cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14173407
title: Graph-Based Equilibrium Metrics for Dynamic Supply–Demand Systems With Applications to Ride-sourcing Platforms

description: How to dynamically measure the local-to-global spatio-temporal coherence between demand and supply networks is a fundamental task for ride-sourcing platforms, such as DiDi. Such coherence measurement is critically important for the quantification of the market efficiency and the comparison of different platform policies, such as dispatching. The aim of this paper is to introduce a graph-based equilibrium metric (GEM) to quantify the distance between demand and supply networks based on a weighted graph structure. We formulate GEM as the optimal objective value of an unbalanced optimal transport problem, which can be formulated as an equivalent linear programming and efficiently solved. We examine how the GEM can help solve three operational tasks of ride-sourcing platforms. The first one is that GEM achieves up to 70.6% reduction in root-mean-square error over the second-best distance measurement for the prediction accuracy of order answer rate. The second one is that the use of GEM for designing order dispatching policy increases drivers’ revenue for more than 1%, representing a huge improvement in number. The third one is that GEM can serve as an endpoint for comparing different platform policies in AB test. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.13647119.v1
title: Additional file 1 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 1: Table S1. Table of specimens used in study, patient clinical data, and tumor mutational profiles.
DOI: 10.6084/m9.figshare.13647131
title: Additional file 4 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 4: Table S3. GBM-specific neojunctions derived from public data analysis.
DOI: 10.6084/m9.figshare.6831377
title: MOESM4 of Transcriptional network analysis on brains reveals a potential regulatory role of PPP1R3F in autism spectrum disorders

description: Additional file 3. The constructed networks from the Gupta et al. dataset [17].
DOI: 10.6084/m9.figshare.13647146.v1
title: Additional file 9 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 9: Table S8. Differential expression test between primary and recurrent in-house GBM RNA-seq.
DOI: 10.6084/m9.figshare.13647134
title: Additional file 5 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 5: Table S4. Differential splicing test between all in-house GBM RNA-seq vs. non-malignant brain RNA-seq.
DOI: 10.6084/m9.figshare.13647128
title: Additional file 3 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 3: Supplementary figures. Supplementary figures and legends.
DOI: 10.6084/m9.figshare.13647134.v1
title: Additional file 5 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 5: Table S4. Differential splicing test between all in-house GBM RNA-seq vs. non-malignant brain RNA-seq.
DOI: 10.6084/m9.figshare.13647140.v1
title: Additional file 7 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 7: Table S6. Putative neojunction-derived neoantigens and HLA serotypes.
DOI: 10.6084/m9.figshare.13647143.v1
title: Additional file 8 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 8: Table S7. Differential splicing test between primary and recurrent in-house GBM RNA-seq.
DOI: 10.6084/m9.figshare.6831377.v1
title: MOESM4 of Transcriptional network analysis on brains reveals a potential regulatory role of PPP1R3F in autism spectrum disorders

description: Additional file 3. The constructed networks from the Gupta et al. dataset [17].
DOI: 10.6084/m9.figshare.13647131.v1
title: Additional file 4 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 4: Table S3. GBM-specific neojunctions derived from public data analysis.
DOI: 10.6084/m9.figshare.13647086
title: Additional file 2 of Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

description: Additional file 2 The metadata of the full list of 114 GWASs
DOI: 10.6084/m9.figshare.13647143
title: Additional file 8 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 8: Table S7. Differential splicing test between primary and recurrent in-house GBM RNA-seq.
DOI: 10.6084/m9.figshare.13647128.v1
title: Additional file 3 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 3: Supplementary figures. Supplementary figures and legends.
DOI: 10.6084/m9.figshare.13647140
title: Additional file 7 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 7: Table S6. Putative neojunction-derived neoantigens and HLA serotypes.
DOI: 10.6084/m9.figshare.13647146
title: Additional file 9 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 9: Table S8. Differential expression test between primary and recurrent in-house GBM RNA-seq.
DOI: 10.6084/m9.figshare.6831521
title: MOESM4 of Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

