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Objetivo El test del aliento con 13C-urea (TAU) es la prueba no invasiva más utilizada para diagnosticar Helicobacter pylori (H. pylori). La posible interferencia de la toma de antiácidos en su resultado es aún controvertida. El estudio se dirige a confirmar la no interferencia del almagato en la determinación de H. pylori mediante el TAU. Pacientes y métodos Estudio observacional, multicéntrico, en pacientes adultos en tratamiento con almagato y a los que se indicó un TAU (TAUKIT®). Cuando el resultado del TAU fue negativo, se suprimió la toma de almagato durante 30 días y se repitió un segundo TAU. En los pacientes cuyo resultado fue positivo, no se realizaron más determinaciones. La variable principal a estudio fue el porcentaje de pacientes que teniendo resultado negativo en la primera prueba de aliento, tras suprimir la toma de almagato y repetirla, ésta se positivizó (falsos negativos del TAU, posiblemente atribuibles a almagato). Resultados De los 167 pacientes evaluables, 59% fueron mujeres, la media de edad fue de 49 años y 97% de los casos presentaban sintomatología digestiva. El resultado del primer TAU fue negativo en un 71% de casos. De éstos, en la segunda prueba de TAU tras suprimir almagato, este resultado se confirmó en el 97,5%. El porcentaje de falsos negativos sobre el total de casos evaluados fue del 1,8%. Conclusiones La toma de almagato tiene una interferencia mínima o nula en el resultado del TAU para el diagnóstico de la infección por H. pylori; por tanto, se puede utilizar en las semanas previas a la realización del TAU, Objective The 13C-urea breath test (UBT) is the most widely used non-invasive diagnostic test for Helicobacter pylori. Debate continues to surround the possible interference of antacid intake on its result. This study aims to confirm the non-interference of almagate in the determination of H. pylori by UBT. Patients and methods Observational, multicentre study in adult patients treated with almagate in whom a UBT (TAUKIT®) was indicated. When the UBT result was negative, use of almagate was stopped for 30 days and the UBT was repeated. When the result was positive, no further determinations were made. The primary endpoint was the percentage of patients who, having had a negative result in the first breath test, were positive in the second after having stopped taking almagate (UBT false negatives, possibly attributable to almagate). Results Of the 167 evaluable patients, 59% were female, average age was 49 and 97% had gastrointestinal symptoms. The result of the first UBT was negative in 71% of cases. Of these, in the second UBT test after stopping the almagate, the negative result was confirmed in 97.5%. Out of the total number of cases evaluated, the rate of false negatives was 1.8%. Conclusions Taking almagate has minimal or no interference in the result of UBT for the diagnosis of H. pylori infection. It can therefore be used in the weeks prior to a UBT, El presente trabajo ha sido financiado por Almirall, S.A., Barcelona y también ha sido posible gracias a la aportación gratuita de los test de urea por parte de Isomed Pharma (kit TAUKIT 100 mg de 13C).

Objective The 13C-urea breath test (UBT) is the most widely used non-invasive diagnostic test for Helicobacter pylori. Debate continues to surround the possible interference of antacid intake on its result. This study aims to confirm the non-interference of almagate in the determination of H. pylori by UBT. Patients and methods Observational, multicentre study in adult patients treated with almagate in whom a UBT (TAUKIT®) was indicated. When the UBT result was negative, use of almagate was stopped for 30 days and the UBT was repeated. When the result was positive, no further determinations were made. The primary endpoint was the percentage of patients who, having had a negative result in the first breath test, were positive in the second after having stopped taking almagate (UBT false negatives, possibly attributable to almagate). Results Of the 167 evaluable patients, 59% were female, average age was 49 and 97% had gastrointestinal symptoms. The result of the first UBT was negative in 71% of cases. Of these, in the second UBT test after stopping the almagate, the negative result was confirmed in 97.5%. Out of the total number of cases evaluated, the rate of false negatives was 1.8%. Conclusions Taking almagate has minimal or no interference in the result of UBT for the diagnosis of H. pylori infection. It can therefore be used in the weeks prior to a UBT.

The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses., US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility [DE-AC02-05CH11231] and used resources of the National Energy Research Scientific Computing Center, supported by the Office of Science of the US Department of Energy. J.C.P. and M.L. were partially supported by the Spanish Ministry of Economy and Competitiveness and European Regional Development Fund [DPI2015-67082-P] (MINECO/FEDER). Funding for open access charge: The corresponding author will pay for publication charges.

