Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Teratoma of the anterior mediastinum presenting as a cystic neck mass: a case report

<p>Abstract</p> <p>Introduction</p> <p>Teratomas of anterior mediastinum are rare tumors and are often slow growing, asymptomatic and detected incidentally on chest imaging. Results of surgical resection are very satisfactory.</p> <p>Case presentation</p> <p>A 19-years old male presented with an asymptomatic cystic neck mass. X-ray and CT scan of chest and neck showed an extrathyroidal multi-septate, predominantly cystic neck mass, that was continuous with a solid intrathoracic mass extending up to the level of right atrium and which contained areas of calcification and cystic necrosis. The mediastinal structures did not show any features of compression or infiltration. Fine needle aspiration cytology from the neck mass was suggestive of a dermoid cyst. In view of the extent and uncertain pathological nature of the tumor, it was excised via a combined cervical and trans-sternal route. Histo-pathology of the resected specimen confirmed the diagnosis of a mature cystic teratoma. The patient made an uneventful recovery, and after five years of follow-up, he has been symptom free with no clinical or radiological evidence of recurrent disease. We discuss the role of imaging and the need for surgical treatment to avoid possible catastrophic complications in patients with cervical and mediastinal masses of uncertain histological nature.</p> <p>Conclusion</p> <p>A mediastinal teratoma may rarely present as a cystic neck swelling due to its cephalad extension. This entity needs to be considered in cases where clinical and investigative work-up fail to provide a convincing clue to a primary neck pathology as cause of a cystic neck swelling.</p

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)

BACKGROUND: Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced. RESULTS: Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes. CONCLUSION: The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species

Discovery of molecular hydrogen in a high-velocity cloud of the Galactic halo

We report the discovery of molecular hydrogen absorption in a Galactic high-velocity cloud (HVC) in the direction of the Large Magellanic Cloud. For the same HVC we derive an iron abundance which is half of the solar value. Thus, all evidence points to a Galactic origin for high-velocity cloud complex in front of the LMC.Comment: Published in Nature, this week; 14 pages, 3 figure

GNSS remote sensing of the Australian tropopause

Radio occultation (RO) techniques that use signals transmitted by Global Navigation Satellite Systems (GNSS) have emerged over the past decade as an important tool for measuring global changes in tropopause temperature and height, a valuable capacity given the tropopause’s sensitivity to temperature variations. This study uses 45,091 RO data from the CHAMP (CHAllenging Minisatellite Payload, 80 months), GRACE (Gravity Recovery And Climate Experiment, 23 months) and COSMIC (Constellation Observing System for Meteorology, Ionosphere, and Climate, 20 months) satellites to analyse the variability of the tropopause’s height and temperature over Australia. GNSS RO temperature profiles from CHAMP, GRACE, and COSMIC are first validated using radiosonde observations provided by the Bureau of Meteorology (Australia). These are compared to RO soundings from between 2001 and 2007 that occurred within 3 h and 100 km of a radiosonde.The results indicate that RO soundings provide data of a comparable quality to radiosonde observations in the tropopause region, with temperature deviations of less than 0.5 ± 1.5 K. An analysis of tropopause height and temperature anomalies indicates a height increase over Australia as a whole of ca. 4.8 ± 1.3 m between September 2001 and April 2008, with a corresponding temperature decrease of −0.019 ± 0.007 K. A similar pattern of increasing height/decreasing temperature was generally observed when determining the spatial distribution of the tropopause height and temperature rate of change over Australia. Although only a short period has been considered in this study, a function of the operating time of these satellites, the results nonetheless show an increase in the height of the tropopause over Australia during this period and thus may indicate regional warming. Several mechanisms could be responsible for these changes, such as an increase in the concentration of greenhouse gases in the atmosphere, and lower stratospheric cooling due to ozone loss, both of which have been observed during the last decades

A first generation BAC-based physical map of the rainbow trout genome

Background: Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species.[br/] Results: The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map.[br/] Conclusion: The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of MAS into rainbow trout breeding programs

Factors associated with severe dry eye in primary Sjögren´s syndrome diagnosed patients

