Identification of DNA-binding proteins using support vector machines and evolutionary profiles

<p>Abstract</p> <p>Background</p> <p>Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation, as these proteins play a crucial role in gene-regulation. In this paper, we developed various SVM modules for predicting DNA-binding domains and proteins. All models were trained and tested on multiple datasets of non-redundant proteins.</p> <p>Results</p> <p>SVM models have been developed on DNAaset, which consists of 1153 DNA-binding and equal number of non DNA-binding proteins, and achieved the maximum accuracy of 72.42% and 71.59% using amino acid and dipeptide compositions, respectively. The performance of SVM model improved from 72.42% to 74.22%, when evolutionary information in form of PSSM profiles was used as input instead of amino acid composition. In addition, SVM models have been developed on DNAset, which consists of 146 DNA-binding and 250 non-binding chains/domains, and achieved the maximum accuracy of 79.80% and 86.62% using amino acid composition and PSSM profiles. The SVM models developed in this study perform better than existing methods on a blind dataset.</p> <p>Conclusion</p> <p>A highly accurate method has been developed for predicting DNA-binding proteins using SVM and PSSM profiles. This is the first study in which evolutionary information in form of PSSM profiles has been used successfully for predicting DNA-binding proteins. A web-server DNAbinder has been developed for identifying DNA-binding proteins and domains from query amino acid sequences <url>http://www.imtech.res.in/raghava/dnabinder/</url>.</p

Biophysical studies in polymer therapeutics: the interactions of anionic and cationic PAMAM dendrimers with lipid monolayers

Understanding how polymers interact with biological membranes is important for the development of polymer based therapeutics and wider biomedical applications. Here, biophysical methods (surface pressure measurements, external reflection FTIR) have been used to investigate the interaction between PAMAM dendrimers (Generation 5 or 4.5) and anionic (DPPG) or zwitterionic (DPPC) model membranes. We observed a concentration-dependent binding behaviour of both PAMAM species to both model membranes; however, equivalent levels of penetration into DPPC monolayers required approximately 10-fold higher dendrimer concentrations than for penetration into DPPG monolayers. Overall, the anionic PAMAM G4.5 showed a slightly better penetration ability which could be caused by repulsive forces towards the lipid layers. In comparison, increasing concentration of cationic PAMAM G5 leads to saturation of adsorption at the anionic lipid surface before penetration into the lipid layer likely driven by electrostatic attraction. Our studies also showed that physiologically relevant concentrations of sodium chloride (144 mM) decreased PAMAM penetration into DPPG monolayers but did not significantly affect the dendrimer-DPPC interaction. These results provide an insight into the mechanism of interaction between charged dendritic polymers with a lipid interface and show that the nature of such interactions are affected by lipid headgroup, dendrimer charge and solution salinity

Beyond inpatient and outpatient care: alternative model for hypertension management

Hypertension is a major contributor to worldwide cardiovascular mortality, however, only one-third of patients with hypertension have their blood pressure treated to guideline recommended levels. To improve hypertension control, there may need to be a fundamental shift in care delivery, one that is population-based and simultaneously addresses patient, provider and system barriers. One potential approach is home-based disease management, based on the triad of home monitoring, team care, and patient self-care. Although there may be challenges to achieving the vision of home-based disease management, there are tremendous potential benefits of such an approach for reducing the global burden of cardiovascular disease

Stringy KLT relations, global symmetries, and E_7(7) violation

We study consequences of the Kawai-Lewellen-Tye (KLT) relations applied to tree amplitudes in toroidal compactifications of string theory to four dimensions. The closed string tree amplitudes with massless external states respect a global SU(4)xSU(4) symmetry, which is enhanced to the SU(8) R-symmetry of N=8 supergravity in the field theory limit. Our analysis focuses on two aspects: (i) We provide a detailed account of the simplest SU(8)-violating amplitudes. We classify these processes and derive explicit superamplitudes for all local 5- and 6-point operators with SU(4)xSU(4) symmetry at order alpha'^3. Their origin is the dilatonic operator exp(-6 phi) R^4 in the closed-string effective action. (ii) We expand the 6-point closed string tree amplitudes to order alpha'^3 and use two different methods to isolate the SU(8)-singlet contribution from exp(-6 phi) R^4. This allows us to extract the matrix elements of the unique SU(8)-invariant supersymmetrization of R^4. Their single-soft scalar limits are non-vanishing. This demonstrates that the N=8 supergravity candidate counterterm R^4 is incompatible with continuous E_7(7) symmetry. From the soft scalar limits, we reconstruct to quadratic order the SU(8)-invariant function of scalars that multiplies R^4, and show that it satisfies the Laplace eigenvalue equation derived recently from supersymmetry and duality constraints.Comment: 23 pages, published versio

The influence of magnetic anisotropy on the Zeeman spectra of lanthanide doped nanoparticles

