bluuebunny/crossref_metadata_2025 huggingface dataset:
A Case Study of White Teacher Candidates’ Conceptions of Racial Profiling in Educational Contexts
Authors: Baggett Hannah Carson , Simmons Crystal G.
Published: November 2017

Few studies have investigated how current events surrounding issues of racial profiling are understood by preservice teachers or how they affect their understandings and conceptions of race and racism in society and more importantly, in educational contexts. This qualitative case study explored how two White teacher candidates understood and conceptualized racial profiling in the wake of Trayvon Martin's murder. By interviewing teacher candidates about their own experiences with profiling, we hoped to prompt reflection and perspective-taking, especially in White teacher candidates who might hold beliefs that may not be adaptive for meeting the needs of students of color. In this study, one participant conceptualized racial profiling as intrinsic to her understanding of the educational experiences of students of color and articulated that profiling contributed to her broader understanding of racism. While the other participant regarded profiling as relevant to educational contexts, she implied that she found some truth in profiles and stereotypes of people of color and reported ‘colorblind’ approaches to teaching and learning. Implications for teacher education and future research are discussed.
When disaster strikes: Under-insurance in Australian households
Authors: Booth Kate , Tranter Bruce
Published: November 2017

In undertaking what we believe is the first national-scale study of its kind, we provide methodologically transparent, statistically robust insights into associations and potential unfolding effects of house and contents under-insurance. We identify new dimensions in the complex relationship between householders and insurance, including the salience of interpersonal – and likely institutional – trust. Under-insurance is (re)produced along socio-economic and geographical lines, with those of lower socio-economic status or living in cities more likely to be under-insured. Should a disaster strike, such communities are likely to suffer further disadvantage, especially if governments continue to shift the responsibility for risk onto households. Our findings support the observation that insurance can contribute to increasing socio-economic urban polarisation in light of natural disasters. We conclude by considering how under-insurance may contribute to growing urban social stratification, as well as how it may produce situated ethical and political responses that exceed neoliberal aspirations.
A power quality enhanced grid voltage sensorless predictive direct power control for active front end rectifiers
Authors: Kumar Amit , Srungavarapu Gopalakrishna
Published: November 2017

In this research work, a power quality enhanced grid voltage sensorless deadbeat predictive direct power control (DB-DPC) approach for AC/DC power converters based on latest virtual flux (VF) estimation, DB-DPC and space vector pulse width modulation (SVPWM) is proposed. At first, the grid voltage sensorless technique with switching table based DPC, which is a conventional approach, is discussed and its performance is analyzed under both increase of load as well as decrease of load conditions. Further, the proposed technique performance is also analyzed under the same circumstance and its performance is compared with the traditional method. The proposed technique has numerous advantages over the conventional method such as constant switching frequency, better active and reactive power control, good regulation of dc bus voltage, and enhanced power quality performance. As the proposed approach utilizes VF, DB-PC, and SVPWM techniques, this ensure line voltage sensorless approach, excellent control dynamics and constant switching frequency, respectively. At the end, experimental validation is done to confirm the supremacy of the proposed technique under load varying conditions and has a phenomenal performance under these circumstances.
Systematic Review of Differential Reinforcement of Alternative Behavior Without Extinction for Individuals With Autism
Authors: MacNaul Hannah L. , Neely Leslie C.
Published: November 2017

The purpose of this article is to review the literature on differential reinforcement of alternative behavior procedures without extinction for individuals with autism. Using predetermined inclusion criteria, a total of 10 studies were included and summarized in terms of the following: (a) participant characteristics (e.g., sex, age, and diagnosis), (b) treatment setting, (c) problem behavior, (d) function, (e) alternative behavior, (f) intervention, (g) outcomes, and (h) conclusiveness of evidence. Of the 10 studies, nine demonstrated positive effects and one mixed effects. Five studies successfully reduced problem behavior by manipulating different reinforcement parameters (magnitude, immediacy, and quality) and four manipulated the schedule of reinforcement. One study had mixed results with two of the three participants requiring extinction. The findings of this review suggest that variations of differential reinforcement of alternative behavior interventions without an extinction component may be considered promising practices for the treatment of challenging behavior in individuals with autism.
Ongoing Narrative Meaning-Making Within Events and Across the Life Span
Authors: Fivush Robyn , Booker Jordan A. , Graci Matthew E.
Published: November 2017

