bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part I: Theoretical basis
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy
Published: August 2015

Background

Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. Recently, such probabilistic models are mostly based on either hidden Markov models (HMMs) or transducer theories, both of which give the indel component of the probability of a given sequence alignment as a product of either probabilities of column-to-column transitions or block-wise contributions along the alignment. However, it is nota prioriclear how these models are related with anygenuinestochastic evolutionary model, which describes the stochastic evolution of anentiresequence along the time-axis. Moreover, none of these models can fully accommodate biologically realistic features, such as overlapping indels, power-law indel-length distributions, and indel rate variation across regions.

Results

Here, we theoretically tackle theab initiocalculation of the probability of a given sequence alignment under agenuineevolutionary model, more specifically, a general continuous-time Markov model of the evolution of anentiresequence via insertions and deletions. Our model allows general indel rate parameters including length distributions but does not impose any unrealistic restrictions on indels. Using techniques of the perturbation theory in physics, we expand the probability into a series over different numbers of indels. Our derivation of this perturbation expansion elegantly bridges the gap between Gillespie’s (1977) intuitive derivation of his own stochastic simulation method, which is now widely used in evolutionary simulators, and Feller’s (1940) mathematically rigorous theorems that underpin Gillespie′s method. We find a sufficient and nearly necessary set of conditions under which the probability can be expressed as the product of an overall factor and the contributions from regions separated by gapless columns of the alignment. The indel models satisfying these conditions include those with some kind of rate variation across regions, as well as space-homogeneous models. We also prove that, though with a caveat, pairwise probabilities calculated by the method of Miklós et al. (2004) are equivalent to those calculated by ourab initioformulation, at least under a space-homogenous model.

Conclusions

Our ab initio perturbative formulation provides a firm theoretical ground that other indel models can rest on.

[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part II: Perturbation analyses
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy
Published: August 2015

Background

Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established a theoretical basis of ourab initioperturbative formulation of agenuineevolutionary model, more specifically, a continuous-time Markov model of the evolution of anentiresequence via insertions and deletions. And we showed that, under some conditions, theab initioprobability of an alignment can be factorized into the product of an overall factor and contributions from regions (or local alignments) separated by gapless columns.

Results

This paper describes how ourab initioperturbative formulation can be concretely used to approximately calculate the probabilities of all types of local pairwise alignments (PWAs) and some typical types of local multiple sequence alignments (MSAs). For each local alignment type, we calculated the fewest-indel contribution and the next-fewest-indel contribution to its probability, and we compared them under various conditions. We also derived a system of integral equations that can be numerically solved to give “exact solutions” for some common types of local PWAs. And we compared the obtained “exact solutions” with the fewest-indel contributions. The results indicated that even the fewest-indel terms alone can quite accurately approximate the probabilities of local alignments, as long as the segments and the branches in the tree are of modest lengths. Moreover, in the light of our formulation, we examined parameter regions where other indel models can safely approximate the correct evolutionary probabilities. The analyses also suggested some modifications necessary for these models to improve the accuracy of their probability estimations.

Conclusions

At least under modest conditions, ourab initioperturbative formulation can quite accurately calculate alignment probabilities under biologically realistic indel models. It also provides a sound reference point that other indel models can be compared to. [This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]
Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations
Authors: Ezawa Kiyoshi , Graur Dan , Landan Giddy
Published: August 2015

Background

Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established the theoretical basis of ourab initioperturbative formulation of a continuous-time Markov model of the evolution of anentiresequence via insertions and deletions along time axis. In other separate papers (Ezawa, Graur and Landan 2015b,c), we also developed various analytical and computational methods to concretely calculate alignment probabilities via our formulation. In terms of frequencies, however, substitutions are usually more common than indels. Moreover, many experiments suggest that other mutations, such as genomic rearrangements and recombination, also play some important roles in sequence evolution.

Results

Here, we extend ourab initioperturbative formulation of agenuineevolutionary model so that it can incorporate other mutations. We give a sufficient set of conditions that the probability of evolution via both indels and substitutions is factorable into the product of an overall factor and local contributions. We also show that, under a set of conditions, the probability can be factorized into two sub-probabilities, one via indels alone and the other via substitutions alone. Moreover, we show that our formulation can be extended so that it can also incorporate genomic rearrangements, such as inversions and duplications. We also discuss how to accommodate some other types of mutations within our formulation.

Conclusions

Ourab initioperturbative formulation thus extended could in principle describe the stochastic evolution of anentiresequence along time axis via major types of mutations.