description: Additional file 4: Table S2. Possible donors of HGT genes in each strain.
DOI: 10.6084/m9.figshare.13647107
title: Additional file 9 of Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

description: Additional file 9 PrediXcan and enloc results for presumed causal genes in the rare variant based silver standard
DOI: 10.6084/m9.figshare.6831470.v1
title: MOESM1 of Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

description: Additional file 1: Table S1. Summary of homologous genes identified by OrthoMCL. Protein sequences from 24 Shewanella genomes were used as input for OrthoMCL orthologous gene clustering (Input Genes). Clusters containing single genes or genes from a single strain were eliminated (Clusters). Genes from a single strain (Clustered as single strain).
DOI: 10.6084/m9.figshare.19938783.v1
title: High-throughput sequencing to evaluate the effects of methamphetamine on the succession of the bacterial community to estimate the postmortem interval

description: In forensic medical examinations, estimating the postmortem interval (PMI) is an important factor. Methamphetamine (MA) is a synthetic stimulant that is commonly abused, and estimation of the PMI after MA abuse has become one of the main tasks in forensic investigation. Microorganisms play a vital role in carrion decomposition. Analysing the bacterial succession patterns can be used as a forensic tool to estimate the PMI. The present study aimed to analyse bacterial succession changes during the decomposition of MA to estimate the PMI. We analysed bacterial communities in rabbits treated with three different concentrations of MA (0, 22.5, and 90 mg/kg) under the natural conditions of 20 °C and 70% humidity by sequencing 16S rRNA gene amplicons using the Illumina MiSeq system. We obtained 2 374 209 high-quality sequences and 2 937 operational taxonomic units (OTUs). The relative abundances of the bacterial communities varied markedly in response to different MA concentrations. Interestingly, in response to the different concentrations of MA, Bacteroidetes became disparate in the rectum in the late PMI. Increased numbers of bacterial taxa were identified in the rectum and buccal cavity samples, except at the highest concentration of MA in the rectum samples when PMI was 0–h, than were present in live rabbits. Meanwhile, the PMI correlated significantly with bacterial succession at different taxonomic levels. Our results suggested that bacterial community succession could be used as a “microbial clock” to estimate the PMI in cases of MA-related death; however, further study is required to gain a deeper understanding of this concept. As a forensic tool, microbiome succession patterns have great potential for PMI estimation. At different taxonomic levels, the variation in the succession of microorganisms under three different concentrations of MA during the processes of decomposition is significantly related to PMI for estimating MA abuse. These findings provide a new idea for the estimation of PMI of MA abused by changes in microorganisms.
DOI: 10.6084/m9.figshare.6831428.v1
title: MOESM5 of Transcriptional network analysis on brains reveals a potential regulatory role of PPP1R3F in autism spectrum disorders

description: Additional file 5. The list of the combined set of target genes of PPP1R3F.
DOI: 10.6084/m9.figshare.7355906.v1
title: Data File 2.csv

description: Data File 2 provides the underlying values in Dataset_3
DOI: 10.6084/m9.figshare.6831389.v1
title: MOESM2 of Identification of long non-coding RNA signatures in triple-negative breast cancer

description: Additional file 2: Table S2. Functional enrichment terms of DEGs.
DOI: 10.6084/m9.figshare.6831581
title: MOESM8 of Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

description: Additional file 8: Table S3. Genomes and strains used in this study. Organism information is collected from NCBI.
DOI: 10.6084/m9.figshare.13647137
title: Additional file 6 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 6: Table S5. Annotated lists of GBM-specific neojunctions derived from in-house data analysis.
DOI: 10.6084/m9.figshare.13647137.v1
title: Additional file 6 of The evolution of alternative splicing in glioblastoma under therapy

description: Additional file 6: Table S5. Annotated lists of GBM-specific neojunctions derived from in-house data analysis.
DOI: 10.6084/m9.figshare.6831470
title: MOESM1 of Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

