cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8075039.v1
title: Supplementary Material for: Augmentation of Urinary Lactoferrin Enhances Host Innate Immune Clearance of Uropathogenic <b><i>Escherichia coli</i></b>

description: Urinary tract infection (UTI) is a prominent global health care burden. Although UTI is readily treated with antibiotics in healthy adults, complicated cases in immune-compromised individuals and the emerging antibiotic resistance of several uropathogens have accelerated the need for new treatment strategies. Here, we surveyed the composition of urinary exosomes in a mouse model of uropathgenic <i>Escherichia coli</i> (UPEC) UTI to identify specific urinary tract defense constituents for therapeutic development. We found an enrichment of the iron-binding glycoprotein lactoferrin in the urinary exosomes of infected mice. In subsequent in vitro studies, we identified human bladder epithelial cells as a source of lactoferrin during UPEC infection. We further established that exogenous treatment with human lactoferrin (hLf) reduces UPEC epithelial adherence and enhances neutrophil antimicrobial functions including bacterial killing and extracellular trap production. Notably, a single intravesicular dose of hLf drastically reduced bladder bacterial burden and neutrophil infiltration in our murine UTI model. We propose that lactoferrin is an important modulator of innate immune responses in the urinary tract and has potential application in novel therapeutic design for UTI.
DOI: 10.6084/m9.figshare.8074964
title: Combined genetic and epigenetic effects on variably methylated regions

description: We first identified candidate VMRs, defined as regions of CpG-sites showing the highest variability across all methylation sites.To examine the factors that best explain the variance in methylation in these functionally relevant sites, we chose the CpG-site with the highest MAD-score as representative of the VMR. These CpGs are named tagCpGs. We next compared the fit of four models for each of the 3,782 tagCpGs: best SNP (G model), best environment (E model), SNP + environment (G+E model) and SNP x environment (GxE model). For each tagCpG, the model with the lowest AIC was chosen as the best model.<br><br>
DOI: 10.6084/m9.figshare.8074955
title: Supplementary Material for: Intragenic Deletion in MACROD2: A Family with Complex Phenotypes Including Microcephaly, Intellectual Disability, Polydactyly, Renal and Pancreatic Malformations

description: Diagnosing a complex genetic syndrome and correctly assigning the concomitant phenotypic traits to a well-defined clinical form is often a medical challenge. In this work, we report the analysis of a family with complex phenotypes, including microcephaly, intellectual disability, dysmorphic features, and polydactyly in the proband, with the aim of adding new aspects for obtaining a clear diagnosis. We performed array-comparative genomic hybridization and quantitative reverse transcriptase PCR (qRT-PCR) analyses. We identified a deletion of chromosome 20p12.1 involving the macrodomain containing 2/mono-ADP ribosylhydrolase 2 gene (<i>MACROD2</i>) in several members of the family. This gene is actually not associated with a specific syndrome but with congenital anomalies of multiple organs. qRT-PCR showed higher levels of a <i>MACROD2</i> mRNA isoform in the individuals carrying the deletion. Our results, together with other data reported in the literature, support the hypothesis that the deletion in <i>MACROD2</i> can affect correct embryonic development and that the presence of another associated event, such as epigenetic modifications at the <i>MACROD2</i> locus, can influence the level of severity of the pathology.
DOI: 10.6084/m9.figshare.8074955.v1
title: Supplementary Material for: Intragenic Deletion in MACROD2: A Family with Complex Phenotypes Including Microcephaly, Intellectual Disability, Polydactyly, Renal and Pancreatic Malformations