Secondary bacterial peritonitis in cirrhotic patients is an uncommon entity that has been little reported. Our aim is to analyse the frequency, clinical characteristics, treatment and prognosis of patients with secondary peritonitis in comparison to those of patients with spontaneous bacterial peritonitis (SBP).Retrospective analysis of 24 cirrhotic patients with secondary peritonitis compared with 106 SBP episodes.Secondary peritonitis represented 4.5% of all peritonitis in cirrhotic patients. Patients with secondary peritonitis showed a significantly more severe local inflammatory response than patients with SBP. Considering diagnosis of secondary peritonitis, the sensitivity of Runyon's criteria was 66.6% and specificity 89.7%, Runyon's criteria and/or polymicrobial ascitic fluid culture were present in 95.6%, and abdominal computed tomography was diagnostic in 85% of patients in whom diagnosis was confirmed by surgery or autopsy. Mortality during hospitalization was higher in patients with secondary peritonitis than in those with SBP (16/24, 66.6% vs. 28/106, 26.4%) (p0.001). There was a trend to lower mortality in secondary peritonitis patients who underwent surgery (7/13, 53.8%) than in those who received medical treatment only (9/11, 81.8%) (p=0.21). Considering surgically treated patients, the time between diagnostic paracentesis and surgery was shorter in survivors than in non-survivors (3.2+/-2.4 vs. 7.2+/-6.1 days, p=0.31).Secondary peritonitis is an infrequent complication in cirrhotic patients but mortality is high. A low threshold of suspicion on the basis of Runyon's criteria and microbiological data, together with an aggressive approach that includes prompt abdominal computed tomography and early surgical evaluation, could improve prognosis in these patients.

An entire family of methodologies for predicting protein interactions is based on the observed fact that families of interacting proteins tend to have similar phylogenetic trees due to co-evolution. One application of this concept is the prediction of the mapping between the members of two interacting protein families (which protein within one family interacts with which protein within the other). The idea is that the real mapping would be the one maximizing the similarity between the trees. Since the exhaustive exploration of all possible mappings is not feasible for large families, current approaches use heuristic techniques which do not ensure the best solution to be found. This is why it is important to check the results proposed by heuristic techniques and to manually explore other solutions. Here we present TSEMA, the server for efficient mapping assessment. This system calculates an initial mapping between two families of proteins based on a Monte Carlo approach and allows the user to interactively modify it based on performance figures and/or specific biological knowledge. All the explored mappings are graphically shown over a representation of the phylogenetic trees. The system is freely available at http://pdg.cnb.uam.es/TSEMA. Standalone versions of the software behind the interface are available upon request from the authors.

Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein–protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein–protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction. Programa Estatal I+D+i, the SpanishMinistry of Economy andCompetitiveness [BIO2013-48213-R to J.F.-R.]; Agence Nationale de la Recherche [SPIN-HD-ANR-CHEX-2011 and ATIP-Avenir Program to P.B.]; FPU Fellowship, the Spanish Ministry of Science and Innovation [BES-2011-045634 to B.J.G.]. Funding for open access charge: Spanish Ministry of Economy and Competitiveness [BIO2013-48213-R]; Agence Nationale de la Recherche [SPIN-HDANR- CHEX-2011].

Summary: The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200×, while achieving results of similar quality. Availability and implementation: The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock. Contact: djimenez@ac.upc.edu or juanf@bsc.es Supplementary Information: Supplementary data are available at Bioinformatics online.

A 74-year-old woman presented obstructive jaundice. Computed tomography revealed a pancreatic head tumor with dilatation of the common bile duct (CBD) and pulmonary metastases. Biliary drainage by ERCP was indicated. Papilla had tumoral signs of infiltration. Cannulation was not achieved after several attempts with a papillotome. We accessed the distal CBD after performing a pre-cut, but the guidewire could not pass deeply. After replacing the duodenoscope with a linear echoendoscope with the intention of performing biliary drainage guided by EUS, a 10 mm duodenal perforation (type I, Stapfer) was visualized in the posterior wall of the duodenal bulb (Fig. 1A), surely caused by the tip of the echoenEndoscopic closure of duodenal perforation with an over-the-scope clip during endoscopic ultrasound-guided cholangiopancreatography

This short communication describes the diagnosis, treatment, and clinical course of a domestic short-haired cat with diaphragmatic hernia in which the herniated structure in the thoracic cavity contained a mummified fetus. The cat was pregnant when rescued from the street and, days later, gave birth without abnormalities. Some months later, during an ovariohysterectomy, an abnormal localization of the uterus was observed, and at that time the case was referred to our center. A thoracic radiograph showed an abnormal thoracic mass cranial to the heart. The main suspicion was the presence of a thoracic hernia with the uterus herniated and containing a mummified fetus. A thoracotomy was performed to confirm the nature of the mass and reduce the diaphragmatic hernia. Although this clinical case is quite rare, a mummified fetus can be observed in thoracic hernias.

International audience; The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder.

