cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5903350
title: Additional file 3: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S2. ChIP-seq sample replicates correlation. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.14816259.v1
title: N-terminal region is required for functions of the HAM family member

description: Shoot meristems contain stem cells, and they sustain growth and development of the above-ground tissues in land plants. The <i>HAIRY MERISTEM</i> (<i>HAM</i>) family genes, encoding GRAS-domain transcriptional regulators, play essential roles in the control of shoot meristem development and stem cell homeostasis in several flowering plants. Similar to other GRAS proteins, the C-terminal regions of HAM family proteins across land plants are conserved, containing signature motifs that define the GRAS domain. In contrast, the N-terminal regions of HAM family proteins display substantial divergence in sequence and length. Whether the variable and divergent N-termini are required for the conserved functions of HAM proteins is unknown. Our recent work showed that <i>CrHAM</i> – the <i>HAM</i> homolog in the fern <i>Ceratopteris richardii</i> was able to replace the role of type-II <i>HAM</i> genes in Arabidopsis, maintaining established shoot apical meristems and promoting the initiation of new stem cell niches. Here, we provide additional information and show that CrHAM contains a much longer N-terminal region compared to Arabidopsis HAM proteins, which is conserved among different fern HAM homologs. The deletion of this region largely compromises the ability of CrHAM to replace the function of Arabidopsis HAM proteins in shoot meristems. These new data together with previous results suggest that, although lacking the sequence conservation among HAM homologs from different plant lineages, the N-termini are important for the conserved functions of HAM family proteins.
DOI: 10.6084/m9.figshare.5903383
title: Additional file 9: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

description: Table S4. List of genes with subtype specific active transcription states. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.7842596.v1
title: Additional file 9: of Identification and analysis of oxygen responsive microRNAs in the root of wild tomato (S. habrochaites)

description: Predicted targets of novel miRNAs identified in this study by psRNATarget. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6427859
title: Liposuction-assisted circumferential trimming in treatment of axillary osmidrosis (AO)

description: <b>Background:</b> The study is to investigate the effectiveness and safety of the minimally invasive treatment for axillary osmidrosis by liposuction assisted circumferential trimming. <b>Methods:</b> It was a retrospective study. From July 2014 to July 2017, 79 patients underwent superficial liposuction and circumferential trimming for bilateral axillary osmidrosis. The preoperative and postoperative degree of axillary malodor was measured by doctors and the patients themselves. In the doctor’s evaluation, the odor levels were scored by the sniffing method before and 1 year after treatment. In the patient’s self-assessment, each patient selected a scale value to convey his/her satisfaction during the visits after 1 year. The complications were recorded. <b>Results:</b> The follow-up period ranged from 12 to 24 months after surgery, and the mean follow-up period was 16 months. 75 (94.9%) had good results, four (5.1%) had moderate malodor or recurrence after one year. When considering patient’s own satisfaction, 93.7% (74/79) of patients were satisfied with the outcomes after one year. The partial epidermis necrosis was observed in four patients, it healed spontaneously without scarring. Three patients had a small amount of hematoma which was easily evacuated through the central primary incision. There was no other serious side effect. <b>Conclusions:</b> The liposuction assisted circumferential trimming technique is proved reliable and safe in treatment for axillary osmidrosis.
DOI: 10.6084/m9.figshare.6427859.v1
title: Liposuction-assisted circumferential trimming in treatment of axillary osmidrosis (AO)

