Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Barcoding and Molecular Phylogeny of Drosophila lini and Its Sibling Species

Drosophila lini and its two sibling species, D. ohnishii and D. ogumai, are hardly distinguishable from one another in morphology. These species are more or less reproductively isolated. The mitochondrial ND2 and COI-COII and the nuclear ITS1-ITS2 regions were sequenced to seek for the possibility of DNA barcoding and to reconstruct the phylogeny of them. The character-based approach for DNA barcoding detected some diagnostic nucleotides only for monophyletic D. ogumai, but no informative sites for the other two very closely species, D. lini and D. ohnishii, of which strains intermingled in the molecular phylogenetic trees. Thus, this study provides another case of limited applicability of DNA barcoding in species delineation, as in other cases of related Drosophila species. The molecular phylogenetic tree inferred from the concatenated sequences strongly supported the monophyly of the cluster of the three species, that is, the lini clade. We propose some hypotheses of evolutionary events in this clade.
Immune inflammation indicators in anal cancer patients treated with concurrent chemoradiation: training and validation cohort with online calculator (ARC: Anal Cancer Response Classifier)

Background: In anal cancer, there are no markers nor other laboratory indexes that can predict prognosis and guide clinical practice for patients treated with concurrent chemoradiation. In this study, we retrospectively investigated the influence of immune inflammation indicators on treatment outcome of anal cancer patients undergoing concurrent chemoradiotherapy. Methods: All patients had a histologically proven diagnosis of squamous cell carcinoma of the anal canal/margin treated with chemoradiotherapy according to the Nigro’s regimen. Impact on prognosis of pre-treatment systemic index of inflammation (SII) (platelet x neutrophil/lymphocyte), neutrophil-lymphocyte ratio (NLR) and platelet-lymphocyte ratio (PLR) were analyzed. Results: A total of 161 consecutive patients were available for the analysis. Response to treatment was the single most important factor for progression-free survival (PFS) and overall survival (OS). At univariate analysis, higher SII level was significantly correlated to lower PFS (p<0.01) and OS (p=0.046). NLR level was significantly correlated to PFS (p=0.05), but not to OS (p=0.06). PLR level significantly affected both PFS (p<0.01) and OS (p=0.02). On multivariate analysis pre-treatment, SII level was significantly correlated to PFS (p=0.0079), but not to OS (p=0.15). We developed and externally validated on a cohort of 147 patients a logistic nomogram using SII, nodal status and pre-treatment Hb levels. Results showed a good predictive ability with C-index of 0.74. An online available calculator has also been developed. Conclusion: The low cost and easy profile in terms of determination and reproducibility make SII a promising tool for prognostic assessment in this oncological setting.
Switching time optimization in discretized hybrid dynamical systems

Switching time optimization (STO) arises in systems that have a finite set of control modes, where a particular mode can be chosen to govern the system evolution at any given time. The STO problem has been extensively studied for switched systems that consists of time continuous ordinary differential equations with switching laws. However, it is rare that an STO problem can be solved analytically, leading to the use of numerical approximation using time discretized approximations of trajectories. Unlike the smooth optimal control problem, where differentiability of the discrete time control problem is inherited from the continuous time problem, in this contribution we show that the STO problem will in general be nondifferentiable in discrete time. Nevertheless, at times when it is differentiable the derivative can be computed using adjoint equations and when it is nondifferentiable the left and right derivatives can be computed using the same adjoint equation. We illustrate the results by a hybrid model of a double pendulum.
A simple tube controller for efficient robust model predictive control of constrained linear discret

Abstract We present a simple tube controller for efficient robust model predictive control of constrained linear, discrete-time systems in the presence of bounded disturbances. The proposed control policy ensures that controlled trajectories are confined to a given tube despite uncertainty. The robust optimal control problem that is solved on-line is a standard quadratic programming problem of marginally increased complexity compared with that required for model predictive control in the deterministic case. We show how to optimize the tube cross section, how to construct an adequate tube terminal set and we establish robust exponential stability of a suitable robust control invariant set (the ‘origin’ for uncertain system) with enlarged domain of attraction.
Galaxy cores as relics of black hole mergers

ABSTRA C T We investigate the hypothesis that the cores of elliptical galaxies and bulges are created from the binding energy liberated by the coalescence of supermassive binary black holes during galaxy mergers. Assuming that the central density profiles of galaxies were initially steep power laws, r , r 22 , we define the ‘mass deficit’ as the mass in stars that had to be removed from the nucleus in order to produce the observed core. We use non-parametric deprojection to compute the mass deficit in a sample of 35 early-type galaxies with high-resolution imaging data. We find that the mass deficit correlates well with the mass of the nuclear black hole, consistent with the predictions of merger models. We argue that cores in haloes of noninteracting dark matter particles should be comparable in size to those observed in the stars.
Fast block matching algorithms using frequency domain

