bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding Parkinson’s through visual narratives: “I’m not Mrs. Parkinson’s”
Authors: Lutz Sara G , Holmes Jeffrey D , Rudman Debbie Laliberte , Johnson Andrew M , LaDonna Kori A , Jenkins Mary E
Published: November 2017

Introduction

Although it is accepted that individuals with Parkinson’s disease must navigate challenges such as receiving their diagnosis and changing daily occupations, little is known about how they navigate. The purpose of this study is to deepen the current understanding of the experience of living with Parkinson’s disease and its implications for occupation through a narrative visual methodology (photo-elicitation).

Method

Six individuals with Parkinson’s disease were asked to take photographs and share verbal narrative accounts to illustrate their experience of living with Parkinson’s disease.

Findings

Results highlight the interrelationship between occupation and identity, as many of the participants’ stories were interpreted as foregrounding the negotiation of occupation, and how such negotiation shaped their sense of identity. Overall, three major themes were identified: (1) Framing the meaning of Parkinson’s disease (accepting the disease as part of who they were); (2) Negotiating engagement in occupation (ongoing deliberation over whether to continue engaging in certain aspects of life as Parkinson’s disease progressed); and (3) Being ready to accept changes that impact personal or social identity (readiness to accept help and to identify as someone with Parkinson’s disease).

Conclusion

Attending to insights regarding the lived experience of Parkinson’s disease will enhance quality of care through informing an enriched client-centered, occupation-based approach.
Presidential campaign talk: Question-answering in ‘Neutral Informational Interviews’
Authors: Garcia Angela Cora
Published: November 2017

This article is a dual-case analysis of presidential campaign interviews conducted with former President George HW Bush when he was campaigning for the Republican presidential nomination in 1980, and former President William J. Clinton when he was campaigning for the presidency in 1991. Both interviews were conducted at high schools in New Hampshire and are publicly available on the C-SPAN website. The purpose of this analysis is to investigate how the success or failure of political campaigns may be tied to candidates’ interactional competence and pragmatic skills. This will be done through an examination of the strengths and weaknesses of the answers each candidate produced in the context of these non-adversarial interviews. This conversation analytic investigation reveals key differences between the two candidates in the successful display of various types of knowledge, interactional competency, sensitivity to audience design, fluency of speech and organization of their responses. The results are discussed in terms of the importance of interactional skills for the success of political campaigns and the effectiveness of ‘Neutral Informational Interviews’ for educating the audience.
A stochastic estimation procedure for intermittently-observed semi-Markov multistate models with back transitions
Authors: Aralis Hilary , Brookmeyer Ron
Published: November 2017

Multistate models provide an important method for analyzing a wide range of life history processes including disease progression and patient recovery following medical intervention. Panel data consisting of the states occupied by an individual at a series of discrete time points are often used to estimate transition intensities of the underlying continuous-time process. When transition intensities depend on the time elapsed in the current state and back transitions between states are possible, this intermittent observation process presents difficulties in estimation due to intractability of the likelihood function. In this manuscript, we present an iterative stochastic expectation-maximization algorithm that relies on a simulation-based approximation to the likelihood function and implement this algorithm using rejection sampling. In a simulation study, we demonstrate the feasibility and performance of the proposed procedure. We then demonstrate application of the algorithm to a study of dementia, the Nun Study, consisting of intermittently-observed elderly subjects in one of four possible states corresponding to intact cognition, impaired cognition, dementia, and death. We show that the proposed stochastic expectation-maximization algorithm substantially reduces bias in model parameter estimates compared to an alternative approach used in the literature, minimal path estimation. We conclude that in estimating intermittently observed semi-Markov models, the proposed approach is a computationally feasible and accurate estimation procedure that leads to substantial improvements in back transition estimates.
The resignation of Sir William Charles Ellis
Authors: Howe Andrew J
Published: November 2017

