cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24073172.v2
title: Heterodyning, Dataset 1

description: Update: use process_data_v2.py. Delete all files in the root folder (processing results) to regenerate these files.Original description:Within the zip archive, you will find three main components:<br><b>Measurement Data:</b>The raw measurement data collected during the experiments conducted as part of the research is organized within directories or folders. These directories contain the structured view of the experimental data.<br><b>Signal Processing Software:</b>The signal processing software, <code>process_data.py</code>, is located in the root folder of the zip archive. This software module is a fundamental tool used in the signal processing and analysis of the experimental data presented in the research paper. It provides essential functionality for data manipulation and interpretation.<br><b>Processing Results:</b>Similarly, the processing results obtained from the application of the <code>process_data.py</code> software are also stored in the root folder of the zip archive. These results are pivotal in understanding the outcomes and conclusions presented in the research paper.<br>
DOI: 10.5281/zenodo.10866386
title: [IO Islamic 490] كلّيّات نعمتخان عالى

description: Kulliyyât-i-Ni’matkhân-‘Âlî

This manuscript is now IO Islamic 1669 in the India Office collections.

[metadata: Hermann Ethé, Catalogue of Persian Manuscripts in the Library of the India Office, 2 vols. (Oxford: India Office, 1903): volume 1, number 490 here with notations and hyperlinks].


1669

Another copy of Ḥusn u ‘Ishḳ.

Beginning as usual. No date.

No. 490, ff. 89-95, 20-27 diagonal lines in the page; Shikasta; size, 83/8 in. by 43/4 in.
DOI: 10.5281/zenodo.10866387
title: [IO Islamic 490] كلّيّات نعمتخان عالى

description: Kulliyyât-i-Ni’matkhân-‘Âlî

This manuscript is now IO Islamic 1669 in the India Office collections.

[metadata: Hermann Ethé, Catalogue of Persian Manuscripts in the Library of the India Office, 2 vols. (Oxford: India Office, 1903): volume 1, number 490 here with notations and hyperlinks].


1669

Another copy of Ḥusn u ‘Ishḳ.

Beginning as usual. No date.

No. 490, ff. 89-95, 20-27 diagonal lines in the page; Shikasta; size, 83/8 in. by 43/4 in.
DOI: 10.6084/m9.figshare.4476377
title: Increased complexity of circRNA expression during species evolution

description: Circular RNAs (circRNAs) are broadly identified from precursor mRNA (pre-mRNA) back-splicing across various species. Recent studies have suggested a cell-/tissue- specific manner of circRNA expression. However, the distinct expression pattern of circRNAs among species and its underlying mechanism still remain to be explored. Here, we systematically compared circRNA expression from human and mouse, and found that only a small portion of human circRNAs could be determined in parallel mouse samples. The conserved circRNA expression between human and mouse is correlated with the existence of orientation-opposite complementary sequences in introns that flank back-spliced exons in both species, but not the circRNA sequences themselves. Quantification of RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns by Complementary Sequence Index (CSI) identifies that among all types of complementary sequences, <i>SINE</i>s, especially <i>Alu</i> elements in human, contribute the most for circRNA formation and that their diverse distribution across species leads to the increased complexity of circRNA expression during species evolution. Together, our integrated and comparative reference catalog of circRNAs in different species reveals a species-specific pattern of circRNA expression and suggests a previously under-appreciated impact of fast-evolved <i>SINE</i>s on the regulation of (circRNA) gene expression.
DOI: 10.6084/m9.figshare.4476377.v1
title: Increased complexity of circRNA expression during species evolution

