Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty

Background: Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise statistical significance with database statistical significance was conducted. In this paper, we extend the earlier work on pairwise statistical significance by incorporating with it the use of multiple parameter sets. Results: Results for a knowledge discovery application of homology detection reveal that using multiple parameter sets for pairwise statistical significance estimates gives better coverage than using a single parameter set, at least at some error levels. Further, the results of pairwise statistical significance using multiple parameter sets are shown to be significantly better than database statistical significance estimates reported by BLAST and PSI-BLAST, and comparable and at times significantly better than SSEARCH. Using non-zero parameter set change penalty values give better performance than zero penalty. Conclusion: The fact that the homology detection performance does not degrade when using multiple parameter sets is a strong evidence for the validity of the assumption that the alignment score distribution follows an extreme value distribution even when using multiple parameter sets. Parameter set change penalty is a useful parameter for alignment using multiple parameter sets. Pairwise statistical significance using multiple parameter sets can be effectively used to determine the relatedness of a (or a few) pair(s) of sequences without performing a time-consuming database search

Appendix perforation in appendix duplication in a man: a case report

<p>Abstract</p> <p>Introduction</p> <p>Although appendix duplication is diagnosed as a rare congenital anomaly of the alimentary tract in childhood, a few adult cases have also been reported. Here we report a case of appendix duplication with perforated appendicitis co-existing with acute appendicitis in an adult patient.</p> <p>Case presentation</p> <p>A 33-year-old Caucasian man was admitted to our Emergency Department with right-sided lower-quadrant pain that we explored for presumed complicated appendicitis. On exploration, a perforated inflamed appendix was found coexisting with a second inflamed appendix which was subserosal and retrocecal. Appendectomies were performed, and the pathological examination confirmed the signs of acute inflammation in both appendixes.</p> <p>Conclusion</p> <p>Surgeons in emergency services should be aware of anatomical anomalies such as duplication and malposition of the appendix, even in patients with a history of previous appendectomy, because misdiagnosis of appendix duplication may lead to a poor clinical outcome and medicolegal issues.</p

Pathogen survival trajectories: an eco-environmental approach to the modeling of human campylobacteriosis ecology.

Campylobacteriosis, like many human diseases, has its own ecology in which the propagation of human infection and disease depends on pathogen survival and finding new hosts in order to replicate and sustain the pathogen population. The complexity of this process, a process common to other enteric pathogens, has hampered control efforts. Many unknowns remain, resulting in a poorly understood disease ecology. To provide structure to these unknowns and help direct further research and intervention, we propose an eco-environmental modeling approach for campylobacteriosis. This modeling approach follows the pathogen population as it moves through the environments that define the physical structure of its ecology. In this paper, we term the ecologic processes and environments through which these populations move "pathogen survival trajectories." Although such a modeling approach could have veterinary applications, our emphasis is on human campylobacteriosis and focuses on human exposures to Campylobacter through feces, food, and aquatic environments. The pathogen survival trajectories that lead to human exposure include ecologic filters that limit population size, e.g., cooking food to kill Campylobacter. Environmental factors that influence the size of the pathogen reservoirs include temperature, nutrient availability, and moisture availability during the period of time the pathogen population is moving through the environment between infected and susceptible hosts. We anticipate that the modeling approach proposed here will work symbiotically with traditional epidemiologic and microbiologic research to help guide and evaluate the acquisition of new knowledge about the ecology, eventual intervention, and control of campylobacteriosis

Multi-parallel qPCR provides increased sensitivity and diagnostic breadth for gastrointestinal parasites of humans: field-based inferences on the impact of mass deworming

