riboSeed:leveraging prokaryotic genomic architecture to assemble across ribosomal regions

The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only similar to 10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome's rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome

Outcomes of left split graft transplantation in Europe: report from the European Liver Transplant Registry

Split liver transplantation (SLT) has been widely adopted across Europe, resulting in remarkable reduction in the paediatric waiting-list mortality. Left split graft (LSG) is commonly used for paediatric recipients; however, deceased donor criteria selection are not universal. The aim of this study was to analyse the LSG outcome from the European Liver Transplant Registry and to identify risk factors for graft failure. Data from 1500 children transplanted in 2006-2014 with LSG from deceased donors were retrospectively analysed. Overall, graft losses were 343(22.9%) after 5 years from transplantation, 240(70.0%) occurred within the first 3 months. Estimated patient survival was 89.1% at 3 months and 82.9% at 5 years from SLT. Re-transplantation rate was 11.5%. At multivariable analysis, significant risk factors for graft failure at 3 months included the following: urgent SLT (HR = 1.73, P = 0.0012), recipient body weight ≤6 kg (HR = 1.91, P = 0.0029), donor age >50 years (HR = 1.87, P = 0.0039), and cold ischaemic time (CIT) [HR = 1.07 per hour, P = 0.0227]. LSG has good outcomes and SLT is excellent option for paediatric recipients in the current organ shortage era. We identified practical guidelines for LSG donor and recipient selection criteria: donor age may be safely extended up to 50 years in the absence of additional risk factors; thus, children <6 kg and urgent transplantation need CIT <6 h and appropriate graft/recipient size-matching to achieve good outcomes

Chimera: a Bioconductor package for secondary analysis of fusion products

Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. Fusions are then easily manipulated with standard R functions or through the set of functionalities specifically developed in Chimera with the aim of supporting the user in managing fusions and discriminating falsepositive results

ProBiota | Serie Documentos | Un congreso para el Bicentenario : Juanito de las pampas y el primer congreso de Limnología

–El agua es vida –dijo Jack Vallentyne mirando a los ojos a un desconcertado “Palito” Ortega, gobernador de Tucumán por aquel entonces. Luego se sentó y creó un instante por lo menos curioso, según recuerda Hurlbert (2011) de aquel caluroso día de septiembre de 1994 en casa de gobierno. Aquella visita protocolar se hizo dentro del primer Congreso argentino de Limnología, después de una serie de reuniones previas en La Plata. Aclaremos que la Limnología es una rama (si cabe) de la Ecología que se encarga del estudio de los ecosistemas acuáticos continentales. Ahora, volvamos a “Juanito de las pampas” como tituló Hurlbert el párrafo final de sus recuerdos sobre Jack Vallentyne (alias Johnny Biosphere) en ocasión de su encuentro en esta reunión científica. No encontré muchos otros aquí en Tucumán que habiendo estado en aquella reunión, recordaran aquel momento singular. Mucho menos alguna foto que inmortalizara aquella visita…Facultad de Ciencias Naturales y Muse

ProBiota | Serie Documentos | Un congreso para el Bicentenario : Juanito de las pampas y el primer congreso de Limnología

–El agua es vida –dijo Jack Vallentyne mirando a los ojos a un desconcertado “Palito” Ortega, gobernador de Tucumán por aquel entonces. Luego se sentó y creó un instante por lo menos curioso, según recuerda Hurlbert (2011) de aquel caluroso día de septiembre de 1994 en casa de gobierno. Aquella visita protocolar se hizo dentro del primer Congreso argentino de Limnología, después de una serie de reuniones previas en La Plata. Aclaremos que la Limnología es una rama (si cabe) de la Ecología que se encarga del estudio de los ecosistemas acuáticos continentales. Ahora, volvamos a “Juanito de las pampas” como tituló Hurlbert el párrafo final de sus recuerdos sobre Jack Vallentyne (alias Johnny Biosphere) en ocasión de su encuentro en esta reunión científica. No encontré muchos otros aquí en Tucumán que habiendo estado en aquella reunión, recordaran aquel momento singular. Mucho menos alguna foto que inmortalizara aquella visita…Facultad de Ciencias Naturales y Muse

Inheritance of chromosome 7 is associated with a drug-resistant phenotype in somatic cell hybrids.

A major form of drug resistance in tumour cells known as classical multidrug resistance (MDR) is associated with the overexpression of the mdr1 gene product, the membrane protein P-glycoprotein (P-gp), which acts as an energy-dependent drug efflux pump. In this study the inheritance of P-gp expression was examined using hybrids formed after somatic cell fusion between a drug-sensitive human T-cell leukaemia cell line, CEM/CCRF, and a drug-resistant derivative, CEM/A7, which is characterized by a clonal chromosomal duplication dup(7)(q11.23q31.2). Fourteen hybrids, chosen at random, were analysed by reverse transcriptase-polymerase chain reaction (RT-PCR) and by binding studies involving the monoclonal antibody MRK16, which recognises an external P-gp epitope. Only two hybrids were positive for both MRK16 antibody labelling and mdr1 mRNA. Partial karyotypic analysis of all hybrids revealed that only the MRK16-positive hybrids contained the duplication in chromosome 7 seen in the CEM/A7 parental MDR line. Therefore, P-gp overexpression in the MRK16-positive hybrids may be linked to the inheritance of chromosome 7 from CEM/A7 and possibly associated with the chromosome 7 abnormality

Actual 10-year survival after resection of perihilar cholangiocarcinoma: What factors preclude a chance for cure?

