bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the treatment effect from multiple trials in idiopathic pulmonary fibrosis
Authors: Richeldi Luca 
Published: June 2012

The magnitude of treatment effect can be assessed by a number of methods. One method of collectively analysing data is that used by the Cochrane Collaboration. Their systematic reviews identify, analyse and present research-based evidence in an accessible format. These reviews may contain meta-analyses combining data from multiple studies to provide robust evaluations of overall treatment effects.In 2003, Cochrane reviews of data for treatment with corticosteroids in idiopathic pulmonary fibrosis (IPF) found no evidence supporting their use; similarly, reviews of immunomodulatory agents found very little evidence to support their use.A recent update of these Cochrane reviews failed to identify any evidence supporting the use of corticosteroids in IPF; however, a review of non-steroid agents in the treatment of IPF identified 15 clinical trials suitable for analysis. Two trials of interferon-γ-1b were combined, and no treatment effect was observed in terms of survival. Two Japanese trials of treatment with pirfenidone were combined, and a positive effect of pirfenidone on pulmonary function decline was observed. Meta-analysis of three phase III studies suggested that pirfenidone significantly increased progression-free survival by 30%.The findings of this systematic review, although not presenting new original data, together with an acceptable safety profile, suggest that pirfenidone may have a role in IPF treatment.
The management of work-related asthma guidelines: a broader perspective
Authors: Baur Xaver , Aasen Tor Brøvig , Burge P. Sherwood , Heederik Dick , Henneberger Paul K. , Maestrelli Piero , Schlünssen Vivi , Vandenplas Olivier , Wilken Dennis 
Published: June 2012

The aim of the European Respiratory Society work-related asthma guidelines is to present the management and prevention options of work-related asthma and their effectiveness.Work-related asthma accounts for 5–25% of all adult asthma cases and is responsible for a significant socioeconomic burden. Several hundred occupational agents, mainly allergens but also irritants and substances with unknown pathological mechanisms, have been identified as causing work-related asthma.The essential message of these guidelines is that the management of work-related asthma can be considerably optimised based on the present knowledge of causes, risk factors, pathomechanisms, and realistic and effective interventions. To reach this goal we urgently require greatly intensified primary preventive measures and improved case management. There is now a substantial body of evidence supporting the implementation of comprehensive medical surveillance programmes for workers at risk. Those workers who fail surveillance programmes need to be referred to a clinician who can confirm or exclude an occupational cause. Once work-related asthma is confirmed, a revised risk assessment in the workplace is needed to prevent further cases. These new guidelines confirm and extend already existing statements and recommendations.We hope that these guidelines will initiate the much-needed research that is required to fill the gaps in our knowledge and to initiate substantial improvements in preventative measures.
Contribution of host factors and workplace exposure to the outcome of occupational asthma
Authors: Maestrelli Piero , Schlünssen Vivi , Mason Paola , Sigsgaard Torben 
Published: June 2012

The outcome of occupational asthma after diagnosis is often poor. The identification of factors associated with a worse outcome may help in the management of the disease, determining its prognosis and assessing the permanent impairment attributable to occupational exposure.The aim of this systematic review was to provide the available evidence from the medical literature to answer the question: “What is the contribution of host factors and workplace exposure to the risk of a bad outcome of occupational asthma?”A systematic literature search was conducted in March 2010. We retrieved 177 abstracts. Of these, 67 were assessed as potentially relevant. After full text evaluation, 35 articles that were actually relevant for the question were included in the analysis.The information obtained was sufficient to establish that older age, high-molecular-weight agents, impaired lung function and longer duration of exposure to the offending agent at the time of diagnosis had a negative role on the outcome of occupational asthma. Atopy and smoking at diagnosis did not seem to influence the outcome of occupational asthma. A limited number of studies considered sex and the pattern of asthmatic reaction on specific inhalation challenge and their findings were contradictory.
What is the optimal management option for occupational asthma?
Authors: Vandenplas Olivier , Dressel Holger , Nowak Dennis , Jamart Jacques 
Published: June 2012

