Miracle-dz/UniFAR-FTUs huggingface dataset:
INITIATION OF SELECTION IN SENTUL NATIVE CHICKEN: TEN WEEKS GROWTH RATE

Sentul chicken is one of native chicken breeds in Indonesia, which is originally raised by villagers in Ciamis district, West Jawa Province. Sentul chicken has specific grey plumage and medium fighting cock posture. The initiation of study on improving productivity of indigenous chicken in Indonesia, especially for growth rate has been carried out using 54 roosters and 164 hens of Sentul chicken (P 0). First selection (G0) was conducted using selection criteria of the highest 10 weeks bodyweight of male chicken, so it resulted in 16 G0 roosters and 64 G0 hens were mated artificially. Ten roosters and 20 hens randomly selected to be used as control population (C0). The fertile eggs of G0 and C0 were incubated in IRIAP facilities. The offspring (SF1 and CF1) were raised in colony cages placed inside the brooder building provided with heating lamps. Feed and drinking water were provided ad libitum. Results showed that the 10 weeks old male and female SF1 reached 1154 ± 170 g/bird and 953 ± 175 g/bird, respectively. Whilst the male and female CF1 were 1054 ± 141 g/bird and 936 ± 150 g/bird respectively. Ten weeks food consumption of SF1 was 2602 ± 383 g/bird with feed conversion ratio (FCR) of 2.565 ± 0.364. The 10 weeks food consumption of CF1 was 2649 ± 434 g/bird with FCR of 2.767 ± 0.410. The results showed that there was an increase in bodyweight of the offspring both selected and control population. Carcass and carcass cuts are also discussed.
Comparison and Characterisation of Mutation Calling from Whole Exome and RNA Sequencing Data for Liver and Muscle Tissue in Lactating Holstein Cows Divergent for Fertility

Whole exome sequencing has had low uptake in livestock species, despite allowing accurate analysis of single nucleotide variant (SNV) mutations. Transcriptomic data in the form of RNA sequencing has been generated for many livestock species and also represents a source of mutational information. However, there is little information on the accuracy of using this data for the identification of SNVs. We generated a bovine exome capture design and used it to sequence and call mutations from a lactating dairy cow model genetically divergent for fertility (Fert+, n=8; Fert-, n=8). We compared mutations called from liver and muscle transcriptomes from the same animals. Our exome capture demonstrated 99.1% coverage of the exome design of 56.7MB, whereas transcriptomes covered 55 and 46.5% of the exome, or 24.4 and 20.7MB, in liver and muscle respectively after filtering. We found that specificity of SNVs in the transcriptome data is approximately 75% following basic hard-filtering, and could be increased to above 80% by increasing the minimum threshold of reads covering SNVs, but this effect was negated in more highly covered SNVs. RNA-DNA differences, SNVs found in transcriptome but not exome, were discovered and shown to have significantly increased levels of transition mutations in both tissues. Functional annotation of non-synonymous SNVs specific to the high and low fertility phenotypes identified immune response-related genes, supporting previous work that has identified differential expression in the same genes. Publically available RNAseq data may be analysed in a similar way to further increase the utility of this resource. Summary The exome and transcriptome both relate to the same protein-coding regions of the genome. There has been sparse research on characterising mutations in RNA and DNA within the same individuals. Here we characterise the similarities in our Holstein dairy cow animal model. We offer practical and biological results indicating that RNA sequencing is a useful proxy of exome sequencing, itself shown to be applicable to this livestock species using a previously untested commercial application. This potentially unlocks public RNA sequencing data for further analysis, also indicating that RNA-DNA differences may associate with transcriptomic divergence.
Climate-sensitive radial increment model of Norway spruce in Tyrol based on a distributed lag model with penalized splines for year-ring time series

