cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/rysm7p5pb5.1
title: Energy and protein gap analysis in dairy cows kept under fodder based diet with cut and carry feeding system.

description: There is a gap in dry matter, water, energy and protein intake of dairy cows kept in fodder- based diet under cut and carry feeding system in Sub- Saharan countries, Rwanda included. A study was conducted in two contrasting areas of Rwanda: Eastern Savana (altitude of 1,566 m, latitude is 1o56’55’S and longitude 30o26’5’’E; rainfall average of 900 mm, with temperatures of 25oC) and Volcanic highlands (altitude of 2250 m, latitude is -1o 29’59.42’’S and longitude is 29o 38’5.89’’E; the rainfall average is 1,845 mm; the average annual temperature is 15.9oC). The objective was to determine dry matter, water, protein and energy intake in comparison to their requirements for meeting the potential milk production. Ninety households, including 60 from lowlands and 30 from highlands, were randomly selected, and a total of 96 cows were included in the data collection process. About 90 samples which corresponded to different fodder mixture fed to lactating dairy cows in surveyed household were analysed for their dry matter (DM), crude protein (CP), neutral detergent fibre (NDF), and metabolizable energy (ME). Data on NDF intake, ME and CP intake, water, DM intake, body weight and milk performance well also collected. Data on feeds characterization were computed with Farm DESIGN Manual models by Groot and Oomen, while data for the production requirement of dairy cows under lactation were computed using LIGAPS dairy models. Data were analysed using general linear model with univariate analysis of statistical package for social sciences (SPSS). Results on feed characteristics showed that the average nutritive value of offered fodder was 25% of dry matter (DM), 58.5% neutral detergent fibre, 9.8% crude protein and of 6 mega joules (MJ) per kg DM. Results on production management showed that the average daily intake was 9kg DM; 35 litres of water; 898g of crude protein (CP) and 55 MJ ME, resulting in a milk production of 8.8 litres per day in both sites. However, the average requirement for both maintenance and a target milk production of 16.5litres per day were 15kg of DM; 57 Litres of water, 1907g of CP and 137 MJ of ME. This indicated daily deficits of 6kg DM, 21.6litres of water, 1094g of crude protein and 83.7 MJ of ME, along with a 7.6litres shortfall in milk yield per day. Results of the present study demonstrate the hypothesis previously posed. Findings from this analysis will serve as instruments for researchers in developing dairy diet models to improve dairy cow productivity at household level. Demonstrating the gap of available feeds resources would trigger the uptake of new feeding technologies by farmers. For dairy feeds manufacturers, this would serve as a guide for proper rationing of high concentrates ingredients rich in energy and protein in consideration of their requirements. This would contribute to improved milk production resulting in better remuneration to farmers, increased national milk pool and per capita milk consumption.
DOI: 10.17632/sg634gy9v2.1
title: Sahu, Villa et al.

description: The data in this study were derived from a variety of sources, including various cell lines, mice, and a yeast strain (Saccharomyces cerevisiae), all of which are comprehensively detailed in the main text and the supplemental materials and methods document. Our assessment of protein levels and metabolic activity was conducted through biochemical methods such as immunoblotting and mass spectrometry (metabolomics). To quantify the levels of proteins of interest, we followed the purification procedures outlined in the manuscript (Sahu, Villa, et al.), subsequently running them on SDS-PAGE gels. These gels were then transferred onto nitrocellulose membranes and subjected to hybridization with specific antibodies for chemiluminescent detection.
In the case of metabolite extraction, cultured cells or segments of mouse livers were either scraped or ground into the indicated solutions specified in the supplemental methods. The resulting metabolite suspensions were then prepared for mass spectrometry analysis.
Furthermore, we captured images of cells and lipid droplets by employing an optical microscope after staining them with Oil Red O.
The files are systematically organized to align with the sequence of data presentation in the manuscript. Each image file is available in PDF format and contains the original, untreated images of western blots, cells, and figures, encompassing both those featured in the main text and supplementary materials.
Additionally, the numerical data points for each graph in both the main and supplementary figures have been meticulously cataloged in separate Excel files, corresponding to the respective figure panels for ease of reference.
DOI: 10.17632/tkh39ck93y
title: A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression. Hofbauer et al.