Sir William Ellis (1780–1839) was superintendent of the West Riding Pauper Lunatic Asylum and Hanwell Asylum. He was a practitioner of moral therapy and non-restraint. He added his own religious aspects to his treatment based on his personal experiences. These interventions were novel and benefitted his patients. However, he is less well known in the present day than his contemporaries who also championed non-restraint. In 1838, he left Hanwell Asylum, as he disagreed with plans to expand patient capacity. The resurgence of Whig politics at the time also played its part in his resignation. Ellis died one year later, his contributions to modern psychiatry remaining in relative obscurity. This paper seeks to shed light on Ellis and analyse his resignation as an example of how politics can affect healthcare.
The effect of nurses’ ethical leadership and ethical climate perceptions on job satisfaction
Authors: Özden Dilek , Arslan Gülşah Gürol , Ertuğrul Büşra , Karakaya Salih
Published: November 2017

Background:

The development of ethical leadership approaches plays an important role in achieving better patient care. Although studies that analyze the impact of ethical leadership on ethical climate and job satisfaction have gained importance in recent years, there is no study on ethical leadership and its relation to ethical climate and job satisfaction in our country.

Objectives:

This descriptive and cross-sectional study aimed to determine the effect of nurses’ ethical leadership and ethical climate perceptions on their job satisfaction.

Methods:

The study sample is composed of 285 nurses who agreed to participate in this research and who work at the internal, surgical, and intensive care units of a university hospital and a training and research hospital in İzmir, Turkey. Data were collected using Ethical Leadership Scale, Hospital Ethical Climate Scale, and Minnesota Satisfaction Scale. While the independent sample t-test, analysis of variance, Mann–Whitney U test, and Kruskal–Wallis test were used to analyze the data, the correlation analysis was used to determine the relationship between the scales.

Ethical considerations:

The study proposal was approved by the ethics committee of the Faculty of Medicine, Dokuz Eylül University.

Findings:

The nurses’ mean scores were 59.05 ± 14.78 for the ethical leadership, 92.62 ± 17 for the ethical climate, and 62.15 ± 13.46 for the job satisfaction. The correlation between the nurses’ ethical leadership and ethical climate mean scores was moderately positive and statistically significant (r = +0.625, p = 0.000), was weak but statistically significant between their ethical leadership and job satisfaction mean scores (r = +0.461, p = 0.000), and was moderately positive and statistically significant between their ethical climate and job satisfaction mean scores (r = +0.603, p = 0.000).

Conclusion:

The nurses’ ethical leadership, ethical climate, and job satisfaction levels are moderate, and there is a positive relationship between them. The nurses’ perceptions of ethical leadership are influenced by their educational status, workplace, and length of service.
Information Security Management Practices: Case Studies from India
Authors: Singh Abhishek Narain , Gupta M.P.
Published: November 2017

In recent years, information security has gained attention in organizations across diverse businesses and sectors. Primary reasons of this can be the new and innovative ways of information handling (during generation, processing, storage and distribution), and dependence of business processes on new and emerging IT/ICT mediums in organizations to carry out daily business activities. This has made organizations agile in terms of functioning and, at the same time, has posed new challenges. In this direction, the present study aims to explore and examine information security management (ISM) practices of two IT development and services organizations in India. In case study design, the study adopts qualitative research route to understand the current ISM practices of the case organizations. The observations derived from semi-structured interviews are presented using descriptive analysis methodology. Further, SAP-LAP (Situation, Actor, Process—Learning, Action, Performance) method of inquiry is used to analyse the findings from case studies. Results highlight the importance of consistent top management support, organizational information security culture and a proper monitoring system for ISM effectiveness in organizations. Insights derived from the study can be helpful for managers and decision makers in managing organizational information security practices.
From “Silent Birth” to Voices Heard: Volunteering, Meaning, and Posttraumatic Growth After Stillbirth
Authors: Cacciatore Joanne , Blood Cybele , Kurker Sarah
Published: November 2017