description: Diagnosing a complex genetic syndrome and correctly assigning the concomitant phenotypic traits to a well-defined clinical form is often a medical challenge. In this work, we report the analysis of a family with complex phenotypes, including microcephaly, intellectual disability, dysmorphic features, and polydactyly in the proband, with the aim of adding new aspects for obtaining a clear diagnosis. We performed array-comparative genomic hybridization and quantitative reverse transcriptase PCR (qRT-PCR) analyses. We identified a deletion of chromosome 20p12.1 involving the macrodomain containing 2/mono-ADP ribosylhydrolase 2 gene (<i>MACROD2</i>) in several members of the family. This gene is actually not associated with a specific syndrome but with congenital anomalies of multiple organs. qRT-PCR showed higher levels of a <i>MACROD2</i> mRNA isoform in the individuals carrying the deletion. Our results, together with other data reported in the literature, support the hypothesis that the deletion in <i>MACROD2</i> can affect correct embryonic development and that the presence of another associated event, such as epigenetic modifications at the <i>MACROD2</i> locus, can influence the level of severity of the pathology.
DOI: 10.6084/m9.figshare.8074832
title: Fluctuating pond water levels and aquatic insect persistence raw data

description: This dataset includes the results from a study on the responses of aquatic insects to receding water levels in a Mediterranean-type climate. In addition, physicochemical parameters of water bodies are given.
DOI: 10.6084/m9.figshare.8074820
title: Supplementary Material for: Polymorphisms of MAMLD1, SRD5A2, and AR Candidate Genes in Seven Dogs (78,XY; SRY-Positive) Affected by Hypospadias or Cryptorchidism

description: Knowledge of the molecular background of disorders of sex development (DSD) in dogs with normal sets of XY chromosomes (XY DSD) is very scarce. However, extensive studies have been carried out in humans, showing that polymorphisms and mutations of numerous genes, including <i>SRY, MAMLD1, SRD5A2</i>, and<i> AR, </i>are associated with or responsible for XY DSD. In this study, we analyzed the entire coding sequence of these genes in 7 dogs (78,XY) with ambiguous external genitalia (hypospadias, cryptorchidism, bifid scrotum, or rudimentary penis). The most common disorder was hypospadias (6 cases), followed by cryptorchidism (4 cases). The co-occurrence of both abnormalities was observed in 3 dogs. Polymorphisms were found in <i>MAMLD1 </i>(3 SNPs), <i>SRD5A2</i> (5 SNPs), and <i>AR</i> (2 STRs and 1 SNP), while <i>SRY</i> was monomorphic. However, the distribution of the polymorphic variants in the DSD dogs and 11 control XY dogs did not differ significantly. Our study suggests that an association between the polymorphisms of the studied candidate genes and hypospadias or cryptorchidism is unlikely in dogs. We thus support the recent suggestion that hypospadias is not rare in this species, and moreover, we show that co-occurrence of hypospadias and cryptorchidism can be quite frequent.
DOI: 10.6084/m9.figshare.8074832.v1
title: Fluctuating pond water levels and aquatic insect persistence raw data

description: This dataset includes the results from a study on the responses of aquatic insects to receding water levels in a Mediterranean-type climate. In addition, physicochemical parameters of water bodies are given.
DOI: 10.6084/m9.figshare.8074832.v2
title: Fluctuating pond water levels and aquatic insect persistence raw data

description: This dataset includes the results from a study on the responses of aquatic insects to receding water levels in a Mediterranean-type climate. In addition, physicochemical parameters of water bodies are given.
DOI: 10.6084/m9.figshare.8074577.v1
title: Posters (Knight DR et al)

description: Collection of conference proceedings
DOI: 10.6084/m9.figshare.8074478
title: Distributed representation of discrete sequential vocalization in the Bengalese finch (<i>Lonchura striata var. domestica</i>)

description: Bengalese finches learn and produce sequential vocalizations with a complex song syntax. Various models for the song syntax have been proposed, each of which focuses on several different characteristics of the syntax. However, methods to model these multiple characteristics in a single framework have not been well studied. Here, we propose a model that explains three prominent characteristics of the song syntax in Bengalese finches in a single unified framework. First, the generation of a vocal element depends on multiple preceding elements. Second, a song often contains repetitions of a single element type. Third, a song often begins with a special sequence called an introductory sequence. In this study, an effective way was sought to model these three characteristics in the framework of a conditional probability in symbol sequences. The model takes a distributed representation of a preceding sequence as an input, which is defined by a set of decaying values activated when the vocal elements are generated. The proposed model is shown to outperform conventional syntax models in predicting sequences in novel songs. The results suggest that the song syntax of the bird’s brain might also be represented by decaying activities of populations of neurons.
DOI: 10.6084/m9.figshare.8074478.v1
title: Distributed representation of discrete sequential vocalization in the Bengalese finch (<i>Lonchura striata var. domestica</i>)

