bluuebunny/crossref_metadata_2025 huggingface dataset:
Parsimony and likelihood reconstruction of human segmental duplications
Authors: Kahn Crystal L. , Hristov Borislav H. , Raphael Benjamin J.
Published: September 2010

Motivation: Segmental duplications > 1 kb in length with ≥ 90% sequence identity between copies comprise nearly 5% of the human genome. They are frequently found in large, contiguous regions known as duplication blocks that can contain mosaic patterns of thousands of segmental duplications. Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but important task.

Results: We introduce parsimony and likelihood techniques to analyze the evolutionary relationships between duplication blocks. Both techniques rely on a generic model of duplication in which long, contiguous substrings are copied and reinserted over large physical distances, allowing for a duplication block to be constructed by aggregating substrings of other blocks. For the likelihood method, we give an efficient dynamic programming algorithm to compute the weighted ensemble of all duplication scenarios that account for the construction of a duplication block. Using this ensemble, we derive the probabilities of various duplication scenarios. We formalize the task of reconstructing the evolutionary history of segmental duplications as an optimization problem on the space of directed acyclic graphs. We use a simulated annealing heuristic to solve the problem for a set of segmental duplications in the human genome in both parsimony and likelihood settings.

Availability:  Supplementary information is available at http://www.cs.brown.edu/people/braphael/supplements/.

Contact:  clkahn@cs.brown.edu; braphael@cs.brown.edu.
Solenoid and non-solenoid protein recognition using stationary wavelet packet transform
Authors: Vo An , Nguyen Nha , Huang Heng
Published: September 2010

Motivation: Solenoid proteins are emerging as a protein class with properties intermediate between structured and intrinsically unstructured proteins. Containing repeating structural units, solenoid proteins are expected to share sequence similarities. However, in many cases, the sequence similarities are weak and non-detectable. Moreover, solenoids can be degenerated and widely vary in the number of units. So that it is difficult to detect them. Recently, several solenoid repeats detection methods have been proposed, such as self-alignment of the sequence, spectral analysis and discrete Fourier transform of sequence. Although these methods have shown good performance on certain data sets, they often fail to detect repeats with weak similarities. In this article, we propose a new approach to recognize solenoid repeats and non-solenoid proteins using stationary wavelet packet transform (SWPT). Our method associates with three advantages: (i) naturally representing five main factors of protein structure and properties by wavelet analysis technique; (ii) extracting novel wavelet features that can capture hidden components from solenoid sequence similarities and distinguish them from global proteins; (iii) obtaining statistics features that capture repeating motifs of solenoid proteins.

Results: Our method analyzes the characteristics of amino acid sequence in both spectral and temporal domains using SWPT. Both global and local information of proteins are captured by SWPT coefficients. We obtain and integrate wavelet-based features and statistics-based features of amino acid sequence to improve the classification task. Our proposed method is evaluated by comparing to state-of-the-art methods such as HHrepID and REPETITA. The experimental results show that our algorithm consistently outperforms them in areas under ROC curve. At the same false positive rate, the sensitivity of our WAVELET method is higher than other methods.

Availability:  http://www.naaan.org/anvo/Software/Software.htm

Contact:  anphuocnhu.vo@mavs.uta.edu
Prototypes of elementary functional loops unravel evolutionary connections between protein functions
Authors: Goncearenco Alexander , Berezovsky Igor N.
Published: September 2010

Motivation: Earlier studies of protein structure revealed closed loops with a characteristic size 25–30 residues and ring-like shape as a basic universal structural element of globular proteins. Elementary functional loops (EFLs) have specific signatures and provide functional residues important for binding/activation and principal chemical transformation steps of the enzymatic reaction. The goal of this work is to show how these functional loops evolved from pre-domain peptides and to find a set of prototypes from which the EFLs of contemporary proteins originated.

Results: This article describes a computational method for deriving prototypes of EFLs based on the sequences of complete genomes. The procedure comprises the iterative derivation of sequence profiles followed by their hierarchical clustering. The scoring function takes into account information content on profile positions, thus preserving the signature. The statistical significance of scores is evaluated from the empirical distribution of scores of the background model. A set of prototypes of EFLs from archaeal proteomes is derived. This set delineates evolutionary connections between major functions and illuminates how folds and functions emerged in pre-domain evolution as a combination of prototypes.

Contact:  Igor.Berezovsky@uni.no
A graphical method for reducing and relating models in systems biology
Authors: Gay Steven , Soliman Sylvain , Fages François
Published: September 2010

Motivation: In Systems Biology, an increasing collection of models of various biological processes is currently developed and made available in publicly accessible repositories, such as biomodels.net for instance, through common exchange formats such as SBML. To date, however, there is no general method to relate different models to each other by abstraction or reduction relationships, and this task is left to the modeler for re-using and coupling models. In mathematical biology, model reduction techniques have been studied for a long time, mainly in the case where a model exhibits different time scales, or different spatial phases, which can be analyzed separately. These techniques are however far too restrictive to be applied on a large scale in systems biology, and do not take into account abstractions other than time or phase decompositions. Our purpose here is to propose a general computational method for relating models together, by considering primarily the structure of the interactions and abstracting from their dynamics in a first step.

