cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24161109.v1
title: Supplementary Material for: Sex Hormone-Binding Globulin and Risk of Incident Dementia in Middle-aged to older Women: Results from the UK Biobank Cohort Study

description: Introduction: The association of serum sex hormone-binding globulin (SHBG) concentrations with dementia risk remains uncertain in middle-aged to older women. We examined associations of serum SHBG levels with incidence of all-cause dementia and its subtypes in middle-aged to older women from the large population-based UK Biobank cohort study. Methods: Serum total SHBG levels were measured by immunoassay. The incidence of all-cause dementia and its subtypes was recorded. Cox proportional hazards models were used to calculate hazard ratios (HR) for main outcomes. Results: Among 171,482 community-dwelling women (mean (SD) age was 59.9 (5.4) years, median follow-up of 11.8 years), 2,368 developed dementia, including 1,088 from Alzheimer's disease (AD), 451 from vascular dementia (VAD), and 1,609 from other dementia. After multivariable adjustments, higher serum SHBG levels were significantly associated with higher risks of all-cause dementia, AD and other dementia (All P&lt;0.05). Compared to those in the lowest quartile of SHBG levels, participants in the highest quartile of SHBG levels had a higher risk of all-cause dementia (HR 1.34; 95% confidence interval [CI] 1.16-1.53), AD (HR 1.32; 95% CI 1.07-1.62), and other dementia (HR 1.44; 95% CI 1.21-1.70). However, this relationship was not significant for VAD (HR 1.16; 95% CI 0.86-1.56). Conclusion: These findings indicated that higher serum SHBG concentrations were independently associated with higher risks of incident all-cause dementia, as well as AD and other dementia among middle-aged to older women. No association was found for VAD.
DOI: 10.5281/zenodo.10020468
title: SPR, judgements, and judgement times
DOI: 10.5281/zenodo.10020469
title: SPR, judgements, and judgement times
DOI: 10.6084/m9.figshare.24174570
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.6084/m9.figshare.24174570.v1
title: Supplementary Material for: Green tea polyphenols alleviate kidney injury induced by di(2-ethylhexyl) phthalate in mice

description: Background: Di(2-ethylhexyl) phthalate (DEHP) is a common plasticizer. Studies have revealed that DEHP exposure can cause kidney damage. Green tea is among the most popular beverages in China. Green tea polyphenols (GTPs) have been proven to have therapeutic effects on organ damage induced by heavy metal exposure. However, few studies have reported on GTP relieving DEHP-induced kidney damage. Methods: C57BL/6J male mice aged 6–8 weeks were treated with distilled water (control group), 1500 mg/kg/d DEHP + corn oil (model group), 1500 mg/kg/d DEHP + corn oil + 70 mg/kg GTP (treatment group), corn oil (oil group), and 70 mg/kg GTP (GTP group) by gavage for 8 weeks, respectively. The renal function of mice and renal tissue histopathology of each group were evaluated. The renal tissues of mice in the model, treatment, and control groups were analyzed using high-throughput sequencing. We calculated the differentially expressed miRNAs and mRNAs using the limma R package, the CIBERSORT algorithm was used to predict immune infiltration, the starBase database was used to screen the miRNA–mRNA regulatory axis, and immunohistochemical analyses were performed to verify protein expression. Results: GTP alleviated the deterioration of renal function, renal inflammation and fibrosis, and mitochondrial and endoplasmic reticulum lesions induced by DEHP in mice. Differential immune infiltrations of plasma, dendritic, T, and B cells were noted between the model and treatment groups. We found that three differentially expressed miRNAs (mmu-miR-383-5p, mmu-miR-152-3p, and mmu-miR-144-3p), three differentially expressed mRNAs (Ddit4, Dusp1, and Snx18), and three differentially expressed proteins (Ddit4, Dusp1, and Snx18) played crucial roles in the miRNA–mRNA–protein regulatory axes when GTPs mitigate DEHP-induced kidney damage in mice. Conclusion: GTP can alleviate DEHP-induced kidney damage and regulate immune cell infiltration. We screened four important miRNA–mRNA–protein regulatory axes of GTP mitigating DEHP-induced kidney damage in mice.
DOI: 10.25716/gude.0ta9-9nkc
title: Molecular Mechanisms and Evolutionary Robustness of a Color Switch in Proteorhodopsins

