Miracle-dz/UniFAR-FTUs huggingface dataset:
PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees

PSeq-Gen will simulate the evolution of protein sequences along evolutionary trees following the procedures previously reported for the DNA sequence simulator Seq-Gen (Sequence-Generator, Rambaut and Grassly, 1997). Statistics calculated from these sequences can be used to give expectations under specific null hypotheses of protein evolution. This Monte Carlo simulation approach to testing hypotheses is often termed 'parametric bootstrapping' (see, for example, Efron, 1985; Huelsenbeck et al., 19%; Huelsenbeck and Rannala, 1997), and has many powerful applications, such as testing the molecular clock (Goldman, 1993), detecting recombination (Grassly and Holmes, 1997), and evaluating competing phylogenetic hypotheses (Hillis et al., 19%). Three common models of amino acid substitution are implemented (PAM: Dayhoff et al., 1978; JTT: Jones et al., 1992; mtREV: Adachi and Hasegawa, 1995). These models use instantaneous rate matrices derived from observed patterns of accepted point mutations for aligned nuclear (PAM, JTT) and mitochondrial (mtREV) genes. The amino acid frequencies found for these alignments are the default in each model, but it is also possible to specify their frequencies independently in the implementation here [following Adachi (1995), but see also Kishino et al. (1990)]. In addition, sitespecific rate heterogeneity following a gamma distribution is allowed (as described in Rambaut and Grassly, 1997; Yang, 1993). As with Seq-Gen, any number of trees may be read in and any number of data sets can be simulated for each tree, allowing large sets of replicate simulations to be created easily. Maximum-likelihood algorithms exist which will reconstruct phylogenies from protein sequences using the PAM, JTT and mtREV substitution models (e.g. Adachi and Hasegawa, 1995; Yang, 1996), and hence bootstrapping to obtain confidence limits about phylogenetic parameters is easily achieved.
Symmetric instantons and Skyrme fields

By explicit construction of the ADHM data, we prove the existence of a charge-seven instanton with icosahedral symmetry. By computing the holonomy of this instanton we obtain a Skyrme field which approximates the minimal energy charge-seven skyrmion. We also present a one-parameter family of tetrahedrally symmetric instantons whose holonomy gives a family of Skyrme fields which models a skyrmion scattering process, where seven well-separated skyrmions collide to form the icosahedrally symmetric skyrmion.
Risky health behavior among adolescents in the childhood cancer survivor study cohort.

OBJECTIVE To report the prevalence and comparison of cancer-linked health behaviors and identify risk factors associated with unhealthy behavior among adolescent siblings and cancer survivors. METHODS The Child Health and Illness Profile--Adolescent Edition (CHIP--AE) was completed by 307 survivors and 97 sibling controls 14-20 years of age. RESULTS Risky behavior ranged from 0.7% to 35.8% for survivors and 1.0% to 41.2% for siblings. Comparisons of sexual behavior, tobacco, alcohol, or illicit drug use utilizing continuous data revealed no differences between groups. Categorically, survivors were less likely to report past smokeless tobacco use or current use of beer/wine or binge drinking (p-values range from .01 to .04). Survivors with better mental health were at lower risk for poor behavioral outcomes. CONCLUSIONS Adolescent survivors engage in risky health behaviors at rates generally equivalent to their siblings. Aggressive health education efforts should be directed toward this high-risk population.
Is there a relation between onset age of bilingualism and enhancement of cognitive control?*

Young English-speaking monolingual and bilingual adults were examined for English proficiency, language use history, and performance on a flanker task. The bilinguals, who were about twenty years old, were divided into two groups (early bilinguals and late bilinguals) according to whether they became actively bilingual before or after the age of ten years. Early bilinguals and monolinguals demonstrated similar levels of English proficiency, and both groups were more proficient in English than late bilinguals. In contrast, early bilinguals produced the smallest response time cost for incongruent trials (flanker effect) with no difference between monolinguals and late bilinguals. Moreover, across the whole sample of bilinguals, onset age of active bilingualism was negatively correlated with English proficiency and positively correlated with the flanker effect. These results suggest a gradient in which more experience in being actively bilingual is associated with greater advantages in cognitive control and higher language proficiency.
Preparation of a Nanoemulsion with Carapa guianensis Aublet (Meliaceae) Oil by a Low-Energy/Solvent-Free Method and Evaluation of Its Preliminary Residual Larvicidal Activity

