Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects

Background  

Published molecular phylogenies are usually based on data whose quality has not been explored prior to tree inference. This leads to errors because trees obtained with conventional methods suppress conflicting evidence, and because support values may be high even if there is no distinct phylogenetic signal. Tools that allow an a priori examination of data quality are rarely applied.     

The association of garlic with Helicobacter pylori infection and gastric cancer risk: A systematic review and meta‐analysis

Background

Garlic may be protective against Helicobacter pylori infection and gastric cancer development. We conducted this study to quantitatively update evidence on garlic intake and gastric cancer with the inclusion of most recent cohort studies and qualitatively summarize epidemiological studies of garlic consumption and Helicobacter pylori infection.

Materials and Methods

PubMed, Embase, MEDLINE, and Cochrane Library were searched on April 2018. We conducted a meta‐analysis to determine whether garlic intake reduced gastric cancer risk using random‐effect models and a systematic review to summarize evidence on the association between garlic consumption and Helicobacter pylori infection. Risk of bias was assessed using tools of Cochrane risk of bias and Robins‐I for randomized and nonrandomized studies, respectively.

Results

Meta‐analysis of 18 studies (142 921 subjects) demonstrated high garlic consumption (as comparing the highest category to the lowest) was associated with a reduced gastric cancer risk (OR = 0.51, 95% CI = 0.44‐0.57). This association became nonsignificant if only derived from the prospective studies (OR = 0.95, 95% CI = 0.66‐1.24). Thirteen studies (4889 participants) were included in the systematic review for garlic consumption and Helicobacter pylori infection; ten of which found no significant results. The majority of these studies were poor in quality given the small sample size and high risk of bias.

Conclusions

Pooled evidence, mainly from case‐control studies, suggested a significant inverse association of garlic intake with gastric cancer risk. Given the limitations of included studies, current epidemiological evidence is not sufficient to reach any definite conclusion regarding the association of garlic with Helicobacter pylori infection.     

Sperm DNA fragmentation and oxidation are independent of malondialdheyde

Background  

There is clinical evidence to show that sperm DNA damage could be a marker of sperm quality and extensive data exist on the relationship between DNA damage and male fertility status. Detecting such damage in sperm could provide new elements besides semen parameters in diagnosing male infertility. We aimed to assess sperm DNA fragmentation and oxidation and to study the association between these two markers, routine semen parameters and malondialdehyde formation.     

Charting the progression of disability in parkinson disease: study protocol for a prospective longitudinal cohort study

Background  

People with Parkinson disease (PD), even in the presence of symptomatic relief from medical, surgical, and rehabilitative interventions, face a persistent worsening of disability. This disability is characterized by diminished quality of life, reduced functional mobility, declining performance in activities of daily living and worsening neurological impairments. While evidence has emerged supporting the clinically meaningful benefits of short-term exercise programs on these underlying factors, assertions regarding the effects of sustained programs of exercise and physical activity on the trajectory of disablement in PD are made in the absence of direct evidence. Indeed, the natural decline in quality of life and functional mobility in people diagnosed with PD is poorly understood. Moreover, outcome measures commonly used in clinical exercise trials typically do not capture the full spectrum of disability as defined by the World Health Organization (WHO).     

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

Background  

In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence.     

Health-related quality of life in adults with epilepsy: the effect of age,age at onset and duration of epilepsy in a multicentre Italian study

Background  

The potential effect of age-related factors on health-related quality of life (HRQOL) of patients with epilepsy has rarely been analyzed in the literature.     

Female philopatry in a heterogeneous environment: ordinary conditions leading to extraordinary ESS sex ratios

Background  

We use a simulation-based model to study the impact of female philopatry and heterogeneity of habitat quality on the evolution of primary sex ratio.     

Do Strategies to Improve Quality of Maternal and Child Health Care in Lower and Middle Income Countries Lead to Improved Outcomes? A Review of the Evidence

Objectives

Efforts to scale-up maternal and child health services in lower and middle income countries will fail if services delivered are not of good quality. Although there is evidence of strategies to increase the quality of health services, less is known about the way these strategies affect health system goals and outcomes. We conducted a systematic review of the literature to examine this relationship.

Methods

We undertook a search of MEDLINE, SCOPUS and CINAHL databases, limiting the results to studies including strategies specifically aimed at improving quality that also reported a measure of quality and at least one indicator related to health system outcomes. Variation in study methodologies prevented further quantitative analysis; instead we present a narrative review of the evidence.

Findings

Methodologically, the quality of evidence was poor, and dominated by studies of individual facilities. Studies relied heavily on service utilisation as a measure of strategy success, which did not always correspond to improved quality. The majority of studies targeted the competency of staff and adequacy of facilities. No strategies addressed distribution systems, public-private partnership or equity. Key themes identified were the conflict between perceptions of patients and clinical measures of quality and the need for holistic approaches to health system interventions.

Conclusion

Existing evidence linking quality improvement strategies to improved MNCH outcomes is extremely limited. Future research would benefit from the inclusion of more appropriate indicators and additional focus on non-facility determinants of health service quality such as health policy, supply distribution, community acceptability and equity of care.     

