapy followed by haploidentical HSCT for relapsed/refractory acute lymphoblastic leukemia: a multi-center retrospective study

description: Additional file 1: Supplementary Table S1. The case number enrolled by each clinical center. Table S2. CAR-T therapy associated toxicities. Table S3. Univariate analyses for factors impacting LFS in patients who received CAR-T therapy followed by haplo-HSCT. Table S4. Univariate analyses for factors impacting OS in patients who received CAR-T therapy followed by haplo-HSCT. Table S5. Univariate analyses for factors impacting cumulative incidence of relapse in patients who received CAR-T therapy followed by haplo-HSCT. Table S6. Transplant-associated complications. Figure S1. Cumulative incidence of grade III-IV acute graft versus host disease (aGVHD), chronic graft versus host disease (cGVHD) requiring systemic steroid therapy, CMV viremia and EBV viremia in transplant group.
DOI: 10.6084/m9.figshare.7538447
title: Additional file 2 of Hot spot prediction in protein-protein interactions by an ensemble system

description: All relevant MATLAB code. A simple Matlab implement of our predictor. (ZIP 19,742 kb)
DOI: 10.6084/m9.figshare.19597093
title: Darwin’s naturalization conundrum disentangled: the role of phylogenetic relatedness depends on the invasion stages

description: We collected data on 5,091 alien angiosperm species that have been introduced to Southern Africa for cultivation. Then combined with lists of the global flora non-native to Southern Africa (n= 24,974 species), the naturalized and native species within the region of Southern Africa, and the species that have become invasive within the country of South Africa. This novel combination of datasets was used to test the Darwin’s naturalization conundrum at the different stages of the invasion process. Specifically, we showed how phylogenetic relatedness to native species is correlated with the subsequent stages of introduction, naturalization and invasiveness of alien species.
DOI: 10.6084/m9.figshare.7538489
title: Additional file 9: of CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

description: Predict results. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.12246755.v1
title: Additional file 1 of Pre-transplant MRD negativity predicts favorable outcomes of CAR-T therapy followed by haploidentical HSCT for relapsed/refractory acute lymphoblastic leukemia: a multi-center retrospective study

description: Additional file 1: Supplementary Table S1. The case number enrolled by each clinical center. Table S2. CAR-T therapy associated toxicities. Table S3. Univariate analyses for factors impacting LFS in patients who received CAR-T therapy followed by haplo-HSCT. Table S4. Univariate analyses for factors impacting OS in patients who received CAR-T therapy followed by haplo-HSCT. Table S5. Univariate analyses for factors impacting cumulative incidence of relapse in patients who received CAR-T therapy followed by haplo-HSCT. Table S6. Transplant-associated complications. Figure S1. Cumulative incidence of grade III-IV acute graft versus host disease (aGVHD), chronic graft versus host disease (cGVHD) requiring systemic steroid therapy, CMV viremia and EBV viremia in transplant group.
DOI: 10.6084/m9.figshare.7538501.v1
title: Additional file 1 of Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes

description: Table S1. Genes used in cellular condition (i.e. healthy or T2D) prediction. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7538507
title: Additional file 2 of Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes

description: Tables S2-S3. Entropy, joint entropy and mutual information between TEDECs and the genes in the apoptosis pathway. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.12246758.v1
title: Additional file 1 of TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data

description: Additional file 1 The TS and the other comparison methods are applied to the SCZ data.
DOI: 10.6084/m9.figshare.25211873
title: Supplementary Material for: Management of Locally Advanced Basal Cell Carcinoma with Sonic Hedgehog Pathway Targeted Therapy: A Case Report and Discussion

description: Introduction
Basal Cell Carcinoma (BCC) is the most common skin malignancy in the world. While most lesions are treated using surgical methods, others may present as locally advanced or metastatic disease and are not amenable to surgical therapy alone. Treatment with sonic hedgehog pathway inhibitors (vismodegib, sonidegib) is designed to inhibit key signaling proteins and gene pathways involved with BCC to reduce the uncontrolled proliferation of basal cells in complicated disease and can be invaluable in treating patients with advanced disease. 

