cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19722679.v1
title: Proteotoxic stress disrupts epithelial integrity by inducing MTOR sequestration and autophagy overactivation

description: Macroautophagy/autophagy, an evolutionarily conserved degradation system, serves to clear intracellular components through the lysosomal pathway. Mounting evidence has revealed cytoprotective roles of autophagy; however, the intracellular causes of overactivated autophagy, which has cytotoxic effects, remain elusive. Here we show that sustained proteotoxic stress induced by loss of the RING and Kelch repeat-containing protein C53A5.6/RIKE-1 induces sequestration of LET-363/MTOR complex and overactivation of autophagy, and consequently impairs epithelial integrity in <i>C. elegans</i>. In C53A5.6/RIKE-1-deficient animals, blocking autophagosome formation effectively prevents excessive endosomal degradation, mitigates mislocalization of intestinal membrane components and restores intestinal lumen morphology. However, autophagy inhibition does not affect LET-363/MTOR aggregation in animals with compromised C53A5.6/RIKE-1 function. Improving proteostasis capacity by reducing DAF-2 insulin/IGF1 signaling markedly relieves the aggregation of LET-363/MTOR and alleviates autophagy overactivation, which in turn reverses derailed endosomal trafficking and rescues epithelial morphogenesis defects in C53A5.6/RIKE-1-deficient animals. Hence, our studies reveal that C53A5.6/RIKE-1-mediated proteostasis is critical for maintaining the basal level of autophagy and epithelial integrity. <b>Abbreviations:</b> ACT-5: actin 5; ACTB: actin beta; ALs: autolysosomes; APs: autophagosomes; AJM-1: apical junction molecule; ATG: autophagy related; C. elegans: Caenorhabditis elegans; CPL-1: cathepsin L family; DAF: abnormal dauer formation; DLG-1: Drosophila discs large homolog; ERM-1: ezrin/radixin/moesin; EPG: ectopic P granule; GFP: freen fluorescent protein; HLH-30: helix loop helix; HSP: heat shock protein; LAAT-1: lysosome associated amino acid transporter; LET: lethal; LGG-1: LC3, GABARAP and GATE-16 family; LMP-1: LAMP (lysosome-associated membrane protein) homolog; MTOR: mechanistic target of rapamycin kinase; NUC-1: abnormal nuclease; PEPT-1/OPT-2: Peptide transporter family; PGP-1: P-glycoprotein related; RAB: RAB family; RIKE-1: RING and Kelch repeat-containing protein; SLCF-1: solute carrier family; SQST-1: sequestosome related; SPTL-1: serine palmitoyl transferase family.
DOI: 10.6084/m9.figshare.9761222
title: MEP_Olfactory_Data

description: Head-fixed mice were trained to perform an olfactory delayed non-match to sample task. For each trial, an olfactory stimulus (ethyl acetate, EA, or 2-pentanone, 2P) was presented as the sample, followed by a delay period (5 s) and then a testing olfactory stimulus, either matched or non-matched to the sample. Water-restricted mice were rewarded with water if they licked within a response time window in the non-match but not match trials. The mouse performed tasks continuously with a 10 s rest between neighboring trials. The experiment is designed to separate the working memory period and decision-making period.
DOI: 10.6084/m9.figshare.23917014
title: Additional file 1 of An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

description: Additional file 1: Table S1. RSCU and RFSC values of the codons in chloroplast genomes of three Coffea species.
DOI: 10.6084/m9.figshare.23917014.v1
title: Additional file 1 of An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

description: Additional file 1: Table S1. RSCU and RFSC values of the codons in chloroplast genomes of three Coffea species.
DOI: 10.6084/m9.figshare.23917017
title: Additional file 2 of An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

description: Additional file 2: Table S2. The RSCU values and Δ RSCU value in the high and low expression library of three Coffea species.
DOI: 10.6084/m9.figshare.23917017.v1
title: Additional file 2 of An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

