Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Developments in the Conquest Code;Accurate and Efficient Molecular Dynamics

More and more developments and use of first-principles molecular dynamics (FPMD) simulations have been of particular note. Its applictaions to complex and massive systems are anticipated to increase in the near future whereas its inherent tremendous computational costs and memory requirement become grit in the gears of its application properties. In order to overcome those difficulties, we have developed a linear-scaling DFT code Conquest and implemented an efficient and accurate Born-Oppenheimer dynamics. The main part of the thesis introduces its algorithm with the aid of the extended-Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) technique and demonstrates that we can now put into practice a stable, accurate and efficient FPMD on massive systems. We also deal with implementations of the partial core correction and DFT-D2 scheme. The former method is necessary when the core and valence charge density overlap in the same magnitude. The latter takes account of dispersions in an empirical manner. This effect is considered very important in applications to, such as, large biological systems. This thesis is organised by nine chapters. First, we give some fundamental mathematical tools to understand the kernel algorithms in the Conquest code (Chapter 1). Next, we introduce and derive a basic but very important approximation; BornOppenheimer approximation, which is premised in density functional theory (DFT) (Chapter 2). Then, we present how the Conquest code carries out an electornic structure calculation in detail (Chapter 3). Chapter 4 deals with the partial core correction. There, the energy and force formalisms are given in the case of a non self-consistent (NSC) calculation. In Chapter 5, the DFT-D2 scheme is introduced with an efficient linear-scaling algorithm and some benchmark results are presented. Chapter 6 presents an application of the Conquest code to a large biological system containing an ion channel embedded in lipid membranes. Chapter 7 and 8 handle FPMD in Conquest. In the former, some inherent detriments and their solution methods are outlined with detail algorithms. The latter copes with the methodologies to realise accurate and efficient FPMD, and provides some test results on practical cases. Finally, concluding remarks come last in Chapter 9.
Age determination and body growth of the common duiker Sylvicapra grimmia (Mammalia)

Age determination in the Common duiker Sylvicapra grimmia was investigated by analysis of tooth eruption and replacement sequence, incremental lines of tooth cementum and tooth wear in a unique collection of 48 known-age skulls, and also by analysis by post-natal body growth in known-age duiker. In both the mandible and maxilla, permanent molariform teeth were fully erupted and in wear by 26 months of age. There was little variation in the age of eruption and replacement of all molariform teeth, making this a particularly useful feature of the duiker for age determination purposes. In contrast, the variability in eruption of the incisiforms, coupled with the difficulty in distinguishing deciduous incisiforms from the permanent counterparts, placed an unexpected limitation on the use of these teeth. Although the apparent linear relationship between tooth attrition and age has potential for further investigation as an age determination technique, the cementum annuli were not correlated with chronological age. Theoretical Von Bertalanffy equations were used to analyse body growth with age. It was concluded that because the asymptote of growth was reached at such an early age, and because there is so much individual variation in growth, body growth, including horn growth, is of very limited value for age determination. Female duiker were significantly larger than males.
Colostrum and milk of current and rare cattle breeds: protein content and amino acid composition

The dry matter, crude protein, and amino acid content of colostrum and milk of different dairy cow breeds that were kept under the same conditions were determined. There were not notable differences between breeds regarding the dry matter, crude protein, and amino acid content of colostrum samples obtained on the first, third, and fifth days of lactation. The single exception was the third-day-colostrum from Holstein-Friesian that contained more of these compounds than the other breeds. The amino acid composition of protein from the colostrum of breeds under investigation was also very similar. The milk samples of Jersey and Swedish red contained the highest amount of dry matter, crude protein, and that of amino acids in the examined lactation period (3-5 months after calving). The ratios of the individual essential amino acids within milk protein did not differ notably among breeds. Based on the Morup-Olesen biological value calculation, among the studied breeds, the amino acid composition of milk proteins from Holstein-Friesian was the most similar to the reference protein in the average of the 3-5 months of lactation.
Studies on mixtures of maize and beans (Phaseolus vulgaris) with particular reference to plant population