The optimal management of occupational asthma remains uncertain in clinical practice. The aim of this review was to analyse the published information pertaining to the management of occupational asthma in order to produce evidence-based statements and recommendations.A systematic literature search was conducted up to March 2010 to identify original studies addressing the following different treatment options: 1) persistence of exposure; 2) pharmacological treatment; 3) complete avoidance of exposure; 4) reduction of exposure; and 5) the use of personal protective equipment.After full text evaluation of 83 potentially relevant articles, 52 studies were retained for analysis.The conclusions from this systematic review are limited by the methodological weaknesses of most published studies. Critical analysis of available evidence indicates that: 1) persistent exposure to the causal agent is more likely to result in asthma worsening than complete avoidance; 2) there is insufficient evidence to determine whether pharmacological treatment can alter the course of asthma in subjects who remain exposed; 3) avoidance of exposure leads to recovery of asthma in less than one-third of affected workers; 4) reduction of exposure seems to be less beneficial than complete avoidance of exposure; and 5) personal respiratory equipment does not provide complete protection.
What are the benefits of medical screening and surveillance?
Authors: Wilken Dennis , Baur Xaver , Barbinova Lioubov , Preisser Alexandra , Meijer Evert , Rooyackers Jos , Heederik Dick 
Published: June 2012

Pre-employment examination is considered to be an important practice and is commonly performed in several countries within the European Union. The benefits of medical surveillance programmes are not generally accepted and their structure is often inconsistent.The aim of this review was to evaluate, on the basis of the available literature, the usefulness of medical screening and surveillance. MEDLINE was searched from its inception up to March 2010. Retrieved literature was evaluated in a peer-review process and relevant data was collected following a systematic extraction schema.Pre-placement screening identifies subjects who are at an increased risk for developing work-related allergic disease, but pre-employment screening is too low to be used as exclusion criteria. Medical surveillance programmes can identify workers who have, or who are developing, work-related asthma. These programmes can also be used to avoid worsening of symptoms by implementing preventive measures. A combination of different tools within the surveillance programme, adjusted for the risk of the individual worker, improves the predictive value.Medical surveillance programmes provide medical as well as socioeconomic benefits. However, pre-employment screening cannot be used to exclude workers. They may act as a starting point for surveillance strategies. A stratified approach can increase the effectiveness and reduce the costs for such programmes.
Comparing thousands of circular genomes using the CGView Comparison Tool
Authors: Grant Jason R , Arantes Adriano S , Stothard Paul 
Published: June 2012

Abstract

Background
Continued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the biology and evolution of the source organism. Visualization of the results is important, as it allows information from a variety of sources to be integrated and interpreted. However, existing graphical comparison tools lack features needed for efficiently comparing a new genome to hundreds or thousands of existing sequences. Moreover, existing tools are limited in terms of the types of comparisons that can be performed, the extent to which the output can be customized, and the ease with which the entire process can be automated.

Results
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG (Clusters of Orthologous Groups of proteins) category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.

Conclusion
CCT can be used to visually compare a reference sequence to thousands of existing genomes or sequence collections (next-generation sequencing reads for example) on a standard desktop computer. It provides analysis and visualization functionality not available in any existing circular genome visualization tool. By visually presenting sequence conservation information along with functional classifications and sequence composition characteristics, CCT can be a useful tool for identifying rapidly evolving or novel sequences, horizontally transferred sequences, or unusual functional properties in newly sequenced genomes. CCT is freely available for download at http://stothard.afns.ualberta.ca/downloads/CCT/.
Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae
Authors: Lam Connie , Octavia Sophie , Reeves Peter R , Lan Ruiting 
Published: June 2012

Abstract

Background
Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs) analysis (MLVA) to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae.

Results
MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP) typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus.

Conclusions
MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing.
Association between polymorphisms in the adiponectin gene and cardiovascular disease: a meta-analysis
Authors: Zhang Huan , Mo Xingbo , Hao Yongchen , Gu Dongfeng 
Published: June 2012

Abstract

Background
Previous studies have examined the associations between polymorphisms of adiponectin gene (ADIPOQ) and cardiovascular disease (CVD), but those studies have been inconclusive. The aim of this study was to access the relationship between three single nucleotide polymorphisms (SNPs), +45 T > G (rs2241766), +276 G > T (rs1501299) and -11377 C > G (rs266729) in ADIPOQ and CVD.

