Primary tubercular liver abscess in an immunocompetent adult: a case report

<p>Abstract</p> <p>Introduction</p> <p>Isolated primary tubercular abscess is one of the rare forms of extrapulmonary tuberculosis. A greater awareness of this rare clinical entity may help in commencing specific evidence-based therapy quickly and preventing undue morbidity and mortality.</p> <p>Case presentation</p> <p>A 30-year-old man, of Asian origin, developed a hepatic tubercular abscess which was not associated with any pulmonary or gastrointestinal tract foci of tuberculosis. An ultrasonogram of the abdomen showed an abscess in the right lobe of his liver which was initially diagnosed as an amoebic liver abscess. Subsequently, the pus from the lesion yielded <it>Mycobacterium tuberculosis </it>using the BACTEC TB 460 instrument and <it>Mycobacterium tuberculosis </it>deoxyribonucleic acid by polymerase chain reaction. The patient was started on systemic antitubercular therapy to which he responded favorably.</p> <p>Conclusion</p> <p>This report emphasizes the fact that, although a tuberculous liver abscess is a very rare entity, it should be included in the differential diagnosis of unknown hepatic mass lesions.</p

bioNMF: a versatile tool for non-negative matrix factorization in biology

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at

On the complexity of resource-bounded logics

We revisit decidability results for resource-bounded logics and use decision problems for vector addition systems with states (VASS) to characterise the complexity of (decidable) model-checking problems. We show that the model-checking problem for the logic RB+-ATL is 2EXPTIME-complete by using recent results on alternating VASS. In addition, we establish that the model-checking problem for RBTL is decidable and has the same complexity as for RBTL* (the extension of RBTL with arbitrary path formulae), namely EXPSPACE-complete, proving a new decidability result as a by-product of the approach. Finally, we establish that the model-checking problem for RB+-ATL* is decidable by a reduction to parity games, and show how to synthesise values for resource parameters

Kerr/CFT, dipole theories and nonrelativistic CFTs

We study solutions of type IIB supergravity which are SL(2,R) x SU(2) x U(1)^2 invariant deformations of AdS_3 x S^3 x K3 and take the form of products of self-dual spacelike warped AdS_3 and a deformed three-sphere. One of these backgrounds has been recently argued to be relevant for a derivation of Kerr/CFT from string theory, whereas the remaining ones are holographic duals of two-dimensional dipole theories and their S-duals. We show that each of these backgrounds is holographically dual to a deformation of the DLCQ of the D1-D5 CFT by a specific supersymmetric (1,2) operator, which we write down explicitly in terms of twist operators at the free orbifold point. The deforming operator is argued to be exactly marginal with respect to the zero-dimensional nonrelativistic conformal (or Schroedinger) group - which is simply SL(2,R)_L x U(1)_R. Moreover, in the supergravity limit of large N and strong coupling, no other single-trace operators are turned on. We thus propose that the field theory duals to the backgrounds of interest are nonrelativistic CFTs defined by adding the single Schroedinger-invariant (1,2) operator mentioned above to the original CFT action. Our analysis indicates that the rotating extremal black holes we study are best thought of as finite right-moving temperature (non-supersymmetric) states in the above-defined supersymmetric nonrelativistic CFT and hints towards a more general connection between Kerr/CFT and two-dimensional non-relativistic CFTs.Comment: 48+8 pages, 4 figures; minor corrections and references adde

Can type of school be used as an alternative indicator of socioeconomic status in dental caries studies? A cross-sectional study

<p>Abstract</p> <p>Background</p> <p>Despite the importance of collecting individual data of socioeconomic status (SES) in epidemiological oral health surveys with children, this procedure relies on the parents as respondents. Therefore, type of school (public or private schools) could be used as an alternative indicator of SES, instead of collecting data individually. The aim of this study was to evaluate the use of the variable type of school as an indicator of socioeconomic status as a substitute of individual data in an epidemiological survey about dental caries in Brazilian preschool children.</p> <p>Methods</p> <p>This study followed a cross-sectional design, with a random sample of 411 preschool children aged 1 to 5 years, representative of Catalão, Brazil. A calibrated examiner evaluated the prevalence of dental caries and parents or guardians provided information about several individual socioeconomic indicators by means of a semi-structured questionnaire. A multilevel approach was used to investigate the association among individual socioeconomic variables, as well as the type of school, and the outcome.</p> <p>Results</p> <p>When all significant variables in the univariate analysis were used in the multiple model, only mother's schooling and household income (individual socioeconomic variables) presented significant associations with presence of dental caries, and the type of school was not significantly associated. However, when the type of school was used alone, children of public school presented significantly higher prevalence of dental caries than those enrolled in private schools.</p> <p>Conclusions</p> <p>The type of school used as an alternative indicator for socioeconomic status is a feasible predictor for caries experience in epidemiological dental caries studies involving preschool children in Brazilian context.</p

Prediction of function in daily life following multidisciplinary rehabilitation for individuals with chronic musculoskeletal pain; a prospective study

