PineappleDB: An online pineapple bioinformatics resource

Background  

A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences.     

Comparative Analysis of Protein Structure Alignments

Background  

Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods.     

Characterisation of physiological and immunological responses in beef cows to abrupt weaning and subsequent housing

Background  

Weaning involves the permanent separation of the calf from the dam and has been shown to be stressful for both. The objectives of this study were to characterise the effect of i) abrupt weaning and ii) subsequent housing on the extended physiological and immunological responses of beef cows. At weaning (day (d) 0, mean age of calf (s.d.) 212 (24.5) d), cows were abruptly separated from their calves and returned to the grazing area. After 35 d at pasture, cows were housed in a slatted floor shed and offered grass silage ad libitum plus a mineral-vitamin supplement daily. Rectal body temperature was recorded and blood samples were obtained on i) d 0 (weaning), 2, 7, 14, 21, 28, 35 and subsequently on ii) d 0 (housing), 2, 7, 14 and 21 for physiological, haematological and immunological measurements.     

Environmental assessment of cod (<Emphasis Type="BoldItalic">Gadus morhua</Emphasis>) from autoline fisheries

Purpose  

The main purpose of this study has been to document the environmental performance of products based on autoline-caught cod and the distribution of environmental impacts in the value chain from fishing to retail. Another aim has been to document the performed environmental improvement analyses.     

Prediction of protein binding sites in protein structures using hidden Markov support vector machine

Background  

Predicting the binding sites between two interacting proteins provides important clues to the function of a protein. Recent research on protein binding site prediction has been mainly based on widely known machine learning techniques, such as artificial neural networks, support vector machines, conditional random field, etc. However, the prediction performance is still too low to be used in practice. It is necessary to explore new algorithms, theories and features to further improve the performance.     

Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

Background  

Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported.     

High sensitivity assays for docetaxel and paclitaxel in plasma using solid-phase extraction and high-performance liquid chromatography with UV detection

Background  

The taxanes paclitaxel and docetaxel have traditionally been used in high doses every third week in the treatment of cancer. Lately there has been a trend towards giving weekly low doses to improve the therapeutic index. This article describes the development of high performance liquid chromatographic (HPLC) methods suitable for monitoring taxane levels in patients, focusing on patients receiving low-dose therapy.     

Antibodies to mutated citrullinated vimentin and disease activity score in early arthritis: a cohort study

Introduction  

The aim of our study was to investigate the association between arthritic disease activity and antibodies to mutated citrullinated vimentin (anti-MCV), because such a relation has been suggested.     

Shift from facilitative to neutral interactions by the cushion plant Silene acaulis along a primary succession gradient

Background

The stress‐gradient hypothesis predicts a shift from facilitative to competitive plant interactions with decreasing abiotic stress. This has been supported by studies along elevation and temperature gradients, but also challenged by the hypothesis of a facilitation collapse at extremely harsh sites. Although facilitation is known to be important in primary succession, few studies have examined these hypotheses along primary succession gradients.

Aim

To examine whether there is a relationship between the presence of the circumpolar cushion plant Silene acaulis and other species, and if so, whether there is a shift between positive and negative interactions along a primary succession gradient in a glacier foreland.

Location

Finse, southern Norway.

Methods

We examined the performance of the common alpine forb Bistorta vivipara, species richness of vascular plants, bryophytes and lichens, and the number of seedlings and fertile vascular plants in S. acaulis cushions, and control plots without S. acaulis, along a succession gradient with increasing distance from a glacier front, and thus decreasing abiotic stress. To examine if S. acaulis cushions modify the abiotic environment, we recorded soil temperature, moisture, organic content and pH in cushions and control plots.

Results

Bistorta vivipara performed better, as shown by bigger leaves in S. acaulis cushions compared to control plots in the harshest part of the gradient close to the glacier. There were few differences in B. vivipara performance between cushion and control plots in the more benign environment further away from the glacier. This suggests a shift from facilitative to mainly neutral interactions by S. acaulis on the performance of B. vivipara with decreasing abiotic stress. A trend, although not significant, of higher vascular species richness and fertility inside S. acaulis cushions along the whole gradient, suggests that S. acaulis also facilitates community‐level species richness. The causal mechanism of this facilitation is likely that the cushions buffer extreme temperatures.

Conclusions

Our results support the stress‐gradient hypothesis for the relationship between the cushion plant S. acaulis and the performance of a single species along a primary succession gradient in a glacier foreland. S. acaulis also tended to increase vascular plant species richness and fertility regardless of stress level along the gradient, suggesting facilitation at the community level. We found no collapse of facilitation at the most stressful end of the gradient in this alpine glacier foreland.     

Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes

Background  

Gene expression divergence is one manifestation of functional differences between duplicate genes. Although rapid accumulation of expression divergence between duplicate gene copies has been observed, the driving mechanisms behind this phenomenon have not been explored in detail.     

Preferred analysis methods for Affymetrix GeneChips. II. An expanded,balanced, wholly-defined spike-in dataset

Background  

Concomitant with the rise in the popularity of DNA microarrays has been a surge of proposed methods for the analysis of microarray data. Fully controlled "spike-in" datasets are an invaluable but rare tool for assessing the performance of various methods.     

Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols

Background  

The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications.     

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.     

Constraints to virus infection in <Emphasis Type="Italic">Nicotiana benthamiana</Emphasis> plants transformed with a potyvirus amplicon

Background  

Plant genomes have been transformed with full-length cDNA copies of viral genomes, giving rise to what has been called 'amplicon' systems, trying to combine the genetic stability of transgenic plants with the elevated replication rate of plant viruses. However, amplicons' performance has been very variable regardless of the virus on which they are based. This has boosted further interest in understanding the underlying mechanisms that cause this behavior differences, and in developing strategies to control amplicon expression.     

Framingham Stroke Risk Profile and poor cognitive function: a population-based study

Background  

The relationship between stroke risk and cognitive function has not previously been examined in a large community living sample other than the Framingham cohort. The objective of this study was to examine the relationship between 10-year risk for incident stroke and cognitive function in a large population-based sample.     

Reciprocity between abscisic acid and ethylene at the onset of berry ripening and after harvest

Background  

The ripening of grape berry is generally regulated by abscisic acid (ABA), and has no relationship with ethylene function. However, functional interaction and synergism between ABA and ethylene during the beginning of grape berry ripening (véraison) has been found recently.     

Reproductive Performance,Udder Health,and Antibiotic Resistance in Mastitis Bacteria isolated from Norwegian Red cows in Conventional and Organic Farming

Background  

The objectives of this study were to investigate whether there were differences between Norwegian Red cows in conventional and organic farming with respect to reproductive performance, udder health, and antibiotic resistance in udder pathogens.     

Psychological and weight-related characteristics of patients with anorexia nervosa-restricting type who later develop bulimia nervosa

Background  

Over the last five to ten years there has been an increase in psychosomatic complaints (PSC) in Swedish children. The objective of the study was to examine the relation between PSC and sense of coherence (SOC).     

Universal seeds for cDNA-to-genome comparison

Background  

To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of a related species. So far, seed performance has been tested for comparisons between closely related species, such as human and mouse, or on simulated data. As the number and variety of genomes increases, it becomes desirable to identify a small set of universal seeds that perform optimally or near-optimally on a large range of comparisons.