Translational template matching addresses the registration problem and has long been a problem of interest in such areas as video compression, robot vision, and biomedical engineering. In this paper, we will present new fast algorithms developed in our group for template and block matching purposes using either second or higher order statistics. Fast Fourier transforms (FFTs) have been called one of the ten most important algorithms of the twentieth century. Using some substitutions and complex arithmetic, computation of the sum square differences sum absolute difference and sum fourth order moment are derived to be correlation functions of substituting functions. The former can be computed using the fast Fourier transform (FFT) approach, which is greatly less computationally expensive than the direct computation. The performance of the proposed methods, as well as some illustrative comparisons with other matching algorithms in the literature, are verified through simulations. The algorithm based on the higher order moment is seen to have better performance in terms of fastness and robustness even in low SNR meanwhile the extra computational cost is negligible.
Association between Common Polymorphism near the MC4R Gene and Obesity Risk: A Systematic Review and Meta-Analysis

Background Genome-wide association studies on Europeans have shown that two polymorphisms (rs17782313, rs12970134) near the melanocortin 4 receptor (MC4R) gene were associated with increased risk of obesity. Subsequently studies among different ethnic populations have shown mixed results with some confirming and others showing inconsistent results, especially among East Asians and Africans. We performed a comprehensive meta-analysis of various studies from different ethnic populations to assess the association of the MC4R polymorphism with obesity risk. Methods We retrieved all published literature that investigated association of MC4R variants with obesity from PubMed and Embase. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effects model. Results A total of 61 studies (80,957 cases/220,223 controls) for rs17782313 polymorphism (or proxy) were included in the meta-analysis. The results suggested that rs17782313 polymorphism was significantly associated with obesity risk (OR = 1.18, 95%CI = 1.15–1.21, p<0.001). Similar trends were observed among subgroups of Europeans and East Asians, adults and children, studies with high quality score, and for each five MC4R polymorphisms independently. Conclusions The present meta-analysis confirms the significant association of MC4R polymorphism with risk of obesity. Further studies should be conducted to identify the causal variant and the underlying mechanisms of the identified association.
Integration of leadership training for graduate and medical students engaged in translational biomedical research: Examining self-efficacy and self-insight

Introduction Formal training in team leadership is not taught in biomedical research graduate training programs or medical schools. Methods We piloted a Leadership Training Workshop for graduate biomedical and medical students enrolled in our Interprofessional Research Design Course. Results The Kane–Baltes self-efficacy survey demonstrated improved leadership skills (median scores pretraining and post-training were 71 and 76.6; paired t-test, p=0.04). Conclusions Most students demonstrated significant improvement in self-awareness pertaining to their own innate leadership styles.
Cancer Incidence and Mortality Survey in Wuwei, Gansu Province, Northwestern China from 2003 to 2012: A Retrospective Population-based Study

Background: Population-based cancer registry collects the data on cancer incidence and mortality deaths from covered population to describe and survey the epidemics in certain areas. The aim of this study was to estimate the cancer incidence and mortality in Wuwei, Gansu province, Northwestern China from 2003 to 2012. The goal is to better understand cancer distribution and long-term development of cancer prevention and treatment in Wuwei. Methods: Data were collected from the Wuwei Cancer Registry between 2003 and 2012. In this registry, data from 46 cancer report centers were included in this analysis. Incidence/mortality rates, age-specific incidence/mortality rates, age-standardized incidence/mortality rates, and cumulative incidence/mortality rates were calculated. Totally, 9,836,740 person-years (5,110,342 for males and 4,726,398 for females) had been monitored over this time period. The gender ratio of male/female was 1.08:1. The number of new cancer cases and related deaths was 24,705 and 17,287 from 2003 to 2012, respectively. Results: The proportion of morphological verification was 74.43%. The incidence of cases identified through death certification only was 1.21%, and the mortality to incidence ratio was 0.70. The average crude incidence was 251.15/100,000 persons (310.61 and 186.87 for males and females per 100,000 persons, respectively). The age-standardized rates by Chinese standard population (ASR-China) and by world standard population (ASR-world) were 207.76 and 245.42 per 100,000 persons, respectively. The crude cancer mortality was 175.74/100,000 persons (228.34 and 118.86 for males and females per 100,000 persons). ASR for China and the world was 149.57 and 175.13/100,000 persons, respectively. The most common cancers and leading causes of cancer-related deaths in Wuwei were as follows: cancers of stomach, esophagus, liver, lung, colorectum, breast, cervix, lymphoma, blood (leukemia), brain, and central nervous system. In Wuwei, during 2003 and 2012, cancer incidence and mortality rates increased by 1.32% and 1.31%/year, respectively. During this time, colorectum cancer incidence and mortality rates increased by 2.69% and 7.54%/year, respectively, in Wuwei. The incidence and mortality of other gastric, esophageal, liver, and lung cancers also all increased. Conclusions: The results of this study report a more accurate cancer burden among the population of Wuwei, China. Active research of cancers etiology and effective prevention should be established to reduce the incidence and mortality associated with cancers.
Early Childhood Educators’ Perceptions of Parent–child Relationships: A Qualitative Study