Results: We present a graph-theoretic formalism with node merge and delete operations, in which model reductions can be studied as graph matching problems. From this setting, we derive an algorithm for deciding whether there exists a reduction from one model to another, and evaluate it on the computation of the reduction relations between all SBML models of the biomodels.net repository. In particular, in the case of the numerous models of MAPK signalling, and of the circadian clock, biologically meaningful mappings between models of each class are automatically inferred from the structure of the interactions. We conclude on the generality of our graphical method, on its limits with respect to the representation of the structure of the interactions in SBML, and on some perspectives for dealing with the dynamics.

Availability: The algorithms described in this article are implemented in the open-source software modeling platform BIOCHAM available at http://contraintes.inria.fr/biocham The models used in the experiments are available from http://www.biomodels.net/

Contact:  francois.fages@inria.fr
Temporal waves of coherent gene expression during Drosophila embryogenesis
Authors: Papatsenko Ilya , Levine Mike , Papatsenko Dmitri
Published: September 2010

Motivation: Animal development depends on localized patterns of gene expression. Whole-genome methods permit the global identification of differential expression patterns. However, most gene-expression-clustering methods focus on the analysis of entire expression profiles, rather than temporal segments or time windows.

Results: In the current study, local clustering of temporal time windows was applied to developing embryos of the fruitfly, Drosophila melanogaster. Large-scale developmental events, involving temporal activation of hundreds of genes, were identified as discrete gene clusters. The time-duration analysis revealed six temporal waves of coherent gene expression during Drosophila embryogenesis. The most powerful expression waves preceded major morphogenetic movements, such as germ band elongation and dorsal closure. These waves of gene expression coincide with the inhibition of maternal transcripts during early development, the specification of ectoderm, differentiation of the nervous system, differentiation of the digestive tract, deposition of the larval cuticle and the reorganization of the cytoskeleton during global morphogenetic events. We discuss the implications of these findings with respect to the gene regulatory networks governing Drosophila development.

Availability: Data and software are available from the UC Berkeley web resource http://flydev.berkeley.edu/cgi-bin/GTEM/dmap_dm-ag/index_dmap.htm

Contact:  dimitri.papatsenko@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Adaptation to sea level rise: does local adaptation influence the demography of coastal fish populations?
Authors: Purcell K. M. , Klerks P. L. , Leberg P. L.
Published: September 2010

This study compared the growth of two western mosquitofish Gambusia affinis populations that were previously demonstrated to have genetic adaptations that increased survival under lethal salinity exposures. The objective was to evaluate how genetic adaptations to lethal salinity stress affect population demography when exposed to sublethal salinity stress. Results indicate that chronic salinity exposure had a generally negative impact on population size, but fish originating from one of the two populations established with fish from a brackish site exhibited an increase in population size. Saltwater intrusion seems to result in reduced population size for most populations. Some populations inhabiting more saline sites, however, may develop localized adaptations, mitigating the consequences of increased salinity on population productivity.
Retinoic acids exhibit anti‐fibrotic activity through the inhibition of 5‐lipoxygenase expression in scleroderma fibroblasts
Authors: XIAO Rong , YOSHIDA Nobuyo , HIGASHI Yuko , LU Qian‐Jin , FUKUSHIGE Tomoko , KANZAKI Tamotsu , KANEKURA Takuro
Published: September 2010

The pathogenesis of systemic sclerosis (SSc) is not fully understood and there is no effective treatment for this disease. Retinoic acid (RA) can modulate connective tissue metabolism, exhibit anti‐fibrotic activity, and improve the clinical symptoms of SSc. However, the mechanisms by which RA elicits its anti‐fibrotic actions remain to be determined. The aim of this study was to elucidate the underlying mechanisms by which RA exerts beneficial effects on scleroderma. Cultured skin fibroblasts from patients with scleroderma were treated with RA and their effect on the expression of 5‐lipoxygenase (LOX), transforming growth factor (TGF)‐β1, connective tissue growth factor (CTGF), type I and type III collagen was tested by reverse transcription polymerase chain reaction (RT–PCR) and western immunoblotting. The effect of MK886, a 5‐LOX‐specific inhibitor, on the expression of TGF‐β1, CTGF, type I and type III collagen was also examined by RT–PCR. In cultured scleroderma fibroblasts, the expression of 5‐LOX was elevated compared with normal human dermal fibroblasts. RA significantly inhibited the expression of 5‐LOX and of TGF‐β1, CTGF, type I and type III collagen. We further found that the expression of TGF‐β1, CTGF and type I and type III collagen mRNA was inhibited by MK886 in scleroderma fibroblasts. In vitro, RA reduced 5‐LOX expression in scleroderma fibroblasts and downregulated TGF‐β1 and CTGF expression, leading to the inhibition of type I and type III collagen synthesis. Our results indicate that the clinical effects of RA on scleroderma are, at least in part, attributable to the reduction of 5‐LOX expression and the subsequent suppression of TGF‐β1 and CTGF expression that results in the blockade of collagenogenesis.
Variation in inflorescence characters and inflorescence development in ecotypes and cultivars of Lolium perenne L.
Authors: McGrath S. , Hodkinson T. R. , Charles T. M. , Zen D. G. , Barth S.
Published: September 2010

