bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Meaning of Best Practice: A Discussion on the Way Client-Centred Psychosocial Rehabilitation Services Might Address the Needs of Australian Veterans in the Future
Authors: Hanley Francine T. , Matthews Lynda R. , Lewis Virginia J. 
Published: May 2012

AbstractThis article presents a summary of 10 priorities for the delivery of best practices in psychosocial rehabilitation relevant to the Australian veteran population. The first section interrogates the empirical principles characteristically identified with best practices before presenting an alternative, heuristic framework organised by three reference points and informed by principles of efficacy, external validity, and the meaning of efficacy in the context of parity. The article presents the strategy used in reviewing the literature, before presenting the findings according to 10 key priorities. The 10 priorities are described in the context of the literature informing them and are set out with regard to the centrality of the client-centred service model in the design and delivery of pertinent and effective services into the future.
The Limits to Parapatric Speciation: Dobzhansky–Muller Incompatibilities in a Continent–Island Model
Authors: Bank Claudia , Bürger Reinhard , Hermisson Joachim 
Published: April 2012

AbstractHow much gene flow is needed to inhibit speciation by the accumulation of Dobzhansky–Muller incompatibilities (DMIs) in a structured population? Here, we derive these limits in a classical migration–selection model with two haploid or diploid loci and unidirectional gene flow from a continent to an island. We discuss the dependence of the maximum gene-flow rate on ecological factors (exogeneous selection), genetic factors (epistasis, recombination), and the evolutionary history. Extensive analytical and numerical results show the following: (1) The maximum rate of gene flow is limited by exogeneous selection. In particular, maintenance of neutral DMIs is impossible with gene flow. (2) There are two distinct mechanisms that drive DMI evolution in parapatry, selection against immigrants in a heterogeneous environment and selection against hybrids due to the incompatibility. (3) Depending on the mechanism, opposite predictions result concerning the genetic architecture that maximizes the rate of gene flow a DMI can sustain. Selection against immigrants favors evolution of tightly linked DMIs of arbitrary strength, whereas selection against hybrids promotes the evolution of strong unlinked DMIs. In diploids, the fitness of the double heterozygotes is the decisive factor to predict the pattern of DMI stability.
Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize
Authors: Fang Zhou , Pyhäjärvi Tanja , Weber Allison L , Dawe R Kelly , Glaubitz Jeffrey C , González José de Jesus Sánchez , Ross-Ibarra Claudia , Doebley John , Morrell Peter L , Ross-Ibarra Jeffrey 
Published: April 2012

Abstract
Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an ∼50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures &gt;700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.
A Network of Genes Antagonistic to the LIN-35 Retinoblastoma Protein ofCaenorhabditis elegans
Authors: Polley Stanley R G , Fay David S 
Published: April 2012

AbstractThe Caenorhabditis elegans pRb ortholog, LIN-35, functions in a wide range of cellular and developmental processes. This includes a role of LIN-35 in nutrient utilization by the intestine, which it carries out redundantly with SLR-2, a zinc-finger protein. This and other redundant functions of LIN-35 were identified in genetic screens for mutations that display synthetic phenotypes in conjunction with loss of lin-35. To explore the intestinal role of LIN-35, we conducted a genome-wide RNA-interference-feeding screen for suppressors of lin-35; slr-2 early larval arrest. Of the 26 suppressors identified, 17 fall into three functional classes: (1) ribosome biogenesis genes, (2) mitochondrial prohibitins, and (3) chromatin regulators. Further characterization indicates that different categories of suppressors act through distinct molecular mechanisms. We also tested lin-35; slr-2 suppressors, as well as suppressors of the synthetic multivulval phenotype, to determine the spectrum of lin-35-synthetic phenotypes that could be suppressed following inhibition of these genes. We identified 19 genes, most of which are evolutionarily conserved, that can suppress multiple unrelated lin-35-synthetic phenotypes. Our study reveals a network of genes broadly antagonistic to LIN-35 as well as genes specific to the role of LIN-35 in intestinal and vulval development. Suppressors of multiple lin-35 phenotypes may be candidate targets for anticancer therapies. Moreover, screening for suppressors of phenotypically distinct synthetic interactions, which share a common altered gene, may prove to be a novel and effective approach for identifying genes whose activities are most directly relevant to the core functions of the shared gene.
Chromatin Modulation at the FLO11 Promoter of Saccharomyces cerevisiae by HDAC and Swi/Snf Complexes
Authors: Barrales Ramón R , Korber Philipp , Jimenez Juan , Ibeas José I 
Published: April 2012

