cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13378712
title: MRI characteristics of the fetal tethered spinal cord: a comparative study

description: <b>Purpose:</b> To compare fetuses and children with confirmed tethered cord syndrome to age-matched controls to provide a reference for prenatally identifying tethered spinal cord and to identify salient points on MRI for diagnosis. <b>Materials and Methods:</b> This retrospective study enrolled 13 fetuses and 20 children with tethered cord syndrome, and age-matched counterparts were included as controls. The MRI features including concomitant malformations, position of the conus medullaris, and thickened filum terminale of the two patient groups were evaluated and compared. Levels of the conus medullaris were discriminated between patients and an equivalent number of controls. <b>Results:</b> Various concomitant malformations manifested on the MRI of all patients, and there were differences between the two patient groups. Significant differences of the level of the conus medullaris were found between the fetal and child patients (<i>U</i>, 26.50; <i>Z</i>, −3.87; <i>p</i> &lt; 0.001) and between the normal fetus and child controls (<i>U</i>, 23.50; <i>Z</i>, −4.13; <i>p</i> &lt; 0.001). The position of the conus medullaris was visibly lower in the patient groups than in the control groups. No significant difference in the diameters of the filum terminale was found between the fetal and child patients (<i>p</i> = 0.67). <b>Conclusions:</b> The current study<b>’</b>s results indicate that tethered spinal cord syndrome can be diagnosed in utero with MRI combined with several characteristics, particularly the position of the conus medullaris. Special attention should be paid to the gestational age of the fetus because normal changes in spinal cord position occur with gestational development.
DOI: 10.6084/m9.figshare.13378712.v1
title: MRI characteristics of the fetal tethered spinal cord: a comparative study

description: <b>Purpose:</b> To compare fetuses and children with confirmed tethered cord syndrome to age-matched controls to provide a reference for prenatally identifying tethered spinal cord and to identify salient points on MRI for diagnosis. <b>Materials and Methods:</b> This retrospective study enrolled 13 fetuses and 20 children with tethered cord syndrome, and age-matched counterparts were included as controls. The MRI features including concomitant malformations, position of the conus medullaris, and thickened filum terminale of the two patient groups were evaluated and compared. Levels of the conus medullaris were discriminated between patients and an equivalent number of controls. <b>Results:</b> Various concomitant malformations manifested on the MRI of all patients, and there were differences between the two patient groups. Significant differences of the level of the conus medullaris were found between the fetal and child patients (<i>U</i>, 26.50; <i>Z</i>, −3.87; <i>p</i> &lt; 0.001) and between the normal fetus and child controls (<i>U</i>, 23.50; <i>Z</i>, −4.13; <i>p</i> &lt; 0.001). The position of the conus medullaris was visibly lower in the patient groups than in the control groups. No significant difference in the diameters of the filum terminale was found between the fetal and child patients (<i>p</i> = 0.67). <b>Conclusions:</b> The current study<b>’</b>s results indicate that tethered spinal cord syndrome can be diagnosed in utero with MRI combined with several characteristics, particularly the position of the conus medullaris. Special attention should be paid to the gestational age of the fetus because normal changes in spinal cord position occur with gestational development.
DOI: 10.5281/zenodo.10663989
title: Datasets and results of 'Glacier mass balance and its climatic and non-climatic drivers in the Ladakh region during 2000-2021 from remote sensing data'

description: In this repository, we provide processed elevation change rasters, CSV files containing individual glacier mass balance and other attributes, as well as processed elevation change points using ICESat-2 datasets for both WL and EL regions. These datasets and results are associated with the article 'Glacier mass balance and its climatic and non-climatic drivers in the Ladakh region during 2000-2021 from remote sensing data', published in Journal of Glaciology. Further details for each data file are provided below.

Elevation change raster files (.tif) have undergone several processing steps. Please refer to Sections 3.2, 3.3, and 3.5 in the published paper. 'WL_ASTER2017_', 'WL_ASTER_2021', 'EL_ASTER_2020', 'EL_ASTER_2021' represent the elevation change between 2000-2017, 2000-2021, 2000-2020, and 2000-2021.

