cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21385904.v1
title: Additional file 2 of Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards

description: Additional file 2: Table S1. Reports all gene names and corresponding number of alterations, including SNV, gene expression outliers, indels and gene fusions that were identified in the cohort. Table S2. Lists the genetic alterations that were identified as predictive biomarkers and corresponding treatment options per patient by Heidelberg (HD) and Berlin (BLN) MTBs. Results from a second sequencing for the same patient are indicated by a comma. Table S3. Provides information on treatment options and respective biomarkers for the analyzed cohort. Results from a second sequencing for the same patient are indicated by a comma.
DOI: 10.6084/m9.figshare.5657269
title: Reconstruction of mitogenomes by NGS and phylogenetic implications for leaf beetles

description: Mitochondrial genome (mitogenome) sequences are frequently used to infer phylogenetic relationships of insects at different taxonomic levels. Next-generation sequencing (NGS) techniques are revolutionizing many fields of biology, and allow for acquisition of insect mitogenomes for large number of species simultaneously. In this study, 20 full or partial mitogenomes were sequenced from pooled genomic DNA samples by NGS for leaf beetles (Chrysomelidae). Combined with published mitogenome sequences, a higher level phylogeny of Chrysomelidae was reconstructed under maximum likelihood and Bayesian inference with different models and various data treatments. The results revealed support for a basal position of Bruchinae within Chrysomelidae. In addition, two major subfamily groupings were recovered: one including seven subfamilies, namely Donaciinae, Criocerinae, Spilopyrinae, Cassidinae, Cryptocephalinae, Chlamisinae and Eumolpinae, another containing a non-monophyletic Chrysomelinae and a monophyletic Galerucinae.
DOI: 10.6084/m9.figshare.5657269.v1
title: Reconstruction of mitogenomes by NGS and phylogenetic implications for leaf beetles

description: Mitochondrial genome (mitogenome) sequences are frequently used to infer phylogenetic relationships of insects at different taxonomic levels. Next-generation sequencing (NGS) techniques are revolutionizing many fields of biology, and allow for acquisition of insect mitogenomes for large number of species simultaneously. In this study, 20 full or partial mitogenomes were sequenced from pooled genomic DNA samples by NGS for leaf beetles (Chrysomelidae). Combined with published mitogenome sequences, a higher level phylogeny of Chrysomelidae was reconstructed under maximum likelihood and Bayesian inference with different models and various data treatments. The results revealed support for a basal position of Bruchinae within Chrysomelidae. In addition, two major subfamily groupings were recovered: one including seven subfamilies, namely Donaciinae, Criocerinae, Spilopyrinae, Cassidinae, Cryptocephalinae, Chlamisinae and Eumolpinae, another containing a non-monophyletic Chrysomelinae and a monophyletic Galerucinae.
DOI: 10.26036/cnp0003101
title: Virome in bats and rodents of East Africa

description: A broad-scale RNA virus screening of bat and rodent individuals from Kenya and Uganda using metatranscriptomic sequencing
DOI: 10.26036/cnp0004910
title: StereoSiTE: A framework to spatially and quantitatively profile the cellular neighborhood organized iTME

description: With emerging of Spatial Transcriptomics (ST) technology, a powerful algorithmic framework to quantitatively evaluate the active cell-cell interactions in the bio-function associated iTME unit will pave the ways to understand the mechanism underlying tumor biology. This study provides the StereoSiTE incorporating open source bioinformatics tools with the self-developed algorithm, SCII, to dissect a cellular neighborhood (CN) organized iTME based on cellular compositions, and to accurately infer the functional cell-cell communications with quantitatively defined interaction intensity in ST data. We applied StereoSiTE to deeply decode ST data of the xenograft models receiving immunoagonist. Results demonstrated that the neutrophils dominated CN5 might attribute to iTME remodeling after treatment. To be noted, SCII analyzed the spatially resolved interaction intensity inferring a neutrophil leading communication network which was proved to actively function by analysis of Transcriptional Factor Regulon and Protein-Protein Interaction. Altogether, StereoSiTE is a promising framework for ST data to spatially reveal tumoribiology mechanisms.
DOI: 10.6084/m9.figshare.20337344
title: STUDY ON SPORTS INJURIES AND REHABILITATION IN BADMINTON PLAYERS

