cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/25g6hhw5db.2
title: O-GlcNAcylation drives calcium signaling towards osteoblast differentiation: a bioinformatics-oriented study

description: Objective: This study aimed to reveal the possible mechanisms by which O-linked-N-acetylglucosaminylation (O-GlcNAcylation) regulates osteoblast differentiation using a series of bioinformatics-oriented experiments. Methods: To examine the influence of O-GlcNAcylation levels on osteoblast differentiation, osteoblastic MC3T3-E1 cells were treated with O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) inhibitors. Correlations between the levels of O-GlcNAcylation and the expression of osteogenic markers as well as OGT were evaluated by qPCR and western blotting. The O-GlcNAcylated proteins assumed to correlate with Runx2 expression were retrieved from several public databases and used for further bioinformatics analysis. Following the findings of the bioinformatics analysis, intracellular calcium ([Ca2+]i) was monitored in the cells treated with OGT and OGA inhibitors using a confocal laser-scanning microscope (CLS). The interaction effect between O-GlcNAcylation and [Ca2+]i on osteogenic marker expression was determined using stable OGT knockdown MC3T3-E1 cells. Results: O-GlcNAcylation was positively and negatively associated with osteoblast differentiation. The time-course profile of global O-GlcNAcylated proteins showed a distinctive pattern with different molecular weights during osteoblast differentiation. The expression pattern of several O-GlcNAcylated proteins was significantly similar to that of Runx2 expression. Bioinformatic analysis of the retrieved Runx2-related-O-GlcNAcylated-proteins revealed the importance of [Ca2+]i. CLS showed that alteration of O-GlcNAcylation rapidly changed [Ca2+]i in MC3T3-E1 cells. O-GlcNAcylation and [Ca2+]i showed an interaction effect on the expression of osteogenic markers. OGT knockdown disrupted the [Ca2+]i-induced expression changes of osteogenic markers. Conclusions: O-GlcNAcylation interacts with [Ca2+]i and elicits osteoblast differentiation by regulating the expression of osteogenic markers. KEYWORDS: Osteoblast differentiation; O-linked-N-acetylglucosaminylation; Calcium; Bioinformatics; Literature-mining
DOI: 10.17632/25g6hhw5db.3
title: O-GlcNAcylation drives calcium signaling towards osteoblast differentiation: a bioinformatics-oriented study

description: Objective: This study aimed to reveal the possible mechanisms by which O-linked-N-acetylglucosaminylation (O-GlcNAcylation) regulates osteoblast differentiation using a series of bioinformatics-oriented experiments. Methods: To examine the influence of O-GlcNAcylation levels on osteoblast differentiation, osteoblastic MC3T3-E1 cells were treated with O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) inhibitors. Correlations between the levels of O-GlcNAcylation and the expression of osteogenic markers as well as OGT were evaluated by qPCR and western blotting. The O-GlcNAcylated proteins assumed to correlate with Runx2 expression were retrieved from several public databases and used for further bioinformatics analysis. Following the findings of the bioinformatics analysis, intracellular calcium ([Ca2+]i) was monitored in the cells treated with OGT and OGA inhibitors using a confocal laser-scanning microscope (CLS). The interaction effect between O-GlcNAcylation and [Ca2+]i on osteogenic marker expression was determined using stable OGT knockdown MC3T3-E1 cells. Results: O-GlcNAcylation was positively and negatively associated with osteoblast differentiation. The time-course profile of global O-GlcNAcylated proteins showed a distinctive pattern with different molecular weights during osteoblast differentiation. The expression pattern of several O-GlcNAcylated proteins was significantly similar to that of Runx2 expression. Bioinformatic analysis of the retrieved Runx2-related-O-GlcNAcylated-proteins revealed the importance of [Ca2+]i. CLS showed that alteration of O-GlcNAcylation rapidly changed [Ca2+]i in MC3T3-E1 cells. O-GlcNAcylation and [Ca2+]i showed an interaction effect on the expression of osteogenic markers. OGT knockdown disrupted the [Ca2+]i-induced expression changes of osteogenic markers. Conclusions: O-GlcNAcylation interacts with [Ca2+]i and elicits osteoblast differentiation by regulating the expression of osteogenic markers. KEYWORDS: Osteoblast differentiation; O-linked-N-acetylglucosaminylation; Calcium; Bioinformatics; Literature-mining
DOI: 10.17632/x594wrcw9j.1
title: Indian Medicinal Plant Dataset