Andiroba (Carapa guianensis) seeds are the source of an oil with a wide range of biological activities and ethnopharmacological uses. However, few studies have devoted attention to innovative formulations, including nanoemulsions. The present study aimed to obtain a colloidal system with the andiroba oil using a low-energy and organic-solvent-free method. Moreover, the preliminary residual larvicidal activity of the nanoemulsion against Aedes aegypti was evaluated. Oleic and palmitic acids were the major fatty acids, in addition to the phytosterol β-sitosterol and limonoids (tetranortriterpenoids). The required hydrophile-lipophile was around 11.0 and the optimal nanoemulsion was obtained using polysorbate 85. The particle size distribution suggested the presence of small droplets (mean diameter around 150 nm) and low polydispersity index (around 0.150). The effect of temperature on particle size distribution revealed that no major droplet size increase occurred. The preliminary residual larvicidal assay suggested that the mortality increased as a function of time. The present study allowed achievement of a potential bioactive oil in water nanoemulsion that may be a promising controlled release system. Moreover, the ecofriendly approach involved in the preparation associated with the great bioactive potential of C. guianensis makes this nanoemulsion very promising for valorization of this Amazon raw material.
A PREDICTIVE MODEL OF THE STATES OF FINANCIAL HEALTH IN SOUTH AFRICAN BUSINESSES

This paper is a move away from the traditional financial health/distress models and follows a two-stage approach – in the first stage identifying, and in the second stage analysing, the financial health of South African businesses. In the first stage, multi-state models are developed to predict the state of health of a company. The second stage is a contemporary approach developed to provide underlying information or clues, independent of the first stage model, so as to enable the stakeholder, especially management, to establish a more meaningful picture of the company. Two independent holdout samples, spanning different time periods, are used to test the predicted accuracy of the models.
Towards a Cognitive Accessibility Guideline based on Empirical Evidences of Deaf Users Web Interaction

The analysis of the cognitive processes involved in web users’ interaction is specially important when designing for users with some kind of permanent or temporal cognitive limitations, like deaf persons. Theoretic constructs and principles of cognitive psychology describing and explaining these processes could be applied and adapted to analyse users’ and web tasks’ characteristics (Xu and col., 2001). In this paper we provide an example of applying cognitive models (working memory models) to derive hypotheses about deaf users’ web interaction. In addition, we tested these hypotheses in a controlled experiment. The results of the experiment allowed us to derive a guideline for cognitive accessibility. The proposed guideline states that is better to distribute semantic related verbal content of web pages in deep web structures than on wide ones. This guideline could be applied to other groups of users with similar cognitive limitations.
Analysis of GNAQ mutations, proliferation and MAPK pathway activation in uveal melanomas

Aim To study the GNAQ mutational status in a series of uveal melanomas and evaluate possible associations with mitogen-activated protein kinase (MAPK) pathway protein expression and tumour proliferation markers. Methods Mutational analysis was performed by PCR/sequencing of exon 5 of the GNAQ gene in a series of 22 uveal melanomas in which total and phosphorylated extracellular signal-regulated kinase (ERK) 1/2 overexpression without coexistent BRAF and NRAS mutations had previously been observed. Expression of the cell cycle markers (Ki-67, cyclin D1 and p27) was evaluated by immunohistochemistry. The association between GNAQ mutational status, ERK1/2, phospho-ERK1/2, Ki-67, cyclin D1 and p27 expression levels and the clinicopathological prognostic parameters of uveal melanomas was also assessed. Results GNAQ mutations were found in 36% of uveal melanomas. No associations were found between the GNAQ mutational status and prognostic parameters, the expression of ERK1/2, pERK1/2 and cell cycle markers. Conclusion The results of this study suggest that GNAQ mutated uveal melanomas do not exhibit a higher deregulation of proliferation or higher activation of the MAPK signalling pathway than uveal melanomas without GNAQ overactivation.
Öğretmen Profesyonelizminin Yordayıcıları Olarak Okul Müdürüne Güven ve Öz Yeterlik

This study examined the relationships between teacher professionalism of primary and secondary school teachers, their perceptions of trust in school principal and levels of their self-efficacy. The present study was designed in correlational research model. A total of 279 primary and secondary school teachers participated in the study. Research data was analyzed through descriptive statistics, Pearson product-moment correlation coefficients and multiple linear regression. Results indicated that there were positive and significant relationships between teacher self-efficacy, trust in school principal and teacher professionalism. Furthermore, results revealed that teachers’ levels of trust and perceptions of self-efficacy were significant predictors of teacher professionalism. In the study, suggestions were made for improving teacher professionalism and following researches.
High redshift detection of the integrated Sachs-Wolfe effect

We present evidence of a large angle correlation between the cosmic microwave background measured by WMAP and a catalog of photometrically detected quasars from the SDSS. The observed cross correlation is 0.30{+-}0.14 {mu}K at zero lag, with a shape consistent with that expected for correlations arising from the integrated Sachs-Wolfe effect. The photometric redshifts of the quasars are centered at z{approx}1.5, making this the deepest survey in which such a correlation has been observed. Assuming this correlation is due to the ISW effect, this constitutes the earliest evidence yet for dark energy and it can be used to constrain exotic dark energy models.
An obligate role for T-cell receptor alphabeta+ T cells but not T-cell receptor gammadelta+ T cells, B cells, or CD40/CD40L interactions in a mouse model of atopic dermatitis.

