Homoplasy in Bacterial Evolution

This study addressed the following research goals: (1) a reevaluation of Lifelong Learning (LLL) scale’s reliability and validity measuring LLL skills, (2) reevaluation of Engineering Attitude Survey’s (EAS) reliability and validity of measuring students’ attitudes toward STEM fields, (3) effects of an evidence-based pedological (EBP) treatment on students’ LLL and engineering attitudes (EA) during a Computer-Aided Design course. The appearance of homoplasy occurs when mutations are not derived from a common ancestor but arise independently in multiple branches of a phylogenetic tree. For bacteria, it suggests that genetic recombination events occur or positive selection exists during evolution, affecting the accuracy of phylogeny estimation. Without considering recombination, the reconstruction of phylogenetic trees based on an alignment of bacterial strains could be misleading. Hence, to better understand their true evolutionary histories among a bacterial population, it is essential to identify recombination breakpoints before estimating their phylogeny. We developed an average compatibility ratio method with a permutation test, ptACR, to detect recombination breakpoints in a multiple sequence alignment without requiring a tree. We use a sliding window to evaluate the local compatibility of adjacent polymorphic sites to locate potential breakpoints and then assess the statistical significance of candidate breakpoints by applying a permutation test. We evaluate the performance of ptACR on both simulated and empirical datasets. The simulation results show that it has similar sensitivity but higher specificity and better F1 score compared to existing methods. Also, ptACR detects recombination events in a collection of clinical isolates of Mycobacterium avium and Staphylococcus aureus, and identifies boundaries of regions with statistical significance, where the adjacent regions exhibit distinct phylogenies. For clonal species, since recombination is less likely to occur, the occurrence of homoplasy is a strong indicator of positive selection, such as antibiotic resistance. To identify mutations conferring resistance, genome-wide association studies are commonly applied to identify statistically significant associations between genotypes (polymorphisms) and phenotypes of interests (antibiotic resistance) across the entire genome. However, homoplasy is not well accounted for by most bacterial genome-wide association analyses, producing false positives or false negatives. Also, existing association methods usually use an individual site or group polymorphisms within a gene as genotypes without considering the frequency of evolutionary convergence and the mutation rate in different regions. To better exploit homoplasy, we developed a two-phase evolutionary cluster-based convergence test (ECC) to identify regions harboring mutations under selection pressure associated with antibiotic resistance. In the first-phase step, we apply a Poisson distribution to detect regions exhibiting more changes (distinct mutational events) than expected by optimizing the grouping of SNPs within windows. Next, we test associations between the clustered regions and drug resistance using a hypergeometric distribution based on the concept of convergence test in the second phase. We model the distribution of changes occurring in the resistant or sensitive branches for each clustered region and compare it to the background. We evaluate the ECC method on empirical datasets of clinical isolates of Mycobacterium tuberculosis with seven phenotypes from drug susceptibility tests. Our two-phase evolutionary cluster-based convergence method is able to identify known resistant-associated sites within genes or intergenic regions corresponding to seven anti-tuberculous drugs. It also identifies two novel clustered regions in Rv2571 and Rv1830, potentially linked to isoniazid resistance. It improves the potential over existing methods for association tests to find more novel resistant-associated mutations, which will ultimately help in developing new antibiotic treatments. In sum, we present two models for identifying genomic regions affected by recombination (ptACR) and clustered regions associated with antibiotic resistance driven by selection pressure (ECC) in bacterial genomes

Physician Acceptance Behavior of the Electronic Medical Records Exchange: An Extended Decomposed Theory of Planned Behavior

In this study, we examined physician acceptance behavior of the electronic medical record (EMR) exchange. Although several prior studies have focused on factors that affect the adoption or use of EMRs, empirical study that captures the success factors that encourage physicians to adopt the EMR exchange is limited. Therefore, drawing on institutional trust integrated with the decomposed theory of planned behavior (TPB) model, we propose a theoretical model to examine physician intentions of using the EMR exchange. A field survey was conducted in Taiwan to collect data from physicians. Structural equation modeling (SEM) using the partial least squares (PLS) method was employed to test the research model. The results showed that the usage intention of physicians is significantly influenced by 4 factors (i.e., attitude, subjective norm, perceived behavior control, and institutional trust). These 4 factors were assessed by their perceived usefulness and compatibility, facilitating conditions and self-efficacy, situational normality, and structural assurance, respectively. The results also indicated that institutional trust integrated with the decomposed TPB model provides an improved method for predicting physician intentions to use the EMR exchange. Finally, the implications of this study are discussed

Semidefinite programming bounds on the size of entanglement-assisted codeword stabilized quantum codes

In this paper, we explore the application of semidefinite programming to the realm of quantum codes, specifically focusing on codeword stabilized (CWS) codes with entanglement assistance. Notably, we utilize the isotropic subgroup of the CWS group and the set of word operators of a CWS-type quantum code to derive an upper bound on the minimum distance. Furthermore, this characterization can be incorporated into the associated distance enumerators, enabling us to construct semidefinite constraints that lead to SDP bounds on the minimum distance or size of CWS-type quantum codes. We illustrate several instances where SDP bounds outperform LP bounds, and there are even cases where LP fails to yield meaningful results, while SDP consistently provides tight and relevant bounds. Finally, we also provide interpretations of the Shor-Laflamme weight enumerators and shadow enumerators for codeword stabilized codes, enhancing our understanding of quantum codes.Comment: 20 pages, 1 tabl

Energy saving evaluation of the ventilated BIPV walls."