Introduction Primary Sjögren?s syndrome (pSS) is an autoimmune disease, characterized by lymphocytic infiltration of exocrine glands and other organs, resulting in dry eye, dry mouth and extraglandular systemic findings. Objective To explore the association of severe or very severe dry eye with extraocular involvement in patients diagnosed with primary Sjögren?s syndrome. Methods SJOGRENSER registry is a multicenter cross-sectional study of pSS patients. For the construction of our main variable, severe/very severe dry eye, we used those variables that represented a degree 3?4 of severity according to the 2007 Dry Eye Workshop classification. First, bivariate logistic regression models were used to identify the effect of each independent variable on severe/very severe dry eye. Secondly, multivariate analysis using regression model was used to establish the independent effect of patient characteristics. Results Four hundred and thirty-seven patients were included in SJOGRENSER registry; 94% of the patients complained of dry eye and 16% developed corneal ulcer. Schirmer?s test was pathological in 92% of the patients; 378 patients presented severe/very severe dry eye. Inflammatory articular involvement was significantly more frequent in patients with severe/very severe dry eye than in those without severe/very severe dry eye (82.5 vs 69.5%, p = 0,028). Inflammatory joint involvement was associated with severe/very severe dry eye in the multivariate analysis, OR 2.079 (95% CI 1.096?3.941). Conclusion Severe or very severe dry eye is associated with the presence of inflammatory joint involvement in patients with pSS. These results suggest that a directed anamnesis including systemic comorbidities, such as the presence of inflammatory joint involvement or dry mouth in patients with dry eye, would be useful to suspect a pSS

Meibum Lipid Composition in Asians with Dry Eye Disease

10.1371/journal.pone.0024339PLoS ONE610

Medicines information and adherence in HIV/AIDS patients

Background: Providing written medicines information is being legislated in an increasing number of countries worldwide, with the patient information leaflet (PIL) being the most widely used method for conveying health information. The impact of providing such information on adherence to therapy is reportedly unpredictable. Therapy for human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) and related opportunistic infections usually involves polytherapy and complex regimens, both of which are risk factors for non-adherence. The objective of this study was to assess the impact of medicines information on adherence to chronic co-trimoxazole therapy in low-literate HIV/AIDS patients. Methods: Two different PILs were designed for co-trimoxazole tablets and were available in both English and isiXhosa. Participants were randomly allocated to a control group (receiving no PIL), group A (receiving a 'complex PIL') and group B (receiving a 'simple PIL' incorporating pictograms). At the first interview, demographic data were collected and the time, date and day that the participant would take his/her first tablet of the month's course was also documented. In a follow-up interview adherence to therapy was assessed using two methods; self-report and tablet count. Results: The medicines information materials incorporating simple text and pictograms resulted in significantly improved adherence to therapy in the short term, whereas a non-significant increase in adherence was associated with the availability of the more complex information. This was shown by both the self-reported assessment as well as the tablet count. Conclusion: This research suggests that appropriately designed written material can have a positive impact in improving adherence and, together with verbal consultation, are essential for enabling patients to make appropriate decisions about their medicine taking

Intra-operative spectroscopic assessment of surgical margins during breast conserving surgery

Background: In over 20% of breast conserving operations, postoperative pathological assessment of the excised tissue reveals positive margins, requiring additional surgery. Current techniques for intra-operative assessment of tumor margins are insufficient in accuracy or resolution to reliably detect small tumors. There is a distinct need for a fast technique to accurately identify tumors smaller than 1 mm2 in large tissue surfaces within 30 min. Methods: Multi-modal spectral histopathology (MSH), a multimodal imaging technique combining tissue auto-fluorescence and Raman spectroscopy was used to detect microscopic residual tumor at the surface of the excised breast tissue. New algorithms were developed to optimally utilize auto-fluorescence images to guide Raman measurements and achieve the required detection accuracy over large tissue surfaces (up to 4 × 6.5 cm2). Algorithms were trained on 91 breast tissue samples from 65 patients. Results: Independent tests on 121 samples from 107 patients - including 51 fresh, whole excision specimens - detected breast carcinoma on the tissue surface with 95% sensitivity and 82% specificity. One surface of each uncut excision specimen was measured in 12–24 min. The combination of high spatial-resolution auto-fluorescence with specific diagnosis by Raman spectroscopy allows reliable detection even for invasive carcinoma or ductal carcinoma in situ smaller than 1 mm2. Conclusions: This study provides evidence that this multimodal approach could provide an objective tool for intra-operative assessment of breast conserving surgery margins, reducing the risk for unnecessary second operations