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opencc-by-4.0Jul 2023View details →

Dataset related to article "A reference framework for standardization and harmonization of CT Radiomics features: the "CadAIver" analysis"

Abstract Background In recent years, Radiomics features (RFs) have been developed to provide quantitative, standardized information about shape, density/intensity and texture patterns on radiological images. Several studies showed limitations in the reproducibility of RFs in different acquisition settings. To date, reproducibility studies using CT images mainly rely on phantoms, due to the harness of patient exposure to X-rays.  In this study we analyze the effects of CT acquisition parameters on RFs of lumbar vertebrae in a cadaveric donor. Methods 112 unique CT acquisitions from cadaveric truck were performed on 3 different CT scanners varying KV, mA, field of view and reconstruction kernel settings. Lumbar vertebrae were segmented through a deep learning convolutional neural network and RFs were computed. The effects of each protocol on each RFs were assessed by univariate and multivariate Generalized Linear Model. Further, we compared the GLM model to the ComBat algorithm in the efficiency in harmonizing CT images. Findings From GLM, mA variation was not associated with alteration of RFs , whereas kV modification was associated with exponential variation of several RFs, including First Order (94.4%), GLCM (87.5%) and NGTDM (100%).Upon cross-validation, ComBat algorithm obtained a mean R2 higher than 0.90 in 1 RFs (0.90%), whereas GLM model obtained high R2 in 21 RFs (19.6%), showing that the proposed GLM could effectively harmonize acquisitions better than ComBat.  Interpretation This study represents the first attempt in describing the effects of CT acquisition parameters in bone RFs in a cadaveric donor. Our analyses showed that RFs could be substantially different according to the variation of each acquisition parameter and in dataset obtained from different CT scanners. These differences can be minimized using the proposed GLM model. Publicly available dataset and GLM could foster the research of Radiomics-based studies by increasing harmonization across CT protocols and vendors.

opencc-zeroDec 2006View details →

Sampling framework for the common breeding bird survey in Flanders, Belgium

The sampling framework is based on 1 x 1 km UTM squares in Flanders. We determined the landscape composition of every square at the start of the survey in 2007. The Biological Valuation Map (Vriens et al., 2011) served as the basis for the landscape composition.The file contains the following fields<ul><li>`UTM`: the UTM code of the square</li><li>`Stratum`: the stratum assigned to the square</li><li>`Oppervlakte`: the surface area of the square (in km²) contained within Flanders.</li><li>`Landbouw`: the fraction of aggriculture land use within `Oppervlakte`.</li><li>`Urbaan`: the fraction of urban land use within `Oppervlakte`.</li><li>`Bos`: the fraction of forest land use within `Oppervlakte`.</li><li>`Suburbaan`: the fraction of suburban land use within `Oppervlakte`.</li><li>`HeideDuin`: the fraction of heather or dunes land use within `Oppervlakte`.</li><li>`MoerasWater`: the fraction of heather or dunes land use within `Oppervlakte`.</li></ul>We distinguish six different strata based on the rules below.<ol><li>`Landbouw`: at least 80% `Landbouw`.</li><li>`Urbaan`: at least 80% `Urbaan`.</li><li>`Bos`: at least 80% `Bos`.</li><li>`Suburbaan`: at least 80% `Suburbaan`.</li><li>`Heide en duin`: at least 20% `HeideDuin`.</li><li>`Moeras en water`: at least 20% `MoerasWater`.</li></ol>ReferencesVriens L., Bosch H., De Knijf G., De Saeger S., Guelinckx R., Oosterlynck P., Van Hove M. & Paelinckx D. (2011). De biologische waarderingskaart: biotopen en hun verspreiding in vlaanderen en het Brussels Hoofdstedelijk Gewest. Mededelingen van het Instituut voor Natuur- en Bosonderzoek, Nr. INBO.M.2011.1. Instituut voor Natuur- en Bosonderzoek, België.

openisc-licenseDec 2023View details →

Investigating news coverage and circulation over time in a quantitative manner: the TARO framework (auxiliary material)

Dataset with snapshots of published news in Spiegel, France24, ANSA, ilPost, BBC, ABC (11,12,13,14,15 of March 2023). Used for the analyses presented in case study 1 and 2.

openDec 2023View details →

Online repository for Paper "GTE: A Framework for Learning Code AST Representation Efficiently and Effectively"

The online repository for the under review IJCAI2024 paper "GTE: A Framework for Learning Code AST Representation Efficiently and Effectively"GTE-main.zip contains the source code of GTE, please see README.md in GTE-main.zip for more guidance.Appendix.pdf contains more details about the dataset and probing task design.