description: Indian Medicinal Plant Dataset
DOI: 10.17632/rjwwjys324.1
title: Figure S1

description: Standardized differences before and after IPTW weighting in individuals with psoriasis (Fig 1a) and arthritic psoriasis (Fig 1b)
DOI: 10.17632/ywhj9s8z6j.1
title: data for multi-objective optimisationof nanocavity diffusion with OKMC

description: Results of OKMC based on different diffusion properties of nanocavities and simulating the implantation and annealing of irradiated samples
DOI: 10.17632/65pfcj4j4m.1
title: Protocol of CRISPR-Cas9 knockout screens for identifying ferroptosis regulators

description: Ferroptosis, an iron-dependent programmed cell death triggered by excessive lipid peroxidation, has shown promising therapeutic potentials in human diseases. Here, we describe a protocol of a CRISPR-Cas9 loss-of-function screen to identify regulators in response to different inducers of ferroptosis. We emphasize the steps of library amplification, drug treatment, high-throughput sequencing preparation, and bioinformatics analysis using Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK). We also present a method to discover the regulators of ferroptosis and verify the potential targets efficiently.
DOI: 10.17632/ndbyjgcsbh.1
title: Double cropping data

description: Verification of wheat chickpea double cropping on the vertisol of West Shewa, Ethiopia
DOI: 10.17632/3rbcwknkbb.1
title: Nurse-Tailored Interventions on Therapeutic Compliance among End-Stage Renal Disease Patients Undergoing Hemodialysis: Randomised controlled trial

description: Part 1 – Socio-demographic questionaries include sex, age, marital status, level of education, smoking, occupation, monthly income, dietary habits, and residency. Part 2- Clinical Variables includes the duration of illness, comorbid illness, duration of hemodialysis treatment. Vascular access, and erythropoietin therapy Part 3 – ESRD –AQ scale ( Reliability- 0.83-1.00 ,Validity- 0.99 ) This tool was developed by Youngmee Kim, PhD, RN, FNP, (2010) to measure the treatment adherence to hemodialysis (HD) attendance, medications, fluid restrictions, and diet prescription among patients with ESRD and got permission to use in this study. • Consists 46 questions • Section 1- 5 items (ESRD and RRT related history) • Section 2 – 14 items (adherence to HD) • Section 3 – 9 items (adherence to medications) • Section 4 – 10 items (adherence to fluid ) • Section 5 – 8 items ( adherence to diet) Interpretation: S.NO SCORE LEVEL OF ADHERENCE 1. &lt; 700 Poor adherence 2. 700-999 Moderate adherence 3. 1000-1200 Good adherence
DOI: 10.17632/j2d4tjh7k2.1
title: The Effect of Negative Written Emotional Disclosure on Eye Movements Changes, Static Balance and Symptoms of Depression of Anxious Athletes

description: data for article in SPSS (version 25)
DOI: 10.17632/tr29mhkjh8.1
title: Monte Carlo simulation of phonon transport from ab-initio data with Nano-κ

description: Understanding of heat transport in nanodevices is a challenging issue for several new technologies. It requires specific modelling approaches and dedicated simulation tools. Yet the latter are not numerous, and are often adapted to some “classic” materials or restricted to simple geometries (i.e. thin films, nanowires). Looking to address this deficiency, the present work brings Nano-κ, a Python code to simulate the phonon transport in nano and micro scale devices from ab-initio phonon data. The code has personalizing capabilities that allow to simulate several geometries and materials, offering insights of temperature distribution, heat flux, thermal conductivity, and mode contribution to energy transport. In the present work, a detailed description of the physical model implementation is provided and several simulation test cases are discussed. Nano-κ provides reliable predictions of the thermal conductivity in different materials, and is able to correctly predict the relative effect of size, temperature, and surface roughness on thermal transport properties.
DOI: 10.17632/xwx83vzmf6.1
title: Horizontal Levee Monitoring Data

