Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of viral and host proteins and RNA elements in tombusvirus replication

OF DISSERTATION CHARACTERIZATION OF VIRAL AND HOST PROTEINS AND RNA ELEMENTS IN TOMBUSVIRUS REPLICATION Two thirds of plant viruses are positive-strand RNA viruses including the family Tombusviridae. One of the best-studied members of this family is Tomato bushy stunt virus (TBSV). Like many other viruses, TBSV has much fewer genes when compared to its hosts’ genome. Nevertheless, TBSV utilizes its genome very judiciously. To compensate for a lack of many proteins of its own, it codes for multi-functional replication protein p33 and also co-opts host factors to facilitate its replication. By using recombinant replication proteins p33 and p92 containing single amino acid changes in protein-protein interaction domains (S1 and S2), I demonstrated that the replication proteins are required in sequential steps during virus replication. The in vitro cell-free extract (CFE) based TBSV replication assays revealed that mutations in S1 and S2 domains affected RNA template selection, recruitment and assembly of replicase complex. TBSV replicates on the cytosolic surface of peroxisomal membranes. To identify the host factor involved in this process of transporting viral replication proteins to peroxisome, I tested the peroxisomal transporter proteins for their ability to bind to p33 in vitro, which led to the discovery of Pex19p. Pull-down and co-purification experiments revealed transient nature of p33-Pex19p binding as expected from a transporter. When pex19p was retargeted to mitochondria, a large fraction of p33 was also re-distributed to the mitochondria validating the importance of Pex19p in p33 localization. TBSV also utilizes its genomic RNA for non-template activities during its replication. Accordingly, TBSV RNA serves as a platform for the assembly of replicase complex. To further characterize the regulatory cis-elements involved in this process, I utilized CFE and different TBSV RNA mutants together with recombinant p33 and p92 in vitro replication assays. These experiments revealed the role of RNA recruitment element [RIISL(+)] and 3’ non-coding regions as minimal cis-elements required to assemble functional replicase complex. The experiments also indicated that the RIISL(+) and 3’ non coding regions could be physically separated on two different RNA molecules to assemble TBSV replicase, suggesting insights into viral evolution.
Estimation of optimal laying period by hybrids of Hy-line Brown production.

Bu arastirma, ticari yumurta tavukculugunda optimal uretim suresinin tespit edilmesi amaciyla yapilmistir. Ozel bir ticari isletmede 34900 adet kahverengi hibritlerle (Hy-line Brown) yurutulen arastirma, Aralik 2002-Temmuz 2004 arasinda tamamlanmistir. Uretimin ilk 20 haftasi civciv buyutme, 21-80. haftalar arasi yumurta verim donemi olarak gerceklesmistir. Optimum uretim suresinin tayininde Azalan Marjinal Verimler Kanunu dikkate alinmistir. Yumurta verim doneminde mortalite %8.17; FCR 2.55 kg, yumurta randimani %72, toplam yumurta verimi 302 adet/tavuk ve kirik-catlak yumurta orani %1.70 olarak tespit edilmistir. Bu donemde maliyet unsurlarindan yarka %15.16; yem %58.50; iscilik %1.87; veteriner-saglik %2.31; enerji %2.01; viyol %4.22; genel idare giderleri %1.83; bakim-onarim %1.66; bina-ekipman amortismani %2.78 ve canli demirbas amortismani %9.66 olarak hesaplanmistir. Mali rantabilite -0.01, rantabilite faktoru -0.01 ve masraf hasila orani da 0.96 degerinde bulunmustur. Isletme 40 ile 41. haftalar arasinda kara gecmis (basabas noktasi), 54 ile 55. haftalarda maksimum karliliga ulasmistir. Uretimin bu noktadan sonra surdurulmesi isletmenin bu uretim donemini zararla kapatmasina neden olmustur. Bu nedenle piyasadaki girdi ve urun fiyatlari da dikkate alinarak, uretimin Azalan Marjinal Verimler Kanunu cercevesinde sonlandirilmasi isletme karliligi acisindan oldukca onemlidir
Ruminal variables in steers fed with Tifton 85 (Cynodon spp.) hay with different particle sizes.

