Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Patterns of Gene Evolution.

One of the most distinctive characteristics of humans among primates is the size, organization and function of the brain. A recent study has proposed that there was widespread accelerated sequence evolution of genes functioning in the nervous system during human origins. Here we test this hypothesis by a genome-wide analysis of genes that are expressed predominantly or specifically in brain tissues and genes that have important roles in the brain, identified on the basis of five different definitions of brain specificity. Although there is little overlap among the five sets of brain-specific genes, none of them supports human acceleration. On the contrary, some datasets show significantly fewer nonsynonymous substitutions in humans than in chimpanzees for brain-specific genes relative to other genes in the genome. Our results suggest that the unique features of the human brain did not arise by a large number of adaptive amino acid changes in many proteins. Introduction The human brain differs substantially from those of other primates in size, organization and function. For instance, in comparison to that of chimpanzees, the brain weight of humans is over 300% greater but the body is only 35% heavier (Williams 2002) (Figure 2.1). The structural asymmetry between the left and right hemispheres is especially pronounced in human brains (Deacon 1994). Humans also have speech or language and other high-order cognitive functions that are absent in non-human primates. The genetic changes that have been responsible for the emergence of these human-unique brain features are a topic of enduring interest. Generally
Genetic and non genetic variability in selective value of Hariana cows.

Data from the calving records of 660 Hariana cows were utilized to study the overall descriptive statistics for total calves born and survived up to first calving in the milking herd from each cow. Average number of total calves produced, total alive calves, total female calves and total female calves reached at milking age per cow during its life time in the herd were 5.2±0.16, 4.9±1.5, 2.38±0.15 and 1.2±0.21. Cow longevity for this herd was 9.12 years, whereas productive herd life was 5.38 years. Average coefficient of gene replication (CGR) was 0.6 ±0.11 for this herd and indicated that this value is higher than one time gene replication (0.5). There was an increasing trend for the total calves born with the increase in the first lactation milk yield (FLMY), higher milk producing cows produced more number of calves as compared to low milk producers. This varied from 2.1±0.28 calves produced by low milk producers ( 1550 kg FLMY). The percentage of cows which left the herd after giving only 1 calf was 21.2, and 11.3% cows produced 10 or more calves in the herd. Effect of age at first calving was not significant on these traits except total alive calves born. Period of birth and FLMY had highly significant effect on these traits. Per cent distribution of cows indicated that 19.3% cows in the herd could not produce any female calf, 25.3% cows left the herd after producing only 1 female calf. About 50% cows left the herd without giving any replacement heifer, whereas 21.4, 12.9 and 8.7% of cows left only 1, 2 and 3 replacements, respectively.
Cross-Reactive Memory CD4 + and CD8 + T Cells Alter the Immune Response to Heterologous Secondary Dengue Virus Infections in Mice: A Dissertation

Dengue virus (DENV) infects 50-100 million people worldwide every year and is the causative agent of dengue fever (DF) and the more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). There are four genetically and immunologically distinct DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4). Evidence suggests that an increased risk for DHF/DSS during secondary infection with a heterologous DENV serotype is due to an immunopathological response mediated by serotype-cross-reactive memory T cells from the primary infection. Furthermore, epidemiological studies have shown that the sequence of infection with different DENV serotypes affects disease severity. Though much has been learned from human studies, there exist uncontrollable variables that are intrinsic in this system such as genetic factors and unknown infection histories. These factors can skew experimental results, making interpretations difficult. Therefore, a murine model to study the immunologic aspects of sequential dengue infections would be an asset to the field of dengue research. To examine the effect of sequential infection with different DENV serotypes on the CD8 + T cell response, we immunized Balb/c mice with a primary DENV infection on day 0 and subsequently challenged with a heterologous secondary DENV infection on day 28. We tested all possible sequences of infection with the four serotypes. We analyzed the T cell response to two previously defined epitopes on the DENV E (L d -restricted) and NS3 (K d -restricted) proteins. Using ELISPOT and intracellular cytokine staining, we measured the frequency of T cells secreting IFNγ and TNFα in response to stimulation with these epitopes during three phases: acute primary, acute secondary, and the memory phase after primary infection. We found that the T cell response in heterologous secondary infections was higher in magnitude than the response in acute primary infection or during the memory phase. We also found that the hierarchy of epitope specific responses, as measured by IFNγ secretion, was influenced by the sequence of infections. The adoptive transfer of immune serum or immune splenocytes suggested that memory T cells from the primary infection responded to antigens from the secondary infection. In vitro experiments with T cell lines generated from mice with primary and secondary DENV infections suggested the preferential expansion of crossreactive memory T cells. In testing all of the different possible sequences of infection, we observed that two different sequences of infection (e.g., DENV-2 followed by DENV-1 versus DENV-2 followed by DENV-3) resulted in differential CD8 + T cell responses to the NS3 peptide even though both secondary infection serotypes contain the identical peptide sequence. To investigate this phenomenon, we examined the role of CD4 + T cell help on the memory CD8 + T cell response. We found that CD4 + T cell cytokine responses differ depending on the sequence of…
Nursing Students’ Perception of the Clinical Learning Environment

