bluuebunny/crossref_metadata_2025 huggingface dataset:
Haplotype assembly in polyploid genomes and identical by descent shared tracts
Authors: Aguiar Derek , Istrail Sorin
Published: June 2013

Motivation: Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction.

Results: In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory–based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data.

Availability and Implementation: HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/.

Contact:  Sorin_Istrail@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Short read alignment with populations of genomes
Authors: Huang Lin , Popic Victoria , Batzoglou Serafim
Published: June 2013

Summary: The increasing availability of high-throughput sequencing technologies has led to thousands of human genomes having been sequenced in the past years. Efforts such as the 1000 Genomes Project further add to the availability of human genome variation data. However, to date, there is no method that can map reads of a newly sequenced human genome to a large collection of genomes. Instead, methods rely on aligning reads to a single reference genome. This leads to inherent biases and lower accuracy. To tackle this problem, a new alignment tool BWBBLE is introduced in this article. We (i) introduce a new compressed representation of a collection of genomes, which explicitly tackles the genomic variation observed at every position, and (ii) design a new alignment algorithm based on the Burrows–Wheeler transform that maps short reads from a newly sequenced genome to an arbitrary collection of two or more (up to millions of) genomes with high accuracy and no inherent bias to one specific genome.

Availability: http://viq854.github.com/bwbble.

Contact: serafim@cs.stanford.edu
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
Authors: Miwa Makoto , Ohta Tomoko , Rak Rafal , Rowley Andrew , Kell Douglas B. , Pyysalo Sampo , Ananiadou Sophia
Published: June 2013

Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge.

Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches.

Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText.

Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/.

Contact:  makoto.miwa@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identifying proteins controlling key disease signaling pathways
Authors: Gitter Anthony , Bar-Joseph Ziv
Published: June 2013

Motivation: Several types of studies, including genome-wide association studies and RNA interference screens, strive to link genes to diseases. Although these approaches have had some success, genetic variants are often only present in a small subset of the population, and screens are noisy with low overlap between experiments in different labs. Neither provides a mechanistic model explaining how identified genes impact the disease of interest or the dynamics of the pathways those genes regulate. Such mechanistic models could be used to accurately predict downstream effects of knocking down pathway members and allow comprehensive exploration of the effects of targeting pairs or higher-order combinations of genes.

Results: We developed methods to model the activation of signaling and dynamic regulatory networks involved in disease progression. Our model, SDREM, integrates static and time series data to link proteins and the pathways they regulate in these networks. SDREM uses prior information about proteins’ likelihood of involvement in a disease (e.g. from screens) to improve the quality of the predicted signaling pathways. We used our algorithms to study the human immune response to H1N1 influenza infection. The resulting networks correctly identified many of the known pathways and transcriptional regulators of this disease. Furthermore, they accurately predict RNA interference effects and can be used to infer genetic interactions, greatly improving over other methods suggested for this task. Applying our method to the more pathogenic H5N1 influenza allowed us to identify several strain-specific targets of this infection.

Availability: SDREM is available from http://sb.cs.cmu.edu/sdrem

Contact: zivbj@cs.cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Experimental characterization of strain localization in rock
Authors: Zhang Hao , Huang Ganyun , Song Haipeng , Kang Yilan
Published: June 2013

In this study, damage evolution and strain localization in sandstone have been experimentally investigated in uniaxial compression tests. A digital image correlation technique has been applied to obtain apparent strain fields which can visually display the deformation and damage evolution of rock. The experimental results show that regions with apparent strain concentration (RASC) develop at the initial loading stage and distribute diffusely on the sample surface which may correspond to the damaged areas. With incremental load, the RASCs localize spatially, probably via coalescence into a line-shaped area that behaves like a macroscopic crack leading to the eventual failure of the specimen. A factor DRASC representing the deviation of the average apparent strain in RASCs from the average on the whole sample surface and a localization factor Lf, are proposed to characterize the evolution of damage and localization. DRASC increases slowly in the initial phase of loading and rises rapidly after the onset of localization. Lf decreases during loading which indicate the localization of spatial distribution of damage. The two factors can be used to well reflect the damage evolution and strain localization of rock specimens under compression.
Diversity of picornaviruses in rural Bolivia
Authors: Nix W. Allan , Khetsuriani Nino , Peñaranda Silvia , Maher Kaija , Venczel Linda , Cselkó Zsuzsa , Freire Maria Cecilia , Cisterna Daniel , Lema Cristina L. , Rosales Patricia , Rodriguez Jacqueline R. , Rodriguez Wilma , Halkyer Percy , Ronveaux Olivier , Pallansch Mark A. , Oberste M. Steven
Published: June 2013