Volunteerism after stillbirth has not been adequately explored despite recent advances in research on volunteering after trauma and the voluminous research on posttraumatic growth (PTG). Previous research on PTG, “altruism born of suffering,” and constructivist theories of grief, meaning, and social narrative provide applicable frameworks. Parents ( N = 191) in the present study were assessed for self-reported growth factors with the Posttraumatic Growth Inventory (PTGI) scale and gave narrative reports describing the importance of volunteering for them after their baby's death. Parents who volunteered after their baby's death self-reported significantly higher mean scores on the PGTI than parents who did not volunteer. Qualitative analysis with parents who volunteered only after their baby's death ( n = 39) discovered salient categories that confirm and connect theoretically similar explorations from prior research, and also illuminate new directions for research. Clinical implications and caveats are presented.
Navigating an Uncertain Journey of Pregnancy After Perinatal Loss
Authors: Moore Sarah E. , Côté-Arsenault Denise
Published: November 2017

The purpose of this qualitative data analysis was to gain insights into women's experiences over the course of pregnancy subsequent to prior perinatal loss. Diaries from 19 pregnant women with a history of miscarriage, stillbirth, or neonatal death who participated in an intervention study were the data source. The participants were primarily Caucasian, 23 to 41 years old, with a history of one to six prior losses, high school to graduate school education, and a wide range of incomes. Inductive thematic analysis of pregnancy diary entries was done. A metaphor of navigating a pregnancy journey that feels scary and uncertain, toward the goal of reaching their desired destination, a healthy infant, was identified from women's personal accounts. Six themes were identified: (a) Staying Alert: Noting Physical Symptoms, (b) Dealing with Uncertainty: Expressing Emotions, (c) Dreaming of the Destination: Evolving Thoughts of Baby, (d) Traveling Together: Connecting with Others, and (e) Moving Forward: Reflecting on Sense of Self. The interaction of several themes is described as (f) Staying on Track: Navigating through Pregnancy. Women may find journaling helpful in dealing with the anxiety and fear that characterize pregnancy after loss. Viewing pregnancy after perinatal loss as similar to navigating an uncertain journey may provide greater understanding of the emotional, physical, and social challenges that women may experience. Recognition that women with a history of perinatal loss may be anxious and fearful during pregnancy will increase sensitive care.
Give Us Your Tired, Your Poor and We Might Buy Them Dinner: Social Capital, Immigration, and Welfare Generosity in the American States
Authors: Hawes Daniel P. , McCrea Austin Michael
Published: November 2017

A long-standing debate persists regarding how social capital relates to diversity and inequality in the American states. Putnam argues social capital leads to greater equality and tolerance; however, others find that it increases racial inequality. We build on Soss, Fording, and Schram’s Racial Classification Model (RCM) and theorize that social capital enhances social trust and empathy in homogeneous contexts and favors paternalistic and punitive social controls in diverse contexts. We test this using the case of immigration and welfare generosity following the Personal Responsibility and Work Opportunity Reconciliation Act (PRWORA) of 1996. Using state-level data from 1997 to 2009, we find that under conditions of low immigration, social capital is associated with increased social trust and empathy; however, as immigration increases, social capital pivots toward favoring mechanisms of social control. Specifically, social capital increases Temporary Assistance for Needy Families (TANF) cash benefit levels, but only when immigration levels are low. In high-immigration contexts, social capital is associated with decreased welfare generosity.
An Integrated Approach to Bias in a Longitudinal Survey in the United Kingdom: Assessing Construct, Method, and Item Bias in the General Health Questionnaire (GHQ-12)
Authors: Benítez Isabel , Adams Byron G. , He Jia
Published: November 2017

Construct, method, and item bias are three levels of measurement bias (i.e., internal bias) essential for valid group comparisons. While many studies often focus on only one level of bias, an integrated perspective on bias is still missing, especially in longitudinal designs. The aim of this study is to address bias in an integrated manner, using four waves of data in the U.K. Longitudinal Household Panel Survey. Responses to the General Health Questionnaire (GHQ-12) from natives and two generations of immigrants were used to analyze the three levels of bias. While the basic structure of the GHQ-12 was stable across groups and time, item and method bias decreased with repeated administrations. Results were confirmed with a sensitivity test. The integrated results allowed for a distinction between temporal sources of bias that became smaller over time and sources affecting valid comparisons persistently. We discuss the implications for mental health assessment.
Dispersion curves of magneto-electro-elastic imperfect cylinders filled with fluid
Authors: Jiang Jiqing , Zhu Jun , Chen Weiqiu
Published: November 2017