Individuals create meaning from the events in their lives, and the ways in which they do this has important implications for identity and well-being. We argue that this is a deeply developmental process. Narrative meaning-making consists of a set of developmentally acquired skills and abilities such that individuals are capable of different forms of meaning creation at different developmental periods. Further, narrative meaning-making emerges differentially across days, weeks, months, and years after an experience, and this event processing takes place within ongoing developmental change. Narrating life experiences both reflects and creates modes of meaning-making in a complex, reciprocal system.
Multi-Image Pinhole Viewer Using a Biscuit
Authors: Cabe Patrick A.
Published: November 2017

A camera obscura-type viewer based on pinhole optics, with the apertures being the holes in a commercial snack biscuit (or cracker), produces interesting and easily obtainable projected images, as demonstrated during the 2017 solar eclipse.
The Criminogenic and Noncriminogenic Treatment Needs of Intimate Partner Violence Offenders
Authors: Hilton N. Zoe , Radatz Dana L.
Published: November 2017

The criminogenic needs of general offenders have been empirically studied, but the criminogenic treatment needs of intimate partner violence (IPV) offenders, or how they compare with other violent or nonviolent offenders, have not been as thoroughly explored. Therefore, we examined and compared the criminogenic and noncriminogenic needs of 99 IPV offenders, 233 non-IPV violent offenders, and 103 nonviolent offenders, all of whom were men who had undergone institutional forensic assessment. Results indicated that IPV offenders had more treatment needs than the other two offender groups, including the Central Eight criminogenic needs. These findings support a focus on criminogenic treatment needs in batterer intervention programs for men, consistent with the principles of effective intervention for offenders.
Rethinking Varieties of Capitalism from the Latin American Periphery
Authors: Fernández Víctor Ramiro , Ebenau Matthias , Bazza Alcides
Published: November 2017

The article reconsiders how capitalist diversity is conceived of in the mainstream institutionalist “comparative capitalisms” literature. It highlights the division between centers and peripheries as a differentiation prior to national varieties, subsequently introducing the concepts of “nuclei of accumulation” and “nuclei of state implication.” It proposes to analyze (peripheral) varieties of capitalism as results of the conformation and change of these nuclei, their interrelations, and their insertion into global economic and political networks.
eBay Memorabilia Auctions vis-à-vis Predictions for the 2016 U.S. Presidential Election
Authors: Highfill Jannett , O’Brien Kevin M.
Published: November 2017

The present paper investigates whether there is a relationship between eBay auction outcomes for memorabilia and various predictions from the FiveThirtyEight site for the 2016 U.S. presidential election. We find that changes in the value of various FiveThirtyEight prediction variables were almost always correlated with the number of bids. For the national prediction, an increase in the probability of a Clinton victory was associated with a reduction in the number of bids and the willingness to pay for an item. Similar results were found for the subsample of Trump items, suggesting that the auctions for his items dominated the results for the full sample.

JEL Classifications: A20, D44, L81
Flange buckling behaviour of FRP box-beams: A parametric study
Authors: Kasiviswanathan M , Upadhyay Akhil
Published: November 2017

FRP is gaining popularity in civil engineering applications due to their high specific strength and stiffness, lightweight and tailoring ability. Meantime, box beam applications have also been increased in bridges due to their high inherent torsional stiffness. The combination of FRP and box-beam is ideal in lightweight bridges. However, being a thin-walled structure, designs are often governed by stability. In the FRP box-beam, two types of buckling are possible, i.e. flange and web buckling. In this paper, flange buckling behaviour of simply supported FRP box-beam subjected to lateral load has been studied with emphasis on the effect of moment gradient and rotational restraint. Web buckling is precluded by adopting thicker webs. Extensive numerical studies have been conducted to identify the parameters which significantly affect the flange buckling. The significance of defined parameters has been shown with the help of generic curves and bar charts, which will be helpful to the designers at the preliminary stage.
Magnesium and zinc borate enhance osteoblastic differentiation of stem cells from human exfoliated deciduous teeth in vitro
Authors: Liu Yao-Jen , Su Wen-Ta , Chen Po-Hung
Published: November 2017

