cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22133961.v1
title: Joint Diagnosis of High-dimensional Process Mean and Covariance Matrix based on Bayesian Model Selection

description: Apart from the quick detection of abnormal changes in a process, it is also critical to pinpoint faulty variables after an out-of-control signal. The existing diagnostic procedures mainly focus on the diagnosis of changes in the process mean. This paper investigates the joint diagnosis of high-dimensional process mean and covariance matrix based on Bayesian model selection with nonlocal priors. The proposed procedure enjoys two promising features. First, in addition to the isolation of shifted components, it can also provide a probability that the identified components are true, which is very useful for elimination of root causes of abnormal changes. Second, it possesses the model consistency property in the sense that the probability of identifying the true components with shifts approaches one as the sample size increases. The performance comparisons favor the proposed procedure. A real example based on the urban waste water treatment process is provided to illustrate the implementation of the proposed method.
DOI: 10.6084/m9.figshare.23707019
title: Additional file 4 of Immediate and long-term changes in infectious diseases in China at the “First-level-response”, “Normalized-control” and “Dynamic-COVID-zero” stages from 2020 to 2022: a multistage interrupted-time-series-analysis

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.22133961
title: Joint Diagnosis of High-Dimensional Process Mean and Covariance Matrix based on Bayesian Model Selection

description: Apart from the quick detection of abnormal changes in a process, it is also critical to pinpoint faulty variables after an out-of-control signal. The existing diagnostic procedures mainly focus on the diagnosis of changes in the process mean. This article investigates the joint diagnosis of high-dimensional process mean and covariance matrix based on Bayesian model selection with nonlocal priors. The proposed procedure enjoys two promising features. First, in addition to the isolation of shifted components, it can also provide a probability that the identified components are true, which is very useful for elimination of root causes of abnormal changes. Second, it possesses the model consistency property in the sense that the probability of identifying the true components with shifts approaches one as the sample size increases. The performance comparisons favor the proposed procedure. A real example based on the urban waste water treatment process is provided to illustrate the implementation of the proposed method.
DOI: 10.6084/m9.figshare.7460042
title: Additional file 1: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

description: Table S1. All protein sequences used in this study. (XLSX 71â kb)
DOI: 10.6084/m9.figshare.20033151.v1
title: Additional file 2 of Characterization of a prognostic model for lung squamous cell carcinoma based on eight stemness index-related genes

description: Additional file 2: Table S1. The results of differential expression analysis.
DOI: 10.6084/m9.figshare.20033190.v1
title: Additional file 3 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 3: Table S1. HML-9 proviral sequences colocalized with genes.
DOI: 10.6084/m9.figshare.20033202
title: Additional file 5 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 5: Table S3. The associations between each solo LTR and its putative regulated gene(s).
DOI: 10.6084/m9.figshare.14269912
title: Jingzhaotoxin-X, a gating modifier of Kv4.2 and Kv4.3 potassium channels purified from the venom of the Chinese tarantula Chilobrachys jingzhao

description: Abstract Background: The tarantula Chilobrachys jingzhao is one of the largest venomous spiders in China. In previous studies, we purified and characterized at least eight peptides from C. jingzhao venom. In this report, we describe the purification and characterization of Jingzhaotoxin-X (JZTX-X), which selectively blocks Kv4.2 and Kv4.3 potassium channels. Methods: JZTX-X was purified using a combination of cation-exchange HPLC and reverse-phase HPLC. The amino-acid sequence was determined by automated Edman degradation and confirmed by mass spectrometry (MS). Voltage-gated ion channel currents were recorded in HEK293t cells transiently transfected with a variety of ion channel constructs. In addition, the hyperalgesic activity of JZTX-X and the toxin´s effect on motor function were assessed in mice. Results: JZTX-X contained 31 amino acids, with six cysteine residues that formed three disulfide bonds within an inhibitory cysteine knot (ICK) topology. In whole-cell voltage-clamp experiments, JZTX-X inhibited Kv4.2 and Kv4.3 potassium channels in a concentration- and voltage-dependent manner, without affecting other ion channels (Kv1.1, 1.2, 1.3, 2.1, delayed rectifier potassium channels, high- and low-voltage-activated Ca2+ channels, and voltage-gated sodium channels Nav1.5 and 1.7). JZTX-X also shifted the voltage-dependent channel activation to more depolarized potentials, whereas extreme depolarization caused reversible toxin binding to Kv4.2 channels. JZTX-X shifted the Kv4.2 and Kv4.3 activities towards a resting state, since at the resting potential the toxin completely inhibited the channels, even in the absence of an applied physical stimulus. Intrathecal or intraplantar injection of JZTX-X caused a long-lasting decrease in the mechanical nociceptive threshold (hyperalgesia) but had no effect on motor function as assessed in the rotarod test. Conclusions: JZTX-X selectively suppresses Kv4.2 and Kv4.3 potassium channel activity in a concentration- and voltage-dependent manner and causes long-lasting mechanical hyperalgesia.
DOI: 10.6084/m9.figshare.20033184.v1
title: Additional file 1 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 1: Dataset S1. The nucleotide sequence of HML-9 proviral elements.
DOI: 10.6084/m9.figshare.14269979.v1
title: Diagnostic value of miR-145 and its regulatory role in macrophage immune response in tuberculosis

