cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3840732
title: Supplementary Material for: A Case of Transforming Growth Factor-β-Induced Gene-Related Oculorenal Syndrome: Granular Corneal Dystrophy Type II with a Unique Nephropathy

description: Many types of inherited renal diseases have ocular features that occasionally support a diagnosis. The following study describes an unusual example of a 40-year-old woman with granular corneal dystrophy type II complicated by renal involvement. These two conditions may coincidentally coexist; however, there are some reports that demonstrate an association between renal involvement and granular corneal dystrophy type II. Granular corneal dystrophy type II is caused by a mutation in the<i>transforming growth factor-β-induced</i> <i>(TGFBI)</i> gene. The patient was referred to us because of the presence of mild proteinuria without hematuria that was subsequently suggested to be granular corneal dystrophy type II. A kidney biopsy revealed various glomerular and tubular basement membrane changes and widening of the subendothelial space of the glomerular basement membrane by electron microscopy. However, next-generation sequencing revealed that she had no mutation in a gene that is known to be associated with monogenic kidney diseases. Conversely, real-time polymerase chain reaction, using a simple buccal swab, revealed <i>TGFBI</i>heteromutation (R124H). The TGFBI protein plays an important role in cell-collagen signaling interactions, including extracellular matrix proteins which compose the renal basement membrane. This mutation can present not only as corneal dystrophy but also as renal disease. <i>TGFBI</i>-related oculorenal syndrome may have been unrecognized. It is difficult to diagnose this condition without renal electron microscopic studies. To the best of our knowledge, this is the first detailed report of nephropathy associated with a <i>TGFBI</i> mutation.
DOI: 10.7910/dvn/v1rjpf/wkvpnh
title: mea20160826_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840738
title: Supplementary Material for: Isolated Cystic Periventricular Leukomalacia Differs from Cystic Periventricular Leukomalacia with Intraventricular Hemorrhage in Prevalence, Risk Factors and Outcomes in Preterm Infants

description: <i>Background:</i> Cystic periventricular leukomalacia (cPVL) is the most severe white matter injury and is often associated with intraventricular hemorrhage (IVH) in preterm infants. <i>Objective:</i> The aim of this study was to investigate the prevalence, risk factors and neurodevelopmental outcomes of isolated cPVL and cPVL with low-grade and high-grade IVH in premature infants. <i>Methods:</i> From 2001 to 2012, 9,964 infants with &lt;31 weeks' gestational age (GA) admitted to Taiwan hospitals were enrolled. cPVL was classified into three groups: isolated cPVL, cPVL with low-grade (I/II) IVH, and cPVL with high-grade (III) IVH. <i>Results:</i> Of 7,805 infants with complete ultrasound data, 286 (3.7%) had cPVL. Among the cPVL infants, 93 (32.5%) were isolated, 118 (41.3%) had low-grade IVH and 75 (26.2%) had high-grade IVH. The risk of cPVL with IVH was significantly higher among infants with &lt;27 weeks' GA than those with ≥27 weeks' GA, in contrast to that of isolated cPVL. Using infants without cPVL and IVH as the reference group, the most significant predictor of isolated cPVL was neonatal sepsis (odds ratio 2.39; 95% confidence interval 1.52-3.77), while 5-min Apgar score &lt;5 (2.50; 1.48-4.21) and prolonged mechanical ventilation (2.19; 1.42-3.42) were associated with cPVL with low-grade IVH, and GA &lt;27 weeks (2.63; 1.56-4.42), pneumothorax (3.04; 1.40-6.65) and prolonged mechanical ventilation (3.36; 1.88-6.01) contributed to cPVL with high-grade IVH. cPVL infants with low-grade and high-grade IVH had a higher risk of abnormal neurodevelopmental outcomes than infants with isolated cPVL at the age of 24 months. <i>Conclusions:</i> Isolated cPVL, cPVL with low-grade IVH and cPVL with high-grade IVH had different risk factors and neurodevelopmental outcomes, suggestive of different causal pathways.
DOI: 10.7910/dvn/v1rjpf/cx4ncy
title: mea20151223_03.txt.gz

description: :unav
DOI: 10.21227/p51e-4g16
title: FallAllD: A Comprehensive Dataset of Human Falls and Activities of Daily Living