A detailed and complete structural knowledge of the interactome is one of the grand challenges in Biology, and a variety of computational docking approaches have been developed to complement experimental efforts and help in the characterization of protein-protein interactions. Among the different docking scoring methods, those based on physicochemical considerations can give the maximum accuracy at the atomic level, but they are usually computationally demanding and necessarily noisy when implemented in rigid-body approaches. Coarser-grained knowledge-based potentials are less sensitive to details of atomic arrangements, thus providing an efficient alternative for scoring of rigid-body docking poses. In this study, we have extracted new statistical potentials from intermolecular pairs of exposed residues in known complex structures, which were then used to score protein-protein docking poses. The new method, called SIPPER (scoring by intermolecular pairwise propensities of exposed residues), combines the value of residue desolvation based on solvent-exposed area with the propensity-based contribution of intermolecular residue pairs. This new scoring function found a near-native orientation within the top 10 predictions in nearly one-third of the cases of a standard docking benchmark and proved to be also useful as a filtering step, drastically reducing the number of docking candidates needed by energy-based methods like pyDock. © 2011 American Chemical Society., This work was supported by the Spanish Ministry of Science (grants BIO2006-15557, BIO2008-02882, BIO2009-10964, and BFU2009-11527), the Consejo Superior de Investigaciones Científicas (grant 200420E578), the Consolider E-science project, the COMBIOMED ISCIII project, and the Fundacion Marcelino Botin.

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy.The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock.Supplementary data are available at Bioinformatics online.

AIM To evaluate the rate of adverse events (AEs) during consecutive gastric and duodenal polypectomies in several Spanish centers. METHODS Polypectomies of protruded gastric or duodenal polyps >= 5 mm using hot snare were prospectively included. Prophylactic measures of hemorrhage were allowed in predefined cases. AEs were defined and graded according to the lexicon recommended by the American Society for Gastrointestinal Endoscopy. Patients were followed for 48 h, one week and 1 mo after the procedure. RESULTS 308 patients were included and a single polypectomy was performed in 205. Only 36 (11.7%) were on prior anticoagulant therapy. Mean polyp size was 15 +/- 8.9 mm (5-60) and in 294 cases (95.4%) were located in the stomach. Hemorrhage prophylaxis was performed in 219 (71.1%) patients. Nine patients presented AEs (2.9%), and 6 of them were bleeding (n = 6, 1.9%) (in 5 out of 6 AE, different types of endoscopic treatment were performed). Other 24 hemorrhagic episodes could be managed without any change in the outcome of the endoscopy and, consequently, were considered incidents. We did not find any independent risk factor of bleeding. CONCLUSION Gastroduodenal polypectomy using prophylactic measures has a rate of AEs small enough to consider this procedure a safe and effective method for polyp resection independently of the polyp size and location. OBJETIVO Evaluar la tasa de eventos adversos (AA) durante las polipectomías gástricas y duodenales consecutivas en varios centros españoles. MÉTODOS Se incluyeron prospectivamente polipectomías de pólipos gástricos o duodenales protruidos> = 5 mm con trampa de calor. Se permitieron medidas profilácticas de hemorragia en casos predefinidos. Los AA se definieron y clasificaron de acuerdo con el léxico recomendado por la Sociedad Estadounidense de Endoscopia Gastrointestinal. Los pacientes fueron seguidos durante 48 h, una semana y 1 mes después del procedimiento. RESULTADOS Se incluyeron 308 pacientes y se realizó una única polipectomía en 205. Solo 36 (11,7%) recibieron terapia anticoagulante previa. El tamaño medio de pólipo fue 15 +/- 8.9 mm (5-60) y en 294 casos (95.4%) se localizaron en el estómago. La profilaxis de hemorragia se realizó en 219 (71,1%) pacientes. Nueve pacientes presentaron AA (2,9%) y 6 de ellos sangraron (n = 6, 1,9%) (en 5 de 6 EA, se realizaron diferentes tipos de tratamiento endoscópico). Otros 24 episodios hemorrágicos podrían ser manejados sin ningún cambio en el resultado de la endoscopia y, en consecuencia, se consideraron incidentes. No encontramos ningún factor de riesgo de hemorragia independiente. CONCLUSIÓN La polipectomía gastroduodenal utilizando medidas profilácticas tiene una tasa de eventos adversos suficientemente pequeña como para considerar este procedimiento como un método seguro y efectivo para la resección de pólipos independientemente del tamaño y la ubicación del pólipo.

Despite the importance of protein-RNA interactions in the cellular context, the number of available protein-RNA complex structures is still much lower than those of other biomolecules. As a consequence, few computational studies have been addressed towards protein-RNA complexes, and to our knowledge, no systematic benchmarking of protein-RNA docking has been reported. In this study we have extracted new pairwise residue-ribonucleotide interface propensities for protein-RNA, which can be used as statistical potentials for scoring of protein-RNA docking poses. We show here a new protein-RNA docking approach based on FTDock generation of rigid-body docking poses, which are later scored by these statistical residue-ribonucleotide potentials. The method has been successfully benchmarked in a set of 12 protein-RNA cases. The results show that FTDock is able to generate near-native solutions in more than half of the cases, and that it can rank near-native solutions significantly above random. In practically all these cases, our propensity-based scoring helps to improve the docking results, finding a near-native solution within rank 100 in 43% of them. In a remarkable case, the near-native solution was ranked 1 after the propensity-based scoring. Other previously described propensity potentials can also be used for scoring, with slightly worse performance. This new protein-RNA docking protocol permits a fast scoring of rigid-body docking poses in order to select a small number of docking orientations, which can be later evaluated with more sophisticated energy-based scoring functions.