description: Additional file 1: Table S1. Summary of homologous genes identified by OrthoMCL. Protein sequences from 24 Shewanella genomes were used as input for OrthoMCL orthologous gene clustering (Input Genes). Clusters containing single genes or genes from a single strain were eliminated (Clusters). Genes from a single strain (Clustered as single strain).
DOI: 10.6084/m9.figshare.6831428
title: MOESM5 of Transcriptional network analysis on brains reveals a potential regulatory role of PPP1R3F in autism spectrum disorders

description: Additional file 5. The list of the combined set of target genes of PPP1R3F.
DOI: 10.17028/rd.lboro.22560106.v1
title: Supplementary information files for Fast in-situ synchrotron X-ray imaging of the interfacial reaction during self-propagating exothermic reactive bonding

description: Supplementary files for article Fast in-situ synchrotron X-ray imaging of the interfacial reaction during self-propagating exothermic reactive bonding
<br>
Self-Propagating Exothermic Reactive (SPER) bonding with lead-free solders is potentially attractive for microelectronics assembly due to its highly localised heating and minimal thermal loading of the components and substrates. The transient dynamics of melting, wetting, solidification and defect formation during SPER bonding were observed using in-situ synchrotron X-ray imaging with sub-millisecond temporal resolution and the results were further analysed using electron microscopy and thermal modelling. In-situ imaging revealed the preferential melting of the solder and subsequent wetting of the substrate. Numerous air bubbles were observed to form at the bonding interface. The distribution of these bubbles was found to vary with the thermal conductivity and wettability of the substrates. These bubbles appear to reduce the effectiveness of bonding by promoting the formation of cracks and voids within the solder joint. Our results show that metallisation layers on the bonding substrate can influence the dynamics of melting for the solder materials and thereby directly influence the reliability of SPER interconnects.
DOI: 10.6084/m9.figshare.6831581.v1
title: MOESM8 of Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

description: Additional file 8: Table S3. Genomes and strains used in this study. Organism information is collected from NCBI.
DOI: 10.6084/m9.figshare.7355906
title: Data File 2.csv

description: Data File 2 provides the underlying values in Dataset_3
DOI: 10.6084/m9.figshare.19938783
title: High-throughput sequencing to evaluate the effects of methamphetamine on the succession of the bacterial community to estimate the postmortem interval

description: In forensic medical examinations, estimating the postmortem interval (PMI) is an important factor. Methamphetamine (MA) is a synthetic stimulant that is commonly abused, and estimation of the PMI after MA abuse has become one of the main tasks in forensic investigation. Microorganisms play a vital role in carrion decomposition. Analysing the bacterial succession patterns can be used as a forensic tool to estimate the PMI. The present study aimed to analyse bacterial succession changes during the decomposition of MA to estimate the PMI. We analysed bacterial communities in rabbits treated with three different concentrations of MA (0, 22.5, and 90 mg/kg) under the natural conditions of 20 °C and 70% humidity by sequencing 16S rRNA gene amplicons using the Illumina MiSeq system. We obtained 2 374 209 high-quality sequences and 2 937 operational taxonomic units (OTUs). The relative abundances of the bacterial communities varied markedly in response to different MA concentrations. Interestingly, in response to the different concentrations of MA, Bacteroidetes became disparate in the rectum in the late PMI. Increased numbers of bacterial taxa were identified in the rectum and buccal cavity samples, except at the highest concentration of MA in the rectum samples when PMI was 0–h, than were present in live rabbits. Meanwhile, the PMI correlated significantly with bacterial succession at different taxonomic levels. Our results suggested that bacterial community succession could be used as a “microbial clock” to estimate the PMI in cases of MA-related death; however, further study is required to gain a deeper understanding of this concept. As a forensic tool, microbiome succession patterns have great potential for PMI estimation. At different taxonomic levels, the variation in the succession of microorganisms under three different concentrations of MA during the processes of decomposition is significantly related to PMI for estimating MA abuse. These findings provide a new idea for the estimation of PMI of MA abused by changes in microorganisms.
DOI: 10.6084/m9.figshare.13123377
title: Rapid humoral immune responses are required for recovery from haemorrhagic fever with renal syndrome patients