description: ABSTRACT Introduction Badminton has a wide audience and a large development market in China. Although it benefits the flexibility of sedentary workers by recruiting the whole body’s musculature, it can also cause a harmful effect due to lack of preparation or intensity during matches. Objective Study the methods of sports injury and rehabilitation of badminton players. Methods 60 badminton players with low back injuries were randomly divided into experimental and control groups. The control group used the traditional method of recovery by manual techniques. An intervention with core stability training lasting 40 minutes three times a week for six weeks was added to the experimental group. Results The degree of injury of badminton players is mostly mild, with some cases of moderate and severe injury. The combination of core strengthening associated with manual therapy rehabilitation and stretching can accelerate the muscular rehabilitation of the lumbar spine. Conclusion In the rehabilitation process of badminton injuries, we should combine physical training with traditional rehabilitation techniques, increasing the effectiveness of sports rehabilitation. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.
DOI: 10.6084/m9.figshare.20337344.v1
title: STUDY ON SPORTS INJURIES AND REHABILITATION IN BADMINTON PLAYERS

description: ABSTRACT Introduction Badminton has a wide audience and a large development market in China. Although it benefits the flexibility of sedentary workers by recruiting the whole body’s musculature, it can also cause a harmful effect due to lack of preparation or intensity during matches. Objective Study the methods of sports injury and rehabilitation of badminton players. Methods 60 badminton players with low back injuries were randomly divided into experimental and control groups. The control group used the traditional method of recovery by manual techniques. An intervention with core stability training lasting 40 minutes three times a week for six weeks was added to the experimental group. Results The degree of injury of badminton players is mostly mild, with some cases of moderate and severe injury. The combination of core strengthening associated with manual therapy rehabilitation and stretching can accelerate the muscular rehabilitation of the lumbar spine. Conclusion In the rehabilitation process of badminton injuries, we should combine physical training with traditional rehabilitation techniques, increasing the effectiveness of sports rehabilitation. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.
DOI: 10.3886/e183842v1-146450
title: Data and Code for: Interest rates and the spatial polarization of housing markets

description: Rising within-country differences in house values are a much debated trend in<br>the U.S. and internationally. Using new long-run regional data for 15 advanced<br>economies, we first show that standard explanations linking growing price dispersion<br>to rent dispersion are contradicted by an important stylized fact: rent dispersion<br>has increased far less than price dispersion. We then propose a new explanation: a<br>uniform decline in real risk-free interest rates can have heterogeneous spatial effects<br>on house values. Falling real safe rates disproportionately push up prices in large<br>agglomerations where initial rent-price ratios are low, leading to housing market<br>polarization on the national level.
DOI: 10.6084/m9.figshare.11948820.v1
title: Sulforaphane Activates a Lysosome-dependent Transcriptional Program to Mitigate Oxidative Stress

description: Oxidative stress underlies a number of pathological conditions, including cancer, neurodegeneration, and aging. Antioxidant-rich foods help maintain cellular redox homeostasis and mitigate oxidative stress, but the underlying mechanisms are not clear. For example, sulforaphane (SFN), an electrophilic compound that is enriched in cruciferous vegetables such as broccoli, is a potent inducer of cellular antioxidant responses. NFE2L2/NRF2 (nuclear factor, erythroid 2 like 2), a transcriptional factor that controls the expression of multiple detoxifying enzymes through antioxidant response elements (AREs), is a proposed target of SFN. <i>NFE2L2/NRF2</i> is a target gene of TFEB (transcription factor EB), a master regulator of autophagic and lysosomal functions, which we show here to be potently activated by SFN. SFN induces TFEB nuclear translocation via a Ca<sup>2+</sup>-dependent but MTOR (mechanistic target of rapamycin kinase)-independent mechanism through a moderate increase in reactive oxygen species (ROS). Activated TFEB then boosts the expression of genes required for autophagosome and lysosome biogenesis, which are known to facilitate the clearance of damaged mitochondria. Notably, TFEB activity is required for SFN-induced protection against both acute oxidant bursts and chronic oxidative stress. Hence, by simultaneously activating macroautophagy/autophagy and detoxifying pathways, natural compound SFN may trigger a self-defense cellular mechanism that can effectively mitigate oxidative stress commonly associated with many metabolic and age-related diseases.
DOI: 10.6084/m9.figshare.11948820.v2
title: Sulforaphane Activates a lysosome-dependent transcriptional program to mitigate oxidative stress