The ammonia nitrogen (N-NH 3 ) concentration and the pH were determined with the objective of evaluating the effect of different particle sizes (5, 7, 10mm and whole) of Tifton 85 hay in the diet of Holstein steers, with average live weight of 300kg and age of 20 months. A completely randomized design, with four replicates, in a split-plot arrangement was used. The plots were the experimental treatments (5, 7, 10mm and whole hay) and the subplots were the times of collection (0, 2, 4, 6, 8h). The use of diets including hay with particle sizes of 5mm and whole, did not affect (P>0,05) the ruminal pH; average values were 6.14 and 6.61, respectively. A linear reduction in the ruminal pH was verified in the steers fed on diets constituted by 10mm particles. For the diets including Tifton hay with particle size of 7mm, it was observed a quadratic effect, where the minimum pH (5.39) was observed 8:00 h after the feed was furnished. Concentrations of N-NH 3 were affected by collection time in a quadratic way. Maximum concentrations of N-NH 3 , 15.55, 15.83, 18.32, 12.0 mg/100 mL, were observed at 4:28, 3:58, 2:99 and 2:80h after feeding, for the diets including Tifton 85 hay with 5, 7, 10mm and whole particle sizes, respectively. It was concluded that all diets allowed normal nycterohemeral patterns of fermentation.
Study on reproductive characteristics of Pinus tabulaeformis f. shekannesis populations in Ziwuling region of the Loess Plateau.

【Objective】 The study was done in order to characterize reproduction ecology of Pinus tabulaeformis f.shekannesis populations and to produce some theoretical basis for reasonable exploitation and utilization. 【Method】 Reproductive age,fecundity table and the environmental factors of P.tabulaeformis f.shekannesis populations in different natural habitats,and 12 plots(shade slope,semi-shade slope and semi-sunny slope) located in the better sections of growth and development were investigated through comprehensive investigation in concentrated distribution area of P.tabulaeformis f.shekannesis populations in Ziwuling region of the Loess Plateau. 【Result】(1) The values of Armin,Armax,and Apc of P.tabulaeformis f.shekannesis populations were 18,130,48 and 112 years respectively;The values of Armin and r were cloudy slopesemi-cloudy slopesemi-sunny slope,and the values of Armax and Apc were Semi-sunny slopesemi-cloudy slopecloudy slope;(2) The results showed that 3 populations had potential to produce seeds,and the higher yield occurred in the population located in the shade slope;The most cones appeared on the upper foliage of the tree,and the south and east aspects of the crown;(3) The fecundity table showed that reproductive ability and value took on low → high → low tendency with age increasing,and the booming of cloudy slope and semi-cloudy slope were 50-90 years and the booming of semi-sunny slope was 30-50 years;Furthermore,P.tabulaeformis f.shekannesis population in cloudy slope had the longest life span and the greatest fitness;(4) According to the principal components analysis(PCA) of the main environmental factors,the human disturbance(0.984) and water content of soil(-0.974) were the most important factors. 【Conclusion】 Site conservation and classification management based on different habitats should be carried out in the future for the P.tabulaeformis f.shekannesi.
The fibrolytic potential of domestic and wild herbivores microbial ecosystems on maize stover.

The objectives of this study were to; (i) preserve whole rumen fluid (RF) or faecal fluid (FF) in the laboratory by culturing using very simple laboratory techniques and (ii) study the effect of substituting fresh RF with fresh or laboratory cultured FF as an alternative inoculum source for in vitro dry matter digestibility. Rumen fluid and faeces were collected from two non-lactating fistulated jersey cows (3.5 yr old). Cultured inocula were prepared by incubating RF or FF with salivary buffer, maize stover (MS) and lucerne (1:1) at 39°C for three days. For fresh incubation (FI) or cultured incubation (CI) systems, RF or FF were mixed with salivary buffer containing MS (1g) and incubated at 39°C for 72 h. Apparent degradability (APD), true degradability (TD), total gas produced (GP), total short chain fatty acids (SCFA) and gas kinetic parameters were determined after incubation. Faecal fluid activity was also monitored for 42 d by measuring the GP from fermentation. For enzyme assays crude proteins precipitated by 60% ammonium sulphate from RF or FF were assayed for exocellulase, endocellulase and hemicellulase specific activities (μg reducing sugar/mg crude protein). Exocellulase specific activity was higher (P<0.001) in RF than FF for FI whereas in CI, RF exocellulase specific activity was lower than that of FF. True degradability and GP in both FI and CI systems were higher (P<0.001) in RF than in FF. The rate of MS fermentation (C) did not differ among systems and between incubations. Partitioning factor and degradability efficiency for both RF and FF were similar in FI but differed (P<0.001) in CI. Gas from slowly but degradable fraction of MS was higher (P<0.001) for RF in both FI and CI when compared to FF. Total SCFA was higher (P<0.001) in RF than FF in FI but was lower for RF in CI. Laboratory cultured FF were active (P<0.001) for up to 6 weeks but with better results obtained in week 1. Cultured FF is a better substitute for fresh RF as shown by their percentage differences in exocellulase activity (0.4%) and TD (7%), compared to the differences observed between fresh RF and FF for exocellulase activity (33%) and TD (14%). This study suggests that cultured inocula would reduce the cost of experimentation without compromising the reliability of results.
An overview of ecological and habitat aspects in the genus Fusarium with special emphasis on the soil-borne pathogenic forms.