Imperfect interfaces due to manufacturing errors can affect the dynamic performance of multiferroic composite cylinders, especially in the high frequency range. However, the traditional transfer matrix method will encounter numerical instability when high frequency is involved. In this paper, an alternative approach called the reverberation-ray matrix method is presented for the wave propagation of a fluid-filled multiferroic composite cylinder with imperfect interfaces, which is unconditionally numerically stable for high frequency analysis. Based on the three-dimensional magneto-electro-elastic theory and the Hamiltonian state equation, the reverberation-ray formulations are established to analyze the dispersion relations of laminate composite cylinders. The effects of interfacial imperfection as well as different material and geometric parameters on the dispersion curves of multiferroic composite cylinders are investigated. The present method could be useful for the analysis and damage detection of layered composite cylinders.
Why Bacteriophage Encode Exotoxins and other Virulence Factors
Authors: Abedon Stephen T. , LeJeune Jeffrey T.
Published: November 2017

This study considers gene location within bacteria as a function of genetic element mobility. Our emphasis is on prophage encoding of bacterial virulence factors (VFs). At least four mechanisms potentially contribute to phage encoding of bacterial VFs: (i) Enhanced gene mobility could result in greater VF gene representation within bacterial populations. We question, though, why certain genes but not others might benefit from this mobility. (ii) Epistatic interactions—between VF genes and phage genes that enhance VF utility to bacteria—could maintain phage genes via selection acting on individual, VF-expressing bacteria. However, is this mechanism sufficient to maintain the rest of phage genomes or, without gene co-regulation, even genetic linkage between phage and VF genes? (iii) Phage could amplify VFs during disease progression by carrying them to otherwise commensal bacteria colocated within the same environment. However, lytic phage kill bacteria, thus requiring assumptions of inclusive fitness within bacterial populations to explain retention of phage-mediated VF amplification for the sake of bacterial utility. Finally, (iv) phage-encoded VFs could enhance phage Darwinian fitness, particularly by acting as ecosystem-modifying agents. That is, VF-supplied nutrients could enhance phage growth by increasing the density or by improving the physiology of phage-susceptible bacteria. Alternatively, VF-mediated break down of diffusion-inhibiting spatial structure found within the multicellular bodies of host organisms could augment phage dissemination to new bacteria or to environments. Such phage-fitness enhancing mechanisms could apply particularly given VF expression within microbiologically heterogeneous environments, ie, ones where phage have some reasonable potential to acquire phage-susceptible bacteria.
Evolution of Proteins and Proteomes: A Phylogenetics Approach
Authors: Gabaldón Toni
Published: November 2017

The study of evolutionary relationships among protein sequences was one of the first applications of bioinformatics. Since then, and accompanying the wealth of biological data produced by genome sequencing and other high-throughput techniques, the use of bioinformatics in general and phylogenetics in particular has been gaining ground in the study of protein and proteome evolution. Nowadays, the use of phylogenetics is instrumental not only to infer the evolutionary relationships among species and their genome sequences, but also to reconstruct ancestral states of proteins and proteomes and hence trace the paths followed by evolution. Here I survey recent progress in the elucidation of mechanisms of protein and proteome evolution in which phylogenetics has played a determinant role.
Estimation of Phylogeny Using a General Markov Model
Authors: Jayaswal Vivek , Jermiin Lars S. , Robinson John
Published: November 2017

