cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12452057.v1
title: Additional file 11 of The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation

description: Additional file 11:. Supplementary table 11. Multivariate linear regression of 4325 CpG sites using group and HBV marker
DOI: 10.15468/8r6dbk
title: Arachnids of Giant Mountains National Park

description: Spider and opilionid species found in pitfall traps in Giant Mountains in the Czech Republic during 2018-2020.
DOI: 10.15468/c25vax
title: Upper Aptian Serre Chaitieu (Niveau Fallot) G. ferreolensis and G. blowi per gram sediment, SE France
DOI: 10.6084/m9.figshare.24923472
title: <i>Ziziphus jujuba</i> genome assembly and annotation

description: The jujube (Ziziphus jujuba Mill.), a member of the Rhamnaceae family, is a major perennial fruit crops with enormous productive, ecological as well as traditional herbal values. Here, we present the population structure, genetic diversity, genomic variations of a diverse collection of 1,057 jujube accessions. We de novo assembled four high-quality jujube genomes and constructed a gene-based pan-genome coupling with two previously released genomes. Among pan-genome, a large number of genomic variations encompassing SNP, InDel and SVs were identified. Especially, a MADS-box family gene ZjFGD1 harboring a 12-bp InDel underlies flowering time and fruit ripening. Graph-based genome enables us to perform SV-based GWAS for 17 horticultural traits and identified 109 associated SVs. Notably, a 2.3-kb PAV in the upstream of ZjMED12 was strong associated with seed-setting rate and knocking out of ZjMED12 ortholog in rice led to low seed-setting rate. Integrating SNP-based GWAS, expression analysis and transgenic validation, we identified a causal gene ZjCDKI5, which pleiotropically regulates bearing-shoot length and leaf size in jujube. Our study not only illuminates the genetic basis of key domestication traits, but also provides a deep and rich genomic resource to promote hypothesis-driven basic research and genomics-assisted crop improvement for this unique perennial fruit tree.
DOI: 10.6084/m9.figshare.12452111
title: Additional file 6 of The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation

description: Additional file 6:. Supplementary table 6. Multivariate linear regression of 4325 CpG sites
DOI: 10.6084/m9.figshare.12452111.v1
title: Additional file 6 of The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation

description: Additional file 6:. Supplementary table 6. Multivariate linear regression of 4325 CpG sites
DOI: 10.6084/m9.figshare.12452120
title: Additional file 9 of The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation

description: Additional file 9:. Supplementary table 9. IPA canonical pathways analysis revealed 113 enriched immune-related pathways between LC and CHB
DOI: 10.6084/m9.figshare.12452120.v1
title: Additional file 9 of The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation

description: Additional file 9:. Supplementary table 9. IPA canonical pathways analysis revealed 113 enriched immune-related pathways between LC and CHB
DOI: 10.15468/h3su5n
title: Three recorded Ostreopsis spp. (Dinophyceae) in New Zealand: in the upper North Island from 1995 to 1997

description: Three species of epiphytic dinoflagellates - Ostreopsis siamensis, O. lenticularis, and O. ovata have recently been found on both the east and west coasts of the upper North Island, New Zealand. The morphological differences of all three Ostreopsis spp. have been studied with both light and scanning electron microscopes. Detailed studies of the inner face of the thecal wall of Ostreopsis siamensis revealed two types of trichocyst pores: small, simple pores and large multipore structures. The multipore structures apparently have not been previously reported. Surveys conducted during the period from November 1995 to April 1997 showed that all three Ostreopsis spp. were fairly widespread in northern New Zealand, and all three species were found to occur south of 35°S latitude. Cell concentrations of Ostreopsis spp. in summer were substantially higher than in early spring. There was also a clear regional difference in distribution; cell concentrations of the dominant species, O. siamensis, were greatest in Rarawa and Tokerau on the north-east coast. Other less abundant epiphytic species recorded during the same period included Prorocentrum lima, P. compressum, and Coolia monotis. These species were generally more sporadic in distribution than Ostreopsis spp.
DOI: 10.6084/m9.figshare.25256614
title: <b>Understanding Genotypes by Environment Interaction and Yield Stability Analysis in Common Bean Genotypes Grown in Dawuro Zone, Ethiopia</b>

description: G by E analysis is useful for improving crop productivity.
DOI: 10.6084/m9.figshare.25256614.v1
title: <b>Understanding Genotypes by Environment Interaction and Yield Stability Analysis in Common Bean Genotypes Grown in Dawuro Zone, Ethiopia</b>

description: G by E analysis is useful for improving crop productivity.
DOI: 10.15468/2e4pzg
title: The Characeae held at PSUB Herbarium

description: Basic data from specimen labels on all the sheets currently held in PSUB collection shown together with digital images from high resolution scans of each sheet. Characeae is a family of freshwater green algae in the order Charales, commonly known as stoneworts. They are also known as brittleworts from the fragility of their lime-encrusted stems. The most commonly recorded species belong to the genera Chara and Nitella
DOI: 10.6084/m9.figshare.25256704
title: Supplementary Material for: The association between urinary sodium-potassium ratio, kidney function, and blood pressure in a cohort from the general population.