description: Cell type-specific gene transcription is a profoundly regulated process that enables development and homeostasis in all animals. Two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers, activate or repress transcription, respectively. However, while enhancers have been thoroughly characterized, the sequence and chromatin properties of silencers, as well as their mechanisms of distal transcriptional repression, remain largely unknown. We performed an unbiased genome-wide silencer screen in Drosophila melanogaster S2 cells and discover a novel class of silencers, which recruit one of three different zinc finger transcription factors (TFs) through conserved DNA motifs. Surprisingly, these silencers lack detectable DNA accessibility, placing them outside current chromatin-defined catalogs of CREs (e.g. modENCODE). Further we find that the TF CG11247, which we term Saft, binds to one type of silencers via the orphan DLM3 motif and seems to safeguard cell fate decisions by repressing trachea- and cuticle-specific genes in non- trachea/non-cuticle tissues, such as the ovary or brain. Saft contains the previously unknown, highly conserved effector domain ZAC and functions via the corepressor G9a, yet independently of G9a’s H3K9 methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanism of action has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.
DOI: 10.17632/tkh39ck93y.1
title: A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression. Hofbauer et al.

description: Cell type-specific gene transcription is a profoundly regulated process that enables development and homeostasis in all animals. Two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers, activate or repress transcription, respectively. However, while enhancers have been thoroughly characterized, the sequence and chromatin properties of silencers, as well as their mechanisms of distal transcriptional repression, remain largely unknown. We performed an unbiased genome-wide silencer screen in Drosophila melanogaster S2 cells and discover a novel class of silencers, which recruit one of three different zinc finger transcription factors (TFs) through conserved DNA motifs. Surprisingly, these silencers lack detectable DNA accessibility, placing them outside current chromatin-defined catalogs of CREs (e.g. modENCODE). Further we find that the TF CG11247, which we term Saft, binds to one type of silencers via the orphan DLM3 motif and seems to safeguard cell fate decisions by repressing trachea- and cuticle-specific genes in non- trachea/non-cuticle tissues, such as the ovary or brain. Saft contains the previously unknown, highly conserved effector domain ZAC and functions via the corepressor G9a, yet independently of G9a’s H3K9 methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanism of action has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.
DOI: 10.17632/svsf92vwbr.1
title: soil physical properties,Tahanovce 2023

description: This dataset contains measured and calculated physical properties of closed and rehabilitated skid trails after 12 years in Ťahanovce, Košice (Slovakia).
Soil samples were taken from several site types: skid trail ruts, rehabilitated pits rehabilitated mounds , and undisturbed soil, which served as control samples. The samples were collected from two different depths: 0–5 cm and 5–10 cm, with RS-m samples collected only from the 0–5 cm depth. A total of 171 soil samples were collected using a steel ring (3.1 cm diameter, 3.3 cm height, 101.51 cm³ volume). Each sample was labeled with a unique code, sealed in plastic bags, and sent to the laboratory for analysis.

In the lab, the samples were dried at 105°C for 24 hours and reweighed using a highly accurate laboratory scale (precision of 0.01 g). Soil moisture content was calculated by comparing the wet and dry weights of the samples. Bulk density (BD) was determined by dividing the dry soil weight by the volume of the steel ring. Particle density (PD) was measured for fine soil particles (&lt;2 mm) using an air pycnometer. Total porosity (TP) was then calculated as the difference between PD and BD, expressed as a percentage. The particle size distribution was determined using the laser diffraction method, following the procedures outlined by Makó et al. (2022). Soil texture was classified according to the USDA soil texture system (shown in Fig. 7 of the article). Soil organic carbon (SOC) was measured using a spectrophotometric method based on dry combustion. Additionally, all samples underwent a visual inspection for mottling, which can indicate anaerobic conditions possibly caused by waterlogging and soil compaction. The dataset provides comprehensive data on soil properties in the rehabilitated and unrehabilitated skid trail sections, offering insights into the long-term impact of skid trail rehabilitation on soil recovery, specifically in terms of bulk density, porosity, soil organic carbon content, and particle size distribution. This information is crucial for evaluating the effectiveness of rehabilitation methods in promoting forest ecosystem recovery. Metadata included.
DOI: 10.17632/svsf92vwbr.2
title: Soil physical properties of Rehabilitated and Closed skid trails, Ťahanovce, Košice (Slovakia), 2023