Various biocompatible and biodegradable scaffolds blended with biochemical signal molecules with adequate osteoinductive and osteoconductive properties have attracted significant interest in hard tissue engineering regeneration. We evaluated the distinct effects of magnesium borate, zinc borate, and boric acid blended into chitosan scaffold for osteogenic differentiation of stem cells from exfoliated deciduous teeth. Stem cells from exfoliated deciduous teeth cells are a potential source of functional osteoblasts for applications in bone tissue engineering, but the efficiency of osteoblastic differentiation is low, thereby significantly limiting their clinical applications. Divalent metal borates have potential function in bone remodeling because they can simulate bone formation and decrease bone resorption. These magnesium, zinc, and B ions can gradually be released into the culture medium from the scaffold and induce advanced osteoblastic differentiation from stem cells from exfoliated deciduous teeth. Stem cells from exfoliated deciduous teeth with magnesium borate or zinc borate as inducer demonstrated more osteoblastic differentiation after 21 days of culture. Differentiated cells exhibited activity of alkaline phosphatase, bone-related gene expression of collagen type I, runt-related transcription factor 2, osteopontin, osteocalcin, vascular endothelial growth factor, and angiopoietin-1, as noted via real-time polymerase chain reaction analysis, as well as significant deposits of calcium minerals. Divalent mental magnesium and zinc and nonmetal boron can be an effective inducer of osteogenesis for stem cells from exfoliated deciduous teeth. This experiment might provide useful inducers for osteoblastic differentiation of stem cells from exfoliated deciduous teeth for tissue engineering and bone repair.
Prevalence and Risk Factors of Women’s Past-Year Physical IPV Perpetration and Victimization in Tanzania
Authors: Reese Bianka M. , Chen May S. , Nekkanti Manali , Mulawa Marta I.
Published: November 2017

Recent studies of intimate partner violence (IPV) in high-resource countries suggest that men and women may perpetrate similar rates of violence against their partners, yet the prevalence and etiology of female-perpetrated IPV, especially in comparison with IPV victimization among females, remains largely understudied in low-resource, high-prevalence countries, particularly in sub-Saharan Africa. Using multivariate logistic regression models, the current study examines the prevalence of and risk factors associated with past 12-month experiences of isolated physical IPV perpetration (i.e., violence perpetrated against an intimate partner not in self-defense) and physical IPV victimization among a nationally representative sample of women of reproductive age (15-49 years) from Tanzania who completed the Tanzanian Demographic and Health Survey Domestic Violence Module ( n = 5,372). Approximately 1.5% reported perpetrating violence in the past 12 months, whereas 35% reported victimization in the same time period. Risk factors of past 12-month IPV perpetration included past 12-month IPV victimization, making cash or in-kind earnings, having autonomy in decision making, and acceptance of justifications for wife beating. Women much younger than their partners had lower odds of IPV perpetration. Risk factors of past 12-month IPV victimization included past 12-month IPV perpetration, educational attainment, having children, partner’s alcohol consumption, partner’s decision making, acceptance of justifications for wife beating, and exposure to parental IPV. Making cash or in-kind earnings was the only protective factor against victimization. Findings suggest that female IPV perpetration and victimization may result from a combination of factors including power differentials between partners and attitudes about the acceptability of using violence. Future research directions and implications for policy and prevention efforts to reduce IPV in Tanzania are discussed.
Financial Compensation and Organizational Commitment: Differences Among Mexican and Malaysian Bankers
Authors: Llanos Luis Felipe , Bin Ahmad Rusli
Published: November 2017

Mexico and Malaysia are contrasting countries, geographically on opposite sides of the globe, with plenty of cultural differences, but with a similar gross domestic product per capita, and a similar banking commercial system. The hypothesis is the the economic compensation systems of bank employees in both countries, salaries, bonus and merit based pay, correlate with the same labor commitment. The research uses the same data collection instrument and results recently obtained in a Malaysian study to compare them to the Mexican case, through multivariate analysis. First results show that the Malaysian instrument is consistently valid and reliable in the case of Mexico. Second, the study confirms that Mexico’s strategy of raising the salary of bankers, or their bonuses, or merit-based payments, may increase organizational commitment but not altogether. Third, results suggest that merit-based compensation schemes are more efficient in countries with low uncertainty aversion, such as Malaysia, and less efficient in countries with high risk aversion, as in the case of Mexico.
Effect of Preservice Classroom Management Training on Attitudes and Skills for Teaching Children With Emotional and Behavioral Problems: A Randomized Control Trial
Authors: Klopfer Kristina M. , Scott Katreena , Jenkins Jennifer , Ducharme Joe
Published: November 2017