The family Picornaviridae is a large and diverse group of viruses that infect humans and animals. Picornaviruses are among the most common infections of humans and cause a wide spectrum of acute human disease. This study began as an investigation of acute flaccid paralysis (AFP) in a small area of eastern Bolivia, where surveillance had identified a persistently high AFP rate in children. Stools were collected and diagnostic studies ruled out poliovirus. We tested stool specimens from 51 AFP cases and 34 healthy household or community contacts collected during 2002–2003 using real-time and semi-nested reverse transcription polymerase chain reaction assays for enterovirus, parechovirus, cardiovirus, kobuvirus, salivirus and cosavirus. Anecdotal reports suggested a temporal association with neurological disease in domestic pigs, so six porcine stools were also collected and tested with the same set of assays, with the addition of an assay for porcine teschovirus. A total of 126 picornaviruses were detected in 73 of 85 human individuals, consisting of 53 different picornavirus types encompassing five genera (all except Kobuvirus). All six porcine stools contained porcine and/or human picornaviruses. No single virus, or combination of viruses, specifically correlated with AFP; however, the study revealed a surprising complexity of enteric picornaviruses in a single community.
Complete genome sequence of invertebrate iridescent virus 22 isolated from a blackfly larva
Authors: Piégu Benoît , Guizard Sébastien , Spears Tatsinda , Cruaud Corinne , Couloux Arnault , Bideshi Dennis K. , Federici Brian A. , Bigot Yves
Published: June 2013

Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. Invertebrate iridescent virus 22 (IIV-22) was originally isolated from the larva of a blackfly (Simulium sp., order Diptera) found in the Ystwyth river, near Aberystwyth, Wales, UK. IIV-22 virions are icosahedral, with a diameter of about 130 nm and contain a dsDNA genome that is 197.7 kb in length, has a G+C content of 28.05 mol% and contains 167 coding sequences. Here, we describe the complete genome sequence of this virus and its annotation. This is the fourth genome sequence of an invertebrate iridovirus to be reported.
Estimation of Errors in “Raw” DNA Sequences: A Validation Study
Authors: Richterich Peter
Published: June 2013

As DNA sequencing is performed more and more in a mass-production-like manner, efficient quality control measures become increasingly important for process control, but so also does the ability to compare different methods and projects. One of the fundamental quality measures in sequencing projects is the position-specific error probability at all bases in each individual sequence. Accurate prediction of base-specific error rates from “raw” sequence data would allow immediate quality control as well as benchmarking different methods and projects while avoiding the inefficiencies and time delays associated with resequencing and assessments after “finishing” a sequence. The program PHRED provides base-specific quality scores that are logarythmically related to error probabilities. This study assessed the accuracy of PHRED’s error-rate prediction by analyzing sequencing projects from six different large-scale sequencing laboratories. All projects used four-color fluorescent sequencing, but the sequencing methods used varied widely between the different projects. The results indicate that the error-rate predictions such as those given by PHRED can be highly accurate for a large variety of different sequencing methods as well as over a wide range of sequence quality.
Predicting house price via gene expression programming
Authors: Shekarian Ehsan , Fallahpour Alireza
Published: June 2013

Purpose

The housing sector is one of the main sources of economic growth in both developing and developed countries. Although many methods for modeling house prices have been proposed, each has its own limitations. The present paper aims to propose gene expression programming (GEP) as a new approach for prediction of housing price.

Design/methodology/approach

This study introduces gene expression programming (GEP) as a new approach for predicting housing price. This is the first time that this metaheuristic method is used in the housing literature.

Findings

The housing price model based on the gene expression programming is compared with a least square regression model that is derived from a stepwise process. The results indicate that the GEP‐based model provides superior performance to the traditional regression.

Originality/value

Data used in this study is derived from the Household Income and Expenditure Survey (HIES) in Iran that is conducted by the Statistical Center of Iran (SCI). Housing price model is estimated by administering the questionnaires of this survey in Hamedan Province. To show the applicability of the derived model by GEP technique, it is verified applying parts of the data, namely test data sets that were not included in the modeling process.
Formal housing finance outreach and the urban poor in India
Authors: Sandhu Kiran
Published: June 2013

Purpose

Access to housing remains high on the agenda of the governments in the developing countries. One of the responses to low income housing access is by making the housing finance conduits reachable to the poor. But is this objective really achieved? The purpose of the research paper is to evaluate the access of formal housing finance specifically in the context of the urban poor in India.

Design/methodology/approach

The purpose of the research is achieved by conducting a review into the available literature as well as drawing inferences from data in order to support the argument that the formal housing finance structures in India are failing to deliver to a majority of the population and primarily the urban poor when it comes to providing access to equitable housing. The paper uses qualitative method of research and analysis and presents the analysis in a descriptive approach.

Findings

Based upon a comprehensive review of literature in terms of work of other authors, reports and documents, the paper generates evidence and critically examines the context of housing finance provision for the urban poor in India. It is found that the housing finance set‐up favours the higher income groups and sidelines the low income groups, largely due to the prerequisites for accessing housing finance.

Practical implications

The research is perceived to be useful to policymakers and government organizations engaged in social housing to reflect on the fact that despite efforts, the outreach of finance is not adequate. It shall motivate them to re‐examine their credit policies and devise innovative mechanisms for housing finance delivery to the low income groups.