In the CSV files (WL_MB_, EL_MB_), individual glaciers are labeled with their RGIId. Columns such as dh_mean, dh_mean_err, mb, mb_err, mb_err_year represent the total elevation change (m), total elevation change error (m), total mass balance (m w.e.), mass balance error (m w.e.), and mass balance per year (m w.e./year). Additionally, other topographical attributes are provided for each surveyed glacier.

In the CSV files (icesat2_dh_.. for WL and EL), x, y, and h_li refer to the x and y coordinates of the ICESat-2 laser pulse footprint, with its land ice elevation (m). Columns dem_elev and diff_elev refer to the elevation (m) of the same data point in SRTM DEM (of the year 2000) and the elevation difference between ICESat-2 and SRTM points, respectively. The 'on_ice' column indicates whether the point was taken over ice or bare surfaces.





Please contact the corresponding author of the article (Arindan Mandal; arindan.141@gmail.com) if you need any further information regarding the datasets.
DOI: 10.5281/zenodo.10663990
title: Datasets and results of 'Glacier mass balance and its climatic and non-climatic drivers in the Ladakh region during 2000-2021 from remote sensing data'

description: In this repository, we provide processed elevation change rasters, CSV files containing individual glacier mass balance and other attributes, as well as processed elevation change points using ICESat-2 datasets for both WL and EL regions. These datasets and results are associated with the article 'Glacier mass balance and its climatic and non-climatic drivers in the Ladakh region during 2000-2021 from remote sensing data', published in Journal of Glaciology. Further details for each data file are provided below.

Elevation change raster files (.tif) have undergone several processing steps. Please refer to Sections 3.2, 3.3, and 3.5 in the published paper. 'WL_ASTER2017_', 'WL_ASTER_2021', 'EL_ASTER_2020', 'EL_ASTER_2021' represent the elevation change between 2000-2017, 2000-2021, 2000-2020, and 2000-2021.

In the CSV files (WL_MB_, EL_MB_), individual glaciers are labeled with their RGIId. Columns such as dh_mean, dh_mean_err, mb, mb_err, mb_err_year represent the total elevation change (m), total elevation change error (m), total mass balance (m w.e.), mass balance error (m w.e.), and mass balance per year (m w.e./year). Additionally, other topographical attributes are provided for each surveyed glacier.

In the CSV files (icesat2_dh_.. for WL and EL), x, y, and h_li refer to the x and y coordinates of the ICESat-2 laser pulse footprint, with its land ice elevation (m). Columns dem_elev and diff_elev refer to the elevation (m) of the same data point in SRTM DEM (of the year 2000) and the elevation difference between ICESat-2 and SRTM points, respectively. The 'on_ice' column indicates whether the point was taken over ice or bare surfaces.





Please contact the corresponding author of the article (Arindan Mandal; arindan.141@gmail.com) if you need any further information regarding the datasets.
DOI: 10.6084/m9.figshare.12854426
title: Identification of CDF family members in apple and their expression in response to sucrose during floral induction

description: Plant-specific CDF genes encode a class of transcription factors which play crucial roles in plant flowering, especially in photoperiod-regulated flowering. But little is known about the potential functions of <i>MdCDF</i>s during flower induction in apple. In this study, 11 putative <i>MdCDF</i>s were identified and named systematically. Bioinformatic analysis revealed a functional and structural similarity among the <i>MdCDF</i>s. Analysis of tandem and synteny revealed several paired <i>CDF</i> homologs between apple and <i>Arabidopsis</i>. RT-qPCR revealed that <i>MdCDF</i>s exhibited distinct expression patterns in different apple tissues and most of them displayed high expression levels in flowers and leaves. Further expression profiles of <i>MdCDF</i>s were investigated in different-flowering varieties of apple and in response to sugar treatment. The results indicated that <i>MdCDF</i>s were responsive to floral induction. Meanwhile, the expressions of all <i>MdCDF</i>s were inhibited in buds during different floral induction stages after sugar treatment. The expressions of flowering-related and photoperiod pathway-related genes showed differences and may indicate that most of the <i>MdCDF</i>s may function as a light response flowering inhibitor and could be repressed by the sugar-mediated floral induction. Collectively, the comprehensive analysis of <i>MdCDF</i>s provides valuable information on their expression during floral induction that will serve as a foundation for further studies.
DOI: 10.6084/m9.figshare.12854426.v1
title: Identification of CDF family members in apple and their expression in response to sucrose during floral induction

