Div-BLAST: Diversification of sequence search results

Cataloged from PDF version of article.Sequence similarity tools, such as BLAST, seek sequences most similar to a query from a database of sequences. They return results significantly similar to the query sequence and that are typically highly similar to each other. Most sequence analysis tasks in bioinformatics require an exploratory approach, where the initial results guide the user to new searches. However, diversity has not yet been considered an integral component of sequence search tools for this discipline. Some redundancy can be avoided by introducing non-redundancy during database construction, but it is not feasible to dynamically set a level of non-redundancy tailored to a query sequence. We introduce the problem of diverse search and browsing in sequence databases that produce non-redundant results optimized for any given query. We define diversity measures for sequences and propose methods to obtain diverse results extracted from current sequence similarity search tools. We also propose a new measure to evaluate the diversity of a set of sequences that is returned as a result of a sequence similarity query. We evaluate the effectiveness of the proposed methods in post-processing BLAST and PSI-BLAST results. We also assess the functional diversity of the returned results based on available Gene Ontology annotations. Additionally, we include a comparison with a current redundancy elimination tool, CD-HIT. Our experiments show that the proposed methods are able to achieve more diverse yet significant result sets compared to static non-redundancy approaches. In both sequence-based and functional diversity evaluation, the proposed diversification methods significantly outperform original BLAST results and other baselines. A web based tool implementing the proposed methods, Div-BLAST, can be accessed at cedar.cs.bilkent.edu.tr/Div-BLAS

Binomial Ideals and Congruences on Nn

Producción CientíficaA congruence on Nn is an equivalence relation on Nn that is compatible with the additive structure. If k is a field, and I is a binomial ideal in k[X1,…,Xn] (that is, an ideal generated by polynomials with at most two terms), then I induces a congruence on Nn by declaring u and v to be equivalent if there is a linear combination with nonzero coefficients of Xu and Xv that belongs to I. While every congruence on Nn arises this way, this is not a one-to-one correspondence, as many binomial ideals may induce the same congruence. Nevertheless, the link between a binomial ideal and its corresponding congruence is strong, and one may think of congruences as the underlying combinatorial structures of binomial ideals. In the current literature, the theories of binomial ideals and congruences on Nn are developed separately. The aim of this survey paper is to provide a detailed parallel exposition, that provides algebraic intuition for the combinatorial analysis of congruences. For the elaboration of this survey paper, we followed mainly (Kahle and Miller Algebra Number Theory 8(6):1297–1364, 2014) with an eye on Eisenbud and Sturmfels (Duke Math J 84(1):1–45, 1996) and Ojeda and Piedra Sánchez (J Symbolic Comput 30(4):383–400, 2000).National Science Foundation (grant DMS-1500832)Ministerio de Economía, Industria y Competitividad (project MTM2015-65764-C3-1)Junta de Extremadura (grupo de investigación FQM-024

Ultraluminous Infrared Galaxies in the AKARI All Sky Survey

We present a new catalog of 118 Ultraluminous Infrared Galaxies (ULIRGs) and one Hyperluminous Infrared Galaxy (HLIRG) by crossmatching AKARI all-sky survey with the Sloan Digital Sky Survey Data Release 10 (SDSS DR10) and the Final Data Release of the Two-Degree Field Galaxy Redshift Survey (2dFGRS). 40 of the ULIRGs and one HLIRG are new identifications. We find that ULIRGs are interacting pair galaxies or ongoing/post mergers. This is consistent with the widely accepted view: ULIRGs are major mergers of disk galaxies. We confirm the previously known positive trend between the AGN fraction and IR luminosity. We show that ULIRGs have a large off-set from the 'main sequence' up to z~1; their off-set from the z~2 'main sequence' is relatively smaller. We find a consistent result with the previous studies showing that compared to local star forming SDSS galaxies of similar mass, local ULIRGs have lower oxygen abundances. We for the first time demonstrate that ULIRGs follow the fundamental metallicity relation (FMR). The scatter of ULIRGs around the FMR (0.09 dex - 0.5 dex) is comparable with the scatter of z~2-3 galaxies. Their optical colors show that ULIRGs are mostly blue galaxies and this agrees with previous findings. We provide the largest local (0.050 < z < 0.487) ULIRG catalog with stellar masses, SFRs, gas metallicities and optical colors. Our catalog provides us active galaxies analogous to high-z galaxies in the local Universe where they can be rigorously scrutinized.Comment: 31 pages, 19 figure