description: The data set is associated with manuscript: Jiafei Mao, Xinsheng Jin, Man Shi, David Heidenreich, Lynda J. Brown, Richard C.D. Brown, Moreno Lelli, Xiao He, Clemens Glaubitz: Molecular Mechanisms and Evolutionary Robustness of a Color Switch in Proteorhodopsins; submitted to Science Advances (adj0384). It contains the NMR data from Figures 2, 3, 4, S2-15 as well as data for the bioinformatics analysis in Figues 1d, 7, S22-S24. An overview of all samples and spectra is provided in Table S1 of the manuscript.
description: The file 850.zip contains raw and processed data of the NMR spectra shown in Figures 2d, S2, S3. The file DNP.zip contains raw and processed data of the NMR spectra shown in Figures 2b, 2c, 3d, 3e, S4, S5, S6, S7a, S7b, S9, S10, S11c, S11d, S12c, S12d, S13a, S13b, S13c, S14, S15. The file hNOE.zip contains raw and processed data of the NMR spectra used to prepare Figures 4b and S8. The file VFMAS.zip contains raw and processed data of the NMR spectra used to prepare Figure 2d. The file SciAdv_Bio_Info_Data.zip contains information for the bioinformatics analysis in Figures 1d, 7, S22, S23, S24.
DOI: 10.4121/12437ba3-4cf4-47c4-928b-94dc9bdec663
title: Data, Code and trained models of RainGuru

description: The RainGuRu is a deep-learning rainfall nowcasting model developed by TU Delft and HKV, with the use of RNN model - TrajGRU. This dataset is built to store all code files, trained models and diverse visual results which are not available in the MSc thesis report of Yanghuan.
DOI: 10.4121/12437ba3-4cf4-47c4-928b-94dc9bdec663.v1
title: Data, Code and trained models of RainGuru

description: The RainGuRu is a deep-learning rainfall nowcasting model developed by TU Delft and HKV, with the use of RNN model - TrajGRU. This dataset is built to store all code files, trained models and diverse visual results which are not available in the MSc thesis report of Yanghuan.
DOI: 10.6084/m9.figshare.20452197
title: No sex-specific effects of artificial selection for relative telencephalon size in detour learning and spatial discrimination in guppies (<i>Poecilia reticulata</i>)

description: Over recent decades, substantial research has focused on fish cognitive evolution to increase our understanding of the evolution of the enormous diversity of cognitive abilities that exists in fishes. One important but understudied aspect of cognitive evolution is sexual dimorphism in cognitive abilities. Sex-specific variation in brain region morphology has been proposed to be an important mechanism in this context. However, it is also common to find sex-specific variation in behaviour and cognition without associated differences in brain morphology among the sexes. The telencephalon is the major cognitive center in the vertebrate brain and variation in telencephalon size has been associated with variation in cognition. Here we utilize recently developed guppy artificial selection lines with ca 10% differences in relative telencephalon size to investigate if similar responses to selection of the size of this region may affect cognitive abilities differently in males and females. We compared two ecologically relevant aspects of cognition, detour learning and binary spatial discrimination. We tested the significance of the interaction between telencephalon size and sex, and found no sex-specific effects of evolutionary increases in telencephalon size in the cognitive abilities tested. This study indicates that no clear cognitive sex-specific responses occur in response to rapid selection on telencephalon size. We suggest that future research on sexual dimorphism in cognitive abilities in fish could examine various cognitive tests and telencephalic subregions to gain a more comprehensive understanding of their evolution.<br>
DOI: 10.6084/m9.figshare.20452197.v1
title: No sex-specific effects of artificial selection for relative telencephalon size in detour learning and spatial discrimination in guppies (<i>Poecilia reticulata</i>)