description: DescriptionFallAllD is a large open dataset of human falls and activities of daily living simulated by 15 participants. FallAllD consists of 26420 files collected using three data-loggers worn on the waist, wrist and neck of the subjects. Motion signals are captured using an accelerometer, gyroscope, magnetometer and barometer with efficient configurations that suit the potential applications e.g. fall detection, fall prevention and human activity recognition.FallAllD is described in detail in the following journal article:M. Saleh, M. Abbas and R. L. B. Jeannès, "FallAllD: An Open Dataset of Human Falls and Activities of Daily Living for Classical and Deep Learning Applications," in IEEE Sensors Journal, doi: 10.1109/JSEN.2020.3018335.Data AcquisitionThree identical data-loggers developed by the society RF-Track have been used. They are waist, wrist and neck-worn devices equipped with:· LSM9DS1: 3-axial accelerometer, 3-axial gyroscope and 3-axial magnetometer.· MS5607-02BA03: barometer.Sensors configurations· Accelerometer: Sampling frequency = 238 Hz. Measurement range = ±8 g.· Gyroscope: Sampling frequency = 238 Hz. Angular rate = ± 2000 dps.· Magnetometer: Sampling frequency = 80 Hz. Full scale magnetic field = ±4 Gauss.· Barometer: Sampling frequency = 10 Hz.
DOI: 10.6084/m9.figshare.3840729
title: LAB bacteriocin applications in the last decade

description: In the early 2000s, the expectations about bacteriocins produced by lactic acid bacteria (LABs) were aimed at food applications. However, the effectiveness of bacteriocins against undesirable micro-organisms opened endless possibilities for innovative research. In the present review, we collected a database including 429 published papers and 245 granted patents (from 2004 to 2015). Based on bibliometric analysis, the progress of bacteriocin research in the last 11 years was discussed in detail. It was found that 164 patents were granted in 2010–2015, which is equivalent to 60% in comparison with previous years (i.e. only 81 patents were granted in 2004–2009). Currently, the research on bacteriocins is still gaining importance. In the realm of therapeutic strategies, about a 37% of the published research was focused on biomedical applications in the last decade. This vein of research is currently seeking for alternative solutions to problems such as cancer, systemic infections, oral-care, vaginal infections, contraception and skincare. On the other hand, food preservation, bio-nanomaterial and veterinary applications represent 29%, 25% and 9%, respectively. All this technology is being applied and will surely grow in the future, since about 31% of the patents granted since 2004 are focused on the biomedical area, 29% on food preservation, 5% on veterinary use; whereas 13% and 16% correspond to patents granted on production–purification systems and recombinant proteins or molecular modifications in the producer strains. This review contributes to the analysis of recent LAB bacteriocin applications and their role in safety, quality and improvement of human health.
DOI: 10.6084/m9.figshare.3840732.v1
title: Supplementary Material for: A Case of Transforming Growth Factor-β-Induced Gene-Related Oculorenal Syndrome: Granular Corneal Dystrophy Type II with a Unique Nephropathy

description: Many types of inherited renal diseases have ocular features that occasionally support a diagnosis. The following study describes an unusual example of a 40-year-old woman with granular corneal dystrophy type II complicated by renal involvement. These two conditions may coincidentally coexist; however, there are some reports that demonstrate an association between renal involvement and granular corneal dystrophy type II. Granular corneal dystrophy type II is caused by a mutation in the<i>transforming growth factor-β-induced</i> <i>(TGFBI)</i> gene. The patient was referred to us because of the presence of mild proteinuria without hematuria that was subsequently suggested to be granular corneal dystrophy type II. A kidney biopsy revealed various glomerular and tubular basement membrane changes and widening of the subendothelial space of the glomerular basement membrane by electron microscopy. However, next-generation sequencing revealed that she had no mutation in a gene that is known to be associated with monogenic kidney diseases. Conversely, real-time polymerase chain reaction, using a simple buccal swab, revealed <i>TGFBI</i>heteromutation (R124H). The TGFBI protein plays an important role in cell-collagen signaling interactions, including extracellular matrix proteins which compose the renal basement membrane. This mutation can present not only as corneal dystrophy but also as renal disease. <i>TGFBI</i>-related oculorenal syndrome may have been unrecognized. It is difficult to diagnose this condition without renal electron microscopic studies. To the best of our knowledge, this is the first detailed report of nephropathy associated with a <i>TGFBI</i> mutation.
DOI: 10.7910/dvn/v1rjpf/gxfp45
title: mea20150812_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840720
title: Allometric models for height and aboveground biomass of dominant tree species in South African Mistbelt forests