Role of peripheral quantitative computed tomography in identifying disuse osteoporosis in paraplegia

Objective: Disuse osteoporosis is a major long-term health consequence of spinal cord injury (SCI) that still needs to be addressed. Its management in SCI should begin with accurate diagnosis, followed by targeted treatments in the most vulnerable subgroups. We present data quantifying disuse osteoporosis in a cross-section of the Scottish paraplegic population to identify subgroups with lowest bone mineral density (BMD). Materials and Methods: Forty-seven people with chronic SCI at levels T2-L2 were scanned using peripheral Quantitative Computed Tomography (pQCT) at four tibial sites and two femoral sites, at the Queen Elizabeth National Spinal Injuries Unit, Glasgow (U.K.). At the distal epiphyses, trabecular BMD (BMDtrab), total BMD, total bone cross-sectional area (CSA), and bone mineral content (BMC) were determined. In the diaphyses, cortical BMD, total bone CSA, cortical CSA, and BMC were calculated. Bone, muscle and fat CSAs were estimated in the lower leg and thigh. Results: BMDtrab decreased exponentially with time since injury, at different rates in the tibia and femur. At most sites, female paraplegics had significantly lower BMC, total bone CSA and muscle CSA than male paraplegics. Subjects with lumbar SCI tended to have lower bone values and smaller muscle CSAs than in thoracic SCI. Conclusion: At the distal epiphyses of the tibia and femur, there is generally a rapid and extensive reduction in BMDtrab after SCI. Female subjects, and those with lumbar SCI, tend to have lower bone values than males or those with thoracic SCI, respectively. Keywords: Bone loss, osteoporosis, paraplegia, peripheral Quantitative Computed Tomography, spinal cord injur

Comparison of pQCT parameters between ulna and radius in retired elite gymnasts : the skeletal benefits associated with long-term gymnastics are bone- and site-specific

Objectives: To compare the skeletal benefits associated with gymnastics between ulna and radius. Methods: 19 retired artistic gymnasts, aged 18-36 years, were compared to 24 sedentary women. Bone mineral content (BMC), total and cortical bone area (ToA, CoA), trabecular and cortical volumetric density (TrD, CoD) and cortical thickness (CoTh) were measured by pQCT at the 4% and 66% forearm. Results: At the 4% site, BMC and ToA were more than twice greater at the radius than ulna whereas at the 66% site, BMC, ToA, CoA, CoTh and SSIpol were 20 to 51% greater at the ulna than radius in both groups (p&lt;0.0001). At the 4% site, the skeletal benefits in BMC of the retired gymnasts over the non-gymnasts were 1.9 times greater at the radius than ulna (p&lt;0.001), with enlarged bone size at the distal radius only. In contrast, the skeletal benefits at the 66% site were twice greater at the ulna than radius for BMC and CoA (p&lt;0.01).Conclusion: Whereas the skeletal benefits associated with long-term gymnastics were greater at the radius than ulna in the distal forearm, the reverse was found in the proximal forearm, suggesting both bones should be analysed when investigating forearm strength.<br /

Editorial: Green chemistry biocatalysis

Editorial on the Research Topic: Green chemistry biocatalysi

Solution of the Bosonic and Algebraic Hamiltonians by using AIM

We apply the notion of asymptotic iteration method (AIM) to determine eigenvalues of the bosonic Hamiltonians that include a wide class of quantum optical models. We consider solutions of the Hamiltonians, which are even polynomials of the fourth order with the respect to Boson operators. We also demonstrate applicability of the method for obtaining eigenvalues of the simple Lie algebraic structures. Eigenvalues of the multi-boson Hamiltonians have been obtained by transforming in the form of the single boson Hamiltonian in the framework of AIM