description: This dataset contains measured and calculated physical properties of closed and rehabilitated skid trails after 12 years in Ťahanovce, Košice (Slovakia).
Soil samples were taken from several site types: skid trail ruts (CS), rehabilitated pits (RS-p), rehabilitated mounds (RS-m), and undisturbed soil (UND). The samples were collected from two different depths: 0–5 cm and 5–10 cm, with RS-m samples collected only from the 0–5 cm depth. A total of 171 soil samples were collected using a steel ring (3.1 cm diameter, 3.3 cm height, 101.51 cm³ volume). Each sample was labeled with a unique code, sealed in plastic bags, and sent to the laboratory for analysis.

In the lab, the samples were dried at 105°C for 24 hours and reweighed using a highly accurate laboratory scale (precision of 0.01 g). Soil moisture content was calculated by comparing the wet and dry weights of the samples. Bulk density (BD) was determined by dividing the dry soil weight by the volume of the steel ring. Particle density (PD) was measured for fine soil particles (&lt;2 mm) using an air pycnometer. Total porosity (TP) was then calculated as the difference between PD and BD, expressed as a percentage. The particle size distribution was determined using the laser diffraction method. Soil texture was classified according to the USDA soil texture system. Soil organic carbon (SOC) was measured using a spectrophotometric method based on dry combustion. Additionally, all samples underwent a visual inspection for mottling, which can indicate anaerobic conditions possibly caused by waterlogging and soil compaction. The dataset provides comprehensive data on soil properties in the rehabilitated and unrehabilitated skid trail sections, offering insights into the long-term impact of skid trail rehabilitation on soil recovery, specifically in terms of bulk density, porosity and soil organic carbon content. This information is crucial for evaluating the effectiveness of rehabilitation methods in promoting forest ecosystem recovery.
Metadata included.
DOI: 10.17632/3rrptycphs
title: [dataset] Field Observations of Breeding Individuals of the Yellow-browed Tit: Insights into Brood Provisioning Behaviors, Nestling Diet, Vocalizations, and Habitat Preference

description: This dataset and R code provide results and figures for the article submission entitled 'Field Observations of Breeding Individuals of the Yellow-browed Tit: Insights into Brood Provisioning Behaviors, Nestling Diet, Vocalizations, and Habitat Preference.'
DOI: 10.17632/svsf92vwbr.3
title: Soil physical properties of Rehabilitated and Closed skid trails, Ťahanovce, Košice (Slovakia), 2023

description: This dataset contains measured and calculated physical properties of closed and rehabilitated skid trails after 12 years in Ťahanovce, Košice (Slovakia).
Soil samples were taken from several site types: skid trail ruts (CS), rehabilitated pits (RS-p), rehabilitated mounds (RS-m), and undisturbed soil (UND). The samples were collected from two different depths: 0–5 cm and 5–10 cm, with RS-m samples collected only from the 0–5 cm depth. A total of 171 soil samples were collected using a steel ring (3.1 cm diameter, 3.3 cm height, 101.51 cm³ volume). Each sample was labeled with a unique code, sealed in plastic bags, and sent to the laboratory for analysis.