The genus Fusarium is diverse, widespread and commonly found world-wide. This ubiquitous fungus exists in soils, gross s in and on living and dead plants and plant products, on living and dead animals; its conidia are water-borne, but in some instances may be air-borne and its chlamydospores are typically soil-borne. When a sexual stage exists, the ascospores are air-borne, some spores may be found at rather high altitudes. There are salt-water forms, living in the deep sea, souse in the shells of sea turtles, causing the shells to break up. Some forms have been isolated from within the corneas of diseased eyes of humans and animals, and cited as the cause of a serious problem leading to vision loss. Species of Fusarium vary greatly in growth rates, substrate and optimal climatic preferences, there are those found only in the tropics, while others are the causative agent of snow mold. They contain a wide range of pigments, ranging from light tans and yellows, carmine red, green, bright blue to blue-black, some that are water soluble (quinone-type compounds), others fat soluble (carotinoids) and some that are closely bound to spore walls. Four different kinds of spores are recognized in the genus- macro- and microconidia. chlamydospores and ascospores. Sclerotia of variable sizes can also occur in culture and are brown, some blue black and there even some white ones. Most Fusarium spp. grow well on typical laboratory media and are easy to culture.
Predictores de mortalidad en pacientes con sepsis obstétrica mediante uso de score de sepsis obstétrica y evaluación secuencial de falla orgánica-obstétrica

y SOFA-O (10-18) puntos. una mortalidad de 7.8% (cuatro pacientes) de la población estudiada. La incidencia de sepsis obstétrica se encuentra en aumento, por lo que el reconocimiento rápido de ésta y la terapia adecuada en la supervivencia de la paciente. Palabras clave: Escala SUMMARYObjective: To determine the predictors of mortality in patients with obstetric sepsis using Sepsis Obsessional Score (SOS) and Sequential Organ Failure Assessment-Obstetric (SOFA-O). Material and methods: An observational, retrospective, descriptive study was carried out, where data were collected from patients who entered an intensive care unit of second level hospitals in the period June 30 2015, to June 30 2017, who had a diagnosis of sepsis Obstetric, where SOS and SOFA-O instruments were applied, correlating the variables with maternal mortality. Results: From a universe of 284 patients who entered the ICU of second level hospitals, 51 patients were selected who had inclusion criteria for sepsis, correlating with SOS and SOFA-O scale variables, finding it to be a major risk factor for development of sepsis being multigested, having preeclampsia, anemia, cesarean section, prenatal poor control and having invasive procedures, the quantitative variables related to maternal death were: creatinine, PaO 2 /FiO 2 ratio, heart rate, lactate, venous saturation. With a minimum and maximum SOS score for maternal death (7-22) and SOFA-O (10-18) points. There was a mortality of 7.8% (four patients) of the study population. Conclusions: The incidence of obstetric sepsis is increasing, so rapid recognition and appropriate therapy will impact patient survival.
Variation in male reproductive traits among three bitterling fishes (Acheilognathinae: Cyprinidae) in relation to the mating system

