cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24174573
title: Supplementary Material for: The microcirculation of vaginal tissue in women with obstetric vesicovaginal fistula and short-term effects of surgical repair on microvascular parameters

description: Objectives: To better understand the extent of the ischemic trauma and the effects of surgical repair on the vaginal microcirculation in patients with obstetric vesicovaginal fistula (VVF). Design: In this observational study, we evaluated the vaginal microvasculature surrounding VVF using handheld vital microscopy (HVM) before, during and two weeks after surgical VVF repair. Participants: Seventeen women undergoing VVF repair were included in this study. Setting: The study was conducted in the Fistula Care Centre in Lilongwe, Malawi. Methods: We used HVM with incident dark-field (IDF) imaging to non-invasively visualize the microvasculature of the vaginal tissue surrounding fistulas. The primary outcome was the presence of microvascular flow. Secondary outcomes included angioarchitecture, fistula closure (postoperative dye test) and urinary continence (pad weight test). Results: Microvascular flow was present before, during and after surgical repair in respectively 83.8%, 83.9% and 93.4% of obtained image sequences. The angioarchitecture was normal in 75.8% of the image sequences before surgery, 69.4% at fistula closure and 89.1% two weeks after VVF repair. Fourteen (82.4%) patients had a closed fistula after surgical repair. Limitations: The study was limited by the lack of a control group and the relatively small sample size. Conclusion: Although the vaginal microcirculation in women with VVF is compromised, extensive ischemic damage is not observed in the tissue surrounding fistulas. This suggests significant regenerative capacity of the vaginal vasculature in young women, or less extensive ischemic damage than presumed. Following surgical repair, we observed improvement of microcirculatory flow and angioarchitecture, suggesting that surgery is a good option for patients with obstetric VVF.
DOI: 10.6084/m9.figshare.24174573.v1
title: Supplementary Material for: The microcirculation of vaginal tissue in women with obstetric vesicovaginal fistula and short-term effects of surgical repair on microvascular parameters

description: Objectives: To better understand the extent of the ischemic trauma and the effects of surgical repair on the vaginal microcirculation in patients with obstetric vesicovaginal fistula (VVF). Design: In this observational study, we evaluated the vaginal microvasculature surrounding VVF using handheld vital microscopy (HVM) before, during and two weeks after surgical VVF repair. Participants: Seventeen women undergoing VVF repair were included in this study. Setting: The study was conducted in the Fistula Care Centre in Lilongwe, Malawi. Methods: We used HVM with incident dark-field (IDF) imaging to non-invasively visualize the microvasculature of the vaginal tissue surrounding fistulas. The primary outcome was the presence of microvascular flow. Secondary outcomes included angioarchitecture, fistula closure (postoperative dye test) and urinary continence (pad weight test). Results: Microvascular flow was present before, during and after surgical repair in respectively 83.8%, 83.9% and 93.4% of obtained image sequences. The angioarchitecture was normal in 75.8% of the image sequences before surgery, 69.4% at fistula closure and 89.1% two weeks after VVF repair. Fourteen (82.4%) patients had a closed fistula after surgical repair. Limitations: The study was limited by the lack of a control group and the relatively small sample size. Conclusion: Although the vaginal microcirculation in women with VVF is compromised, extensive ischemic damage is not observed in the tissue surrounding fistulas. This suggests significant regenerative capacity of the vaginal vasculature in young women, or less extensive ischemic damage than presumed. Following surgical repair, we observed improvement of microcirculatory flow and angioarchitecture, suggesting that surgery is a good option for patients with obstetric VVF.
DOI: 10.6084/m9.figshare.24160887
title: Supplementary Material for: Inhibition of Piezo1 ameliorates intestinal inflammation and limits the activation of group 3 innate lymphoid cells in experimental colitis