SUMMARY Two experiments are described in which the possible yield benefits of mixing maize and beans were examined under intensive farming conditions. A ‘replacement series’ of pure maize, two-thirds maize/one-third beans, one-third maize/two-thirds beans and pure beans was used at four plant populations. A high level of nitrogen was applied on the maize to eliminate the effects of nitrogen transfer from the beans. Yields of the mixtures were up to 38% higher than could be achieved by growing the crops separately. It is concluded that this occurred because the mixtures achieved a greater utilization of environmental resources; it is suggested that, because of the marked height differences of the two crops, an increased utilization of light was probably a major contributing factor. The need for high populations in mixtures is indicated, partly because the largest yield increases were achieved at high populations and partly because the mixtures required a higher population pressure to produce their maximum yield. The maize was found to have the higher relative competitive ability, and this increased with increase in plant population pressure. It is suggested that this was probably due to the shading effect which the maize had on the beans. The effects of a change in relative competitive abilities, or in relative selling prices, on the optimum proportion of two species in a mixture are also considered.
The Impacts of Biotechnology on Biodiversity in Global Health: a Case Study on Avian Influenza in Bangladesh

Biodiversity is the variability of between genetics, species, or ecosystems of living organisms within a specific region. Biodiversity is essential for sustaining healthy living networks and systems because it allows for a variety of food sources, medicine, and biological control, while also playing a significant role in atmospheric regulation, nutrient cycling, and pollination. Loss of biodiversity and ecosystem change increases the risk of the emergence or spreading of infectious diseases and global pandemics such as the Avian Influenza (AI H5N1). Biotechnology is one solution for reducing, and ultimately eliminating, the transmission of avian influenza. Traditional methods of treating infected animals, such as common vaccines, are temporary solutions that have no effect on the biodiversity of an ecosystem. Methods in animal biotechnology such as artificial insemination, embryo transfer, and in vitro fertilization have led to developments of cheaper, safer, and more effective vaccines. Livestock that have been treated for H5N1, as well as those that are healthy and have never been infected have proven to increase the diversity, leading to the elimination of specific issues. Similar effects are attainable if these animal biotechnology methods were to be used on poultry infected with the avian influenza virus.
Helicobacter pylori: Associação com o câncer gástrico e novas descobertas sobre os fatores de virulência

Objetivo: Realizar uma revisao bibliografica sobre a acao da bacteria Helicobacter pylori nas alteracoes gastrointestinais visando a entender o papel dos chamados “fatores de virulencia”, assim como estudar a associacao do H. pylori com doencas gastrointestinais e os mecanismos imunologicos desencadeados pela presenca desta bacteria. Metodo: Foram selecionados os trabalhos publicados em revistas indexadas nas bases de dados MedLine e PubMed, sob os unitermos “H. pylori”, “gastrite”, “câncer”, “resposta imune”, “Cag A” e “VacA” com maior enfase nos artigos publicados nos ultimos 5 anos. Resultado: Trinta e dois artigos foram selecionados, todos de revistas estrangeiras, sendo um dos trabalhos desenvolvido por grupo de cientistas brasileiros. Os artigos selecionados mostraram o amplo espectro de acao da H. pylori atraves de seus “fatores de virulencia” tais como a vacuolizacao de celulas infectadas provocada pela proteina VacA e a adesao da bacteria as celulas atraves da atividade das adesinas e proteinas de membrana. Tambem foram descritas as interacoes da H. pylori com doencas gastrointestinais e com o sistema endocrino assim como as peculiaridades da resposta imunologica humoral e celular contra esta bacteria. Conclusoes: Fica clara a importância epidemiologica da H. pylori por sua evidente associacao com o câncer gastrico e o importante papel desempenhado pelos fatores de virulencia codificados pela bacteria.
The effect of time from hatch on the yolk conversion efficiency of rainbow trout, Salmo gairdneri