description: Novel species-specific equations for the estimation of height and aboveground biomass were established for four dominant tree species (<i>Syzygium gerrardii</i> Burtt Davy, <i>Combretum kraussii</i> Hochst., <i>Trichilia dregeana</i> Sond. and <i>Croton sylvaticus</i> Hochst.), in the Northern Mistbelt Forests of South Africa. A non-destructive sampling methodology was applied, which was based on measuring standing trees, selecting smaller branches and taking core samples. The species-specific aboveground biomass equations were fitted using predictor variables such as diameter at breast height (DBH) and total height (<i>H</i>). The relative error of estimation was used to examine the accuracy of a pantropical biomass equation versus our established specific model. Biomass values were afterwards up-scaled from tree to stand level for each species, based on the selected models and the forest inventory data. As expected, the DBH–height relationship varied among studied species. The incorporation of both DBH and <i>H</i> in the biomass models significantly improved their precision. A model with DBH<sup>2</sup> × <i>H</i> as a single variable was suitable for three out of the four studied species, with more than 98% of explained variance. An existing pantropical biomass equation for moist forests showed larger relative error of estimation, especially in the upper range of tree diameter. The estimated aboveground biomass density varied significantly among studied species, with the highest values recorded for <i>S. gerrardii</i> (87.7 ± 15.4 Mg ha<sup>−1</sup>), followed by <i>T. dregeana</i> (29.4 ± 14.7 Mg ha<sup>−1</sup>), <i>C. sylvaticus</i> (24.3 ± 11.5 Mg ha<sup>−1</sup>) and <i>C. kraussii</i> (20.1 ± 6.7 Mg ha<sup>−1</sup>). It is also found that species-specific production of biomass at the tree level is not always sufficient to reflect the stand-level biomass density. The results from this study contribute to accurately predict aboveground biomass, thereby improving the reliability of the estimates of forest biomass and carbon balance.
DOI: 10.6084/m9.figshare.3840729.v2
title: LAB bacteriocin applications in the last decade

description: In the early 2000s, the expectations about bacteriocins produced by lactic acid bacteria (LABs) were aimed at food applications. However, the effectiveness of bacteriocins against undesirable micro-organisms opened endless possibilities for innovative research. In the present review, we collected a database including 429 published papers and 245 granted patents (from 2004 to 2015). Based on bibliometric analysis, the progress of bacteriocin research in the last 11 years was discussed in detail. It was found that 164 patents were granted in 2010–2015, which is equivalent to 60% in comparison with previous years (i.e. only 81 patents were granted in 2004–2009). Currently, the research on bacteriocins is still gaining importance. In the realm of therapeutic strategies, about a 37% of the published research was focused on biomedical applications in the last decade. This vein of research is currently seeking for alternative solutions to problems such as cancer, systemic infections, oral-care, vaginal infections, contraception and skincare. On the other hand, food preservation, bio-nanomaterial and veterinary applications represent 29%, 25% and 9%, respectively. All this technology is being applied and will surely grow in the future, since about 31% of the patents granted since 2004 are focused on the biomedical area, 29% on food preservation, 5% on veterinary use; whereas 13% and 16% correspond to patents granted on production–purification systems and recombinant proteins or molecular modifications in the producer strains. This review contributes to the analysis of recent LAB bacteriocin applications and their role in safety, quality and improvement of human health.
DOI: 10.7910/dvn/v1rjpf/mo3pnl
title: mea20160916_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840720.v2
title: Allometric models for height and aboveground biomass of dominant tree species in South African Mistbelt forests

description: Novel species-specific equations for the estimation of height and aboveground biomass were established for four dominant tree species (<i>Syzygium gerrardii</i> Burtt Davy, <i>Combretum kraussii</i> Hochst., <i>Trichilia dregeana</i> Sond. and <i>Croton sylvaticus</i> Hochst.), in the Northern Mistbelt Forests of South Africa. A non-destructive sampling methodology was applied, which was based on measuring standing trees, selecting smaller branches and taking core samples. The species-specific aboveground biomass equations were fitted using predictor variables such as diameter at breast height (DBH) and total height (<i>H</i>). The relative error of estimation was used to examine the accuracy of a pantropical biomass equation versus our established specific model. Biomass values were afterwards up-scaled from tree to stand level for each species, based on the selected models and the forest inventory data. As expected, the DBH–height relationship varied among studied species. The incorporation of both DBH and <i>H</i> in the biomass models significantly improved their precision. A model with DBH<sup>2</sup> × <i>H</i> as a single variable was suitable for three out of the four studied species, with more than 98% of explained variance. An existing pantropical biomass equation for moist forests showed larger relative error of estimation, especially in the upper range of tree diameter. The estimated aboveground biomass density varied significantly among studied species, with the highest values recorded for <i>S. gerrardii</i> (87.7 ± 15.4 Mg ha<sup>−1</sup>), followed by <i>T. dregeana</i> (29.4 ± 14.7 Mg ha<sup>−1</sup>), <i>C. sylvaticus</i> (24.3 ± 11.5 Mg ha<sup>−1</sup>) and <i>C. kraussii</i> (20.1 ± 6.7 Mg ha<sup>−1</sup>). It is also found that species-specific production of biomass at the tree level is not always sufficient to reflect the stand-level biomass density. The results from this study contribute to accurately predict aboveground biomass, thereby improving the reliability of the estimates of forest biomass and carbon balance.
DOI: 10.7910/dvn/v1rjpf/hiuyqm
title: mea20150802_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840702
title: 83-gene (CDS) matrix