description: Piezo1, the mechanosensory ion channel, has attracted increasing attention for its essential roles in various inflammatory responses and immune-related diseases. Although most of the key immune cells in inflammatory bowel disease (IBD) have been reported to be regulated by Piezo1, the specific role of Piezo1 in colitis has yet to be intensively studied. The present study investigated the impact of pharmacological inhibition of Piezo1 on dextran sulfate sodium (DSS)-induced colitis, and explored the role of Piezo1 in intestinal immune cells in the context of colitis. We observed upregulated expression of Piezo1 in the colon tissue of mice with DSS-induced colitis. Pharmacological inhibition of Piezo1 by GsMTx4 diminished the severity of colitis. Piezo1 inhibition downregulated the expression of pro-inflammatory mediators Il1b, Il6, and Ptgs2 in colonic tissue, and suppressed the production of IL-6 from macrophages and dendritic cells (DCs), without altering the balance of T helper (Th) cells. In particular, Piezo1 did not affect cell viability, but regulated cell proliferation and production of IL-17A in group 3 innate lymphoid cells (ILC3s), which is dependent on the PI3K-Akt-mTOR signaling pathway. Our findings uncover Piezo1 as an effective regulator in gut inflammation. Targeting Piezo1 could be a promising strategy to modulate intestinal immunity in IBD.
DOI: 10.18167/dvn1/ictc6u
title: Gendered Food Mapping Data on Gari and Eba generated by NRCRI in Nigeria

description: This dataset contains data generated during the Activity 3 or Step 2 - Gendered food mapping performed by the NRCRI team in Nigeria on Gari and Eba, within the RTBfoods project (following the Methodological Guidance). This dataset may contain diverse types of anonymized data (e‧g. questionnaires, cleaned and processed data) which is to be available on open access following a 2-years embargo after the end of the RTBfoods project (embargo ending date: 15 March 2025) This dataset may also contain non-anonymized data (e‧g. raw data, consent forms signed by interviewees) which cannot be made publicly available, at any time; non-anonymized data is contained in the .tar‧gz file. For more information about the content of the .tar‧gz file, you are invited to contact the authors mentioned in the metadata.
DOI: 10.6084/m9.figshare.24271027.v1
title: Supplementary Material for: Systemic type 2 inflammation associated atopic dermatitis exacerbates periodontitis

description: Introduction: Atopic dermatitis (AD) is a prevalent and chronic inflammatory skin disease characterized by Th2 cell-mediated type 2 inflammation. Emerging evidence indicated that AD patients exhibit an increased incidence of oral disorders. In the present study, we sought mechanistic insights into how AD affects periodontitis. Methods: Onset of AD was induced by 2,4-dinitrochlorobenzene (DNCB). Furthermore, we induced periodontitis (P) in AD mice. The effect of AD in promoting inflammation and bone resorption in gingiva was evaluated. Hematoxylin and eosin (H&E) staining, tartrate-resistant acid phosphatase staining, immunofluorescence assay, and flow cytometry were used to investigate histomorphology, and cytology analysis, respectively. RNA sequencing (RNAseq) of oral mucosa tissues to further understand the dynamic transcriptome changes. 16S rRNA microbial analysis is used to profile oral microbial composition. Results: Compared control group, mice in AD group showed inflammatory signatures and infiltration of a proallergic Th2 (Th2A)-like subset in oral mucosa, but not periodontitis, identified by not substantial changes in mucosa swelling, alveolar bone loss and TRAP+ osteoclasts infiltration. Similarly, more Th2A-like cell infiltration and IL-4 levels were significantly elevated in the oral mucosa of DNCB-P mice compared to P mice. More importantly, AD exacerbates periodontitis when periodontitis has occurred and the severity of periodontitis increased with aggravation of dermatitis. Transcriptional analysis revealed that aggravated periodontitis was positively correlated with more macrophage infiltration and abundant CCL3 secreted. AD also altered oral microbiota, indicating the re-organization of extracellular matrix. Conclusions: These data provide a solid evidence about exacerbation of periodontitis caused by type 2 dermatitis, advancing our understanding in cellular and microbial changes during AD-periodontitis progression.
DOI: 10.5281/zenodo.10026799
title: ОЦЕНКА ДЛЯ ВЕТВЯЩИХСЯ ПРОЦЕССОВ С НЕПРЕРЫВНЫМ ВРЕМЕНЕМ
DOI: 10.5281/zenodo.10026798
title: ОЦЕНКА ДЛЯ ВЕТВЯЩИХСЯ ПРОЦЕССОВ С НЕПРЕРЫВНЫМ ВРЕМЕНЕМ
DOI: 10.4121/355fc1ac-2f72-47a2-9e4d-73376b905f06
title: Data underlying the publication: The effects of thioredoxin peroxidase from Cysticercus cellulosae excretory-secretory antigens on TGF-β signaling pathway and Th17 cells differentiation in Jurkat cells by transcriptomics