PARENT–CHILD RELATIONSHIPS are the most critical for children's social and emotional development and wellbeing. While parent–child relationship support programs are well documented, there are none designed for educators’ use within early education and care settings. To inform development of an educator program, an understanding of educators’ everyday practices, their role in supporting parent–child relationships and children's social and emotional development was sought. Educators reported the importance of parent– child relationships, yet were hesitant to engage with parents. Educators’ knowledge was primarily implicit—drawing on observations and practical experiences to build their knowledge of relationships and social and emotional development—which contributed to reluctance in sharing their knowledge with parents. Educators requested theoretical, evidence-based approaches to build further knowledge and inform everyday practices in supporting parent–child relationships. These findings are critical to the development of an educator-led parent–child relationship program for use within education and care settings.
The effect of using an alternative irrigant between sodium hypochlorite and chlorhexidine to prevent the formation of para-chloroaniline within the root canal system.

AIM To determine if the formation of para-chloroaniline (PCA) can be avoided by using an alternative irrigant following sodium hypochlorite but before chlorhexidine. METHODOLOGY Fifty-five single-rooted teeth were decoronated, instrumented to size 40, . 06 taper whilst being irrigated with 14% ethylene-diamine-tetra-acetic acid (EDTA) and 6% NaOCl. Samples were then randomly divided into three experimental and two control groups. Group 1 was irrigated with saline followed by 2% chlorhexidine gluconate (CHX). Group 2 was irrigated with 50% citric acid (CA) followed by 2% CHX. Group 3 was irrigated with 14% EDTA followed by 2% CHX. The chemical identity and quantification of the PCA in the formed precipitate was determined using gas chromatography/mass spectrometry (GC/MS). RESULTS All experimental groups contained PCA. The mean level of PCA for group 1 (sterile saline) was 229 ng mL(-1), group 2 (citric acid) 72 ng mL(-1) and group 3 (EDTA) 400 ng mL(-1), respectively. A significant difference was found between the saline and EDTA groups and the negative control (P < 0.05). Although no statistical significance was found between the negative control and citric acid group, PCA was still present in this experimental group. CONCLUSIONS Citric acid used as the intermittent irrigant had the least amount of PCA formation in the canal system. Until the threshold required to cause biological damage in humans is determined, the combination of NaOCl and CHX in root canal treatment should be avoided.
s-Process Nucleosynthesis in Carbon Stars

We present the first detailed and homogeneous analysis of the s-element content in Galactic carbon stars of N type. Abundances of Sr, Y, Zr (low-mass s-elements, or ls), Ba, La, Nd, Sm, and Ce (high-mass s-elements, or hs) are derived using the spectral synthesis technique from high-resolution spectra. The N stars analyzed are of nearly solar metallicity and show moderate s-element enhancements, similar to those found in S stars, but smaller than those found in the only previous similar study (Utsumi 1985), and also smaller than those found in supergiant post-asymptotic giant branch (post-AGB) stars. This is in agreement with the present understanding of the envelope s-element enrichment in giant stars, which is increasing along the spectral sequence M → MS → S → SC → C during the AGB phase. We compare the observational data with recent s-process nucleosynthesis models for different metallicities and stellar masses. Good agreement is obtained between low-mass AGB star models (M ≲ 3 M☉) and s-element observations. In low-mass AGB stars, the 13C(α, n)16O reaction is the main source of neutrons for the s-process; a moderate spread, however, must exist in the abundance of 13C that is burnt in different stars. By combining information deriving from the detection of Tc, the infrared colors, and the theoretical relations between stellar mass, metallicity, and the final C/O ratio, we conclude that most (or maybe all) of the N stars studied in this work are intrinsic, thermally pulsing AGB stars; their abundances are the consequence of the operation of third dredge-up and are not to be ascribed to mass transfer in binary systems.
An integrated model for business process measurement