[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend theab initioperturbative formulation of a general continuous-time Markov model of indels.]
The constant philopater hypothesis: a new life history invariant for dispersal evolution
Authors: Rodrigues António M. M. , Gardner Andy
Published: August 2015

Life history invariants play a pivotal role in the study of social adaptation: they provide theoretical hypotheses that can be empirically tested, and benchmark frameworks against which new theoretical developments can be understood. Here we derive a novel invariant for dispersal evolution: the “constant philopater hypothesis” (CPH). Specifically, we find that, irrespective of variation in maternal fecundity, all mothers are favoured to produce exactly the same number of philopatric offspring, with high-fecundity mothers investing proportionally more, and low-fecundity mothers investing proportionally less, into dispersing offspring. This result holds for female and male dispersal, under haploid, diploid and haplodiploid modes of inheritance, irrespective of the sex ratio, local resource availability, and whether mother or offspring controls the latter’s dispersal propensity. We explore the implications of this result for evolutionary conflicts of interest – and the exchange and withholding of contextual information – both within and between families, and we show that the CPH is the fundamental invariant that underpins and explains a wider family of invariance relationships that emerge from the study of social evolution.
SIMPLEX: simulator and postprocessor for free-electron laser experiments
Authors: Tanaka Takashi
Published: August 2015

SIMPLEXis a computer program developed for simulating the amplification process of free-electron lasers (FELs). It numerically solves the so-called FEL equations describing the evolution of the radiation field and growth of microbunching while the electron beam travels along the undulator. In order to reduce the numerical cost, the FEL equations have been reduced to more convenient forms for numerical implementation by applying reasonable approximations.SIMPLEXis equipped with a postprocessor to facilitate the retrieval of desired information from the simulation results, which is crucial for practical applications such as designing the beamline and analyzing the experimental results.
Explorations into sex, gender and leadership in the UK Civil Service Part 2. Hypotheses and research findings
Authors: Manning Tony , Robertson Bob
Published: August 2015

Purpose

– This is the second part of a three-part paper exploring the intersection between sex, gender and leadership in the UK Civil Service. The first part of this paper outlined the training and development activities carried out by the authors, provided a literature review and drew conclusions, in the form of conjectures. The purpose of this paper is to present a series of null hypotheses derived from the conjectures. It then outlines the research methodology and research findings. The final part of this paper discusses the implications of the research findings, presents an evidence-based leadership framework and offers prescriptions for its use.

Design/methodology/approach

– Information was collected from a wide cross-section of UK Civil Servants between 1993 and 2013. Individuals were participants on training and development activities carried out by the authors. The information collected was a by-product of these activities. Individuals completed a variety of psychometric instruments, including self-assessments and 360-degree assessments, and provided information on their sex, work role and work situation. Statistical analysis was carried out on differences in the behaviour of male and female managers, differences in how such behaviours were assessed, using 360-degree assessments, and differences in behaviour and assessments of behaviour in different contexts.

Findings

– Research evidence presented points to the existence of contrasting gender stereotypes and sex differences in behaviour. It also shows that such differences are small and that there are far greater differences amongst men and women managers than between the average man and women manager. Differences in behaviour and assessments of behaviour were also more strongly linked to context than either sex or gender.

Research limitations/implications

– The research was a by-product of training activities. It was not a wide ranging, purpose-built research programme to explain the “glass ceiling”. It was carried out on a particular population and may not generalise to other contexts. Nonetheless, findings are broadly consistent with previous research.

Practical implications

– The third part of this paper discusses the implications of these findings, particularly for training and development professionals. It also presents and discusses additional research findings on leadership in the UK Civil Service.

Social implications

– The findings are relevant to the understanding of sex and gender differences in the work place. They relate to wider considerations of equality of opportunity and diversity.

Originality/value

– There is an extensive body of theory and research on sex, gender and leadership, although little is directly relevant to the UK Civil Service. This is new research, relevant to this context, that brings together these three themes.
The Millennium Development Goals and Production Engineering training
Authors: Jabbour Charbel Jose Chiappetta , Jabbour Ana Beatriz Lopes de Sousa , Leal Filho Walter , Gunasekaran Angappa
Published: August 2015

Purpose

– The search for a more sustainable society depends on more sustainable organisations and, as such, Production (Industrial) Engineering may contribute to this process through the training of professionals with a greater social and environmental consciousness. The purpose of this paper is to present arguments in favour of the integration of Production Engineering and the Millennium Development Goals and evaluate the potential of Production Engineering subareas in contributing to the Millennium Development Goals.

Design/methodology/approach

– This work is conceptual and integrative in order to provide an original framework. A Brazilian perspective on Production Engineering has been adopted.

Findings

– A framework is proposed to guide this integration process by providing suggestions for an agenda of opportunities for academics and practitioners in favour of a more sustainable society.

Originality/value

– This work presents a new framework integrating Production Engineering and the Millennium Development Goals in order to promote a more sustainable training in Production (Industrial) Engineering field of research.
Does the effect of media influence suicide rates?
Authors: Loureiro Paulo Roberto Amorim , Moreira Tito Belchior Silva , Sachsida Adolfo
Published: August 2015

Purpose

– An important question about the determinants of suicide refers to the role of media. In this context, the purpose of this paper is to investigate if there are groups of people who are susceptible to suicide as a result of the effect of media.