Abstract
Cell adhesion and biofilm formation are critical processes in the pathogenicity of fungi and are mediated through a family of adhesin proteins conserved throughout yeasts and fungi. In Saccharomyces cerevisiae, Flo11 is the main adhesin involved in cell adhesion and biofilm formation, making the study of its function and regulation in this nonpathogenic budding yeast highly relevant. The S. cerevisiae FLO11 gene is driven by a TATA-box-containing promoter that is regulated through one of the longest regulatory upstream regions (3 kb) in yeast. We reported recently that two chromatin cofactor complexes, the Rpd3L deacetylase and the Swi/Snf chromatin-remodeling complexes, contribute significantly to the regulation of FLO11. Here, we analyze directly how these complexes impact on FLO11 promoter chromatin structure and dissect further the interplay between histone deacetylases, chromatin remodeling, and the transcriptional repressor Sfl1. We show that the regulation of chromatin structure represents an important layer of control in the highly complex regulation of the FLO11 promoter.
Remarkably Simple Sequence Requirement of the M-Factor Pheromone ofSchizosaccharomyces pombe
Authors: Seike Taisuke , Yamagishi Yoshikazu , Iio Hideo , Nakamura Taro , Shimoda Chikashi 
Published: April 2012

AbstractThe mating reaction is triggered by specific pheromones in a wide variety of organisms. Small peptides are used as mating pheromones in yeasts and fungi. In the fission yeast Schizosaccharomyces pombe, M-factor is a C terminally farnesylated nonapeptide secreted from M-cells, and its counterpart, P-factor, is a simple peptide composed of 23 amino acids. The primary structure requirements for the biological activity of pheromone peptides remain to be elucidated. Here, we conducted comprehensive substitution of each of the amino acids in M-factor peptide and inspected the mating ability of these missense mutants. Thirty-five sterile mutants were found among an array of 152 mutants with single amino acid substitutions. Mapping of the mutation sites clearly indicated that the sterile mutants were associated exclusively with four amino acid residues (VPYM) in the carboxyl-terminal half. In contrast, the substitution of four amino-terminal residues (YTPK) with any amino acid had no or only a slightly deleterious effect on mating. Furthermore, deletion of the three N-terminal residues caused no sterility, although truncation of a fourth residue had a marked effect. We conclude that a farnesylated hexapeptide (KVPYMCFar–OCH3) is the minimal M-factor that retains pheromone activity. At least 15 nonfunctional peptides were found to be secreted, suggesting that these mutant M-factor peptides are no longer recognized by the cognate receptor.
Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)
Authors: Chen Jun , Källman Thomas , Ma Xiaofei , Gyllenstrand Niclas , Zaina Giusi , Morgante Michele , Bousquet Jean , Eckert Andrew , Wegrzyn Jill , Neale David , Lagercrantz Ulf , Lascoux Martin 
Published: April 2012

AbstractUnderstanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (FST = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to FST. The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.
Establishment of New Mutations in Changing Environments
Authors: Peischl Stephan , Kirkpatrick Mark 
Published: April 2012

AbstractUnderstanding adaptation in changing environments is an important topic in evolutionary genetics, especially in the light of climatic and environmental change. In this work, we study one of the most fundamental aspects of the genetics of adaptation in changing environments: the establishment of new beneficial mutations. We use the framework of time-dependent branching processes to derive simple approximations for the establishment probability of new mutations assuming that temporal changes in the offspring distribution are small. This approach allows us to generalize Haldane’s classic result for the fixation probability in a constant environment to arbitrary patterns of temporal change in selection coefficients. Under weak selection, the only aspect of temporal variation that enters the probability of establishment is a weighted average of selection coefficients. These weights quantify how much earlier generations contribute to determining the establishment probability compared to later generations. We apply our results to several biologically interesting cases such as selection coefficients that change in consistent, periodic, and random ways and to changing population sizes. Comparison with exact results shows that the approximation is very accurate.
A Regulatory Module Controlling Pharyngeal Development and Function in Caenorhabditis elegans
Authors: Fay David S , Polley Stanley R G , Kuang Jujiao , Kuzmanov Aleksandra , Hazel James W , Mani Kumaran , Veo Bethany L , Yochem John 
Published: April 2012