description: Over recent decades, substantial research has focused on fish cognitive evolution to increase our understanding of the evolution of the enormous diversity of cognitive abilities that exists in fishes. One important but understudied aspect of cognitive evolution is sexual dimorphism in cognitive abilities. Sex-specific variation in brain region morphology has been proposed to be an important mechanism in this context. However, it is also common to find sex-specific variation in behaviour and cognition without associated differences in brain morphology among the sexes. The telencephalon is the major cognitive center in the vertebrate brain and variation in telencephalon size has been associated with variation in cognition. Here we utilize recently developed guppy artificial selection lines with ca 10% differences in relative telencephalon size to investigate if similar responses to selection of the size of this region may affect cognitive abilities differently in males and females. We compared two ecologically relevant aspects of cognition, detour learning and binary spatial discrimination. We tested the significance of the interaction between telencephalon size and sex, and found no sex-specific effects of evolutionary increases in telencephalon size in the cognitive abilities tested. This study indicates that no clear cognitive sex-specific responses occur in response to rapid selection on telencephalon size. We suggest that future research on sexual dimorphism in cognitive abilities in fish could examine various cognitive tests and telencephalic subregions to gain a more comprehensive understanding of their evolution.<br>
DOI: 10.6084/m9.figshare.24186324.v1
title: Supplementary Material for: Perilipin1 deficiency prompts lipolysis in lipid droplets and aggravates the pathogenesis of persistent immune activation in Drosophila

description: Lipid droplets (LDs) are highly dynamic intracellular organelles, which are involved in lots of biological processes. However, the dynamic morphogenesis and functions of intracellular LDs during persistent innate immune responses remain obscure. In this study, we induce long-term systemic immune activation in Drosophila through genetic manipulation. Then, the dynamic pattern of LDs is traced in the Drosophila fat body. We find that deficiency of Plin1, a key regulator of LDs’ reconfiguration, blocks LDs minimization at the initial stage of immune hyperactivation but enhances LDs breakdown at the later stage of sustained immune activation via recruiting the lipase Brummer (Bmm, homologous to human ATGL). The high wasting in LDs shortens the lifespan of flies with high-energy-cost immune hyperactivation. Therefore, these results suggest a critical function of LDs during long-term immune activation and provide a potential treatment for the resolution of persistent inflammation.
DOI: 10.6084/m9.figshare.24186324
title: Supplementary Material for: Perilipin1 deficiency prompts lipolysis in lipid droplets and aggravates the pathogenesis of persistent immune activation in Drosophila

description: Lipid droplets (LDs) are highly dynamic intracellular organelles, which are involved in lots of biological processes. However, the dynamic morphogenesis and functions of intracellular LDs during persistent innate immune responses remain obscure. In this study, we induce long-term systemic immune activation in Drosophila through genetic manipulation. Then, the dynamic pattern of LDs is traced in the Drosophila fat body. We find that deficiency of Plin1, a key regulator of LDs’ reconfiguration, blocks LDs minimization at the initial stage of immune hyperactivation but enhances LDs breakdown at the later stage of sustained immune activation via recruiting the lipase Brummer (Bmm, homologous to human ATGL). The high wasting in LDs shortens the lifespan of flies with high-energy-cost immune hyperactivation. Therefore, these results suggest a critical function of LDs during long-term immune activation and provide a potential treatment for the resolution of persistent inflammation.
DOI: 10.6084/m9.figshare.24242140
title: Supplementary Material for: Seroprevalence of Enterovirus D68 infection among humans: A systematic review and meta-analysis