High-resolution infra-red spectra of KY3F10 nanoparticles doped with Nd3+ and Er3+ are measured in magnetic fields of up to 4 T. A simple model of the magnetic splittings of the ground and excited states is used to show that the presence or absence of observable splittings depends on the anisotropy of the response to the magnetic field. Detailed crystal-field calculations accurately model the spectra, including nonlinear effects

Protocol for the "Michigan Awareness Control Study": A prospective, randomized, controlled trial comparing electronic alerts based on bispectral index monitoring or minimum alveolar concentration for the prevention of intraoperative awareness

<p>Abstract</p> <p>Background</p> <p>The incidence of intraoperative awareness with explicit recall is 1-2/1000 cases in the United States. The Bispectral Index monitor is an electroencephalographic method of assessing anesthetic depth that has been shown in one prospective study to reduce the incidence of awareness in the high-risk population. In the B-Aware trial, the number needed to treat in order to prevent one case of awareness in the high-risk population was 138. Since the number needed to treat and the associated cost of treatment would be much higher in the general population, the efficacy of the Bispectral Index monitor in preventing awareness in all anesthetized patients needs to be clearly established. This is especially true given the findings of the B-Unaware trial, which demonstrated no significant difference between protocols based on the Bispectral Index monitor or minimum alveolar concentration for the reduction of awareness in high risk patients.</p> <p>Methods/Design</p> <p>To evaluate efficacy in the general population, we are conducting a prospective, randomized, controlled trial comparing the Bispectral Index monitor to a non-electroencephalographic gauge of anesthetic depth. The total recruitment for the study is targeted for 30,000 patients at both low and high risk for awareness. We have developed a novel algorithm that is capable of real-time analysis of our electronic perioperative information system. In one arm of the study, anesthesia providers will receive an electronic page if the Bispectral Index value is >60. In the other arm of the study, anesthesia providers will receive a page if the age-adjusted minimum alveolar concentration is <0.5. Our minimum alveolar concentration algorithm is sensitive to both inhalational anesthetics and intravenous sedative-hypnotic agents.</p> <p>Discussion</p> <p>Awareness during general anesthesia is a persistent problem and the role of the Bispectral Index monitor in its prevention is still unclear. The Michigan Awareness Control Study is the largest prospective trial of awareness prevention ever conducted.</p> <p>Trial Registration</p> <p>Clinical Trial NCT00689091</p

Non-invasive MR imaging of inflammation in a patient with both asymptomatic carotid atheroma and an abdominal aortic aneurysm: a case report.

Inflammation is a recognized risk factor for the vulnerable atherosclerotic plaque. USPIO-enhanced MRI imaging is a promising non-invasive method to identify high-risk atheromatous plaque inflammation in vivo in humans, in which areas of focal signal loss on MR images have been shown to correspond to the location of activated macrophages, typically at the shoulder regions of the plaque. This is the first report in humans describing simultaneous USPIO uptake within atheroma in two different arterial territories and again emphasises that atherosclerosis is a truly systemic disease. With further work, USPIO-enhanced MR imaging may be useful in identifying inflamed vulnerable atheromatous plaques in vivo, so refining patient selection for intervention and allowing appropriate early aggressive pharmacotherapy to prevent plaque rupture.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

Extraction of bodily features for gait recognition and gait attractiveness evaluation

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s11042-012-1319-2. Copyright @ 2012 Springer.Although there has been much previous research on which bodily features are most important in gait analysis, the questions of which features should be extracted from gait, and why these features in particular should be extracted, have not been convincingly answered. The primary goal of the study reported here was to take an analytical approach to answering these questions, in the context of identifying the features that are most important for gait recognition and gait attractiveness evaluation. Using precise 3D gait motion data obtained from motion capture, we analyzed the relative motions from different body segments to a root marker (located on the lower back) of 30 males by the fixed root method, and compared them with the original motions without fixing root. Some particular features were obtained by principal component analysis (PCA). The left lower arm, lower legs and hips were identified as important features for gait recognition. For gait attractiveness evaluation, the lower legs were recognized as important features.Dorothy Hodgkin Postgraduate Award and HEFCE

Solution to the Ward Identities for Superamplitudes

Supersymmetry and R-symmetry Ward identities relate on-shell amplitudes in a supersymmetric field theory. We solve these Ward identities for (Next-to)^K MHV amplitudes of the maximally supersymmetric N=4 and N=8 theories. The resulting superamplitude is written in a new, manifestly supersymmetric and R-invariant form: it is expressed as a sum of very simple SUSY and SU(N)_R-invariant Grassmann polynomials, each multiplied by a "basis amplitude". For (Next-to)^K MHV n-point superamplitudes the number of basis amplitudes is equal to the dimension of the irreducible representation of SU(n-4) corresponding to the rectangular Young diagram with N columns and K rows. The linearly independent amplitudes in this algebraic basis may still be functionally related by permutation of momenta. We show how cyclic and reflection symmetries can be used to obtain a smaller functional basis of color-ordered single-trace amplitudes in N=4 gauge theory. We also analyze the more significant reduction that occurs in N=8 supergravity because gravity amplitudes are not ordered. All results are valid at both tree and loop level.Comment: 29 pages, published versio