Originality/value

The paper presents a thorough and critical review of the housing finance structure with focus on the urban poor using current trends. It reflects on the issues and evidence so generated during research. The paper shall be useful to researchers in social housing and housing finance as well as decision makers in the Government in India and as a reference case for other countries in the developing world.
Management of the master data lifecycle: a framework for analysis
Authors: Hubert Ofner Martin , Straub Kevin , Otto Boris , Oesterle Hubert
Published: June 2013

Purpose

The purpose of the paper is to propose a reference model describing a holistic view of the master data lifecycle, including strategic, tactical and operational aspects. The Master Data Lifecycle Management (MDLM) map provides a structured approach to analyze the master data lifecycle.

Design/methodology/approach

Embedded in a design oriented research process, the paper applies the Component Business Model (CBM) method and suggests a reference model which identifies the business components required to manage the master data lifecycle. CBM is a patented IBM method to analyze the key components of a business domain. The paper uses a participative case study to evaluate the suggested model.

Findings

Based on a participative case study, the paper shows how the reference model makes it possible to analyze the master data lifecycle on a strategic, a tactical and an operational level, and how it helps identify areas of improvement.

Research limitations/implications

The paper presents design work and a participative case study. The reference model is grounded in existing literature and represents a comprehensive framework forming the foundation for future analysis of the master data lifecycle. Furthermore, the model represents an abstraction of an organization's master data lifecycle. Hence, it forms a “theory for designing”. More research is needed in order to more thoroughly evaluate the presented model in a variety of real‐life settings.

Practical implications

The paper shows how the reference model enables practitioners to analyze the master data lifecycle and how it helps identify areas of improvement.

Originality/value

The paper reports on an attempt to establish a holistic view of the master data lifecycle, including strategic, tactical and operational aspects, in order to provide more comprehensive support for its analysis and improvement.
Selected FINRA notices and disciplinary actions, September 2012‐April 2013
Authors: Davis Henry A.
Published: June 2013

Purpose

The purpose of this paper is to provide selected Financial Industry Regulatory Authority (FINRA) Regulatory Notices and Disciplinary Actions issued in June, July, and August 2012.

Design/methodology/approach

The paper provides FINRA Regulatory Notice 12‐40, SEC Approves New FINRA Rule 5123 Regarding Private Placements of Securities; Regulatory Notice 12‐44, SEC Approves Amendments to FINRA Rule 4210 (Margin Requirements); Regulatory Notice 12‐55, Guidance on FINRA's Suitability Rule; and Regulatory Notice 13‐13, Trading and Quotation Halts in OTC Equity Securities; Trade Reporting Notice of April 17, 2013: Reduction of Reporting Times for Agency Pass‐Through Mortgage‐Backed Securities Traded TBA.

Findings

Notice 12‐40: FINRA Rule 5123 is part of a multi‐pronged approach to enhance oversight and investor protection in private placements; the rule will provide FINRA with more timely and complete information about the private placement activities of firms on behalf of other issuers. Notice 12‐44: The SEC approved amendments to FINRA Rule 4210 (Margin Requirements) related to option spread strategies, maintenance margin requirements for non‐margin eligible equity securities, free‐riding, “exempt accounts” and stress testing in portfolio margin accounts. Notice 12‐55: This Notice addresses two issues discussed in Regulatory Notice 12‐25: the scope of the terms “customer” and “investment strategy.” Notice 12‐25 provided guidance in a “frequently asked questions” format in FINRA Rule 2111 (Suitability). Notice 13‐13: The SEC approved amendments to FINRA Rule 6440, which provides authority for FINRA to initiate trading and quotation halts in OTC equity securities in circumstances where it is necessary to protect investors and the public; the rule provides authority to impose foreign regulatory halts, derivative halts and extraordinary event halts. Trade Reporting Notice of April 17, 2013: FINRA reminds firms of the coming reduction in reporting periods for the timely reporting of transactions in agency pass‐through mortgage‐backed securities traded TBA (to be announced) for good delivery and products not traded for good delivery.

Originality/value

These FINRA notices are selected to provide a useful indication of regulatory trends.
Critical theory for women empowerment through ICT studies
Authors: Kenkarasseril Joseph Meera
Published: June 2013

Purpose

Information and communication technology (ICT) is a powerful tool and an enabler of economic growth in under‐developed areas. ICTs have played an important role in women's development and provided opportunities for empowerment. ICTs have the potential to exchange information and empower marginalised communities. The purpose of this paper is to cover Habermas‐based critical theory to understand the politics of women's empowerment through the use of ICTs.

Design/methodology/approach

The paper examines the role of ICTs in developing marginalised women from the coastal areas of southern India. The paper is based on a qualitative study and presents a set of questionnaires developed specifically to assess women's development through the use of ICTs.

Findings

This study presents Habermasian based approach to address women's developmental goals.