description: Introduction : Human enterovirus D68 (EV-D68), which belongs to enteroviruses of the small RNA family, is a type of enterovirus that can cause acute respiratory tract infection and central nervous system diseases. This study systematically analysed and summarized EV-D68 antibody studies in databases and identified the seropositivity rates of different regions, ages, and sexes. Methods: Meta-analysis was performed using STATA 16.0 software. I2 and Q tests were used to analyse the heterogeneity of the included studies. Meta-regression analysis was performed for different groups, and Egger's linear regression analysis was used to evaluate publication bias. Results: The results of multiple studies indicated that the serological prevalence range of EV-D68 antibody was 17.78%-96.69%. The results of the meta-analysis showed that the seropositivity rate of EV-D68 antibody was 76% (95% CI: 67%-84%), among which that of the Chinese population was 74% (95% CI: 61%-86%) and that of other countries was 79% (95% CI: 65%-91%). At the same time, a subgroup analysis was conducted. The seroprevalence of EV-D68 antibody was related to age but not sex or region. Conclusion: The seropositivity rate was lower in the below 5 years age group; however, it gradually increased with age. The results of this study showed that EV-D68 infection was widespread in the population, and the current clinical infection situation could not reflect the actual epidemic situation of the virus, among which children under 5 years old were vulnerable to infection, which should be given greater attention for epidemic prevention and control.
DOI: 10.6084/m9.figshare.24242140.v1
title: Supplementary Material for: Seroprevalence of Enterovirus D68 infection among humans: A systematic review and meta-analysis

description: Introduction : Human enterovirus D68 (EV-D68), which belongs to enteroviruses of the small RNA family, is a type of enterovirus that can cause acute respiratory tract infection and central nervous system diseases. This study systematically analysed and summarized EV-D68 antibody studies in databases and identified the seropositivity rates of different regions, ages, and sexes. Methods: Meta-analysis was performed using STATA 16.0 software. I2 and Q tests were used to analyse the heterogeneity of the included studies. Meta-regression analysis was performed for different groups, and Egger's linear regression analysis was used to evaluate publication bias. Results: The results of multiple studies indicated that the serological prevalence range of EV-D68 antibody was 17.78%-96.69%. The results of the meta-analysis showed that the seropositivity rate of EV-D68 antibody was 76% (95% CI: 67%-84%), among which that of the Chinese population was 74% (95% CI: 61%-86%) and that of other countries was 79% (95% CI: 65%-91%). At the same time, a subgroup analysis was conducted. The seroprevalence of EV-D68 antibody was related to age but not sex or region. Conclusion: The seropositivity rate was lower in the below 5 years age group; however, it gradually increased with age. The results of this study showed that EV-D68 infection was widespread in the population, and the current clinical infection situation could not reflect the actual epidemic situation of the virus, among which children under 5 years old were vulnerable to infection, which should be given greater attention for epidemic prevention and control.
DOI: 10.17909/3a8n-th45
title: Data from paper
DOI: 10.6084/m9.figshare.24228664
title: Supplementary Material for: Risk factors for fractures in renal transplantation: a population-based cohort study

description: Introduction: Kidney transplant recipients are at an increased risk of fractures, and targeted preventive strategies are needed. Therefore, in this retrospective cohort study, we investigated a large population-based cohort to identify the transplant recipient-specific risk factors for fractures in Taiwanese kidney transplant recipients. Methods: We conducted a retrospective cohort study using the National Health Insurance Research Database. Patients who underwent renal transplantation between 2003 and 2015 were identified and followed until December 31, 2015 to observe the development of fractures. Variables associated with the development of post-transplant fractures were identified by calculating hazard ratios in a Cox regression model. Results: 5309 renal transplant recipients were identified, of whom 553 (10.4%) were diagnosed with post-transplant fractures. Independent predictors of post-transplant fractures included an age at transplant ≥65 years (p&lt;0.001), female sex (p&lt;0.001), fractures within 3 years prior to transplantation (p&lt;0.001), and diabetes mellitus (p&lt;0.001). In addition, daily prednisolone dose &gt;2.9-5.3 mg/day (p&lt;0.001), &gt;5.3-8.7 mg/day (p&lt;0.001) and &gt;8.7 mg/day (p&lt;0.001) were also independent predictors of post-transplant fractures. Conversely, the use of peritoneal dialysis before renal transplantation (p=0.021), hypertension (p=0.005), and the use of tacrolimus (p&lt;0.001), azathioprine (p=0.006), mycophenolate mofetil/mycophenolic acid (p=0.002), mTOR inhibitors (p=0.004) and calcium supplements (p=0.009) were inversely correlated with post-transplant fractures. Conclusion: We recommend minimizing daily glucocorticoids as early and as far as possible in conjunction with immunosuppressive regimens such as tacrolimus, azathioprine, mycophenolate mofetil/mycophenolic acid, mTOR inhibitors and calcium supplements, especially in older female recipients, and in recipients with diabetes and a history of prior fractures.
DOI: 10.6084/m9.figshare.24228664.v1
title: Supplementary Material for: Risk factors for fractures in renal transplantation: a population-based cohort study