The growth and development of rainbow trout, Salmo gairdneri, from hatch to first feeding depends upon the nutrients stored in the yolk sac. The efficiency (E) with which yolk can be converted to larval biomass is a useful measurement in chronic toxicity tests, and it can be simply estimated by comparing the gain in larval weight (L) to the loss in yolk weight (Y) at hatch (time 0) and at any time t after hatch: E=(L1−L0)/(Y0−Y1); E may be calculated on a wet or dry weight basis. Although the rates of weight change were constant for the first 15 days after hatch at 10.5° C, E was not. E increased from near 0 and approached a value of 2.1 on a wet weight basis or 0.70 on a dry weight basis after 5–8 days. The variability of E was also very high shortly after hatch, but declined and stabilized within 5–9 days. For toxicity testing, we recommend that E be measured 10–15 days post-hatch to ensure precision with a minimum bias due to dissection error.
Use of Paper-mill Wastes on Agricultural Soils: Is This a Way to Reduce Nitrate Leaching?

The term paper-mill waste is used for different products: de-inked fiber sludge, primary fiber sludge, secondary sludge and mixtures. The aim of this study was to find out if any of these materials can be safely used on agricultural soils to induce net N immobilization of N, and thereby decrease nitrate (NO 3 ) leaching. Chemical characterization showed that secondary sludge derived from biological waste water treatment was a nutrient-rich material low in fiber content, whereas primary and de-inked fiber sludge were high in fiber content and low in nutrient content. Cellulose-C and hemi-cellulose-C amounted to 46% and 36% of the organic C present, respectively, and C/N ratios were around 130 in primary and de-inked fiber sludge. Incubation studies at 8°C over 2 months showed that the decomposability of primary and de-inked fiber sludge in soil was not significantly different. Both showed lower decomposability than secondary sludge. Concentrations of inorganic N in soil declined to very low levels after application of primary and deinked fiber sludge and their capacity for net N immobilization was 4.8-7.2 kg N t - 1 C added at 5°C. However, contents of Cu, Cd and polycyclic aromatic hydrocarbons in de-inked fiber sludge limit its use on arable land. Only primary fiber sludge was found to be suitable as a introgen catch fiber material for use on agricultural soils.
Fourteen years of population fluctuations of Microtus ochrogaster and M. pennsylvanicus in east central Illinois

Population densities of Microtus ochrogaster and M. pennsylvanicus were monitored from 1972 to 1986 in three habitats: alfalfa, bluegrass, and tallgrass prairie. Microtus ochrogaster displayed two apparent multiannual population cycles in alfalfa and bluegrass from 1972 to 1976; thereafter only annual (alfalfa) or erratic (bluegrass) fluctuations were apparent. Except for extremely high densities during 1984–1985, population fluctuations of M. ochrogaster in tallgrass were erratically low and there was no evidence of multiannual cycles. During 15 of 29 changes in population density of M. ochrogaster, the amplitude of fluctuations was more than 10-fold; 14 of these changes were preceded by marked population declines or very low densities the previous winter and spring. Microtus pennsylvanicus displayed annual fluctuations in abundance in alfalfa and bluegrass and was erratically high at all times in tallgrass. Only 7 of 32 population fluctuations of M. pennsylvanicus had amplitudes of at least 10-fold; in .
Fishes of North America Endangered, Threatened, or of Special Concern: 1989

Abstract The American Fisheries Society herein provides an update of their now decade-old list of rare North American fishes. The 1989 list adds 139 new taxa to the list developed by Deacon et al. (1979) of 251 fishes and removes 26 for a total of 364 fishes in Canada, United States, and Mexico that warrant protection because of their rarity. The 26 taxa removed from the 1979 list include 16 removed because of better information on their taxonomy or status and 10 because they have become extinct. Not a single fish warranted removal from the list because of successful recovery efforts. In addition, 49 fishes have changed in status but remain on the list: 7 have improved in status, 24 have declined, and 18 have been reclassified because new information revealed that they were either more common or rarer than was earlier believed and, therefore, were incorrectly classified in 1979. Comparison of the 1979 and 1989 lists indicates that recovery efforts have been locally effective for some species, but are clea.
Nitrification: A Significant Cause of Oxygen Depletion Under Winter Ice