Childhood emotional and behavioral problems are prevalent in elementary classroom settings, making it imperative that high-quality, efficacious training be available to support teachers in managing disruptive and distressed child behaviors. Our study used a randomized control design to examine the impact of 36 hours of preservice education targeted at improving the attitudes of teachers toward children with emotional and behavioral difficulties, and developing their skills in using proactive and preventative strategies to address anticipated behavioral challenges. Eighty-two preservice teachers were randomly assigned to an elective course on management of emotional and behavioral problems (50 teachers) or to an alternate elective of their choice (32 teachers). Results highlight the positive influence of targeted preservice instruction; specifically, there were medium to large posttest effect size differences between preservice teachers who received this elective as compared with those who did not on measures of teachers’ use of psychological pressure (e.g., teacher disappointment and shaming; d = 0.76), their positive emotions ( d = 0.69), negative reactions ( d = 1.05), and their use of proactive strategies ( d = 1.43 and 1.59), inadequate strategies ( d = 0.73), and reactive strategies ( d = 1.01) in response to challenging child behaviors in simulated classrooms. No significant intervention-related differences were noted in preservice teacher self-efficacy, endorsement of rules and control, warmth and support, or negative beliefs. Overall, results provide promising evidence that preservice training can effectively affect the immediate attitudes and skills of teachers for supporting children with emotional and behavioral problems in a regular classroom context.
Recurrent Admissions for Hypothermia From Concomitant Topiramate and Phenobarbital: A Case Report
Authors: Mutch Alisha M.
Published: November 2017

Introduction:

This article presents an additional case of concomitant topiramate and phenobarbital administration that resulted in 8 hospital admissions for hypothermia that resolved after discontinuation of phenobarbital.

Case:

A 56-year-old white female with cerebral palsy and quadriplegia, epilepsy, and hypothyroidism was admitted to a community teaching hospital multiple times with documented hypothermia. These admissions followed a subsequent dose increase of topiramate in December 2014. In February 2015, the patient was admitted with 35°C rectal temperature. Her 2 admissions in April were for hypothermia with temperatures of 34.6°C and 33.6°C, respectively. The patient had 5 other admissions with hypothermia through December 2015. All other causes of hypothermia were ruled out. The hypothermia resolved when phenobarbital was discontinued.

Discussion:

A recent case series noted an association between phenobarbital and topiramate causing hypothermia. The patient’s hypothermia developed while on concomitant phenobarbital and topiramate but only after an increase in topiramate. No other causes for hypothermia were found based upon physical examination or lab work. The Naranjo nomogram noted a probable causation.

Conclusion:

This case report points to an association of hypothermia with concomitant topiramate and phenobarbital with resolution after phenobarbital discontinuation. Improvement after discontinuation of phenobarbital seems to support a drug-effect relationship.
A joint model for multivariate hierarchical semicontinuous data with replications
Authors: Kassahun-Yimer Wondwosen , Albert Paul S , Lipsky Leah M , Nansel Tonja R , Liu Aiyi
Published: November 2017

Longitudinal data are often collected in biomedical applications in such a way that measurements on more than one response are taken from a given subject repeatedly overtime. For some problems, these multiple profiles need to be modeled jointly to get insight on the joint evolution and/or association of these responses over time. In practice, such longitudinal outcomes may have many zeros that need to be accounted for in the analysis. For example, in dietary intake studies, as we focus on in this paper, some food components are eaten daily by almost all subjects, while others are consumed episodically, where individuals have time periods where they do not eat these components followed by periods where they do. These episodically consumed foods need to be adequately modeled to account for the many zeros that are encountered. In this paper, we propose a joint model to analyze multivariate hierarchical semicontinuous data characterized by many zeros and more than one replicate observations at each measurement occasion. This approach allows for different probability mechanisms for describing the zero behavior as compared with the mean intake given that the individual consumes the food. To deal with the potentially large number of multivariate profiles, we use a pairwise model fitting approach that was developed in the context of multivariate Gaussian random effects models with large number of multivariate components. The novelty of the proposed approach is that it incorporates: (1) multivariate, possibly correlated, response variables; (2) within subject correlation resulting from repeated measurements taken from each subject; (3) many zero observations; (4) overdispersion; and (5) replicate measurements at each visit time.
The Development of Gratitude in the United States
Authors: O’Brien Lia , Mendonça Sara E. , Price Uzama S.
Published: November 2017