Design/methodology/approach

– Using data for the 27 Brazilian states, for the period 1980-2009, to investigate the impact of the media index, unemployment rate, divorce rate and other explanatory variables on the rate of suicide by gender and age. First of all, the authors estimated a model of fixed effects panel. The second estimation method makes use of dynamic panel data with instrumental variables. Each of the results generated by these two estimated models is compared with those obtained by ordinary least squares in stacked data. The authors develop a model about the suicide epidemic where the media works as a contagion effect to disseminate suicidal behavior.

Findings

– The authors observe that, the media index is the third motivator of suicide, after unemployment and violence, for all groups of people. The estimated model shows that 1 percent increase in media index increases suicide rate of young men (aged between 15 and 29 years) at 4.22 percent.

Research limitations/implications

– The empirical results are limited because the authors developed a media index based on quantities of televisions and radios. The authors suggest other research include social media in the index as well.

Originality/value

– This result seems to suggest a type of contagion effect on suicide rates, which reinforces the results obtained by Cutler et al. (2001).
Assessing retail market competition for multi-aquaculture products
Authors: Fofana Abdulai , Jaffry Shabbar
Published: August 2015

Purpose

– The purpose of this paper is to investigate market competition for three product types of salmon (smoke, fresh and whole salmon) to understand whether supermarkets are exercising market power over salmon consumers in the UK retail market.

Design/methodology/approach

– Competition and the corresponding pricing conduct among supermarkets are tested by applying dynamic structural simultaneous system equations and using similar data set used by Jaffryet al.(2003).

Findings

– The results indicate that the market is competitive for fresh fillets and whole salmon but retailers appeared to exert some level of market power for smoke salmon. The hypothesis that market power is the same for all three products in the study was rejected; further indicating that the market for fresh products are competitive while retailers may be exercising market power over consumers for smoke salmon.

Research limitations/implications

– Current data limitations did not allow the investigation to cover the past few years in the modelling process. However, the results are still relevant as there have been no major structural changes in aquaculture products retailing landscape in the recent past.

Practical implications

– Concerns over the supermarkets’ exercise of market power over consumers have prompted the competition authorities to continue investigating the situation in the UK supermarket sector since 1996. The most recent investigation by competition authorities was in 2006. In all cases, no evidence of market power was found despite increased market concentration. Results from this study generally uphold the claim of the competition authorities in the UK.

Originality/value

– This is the first study to use a model within a structural econometric framework of firms to test for competitiveness of salmon products in the UK market place.
Firing costs in a business cycle model with endogenous separations
Authors: Wesselbaum Dennis
Published: August 2015

Purpose

– The purpose of this paper is to introduce productivity-dependent firing costs into an otherwise standard endogenous separations matching model. The authors suggest an alternative to the standard fix cost approach and account for empirical evidence emphasizing that firing costs vary across workers. The authors show that the model with firing costs outperformes the model without firing costs and replicates the empirical facts fairly well. Furthermore, the authors present cross-country evidence that countries with stricter employment protection have a weaker Beveridge curve relation and surprisingly more volatile job flow rates.

Design/methodology/approach

– The authors begin the analysis at the intersection of labor and product markets. For this purpose, the authors derive a real business cycle model with search and matching frictions and endogenous separations. The authors enrich this set-up by introducing productivity-dependent firing costs.

Findings

– The authors show that the model with firing costs outperformes the model without firing costs and replicates the empirical facts fairly well. Furthermore, the authors present cross-country evidence that countries with stricter employment protection have a weaker Beveridge curve relation and surprisingly more volatile job flow rates.

Originality/value

– This paper introduces productivity-dependent firing costs into an otherwise standard endogenous separations matching model. The authors suggest an alternative to the standard fix cost approach and account for empirical evidence emphasizing that firing costs vary across workers. The authors show that the model with firing costs outperformes the model without firing costs and replicates the empirical facts fairly well. Furthermore, the authors present cross-country evidence that countries with stricter employment protection have a weaker Beveridge curve relation and surprisingly more volatile job flow rates.
HPLC‐MSn Identification of Betalain Profile of Different Beetroot (Beta vulgaris L. ssp. vulgaris) Parts and Cultivars
Authors: Slatnar Ana , Stampar Franci , Veberic Robert , Jakopic Jerneja
Published: August 2015

The distribution of betalains in peel, flesh, and petioles of yellow and red beetroot cultivars has been investigated using an High‐performance liquid chromatography (HPLC) system with electrospray mass spectrometry. Differences in the levels of betacyanins and betaxanthins between different colored cultivars were individually determined for 3 plant parts. The content of almost all analyzed compounds decreased in the following order: peel > flesh > petiole. Betanin/isobetanin pigments comprised a major portion of the relative peak area measured in red beetroot peel. Isobetanin relative peak areas were also high in leaf petioles (68.94% to 74.16%) of red colored cultivars. However, betacyanins were completely absent from the extracts of all analyzed parts of yellow beet. Glutamine‐bx represented a very high relative peak area (59.54% to 64.18%) in flesh of red‐colored cultivars analyzed in the study. Our results indicate that red beet cultivars can be utilized as a potential source of red and yellow natural colorants. However, differences in pigment composition among different beetroot parts must be considered and in order to maximize the pigment yields petioles can also be used as a source rich in specific betalain compounds.
Membrane biofilm development improves COD removal in anaerobic membrane bioreactor wastewater treatment
Authors: Smith Adam L. , Skerlos Steven J. , Raskin Lutgarde
Published: August 2015