A novel methodological framework is presented for climate-sensitive modeling of annual radial stem increment using year-ring width time series. The approach is based on a generalized additive model with penalized regression splines together with a distributed time lag model taking into account smooth nonlinear effects of a series of monthly temperature and precipitation values, as well as their interactions. Climate effects are also assumed to vary smoothly with time lag. The model framework enables both the detrending of the individual time series and the regression modeling to be performed simultaneously in a single model step. The approach is applied to year-ring width time series of Norway spruce (Picea abies (L.) H. Karst. ) trees in Tyrol, Austria. The marginal response curves show that tree growth is mainly promoted by high temperatures in late spring and early summer and by precipitation in fall and winter. Summer drought does not have a negative influence on the current year’s radial increment; however, when it is associated with high temperatures, it lowers the increment in the subsequent growth period. Higher winter precipitation in conjunction with lower temperatures has a positive effect. A significant non-climate related long-term growth trend is demonstrated, probably reflecting NOx and SO2 emission trends in Austria.
Nanomechanics of graphene

Abstract The super-high strength of single-layer graphene has attracted great interest. In practice, defects resulting from thermodynamics or introduced by fabrication, naturally or artificially, play a pivotal role in the mechanical behaviors of graphene. More importantly, high strength is just one aspect of the magnificent mechanical properties of graphene: its atomic-thin geometry not only leads to ultra-low bending rigidity, but also brings in many other unique properties of graphene in terms of mechanics in contrast to other carbon allotropes, including fullerenes and carbon nanotubes. The out-of-plane deformation is of a ‘soft’ nature, which gives rise to rich morphology and is crucial for morphology control. In this review article, we aim to summarize current theoretical advances in describing the mechanics of defects in graphene and the theory to capture the out-of-plane deformation. The structure–mechanical property relationship in graphene, in terms of its elasticity, strength, bending and wrinkling, with or without the influence of imperfections, is presented.
Caractérisation du mécanisme de transport nucléo-cytoplasmique de la protéine P25 et mise en évidence d'interactions entre les protéines de mouvement du virus des nervures jaunes et nécrotiques de la betterave

Le BNYVV est responsable de la rhizomanie de la betterave sucriere. Son genome est consitue de 4 a 5 RNA de polarite positive. Les resultats decrits dans ce memoire concernent, d'une part, l'etude du transport nucleo-cytoplasmique de la proteine P25 codee par le RNA3 ainsi que son influence sur la symptomatologie, et d'autre part, la localisation subcellulaire et l'etude des interactions entre les trois proteines virales impliquees dans le mouvement a courte distance du virus. Des etudes anterieures ont montre que la P25 est responsable des symptomes typiques de la rhizomanie. Grâce a des observations en microscopie confocale, j'ai montre que la P25 fusionnee a la GFP, se localise dans le cytoplasme et dans le noyau des cellules infectees. J'ai mis alors en evidence sur la P25, un signal de localisation nucleaire (NLS) ainsi qu'un signal d'exportation nucleaire (NEMS). Le transport de la P25 du cytoplasme vers le noyau fait intervenir une interaction directe entre la sequence NLS et l'importine a. L'exportation nucleaire, quant a elle, se fait grâce a la sequence NEMS par la voie des Exportines1. Des experiences de mutagenese dirigee sur des sites potentiels de phosphorylation semblent montrer que la regulation du transport nucleo-cytoplasmique fait intervenir des proteines kinases. Des etudes sur la symptomatologie foliaire et la localisation subcellulaire des P25, sauvage ou mutees, exprimees en contexte viral, montrent que les formes mutees de la P25, incapables de transiter dans le noyau, n'induisent plus les symptomes associes a l'expression de la P25. Enfin, des experiences de "simple hybride" ont revele que la P25 etait capable d'activer la transcription de genes rapporteurs de levure. L'ensemble de ces resultats, nous laisse penser que la P25, qui contient en outre un motif " doigt a zinc " et un domaine C-terminal acide, pourrait moduler la transcription de genes cellulaires, ce qui expliquerait les symptomes caracteristiques de la rhizomanie. Dans une deuxieme partie, j'ai montre, par microscopie electronique que les proteines de mouvement TGBp1 et TGBp2 colocalisaient au niveau des plasmodesmes de cellules infectees par le BNYVV. L'existence d'interactions entre ces deux proteines a ete confirmee par des experiences de farwestern et de co-immunoprecipitation.
The Stone Age Plague: 1000 years of Persistence in Eurasia

Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis caused some form of disease in humans prior to the first historically documented pandemic. Here, we present six new Y. pestis genomes spanning from the European Late Neolithic to the Bronze Age (LNBA) dating from 4,800 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe people, persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in parallel with subsequent human population movements.
12 Mating and Sporulation in Schizosaccharomyces pombe

I. INTRODUCTION Haploid cells of the fission yeast Schizosaccharomyces pombe display one of the two mating types denoted as h + (or P) and h − (or M). Homothallic strains, denoted as h 90 , change their mating type during proliferation (for review, see Klar, these volumes), whereas heterothallic strains are fixed as either h + or h − . S. pombe cells are most stable in the haploid state and are essentially asexual as long as they are well fed. They initiate sexual development only under starvation conditions. Thus, unlike Saccharomyces cerevisiae , homothallic S. pombe cells keep growing as haploids and do not undergo conjugation in rich medium. When starved for nutrients, especially for nitrogen, haploid cells mate to form zygotes, which then undergo meiosis and generate haploid spores (zygotic ascospores). Zygotes can grow as diploids if they are transferred to rich medium immediately after conjugation. However, these diploid cells undergo meiosis and form spores (azygotic ascospores) at the end of vegetative growth. The absence of glucose is not mandatory for mating and meiosis in S. pombe , but these events proceed more efficiently if the concentration of glucose in the medium is lowered. Nitrogen starvation induces expression of genes essential for sexual development, which results in the enhanced production of mating pheromones and their receptors. Cells are then able to recognize the pheromone secreted by cells of the opposite mating type, and h + and h − cells elongate conjugation tubes toward each other. The cells agglutinate in pairs at the tips of these tubes, fuse, and then.
The Impact of the Splanchnic Bed on the Dietary Requirements of Threonine and Lysine in Humans

The splanchnic bed is a group of organs (liver, intestines, stomach, pancreas and spleen) which are active in the metabolism of amino acids. However, the impact of this group of organs on the dietary requirements of humans has yet to be determined. The focus of this research will be the requirements of two indispensable amino acids, threonine and lysine, and the impact of the splanchnic bed on amino acid kinetics. Threonine is an indispensable amino acid which is critical in the production of mucins in the gut and contributes significantly to collagen, elastin and tooth enamel formation in mammals. The first study was designed to determine the threonine requirement for the parenterally-fed, stable, post-surgical neonate. The mean threonine parenteral requirement, as experimentally derived in human neonates, was 32.8 mg·kg -1 ·d -1 which was less than the recommended enteral intake of 76 mg·kg -1 ·d -1 suggesting a splanchnic uptake in humans of 57%.
HIV and schistosomiasis : studies in Tanzania

Schistosomiasis is a helminthic worm infection that affects 260 million people worldwide, 90% of whom live in sub-Saharan Africa. In Tanzania, where the research in this thesis was conducted, two species of schistosomes are highly endemic (Schistosoma haematobium and S. mansoni), with more than 50% of adults infected with one or both schistosome species in many regions. In and of itself, schistosomiasis causes significant morbidity and mortality, with an estimated 200,000 deaths annually and 3.31 million disability-adjusted life-years. The possibility that it additionally impacts HIV transmission and disease progression render treatment and control of this neglected tropical disease even more urgent. This thesis focuses on HIV prevention and disease management in sub-Saharan Africa. It will first describe population-based epidemiological work in Tanzania associating HIV with S. haematobium and with S. mansoni. Subsequent chapters focus on treatment of S. haematobium infection in women, where it causes genital tract disease, and on the effects of schistosome infection on immunological response to treatment in people living with HIV infection. The final chapter focuses on implementation science work with high potential to improve HIV prevention and early diagnosis in Tanzania.
Grand Challenges in the Management and Conservation of North American Inland Fishes and Fisheries

