What can we learn from noncoding regions of similarity between genomes?

BACKGROUND: In addition to known protein-coding genes, large amounts of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain functional elements than less-conserved portions of the genome. METHODS: Here we used a motif-oriented machine learning method based on the Relevance Vector Machine algorithm to extract the strongest signal from a set of non-coding conserved sequences. RESULTS: We successfully fitted models to reflect the non-coding sequences, and showed that the results were quite consistent for repeated training runs. Using the learned models to scan genomic sequence, we found that they often made predictions close to the start of annotated genes. We compared this method with other published promoter-prediction systems, and showed that the set of promoters which are detected by this method is substantially similar to that detected by existing methods. CONCLUSIONS: The results presented here indicate that the promoter signal is the strongest single motif-based signal in the non-coding functional fraction of the genome. They also lend support to the belief that there exists a substantial subset of promoter regions which share several common features including, but not restricted to, a relative abundance of CpG dinucleotides. This subset is detectable by a variety of distinct computational methods

Use of long-term microdialysis subcutaneous glucose monitoring in the management of neonatal diabetes - A first case report

In neonatal diabetes mellitus (NDM), a rare genetic disorder, insulin therapy is required but the management is difficult. Frequent blood glucose determinations are necessary in most cases. Microdialysis subcutaneous glucose monitoring (MSGM) is feasible in neonates and has been proposed to reduce painful blood sampling and blood loss. We have applied long-term MSGM to a small-fordate female newborn with transient NDM. We found a good correlation of subcutaneous and blood glucose concentration over a wide range of values. MSGM enabled a reduction in blood glucose determinations during optimization of intravenous insulin treatment and initiation of continuous subcutaneous insulin infusion. We conclude that long-term MSGM is feasible and may reduce painful blood sampling and blood loss in NDM. Furthermore, long-term MSGM may hold a potential for avoiding hypoglycemic episodes and earlier discharge. Copyright (C) 2006 S. Karger AG, Basel

A machine learning strategy to identify candidate binding sites in human protein-coding sequence

BACKGROUND: The splicing of RNA transcripts is thought to be partly promoted and regulated by sequences embedded within exons. Known sequences include binding sites for SR proteins, which are thought to mediate interactions between splicing factors bound to the 5' and 3' splice sites. It would be useful to identify further candidate sequences, however identifying them computationally is hard since exon sequences are also constrained by their functional role in coding for proteins. RESULTS: This strategy identified a collection of motifs including several previously reported splice enhancer elements. Although only trained on coding exons, the model discriminates both coding and non-coding exons from intragenic sequence. CONCLUSION: We have trained a computational model able to detect signals in coding exons which seem to be orthogonal to the sequences' primary function of coding for proteins. We believe that many of the motifs detected here represent binding sites for both previously unrecognized proteins which influence RNA splicing as well as other regulatory elements

NestedMICA as an ab initio protein motif discovery tool.

BACKGROUND: Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. RESULTS: Generally NestedMICA recovered most of the short (3-9 amino acid long) test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. CONCLUSION: NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. AVAILABILITY: NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Quality of perception to quality of service mapping using a dynamically reconfigurable communication system

We present an innovative approach for providing en-to-end Quality of Service (QoS) guarantees in a distributed multimedia setting. Quality of Perception (QoP) is a term which encompasses not only a user's satisfaction with the quality of multimedia presentations, but also his/her ability to analyse, synthesise and assimilate the informational content of multimedia displays. The basics of a mapping linking QoP to QoS are then presented and the case for including it in an adaptable protocol is made. A proof of concept implementation based on the Dynamically Reconfigurable Protocol Stacks (DRoPS) project show that such applications can be used to improve QoP, especially in the case of dynamic and complex sequences

Metamotifs--a generative model for building families of nucleotide position weight matrices.

BACKGROUND: Development of high-throughput methods for measuring DNA interactions of transcription factors together with computational advances in short motif inference algorithms is expanding our understanding of transcription factor binding site motifs. The consequential growth of sequence motif data sets makes it important to systematically group and categorise regulatory motifs. It has been shown that there are familial tendencies in DNA sequence motifs that are predictive of the family of factors that binds them. Further development of methods that detect and describe familial motif trends has the potential to help in measuring the similarity of novel computational motif predictions to previously known data and sensitively detecting regulatory motifs similar to previously known ones from novel sequence. RESULTS: We propose a probabilistic model for position weight matrix (PWM) sequence motif families. The model, which we call the 'metamotif' describes recurring familial patterns in a set of motifs. The metamotif framework models variation within a family of sequence motifs. It allows for simultaneous estimation of a series of independent metamotifs from input position weight matrix (PWM) motif data and does not assume that all input motif columns contribute to a familial pattern. We describe an algorithm for inferring metamotifs from weight matrix data. We then demonstrate the use of the model in two practical tasks: in the Bayesian NestedMICA model inference algorithm as a PWM prior to enhance motif inference sensitivity, and in a motif classification task where motifs are labelled according to their interacting DNA binding domain. CONCLUSIONS: We show that metamotifs can be used as PWM priors in the NestedMICA motif inference algorithm to dramatically increase the sensitivity to infer motifs. Metamotifs were also successfully applied to a motif classification problem where sequence motif features were used to predict the family of protein DNA binding domains that would interact with it. The metamotif based classifier is shown to compare favourably to previous related methods. The metamotif has great potential for further use in machine learning tasks related to especially de novo computational sequence motif inference. The metamotif methods presented have been incorporated into the NestedMICA suite.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The Word Problem for Omega-Terms over the Trotter-Weil Hierarchy

