cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5032250.v1
title: Microscopic recognition and identification of fish meal in compound feeds

description: Fish meal is an accepted ingredient in compound feed. Unauthorised application is primarily enforced by visual inspection, i.e., microscopy. In order to document the visually available diversity, fragments of bones and scales of 17 teleost fish species belonging to seven different orders were investigated for their diversity in the presence of structural elements: lacunae and canaliculae in bone fragments and type of growth rings and teeth of scale fragments. Despite the classical division into cellular bones and acellular bones of teleost fish, i.e., whether or not possessing osteocytes, the current examinations revealed patterns of lacunae, in some types accompanied with canaliculae, in all 17 species investigated. In total seven types of bone structures were defined, and six types of scale structures. Profiles with the relative frequency of each bone type per species were established. The share of acellular bone fragments appeared to be related to the evolutionary position of the species. Results of proficiency tests for the detection of fish meal reveal that in most cases the sensitivity and specificity for the detection of fish meal ranges from sufficient to perfect. Only some specified circumstances can hamper proper recognition and identification, most notably salmon bone fragments mimicking bone fragments from terrestrial animals, and pieces of hydrolysed proteins or minerals mimicking acellular fish bone fragments. The expertise gained in this study would help to improve the distinction between fish meal and terrestrial animal material in compound feed, and it supports the application of the species-to-species ban with respect to the valorisation of by-products from fish farms in aquafeed. In a broader perspective, the current expertise might be helpful to detect fraud throughout the feed/food production chain. The matrix of characteristics versus species is implemented in a data model running in the expert system ‘Determinator’ for facilitating identification.
DOI: 10.6084/m9.figshare.12601348
title: Biologically-based modeling of radiation risk and biomarker prevalence for papillary thyroid cancer in Japanese a-bomb survivors 1958–2005

description: Thyroid cancer of papillary histology (PTC) is the dominant type in radio-epidemiological cohorts established after nuclear accidents or warfare. Studies on post-Chernobyl PTC and on thyroid cancer in the life span study (LSS) of Japanese a-bomb survivors consistently revealed high radiation risk after exposure during childhood and adolescence. For post-Chernobyl risk assessment overexpression of the CLIP2 gene was proposed as molecular biomarker to separate radiogenic from sporadic PTC. Based on such binary marker a biologically-based risk model of PTC carcinogenesis has been developed for observational Chernobyl data. The model featured two independent molecular pathways of disease development, of which one was associated with radiation exposure. To gain credibility the concept for a mechanistic risk model must be based on general biological features which transcend findings in a single cohort. The purpose of the present study is therefore to demonstrate portability of the model concept by application to PTC incidence data in the LSS. By exploiting the molecular two-path concept we improve the determination of the probability of radiation causing cancer (POC). The current analysis uses thyroid cancer incidence data of the LSS with thyroid cancer diagnoses and papillary histology (<i>n</i> = 292) from the follow-up period between 1958 and 2005. Risk analysis was performed with both descriptive and biologically-based models. Judged by goodness-of-fit all applied models described the data almost equally well. They yielded similar risk estimates in cohorts post-Chernobyl and LSS. The preferred mechanistic model was selected by biological plausibility. It reflected important features of an imperfect radiation marker which are not easily addressed by descriptive models. Precise model predictions of marker prevalence in strata of epidemiological covariables can be tested by molecular measurements. Application of the radiation-related molecular pathway from our preferred model in retrospective risk assessment decreases the threshold dose for 50% POC from 0.33 (95% confidence interval (CI) 0.18; 0.64) Gy to 0.04 (95% CI 0.01; 0.19) Gy for females and from 0.43 (95% CI 0.17; 1.84) Gy to 0.19 (95% CI 0.05; 1.00) Gy for males. These improvements are still not sufficient to separate radiation-induced from sporadic PTC cases at very low doses &lt;0.015 Gy typical for the Fukushima accident. Successful application of our preferred mechanistic model to LSS incidence data confirms and improves the biological two-path concept of radiation-induced PTC. Model predictions suggest further molecular validation studies to consolidate the basis of biologically-based risk estimation.
DOI: 10.6084/m9.figshare.4985195.v2
title: Genetic polymorphism of 29 STR loci in the Hunan Han population from China

description: Genetic polymorphism of 29 STR loci in the Hunan Han population from China
DOI: 10.6084/m9.figshare.4985195.v1
title: Genetic polymorphism of 29 STR loci in the Hunan Han population from China

description: Genetic polymorphism of 29 STR loci in the Hunan Han population from China
DOI: 10.6084/m9.figshare.14792100.v3
title: MLSA phylogeny of 40 Agrobacterium spp.