description: Translated Chinese text by ChatGPT:Background: The sulfur oxygen reductase peroxidase (TPx) protein from Cellulosimicrobium cellulans excretory-secretory antigen (ESA) has been shown to regulate the differentiation of host Treg and Th17 cells, resulting in an immune suppression response dominated by Treg cells. However, the molecular mechanisms by which the TPx protein from Cellulosimicrobium cellulans ESA regulates the differentiation of host Treg/Th17 cells have not been reported. <br>Methods: Jurkat cells stimulated with TPx protein from porcine Cellulosimicrobium cellulans ESAs at 0, 24, 48, and 72 hours with PMA and ionomycin activation. Transcriptomic analysis was performed to study the signaling pathways related to Jurkat cell differentiation regulated by TPx protein from porcine Cellulosimicrobium cellulans ESA.<br>Results: Gene Set Enrichment Analysis (GSEA) showed that TPx protein from porcine Cellulosimicrobium cellulans ESAs can induce upregulation of the TGF-β signaling pathway in Jurkat cells and downregulation of Th17 cell differentiation.<br>Conclusion: The TPx protein from porcine Cellulosimicrobium cellulans ESA can activate the TGF-β signaling pathway in Jurkat cells, thereby regulating the differentiation of Treg/Th17 cells, resulting in an immune suppression response dominated by Treg cells and evading host immune attacks. This study provides a foundation for further validating these pathways and elucidating the molecular mechanisms of immune escape caused by porcine Cellulosimicrobium cellulans.<br>Original text: 背景：来自<em>纤维素囊尾蚴</em>（<em>C. cellulosae</em>）排泄分泌抗原（ESA）的硫氧还原蛋白过氧化物酶（TPx）蛋白已被证明可以调节宿主Treg和Th17细胞的分化，导致由Treg细胞主导的免疫抑制反应。然而，来自<em>纤维素梭菌</em>ESA的TPx蛋白调节宿主Treg/Th17细胞分化失衡的分子机制尚未报道。（2）方法：采用猪<em>纤维素梭菌</em>ESAs的TPx蛋白在第0、24、48和72小时刺激PMA和电离霉素活化的Jurkat细胞。进行转录组学分析以研究与来自<em>纤维素梭菌</em>ESA的TPx蛋白调控的Jurkat细胞分化相关的信号通路。（3）结果：基因集富集分析（GSEA）显示，来自猪<em>纤维素梭菌</em>ESAs的TPx蛋白可诱导Jurkat细胞TGF-β信号通路上调和Th17细胞分化下调。（4）结论：猪<em>纤维素梭菌</em>ESA的TPx蛋白可激活Jurkat细胞中的TGF-β信号通路，从而调节Treg/Th17细胞的分化，导致以Treg细胞为主的免疫抑制反应，从而逃避宿主免疫攻击。本研究为进一步验证这些途径提供了基础，并进一步阐明了猪<em>纤维素梭菌</em>引起的免疫逃逸的分子机制。<br>
DOI: 10.4121/355fc1ac-2f72-47a2-9e4d-73376b905f06.v1
title: Data underlying the publication: The effects of thioredoxin peroxidase from Cysticercus cellulosae excretory-secretory antigens on TGF-β signaling pathway and Th17 cells differentiation in Jurkat cells by transcriptomics