description: Introduction: Kidney transplant recipients are at an increased risk of fractures, and targeted preventive strategies are needed. Therefore, in this retrospective cohort study, we investigated a large population-based cohort to identify the transplant recipient-specific risk factors for fractures in Taiwanese kidney transplant recipients. Methods: We conducted a retrospective cohort study using the National Health Insurance Research Database. Patients who underwent renal transplantation between 2003 and 2015 were identified and followed until December 31, 2015 to observe the development of fractures. Variables associated with the development of post-transplant fractures were identified by calculating hazard ratios in a Cox regression model. Results: 5309 renal transplant recipients were identified, of whom 553 (10.4%) were diagnosed with post-transplant fractures. Independent predictors of post-transplant fractures included an age at transplant ≥65 years (p&lt;0.001), female sex (p&lt;0.001), fractures within 3 years prior to transplantation (p&lt;0.001), and diabetes mellitus (p&lt;0.001). In addition, daily prednisolone dose &gt;2.9-5.3 mg/day (p&lt;0.001), &gt;5.3-8.7 mg/day (p&lt;0.001) and &gt;8.7 mg/day (p&lt;0.001) were also independent predictors of post-transplant fractures. Conversely, the use of peritoneal dialysis before renal transplantation (p=0.021), hypertension (p=0.005), and the use of tacrolimus (p&lt;0.001), azathioprine (p=0.006), mycophenolate mofetil/mycophenolic acid (p=0.002), mTOR inhibitors (p=0.004) and calcium supplements (p=0.009) were inversely correlated with post-transplant fractures. Conclusion: We recommend minimizing daily glucocorticoids as early and as far as possible in conjunction with immunosuppressive regimens such as tacrolimus, azathioprine, mycophenolate mofetil/mycophenolic acid, mTOR inhibitors and calcium supplements, especially in older female recipients, and in recipients with diabetes and a history of prior fractures.
DOI: 10.6084/m9.figshare.24298204
title: Supplementary Material for: Use of amniotic membrane transplant and deep anterior keratoplasty in a patient with bilateral acanthamoeba infectious keratitis: a case report

description: To report a case with the use of amniotic membrane transplant and deep anterior keratoplasty in a patient with bilateral acanthamoeba infectious keratitis as a treatment. A 20-year-old male presented with bilateral acanthamoeba keratitis (AK) who was initially diagnosed with herpetic keratitis receiving full antiviral and corticosteroids topical treatment without any improvement. Corneal biopsy was performed to confirm the suspected diagnosis and Acanthamoeba stromal cysts were identified in the sample. Treatment was initiated with 0.02% chlorhexidine, 0.1% propamidine isethionate, neomycin, and tropicamide/phenylephrine. Symptoms and clinical improvement were achieved between the 8th-10th week so corticosteroids were initiated. Treatment was continued until we observed a poor response in the left eye therefore, an epithelial scraping and amniotic membrane placement were performed. Lately, Right eye underwent a deep anterior lamellar keratoplasty (DALK). A challenging case of bilateral acanthamoeba keratitis managed with topical medications, amniotic membrane, and cornea keratoplasty. The earlier the disease is diagnosed, the better the outcome. If the diagnosis is delayed, the amoebas have penetrated deep into the corneal stroma and successful therapy becomes difficult. A surgical option can be an early solution with a good prognosis for these cases.
DOI: 10.34740/kaggle/dsv/6748560
title: 2021 World Population (updated daily)