description: <b>Background:</b> The study is to investigate the effectiveness and safety of the minimally invasive treatment for axillary osmidrosis by liposuction assisted circumferential trimming. <b>Methods:</b> It was a retrospective study. From July 2014 to July 2017, 79 patients underwent superficial liposuction and circumferential trimming for bilateral axillary osmidrosis. The preoperative and postoperative degree of axillary malodor was measured by doctors and the patients themselves. In the doctor’s evaluation, the odor levels were scored by the sniffing method before and 1 year after treatment. In the patient’s self-assessment, each patient selected a scale value to convey his/her satisfaction during the visits after 1 year. The complications were recorded. <b>Results:</b> The follow-up period ranged from 12 to 24 months after surgery, and the mean follow-up period was 16 months. 75 (94.9%) had good results, four (5.1%) had moderate malodor or recurrence after one year. When considering patient’s own satisfaction, 93.7% (74/79) of patients were satisfied with the outcomes after one year. The partial epidermis necrosis was observed in four patients, it healed spontaneously without scarring. Three patients had a small amount of hematoma which was easily evacuated through the central primary incision. There was no other serious side effect. <b>Conclusions:</b> The liposuction assisted circumferential trimming technique is proved reliable and safe in treatment for axillary osmidrosis.
DOI: 10.6084/m9.figshare.7842596
title: Additional file 9: of Identification and analysis of oxygen responsive microRNAs in the root of wild tomato (S. habrochaites)

description: Predicted targets of novel miRNAs identified in this study by psRNATarget. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6427859.v2
title: Liposuction-assisted circumferential trimming in treatment of axillary osmidrosis (AO)

description: <b>Background:</b> The study is to investigate the effectiveness and safety of the minimally invasive treatment for axillary osmidrosis by liposuction assisted circumferential trimming. <b>Methods:</b> It was a retrospective study. From July 2014 to July 2017, 79 patients underwent superficial liposuction and circumferential trimming for bilateral axillary osmidrosis. The preoperative and postoperative degree of axillary malodor was measured by doctors and the patients themselves. In the doctor’s evaluation, the odor levels were scored by the sniffing method before and 1 year after treatment. In the patient’s self-assessment, each patient selected a scale value to convey his/her satisfaction during the visits after 1 year. The complications were recorded. <b>Results:</b> The follow-up period ranged from 12 to 24 months after surgery, and the mean follow-up period was 16 months. 75 (94.9%) had good results, four (5.1%) had moderate malodor or recurrence after one year. When considering patient’s own satisfaction, 93.7% (74/79) of patients were satisfied with the outcomes after one year. The partial epidermis necrosis was observed in four patients, it healed spontaneously without scarring. Three patients had a small amount of hematoma which was easily evacuated through the central primary incision. There was no other serious side effect. <b>Conclusions:</b> The liposuction assisted circumferential trimming technique is proved reliable and safe in treatment for axillary osmidrosis.
DOI: 10.6084/m9.figshare.16912556.v1
title: Differences in the biological properties of mesenchymal stromal cells from traumatic temporomandibular joint fibrous and bony ankylosis: a comparative study

description: The aim of this study was to compare the functional characteristics of mesenchymal stromal cells (MSCs) from a sheep model of traumatic temporomandibular joint (TMJ) fibrous and bony ankylosis. A sheep model of bilateral TMJ trauma-induced fibrous ankylosis on one side and bony ankylosis on the contralateral side was used. MSCs from fibrous ankylosed callus (FA-MSCs) or bony ankylosed callus (BA-MSCs) at weeks 1, 2, 4, and 8 after surgery were isolated and cultured. MSCs derived from the bone marrow of the mandibular condyle (BM-MSCs) were used as controls. The MSCs from the different sources were characterized morphologically, phenotypically, and functionally. Adherence and trilineage differentiation potential were presented in the ovine MSCs. These cell populations highly positively expressed MSC-associated specific markers, namely CD29, CD44, and CD166, but lacked CD31 and CD45 expressions. The BA-MSCs had higher clonogenic and proliferative potentials than the FA-MSCs. The BA-MSCs also showed higher osteogenic and chondrogenic potentials, but lower adipogenic capacity than the FA-MSCs. In addition, the BA-MSCs demonstrated higher chondrogenic, but lower osteogenic capacity than the BM-MSCs. Our study suggests that inhibition of the osteogenic and chondrogenic differentiations of MSCs might be a promising strategy for preventing bony ankylosis in the future.
DOI: 10.6084/m9.figshare.14812548.v1
title: Additional file 2 of Expressional diversity of grapevine 3-Hydroxy-3-methylglutaryl-CoA reductase (VvHMGR) in different grapes genotypes