The non-homogeneous model of nucleotide substitution proposed by Barry and Hartigan ( Stat Sci, 2: 191–210) is the most general model of DNA evolution assuming an independent and identical process at each site. We present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. The log likelihood values returned by programs based on the F84 model ( J Mol Evol, 29: 170–179), the general time reversible model ( J Mol Evol, 20: 86–93), and Barry and Hartigan's model are compared to determine the validity of the assumptions made by the first two models. In addition, we present a method for assessing whether sequences have evolved under reversible conditions and discover that this is not so for the two data sets. Finally, we determine the most likely tree under the three models of DNA evolution and compare these with the one favoured by the tests for symmetry.
ALFRED: An Allele Frequency Database for Microevolutionary Studies
Authors: Rajeevan Haseena , Cheung Kei-Hoi , Gadagkar Rohit , Stein Shannon , Soundararajan Usha , Kidd Judith R , Pakstis Andrew J , Miller Perry L , Kidd Kenneth K
Published: November 2017

Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.
Fast Structural Search in Phylogenetic Databases
Authors: Wang Jason T. L. , Shan Huiyuan , Shasha Dennis , Piel William H.
Published: November 2017

As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P. The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising.
Phylogenetic Diversity (PD) and Biodiversity Conservation: Some Bioinformatics Challenges
Authors: Faith Daniel P. , Baker Andrew M.
Published: November 2017

Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bioinformatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socioeconomic data.
Gaussian Quadrature Formulae for Arbitrary Positive Measures
Authors: Fernandes Andrew D. , Atchley William R.
Published: November 2017

We present computational methods and subroutines to compute Gaussian quadrature integration formulas for arbitrary positive measures. For expensive integrands that can be factored into well-known forms, Gaussian quadrature schemes allow for efficient evaluation of high-accuracy and -precision numerical integrals, especially compared to general ad hoc schemes. In addition, for certain well-known density measures (the normal, gamma, log-normal, Student's t, inverse-gamma, beta, and Fisher's F) we present exact formulae for computing the respective quadrature scheme.

Availability: Source code is freely available online as a C-linkable ISO C++ library under a BSD-style license from http://www.fernandes.org/gaussqr . The library may be built using single, double, or extended precision arithmetic.
Finding Common Protein Interaction Patterns Across Organisms
Authors: Gerke Mirco , Bornberg-Bauer Erich , Jiang Xiaoyi , Fuellen Georg
Published: November 2017

Protein interactions are an important resource to obtain an understanding of cell function. Recently, researchers have compared networks of interactions in order to understand network evolution. While current methods first infer homologs and then compare topologies, we here present a method which first searches for interesting topologies and then looks for homologs. PINA (protein interaction network analysis) takes the protein interaction networks of two organisms, scans both networks for subnetworks deemed interesting, and then tries to find orthologs among the interesting subnetworks. The application is very fast because orthology investigations are restricted to subnetworks like hubs and clusters that fulfill certain criteria regarding neighborhood and connectivity. Finally, the hubs or clusters found to be related can be visualized and analyzed according to protein annotation.
The Rv3799-Rv3807 Gene Cluster in Mycobacterium Tuberculosis Genome Corresponds to the ‘Ancient Conserved Region’ in CMN Mycolyltransferases
Authors: Ramulu Hemalatha G. , Swathi Adindla , Guruprasad Lalitha
Published: November 2017

We have identified based on gene cluster analysis that the genes between Rv3799–Rv3807 in M. tuberculosis have orthologs in Corynebacteria, Mycobacteria and Nocardia (CMN) genomes. Therefore, this gene cluster possibly corresponds to the ‘Ancient Conserved Region’ of CMN mycolyltransferases. The evolutionary trace analysis suggests that twelve amino acid residues; Leu39, Trp51, Pro71, Trp82, Trp97, Phe100, Gly124, Ser126, Asp192, Glu230, Gly260 and Trp264 are ‘absolutely conserved’. These amino acid residues constitute the active site and conserved hydrophobic tunnel in CMN mycolyltransferases.
Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction
Authors: Höhl Michael , Rigoutsos Isidore , Ragan Mark A.
Published: November 2017

We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au ), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees.