description: Additional file 2: Table S2. The RSCU values and Δ RSCU value in the high and low expression library of three Coffea species.
DOI: 10.6084/m9.figshare.23917020
title: Additional file 3 of An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

description: Additional file 3: Table S3. Comparison of codon usage frequency between three Coffea species and four organisms.
DOI: 10.6084/m9.figshare.23917020.v1
title: Additional file 3 of An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

description: Additional file 3: Table S3. Comparison of codon usage frequency between three Coffea species and four organisms.
DOI: 10.6084/m9.figshare.14479985
title: Additional file 1 of Highly efficient generation of bacterial leaf blight-resistant and transgene-free rice using a genome editing and multiplexed selection system

description: Additional file 1: Supplementary Table 1. Sequence analysis of mutations in the Xa13 promoter of T0 lines.
DOI: 10.6084/m9.figshare.14479985.v1
title: Additional file 1 of Highly efficient generation of bacterial leaf blight-resistant and transgene-free rice using a genome editing and multiplexed selection system

description: Additional file 1: Supplementary Table 1. Sequence analysis of mutations in the Xa13 promoter of T0 lines.
DOI: 10.6084/m9.figshare.14479988
title: Additional file 2 of Highly efficient generation of bacterial leaf blight-resistant and transgene-free rice using a genome editing and multiplexed selection system

description: Additional file 2: Supplementary Table 2. Raw data and ANOVA analysis of lesion length and area of mutant lines and the WT after infection.
DOI: 10.6084/m9.figshare.14479988.v1
title: Additional file 2 of Highly efficient generation of bacterial leaf blight-resistant and transgene-free rice using a genome editing and multiplexed selection system

description: Additional file 2: Supplementary Table 2. Raw data and ANOVA analysis of lesion length and area of mutant lines and the WT after infection.
DOI: 10.5281/zenodo.10677355
title: Removal of mercury from industrial waste water using low absorbent charcoal (black babul shell)
DOI: 10.5281/zenodo.10677356
title: Removal of mercury from industrial waste water using low absorbent charcoal (black babul shell)
DOI: 10.6084/m9.figshare.11858616
title: Additional file 1 of Should compression bandage be performed after total knee arthroplasty? A meta-analysis of randomized controlled trials

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.11858616.v1
title: Additional file 1 of Should compression bandage be performed after total knee arthroplasty? A meta-analysis of randomized controlled trials

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.11858733
title: Additional file 1 of Genetic diversity of Bacillus anthracis Ames lineage strains in China

description: Additional file 1: Table S1. B. anthracis Ames lineage strains and the MLVA profiles identified in this study.
DOI: 10.6084/m9.figshare.11858733.v1
title: Additional file 1 of Genetic diversity of Bacillus anthracis Ames lineage strains in China

description: Additional file 1: Table S1. B. anthracis Ames lineage strains and the MLVA profiles identified in this study.
DOI: 10.6084/m9.figshare.24965941
title: Additional file 1 of Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice

description: Additional file 1: Table S1. Summary statistics of the five traits for the two populations in different environments. Table S2. Detail information of all QTLs detected by BIP. Table S3. Detail information of all QTLs detected by REG. Table S4. Detail information of all QTLs detected by CSL. Table S5. Detail information of all QTLs detected by MET. Table S6. Predicted genotypic values of the selected lines and target genotype in each population and environment. Additive effect of each QTL for calculating the genotypic values was picked up from the BIP mapping results at the nearest position of the average QTL position across in Table 7. Table S7. Nine regions harboring QTLs for MQ-GS traits.
DOI: 10.6084/m9.figshare.24965941.v1
title: Additional file 1 of Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice

description: Additional file 1: Table S1. Summary statistics of the five traits for the two populations in different environments. Table S2. Detail information of all QTLs detected by BIP. Table S3. Detail information of all QTLs detected by REG. Table S4. Detail information of all QTLs detected by CSL. Table S5. Detail information of all QTLs detected by MET. Table S6. Predicted genotypic values of the selected lines and target genotype in each population and environment. Additive effect of each QTL for calculating the genotypic values was picked up from the BIP mapping results at the nearest position of the average QTL position across in Table 7. Table S7. Nine regions harboring QTLs for MQ-GS traits.
DOI: 10.6084/m9.figshare.11858748
title: Additional file 2 of Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China

description: Additional file 2: Table S2. Posterior probabilities supporting undescribed species/species using different algorithms and priors.
DOI: 10.6084/m9.figshare.11858748.v1
title: Additional file 2 of Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China

description: Additional file 2: Table S2. Posterior probabilities supporting undescribed species/species using different algorithms and priors.
DOI: 10.6084/m9.figshare.9761612
title: Generation of navigation networks for corridor spaces based on indoor visibility map

description: In
this study, we proposed a method for building navigation networks of indoor
spaces based on a quantitative visibility analysis. we shared data and core codes in the figshare repository.
DOI: 10.6084/m9.figshare.24965985
title: Additional file 1 of Effects of electroconvulsive therapy on functional brain networks in patients with schizophrenia

description: Additional file 1.
DOI: 10.6084/m9.figshare.24965985.v1
title: Additional file 1 of Effects of electroconvulsive therapy on functional brain networks in patients with schizophrenia

description: Additional file 1.
DOI: 10.6084/m9.figshare.13955978
title: Directed Community Detection With Network Embedding

description: Community detection in network data aims at grouping similar nodes sharing certain characteristics together. Most existing methods focus on detecting communities in undirected networks, where similarity between nodes is measured by their node features and whether they are connected. In this article, we propose a novel method to conduct network embedding and community detection simultaneously in a directed network. The network embedding model introduces two sets of vectors to represent the out- and in-nodes separately, and thus allows the same nodes belong to different out- and in-communities. The community detection formulation equips the negative log-likelihood with a novel regularization term to encourage community structure among the nodes representations, and thus achieves better performance by jointly estimating the nodes embeddings and their community structures. To tackle the resultant optimization task, an efficient alternative updating scheme is developed. More importantly, the asymptotic properties of the proposed method are established in terms of both network embedding and community detection, which are also supported by numerical experiments on some simulated and real examples.
DOI: 10.6084/m9.figshare.13955978.v2
title: Directed Community Detection With Network Embedding

description: Community detection in network data aims at grouping similar nodes sharing certain characteristics together. Most existing methods focus on detecting communities in undirected networks, where similarity between nodes is measured by their node features and whether they are connected. In this article, we propose a novel method to conduct network embedding and community detection simultaneously in a directed network. The network embedding model introduces two sets of vectors to represent the out- and in-nodes separately, and thus allows the same nodes belong to different out- and in-communities. The community detection formulation equips the negative log-likelihood with a novel regularization term to encourage community structure among the nodes representations, and thus achieves better performance by jointly estimating the nodes embeddings and their community structures. To tackle the resultant optimization task, an efficient alternative updating scheme is developed. More importantly, the asymptotic properties of the proposed method are established in terms of both network embedding and community detection, which are also supported by numerical experiments on some simulated and real examples.
DOI: 10.5281/zenodo.10677363
title: Exploring Green Extracts for Silver Nanoparticle Synthesis
DOI: 10.5281/zenodo.10677364
title: Exploring Green Extracts for Silver Nanoparticle Synthesis
DOI: 10.6084/m9.figshare.13955978.v1
title: Directed community detection with network embedding*