description: Circular RNAs (circRNAs) are broadly identified from precursor mRNA (pre-mRNA) back-splicing across various species. Recent studies have suggested a cell-/tissue- specific manner of circRNA expression. However, the distinct expression pattern of circRNAs among species and its underlying mechanism still remain to be explored. Here, we systematically compared circRNA expression from human and mouse, and found that only a small portion of human circRNAs could be determined in parallel mouse samples. The conserved circRNA expression between human and mouse is correlated with the existence of orientation-opposite complementary sequences in introns that flank back-spliced exons in both species, but not the circRNA sequences themselves. Quantification of RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns by Complementary Sequence Index (CSI) identifies that among all types of complementary sequences, <i>SINE</i>s, especially <i>Alu</i> elements in human, contribute the most for circRNA formation and that their diverse distribution across species leads to the increased complexity of circRNA expression during species evolution. Together, our integrated and comparative reference catalog of circRNAs in different species reveals a species-specific pattern of circRNA expression and suggests a previously under-appreciated impact of fast-evolved <i>SINE</i>s on the regulation of (circRNA) gene expression.
DOI: 10.6084/m9.figshare.4476629
title: Differential analysis of genome-wide methylation and gene expression in mesenchymal stem cells of patients with fractures and osteoarthritis

description: Insufficient activity of the bone-forming osteoblasts leads to low bone mass and predisposes to fragility fractures. The functional capacity of human mesenchymal stem cells (hMSCs), the precursors of osteoblasts, may be compromised in elderly individuals, in relation with the epigenetic changes associated with aging. However, the role of hMSCs in the pathogenesis of osteoporosis is still unclear. Therefore, we aimed to characterize the genome-wide methylation and gene expression signatures and the differentiation capacity of hMSCs from patients with hip fractures. We obtained hMSCs from the femoral heads of women undergoing hip replacement due to hip fractures and controls with hip osteoarthritis. DNA methylation was explored with the Infinium 450K bead array. Transcriptome analysis was done by RNA sequencing. The genomic analyses revealed that most differentially methylated loci were situated in genomic regions with enhancer activity, distant from gene bodies and promoters. These regions were associated with differentially expressed genes enriched in pathways related to hMSC growth and osteoblast differentiation. hMSCs from patients with fractures showed enhanced proliferation and upregulation of the osteogenic drivers RUNX2/OSX. Also, they showed some signs of accelerated methylation aging. When cultured in osteogenic medium, hMSCs from patients with fractures showed an impaired differentiation capacity, with reduced alkaline phosphatase activity and poor accumulation of a mineralized matrix. Our results point to 2 areas of potential interest for discovering new therapeutic targets for low bone mass disorders and bone regeneration: the mechanisms stimulating MSCs proliferation after fracture and those impairing their terminal differentiation.
DOI: 10.6084/m9.figshare.4476629.v1
title: Differential analysis of genome-wide methylation and gene expression in mesenchymal stem cells of patients with fractures and osteoarthritis

description: Insufficient activity of the bone-forming osteoblasts leads to low bone mass and predisposes to fragility fractures. The functional capacity of human mesenchymal stem cells (hMSCs), the precursors of osteoblasts, may be compromised in elderly individuals, in relation with the epigenetic changes associated with aging. However, the role of hMSCs in the pathogenesis of osteoporosis is still unclear. Therefore, we aimed to characterize the genome-wide methylation and gene expression signatures and the differentiation capacity of hMSCs from patients with hip fractures. We obtained hMSCs from the femoral heads of women undergoing hip replacement due to hip fractures and controls with hip osteoarthritis. DNA methylation was explored with the Infinium 450K bead array. Transcriptome analysis was done by RNA sequencing. The genomic analyses revealed that most differentially methylated loci were situated in genomic regions with enhancer activity, distant from gene bodies and promoters. These regions were associated with differentially expressed genes enriched in pathways related to hMSC growth and osteoblast differentiation. hMSCs from patients with fractures showed enhanced proliferation and upregulation of the osteogenic drivers RUNX2/OSX. Also, they showed some signs of accelerated methylation aging. When cultured in osteogenic medium, hMSCs from patients with fractures showed an impaired differentiation capacity, with reduced alkaline phosphatase activity and poor accumulation of a mineralized matrix. Our results point to 2 areas of potential interest for discovering new therapeutic targets for low bone mass disorders and bone regeneration: the mechanisms stimulating MSCs proliferation after fracture and those impairing their terminal differentiation.
DOI: 10.6084/m9.figshare.4478390
title: MWPCR: Multiscale Weighted Principal Component Regression for High-Dimensional Prediction