Membrane biofilm development was evaluated to improve psychrophilic (15°C) anaerobic membrane bioreactor (AnMBR) treatment of domestic wastewater. An AnMBR containing three replicate submerged membrane housings with separate permeate collection was operated at three levels of membrane fouling by independently controlling biogas sparging for each membrane unit. High membrane fouling significantly improved permeate quality, but resulted in dissolved methane in the permeate at a concentration two to three times the equilibrium concentration predicted by Henry's law. Illumina sequencing of 16S rRNA targeting Bacteria and Archaea and reverse transcription‐quantitative polymerase chain reaction targeting the methyl coenzyme‐M reductase (mcrA) gene in methanogens indicated that the membrane biofilm was enriched in highly active methanogens and syntrophic bacteria. Restoring fouled membranes to a transmembrane pressure (TMP) near zero by increasing biogas sparging did not disrupt the biofilm's treatment performance, suggesting that microbes in the foulant layer were tightly adhered and did not significantly contribute to TMP. Dissolved methane oversaturation persisted without high TMP, implying that methanogenesis in the biofilm, rather than high TMP, was the primary driving force in methane oversaturation. The results describe an attractive operational strategy to improve treatment performance in low‐temperature AnMBR by supporting syntrophy and methanogenesis in the membrane biofilm through controlled membrane fouling.
Duloxetine in treating generalized anxiety disorder in adults: A meta‐analysis of published randomized, double‐blind, placebo‐controlled trials
Authors: Zhang Yingli , Huang Guoping , Yang Shichang , Liang Wei , Zhang Lei , Wang Changhong
Published: August 2015

Introduction

We carried out a meta‐analysis of published randomized, double‐blind, placebo‐controlled trails to assess the efficacy and tolerability of duloxetine in treating generalized anxiety disorder (GAD).

Methods

A literature search was conducted using PubMed, ISI Web of Science, Medline, Cochrane Central Register of Controlled Trials databases until October 2014. The search terms used were “anxiety or anxious or generalized anxiety disorder” and “duloxetine or Cymbalta.” Meta‐analysis was conducted using Revman 5.1. A fixed‐effects model was carried out on the response rates, remission rates, and symptom improvement. Risk ratio (RR) and mean difference (MD) were calculated. The overall effect size was calculated with 95% confidence intervals (CIs).

Results

Seven studies (n = 2,674) were found eligible for inclusion in analysis. Six studies provided data on response, which showed a significant difference between duloxetine and placebo (n = 1,975, RR = 1.48, 95% CI, 1.34–1.63). Remission rates revealed significant superiority of duloxetine (n = 2,399, RR = 1.60, 95% CI, 1.43–1.80). Change from baseline scores on Hamilton Rating Scale for Anxiety showed a reduction in anxiety symptoms to be significantly efficient for duloxetine (n = 1,135, MD = 3.34, 95% CI, 2.37–4.32). Duloxetine increased statistically Sheehan Disability Scale total score (n = 1,652, MD = 2.84, 95% CI, 2.08–3.60). The discontinuation of the duloxetine was not significantly different from that of the placebo.

Conclusion

Duloxetine is moderately effective in treating GAD with improvement in overall function and well tolerability.
Toll‐like receptor 2 activators modulate oral tolerance in mice
Authors: Tunis M. C. , Dawod B. , Carson K. R. , Veinotte L. L. , Marshall J. S.
Published: August 2015

Background

Toll‐like receptor 2 (TLR2) is a widely expressed pattern recognition receptor critical for innate immunity. TLR2 is also a key regulator of mucosal immunity implicated in the development of allergic disease. TLR2 activators are found in many common foods, but the role of TLR2 in oral tolerance and allergic sensitization to foods is not well understood.

Objective

The purpose of this study was to evaluate the impacts of TLR2 expression and TLR2 activation on oral tolerance to food antigens in a murine model.

Methods

Mice were fed ovalbumin (OVA) or peanut butter with or without the addition of low doses of TLR2 activators Pam3CSK4 or FSL‐1. Oral tolerance was assessed by analysing antibody responses after a systemic antigen challenge. OVA‐specific Tregs were assessed in the Peyer's patches, mesenteric lymph nodes, and spleen in wild‐type and TLR2−/− mice. Low‐dose Pam3CSK4 was also tested as an oral adjuvant.

