cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19703669
title: Abnormal triaging of misfolded proteins by adult neuronal ceroid lipofuscinosis-associated DNAJC5/CSPα mutants causes lipofuscin accumulation

description: Mutations in <i>DNAJC5/CSPα</i> are associated with adult neuronal ceroid lipofuscinosis (ANCL), a dominant-inherited neurodegenerative disease featuring lysosome-derived autofluorescent <i>s</i>torage materials (AFSMs) termed lipofuscin. Functionally, DNAJC5 has been implicated in chaperoning synaptic proteins and in misfolding-associated protein secretion (MAPS), but how DNAJC5 dysfunction causes lipofuscinosis and neurodegeneration is unclear. Here we report two functionally distinct but coupled chaperoning activities of DNAJC5, which jointly regulate lysosomal homeostasis: While endolysosome-associated DNAJC5 promotes ESCRT-dependent microautophagy, a fraction of perinuclear and non-lysosomal DNAJC5 mediates MAPS. Functional proteomics identifies a previously unknown DNAJC5 interactor SLC3A2/CD98hc that is essential for the perinuclear DNAJC5 localization and MAPS but dispensable for microautophagy. Importantly, uncoupling these two processes, as seen in cells lacking SLC3A2 or expressing ANCL-associated DNAJC5 mutants, generates DNAJC5-containing AFSMs resembling NCL patient-derived lipofuscin and induces neurodegeneration in a <i>Drosophila</i> ANCL model. These findings suggest that MAPS safeguards microautophagy to avoid DNAJC5-associated lipofuscinosis and neurodegeneration. <b>Abbreviations:</b> 3-MA: 3-methyladenine; ACTB: actin beta; AFSM: autofluorescent storage materials; ANCL: adult neuronal ceroid lipofuscinosis; Baf. A1: bafilomycin A<sub>1</sub>; CLN: ceroid lipofuscinosis neuronal; CLU: clusterin; CS: cysteine string domain of DNAJC5/CSPα; CUPS: compartment for unconventional protein secretion; DN: dominant negative; DNAJC5/CSPα: DnaJ heat shock protein family (Hsp40) member C5; eMI: endosomal microautophagy; ESCRT: endosomal sorting complex required for transport; GFP: green fluorescent protein; HSPA8/HSC70: heat shock protein family A (Hsp70) member 8; INCL: infant neuronal ceroid lipofuscinosis; JNCL: juvenile neuronal ceroid lipofuscinosis; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LAPTM4B: lysosomal protein transmembrane 4 beta; LN: linker domain of DNAJC5/CSPα; MAPS: misfolding-associated protein secretion; mCh/Ch: mCherry; mCi/Ci: mCitrine; MTOR: mechanistic target of rapamycin kinase; NCL: neuronal ceroid lipofuscinosis; PPT1: palmitoyl-protein thioesterase 1; PQC: protein quality control; SBP: streptavidin binding protein; SGT: small glutamine-rich tetratricopeptide repeat; shRNA: short hairpin RNA; SLC3A2/CD98hc: solute carrier family 3 member 2; SNCA/α-synuclein: synuclein alpha; TMED10: transmembrane p24 trafficking protein 10; UV: ultraviolet; VPS4: vacuolar protein sorting 4 homolog; WT: wild type.
DOI: 10.6084/m9.figshare.7645061.v1
title: Electronic supplementary material from Study on ground settlement and structural deformation for large span subway station using a new pre-supporting system

description: Data used in the manuscript
DOI: 10.6084/m9.figshare.19703669.v1
title: Abnormal triaging of misfolded proteins by adult neuronal ceroid lipofuscinosis-associated DNAJC5/CSPα mutants causes lipofuscin accumulation