Clinical learning environment placements provide opportunities for students to develop their skills, socialize to the profession and bridge the gap between academic and workplace learning. This study was conducted to investigate Saudi nursing students’ perceptions of their clinical learning environment and supervision in the hospital setting. A sample of 90 final year student nurses completing practicums at a tertiary hospital in Riyadh was included in this cross-sectional study utilizing the Clinical Learning Environment and Supervision plus Nurse Teacher scale. Overall, students perceived their clinical learning environment positively. Among sub-scores, that for the leadership style of ward manager was the highest. Supervision types, nursing-teacher teacher-visit frequency and grade point average positively and significantly impacted student’s perceptions, while university type and practicum duration did not. Students confirmed the ward manager’s leadership style as the most significant influencing their perceptions. However, the nursing teacher’s role had the lowest mean score, suggesting the need for its enhancement and clarification and indicating the need for better communication and collaboration between nursing schools and the clinical training hospital.
CARNIVORI DELLA SOMALIA EX ITALIANA

RIASSUNTO Gli Autori presentano una revisione dei Carnivori della Somalia ex italiana. Nel territorio risultano finora presenti 26 specie e Civettictis civetta viene segnalata per la prima volta. Risulta ampliata la distribuzione di varie specie. Numerose forme sono passate in sinonimia. Genetta deorum e considerata sottospecie valida di Genetta rubiginosa. Viene documentata la validita specifica di Herpestes ochraceus e di Helogale hirtula e undulata. Panthera leo somaliensis e dimostrata forma valida anche se il nome non puo essere attribuito a Noack e, in base alle regole di nomenclatura, vi sono dubbi sulla sua disponibilita.
Fractional SIR Epidemiological Models

The purpose of this work is to make a case for epidemiological models with fractional exponent in the contribution of sub-populations to the transmission rate. More specifically, we question the standard assumption in the literature on epidemiological models, where the transmission rate dictating propagation of infections is taken to be proportional to the product between the infected and susceptible sub-populations; a model that relies on strong mixing between the two groups and widespread contact between members of the groups. We content, that contact between infected and susceptible individuals, especially during the early phases of an epidemic, takes place over a (possibly diffused) boundary between the respective sub-populations. As a result, the rate of transmission depends on the product of fractional powers instead. The intuition relies on the fact that infection grows in geographically concentrated cells, in contrast to the standard product model that relies on complete mixing of the susceptible to infected sub-populations. We validate the hypothesis of fractional exponents i) by numerical simulation for disease propagation in graphs imposing a local structure to allowed disease transmissions and ii) by fitting the model to a COVID-19 data set provided by John Hopkins University (JHUCSSE) for the period Jan-31-20 to Mar-24-20, for the countries of Italy, Germany, Iran, and France.
High Frequency of SARS-CoV-2 RNAemia and Association With Severe Disease

Background: Detection of SARS-CoV-2 RNA in the blood, also known as RNAemia, has been reported, but its prognostic implications are not well understood. This study aimed to determine the frequency of SARS-CoV-2 RNA in plasma and its association with the clinical severity of COVID-19. Methods: An analytical cross-sectional study was performed in a single-center tertiary care institution in northern California and included consecutive inpatients and outpatients with COVID-19 confirmed by detection of SARS-CoV-2 RNA in nasopharyngeal swab specimens. The prevalence of SARS CoV-2 RNAemia and the strength of its association with clinical severity variables were examined and included the need for transfer to an intensive care unit (ICU), mechanical ventilation and 30-day all-cause mortality. Results: Paired nasopharyngeal and plasma samples were included from 85 patients. The overall median age was 55 years, and individuals with RNAemia were older than those with undetectable SARS-CoV-2 RNA in plasma (63 vs 50 years; p=0.001). Comorbidities were frequent including obesity (37.7%), hypertension (30.6%) and diabetes mellitus (22.4%). RNAemia was detected in a total of 28/85 (32.9%) individual patients, including 22/28 (78.6%) who required hospital admission. RNAemia was detected more frequently in individuals who developed severe disease including the need for ICU transfer (32.1% vs 14.0%; p=0.05), mechanical ventilation (21.4% vs 3.5%; p=0.01) and 30-day all-cause mortality (14.3% vs 0%; p=0.01). No association was detected between RNAemia and estimated levels of viral RNA in the nasopharynx. An additional 121 plasma samples from 28 individuals with RNAemia were assessed longitudinally, and RNA was detected for a maximum duration of 10 days. Conclusion: This study demonstrated a high proportion of SARS-CoV-2 RNAemia, and an association between RNAemia and clinical severity suggesting the potential utility of plasma viral testing as a prognostic indicator for COVID-19.
Evaluación fenológica y digestibilidad in vivo de la Leguminosa Forrajera (Arachis pintoi) en diferentes edades de corte.