Exercise therapy and cognitive behavioural therapy to improve fatigue,daily activity performance and quality of life in Postpoliomyelitis Syndrome: the protocol of the FACTS-2-PPS trial

Background  

Postpoliomyelitis Syndrome (PPS) is a complex of late onset neuromuscular symptoms with new or increased muscle weakness and muscle fatigability as key symptoms. Main clinical complaints are severe fatigue, deterioration in functional abilities and health related quality of life. Rehabilitation management is the mainstay of treatment. Two different therapeutic interventions may be prescribed (1) exercise therapy or (2) cognitive behavioural therapy (CBT). However, the evidence on the effectiveness of both interventions is limited. The primary aim of the FACTS-2-PPS trial is to study the efficacy of exercise therapy and CBT for reducing fatigue and improving activities and quality of life in patients with PPS. Additionally, the working mechanisms, patients' and therapists' expectations of and experiences with both interventions and cost-effectiveness will be evaluated.     

Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries

Background  

We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis.     

Intra- and inter-observer analysis in the morphological assessment of early-stage embryos

Background  

The aim of this study was to determine the intra- and inter-observer variability in the evaluation of embryo quality. Multilevel images of embryos on day 1, day 2 and day 3, were analysed using different morphological parameters.     

Reporting randomised clinical trials of analgesics after traumatic or orthopaedic surgery is inadequate: a systematic review

Background  

Several randomised clinical trials (RCTs) of analgesics in postoperative pain after traumatic or orthopaedic surgery (TOS) have been published, but no studies have assessed the quality of these reports. We aimed to examine the quality of reporting RCTs on analgesics for postoperative pain after TOS.     

Health Reporting in Print Media in Lebanon: Evidence,Quality and Role in Informing Policymaking

Background

Media plays a vital role in shaping public policies and opinions through disseminating health-related information. This study aims at exploring the role of media in informing health policies in Lebanon, identifying the factors influencing health reporting and investigating the role of evidence in health journalism and the quality of health reporting. It also identifies strategies to enhance the use of evidence in health journalism and improve the quality of health reporting.

Methods

Media analysis was conducted to assess the way media reports on health-related issues and the quality of reporting using a quality assessment tool. Semi-structured interviews were also conducted with 27 journalists, researchers and policymakers to explore their perception on the role of media in health policymaking and the factors influencing health reporting. In addition, a validation workshop was conducted.

Results

Out of 1,279 health-related news articles identified, 318 articles used certain type of evidence to report health issues 39.8% of which relied on experts’ opinions as their source of evidence while only 5.9% referenced peer-reviewed research studies. The quality of health reporting was judged to be low based on a quality assessment tool consisting of a set of ten criteria. Journalists raised concerns about issues impeding them from referring to evidence. Journalists also reported difficulties with the investigative health journalism. Policymakers and researchers viewed media as an important tool for evidence-informed health policies, however, serious concerns were voiced in terms of the current practice and capacities.

Conclusion

Our study provides a structured reflection on the role of media and the factors that influence health reporting including context-specific strategies that would enhance the quality and promote the use of evidence in health reporting. In the light of the political changes in many Middle Eastern countries, findings from this study can contribute to redefining the role of media in strengthening health systems.     

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

Background  

Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data.     

Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family

Background  

Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlying alignments is therefore crucial for phylogenetic analysis.     

Canakinumab relieves symptoms of acute flares and improves health-related quality of life in patients with difficult-to-treat Gouty Arthritis by suppressing inflammation: results of a randomized,dose-ranging study

Introduction  

We report the impact of canakinumab, a fully human anti-interleukin-1β monoclonal antibody, on inflammation and health-related quality of life (HRQoL) in patients with difficult-to-treat Gouty Arthritis.     

Prolactin signaling through the short isoform of the mouse prolactin receptor regulates DNA binding of specific transcription factors, often with opposite effects in different reproductive issues

Background  

Externalization of phosphatidylserine (EPS) occurs in apoptotic-like spermatozoa and could be used to remove them from sperm preparations to enhance sperm quality for assisted medical procreation. We first characterized EPS in sperms from infertile patients in terms of frequency of EPS spermatozoa as well as localization of phosphatidylserine (PS) on spermatozoa. Subsequently, we determined the impact of depleting EPS spermatozoa on sperm quality.     

Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas

Background  

Expression microarrays represent a powerful technique for the simultaneous investigation of thousands of genes. The evidence that genes are not randomly distributed in the genome and that their coordinated expression depends on their position on chromosomes has highlighted the need for mathematical approaches to exploit this dependency for the analysis of expression data-sets.     

Arabidopsis brassinosteroid biosynthetic mutant <Emphasis Type="Italic">dwarf7-1</Emphasis>exhibits slower rates of cell division and shoot induction

Background  

Plant growth depends on both cell division and cell expansion. Plant hormones, including brassinosteroids (BRs), are central to the control of these two cellular processes. Despite clear evidence that BRs regulate cell elongation, their roles in cell division have remained elusive.