Methods
A comprehensive search was conducted to identify all studies on the association of ADIPOQ gene polymorphisms with CVD risk. The fixed and random effect pooled measures (i.e. odds ratio (OR) and 95% confidence interval (CI)) were calculated in the meta-analysis. Heterogeneity among studies was evaluated using Q test and the I2. Publication bias was estimated using modified Egger’s linear regression test.

Results
Thirty-seven studies concerning the associations between the three polymorphisms of ADIPOQ gene and CVD risk were enrolled in this meta-analysis, including 6,398 cases and 10,829 controls for rs2241766, 8,392 cases and 18,730 controls for rs1501299 and 7,835 cases and 14,023 controls for rs266729. The three SNPs were significantly associated with CVD, yielding pooled ORs of 1.22 (95%CI: 1.07, 1.39; P = 0.004), 0.90 (95%CI: 0.83, 0.97; P = 0.007) and 1.09(95%CI: 1.01, 1.17; P = 0.032) for rs2241766, rs1501299 and rs266729, respectively. Rs2241766 and rs1501299 were significantly associated with coronary heart disease (CHD), yielding pooled ORs of 1.29 (95%CI: 1.09, 1.52; P = 0.004) and 0.89 (95%CI: 0.81, 0.99; P = 0.025), respectively. The pooled OR for rs266729 and CHD was 1.09 (95%CI: 0.99, 1.19; P = 0.090). Significant between-study heterogeneity was found in our meta-analysis. Evidence of publication bias was observed in the meta-analysis.

Conclusions
The present meta-analysis showed that the associations between rs2241766, rs1501299 and rs266729 in the ADIPOQ and CVD were significant but weak. High quality studies are still needed to confirm the associations, especially for rs2241766.
Barriers to condom use among women at risk of HIV/AIDS: a qualitative study from Iran
Authors: Lotfi Razieh , Tehrani Fahimeh Ramezani , Yaghmaei Farideh , Hajizadeh Ebrahim 
Published: June 2012

Abstract

Background
The growing trend of women infected with HIV through sexual transmission is alarming. Factors influencing condom use have not yet been fully identified, especially in countries with conservative cultures and backgrounds. The present study aimed to explore the barriers of condom use in Iranian women at risk of HIV.

Methods
Using the grounded theory methodology, participants’ experiences and their perceptions regarding condom were collected during semi structured in depth interviews. Participants were 22 women, aged 21–49 years, considered to be at risk for HIV, due to their own or their partner’s sexual behaviors. Qualitative analysis of the data was conducted manually and was guided by constant comparative analysis.

Results
Two main barriers, personal and socio-environmental emerged from data analysis. Lack of perceived threat, absence of protective motivation, inadequate knowledge, perceived lack of control, negative attitudes towards condom and misperception were the major personal barriers, while unsupportive environments and cultural norms were the common socio-environmental barriers to condom use among these at risk women.

Conclusions
These critical barriers have to be addressed for implementing effective prevention programs against HIV among populations at risk for HIV.
The effect of yoga on women with secondary arm lymphoedema from breast cancer treatment
Authors: Loudon Annette , Barnett Tony , Piller Neil , Immink Maarten A , Visentin Denis , Williams Andrew D 
Published: June 2012

Abstract

Background
Women who develop secondary arm lymphoedema subsequent to treatment associated with breast cancer require life-long management for a range of symptoms including arm swelling, heaviness, tightness in the arm and sometimes the chest, upper body impairment and changes to a range of parameters relating to quality of life. While exercise under controlled conditions has had positive outcomes, the impact of yoga has not been investigated. The aim of this study is to determine the effectiveness of yoga in the physical and psycho-social domains, in the hope that women can be offered another safe, holistic modality to help control many, if not all, of the effects of secondary arm lymphoedema.