A sufficient database of seed yield components is the prerequisite to predict which component contributes most to the seed yield complex and to dissect the biology of the complex quantitative trait seed yield. Phenotypic variation of eleven vegetative and reproductive traits was characterized for 2481 individuals from fifty Lolium perenne L. (perennial ryegrass) ecotypes and cultivars. Considerable levels of among‐ and within‐population variation were found across several inflorescence characters. Principal component and canonical variate analysis separated ecotypes from cultivars, and cultivars generally had later dates of ear emergence, better spring and summer growth, longer rachis length and more spikelets per spike than ecotypes. Strong positive relationships were seen between inflorescence characters using both correlation and regression analyses. The strong relationship between rachis length and other inflorescence characters suggested that rachis length could be used as a performance predictor for several other characters of the spike. This phenotypic study has helped to determine basic patterns of morphological diversity and correlations between characters. It is discussed in which way further developmental genetic studies can be directed.
Laparoscopic surgery for endometrial cancer: a phenomenological study
Authors: Hughes Cathy , Knibb Wendy , Allan Helen
Published: September 2010

hughes c., knibb w. & allan h. (2010) Laparoscopic surgery for endometrial cancer: a phenomenological study. Journal of Advanced Nursing 66(11), 2500–2509.

Aim.  This paper is a report of a study of women’s perspectives on the experience of laparoscopic surgery for endometrial cancer.

Background.  Laparoscopic surgery is increasingly used to treat early endometrial cancer. It is associated with low levels of morbidity and is considered safe as cancer surgery, but research on quality of life and women’s experiences is limited.

Method.  Heideggerian hermeneutic phenomenology was used to explore the experiences of 14 women who had undergone the procedure in two English cancer centres between February 2008 and July 2009. In‐depth interviews were taped, transcribed and analysed using Colaizzi’s framework.

Findings.  A phenomenological description was produced from five identified themes: having cancer, transfer of responsibility to the surgeon, information and support, independence, and normality. The experience of laparoscopic surgery was overshadowed by the presence of cancer. Fear and lack of knowledge played an important role in entrusting the surgeon with the responsibility for decision‐making. Individual, unmet information needs focused on the practicalities of treatment and being in an unfamiliar situation and environment. Loss of control and vulnerability were associated with illness and surgery, but early postoperative mobility and reduced pain, facilitated rapid return to independence and maintained a sense of normality.

Conclusion.  Healthcare professionals should deliver care in early endometrial cancer in a way that recognizes the significance of the cancer diagnosis, the role of the surgeon in decision‐making and the need for practical information. Women with endometrial cancer should have access to treatments that reduce dependency and maintain normality.
Center for Epidemiologic Studies Depression Scale for Children: psychometric testing of the Chinese version
Authors: William Li Ho Cheung , Chung Oi Kwan Joyce , Ho Ka Yan
Published: September 2010

li h.c.w., chung o.k.j. & ho k.y. (2010) Center for Epidemiologic Studies Depression Scale for Children: psychometric testing of the Chinese version. Journal of Advanced Nursing 66(11), 2582–2591.

Aim.  This paper is a report of psychometric testing of the Chinese version of the Center for Epidemiologic Studies Depression Scale for Children.

Background.  The availability of a valid and reliable instrument that accurately detects depressive symptoms in children is crucial before any psychological intervention can be appropriately planned and evaluated. There is no such an instrument for Chinese children.

Methods.  A test–retest, within‐subjects design was used. A total of 313 primary school students between the ages of 8 and 12 years were invited to participate in the study in 2009. Participants were asked to respond to the Chinese version of the Center for Epidemiologic Studies Depression Scale for Children, short form of the State Anxiety Scale for Children and Rosenberg’s Self‐Esteem Scale. The internal consistency, content validity and construct validity and test–retest reliability of the Chinese version of the Center for Epidemiologic Studies Depression Scale for Children were assessed.

Results.  The newly‐translated scale demonstrated adequate internal consistency, good content validity and appropriate convergent and discriminant validity. Confirmatory factor analysis added further evidence of the construct validity of the scale.

Conclusion.  Results suggest that the newly‐translated scale can be used as a self‐report assessment tool in detecting depressive symptoms of Chinese children aged between 8 and 12 years.
Resetting the Dynamic Range of Hypothalamic‐Pituitary‐Adrenal Axis Stress Responses Through Pregnancy
Authors: Brunton P. J.
Published: September 2010

The hypothalamic‐pituitary‐adrenal (HPA) axis plays a key role in the neuroendocrine response to stress. Dynamic changes in HPA axis regulation and hence HPA responsivity occur over the lifetime of an animal. This article focuses on two extremes of the spectrum. The first occurs naturally during pregnancy when stress responses are dampened. The second, at the opposite end of the scale, occurs in offspring of mothers who were exposed to stress during pregnancy and display exaggerated HPA axis stress responses. Reduced glucocorticoid output in response to stress in pregnancy may have important consequences for conserving energy supply to the foetus(es), in modulating immune system adaptations and in protecting against adverse foetal programming by glucocorticoids. Understanding the mechanisms underpinning this adaptation in pregnancy may provide insights for manipulating HPA axis responsiveness in later life, particularly in the context of resetting HPA axis hyperactivity associated with prenatal stress exposure, which may underlie several major pathologies, including cardiovascular disease, diabetes mellitus type 2, obesity, cognitive decline and mood disorders.
Reduced small‐intestinal injury induced by indomethacin in interleukin‐17A‐deficient mice
Authors: Yamada Shinya , Naito Yuji , Takagi Tomohisa , Mizushima Katsura , Hirai Yasuko , Horie Ryusuke , Fukumoto Kohei , Inoue Ken , Harusato Akihito , Yoshida Naohisa , Uchiyama Kazuhiko , Handa Osamu , Ishikawa Takeshi , Konishi Hideyuki , Wakabayashi Naoki , Yagi Nobuaki , Kokura Satoshi , Kita Masakazu , Yoshikawa Toshikazu
Published: September 2010