We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.
Assessing the Applicability of the GTR Nucleotide Substitution Model through Simulations
Authors: Gatto Laurent , Catanzaro Daniele , Milinkovitch Michel C.
Published: November 2017

The General Time Reversible (GTR) model of nucleotide substitution is at the core of many distance-based and character-based phylogeny inference methods. The procedure described by Waddell and Steel (1997), for estimating distances and instantaneous substitution rate matrices, R, under the GTR model, is known to be inapplicable under some conditions, ie, it leads to the inapplicability of the GTR model. Here, we simulate the evolution of DNA sequences along 12 trees characterized by different combinations of tree length, (non-)homogeneity of the substitution rate matrix R, and sequence length. We then evaluate both the frequency of the GTR model inapplicability for estimating distances and the accuracy of inferred alignments. Our results indicate that, inapplicability of the Waddel and Steel's procedure can be considered a real practical issue, and illustrate that the probability of this inapplicability is a function of substitution rates and sequence length.

We also discuss the implications of our results on the current implementations of maximum likelihood and Bayesian methods.
Outsourcing the Nucleus: Nuclear Pore Complex Genes are no Longer Encoded in Nucleomorph Genomes
Authors: Neumann Nadja , Jeffares Daniel C. , Poole Anthony M.
Published: November 2017

The nuclear pore complex (NPC) facilitates transport between nucleus and cytoplasm. The protein constituents of the NPC, termed nucleoporins (Nups), are conserved across a wide diversity of eukaryotes. In apparent exception to this, no nucleoporin genes have been identified in nucleomorph genomes. Nucleomorphs, nuclear remnants of once free-living eukaryotes, took up residence as secondary endosymbionts in cryptomonad and chlorarachniophyte algae. As these genomes are highly reduced, Nup genes may have been lost, or relocated to the host nucleus. However, Nup genes are often poorly conserved between species, so absence may be an artifact of low sequence similarity. We therefore constructed an evolutionary bioinformatic screen to establish whether the apparent absence of Nup genes in nucleomorph genomes is due to genuine absence or the inability of current methods to detect homologues. We searched green plant ( Arabidopsis and rice), green alga ( Chlamydomonas reinhardtii) and red alga ( Cyanidioschyzon merolae) genomes, plus two nucleomorph genomes ( Bigelowiella natans and Guillardia theta) with profile hidden Markov models (HMMs) from curated alignments of known vertebrate/yeast Nups. Since the plant, algal and nucleomorph genomes all belong to the kingdom Plantae, and are evolutionarily distant from the outgroup (vertebrate/yeast) training set, we use the plant and algal genomes as internal positive controls for the sensitivity of the searches in nucleomorph genomes. We find numerous Nup homologues in all plant and free-living algal species, but none in either nucleomorph genome. BLAST searches using identified plant and algal Nups also failed to detect nucleomorph homologues. We conclude that nucleomorph Nup genes have either been lost, being replaced by host Nup genes, or, that nucleomorph Nup genes have been transferred to the host nucleus twice independently; once in the evolution of the red algal nucleomorph and once in the green algal nucleomorph.
A Fast and Specific Alignment Method for Minisatellite Maps
Authors: Bérard Sèverine , Nicolas François , Buard Jérôme , Gascuel Olivier , Rivals Eric
Published: November 2017

Background

Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length ( i.e., in number of copies) of minisatellites proved useful in population genetics.

Motivation

In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications.

Results

We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1) human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases.