description: Bengalese finches learn and produce sequential vocalizations with a complex song syntax. Various models for the song syntax have been proposed, each of which focuses on several different characteristics of the syntax. However, methods to model these multiple characteristics in a single framework have not been well studied. Here, we propose a model that explains three prominent characteristics of the song syntax in Bengalese finches in a single unified framework. First, the generation of a vocal element depends on multiple preceding elements. Second, a song often contains repetitions of a single element type. Third, a song often begins with a special sequence called an introductory sequence. In this study, an effective way was sought to model these three characteristics in the framework of a conditional probability in symbol sequences. The model takes a distributed representation of a preceding sequence as an input, which is defined by a set of decaying values activated when the vocal elements are generated. The proposed model is shown to outperform conventional syntax models in predicting sequences in novel songs. The results suggest that the song syntax of the bird’s brain might also be represented by decaying activities of populations of neurons.
DOI: 10.6084/m9.figshare.8074430
title: Supplementary Material for: Age- and Sex-Specific Risk Profiles and In-Hospital Mortality in 13,932 Spanish Stroke Patients

description: <b><i>Background:</i></b> In-hospital stroke death rate is an important sanitary issue. Despite advances in the acute phase management of stroke patients, mortality and disability rates remain high. In aging populations and with different mortality between the sexes in general, the study of sex- and age-related differences becomes increasingly relevant for optimization of post-acute clinical care of stroke patients. <b><i>Methods:</i></b> We designed a cohort follow-up study with 13,932 consecutive ischemic stroke (IS) patients from 19 Spanish hospitals. Data was obtained from the Spanish Stroke Registry; transient ischemic attacks and ages &lt;18 years were excluded. Patients were organised by age group and sex. We compared female and male patient cohorts within and across age groups univariately and used multivariable logistic regression to adjust for confounders in differential in-hospital mortality. <b><i>Results:</i></b> The median (percentiles 2.5 and 97.5%) age was 78 (41–92) years old for women and 71 (41–92) for men. IS women were more likely to be older, to exhibit cardio-embolic aetiology, and less likely to have been admitted to a stroke unit or to have had a stroke code activated. Both pre-stroke modified Rankin Scale and National Institute of Health Stroke Scale (NIHSS) scores at admission increased significantly with age and were higher in women than those in men. Differences in distributions of common risk factors for IS and of in-hospital outcomes between women and men actually changed with patient’s age. It is to be noted here that although there were no statistically significant differences (<i>p</i> &gt; 0.05) between the sexes within any age group, in-hospital mortality appeared significantly higher in women than that in men when analysed overall, due to confounding. Death was more closely related to stroke in women than in men and occurred earlier. Although there were some age-specific sex differences between the predictors for in-hospital mortality, stroke severity measured by NIHSS was the main predictor of in-hospital mortality for both sexes. Topographic classifications – partial anterior circulatory infarct and total anterior circulatory infarct – were significant prognostic factors for men aged &lt;60 years and for those in the 60–69 years range respectively. <b><i>Conclusion:</i></b> Although most of our findings were consistent with previous studies, it is important to take into account and highlight differences in in-hospital mortality between the sex and age group. Not to account for age-related differences between the sexes can give false results that may mislead management decisions. As most deaths in women were related to stroke, it is important to improve their early management, stroke code activation, access to stroke units and/or revascularisation therapies, especially in the older age groups.
DOI: 10.6084/m9.figshare.8074433
title: Supplementary Material for: Daily Habit of Water Intake in Patients with Cerebral Infarction before its Onset; Comparison with a Healthy Population: A Cross-Sectional Study