Background and Aims:  The pathogenesis of enteropathy induced by non‐steroidal anti‐inflammatory drugs (NSAIDs) is still unclear, and there are no established treatments. Interleukin‐17A (IL‐17A) is a pro‐inflammatory cytokine that has been associated with the development of chronic inflammatory diseases, including autoimmune diseases. To define the role of IL‐17A in small intestinal injury and inflammation, we studied the effects of indomethacin administration in mice with targeted deletions of the IL‐17A gene.

Methods:  Male C57BL/6 (wild‐type) and homozygous IL‐17A‐/‐ C57BL/6 mice were subjected to this study. Indomethacin (10 mg/kg) was subcutaneously administered to induce small‐intestinal damage. Indomethacin‐induced lesions in the small intestine were evaluated by measuring the injured area and by histopathology. Also assessed were myeloperoxidase (MPO) activity, as an index of neutrophil accumulation, and intestinal mRNA expression for inflammatory cytokines.

Results:  The area of macroscopic ulcerative lesions, the MPO activity and the mRNA expression of inflammatory‐associated chemokines, such as keratinocyte chemoattractant (KC), monocyte chemotactic protein‐1 (MCP‐1), and granulocyte‐colony stimulating factor (G‐CSF), were significantly increased in indomethacin‐treated groups compared with the sham groups. The development of intestinal lesions by indomethacin was inhibited in IL‐17A‐/‐ mice compared with wild‐type mice, together with significant suppression of the increased levels of MPO activities and KC, MCP‐1, and G‐CSF levels.

Conclusion:  These findings demonstrate that IL‐17A contributes to the development of indomethacin‐induced small intestinal injury through upregulation of G‐CSF, KC, and MCP‐1. IL‐17A might be a promising new therapeutic target to treat NSAID‐induced enteritis.
Effect of Lactobacillus plantarum LP‐Onlly on gut flora and colitis in interleukin‐10 knockout mice
Authors: Xia Yang , Chen Hong‐Qi , Zhang Min , Jiang Yan‐Qun , Hang Xiao‐Min , Qin Huan‐Long
Published: September 2010

Background and Aim:  Probiotics are used in the therapy of inflammatory bowel disease. This study aimed to determine the effects of probiotic Lactobacillus plantarum LP‐Onlly (LP) on gut flora and colitis in interleukin‐10 knockout (IL‐10−/−) mice, a model of spontaneous colitis.

Methods:  IL‐10−/− and wild‐type mice were used at 8 weeks of age and LP by gavage was administered at a dose of 109 cells/day per mice for 4 weeks. Mice were maintained for another one week without LP treatment. The colonic tissues were collected for histological and ultrastructural analysis at death after 4 weeks treatment of LP, and the feces were collected at 1‐week intervals throughout the experiment for the analysis of gut flora and LP using selective culture‐based techniques.

Results:  Compared with control mice, IL‐10−/− mice developed a severe intestinal inflammation and tissue damage, and had an abnormal composition of gut microflora. LP administration attenuated colitis with the decreased inflammatory scoring and histological injury in the colon of IL‐10−/− mice. In addition, LP administration increased the numbers of beneficial total bifidobacteria and lactobacilli, and decreased the numbers of potential pathogenic enterococci and Clostridium perfringens, although the decrease of coliforms was not significant after LP treatment in IL‐10−/− mice.

Conclusions:  Oral administration of LP was effective in the treatment of colitis, with the direct modification of gut microflora in IL‐10−/− mice. This probiotic strain could be used as a potential adjuvant in the therapy of inflammatory bowel disease, although further studies are required in human.
Urinary matrix metalloproteinase‐7 level is associated with the presence of metastasis in bladder cancer
Authors: Szarvas Tibor , Singer Bernhard B. , Becker Markus , vom Dorp Frank , Jäger Tobias , Szendrői Attila , Riesz Péter , Romics Imre , Rübben Herbert , Ergün Süleyman
Published: September 2010

Study Type – Therapy (case series) Level of Evidence 4

What’s known on the subject? and What does the study add?

Recent data suggest that MMP‐7 is critically involved in metastasis formation. In accordance, we formerly found significantly elevated MMP‐7 tissue expression and serum concentration in samples of patients with metastatic bladder cancer and observed an independent correlation between MMP‐7 levels and patients’ prognosis. In the present study we demonstrated that high preoperative urinary MMP‐7 concentrations are associated with metastatic bladder cancer.

OBJECTIVE

• To assess the presence of matrix metalloproteinase (MMP)‐7 in urine samples of patients with bladder cancer and to investigate the correlation between MMP‐7 urine concentration and clinicopathological variables.

PATIENTS AND METHODS

• The presence of MMP‐7 in the urine of patients with bladder cancer was tested in 32 representative cases using immunoprecipitation followed by western blot analysis.