description: Concatenated alignment of 83 genes (CDS) for Wei et al. article, Plastid phylogenomics resolve deep relationships among eupolypod II ferns with rapid radiation and rate heterogeneity'', submitted to <i>Genome Biology and Evolution</i>.<br>This version excludes all introns in relevant genes.<br>
DOI: 10.6084/m9.figshare.3840708
title: Identification of radiation response genes and proteins from mouse pulmonary tissues after high-dose per fraction irradiation of limited lung volumes

description: <b>Purpose:</b> The molecular effects of focal exposure of limited lung volumes to high-dose per fraction irradiation (HDFR) such as stereotactic body radiotherapy (SBRT) have not been fully characterized. In this study, we used such an irradiation system and identified the genes and proteins after HDFR to mouse lung, similar to those associated with human therapy. <b>Methods and materials:</b> High focal radiation (90 Gy) was applied to a 3-mm volume of the left lung of C57BL6 mice using a small-animal stereotactic irradiator. As well as histological examination for lungs, a cDNA micro array using irradiated lung tissues and a protein array of sera were performed until 4 weeks after irradiation, and radiation-responsive genes and proteins were identified. For comparison, the long-term effects (12 months) of 20 Gy radiation wide-field dose to the left lung were also investigated. <b>Results:</b> The genes <i>ermap</i>, <i>epb4.2</i>, <i>cd200r3</i> (up regulation) and <i>krt15</i>, <i>hoxc4</i>, <i>gdf2</i>, <i>cst9</i>, <i>cidec</i>, and <i>bnc1</i> (down-regulation) and the proteins of AIF, laminin, bNOS, HSP27, β-amyloid (upregulation), and calponin (downregulation) were identified as being responsive to 90 Gy HDFR. The <i>gdf2</i>, <i>cst9</i>, and <i>cidec</i> genes also responded to 20 Gy, suggesting that they are universal responsive genes in irradiated lungs. No universal proteins were identified in both 90 Gy and 20 Gy. Calponin, which was downregulated in protein antibody array analysis, showed a similar pattern in microarray data, suggesting a possible HDFR responsive serum biomarker that reflects gene alteration of irradiated lung tissue. These genes and proteins also responded to the lower doses of 20 Gy and 50 Gy HDFR. <b>Conclusions:</b> These results suggest that identified candidate genes and proteins are HDFR-specifically expressed in lung damage induced by HDFR relevant to SBRT in humans.
DOI: 10.7910/dvn/v1rjpf/j8kqt0
title: mea20160901_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840708.v2
title: Identification of radiation response genes and proteins from mouse pulmonary tissues after high-dose per fraction irradiation of limited lung volumes