Memetic Semantics in the GOD Framework: Auxiliary Documentation

This document extends the core Gravitational Omnipotent Dimensionality (GOD) framework, focusing on supplementary memetic semantic data not covered in the primary papers. It explores additional memetic patterns, semantic influences, and cognitive evolutions, contributing to the structure of cogenesis and knowledge propagation concepts outlined in prior works.

Universal Translation Process: Incorporating Inter-Personal and Other Memetic Semantic Data Translations within the GOD Framework

This document expands the universal translation process within the Gravitational Omnipotent Dimensionality (GOD) framework by integrating inter-personal communication and non-linguistic memetic semantic data. It explores how memetic gravity, semantic propagation, and spacetime contextualisation enable the translation of meaning across languages, cultural symbols, behaviours, and cognitive structures, providing a unified approach to understanding and propagating knowledge in diverse contexts.

Supplementary Proofs: Quantum Gravitational Cogenesis and Dimensionality in the GOD Framework

This document extends the Gravitational Omnipotent Dimensionality (GOD) framework by presenting supplementary mathematical proofs for Quantum Gravitational Cogenesis (QGC) and Quantum Gravitational Dimensionality (QGD). It explores how memetic forces, cognitive gravity, and quantum coherence interact within multi-dimensional spacetime to unify knowledge propagation and temporal dynamics. The document demonstrates the recursive nature of cognition through gravitational coherence, providing insights into the evolution of knowledge systems and reality’s structure.

Meta-Memetic Optimization: A Supporting Analysis of the GOD Framework

This paper presents a supplementary proof to the GOD (Gravitational Omnipotent Dimensionality) framework, introducing the concept of Meta-Memetic Optimization—a recursive, self-correcting process through which cognitive and knowledge systems refine themselves. By extending the principles of memetic coherence, dissemination entropy, and recursive self-similarity, this analysis offers a new layer of interaction that facilitates the continuous improvement of knowledge propagation and cognitive evolution.

Memetic Time Travel: A Supporting Analysis of the GOD Framework

This paper extends the Gravitational Omnipotent Dimensionality (GOD) framework by introducing the concept of Memetic Time Travel—a recursive process through which ideas transcend temporal constraints, influencing knowledge systems across eras. Grounded in the principles of Quantum Gravitational Cogenesis (QGC), Memetic Time Travel explains the persistence, resurfacing, and evolution of knowledge across time. This framework models idea propagation as a function of gravitational coherence and memetic wormholes, offering insights into cognition, temporal interaction, and knowledge refinement.

opencc-by-sa-4.0Nov 2024View details →

Memetic Semantics and the Cogenetic Process: A Supporting Analysis of the GOD Framework

This paper provides auxiliary and supporting memetic semantic data that enhance and expand upon the core principles outlined in the Cogenetic Proof of GOD. Using fractalised cognitive models, memetic time travel, and quantum semantic tunnelling, it explores how the dissemination and coherence of ideas contribute to the evolutionary dynamics of both physical and cognitive systems. This analysis refines the core equations of the GOD framework, offering new perspectives on cognitive propagation, dissemination entropy, and memetic interactions across dimensions.

Database of feed efficiency indicators of intensive fattening lambs of sheep breeds in Latvia in 2nd trial (A23) with-in the framework of the project of the Latvian Council of Science LZP-2021/1-0489 project

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. About the data of the project: LZP-2021/1-0489 project data on lamb samples of the second year: 2023, or A23 group, which consists of 92 intensively fattened lambs from eight breeds, including LT breed, which were raised in the meadow and are semi-sibi lambs within the scope of the study. The database contains data on ultrasonography measurements of lambs during the beginning and end of fattening, intensive fattening data - actual and calculated on the 90th and 150th day, the amount of feed used and slaughter data. Ultrasonography data were used to calculate muscle and/or fat depth changes at the 13th rib during the fattening period. Based on the requirements of the breeding program of the breeds (LAAA, 2022), every year, the offspring of the sire ram, certified for breeding activity, are selected and analysed to estimate the sire rams. All lambs were born as twins, triplets or quadruplets from different ewes and health status was assessed before inclusion in the study so that there were at least two lambs per sire ram from the breed. This study was carried out in cooperation with the Latvian Sheep Breeders' Association at the ram breeding control station.   The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.