Even with long-standing management and extensive science support, North American inland fish and fisheries still face many conservation and management challenges. We used a grand challenges approach to identify critical roadblocks that if removed would help solve important problems in the management and long-term conservation of North American inland fish and fisheries. We identified seven grand challenges within three themes (valuation, governance, and externalities) and 34 research needs and management actions. The major themes identified are to (1) raise awareness of diverse values associated with inland fish and fisheries, (2) govern inland fish and fisheries to satisfy multiple use and conservation objectives, and (3) ensure productive inland fisheries given nonfishing sector externalities. Addressing these grand challenges will help the broader community understand the diverse values of inland fish and fisheries, promote open forums for engagement of diverse stakeholders in fisheries management, and.
Large changes in the avifauna in an extant hotspot of farmland biodiversity in the Alps

Summary Large declines of farmland bird species have been observed in the lowlands of Western Europe, whereas important populations of some of these species have survived in parts of Eastern and Southern Europe and in small areas within Western Europe, e.g. in parts of the Alps. However, such extant hotspots of farmland biodiversity are at risk: The economic and technical developments threaten to erode biodiversity in existing hotspots, potentially repeating the collapse previously observed in Western Europe. We here present changes in the abundance of farmland birds in the Engadin in the Swiss Alps. Farmland birds such as Whinchat Saxicola rubetra and Skylark Alauda arvensis were still numerous in 1987/1988 when we first censused the area. During our second census period in 2009/2010, we noticed strong declines of such open country species, while several hedge and tree breeders as well as some species preferring warmer climate increased. We observed a good correlation between the change in the vegetation and in the birds. Both these changes were especially pronounced in areas with a recent agricultural improvement project. Thus, we believe that the change in farmland practices, which affected our mountainous study area much later than the lowlands, and possibly climate change, have led to a profound change in the regional avifauna. Using our data as a case study, we argue that similar, and similarly fast, changes may be on-going or imminent in many other areas with extant important populations of farmland species such as Whinchat and Skylark. Thus, our data add to the repeatedly declared urgency to adjust the advancement of agricultural subsidy systems to better accommodate biodiversity considerations, both in depauperated areas as well as in extant hotspots.
Pollen analysis and interaction networks of floral visitor bees of Eugenia uniflora L. (Myrtaceae), in Atlantic Forest areas in southern Brazil

Studies performed using interaction networks have helped in the understanding of mutualistic relation- ships, allowing for the representation of complex community structure. Conservation of the species that form the networks is a prerequisite for the conservation of the very networks. Pollen analysis allows knowledge of bee visitation history and is a complementary tool in studying interactions between bees and flowers. This research had as its aim the mapping of interactions between Eugenia uni- flora flowers and floral visitor bees and with palynological studies also know the other plants that interact to form the network. Twenty-nine bee species were found with pollen load and 20 pollen types, and E. uniflora was the only plant that interacted with all bee species. Studied networks are nested, revealing stability for the community of bees and plants. E. uniflora flowers are an important source of resources to visiting bees, and this plant native to the Atlantic Forest is contributing to the stability of biodiver- sity of the bees in these areas.
Migratory bird protection, a crack in the armor: the case of the Double-crested Cormorant