Gratitude develops over the course of childhood and adolescence. However, the processes involved are largely unknown. We propose that cultural context may play an important role in gratitude development. As a whole, this special issue examines cultural influences on the development of gratitude. In this article, we focus on the development of gratitude in the United States. According to Kağıtçıbaşı, the United States would demonstrate features of autonomy and separateness. We describe the culture of the United States and Greensboro, North Carolina, specifically. To examine gratitude development in the United States, we recruited 426 children between 7 and 14 years of age ( M = 10.23 years) in Greensboro, North Carolina. In this sample, we found that older children were more likely to express connective gratitude and also to save their money. It is important to understand the features of culture that encourages the expression of gratitude.
Sustaining Engagement in Longitudinal Research With Vulnerable Families: A Mixed-Methods Study of Attrition
Authors: Ginn Carla S. , Mughal Muhammad Kashif , Syed Hafsa , Storteboom Amanda Rae , Benzies Karen M.
Published: November 2017

The aim of this mixed-methods study was to investigate attrition at the age 10-year follow-up in a study of vulnerable children and their families living with low income following a two-generation preschool program in Calgary, Alberta, Canada. Quantitative factors associated with attrition included: (a) food bank use; (b) unstable housing; (c) child welfare involvement; (d) unpartnered status; and (e) caregiver noncompletion of high school. Qualitative themes related to attrition included: (a) income and employment; (b) health; (c) unstable housing; (d) change of guardianship; (e) domestic violence; (f) work and time management challenges; and (g) negative caregiver–child relationships. Triangulation of quantitative and qualitative results occurred using Maslow’s Hierarchy of Needs; families with unmet physiological, safety, belongingness and love needs, and esteem needs were more likely to attrite. Attrition in longitudinal studies with vulnerable families is complex, affected by frequently changing life circumstances, and struggles to access necessities of life. Strategies for retaining vulnerable families in longitudinal research are offered.
Experiencing Financial Hardship Associated With Medical Bills and Its Effects on Health Care Behavior: A 2-Year Panel Study
Authors: Choi Sunha
Published: November 2017

Using 2-year panel data, this study examined (1) whether experiencing financial hardship associated with out-of-pocket medical expenditures affected delaying/missing necessary health care in the following year; (2) whether such financial hardship mediated the effects of predisposing, enabling, and need characteristics on timely health care access (i.e., significant indirect effects); and (3)whether such mediating effects are different by chronic health status (i.e., moderated mediation) among U.S. adults. The 2011 National Health Interview Survey was linked to the 2012 Medical Expenditure Panel Survey. The sample includes 8,993 adults aged between 26 and 64 years. Among them, 1,089 reported having at least one chronic health condition that had caused activity limitations. Multiple-group path analysis was conducted using Mplus 7.2. Approximately 35% experienced financial difficulties paying medical bills, including 28% who were currently paying off medical debts. Almost 14% of the respondents reported delayed/missed necessary medical treatments. In addition to direct effects, predisposing, enabling, and need factors affected access to care indirectly via financial hardship, although significant moderated mediation was found by chronic health status. However, different from the Andersen’s behavioral model of health service utilization, the effect of financial hardship due to medical bills as a barrier to the timely use of necessary health services was not smaller among adults with chronic health conditions. Policy alternatives should be explored to provide affordable financing programs and adequate safety net health services to reduce the financial burden of health care for those who are financially vulnerable, especially those suffering from chronic health conditions.
Examining College Students’ Social Environment, Normative Beliefs, and Attitudes in Subsequent Initiation of Electronic Nicotine Delivery Systems
Authors: Agarwal Deepti , Loukas Alexandra , Perry Cheryl L.
Published: November 2017