description: Mutations in <i>DNAJC5/CSPα</i> are associated with adult neuronal ceroid lipofuscinosis (ANCL), a dominant-inherited neurodegenerative disease featuring lysosome-derived autofluorescent <i>s</i>torage materials (AFSMs) termed lipofuscin. Functionally, DNAJC5 has been implicated in chaperoning synaptic proteins and in misfolding-associated protein secretion (MAPS), but how DNAJC5 dysfunction causes lipofuscinosis and neurodegeneration is unclear. Here we report two functionally distinct but coupled chaperoning activities of DNAJC5, which jointly regulate lysosomal homeostasis: While endolysosome-associated DNAJC5 promotes ESCRT-dependent microautophagy, a fraction of perinuclear and non-lysosomal DNAJC5 mediates MAPS. Functional proteomics identifies a previously unknown DNAJC5 interactor SLC3A2/CD98hc that is essential for the perinuclear DNAJC5 localization and MAPS but dispensable for microautophagy. Importantly, uncoupling these two processes, as seen in cells lacking SLC3A2 or expressing ANCL-associated DNAJC5 mutants, generates DNAJC5-containing AFSMs resembling NCL patient-derived lipofuscin and induces neurodegeneration in a <i>Drosophila</i> ANCL model. These findings suggest that MAPS safeguards microautophagy to avoid DNAJC5-associated lipofuscinosis and neurodegeneration. <b>Abbreviations:</b> 3-MA: 3-methyladenine; ACTB: actin beta; AFSM: autofluorescent storage materials; ANCL: adult neuronal ceroid lipofuscinosis; Baf. A1: bafilomycin A<sub>1</sub>; CLN: ceroid lipofuscinosis neuronal; CLU: clusterin; CS: cysteine string domain of DNAJC5/CSPα; CUPS: compartment for unconventional protein secretion; DN: dominant negative; DNAJC5/CSPα: DnaJ heat shock protein family (Hsp40) member C5; eMI: endosomal microautophagy; ESCRT: endosomal sorting complex required for transport; GFP: green fluorescent protein; HSPA8/HSC70: heat shock protein family A (Hsp70) member 8; INCL: infant neuronal ceroid lipofuscinosis; JNCL: juvenile neuronal ceroid lipofuscinosis; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LAPTM4B: lysosomal protein transmembrane 4 beta; LN: linker domain of DNAJC5/CSPα; MAPS: misfolding-associated protein secretion; mCh/Ch: mCherry; mCi/Ci: mCitrine; MTOR: mechanistic target of rapamycin kinase; NCL: neuronal ceroid lipofuscinosis; PPT1: palmitoyl-protein thioesterase 1; PQC: protein quality control; SBP: streptavidin binding protein; SGT: small glutamine-rich tetratricopeptide repeat; shRNA: short hairpin RNA; SLC3A2/CD98hc: solute carrier family 3 member 2; SNCA/α-synuclein: synuclein alpha; TMED10: transmembrane p24 trafficking protein 10; UV: ultraviolet; VPS4: vacuolar protein sorting 4 homolog; WT: wild type.
DOI: 10.6084/m9.figshare.14985057
title: Additional file 7 of Somatic mutations in benign breast disease tissues and association with breast cancer risk

description: Additional file 7. Table S3: Gene-level results for case-control comparisons for all 12 combinations of QC filters and analysis methods.
DOI: 10.6084/m9.figshare.7648265.v1
title: Additional file 1: of Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses

description: Table S1. Primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8172566.v1
title: Additional file 3: of Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

description: Table S3. The tissue specifically expressed genes (TPMâ â Ľâ 500) in three tissues of ad libitum group. (XLSX 215 kb)
DOI: 10.6084/m9.figshare.14984997.v1
title: Additional file 1 of Haplotype-resolved germline and somatic alterations in renal medullary carcinomas

description: Additional file 1: Tables S1-S10. Supplementary tables include the following: clinical info (Table S1), inferred sex (Table S2), Longranger statistics (Table S3), germline variants (Table S4), SMARCB1 SVs (Table S5), somatic variants (Table S6), sickle cell locus (Table S7), HBB variants (Table S8), breakpoint repeats (Table S9), and breakpoint microhomology (Table S10). Legends for each table are included at the top of each table in the Microsoft Excel file.
DOI: 10.6084/m9.figshare.9745502
title: Additional file 2: of Isolation of T cell receptor specifically reactive with autologous tumour cells from tumour-infiltrating lymphocytes and construction of T cell receptor engineered T cells for esophageal squamous cell carcinoma