For two given $\omega$-terms $\alpha$ and $\beta$, the word problem for $\omega$-terms over a variety $\boldsymbol{\mathrm{V}}$ asks whether $\alpha=\beta$ in all monoids in $\boldsymbol{\mathrm{V}}$. We show that the word problem for $\omega$-terms over each level of the Trotter-Weil Hierarchy is decidable. More precisely, for every fixed variety in the Trotter-Weil Hierarchy, our approach yields an algorithm in nondeterministic logarithmic space (NL). In addition, we provide deterministic polynomial time algorithms which are more efficient than straightforward translations of the NL-algorithms. As an application of our results, we show that separability by the so-called corners of the Trotter-Weil Hierarchy is witnessed by $\omega$-terms (this property is also known as $\omega$-reducibility). In particular, the separation problem for the corners of the Trotter-Weil Hierarchy is decidable

Dynamics of excited-state proton transfer systems via time-resolved photoelectron spectroscopy

The use of time-resolved photoelectron spectroscopy for analyzing excited state intramolecular proton transfer (ESIPT) and internal conversion dynamics in a model system was investigated. The photoelectron spectra of both the excited state enol and keto tautomers were presented as a function of pump laser wavelength and pump-probe time delay. It was found that the internal conversion dynamics in o-hydroxybenzaldehyde (OHBA) was influenced by interactions with a close-lying n??* state.open958

Board review course effect on resident in-training examination

Background The in-training examination is a national and yearly exam administered by the American Board of Emergency Medicine to all emergency medicine residents in the USA. The purpose of the examination is to evaluate a resident’s progress toward obtaining the fundamental knowledge to practice independent emergency medicine. Aims The purpose of this study was to determine the effects of a 40 hour board review lecture course on the resident in-training examination in emergency medicine. Methods A 40 hour board review lecture course was designed and implemented during the weekly 5 hour long resident conferences during the 8 weeks preceding the in-training examination date in 2006. Attendance was manda-tory at the Accreditation Council for Graduate Medical Education (ACGME) standard of 70 % or greater. A positive result was considered to be a 10 % increase or greater in the resident’s individual national class percentile ranking among their national peers for their class year for the emergency medicine in-training examination. A resident was excluded from the study if there was no 2005 in-training examination score for self-comparison. The 95% confidence intervals (CI) were used to analyze the results. Results Of 16 residents, 1 (6.25%; 95 % CI: 0–18%) showed a positive result of increasing their national class percentile ranking by 10 % or greater. For the PGY2, one of the eight had a positive result (12.5%; 95 % CI: 0–35.4%). For PGY3, no resident (0%; 95 % CI: 0–35.4%) had a positive result. Conclusions A 40 hour board review lecture course has no positive effect on improving a resident’s in-training examination score

Exposure to Polyfluoroalkyl Chemicals and Cholesterol, Body Weight, and Insulin Resistance in the General U.S. Population

BACKGROUND. Polyfluoroalkyl chemicals (PFCs) are used commonly in commercial applications and are detected in humans and the environment worldwide. Concern has been raised that they may disrupt lipid and weight regulation. OBJECTIVES. We investigated the relationship between PFC serum concentrations and lipid and weight outcomes in a large publicly available data set. METHODS. We analyzed data from the 2003-2004 National Health and Nutrition Examination Survey (NHANES) for participants 12-80 years of age. Using linear regression to control for covariates, we studied the association between serum concentrations of perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorooctane sulfonic acid (PFOS), and perfluorohexane sulfonic acid (PFHxS) and measures of cholesterol, body size, and insulin resistance. RESULTS. We observed a positive association between concentrations of PFOS, PFOA, and PFNA and total and non-high-density cholesterol. We found the opposite for PFHxS. Those in the highest quartile of PFOS exposure had total cholesterol levels 13.4 mg/dL [95% confidence interval (CI), 3.8-23.0] higher than those in the lowest quartile. For PFOA, PFNA, and PFHxS, effect estimates were 9.8 (95% CI, -0.2 to 19.7), 13.9 (95% CI, 1.9-25.9), and -7.0 (95% CI, -13.2 to -0.8), respectively. A similar pattern emerged when exposures were modeled continuously. We saw little evidence of a consistent association with body size or insulin resistance. CONCLUSIONS. This exploratory cross-sectional study is consistent with other epidemiologic studies in finding a positive association between PFOS and PFOA and cholesterol, despite much lower exposures in NHANES. Results for PFNA and PFHxS are novel, emphasizing the need to study PFCs other than PFOS and PFOA.National Institute of Environmental Health Sciences (R21ES013724, T32ES014562