Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras

Evolving better RNAfold structure prediction

Grow and graft genetic programming (GGGP) evolves more than 50000 parameters in a state-of-the-art C program to make functional source code changes which give more accurate predictions of how RNA molecules fold up. Genetic improvement updates 29% of the dynamic programming free energy model parameters. In most cases (50.3%) GI gives better results on 4655 known secondary structures from RNA_STRAND (29.0% are worse and 20.7% are unchanged). Indeed it also does better than parameters recommended by Andronescu, M., et al.: Bioinformatics 23(13) (2007) i19–i28

Production of TGF-alpha and TGF-beta by cultured keratinocytes, skin and oral squamous cell carcinomas--potential autocrine regulation of normal and malignant epithelial cell proliferation.

Transforming growth factors have a wide range of biological activities related to cell proliferation and differentiation. In general TGF-alpha promotes cell proliferation while TGF-beta may stimulate or inhibit proliferation depending on the cell type and growth factor environment. Cultured human keratinocytes, skin and oral squamous cell carcinomas were analysed for the presence of transcripts and protein for the transforming growth factors alpha & beta. Both growth factors were detected in cultured keratinocytes (which have receptors for and respond to both ligands), and in medium conditioned by these cells. Additionally transcripts for TGF-alpha were found preferentially in the basal, proliferative compartment of cultured keratinocytes. Similarly both growth factors were detected in oral squamous cell carcinomas and a highly significant inverse correlation was found between the levels of TGF-alpha and the epidermal growth factor receptor in these tumours. The data for TGF-alpha are consistent with the existence of an autocrine growth control loop influencing cell proliferation in both a normal cell type and malignant epithelial tissues, a process that in keratinocytes and responsive squamous cell carcinomas could be modulated by TGF-beta

Evolving text classification rules with genetic programming

We describe a novel method for using genetic programming to create compact classification rules using combinations of N-grams (character strings). Genetic programs acquire fitness by producing rules that are effective classifiers in terms of precision and recall when evaluated against a set of training documents. We describe a set of functions and terminals and provide results from a classification task using the Reuters 21578 dataset. We also suggest that the rules may have a number of other uses beyond classification and provide a basis for text mining applications

BRCA1 5382insC mutation in sporadic and familial breast and ovarian carcinoma in Scotland.

A restriction site-generating polymerase chain reaction (RG-PCR) assay was developed to detect the BRCA1 5382insC mutation that has been reported in multiple, apparently unrelated breast/ovarian carcinoma families. The assay has been used to screen tumour DNA from 250 breast cancer patients (aged 19-86 years) and from 80 ovarian cancer patients (aged 25-90 years) in a local population of patients with no known family history. Altogether, 0/80 (0%) ovarian and 1/250 (0.4%) breast tumour DNAs were found to have the 5382insC mutation. The sole positive case was a 26-year-old woman (BC185) with no known family history. One of the reasons for carrying out this analysis was that the 5382insC mutation had previously been shown to segregate with the disease in a very large Scottish 'West Lothian' kindred having breast/ovarian carcinoma. To investigate whether this apparently isolated case and the known family might be related, haplotypes for the markers D17S855, D17S1322, D17S1323 and D17S1327 were analysed. The mutant haplotype in the large kindred was identical to that reported in all other 5382insC mutation families for all markers with the exception of D17S1327. This implies that there has been a recombination event at the telomeric end of common ancestral haplotype in this family. Since the isolated case we identified carries the 'complete' common haplotype, it is unlikely that she is closely related to the West Lothian family

Assessment of the ergogenic effect of caffeine supplementation on mood, anticipation timing, and muscular strength in older adults

The effect of caffeine to promote improvements in mood, cognition, and exercise performance has been well established in young and athletic adults. However, little is known about whether such nutritional ergogenic aids are effective in enhancing psychological well-being, physiological or cognitive performance in older adults. This study assesses the ergogenic effect of caffeine on mood, perceptual-motor coupling, and muscular strength in an older human population. Following a familiarization session, 12 apparently healthy volunteers (nine females and three males; 69 ± 6 years) completed two laboratory visits. "Pre ingestion" trials of mood state Brunel Mood State Inventory (BRUMS) and coincidence anticipation performance (Bassin anticipation timer) at slow (3 mph) and fast (8 mph) stimulus speeds were completed on both visits. Using a randomized, double-blind, cross-over design, participants consumed either caffeine (3 mg/kg body mass) or a placebo. Sixty minutes postingestion participants repeated the trials before completing a set of 10 consecutive repetitions of maximal knee extension using isokinetic dynamometry. Rating of perceived exertion (RPE) was assessed following the fifth and final repetition. Caffeine ingestion significantly improved mood state scores for vigor by 17% (P = 0.009) and reduced absolute error by 35% (P = 0.045) during coincidence anticipation assessment at 8 mph compared to placebo. There were no other significant effects. Caffeine ingestion failed to augment maximal voluntary contraction of the knee extensors and RPE did not prove to be significantly different to from placebo (P > 0.33 in each case). Acute caffeine ingestion may not be an effective ergogenic aid for improving muscular strength in older adults but could possibly be used as a nutrition supplement for enhancing mood and improving cognitive performance in daily living tasks where interceptive timing skills are required

Psychiatry and neurodevelopmental disorders: experts by experience, clinical care and research.

People with neurodevelopmental disorders often present with challenging behaviours and psychiatric illnesses. Diagnosis and treatment require patients, families and healthcare professionals to work closely together in partnership, acknowledging their respective areas of expertise. Good treatment outcomes should also be underpinned by robust research evidence. Key research priorities are highlighted

Sediment provenance in the Shudu Lake basin, northwest Yunnan Province, China, as revealed by composite fingerprinting

Composite fingerprinting represents an effective method of reconstructing sediment-source changes in remote areas where long-term hydrological and sediment accretion records do not exist. A ca. 50-year record of sediment deposition was determined for a small catchment at Shudu, situated in northwest Yunnan Province, China. Woodland, pasture, shrubland and channel bank material are identified as the most likely sediment sources and this was confirmed using a composite sediment fingerprinting approach. Based on the findings of the fingerprinting technique, variations in the geochemical signature associated with lacustrine sediment deposits indicate that 49.2 % of the total catchment sediment yield over an approximate 50-year period originated from channel banks. In contrast, 19.2 % originated from pasture, 18.6 % originated from shrubland, and 13 % from woodland. The relative contributions of eroded sediment from both woodland and shrubland have generally remained stable over the period investigated, whereas the contribution of material from pasture has increased over recent decades. This is tentatively attributed to increased grazing pressure, which is probably due to increased stocking densities which have gradually exceeded the carrying capacity and regenerative capabilities of the available grassland

Pseudo-Random Streams for Distributed and Parallel Stochastic Simulations on GP-GPU

International audienceRandom number generation is a key element of stochastic simulations. It has been widely studied for sequential applications purposes, enabling us to reliably use pseudo-random numbers in this case. Unfortunately, we cannot be so enthusiastic when dealing with parallel stochastic simulations. Many applications still neglect random stream parallelization, leading to potentially biased results. In particular parallel execution platforms, such as Graphics Processing Units (GPUs), add their constraints to those of Pseudo-Random Number Generators (PRNGs) used in parallel. This results in a situation where potential biases can be combined with performance drops when parallelization of random streams has not been carried out rigorously. Here, we propose criteria guiding the design of good GPU-enabled PRNGs. We enhance our comments with a study of the techniques aiming to parallelize random streams correctly, in the context of GPU-enabled stochastic simulations