description: Plant-specific CDF genes encode a class of transcription factors which play crucial roles in plant flowering, especially in photoperiod-regulated flowering. But little is known about the potential functions of <i>MdCDF</i>s during flower induction in apple. In this study, 11 putative <i>MdCDF</i>s were identified and named systematically. Bioinformatic analysis revealed a functional and structural similarity among the <i>MdCDF</i>s. Analysis of tandem and synteny revealed several paired <i>CDF</i> homologs between apple and <i>Arabidopsis</i>. RT-qPCR revealed that <i>MdCDF</i>s exhibited distinct expression patterns in different apple tissues and most of them displayed high expression levels in flowers and leaves. Further expression profiles of <i>MdCDF</i>s were investigated in different-flowering varieties of apple and in response to sugar treatment. The results indicated that <i>MdCDF</i>s were responsive to floral induction. Meanwhile, the expressions of all <i>MdCDF</i>s were inhibited in buds during different floral induction stages after sugar treatment. The expressions of flowering-related and photoperiod pathway-related genes showed differences and may indicate that most of the <i>MdCDF</i>s may function as a light response flowering inhibitor and could be repressed by the sugar-mediated floral induction. Collectively, the comprehensive analysis of <i>MdCDF</i>s provides valuable information on their expression during floral induction that will serve as a foundation for further studies.
DOI: 10.6084/m9.figshare.12854538
title: Ultra-accurate thermophysical properties of helium-4 and helium-3 at low density. I. Second pressure and acoustic virial coefficients

description: The second pressure and acoustic virial coefficients of helium-4 and helium-3 are computed employing an accurate <i>ab initio</i> potential from the literature. The fully quantum-mechanical formulations are derived for second acoustic virial coefficient, which are not available in the literature. The uncertainty of our calculated values is quantified and evaluated based on the potential inaccuracy. For helium-4, our theoretical values are in excellent agreement with the best measurements and a recent <i>ab initio</i> calculation. Our estimated uncertainty is at least five times smaller than the previous best determination. For helium-3, systematic errors are detected for the widely accepted <i>ab initio</i> data and our new results are probably more reliable. The computed values of this work are given in the supplemental materials over a wide temperature range between 1 and 10 000 K, which are useful especially for primary temperature metrology.
DOI: 10.6084/m9.figshare.12854538.v1
title: Ultra-accurate thermophysical properties of helium-4 and helium-3 at low density. I. Second pressure and acoustic virial coefficients

description: The second pressure and acoustic virial coefficients of helium-4 and helium-3 are computed employing an accurate <i>ab initio</i> potential from the literature. The fully quantum-mechanical formulations are derived for second acoustic virial coefficient, which are not available in the literature. The uncertainty of our calculated values is quantified and evaluated based on the potential inaccuracy. For helium-4, our theoretical values are in excellent agreement with the best measurements and a recent <i>ab initio</i> calculation. Our estimated uncertainty is at least five times smaller than the previous best determination. For helium-3, systematic errors are detected for the widely accepted <i>ab initio</i> data and our new results are probably more reliable. The computed values of this work are given in the supplemental materials over a wide temperature range between 1 and 10 000 K, which are useful especially for primary temperature metrology.
DOI: 10.6084/m9.figshare.19670242
title: Additional file 1 of Preoperative binocular vision characteristics in the age-related cataract population

description: Additional file 1.
DOI: 10.6084/m9.figshare.19670242.v1
title: Additional file 1 of Preoperative binocular vision characteristics in the age-related cataract population

description: Additional file 1.
DOI: 10.6084/m9.figshare.19670251
title: Additional file 1 of Artesunate–amodiaquine and artemether–lumefantrine for the treatment of uncomplicated falciparum malaria in Liberia: in vivo efficacy and frequency of molecular markers

description: Additional file 1. Liberia genotyping raw data.
DOI: 10.6084/m9.figshare.19670251.v1
title: Additional file 1 of Artesunate–amodiaquine and artemether–lumefantrine for the treatment of uncomplicated falciparum malaria in Liberia: in vivo efficacy and frequency of molecular markers