Background. Although use of Electronic Nicotine Delivery Systems (ENDS) is increasingly prevalent among young adults, little is known about predictors of ENDS initiation among this population. Aims. We examined the roles of the social environment (i.e., peer ENDS use and household ENDS use), normative beliefs (i.e., social acceptability of ENDS use), and attitudes (i.e., inclination to date someone who uses ENDS) in prospectively predicting initiation of ENDS over a 1-year period among 18- to 29-year-old college students. Method. Participants were 2,110 (18- to 29-year–old) students ( M = 20.27, SD = 2.17) from 24 colleges in Texas who participated in a three-wave online survey, with 6 months between each wave. All participants reported never using ENDS at baseline. A multivariable, multilevel logistic regression model, accounting for clustering of students within colleges, was used to assess if students’ social environment, normative beliefs, and attitudes predicted subsequent initiation of ENDS up to 1 year later, adjusting for various sociodemographic factors and number of other tobacco products used. Results. In all, 329 college students (16%) initiated ENDS within 1 year. Results from the logistic regression indicated that college students who were younger (18-24 years old), ever used other tobacco products, indicated a more dense peer network of ENDS users, and had a higher inclination to date someone who uses ENDS had higher odds of initiating ENDS than their peers. Conclusion. Preventing ENDS initiation should be included in college health promotion programs, which should highlight the roles of students’ social environment and attitudes regarding ENDS use.
Arlequin (version 3.0): An integrated software package for population genetics data analysis
Authors: Excoffier Laurent , Laval Guillaume , Schneider Stefan
Published: November 2017

Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3 .
MySSP: Non-stationary evolutionary sequence simulation, including indels
Authors: Rosenberg Michael S.
Published: November 2017

MySSP is a new program for the simulation of DNA sequence evolution across a phylogenetic tree. Although many programs are available for sequence simulation, MySSP is unique in its inclusion of indels, flexibility in allowing for non-stationary patterns, and output of ancestral sequences. Some of these features can individually be found in existing programs, but have not all have been previously available in a single package.
The identification of functional motifs in temporal gene expression analysis
Authors: Song Jiuzhou , Bjarnason Jaime , Surette Michael G.
Published: November 2017

The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR) and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur) binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.
Improved Heuristics for Minimum-Flip Supertree Construction
Authors: Chen Duhong , Eulenstein Oliver , Fernández-Baca David , Burleigh J. Gordon
Published: November 2017

The utility of the matrix representation with flipping (MRF) supertree method has been limited by the speed of its heuristic algorithms. We describe a new heuristic algorithm for MRF supertree construction that improves upon the speed of the previous heuristic by a factor of n (the number of taxa in the supertree). This new heuristic makes MRF tractable for large-scale supertree analyses and allows the first comparisons of MRF with other supertree methods using large empirical data sets. Analyses of three published supertree data sets with between 267 to 571 taxa indicate that MRF supertrees are equally or more similar to the input trees on average than matrix representation with parsimony (MRP) and modified mincut supertrees. The results also show that large differences may exist between MRF and MRP supertrees and demonstrate that the MRF supertree method is a practical and potentially more accurate alternative to the nearly ubiquitous MRP super-tree method.
Unravelling Selection Shifts among Foot-and-Mouth Disease virus (FMDV) Serotypes
Authors: Tully Damien C. , Fares Mario A.
Published: November 2017

FMDV virus has been increasingly recognised as the most economically severe animal virus with a remarkable degree of antigenic diversity. Using an integrative evolutionary and computational approach we have compelling evidence for heterogeneity in the selection forces shaping the evolution of the seven different FMDV serotypes. Our results show that positive Darwinian selection has governed the evolution of the major antigenic regions of serotypes A, Asia1, O, SAT1 and SAT2, but not C or SAT3. Co-evolution between sites from antigenic regions under positive selection pinpoints their functional communication to generate immune-escape mutants while maintaining their ability to recognise the host-cell receptors. Neural network and functional divergence analyses strongly point to selection shifts between the different serotypes. Our results suggest that, unlike African FMDV serotypes, serotypes with wide geographical distribution have accumulated compensatory mutations as a strategy to ameliorate the effect of slightly deleterious mutations fixed by genetic drift. This strategy may have provided the virus by a flexibility to generate immune-escape mutants and yet recognise host-cell receptors. African serotypes presented no evidence for compensatory mutations. Our results support heterogeneous selective constraints affecting the different serotypes. This points to the possible accelerated rates of evolution diverging serotypes sharing geographical locations as to ameliorate the competition for the host.
Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations
Authors: Lee Tai-Sung , Potts Steven J. , McGinniss Matthew J. , Strom Charles M.
Published: November 2017

Computational prediction of the impact of a mutation on protein function is still not accurate enough for clinical diagnostics without additional human expert analysis. Sequence alignment-based methods have been extensively used but their results highly depend on the quality of the input alignments and the choice of sequences. Incorporating the structural information with alignments improves prediction accuracy. Here, we present a conservation of amino acid properties method for mutation prediction, Multiple Properties Tolerance Analysis (MuTA), and a new strategy, MuTA/S, to incorporate the solvent accessible surface (SAS) property into MuTA. Instead of combining multiple features by machine learning or mathematical methods, an intuitive strategy is used to divide the residues of a protein into different groups, and in each group the properties used is adjusted.