description: Oxidative stress underlies a number of pathological conditions, including cancer, neurodegeneration, and aging. Antioxidant-rich foods help maintain cellular redox homeostasis and mitigate oxidative stress, but the underlying mechanisms are not clear. For example, sulforaphane (SFN), an electrophilic compound that is enriched in cruciferous vegetables such as broccoli, is a potent inducer of cellular antioxidant responses. NFE2L2/NRF2 (nuclear factor, erythroid 2 like 2), a transcriptional factor that controls the expression of multiple detoxifying enzymes through antioxidant response elements (AREs), is a proposed target of SFN. <i>NFE2L2/NRF2</i> is a target gene of TFEB (transcription factor EB), a master regulator of autophagic and lysosomal functions, which we show here to be potently activated by SFN. SFN induces TFEB nuclear translocation via a Ca<sup>2+</sup>-dependent but MTOR (mechanistic target of rapamycin kinase)-independent mechanism through a moderate increase in reactive oxygen species (ROS). Activated TFEB then boosts the expression of genes required for autophagosome and lysosome biogenesis, which are known to facilitate the clearance of damaged mitochondria. Notably, TFEB activity is required for SFN-induced protection against both acute oxidant bursts and chronic oxidative stress. Hence, by simultaneously activating macroautophagy/autophagy and detoxifying pathways, natural compound SFN may trigger a self-defense cellular mechanism that can effectively mitigate oxidative stress commonly associated with many metabolic and age-related diseases. <b>Abbreviations:</b> ANOVA: analyzes of variance; AREs: antioxidant response elements; Baf-A1: bafilomycin A<sub>1</sub>; BHA: butylhydroxyanisole; CAT: catechin hydrate; CCCP: carbonyl cyanide m- chlorophenylhydrazone; CLEAR: coordinated lysosomal expression and regulation; DCFH-DA: 2ʹ,7ʹ-dichlorofluorescin diacetate; FBS: fetal bovine serum; GFP: green fluorescent protein; HMOX1/HO-1: heme oxygenase 1; KD: knockdown; KEAP1: kelch like ECH associated protein 1; KO: knockout; LAMP1: lysosomal associated membrane protein 1; MCOLN1/TRPML1: mucolipin 1; ML-SA1: mucolipin-specific synthetic agonist 1; ML-SI3: mucolipin-specific synthetic inhibitor 3; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; NAC: N-acetylcysteine; NFE2L2/NRF2: nuclear factor: erythroid 2 like 2; NPC: Niemann–Pick type C; PBS: phosphate-buffered saline; PPP2/PP2A: protein phosphatase 2; Q-PCR: real time polymerase chain reaction; ROS: reactive oxygen species; RPS6KB1/S6K1/p70S6K: ribosomal protein S6 kinase B1; SFN: sulforaphane; TFEB: transcription factor EB; WT, wild-type
DOI: 10.6084/m9.figshare.12997405
title: Additional file 1 of A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples

description: Additional file 1: Table S0. Datasets and their application in this study. Table S1. Gene Ontology (Biological Processes (BP)) annotation for the marker genes identified by LinDeconSeq. Table S2. Gold-standard marker genes. Table S3. Signature matrix of 13 cell types revealed by LinDeconSeq in AML and Healthy samples. Table S4. The estimated cellular fractions by LinDeconSeq for 179 TCGA-AML samples. Table S5. The estimated cellular fractions for the 100 transcriptomic data of the healthy samples in GSE134080 using LinDeconSeq. Table S6. Comparison of the actual and predicted classification for 2138 independent test samples based on the SVM, Random Forest and Logistic Regression. Table S7. Two subgroups derived from TCGA-AML samples using PAM clustering method. Table S8. Differentially expressed genes (DEGs) revealed by DESeq2 between SubgroupA and SubgroupB. Table S9. Gene Ontology analysis for the DEGs with tool DAVID. Table S10. The estimated cellular fractions for the 187 TARGET-AML samples with LinDeconSeq. Table S11. The feature genes selected from the DEGs for training random forest classifier. Table S12. The subgroups predicted by the trained random forest classifier for TARGET-AML samples.
DOI: 10.6084/m9.figshare.12997405.v1
title: Additional file 1 of A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples

description: Additional file 1: Table S0. Datasets and their application in this study. Table S1. Gene Ontology (Biological Processes (BP)) annotation for the marker genes identified by LinDeconSeq. Table S2. Gold-standard marker genes. Table S3. Signature matrix of 13 cell types revealed by LinDeconSeq in AML and Healthy samples. Table S4. The estimated cellular fractions by LinDeconSeq for 179 TCGA-AML samples. Table S5. The estimated cellular fractions for the 100 transcriptomic data of the healthy samples in GSE134080 using LinDeconSeq. Table S6. Comparison of the actual and predicted classification for 2138 independent test samples based on the SVM, Random Forest and Logistic Regression. Table S7. Two subgroups derived from TCGA-AML samples using PAM clustering method. Table S8. Differentially expressed genes (DEGs) revealed by DESeq2 between SubgroupA and SubgroupB. Table S9. Gene Ontology analysis for the DEGs with tool DAVID. Table S10. The estimated cellular fractions for the 187 TARGET-AML samples with LinDeconSeq. Table S11. The feature genes selected from the DEGs for training random forest classifier. Table S12. The subgroups predicted by the trained random forest classifier for TARGET-AML samples.
DOI: 10.6084/m9.figshare.14570281
title: Additional file 2 of A novel nonsense mutation in ARMC5 causes primary bilateral macronodular adrenocortical hyperplasia

description: Additional file 2: Table S2. In silico predictions of ARMC5 c.1369C&gt;T (p.Arg457Trp) on functional impacts using VarCards ( http://varcards.biols.ac.cn/ ).
DOI: 10.6084/m9.figshare.14570281.v1
title: Additional file 2 of A novel nonsense mutation in ARMC5 causes primary bilateral macronodular adrenocortical hyperplasia

description: Additional file 2: Table S2. In silico predictions of ARMC5 c.1369C&gt;T (p.Arg457Trp) on functional impacts using VarCards ( http://varcards.biols.ac.cn/ ).
DOI: 10.25430/researchdata.cab.unipd.it.00001207
title: SVRUM: Safety-system for Vulnerable Road User's Mobility

description: The dataset contains measurements generated by different types of sensors (3-axis accelerometer, sonar, GPS) mounted on a city bicycle, which was run over different types of roads. The dataset is meant to facilitate the testing and comparison of different data analysis techniques for road hazard identification.
DOI: 10.6084/m9.figshare.19288900
title: Additional file 2 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 2: Table S2. Annotation information of uingenes from RNA-Seq. (XLS 48557 kb)
DOI: 10.6084/m9.figshare.19288900.v1
title: Additional file 2 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 2: Table S2. Annotation information of uingenes from RNA-Seq. (XLS 48557 kb)
DOI: 10.6084/m9.figshare.19288902
title: Additional file 1 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 1. Differentially expressed genes (DEGs) in KY 131 under cold stress.
DOI: 10.6084/m9.figshare.19288902.v1
title: Additional file 1 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 1. Differentially expressed genes (DEGs) in KY 131 under cold stress.
DOI: 10.6084/m9.figshare.19288905
title: Additional file 2 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 2. Differentially expressed genes (DEGs) in DN 422 under cold stress.
DOI: 10.6084/m9.figshare.19288905.v1
title: Additional file 2 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 2. Differentially expressed genes (DEGs) in DN 422 under cold stress.
DOI: 10.6084/m9.figshare.19288906
title: Additional file 3 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 3: Table S3. Read count statistics of genes from RNA-Seq.
DOI: 10.6084/m9.figshare.19288906.v1
title: Additional file 3 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 3: Table S3. Read count statistics of genes from RNA-Seq.
DOI: 10.6084/m9.figshare.19288908
title: Additional file 3 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 3. Go enrichment analysis of differentially expressed genes (DEGs) in KY 131 under cold stress.
DOI: 10.6084/m9.figshare.19288908.v1
title: Additional file 3 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 3. Go enrichment analysis of differentially expressed genes (DEGs) in KY 131 under cold stress.
DOI: 10.6084/m9.figshare.14570293
title: Additional file 1 of DPSCs treated by TGF-β1 regulate angiogenic sprouting of three-dimensionally co-cultured HUVECs and DPSCs through VEGF-Ang-Tie2 signaling

