CFD modelling of buoyancy-driven natural ventilation opposed by wind

This paper presents CFD simulations of natural displacement ventilation airflows in which the buoyancy force produced by a heat source is opposed by a wind force. Cases investigated focus on windbuoyancy force relationships for which a two-layer stratification is maintained. CFD predictions of the position of the interface separating the two layers and the change in reduced gravity (temperature difference) between them are compared with the analytical work and salt-bath measurements of Hunt and Linden (2000, 2005). Comparisons are good with only minor discrepancies in the interface position and a small under-prediction of the upper layer reduced gravity

Grain refinement in a AlZnMgCuTi alloy by intensive melt shearing: A multi-step nucleation mechanism

This is a post-print version of the article. Copyright @ 2010 Elsevier B.V.Direct chill (DC) cast ingots of wrought Al alloys conventionally require the deliberate addition of a grain refiner to provide a uniform as-cast microstructure for the optimisation of both mechanical properties and processability. Grain refiner additions have been in widespread industrial use for more than half a century. Intensive melt shearing can provide grain refinement without the need for a specific grain refiner addition for both magnesium and aluminium based alloys. In this paper we present experimental evidence of the grain refinement in an experimental wrought aluminium alloy achieved by intensive melt shearing in the liquid state prior to solidification. The mechanisms for high shear induced grain refinement are correlated with the evolution of oxides in alloys. The oxides present in liquid aluminium alloys, normally as oxide films and clusters, can be effectively dispersed by intensive shearing and then provide effective sites for the heterogeneous nucleation of Al3Ti phase. As a result, Al3Ti particles with a narrow size distribution and hence improved efficiency as active nucleation sites of alpha-aluminium grains are responsible for the achieved significant grain refinement. This is termed a multi-step nucleation mechanism.Funding was obtained from the EPRSC

The genetics of cardiovascular disease

Recent advances in genotyping technology and insights into disease mechanisms have increased interest in the genetics of cardiovascular disease. Several candidate genes involved in cardiovascular diseases were identified from studies using animal models, and the translation of these findings to human disease is an exciting challenge. There is a trend towards large-scale genome-wide association studies that are subject to strict quality criteria with regard to both genotyping and phenotyping. Here, we review some of the strategies that have been developed to translate findings from experimental models to human disease and outline the need for optimizing global approaches to analyze such results. Findings from ongoing studies are interpreted in the context of disease pathways instead of the more traditional focus on single genetic variants

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina datasets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as 1 nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures + supplement. Significantly revised for clarity, references added, results not change

The C-Terminal Domain of the Novel Essential Protein Gcp Is Critical for Interaction with Another Essential Protein YeaZ of Staphylococcus aureus

Previous studies have demonstrated that the novel protein Gcp is essential for the viability of various bacterial species including Staphylococcus aureus; however, the reason why it is required for bacterial growth remains unclear. In order to explore the potential mechanisms of this essentiality, we performed RT-PCR analysis and revealed that the gcp gene (sa1854) was co-transcribed with sa1855, yeaZ (sa1856) and sa1857 genes, indicating these genes are located in the same operon. Furthermore, we demonstrated that Gcp interacts with YeaZ using a yeast two-hybrid (Y2H) system and in vitro pull down assays. To characterize the Gcp-YeaZ interaction, we performed alanine scanning mutagenesis on the residues of C-terminal segment of Gcp. We found that the mutations of the C-terminal Y317-F322 region abolished the interaction of Gcp and YeaZ, and the mutations of the D324-N329 and S332-Y336 regions alleviated Gcp binding to YeaZ. More importantly, we demonstrated that these key regions of Gcp are also necessary for the bacterial survival since these mutated Gcp could not complement the depletion of endogenous Gcp. Taken together, our data suggest that the interaction of Gcp and YeaZ may contribute to the essentiality of Gcp for S. aureus survival. Our findings provide new insights into the potential mechanisms and biological functions of this novel essential protein

