Exercise training as a novel primary treatment for localised prostate cancer: a multi-site randomised controlled phase II study

Alternative management strategies for localised prostate cancer are required to reduce morbidity and overtreatment. The aim of this study was to evaluate the feasibility, safety and acceptability of exercise training (ET) with behavioural support as a primary therapy for low/intermediate risk localised prostate cancer. Men with low/intermediate-risk prostate cancer were randomised to 12 months of ET or usual care with physical activity advice (UCwA) in a multi-site open label RCT. Feasibility included acceptability, recruitment, retention, adherence, adverse events and disease progression. Secondary outcomes included quality of life and cardiovascular health indices. Of the 50 men randomised to ET (n=25) or UCwA (n=25), 92% (n=46) completed 12 month assessments. Three men progressed to invasive therapy (two in UCwA). In the ET group, men completed mean: 140 mins per week for 12 months (95% CI 129,152mins) (94% of target dose) at 75% Hrmax. Men in the ET group demonstrated improved body mass (mean reduction: 2.0 kg; 95% CI -2.9,-1.1), reduced systolic (mean: 13 mmHg; 95% CI 7,19) and diastolic blood pressure (mean:8 mmHg; 95% CI 5,12) and improved quality of life (EQ5D mean:13 points; 95% CI 7,18). There were no serious adverse events. ET in men with low/intermediate risk prostate cancer is feasible and acceptable with a low progression rate to radical treatment. Early signals on clinically relevant markers were found which warrant further investigation

Siderite micro-modification for enhanced corrosion protection

Production of oil and gas results in the creation of carbon dioxide (CO₂) which when wet is extremely corrosive owing to the speciation of carbonic acid. Severe production losses and safety incidents occur when carbon steel (CS) is used as a pipeline material if corrosion is not properly managed. Currently corrosion inhibitor (CI) chemicals are used to ensure that the material degradation rates are properly controlled; this imposes operational constraints, costs of deployment and environmental issues. In specific conditions, a naturally growing corrosion product known as siderite or iron carbonate (FeCO₃) precipitates onto the internal pipe wall providing protection from electrochemical degradation. Many parameters influence the thermodynamics of FeCO₃ precipitation which is generally favoured at high values of temperatures, pressure and pH. In this paper, a new approach for corrosion management is presented; micro-modifying the corrosion product. This novel mitigation approach relies on enhancing the crystallisation of FeCO₃ and improving its density, protectiveness and mechanical properties. The addition of a silicon-rich nanofiller is shown to augment the growth of FeCO₃ at lower pH and temperature without affecting the bulk pH. The hybrid FeCO₃ exhibits superior general and localised corrosion properties. The findings herein indicate that it is possible to locally alter the environment in the vicinity of the corroding steel in order to grow a dense and therefore protective FeCO₃ film via the incorporation of hybrid organic-inorganic silsesquioxane moieties. The durability and mechanical integrity of the film is also significantly improved