• Urinary MMP‐7 concentration levels were analyzed in 132 patients with bladder cancer and 96 controls using an enzyme‐linked immunosorbent assay.

RESULTS

• MMP‐7 levels did not differ significantly between patients with localized bladder cancer and controls (P= 0.174). On the other hand, we detected a fourfold, significantly elevated MMP‐7 concentration in urine samples of patients with bladder cancer with regional or distant metastasis (P= 0.003).

• Using a threshold value of 6.88 ng/ml, determined by receiver‐operating characteristic curve analysis, a specificity of 82% and a sensitivity of 78% were observed.

• Western blot analysis revealed that the 55‐kDa tissue inhibitor of metalloproteinase 1 complexed MMP‐7 is the dominant form of urinary matrilysin.

CONCLUSIONS

• MMP‐7 is present in detectable amounts in the urine of patients with bladder cancer. Its concentrations are significantly elevated in patients with metastatic disease.

• Determination of urinary matrilysin level could help to detect bladder cancer metastasis, and may therefore provide a more reliable prognosis and influence therapy decisions.
Acculturation among immigrant nurses in Israel and the United States of America
Authors: Ea E. , Itzhaki M. , Ehrenfeld M. , Fitzpatrick J.
Published: September 2010

EA E., ITZHAKI M., EHRENFELD M. & FITZPATRICK J. (2010) Acculturation among immigrant nurses in Israel and the United States of America. International Nursing Review

Background:  Former Soviet Union (FSU) nurses in Israel and Filipino registered nurses (RNs) in the United States of America (USA) play significant roles in the delivery of health‐care services in their host countries. However, little is known about how they acculturate in a different culture.

Objectives:  The purposes of this study were to determine the levels of and the difference in acculturation of FSU nurses in Israel and Filipino RNs in the USA.

Methods:  Acculturation was assessed using A Short Acculturation Scale for Filipino Americans and t‐test was conducted to determine the difference in acculturation between these two groups of immigrant nurses.

Findings:  Results revealed that Filipino RNs have an acculturation level that leaned towards their host culture while FSU nurses have an acculturation level that was closer to their original culture than the Israeli culture and that there was a significant difference in acculturation between these two groups of immigrant nurses.

Conclusions:  Differences in acculturation between two predominant groups of immigrant nurses in Israel and the USA exist. Understanding the differences and the factors that affect their integration into their host cultures could be used to develop strategies to assist Filipino and FSU immigrant nurses achieve positive personal and work‐related outcomes.
The transcultural nursing concept: a study of nursing students in Turkey
Authors: Ayaz S. , Bilgili N. , Akın B.
Published: September 2010

AYAZ S., BILGILI N. & AKIN B. (2010) The transcultural nursing concept: a study of nursing students in Turkey. International Nursing Review

Background:  Cultural differences are known to be pronounced in Turkey, and some difficulties are encountered in patient care. Cultural sufficiency in providing health care to the patients is of great importance in satisfactory care delivery.

Aim:  To determine the cultural diversity that the students experienced between the patients and themselves while providing care to patients. Knowledge of transcultural nursing was also investigated.

Design and Methods:  This was a descriptive study. The population comprised of 650 undergraduate students attending the nursing schools of three universities. A total of 622 students were included in the sample. The survey method was used for data collection. Percentages and chi‐square test were used.

Results:  Most of the students (85.5%) had experienced cultural differences while giving care to their patients and 73.8% did not know the definition of this concept. The issues where cultural differences were experienced to the highest degree were differences in dialect and pronunciation (53.4%), differences of language (37%), traditions and customs of the individual (30.7%), and religious belief and sect (30.2%). It was found that the grade the students were in had a significant effect on the experience of cultural differences (P < 0.05).

Conclusions:  The majority of students experience cultural diversity in patient care. It is thought that transcultural care placed in curriculum even as a separate course will guide nursing students in all stages of patient care. Thus, the effect of cultural diversity in patient care can be minimized with the help of education.
Weight gain following treatment with valproic acid: pathogenetic mechanisms and clinical implications
Authors: Verrotti A. , D'Egidio C. , Mohn A. , Coppola G. , Chiarelli F.
Published: September 2010

In the last years, a growing body of literature indicates an association between valproic acid therapy and weight gain. Weight gain during valproate treatment can be observed within the first 3 months of therapy and women seem to be more susceptible than men. The mechanism through which valproic acid may induce a weight gain is still controversial. The scope of this paper is to investigate the possible causal link between treatment and weight gain in epileptic patients. Systematic review of published epidemiological studies has been done in order to evaluate the real extent of this side effect of valproic acid and its clinical implications, such as an increased risk of insulin resistance and other secondary metabolic abnormalities. The knowledge of the potential of valproic acid to cause significant changes in body weight will help in appropriate selection and modification of antiepileptic therapy to minimize the risk for weight abnormalities. Measurements of body weight before initiation of valproic acid therapy should be done as part of the monitoring of patients with epilepsy to detect changes before there are serious adverse consequences; an increase of 2 kg of body weight after 1 month of treatment should imply considerations to change antiepileptic drug therapy.
Permanently Provisional: History, Facts & Figures of Portuguese Immigration in Switzerland
Authors: Afonso Alexandre
Published: September 2010