description: Community detection in network data aims at grouping similar nodes sharing certain characteristics together. Most existing methods focus on detecting communities in undirected networks, where similarity between nodes is measured by their node features and whether they are connected. In this article, we propose a novel method to conduct network embedding and community detection simultaneously in a directed network. The network embedding model introduces two sets of vectors to represent the out- and in-nodes separately, and thus allows the same nodes belong to different out- and in-communities. The community detection formulation equips the negative log-likelihood with a novel regularization term to encourage community structure among the nodes representations, and thus achieves better performance by jointly estimating the nodes embeddings and their community structures. To tackle the resultant optimization task, an efficient alternative updating scheme is developed. More importantly, the asymptotic properties of the proposed method are established in terms of both network embedding and community detection, which are also supported by numerical experiments on some simulated and real examples.
DOI: 10.6084/m9.figshare.9761681
title: Myotubularin related protein 7 is essential for the spermatogonial stem cell homeostasis via PI3K/AKT signaling

description: Myotubularin related protein 7 (MTMR7), a key member of the MTMR family, depicts phosphatase activity and is involved in myogenesis and tumor growth. We have previously identified MTMR7 in the proteomic profile of mouse spermatogonial stem cell (SSC) maturation and differentiation, implying that MTMR7 is associated with neonatal testicular development. In this study, to further explore the distribution and function of MTMR7 in mouse testis, we studied the effect of <i>Mtmr7</i> knockdown on neonatal testicular development by testicular and SSC culture methods. Our results revealed that MTMR7 is exclusively located in early germ cells. Deficiency of MTMR7 by morpholino in neonatal testis caused excessive SSC proliferation, which was attributable to the aberrant PI3K/AKT signaling activation. Altogether, our study demonstrates that MTMR7 maintains SSC homeostasis by inhibiting PI3K/AKT signaling activation.
DOI: 10.6084/m9.figshare.9761681.v1
title: Myotubularin related protein 7 is essential for the spermatogonial stem cell homeostasis via PI3K/AKT signaling

description: Myotubularin related protein 7 (MTMR7), a key member of the MTMR family, depicts phosphatase activity and is involved in myogenesis and tumor growth. We have previously identified MTMR7 in the proteomic profile of mouse spermatogonial stem cell (SSC) maturation and differentiation, implying that MTMR7 is associated with neonatal testicular development. In this study, to further explore the distribution and function of MTMR7 in mouse testis, we studied the effect of <i>Mtmr7</i> knockdown on neonatal testicular development by testicular and SSC culture methods. Our results revealed that MTMR7 is exclusively located in early germ cells. Deficiency of MTMR7 by morpholino in neonatal testis caused excessive SSC proliferation, which was attributable to the aberrant PI3K/AKT signaling activation. Altogether, our study demonstrates that MTMR7 maintains SSC homeostasis by inhibiting PI3K/AKT signaling activation.
DOI: 10.6084/m9.figshare.19723189
title: Directed differentiation of human pluripotent stem cells into diverse organ-specific mesenchyme of the digestive and respiratory systems.

description:   Development of visceral organs such as the esophagus, lung, liver and stomach are coordinated by reciprocal signaling interactions between the embryonic endoderm and adjacent mesoderm cells in the fetal foregut. While the recent successes in recapitulating developmental signaling <em>in vitro </em>has enabled the differentiation of human pluripotent stem cells (hPSCs) into various types of organ-specific endodermal epithelium, the generation of organ-specific mesenchyme has received much less attention. This is a major limitation in ongoing efforts to engineer complex human tissue. Here, we describe a series of protocols to differentiate hPSCs into different types of organ-specific mesoderm leveraging signaling networks and new molecular markers recently elucidated from single cell transcriptomic analysis of mouse foregut organogenesis. Building on established methods, hPSC-derived lateral plate mesoderm (LPM) treated with either retinoic acid (RA) or RA and a Hedgehog (HH) agonist generates posterior or anterior foregut splanchnic mesoderm respectively (pFG-SpM or aFG-SpM) after 4 days in cultures. These are then directed into organ-specific mesenchyme lineages by the combinatorial activation or inhibition of WNT, BMP, RA or HH pathways from days 4-7 in monolayer culture. By day 7 the cultures are enriched for different types of mesoderm with distinct molecular signatures: 60~90% pure liver septum transversum/mesothelium (STM/Mesothelium), 70~80% pure liver fibroblasts (LF), and populations of ~35% respiratory mesoderm (RM), gastric mesoderm (GM), or esophageal mesoderm (EM). This protocol can be carried out by anyone with moderate experience differentiating hPSCs and provides a novel platform to study human mesoderm development and can be used to tissue engineer more complex foregut organ tissue for disease modeling and regenerative medicine.
DOI: 10.6084/m9.figshare.12383159
title: Aggregate Inverse Mean Estimation for Sufficient Dimension Reduction