description: Abstract

Introduction
Subclinical kidney dysfunction may contribute to salt sensitive hypertension. We assessed the association between the urinary sodium-potassium ratio (Na/K-ratio) and blood pressure (BP) in a general population cohort without diabetes, chronic kidney disease, cardiovascular disease or treated hypertension. We investigated whether any such association was mediated by the kidney function markers measured glomerular filtration rate (mGFR), urinary albumin creatinine ratio (ACR) and epidermal growth factor – creatinine ratio (EGF-Cr).

Methods
The Tromsø Study is a population-based study of inhabitants of the municipality of Tromsø, Northern Norway. Participants aged 50-62 years, without diabetes, chronic kidney disease or cardiovascular disease, were invited to the substudy Renal Iohexol Clearance Survey in Tromsø 6 (RENIS-T6; 2007-09). For the present study we excluded participants reporting the use of 1 or more antihypertensive agents, leaving 1311 RENIS-T6 participants for a cross-sectional analysis. We measured office BP, 24-hour ambulatory blood pressure (ABP) and mGFR using iohexol-clearance. Na/K-ratio, ACR, and EGF-Cr were measured in morning urine samples. 

Results
Urinary Na/K-ratio was significantly associated with systolic office BP and ABP independently of cardiovascular risk factors and kidney function markers. A one standard deviation unit increase in the Na/K-ratio was associated with increased systolic ABP by 1.0 (0.3-1.6) mmHg. Urinary Na/K-ratio showed a stronger association with office BP than ABP. EGF-Cr, ACR and mGFR did not mediate the relationship between urinary Na/K-ratio and systolic BP. 

Conclusions
In a representative sample of the middle-aged North-European population without diabetes, chronic kidney disease, cardiovascular disease or treated hypertension, there was a consistent association between urinary Na/K-ratio and BP. The association with BP was not mediated through kidney function measures, suggesting a relationship between a diet with high sodium and low potassium and higher BP regardless of kidney function.
DOI: 10.6084/m9.figshare.25256704.v1
title: Supplementary Material for: The association between urinary sodium-potassium ratio, kidney function, and blood pressure in a cohort from the general population.

description: Abstract

Introduction
Subclinical kidney dysfunction may contribute to salt sensitive hypertension. We assessed the association between the urinary sodium-potassium ratio (Na/K-ratio) and blood pressure (BP) in a general population cohort without diabetes, chronic kidney disease, cardiovascular disease or treated hypertension. We investigated whether any such association was mediated by the kidney function markers measured glomerular filtration rate (mGFR), urinary albumin creatinine ratio (ACR) and epidermal growth factor – creatinine ratio (EGF-Cr).

Methods
The Tromsø Study is a population-based study of inhabitants of the municipality of Tromsø, Northern Norway. Participants aged 50-62 years, without diabetes, chronic kidney disease or cardiovascular disease, were invited to the substudy Renal Iohexol Clearance Survey in Tromsø 6 (RENIS-T6; 2007-09). For the present study we excluded participants reporting the use of 1 or more antihypertensive agents, leaving 1311 RENIS-T6 participants for a cross-sectional analysis. We measured office BP, 24-hour ambulatory blood pressure (ABP) and mGFR using iohexol-clearance. Na/K-ratio, ACR, and EGF-Cr were measured in morning urine samples. 

Results
Urinary Na/K-ratio was significantly associated with systolic office BP and ABP independently of cardiovascular risk factors and kidney function markers. A one standard deviation unit increase in the Na/K-ratio was associated with increased systolic ABP by 1.0 (0.3-1.6) mmHg. Urinary Na/K-ratio showed a stronger association with office BP than ABP. EGF-Cr, ACR and mGFR did not mediate the relationship between urinary Na/K-ratio and systolic BP. 

