A general approach to simultaneous model fitting and variable elimination in response models for biological data with many more variables than observations

Background  

With the advent of high throughput biotechnology data acquisition platforms such as micro arrays, SNP chips and mass spectrometers, data sets with many more variables than observations are now routinely being collected. Finding relationships between response variables of interest and variables in such data sets is an important problem akin to finding needles in a haystack. Whilst methods for a number of response types have been developed a general approach has been lacking.     

Psychological correlates of self-reported functional limitation in patients with ankylosing spondylitis

Introduction  

Functional status is an integral component of health-related quality of life in patients with ankylosing spondylitis (AS). The purpose of this study was to investigate the role of psychological variables in self-reported functional limitation in patients with AS, while controlling for demographic and medical variables.     

Restrictive pulmonary function is more prevalent in patients with ankylosing spondylitis than in matched population controls and is associated with impaired spinal mobility: a comparative study

Introduction  

Pulmonary involvement is a known manifestation in patients with ankylosing spondylitis (AS). However, previous studies have been based on small samples and the reported prevalence and associations with typical clinical features vary. The purpose of this study was to compare pulmonary function (PF) in patients with AS and population controls, and to study associations between PF and disease related variables, cardio-respiratory fitness and demographic variables in patients with AS.     

Books from an environmental perspective—Part 1: environmental impacts of paper books sold in traditional and internet bookshops

Purpose  

The sale and distribution of books are activities that have changed through increased use of the internet. The main aim of this paper was to determine the potential environmental impacts of paper books and identify key issues determining the magnitude of those impacts. A second aim was to study the environmental difference between a paper book bought in a traditional bookshop and through an internet bookshop. In addition, areas with a lack of data and major uncertainties were to be noted.     

Effect of menstrual cycle phase and hormonal treatments on evaluation of tubal patency in baboons

Background

We evaluated whether menstrual cycle phase influences the assessment of tubal patency by hysterosalpingography (HSG) in baboons.

Methods

Retrospective analysis of baseline tubal patency studies and serum estradiol (E₂) and progesterone (P4) values obtained from female baboons used as models for development of non‐surgical permanent contraception in women. The main outcome measure was bilateral tubal patency (BTP) in relationship with estradiol level.

Results

Female baboons (n = 110) underwent a single (n = 81), two (n = 26), or three (n = 3) HSG examinations. In 33/142 (23%) HSG examinations, one or both tubes showed functional occlusion (FO). The median E₂ in studies with BTP (49 pg/mL) was significantly higher than in those studies with FO (32 pg/mL, P = .005). Among 18 animals with repeat examinations where serum E₂ changed from <60 to ≥ 60 pg/mL, 13 results changed from FO to BTP (P = .0001). No sets showed a change from BTP to FO with an increase in estradiol.

Conclusion

In baboons, functional occlusion of the fallopian tube is associated with low estradiol levels, supporting a role for estrogen‐mediated relaxation of the utero‐tubal junction.     

Role of accelerated segment switch in exons to alter targeting (ASSET) in the molecular evolution of snake venom proteins

Background  

Snake venom toxins evolve more rapidly than other proteins through accelerated changes in the protein coding regions. Previously we have shown that accelerated segment switch in exons to alter targeting (ASSET) might play an important role in its functional evolution of viperid three-finger toxins. In this phenomenon, short sequences in exons are radically changed to unrelated sequences and hence affect the folding and functional properties of the toxins.     

Increasing polypharmacy - an individual-based study of the Swedish population 2005-2008

Background  

An increase in the use of drugs and polypharmacy have been displayed over time in spite of the fact that polypharmacy represents a well known risk factor as regards patients' health due to the adverse drug reactions, drug-drug interactions, and low adherence to drug therapy arising from polypharmacy. For policymakers, as well as for clinicians, it is important to follow the developing trends in drug use and polypharmacy over time. We wanted to study if the prevalence of polypharmacy in an entire national population has changed during a 4-year period.     

Evidence of recombination among early-vaccination era measles virus strains

Background  

The advent of live-attenuated vaccines against measles virus during the 1960'ies changed the circulation dynamics of the virus. Earlier the virus was indigenous to countries worldwide, but now it is mediated by a limited number of evolutionary lineages causing sporadic outbreaks/epidemics of measles or circulating in geographically restricted endemic areas of Africa, Asia and Europe. We expect that the evolutionary dynamics of measles virus has changed from a situation where a variety of genomic variants co-circulates in an epidemic with relatively high probabilities of co-infection of the individual to a situation where a co-infection with strains from evolutionary different lineages is unlikely.     

Estimating and Modelling Bias of the Hierarchical Partitioning Public-Domain Software: Implications in Environmental Management and Conservation

Background

Hierarchical partitioning (HP) is an analytical method of multiple regression that identifies the most likely causal factors while alleviating multicollinearity problems. Its use is increasing in ecology and conservation by its usefulness for complementing multiple regression analysis. A public-domain software “hier.part package” has been developed for running HP in R software. Its authors highlight a “minor rounding error” for hierarchies constructed from >9 variables, however potential bias by using this module has not yet been examined. Knowing this bias is pivotal because, for example, the ranking obtained in HP is being used as a criterion for establishing priorities of conservation.