description: Water quality and flow monitoring data were collected from the Horizontal Levee test facility at Oro Loma Sanitary District in San Lorenzo, CA. This experimental constructed wetland consists of a set of twelve separate wetland cells that were designed with various "treatments" based on differences in their plant community, soil type and topography. These data were collected to assess the relative influence of various design parameters on water quality improvements observed in these new constructed wetlands. Datasets published herein contain measurements of water quality parameters (e.g., pH, T, etc.), contaminants (e.g., nitrate, ammonium, phosphate) and flows in the influent (which was uniform across all wetland cells) and the effluent from each wetland cell. Additional data was collected from an adjacent free-water surface wetland and is provided as well. Porewater concentrations of nitrate and chloride are also provided that were collected throughout the wetland subsurface. Our data demonstrate the significant influence of hydrological conditions on contaminant removal in these systems. Plants and soil types were shown to have additional impacts on hydrological conditions by modifying subsurface flows.
DOI: 10.17632/xwx83vzmf6.3
title: Monitoring Data from a Pilot-Scale Horizontal Levee

description: Data were collected from a pilot-scale horizontal levee at the Oro Loma Sanitary District wastewater treatment facility in San Lorenzo, CA. The experimental system was constructed in 2017 to test this new type of treatment wetland. Horizontal levees, which are situated between coastal storm control levees and tidal mud flats, were first proposed for use in San Francisco Bay to remove contaminants from wastewater effluent in subsurface treatment layers while simultaneously providing flood control benefits by protecting coastal levees against wave action and storm surges. Additional benefits, such as the establishment of valuable habitat and recreational opportunities, may also be afforded. The experimental constructed wetland consisted of a set of twelve separate wetland cells that were designed with various "treatments" based on differences in their plant community, soil type and topography.

Data were collected to: (1) assess the relative influence of design parameters on water quality improvements; (2) evaluate the importance of various mechanisms to contaminant transformation and removal; and, (3) develop new methods for monitoring nature-based treatment systems. Measurements of water quality parameters, contaminant concentrations, and flows, characterizations of mineral formation and microbial communities in soils, and plant biomass growth measurements and satellite imagery are provided within this dataset. The results of a few of the models used to interpret these data are also provided. Metadata are provided within the spreadsheets or in separate text files to facilitate data interpretation. References are provided where data are related to other spreadsheets, datasets or specific publications.

We expected design parameters to have a significant impact on contaminant removal, but design did not impact fractional removal of contaminants (i.e., nutrients, trace organic contaminants and pathogen indicators). Rather, hydrological conditions controlled fractional removal, with design parameters having an impact on the total mass of contaminants removed. For example, willows increased subsurface flow rates and the mass of contaminants removed in those cells, although the fraction of applied contaminants removed remained the same. We also hypothesized denitrification would be the primary removal mechanism for nitrate. As expected, nitrate removal occurred primarily through microbial processes in the saturated subsurface and plant uptake contributed only 8% of total nitrogen removal. Seasonality was not observed in nitrogen removal, but we observed seasonality with respect to the electron donors used to fuel denitrification. Organic carbon fueled denitrification and iron sulfide deposition in the summer, with iron sulfides partly fueling denitrification in the winter.  Additional information on the key findings of studies associated with these data, as well as guidance on how to interpret those data, are provided for each folder in this dataset.
DOI: 10.17632/xwx83vzmf6.4
title: Monitoring Data from a Pilot-Scale Horizontal Levee