Originality/value

The paper provides meaningful discussion on ICT for Women's Development (ICT4WD) and explores theories related to the feminist inquiry.
Discourses of delusion in demanding times
Authors: Irving Barrie A.
Published: June 2013

Purpose

The purpose of this paper is to demonstrate how critical discourse analysis can help to uncover the dominant discursive formations that underlie policy guidelines within education. Focusing on the policy guidelines for career education and guidance in New Zealand, it illustrates how these have been used by the state in an attempt to normalise ideological standpoints, shape “common‐sense” thinking and delimit the scope of practice.

Design/methodology/approach

Critical discourse analysis was employed as this approach helps to uncover the hidden meanings, political imperatives and uneven workings of power/dominance and oppression that are employed in/through textual representations.

Findings

Neoliberal discourse is infused throughout the policy guidelines for career education and guidance in New Zealand, and demands that career advisers/teachers should produce entrepreneurial and self‐responsibilised global economic subjects.

Research limitations/implications

Although this paper is situated within a New Zealand context, given the creeping influence of neoliberalism in many English‐speaking states, the issues identified have international relevance in relation to the kind of citizen career education is expected to produce.

Originality/value

Much of the literature within the career arena adopts an uncritical, and apolitical, stance, with the truth‐claims made by neoliberal states tending to be positioned as authoritative and inviolable. Drawing from critical theory, this paper contributes a social justice perspective that looks beneath the surface of the seemingly benign and well‐intentioned discourses that permeate the guidelines for career education and guidance in New Zealand.
Long‐term prognosis after surgical excision of basal cell carcinoma: A single institutional study in Japan
Authors: Takenouchi Tatsuya , Takatsuka Sumiko
Published: June 2013

Conventional surgical excision (SE) is commonly used to treat patients with basal cell carcinoma (BCC). There have been few studies, however, evaluating the long‐term prognosis of Japanese patients receiving SE for treatment of BCC. The purpose of this retrospective study is to determine the effectiveness of SE in accomplishing the long‐term cure of patients with BCC. We enrolled 290 patients with primary BCC who underwent SE during 1998–2006. The prognosis of treated patients was subsequently investigated using data obtained through our hospital cancer registration section. In total, 205 patients (70.7%) were treated for BCC lesions located on the face. The mean tumor diameter of excised lesions was 12.8 mm. A majority of patients in the study (256 patients, 88.3%) had pigmented BCC. The mean surgical margin at SE was 3.8 mm. Two patients developed local recurrence during the postoperative course of 290 patients (mean duration, 80 months). One patient developed recurrent disease 21 months after surgery, and the other developed recurrence at 66 months after surgery. The 5‐ and 10‐year cumulative recurrence rates were 0.4% and 0.8%, respectively. In conclusion, this study demonstrated that long‐term high cure rates of BCC in Japanese patients may be achieved through conventional SE. A better prognosis was obtained in this study compared with similar studies reported previously in Caucasians. This may be related to the predominance of pigmented versus non‐pigmented lesions in the Japanese population.
Treatment burden in stage I seminoma: a comparison of surveillance and adjuvant radiation therapy
Authors: Leung Eric , Warde Padraig , Jewett Michael , Panzarella Tony , O'Malley Martin , Sweet Joan , Moore Malcolm , Sturgeon Jeremy , Gospodarowicz Mary , Chung Peter
Published: June 2013

Objective

To examine the management and outcomes of patients with stage I seminoma and to relate these to overall treatment burden.

Patients and Methods

A total of 764 patients with stage I seminoma underwent surveillance or adjuvant radiation therapy (RT) at a single institution.

First relapse on surveillance was managed with RT alone, or with combination chemotherapy (ChT) for more extensive recurrence. Second relapse was managed with ChT.

Relapse after adjuvant RT was treated with ChT.

The treatment burden was measured, according to the specific treatment undertaken after orchiectomy, by defining treatment episodes as follows: surgery – one episode; one course of RT – one episode; one course of ChT – one episode.

Results

In all, 484 patients underwent surveillance and 280 received adjuvant RT.

The 5‐ and 10‐year overall survival rates were 98.6 and 97.7% for surveillance, and 97.2 and 91.4% for adjuvant RT.

A total of 72 (15%) patients in the surveillance group relapsed; treatment for relapse was RT (n = 56), ChT (n = 15) and surgery (n = 1). Second relapse occurred in six patients; these patients were treated with ChT.

Of the patients in the adjuvant RT group, 14 (5%) relapsed: salvage treatment was 10 – ChT (n = 10) surgery (n = 1) and further RT (n = 3).

The overall treatment burden represented by number of treatment episodes per patient was 0.16 in the surveillance group and 1.05 in the adjuvant RT group.

Conclusions

Surveillance reduces the overall treatment burden in patients with stage I seminoma and is the preferred management option.

