Optical observations of the nearby galaxy IC342 with narrow band [SII] and Hα\alpha filters. I

We present observations of the portion of the nearby spiral galaxy IC342 using narrow band [SII] and H$\alpha$ filters. These observations were carried out in November 2011 with the 2m RCC telescope at Rozhen National Astronomical Observatory in Bulgaria. In this paper we report coordinates, diameters, H$\alpha$ and [SII] fluxes for 203 HII regions detected in two fields of view in IC342 galaxy. The number of detected HII regions is 5 times higher than previously known in these two parts of the galaxy.Comment: 9 pages, 3 tables, 4 figures. Table 3 corrected + small corrections in the tex

Can greater muscularity in larger individuals resolve the 3/4 power-law controversy when modelling maximum oxygen uptake?

BACKGROUND: The power function relationship, MR = a.m(b), between metabolic rate (MR) and body mass m has been the source of much controversy amongst biologists for many years. Various studies have reported mass exponents (b) greater than the anticipated 'surface-area' exponent 0.67, often closer to 0.75 originally identified by Kleiber. AIM: The study aimed to provide a biological explanation for these 'inflated' exponents when modelling maximum oxygen uptake (max), based on the observations from this and previous studies that larger individuals develop disproportionately more muscle mass in the arms and legs. RESEARCH DESIGN AND SUBJECTS: A cross-sectional study of 119 professional soccer players from Croatia aged 18-34 was carried out. RESULTS: Here we confirm that the power function relationship between max and body mass of the professional soccer players results in an 'inflated' mass exponent of 0.75 (95% confidence interval from 0.56 to 0.93), but also the larger soccer players have disproportionately greater leg muscle girths. When the analysis was repeated incorporating the calf and thigh muscle girths rather than body mass as predictor variables, the analysis not only explained significantly more of the variance in max, but the sum of the exponents confirmed a surface-area law. CONCLUSIONS: These findings confirm the pitfalls of fitting body-mass power laws and suggest using muscle-girth methodology as a more appropriate way to scale or normalize metabolic variables such as max for individuals of different body sizes

American power and identities in the age of Obama

Although the election of Barack Obama to the US presidency represents a landmark event in the history of that country, questions remain over its broader political significance. What is the likelihood of Obama's foreign and national security policies differing fundamentally from those of the Bush administrations Does Obama's election signal a post-racial phase in American national life What are the factors that suggest opportunities to change and expand American identities as opposed to those that limit Obama's sphere of action This article introduces the special issue and suggests that although Obama's room for manoeuvre is limited by legacies inherited from the Bush administration, Obama's own appointments to high office as well as other actions, despite the availability of alternative courses, indicate that he is not the transformational president he claimed to be. American identities, therefore, are deeply embedded and remain heavily imbued with racial, religious and imperial features

Predicting mostly disordered proteins by using structure-unknown protein data

BACKGROUND: Predicting intrinsically disordered proteins is important in structural biology because they are thought to carry out various cellular functions even though they have no stable three-dimensional structure. We know the structures of far more ordered proteins than disordered proteins. The structural distribution of proteins in nature can therefore be inferred to differ from that of proteins whose structures have been determined experimentally. We know many more protein sequences than we do protein structures, and many of the known sequences can be expected to be those of disordered proteins. Thus it would be efficient to use the information of structure-unknown proteins in order to avoid training data sparseness. We propose a novel method for predicting which proteins are mostly disordered by using spectral graph transducer and training with a huge amount of structure-unknown sequences as well as structure-known sequences. RESULTS: When the proposed method was evaluated on data that included 82 disordered proteins and 526 ordered proteins, its sensitivity was 0.723 and its specificity was 0.977. It resulted in a Matthews correlation coefficient 0.202 points higher than that obtained using FoldIndex, 0.221 points higher than that obtained using the method based on plotting hydrophobicity against the number of contacts and 0.07 points higher than that obtained using support vector machines (SVMs). To examine robustness against training data sparseness, we investigated the correlation between two results obtained when the method was trained on different datasets and tested on the same dataset. The correlation coefficient for the proposed method is 0.14 higher than that for the method using SVMs. When the proposed SGT-based method was compared with four per-residue predictors (VL3, GlobPlot, DISOPRED2 and IUPred (long)), its sensitivity was 0.834 for disordered proteins, which is 0.052–0.523 higher than that of the per-residue predictors, and its specificity was 0.991 for ordered proteins, which is 0.036–0.153 higher than that of the per-residue predictors. The proposed method was also evaluated on data that included 417 partially disordered proteins. It predicted the frequency of disordered proteins to be 1.95% for the proteins with 5%–10% disordered sequences, 1.46% for the proteins with 10%–20% disordered sequences and 16.57% for proteins with 20%–40% disordered sequences. CONCLUSION: The proposed method, which utilizes the information of structure-unknown data, predicts disordered proteins more accurately than other methods and is less affected by training data sparseness