INTRODUCTION The year 2016 marks the centennial of the convention between the United States and Great Britain (for Canada) for the Protection of Migratory Birds. Signed on 16 August 1916, this historic convention originated out of the need to protect birds from a long tradition of overuse and destruction. In Canada the Migratory Birds Convention Act, 1994 (MBCA) was passed in 1917, while in the United States the Migratory Bird Treaty Act (MBTA) was passed in 1918. These acts resulted in the implementation of the convention in each country and provided protection under the law to migratory birds, their nests, and eggs. This protection represents a milestone in bird conservation efforts. To celebrate the centennial, increase awareness of migratory birds, and prepare for the next century of migratory bird conservation, the U.S. Fish and Wildlife Service (USFWS) is planning multiple activities that will occur throughout 2015-2016 (http://www.fws. gov/birds/MBTreaty100/). Environment Canada has not yet announced plans for centennial celebrations, but presumably will also undertake activities to celebrate this event.
Evaluation of antibacterial activity of some medicinal plants against Isolated Escherichia coli from diseased laying hens

Plant extracts and their phytochemicals with antibacterial properties can be influential on infection treatment. In the present study, inhibitory activity of aqueous and ethanol 90% extracts of Zataria multiflora, Thymus vulgaris, Mentha pulegium, Mentha piperita, Ocimum basilicum, Cassia senna, and Carthamus tinctorius on the growth of Escherichia coli isolated from diseased chickens were tested in vitro using disk diffusion method. Inhibition zone diameters of bacterium were calculated in the presence of the plants extract. All the ethanol 90% extracts with concentration of 0.2-1.0 mg/mL effectively inhibited the growth of the bacterium, while aqueous extracts showed no activity against E. coli. Inhibition zone diameters (IZD) of the bacteria treated with different concentrations of ethanol 90% extracts of the plants raging between 14.6-41.0 mm. Zataria multiflora and M. pulegium with concentration of 1.0 mg/mL exhibited highest antibacterial activity compared with other plants with IZDs of 41.0 ± 0.0 and 39.0 ± 0.0 mm, respectively. According to the results, the order of inhibitory effect of plants extract with concentration of 1.0 mg/mL against E. coli was Z. multiflora> M. pulegium> T. vulgaris> M. piperita> C. angustifolia> C. tinctorius> O. basilicum. Our findings revealed that the tested plants could be considered as suitable source of phytochemicals for prevention of E. coli growth. The extracts of the examined plants are suitable supplementary alternative for control of E. coli in laying hens.
Marker assisted selection of rice (Oryza sativa L.) genotypes for bacterial leaf blight disease resistance

Majority of the cultivated rice ( Oryza sativa L.) varieties are susceptible to Bacterial Leaf Blight disease (BLB), caused by Xanthomonas oryzae pv. Oryzae . Since effective chemical and biological methods are not available, the preferred strategy for disease management is through varietal resistance. To develop BLB resistant varieties, identifying resistance genes in the available germplasm is an urgent need. Molecular characterisation using microsatellite markers is a powerful tool for screening germplasm for resistance gene. Among the various resistance genes, Xa5 is an important recessive bacterial blight resistant gene, which is effective and important in Asian rice breeding programmes. Hence main objective of the present study was marker assisted selection of rice germplasm accessions for Xa5 gene , using RM122, a closely linked microsatellite marker. Forty traditional rice genotypes from the germplasm of Division of Plant Breeding and Genetics, Regional Agricultural Research Station, Pattambi, were initially screened in field for BLB resistance. Out of them, only twenty genotypes which had either no or less symptoms of BLB disease, were utilized for marker assisted selection. The PCR products were subjected to gel Agarose electrophoresis (1.5%). Among the thirteen genotypes which displayed marker specific bands during gel electrophoresis, five genotypes viz . , Karuthakuruka, Kuruva, Kokkankoli, Kochuvithu (Thamarakulam) and Punjaparathu had no symptoms of BLB, indicating that BLB resistance in these genotypes is due to the gene Xa5 . Hence these five resistant genotypes can be utilised as donors for Marker Assisted Breeding, to develop BLB resistant rice varieties.