The selective use of RT at first relapse for patients on surveillance leads to a similar requirement for subsequent ChT to that for patients on adjuvant RT.
Sex Differences in the Cholinergic Basal Forebrain in the Ts65Dn Mouse Model of Down Syndrome and Alzheimer's Disease
Authors: Kelley Christy M. , Powers Brian E. , Velazquez Ramon , Ash Jessica A. , Ginsberg Stephen D. , Strupp Barbara J. , Mufson Elliott J.
Published: June 2013

In the Down syndrome (DS) population, there is an early incidence of dementia and neuropathology similar to that seen in sporadic Alzheimer's disease (AD), including dysfunction of the basal forebrain cholinergic neuron (BFCN) system. Using Ts65Dn mice, a model of DS and AD, we examined differences in the BFCN system between male and female segmentally trisomic (Ts65Dn) and disomic (2N) mice at ages 5–8 months. Quantitative stereology was applied to BFCN subfields immunolabeled for choline acetyltransferase (ChAT) within the medial septum/vertical limb of the diagonal band (MS/VDB), horizontal limb of the diagonal band (HDB) and nucleus basalis of Meynert/substantia innominata (NBM/SI). We found no sex differences in neuron number or subregion area measurement in the MS/VDB or HDB. However, 2N and Ts65Dn females showed an average 34% decrease in BFCN number and an average 20% smaller NBM/SI region area compared with genotype‐matched males. Further, relative to genotype‐matched males, female mice had smaller BFCNs in all subregions. These findings demonstrate that differences between the sexes in BFCNs of young adult Ts65Dn and 2N mice are region and genotype specific. In addition, changes in post‐processing tissue thickness suggest altered parenchymal characteristics between male and female Ts65Dn mice.
Metrics of salbutamol use as predictors of future adverse outcomes in asthma
Authors: Patel M. , Pilcher J. , Reddel H. K. , Pritchard A. , Corin A. , Helm C. , Tofield C. , Shaw D. , Black P. , Weatherall M. , Beasley R.
Published: June 2013

Background

Beta‐agonist overuse is associated with adverse outcomes in asthma, however, the relationships between different metrics of salbutamol use and future risk are uncertain.

Objective

To investigate the relationship between metrics of salbutamol use and adverse outcome.

Methods

In a 24‐week randomized controlled trial of 303 asthma patients at risk of severe exacerbations which compared the efficacy and safety of combination budesonide/formoterol inhaler according to a single inhaler regimen (SMART) with a fixed‐dose regimen with salbutamol as reliever (‘Standard’), actual medication use was measured by electronic monitoring (Australian New Zealand Clinical Trials Registry Number ACTRN12610000515099). A nested cohort study explored the relationship between metrics of baseline salbutamol use over 2 weeks and future severe asthma exacerbations, poor asthma control (ACQ‐5 ≥ 1.5) or ‘extreme’ salbutamol overuse (> 32 salbutamol actuations/24‐h period).

Results

Higher mean daily salbutamol use (per two actuations/day) [Odds ratio (OR) (95% CI) 1.24 (1.06–1.46)], higher days of salbutamol use (per 2 days in 2 weeks) [OR 1.15 (1.00–1.31)] and higher maximal 24‐h use (per two actuations/day) [OR 1.09 (1.02–1.16)] were associated with future severe exacerbations. Higher mean daily salbutamol use was associated with future poor asthma control [OR 1.13 (1.02–1.26)]. Higher mean daily salbutamol use [OR 2.73 (1.84–4.07)], number of days of use [OR 1.46 (1.24–1.71)], and maximal daily use [OR 1.57 (1.31–1.89)] were associated with an increased risk of future extreme salbutamol overuse.

Conclusion and Clinical Relevance

Electronically recorded frequency of current salbutamol use is a strong predictor of risk of future adverse outcomes in asthma, with average daily use performing the best. These findings provide new information for clinicians considering metrics of salbutamol as predictors of future adverse outcomes in asthma.
Perceptions of clinicians treating young people with first‐episode psychosis for post‐traumatic stress disorder
Authors: Gairns Sarah , Alvarez‐Jimenez Mario , Hulbert Carol , McGorry Patrick , Bendall Sarah
Published: June 2013

Aim

Evidence shows that approximately half of young people with first‐episode psychosis have post‐traumatic stress disorder. Yet, post‐traumatic stress disorder is often left untreated in the presence of psychosis. To support the development of a post‐traumatic stress disorder intervention for young people with first‐episode psychosis, clinicians' perceptions of trauma‐focused interventions were sought. Two research questions were explored: What treatment barriers were associated with treating young people with first‐episode psychosis? What supports would be useful to implement post‐traumatic stress disorder intervention?

Methods

A mixed‐methods design incorporated quantitative and qualitative data from a questionnaire with qualitative data from two focus groups. Sixteen (of 20) case managers from an early psychosis intervention centre participated in the study (16 completed a questionnaire, eight participated in focus groups). Descriptive statistics were generated for quantitative data and qualitative material was examined using a grounded theory approach.