description: Table S1. Clinical characteristics of the patient and donors. Table S2. Sequences of the primers used for single cell TCRÎą/Î˛ RT-PCR. Table S3. Contents of 2-step single-cell RT-PCR. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9745502.v1
title: Additional file 2: of Isolation of T cell receptor specifically reactive with autologous tumour cells from tumour-infiltrating lymphocytes and construction of T cell receptor engineered T cells for esophageal squamous cell carcinoma

description: Table S1. Clinical characteristics of the patient and donors. Table S2. Sequences of the primers used for single cell TCRÎą/Î˛ RT-PCR. Table S3. Contents of 2-step single-cell RT-PCR. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.14988433
title: Modeling scale morphogenesis in a Devonian chondrichthyan and scale growth patterns in crown gnathostomes

description: Early chondrichthyans (cartilaginous fishes) possess a rich record of scale fossils that have impacted on taxonomic and phylogenetic studies of early jawed vertebrates, but the significance of these scales remains elusive due to the lack of well-defined characters. <i>Gualepis</i>, a scale-based genus from the Lower Devonian of Yunnan, China, was initially recognized as an early chondrichthyan of uncertain affinity. We investigate new material of <i>Gualepis elegans</i> from the type locality. By combining microtomographic data with morphological and histological examination of specimens at successive growth stages, we have reconstructed the 3D growth pattern of the scales. During growth, <i>Gualepis</i> scales added new odontodes appositionally, which has previously been documented in the dermal skeletons of <i>Seretolepis</i>, <i>Kathemacanthus</i>, <i>Parexus</i>, and other crownward members of the stem chondrichthyans. Phylogenetic analysis resolves <i>Gualepis</i> as a non-acanthodid stem chondrichthyan near the crown chondrichthyan node. Our 3D approach is potentially useful to render more reliable scale-based characters, especially regarding scale growth patterns. This study provides the first 3D virtual growth model of stem chondrichthyan scales with a <i>Seretolepis</i>-type morphogenesis, offering new insights into the early evolution of chondrichthyan dermal skeletons.
DOI: 10.6084/m9.figshare.14985063
title: Additional file 9 of Somatic mutations in benign breast disease tissues and association with breast cancer risk

description: Additional file 9. Table S5: Gene-level results for ER- vs. Control comparisons for all 12 combinations of QC filters and analysis methods.
DOI: 10.6084/m9.figshare.14984882
title: Additional file 3 of Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion

description: Additional file 3. Genes with differential biological responses caused by the expression of Nan and Pex.
DOI: 10.6084/m9.figshare.14984879
title: Additional file 2 of Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion

description: Additional file 2. Common significantly differentially expressed genes in both HA.Nan vs LA.Nan and HA.Pex vs LA.Pex.
DOI: 10.6084/m9.figshare.8172755.v1
title: Additional file 2: of The prognostic value of tumor-infiltrating lymphocytes in colorectal cancer differs by anatomical subsite: a systematic review and meta-analysis

description: Table S2. The quality assessment of all included studies in this meta-analysis (XLSX 12 kb)
DOI: 10.6084/m9.figshare.19703787
title: Additional file 2 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 2: Table S2. The expression of all identified circRNAs.
DOI: 10.6084/m9.figshare.19703808
title: Additional file 9 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 9: Table S9. The miRNA-circRNA interaction pairs and miRNA-mRNA interaction pairs in profile 16.
DOI: 10.6084/m9.figshare.19703796
title: Additional file 5 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 5: Table S5. The circRNAs and mRNAs identified in profile 3.
DOI: 10.6084/m9.figshare.19703772
title: Additional file 10 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 10: Table S10. The circRNA-miRNA-mRNA network of profile 16.
DOI: 10.6084/m9.figshare.19703772.v1
title: Additional file 10 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 10: Table S10. The circRNA-miRNA-mRNA network of profile 16.
DOI: 10.6084/m9.figshare.19703775
title: Additional file 11 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 11: Table S11. The circRNA-miRNA-mRNA network for circRNA225 and circRNA226.
DOI: 10.6084/m9.figshare.19703778
title: Additional file 12 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 12: Table S12. Function annotation of the circRNAs in profile 16.
DOI: 10.6084/m9.figshare.19703796.v1
title: Additional file 5 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 5: Table S5. The circRNAs and mRNAs identified in profile 3.
DOI: 10.6084/m9.figshare.19703790.v1
title: Additional file 3 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 3: Table S3. The differentially expressed circRNAs.
DOI: 10.6084/m9.figshare.19703805
title: Additional file 8 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 8: Table S8. The miRNAs identified in our previous study.
DOI: 10.6084/m9.figshare.14464218
title: Output files(part7)