BACKGROUND: Although chronic morbidity in humans from soil transmitted helminth (STH) infections can be reduced by anthelmintic treatment, inconsistent diagnostic tools make it difficult to reliably measure the impact of deworming programs and often miss light helminth infections. METHODS: Cryopreserved stool samples from 796 people (aged 2-81 years) in four villages in Bungoma County, western Kenya, were assessed using multi-parallel qPCR for 8 parasites and compared to point-of-contact assessments of the same stools by the 2-stool 2-slide Kato-Katz (KK) method. All subjects were treated with albendazole and all Ascaris lumbricoides expelled post-treatment were collected. Three months later, samples from 633 of these people were re-assessed by both qPCR and KK, re-treated with albendazole and the expelled worms collected. RESULTS: Baseline prevalence by qPCR (n = 796) was 17 % for A. lumbricoides, 18 % for Necator americanus, 41 % for Giardia lamblia and 15% for Entamoeba histolytica. The prevalence was <1% for Trichuris trichiura, Ancylostoma duodenale, Strongyloides stercoralis and Cryptosporidium parvum. The sensitivity of qPCR was 98% for A. lumbricoides and N. americanus, whereas KK sensitivity was 70% and 32%, respectively. Furthermore, qPCR detected infections with T. trichiura and S. stercoralis that were missed by KK, and infections with G. lamblia and E. histolytica that cannot be detected by KK. Infection intensities measured by qPCR and by KK were correlated for A. lumbricoides (r = 0.83, p < 0.0001) and N. americanus (r = 0.55, p < 0.0001). The number of A. lumbricoides worms expelled was correlated (p < 0.0001) with both the KK (r = 0.63) and qPCR intensity measurements (r = 0.60). CONCLUSIONS: KK may be an inadequate tool for stool-based surveillance in areas where hookworm or Strongyloides are common or where intensity of helminth infection is low after repeated rounds of chemotherapy. Because deworming programs need to distinguish between populations where parasitic infection is controlled and those where further treatment is required, multi-parallel qPCR (or similar high throughput molecular diagnostics) may provide new and important diagnostic information

QUBIC: The QU Bolometric Interferometer for Cosmology

One of the major challenges of modern cosmology is the detection of B-mode polarization anisotropies in the CMB. These originate from tensor fluctuations of the metric produced during the inflationary phase. Their detection would therefore constitute a major step towards understanding the primordial Universe. The expected level of these anisotropies is however so small that it requires a new generation of instruments with high sensitivity and extremely good control of systematic effects. We propose the QUBIC instrument based on the novel concept of bolometric interferometry, bringing together the sensitivity advantages of bolometric detectors with the systematics effects advantages of interferometry. Methods: The instrument will directly observe the sky through an array of entry horns whose signals will be combined together using an optical combiner. The whole set-up is located inside a cryostat. Polarization modulation will be achieved using a rotating half-wave plate and interference fringes will be imaged on two focal planes (separated by a polarizing grid) tiled with bolometers. We show that QUBIC can be considered as a synthetic imager, exactly similar to a usual imager but with a synthesized beam formed by the array of entry horns. Scanning the sky provides an additional modulation of the signal and improve the sky coverage shape. The usual techniques of map-making and power spectrum estimation can then be applied. We show that the sensitivity of such an instrument is comparable with that of an imager with the same number of horns. We anticipate a low level of beam-related systematics thanks to the fact that the synthesized beam is determined by the location of the primary horns. Other systematics should be under good control thanks to an autocalibration technique, specific to our concept, that will permit the accurate determination of most of the systematics parameters.Comment: 12 pages, 10 figures, submitted to Astronomy and Astrophysic

Socio-Economic Position and Type 2 Diabetes Risk Factors: Patterns in UK Children of South Asian, Black African-Caribbean and White European Origin