description: We propose a multiscale weighted principal component regression (MWPCR) framework for the use of high-dimensional features with strong spatial features (e.g., smoothness and correlation) to predict an outcome variable, such as disease status. This development is motivated by identifying imaging biomarkers that could potentially aid detection, diagnosis, assessment of prognosis, prediction of response to treatment, and monitoring of disease status, among many others. The MWPCR can be regarded as a novel integration of principal components analysis (PCA), kernel methods, and regression models. In MWPCR, we introduce various weight matrices to prewhitten high-dimensional feature vectors, perform matrix decomposition for both dimension reduction and feature extraction, and build a prediction model by using the extracted features. Examples of such weight matrices include an importance score weight matrix for the selection of individual features at each location and a spatial weight matrix for the incorporation of the spatial pattern of feature vectors. We integrate the importance of score weights with the spatial weights to recover the low-dimensional structure of high-dimensional features. We demonstrate the utility of our methods through extensive simulations and real data analyses of the Alzheimer’s disease neuroimaging initiative (ADNI) dataset. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4478390.v2
title: MWPCR: Multiscale Weighted Principal Component Regression for High-Dimensional Prediction

description: We propose a multiscale weighted principal component regression (MWPCR) framework for the use of high-dimensional features with strong spatial features (e.g., smoothness and correlation) to predict an outcome variable, such as disease status. This development is motivated by identifying imaging biomarkers that could potentially aid detection, diagnosis, assessment of prognosis, prediction of response to treatment, and monitoring of disease status, among many others. The MWPCR can be regarded as a novel integration of principal components analysis (PCA), kernel methods, and regression models. In MWPCR, we introduce various weight matrices to prewhitten high-dimensional feature vectors, perform matrix decomposition for both dimension reduction and feature extraction, and build a prediction model by using the extracted features. Examples of such weight matrices include an importance score weight matrix for the selection of individual features at each location and a spatial weight matrix for the incorporation of the spatial pattern of feature vectors. We integrate the importance of score weights with the spatial weights to recover the low-dimensional structure of high-dimensional features. We demonstrate the utility of our methods through extensive simulations and real data analyses of the Alzheimer’s disease neuroimaging initiative (ADNI) dataset. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4478390.v1
title: MWPCR: Multiscale Weighted Principal Component Regression for High-dimensional Prediction

description: We propose a multiscale weighted principal component regression (MWPCR) framework for the use of high dimensional features with strong spatial features (e.g., smoothness and correlation) to predict an outcome variable, such as disease status. This development is motivated by identifying imaging biomarkers that could potentially aid detection, diagnosis, assessment of prognosis, prediction of response to treatment, and monitoring of disease status, among many others. The MWPCR can be regarded as a novel integration of principal components analysis (PCA), kernel methods, and regression models. In MWPCR, we introduce various weight matrices to prewhitten high dimensional feature vectors, perform matrix decomposition for both dimension reduction and feature extraction, and build a prediction model by using the extracted features. Examples of such weight matrices include an importance score weight matrix for the selection of individual features at each location and a spatial weight matrix for the incorporation of the spatial pattern of feature vectors. We integrate the importance score weights with the spatial weights in order to recover the low dimensional structure of high dimensional features. We demonstrate the utility of our methods through extensive simulations and real data analyses of the Alzheimer's disease neuroimaging initiative (ADNI) data set.
DOI: 10.5281/zenodo.10866390
title: [IO Islamic 950] كلّيّات نعمتخان عالى

description: Kulliyyât-i-Ni’matkhân-‘Âlî

This manuscript is now IO Islamic 1670 in the India Office collections.

[metadata: Hermann Ethé, Catalogue of Persian Manuscripts in the Library of the India Office, 2 vols. (Oxford: India Office, 1903): volume 1, number 950 here with notations and hyperlinks].


1670

Another copy of the abridged Bahâdurshâhnâma.

The same abridgment of the Bahâdurshâhnâma, as in No. 1659, 1, beginning in the same way:

بسم الله الرّحمن الرّحيم – دست بر آورده بجود كريم الخ

In the colophon it is styled پادشاهنامه.

No. 950, ff. 74, ll. 13; large and distinct Nasta’lîḳ; size, 73/4 in. by 41/8 in.
DOI: 10.5281/zenodo.10866391
title: [IO Islamic 950] كلّيّات نعمتخان عالى

description: Kulliyyât-i-Ni’matkhân-‘Âlî

This manuscript is now IO Islamic 1670 in the India Office collections.