Availability

Software is available at http://atgc.lirmm.fr/ms_align/
Genome Halving with an Outgroup
Authors: Zheng Chunfang , Zhu Qian , Sankoff David
Published: November 2017

Some genomes are known to have incurred a genome doubling (tetraploidization) event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to “halve” the genome, i.e. to reconstruct the ancestral genome at the moment of tetraploidization, but the solution is often highly non-unique. To resolve this problem, we adapt the genome halving algorithm of El-Mabrouk and Sankoff to take account of an external reference genome. We apply this to reconstruct the tetraploid ancestor of maize, using either rice or sorghum as the reference.
Positional Homology in Bacterial Genomes
Authors: Burgetz Ingrid J. , Shariff Salimah , Pang Andy , Tillier* Elisabeth R. M.
Published: November 2017

In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that orthologous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone.
PIRSF Family Classification System for Protein Functional and Evolutionary Analysis
Authors: Nikolskaya Anastasia N. , Arighi Cecilia N. , Huang Hongzhan , Barker Winona C. , Wu Cathy H.
Published: November 2017

The PIRSF protein classification system ( http://pir.georgetown.edu/pirsf/ ) reflects evolutionary relationships of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain or fold-based searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. Here we demonstrate, with illustrative examples, how to use the web-based PIRSF system as a tool for functional and evolutionary studies of protein families.
Topological Bias in Distance-Based Phylogenetic Methods: Problems with Over- and Underestimated Genetic Distances
Authors: Xia Xuhua
Published: November 2017

I show several types of topological biases in distance-based methods that use the least-squares method to evaluate branch lengths and the minimum evolution (ME) or the Fitch-Margoliash (FM) criterion to choose the best tree. For a 6-species tree, there are two tree shapes, one with three cherries (a cherry is a pair of adjacent leaves descending from the most recent common ancestor), and the other with two. When genetic distances are underestimated, the 3-cherry tree shape is favored with either the ME or FM criterion. When the genetic distances are overestimated, the ME criterion favors the 2-cherry tree, but the direction of bias with the FM criterion depends on whether negative branches are allowed, i.e. allowing negative branches favors the 3-cherry tree shape but disallowing negative branches favors the 2-cherry tree shape. The extent of the bias is explored by computer simulation of sequence evolution.
Fast Genes and Slow Clades: Comparative Rates of Molecular Evolution in Mammals
Authors: Bininda-Emonds Olaf R. P.
Published: November 2017

Although interest in the rate of molecular evolution and the molecular clock remains high, our knowledge for most groups in these areas is derived largely from a patchwork of studies limited in both their taxon coverage and the number of genes examined. Using a comprehensive molecular data set of 44 genes (18 nDNA, 11 tRNA and 15 additional mtDNA genes) together with a virtually complete and dated phylogeny of extant mammals, I 1) describe differences in the rate of molecular evolution (i.e. substitution rate) within this group in an explicit phylogenetic and quantitative framework and 2) present the first attempt to localize the phylogenetic positions of any rate shifts. Significant rate differences were few and confirmed several long-held trends, including a progressive rate slowdown within hominids and a reduced substitution rate within Cetacea. However, many new patterns were also uncovered, including the mammalian orders being characterized generally by basal rate slowdowns. A link between substitution rate and the size of a clade (which derives from its net speciation rate) is also suggested, with the species-poor major clades (“orders”) showing more decreased rates that often extend throughout the entire clade. Significant rate increases were rare, with the rates within (murid) rodents being fast, but not significantly so with respect to other mammals as a whole. Despite clear lineage-specific differences, rates generally change gradually along these lineages, supporting the potential existence of a local molecular clock in mammals. Together, these results will lay the foundation for a broad-scale analysis to establish the correlates and causes of the rate of molecular evolution in mammals.
Phylogenetic Study of the Evolution of PEP-Carboxykinase
Authors: Aich Sanjukta , Delbaere Louis T.J.
Published: November 2017

Phosphoenolpyruvate carboxykinase (PCK) is the key enzyme to initiate the gluconeogenic pathway in vertebrates, yeast, plants and most bacteria. Nucleotide specificity divided all PCKs into two groups. All the eukaryotic mammalian and most archaeal PCKs are GTP-specific. Bacterial and fungal PCKs can be ATP-or GTP-specific but all plant PCKs are ATP-specific. Amino acid sequence alignment of PCK enzymes shows that the nucleotide binding sites are somewhat conserved within each class with few exceptions that do not have any clear ATP- or GTP-specific binding motif. Although the active site residues are mostly conserved in all PCKs, not much significant sequence homology persists between ATP- and GTP-dependent PCK enzymes. There is only one planctomycetes PCK enzyme (from Cadidatus Kuenenia stuttgartiensis) that shows sequence homology with both ATP-and GTP-dependent PCKs. Phylogenetic studies have been performed to understand the evolutionary relationship of various PCKs from different sources. Based on this study a flowchart of the evolution of PCK has been proposed.
Efficient Tree Searches with Available Algorithms
Authors: Giribet Gonzalo
Published: November 2017