Background: The prevalence of chronic musculoskeletal pain is high, with widespread negative economic, psychological, and social consequences for the individual. It is therefore important to find ways to predict the outcome of rehabilitation programmes in terms of function in daily life. The aims of this study were to investigate the improvements over time from multidisciplinary rehabilitation in terms of pain and function, and analyse the relative impact of individual and psychosocial factors as predictors of function in daily life in individuals with chronic musculoskeletal pain. Methods: A prospective study was conducted among one hundred and forty three (N = 143) musculoskeletal pain patients. Measures of pain, function, and functional health status were obtained at baseline, after 5 weeks of intensive training, at the end of the 57-week rehabilitation programme, and at a 1 year follow-up, using validated self-administrated measures. Linear regression analysis was applied to investigate the relative impact of musculoskeletal pain, individual- , and psychosocial factors in function. Results: The participants studied showed a significant increase in function during the 57 weeks rehabilitation period. There was also a significant increase in function from the end of the rehabilitation period (57th week) to the one year follow-up measures. Pain intensity associated significantly with pain experience over all measurement periods. High levels of pain intensity (β = .42**) and pain experience (β = .37*), and poor psychological capacity (β = -.68*) at baseline, as well as poor physiological capacity (β = -.44**) and high levels of anxiety (β = .48**) and depression (β = .58***) at the end of the rehabilitation program were the most important prognostic factors of variance in functioning over the 4 measurement periods. Conclusion: The data suggest that physical capacity, emotional distress and coping skills should be priority areas in rehabilitation programmes to improve functioning in daily life

A literature-based similarity metric for biological processes

BACKGROUND: Recent analyses in systems biology pursue the discovery of functional modules within the cell. Recognition of such modules requires the integrative analysis of genome-wide experimental data together with available functional schemes. In this line, methods to bridge the gap between the abstract definitions of cellular processes in current schemes and the interlinked nature of biological networks are required. RESULTS: This work explores the use of the scientific literature to establish potential relationships among cellular processes. To this end we haveused a document based similarity method to compute pair-wise similarities of the biological processes described in the Gene Ontology (GO). The method has been applied to the biological processes annotated for the Saccharomyces cerevisiae genome. We compared our results with similarities obtained with two ontology-based metrics, as well as with gene product annotation relationships. We show that the literature-based metric conserves most direct ontological relationships, while reveals biologically sounded similarities that are not obtained using ontology-based metrics and/or genome annotation. CONCLUSION: The scientific literature is a valuable source of information from which to compute similarities among biological processes. The associations discovered by literature analysis are a valuable complement to those encoded in existing functional schemes, and those that arise by genome annotation. These similarities can be used to conveniently map the interlinked structure of cellular processes in a particular organism

Mycobacterium tuberculosis ecology in Venezuela: epidemiologic correlates of common spoligotypes and a large clonal cluster defined by MIRU-VNTR-24

<p>Abstract</p> <p>Background</p> <p>Tuberculosis remains an endemic public health problem, but the ecology of the TB strains prevalent, and their transmission, can vary by country and by region. We sought to investigate the prevalence of <it>Mycobacterium tuberculosis </it>strains in different regions of Venezuela. A previous study identified the most prevalent strains in Venezuela but did not show geographical distribution nor identify clonal genotypes. To better understand local strain ecology, we used spoligotyping to analyze 1298 <it>M. tuberculosis </it>strains isolated in Venezuela from 1997 to 2006, predominantly from two large urban centers and two geographically distinct indigenous areas, and then studied a subgroup with MIRU-VNTR 24 loci.</p> <p>Results</p> <p>The distribution of spoligotype families is similar to that previously reported for Venezuela and other South American countries: LAM 53%, T 10%, Haarlem 5%, S 1.9%, X 1.2%, Beijing 0.4%, and EAI 0.2%. The six most common shared types (SIT's 17, 93, 605, 42, 53, 20) accounted for 49% of the isolates and were the most common in almost all regions, but only a minority were clustered by MIRU-VNTR 24. One exception was the third most frequent overall, SIT 605, which is the most common spoligotype in the state of Carabobo but infrequent in other regions. MIRU-VNTR homogeneity suggests it is a clonal group of strains and was named the "Carabobo" genotype. Epidemiologic comparisons showed that patients with SIT 17 were younger and more likely to have had specimens positive for Acid Fast Bacilli on microscopy, and patients with SIT 53 were older and more commonly smear negative. Female TB patients tended to be younger than male patients. Patients from the high incidence, indigenous population in Delta Amacuro state were younger and had a nearly equal male:female distribution.</p> <p>Conclusion</p> <p>Six SIT's cause nearly half of the cases of tuberculosis in Venezuela and dominate in nearly all regions. Strains with SIT 17, the most common pattern overall may be more actively transmitted and SIT 53 strains may be less virulent and associated with reactivation of past infections in older patients. In contrast to other common spoligotypes, strains with SIT 605 form a clonal group centered in the state of Carabobo.</p

Secretion of Novel SEL1L Endogenous Variants Is Promoted by ER Stress/UPR via Endosomes and Shed Vesicles in Human Cancer Cells

We describe here two novel endogenous variants of the human endoplasmic reticulum (ER) cargo receptor SEL1LA, designated p38 and p28. Biochemical and RNA interference studies in tumorigenic and non-tumorigenic cells indicate that p38 and p28 are N-terminal, ER-anchorless and more stable relative to the canonical transmembrane SEL1LA. P38 is expressed and constitutively secreted, with increase after ER stress, in the KMS11 myeloma line and in the breast cancer lines MCF7 and SKBr3, but not in the non-tumorigenic breast epithelial MCF10A line. P28 is detected only in the poorly differentiated SKBr3 cell line, where it is secreted after ER stress. Consistently with the presence of p38 and p28 in culture media, morphological studies of SKBr3 and KMS11 cells detect N-terminal SEL1L immunolabeling in secretory/degradative compartments and extracellularly-released membrane vesicles. Our findings suggest that the two new SEL1L variants are engaged in endosomal trafficking and secretion via vesicles, which could contribute to relieve ER stress in tumorigenic cells. P38 and p28 could therefore be relevant as diagnostic markers and/or therapeutic targets in cancer