This article provides an overview of the main demographic, social, and economic characteristics of Portuguese immigration in Switzerland. Firstly, it outlines the political and economic underpinnings of Portuguese migration flows to Switzerland. Then, it analyzes the demographic and sociological composition of these flows, the composition of the Portuguese population in Switzerland, as well as processes of economic and cultural integration. It is notably argued that the enduring Portuguese “ideology of return migration” has played a central role in the patterns of integration of Portuguese immigrants in Switzerland.
The metabolic theory of ecology: prospects and challenges for plant biology
Authors: Price Charles A. , Gilooly James F. , Allen Andrew P. , Weitz Joshua S. , Niklas Karl J.
Published: September 2010

The metabolic theory of ecology (MTE) as applied to the plant sciences aims to provide a general synthesis for the structure and functioning of plants from organelles to ecosystems. MTE builds from simple assumptions of individual metabolism to make predictions about phenomena across a wide range of scales, from individual plant structure and function to community dynamics and global nutrient cycles. The scope of its predictions include morphological allometry, biomass partitioning, vascular network design, and life history phenomena at the individual level; size‐frequency distributions, population growth rates, and energetic equivalence at the community level; and the flux, turnover and storage of nutrients at the ecosystem level. Here, we provide an overview of MTE, by considering its assumptions and predictions at these different levels of organization and explaining how the model integrates phenomena among all of these scales. We highlight the model’s many successes in predicting novel patterns and draw attention to areas in which gaps remain between observations and MTE’s assumptions and predictions. Considering the theory as a whole, we argue that MTE has made a significant contribution in furthering our understanding of those unifying aspects of the structure and function of plants, populations, communities, and ecosystems.

ContentsSummary696I.Introduction697II.Background and theoretical foundations: assumptions of WBE698III.Background and theoretical foundations: assumptions of MTE699IV.MTE at the individual plant level: metabolism, architecture and demography699V.Metabolism700VI.Morphology701VII.Biomass partitioning701VIII.Hydraulics702IX.Demography702X.MTE at population, community, and ecosystem scales703XI.Plant population density703XII.Plant population density within a site704XIII.Population growth rates704XIV.Ecosystem dynamics705XV.Discussion706Acknowledgements708References708
Lizard predation alters the effect of habitat area on the species richness of insect assemblages on Bahamian isles
Authors: Murakami Masashi , Hirao Toshihide
Published: September 2010

Aim Anolis lizard invasions are a serious threat world‐wide, and information about how this invasive predator affects the diversity of prey assemblages is important for many strategic conservation goals. It is hypothesized that these predators reduce the slope of species–area relationships (SARs) of their prey assemblages. The effects of island area and predation by anolis lizards on the species richness of insular insect assemblages were investigated.

Location Twenty‐four isles around Staniel Cay, Exuma Cays, Bahamas.

Methods Flying insects were sampled using half‐sized Malaise traps for three consecutive days on each island in May 2007. First, the effect of island area on the probability of lizard presence was evaluated. Then, the effects of the presence–absence of predatory lizards on SARs were analysed for the overall insect assemblage and for the assemblages of five dominant insect orders.

Results Our results indicated that anolis lizards occurred primarily on larger islands. The species richness of the overall insect assemblage and five dominant insect orders significantly increased with island area. The interaction between island area and predator presence–absence significantly affected the overall insect assemblage and Diptera and Hymenoptera assemblages (but not Coleoptera, Hemiptera and Lepidoptera assemblages). The presence of predators caused decreases in the slope of the SARs.

Main conclusions The presence of predatory lizards strongly affects species richness of insular insect assemblages with the island area being a crucial determinant of the species richness. Therefore, the slope of the SAR can serve as a measure of the consequence of invasive predatory species on native insect assemblages.
First‐Principles Thermochemistry and Thermodynamic Modeling of the Al2O3–Nd2O3–SiO2–Y2O3 Pseudoquaternary System
Authors: Saal James E. , Shin Dongwon , Stevenson Adam J. , Messing Gary L. , Liu Zi‐Kui
Published: September 2010

The Al2O3–Nd2O3–SiO2–Y2O3 pseudoquaternary system was thermodynamically modeled with a focus on the phase equilibria concerning the sintering of neodymium‐doped yttrium aluminum garnet, Nd:YAG ((Y1−xNdx)3Al5O12). The Nd2O3–SiO2 and Nd2O3–Y2O3 systems were evaluated. Due to the lack of experimental thermochemical data, first‐principles calculations were used to predict the enthalpy of formation of Nd2SiO5 and the enthalpy of mixing of Nd in YAG. Isothermal sections of the Al2O3–Nd2O3–SiO2, Al2O3–Nd2O3–Y2O3, and Nd2O3–SiO2–Y2O3 pseudoternary systems are presented.
Prevention of retinopathy of prematurity in preterm infants through changes in clinical practice and SpO2technology
Authors: Castillo Armando , Deulofeut Richard , Critz Ann , Sola Augusto
Published: September 2010

Aim: To identify whether pulse oximetry technology is associated with decreased retinopathy of prematurity (ROP) and laser treatment.

Methods: Inborn infants <1250 g who had eye exams were compared at two centres in three periods. In Period 1, SpO2target was ≥93% and pulse oximetry technology was the same in both Centres. In Period 2, guidelines for SpO288–93% were implemented at both centres and Centre B changed to oximeters with signal extraction technology (SET®) while Centre A did not, but did so in Period 3. One ophthalmology department performed eye exams using international criteria.

