IMG/M: the integrated metagenome data management and comparative analysis system

The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M’s data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer)

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions

The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov

IMG/M: a data management and analysis system for metagenomes

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/

IMG/M: the integrated metagenome data management and comparative analysis system

The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M's data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer)

ТРАНСАНАЛЬНАЯ ЭНДОСКОПИЧЕСКАЯ ХИРУРГИЯ В ЛЕЧЕНИИ ОПУХОЛЕЙ ПРЯМОЙ КИШКИ

Relevance. Endoscopic electroexcision through the colonoscope, transanal removal of tumors, as well as their transabdominal removal are used For the treatment of benign and malignant tumors of the rectum. These methods have both advantages and indications, as the limitations and drawbacks. Priorities of the modern oncology to develop organ-preserving methods of treatment have led to development of transanal endoscopic surgery method. Full visual control and microsurgical technique allow to achieve precise en-bloc removal of tumors with adequate lateral margins, with the possibility of excision of the entire thickness of the bowel wall.Aim. To evaluate the results of transanal endoscopic removal of rectal tumors.Materials and methods: The study included 46 patients operated by transanal endoscopic surgery for adenoma and early rectal cancer. Tumors were located at a distance of 3 to 13 cm from the dentate line, their size ranged from 1.2 to 5 cm, 85% of tumors had a wide base. Rectum polyps (65%) were removed with entire wall of the rectum, polyps with signs of malignancy and early rectal cancer (35%) were removed with the mesorectal tissue. Final pathological examination revealed adenocarcinoma in situ in 15% of patients with adenomas.Results: Postoperative complications occurred in 3 patients (6.5%). Two patients had a febrile temperature reaction. One patient had an intestinal bleeding, that was stopped by conservative measures. Follow-up of these patients ranges from 3 months to 2 years. In follow-up period rectal tumor recurrence was detected in 2 patients (4.3%) during 10-14 months after surgery. Transanal endosurgical intervention didn’t have any significant impact on the function of the rectum.Conclusion. Described capabilities allow to recommend this method for widespread introduction into surgical practice. Based on these results we can conclude that transanal endoscopic removal of tumors may become the treatment of choice in patients with early cancer of the rectum.Актуальность.  Для лечения доброкачественных и злокачественных опухолей прямой кишки применяется эндоскопическая электроэксцизия через  колоноскоп, трансанальное удаление опухолей, а также и их трансабдоминальное удаление. Эти методы имеют как определенные преимущества и показания, так и ограничения и недостатки. Приоритеты современной онкологии в разработке органосохраняющих методов лечения привели к появлению метода трансанальной эндоскопической хирургии. Полный визуальный контроль и микрохирургическая техника обеспечивают возможность прецизионного удаления опухолей n-блоком с адекватными латеральными границами, с возможностью иссечения на всю толщину стенки кишки.Цель работы. Оценить результаты трансанального эндоскопического удаления опухолей прямой кишки.Материалы и методы. 46 больных, оперированных методом трансанальной эндоскопической хирургии по поводу аденом и начальных форм рака прямой кишки. Опухоли располагались  на расстоянии от 3 до13 смот зубчатой линии, их размер  был от 1,2 до5 см, у 85% опухолей было широкое основание.  Полностенному удалению подвергались  полипы прямой кишки (65%), удаление опухоли вместе  с подлежащей мезоректальной  клетчаткой осуществлялось при полипах с признаками малигнизации, начальном раке прямой кишки (35%). Послеоперационное патоморфологическое  исследование  у 15% больных в аденомах прямой кишки выявило участки аденокарциномы  in situ.Результаты:  Послеоперационные осложнения развились у 3 больных (6,5%).  В 2 случаях возникла фебрильная температурная реакция. В 1 случае наблюдалось кишечное кровотечение, остановленное консервативными мероприятиями. Больные находятся под наблюдением от 3 месяцев до 2 лет. За время наблюдения  рецидив опухоли прямой кишки выявлен у 2 больных (4,3%) через 10–14  месяцев после операции. Трансанальное эндохирургическое вмешательство  на прямой кишке не оказало существенного влияния на функцию прямой кишки.Заключение. Описанные возможности позволяют рекомендовать данный метод к широкому внедрению в хирургическую практику. На основании полученных результатов  можно заключить, что трансанальное  эндоскопическое  удаление опухолей вполне может стать методом  выбора у больных  с начальными формами рака прямой кишки