description: The output files of MIP3D.
DOI: 10.6084/m9.figshare.14464218.v1
title: Output files(part7)

description: The output files of MIP3D.
DOI: 10.6084/m9.figshare.14464221
title: Output files(part8)

description: The output files of MIP3D.
DOI: 10.6084/m9.figshare.14464221.v1
title: Output files(part8)

description: The output files of MIP3D.
DOI: 10.6084/m9.figshare.9745634
title: Additional file 2: of Bos taurusâ indicus hybridization correlates with intralocus sexual-conflict effects of PRDM9 on male and female fertility in Holstein cattle

description: The dataset of IL sires, including genotyping data and SCR values. (XLSX 218 kb)
DOI: 10.6084/m9.figshare.9745634.v1
title: Additional file 2: of Bos taurusâ indicus hybridization correlates with intralocus sexual-conflict effects of PRDM9 on male and female fertility in Holstein cattle

description: The dataset of IL sires, including genotyping data and SCR values. (XLSX 218 kb)
DOI: 10.6084/m9.figshare.9745652
title: Additional file 2: of Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics

description: Supplementary datasets. (XLSX 1717 kb)
DOI: 10.6084/m9.figshare.9745652.v1
title: Additional file 2: of Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics

description: Supplementary datasets. (XLSX 1717 kb)
DOI: 10.6084/m9.figshare.18130887.v1
title: The circ-PITX1 promotes non-small cell lung cancer development via the miR-30e-5p/ITGA6 axis

description: Non-small cell lung cancer (NSCLC) is one of the most prevalent tumors with high incidence and mortality across the globe. Recently, increasing studies have demonstrated that circular RNAs (circRNAs) exert outstanding functions in NSCLC progression. Notwithstanding, we are still in the dark about the function and exact mechanism of circ-PITX1, a newly discovered circRNA. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) confirmed the profile of circ-PITX1 in NSCLC tissues and adjacent normal tissues. Gain- and loss- of function assay verified the impact of circ-PITX1 and miR-30e-5p on the proliferation, invasion, and migration of NSCLC cells (H1975 and A549). Bioinformatics analysis corroborated the downstream mechanisms of circ-PITX1. Dual-luciferase reporter gene assay and RNA immunoprecipitation (RIP) examined the interactions between circ-PITX1 and miR-30e-5p, miR-30e-5p and ITGA6. The protein levels of ITGA6, PI3K, AKT were determined by Western blot. circ-PITX1 was substantially up-regulated in NSCLC tissues and cells, and circ-PITX1 up-regulation was correlated with NSCLC patients’ poor survival. Functionally, circ-PITX1 overexpression or miR-30e-5p inhibition markedly facilitated proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), reduced apoptosis, and enhanced ITGA6/PI3K/AKT expression in NSCLC cells, whereas circ-PITX1 knockdown or miR-30e-5p up-regulation resulted in the opposite results. Mechanistically, circ-PITX1 acted as a sponge of miR-30e-5p, which targeted the 3ʹuntranslated region (UTR) of ITGA6. Knockdown of circ-PITX1 or overexpressing miR-30e-5p reduced ITGA6/PI3K/AKT axis. circ-PITX1 modulates the miR-30e-5p/ITGA6 axis to boost NSCLC progression, hence functioning as an oncogene.
DOI: 10.6084/m9.figshare.19703793.v1
title: Additional file 4 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 4: Table S4. The DE-mRNAs identified in our previous study.
DOI: 10.6084/m9.figshare.11839431.v1
title: A functional polymorphism in the paired basic amino acid-cleaving enzyme 4 gene confers osteoarthritis risk in a population of Eastern China