Results

Oral tolerance was successfully induced in both wild‐type and TLR2−/− recipient mice, with an associated regulatory T‐cell response. Oral TLR2 activation, with low‐dose Pam3CSK4 or FSL‐1, during oral antigen exposure was found to alter oral tolerance and was associated with the development of substantial IgE and IgA responses to foods upon systemic challenge. Low‐dose oral Pam3CSK4 treatment also selectively enhanced antigen‐specific IgA responses to oral antigen exposure.

Conclusions and Clinical Relevance

TLR2 is not necessary for oral tolerance induction, but oral TLR2 activation modulates humoral IgE and IgA responses during tolerance development. Low‐dose Pam3CSK4 is also an effective oral adjuvant that selectively enhances IgA production. These observations are pertinent to the optimization of oral allergen immunotherapy and oral vaccine development.
Rho‐kinase inhibitor fasudil reduces allergic airway inflammation and mucus hypersecretion by regulating STAT6 and NFκB
Authors: Xie T. , Luo GY. , Zhang Y. , Wang X. , Wang XY. , Wu M. , Li GP.
Published: August 2015

Background

Airway mucus hypersecretion is a key pathophysiological feature in asthma. Fasudil, a selective Rho‐A/Rho kinase inhibitor, has been used in clinical trials to treat pulmonary hypertension. However, its function in modulating airway mucus hypersecretion in asthma remains undefined.

Objective

We examined whether fasudil, a selective Rho‐A/Rho kinase inhibitor, affects the mucus hypersecretion by suppressing MUC5AC via signal transducer and activator of transcription factor 6 (STAT6) and nuclear factor‐kappa B (NFκB) in mice and cells.

Methods

We measured mucus secretion and the expression of Rho‐kinase in the airway tissue of patients with asthma. BALB/c mice were sensitized and challenged with ovalbumin (OVA) followed with fasudil treatment. The lung tissues were assessed for airway inflammation and mucus secretion. Cytokine levels and airway responsiveness were determined. STAT6 and NFκB were quantified by Western blot. 16HBE cells were stimulated with house dust mite (HDM) extracts. MUC5AC and muc5ac promoter activities were measured. Using siRNA to knockdown STAT6 in epithelial cells, we determined the impact of STAT6 on muc5ac promoter activity. NFκB nuclear translocation was observed with immunostaining.

Results

Fasudil administration significantly decreased the number of inflammatory cells, inflammation index in the lung and airway responsiveness. Fasudil also reduced mucous secretion and MUC5AC expression in OVA‐challenged mice. Fasudil down‐regulated the levels of IL‐17, IL‐4 and IL‐13 in the lung tissue of OVA‐challenged mice. Fasudil also decreased the expression and phosphorylation of NFκB and STAT6 as well as the nuclear translocation of NFκB. In addition, human airway epithelial cells (16HBE) were challenged with HDM extracts and then treated with fasudil. Fasudil inhibited HDM extract‐induced MUC5AC expression, which is associated with a reduction in STAT6 and NFκB in epithelial cells.

Conclusions and Clinical Relevance

These findings indicate that the Rho‐A/Rho kinase inhibitor, fasudil, plays a negative regulatory role in allergen‐induced mucus secretion and MUC5AC expression by regulating STAT6 and NFκB.
Secretion of matrix metalloproteinase‐3 by co‐cultured pigmented and non‐pigmented human trabecular meshwork cells following selective laser trabeculoplasty
Authors: Lee James YJ , Kagan Dov B , Roumeliotis Grayson , Liu Hong , Hutnik Cindy ML
Published: August 2015

Background

Matrix metalloproteinases (MMPs) are reported to contribute to the mechanism of argon laser trabeculoplasty, but it is unknown whether they are also secreted after selective laser trabeculoplasty (SLT). The aim of this study was to investigate whether human primary trabecular meshwork (HTM) cells secrete MMP‐3 after stimulation by SLT. The relationship between SLT and the two principal forms of cell death, apoptosis and necrosis, was also examined.

Methods

Non‐pigmented primary HTM cells were challenged with melanin granules to artificially introduce pigmentation. Isolated non‐pigmented HTM cells and 1:1 co‐cultures of pigmented and non‐pigmented cells were treated with 0.5–1.5 mJ SLT. Cellular metabolic activity (CMA) was quantified using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay. Apoptosis and necrosis were measured using a cell death ELISA and a lactate dehydrogenase assay, respectively. MMP‐3 secretion was measured by ELISA.

Results

Co‐cultures exhibited a dose‐dependent decline in CMA and a dose‐dependent increase in necrosis 4 and 24 h after SLT. Non‐pigmented cells did not undergo necrosis and displayed a trend towards increased CMA. Apoptosis was reduced in non‐pigmented cells but elevated in co‐cultures. Increased MMP‐3 secretion was observed from co‐cultures but not isolated non‐pigmented cells.