Methodology/Principal Findings

Using numerical simulations and two real examples, we assessed the robustness of this HP module in relation to the order the variables have in the analysis. Results indicated a considerable effect of the variable order on the amount of independent variance explained by predictors for models with >9 explanatory variables. For these models the nominal ranking of importance of the predictors changed with variable order, i.e. predictors declared important by its contribution in explaining the response variable frequently changed to be either most or less important with other variable orders. The probability of changing position of a variable was best explained by the difference in independent explanatory power between that variable and the previous one in the nominal ranking of importance. The lesser is this difference, the more likely is the change of position.

Conclusions/Significance

HP should be applied with caution when more than 9 explanatory variables are used to know ranking of covariate importance. The explained variance is not a useful parameter to use in models with more than 9 independent variables. The inconsistency in the results obtained by HP should be considered in future studies as well as in those already published. Some recommendations to improve the analysis with this HP module are given.     

Relationship between salivary haemoglobin and number of remaining teeth in older Koreans

Objective

We investigated the relationship between saliva and dental biofilm characteristics, oral hygiene behaviours and the number of remaining teeth in a sample of older Koreans.

Materials and methods

This cross‐sectional study included 133 participants, aged 65 years and older, recruited from senior welfare facilities in Incheon, South Korea. The outcome variable was the number of remaining teeth, and its associations with the independent variables of participants’ general characteristics, salivary haemoglobin level, dental biofilm acidogenicity, salivary flow rate and oral hygiene behaviours were assessed. For statistical analyses, chi‐squared test and step‐wise multiple linear regression were used.

Results

The multiple linear regression model, which included all related factors identified in the bivariate analyses, showed that older adults who had high salivary haemoglobin levels (P < .05), brushed their teeth using the horizontal scrub method (P< .001), and did not use an interproximal cleaning device (P < .01) were more likely to have fewer remaining teeth. However, dental biofilm acidogenicity was not associated with the number of remaining teeth.

Conclusion

The number of remaining teeth was associated with salivary haemoglobin level, appropriate toothbrushing technique and interdental cleaning. These findings suggest that the monitoring of salivary haemoglobin may contribute to the prevention of tooth loss caused by periodontal disease.     

Causes of mortality in laying hens in different housing systems in 2001 to 2004

Background  

The husbandry systems for laying hens were changed in Sweden during the years 2001 – 2004, and an increase in the number of submissions for necropsy from laying hen farms was noted. Hence, this study was initiated to compare causes of mortality in different housing systems for commercial laying hens during this change.     

Post-Soviet fire and grazing regimes govern the abundance of a key ecosystem engineer on the Eurasian steppe,the yellow ground squirrel Spermophilus fulvus

Aim

Grazing intensity and fire patterns across the Eurasian steppes have changed dramatically over the past decades due to the collapse of the Soviet Union in 1991, and Kazakhstan is now a global fire hotspot. The implications of these changes for ecosystem functioning are largely unclear. We aimed to understand the effects of changed grazing intensity and fire frequency on a key ecosystem engineer, the yellow ground squirrel Spermophilus fulvus, on a very large scale.

Location

Kazakhstan.

Methods

Ground squirrels were surveyed in an area of ca. 100,000 ha in the dry steppe of central Kazakhstan, using hierarchical distance sampling at more than 200 random points, stratified by fire frequency and livestock grazing intensity. We modelled abundance as a function of different variables, grouped at the landscape scale (fire and grazing), meso-scale (soil and vegetation structure) and at burrow scale (plant traits such as palatability, digestibility and nutrient content).

Results

Ground squirrels prefer areas of a high wormwood cover (Artemisia spp.) and high plant species richness, which are moderately grazed, preferably by cattle, with only rare fire occurrence. High squirrel densities were also related to the availability of nitrogen-rich plants of high nutritional value for herbivores.

Main Conclusions

Yellow ground squirrels seem to reach their density optima by balancing trade-offs between optimal foraging in areas of short, nutrient-rich vegetation and a good visibility of approaching predators. Post-Soviet changes in grazing pressure, resulting in higher fire recurrence rates due to grass encroachment and litter accumulation (i.e. fuel for wildfire), have likely affected the abundance of burrowing mammals and associated biodiversity across huge parts of the Eurasian steppes and semideserts.     

Seroma formation after surgery for breast cancer

Background  

Seroma formation is the most frequent postoperative complication after breast cancer surgery. We carried out a study to investigate the effect of various demographic, clinical and therapeutic variables on seroma formation.     

Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

Background  

When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.     

Neural set point for the control of arterial pressure: role of the nucleus tractus solitarius

Background  

Physiological experiments have shown that the mean arterial blood pressure (MAP) can not be regulated after chemo and cardiopulmonary receptor denervation. Neuro-physiological information suggests that the nucleus tractus solitarius (NTS) is the only structure that receives information from its rostral neural nuclei and from the cardiovascular receptors and projects to nuclei that regulate the circulatory variables.     

Effects of dependence in high-dimensional multiple testing problems

Background  

We consider effects of dependence among variables of high-dimensional data in multiple hypothesis testing problems, in particular the False Discovery Rate (FDR) control procedures. Recent simulation studies consider only simple correlation structures among variables, which is hardly inspired by real data features. Our aim is to systematically study effects of several network features like sparsity and correlation strength by imposing dependence structures among variables using random correlation matrices.