Abstract
In Caenorhabditis elegans, the differentiation and morphogenesis of the foregut are controlled by several transcriptional regulators and cell signaling events, and by PHA-1, an essential cytoplasmic protein of unknown function. Previously we have shown that LIN-35 and UBC-18–ARI-1 contribute to the regulation of pha-1 and pharyngeal development through the Zn-finger protein SUP-35/ZTF-21. Here we characterize SUP-37/ZTF-12 as an additional component of the PHA-1 network regulating pharyngeal development. SUP-37 is encoded by four distinct splice isoforms, which contain up to seven C2H2 Zn-finger domains, and is localized to the nucleus, suggesting a role in transcription. Similar to sup-35, sup-37 loss-of-function mutations can suppress both LOF mutations in pha-1 as well as synthetic-lethal double mutants, including lin-35; ubc-18, which are defective in pharyngeal development. Genetic, molecular, and expression data further indicate that SUP-37 and SUP-35 may act at a common step to control pharyngeal morphogenesis, in part through the transcriptional regulation of pha-1. Moreover, we find that SUP-35 and SUP-37 effect pharyngeal development through a mechanism that can genetically bypass the requirement for pha-1 activity. Unlike SUP-35, SUP-37 expression is not regulated by either the LIN-35 or UBC-18–ARI-1 pathways. In addition, SUP-37 carries out two essential functions that are distinct from its role in regulating pharyngeal development with SUP-35. SUP-37 is required within a subset of pharyngeal muscle cells to facilitate coordinated rhythmic pumping and in the somatic gonad to promote ovulation. These latter observations suggest that SUP-37 may be required for the orchestrated contraction of muscle cells within several tissues.
Temporal Variation in Selection Accelerates Mutational Decay by Muller’s Ratchet
Authors: Wardlaw Alison M , Agrawal Aneil F 
Published: April 2012

AbstractAsexual species accumulate deleterious mutations through an irreversible process known as Muller’s ratchet. Attempts to quantify the rate of the ratchet have ignored the role of temporal environmental heterogeneity even though it is common in nature and has the potential to affect overall ratchet rate. Here we examine Muller’s ratchet in the context of conditional neutrality (i.e., mutations that are deleterious in some environmental conditions but neutral in others) as well as more subtle changes in the strength (but not sign) of selection. We find that temporal variation increases the rate of the ratchet (mutation accumulation) and the rate of fitness decline over that of populations experiencing constant selection of equivalent average strength. Temporal autocorrelation magnifies the effects of temporal heterogeneity and can allow the ratchet to operate at large population sizes in which it would be halted under constant selection. Classic studies of Muller’s ratchet show that the rate of fitness decline is maximized when selection is of a low but intermediate strength. This relationship changes quantitatively with all forms of temporal heterogeneity studied and changes qualitatively when there is temporal autocorrelation in selection. In particular, the rate of fitness decline can increase indefinitely with the strength of selection with some forms of temporal heterogeneity. Our finding that temporal autocorrelation in selection dramatically increases ratchet rate and rate of fitness decline may help to explain the paucity of asexual taxa.
Multiple Barriers to Nonhomologous DNA End Joining During Meiosis inDrosophila
Authors: Joyce Eric F , Paul Anshu , Chen Katherine E , Tanneti Nikhila , McKim Kim S 
Published: April 2012

AbstractRepair of meiotic double-strand breaks (DSBs) uses the homolog and recombination to yield crossovers while alternative pathways such as nonhomologous end joining (NHEJ) are suppressed. Our results indicate that NHEJ is blocked at two steps of DSB repair during meiotic prophase: first by the activity of the MCM-like protein MEI-218, which is required for crossover formation, and, second, by Rad51-related proteins SPN-B (XRCC3) and SPN-D (RAD51C), which physically interact and promote homologous recombination (HR). We further show that the MCM-like proteins also promote the activity of the DSB repair checkpoint pathway, indicating an early requirement for these proteins in DSB processing. We propose that when a meiotic DSB is formed in the absence of both MEI-218 and SPN-B or SPN-D, a DSB substrate is generated that can enter the NHEJ repair pathway. Indeed, due to its high error rate, multiple barriers may have evolved to prevent NHEJ activity during meiosis.
Periodontal Disease, Hypertension, and Blood Pressure Among Older Adults in Puerto Rico
Authors: Rivas‐Tumanyan Sona , Campos Maribel , Zevallos Juan C. , Joshipura Kaumudi J. 
Published: May 2012