description: <b><i>Background:</i></b> While water intake is frequently recommended to prevent cerebral infarction (CI), only few studies have been published on this topic. <b><i>Objectives:</i></b> This study retrospectively estimated the daily non-alcohol drink (NAD) intake in CI patients before CI onset and compared it with NAD in healthy subjects. <b><i>Methods:</i></b> We performed a cross-sectional study on CI patients in 3 hospitals and healthy subjects in the Kobe Orthopedic and Biomedical Epidemiologic (KOBE) study. Data from 1,287 subjects (274 CI patients and 1,013 healthy subjects) were used for the analyses. By dividing the CI patients into “increased”, “unchanged”, and “decreased” groups according to their current NAD intake, we compared the NAD intake between these 3 groups and healthy subjects by analyses of covariance and the post hoc test, adjusting for sex, age, surveyed month, body mass index, alcohol drinking history, and smoking history. Under the assumption that the NAD intake in the “unchanged” group was equal to the NAD intake before CI onset, the OR of less NAD intake for CI adjusting for the relevant variables in the “unchanged” group and the healthy subjects was calculated; the cut-off point was chosen using Youden’s index. <b><i>Results:</i></b> The mean age (mean ± SD) of the participants was 62.8 ± 9.3 years. One hundred and fifty-one patients (36 women) were included in the “increased” group; 105 (30 women), in the “unchanged” group; 18 (2 women), in the “decreased” group; and 1,013 (706 women), in the “healthy” group. The mean NAD intake was 1,702.5 ± 670.2 mL in the “increased” group, 1,494.2 ± 611.2 mL in the “unchanged” group, 1,268.0 ± 596.1 mL in the “decreased” group, and 1,720.6 ± 686.0 mL in the “healthy” group. After adjusting for the relevant variables, a significant difference in NAD intake between the groups was observed (F = 6.1, <i>p</i> &lt; 0.001), and a post hoc test demonstrated significant differences (<i>p</i> &lt; 0.05) in NAD intake between the “healthy” and “unchanged” groups, and between the “increased” and “unchanged” groups. The OR of less NAD intake (&lt;1,570 mL/day, chosen using Youden’s index) for CI was 2.48 (95% CI 1.52–4.07). <b><i>Conclusion:</i></b> This study showed that daily NAD intake before CI onset in CI patients was less than that in healthy persons, indicating that sufficient intake of NAD may be protective for CI.
DOI: 10.6084/m9.figshare.8074409
title: Supplementary Material for: Spontaneous Regression of Cervical Intraepithelial Neoplasia 2: A Meta-analysis

description: <b><i>Background:</i></b> Cervical intraepithelial neoplasia (CIN) is a precancerous condition that, if progresses, can cause cervical cancer. Less severe forms such as CIN1 regress spontaneously for most of the cases, but for high-grade CIN (CIN2 or CIN3), have higher potentials for progression. <b><i>Objective:</i></b> Aim of the present study was to obtain reliable estimates of spontaneous regression and progression rates of CIN2. <b><i>Methods:</i></b> Data were extracted from eligible studies identified after literature search in electronic databases, and meta-analyses were performed by pooling the regression and progression rates reported by these studies. Meta-regression analyses were performed for the identification of factors affecting regression rate. <b><i>Results:</i></b> Sixteen studies (1,481 patients; 14.86 months [95% CI 9.25–20.48] follow-up; 28.23 years [95% CI 25.07–31.39] age) were included in the meta-analysis. Overall regression rate in these conservatively observed patients was 42.66% (95% CI 35.41–49.91), but regression rate was higher in studies that recruited patients with CIN2 (50.85% [95% CI 36.11–65.60]) in comparison with those that recruited patients without discrimination of CIN2 with CIN3 (36.31% [95% CI 27.67–44.95]. Progression rate in CIN2 patients was 10.28% [95% CI 3.72–16.84]). Age was significantly negatively associated with regression rate (coefficient –1.72 [–3.53 to 0.10]; <i>p</i> = 0.061). <b><i>Conclusion:</i></b> Spontaneous regression rate of CIN2 is considerably high, especially in younger years.
DOI: 10.6084/m9.figshare.8074436
title: Hourly average pollutant concentrations from RAMPs and BC monitor deployed by CMU in Rwanda