Conclusions
In a representative sample of the middle-aged North-European population without diabetes, chronic kidney disease, cardiovascular disease or treated hypertension, there was a consistent association between urinary Na/K-ratio and BP. The association with BP was not mediated through kidney function measures, suggesting a relationship between a diet with high sodium and low potassium and higher BP regardless of kidney function.
DOI: 10.6084/m9.figshare.12452306
title: Additional file 4 of Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen

description: Additional file 4: Table S3. List of primers and spacer sequences. (a) Primers and spacer sequences for gene knockout and activation experiments. (b) Primers and targeting sequences for off-target detection. (c) Primers for capture experiment. (d) Primers used in the nested PCR of gRNA index library preparation.
DOI: 10.6084/m9.figshare.15073974
title: Aerosol-PBL-monsoon interactions amplify semi-direct effect of biomass smoke on low cloud formation in Southeast Asia

description: Low clouds play a key role in the Earth-atmosphere energy balance and influence agricultural production and solar-power generation. Smoke aloft has been found to enhance marine stratocumulus over the Southeast Atlantic in austral spring through aerosol-cloud interactions, but its role in regions with strong human activities and complex monsoon circulation remains unclear. Here we show that biomass burning aerosols aloft strongly increase the low-cloud coverage over both land and ocean in subtropical southeastern Asia. The degree of this enhancement and its spatial extent are comparable to that in the Southeast Atlantic, even though the total biomass burning emissions in Southeast Asia are only one-fifth of those in Southern Africa. We find that a synergetic effect of aerosol-cloud-boundary layer interaction with the monsoon is the main reason for the strong semi-direct effect and enhanced low-cloud formation in Asia.
DOI: 10.5281/zenodo.10684599
title: Limitations of estimating antibiotic resistance using German hospital consumption data - A comprehensive computational analysis

description: Data and code for the publication: "Limitations of estimating antibiotic resistance using German hospital consumption data - A comprehensive computational analysis" by M. Rank, A. Kather, D. Wilke, M. Steib-Bauert, W. V. Kern, I. Röder, K. de With
description: For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.
DOI: 10.5281/zenodo.10684600
title: Limitations of estimating antibiotic resistance using German hospital consumption data - A comprehensive computational analysis

description: Data and code for the publication: "Limitations of estimating antibiotic resistance using German hospital consumption data - A comprehensive computational analysis" by M. Rank, A. Kather, D. Wilke, M. Steib-Bauert, W. V. Kern, I. Röder, K. de With
description: For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.
DOI: 10.6084/m9.figshare.24511188
title: Effects of anti-inflammatory and digestive-promoting fermented Chinese herbs on cecum microbiota composition and content metabolome of Chinese chickens (<i>Gallus domesticus</i>)

description: In this study, 168 chicks were randomly divided into two groups to elucidate the effect of fermented Chinese herbs (FCHs) on the intestinal microbiota of Chinese chickens (<i>Gallus domesticus</i>) and provide a scientific basis for the development and application of FCHs feed additives. The chicks were fed a basal diet for 7 days during the pre-feeding period. Thereafter, the control group was fed a basal diet, and the experimental group was fed a basal diet supplemented with 1.5% FCHs for 43 days. After being weighed and euthanised, the chickens were dissected to obtain the caecum content to analyse the intestinal microbiota composition using high-throughput sequencing of the 16S rRNA gene and metabolites using ultra-high-performance liquid chromatography high-resolution mass spectrometry. Our results showed that FCHs had no effect on the growth and serum immunological indices of Chinese chickens but significantly increased the bursa of Fabricius index, and reduced the α-diversity and affected composition of the caecum intestinal microbiota. In particular, the relative abundance of <i>Akkermansia</i> increased, and these of <i>Bacteroides</i>, <i>Megamonas</i>, and <i>Faecalibacterium</i> were reduced, accompanied by a change in the composition of caecal metabolites. These results implied that the FCH probably enhance the immune capacity of Chinese chickens. This study provides a scientific basis for developing and applying FCHs as feed additives. However, more research is necessary to elucidate the mode of action, level of inclusion, and the benefits of including the FCH in chicken diets. Fermented Chinese herbs (FCHs) did not change chick growth and serum indices.FCHs changed chick caecal microbiota.FCHs changed chick caecal metabolites. Fermented Chinese herbs (FCHs) did not change chick growth and serum indices. FCHs changed chick caecal microbiota. FCHs changed chick caecal metabolites.
DOI: 10.6084/m9.figshare.24511188.v1
title: Effects of anti-inflammatory and digestive-promoting fermented Chinese herbs on cecum microbiota composition and content metabolome of Chinese chickens (<i>Gallus domesticus</i>)