POEMMA: Probe Of Extreme Multi-Messenger Astrophysics

The Probe Of Extreme Multi-Messenger Astrophysics (POEMMA) mission is being designed to establish charged-particle astronomy with ultra-high energy cosmic rays (UHECRs) and to observe cosmogenic tau neutrinos (CTNs). The study of UHECRs and CTNs from space will yield orders-of-magnitude increase in statistics of observed UHECRs at the highest energies, and the observation of the cosmogenic flux of neutrinos for a range of UHECR models. These observations should solve the long-standing puzzle of the origin of the highest energy particles ever observed, providing a new window onto the most energetic environments and events in the Universe, while studying particle interactions well beyond accelerator energies. The discovery of CTNs will help solve the puzzle of the origin of UHECRs and begin a new field of Astroparticle Physics with the study of neutrino properties at ultra-high energies.Comment: 8 pages, in the Proceedings of the 35th International Cosmic Ray Conference, ICRC217, Busan, Kore

Neuroactive steroids in depression and anxiety disorders: Clinical studies

Certain neuroactive steroids modulate ligand-gated ion channels via non-genomic mechanisms. Especially 3 alpha-reduced pregnane steroids are potent positive allosteric modulators of the gamma-aminobutyric acid type A (GABA(A)) receptor. During major depression, there is a disequilibrium of 3 alpha-reduced neuroactive steroids, which is corrected by clinically effective pharmacological treatment. To investigate whether these alterations are a general principle of successful antidepressant treatment, we studied the impact of nonpharmacological treatment options on neuroactive steroid concentrations during major depression. Neither partial sleep deprivation, transcranial magnetic stimulation, nor electroconvulsive therapy affected neuroactive steroid levels irrespectively of the response to these treatments. These studies suggest that the changes in neuroactive steroid concentrations observed after antidepressant pharmacotherapy more likely reflect distinct pharmacological properties of antidepressants rather than the clinical response. In patients with panic disorder, changes in neuroactive steroid composition have been observed opposite to those seen in depression. However, during experimentally induced panic induction either with cholecystokinine-tetrapeptide or sodium lactate, there was a pronounced decline in the concentrations of 3 alpha-reduced neuroactive steroids in patients with panic disorder, which might result in a decreased GABAergic tone. In contrast, no changes in neuroactive steroid concentrations could be observed in healthy controls with the exception of 3 alpha,5 alpha-tetrahydrodeoxycorticosterone. The modulation of GABA(A) receptors by neuroactive steroids might contribute to the pathophysiology of depression and anxiety disorders and might offer new targets for the development of novel anxiolytic compounds. Copyright (c) 2006 S. Karger AG, Basel

Thoracic and Lumbar Vertebral Bone Mineral Density Changes in a Natural Occurring Dog Model of Diffuse Idiopathic Skeletal Hyperostosis

Ankylosing spinal disorders can be associated with alterations in vertebral bone mineral density (BMD). There is however controversy about vertebral BMD in patients wuse idiopathic skeletal hyperostosis (DISH). DISH in Boxer dogs has been considered a natural occurring disease model for DISH in people. The purpose of this study was to compare vertebral BMD between Boxers with and without DISH. Fifty-nine Boxers with (n=30) or without (n=29) DISH that underwent computed tomography were included. Vertebral BMD was calculated for each thoracic and lumbar vertebra by using an earlier reported and validated protocol. For each vertebral body, a region of interest was drawn on the axial computed tomographic images at three separate locations: immediately inferior to the superior end plate, in the middle of the vertebral body, and superior to the inferior end plate. Values from the three axial slices were averaged to give a mean Hounsfield Unit value for each vertebral body. Univariate statistical analysis was performed to identify factors to be included in a multivariate model. The multivariate model including all dogs demonstrated that vertebral DISH status (Coefficient 24.63; 95% CI 16.07 to 33.19; p <0.001), lumbar vertebrae (Coefficient -17.25; 95% CI -23.42 to -11.09; p < 0.01), and to a lesser extent higher age (Coefficient -0.56; 95% CI -1.07 to -0.05; p = 0.03) were significant predictors for vertebral BMD. When the multivariate model was repeated using only dogs with DISH, vertebral DISH status (Coefficient 20.67; 95% CI, 10.98 to 30.37; p < 0.001) and lumbar anatomical region (Coefficient -38.24; 95% CI, -47.75 to -28.73; p < 0.001) were again predictors for vertebral BMD but age was not. The results of this study indicate that DISH can be associated with decreased vertebral BMD. Further studies are necessary to evaluate the clinical importance and pathophysiology of this finding