[metadata: Hermann Ethé, Catalogue of Persian Manuscripts in the Library of the India Office, 2 vols. (Oxford: India Office, 1903): volume 1, number 950 here with notations and hyperlinks].


1670

Another copy of the abridged Bahâdurshâhnâma.

The same abridgment of the Bahâdurshâhnâma, as in No. 1659, 1, beginning in the same way:

بسم الله الرّحمن الرّحيم – دست بر آورده بجود كريم الخ

In the colophon it is styled پادشاهنامه.

No. 950, ff. 74, ll. 13; large and distinct Nasta’lîḳ; size, 73/4 in. by 41/8 in.
DOI: 10.6084/m9.figshare.4487702.v2
title: Molecular characteristics of tara galactomannans: Effect of degradation with hydrogen peroxide

description: Tara gum (<i>M</i><sub>w</sub> = 1519 × 10<sup>3</sup> g/mol) was degraded by hydrogen peroxide in the presence/absence of ascorbic acid, and properties of the products were investigated using gel permeation chromatography, Fourier transform infrared spectroscopy, atomic force microscope, and rheometer methods. Results showed that molecular weight of tara gum decreased with increasing concentration of hydrogen peroxide. The addition of ascorbic acid could sharply increase the degradation rate and degree of tara gum by hydrogen peroxide, which is also confirmed by atomic force microscope. The degradation products kept the structure characteristics of galactomannan. However, they performed different rheological properties. At 1% (w/v) of concentration, DP1 (941 × 10<sup>3</sup> g/mol) and DP2 (335 × 10<sup>3</sup> g/mol) prepared by H<sub>2</sub>O<sub>2</sub> exhibited non-Newtonian behavior, while DP3 (35.1 × 10<sup>3</sup> g/mol) and DP4 (14.2 × 10<sup>3</sup> g/mol) obtained by hydrogen peroxide plus ascorbic acid displayed Newtonian property. These results may promote the application of tara gum in diverse fields.
DOI: 10.6084/m9.figshare.4487702.v1
title: Molecular characteristics of tara galactomannans: effect of degradation with hydrogen peroxide

description: Tara gum (M<sub>w</sub>=1519×10<sup>3</sup> g/mol) was degraded by hydrogen peroxide in the presence/absence of ascorbic acid, and properties of the products were investigated using gel permeation chromatography, Fourier transform infrared, atomic force microscope and rheometer methods. Results showed that molecular weight of tara gum decreased with increasing concentration of hydrogen peroxide. The addition of ascorbic acid could sharply increase the degradation rate and degree of tara gum by hydrogen peroxide, which were also confirmed by atomic force microscope. The degradation products (DPs) kept the structure characteristics of galactomannan. However, they performed different rheological properties. At 1% (w/v) of concentration, DP1 (941×10<sup>3</sup> g/mol) and DP2 (335×10<sup>3</sup> g/mol) prepared by H<sub>2</sub>O<sub>2</sub> exhibited non-Newtonian behavior, while DP3 (35.1×10<sup>3</sup> g/mol) and DP4 (14.2 ×10<sup>3</sup> g/mol) obtained by hydrogen peroxide plus ascorbic acid displayed Newtonian-like property. These results may promote the application of tara gum in diverse fields.
DOI: 10.6084/m9.figshare.4490258
title: MyGeoHub Science Gateway for Spatial Data and a Model for Sustainability

description: Science gateways have gained popularity and adoption in the past few years as an efficient and user friendly way to share scientific data, models, tools, and workflows in a community. However, all science gateways face a major hurdle of sustainability in the long term. When funding ends, the gateway developed for the project is likely to become obsolete due to non-trivial maintenance costs. We describe here a cost-sharing solution based on the HUBzero gateway framework. Instead of dedicating one hub for each project, this solution hosts multiple projects with synergies on one physical hub while at the same time providing branded individual web space for each project by leveraging HUBzero’s support of super groups. This reduces the cost in maintaining the underlying infrastructure, which is further shared among multiple projects, keeping the hosted gateways alive in the long term. We applied this model to MyGeoHub and will discuss our implementation experience.
DOI: 10.6084/m9.figshare.4490258.v2
title: MyGeoHub Science Gateway for Spatial Data and a Model for Sustainability