In the lab, the samples were dried at 105°C for 24 hours and reweighed using a highly accurate laboratory scale (precision of 0.01 g). Soil moisture content was calculated by comparing the wet and dry weights of the samples. Bulk density (BD) was determined by dividing the dry soil weight by the volume of the steel ring. Particle density (PD) was measured for fine soil particles (&lt;2 mm) using an air pycnometer. Total porosity (TP) was then calculated as the difference between PD and BD, expressed as a percentage. The particle size distribution was determined using the laser diffraction method. Soil texture was classified according to the USDA soil texture system. Soil organic carbon (SOC) was measured using a spectrophotometric method based on dry combustion. Additionally, all samples underwent a visual inspection for mottling, which can indicate anaerobic conditions possibly caused by waterlogging and soil compaction. The dataset provides comprehensive data on soil properties in the rehabilitated and unrehabilitated skid trail sections, offering insights into the long-term impact of skid trail rehabilitation on soil recovery, specifically in terms of bulk density, porosity and soil organic carbon content. This information is crucial for evaluating the effectiveness of rehabilitation methods in promoting forest ecosystem recovery.
Metadata included.
DOI: 10.17632/3rrptycphs.1
title: [dataset] Field Observations of Breeding Individuals of the Yellow-browed Tit: Insights into Brood Provisioning Behaviors, Nestling Diet, Vocalizations, and Habitat Preference

description: This dataset and R code provide results and figures for the article submission entitled 'Field Observations of Breeding Individuals of the Yellow-browed Tit: Insights into Brood Provisioning Behaviors, Nestling Diet, Vocalizations, and Habitat Preference.'
DOI: 10.17632/p24z49w44z.1
title: ACW1B - A Weighted Accelerometer 1B Dataset from GRACE C Satellite

description: The dataset consists of the weighted accelerometer 1B data from the GRACE C satellite of the GRACE-FO mission, sampled at 1 Hz along the three axes of the Science Reference Frame (SRF). This data was derived from the official ACC1A dataset (10 Hz) by applying a 35 mHz low-pass Gaussian filter, which concurrently downsampled the data to avoid aliasing. All time corrections from 1A to 1B align with the GRACE-FO mission handbook.

During filtering, the initial variances from the 1A measurements were propagated, and a covariance matrix was utilized to calculate the final variance for each measurement. The autocorrelation function was used to derive initial variances in 1A, incorporated into the filtering process to maintain error information in the final variances and eliminate spikes.

The dataset includes the following columns:
1. GPS Time
2. Geographic Latitude (degrees)
3. Geographic Longitude (degrees)
4. XSRF linear non-gravitational accelerations (nm/s²)
5. YSRF linear non-gravitational accelerations (nm/s²)
6. ZSRF linear non-gravitational accelerations (nm/s²)
7. Standard deviation in XSRF (nm/s²)
8. Standard deviation in YSRF (nm/s²)
9. Standard deviation in ZSRF (nm/s²)


All files are in .txt format and follow the naming convention: ACW1B_year-month-day. Single-digit months and days are not padded with a leading zero. 
The available dataset spans from August 1, 2018, to October 15, 2020, with additional dates expected to be added in the future.
DOI: 10.17632/zg89423tkb.1
title: NIRS intact green coffee beans with CGA content, species and Geographical origins from Java, Indonesia

description: Presented dataset contains spectral data of intact green beans coffee samples from Java Island, Indonesia. 
Spectral data were acquired in wavelength range from 1000 to 2500 nm. 

data can be analyzed for quantitative and qualitative purposes. 
presented data on .txt and .unsb format that can be run directly in The Unscrambler X
DOI: 10.17632/9rmx5jcwsv.1
title: Student Motivation, Artificial Intelligence, Extended Reality

description: Research strings of ARCS Motivation model with artificial intelligence and extended technologies. 
It includes every string, its number of findings, date, and sample within the scope.
DOI: 10.17632/t6c2kfp852.1
title: Supplementary Information for Flexible Carbon Capture Using MOF Fixed Bed Reactors at an NGCC Plant

description: This supplementary data supports the paper titled Flexible Carbon Capture Using MOF Fixed Bed Reactors at an NGCC Plant.
DOI: 10.17632/36k59tkp7c.1
title: Aaltonen H. et al. 2021. "The effects of glucose addition and water table manipulation on peat quality of drained peatland forests with different management practices"