description: Haemorrhagic fever with renal syndrome (HFRS) following Hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses elicited during HTNV infections are considered important, however, this process remains poorly understood. Herein, we have investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor (BCR) repertoire in an HFRS cohort. The serological proﬁles were characterized by a lowered expression level of nucleoprotein (NP)-speciﬁc antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the first two weeks of symptom onset and moderate cases reacted more rapidly. BCR analysis in the recovery phase revealed a dramatic increase in the immunoglobulin gene diversity which was more significantly progressed in moderate infections. In severe cases, B-cell-related transcription was lower with inflammatory sets overactivated. Taken together, these data suggest the clinical signs and disease recovery in HFRS patients were positively impacted by rapid and efficacious humoral responses.
DOI: 10.17028/rd.lboro.22560106
title: Supplementary information files for Fast in-situ synchrotron X-ray imaging of the interfacial reaction during self-propagating exothermic reactive bonding

description: Supplementary files for article Fast in-situ synchrotron X-ray imaging of the interfacial reaction during self-propagating exothermic reactive bonding
<br>
Self-Propagating Exothermic Reactive (SPER) bonding with lead-free solders is potentially attractive for microelectronics assembly due to its highly localised heating and minimal thermal loading of the components and substrates. The transient dynamics of melting, wetting, solidification and defect formation during SPER bonding were observed using in-situ synchrotron X-ray imaging with sub-millisecond temporal resolution and the results were further analysed using electron microscopy and thermal modelling. In-situ imaging revealed the preferential melting of the solder and subsequent wetting of the substrate. Numerous air bubbles were observed to form at the bonding interface. The distribution of these bubbles was found to vary with the thermal conductivity and wettability of the substrates. These bubbles appear to reduce the effectiveness of bonding by promoting the formation of cracks and voids within the solder joint. Our results show that metallisation layers on the bonding substrate can influence the dynamics of melting for the solder materials and thereby directly influence the reliability of SPER interconnects.
DOI: 10.6084/m9.figshare.12599220.v1
title: Additional file 1 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 1: Table S1. List of NbFLA CDS and protein sequences.
DOI: 10.6084/m9.figshare.20987831
title: MiR-200c regulates invasion, proliferation and EMT of anaplastic thyroid cancer cells by targeting parathyroid hormone like hormone

description: This study aimed to explore the specific effect of miR-200c in anaplastic thyroid cancer (ATC). Hth74 and ARO cell lines were used. Proliferation, invasion, and colony formation activities of Hth74 and ARO cell lines affected by miR-200c were studied. Expression of epithelial-to-mesenchymal transition (EMT) markers (E-cadherin, N-cadherin, Slug, and Snail) in the Hth74 and ARO cell lines were validated by western blot and qRT-PCR. In addition, the regulation of the parathyroid hormone-like hormone (PTHLH) by miR-200c was assessed. Overexpression of miR-200c inhibited the invasion, proliferation, and colony formation of the ATC cell lines, whereas its downregulation achieved the opposite results. PTHLH was found to be regulated negatively by miR-200c through a miR-200c binding site within the 3′-UTR of PTHLH. miR-200c repressed the proliferation, invasion, and EMT process of cells in ATC cell lines by targeting PTHLH post-transcriptionally, which indicates that miR-200c may be a potential target for the treatment of ATC.
DOI: 10.6084/m9.figshare.12599226.v1
title: Additional file 3 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 3: Table S2. The MEME motif sequences and length of NbFLAs.
DOI: 10.6084/m9.figshare.12599232.v1
title: Additional file 5 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 5: Table S4. Potential transcription factors of NbFLAs.
DOI: 10.6084/m9.figshare.20987831.v1
title: MiR-200c regulates invasion, proliferation and EMT of anaplastic thyroid cancer cells by targeting parathyroid hormone like hormone