Case Presentation
We describe the course of a 68-year-old man who presented with a 7.2x6cm exophytic and ulcerated locally invasive BCC of his upper back. The patient was started on daily vismodegib treatment with the goal of eventual surgical resection. After 11 weeks of therapy, he had significant improvement in both wound size and appearance. After 18 weeks of therapy, he had achieved a near complete clinical response of the central aspect of lesion with three remaining small peripheral lesions. These lesions were biopsied and two were found to be negative for malignancy while a small inferior nodule was positive for squamous cell carcinoma (SCC). Vismodegib therapy was discontinued after a total of 26 weeks of therapy. Excision of the SCC was performed, and the patient remains disease free at 2 years.

Conclusion
This case report shows the efficacy of hedgehog pathway inhibitor therapy in the treatment of a locally advanced BCC with complete pathologic response, not requiring surgical intervention.
DOI: 10.6084/m9.figshare.7538537.v1
title: Additional file 1: of Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimerâ s disease patients

description: Table S1. Comparison of module genes identified by lmQCM and WGCNA from GSE48350 AD samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.12246722.v1
title: Additional file 2 of Cytochrome P450 1A1 enhances inflammatory responses and impedes phagocytosis of bacteria in macrophages during sepsis

description: Additional file 1: Figure S1. Confirmation of transfections. Figure S2. Relative expression levels of inflammatory factors in overactivated macrophages. Figure S3. The inhibitory effects of Rhapontigenin on LPS-induced TNF-α and IL-6 secretion in PMs. Figure S4. Validation of the NF-κB signalling pathway and different MAPK signalling pathways in LPS-stimulated CYP1A1/RAW and NC/RAW. Figure S5. The levels of 12(S)-HETE in PLFs from E.coli- and CLP-induced septic mice. Figure S6. Detection of lentivirus infection rate in PMs. Figure S7. The regulation of CYP1A1-JNK-AP-1 axis in septic mice. Figure S8. Platelet count in PLFs from CYP1A1-overexpressed macrophages transferred septic mice. Figure S9. CYP1A1 is involved in phagocytosis of bacteria in macrophages during sepsis.
DOI: 10.6084/m9.figshare.16965496.v1
title: Table S1 Correlation between isoaccepting tRNA gene frequencies and synonymous codon usage in the transcriptome of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.7538576.v1
title: Additional file 3 of Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

description: The disease-gene associations. This file contains the researched diseases and their associated genes extracted from CTD. (CSV 7229 kb)
DOI: 10.6084/m9.figshare.7538591
title: Additional file 2 of FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

description: Table S2. The top 50 predicted miRNAs related to Gastric Neoplasms. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.12247052.v1
title: Additional file 4 of Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions

description: Additional file 4. The top 10 predicted results for miRNAs in MeSHSim.
DOI: 10.6084/m9.figshare.14337595
title: Additional file 12 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 12: Table S5. Primer sequences used in expression analysis of BBX genes in grapevine
DOI: 10.6084/m9.figshare.16965487.v1
title: Dataset S2 Co-adaption between of tRNA gene frequency and codon usage at the synonymous codon level and the amino acid level of individual genes of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.8063306
title: Fuzzy optimization model for electric vehicle routing problem with time windows and recharging stations

description: This is the experimental data of the manuscript entitled "Fuzzy optimization model for electric vehicle routing problem with time windows and recharging stations". All data are saved in the file with txt format.
DOI: 10.6084/m9.figshare.14337616
title: Additional file 6 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 6: Table S2. Segmental duplications within grapevine VviBBX genes and Ka/Ks ratios analysis of segmental duplicate gene pairs
DOI: 10.6084/m9.figshare.14337604.v1
title: Additional file 2 of Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

description: Additional file 2: Text S2. The protein sequences of BBX family in six species
DOI: 10.15156/bio/sh1919221.08fu
title: SH1919221.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919222.08fu
title: SH1919222.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919223.08fu
title: SH1919223.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919224.08fu
title: SH1919224.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919225.08fu
title: SH1919225.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919226.08fu
title: SH1919226.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919227.08fu
title: SH1919227.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1919228.08fu
title: SH1919228.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.