description: Additional file 2: Table S1. Primer used for qRT-PCR on the grape. Table S2. Information on HMGR genes. Table S3. Analysis of protein secondary structure. Table S4. Prediction of subcellular localization. Table S5. Aroma components of 10 varieties in berry skin and berry flesh.
DOI: 10.6084/m9.figshare.14816693.v1
title: BECN2 (beclin 2) Negatively Regulates Inflammasome Sensors Through ATG9A-Dependent but ATG16L1- and LC3-Independent Non-Canonical Autophagy

description: Macroautophagy/autophagy-related proteins regulate infectious and inflammatory diseases in autophagy-dependent or -independent manner. However, the role of a newly identified mammalian-specific autophagy protein-BECN2 (beclin 2) in innate immune regulation is largely unknown. Here we showed that loss of BECN2 enhanced the activities of NLRP3, AIM2, NLRP1, and NLRC4 inflammasomes upon ligand stimulations. Mechanistically, BECN2 interacted with inflammasome sensors and mediated their degradation through a ULK1- and ATG9A-dependent, but BECN1-WIPI2-ATG16L1-LC3-independent, non-canonical autophagic pathway. BECN2 recruited inflammasome sensors on ATG9A<sup>+</sup> vesicles to form a complex (BECN2-ATG9A-sensors) upon ULK1 activation. Three soluble NSF attachment protein receptor (SNARE) proteins (SEC22A, STX5, and STX6) were further shown to mediate the BECN2-ATG9A-dependent inflammasome sensor degradation. Loss of BECN2 promoted alum-induced peritonitis, which could be rescued by the ablation of CASP1 in <i>Becn2</i>-deficient mice. Hence, BECN2 negatively regulated inflammasome activation to control inflammation, serving as a potential therapeutic target for the treatment of infectious and inflammatory diseases. <b>Abbreviations</b>: AIM2: absent in melanoma 2; ATG: autophagy related; BECN1: beclin 1; BMDC: bone marrow-derived dendritic cells; BMDM: bone marrow-derived macrophages; CASP1: caspase 1; CQ: chloroquine; gMDSC: granulocytic myeloid-derived suppressor cells; IL: interleukin; LPS: lipopolysaccharide; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; mMDSC: monocytic myeloid-derived suppressor cells; NLRC4: NLR family CARD domain containing 4; NLRP1: NLR family pyrin domain containing 1; NLRP3: NLR family pyrin domain containing 3; PECs: peritoneal exudate cells; PYCARD/ASC: apoptosis-associated speck-like protein containing a caspase activation and recruitment domain; SNAREs: soluble NSF attachment protein receptors; STX5: syntaxin 5; STX6: syntaxin 6; ULK1: unc-51 like autophagy activating kinase 1; WIPI: WD repeat domain, phosphoinositide interacting.
DOI: 10.6084/m9.figshare.20579766.v1
title: Additional file 4 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 4: Table S2. Summary of DMR analysis across all studies used in study that overlapped DMRs identified in FAP study. Positive "meandiff" corresponds to increased beta values (DNA methylation) in FAP (or tumor samples).
DOI: 10.6084/m9.figshare.20579772.v1
title: Additional file 6 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 6: Table S4. Summary of qPCR and RNA-seq analysis performed on selected gene targets. Positive fold changes and t values indicate increased expression in TCGA-COAD tumor and FAP colon organoids, respectively.
DOI: 10.6084/m9.figshare.20579760.v1
title: Additional file 2 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 2: Table S1. Phenotype information for cohort.
DOI: 10.6084/m9.figshare.20579769.v1
title: Additional file 5 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 5: Table S3. Summary of gene ontology analysis for FAP versus healthy colon organoids.
DOI: 10.6084/m9.figshare.14816622
title: Metabolomic and Lipidomic Analysis of human CSF