Results

The results showed that perceived barriers to delivering trauma‐focused intervention were increased mental health risks for clients with psychosis, workload pressures and poor client engagement. Targeted training and formal professional guidance were thought to best scaffold an intervention.

Conclusions

Post‐traumatic stress disorder intervention for first‐episode psychosis clients should address engagement, make safeguarded provisions for family involvement and be sufficiently paced and flexible. Trauma‐focused intervention is perceived with a degree of caution, is often not prioritized, lacks institutional support and requires more targeted training. It is important to conduct further research regarding the safety of trauma interventions alongside psychosis in order to address widespread concerns.
Neuropeptidergic input pathways to the circadian pacemaker center of the Madeira cockroach analysed with an improved injection technique
Authors: Schulze Julia , Schendzielorz Thomas , Neupert Susanne , Predel Reinhard , Stengl Monika
Published: June 2013

Light entrainment pathways synchronize the circadian clock of almost all species of the animal and plant kingdom to the daily light dark cycle. In the Madeira cockroach Rhyparobia (Leucophaea) maderae, the circadian clock is located in the accessory medulla of the brain's optic lobes. The clock has abundant neuropeptides with unknown functions. Previous studies suggested that myoinhibitory peptides (MIPs), orcokinins (ORCs), and allatotropin (AT) take part in light input pathways to the circadian clock. As the sequences of AT and ORCs of R. maderae have not yet been determined, with matrix‐assisted laser desorption/ionization–time of flight mass spectrometry, the respective Rhyparobia peptides were characterized. To search for light‐like phase‐shifting inputs to the circadian clock, Rhyparobia‐MIP‐1, Rhyparobia‐AT, and Rhyparobia‐ORC were injected at different circadian times, combined with locomotor activity assays. An improved, less invasive injection method was developed that allowed for the analysis of peptide effects within <2 weeks after injection. Rhyparobia‐MIP‐1 and Rhyparobia‐AT injections resulted in dose‐dependent monophasic phase response curves with maximum delays at the beginning of the subjective night, similar to light‐dependent phase delays. In contrast to Manduca sexta‐AT, Rhyparobia‐AT did not phase advance locomotor activity rhythms. Only injections of Rhyparobia‐ORCs resulted in a biphasic light‐like phase response curve. Thus, it is hypothesized that Rhyparobia‐MIP‐1 and ‐AT are candidates for relaying light‐dependent delays and/or non‐photic inputs to the clock, whereas Rhyparobia‐ORCs might be part of the light‐entrainment pathways relaying phase delays and advances to the circadian clock of the Madeira cockroach.
What Is the Value of Sovereign Ratings?
Authors: Gaillard Norbert
Published: June 2013

This article gives a fresh analysis of sovereign ratings, including the recent default of Greece. Section 1 studies the evolution of the sovereign rating business, and Section 2 explains how credit ratings are assigned. Section 3 focuses on sovereign rating methodologies and identifies the key determinants of sovereign ratings. Section 4 measures the accuracy of these ratings between 1 January 2001 and 1 January 2013. Section 5 compares credit ratings to market-based indicators, and Section 6 concludes.
Beer and beer compounds: physiological effects on skin health
Authors: Chen W. , Becker T. , Qian F. , Ring J.
Published: June 2013

Beer is one of the earliest human inventions and globally the most consumed alcoholic beverage in terms of volume. In addition to water, the ‘German Beer Purity Law’, based on the Bavarian Beer Purity Law from 1516, allows only barley, hops, yeasts and water for beer brewing. The extracts of these ingredients, especially the hops, contain an abundance of polyphenols such as kaempferol, quercetin, tyrosol, ferulic acid, xanthohumol/isoxanthohumol/8‐prenylnaringenin, α‐bitter acids like humulone and β‐bitter acids like lupulone. 8‐prenylnaringenin is the most potent phytoestrogen known to date. These compounds have been shown to possess various anti‐bacterial, anti‐inflammatory, anti‐oxidative, anti‐angiogenic, anti‐melanogenic, anti‐osteoporotic and anti‐carcinogenic effects. Epidemiological studies on the association between beer drinking and skin disease are limited while direct evidence of beer compounds in clinical application is lacking. Potential uses of these substances in dermatology may include treatment of atopic eczema, contact dermatitis, pigmentary disorders, skin infections, skin ageing, skin cancers and photoprotections, which require an optimization of the biostability and topical delivery of these compounds. Further studies are needed to determine the bioavailability of these compounds and their possible beneficial health effects when taken by moderate beer consumption.
Relationship between childhood obesity cut‐offs and metabolic and vascular comorbidities: comparative analysis of three growth standards
Authors: Martínez‐Costa C. , Núñez F. , Montal A. , Brines J.
Published: June 2013

Background

To compare the association between metabolic and vascular comorbidities and the body mass (BMI)‐for‐age cut‐off criteria from three growth standards [Centers for Disease Control and Prevention (CDC), 2000; World Health Organization (WHO), 2007; Spanish Reference Criteria (Carrascosa Lezcano et al., 2008)] that are used to define being overweight and obese in childhood.