Conclusions

Pigmentation is necessary for both post‐SLT cell death and MMP‐3 secretion. SLT appears to have a hormetic effect on non‐pigmented HTM cells.
Obstetric risk factors and time trends of neurodevelopmental outcome at 2 years in very‐low‐birthweight infants: a single institution study
Authors: Gardella Barbara , Iacobone Anna Daniela , Bogliolo Stefano , Musacchi Valentina , Orcesi Simona , Tzialla Chryssoulla , Spinillo Arsenio
Published: August 2015

Aim

To assess the time trends of neonatal survival and infant neurodevelopmental outcome in very‐low‐birthweight children at 24 months corrected age over a 20‐year period.

Method

The study cohort comprised 857 infants (439 males and 418 females) weighing less than 1500g at birth or delivered before 32 weeks gestational age in the period 1989 to 2008. Neurological examination and cognitive assessment of the infants (Bayley Scales of Infant Development and Griffiths Mental Developmental Scale) were performed at 24 months corrected age.

Results

The prevalence of neonatal survival with normal neurodevelopmental outcome increased from 55.3% (104/188) in 1989 to 1993, to 61.4% in 1994–1998 (116/189), 68.3% in 1999 to 2003 (138/202), and 84.5% in 2004 to 2008 (235/278) (annual increase=1%, 95% CI 2.1–4.1; p<0.001). In logistic models, the increase in the rate of normal neurodevelopmental outcome during the periods studied was consistent across the categories of birthweight (≤1000g as opposed to >1000g), gestational age (≤28wks as opposed to >28wks), and clinical characteristics (pre‐eclampsia/growth restriction as opposed to spontaneous prematurity/rupture of membranes).

Interpretation

The increased rate of normal neurodevelopmental outcome at 2 years among very‐low‐birthweight infants is independent of obstetric risk factors.
Plant module size influences the intra‐tree distribution and abundance of a shoot‐boring sawfly in young balsam fir
Authors: Johns Rob C. , Edwards Sara , Carleton Drew , Morrison Andrew , Morin Benoit
Published: August 2015

Field surveys were carried out to assess the effects of intra‐tree variation in developing shoot length within and among crown levels on the density and abundance of the balsam shoot‐boring sawfly, Pleroneura brunneicornis Rohwer (Hymenoptera: Xyelidae), in young balsam fir, Abies balsamea (L.) Mill. (Pinaceae). Overall, cardinal direction had no influence on shoot‐borer density or abundance; however, the highest percentage and abundance of bored shoots occurred on intermediate‐sized shoots within the crown (i.e., in the mid‐crown and on the distal‐lateral and medial‐lateral shoots). Comparatively, few shoot borers occurred in the upper or lower crown levels, or on the relatively large terminal shoots within branches. This distribution appears indicative of the higher suitability of intermediate‐sized shoots within hosts for either egg lay or larval performance. Results of this study are most consistent with predictions of the ‘optimal module size’ hypothesis, which posits that herbivore responses to plant module size should reflect the balance of tradeoffs between utilizing relatively large, nutritious shoots vs. small, more easily exploited shoots.
Fungal root endophytes ofQuercus robursubjected to flooding
Authors: Kwaśna H. , Szewczyk W. , Behnke‐Borowczyk J.
Published: August 2015

In August 2011, fungal endophytes were isolated from fine (0.1–0.5 cm diameter) and structural (0.6–2.0 cm) roots from eighteenQ. roburtrees at six sites in aQ. robur‐dominated forest displaying symptoms of oak decline. Five sites were subjected to periodic flooding for 3 months in 1997 and 1 month in 2010. Fungal colonization was detected in 94% of 1296 root fragments examined. Fungi representing 126 taxa from Zygomycota (four species), Ascomycota (117 species) and Basidiomycota (five species) were isolated using culture‐based methods and identified by morphotyping and sequencing of theITS1 and 2rDNA. The most frequent eudominants (with colonization frequencies ≥10%) wereAspergillusspp.,Cosmosporasp.,Ilyonectria radicicola, Pezicula radicicola, Pyrenochaeta cavaand six species ofTrichoderma. Species composition did not vary greatly between sites, but only 3% of species occurred in all sites. Number of species was higher in roots subjected to floods. Eudominants and dominants present only on flooded sites includedAspergillusspp.,Chaetomium globosum, Cosmosporasp.,I. radicicola, Sporothrix inflata,Trichoderma harzianum, T. pubescensandT. virens. Structural roots were usually colonized by a higher number of species than fine roots. The majority of species detected belong to Class 2NC‐endophytes.Pezicula radicicolaandPhialocephala fortiniibelong to Class 4NC‐endophytes.
Weight functions and stress intensity factors for pin‐loaded single‐edge notch bend specimen
Authors: Zhao X.  C. , Wu X.  R. , Tong D.  H.
Published: August 2015