Measuring the effects through time of the influence of visuomotor and visuotactile synchronous stimulation on a virtual body ownership illusion

Previous studies have examined the experience of owning a virtual surrogate body or body part through specific combinations of cross-modal multisensory stimulation. Both visuomotor (VM) and visuotactile (VT) synchronous stimulation have been shown to be important for inducing a body ownership illusion, each tested separately or both in combination. In this study we compared the relative importance of these two cross-modal correlations, when both are provided in the same immersive virtual reality setup and the same experiment. We systematically manipulated VT and VM contingencies in order to assess their relative role and mutual interaction. Moreover, we present a new method for measuring the induced body ownership illusion through time, by recording reports of breaks in the illusion of ownership ("breaks") throughout the experimental phase. The balance of the evidence, from both questionnaires and analysis of the breaks, suggests that while VM synchronous stimulation contributes the greatest to the attainment of the illusion, a disruption of either (through asynchronous stimulation) contributes equally to the probability of a break in the illusion

Hormonal and transcriptional profiles highlight common and differential host responses to arbuscular mycorrhizal fungi and the regulation of the oxylipin pathway

Arbuscular mycorrhizal (AM) symbioses are mutualistic associations between soil fungi and most vascular plants. The symbiosis significantly affects the host physiology in terms of nutrition and stress resistance. Despite the lack of host range specificity of the interaction, functional diversity between AM fungal species exists. The interaction is finely regulated according to plant and fungal characters, and plant hormones are believed to orchestrate the modifications in the host plant. Using tomato as a model, an integrative analysis of the host response to different mycorrhizal fungi was performed combining multiple hormone determination and transcriptional profiling. Analysis of ethylene-, abscisic acid-, salicylic acid-, and jasmonate-related compounds evidenced common and divergent responses of tomato roots to Glomus mosseae and Glomus intraradices, two fungi differing in their colonization abilities and impact on the host. Both hormonal and transcriptional analyses revealed, among others, regulation of the oxylipin pathway during the AM symbiosis and point to a key regulatory role for jasmonates. In addition, the results suggest that specific responses to particular fungi underlie the differential impact of individual AM fungi on plant physiology, and particularly on its ability to cope with biotic stresses

Altered visual feedback from an embodied avatar unconsciously influences movement amplitude and muscle activity

Evidence suggests that the sense of the position of our body parts can be surreptitiously deceived, for instance through illusory visual inputs. However, whether altered visual feedback during limb movement can induce substantial unconscious motor and muscular adjustments is not known. To address this question, we covertly manipulated virtual body movements in immersive virtual reality. Participants were instructed to flex their elbow to 90° while tensing an elastic band, as their virtual arm reproduced the same, a reduced (75°), or an amplified (105°) movement. We recorded muscle activity using electromyography, and assessed body ownership, agency and proprioception of the arm. Our results not only show that participants compensated for the avatar’s manipulated arm movement while being completely unaware of it, but also that it is possible to induce unconscious motor adaptations requiring significant changes in muscular activity. Altered visual feedback through body ownership illusions can influence motor performance in a process that bypasses awareness

Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides

The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Endophytes represent a promising group of organisms, as they are a mostly untapped reservoir of metabolic diversity. They are often able to degrade cellulose, and they can produce an extraordinary diversity of metabolites. The filamentous fungal endophyte Ascocoryne sarcoides was shown to produce potential-biofuel metabolites when grown on a cellulose-based medium; however, the genetic pathways needed for this production are unknown and the lack of genetic tools makes traditional reverse genetics difficult. We present the genomic characterization of A. sarcoides and use transcriptomic and metabolomic data to describe the genes involved in cellulose degradation and to provide hypotheses for the biofuel production pathways. In total, almost 80 biosynthetic clusters were identified, including several previously found only in plants. Additionally, many transcriptionally active regions outside of genes showed condition-specific expression, offering more evidence for the role of long non-coding RNA in gene regulation. This is one of the highest quality fungal genomes and, to our knowledge, the only thoroughly annotated and transcriptionally profiled fungal endophyte genome currently available. The analyses and datasets contribute to the study of cellulose degradation and biofuel production and provide the genomic foundation for the study of a model endophyte system

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.Peer reviewe