BACKGROUND We recently described a murine model of atopic dermatitis (AD) elicited by epicutaneous sensitization with ovalbumin (OVA). The skin lesions in these mice were characterized by a dermal infiltrate consisting of eosinophils and T cells and by increased expression of the TH2 cytokines IL-4 and IL-5. Epicutaneous sensitization induces a rise in the levels of serum total IgE and OVA-specific antibodies, further indicating that it elicits a predominantly TH2 response. OBJECTIVE This study was undertaken to assess the roles of T cells, B cells, and CD40L-CD40 interactions in AD. METHODS Mice with targeted gene deletions were sensitized with OVA. Histologic and immunohistochemical examinations, as well as measurements of IL-4 mRNA, were performed on OVA-sensitized skin. Total and antigen-specific serum IgE levels were determined. RESULTS RAG2(-/-) mice, which lack both T and B cells, did not exhibit cellular infiltration, induction of dermal IL-4 mRNA, or elevation of serum IgE after OVA sensitization; all of these features were present in B-cell-deficient IgH(-/-) mice. T-cell receptor alpha(-/-) mice did not display cellular infiltration, IL-4 mRNA expression, or increased IgE levels after OVA sensitization, but these responses were elicited in T-cell receptor delta(-/-) mice after sensitization. Absence of CD40 had no effect on these responses. CONCLUSION These results suggest that alphabeta T cells, but not gammadelta T cells, B cells, or CD40L-CD40 interactions, are critical for skin inflammation and the TH2 response in AD.
Cost Optimization Method for Workflows with Deadline Constraints in Grids

Cost optimization for workflow applications with deadline constraints is fundamental and intractable in grids. In this paper, early tree is introduced to find an early feasible schedule for a workflow application. According to the early tree, a cost optimization algorithm is proposed. Taking into account the workflow total float, the workflow deadline is segmented to activity deadlines while keeping precedence constraints. Costs of all activities are locally optimized, so does the workflow cost. Experimental results show that the proposal that this approach can dramatically decrease workflow cost with different deadlines. Moreover, it outperforms other two leveling algorithms in performance on average.
Full Diversity Unitary Precoded Integer-Forcing

We consider a point-to-point flat-fading MIMO channel with channel state information known both at transmitter and receiver. At the transmitter side, a lattice coding scheme is employed at each antenna to map information symbols to independent lattice codewords drawn from the same codebook. Each lattice codeword is then multiplied by a unitary precoding matrix P and sent through the channel. At the receiver side, an integer-forcing (IF) linear receiver is employed. We denote this scheme as unitary precoded integer-forcing (UPIF). We show that UPIF can achieve full-diversity under a constraint based on the shortest vector of a lattice generated by the precoding matrix P. This constraint and a simpler version of that provide design criteria for two types of full-diversity UPIF. Type I uses a unitary precoder that adapts at each channel realization. Type II uses a unitary precoder, which remains fixed for all channel realizations. We then verify our results by computer simulations in 2×2, and 4×4 MIMO using different QAM constellations. We finally show that the proposed Type II UPIF outperform the MIMO precoding X-codes at high data rates.
Four Centuries of Portuguese Expansion, 1415-1825: A Succinct Survey

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Optical-IR Spectral Energy Distribution of the Protogalaxy Candidate MS 1512–cB58

The spectral energy distribution of the protogalaxy candidate MS 1512-cB58 at z = 2.72 is presented. Photometry in seven bands ranging from g to K' (1300-6000 Å rest wavelength) are fitted with population synthesis models. The data confirm a very young age for this galaxy in agreement with ages estimated from preliminary C IV λ1550 P Cygni profile modeling. Single-burst models with ages greater than about 20 Myr can be discarded at the 99% confidence level, and continuous star formation models with ages greater than about 35 Myr can be discarded at the 95% confidence level. The spectral energy distribution is most consistent with a continuous star formation model of about 10-20 Myr, with reddening of E(B - V) ~ 0.3. No evidence for an older population of stars is seen, but the possibility of an older population with as much as 90% of the galaxy mass cannot be ruled out. We discuss the possible ramifications of a nonstandard IMF and gravitational lensing on the galaxy's age and mass.
Influence of aerobic and anaerobic interval training compared with yogic practices on selected physical fitness variables of high school football players