description: The data consist of lipidomic and metabolomic assays from the cerrebrospinal fluid of one hundred ninety-eight CSF samples, collected from 85 controls, 57 Alzheimer's (AD) patients, and 56 Parksinson's (PD) patients (note the PD data is currently not available, but will be pending approval). For each subject we also record age and sex. subject_info contains the age, type (AD, PD or control), and sex of the subjects. lipids.csv contains normalized lipid abundances for each subject, targeted.csv contains abundances of 108 known metabolites and untargeted.csv contains abundances of thousands of features, identified only by their mass-to-charge ratio (m/z).
DOI: 10.6084/m9.figshare.23265015
title: Additional file 4 of MPC-n (IgG) improves long-term cognitive impairment in the mouse model of repetitive mild traumatic brain injury

description: Additional file 4: Table S2. All differentially expressed genes between the rmTBI group and the sham group.
DOI: 10.6084/m9.figshare.14816693
title: BECN2 (beclin 2) Negatively Regulates Inflammasome Sensors Through ATG9A-Dependent but ATG16L1- and LC3-Independent Non-Canonical Autophagy

description: Macroautophagy/autophagy-related proteins regulate infectious and inflammatory diseases in autophagy-dependent or -independent manner. However, the role of a newly identified mammalian-specific autophagy protein-BECN2 (beclin 2) in innate immune regulation is largely unknown. Here we showed that loss of BECN2 enhanced the activities of NLRP3, AIM2, NLRP1, and NLRC4 inflammasomes upon ligand stimulations. Mechanistically, BECN2 interacted with inflammasome sensors and mediated their degradation through a ULK1- and ATG9A-dependent, but BECN1-WIPI2-ATG16L1-LC3-independent, non-canonical autophagic pathway. BECN2 recruited inflammasome sensors on ATG9A<sup>+</sup> vesicles to form a complex (BECN2-ATG9A-sensors) upon ULK1 activation. Three soluble NSF attachment protein receptor (SNARE) proteins (SEC22A, STX5, and STX6) were further shown to mediate the BECN2-ATG9A-dependent inflammasome sensor degradation. Loss of BECN2 promoted alum-induced peritonitis, which could be rescued by the ablation of CASP1 in <i>Becn2</i>-deficient mice. Hence, BECN2 negatively regulated inflammasome activation to control inflammation, serving as a potential therapeutic target for the treatment of infectious and inflammatory diseases. <b>Abbreviations</b>: AIM2: absent in melanoma 2; ATG: autophagy related; BECN1: beclin 1; BMDC: bone marrow-derived dendritic cells; BMDM: bone marrow-derived macrophages; CASP1: caspase 1; CQ: chloroquine; gMDSC: granulocytic myeloid-derived suppressor cells; IL: interleukin; LPS: lipopolysaccharide; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; mMDSC: monocytic myeloid-derived suppressor cells; NLRC4: NLR family CARD domain containing 4; NLRP1: NLR family pyrin domain containing 1; NLRP3: NLR family pyrin domain containing 3; PECs: peritoneal exudate cells; PYCARD/ASC: apoptosis-associated speck-like protein containing a caspase activation and recruitment domain; SNAREs: soluble NSF attachment protein receptors; STX5: syntaxin 5; STX6: syntaxin 6; ULK1: unc-51 like autophagy activating kinase 1; WIPI: WD repeat domain, phosphoinositide interacting.
DOI: 10.6084/m9.figshare.16909933.v1
title: Additional file 2 of Cancer-associated fibroblasts impact the clinical outcome and treatment response in colorectal cancer via immune system modulation: a comprehensive genome-wide analysis

description: Additional file 2: Data S1. The risk of each patient in the six cohorts.
DOI: 10.6084/m9.figshare.16909902
title: Additional file 1 of Identification of stem cell-related subtypes and risk scoring for gastric cancer based on stem genomic profiling

description: Additional file 1. Table S1: The clinical and demographic features of gastric cancer patients from Renmin Hospital of Wuhan University.
DOI: 10.6084/m9.figshare.20579760
title: Additional file 2 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 2: Table S1. Phenotype information for cohort.
DOI: 10.6084/m9.figshare.20579769
title: Additional file 5 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 5: Table S3. Summary of gene ontology analysis for FAP versus healthy colon organoids.
DOI: 10.6084/m9.figshare.16913416.v1
title: ANXA1 (Annexin A1) regulated by MYC (MYC proto-oncogene) promotes the growth of papillary thyroid carcinoma