description: <b>Purpose:</b> The molecular effects of focal exposure of limited lung volumes to high-dose per fraction irradiation (HDFR) such as stereotactic body radiotherapy (SBRT) have not been fully characterized. In this study, we used such an irradiation system and identified the genes and proteins after HDFR to mouse lung, similar to those associated with human therapy. <b>Methods and materials:</b> High focal radiation (90 Gy) was applied to a 3-mm volume of the left lung of C57BL6 mice using a small-animal stereotactic irradiator. As well as histological examination for lungs, a cDNA micro array using irradiated lung tissues and a protein array of sera were performed until 4 weeks after irradiation, and radiation-responsive genes and proteins were identified. For comparison, the long-term effects (12 months) of 20 Gy radiation wide-field dose to the left lung were also investigated. <b>Results:</b> The genes <i>ermap</i>, <i>epb4.2</i>, <i>cd200r3</i> (up regulation) and <i>krt15</i>, <i>hoxc4</i>, <i>gdf2</i>, <i>cst9</i>, <i>cidec</i>, and <i>bnc1</i> (down-regulation) and the proteins of AIF, laminin, bNOS, HSP27, β-amyloid (upregulation), and calponin (downregulation) were identified as being responsive to 90 Gy HDFR. The <i>gdf2</i>, <i>cst9</i>, and <i>cidec</i> genes also responded to 20 Gy, suggesting that they are universal responsive genes in irradiated lungs. No universal proteins were identified in both 90 Gy and 20 Gy. Calponin, which was downregulated in protein antibody array analysis, showed a similar pattern in microarray data, suggesting a possible HDFR responsive serum biomarker that reflects gene alteration of irradiated lung tissue. These genes and proteins also responded to the lower doses of 20 Gy and 50 Gy HDFR. <b>Conclusions:</b> These results suggest that identified candidate genes and proteins are HDFR-specifically expressed in lung damage induced by HDFR relevant to SBRT in humans.
DOI: 10.6084/m9.figshare.3840708.v1
title: Identification of Radiation Response Genes and Proteins from Mouse Pulmonary Tissues after High-Dose per Fraction Irradiation of Limited Lung Volumes

description: <b>Purpose:</b> The molecular effects of focal exposure of limited lung volumes to high-dose per fraction irradiation (HDFR) such as stereotactic body radiotherapy (SBRT) have not been fully characterized. In this study, we used such an irradiation system and identified the genes and proteins after HDFR to mouse lung, similar to those associated with human therapy. <b>Methods and Materials:</b> High focal radiation (90 Gy) was applied to a 3-mm volume of the left lung of C57BL6 mice using a small-animal stereotactic irradiator. As well as histological examination for lungs, a cDNA micro array using irradiated lung tissues and a protein array of sera were performed until 4 weeks after irradiation, and radiation-responsive genes and proteins were identified. For comparison, the long-term effects (12 months) of 20 Gy radiation wide-field dose to the left lung were also investigated. <b>Results:</b> The genes <i>ermap, epb4.2, cd200r3</i> (up regulation) and <i>krt15, hoxc4, gdf2, cst9, cidec,</i> and <i>bnc1</i> (down-regulation) and the proteins of AIF, laminin, bNOS, HSP27, β-amyloid (upregulation), and calponin (downregulation) were identified as being responsive to 90 Gy HDFR. The <i>gdf2, cst9,</i> and <i>cidec</i> genes also responded to 20 Gy, suggesting that they are universal responsive genes in irradiated lungs. No universal proteins were identified in both 90 Gy and 20 Gy. Calponin, which was downregulated in protein antibody array analysis, showed a similar pattern in microarray data, suggesting a possible HDFR responsive serum biomarker that reflects gene alteration of irradiated lung tissue. These genes and proteins also responded to the lower doses of 20 Gy and 50 Gy HDFR. <b>Conclusions:</b> These results suggest that identified candidate genes and proteins are HDFR-spcifically expressed in lung damage induced by HDFR relevant to SBRT in humans.
DOI: 10.7910/dvn/v1rjpf/v0d07t
title: mea20150308_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840696
title: GWAS summary statistics on Major Depressive Disorder

description: This file contains the summary statistics from genome wide association study of Major Depressive Disorder in 10,640 Han Chinese women in the CONVERGE Consortium<br>The columns are: <br>chr: ChromosomeSNP: PositionRSID: RSIDA1: Effect allele (usually minor) A2: Other allele (usually major)FRQ: frequency of effect allele OR: Odds ratio from logistic regression (with 10 PCs as covariates)SE: Standard error of ORP: P value of association from logistic regressionfrq_1kgp: Minor allele frequency at this locus in 1000 Genomes Phase 1 ASN hwe_p: P value for HWE info: Imputation information score at this locus <br>Note: This page has been updated to provide summary stats from logistic regression as odds ratios from logistic regression have proven to be more useful and less prone to ascertainment bias in a number of downstream analyses such as heritability and genetic correlation estimation. This is particularly the case for ascertained case-control data like CONVERGE. Previous summary stats from FastLMM are removed from this site to prevent confusion, but can be requested through email. The P values of association between the two sets are comparable (see Cai et al, Nature 2015 for details). <br>
DOI: 10.6084/m9.figshare.3840702.v2
title: 83-gene (CDS) matrix

description: Concatenated alignment of 83 genes (CDS) for Wei et al. article, Plastid phylogenomics resolve deep relationships among eupolypod II ferns with rapid radiation and rate heterogeneity'', submitted to <i>Genome Biology and Evolution</i>.<br>This version excludes all introns in relevant genes.<br>