Phylogenetic methods based on optimality criteria are highly desirable for their logic properties, but time-consuming when compared to other methods of tree construction. Traditionally, researchers have been limited to exploring tree space by using multiple replicates of Wagner addition followed by typical hill climbing algorithms such as SPR or/and TBR branch swapping but these methods have been shown to be insuficient for “large” data sets (or even for small data sets with a complex tree space). Here, I review different algorithms and search strategies used for phylogenetic analysis with the aim of clarifying certain aspects of this important part of the phylogenetic inference exercise. The techniques discussed here apply to both major families of methods based on optimality criteria—parsimony and maximum likelihood—and allow the thorough analysis of complex data sets with hundreds to thousands of terminal taxa. A new technique, called pre-processed searches is proposed for reusing phylogenetic results obtained in previous analyses, to increase the applicability of the previously proposed jumpstarting phylogenetics method. This article is aimed to serve as an educational and algorithmic reference to biologists interested in phylogenetic analysis.
MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes
Authors: Putta Srikrishna , Smith Jeramiah J. , Staben Chuck , Voss S. Randal
Published: November 2017

Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome sequence while accounting for the presence of intronic sequences, and assigns orthology based on user-defined parameters. To illustrate the utility of this program, we used MapToGenome to process alignments between vertebrate genetic maps and genome assemblies 1) self/self alignments for maps and assemblies of the rat and zebrafish genome; 2) alignments between vertebrate transcript maps (rat, salamander, zebrafish, and medaka) and the chicken genome; and 3) alignments of the medaka and zebrafish maps to the pufferfish ( Tetraodon nigroviridis) genome. Our results show that map-genome alignments can be improved by combining alignments across presumptive intron breaks and ignoring alignments for simple sequence length polymorphism (SSLP) marker sequences. Comparisons between vertebrate maps and genomes reveal broad patterns of conservation among vertebrate genomes and the differential effects of genome rearrangement over time and across lineages.
Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity
Authors: Steel Mike , Mimoto Aki , Mooers Arne Ø
Published: November 2017

If predictions for species extinctions hold, then the ‘tree of life’ today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as measured by its expected contribution to phylogenetic diversity. Our approach considers all possible scenarios for the set of species that will be extant at some future time, and weights them according to their likelihood under an independent (but not identical) distribution on species extinctions. Although the number of extinction scenarios can typically be very large, we show that there is a simple algorithm that will quickly compute this index. The method is implemented and applied to the prosimian primates as a test case, and the associated species ranking is compared to a related measure (the ‘Shapley index’). We describe indices for rooted and unrooted trees, and a modification that also includes the focal taxon's probability of extinction and which links two complementary approaches to conserving phylogenetic diversity.
A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores
Authors: Bastien Olivier
Published: November 2017

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. In the asymptotic limit of long sequences, the Karlin-Altschul model computes a P-value assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Using a simple approach combined with recent results in reliability theory, we demonstrate here that the Karlin-Altshul model can be derived with no reference to the extreme events theory.

Sequences were considered as systems in which components are amino acids and having a high redundancy of Information reflected by their alignment scores. Evolution of the information shared between aligned components determined the Shared Amount of Information (SA.I.) between sequences, i.e. the score. The Gumbel distribution parameters of aligned sequences scores find here some theoretical rationale. The first is the Hazard Rate of the distribution of scores between residues and the second is the probability that two aligned residues do not lose bits of information (i.e. conserve an initial pairing score) when a mutation occurs.