description: Thyroid carcinoma is one of the most common endocrine malignancies, in which papillary thyroid carcinoma (PTC) is the main pathotype. ANXA1 plays a significant role in many cancer types, but how it works in PTC has not been identified. MYC is a common transcript factor involved in tumorigenesis, development, invasion, and metastasis. The relation between ANXA1 and MYC has not been proved in PTC. In this study, firstly, we analyzed the expression and prognostic value of ANXA1 in pan-cancer using the data from the UCSC database. Then we explore the role of ANXA1 in PTC, including expression, prognostic value, and immune infiltration. In addition, we evaluated the relation between ANXA1 and the transcription factor MYC. Finally, we identified the expression of ANXA1 and MYC and then evaluated their function associated with proliferation and apoptosis in PTC cell lines by CCK8 proliferation and flow cytometry apoptosis experiment. We found that ANXA1 is up-regulated in PTC comparing with normal patients. High expression of ANXA1 was associated with adverse overall survival of PTC. ANXA1 may be regulated by MYC to promote the proliferation of PTC. MYC may regulate the expression of ANXA and thus affect the proliferation of PTC.
DOI: 10.6084/m9.figshare.20579766
title: Additional file 4 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 4: Table S2. Summary of DMR analysis across all studies used in study that overlapped DMRs identified in FAP study. Positive "meandiff" corresponds to increased beta values (DNA methylation) in FAP (or tumor samples).
DOI: 10.6084/m9.figshare.21628668.v1
title: Additional file 2 of Whole transcriptome analysis of HCT-8 cells infected by Cryptosporidium parvum

description: Additional file 2: Table S2. The differentially expressed mRNAs, lncRNAs, miRNAs and circRNA at 3 hpi and 12 hpi.
DOI: 10.6084/m9.figshare.16909902.v1
title: Additional file 1 of Identification of stem cell-related subtypes and risk scoring for gastric cancer based on stem genomic profiling

description: Additional file 1. Table S1: The clinical and demographic features of gastric cancer patients from Renmin Hospital of Wuhan University.
DOI: 10.6084/m9.figshare.20579772
title: Additional file 6 of DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development

description: Additional file 6: Table S4. Summary of qPCR and RNA-seq analysis performed on selected gene targets. Positive fold changes and t values indicate increased expression in TCGA-COAD tumor and FAP colon organoids, respectively.
DOI: 10.6084/m9.figshare.21628671
title: Additional file 3 of Whole transcriptome analysis of HCT-8 cells infected by Cryptosporidium parvum

description: Additional file 3: Table S3. The cis- and trans- target genes predicted for dif-lncRNAs at 3 hpi and 12 hpi.
DOI: 10.5281/zenodo.10155766
title: Datasets for JEB-2023-00176
DOI: 10.6084/m9.figshare.16910013.v1
title: Additional file 2 of Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)

description: Additional file 2: Table S2. Analysis and distribution of conserved motifs in S. italica bHLH proteins.
DOI: 10.6084/m9.figshare.16910022.v1
title: Additional file 5 of Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)

description: Additional file 5: Table S5. One-to-one orthologous genes relationships between S. italica and other plants.
DOI: 10.6084/m9.figshare.21628704
title: Additional file 2 of Whole-genome methylation analysis reveals epigenetic variation between wild-type and nontransgenic cloned, ASMT transgenic cloned dairy goats generated by the somatic cell nuclear transfer

description: Additional file 2: Fig. S2. Methylation sequencing quality and statistical analyses (A, ASMT transgenic cloned goat (K2020); B, control goat (S2); C, Nontransgenic cloned goat (K03)).
DOI: 10.6084/m9.figshare.16909938
title: Additional file 5 of Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus

description: Additional file 5: Table S1. The relative synonymous codon usage (RSCU) of synonymous codons. Table S2. The RSCU datasets of high and low expression genes. Table S3. Genome information of nine species.
DOI: 10.6084/m9.figshare.16910013
title: Additional file 2 of Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)

description: Additional file 2: Table S2. Analysis and distribution of conserved motifs in S. italica bHLH proteins.