description: Science gateways have gained popularity and adoption in the past few years as an efficient and user friendly way to share scientific data, models, tools, and workflows in a community. However, all science gateways face a major hurdle of sustainability in the long term. When funding ends, the gateway developed for the project is likely to become obsolete due to non-trivial maintenance costs. We describe here a cost-sharing solution based on the HUBzero gateway framework. Instead of dedicating one hub for each project, this solution hosts multiple projects with synergies on one physical hub while at the same time providing branded individual web space for each project by leveraging HUBzero’s support of super groups. This reduces the cost in maintaining the underlying infrastructure, which is further shared among multiple projects, keeping the hosted gateways alive in the long term. We applied this model to MyGeoHub and will discuss our implementation experience.
DOI: 10.6084/m9.figshare.4490492
title: Tobacco smoking and smoking-related DNA methylation are associated with the development of frailty among older adults

description: Tobacco smoking is a preventable environmental factor that contributes to a wide spectrum of age-related health outcomes; however, its association with the development of frailty is not yet well established. We examined the associations of self-reported smoking indicators, serum cotinine levels and smoking-related DNA methylation biomarkers with a quantitative frailty index (FI) in 2 independent subsets of older adults (age 50–75) recruited in Saarland, Germany in 2000 – 2002 (discovery set: n = 978, validation set: n = 531). We obtained DNA methylation profiles in whole blood samples by Illumina HumanMethylation450 BeadChip and calculated the FI according to the method of Mitnitski and Rockwood. Mixed linear regression models were implemented to assess the associations between smoking indicators and the FI. After controlling for potential covariates, current smoking, cumulative smoking exposure (pack-years), and time after smoking cessation (years) were significantly associated with the FI (<i>P</i>-value &lt; 0.05). In the discovery panel, 17 out of 151 previously identified smoking-related CpG sites were associated with the FI after correction for multiple testing (FDR &lt; 0.05). Nine of them survived in the validation phase and were designated as frailty-associated loci. A smoking index (SI) based on the 9 loci manifested a monotonic association with the FI. In conclusion, this study suggested that epigenetic alterations could play a role in smoking-associated development of frailty. The identified CpG sites have the potential to be prognostic biomarkers of frailty and frailty-related health outcomes. Our findings and the underlying mechanisms should be followed up in further, preferably longitudinal studies.
DOI: 10.6084/m9.figshare.4490492.v1
title: Tobacco smoking and smoking-related DNA methylation are associated with the development of frailty among older adults

description: Tobacco smoking is a preventable environmental factor that contributes to a wide spectrum of age-related health outcomes; however, its association with the development of frailty is not yet well established. We examined the associations of self-reported smoking indicators, serum cotinine levels and smoking-related DNA methylation biomarkers with a quantitative frailty index (FI) in 2 independent subsets of older adults (age 50–75) recruited in Saarland, Germany in 2000 – 2002 (discovery set: n = 978, validation set: n = 531). We obtained DNA methylation profiles in whole blood samples by Illumina HumanMethylation450 BeadChip and calculated the FI according to the method of Mitnitski and Rockwood. Mixed linear regression models were implemented to assess the associations between smoking indicators and the FI. After controlling for potential covariates, current smoking, cumulative smoking exposure (pack-years), and time after smoking cessation (years) were significantly associated with the FI (<i>P</i>-value &lt; 0.05). In the discovery panel, 17 out of 151 previously identified smoking-related CpG sites were associated with the FI after correction for multiple testing (FDR &lt; 0.05). Nine of them survived in the validation phase and were designated as frailty-associated loci. A smoking index (SI) based on the 9 loci manifested a monotonic association with the FI. In conclusion, this study suggested that epigenetic alterations could play a role in smoking-associated development of frailty. The identified CpG sites have the potential to be prognostic biomarkers of frailty and frailty-related health outcomes. Our findings and the underlying mechanisms should be followed up in further, preferably longitudinal studies.