description: The dataset contains data of the peat column priming experiment carried out in the project "Reducing the effects of forest management on inland water (REFORMWATER) funded by the Water-JPI. The overarching aim of this study was to look for less invasive practices to reduce the harmful effects of peatland
forest management at the time of climate change and increasing demands for tree biomass. We postulated a main hypothesis that the ditch network maintenance operation lowers the water table depth, the availability of oxygen increases and this increases the abundance and 
activity of decomposing microbes in peat, leading to increased release of dissolved organic matter and nutrients. The data is based on a peat column experiment where 50 cm-long peat columns were collected from drained peatland forests and exposed to different water table and glucose manipulation treatments. The decomposition stage of peat was measured using soil organic matter fractionation based on acid-water extractions and the decomposition of peat was measured by measuring soil respiration. Also dissolved organic carbon and its quality were measured from water samples collected from the columns.
DOI: 10.17632/x84h9b6bw6.1
title: Landscape and Class metrics calculated in microlandscapes in Chingaza National Natural Park, Colombia

description: Data set with the information of landscape metrics and class metrics calculated at diferente spatial scales (50m, 100m and 200m) in microlandscape in the Chingaza Natural National Park, Colombia. We calculated 18 class metrics and 25 landscape metrics for each Micro-landscape based on area, aggregation, shape, core area, and diversity, using the landscapemetrics package for R .
DOI: 10.17632/x84h9b6bw6.2
title: Landscape and Class metrics calculated in microlandscapes in Chingaza National Natural Park, Colombia

description: Data set with the information of landscape metrics and class metrics calculated at diferente spatial scales (50m, 100m and 200m) in microlandscape in the Chingaza Natural National Park, Colombia. We calculated 18 class metrics and 25 landscape metrics for each Micro-landscape based on area, aggregation, shape, core area, and diversity, using the landscapemetrics package for R .
DOI: 10.17632/gsrrtr28hp.1
title: Data and code for: Ice load measurements on Rätan concrete dam using different sensor types

description: Data and code for: Ice load measurements on Rätan concrete dam using different sensor types
https://doi.org/10.1016/j.coldregions.2021.103425

Run main.py in the Command Files folder to re-create figures and tables in the paper, read the Readme file.

V2

No change to version 2
DOI: 10.17632/m5h5fw872g.1
title: Brazil-FluxMet-Stf

description: This dataset contributes to a better understanding of the influence of atmospheric aerosols on the functioning of Brazilian Amazon ecosystems, particularly on the Net Ecosystem Exchange (NEE). The radiative effects of aerosols and clouds (from the emitted by Biomass Burning ), until then unknown for a wide variety of species and vegetation types present in the Amazon Basin, have been evaluated through CO2 flux tower systems and meteorological data in the Amazon biomes. Our data allowed us to examine the radiative effects of atmospheric aerosols on solar radiation and its impacts on the Net Ecosystem Exchange (NEE) of an area of semi-deciduous tropical forest located in the south of the Amazon basin in the north of the state of Mato Thick. The data for the development of this research will be made available soon on the AmericFlux website (https://ameriflux.lbl.gov). All the data collected are under the citation: Vourlitis, George (2011), Spatial and temporal variations in aboveground woody carbon storage for cerrado forests and woodlands of Mato Grosso, Brazil. Here, the dataset contains: (1) Net Ecosystem Exchange (NEE of CO2); from the turbulent covariance system (eddy-covariance); and (2) meteorological data, both collected between June 2005 and July 2008.
DOI: 10.17632/srrsntpghy.1
title: Comparison of Bacterial and Secreted Proteins produced in Milk Versus Medium for Escherichia coli by Proteomic Analysis

description: Escherichia coli, Quantitative proteomics, Bacterial proteins, Secretory proteins
DOI: 10.17632/5h3565w2p7.1
title: Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains. Bryan et al.

description: This repository contains uncropped Western blot and microscopy images for the manuscript "Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains". See manuscript for details.
DOI: 10.17632/zg89423tkb.2
title: NIRS intact green coffee beans with CGA content, species and Geographical origins from Java, Indonesia

description: Presented dataset contains spectral data of intact green beans coffee samples from Java Island, Indonesia. 
Spectral data were acquired in wavelength range from 1000 to 2500 nm. 

data can be analyzed for quantitative and qualitative purposes. 
presented data on .txt and .unsb format that can be run directly in The Unscrambler X