Changes in concentrations of ammonium, nitrite, nitrate, and oxygen suggested the occurrence of significant nitrification throughout the water column of mesotrophic Lake St. George, Ontario, during the winter months from 1976 to 1984. The existence of nitrapyrin- and acetylene-sensitive 14C-bicarbonate incorporation confirmed that bacterial nitrification occurred. During late January to early March (water temperature 2–3 °C), nitrification occurred at an average rate of about 13 μg N∙L−1∙d−1 for the years studied. Numbers of detectable nitrifying bacteria appeared too low (by 2 to 4 orders of magnitude) to account for the observed activity. The nitrification activity observed would result in average oxygen consumption amounting to 71% of the observed oxygen depletion. This shows that winter nitrification can be an important factor in promoting oxygen depletion and possibly winter-kill of fish.
Reserve site selection for data‐poor invertebrate fisheries using patch scale and dispersal dynamics: a case study of sea cucumber (Cucumaria frondosa)

Globally, management decisions for recently established invertebrate fisheries are based on limited information. The negative consequences are being realized as now at least one-third of invertebrate fisheries are over-exploited, collapsed or closed. Management of a fishery should be based on abundance and productivity data. This information is often unavailable but in some jurisdictions, spatial distributions are known. A methodology for designating a network of reserves for sedentary invertebrates, using sea cucumber (Cucumaria frondosa) on the Scotian Shelf, Canada is proposed, as a case study. It is assumed that there is a positive relationship between spawner density and per capita population growth rate in sedentary broadcast spawners and that fertilization success declines rapidly at low densities. Protection of high-density habitat would safeguard critical spawner density, especially when the critical density is unknown. Using spatial distribution, a method to identify size and location of reserves designed to protect high-density habitat was developed. First, geographically distinct regional-scale clusters are identified. Within clusters, the characteristic patch scale was determined through spatial autocorrelation analysis. The size of reserves can be set as 50% of each high-density patch based on an appropriate risk-averse approach. The allocation of reserve size and location is not dependent on results of a numerical circulation model. However, the analysis was refined by using one to predict larval drift patterns, and connectivity among patches. Reserve boxes were then designated to safeguard from 30 to 65% of each high-density patch. Marine reserves do not work if inappropriately sited. In the absence of any other information, it is argued that siting reserves on high-density areas is an essential and appropriate approach to data-poor invertebrate fisheries management. A high percentage of each high-density patch could serve as risk-averse ‘spatial management’ reference points, and could be modified once replenishment rates are known. Copyright © Her Majesty the Queen in Right of Canada 2013
Application of aggregate genotype in beef cattle breeding

Abstract When developing total merit indices (TMI's), estimated breeding values (EBV's) may be lacking for several traits. Methodology exists to address these challenges, calculating index weights using economic values and genetic (co)variances between traits included in the TMI and aggregate genotype. TMI's including production and functional traits were developed for beef breeds in the Norwegian breeding scheme, and potential for genetic gain was evaluated. Selection based on the TMI developed in this study was found to improve growth and carcass quality, while genetic deterioration was expected for calving difficulty. Alternative selection indices were applied to avoid these effects, but reduced the genetic gain for production traits. The results of our study show that is possible to achieve genetic gain in most economically important traits for beef cattle by using a TMI. When additional EBV's and genetic correlations become available, these should be included into the TMI for further improvement.
Comparative study of the internal conformation of the posdiaphragmatic digestive tract in the dog (Canis lupus familiaris) and in the cat (Felis catus).