BACKGROUND: Socio-economic position (SEP) and ethnicity influence type 2 diabetes mellitus (T2DM) risk in adults. However, the influence of SEP on emerging T2DM risks in different ethnic groups and the contribution of SEP to ethnic differences in T2DM risk in young people have been little studied. We examined the relationships between SEP and T2DM risk factors in UK children of South Asian, black African-Caribbean and white European origin, using the official UK National Statistics Socio-economic Classification (NS-SEC) and assessed the extent to which NS-SEC explained ethnic differences in T2DM risk factors. METHODS AND FINDINGS: Cross-sectional school-based study of 4,804 UK children aged 9-10 years, including anthropometry and fasting blood analytes (response rates 70%, 68% and 58% for schools, individuals and blood measurements). Assessment of SEP was based on parental occupation defined using NS-SEC and ethnicity on parental self-report. Associations between NS-SEC and adiposity, insulin resistance (IR) and triglyceride differed between ethnic groups. In white Europeans, lower NS-SEC status was related to higher ponderal index (PI), fat mass index, IR and triglyceride (increases per NS-SEC decrement [95%CI] were 1.71% [0.75, 2.68], 4.32% [1.24, 7.48], 5.69% [2.01, 9.51] and 3.17% [0.96, 5.42], respectively). In black African-Caribbeans, lower NS-SEC was associated with lower PI (-1.12%; [-2.01, -0.21]), IR and triglyceride, while in South Asians there were no consistent associations between NS-SEC and T2DM risk factors. Adjustment for NS-SEC did not appear to explain ethnic differences in T2DM risk factors, which were particularly marked in high NS-SEC groups. CONCLUSIONS: SEP is associated with T2DM risk factors in children but patterns of association differ by ethnic groups. Consequently, ethnic differences (which tend to be largest in affluent socio-economic groups) are not explained by NS-SEC. This suggests that strategies aimed at reducing social inequalities in T2DM risk are unlikely to reduce emerging ethnic differences in T2DM risk

Imaging the spinning gas and dust in the disc around the supergiant A[e] star HD62623

Context. To progress in the understanding of evolution of massive stars one needs to constrain the mass-loss and determine the phenomenon responsible for the ejection of matter an its reorganization in the circumstellar environment Aims. In order to test various mass-ejection processes, we probed the geometry and kinematics of the dust and gas surrounding the A[e] supergiant HD 62623. Methods. We used the combined high spectral and spatial resolution covered by the VLTI/AMBER instrument. Thanks to a new multiwavelength optical/IR interferometry imaging technique, we reconstructed the first velocity-resolved images with a milliarcsecond resolution in the infrared domain. Results. We managed to disentangle the dust and gas emission in the HD 62623 circumstellar disc.We measured the dusty disc inner inner rim, i.e. 6 mas, constrained the inclination angle and the position angle of the major-axis of the disc.We also measured the inner gaseous disc extension (2 mas) and probed its velocity field thanks to AMBER high spectral resolution. We find that the expansion velocity is negligible, and that Keplerian rotation is a favoured velocity field. Such a velocity field is unexpected if fast rotation of the central star alone is the main mechanism of matter ejection. Conclusions. As the star itself seems to rotate below its breakup-up velocity, rotation cannot explain the formation of the dense equatorial disc. Moreover, as the expansion velocity is negligible, radiatively driven wind is also not a suitable explanation to explain the disc formation. Consequently, the most probable hypothesis is that the accumulation of matter in the equatorial plane is due to the presence of the spectroscopic low mass companion.Comment: To be published soon in A\&

Isospin Physics in Heavy-Ion Collisions at Intermediate Energies

In nuclear collisions induced by stable or radioactive neutron-rich nuclei a transient state of nuclear matter with an appreciable isospin asymmetry as well as thermal and compressional excitation can be created. This offers the possibility to study the properties of nuclear matter in the region between symmetric nuclear matter and pure neutron matter. In this review, we discuss recent theoretical studies of the equation of state of isospin-asymmetric nuclear matter and its relations to the properties of neutron stars and radioactive nuclei. Chemical and mechanical instabilities as well as the liquid-gas phase transition in asymmetric nuclear matter are investigated. The in-medium nucleon-nucleon cross sections at different isospin states are reviewed as they affect significantly the dynamics of heavy ion collisions induced by radioactive beams. We then discuss an isospin-dependent transport model, which includes different mean-field potentials and cross sections for the proton and neutron, and its application to these reactions. Furthermore, we review the comparisons between theoretical predictions and available experimental data. In particular, we discuss the study of nuclear stopping in terms of isospin equilibration, the dependence of nuclear collective flow and balance energy on the isospin-dependent nuclear equation of state and cross sections, the isospin dependence of total nuclear reaction cross sections, and the role of isospin in preequilibrium nucleon emissions and subthreshold pion production.Comment: 101 pages with embedded epsf figures, review article for "International Journal of Modern Physics E: Nuclear Physics". Send request for a hard copy to 1/author