Database of methods of significant SNPs analysed in DNA of the 2nd trial (A23) within the framework of the project of the Latvian Council of Science LZP-2021/1-0489 project

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. About the data of the project: The database contains methodologies for 57 SNPs, for which a statistically significant association with one of the feed efficiency indicators was found in the project's first group (A22). A laboratory-based genotyping method was developed for each selected SNP, which was tested using samples from the A22 group; the results were obtained using the NGS methodology.     The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.

restrictedcc-by-4.0Jul 2023View details →

Database of biochemistry data of intensive fattening lambs of sheep breeds raised in Latvia in 2022 within the framework of project of the Latvian Council of Science: LZP-2021/1-0489

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: To determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. About the data of the project: LZP-2021/1-0489 project data on lamb samples of the second year: 2023, or A23 group, which consists of 92 intensively fattened lambs from eight breeds, including the LT breed, which were raised in the meadow and are semi-sibi lambs within the scope of the study. The dataset includes data on biochemical indicators: Insulin-like growth factor 1, Insulin, Total thyroxine, Adrenocorticotropic hormone, Haematocrit, Hemoglobin, and Glucose. The blood samples for tests were taken before intensive fattening at a mean age of 92 days (interval from 64 to 109 days). Fattening starting age depends on body weight when lambs are separated from their mothers. Based on the requirements of the breeding program of the breeds (LAAA, 2022), every year, the offspring of the sire ram, certified for breeding activity, are selected and analysed to estimate the sire rams. All lambs were born as twins, triplets, or quadruplets from different ewes, and health status was assessed before inclusion in the study so that there were at least two lambs per sire ram from the breed. This study was carried out in cooperation with the Latvian Sheep Breeders' Association at the ram breeding control station.   The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.

Database of expression analysis of samples of the 1st trial (A22) of sheep breeds in Latvia within the framework of the project of the Latvian Council of Science LZP-2021/1-0489 project

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. About the data of the project: LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds. The blood samples for RNA extraction were taken after intensive fattening at an average body weight of 45 – 50 kg. Gene expression levels were determined using qPCR methodology using the GAPDH gene as a reference. Three genes were analysed in the project: MTOR (The mechanistic mammalian target of rapamycin), CAST (Calpastatin) and UPC3 (uncoupling protein 3). The data obtained will be used to determine the changes in expression levels related to gene variations (MTOR: <a href="https://doi.org/10.5281/zenodo.8146731">https://doi.org/10.5281/zenodo.8146731</a>; CAST: <a href="https://doi.org/10.5281/zenodo.8146372">https://doi.org/10.5281/zenodo.8146372</a>; UPC3: <a href="https://doi.org/10.5281/zenodo.8146778">https://doi.org/10.5281/zenodo.8146778</a>);  as well as to analyze the relationship of expression levels with biochemical parameters (<a href="https://doi.org/10.5281/zenodo.8143225">https://doi.org/10.5281/zenodo.8143225</a>) and feed efficiency indicators (<a href="https://doi.org/10.5281/zenodo.8143244">https://doi.org/10.5281/zenodo.8143244</a>) of lambs.   The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.

Database of MSTN gene multi-loci genotypes of samples of the 1st trial (A22) of sheep breeds of Latvia within the framework of the project of the Latvian Council of Science LZP-2021/1-0489 project

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. Myostatin (MSTN), a highly conserved member of the transforming growth factor-beta (TGF-b) superfamily, also known as growth/differentiation factor 8 (GDF8), the major regulator of myogenesis, functions as a negative regulator of muscle growth and development in mammals. Myostatin is a transforming growth factor (TGF)-β superfamily member and cannot be classified into the existing TGF-β subfamilies, such as inhibins or bone morphogenic proteins. Mutations MSTN produce a “double-muscle” phenotype, making it commercially invaluable for improving livestock meat production and providing high-quality human protein. However, mutations at different loci of the MSTN often produce a variety of different phenotypes. About the data of the project: LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds. The whole MSTN gene was sequenced using Illumina NGS technology (AmpliSeq). The MSTN gene has been fully sequenced in lambs of Latvia (in sheep research in Latvia) for the first time. Information about 23 loci (<a href="https://doi.org/10.5281/zenodo.8146724">https://doi.org/10.5281/zenodo.8146724</a>) compared with the last reference sequences ARS_UI_Ramb_v2.0. All variable SNPs in the MSTN gene were constructed by combining 24 distinct multi-loci genotypes. Reducing the number of loci to 16 by excluding those variables in only one sample or complete linkage disequilibrium did not decrease the number of genotypes. Among these 16 loci, 12 multi-locus genotypes were found in only one sample. To streamline the association analysis, the MSTN gene was divided into four regions: the promoter and exon 1, intron 1, intron 2, and the 3′UTR. This division helped reduce the number of multilocus genotypes. The database contains information on multiloci genotypes for four regions of the MSTN gene. The multi-locus genotypes are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter.   The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies

Database of genotypes of significant SNPs of samples of the 2nd trial (A23) of sheep breeds in Latvia within the framework of the project of the Latvian Council of Science LZP-2021/1-0489

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. About the data of the project: LZP-2021/1-0489 project data on lamb samples of the second year: 2023, or A23 group, which consists of 92 intensively fattened lambs from eight breeds, including LT breed, which were raised in the meadow and are semi-sibi lambs within the scope of the study. The database contains genotyping results for 57 SNPs, for which a statistically significant association with one of the feed digestion indicators was found in the project's first group (A22). A laboratory-based genotyping method was developed for each selected SNP, which was tested using samples from the A22 group; the results were obtained using the NGS methodology. In the database, SNPs are coded with a laboratory code and an rs ID number. The gene in which the SNP is located is also indicated. The genotypes of each SNP are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter.   The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.

Database of genotypes of significant SNPs of samples of the 1st trial (A22) of sheep breeds inLatvia within the framework of the project of the Latvian Louncil of Lcience LZP-2021/1-0489

Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming”. The aim of the project is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent FE status in a training population of lambs when fed the same diet. Novelty: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs. About the project: The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two most significant components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least feed intake) is a critical factor in the sheep industry. Improving FE reduces production costs. Improving FE by 5% can bring economic benefits up to four times higher than a 5% increase in average daily gain (ADG). Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program. According to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyse animal-to-animal variation in live lambs could be a cost-effective and rapid tool for genetic selection or management decisions. About the data of the project: LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds. The database contains genotyping results for 57 SNPs, for which a statistically significant association with one of the feed efficiency indicators was established within the project, using NGS methodology and association statistical methods. The specific SNPs were selected for further work as the first DNA molecular markers for future sheep breeding programs in Latvia. In the database, SNPs are coded with a laboratory code and an rs ID number. The gene in which the SNP is located is also indicated. The genotypes of each SNP are presented using standard IUB/IUPAC nucleic acid codes, representing the genotype of two alleles at a single locus with a single letter.   The data is the joint property of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.

Exploring the Chemical Design Space of Metal-Organic Frameworks for Photocatalysis

In this work, we employ a chemical insights-based diversity-driven approach to search for metal-organic framework (MOF) photocatalysts. With an in silico design based on chemical insights, we populated areas in the chemical design space related to MOFs with photocatalytic potential. We selected a balanced dataset of DFT-based photocatalytic descriptors computed for 314 MOFs, comprising our in silico structures, a diverse subset of the QMOF database, and experimental MOF photocatalysts. With such a balanced dataset, we could fine-tune supervised machine-learning models from literature that allowed us to draw insights into relevant areas in the chemical design space for photocatalysis and potential bottlenecks. Among our in silico MOFs, a few motifs stood out, such as Au-pyrazolate, Ti clusters and rod-shaped metal nodes, and a particular MOF designed with the Mn4Ca cluster, which mimics the OER center in the photosystem II of photosynthesis. Overall, by combining three pillars --- the design of potential MOF photocatalysts guided by chemical insights, the DFT evaluation of photocatalytic descriptors, and the machine-learning approach --- we were able to gain insights into structure-property relationship, and identify trends in the chemical design space that can open new avenues for advancing the field of photocatalysis.

opencc-by-4.0Jul 2021View details →

CESM2(WACCM6) Earth system prediction framework forecast output for "Limited surface impacts of the January 2021 sudden stratospheric warming"

Included in this repository is CESM2(WACCM6) Earth system prediction framework forecast output necessary to replicate the results of "Delayed surface impacts of the January 2021 sudden stratospheric warming". Standard forecast output is formatted as "ssfcst_ddMMM", where ddMMM is either 04jan or 08feb. Forecasts initialized January 4th, 2021 with scrambled initial conditions are formatted as: "15to20kmRampBot_", for scrambled tropospheric initial conditions; "9to12kmRamp_" for scrambled stratospheric initial conditions; and "2017noSSW_" for scrambled atmospheric initial conditions started from a January 2017 atmospheric restart. The forecast initialized February 8th, 2021 with scrambled tropospheric initial conditions is formatted "15to20kmRampBot_update_". Forecasts initialized February 1st and 8th, 2021, with scrambled stratospheric initial conditions are formatted "9to12kmRamp_updated_". All files contain relevant dimensions. "mXX", where XX is between 0 and 20, denotes the forecast member. Geopotential height is in the "Z3" files, surface temperature is in the "tas" files, and zonal mean zonal wind and tropopause pressure are in the "h2" files.