description: <i>Abstract–</i>Many well-known sufficient dimension reduction methods investigate the inverse conditional moments of the predictors given the response. The required linearity condition, the number and arrangement of slices, and the inability to detect symmetric dependence are among several long-standing issues that have negatively impacted on the use of these approaches. Motivated by two recent works dealing with the choice of number of slices, we propose a novel and effective method based on the aggregation of inverse mean estimation. The new approach can substantially improve the estimation accuracy, break down the symmetry to achieve exhaustive estimation, and is much less sensitive to the violation of the linearity condition. Both simulation studies and a real data application show the efficacy of the newly proposed approach.
DOI: 10.6084/m9.figshare.12383159.v2
title: Aggregate Inverse Mean Estimation for Sufficient Dimension Reduction

description: <i>Abstract–</i>Many well-known sufficient dimension reduction methods investigate the inverse conditional moments of the predictors given the response. The required linearity condition, the number and arrangement of slices, and the inability to detect symmetric dependence are among several long-standing issues that have negatively impacted on the use of these approaches. Motivated by two recent works dealing with the choice of number of slices, we propose a novel and effective method based on the aggregation of inverse mean estimation. The new approach can substantially improve the estimation accuracy, break down the symmetry to achieve exhaustive estimation, and is much less sensitive to the violation of the linearity condition. Both simulation studies and a real data application show the efficacy of the newly proposed approach.
DOI: 10.6084/m9.figshare.12383159.v1
title: Aggregate inverse mean estimation for sufficient dimension reduction

description: Many well-known sufficient dimension reduction methods investigate the inverse conditional moments of the predictors given the response. The required linearity condition, the number and arrangement of slices, and the inability to detect symmetric dependence are among several long-standing issues that have negatively impacted on the use of these approaches. Motivated by two recent work dealing with the choice of number of slices, we propose a novel and effective method based on the aggregation of inverse mean estimation (AIME). The new approach can substantially improve the estimation accuracy, break down the symmetry to achieve exhaustive estimation, and is much less sensitive to the violation of the linearity condition. Both simulation studies and a real data application show the efficacy of the newly proposed approach.
DOI: 10.6084/m9.figshare.14480316
title: Whole-exome sequencing in a cohort of high myopia patients in northwest China

description: A total of 201 potential variants were identified in 27 families: 139 ones were well cosegregated with the disease in 15 families. Sixty-two variants were not cosegregated
DOI: 10.6084/m9.figshare.11858892
title: Additional file 10 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 10. Differentially abundant fungal OTUs of wild and domesticated rice
DOI: 10.6084/m9.figshare.11858898
title: Additional file 11 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 11. Degree and betweenness centrality of network nodes of wild rice, domesticated rice, and all rice
DOI: 10.6084/m9.figshare.11858898.v1
title: Additional file 11 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 11. Degree and betweenness centrality of network nodes of wild rice, domesticated rice, and all rice
DOI: 10.6084/m9.figshare.11858904
title: Additional file 12 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 12. Core OTUs based on prevalence
DOI: 10.6084/m9.figshare.11858904.v1
title: Additional file 12 of Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

description: Additional fileÂ 12. Core OTUs based on prevalence