Methods and design
A randomised controlled pilot trial will be conducted in Hobart and Launceston with a total of 40 women receiving either yoga intervention or current best practice care. Intervention will consist of eight weeks of a weekly teacher-led yoga class with a home-based daily yoga practice delivered by DVD. Primary outcome measures will be the effects of yoga on lymphoedema and its associated symptoms and quality of life. Secondary outcome measures will be range of motion of the arm and thoracic spine, shoulder strength, and weekly and daily physical activity. Primary and secondary outcomes will be measured at baseline, weeks four, eight and a four week follow up at week twelve. Range of motion of the spine, in a self-nominated group, will be measured at baseline, weeks eight and twelve. A further outcome will be the women’s perceptions of the yoga collected by interview at week eight.

Discussion
The results of this trial will provide information on the safety and effectiveness of yoga for women with secondary arm lymphoedema from breast cancer treatment. It will also inform methodology for future, larger trials.

Trial registration
ACTRN12611000202965
An electronic health record-enabled obesity database
Authors: Wood G Craig , Chu Xin , Manney Christina , Strodel William , Petrick Anthony , Gabrielsen Jon , Seiler Jamie , Carey David , Argyropoulos George , Benotti Peter , Still Christopher D , Gerhard Glenn S 
Published: June 2012

Abstract

Background
The effectiveness of weight loss therapies is commonly measured using body mass index and other obesity-related variables. Although these data are often stored in electronic health records (EHRs) and potentially very accessible, few studies on obesity and weight loss have used data derived from EHRs. We developed processes for obtaining data from the EHR in order to construct a database on patients undergoing Roux-en-Y gastric bypass (RYGB) surgery.

Methods
Clinical data obtained as part of standard of care in a bariatric surgery program at an integrated health delivery system were extracted from the EHR and deposited into a data warehouse. Data files were extracted, cleaned, and stored in research datasets. To illustrate the utility of the data, Kaplan-Meier analysis was used to estimate length of post-operative follow-up.

Results
Demographic, laboratory, medication, co-morbidity, and survey data were obtained from 2028 patients who had undergone RYGB at the same institution since 2004. Pre-and post-operative diagnostic and prescribing information were available on all patients, while survey laboratory data were available on a majority of patients. The number of patients with post-operative laboratory test results varied by test. Based on Kaplan-Meier estimates, over 74% of patients had post-operative weight data available at 4 years.

Conclusion
A variety of EHR-derived data related to obesity can be efficiently obtained and used to study important outcomes following RYGB.
What is preventable harm in healthcare? A systematic review of definitions
Authors: Nabhan Mohammed , Elraiyah Tarig , Brown Daniel R , Dilling James , LeBlanc Annie , Montori Victor M , Morgenthaler Timothy , Naessens James , Prokop Larry , Roger Veronique , Swensen Stephen , Thompson Rodney L , Murad M Hassan 
Published: June 2012

Abstract

Background
Mitigating or reducing the risk of harm associated with the delivery of healthcare is a policy priority. While the risk of harm can be reduced in some instances (i.e. preventable), what constitutes preventable harm remains unclear. A standardized and clear definition of preventable harm is the first step towards safer and more efficient healthcare delivery system. We aimed to summarize the definitions of preventable harm and its conceptualization in healthcare.

Methods
We conducted a comprehensive electronic search of relevant databases from January 2001 to June 2011 for publications that reported a definition of preventable harm. Only English language publications were included. Definitions were coded for common concepts and themes. We included any study type, both original studies and reviews. Two reviewers screened the references for eligibility and 28% (127/460) were finally included. Data collected from studies included study type, description of the study population and setting, and data corresponding to the outcome of interest. Three reviewers extracted the data. The level of agreement between the reviewers was calculated.

Results
One hundred and twenty seven studies were eligible. The three most prevalent preventable harms in the included studies were: medication adverse events (33/127 studies, 26%), central line infections (7/127, 6%) and venous thromboembolism (5/127, 4%). Seven themes or definitions for preventable harm were encountered. The top three were: presence of an identifiable modifiable cause (58/132 definitions, 44%), reasonable adaptation to a process will prevent future recurrence (30/132, 23%), adherence to guidelines (22/132, 16%). Data on the validity or operational characteristic (e.g., accuracy, reproducibility) of definitions were limited.

Conclusions
There is limited empirical evidence of the validity and reliability of the available definitions of preventable harm, such that no single one is supported by high quality evidence. The most common definition is “presence of an identifiable, modifiable cause of harm”.