The results for LacI, lysozyme, and HIV protease show that MuTA performs as well as the widely used SIFT algorithm while MuTA/S outperforms SIFT and MuTA by 2%–25% in terms of prediction accuracy. By incorporating the SAS term alone, the alignment dependency of overall prediction accuracy is significantly reduced. MuTA/S also defines a new way to incorporate any structural features and knowledge and may lead to more accurate predictions.
Coevolution of Exploiter Specialization and Victim Mimicry can be Cyclic and Saltational
Authors: Norrström Niclas , Getz Wayne M. , Holmgren Noél
Published: November 2017

Darwin's Principle of Divergence explains sympatric speciation as gradual and directional. Contradicting evidence suggests that species' traits evolve saltationally. Here, we model coevolution in exploiter-victim systems. Victims (resource population) have heritable, mutable cue phenotypes with different levels of defense. Exploiters have heritable, mutable perceptual phenotypes. Our simulations reveal coevolution of victim mimicry and exploiter specialization in a saltational and reversible cycle. Evolution is gradual and directional only in the specialization phase of the cycle thereby implying that specialization itself is saltational in such systems. Once linked to assortative mating, exploiter specialization provides conditions for speciation.
LASER: A Maximum Likelihood Toolkit for Detecting Temporal Shifts in Diversification Rates from Molecular Phylogenies
Authors: Rabosky Daniel L.
Published: November 2017

Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods provide a useful framework for inferring temporal variation in diversification rates. LASER is a package for the R programming environment that implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time. LASER contrasts the likelihood of phylogenetic data under models where diversification rates have changed over time to alternative models where rates have remained constant over time. Major strengths of the package include the ability to detect temporal increases in diversification rates and the inference of diversification parameters under multiple rate-variable models of diversification. The program and associated documentation are freely available from the R package archive at http://cran.r-project.org.
Modelling Prokaryote Gene Content
Authors: Spencer Matthew , Susko Edward , Roger Andrew J.
Published: November 2017

The patchy distribution of genes across the prokaryotes may be caused by multiple gene losses or lateral transfer. Probabilistic models of gene gain and loss are needed to distinguish between these possibilities. Existing models allow only single genes to be gained and lost, despite the empirical evidence for multi-gene events. We compare birth-death models (currently the only widely-used models, in which only one gene can be gained or lost at a time) to blocks models (allowing gain and loss of multiple genes within a family). We analyze two pairs of genomes: two E. coli strains, and the distantly-related Archaeoglobus fulgidus (archaea) and Bacillus subtilis (gram positive bacteria). Blocks models describe the data much better than birth-death models. Our models suggest that lateral transfers of multiple genes from the same family are rare (although transfers of single genes are probably common). For both pairs, the estimated median time that a gene will remain in the genome is not much greater than the time separating the common ancestors of the archaea and bacteria. Deep phylogenetic reconstruction from sequence data will therefore depend on choosing genes likely to remain in the genome for a long time. Phylogenies based on the blocks model are more biologically plausible than phylogenies based on the birth-death model.
Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype
Authors: Zhang Xiang-Sun , Wang Rui-Sheng , Wu Ling-Yun , Zhang Wei
Published: November 2017

The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH) as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expected. We first prove the MCIH problem to be NP-hard. To evaluate the practicality of the new model we design an exact algorithm (a dynamic programming procedure) to implement MCIH on a special data structure. The numerical experience indicates that it is fairly effective to use MCIH at the cost of related genotype information, especially in the case of SNP fragments with a high error rate. Moreover, we present a feed-forward neural network algorithm to solve MCIH for general data structure and large size instances. Numerical results on real biological data and simulation data show that the algorithm works well and MCIH is a potential alternative in individual haplotyping.
Phylogenomic Analysis Reveals Extensive Phylogenetic Mosaicism in the Human GPCR Superfamily
Authors: Allaby Robin G. , Woodwark Mathew
Published: November 2017