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

Background: The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results: The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions: ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf. comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.Blanca Postigo, JM.; Pascual Bañuls, L.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Cañizares Sales, J. (2011). Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics. 12:1-8. doi:10.1186/1471-2164-12-285S1812Metzker ML: Sequencing technologies - the next generation. Nature Reviews Genetics. 2010, 11 (1): 31-46. 10.1038/nrg2626.454 sequencing. [ http://www.454.com/ ]Illumina Inc. [ http://www.illumina.com/ ]Flicek P, Birney E: Sense from sequence reads: methods for alignment and assembly (vol 6, pg S6, 2009). Nature Methods. 2010, 7 (6): 479-479.Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WEG, Wetter T, Suhai S: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research. 2004, 14 (6): 1147-1159. 10.1101/gr.1917404.Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009, 10 (3):Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data P: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.1000 Genomes. A deep Catalog of Human Genetic Variation. [ http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 ]The seqanswers internet forum. [ http://seqanswers.com/ ]Blankenberg D, Taylor J, Schenck I, He JB, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Ross CH, Nekrutenko A: A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Research. 2007, 17 (6): 960-964. 10.1101/gr.5578007.CloVR Automated Sequence Analysis from Your Desktop. [ http://clovr.org/ ]Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG: Next generation transcriptomes for next generation genomes using est2assembly. Bmc Bioinformatics. 2009, 10:Applied Biosystems by life technologies. [ http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.html ]Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang HY, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW: Comparison of next generation sequencing technologies for transcriptome characterization. Bmc Genomics. 2009, 10:Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hanon GJ, Papenfuss AT: The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science. 2010, 327 (5961): 84-87. 10.1126/science.1180616.Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. Bmc Genomics. 2010, 11:Babik W, Stuglik M, Qi W, Kuenzli M, Kuduk K, Koteja P, Radwan J: Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics. 2010, 11: 390-10.1186/1471-2164-11-390.Miller JC, Tanksley SD: RFLP analysis of phylogenetic-relationships and genetic-variation in the genus Lycopersicon. Theoretical and Applied Genetics. 1990, 80 (4): 437-448.Williams CE, Stclair DA: Phenetic relationships and levels of variability detected by restriction-fragment-length-polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon-esculentum. Genome. 1993, 36 (3): 619-630. 10.1139/g93-083.Rick CM: Tomato, Lycopersicon esculentum (Solanaceae). Evolution of crop plants. Edited by: Simmonds NW. 1976, London: Longman Group, 268-273.Labate JA, Baldo AM: Tomato SNP discovery by EST mining and resequencing. Molecular Breeding. 2005, 16 (4): 343-349. 10.1007/s11032-005-1911-5.Yano K, Watanabe M, Yamamoto N, Maeda F, Tsugane T, Shibata D: Expressed sequence tags (EST) database of a miniature tomato cultivar, Micro-Tom. Plant and Cell Physiology. 2005, 46: S139-S139.Jimenez-Gomez JM, Maloof JN: Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. Bmc Plant Biology. 2009, 9:Yang WC, Bai XD, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D: Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Molecular Breeding. 2004, 14 (1): 21-34.Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, van der Knaap E, Francis D: Diversity in conserved genes in tomato. Bmc Genomics. 2007, 8:Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM: Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. Bmc Genomics. 2009, 10:Bioinformatics at COMAV. [ http://bioinf.comav.upv.es/ngs_backbone/index.html ]Broad institute. [ http://www.broadinstitute.org/igv ]Bioinformatics at COMAV. [ http://bioinf.comav.upv.es/ngs_backbone/install.html ]Github social coding. [ http://github.com/JoseBlanca/franklin ]Chou HH, Holmes MH: DNA sequence quality trimming and vector removal. Bioinformatics. 2001, 17 (12): 1093-1104. 10.1093/bioinformatics/17.12.1093.Picard. [ http://picard.sourceforge.net/index.shtml ]McKenna A, Hanna M, Banks E, Sivachenko A, Citulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. 2010, 20: 1297-1303. 10.1101/gr.107524.110.Sol Genomics Network. [ ftp://ftp.solgenomics.net/ ]NCBI Genbank. 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Proximal major limb amputations – a retrospective analysis of 45 oncological cases

<p>Abstract</p> <p>Background</p> <p>Proximal major limb amputations due to malignant tumors have become rare but are still a valuable treatment option in palliation and in some cases can even cure. The aim of this retrospective study was to analyse outcome in those patients, including the postoperative course, survival, pain, quality of life, and prosthesis usage.</p> <p>Methods</p> <p>Data of 45 consecutive patients was acquired from patient's charts and contact to patients, and general practitioners. Patients with interscapulothoracic amputation (n = 14), shoulder disarticulation (n = 13), hemipelvectomy (n = 3) or hip disarticulation (n = 15) were included.</p> <p>Results</p> <p>The rate of proximal major limb amputations in patients treated for sarcoma was 2.3% (37 out of 1597). Survival for all patients was 42.9% after one year and 12.7% after five years. Survival was significantly better in patients with complete tumor resections. Postoperative chemotherapy and radiation did not prolong survival. Eighteen percent of the patients with malignant disease developed local recurrence. In 44%, postoperative complications were observed. Different modalities of postoperative pain management and the site of the amputation had no significant influence on long-term pain assessment and quality of life. Eighty-seven percent suffered from phantom pain, 15.6% considered their quality of life worse than before the operation. Thirty-two percent of the patients who received a prosthesis used it regularly.</p> <p>Conclusion</p> <p>Proximal major limb amputations severely interfere with patients' body function and are the last, albeit valuable, option within the treatment concept of extremity malignancies or severe infections. Besides short survival, high complication rates, and postoperative pain, patients' quality of life can be improved for the time they have remaining.</p

Nosocomial infection in a newborn intensive care unit (NICU), South Korea

BACKGROUND: This study aimed to determine the occurrence of nosocomial infections (NIs), including infection rates, main infection sites, and common microorganisms. Patients included in the study were taken from a newborn intensive care unit (NICU), in a hospital in South Korea. METHODS: A retrospective cohort study was performed by reviewing chart. The subjects were 489 neonates who were admitted to the NICU, survived longer than 72 hours, and not transferred to another unit, between Jan. 1. 1995 to Sep. 30, 1999. NIs were identified according to the NNIS definition. Data were analyzed with descriptive statistics. RESULTS: Cumulative incidence rate for NIs was 30.3 neonates out of 100 admissions, with a total of 44.6 infections. The incidence density was average 10.2 neonates and 15.1 infections per 1000 patient days. The most common infections were pneumonia (28%), bloodstream infection (26%), and conjunctivitis (22%). Major pathogens were Gram-positives such as Staphylococcus aureus and coagulase-negative staphylococci. The factors associated with NI was less than 1500 g of birth weight, less than 32 weeks of gestational age, and less than 8 of apgar score. There's no statistical difference in discharge status between two groups, but hospital stay was longer in subjects with nosocomial infection than those without infection. CONCLUSION: Although the distribution of pathogens was similar to previous reports, a high rate of nosocomial infection and in particular conjunctivitis was observed in this study that merits further evaluation