description: Abstract Paired basic amino acid-cleaving enzyme 4 (PACE4), a proprotein convertase, is involved in the activation of aggrecanases (ADAMTS-4 and ADAMTS-5) in osteoarthritic and cytokine-stimulated cartilage. Activated aggrecanases cause aggrecan degradation and thus, contribute to osteoarthritis (OA). In this study, we investigated the association between PACE4 gene polymorphisms and OA risk. One single-nucleotide polymorphism (rs4965833) in the PACE4 gene was genotyped in 432 OA patients and 523 healthy controls using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Quantitative reverse transcription PCR (qRT-PCR) was used to determine the relative expression of PACE4 in blood samples from 90 OA patients (30 for each genotype). The relative expression level of PACE4 mRNA was higher in the GG genotype as compared to the AA/AG group. Moreover, the PACE4 rs4965833 polymorphism was associated with increased risk of OA, especially among individuals aged ≥55 years and with a body mass index ≥25. There was no significant association between the PACE4 rs4965833 polymorphism and clinical parameters of OA patients, such as erythrocyte sedimentation rate, C-reactive protein, Visual Analog Scale for pain and Lequesne’s index. In conclusion, the rs4965833 polymorphism in the 3’-UTR of PACE4 is associated with OA susceptibility.
DOI: 10.6084/m9.figshare.20226845.v1
title: Additional file 21 of Combined nature and human selections reshaped peach fruit metabolome

description: Additional file 21: Table S20. List of eQTL hotspots.
DOI: 10.6084/m9.figshare.19703799.v1
title: Additional file 6 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 6: Table S6. The circRNAs and mRNAs identified in profile 16.
DOI: 10.6084/m9.figshare.19703802.v1
title: Additional file 7 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 7: Table S7. The circRNAs and mRNAs identified in profile 14.
DOI: 10.6084/m9.figshare.19703808.v1
title: Additional file 9 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 9: Table S9. The miRNA-circRNA interaction pairs and miRNA-mRNA interaction pairs in profile 16.
DOI: 10.6084/m9.figshare.19703778.v1
title: Additional file 12 of Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

description: Additional file 12: Table S12. Function annotation of the circRNAs in profile 16.
DOI: 10.6084/m9.figshare.9745676
title: Additional file 1: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S1. Public whole genome sequence data used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9745676.v1
title: Additional file 1: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S1. Public whole genome sequence data used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.9745682
title: Additional file 2: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S2. Sequence comparison of the henny feathering endogenous retrovirus sequence (Hf_ERV) with 140 published avian leukosis viruses. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.9745682.v1
title: Additional file 2: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S2. Sequence comparison of the henny feathering endogenous retrovirus sequence (Hf_ERV) with 140 published avian leukosis viruses. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.9745691
title: Additional file 3: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S3. PCR primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9745691.v1
title: Additional file 3: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S3. PCR primers used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9745700
title: Additional file 4: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S4. List of DNA samples. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9745700.v1
title: Additional file 4: of Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering in chicken

description: Table S4. List of DNA samples. (XLSX 9 kb)
DOI: 10.5281/zenodo.10669566
title: Public Database of Hypsography Interpretation Study Results

description: The Excel file contains the filtered data records of the hypsography interpretation study of the Research Group on Experimental Cartography at the Eötvös Loránd University (ktk.elte.hu). The data collection lasted between 01.10.2017 - 17.10.2017. The file contains two sheets: the "test_questions" sheet holds the questions and correct answers of the test, while the "data" sheet has the 195 data records. The incomplete results were filtered out along with fill times below 2 minutes.