Results: In 571 newborns <1250 g, birth weight and gestational age were similar in the different periods and centres. At Centre A, severe ROP and need for laser remained the same in Periods 1 and 2, decreasing in Period 3–6% and 3%, respectively. At Centre B, severe ROP decreased from 12% (Period 1) to 5% (Period 2) and need for laser decreased from 5% to 3%, remaining low in Period 3.

Conclusion: In a large group of inborn infants <1250 g, a change in clinical practice in combination with pulse oximetry with Masimo SET, but not without it, led to significant reduction in severe ROP and need for laser therapy. Pulse oximetry selection is important in managing critically ill infants.
RADIOGRAPHY AND COMPUTED TOMOGRAPHY IN THE DIAGNOSIS OF NONNEOPLASTIC EQUINE MANDIBULAR DISEASE
Authors: HUGGONS NICK A. , BELL ROBIN J. W. , PUCHALSKI SARAH M.
Published: September 2010

We compared the information gained from computed tomography (CT) vs. radiography in horses with nonneoplastic disease of the mandible. We hypothesized that CT would provide additional diagnostic information. Medical records, radiographs, and CT images of horses with nonneoplastic mandibular disease evaluated between 1994 and 2008 were reviewed. Nineteen horses were identified; 11 had a tooth root abscess and related disease, four had a fracture of the teeth and/or mandible, and four had a nonneoplastic mass. Both CT images and radiographs allowed identification of diseased teeth that appeared clinically normal otherwise. CT allowed identification of teeth that were clinically affected but appeared normal radiographically. Parameters such as tooth pulp involvement, lamina dura destruction, presence of bone fragments, lingual and buccal mandibular bone periosteal reaction, and cortical bone destruction were more conspicuous with CT. Performing radiography and CT in horses with nonneoplastic mandibular disease provides a more complete evaluation than either technique alone. CT contributes additional information that could otherwise be overlooked with radiographs alone in horses with a mandibular fracture. CT provides ancillary information to radiographs in horses with dental infection or a nonneoplastic mass of the mandible.
Mammalian Gup1, a homolog of Saccharomyces cerevisiae glycerol uptake/transporter 1, acts as a negative regulator for N‐terminal palmitoylation of Sonic hedgehog
Authors: Abe Yoichiro , Kita Yoshiko , Niikura Takako
Published: September 2010

Mammalian glycerol uptake/transporter 1 (Gup1), a homolog of Saccharomyces cerevisiae Gup1, is predicted to be a member of the membrane‐bound O‐acyltransferase family and is highly homologous to mammalian hedgehog acyltransferase, known as Skn, the homolog of the Drosophila skinny hedgehog gene product. Although mammalian Gup1 has a sequence conserved among the membrane‐bound O‐acyltransferase family, the histidine residue in the motif that is indispensable to the acyltransferase activity of the family has been replaced with leucine. In this study, we cloned Gup1 cDNA from adult mouse lung and examined whether Gup1 is involved in the regulation of N‐terminal palmitoylation of Sonic hedgehog (Shh). Subcellular localization of mouse Gup1 was indistinguishable from that of mouse Skn detected using the fluorescence of enhanced green fluorescent protein that was fused to each C terminus of these proteins. Gup1 and Skn were co‐localized with an endoplasmic reticulum marker, 78 kDa glucose‐regulated protein, suggesting that these two molecules interact with overlapped targets, including Shh. In fact, full‐length Shh coprecipitated with FLAG‐tagged Gup1 by immunoprecipitation using anti‐FLAG IgG. Ectopic expression of Gup1 with full‐length Shh in cells lacking endogenous Skn showed no hedgehog acyltransferase activity as determined using the monoclonal antibody 5E1, which was found to recognize the palmitoylated N‐terminal signaling domain of Shh under denaturing conditions. On the other hand, Gup1 interfered with the palmitoylation of Shh catalyzed by endogenous Skn in COS7 and NSC34. These results suggest that Gup1 is a negative regulator of N‐terminal palmitoylation of Shh and may contribute to the variety of biological actions of Shh.
Enzymatic control of anhydrobiosis‐related accumulation of trehalose in the sleeping chironomid, Polypedilum vanderplanki
Authors: Mitsumasu Kanako , Kanamori Yasushi , Fujita Mika , Iwata Ken‐ichi , Tanaka Daisuke , Kikuta Shingo , Watanabe Masahiko , Cornette Richard , Okuda Takashi , Kikawada Takahiro
Published: September 2010

Larvae of an anhydrobiotic insect, Polypedilum vanderplanki, accumulate very large amounts of trehalose as a compatible solute on desiccation, but the molecular mechanisms underlying this accumulation are unclear. We therefore isolated the genes coding for trehalose metabolism enzymes, i.e. trehalose‐6‐phosphate synthase (TPS) and trehalose‐6‐phosphate phosphatase (TPP) for the synthesis step, and trehalase (TREH) for the degradation step. Although computational prediction indicated that the alternative splicing variants (PvTpsα/β) obtained encoded probable functional motifs consisting of a typical consensus domain of TPS and a conserved sequence of TPP, PvTpsα did not exert activity as TPP, but only as TPS. Instead, a distinct gene (PvTpp) obtained expressed TPP activity. Previous reports have suggested that insect TPS is, exceptionally, a bifunctional enzyme governing both TPS and TPP. In this article, we propose that TPS and TPP activities in insects can be attributed to discrete genes. The translated product of the TREH ortholog (PvTreh) certainly degraded trehalose to glucose. Trehalose was synthesized abundantly, consistent with increased activities of TPS and TPP and suppressed TREH activity. These results show that trehalose accumulation observed during anhydrobiosis induction in desiccating larvae can be attributed to the activation of the trehalose synthetic pathway and to the depression of trehalose hydrolysis.
Synthesis of the MAX Phases by Pulse Discharge Sintering
Authors: Sun ZhengMing , Hashimoto Hitoshi , Tian Wubian , Zou Yong
Published: September 2010