description: Translated Chinese text by ChatGPT:Background: The sulfur oxygen reductase peroxidase (TPx) protein from Cellulosimicrobium cellulans excretory-secretory antigen (ESA) has been shown to regulate the differentiation of host Treg and Th17 cells, resulting in an immune suppression response dominated by Treg cells. However, the molecular mechanisms by which the TPx protein from Cellulosimicrobium cellulans ESA regulates the differentiation of host Treg/Th17 cells have not been reported. <br>Methods: Jurkat cells stimulated with TPx protein from porcine Cellulosimicrobium cellulans ESAs at 0, 24, 48, and 72 hours with PMA and ionomycin activation. Transcriptomic analysis was performed to study the signaling pathways related to Jurkat cell differentiation regulated by TPx protein from porcine Cellulosimicrobium cellulans ESA.<br>Results: Gene Set Enrichment Analysis (GSEA) showed that TPx protein from porcine Cellulosimicrobium cellulans ESAs can induce upregulation of the TGF-β signaling pathway in Jurkat cells and downregulation of Th17 cell differentiation.<br>Conclusion: The TPx protein from porcine Cellulosimicrobium cellulans ESA can activate the TGF-β signaling pathway in Jurkat cells, thereby regulating the differentiation of Treg/Th17 cells, resulting in an immune suppression response dominated by Treg cells and evading host immune attacks. This study provides a foundation for further validating these pathways and elucidating the molecular mechanisms of immune escape caused by porcine Cellulosimicrobium cellulans.<br>Original text: 背景：来自<em>纤维素囊尾蚴</em>（<em>C. cellulosae</em>）排泄分泌抗原（ESA）的硫氧还原蛋白过氧化物酶（TPx）蛋白已被证明可以调节宿主Treg和Th17细胞的分化，导致由Treg细胞主导的免疫抑制反应。然而，来自<em>纤维素梭菌</em>ESA的TPx蛋白调节宿主Treg/Th17细胞分化失衡的分子机制尚未报道。（2）方法：采用猪<em>纤维素梭菌</em>ESAs的TPx蛋白在第0、24、48和72小时刺激PMA和电离霉素活化的Jurkat细胞。进行转录组学分析以研究与来自<em>纤维素梭菌</em>ESA的TPx蛋白调控的Jurkat细胞分化相关的信号通路。（3）结果：基因集富集分析（GSEA）显示，来自猪<em>纤维素梭菌</em>ESAs的TPx蛋白可诱导Jurkat细胞TGF-β信号通路上调和Th17细胞分化下调。（4）结论：猪<em>纤维素梭菌</em>ESA的TPx蛋白可激活Jurkat细胞中的TGF-β信号通路，从而调节Treg/Th17细胞的分化，导致以Treg细胞为主的免疫抑制反应，从而逃避宿主免疫攻击。本研究为进一步验证这些途径提供了基础，并进一步阐明了猪<em>纤维素梭菌</em>引起的免疫逃逸的分子机制。<br>
DOI: 10.25345/c5xg9fn3g
title: MassIVE MSV000093160 - 231020_Data Marcelo_Q_Exactive
title: Bacterial extracts, Marcelo, Q Exactive Orbitrap measurements on Rosy
DOI: 10.6084/m9.figshare.24162195
title: Supplementary Material for: Histological phenotyping in eosinophilic esophagitis: Localized proximal disease is infrequent, but associated with less severe disease and better disease outcome

description: Introduction: It is still unknown whether eosinophilic esophagitis (EoE) patients with localized disease are different from those with extended disease. Methods: We evaluated prospectively included patients in the Swiss EoE cohort. Data on all patients with active disease at baseline, no concomitant gastro-esophageal reflux disease, no strictures at baseline and at least one follow-up visit were analyzed. We compared patients with histologically localized proximal vs distal vs. extended (=proximal and distal) disease with regards to patient, disease characteristics, disease presentation and development of complications. Results: We included 124 patients with a median of 2.5y of follow-up (73.4% males, median age 35.0y). Ten patients had proximal (8.1%), 46 patients had distal (37.1%), and 68 patients had extended disease (54.8%). Patients with proximal disease were significantly more often females (80%) compared with patients with distal (26.1%, p=0.002) or extended disease (19.1%, p&lt;0.001) and reported less severe symptoms (VAS 0 vs VAS 1, p=0.001). Endoscopic and histological disease was less pronounced in the proximal esophagus of proximal EoE compared to extended disease (EREFS 1.0 vs 3.0, p=0.001; 27.0eos/hpf vs 52.5eos/hpf, p=0.008). Patients with proximal disease were less likely to undergo dilation compared to patients with distal disease in the follow-up (3.3% vs 23.3%, p=0.010). In a multivariate Cox regression model, proximal eosinophilia was less likely to be associated with treatment failure compared to distal eosinophilia. Discussion/Conclusion: Although isolated proximal EoE is infrequent, it is associated with less severe disease and better disease outcome. Proximal disease appears to present a unique EoE phenotype.
DOI: 10.6084/m9.figshare.24162195.v1
title: Supplementary Material for: Histological phenotyping in eosinophilic esophagitis: Localized proximal disease is infrequent, but associated with less severe disease and better disease outcome