The present study offers a detailed anatomical description of the macroscopical characteristicsof the internal conformation of the postdiaphragmatic digestive tract in the main pet species - the dog andthe cat. After domestication, the two species, while of common philogenetic origins, have evolved withcertain differences from the point of view of feeding habits in the modern era, to omnivore for dogs andstrict carnivore for cats. This fact reflects itself in the pathology of this segment and in therapeuticnecessities. This aspect justifies the need for better anatomical knowledge of the differences between thetwo species in the digestive segment. Having discussed in a previous article the differences between thesespecies in terms of external shape, features and organ topography, we have turned to the innerconformation of the gastrointestinal tract. Our study focused on species characteristics description,without underlining race particularities. The study was carried out in the Comparative AnatomyLaboratory of the Faculty of Veterinary Medicine of Cluj-Napoca, on five dog bodies and 5 cat bodieslacking digestive pathological modifications. The research used usual dissection techniques, followed bythe isolation, the section and the examination of the gastro-intestinal segment in all subjects. Commontraits of carnivorous species displayed overall by the digestive tract aside, the main internal conformationdifferences between dogs and cats were mainly registered in the stomach. In this segment, the cat displaysa uniform gastric mucosa, while the linen varies in the dog. The duodenum of both species has similarmucosa and two duodenal papillae, but the placement and presence of the papillae differ. The largeintestine of dogs and cats has lesser differences, aside from the disposition of the lining folds of the colon.
Effect of light on sporulation of Plasmopara viticola

Abstract Sporulation of Plasmopara viticola (Berk. et Curt. ex de Bary) Berl. et de Toni on infected grapevine leaves proceeded in a moist atmosphere in darkness but not in light. Sporulation was inhibited by irradiation either with near-u.v. light of 310–400 nm, or with green of 500–560 nm, at intensities of more than 3, or 3.5 Wm−2 respectively.
Discrimination against 15N in three N2-fixing Trifolium species as influenced by Rhizobium strain and plant age

Abstract When estimating N2 fixation with the 15N natural abundance method, the 15N abundance in plants grown with N2 in air as only N source (B), must be known in order to account for discrimination against 15N during N2 fixation. Trifolium hybridum L. , T. pratense L. and T. repens L. were grown without N in the nutrient solution in a greenhouse. The aim was to establish B values in these species in symbioses with Scandinavian Rhizobium genotypes, and to test the hypothesis that B is related to N2 fixation efficiency and plant age. Choice of Rhizobium strain significantly influenced B in shoots of T. hybridum and T. repens, and N content in all Trifolium species. B in shoots was partly correlated to amounts of N2 fixed, while plant age only had a marginal effect. Soil suspension inoculum or single strain inocula gave very similar B in shoots of T. pratense.
Modelagem e Simulação de Offloading para Computação Móvel em Nuvem

Mobile Cloud Computing (MCC) uses cloud services to spread out the energy and computing resources of mobile devices. Despite these devices have grown in use, we observe a lack of models and simulation tools to study and analyse mobile devices resource limitation using cloud computing as solution. In this paper, we model a typical MCC architecture which focuses on an offloading perspective. Our model provides a development environment to validate offloading strategies without using a real cloud infrastructure. To validate our approach, we simulate the execution time of a task on a local (mobile device) and in a remote cloud. Results show that our models represent MCC scenarios with an maximum accuracy of 98.9%. Moreover, we verified the workload algorithm complexity impacts on the offloading decisions. Resumo. Computação Móvel em Nuvem (Mobile Cloud Computing, MCC) utiliza os serviços de nuvens a fim de estender os recursos energéticos e computacionais de dispositivos móveis. Apesar da sua presença em nosso cotidiano, observamos uma carência de modelos e simuladores para análise de problemas relacionados à escassez de recursos dos dispositivos móveis tendo as nuvens computacionais como solução em perspectiva. Neste artigo, propomos a modelagem e simulação de uma arquitetura tı́pica de MCC compreendendo diferentes abordagens para execução de tarefas computacionais em servidores remotos (offloading). A modelagem foi concebida com vistas à provisão de um ambiente controlado para avaliação e ajuste de polı́ticas de offloading sem a necessidade da implantação fı́sica de uma infraestrutura computacional de larga escala. A validação da proposta foi conduzida através de simulações, a partir de experimentos com imagens entre 0.3 e 8 megapixels, e cujos resultados indicam uma acurácia de até 98.9%. Concluı́mos ainda que a ordem de complexidade algorı́tmica da carga é diretamente proporcional à probabilidade de offloading.