A recently developed pin‐loaded single‐edge notch bend specimen provides an alternative to the single‐edge notch tension specimen commonly used for small‐crack growth testing. In this paper, weight functions for pin‐loaded single‐edge notch bend specimen are derived by using two methods, the classical analytical weight function method and the newly developed numerical weight function complex variable Taylor series expansion method. Excellent agreement between the two methods is achieved. Based on these weight functions, accurate stress intensity factors for two load cases, that is, pin‐loading and Dugdale loading, which is required for plasticity‐induced crack‐closure analysis based on the strip‐yield model, are determined.
Macro‐ and microclimatic interactions can drive variation in species' habitat associations
Authors: Pateman Rachel M. , Thomas Chris D. , Hayward Scott A. L. , Hill Jane K.
Published: August 2015

Many species are more restricted in their habitat associations at the leading edges of their range margins, but some species have broadened their habitat associations in these regions during recent climate change. We examine the effects of multiple, interacting climatic variables on spatial and temporal patterns of species' habitat associations, using the speckled wood butterfly, Pararge aegeria, in Britain, as our model taxon. Our analyses reveal that this species, traditionally regarded as a woodland‐dependent insect, is less restricted to woodland in regions with warmer winters and warmer and wetter summers. In addition, over the past 40 years of climate change, the species has become less restricted to woodland in locations where temperature and summer rainfall have increased most. We show that these patterns arise mechanistically because larval growth rates are slower in open (i.e. nonwoodland) habitats associated with colder microclimates in winter and greater host plant desiccation in summer. We conclude that macro‐ and microclimatic interactions drive variation in species' habitat associations, which for our study species resulted predominantly in a widening of habitat associations under climate change. However, species vary in their climatic and nonclimatic requirements, and so complex spatial and temporal patterns of changes in habitat associations are likely to be observed in future as the climate changes.
Volcanic and structural evolution of Pico do Fogo, Cape Verde
Authors: Carracedo Juan‐Carlos , Perez‐Torrado Francisco J. , Rodriguez‐Gonzalez Alejandro , Paris Raphaël , Troll Valentin R. , Barker Abigail K.
Published: August 2015

In recent months the media have drawn attention to the Cape Verde archipelago, with particular focus on the island of Fogo, the only island presently active and with an eruption that began on 23 November 2014, finally ceasing on 7 February 2015. The Monte Amarelo conical shield forms most of the 476 km2 almost circular island of Fogo. After attaining a critical elevation of about 3500 m, the Monte Amarelo shield volcano was decapitated by a giant landslide that formed a caldera‐like depression (Cha das Caldeiras), which was subsequently partially filled by basaltic nested volcanism. This younger eruptive activity culminated in the construction of the 2829 m‐high Pico do Fogo stratocone, apparently entirely made of layers of basaltic lapilli. Continued growth of the Pico do Fogo summit eruptions was interrupted in 1750, most likely after the stratocone reached a critical height. Since then, at least eight eruptions have taken place inside the landslide depression at the periphery of the Pico do Fogo cone, including the 2014–2015 eruptive event. Strong geological similarities with the Canary Islands, 1400 km to the north, have been frequently noted, probably as a consequence of a common process of origin and evolution associated with a mantle hot‐spot. These similarities are particularly evident when comparing Fogo with the Teide Volcanic Complex on Tenerife, where a lateral collapse of the Las Cañadas stratovolcano also formed a large depression (the Caldera de Las Cañadas), now partially filled with the 3718 m‐high Teide stratocone. However, important geological differences also exist and probably relate to the contrasting evolutionary stages of both islands. The Las Cañadas volcano on Tenerife formed at a late post‐erosional stage, with predominantly evolved (trachyte and phonolite) magmas, while at Fogo basaltic volcanism is still dominant.
Patterns of inpatient dermatology referral and predictors of diagnostic accuracy in non‐dermatologists in a Northern District hospital in Singapore
Authors: Huang Wenhui , Chong Wei‐Sheng
Published: August 2015

Background

A wide range of dermatological conditions is often encountered in the inpatient setting. Many non‐dermatologists experience difficulty in their diagnosis, and referral to a dermatologist is often warranted. In our local setting, this is made through a formal written referral letter, which is usually drafted by the junior doctor on the team.

Objectives

This study was conducted to characterize patterns of inpatient dermatology referral and to investigate whether predictors of diagnostic concordance between the referring non‐dermatologist and the reviewing dermatologist can be identified.

Methods

A total of 168 inpatient dermatology referrals made between June and September 2013 at a Northern District hospital in Singapore were identified and reviewed. Collated variables were broadly divided into: (i) patient demographic details; (ii) the referring details of non‐dermatologists; and (iii) the response details of reviewing dermatologists.

Results

No predictors of diagnostic concordance could be identified statistically. A total of 90.5% (n = 152) of referrals were made for both diagnostic and management purposes, whereas 9.5% (n = 16) of referrals were made purely for management purposes. Of the 152 diagnostic and management referrals, a preliminary diagnosis was reflected in 69.1% (n = 105). In 47.6% of all referrals (n = 80), more than one dermatological condition was identified. The fungal smear was the most commonly requested ancillary investigation (22.6%, n = 38/168). Cutaneous skin infections (32.0%, n = 85/266) and endogenous eczema (32.0%, n = 85/266) were by far the two most commonly identified dermatological conditions in our local cohort of patients.