description: This is the data set used for a manuscript soon to be submitted for peer review.
DOI: 10.6084/m9.figshare.8074430.v1
title: Supplementary Material for: Age- and Sex-Specific Risk Profiles and In-Hospital Mortality in 13,932 Spanish Stroke Patients

description: <b><i>Background:</i></b> In-hospital stroke death rate is an important sanitary issue. Despite advances in the acute phase management of stroke patients, mortality and disability rates remain high. In aging populations and with different mortality between the sexes in general, the study of sex- and age-related differences becomes increasingly relevant for optimization of post-acute clinical care of stroke patients. <b><i>Methods:</i></b> We designed a cohort follow-up study with 13,932 consecutive ischemic stroke (IS) patients from 19 Spanish hospitals. Data was obtained from the Spanish Stroke Registry; transient ischemic attacks and ages &lt;18 years were excluded. Patients were organised by age group and sex. We compared female and male patient cohorts within and across age groups univariately and used multivariable logistic regression to adjust for confounders in differential in-hospital mortality. <b><i>Results:</i></b> The median (percentiles 2.5 and 97.5%) age was 78 (41–92) years old for women and 71 (41–92) for men. IS women were more likely to be older, to exhibit cardio-embolic aetiology, and less likely to have been admitted to a stroke unit or to have had a stroke code activated. Both pre-stroke modified Rankin Scale and National Institute of Health Stroke Scale (NIHSS) scores at admission increased significantly with age and were higher in women than those in men. Differences in distributions of common risk factors for IS and of in-hospital outcomes between women and men actually changed with patient’s age. It is to be noted here that although there were no statistically significant differences (<i>p</i> &gt; 0.05) between the sexes within any age group, in-hospital mortality appeared significantly higher in women than that in men when analysed overall, due to confounding. Death was more closely related to stroke in women than in men and occurred earlier. Although there were some age-specific sex differences between the predictors for in-hospital mortality, stroke severity measured by NIHSS was the main predictor of in-hospital mortality for both sexes. Topographic classifications – partial anterior circulatory infarct and total anterior circulatory infarct – were significant prognostic factors for men aged &lt;60 years and for those in the 60–69 years range respectively. <b><i>Conclusion:</i></b> Although most of our findings were consistent with previous studies, it is important to take into account and highlight differences in in-hospital mortality between the sex and age group. Not to account for age-related differences between the sexes can give false results that may mislead management decisions. As most deaths in women were related to stroke, it is important to improve their early management, stroke code activation, access to stroke units and/or revascularisation therapies, especially in the older age groups.
DOI: 10.6084/m9.figshare.12871736
title: Data NCOMMS-20-17726-T.xlsx

description: Datasets of exciton diffusion length measurement <br>
DOI: 10.6084/m9.figshare.8074388
title: Size Freedom welfare Dataset.sav

description: Dataset for article: Government Effectiveness, Economic Freedom and Citizens’ Welfare: How amenable are nations to adapt network governance?Has two additional variables used during the testing phase
DOI: 10.6084/m9.figshare.12871736.v1
title: Data NCOMMS-20-17726-T.xlsx

description: Datasets of exciton diffusion length measurement <br>
DOI: 10.6084/m9.figshare.8074388.v1
title: Size Freedom welfare Dataset.sav

description: Dataset for articleGovernment Effectiveness, Economic Freedom and Citizens’ Welfare: How amenable are nations to adapt network governance?Has two additional variables used during the testing phase
DOI: 10.6084/m9.figshare.8074373
title: Overseas Study Zhihu Corpus

description: Chinese language corpus containing 621 questions and 10,416 answers posted to Zhihu.com. Questions relate to undertaking overseas study in Australia.Includes R scripts used to extract data. Data extracted in April 2019. Files are questions (Q), answers (A) and question topics (T). The naming convention is the URL of the webpage: For questions: https://www.zhihu.com/question/[<i>question number</i>] For answers: https://www.zhihu.com/question/[<i>question number</i>]/answer/[<i>answer number</i>]<br>Answers are organised by author category: "male", "female", "undisclosed gender", "anonymous", "organisation" using information from the user's profile where publicly accessible.