Metrics for GO based protein semantic similarity: a systematic evaluation

<p>Abstract</p> <p>Background</p> <p>Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However, it is still unclear which is the best approach to semantic similarity in this context, since there is no conclusive evaluation of the various measures. Another issue, is whether electronic annotations should or not be used in semantic similarity calculations.</p> <p>Results</p> <p>We conducted a systematic evaluation of GO-based semantic similarity measures using the relationship with sequence similarity as a means to quantify their performance, and assessed the influence of electronic annotations by testing the measures in the presence and absence of these annotations. We verified that the relationship between semantic and sequence similarity is not linear, but can be well approximated by a rescaled Normal cumulative distribution function. Given that the majority of the semantic similarity measures capture an identical behaviour, but differ in resolution, we used the latter as the main criterion of evaluation.</p> <p>Conclusions</p> <p>This work has provided a basis for the comparison of several semantic similarity measures, and can aid researchers in choosing the most adequate measure for their work. We have found that the hybrid <it>simGIC</it> was the measure with the best overall performance, followed by Resnik's measure using a best-match average combination approach. We have also found that the average and maximum combination approaches are problematic since both are inherently influenced by the number of terms being combined. We suspect that there may be a direct influence of data circularity in the behaviour of the results including electronic annotations, as a result of functional inference from sequence similarity.</p

Repetitive Behavior in Rubinstein–Taybi Syndrome:Parallels with Autism Spectrum Phenomenology

Syndrome specific repetitive behavior profiles have been described previously. A detailed profile is absent for Rubinstein–Taybi syndrome (RTS). The Repetitive Behaviour Questionnaire and Social Communication Questionnaire were completed for children and adults with RTS (N = 87), Fragile-X (N = 196) and Down (N = 132) syndromes, and individuals reaching cut-off for autism spectrum disorder (N = 228). Total and matched group analyses were conducted. A phenotypic profile of repetitive behavior was found in RTS. The majority of behaviors in RTS were not associated with social-communication deficits or degree of disability. Repetitive behavior should be studied at a fine-grained level. A dissociation of the triad of impairments might be evident in RTS

Prevalence of facet joint pain in chronic spinal pain of cervical, thoracic, and lumbar regions

BACKGROUND: Facet joints are a clinically important source of chronic cervical, thoracic, and lumbar spine pain. The purpose of this study was to systematically evaluate the prevalence of facet joint pain by spinal region in patients with chronic spine pain referred to an interventional pain management practice. METHODS: Five hundred consecutive patients with chronic, non-specific spine pain were evaluated. The prevalence of facet joint pain was determined using controlled comparative local anesthetic blocks (1% lidocaine or 1% lidocaine followed by 0.25% bupivacaine), in accordance with the criteria established by the International Association for the Study of Pain (IASP). The study was performed in the United States in a non-university based ambulatory interventional pain management setting. RESULTS: The prevalence of facet joint pain in patients with chronic cervical spine pain was 55% 5(95% CI, 49% – 61%), with thoracic spine pain was 42% (95% CI, 30% – 53%), and in with lumbar spine pain was 31% (95% CI, 27% – 36%). The false-positive rate with single blocks with lidocaine was 63% (95% CI, 54% – 72%) in the cervical spine, 55% (95% CI, 39% – 78%) in the thoracic spine, and 27% (95% CI, 22% – 32%) in the lumbar spine. CONCLUSION: This study demonstrated that in an interventional pain management setting, facet joints are clinically important spinal pain generators in a significant proportion of patients with chronic spinal pain. Because these patients typically have failed conservative management, including physical therapy, chiropractic treatment and analgesics, they may benefit from specific interventions designed to manage facet joint pain

Towards enhancing national capacity for evidence informed policy and practice in falls management: a role for a "Translation Task Group"?