Conclusions

The need for a dedicated inpatient dermatology service is reinforced. However, targeted education may be employed to facilitate the referral process.
A prospective case series evaluating efficacy and safety of combination of itraconazole and potassium iodide in rhinofacial conidiobolomycosis
Authors: Gupta Manish , Narang Tarun , Kaur Rupinder Jeet , Manhas Ashwani , Saikia Uma Nahar , Dogra Sunil
Published: August 2015

Background

Rhinofacial conidiobolomycosis (RFC) is an uncommon subcutaneous fungal infection producing painless swelling with grotesque deformity of the face. Although there are case reports and small case series; there are very few prospective studies evaluating treatment outcome and long‐term follow‐up.

Objective

To evaluate the safety and efficacy of combination of itraconazole (200 mg twice daily) and saturated solution of potassium iodide (SSKI) in patients with RFC.

Methods

Ten patients of RFC were studied over a period of 5 years. Diagnosis was confirmed by clinical, histopathological, and microbiological evaluation. Conidiobolus was cultured in four cases and in the rest of the cases, the histopathology was suggestive of RFC. They were treated with itraconazole (200 mg twice daily) and SSKI and followed up for a minimum of 1 year after stopping treatment.

Results

The mean age was 38.7 years and the mean duration of symptoms was 22.4 months. Males were predominantly involved (9 : 1). Seven patients responded to the combination treatment, five had complete resolution and two had good improvement (50–75%); however, in two patients the response was minimal (<25% regression of the swelling) and one patient did not show any improvement after 6 months of treatment.

Conclusion

Combination of itraconazole and SSKI is an effective treatment modality for RFC with relatively faster onset of action, low relapse rates, and minimal adverse effects. It can be considered as first‐line treatment in patients with RFC.
Evaluation of ocular findings in patients with vitiligo
Authors: Karadag Remzi , Esmer Oktay , Karadag Ayse S. , Bilgili Serap Gunes , Cakici Ozgur , Demircan Yuhanize Tas , Bayramlar Huseyin
Published: August 2015

In this study, we aimed to investigate ocular manifestations in patients with vitiligo. Sixty‐one patients with vitiligo were included in the study. From the patients who referred for examination to the dermatology and ophthalmology clinic, 57 patients without any systemic disease were taken as the control group. In both groups, otorefractometry, keratometry, visual acuity test, intraocular pressure measurement, anterior segment, and fundus examinations of the eye with slit lamp, Schirmer test, and perimetry were carried out. The mean age was 24.54 ± 11.90 years and 23.03 ± 8.72 years in the patients and control group, respectively. The mean Schirmer test results were as follows: 16.74 ± 9.11 mm and 17.64 ± 9.41 mm for the right and left eyes of the patients, and 21.96 ± 12.51 mm and 23.42 ± 12.51 mm for the right and left eyes of controls, respectively. Of the patients, 36 eyes showed lenticular findings. However, only 12 eyes of the controls have some lenticular findings. Twenty‐nine eyes in the vitiligo group and four in the controls showed some fundus findings. When the two groups were compared with each other, there was a statistically significant difference between them in terms of Schirmer test results, lens, and fundus findings (P < 0.05 for all). However, there was no significant difference in terms of age, gender, visual acuity, refraction, keratometry, intraocular pressure, perimetry, and corneal findings (P > 0.05 for all). Patients with vitiligo may have more lenticular and retinal findings than normal. They can be more prone to dry eye syndrome as well.
Sustainable use of marine resources – turning waste into food ingredients
Authors: Nurdiani Rahmi , Dissanayake Muditha , Street Wayne E. , Donkor Osaana N. , Singh Tanoj K. , Vasiljevic Todor
Published: August 2015

Fish by‐products are considered low value and discarded. With proper handling and processing, fish by‐products may provide high nutritional value to consumers. This study aimed at establishing compositional differences in valuable compounds from fish by‐products of selected species, including Salmon, Flathead, Silver warehou and Barramundi. Simple extraction methods were employed, and obtained fractions were analysed for their chemical and physical properties. The chemical composition of four fish species differed significantly (P < 0.05) with the protein content ranging from 14.7 ± 0.09 to 16.8 ± 0.41%. AdjustingpHto 2.5 yielded two times more of extracted oil than atpH4.5. Salmon and Barramundi oils contained high amounts of monounsaturated fatty acids (MUFAs) (39–50%), while Silver warehou and Flathead oils contained 46–49% of saturated fatty acids (SFAs). The particle size of the protein fractions was small, ranging from 126.9 to 489.5 nm. Molecular weight of extracted proteins was fish species dependant – Silver warehou and Barramundi samples contained proteins of 250, 120 and 100 kDa, while these bands were absent from Salmon and Flathead samples. The data obtained indicate that extracted fractions from fish by‐products likely have high nutritional value and could find a potential use in food formulations.