description: Additional file 1.
DOI: 10.6084/m9.figshare.19288909
title: Additional file 4 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 4: Table S4. FPKM of differential expressed genes from RNA-Seq.
DOI: 10.6084/m9.figshare.14570293.v1
title: Additional file 1 of DPSCs treated by TGF-β1 regulate angiogenic sprouting of three-dimensionally co-cultured HUVECs and DPSCs through VEGF-Ang-Tie2 signaling

description: Additional file 1.
DOI: 10.6084/m9.figshare.19288909.v1
title: Additional file 4 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 4: Table S4. FPKM of differential expressed genes from RNA-Seq.
DOI: 10.6084/m9.figshare.19288911
title: Additional file 4 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 4. Go enrichment analysis of differentially expressed genes (DEGs) in DN 422 under cold stress.
DOI: 10.6084/m9.figshare.19288911.v1
title: Additional file 4 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 4. Go enrichment analysis of differentially expressed genes (DEGs) in DN 422 under cold stress.
DOI: 10.6084/m9.figshare.19288912
title: Additional file 5 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 5: Table S5. Hairpin and mature sequences of novel miRNAs from sRNA-Seq.
DOI: 10.6084/m9.figshare.19288912.v1
title: Additional file 5 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 5: Table S5. Hairpin and mature sequences of novel miRNAs from sRNA-Seq.
DOI: 10.7910/dvn/h1zyn3
title: FUE Methode

description: Die FUE Methode (Follicular Unit Extraction) ist ein modernes Verfahren der Haartransplantation, bei dem einzelne Haarfollikel direkt aus der Spenderregion, typischerweise dem Hinterkopf, entnommen und in kahle oder dünner werdende Bereiche des Kopfes transplantiert werden, um natürliche Wachstumsmuster zu erzeugen und Haarausfall zu bekämpfen. Diese Technik minimiert Narbenbildung, da sie ohne große Schnitte auskommt, ermöglicht eine schnellere Heilung und bietet die Flexibilität, Haare auch in andere Körperbereiche zu transplantieren, erfordert jedoch eine hohe Präzision und Erfahrung des Chirurgen, um optimale Ergebnisse zu erzielen.
DOI: 10.6084/m9.figshare.19288914
title: Additional file 5 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 5. KEGG enrichment analysis of differentially expressed genes (DEGs) in KY 131 under cold stress.
DOI: 10.6084/m9.figshare.19288914.v1
title: Additional file 5 of An integrated analysis of the rice transcriptome and lipidome reveals lipid metabolism plays a central role in rice cold tolerance

description: Additional file 5. KEGG enrichment analysis of differentially expressed genes (DEGs) in KY 131 under cold stress.
DOI: 10.6084/m9.figshare.19288915
title: Additional file 6 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 6: Table S6. Read count statistics of miRNAs from sRNA-Seq.
DOI: 10.6084/m9.figshare.12997457
title: Additional file 2 of Both Wnt signaling and epidermal stem cell-derived extracellular vesicles are involved in epidermal cell growth

description: Additional file 2: Supplementary Table S2. Proteome profile of epidermal stem cell (EpSC)-derived extracellular vesicles.
DOI: 10.6084/m9.figshare.19288915.v1
title: Additional file 6 of Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis)

description: Additional file 6: Table S6. Read count statistics of miRNAs from sRNA-Seq.