A Computational Approach to Understand In Vitro Alveolar Morphogenesis

Primary human alveolar type II (AT II) epithelial cells maintained in Matrigel cultures form alveolar-like cysts (ALCs) using a cytogenesis mechanism that is different from that of other studied epithelial cell types: neither proliferation nor death is involved. During ALC formation, AT II cells engage simultaneously in fundamentally different, but not fully characterized activities. Mechanisms enabling these activities and the roles they play during different process stages are virtually unknown. Identifying, characterizing, and understanding the activities and mechanisms are essential to achieving deeper insight into this fundamental feature of morphogenesis. That deeper insight is needed to answer important questions. When and how does an AT cell choose to switch from one activity to another? Why does it choose one action rather than another? We report obtaining plausible answers using a rigorous, multi-attribute modeling and simulation approach that leveraged earlier efforts by using new, agent and object-oriented capabilities. We discovered a set of cell-level operating principles that enabled in silico cells to self-organize and generate systemic cystogenesis phenomena that are quantitatively indistinguishable from those observed in vitro. Success required that the cell components be quasi-autonomous. As simulation time advances, each in silico cell autonomously updates its environment information to reclassify its condition. It then uses the axiomatic operating principles to execute just one action for each possible condition. The quasi-autonomous actions of individual in silico cells were sufficient for developing stable cyst-like structures. The results strengthen in silico to in vitro mappings at three levels: mechanisms, behaviors, and operating principles, thereby achieving a degree of validation and enabling answering the questions posed. We suggest that the in silico operating principles presented may have a biological counterpart and that a semiquantitative mapping exists between in silico causal events and in vitro causal events

Spontaneous rupture of the lateral thoracic artery in patients with liver cirrhosis

Bleeding in patients with liver cirrhosis is primarily caused by gastroesophageal varix in association with extensive collateral circulation, portal hypertensive gastropathy, a Mallory-Weiss tear and peptic ulcer disease. The spontaneous rupture of an artery, as a result of coagulopathy, is extremely rare in patients with liver cirrhosis; however, we recently observed a case of a spontaneous rupture of the lateral thoracic artery in a 47 year-old male patient with alcoholic liver cirrhosis. The patient expired despite repeated transcatheter arterial embolization of the lateral thoracic artery and best supportive care. This is, to our knowledge, the first documented case of the spontaneous rupture of the lateral thoracic artery in a patient with liver cirrhosis

Persistent Anemia in a Patient with Diffuse Large B Cell Lymphoma: Pure Red Cell Aplasia Associated with Latent Epstein-Barr Virus Infection in Bone Marrow

We report a case of pure red cell aplasia (PRCA), which was initially suspected as a result of bone marrow involvement of diffuse large B cell lymphoma. Persistent anemia without an obvious cause was observed in a 47-yr-old man diagnosed with relapsed diffuse large B cell lymphoma. The bone marrow study showed only erythroid hypoplasia without the evidence of bone marrow involvement with lymphoma cells, thus PRCA was suggested. However, parvovirus infection was excluded as a potential cause of PRCA because of negative IgM anti-parvovirus B19 antibody and negative parvovirus PCR in the serum. Latent Epstein-Barr virus (EBV) infection of bone marrow was suggested by in situ hybridization with EBV-encoded small RNA (EBER) that showed a strong positive expression in bone marrow cells. Thus, PRCA was thought to be associated with latent EBV infection in bone marrow cells. Although the finding of unexplained anemia is a possible predictor of bone marrow involvement with lymphoma cells, PRCA as a result of a viral infection including EBV should be considered in lymphoma patients. This is the first report of the occurrence of PRCA associated with latent EBV infection in a patient with non-Hodgkin's lymphoma

Organic matter remineralization in marine sediments : A Pan-Arctic synthesis

Natural Environment Research Council (GrantNumber(s): NE/J023094/1; Grant recipient(s): Ursula Witte) ArcticNet (GrantNumber(s): Hotspot biodiversity project; Grant recipient(s): Philippe Archambault)Peer reviewedPublisher PD