Purpose – Research in the evaluation of business processes (BPs) seems to have missed those of BP modeling techniques. Past studies on evaluations have focused in most cases on a single objective or goal of a BP using quantitative performance measures or qualitative surveys. In this paper, an approach that combines all relevant single purpose measures (relevant to the goals of the BP) into one overall measure is proposed. The overall measure will reflect all stakeholders' perspective and preference ratings on the attributes/criterion of the BP in question. The conceptual model is supported by the analytic hierarchy process (AHP) methodology.Design/methodology/approach – A discussion of factors that might be the root cause of difficulties in defining an appropriate evaluation is given along with a review of major measures used. The synthetic combination of single purpose measures basically follows the AHP, with major stake‐holders represented in defining the relative priority/ranking matrix between criteri.
The Effect of Time Management on Academic Performance among Students of Jazan University

Background: Many students could not manage their times efficiently before being students in college since they did not have any challenges or difficulties in high school. However, the case changed completely when they are attending college. Being a student in college means that the responsibility is bigger and the courses are more difficult than what they were in high school. Aim: The research aimed to determine the relationship between the time management skills and academic performance of students, to assess time management and practice among students, to determine patterns of time management among Jazan University students. In addition to determine whether student participation in extra-curricular activities and social media correlates to his or her cumulative grade point average (CGPA). Method: The study design is a cross-sectional study of the effect of time management on academic performance. Conducted it in Jazan University for medical and non-medical students. Results: The study conducted on 491 participants of female (53.80%) and male (46.20%) students. The Applied Medical Science students (24.20%) stated that they just consumed their time to complete homework, while Faculty of Science students (9.40%) reported that they rarely have time to do. We find that 44.2% of male and 65% of female never participate in student club, while 43.50% of male and 15.60% of female always do sports and 12.90% of male and 4.20% of female always planning for these activities. Conclusion: Students who had opportunities to practice time management skills revield better academic performance in addition to the differences in the time management level between students according to faculty, gender and curriculum.
Pseudocounts for transcription factor binding sites

To represent the sequence specificity of transcription factors, the position weight matrix (PWM) is widely used. In most cases, each element is defined as a log likelihood ratio of a base appearing at a certain position, which is estimated from a finite number of known binding sites. To avoid bias due to this small sample size, a certain numeric value, called a pseudocount, is usually allocated for each position, and its fraction according to the background base composition is added to each element. So far, there has been no consensus on the optimal pseudocount value. In this study, we simulated the sampling process by artificially generating binding sites based on observed nucleotide frequencies in a public PWM database, and then the generated matrix with an added pseudocount value was compared to the original frequency matrix using various measures. Although the results were somewhat different between measures, in many cases, we could find an optimal pseudocount value for each matrix. These optimal values are independent of the sample size and are clearly correlated with the entropy of the original matrices, meaning that larger pseudocount vales are preferable for less conserved binding sites. As a simple representative, we suggest the value of 0.8 for practical uses.
Compressible mixing layer growth rate and turbulence characteristics

Direct numerical simulation databases have been used to study the effect of compressibility on mixing layers. The simulations cover convective Mach numbers from 0.2 to 1.2 and all contain a fully resolved turbulent energy cascade to small spatial scales. Statistical information is extracted from the databases to determine reasons for the reduced growth rate that is observed as the convective Mach number is increased. It is found that the dilatational contribution to dissipation is negligible even when eddy shocklets are observed in the flow. Also pressure-dilatation is not found to be significant. Using an accurate relation between the momentum thickness growth rate and the production of turbulence kinetic energy together with integrated equations for the Reynolds stress tensor it is shown that reduced pressure fluctuations are responsible for the changes in growth rate via the pressure-strain term. A deterministic model for the required pressure fluctuations is given based on the structure of variable-density vortices and the assumption that the limiting eddies are sonic. Simple anisotropy considerations are used to close the averaged equations. Good agreement with turbulence statistics obtained from the simulations is found.
Search-based data-flow test generation

Coverage criteria based on data-flow have long been discussed in the literature, yet to date they are still of surprising little practical relevance. This is in part because 1) manually writing a unit test for a data-flow aspect is more challenging than writing a unit test that simply covers a branch or statement, 2) there is a lack of tools to support data-flow testing, and 3) there is a lack of empirical evidence on how well data-flow testing scales in practice. To overcome these problems, we present 1) a search-based technique to automatically generate unit tests for data-flow criteria, 2) an implementation of this technique in the Evosuite test generation tool, and 3) a large empirical study applying this tool to the SF100 corpus of 100 open source Java projects. On average, the number of coverage objectives is three times as high as for branch coverage. However, the level of coverage achieved by Evosuite is comparable to other criteria, and the increase in size is only 15%, leading to higher mutation scores. These results counter the common assumption that data-flow testing does not scale, and should help to re-establish data-flow testing as a viable alternative in practice.