description: This study aimed to explore the specific effect of miR-200c in anaplastic thyroid cancer (ATC). Hth74 and ARO cell lines were used. Proliferation, invasion, and colony formation activities of Hth74 and ARO cell lines affected by miR-200c were studied. Expression of epithelial-to-mesenchymal transition (EMT) markers (E-cadherin, N-cadherin, Slug, and Snail) in the Hth74 and ARO cell lines were validated by western blot and qRT-PCR. In addition, the regulation of the parathyroid hormone-like hormone (PTHLH) by miR-200c was assessed. Overexpression of miR-200c inhibited the invasion, proliferation, and colony formation of the ATC cell lines, whereas its downregulation achieved the opposite results. PTHLH was found to be regulated negatively by miR-200c through a miR-200c binding site within the 3′-UTR of PTHLH. miR-200c repressed the proliferation, invasion, and EMT process of cells in ATC cell lines by targeting PTHLH post-transcriptionally, which indicates that miR-200c may be a potential target for the treatment of ATC.
DOI: 10.6084/m9.figshare.6831521.v1
title: MOESM4 of Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway

description: Additional file 4: Table S2. Possible donors of HGT genes in each strain.
DOI: 10.6084/m9.figshare.12599226
title: Additional file 3 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 3: Table S2. The MEME motif sequences and length of NbFLAs.
DOI: 10.6084/m9.figshare.7355903
title: Data File 1.csv

description: Data File 1 provides the underlying values in Dataset_1
DOI: 10.5517/ccdc.csd.cc23756r
title: CCDC 1943303: Experimental Crystal Structure Determination

description: Related Article: Ayumu Kawase, Hirotaka Omura, Takayuki Doi, Hirokazu Tsukamoto|2019|Chem.Lett.|48|1402|doi:10.1246/cl.190642
DOI: 10.5517/ccdc.csd.cc23fzfz
title: CCDC 1949851: Experimental Crystal Structure Determination

description: Related Article: Ya-Yun Cai, Li-Yan Xu, Lan-Qin Chai, Yao-Xin Li|2020|J.Mol.Struct.|1204|127552|doi:10.1016/j.molstruc.2019.127552
DOI: 10.5517/ccdc.csd.cc23jj5c
title: CCDC 1952292: Experimental Crystal Structure Determination

description: Related Article: Jieni Liu, Xiaoping Yang, Ting Zhu, Bichen Yuan, Hongfen Chen, Dongliang Shi, Desmond Schipper, Richard A. Jones|2019|RSC Advances|9|40017|doi:10.1039/C9RA09409A
DOI: 10.5517/ccdc.csd.cc23k775
title: CCDC 1952976: Experimental Crystal Structure Determination

description: Related Article: Ji-Young Shin|2019|RSC Advances|9|40031|doi:10.1039/C9RA08850D
DOI: 10.5517/ccdc.csd.cc23l923
title: CCDC 1953994: Experimental Crystal Structure Determination

description: Related Article: Sadie A. Wolfarth, Natasha E. Miner, Nicole E. Wamser, Reilly K. Gwinn, Benny C. Chan, Chip Nataro|2020|J.Organomet.Chem.|906|121049|doi:10.1016/j.jorganchem.2019.121049
DOI: 10.5517/ccdc.csd.cc23l934
title: CCDC 1953995: Experimental Crystal Structure Determination

description: Related Article: Sadie A. Wolfarth, Natasha E. Miner, Nicole E. Wamser, Reilly K. Gwinn, Benny C. Chan, Chip Nataro|2020|J.Organomet.Chem.|906|121049|doi:10.1016/j.jorganchem.2019.121049
DOI: 10.5517/ccdc.csd.cc244mhf
title: CCDC 1970654: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton, Keith A. Stubbs, Mitchell Hattie|2019|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc244mjg
title: CCDC 1970655: Experimental Crystal Structure Determination

description: Related Article: Jerin Susan John, M. Saravana Kumar, Lija K. Joy, D. Sajan, G. Vinitha, N. Vijayan, Nimmy L. John|2019|CSD Communication|||