Male traits that correlate with fertilization success include testis size and structure, ejaculate size, ejaculation frequency, and sperm motility. Two hypotheses potentially explain interspecific differences in these traits: sperm competition and sperm limitation. We examined variation in six traits associated with fertilization success in three closely-related species of bitterling fish; the European bitterling (Rhodeus amarus), the Chinese rose bitterling (Rhodeus ocellatus), and the Chinese bitterling (Rhodeus sinensis). Interspecific differences indicated that the three study species have evolved different sperm allocation strategies. Rhodeus amarus displayed the most developed reproductive apparatus with a number of traits associated with both high levels of sperm production and fertilization efficiency. Rhodeus ocellatus and R. sinensis appear to have more comparable sperm allocation strategies, although relative testis size and spermatozoa head : tail ratio were greater in R. sinensis, suggesting that sperm competition risk may be higher in this species. All three species possessed an unusually well developed sperm duct with evidence of mucin production, which greatly extends the longevity of sperm and, consequently, the period over which fertilization can occur. We discuss these findings in the context of differences in the mating systems of the species examined, and relate the results obtained to differences in the temporal and spatial clustering of fertilizations. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103, 622-632.
Eicosanoids: progress towards manipulating insect immunity

Insect immunity is exclusively innate, lacking the antibody‐based adaptive immunity of vertebrates. Innate immunity is a naturally occurring, non‐specific system that does not require previous infectious experience. In this paper, I describe insect immunity and review the roles of prostaglandins and other eicosanoids as crucial signals that mediate insect immune reactions to challenge. Despite physical barriers (the integument) and robust epithelial immune functions in salivary glands, tracheal systems and midgut, many microbes and parasitoids invade insect haemocoels. Once invaders are detected within the body, insects unleash potent immune effectors, traditionally assorted into cellular (haemocytic) and humoral immunity. Humoral immunity refers to induced expression of genes encoding antimicrobial peptides and the enzymes lysozyme and prophenoloxidase. These proteins appear in haemolymph of infected insects 6–12 h post‐infection. Haemocytic immunity is characterized by direct interactions between invaders and circulating haemocytes. These reactions begin immediately when an infection is detected and, in the case of bacterial infections, are the predominant responses, responsible for clearing the vast majority of infecting bacterial cells within the first 2 h after infection. As a measure of cellular immunity, a recent field study shows that virtually all insects become infected and many fully recover from the infections. Insect immune functions are of such biological significance that they may limit the effectiveness of some biological control programmes. I highlight the efficacy of insect immunity and the importance of eicosanoids as immune signals by reviewing two cases in which microbes have evolved the ability to suppress host insect immunity by inhibiting eicosanoid biosynthesis. I complete the paper with a description of a major research goal in the Biological Control of Insects Research Laboratory, now focused on developing molecular tools to cripple pest insect immunity at the field level.
Toxicity and tunneling ability of Coptotermes heimi (Isoptera: Rhinotermitidae) in response to Biflex®, Termidor® and Tenekil®.

Repellency, toxicity and tunneling ability of Coptotermes heimi (Wasmann) were evaluated against the synthetic pyrethroids, bifenthrin (Biflex ® ), phenyl pyrazole, fipronil (Termidor ® ) and the polychlorinated petroleum hydrocarbon (Tenekil ® ). Different concentrations used to evaluate the toxicity were 1.5625, 3.125, 6.25, 12.5, 25, 50 ppm for Biflex, Termidor and Tenekil, respectively Biflex and termidor were found to be more toxic at 50 ppm in comparison to the tenekil in an 8h assay as observed by F-1 (0.97) mortality. LC 50 values ofbiflex, termidor and tenekil against C. heimi were 0.3467,1.458 and 12.359 ppm respectively for the 8h assay whereas the LC 50 values were 12.560,13.031 and 37.154 ppm for biflex, termidor and tenekil, respectively when the termites were expose to one-month-old treated soil. Biflexwas found to have repellent effects at 50 ppm in fresh and one month old treated soil however; termidor and tenekil did not show repellent effects at any concentration used in this study. These insecticides at different concentrations used in this study also affected survival of the termites and reduced the tunneling ability of termite workers in the treated soil.
Both seedling banks and specialist seed predators promote the evolution of synchronized and intermittent reproduction (masting) in trees

1. Conditions leading to the evolution of masting (intermittent and synchronized reproduction of trees) are examined. According to the dynamics of the resource reserve of individuals, reproductive investment is the proportion of investment in flowers with coefficient k. If k evolves to sufficiently large values, trees show a large between‐year fluctuation in the seed crop even in a constant environment (masting).
Leafy spurge and the species composition of a mixed-grass prairie.