description: For this MLSA of 40 Agrobacterium spp. strains, we extracted the CDS alignments of parE, gyrB, recA, and rpoB from the Pantagruel pangenome database and concatenated into a multi-locus alignment, totaling 9,968 positions. ML Phylogenies were then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.<br>
DOI: 10.5281/zenodo.5535762
title: Data of Eggenberger Andersen et al. 2021

description: Hi,<br> There are nine files containing GW data as well as a notebook that reads the data and make two basic plots of the GW waveforms. Please contact oliver.e.andersen@astro.su.se with any questions (or should your analysis find any inconsistencies with ours). If you use this data, please cite our paper.<br> <br> The data files are named according to our labelling of the simulations in Table 2.<br> <br> The file columns are:<br> 1. time post-bounce<br> 2. h_{+} * D [cm] (plus polarised strain assuming the observer is located at the equator) The notebook generate plots of the gravitational wave signal for all our model runs. EDIT: This data has been corrected from an earlier version which had overestimated the GW amplitude by 25 %. <br> We have also included tables for the EOS and neutrino opacities. <br> The kindest regards, <br> Oliver, Shuai, André, Aurore, Sean, & Evan.<br>
DOI: 10.5281/zenodo.4973545
title: Data of Eggenberger Andersen et al. 2021

description: Hi,<br> There are nine files containing GW data as well as a notebook that reads the data and make two basic plots of the GW waveforms. Please contact oliver.e.andersen@astro.su.se with any questions (or should your analysis find any inconsistencies with ours). If you use this data, please cite our paper.<br> <br> The data files are named according to our labelling of the simulations in Table 2.<br> <br> The file columns are:<br> 1. time post-bounce<br> 2. h_{+} * D [cm] (plus polarised strain assuming the observer is located at the equator) The notebook generate plots of the gravitational wave signal for all our model runs. EDIT: This data has been corrected from an earlier version which had overestimated the GW amplitude by 25 %. <br> We have also included tables for the EOS and neutrino opacities. <br> The kindest regards, <br> Oliver, Shuai, André, Aurore, Sean, & Evan.<br>
DOI: 10.5257/iea/co2/2021
title: Greenhouse Gas Emissions from Energy (2021 Edition)

description: In recognition of the fundamental importance of understanding energy-related environmental issues, the IEA Greenhouse Gas Emissions from Energy provides a full analysis of emissions stemming from energy use. This annual publication has become an essential tool for analysts and policy makers in many international fora. The data in this dataset are designed to assist in understanding the evolution of the emissions of Greenhouse Gases from 1971 for countries and regions by sector and by fuel. Emissions were calculated using IEA energy databases and the default methods and emission factors from the 2006 IPCC Guidelines for National Greenhouse Gas Inventories.
DOI: 10.6084/m9.figshare.13157885.v1
title: Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers

description: South African native chicken breeds are no exception to the declining of local domestic breeds that has long been recognised and found associated with the commercialisation of breeding in domestic animals. The aims of the study were: (i) to provide a comprehensive view of genetic variation in four KwaZulu-Natal indigenous chicken populations (Jozini, Newcastle, Pietermaritzburg, and Port Shepstone), and (ii) to estimate the extent of differentiation of the village populations from three conserved South African indigenous pure breeds (Potchefstroom koekoek, Ovambo, and Venda) by genotyping individuals at 19 autosomal microsatellite loci. Finally, (iii) new information to the history of KwaZulu-Natal indigenous chicken populations was made available by exploring their phylogenetic relationship and their possible maternal origin through the mitochondrial DNA. The results suggested noticeable genetic diversity within and between ecotypes with clear sub-structuring between them. The indigenous populations had high genetic diversity (observed heterozygosity ranging from 0.61 in Pietermaritzburg to 0.70 in Jozini) while conserved populations showed considerable within population inbreeding coefficient (from 0.01 in Potchefstroom koekoek to 0.18 in Ovambo). Median-joining network analyses indicated the dominance of haplogroup E suggesting a likely Southeast Asia and/or Indian subcontinent origin. The presence of haplogroup B and C not only emphasises multiple maternal origin but also highlights genetic introgression of local chickens with commercial genotypes. These results highlighted the importance of local breeds as a genetic reservoir; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.HighlightsThe genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated.The village populations showed a noticeable genetic variability with clear sub-structuring between them.The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes. The genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated. The village populations showed a noticeable genetic variability with clear sub-structuring between them. The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes.
DOI: 10.6084/m9.figshare.13157885
title: Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers

description: South African native chicken breeds are no exception to the declining of local domestic breeds that has long been recognised and found associated with the commercialisation of breeding in domestic animals. The aims of the study were: (i) to provide a comprehensive view of genetic variation in four KwaZulu-Natal indigenous chicken populations (Jozini, Newcastle, Pietermaritzburg, and Port Shepstone), and (ii) to estimate the extent of differentiation of the village populations from three conserved South African indigenous pure breeds (Potchefstroom koekoek, Ovambo, and Venda) by genotyping individuals at 19 autosomal microsatellite loci. Finally, (iii) new information to the history of KwaZulu-Natal indigenous chicken populations was made available by exploring their phylogenetic relationship and their possible maternal origin through the mitochondrial DNA. The results suggested noticeable genetic diversity within and between ecotypes with clear sub-structuring between them. The indigenous populations had high genetic diversity (observed heterozygosity ranging from 0.61 in Pietermaritzburg to 0.70 in Jozini) while conserved populations showed considerable within population inbreeding coefficient (from 0.01 in Potchefstroom koekoek to 0.18 in Ovambo). Median-joining network analyses indicated the dominance of haplogroup E suggesting a likely Southeast Asia and/or Indian subcontinent origin. The presence of haplogroup B and C not only emphasises multiple maternal origin but also highlights genetic introgression of local chickens with commercial genotypes. These results highlighted the importance of local breeds as a genetic reservoir; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.HighlightsThe genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated.The village populations showed a noticeable genetic variability with clear sub-structuring between them.The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes. The genetic variation and differentiation of KwaZulu-Natal indigenous chicken populations and pure South African chicken breeds is investigated. The village populations showed a noticeable genetic variability with clear sub-structuring between them. The results can be used to improve a sustainable breeding and conservation programs to control possible genetic dilution with commercial genotypes.
DOI: 10.6084/m9.figshare.13242417.v1
title: Observational study on application of a selective dry-cow therapy protocol based on individual somatic cell count thresholds

description: Selective dry cow therapy (SDCT) is one measure suggested to reduce the use of antibiotics on dairy farms. This procedure may have a negative impact on dairy herds, affecting both milk yield and quality. The aim of this observational study was to evaluate the implementation of a SDCT protocol based on the treatment only of cows with SCC at last individual milk test before drying-off &gt;100,000 cells/mL (primiparous cows) or &gt;200,000 cells/mL (pluriparous cows) on udder infection status. We also assessed the association between cow and management factors with the likelihood of cure or of new IMI across the dry period. The study considered 516 dairy cows (2064 quarters), and only 53% of the cows were treated with antibiotics. Before drying-off, 999 quarters (49.1%) were bacteriological negative at two consecutive samples. After calving the negative quarters were 1004 (49.3%). The likelihood of a cure across the dry period was significantly associated with parity, drying-off length and teat sealant application, while the likelihood of new IMI across the dry period was associated to all the risk factors considered (parity, dry period length, teat sealant application, infections status at drying-off and type of long-acting antibiotic applied). The application under field conditions of the proposed SDCT protocol showed to feasible, and to largely reduce the use of antimicrobials at drying-off, with a relatively small impact on cow health.HighlightsFirst observational study in of Italian dairy herds on the application of a selective dry-cow therapy protocol based on SCC.The study showed as a reduction of about 50% in antimicrobial usage at drying off can be achieved.Management and cow factors affect the likelihood of a cure of a new intramammary infection across the dry period. First observational study in of Italian dairy herds on the application of a selective dry-cow therapy protocol based on SCC. The study showed as a reduction of about 50% in antimicrobial usage at drying off can be achieved. Management and cow factors affect the likelihood of a cure of a new intramammary infection across the dry period.
DOI: 10.6084/m9.figshare.11961360.v1
title: Effect of genotype and protein source on performance of Pacific white shrimp (<i>Litopenaeus vannamei</i>)

description: Shrimp farming is supported by fast-growth and high-resistance genotypes. Protein requirement is important for shrimp perfomance. Fishmeal is the main source, but their limited production increase feed formulation costs for aquaculture. This study evaluated the effect of genotype and protein source on performance of two shrimp genotypes. Shrimps with fast-growth (FG) and high-resistance (HR) were randomly assigned to two dietary treatments (animal and vegetal protein) in a 2 × 2 factorial design. A 36-day bioassay was realised in clear-water hyper-intensive system to compare FG and HR performance using three replicate tanks for each genotype and dietary treatment. Each tank was seeded with 10 shrimp with average initial weight of 2.03 ± 0.10 g for FG genotype and 2.07 ± 0.02 g for HR genotype, at a density of 250 shrimp/m<sup>3</sup>. A weekly biometry was realised to monitor the shrimp performance. We observed a significant interaction (<i>p 05) between genotype and diet for shrimp growth performance. Compared with HR shrimp, FG shrimp showed higher growth and better feed efficiency. The maximum weight gain was recorded, FG shrimp was significantly higher than HR shrimp independently of protein source. Diet with different protein source significantly influence the performance of FG shrimp, while in HR shrimp there is no significant difference between dietary treatment. The comparison showed that genotype, diet and their interactions influenced the performance of <i>Litopenaeus vannamei</i>. This research may be useful for improving genetic selection programmes, reducing feed costs for shrimp industry and design-feeding strategies for shrimp genotypes.Highlights</i><i>Litopenaeus vannamei</i> genotypes respond differently to diet.Fishmeal reduction on diet is posible in shrimps with high resistance.Genotype and diet interaction influence shrimp performance. <i>Litopenaeus vannamei</i> genotypes respond differently to diet. Fishmeal reduction on diet is posible in shrimps with high resistance. Genotype and diet interaction influence shrimp performance.
DOI: 10.6084/m9.figshare.13242417
title: Observational study on application of a selective dry-cow therapy protocol based on individual somatic cell count thresholds