description: Additional file 1. Liberia genotyping raw data.
DOI: 10.6084/m9.figshare.12854664
title: Development of a TaqMan-based real-time PCR assay for detection and quantification of <i>Pythium aphanidermatum</i> in plant and soil samples

description: The soilborne oomycete pathogen <i>Pythium aphanidermatum</i> causes damping-off and root rot in a wide range of economically important crops and vegetables. Effective <i>P</i>. <i>aphanidermatum</i> disease management is hindered by the lack of accurate pathogen detection methods. We developed a TaqMan-based real-time PCR tool for efficient detection and quantification of <i>P</i>. <i>aphanidermatum</i> presence in plant and soil samples. <i>Eukaryotic peptide chain release factor subunit 1</i> (<i>eRF1</i>) was selected as the marker gene based on bioinformatic analysis. <i>P</i>. <i>aphanidermatum</i> DNA was quantified by using a <i>eRF1</i>-containing plasmid as the reference standard. This approach is sensitive enough to detect as low as 10 fg of <i>P</i>. <i>aphanidermatum</i> genomic DNA or 10 copies of reference plasmid. In a specificity evaluation, eight <i>P</i>. <i>aphanidermatum</i> isolates can be precisely detected out of 44 plant pathogen isolates. Moreover, <i>P</i>. <i>aphanidermatum</i> DNA can be detected in plant leaves 10 min after inoculation when there is no symptom appearance at all. Meanwhile, this assay successfully detected <i>P</i>. <i>aphanidermatum</i> zoospores in the soil at the sensitivity level of 100 zoospores/g, a density sufficient for inhibiting seedling growth. Taken together, the real-time PCR tool could be valuable for the early surveillance and quantification of <i>P</i>. <i>aphanidermatum</i> spread in the field.
DOI: 10.6084/m9.figshare.12854664.v1
title: Development of a TaqMan-based real-time PCR assay for detection and quantification of <i>Pythium aphanidermatum</i> in plant and soil samples

description: The soilborne oomycete pathogen <i>Pythium aphanidermatum</i> causes damping-off and root rot in a wide range of economically important crops and vegetables. Effective <i>P</i>. <i>aphanidermatum</i> disease management is hindered by the lack of accurate pathogen detection methods. We developed a TaqMan-based real-time PCR tool for efficient detection and quantification of <i>P</i>. <i>aphanidermatum</i> presence in plant and soil samples. <i>Eukaryotic peptide chain release factor subunit 1</i> (<i>eRF1</i>) was selected as the marker gene based on bioinformatic analysis. <i>P</i>. <i>aphanidermatum</i> DNA was quantified by using a <i>eRF1</i>-containing plasmid as the reference standard. This approach is sensitive enough to detect as low as 10 fg of <i>P</i>. <i>aphanidermatum</i> genomic DNA or 10 copies of reference plasmid. In a specificity evaluation, eight <i>P</i>. <i>aphanidermatum</i> isolates can be precisely detected out of 44 plant pathogen isolates. Moreover, <i>P</i>. <i>aphanidermatum</i> DNA can be detected in plant leaves 10 min after inoculation when there is no symptom appearance at all. Meanwhile, this assay successfully detected <i>P</i>. <i>aphanidermatum</i> zoospores in the soil at the sensitivity level of 100 zoospores/g, a density sufficient for inhibiting seedling growth. Taken together, the real-time PCR tool could be valuable for the early surveillance and quantification of <i>P</i>. <i>aphanidermatum</i> spread in the field.
DOI: 10.6084/m9.figshare.11806131
title: Let-7 microRNA is a critical regulator in controlling the growth and function of silk gland in the silkworm

description: The silk gland is characterized by high protein synthesis. However, the molecular mechanisms controlling silk gland growth and silk protein synthesis remain undetermined. Here we demonstrated that CRISPR/Cas9-based knockdown of let-7 or the whole cluster promoted endoreduplication and enlargement of the silk gland, accompanied by changing silk yield, whereas transgenic overexpression of let-7 led to atrophy and degeneration of the silk gland. Mechanistically, let-7 controls cell growth in the silk gland through coordinating nutrient metabolism processes and energy signalling pathways. Transgenic overexpression of <i>pyruvate carboxylase</i>, a novel target of let-7, resulted in enlargement of the silk glands, which is consistent with the abnormal phenotype of the let-7 knockdown. Overall, our data reveal a previously unknown miRNA-mediated regulation of silk gland growth and physiology and shed light on involvement of let-7 as a critical stabilizer and booster in carbohydrate metabolism, which may have important implications for understanding of the molecular mechanism and physiological function of specialized organs in other species.
DOI: 10.6084/m9.figshare.11806131.v1
title: let-7 microRNA is a critical regulator in controlling the growth and function of silk gland in the silkworm