description: Data were collected from a pilot-scale horizontal levee at the Oro Loma Sanitary District wastewater treatment facility in San Lorenzo, CA. The experimental system was constructed in 2017 to test this new type of treatment wetland. Horizontal levees, which are situated between coastal storm control levees and tidal mud flats, were first proposed for use in San Francisco Bay to remove contaminants from wastewater effluent in subsurface treatment layers while simultaneously providing flood control benefits by protecting coastal levees against wave action and storm surges. Additional benefits, such as the establishment of valuable habitat and recreational opportunities, may also be afforded. The experimental constructed wetland consisted of a set of twelve separate wetland cells that were designed with various "treatments" based on differences in their plant community, soil type and topography. Data were collected to: (1) assess the relative influence of design parameters on water quality improvements; (2) evaluate the importance of various mechanisms to contaminant transformation and removal; and, (3) develop new methods for monitoring nature-based treatment systems. Measurements of water quality parameters, contaminant concentrations, and flows, characterizations of mineral formation and microbial communities in soils, and plant biomass growth measurements and satellite imagery are provided within this dataset. The results of a few of the models used to interpret these data are also provided. Metadata are provided within the spreadsheets or in separate text files to facilitate data interpretation. References are provided where data are related to other spreadsheets, datasets or specific publications. We expected design parameters to have a significant impact on contaminant removal, but design did not impact fractional removal of contaminants (i.e., nutrients, trace organic contaminants and pathogen indicators). Rather, hydrological conditions controlled fractional removal, with design parameters having an impact on the total mass of contaminants removed. For example, willows increased subsurface flow rates and the mass of contaminants removed in those cells, although the fraction of applied contaminants removed remained the same. We also hypothesized denitrification would be the primary removal mechanism for nitrate. As expected, nitrate removal occurred primarily through microbial processes in the saturated subsurface and plant uptake contributed only 8% of total nitrogen removal. Seasonality was not observed in nitrogen removal, but we observed seasonality with respect to the electron donors used to fuel denitrification. Organic carbon fueled denitrification and iron sulfide deposition in the summer, with iron sulfides partly fueling denitrification in the winter. Additional information on the key findings of studies associated with these data, as well as guidance on how to interpret those data, are provided for each folder in this dataset.
DOI: 10.17632/xnrgv2z76h.1
title: MLAnalysis: An open-source program for high energy physics analyses

description: We present a python-based program for phenomenological investigations in particle physics using machine learning algorithms, called MLAnalysis. The program is able to convert LHE and LHCO files generated by MadGraph5_aMC@NLO into data sets for machine learning algorithms, which can analyze the information of the events. At present, it contains three machine learning (ML) algorithms: isolation forest (IF) algorithm, nested isolation forest (NIF) algorithm, kmeans anomaly detection (KMAD), and some basic functionality to analyze the kinematic features of a data set. Users can use this program to improve the efficiency of searching for new physics signals.
DOI: 10.17632/zytw6vbm2k.1
title: Data Files for the article "Electro-Mechanical and Biomarker Analysis of Muscle Fatigue: Gender Comparisons in an Experimental Setting"

description: The data includes the electromechanical (Force and EMG) and biochemical (CPK, Cr and Ca) results for the evaluation in muscle fatigue for males and females non-trained.
DOI: 10.17632/hyp4ym8hhm.1
title: A direct interaction between CPF and Pol II links RNA 3ʹ-end processing to transcription

description: Carminati et al., 2023 raw data
DOI: 10.17632/j7d5sg9scv.1
title: Bacterial microbiota of Lepidochelys olivacea at the Puerto Arista beach-CHIAPAS

description: The beaches of Chiapas, at the Mexican Pacific, are an important nesting site for the Lepidochelys olivacea species. As they are migratory marine reptiles, they are difficult to study in the natural environment, so the nesting process is important to obtain biological information. Microbiological studies in these species allow us to understand the potential risks of bacterial zoonosis, derived from the handling of turtles and the consumption of eggs. In this work, morphometric data and cloacal and oral samples were obtained from 23 nesting females of L. olivacea, from August-December 2021, at the Puerto Arista beach, Chiapas, Mexico. A total of 18 bacterial taxa were identified through biochemical tests, of which five are genera, and up to 12 species were identified. A significant higher number of taxa were isolated from oral cavity (N=18), of which five were only identified to genus. Six taxa were isolated from the cloaca, two of them were identified to genus and four to species level. The most frequent genus in both cavities was Enterobacter, in addition to Citrobacter, Streptococcus and Staphylococcus. Also, the potentially pathogenic species for humans P. aeruginosa, K. ozaenae and V. alginolyticus were identified. These types of analyzes are essential to determine the infectious potential of bacteria for sea turtle species, as well as for humans. As they are threatened species, it is necessary to have a baseline that allows the care of immunosuppressed and sick animals. Likewise, they allow evaluating the zoonotic potential in the management activities of turtle species, which is of special interest for the staff of the camps installed on the country's beaches.
DOI: 10.17632/sctmp96v7n.1
title: Uniaxial Repeated Load Test Data of Asphalt concrete

