Searching the World-Wide-Web using nucleotide and peptide sequences

*Background:* No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept ‘processed’ queries, the burden of preparing such ‘search strings’ simply defeats the purpose of quickly locating highly relevant information. Unlike ‘sequence similarity’ searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct ‘sequence based’ search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical researchers who would often like to enter a sequence and quickly locate any pertinent information before proceeding to carry out detailed sequence alignment. 

*Results:* Here, we describe the theory and implementation of a web-based front-end for a search engine, like Google, which accepts sequence fragments and interactively retrieves a collection of highly relevant links and documents, in real-time. e.g. flat files like patent records, privately hosted sequence documents and regular databases. 

*Conclusions:* The importance of this simple yet highly relevant tool will be evident when with a little bit of tweaking, the tool can be engineered to carry out searches on all kinds of hosted documents in the World-Wide-Web.

*Availability:* Instaseq is free web based service that can be accessed by visiting the following hyperlink on the WWW
http://instaseq.georgetown.edu 
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Geriatric Inclusive Art and Length of Stay in Acute Care Unit: A Case-Control Pilot Study

International audienc

Whey- vs Casein-Based Enteral Formula and Gastrointestinal Function in Children With Cerebral Palsy.

Objectives: Children with severe cerebral palsy (CP) commonly have gastrointestinal (GI) dysfunction. Whey-based enteral formulas have been postulated to reduce gastroesophageal reflux (GOR) and accelerate gastric emptying (GE). The authors investigated whether whey-based (vs casein-based) enteral formulas reduce GOR and accelerate GE in children who have severe CP with a gastrostomy and fundoplication. Methods: Thirteen children received a casein-based formula for 1 week and either a 50% whey whole protein (50% WWP) or a 100% whey partially hydrolyzed protein (100% WPHP) formula for 1 week. Reflux episodes, gastric half-emptying time (GE t1/2), and reported pain and GI symptoms were measured. Results: Whey formulas emptied significantly faster than casein (median [interquartile range (IQR)] GE t1/2, 33.9 [25.3-166.2] min vs 56.6 [46-191] min; P = .033). Reflux parameters were unchanged. GI symptoms were lower in children who received 50% WWP (visual analog symptom score, median [IQR], 0[0-11.8]) vs 100% WPHP (13.0 [2.5-24.8]) (P = .035). Conclusion: This pilot study shows that in children who have severe CP with a gastrostomy and fundoplication, GE of the whey-based enteral formula is significantly faster than casein. The acceleration in GE does not alter GOR frequency, and there appears to be no effect of whey vs casein in reducing acid, nonacid, and total reflux episodes. The results indicate that enteral formula selection may be particularly important for children with severe CP and delayed GE. (JPEN J Parenter Enteral Nutr. 2012;36:118S-123S

Measurement of the Growth of the Main Commercial Rays (Raja clavata, Raja brachyura, Torpedo marmorata, Dipturus oxyrinchus) in European Waters Using Intercalibration Methods

The intercalibration of age readings represents a crucial step in the ageing procedure; the use of different sampling methods, structures, preparation techniques, and ageing criteria can significantly affect age and growth data. This study evaluated the precision and accuracy of ageing for the most important North Atlantic (NA) and Mediterranean (M) ray species, Raja clavata, Raja brachyura, Torpedo marmorata, and Dipturus oxyrinchus, through exchange exercises carried out by readers from different laboratories. In addition, growth parameters were estimated from the obtained data. A total of 663 individual batoids were analysed. R. clavata and R. brachyura samples were obtained from both the NA and the M, while vertebral centra of T. marmorata and D. oxyrinchus were only available for the M. High reading variability was observed for all four evaluated species in terms of CV, APE, and PA. D. oxyrinchus and T. marmorata showed relatively slow growth and the von Bertalanffy model with fixed t(0) and Gompertz's model were, respectively, the most precise models for each of these species. In R. brachyura, females had a faster growth rate compared to combined sexes. The vbt0p proved the most precise model for describing growth in this species, and no statistical differences were found between the NO and the M. For R. clavata, the best-fitting model was the vbt0p for females and males in the NO and for females from the M, while the best-fitting model for males from the M and sexes combined for both areas was log.p. Distinct growth patterns were observed between the two study areas

Characterizing preclinical sub-phenotypic models of acute respiratory distress syndrome:An experimental ovine study

Abstract The acute respiratory distress syndrome (ARDS) describes a heterogenous population of patients with acute severe respiratory failure. However, contemporary advances have begun to identify distinct sub‐phenotypes that exist within its broader envelope. These sub‐phenotypes have varied outcomes and respond differently to several previously studied interventions. A more precise understanding of their pathobiology and an ability to prospectively identify them, may allow for the development of precision therapies in ARDS. Historically, animal models have played a key role in translational research, although few studies have so far assessed either the ability of animal models to replicate these sub‐phenotypes or investigated the presence of sub‐phenotypes within animal models. Here, in three ovine models of ARDS, using combinations of oleic acid and intravenous, or intratracheal lipopolysaccharide, we investigated the presence of sub‐phenotypes which qualitatively resemble those found in clinical cohorts. Principal Component Analysis and partitional clustering identified two clusters, differentiated by markers of shock, inflammation, and lung injury. This study provides a first exploration of ARDS phenotypes in preclinical models and suggests a methodology for investigating this phenomenon in future studies

T cell lymphoproliferative disorders associated with anti-tumor necrosis factor alpha antibody therapy for ulcerative colitis: literature summary

The enhanced risk of development of lymphoproliferative disorders in patients with inflammatory bowel disease has been attributed to immunosuppressive/immunomodulatory therapies. Infliximab is a chimeric monoclonal immunoglobulin G1 antibody directed against tumor necrosis factor alpha (TNF-α) that was approved by the Food and Drug Administration (FDA) in 1998 as an effective therapeutic agent against inflammatory bowel disease. Malignant lymphomas of both B and T cell lineage have been described in patients undergoing therapy involving TNF-α blockade. To date, eight cases of Epstein–Barr virus (EBV)-negative hepatosplenic T cell lymphoma associated with infliximab have been reported to the FDA’s Adverse Event Reporting System, as well as several other T cell lymphoproliferative disorders with aggressive clinical outcomes. We present the histologic, immunophenotypic, and molecular features of a T cell lymphoproliferative disorder involving the axillary lymph node of a 33-year-old male following infliximab treatment for ulcerative colitis. These EBV-negative lymphomas suggest that lymphoproliferative disorders following infliximab treatment for inflammatory bowel disease may involve EBV-independent immune dysregulation. The spectrum of lymphoproliferative disorders associated with infliximab and the potential mechanisms by which they occur are discussed

Report of the Regional Co-ordination Meeting for the North Sea and Eastern Arctic (RCM NS&EA) 2014

Report of the Regional Co-ordination Meeting for the North Sea and Eastern Arctic (RCM NS&EA) 2014 Swedish University of Agriculture Sciences (SLU Aqua) Lysekil, Sweden 08-12 September 2014The RCM NS&EA met in Lysekil (Sweden) between 8-12 September 2014. The main purpose of the RCM is coordinate the National Programmes (NP) of the Member States (MS) in the North Sea region for 2015