description: The silk gland is characterized by high protein synthesis. However, the molecular mechanisms controlling silk gland growth and silk protein synthesis remain undetermined. Here we demonstrated that CRISPR/Cas9-based knockdown of let-7 or the whole cluster promoted endoreduplication and enlargement of the silk gland, accompanied by changing silk yield, whereas transgenic overexpression of let-7 led to atrophy and degeneration of the silk gland. Mechanistically, let-7 controls cell growth in the silk gland through coordinating nutrient metabolism processes and energy signaling pathways. Transgenic overexpression of <i>pyruvate carboxylase</i>, a novel target of let-7, resulted in enlargement of the silk glands, which is consistent with the abnormal phenotype of the let-7 knockdown. Overall, our data reveal a previously unknown miRNA-mediated regulation of silk gland growth and physiology and shed light on involvement of let-7 as a critical stabilizer and booster in carbohydrate metabolism, which may have important implications for understanding of the molecular mechanism and physiological function of specialized organs in other species.
DOI: 10.6084/m9.figshare.11806131.v2
title: Let-7 microRNA is a critical regulator in controlling the growth and function of silk gland in the silkworm

description: The silk gland is characterized by high protein synthesis. However, the molecular mechanisms controlling silk gland growth and silk protein synthesis remain undetermined. Here we demonstrated that CRISPR/Cas9-based knockdown of let-7 or the whole cluster promoted endoreduplication and enlargement of the silk gland, accompanied by changing silk yield, whereas transgenic overexpression of let-7 led to atrophy and degeneration of the silk gland. Mechanistically, let-7 controls cell growth in the silk gland through coordinating nutrient metabolism processes and energy signalling pathways. Transgenic overexpression of <i>pyruvate carboxylase</i>, a novel target of let-7, resulted in enlargement of the silk glands, which is consistent with the abnormal phenotype of the let-7 knockdown. Overall, our data reveal a previously unknown miRNA-mediated regulation of silk gland growth and physiology and shed light on involvement of let-7 as a critical stabilizer and booster in carbohydrate metabolism, which may have important implications for understanding of the molecular mechanism and physiological function of specialized organs in other species.
DOI: 10.6084/m9.figshare.13379025
title: Epigenome-wide association study and network analysis for IgA Nephropathy from CD19<sup>+</sup> B-cell in Chinese Population

description: IgA nephropathy (IgAN) is the most common primary glomerular disease in China and worldwide. The proliferation of B cells is known to be associated with both risk and prognosis of IgAN, but the epigenetic mechanism underlying this association is unknown. In this study we carried out the first Epigenome-wide Association Study (EWAS) by using the latest Infinium Methylation EPIC BeadChip on 184 B cell-specific samples (92 case/control pairs) for Chinese IgAN population. After rigorous data normalization and residual batch effect correction, linear mixed effect model was used to detect methylation CpG sites associated with IgAN adjusting for age, gender and smoking. False discovery rate (<i>FDR</i>) less than 10% was used to account for multiple testing. Weighted gene co-methylation networks were generated to identify gene modules highly correlated with IgAN. A permutation test was performed to account for the potential effect of overfitting. After adjusting clinical covariates and potential technical batch effects, three CpGs corresponding to <i>PCDH17, TERT, WDR82</i> genes and three in the intergenic regions passed the genome-wide significant threshold. Methylation network analysis identified an additional IgAN associated gene module, containing 72 significant CpGs including <i>GALNT6, IQSEC1, CDC16 and SYS1</i>, involved in the pathway related to tubular atrophy/interstitial fibrosis of IgAN. These results suggested important DNA methylation and gene targets in CD19<sup>+</sup> B cells for the pathogenesis of IgAN.