Complete resection of perihilar cholangiocarcinoma (pCCA) is the only potentially curative treatment. Long-term survival data is rare and prognostic analyses are hindered by the rarity of the disease. This study aimed to determine the cure rate and to identify clinicopathological factors that may preclude cure. All consecutive resections for pathologically confirmed pCCA between 2000 and 2009 in 22 centers worldwide were included in a retrospective cohort study. Each center included its retrospective data series. A total of 460 patients were included with a median followup of 10 years for patients alive at last follow-up. Median overall survival (OS) was 29.9 months and 10-year OS was 12.8%. Twenty-nine (6%) patients reached 10-year OS. The observed cure rate was 5%. Factors that virtually precluded cure (i.e., below 1%) according to the mixture cure model included age above 70, Bismuth-Corlette type IV tumors, hepatic artery reconstruction, and positive resection margins. Cure was unlikely (i.e., below 3%) in patients with positive lymph nodes or poor tumor differentiation. These factors need to be considered in patient counseling and long-term follow-up after surgery

Intentional tanning among adolescents in seven Canadian provinces: Provincial comparisons (CRAYS 2015)

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.ypmed.2018.03.004 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/This report explores intentional tanning behaviors among Canadian high school students in light of provincial restrictions on UV tanning device use among youth. Data are from the Cancer Risk Assessment in Youth Survey (CRAYS), collected from January to December 2015, at randomly selected high schools in 7 provinces. Relevant variables were: tanning methods ever used, demographics, and location and refusal of UV tanning device (beds, lamps) use in the past 12 months. Data were weighted so total survey weights by male/female, grade and province equal actual enrolments in these groups. Analyses were conducted in SAS, mostly for grades 10 and 11. Rao-Scott chi squared tests and p-values were calculated. Among 6803 grade 10 and 11 participants, 82% tanned intentionally, mostly by being/playing outside, or laying in the sun. Spray/self-tanners were used by 15% of participants. UV tanning device use was uncommon (4.4%), lowest in Ontario (2.7%) and British Columbia (3.8%), which have legislation against use among youth. Of 202 who used UV tanning devices in the past 12 months, most did at salons/studios (85%), 35% at home and 30% at a gym. Two hundred and forty-nine participants (3.4%) were refused use of UV tanning devices in the past 12 months. While legislation appears to deter UV tanning device use, it appears to have no impact on UV exposure among high school students overall. Greater prevention efforts are required to deter intentional tanning among high school students.Prevention Research Grant of the Canadian Cancer Society Research Institute (grant #703073)Canadian Institutes of Health Research - Institute of Cancer Research (grant #137732

Intensity modulated radiotherapy for localized prostate cancer: rigid compliance to dose-volume constraints as a warranty of acceptable toxicity?

BACKGROUND: To report the toxicity after intensity modulated radiotherapy (IMRT) for patients with localized prostate cancer, as a sole treatment or after radical prostatectomy. METHODS: Between August 2001 and December 2003, 132 patients with prostate cancer were treated with IMRT and 125 were evaluable to acute and late toxicity analysis, after a minimum follow-up time of one year. Clinical and treatment data, including normal tissue dose-volume histogram (DVH) constraints, were reviewed. Gastro-intestinal (GI) and genito-urinary (GU) signs and symptoms were evaluated according to the Radiation Therapy Oncology Group (RTOG) toxicity scales. Median prescribed dose was 76 Gy. Median follow-up time was of 26.1 months. RESULTS: From the 125 patients, 73 (58.4%) presented acute Grade 1 or Grade 2 GI and 97 (77.2%) presented acute Grade 1 or Grade 2 GU toxicity. Grade 3 GI acute toxicity occurred in only 2 patients (1.6%) and Grade 3 GU acute toxicity in only 3 patients (2.4%). Regarding Grade 1 and 2 late toxicity, 26 patients (20.8%) and 21 patients (16.8%) presented GI and GU toxicity, respectively. Grade 2 GI late toxicity occurred in 6 patients (4.8%) and Grade 2 GU late toxicity in 4 patients (3.2%). None patient presented any Grade 3 or higher late toxicity. Non-conformity to DVH constraints occurred in only 11.2% of treatment plans. On univariate analysis, no significant risk factor was identified for Grade 2 GI late toxicity, but mean dose delivered to the PTV was associated to higher Grade 2 GU late toxicity (p = 0.042). CONCLUSION: IMRT is a well tolerable technique for routine treatment of localized prostate cancer, with short and medium-term acceptable toxicity profiles. According to the data presented here, rigid compliance to DHV constraints might prevent higher incidences of normal tissue complication