There has been a growing interest over recent years, both within Australia and overseas, in enhancing the translation of research into policy and practice. As one mechanism to improve the dissemination and uptake of falls research into policy and practice and to foster the development of policy-appropriate research, a Falls Translation Task Group has formed to facilitate linkage and exchange. There has been a growing interest over recent years, both within Australia and overseas, in enhancing the translation of research into policy and practice. As one mechanism to improve the dissemination and uptake of falls research into policy and practice and to foster the development of policy-appropriate research, a Falls Translation Task Group was formed as part of an NHMRC Population Health Capacity Building grant. This paper reports on the group\u27s first initiative to address issues around the research to policy and practice interface, and identifies a continuing role for such a group. MethodA one day forum brought together falls researchers and decision-makers from across the nation to facilitate linkage and exchange. Observations of the day\u27s proceedings were made by the authors. Participants were asked to complete a questionnaire at the commencement of the forum (to ascertain expectations) and at its completion (to evaluate the event). Observer notes and the questionnaire responses form the basis of analysis. Results: Both researchers and decision-makers have a desire to bridge the gap between research and policy and practice. Significant barriers to research uptake were highlighted and included both health system barriers (for example, a lack of financial and human resources) as well as evidence barriers (such as insufficient economic data and implementation research). Solutions to some of these barriers included the identification of clinical champions within the health sector to enhance evidence uptake, and the sourcing of alternative funding to support implementation research and encourage partnerships between researchers, decision-makers and other stakeholders. Conclusion: Participants sought opportunities for ongoing networking and collaboration. Two activities have been identified as priorities: establishing a policy-sensitive research agenda and partnering researchers and decision-makers in the process; and establishing a National Translation Task Group with a broad membership

Autism as a disorder of neural information processing: directions for research and targets for therapy

The broad variation in phenotypes and severities within autism spectrum disorders suggests the involvement of multiple predisposing factors, interacting in complex ways with normal developmental courses and gradients. Identification of these factors, and the common developmental path into which theyfeed, is hampered bythe large degrees of convergence from causal factors to altered brain development, and divergence from abnormal brain development into altered cognition and behaviour. Genetic, neurochemical, neuroimaging and behavioural findings on autism, as well as studies of normal development and of genetic syndromes that share symptoms with autism, offer hypotheses as to the nature of causal factors and their possible effects on the structure and dynamics of neural systems. Such alterations in neural properties may in turn perturb activity-dependent development, giving rise to a complex behavioural syndrome many steps removed from the root causes. Animal models based on genetic, neurochemical, neurophysiological, and behavioural manipulations offer the possibility of exploring these developmental processes in detail, as do human studies addressing endophenotypes beyond the diagnosis itself

A stable pattern of EEG spectral coherence distinguishes children with autism from neuro-typical controls - a large case control study

<p>Abstract</p> <p>Background</p> <p>The autism rate has recently increased to 1 in 100 children. Genetic studies demonstrate poorly understood complexity. Environmental factors apparently also play a role. Magnetic resonance imaging (MRI) studies demonstrate increased brain sizes and altered connectivity. Electroencephalogram (EEG) coherence studies confirm connectivity changes. However, genetic-, MRI- and/or EEG-based diagnostic tests are not yet available. The varied study results likely reflect methodological and population differences, small samples and, for EEG, lack of attention to group-specific artifact.</p> <p>Methods</p> <p>Of the 1,304 subjects who participated in this study, with ages ranging from 1 to 18 years old and assessed with comparable EEG studies, 463 children were diagnosed with autism spectrum disorder (ASD); 571 children were neuro-typical controls (C). After artifact management, principal components analysis (PCA) identified EEG spectral coherence factors with corresponding loading patterns. The 2- to 12-year-old subsample consisted of 430 ASD- and 554 C-group subjects (n = 984). Discriminant function analysis (DFA) determined the spectral coherence factors' discrimination success for the two groups. Loading patterns on the DFA-selected coherence factors described ASD-specific coherence differences when compared to controls.</p> <p>Results</p> <p>Total sample PCA of coherence data identified 40 factors which explained 50.8% of the total population variance. For the 2- to 12-year-olds, the 40 factors showed highly significant group differences (<it>P </it>< 0.0001). Ten randomly generated split half replications demonstrated high-average classification success (C, 88.5%; ASD, 86.0%). Still higher success was obtained in the more restricted age sub-samples using the jackknifing technique: 2- to 4-year-olds (C, 90.6%; ASD, 98.1%); 4- to 6-year-olds (C, 90.9%; ASD 99.1%); and 6- to 12-year-olds (C, 98.7%; ASD, 93.9%). Coherence loadings demonstrated reduced short-distance and reduced, as well as increased, long-distance coherences for the ASD-groups, when compared to the controls. Average spectral loading per factor was wide (10.1 Hz).</p> <p>Conclusions</p> <p>Classification success suggests a stable coherence loading pattern that differentiates ASD- from C-group subjects. This might constitute an EEG coherence-based phenotype of childhood autism. The predominantly reduced short-distance coherences may indicate poor local network function. The increased long-distance coherences may represent compensatory processes or reduced neural pruning. The wide average spectral range of factor loadings may suggest over-damped neural networks.</p