Production of phi mesons at mid-rapidity in sqrt(s_NN) = 200 GeV Au+Au collisions at RHIC

We present the first results of meson production in the K^+K^- decay channel from Au+Au collisions at sqrt(s_NN) = 200 GeV as measured at mid-rapidity by the PHENIX detector at RHIC. Precision resonance centroid and width values are extracted as a function of collision centrality. No significant variation from the PDG accepted values is observed. The transverse mass spectra are fitted with a linear exponential function for which the derived inverse slope parameter is seen to be constant as a function of centrality. These data are also fitted by a hydrodynamic model with the result that the freeze-out temperature and the expansion velocity values are consistent with the values previously derived from fitting single hadron inclusive data. As a function of transverse momentum the collisions scaled peripheral.to.central yield ratio RCP for the is comparable to that of pions rather than that of protons. This result lends support to theoretical models which distinguish between baryons and mesons instead of particle mass for explaining the anomalous proton yield.Comment: 326 authors, 24 pages text, 23 figures, 6 tables, RevTeX 4. To be submitted to Physical Review C as a regular article. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Preoperative Red Cell Distribution Width and 30-day mortality in older patients undergoing non-cardiac surgery: a retrospective cohort observational study

Increased red cell distribution width (RDW) is associated with poorer outcomes in various patient populations. We investigated the association between preoperative RDW and anaemia on 30-day postoperative mortality among elderly patients undergoing non-cardiac surgery. Medical records of 24,579 patients aged 65 and older who underwent surgery under anaesthesia between 1 January 2012 and 31 October 2016 were retrospectively analysed. Patients who died within 30 days had higher median RDW (15.0%) than those who were alive (13.4%). Based on multivariate logistic regression, in our cohort of elderly patients undergoing non-cardiac surgery, moderate/severe preoperative anaemia (aOR 1.61, p = 0.04) and high preoperative RDW levels in the 3rd quartile (>13.4% and ≤14.3%) and 4th quartile (>14.3%) were significantly associated with increased odds of 30-day mortality - (aOR 2.12, p = 0.02) and (aOR 2.85, p = 0.001) respectively, after adjusting for the effects of transfusion, surgical severity, priority of surgery, and comorbidities. Patients with high RDW, defined as >15.7% (90th centile), and preoperative anaemia have higher odds of 30-day mortality compared to patients with anaemia and normal RDW. Thus, preoperative RDW independently increases risk of 30-day postoperative mortality, and future risk stratification strategies should include RDW as a factor

Identification of genes required for soil survival in Burkholderia thailandensis by transposon-directed insertion site sequencing.

Transposon-directed insertion site sequencing was used to identify genes required by Burkholderia thailandensis to survive in plant/soil microcosms. A total of 1,153 genetic loci fulfilled the criteria as being likely to encode survival characteristics. Of these, 203 (17.6 %) were associated with uptake and transport systems; 463 loci (40.1 %) coded for enzymatic properties, 99 of these (21.4 %) had reduction/oxidation functions; 117 (10.1 %) were gene regulation or sensory loci; 61 (5.3 %) encoded structural proteins found in the cell envelope or with enzymatic activities related to it, distinct from these, 46 (4.0 %) were involved in chemotaxis and flagellum, or pilus synthesis; 39 (3.4 %) were transposase enzymes or were bacteriophage-derived; and 30 (2.6 %) were involved in the production of antibiotics or siderophores. Two hundred and twenty genes (19.1 %) encoded hypothetical proteins or those of unknown function. Given the importance of motility and pilus formation in microcosm persistence the nature of the colonization of the rhizosphere was examined by confocal microscopy. Wild type B. thailandensis expressing red fluorescent protein was inoculated into microcosms. Even though the roots had been washed, the bacteria were still present but they were motile with no attachment having taken place, perhaps being retained in a biofilm

The neural substrate of positive bias in spontaneous emotional processing

Even in the presence of negative information, healthy human beings display an optimistic tendency when thinking of past success and future chances, giving a positive bias to everyday's cognition. The tendency to actively select positive thoughts suggests the existence of a mechanism to exclude negative content, raising the issue of its dependence on mechanisms like those of effortful control. Using perfusion imaging, we examined how brain activations differed according to whether participants were left to prefer positive thoughts spontaneously, or followed an explicit instruction to the same effect, finding a widespread dissociation of brain perfusion patterns. Under spontaneous processing of emotional material, recruitment of areas associated with effortful attention, such as the dorsolateral prefrontal cortex, was reduced relative to instructed avoidance of negative material (F(1,58) = 26.24, p = 0.047, corrected). Under spontaneous avoidance perfusion increments were observed in several areas that were deactivated by the task, including the perigenual medial prefrontal cortex. Furthermore, individual differences in executive capacity were not associated with positive bias. These findings suggest that spontaneous positive cognitive emotion regulation in health may result from processes that, while actively suppressing emotionally salient information, differ from those associated with effortful and directed control