description: Abstract Tuberculosis (TB) induced by Mycobacterium tuberculosis (Mtb) is a serious global health burden. This study sought to investigate the expression and diagnostic value of serum miR-145 in TB patients and explore the biological function of miR-145 using macrophages. Serum expression levels of miR-145 were estimated by quantitative real-time PCR. A receiver operating characteristic curve was plotted to evaluate the diagnostic accuracy of miR-145. This study further focused on the effects of miR-145 on cell viability and inflammation in macrophages upon Mtb infection, and explored the potential target gene of miR-145. Serum expression levels of miR-145 were decreased in TB patients, and the upregulated inflammatory cytokines in TB patients were negatively correlated with the serum expression levels of miR-145. miR-145 had considerable diagnostic accuracy in distinguishing of TB patients from healthy individuals and differentiating between active TB cases and latent TB cases. Mtb infection induced an increase in cell viability and inflammatory responses in macrophages, but these promoting effects were rescued by the overexpression of miR-145. CXCL16 was determined as a target gene of miR-145 in macrophages. Overall, this study demonstrated that the decreased serum miR-145 expression serves a candidate diagnostic biomarker in TB patients. The overexpression of miR-145 in macrophages upon Mtb infection can suppress cell viability and infection-induced inflammation via regulating CXCL16, indicating the potential of miR-145 as a therapeutic target of TB.
DOI: 10.6084/m9.figshare.20033184
title: Additional file 1 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 1: Dataset S1. The nucleotide sequence of HML-9 proviral elements.
DOI: 10.6084/m9.figshare.20033190
title: Additional file 3 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 3: Table S1. HML-9 proviral sequences colocalized with genes.
DOI: 10.6084/m9.figshare.20033202.v1
title: Additional file 5 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 5: Table S3. The associations between each solo LTR and its putative regulated gene(s).
DOI: 10.6084/m9.figshare.25195754
title: Source data file for ChIP, RNA analysis, Nascent RNA transcription analysis

description: Datasets that were used for making figures for ChIP analysis, RNA analysis, and Nascent RNA transcription analysis as described in Talukdar et al. Nature Communication 2024
DOI: 10.6084/m9.figshare.25195754.v1
title: Source data file for ChIP, RNA analysis, Nascent RNA transcription analysis

description: Datasets that were used for making figures for ChIP analysis, RNA analysis, and Nascent RNA transcription analysis as described in Talukdar et al. Nature Communication 2024
DOI: 10.6084/m9.figshare.22140140
title: Bacterial lipoproteins shift cellular metabolism to glycolysis in macrophages causing bone erosion

description:   
Belonging to a group of membrane proteins, bacterial lipoproteins (LPP) are defined by a unique lipid structure at their <em>N</em>-terminus providing the anchor in the bacterial cell membrane. In Gram-positive bacteria, LPP play a key role in host immune activation triggered through a Toll-like receptor 2 (TLR2)-mediated action resulting in macrophage stimulation and subsequent tissue damage demonstrated in <em>in vivo</em> experimental models. Yet, the physiologic links between LPP activation, cytokine release, and any underlying switches in cellular metabolism remain unclear. In this study, we demonstrated that <em>S. aureus</em> Lpl1 not only triggers cytokine production but also confers a shift towards fermentative metabolism in bone marrow derived macrophages (BMDM). Lpl1 consists of di- and tri-acylated LPP variants, hence, the synthetic P2C and P3C, mimicking di-and tri-acylated LPP, were performed to reveal their effect on BMDM. When compared to P3C, P2C was found to shift the metabolism of BMDM and the human mature monocytic MonoMac 6 (MM6) cells more profoundly towards the fermentative pathway as indicated by lactate accumulation, glucose consumption, pH reduction, and oxygen consumption. <em>In vivo</em>, P2C caused more severe joint inflammation, bone erosion and lactate and malate accumulation when compared to P3C. These observed P2C effects were completely abrogated in monocyte/macrophage depleted mice. Taken together, these findings now solidly confirm the hypothesized link between LPP exposure, a macrophage metabolic shift towards fermentation, and ensuing bone destruction.
DOI: 10.6084/m9.figshare.7460237.v1
title: Additional file 5: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: SNPs generated from GLM and MLM analysis when Pâ &lt;â 0.01. (XLSX 364â kb)
DOI: 10.6084/m9.figshare.20033208.v1
title: Additional file 6 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 6: Table S4. The associations between each proviral LTR and its putative regulated gene(s).
DOI: 10.6084/m9.figshare.20033217
title: Additional file 7 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 7: Table S5. PBS types in HML-9.
DOI: 10.15156/bio/sh1054113.09fu
title: SH1054113.09FU

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/sh1054114.09fu
title: SH1054114.09FU

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/sh1054115.09fu
title: SH1054115.09FU

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/sh1054116.09fu
title: SH1054116.09FU

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/sh1054117.09fu
title: SH1054117.09FU

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/sh1054118.09fu
title: SH1054118.09FU

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/sh1054119.09fu
title: SH1054119.09FU

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/sh1054120.09fu
title: SH1054120.09FU

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/sh1054121.09fu
title: SH1054121.09FU

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/sh1054122.09fu
title: SH1054122.09FU

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.