A new measure for functional similarity of gene products based on Gene Ontology

BACKGROUND: Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. RESULTS: We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene products. The method relies on two semantic similarity measures; sim(Rel )and funSim. One measure (sim(Rel)) is applied in the comparison of the biological processes found in different groups of organisms. The other measure (funSim) is used to find functionally related gene products within the same or between different genomes. Results indicate that the method, in addition to being in good agreement with established sequence similarity approaches, also provides a means for the identification of functionally related proteins independent of evolutionary relationships. The method is also applied to estimating functional similarity between all proteins in Saccharomyces cerevisiae and to visualizing the molecular function space of yeast in a map of the functional space. A similar approach is used to visualize the functional relationships between protein families. CONCLUSION: The approach enables the comparison of the underlying molecular biology of different taxonomic groups and provides a new comparative genomics tool identifying functionally related gene products independent of homology. The proposed map of the functional space provides a new global view on the functional relationships between gene products or protein families

Multiple configurations of N-methylpyrrole binding on Si(111)-7×7

The adsorption configurations of N-methylpyrrole on Si(111)-7×7 were investigated using high-resolution electron energy-loss spectroscopy, x-ray photoelectron spectroscopy (XPS), scanning tunneling microscopy (STM), and density function theory calculations. Compared to physisorbed N-methylpyrrole, chemisorbed molecules present a different vibrational feature at 2886 cm-1 attributable to ν[(Si)Csp3-H] in addition to the vibrational features of (sp2)Cα-H (3106 cm-1), (sp2)Cβ-H (3050 cm-1), and C—H of CH3 (2944 cm-1) stretching modes, demonstrating the direct interaction between C=C bonds and Si(111)-7×7. The major change of N 1s XPS spectrum of N-methylpyrrole upon chemisorption strongly suggests the coexistence of two chemisorption states, further confirmed in the strong dependence of STM image features on the sample bias together with statistical analysis. The concurrent occurrence of [4+2] and [2+2] cycloadditions is proposed to account for these two adsorption configurations of N-methylpyrrole on Si(111)-7×

The Effect of a DNA Repair Gene on Cellular Invasiveness: Xrcc3 Over-Expression in Breast Cancer Cells

Over-expression of DNA repair genes has been associated with resistance to radiation and DNA-damage induced by chemotherapeutic agents such as cisplatin. More recently, based on the analysis of genome expression profiling, it was proposed that over-expression of DNA repair genes enhances the invasive behaviour of tumour cells. In this study we present experimental evidence utilizing functional assays to test this hypothesis. We assessed the effect of the DNA repair proteins known as X-ray complementing protein 3 (XRCC3) and RAD51, to the invasive behavior of the MCF-7 luminal epithelial-like and BT20 basal-like triple negative human breast cancer cell lines. We report that stable or transient over-expression of XRCC3 but not RAD51 increased invasiveness in both cell lines in vitro. Moreover, XRCC3 over-expressing MCF-7 cells also showed a higher tumorigenesis in vivo and this phenotype was associated with increased activity of the metalloproteinase MMP-9 and the expression of known modulators of cell-cell adhesion and metastasis such as CD44, ID-1, DDR1 and TFF1. Our results suggest that in addition to its' role in facilitating repair of DNA damage, XRCC3 affects invasiveness of breast cancer cell lines and the expression of genes associated with cell adhesion and invasion