espanolEl objetivo de esta investigacion fue evaluar la fenologia, produccion, composicion quimica nutricional y digestibilidad in vivo de A. pintoi y de establecer modelos matematicos para determinar el valor nutricional y produccion en base a la composicion quimica de la planta. Las evaluaciones fenologicas se realizaron en la hacienda ESPE y la digestibilidad in vivo en la Facultad de Ciencias Pecuarias de la ESPOCH. En la primera fase se utilizaron parcelas experimentales de 10 x15 m con cuatro repeticiones, mientras que en la segunda fase la unidad experimental fue un ovino (n=4). En ambos ensayos se aplico un diseno experimental completamente al azar con un modelo lineal aditivo utilizando un nivel de significancia del 5%. Se realizo un analisis de correlacion y regresion lineal entre variables fenologicas, composicion quimica, digestibilidad y energia. Todos los analisis fueron realizados con el paquete SPSS 10. Las mayores producciones de forraje verde y materia seca (MS) por hectarea se obtuvieron con cortes a los 75 dias con 47,730 y 12,480 kg ha-1, respectivamente. En cuanto a la composicion quimica de la proteina bruta y digestibilidad in vivo de la MS, el forraje cortado a 30 dias obtuvo los mayores valores con 24.50 y 66.42%, respectivamente. El maximo valor de energia neta de lactancia (ENL) se logro en el corte de 30 dias, alcanzando 1.51 para luego disminuir a 1.24 Mcal ENL kg-1 a los 75 dias. EnglishThe objective in this research was to evaluate the phenology, production and to determine nutritional chemistry composition and in vivo digestibility of A. pintoi and, to establish standards for determining the nutritional value and production based according to the chemistry composition of the plant. The phenological evaluations were carried out at ranch ESPE and in vivo digestibility was executed in Animal Science Faculty from ESPOCH. In the first phase were used experimental plots 10 by 15 m. in four replications. In the second phase the experimental unit was an ovine (n=4). In both tests were used at random experimental designs with a linear additive standard applying a significance level of 5%. It was executed an correlation analysis and linear regression among phonological variables, chemistry composition, digestibility and energy. The whole analysis were carried out with SPSS 10 Statistical package. The greatest productions of green fodder and dry matter (DM) per hectare were obtained at cutting to 75 days with 47,730 and 12,480 kg ha-1, respectively. On the other hand, in chemistry composition of grass protein and in vivo digestibility of dry Matter (DM), the clipped forage to 30 days obtained the greatest values with 24.50 and 66.42%, respectively. The maximum value of net energy for lactation (NEL) was achieved at 30 days cutting reaching 1.51 for decreasing to 1.24 Mcal NEL kg-1 to 75 days.
Bayesian inference of COVID-19 spreading rates in South Africa

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has highlighted the need for the development of prompt mitigating responses under conditions of high uncertainty. Fundamental to the design of rapid state reactions is the ability to perform epidemiological model parameter inference for localised trajectory predictions. In this work, we perform Bayesian parameter inference using Markov Chain Monte Carlo (MCMC) methods on the Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological models with time-varying spreading rates for South Africa. The results find two change points in the spreading rate of COVID-19 in South Africa as inferred from the confirmed cases. The first change point coincides with state enactment of a travel ban and the resultant containment of imported infections. The second change point coincides with the start of a state-led mass screening and testing programme which has highlighted community-level disease spread that was not well represented in the initial largely traveller based and private laboratory dominated testing data. The results further suggest that due to the likely effect of the national lockdown, community level transmissions are slower than the original imported case driven spread of the disease.
Evaluation of different plating medias and PCR in the detecting of Salmonella Enteritidis from eggs laid by experimentally infected hens.

Salmonellosis is one of the most important food-borne diseases. Outbreaks of Salmonellosis are mainly related to the consumption of contaminated eggs or egg-products and, less frequently, of poultry meat. In this study fifty 29-week-old broiler breeder hens were randomly divided in two groups of 25 birds. One group of birds inoculated orally with 10log10 CFU and other group inoculated intravenously with 6log10 CFU of S. Enteritidis parent strain bacteria. During 35 days of experimental period, produced eggs were cultured using different medias and S.Enteritidis was detected using different cultural and PCR method. SE was isolated during 32.5 % of experimental days and more isolation rate of Salmonella was during the first two weeks of post infection period. In contrast, using pre-enrichment media resulted more isolation rate of Salmonella cells and SS agar was more sensitive than BG agar. PCR was more sensitive than cultural methods for detection of Salmonella Enteritidis from contaminated eggs.
Growth and biochemistry of the common hyacinth (Hyacinthus orientalis L.) and the lily (Lilium longiflorum L.)