Correlation between disability and MRI findings in lumbar spinal stenosis: A prospective study of 109 patients operated on by decompression

Background and purpose MRI is the modality of choice when diagnosing spinal stenosis but it also shows that stenosis is prevalent in asymptomatic subjects over 60. The relationship between preoperative health-related quality of life, functional status, leg and back pain, and the objectively measured dural sac area in single and multilevel stenosis is unknown. We assessed this relationship in a prospective study. Patients and methods The cohort included 109 consecutive patients with central spinal stenosis operated on with decompressive laminectomy or laminotomy. Preoperatively, all patients completed the questionnaires for EQ-5D, SF-36, Oswestry disability index (ODI), estimated walking distance and leg and back pain (VAS). The cross-sectional area of the dural sac was measured at relevant disc levels in mm(2), and spondylolisthesis was measured in mm. For comparison, the area of the most narrow level, the number of levels with dural sac area < 70 mm(2), and spondylolisthesis were studied. Results Before surgery, patients with central spinal stenosis had low HRLQoL and functional status, and high pain levels. Patients with multilevel stenosis had better general health (p = 0.04) and less leg and back pain despite having smaller dural sac area than patients with single-level stenosis. There was a poor correlation between walking distance, ODI, the SF-36, EQ-5D, and leg and back pain levels on the one hand and dural sac area on the other. Women more often had multilevel spinal stenosis (p = 0.05) and spondylolisthesis (p < 0.001). Spondylolisthetic patients more often had small dural sac area (p = 0.04) and multilevel stenosis (p = 0.06). Interpretation Our findings indicate that HRQoL, function, and pain measured preoperatively correlate with morphological changes on MRI to a limited extent

The critical role of ERK in death resistance and invasiveness of hypoxia-selected glioblastoma cells

<p>Abstract</p> <p>Background</p> <p>The rapid growth of tumor parenchyma leads to chronic hypoxia that can result in the selection of cancer cells with a more aggressive behavior and death-resistant potential to survive and proliferate. Thus, identifying the key molecules and molecular mechanisms responsible for the phenotypic changes associated with chronic hypoxia has valuable implications for the development of a therapeutic modality. The aim of this study was to identify the molecular basis of the phenotypic changes triggered by chronic repeated hypoxia.</p> <p>Methods</p> <p>Hypoxia-resistant T98G (HRT98G) cells were selected by repeated exposure to hypoxia and reoxygenation. Cell death rate was determined by the trypan blue exclusion method and protein expression levels were examined by western blot analysis. The invasive phenotype of the tumor cells was determined by the Matrigel invasion assay. Immunohistochemistry was performed to analyze the expression of proteins in the brain tumor samples. The Student T-test and Pearson Chi-Square test was used for statistical analyses.</p> <p>Results</p> <p>We demonstrate that chronic repeated hypoxic exposures cause T98G cells to survive low oxygen tension. As compared with parent cells, hypoxia-selected T98G cells not only express higher levels of anti-apoptotic proteins such as Bcl-2, Bcl-X_L, and phosphorylated ERK, but they also have a more invasive potential in Matrigel invasion chambers. Activation or suppression of ERK pathways with a specific activator or inhibitor, respectively, indicates that ERK is a key molecule responsible for death resistance under hypoxic conditions and a more invasive phenotype. Finally, we show that the activation of ERK is more prominent in malignant glioblastomas exposed to hypoxia than in low grade astrocytic glial tumors.</p> <p>Conclusion</p> <p>Our study suggests that activation of ERK plays a pivotal role in death resistance under chronic hypoxia and phenotypic changes related to the invasive phenotype of HRT98G cells compared to parent cells.</p