The aim of this study was to determine whether aerobic interval training with yogic practices (AeIYG) or anaerobic interval training with yogic practices (AnIYG) has greater effect on selected physical fitness variables, speed and agility among high school football players. For this purpose, the investigator selected find out the influence of aerobic and anaerobic interval 90 football players divided into three groups, namely, AeIYG, AnIYG and control group (CG). The subjects were tested for speed and agility initially and after 12 weeks of experiment on respective training on the subjects. The results proved that there was significant improvement in speed (F: 45.52) and agility (F 8.37) on adjusted means, against required F value of 3.1. The post hoc analysis proved that AeIYG was better than CG and AnIYG in improving speed and agility of school level football players. It was concluded that aerobic interval training with yogic practices significantly improved speed and agility of the school level football players than anaerobic power with yogic practices.
The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins

DNA polymerase zeta (pol ζ) participates in several DNA transactions in eukaryotic cells that increase spontaneous and damage-induced mutagenesis. To better understand this central role in mutagenesis in vivo, here we report the fidelity of DNA synthesis in vitro by yeast pol ζ alone and with RFC, PCNA and RPA. Overall, the accessory proteins have little effect on the fidelity of pol ζ. Pol ζ is relatively accurate for single base insertion/deletion errors. However, the average base substitution fidelity of pol ζ is substantially lower than that of homologous B family pols α, δ and ɛ. Pol ζ is particularly error prone for substitutions in specific sequence contexts and generates multiple single base errors clustered in short patches at a rate that is unprecedented in comparison with other polymerases. The unique error specificity of pol ζ in vitro is consistent with Pol ζ-dependent mutagenic specificity reported in vivo. This fact, combined with the high rate of single base substitution errors and complex mutations observed here, indicates that pol ζ contributes to mutagenesis in vivo not only by extending mismatches made by other polymerases, but also by directly generating its own mismatches and then extending them.
Two-way quantize-and-forward relaying with STBC

In this paper we propose a new two-way relaying scheme using a quantize-and-forward strategy with space-time block coding (STBC). In this scheme two nodes use STBC to simultaneously transmit their signals to the relay. At the relay these signals are estimated by using minimum mean square error ordered successive interference cancellation and then are quantized to the nearest signal constellation point. The relay linearly combines the quantized signals and broadcasts the combined signal to both nodes using a STBC. The performance of the proposed scheme is evaluated numerically in an uncorrelated flat fading channel and compared to a space division duplex reference scheme. We also investigate the effect of power-splitting on the performance of the scheme.
Insomnia Subtypes and the Subsequent Risks of Stroke: Report From a Nationally Representative Cohort

Background and Purpose— The studies assessing the impact of insomnia on stroke are still lacking. We aim to investigate insomnia in relation to subsequent stroke during the 4-year follow-up. Methods— Data from the Taiwan National Health Insurance Research Database were used. Enrollees with International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis code for insomnia were compared with randomly selected, age- and sex-matched noninsomnia enrollees with subsequent hospitalization for stroke during the 4-year follow-up. All enrollees, insomniacs and noninsomniacs, did not have previous diagnosis of stroke, sleep apnea, and insomnia. Individuals with insomnia were further categorized into different subgroups based on their insomnia patterns to explore whether the risk of stroke varies by subtype. The risk of outcomes was assessed with Kaplan–Meier curves and the impact of insomnia was estimated using Poisson regression analysis and Cox proportional hazards models. Results— The study included 21 438 (mean age, 52±16 years) insomniacs and 64 314 matched noninsomniacs (mean age, 51±16 years). Compared with noninsomniacs, insomniacs had 54% higher risk of developing stroke (adjusted hazard ratio, 1.54; 95% confidence interval, 1.38–1.72). When breaking down into insomnia subgroups, the persistent insomniacs had a higher 3-year cumulative incidence rate of stroke than those in the remission group (P=0.024). The insomniacs-to-noninsomniacs incidence rate ratio for stroke was highest among those aged 18 to 34 years (incidence rate ratio, 8.06). Conclusions— Insomnia predisposes individuals to increased risk of stroke and this association is profound among young adults. Our results underscore the clinical importance of identifying and treating insomnia. A novel behavioral intervention targeting insomnia that may prevent stroke should be explored.