The relationship between leafy spurge (Euphorbia esula L.) and the species composition of mixed-grass prairie was examined on both a large scale, within a 200-km2 area, and on a local scale, within a single infestation. On the large scale, cover values of 8 of the 10 most common species varied significantly (P & 0.05) between native prairie and spurge-dominated vegetation. Cover values of all common native species were negatively correlated with cover of leafy spurge. Within a single infestation of leafy spurge, the frequency of 5 common native species decreased significantly with leafy spurge. Most native species were absent where leafy spurge was most abundant and species richness declined from 11 outside the infestation to 3 at the center. Ninety-five percent of leafy spurge infestations within a 374-ha area were associated with anthropogenic disturbances (vehicle tracks, road construction and fireguards) which removed native plant cover and exposed mineral soil. These observations corroborate experimental studies which show that leafy spurge establishes more readily in disturbed soil and indicate that the result of such disturbances is the replacement of native species with leafy spurge.
Avaliação do IPO da Stone pagamentos na Nasdaq : estudo de caso da abertura de capital da fintech brasileira no mercado de capitais estrangeiro

Em razao do desenvolvimento economico global, cada vez mais as empresas de capital fechado buscam aprimorar suas fontes de financiamento de maneira que possam alavancar e sustentar seu crescimento enquanto continuam a gerar retornos consideraveis. Nesse cenario, a StoneCo Ltd, empresa de processamento de pagamentos que opera no Brasil, recorreu a abertura de seu capital para captacao de recursos. O processo de abertura de capital e coordenado por instuicoes financeiras que tem, dentre outras atribuicoes, mensurar o valor da empresa que deseja se tornar emissora publica de acoes e o potencial capital a ser levantado durante um IPO. Esse estudo investigou as melhores praticas de avaliacao de empresas a fim de realizar uma avaliacao independente e determinar se, pela metodologia adotada, o preco das acoes na oferta publica inicial foram super ou subvalorizados quando comparados ao preco de negociacao dado pelo mercado. Os resultados obtidos mostraram que o preco de negociacao no fechamento do primeiro dia apos a oferta publica inicial da Stone foi 31% maior que o preco de oferta e apenas 3,3% maior que o preco obtido pela metodologia adotada nesse estudo, envidenciando sua maior eficacia.
Development of an organically certifiable growth medium for N-fixing cyanobacteria in a raceway biofertilizer production system

ii ACKNOWLEDGEMENTS.v CHAPTER 1: INTRODUCTION.1 References.5 CHAPTER 2: COMPARISON OF CYANOBACTERIAL GROWTH AND NITROGEN FIXATION IN A NEWLY DEVELOPED ORGANICALLY CERTIFIABLE GROWTH MEDIUM AND ALLEN AND ARNON MEDIUM.6 Preface.6 Introduction.7 Methods.8 Nutrient substitutions . 8 Microorganism.9 Lab study.9 Field study.11 N dissolution from bone meal.12 Field bone meal reduction study . 13 Statistical analysis.13 Results and discussion . 14 Lab study: cyanobacterial growth and N-fixation in RB medium versus AA medium.14 Lab study: nutrient concentrations in RB medium versus AA medium . 15 Field study: effect on measurements due to varying paddlewheel speeds.16
Influence of site conditions on the diversity of endophytic fungi of fir clubmoss Huperzia selago (L.) Bernh. ex Schrank et Mart

The aim of the study was to assess the influence of environmental conditions on the composition of endophytic assemblages associated with fir clubmoss, Huperzia selago (L.) Bernh. ex Schrank et Mart. This clubmoss is a cosmopolitan species widely spread in Eurasia and North America, and its gametophytes and sporophytes are colonised by endophytic fungi. Plants for this study were collected in October 2004 and between April and October 2007 from seven European sites, differing in altitude, average annual precipitation, temperature and plant community. Endophytes were isolated on PDA medium (4% potato-dextrose agar) and identified through morphological observations. Different ecological indices were calculated for each site like colonization factor, Fisher’s alpha, Shannon’s diversity, Morista-Horn and Jaccard’s indices. Our results prove that altitude positively correlates with species diversity (Fisher’s alpha) and species richness (number of species). Moreover, the similarity assessed from Jaccard’s (0.66 for Larici-Piceetum sites) and Morista-Horn indices (0.77 for Juncetea trifidi sites) suggest the influence of plant community on fungal endophyte composition.