Methods

A prospective study was conducted in 137 children (aged 8–16 years). Based on BMI‐for‐age Z‐scores according to WHO cut‐offs, 59 participants were obese, 35 were overweight and 43 were normal‐weight. All participating children were subsequently reclassified applying the CDC and Spanish Reference Criteria. Blood pressure (BP), biochemical variables and vascular parameters (stiffness and intima‐media thickness) were analysed.

Results

According to WHO and CDC references, 48% and 43% of the children, respectively, were categorised as obese, whereas 16% were considered as obese using the Spanish Reference Criteria. Applying WHO criteria, obese children showed significantly higher levels of insulin, homeostasis model assessment index and most vascular parameters, as well as lower high‐density lipoprotein (HDL)‐cholesterol than overweight children. Moreover, overweight children showed higher BP, insulin and uric acid, and lower HDL‐cholesterol than normal weight children. The CDC criteria yielded similar results, although with fewer differences between obese and overweight children. Applying Spanish criteria, the differences between obese and overweight children disappeared.

Conclusions

WHO and CDC BMI‐for‐age references and cut‐offs are useful for defining obesity and being overweight in children because they clearly identify metabolic and vascular comorbidities. The Spanish Reference Criteria underdiagnose obesity because overweight children show comorbidities typical of the obese.
Effects of bipolar electrocoagulation versus suture after laparoscopic excision of ovarian endometrioma on the ovarian reserve and outcome of in vitro fertilization
Authors: Takashima Akiko , Takeshita Naoki , Otaka Kiwamu , Kinoshita Toshihiko
Published: June 2013

Aim

The aim of this study was to assess the effect of coagulation versus suture used for hemostasis during laparoscopic excision of a unilateral endometrioma for outcome of in vitro fertilization (IVF).

Material and Methods

This retrospective study was set in a university hospital. A total of 44 sterile patients underwent laparoscopic excision of a unilateral ovarian endometrioma. Bipolar electrocoagulation was performed for hemostasis in 21 patients and the remaining 23 patients underwent suturing. Samples of blood were taken on day 3 of menstruation before the operation. Serum levels of anti‐Müllerian hormone, follicle‐stimulating hormone and estradiol were measured. Number of antral follicles, follicular flushings, oocytes retrieved, and embryos were counted and the outcomes of IVF were recorded.

Results

No significant differences in the serum levels of any of the hormones were found between the pre‐ and postoperative samples, in either group. The mean antral follicle count, number of follicular flushings, oocytes retrieved and embryos obtained were significantly lower in the treated ovary as compared with the corresponding values in the contralateral intact ovary in the suture group. The pregnancy rates were similar in the two groups.

Conclusions

There was no difference in the outcome of IVF between the two different methods of hemostasis.
Erectile Dysfunction, Penile Atherosclerosis, and Coronary Artery Vasculopathy in Heart Transplant Recipients
Authors: Caretta Nicola , Feltrin Giuseppe , Tarantini Giuseppe , D'Agostino Chiara , Tona Francesco , Schipilliti Mirko , Selice Riccardo , Minicuci Nadia , Gerosa Gino , Foresta Carlo
Published: June 2013

Introduction

Vascular erectile dysfunction (ED) is the expression of a systemic vascular disease and in particular of endothelial dysfunction. Dysfunctional endothelium plays also a significant role in the onset and progression of coronary artery vasculopathy (CAV).

Aim

This pilot study was designed to evaluate the prevalence and pathogenesis of ED and its correlation with CAV in heart transplanted male.

Methods

A total of 77 male heart transplanted patients (HTx) evaluated in our center (mean age 61.6+10.6 years) were enrolled in the study.

Main Outcome Measures

All subjects underwent accurate medical history collection, including lifestyle (cigarette smoking, dietary and sedentary habits, drug intake, and erectile function before cardiac transplantation), physical examination (body mass index and arterial pressure), biochemical blood tests (fasting glucose, total cholesterol, high-density lipoprotein cholesterol, and triglycerides), and hormones (prolactin, luteinizing hormone and total testosterone). Furthermore, they were studied with penile, carotid, femoral echo-color Doppler ultrasonography and coronary angiogram.

Results

Incidence of ED was 24% before HTx and increased up to 65% after. Postischemic cardiomiopathy was an indication to HTx in ED group more frequently than in patients without ED (No-ED group) (45.1% vs. 20%). ED patients showed a lower peak systolic velocity, a higher cavernosal intima-media thickness (IMT), a higher prevalence of cavernosal plaques (26.7% vs. 5.2%, P <0.05), peripheral vascular disease (60.87% vs. 26.1%, P <0.05) and CAV (45.8% vs. 25.8%, P <0.05) with respect to No-ED patients. Coronary flow reserve was significantly reduced in ED vs. No-ED patients (2.43+0.7 vs. 2.9+0.8, P <0.04). Finally, cavernous plaque and testosterone plasma levels were statistically associated with CAV.