Background: Current scientific evidence addressing the relationship between periodontitis and hypertension is limited to studies producing inconsistent results.Methods: All participants of an ongoing representative cohort of Puerto Rican elderly who were ≥70 years old and residing in the San Juan metropolitan area were invited to this cross‐sectional study. Periodontal probing depth (PD) and attachment loss (AL) were summarized using the Centers for Disease Control and Prevention and the American Academy of Periodontology definition for severe periodontitis (≥2 teeth with AL ≥6 mm and ≥1 tooth with PD ≥5 mm). Three repeated blood pressure (BP) measurements taken were averaged using a standardized auscultatory method. Information on hypertension history, use of antihypertensive medications, and potential confounders (age, sex, smoking, heavy and binge drinking, diabetes, use of preventive dental services, flossing, body mass index, consumption of fruits, vegetables, whole wheat bread, and high‐fiber cereal) was collected during in‐person interviews. High BP was defined as average systolic BP ≥140 mm Hg or diastolic ≥90 mm Hg. Multivariate logistic regression models were used to study the relationship between severe periodontitis, hypertension history, and high BP.Results: The study population comprised 182 adults. In multivariate analysis, there was no association between severe periodontitis and hypertension history (odds ratio [OR] = 0.99; 95% confidence interval [CI]: 0.40 to 2.48). Severe periodontitis was associated with high BP, with OR of 2.93 (95% CI: 1.25 to 6.84), after adjusting for age, sex, smoking, and binge drinking. This association was stronger when restricted to those with hypertension or taking antihypertensive medications: OR = 4.20 (95% CI: 1.28 to 13.80).Conclusion: The results of this study suggest that periodontitis may contribute to poor BP control among older adults.
Severe Loss of Clinical Attachment Level: An Independent Association With Low Hip Bone Mineral Density in Postmenopausal Females
Authors: Gondim Valéria , Aun Juliana , Fukuda Cassia Tiemi , Takayama Liliam , Latorre Maria do Rosário , Pannuti Cláudio Mendes , Rodrigues Pereira Rosa Maria , Romito Giuseppe Alexandre 
Published: May 2012

Background: Bone loss is a feature of both periodontitis and osteoporosis, and several studies have analyzed whether the periodontal destruction could have been influenced by systemic bone loss. The aim of this study is to assess the association between clinical attachment level (CAL) and bone mineral density (BMD) at the lumbar spine and hip, lifestyle, smoking, sociodemographic factors, and dental clinical variables in postmenopausal women.Methods: One hundred forty‐eight women were interviewed using a structured written questionnaire and clinically examined. The periodontal examination, which was performed by calibrated investigators, included CAL, probing depth, gingival recession, bleeding on probing (BOP), visible plaque, supragingival calculus, and mean tooth loss. The sample was stratified into two groups: moderate and severe CAL. The moderate group had all sites with CAL ≤5 mm. The severe group had ≥1 site with CAL >5 mm. BMD, measured using dual‐energy x‐ray absorptiometry, was assessed at the lumbar spine, femoral neck, and total femur (grams per square centimeters).Results: Severe CAL was identified in 86 women (58.1%). The multiple linear regression analysis using CAL (dependent variable), adjusted by menopause, education, and family income, demonstrated an inverse relationship of severe CAL with the BMD of the femoral neck (P = 0.015), as well as a positive association of severe CAL with tooth loss (P = 0.000), BOP (P = 0.004), and heavy smokers (P = 0.001).Conclusions: Our study demonstrated that severe CAL was associated with low BMD of the femoral neck and deleterious clinical dental parameters and smoking. Our findings suggest that, in addition to appropriate oral care, individuals with severe CAL may also require additional attention to their systemic bone health.
Tar Characterization for Optimum Reservoir Management Strategy
Authors: Al-Harthi Muhammad , Al-Ali Mohammed , Gunarto Ronny 
Published: May 2012

Abstract
Tar mats are extra-heavy bitumen that occur between aquifers and overlaying oil columns. They seal either partially or completely an oil reservoir from its aquifer and reduces aquifer support. Tar characterization includes evaluation of the tar distribution and its sealing degree. It is an important prerequisite to optimize the water injection well's requirement and placement to maximize sweep and recovery.
This paper discusses a case study and demonstrates an integrated methodology by using static and dynamic data to determine the tar distribution and its sealing degree. The study includes both early life data before the subject field was put in production, as put on production, and post-production data to refine the characterization. Additionally, the use of formation pressure while drilling and Pyrolytic Oil-Productivity Index (POPI) analysis to optimize the injector's placement will also be highlighted. Moreover, saturation and production logging tool analysis were incorporated to determine if there is aquifer influx across the tar mat. The degree of the aquifer influx is also evaluated using material balance and reservoir simulation.