description: Introduction: It is still unknown whether eosinophilic esophagitis (EoE) patients with localized disease are different from those with extended disease. Methods: We evaluated prospectively included patients in the Swiss EoE cohort. Data on all patients with active disease at baseline, no concomitant gastro-esophageal reflux disease, no strictures at baseline and at least one follow-up visit were analyzed. We compared patients with histologically localized proximal vs distal vs. extended (=proximal and distal) disease with regards to patient, disease characteristics, disease presentation and development of complications. Results: We included 124 patients with a median of 2.5y of follow-up (73.4% males, median age 35.0y). Ten patients had proximal (8.1%), 46 patients had distal (37.1%), and 68 patients had extended disease (54.8%). Patients with proximal disease were significantly more often females (80%) compared with patients with distal (26.1%, p=0.002) or extended disease (19.1%, p&lt;0.001) and reported less severe symptoms (VAS 0 vs VAS 1, p=0.001). Endoscopic and histological disease was less pronounced in the proximal esophagus of proximal EoE compared to extended disease (EREFS 1.0 vs 3.0, p=0.001; 27.0eos/hpf vs 52.5eos/hpf, p=0.008). Patients with proximal disease were less likely to undergo dilation compared to patients with distal disease in the follow-up (3.3% vs 23.3%, p=0.010). In a multivariate Cox regression model, proximal eosinophilia was less likely to be associated with treatment failure compared to distal eosinophilia. Discussion/Conclusion: Although isolated proximal EoE is infrequent, it is associated with less severe disease and better disease outcome. Proximal disease appears to present a unique EoE phenotype.
DOI: 10.6084/m9.figshare.24161571
title: Supplementary Material for: Clinicopathological Features and Outcomes of IgA Nephropathy with Serum Antineutrophil Cytoplasmic Autoantibody Positivity

description: Objective: IgA nephropathy (IgAN) with serum Antineutrophil Cytoplasmic Autoantibody (ANCA) positivity is uncommon. This study analyzed the clinicopathologic features and prognosis of IgAN patients with serum ANCA positivity. Methods: 2864 IgAN patients were tested for ANCA by the indirect immunofluorescence assay and chemiluminescence immunoassay. Patients with serum ANCA positivity (n=85) were identified and their clinical, pathological and prognostic characteristics were analyzed. They were compared with ANCA negative IgAN patients (n=170) and ANCA-associated systemic vasculitis (AAV) with renal involvement patients (n=85) selected randomly. Result：2.97% (85/2864) of IgAN were ANCA positive and 4 patients were diagnosed as crescentic IgAN with ANCA positivity. The clinicopathological characteristics of ANCA-positive IgAN patients were comparable to ANCA-negative IgAN patients, but they had higher antinuclear antibodies (ANA) positive rates and lower levels of renal interstitial inflammation and less immune depositions than ANCA-negative IgAN patients. Compared with AAV patients, ANCA-positive IgAN patients were younger, fewer extrarenal manifestations, milder renal damage and more immune complexes depositions. The renal outcomes were similar between IgAN patients with and without ANCA positivity. Multivariate Cox analysis revealed that in IgAN patients with ANCA positivity, male, ANA positivity, higher serum creatinine and proteinuria, and more severe renal tubular atrophy/interstitial fibrosis were risk factors for adverse renal outcomes. Conclusion: The clinical, pathological features and prognosis of ANCA-positive IgAN patients were similar with ANCA-negative IgAN patients except for higher ANA positive rate, milder renal inflammation and less immune depositions. ANA positivity was an independent risk factor for adverse renal outcomes in ANCA-positive IgAN patients.
DOI: 10.6084/m9.figshare.24161571.v1
title: Supplementary Material for: Clinicopathological Features and Outcomes of IgA Nephropathy with Serum Antineutrophil Cytoplasmic Autoantibody Positivity