A novel high throughput phylogenomic analysis (HTP) was applied to the rhodopsin G-protein coupled receptor (GPCR) family. Instances of phylogenetic mosaicism between receptors were found to be frequent, often as instances of correlated mosaicism and repeated mosaicism. A null data set was constructed with the same phylogenetic topology as the rhodopsin GPCRs. Comparison of the two data sets revealed that mosaicism was found in GPCRs in a higher frequency than would be expected by homoplasy or the effects of topology alone. Various evolutionary models of differential conservation, recombination and homoplasy are explored which could result in the patterns observed in this analysis. We find that the results are most consistent with frequent recombination events. A complex evolutionary history is illustrated in which it is likely frequent recombination has endowed GPCRs with new functions. The pattern of mosaicism is shown to be informative for functional prediction for orphan receptors. HTP analysis is complementary to conventional phylogenomic analyses revealing mosaicism that would not otherwise have been detectable through conventional phylogenetics.
Gathering Computational Genomics and Proteomics to Unravel Adaptive Evolution
Authors: Antunes Agostinho , Ramos Maria João
Published: November 2017

A recent editorial in PLoS Biology by MacCallum and Hill (2006) pointed out the inappropriateness of studies evaluating signatures of positive selection based solely in single-site analyses. Therefore the rising number of articles claiming positive selection that have been recently published urges the question of how to improve the bioinformatics standards for reliably unravel positive selection? Deeper integrative efforts using state-of-the-art methodologies at the gene-level and protein-level are improving positive selection studies. Here we provide some computational guidelines to thoroughly document molecular adaptation.
Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes
Authors: Vitulo Nicola , Vezzi Alessandro , Galla Giulio , Citterio Sandra , Marino Giada , Ruperti Benedetto , Zermiani Monica , Albertini Emidio , Valle Giorgio , Barcaccia Gianni
Published: November 2017

The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle progression with cell polarity and morphogenesis. Here we report the characterization and evolution of the MOB domain-containing proteins as inferred from the 43 eukaryotic genomes so far sequenced. We show that genes for Mob-like proteins are present in at least 41 of these genomes, confirming the universal distribution of this protein family and suggesting its prominent biological function. The phylogenetic analysis reveals five distinct MOB domain classes, showing a progressive expansion of this family from unicellular to multicellular organisms, reaching the highest number in mammals. Plant Mob genes appear to have evolved from a single ancestor, most likely after the loss of one or more genes during the early stage of Viridiplantae evolutionary history. Three of the Mob classes are widespread among most of the analyzed organisms. The possible biological and molecular function of Mob proteins and their role in conserved signaling pathways related to cell proliferation, cell death and cell polarity are also presented and critically discussed.
On the Adaptive Design Rules of Biochemical Networks in Evolution
Authors: Chen Bor-Sen , Wu Wan-Shian , Wu Wei-Sheng , Li Wen-Hsiung
Published: November 2017

Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive) to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process.

We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.
Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach
Authors: Chen Bor-Sen , Wu Wei-Sheng
Published: November 2017

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective.
A Reduction Algorithm for Computing the Hybridization Number of Two Trees
Authors: Bordewich Magnus , Linz Simone , John Katherine St. , Semple Charles
Published: November 2017

Hybridization is an important evolutionary process for many groups of species. Thus, conflicting signals in a data set may not be the result of sampling or modeling errors, but due to the fact that hybridization has played a significant role in the evolutionary history of the species under consideration. Assuming that the initial set of gene trees is correct, a basic problem for biologists is to compute this minimum number of hybridization events to explain this set. In this paper, we describe a new reduction-based algorithm for computing the minimum number, when the initial data set consists of two trees. Although the two-tree problem is NP-hard, our algorithm always gives the exact solution and runs efficiently on many real biological problems. Previous algorithms for the two-tree problem either solve a restricted version of the problem or give an answer with no guarantee of the closeness to the exact solution. We illustrate our algorithm on a grass data set. This new algorithm is freely available for application at either http://www.bi.uni-duesseldorf.de/~linz or http://www.math.canterbury.ac.nz/~cas83 .