description: In this study, 168 chicks were randomly divided into two groups to elucidate the effect of fermented Chinese herbs (FCHs) on the intestinal microbiota of Chinese chickens (<i>Gallus domesticus</i>) and provide a scientific basis for the development and application of FCHs feed additives. The chicks were fed a basal diet for 7 days during the pre-feeding period. Thereafter, the control group was fed a basal diet, and the experimental group was fed a basal diet supplemented with 1.5% FCHs for 43 days. After being weighed and euthanised, the chickens were dissected to obtain the caecum content to analyse the intestinal microbiota composition using high-throughput sequencing of the 16S rRNA gene and metabolites using ultra-high-performance liquid chromatography high-resolution mass spectrometry. Our results showed that FCHs had no effect on the growth and serum immunological indices of Chinese chickens but significantly increased the bursa of Fabricius index, and reduced the α-diversity and affected composition of the caecum intestinal microbiota. In particular, the relative abundance of <i>Akkermansia</i> increased, and these of <i>Bacteroides</i>, <i>Megamonas</i>, and <i>Faecalibacterium</i> were reduced, accompanied by a change in the composition of caecal metabolites. These results implied that the FCH probably enhance the immune capacity of Chinese chickens. This study provides a scientific basis for developing and applying FCHs as feed additives. However, more research is necessary to elucidate the mode of action, level of inclusion, and the benefits of including the FCH in chicken diets. Fermented Chinese herbs (FCHs) did not change chick growth and serum indices.FCHs changed chick caecal microbiota.FCHs changed chick caecal metabolites. Fermented Chinese herbs (FCHs) did not change chick growth and serum indices. FCHs changed chick caecal microbiota. FCHs changed chick caecal metabolites.
DOI: 10.6084/m9.figshare.6161249
title: Sliced Rotated Sphere Packing Designs

description: Space-filling designs are popular choices for computer experiments. A sliced design is a design that can be partitioned into several subdesigns. We propose a new type of sliced space-filling design called sliced rotated sphere packing designs. Their full designs and subdesigns are rotated sphere packing designs. They are constructed by rescaling, rotating, translating, and extracting the points from a sliced lattice. We provide two fast algorithms to generate such designs. Furthermore, we propose a strategy to use sliced rotated sphere packing designs adaptively. Under this strategy, initial runs are uniformly distributed in the design space, follow-up runs are added by incorporating information gained from initial runs, and the combined design is space-filling for any local region. Examples are given to illustrate its potential application.
DOI: 10.6084/m9.figshare.7734236
title: Additional file 1: of DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins

description: Table S1. The 31 informative physicochemical properties and their corresponding MED (main effect difference) scores. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7734236.v1
title: Additional file 1: of DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins

description: Table S1. The 31 informative physicochemical properties and their corresponding MED (main effect difference) scores. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.20317233
title: Supplementary data of "The oldest complete jawed vertebrates from the early Silurian of China"

description: The supplementary data of "The oldest complete jawed vertebrates from the early Silurian of China" include 3D surface files and photos of Xiushanosteus and Shenacanthus from early Silurian Chongqing Lagerstätte.
DOI: 10.34740/kaggle/dsv/7669333
title: Egypt Gold Prices | Daily Updated
DOI: 10.25345/c5ff3mb03
title: MassIVE MSV000094139 - Identification of secreted proteins in GSNOR-deficient endothelial cells
title: In mammals, DNA is generally confined to the cell nucleus and mitochondria. Its presence in the cytosol is abnormal and may indicate threatening conditions. Therefore, the detection of cytoplasmic DNA is fundamental to control cellular homeostasis. One of pivotal post-translational modifications governing cellular fate is S-nitrosation. Our preliminary results indicate an absolute colocalisation of cytDNA with protein aggregates. We suspect that protein aggregates accumulate on cytDNA to serve as a direct signal for cytDNA clearance by autophagy. We want to figure out which proteins are aggregating, which of them are crucial to trigger autophagy signal and which step of cytDNA clearance is blocked in GSNOR-deficient cells, characterized by increased S-nitrosation. To gain insights into putative regulators of the process, we performed mass spectrometry analysis of proteins secreted from GSNOR-deficient ECs. Based on our observations, the DNA secretion is facilitated by concomitant KEAP1 knockdown. Analysis of these cells permits to identify the major regulators of the release of DNA from endothelial cells. Moreover, we compare the results to lamin B1-deficient cells, which were previously reported to be characterized by enhanced cytDNA presence. To sum up, our data identifies proteins involved in S-nitrosation-dependent modulation of innate immunity of endothelial cells.