description: Objective: IgA nephropathy (IgAN) with serum Antineutrophil Cytoplasmic Autoantibody (ANCA) positivity is uncommon. This study analyzed the clinicopathologic features and prognosis of IgAN patients with serum ANCA positivity. Methods: 2864 IgAN patients were tested for ANCA by the indirect immunofluorescence assay and chemiluminescence immunoassay. Patients with serum ANCA positivity (n=85) were identified and their clinical, pathological and prognostic characteristics were analyzed. They were compared with ANCA negative IgAN patients (n=170) and ANCA-associated systemic vasculitis (AAV) with renal involvement patients (n=85) selected randomly. Result：2.97% (85/2864) of IgAN were ANCA positive and 4 patients were diagnosed as crescentic IgAN with ANCA positivity. The clinicopathological characteristics of ANCA-positive IgAN patients were comparable to ANCA-negative IgAN patients, but they had higher antinuclear antibodies (ANA) positive rates and lower levels of renal interstitial inflammation and less immune depositions than ANCA-negative IgAN patients. Compared with AAV patients, ANCA-positive IgAN patients were younger, fewer extrarenal manifestations, milder renal damage and more immune complexes depositions. The renal outcomes were similar between IgAN patients with and without ANCA positivity. Multivariate Cox analysis revealed that in IgAN patients with ANCA positivity, male, ANA positivity, higher serum creatinine and proteinuria, and more severe renal tubular atrophy/interstitial fibrosis were risk factors for adverse renal outcomes. Conclusion: The clinical, pathological features and prognosis of ANCA-positive IgAN patients were similar with ANCA-negative IgAN patients except for higher ANA positive rate, milder renal inflammation and less immune depositions. ANA positivity was an independent risk factor for adverse renal outcomes in ANCA-positive IgAN patients.
DOI: 10.5281/zenodo.10003274
title: XJ_COTTON10: The 10-m cotton maps in Xinjiang, China during 2018-2021

description: The datasets accompany the paper "The 10-m cotton maps in Xinjiang, China during 2018–2021" that was published in Scientific Data on Oct. 10, 2023. The datasets contain the 10-m cotton maps of Xinjiang (XJ_COTTON10) from 2018 to 2021. They were developed through supervised classification using high-quality in-field samples and multi-source remote sensing data on the Google Earth Engine (GEE) platform.
Citation:
[1] Kang, X., Huang, C., Chen, J.M., Lv, X., Wang, J., Zhong, T., Wang, H., Fan, X., Ma, Y., Yi, X., Zhang, Z., Zhang, L., Tong, Q., 2023. The 10-m cotton maps in Xinjiang, China during 2018-2021. Sci Data 10, 688. doi:10.1038/s41597-023-02584-3
[2] Lang, P., Zhang, L., Huang, C., Chen, J., Kang, X., Zhang, Z., Tong, Q., 2023. Integrating environmental and satellite data to estimate county-level cotton yield in Xinjiang Province. Frontiers in Plant Science 13, 1048479. doi:10.3389/fpls.2022.1048479
[3] Kang, X., Huang, C., Zhang, L., Zhang, Z., Lv, X., 2022. Downscaling solar-induced chlorophyll fluorescence for field-scale cotton yield estimation by a two-step convolutional neural network. Computers and Electronics in Agriculture 201, 107260. doi:10.1016/j.compag.2022.107260
[4] Kang, X., Huang, C., Zhang, L., Wang, H., Zhang, Z., Lv, X., 2023. Regional-scale cotton yield forecast via data-driven spatio-temporal prediction (STP) of solar-induced chlorophyll fluorescence (SIF). Remote Sensing of Environment 299, 113861. doi:10.1016/j.rse.2023.113861
DOI: 10.5281/zenodo.7266101
title: XJ_COTTON10: The 10-m cotton field maps in Xinjiang, China during 2018-2021

description: The datasets will accompany the paper "The 10-m cotton field maps in Xinjiang, China during 2018–2021". The datasets contain the 10-m cotton field maps of Xinjiang (XJ_COTTON10) from 2018 to 2021. They were developed through supervised classification using high-quality in-field samples and multi-source remote sensing data on the Google Earth Engine (GEE) platform.