Conclusions

We showed that ED is a frequent disease in HTx patients, more common when the original pathology is postischemic cardiomiopathy and associated with higher prevalence of cavernous plaques and CAV. Its evaluation should be integral to an HTx rehab program.
The CLOSER (

CL

arifying Vaginal Atrophy's Impact

O

n

SE

x and

R

elationships) Survey: Implications of Vaginal Discomfort in Postmenopausal Women and in Male Partners
Authors: Nappi Rossella E. , Kingsberg Sheryl , Maamari Ricardo , Simon James
Published: June 2013

Introduction

Postmenopausal vaginal atrophy (VA) is a chronic condition with symptoms that include vaginal dryness, soreness, itching, burning, and dyspareunia.

Aim

The CLarifying Vaginal Atrophy's Impact On SEx and Relationships survey evaluated the impact of VA on the physical and emotional aspects of sexual relationships between postmenopausal women and their male partners.

Methods

Four thousand one hundred females and 4,100 males representing the United Kingdom, Finland, Norway, Sweden, Denmark, Italy, France, Canada, and the United States were surveyed. Assessments included: (i) talking about VA and its symptoms; (ii) the impact of VA on intimacy, relationships, and women's self-esteem; (iii) talking about VA and erectile dysfunction (ED); and (iv) the impact of local estrogen therapy (LET) on intimacy and relationships.

Main Outcome Measures

Descriptive data on the impact of VA.

Results

Twenty-eight percent of women did not tell their partners when they first encountered vaginal discomfort, mainly because they felt “it was just a natural part of growing older” (52%) or because of “embarrassment” (21%). Eighty-two percent of males wanted their partner to share their experiences with VA; males were also more comfortable discussing VA than females (68% vs. 58%, respectively). Having sex less often (women: 58%, men: 61%), less satisfying sex (women: 49%, men: 28%), and putting off having sex (women: 35%, men: 14%) were the main effects of VA. Intimacy avoidance was attributed to painful sex (women: 55%, men: 61%) and women's reduced sexual desire (women: 46%, men: 43%). Discussions about vaginal discomfort and ED were generally limited to partners and healthcare providers (HCPs). LET use resulted in less painful sex (women: 62%, men: 59%) and more satisfying sex (women: 47%, men: 49%).

Conclusions

VA has an adverse emotional and physical impact on postmenopausal women and their partners. These findings may encourage more open communication about VA between couples and their HCPs.
High level of IL‐27 positively correlated with Th17 cells may indicate liver injury in patients infected with HBV
Authors: Zhang Geng‐Lin , Xie Dong‐Ying , Ye Yi‐Nong , Lin Chao‐Shuang , Zhang Xiao‐Hong , Zheng Yu‐Bao , Huang Zhan‐Lian , Peng Liang , Gao Zhi‐Liang
Published: June 2013

Background

Interleukin‐6/IL‐12 family cytokines play a key role in inflammatory diseases via their effects on the differentiation or regulation of T helper cells.

Aims

The aim of this study was to determine the role of interleukin‐27 (IL‐27) and its association with helper T cells in hepatitis B virus (HBV)‐infected patients.

Methods

Samples were assessed from 51 HBV‐infected patients [28 chronic hepatitis B (CHB) subjects and 23 acute‐on‐chronic liver failure (ACLF) subjects] and 18 normal controls (NC). Serum IL‐27 levels were examined by enzyme‐linked immunosorbent assay. Circulating helper T cells were determined using flow cytometry and associations between IL‐27 expression and helper T cells were analysed.

Results

Serum IL‐27 levels rose in HBV‐infected patients (502.88 ± 23.35 pg/ml) compared to (NC, 277.14 ± 23.96 pg/ml, P < 0.0001). Furthermore, it significantly increased in patients with ACLF (587.90 ± 33.08 pg/ml) when compared with CHB (433.04 ± 26.57 pg/ml, P = 0.001). However, no statistically significant differences were observed between IL‐27 and the presence of HBeAg. High levels of IL‐27 then positively correlated with Tbil levels (r = 0.401, P = 0.004), but negatively associated with prothrombin time activity levels (r = −0.496, P < 0.001), and a slightly negative correlation trend with HBV‐DNA loads (r = −0.228, P = 0.107) existed in these HBV‐infected subjects. Additionally, frequency of circulating interleukin‐17‐producing CD4+T cells (Th17 cells) increased in HBV‐infected patients (ACLF, mean, 5.39%; CHB, median, 3.12%) as compared to NC subjects (median, 2.22%, P < 0.0001). Moreover, correlation analysis showed that serum IL‐27 level was positively associated with circulating Th17 cells (r = 0.342, P = 0.036).

Conclusion

These results provided evidence that IL‐27 was positively correlated with Th17 cells commitment, and may exerted a proinflammatory effect in the development of liver injury in HBV‐infected patients.