description: The file provides a comprehensive dataset obtained from uniaxial repeated load tests on 108 asphalt concrete samples. Each sample underwent systematic evaluation under varied test temperatures, loading conditions, and mixture properties, ensuring the data’s comprehensiveness and reliability
DOI: 10.17632/3cxt36v48p.1
title: Phenols HPLC

description: To investigate the potential role of photoprotective and antioxidant mechanisms in response to future increases in sea surface temperatures caused by climate change, we conducted laboratory experiments using three intertidal macroalgae model species: Adenocystis utricularis (Ochrophyta, Phaeophyceae), Pyropia endiviifolia (Rhodophyta, Bangiophyceae), and Monostroma hariotii (Chlorophyta, Ulvophyceae). These algae were collected in Punta Artigas (King George Island, Antarctica) and acclimated at 2°C for 48 hours. They were then assessed in laboratory experiments for up to 5 days under two treatments: 1) control conditions at 2°C, and 2) elevated temperature conditions at 8°C, representing the most negative increment in SSTs estimated by the end of the 21st century. Pigments (chlorophylls and carotenoids), Mycosporine-like amino acids (MAAs), and Phenolic compounds were quantified after 3 and 5 days of exposure.
DOI: 10.17632/dk74jscsww.2
title: Dietary restriction of isoleucine increases healthspan and lifespan of genetically heterogeneous mice

description: This is the raw data allowing the recreation of figures from the paper "Dietary restriction of isoleucine increases healthspan and lifespan of genetically heterogeneous mice".
DOI: 10.17632/p5k7y76pmr.1
title: The video link of the ASCD operation

description: ASCD operation movie.
DOI: 10.17632/y5rvt5cbd3.1
title: EXPLORING THE IMPACT OF EDUCATION ON THE SOCIOECONOMIC DEVELOPMENT OF HISTORICALLY DISADVANTAGED GROUPS IN INDIA: AN EMPIRICAL ANALYSIS

description: Abstract : The objective of this study is to ascertain the socioeconomic status of the Scheduled Castes and examine the determinants that influence intergenerational mobility within this population. The examination of educational initiatives aimed at promoting the advancement of scheduled castes and the growth of higher education, within the framework of preferential treatment and supportive policies for diverse socioeconomic groups, including scheduled castes and tribes, is explored in the context of intergenerational educational mobility in India. The researcher discussed the topic of higher education for Scheduled Castes and Tribes, focusing on the experiences of students from these communities who are pursuing advanced education and successfully navigating various obstacles. This study examines the primary barriers and many social, personal, economic, and educational difficulties faced by Scheduled Caste Students (SCS) within their social environments. The research specifically concentrates on SCS individuals who have chosen to pursue higher education, as well as those who have not pursued such opportunities. The study will additionally demonstrate the differential ability of certain pupils from scheduled castes to surmount these challenges, in contrast to their counterparts who were unable to do so. The collection and analysis of data were conducted via interviews. The poll revealed that students belonging to the scheduled caste had a diverse array of aspirations, encompassing both individuals with intentions to pursue higher education and those without such aspirations. The study's findings indicate that despite historical instances of educational discrimination against scheduled tribes, contemporary lower-caste college students exhibit significant aspirations in both vocational and scholarly pursuits.The topic of discussion pertains to the concept of reservation in the context of caste. The topics under consideration encompass institutional habitus, educational experiences, professional education, occupational mobility, caste, inequality, generational dynamics, and the role of education.
DOI: 10.17632/3wydxdxspw.1
title: JDS_23602 Supplementary material

description: Supplementary material for Subclinical ketosis leads to lipid metabolism disorder by down-regulating the expression of Acetyl-CoA acetyltransferase 2 (ACAT2) in dairy cows
DOI: 10.17632/s42zcdb6dg.1
title: SustainabilityRepository

description: Repository of the paper "How much do carbon emission reduction strategies comply with a sustainable developement of the power sector?"