StochNetV2: A Tool for Automated Deep Abstractions for Stochastic Reaction Networks

We present a toolbox for stochastic simulations with CRN models and their (automated) deep abstractions: a mixture density deep neural network trained on time-series data produced by the CRN. The optimal neural network architecture is learnt along with learning the transition kernel of the abstract process. Automated search of the architecture makes the method applicable directly to any given CRN, which is time-saving for deep learning experts and crucial for non-specialists. The tool was primarily designed to efficiently reproduce simulation traces of given complex stochastic reaction networks arising in systems biology research, possibly with multi-modal emergent phenotypes. It is at the same time applicable to any other application domain, where time-series measurements of a Markovian stochastic process are available by experiment or synthesised with simulation (e.g. are obtained from a rule-based description of the CRN)

A Bacterial Toxin Inhibits DNA Replication Elongation through a Direct Interaction with the β Sliding Clamp

Toxin-antitoxin (TA) systems are ubiquitous on bacterial chromosomes, yet the mechanisms regulating their activity and the molecular targets of toxins remain incompletely defined. Here, we identify SocAB, an atypical TA system in Caulobacter crescentus. Unlike canonical TA systems, the toxin SocB is unstable and constitutively degraded by the protease ClpXP; this degradation requires the antitoxin, SocA, as a proteolytic adaptor. We find that the toxin, SocB, blocks replication elongation through an interaction with the sliding clamp, driving replication fork collapse. Mutations that suppress SocB toxicity map to either the hydrophobic cleft on the clamp that binds DNA polymerase III or a clamp-binding motif in SocB. Our findings suggest that SocB disrupts replication by outcompeting other clamp-binding proteins. Collectively, our results expand the diversity of mechanisms employed by TA systems to regulate toxin activity and inhibit bacterial growth, and they suggest that inhibiting clamp function may be a generalizable antibacterial strategy.Howard Hughes Medical Institute (Summer Medical Fellowship)National Science Foundation (U.S.). Graduate Research Fellowship ProgramNational Institutes of Health (U.S.) (R01GM082899

Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development

Histological Evaluation of the Biocompatibility of Polyurea Crosslinked Silica Aerogel Implants in a Rat Model: A Pilot Study

Background: Aerogels are a versatile group of nanostructured/nanoporous materials with physical and chemical properties that can be adjusted to suit the application of interest. In terms of biomedical applications, aerogels are particularly suitable for implants such as membranes, tissue growth scaffolds, and nerve regeneration and guidance inserts. The mesoporous nature of aerogels can also be used for diffusion based release of drugs that are loaded during the drying stage of the material. From the variety of aerogels polyurea crosslinked silica aerogels have the most potential for future biomedical applications and are explored here. Methodology: This study assessed the short and long term biocompatibility of polyurea crosslinked silica aerogel implants in a Sprague-Dawley rat model. Implants were inserted at two different locations a) subcutaneously (SC), at the dorsum and b) intramuscularly (IM), between the gluteus maximus and biceps femoris of the left hind extremity. Nearby muscle and other internal organs were evaluated histologically for inflammation, tissue damage, fibrosis and movement (travel) of implant. Conclusion/Significance: In general polyurea crosslinked silica aerogel (PCSA) was well tolerated as a subcutaneous and an intramuscular implant in the Sprague-Dawley rat with a maximum incubation time of twenty months. In some cases a thin fibrous capsule surrounded the aerogel implant and was interpreted as a normal response to foreign material. No noticeable toxicity was found in the tissues surrounding the implants nor in distant organs. Comparison was made with control rats without any implants inserted, and animals with suture material present. No obvious or noticeable changes were sustained by the implants at either location. Careful necropsy and tissue histology showed age-related changes only. An effective sterilization technique for PCSA implants as well as staining and sectioning protocol has been established. These studies further support the notion that silica-based aerogels could be useful as biomaterials. © 2012 Sabri et al

Transport Phenomena and Structuring in Shear Flow of Suspensions near Solid Walls

In this paper we apply the lattice-Boltzmann method and an extension to particle suspensions as introduced by Ladd et al. to study transport phenomena and structuring effects of particles suspended in a fluid near sheared solid walls. We find that a particle free region arises near walls, which has a width depending on the shear rate and the particle concentration. The wall causes the formation of parallel particle layers at low concentrations, where the number of particles per layer decreases with increasing distance to the wall.Comment: 14 pages, 14 figure

Team knowledge sharing: A game-based learning approach

Introduction. Business simulation games that have been widely used in teaching in recent years have been proven to help students develop teamwork and problem-solving skills. Aim. The current research aims to assess how team cohesion and knowledge sharing attitudes relate to organisational climate and knowledge sharing (KS) intentions. Methodology and research methods. Through the use of a game-based team learning environment, this study examined the students’ attitudes and intentions regarding KS. As part of the study, questionnaires were also administered to 202 students at business colleges in Ho Chi Minh City, Vietnam. Bootstrapping estimation was used to test all hypotheses using a structural equation model (SEM). Results. The research findings showed that (1) organisational climate positively influenced team cohesion, as well as KS attitudes positively influencing KS intentions; (2) organisational climate was positively related to KS attitudes and intentions; (3) team cohesion was positively associated with KS attitudes and intentions; and (4) a significant relationship exists between organisational climate and KS intentions through the mediation of team cohesion and KS attitudes. Scientific novelty. The study helps to examine the relationships between the four variables that have been done before. Practical significance. The research findings suggest that teachers should establish grading standards and encourage students to express their opinions. In addition, it is crucial to create a good atmosphere and enhance cohesion in the class so that they can trigger students’ KS attitudes and intentions.Введение. Было доказано, что игровые бизнес-симуляторы, которые широко используются в преподавании в последние годы, помогают студентам развивать командную работу и навыки решения проблем. Цель исследования – оценить, как сплоченность команды и отношение к обмену знаниями связаны с намерениями создавать организационный климат и обмениваться знаниями. Методология, методы и методики. Используя игровую среду обучения, авторы изучили отношения и намерения студентов, касающиеся обмена знаниями. В рамках исследования анкеты были направлены 202 студентам бизнес-колледжей в Хошимине, Вьетнам. Оценка методом бутстрепа использовалась для проверки всех гипотез с использованием модели структурных уравнений (SEM). Результаты. Результаты исследования показали, что: 1) организационный климат положительно повлиял на сплоченность команды, а также на отношение к обмену знаниями, позитивно воздействующее на намерения обмениваться знаниями; 2) организационный климат был положительно связан с отношением к обмену знаниями и намерениями обмениваться знаниями; 3) сплоченность команды была положительно связана с отношением к обмену знаниями и намерениями обмениваться знаниями; 4) существует значительная связь между организационным климатом и намерениями обмениваться знаниями через посредничество сплоченности команды и отношения к обмену знаниями. Научная новизна. Исследование помогает изучить взаимосвязи между четырьмя переменными, которые были упомянуты выше. Практическая значимость. Результаты исследования показывают, что преподаватели должны устанавливать стандарты оценивания и побуждать учащихся выражать свое мнение. Кроме того, крайне важно создать хорошую атмосферу и повысить сплоченность в классе, для того чтобы формировать положительное отношение к обмену знаниями и намерения студентов использовать эти навыки