ABSTRACT This study integrates photovoltaic (PV) system, building structure, and heat flow mechanism to propose the ventilated building-integrated photovoltaics (BIPV) walls. Energy-saving potential of the ventilated BIPV walls was investigated via engineering considerations and computational fluid dynamics (CFD) simulations. The results show that the heat removal rate and indoor heat gain of the proposed ventilated BIPV walls were dominantly affected by outdoor wind velocity and airflow channel width. Correlations for predicting the heat removal rate and indoor heat gain are introduced. After considering building construction practices, this prototype was transformed into a curtain wall structure that complemented the design of the overall construction

Measuring the Quality of Financial Electronic Payment System: Combined with Fuzzy AHP and Fuzzy TOPSIS

The study aims to apply Fuzzy AHP in TOPSIS to discuss the key factors that foster the success of current third-party online payment platforms. This study organized the quality measurements into four categories and eleven sub-categories. The AHP in TOPSIS is applied to calculate the weighted averages of all categories and sub-categories to measure the quality of third-party online payment platforms. This study finds that “safety quality” is the most emphasized category, “system quality” is the second, “communication quality” is the third, and “service quality” is the least emphasized

Bian Zheng Lun Zhi

Background. Limited scientific evidence supports the positive effects of traditional Chinese medicine (TCM) for treating dysmenorrhea. Thus, an observation period of 3 months could verify the ancient indication that TCM treatments effectively alleviate menstrual cramps in women with primary dysmenorrhea or endometriosis. Methods. A prospective, nonrandomized study (primary dysmenorrhea and endometriosis groups) was conducted in women with dysmenorrhea for more than three consecutive menstrual cycles. All patients received TCM prescriptions based on bian zheng lun zhi theory 14 days before menstruation for a period of 12 weeks. Pain intensity was evaluated using a 10-cm visual analogue scale and two validated questionnaires (the Menstrual Distress Questionnaire and the World Health Organization Quality of Life questionnaire). Results. Of the initial 70 intent-to-treat participants, the women with dysmenorrhea reported significant alleviation of cramps during menstruation after the 12-week TCM treatment. Mixed model analysis revealed that TCM prescriptions were more effective in alleviating fatigue, hot flashes, dizziness, painful breasts, excitement, and irritability in the primary dysmenorrhea group (N=36) than in the endometriosis group (N=34). Conclusion. TCM prescriptions based on syndrome differentiation theory might be a potentially viable choice for treating painful menstruation and premenstrual symptoms after ruling out endometriosis

On the size of maximal binary codes with 2, 3, and 4 distances

We address the maximum size of binary codes and binary constant weight codes with few distances. Previous works established a number of bounds for these quantities as well as the exact values for a range of small code lengths. As our main results, we determine the exact size of maximal binary codes with two distances for all lengths $n\ge 6$ as well as the exact size of maximal binary constant weight codes with 2,3, and 4 distances for several values of the weight and for all but small lengths.Comment: Main text 23 pp. and Appendix 17p

On the size of maximal binary codes with 2, 3, and 4 distances

We address the maximum size of binary codes and binary constant weight codes with few distances. Previous works established a number of bounds for these quantities as well as the exact values for a range of small code lengths. As our main results, we determine the exact size of maximal binary codes with two distances for all lengths n≥6 as well as the exact size of maximal binary constant weight codes with 2,3, and 4 distances for several values of the weight and for all but small lengths

Web-based computer adaptive assessment of individual perceptions of job satisfaction for hospital workplace employees

<p>Abstract</p> <p>Background</p> <p>To develop a web-based computer adaptive testing (CAT) application for efficiently collecting data regarding workers' perceptions of job satisfaction, we examined whether a 37-item Job Content Questionnaire (JCQ-37) could evaluate the job satisfaction of individual employees as a single construct.</p> <p>Methods</p> <p>The JCQ-37 makes data collection via CAT on the internet easy, viable and fast. A Rasch rating scale model was applied to analyze data from 300 randomly selected hospital employees who participated in job-satisfaction surveys in 2008 and 2009 via non-adaptive and computer-adaptive testing, respectively.</p> <p>Results</p> <p>Of the 37 items on the questionnaire, 24 items fit the model fairly well. Person-separation reliability for the 2008 surveys was 0.88. Measures from both years and item-8 job satisfaction for groups were successfully evaluated through item-by-item analyses by using <it>t</it>-test. Workers aged 26 - 35 felt that job satisfaction was significantly worse in 2009 than in 2008.</p> <p>Conclusions</p> <p>A Web-CAT developed in the present paper was shown to be more efficient than traditional computer-based or pen-and-paper assessments at collecting data regarding workers' perceptions of job content.</p