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

Health-related quality of life in patients with surgically treated lumbar disc herniation: 2- and 7-year follow-up of 117 patients

To access publisher full text version of this article. Please click on the hyperlink in Additional Links field.BACKGROUND AND PURPOSE: Health-related quality of life (HRQoL) instruments have been of increasing interest for evaluation of medical treatments over the past 10-15 years. In this prospective, long-term follow-up study we investigated the influence of preoperative factors and the change in HRQoL over time after lumbar disc herniation surgery. METHODS: 117 patients surgically treated for lumbar disc herniation (L4-L5 or L5-S1) were evaluated with a self-completion HRQoL instrument (EQ-5D) preoperatively, after 2 years (96 patients) and after 7 years (89 patients). Baseline data (age, sex, duration of leg pain, surgical level) and degree of leg and back pain (VAS) were obtained preoperatively. The mean age was 39 (18-66) years, 54% were men, and the surgical level was L5-S1 in 58% of the patients. The change in EQ-5D score at the 2-year follow-up was analyzed by testing for correlation and by using a multiple regression model including all baseline factors (age, sex, duration of pain, degree of leg and back pain, and baseline EQ-5D score) as potential predictors. RESULTS: 85% of the patients reported improvement in EQ-5D two years after surgery and this result remained at the long-term follow-up. The mean difference (change) between the preoperative EQ-5D score and the 2-year and 7-year scores was 0.59 (p < 0.001) and 0.62 (p < 0.001), respectively. However, the HRQoL for this patient group did not reach the mean level of previously reported values for a normal population of the same age range at any of the follow-ups. The changes in EQ-5D score between the 2- and 7-year follow-ups were not statistically significant (mean change 0.03, p = 0.2). There was a correlation between baseline leg pain and the change in EQ-5D at the 2-year (r = 0.33, p = 0.002) and 7-year follow-up (r = 0.23, p = 0.04). However, when using regression analysis the only statistically significant predictor for change in EQ-5D was baseline EQ-5D score. INTERPRETATION: Our findings suggest that HRQoL (as measured by EQ-5D) improved 2 years after lumbar disc herniation surgery, but there was no further improvement after 5 more years. Low quality of life and severe leg pain at baseline are important predictors of improvement in quality of life after lumbar disc herniation surgery.Marianne och Marcus Wallenberg Foundation ALF Vastra Gotaland. Gothenburg Medical Association. Swedish Society of Medicine. Felix Neubergh Foundation

Utilizing associational resistance for biocontrol: impacted by temperature, supported by indirect defence

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Interrogating domain-domain interactions with parsimony based approaches

<p>Abstract</p> <p>Background</p> <p>The identification and characterization of interacting domain pairs is an important step towards understanding protein interactions. In the last few years, several methods to predict domain interactions have been proposed. Understanding the power and the limitations of these methods is key to the development of improved approaches and better understanding of the nature of these interactions.</p> <p>Results</p> <p>Building on the previously published Parsimonious Explanation method (PE) to predict domain-domain interactions, we introduced a new Generalized Parsimonious Explanation (GPE) method, which (i) adjusts the granularity of the domain definition to the granularity of the input data set and (ii) permits domain interactions to have different costs. This allowed for preferential selection of the so-called "co-occurring domains" as possible mediators of interactions between proteins. The performance of both variants of the parsimony method are competitive to the performance of the top algorithms for this problem even though parsimony methods use less information than some of the other methods. We also examined possible enrichment of co-occurring domains and homo-domains among domain interactions mediating the interaction of proteins in the network. The corresponding study was performed by surveying domain interactions predicted by the GPE method as well as by using a combinatorial counting approach independent of any prediction method. Our findings indicate that, while there is a considerable propensity towards these special domain pairs among predicted domain interactions, this overrepresentation is significantly lower than in the iPfam dataset.</p> <p>Conclusion</p> <p>The Generalized Parsimonious Explanation approach provides a new means to predict and study domain-domain interactions. We showed that, under the assumption that all protein interactions in the network are mediated by domain interactions, there exists a significant deviation of the properties of domain interactions mediating interactions in the network from that of iPfam data.</p