As an invited paper with the designated title to this focused session, this is to introduce the pulse discharge sintering process applied for the sintering and/or synthesis of a few representative MAX phases, such as Ti3SiC2, Ti3AlC2, Ti2AlC, Ti2AlN, Cr2AlC, Cr2GaC, Ti2GaC, as well as the MAX‐based solid solutions and some composites. The effects of processing parameters on the synthesis reactions, densification, microstructure, as well as the properties have been investigated. This paper not only briefly reviews our synthesis work on the MAX phases but also presents new results such as the comparison of PDS with conventional hot pressing, the newly obtained results on the synthesis of Cr2GaC, Ti2GaC, as well as some solid solutions and composites. With the results presented herein as summarized in tables and figures, none of which were published elsewhere, this article aims at a better understanding of the PDS process in the research and development of the MAX phases and related materials.
A case study and comprehensive differential diagnosis and care plan for the three Ds of women's health: Primary dysmenorrhea, secondary dysmenorrhea, and dyspareunia
Authors: Stoelting‐Gettelfinger Wendy
Published: September 2010

Abstract  Purpose: To provide a case study for the discussion, diagnosis, management, and comprehensive plan of care for primary dysmenorrhea, secondary dysmenorrhea, and dyspareunia for the advanced practice registered nurse (APRN) working in primary care.

Data sources: Selected text, research, clinical articles, and personal communication with expert APRNs.

Conclusions: Three of the most commonly presenting women's health related conditions include primary dysmenorrhea, secondary dysmenorrhea, and dyspareunia. These conditions can present a challenge in developing an accurate differential diagnosis and appropriate plan of care. This article presents the reader with a detailed case study that provides an analysis of each potential differential diagnosis with rationale. A recommended diagnostic and therapeutic plan of care is included for the reader's review.

Implications for practice: If left untreated, primary dysmenorrhea, secondary dysmenorrhea, and dyspareunia can result in pain, suffering, and impaired fertility and sexual function. Patients frequently experience symptoms for months to years prior to accurate diagnosis.
A brief review of pharmacotherapeutic treatment options in smoking cessation: bupropion versus varenicline
Authors: Johnson Tam Spitzer
Published: September 2010

Abstract  Purpose: The purpose of this article is to compare the efficacy of two prominent medications utilized in smoking cessation: bupropion and varenicline.

Data sources: Comprehensive review of the literature on bupropion and varenicline including randomized control trials, government reports, journal reviews, and pharmaceutical inserts.

Conclusions: In all studies comparing varenicline to bupropion and/or placebo, varenicline yielded a greater cessation rate at both 3 and 12 months. Additionally, varenicline 1 mg indicated an increased potential for long‐term cessation success when compared with varenicline 0.5 mg. When compared with only placebo, bupropion demonstrated a higher efficacy for cessation both at 3 and 12 months.

Implications for practice: Only 6% of the 20 million smokers who attempt to quit will succeed in long term. Clinicians must assess their patient's willingness to quit and educate them about cessation options. Knowing the efficacy of various treatment options for patients will potentially increase their success at quitting smoking. Understanding the treatment options available, allows for clinicians to provide the best possible method for smoking cessation for their patient population.
Hydrophobic substances induce water stress in microbial cells
Authors: Bhaganna Prashanth , Volkers Rita J. M. , Bell Andrew N. W. , Kluge Kathrin , Timson David J. , McGrath John W. , Ruijssenaars Harald J. , Hallsworth John E.
Published: September 2010

Ubiquitous noxious hydrophobic substances, such as hydrocarbons, pesticides and diverse industrial chemicals, stress biological systems and thereby affect their ability to mediate biosphere functions like element and energy cycling vital to biosphere health. Such chemically diverse compounds may have distinct toxic activities for cellular systems; they may also share a common mechanism of stress induction mediated by their hydrophobicity. We hypothesized that the stressful effects of, and cellular adaptations to, hydrophobic stressors operate at the level of water : macromolecule interactions. Here, we present evidence that: (i) hydrocarbons reduce structural interactions within and between cellular macromolecules, (ii) organic compatible solutes – metabolites that protect against osmotic and chaotrope‐induced stresses – ameliorate this effect, (iii) toxic hydrophobic substances induce a potent form of water stress in macromolecular and cellular systems, and (iv) the stress mechanism of, and cellular responses to, hydrophobic substances are remarkably similar to those associated with chaotrope‐induced water stress. These findings suggest that it may be possible to devise new interventions for microbial processes in both natural environments and industrial reactors to expand microbial tolerance of hydrophobic substances, and hence the biotic windows for such processes.