description: Selective dry cow therapy (SDCT) is one measure suggested to reduce the use of antibiotics on dairy farms. This procedure may have a negative impact on dairy herds, affecting both milk yield and quality. The aim of this observational study was to evaluate the implementation of a SDCT protocol based on the treatment only of cows with SCC at last individual milk test before drying-off &gt;100,000 cells/mL (primiparous cows) or &gt;200,000 cells/mL (pluriparous cows) on udder infection status. We also assessed the association between cow and management factors with the likelihood of cure or of new IMI across the dry period. The study considered 516 dairy cows (2064 quarters), and only 53% of the cows were treated with antibiotics. Before drying-off, 999 quarters (49.1%) were bacteriological negative at two consecutive samples. After calving the negative quarters were 1004 (49.3%). The likelihood of a cure across the dry period was significantly associated with parity, drying-off length and teat sealant application, while the likelihood of new IMI across the dry period was associated to all the risk factors considered (parity, dry period length, teat sealant application, infections status at drying-off and type of long-acting antibiotic applied). The application under field conditions of the proposed SDCT protocol showed to feasible, and to largely reduce the use of antimicrobials at drying-off, with a relatively small impact on cow health.HighlightsFirst observational study in of Italian dairy herds on the application of a selective dry-cow therapy protocol based on SCC.The study showed as a reduction of about 50% in antimicrobial usage at drying off can be achieved.Management and cow factors affect the likelihood of a cure of a new intramammary infection across the dry period. First observational study in of Italian dairy herds on the application of a selective dry-cow therapy protocol based on SCC. The study showed as a reduction of about 50% in antimicrobial usage at drying off can be achieved. Management and cow factors affect the likelihood of a cure of a new intramammary infection across the dry period.
DOI: 10.6084/m9.figshare.11961360
title: Effect of genotype and protein source on performance of Pacific white shrimp (<i>Litopenaeus vannamei</i>)

description: Shrimp farming is supported by fast-growth and high-resistance genotypes. Protein requirement is important for shrimp perfomance. Fishmeal is the main source, but their limited production increase feed formulation costs for aquaculture. This study evaluated the effect of genotype and protein source on performance of two shrimp genotypes. Shrimps with fast-growth (FG) and high-resistance (HR) were randomly assigned to two dietary treatments (animal and vegetal protein) in a 2 × 2 factorial design. A 36-day bioassay was realised in clear-water hyper-intensive system to compare FG and HR performance using three replicate tanks for each genotype and dietary treatment. Each tank was seeded with 10 shrimp with average initial weight of 2.03 ± 0.10 g for FG genotype and 2.07 ± 0.02 g for HR genotype, at a density of 250 shrimp/m<sup>3</sup>. A weekly biometry was realised to monitor the shrimp performance. We observed a significant interaction (<i>p 05) between genotype and diet for shrimp growth performance. Compared with HR shrimp, FG shrimp showed higher growth and better feed efficiency. The maximum weight gain was recorded, FG shrimp was significantly higher than HR shrimp independently of protein source. Diet with different protein source significantly influence the performance of FG shrimp, while in HR shrimp there is no significant difference between dietary treatment. The comparison showed that genotype, diet and their interactions influenced the performance of <i>Litopenaeus vannamei</i>. This research may be useful for improving genetic selection programmes, reducing feed costs for shrimp industry and design-feeding strategies for shrimp genotypes.Highlights</i><i>Litopenaeus vannamei</i> genotypes respond differently to diet.Fishmeal reduction on diet is posible in shrimps with high resistance.Genotype and diet interaction influence shrimp performance. <i>Litopenaeus vannamei</i> genotypes respond differently to diet. Fishmeal reduction on diet is posible in shrimps with high resistance. Genotype and diet interaction influence shrimp performance.