The biochemical principles underlining carbohydrate metabolism of ornamental geophytes such as hyacinth and the lily are poorly understood. The present studies were therefore undertaken to investigate the regulation and partitioning of carbohydrates, as well as growth and development of these flower bulbs. Results indicated that starch was the major storage carbohydrate in these bulbs. Starch degradation occurred through amylolysis rather than phosphorolysis. The flower accumulated the highest amount of the reserves in hyacinth, following the depletion of these substances in the bulb scales, whilst in the case of the lily; it was the stem and roots, which accumulated the highest amount of reserves. The isolation of gene fragments of starch phosphorylase and starch synthase from hyacinth as well as the sequences generated for these enzymes implies that primers which are specific to hyacinth can be designed, and full characterisation of the genes can be made in the future by making and probing genomic libraries and isolating clones from cDNA libraries. In general, peeling of bulbs prior to planting resulted in a delay in emergence and reductions in vegetative growth as well as flower quality. Hyacinth plants subjected to defoliation did not show any compensation for leaf loss because growth was always reduced whilst flowering was unaffected, however, the lily responded positively to complete shoots removal especially when herbivory occurred at the beginning of their growth. Plants produced from large bulbs, just like those from the shallow planting regimes performed better in terms of growth and flower quality as compared to those of small bulbs and deep planting. Also, the application of (NH4)2SO4 enhanced more vigorous growth and bulb yield in both species of flower bulbs than did Na2HPO4, but in hyacinth it was Na2HPO4 that produced better flower quality than the former. Varieties such as Sky Jackets and Purple Voice produced the highest vegetative growth and bulb yield, whilst Fondant and Blue Jacket recorded the highest flower quality.
Influence of light intensity, water volume and density in tadpoles raised in mesocosm experiments

The ability of an organism to produce different phenotypes under different environmental conditions is a common adaptation in nature. Biotic factors like competition, community structure and predation can influence the survival and time to metamorphosis in amphibians. However, abiotic factors such as the hydroperiod and light intensity can be as important as biotic ones. We examine the influence of abiotic (light, hydroperiod) and biotic (density) factors on the morphology, growth and development of Argenteohyla siemersi pederseni tadpoles. Our main goal was to determine whether the morphology, growth and development vary in relation to changes in water volume, light intensity and number of conspecifics. The experiment was conducted under mesocosm conditions. We used a randomized block design with a factorial combination of two densities of tadpoles, two volumes of water and two light intensity conditions. The main findings were as follows: (1) Tadpole morphology was significantly affected by density and water volume but not by light intensity. Tadpoles maintained at low density increased their tail length and tail depth, tadpoles exposed to low volumes of water increased their tail length and tail muscle depth; (2) The growth rate and development rate of tadpoles were significantly affected by the effects of volume of water and density. Tadpoles maintained at low densities and low volume of water showed a significant increase in growth and development rate; (3) The growth and development rates of tadpoles were significantly affected by the effect of light intensity. Tadpoles exposed to lower light intensity showed an increase in their growth and development rates.
Genetic and ecological analysis of the putative natural hybrid zone formed Banksia robur Cav. and Banksia oblongifolia Cav.

Natural hybridization provides the opportunity to study the processes involved in speciation, since hybridizing populations are thought to represent some intermediate stage between a common ancestral population and the complete divergence of two species. The presence of hybrids within a population indicates that reproductive isolation has at some stage been incomplete. Therefore, the determination of the current level of gene flow can indicate the degree to which speciation is complete. Further, the fitness of the hybrids in comparison to that of the parent species can indicate the mode of formation and maintenance of the hybrid zone: either (i) a genetic/morphological cline can form in association with an environmental cline if the species are suited to conditions on different extremes of the cline or if the hybrid are as fit as the parents in the ecotone (environmental cline) and (ii) a cline may be formed as a result of an equilibrium formed between the constant gene flow into, and the selection against hybrids within, the hybrid zone (tension zone). Banksia robur Cav. and Banksia oblongifolia Cav. form the most commonly reported hybrid zone within the genus. The two species are morphologically different and are also closely associated with very different soil water regimes. Morphologically intermediate individuals, present in regions where the two species coexist, are thought to be hybrids. This hybrid zone, therefore, provides the opportunity to compare the "environmental cline" versus "tension zone" modes of hybrid zone formation, because while the Banksia hybrid zone seems to be associated with an environmental cline, there is also evidence that hybrids are selectively disadvantaged. In order to make this comparison, there are three general aims of this thesis: 1. To describe the "parental species", hybrids, and the hybrid zones as they are at present; 2. To determine if hybrids are selected against at some stage