Topological correlations in soap froths

Correlation in two-dimensional soap froth is analysed with an effective potential for the first time. Cells with equal number of sides repel (with linear correlation) while cells with different number of sides attract (with NON-bilinear) for nearest neighbours, which cannot be explained by the maximum entropy argument. Also, the analysis indicates that froth is correlated up to the third shell neighbours at least, contradicting the conventional ideas that froth is not strongly correlated.Comment: 10 Pages LaTeX, 6 Postscript figure

Topological model of soap froth evolution with deterministic T2-processes

We introduce a topological model for the evolution of 2d soap froth. The topological rearrangements (T2 processes) are deterministic (unlike the standard stochastic model): the final topology depends on the areas of the neighboring cells. The new model gives agreement with experiments in the transient regime, where the previous models failed qualitatively, and also improves agreement in the scaling state.Comment: latex, 12 pages, 2 figure

Desmoglein 2 promotes vasculogenic mimicry in melanoma and is associated with poor clinical outcome

Tumors can develop a blood supply not only by promoting angiogenesis but also by forming vessel-like structures directly from tumor cells, known as vasculogenic mimicry (VM). Understanding mechanisms that regulate VM is important, as these might be exploitable to inhibit tumor progression. Here, we reveal the adhesion molecule desmoglein 2 (DSG2) as a novel mediator of VM in melanoma. Analysis of patient-derived melanoma cell lines and tumor tissues, and interrogation of The Cancer Genome Atlas (TCGA) data, revealed that DSG2 is frequently overexpressed in primary and metastatic melanomas compared to normal melanocytes. Notably, this overexpression was associated with poor clinical outcome. DSG2+ melanoma cells self-organized into tube-like structures on Matrigel, indicative of VM activity, which was inhibited by DSG2 knockdown or treatment with a DSG2-blocking peptide. Mechanistic studies revealed that DSG2 regulates adhesion and cell-cell interactions during tube formation, but does not control melanoma cell viability, proliferation or motility. Finally, analysis of patient tumors revealed a correlation between DSG2 expression, VM network density and expression of VM-associated genes. These studies identify DSG2 as a key regulator of VM activity in human melanoma and suggest this molecule might be therapeutically targeted to reduce tumor blood supply and metastatic spread.Lih Yin Tan, Chris Mintoff, M. Zahied Johan, Brenton W. Ebert, Clare Fedele, You Fang Zhang, Pacman Szeto, Karen E. Sheppard, Grant A. McArthur, Erwin Foster-Smith, Andrew Ruszkiewicz, Michael P. Brown, Claudine S. Bonder, Mark Shackleton, Lisa M. Eber

The concerns and experiences of patients with lumbar spinal stenosis regarding prehabilitation and recovery after spine surgery: A qualitative study

Objectives To improve our understanding of patients’ perspectives regarding: (1) the decision making and prehabilitation before lumbar spinal stenosis (LSS) surgery; and (2) their postoperative experiences. Design Qualitative research with semi-structured interviews. Setting General community Participants Individuals received (n=10) and did not receive (n=15) prehabilitation before LSS surgery were recruited at the 6-month postoperative follow-up (8 females; average age: 67.7±6.7 years) by purposive sampling. Additionally, one participant invited her daughter to accompany her in an interview. Interventions Not applicable Main outcome measures Concerns and experiences of patients with LSS regarding prehabilitation and recovery after spine surgery. Results Thematic analysis was conducted to identify four themes inductively: (1) sources of information about LSS surgery; (2) factors affecting the surgical decision making; (3) attitudes toward prehabilitation; and (4) postoperative recovery. All participants desired to have more preoperative education to inform their surgical decision making. There were mixed opinions regarding the perceived benefits of prehabilitation because some individuals hesitated to participate in prehabilitaiotn due to their symptoms, or the cost or time of travelling. Many participants expected some or even complete relief of LSS-related symptoms after surgery. However, not all participants experienced the expected postoperative improvements. Some participants only experienced temporary symptomatic relief, while others experienced new postoperative symptoms. Patients generally found that postoperative exercises taught by physiotherapists were useful although their compliance decreased over time. Conclusions Our study highlights the need for better preoperative LSS education. Since face-to-face prehabilitation or postoperative rehabilitation may not be feasible for all patients, future studies should explore whether online-based prehabilitation or postoperative rehabilitation may benefit certain patient subgroups

Evaluation of flow after transcatheter aortic valve replacement in patients with low-flow aortic stenosis : a secondary analysis of the PARTNER randomized clinical trial

Importance: Low-flow (LF) severe aortic stenosis (AS) is an independent predictor of mortality in patients undergoing aortic valve replacement (AVR). Little is known about improvement in flow after AVR and its effects on survival. Objective: To determine whether higher flow (left-ventricular stroke volume index [LVSVI]) after transcatheter AVR (TAVR) would indicate better clinical outcomes in this at-risk population. Design, Setting, and Participants: A substudy analysis of data from the Placement of Aortic Transcatheter Valves (PARTNER) randomized clinical trial and continued-access registry was conducted. A total of 984 participants with evaluable echocardiograms and baseline LF AS (LVSVI =35 mL/m2) were included. The trial was conducted at 26 sites in the United States and Canada. Patients were stratified after TAVR into tertiles by discharge LVSVI status (severe low flow [SLF], moderate low flow [MLF], and normal flow [(NF]). The present study was conducted from May 11, 2007, to January 9, 2012, with data analysis performed from April 25, 2014, to January 21, 2016. Main Outcomes and Measures: The primary end point was all-cause mortality at 1 year. Results: Baseline characteristics of 984 patients with LF AS included mean (SD) age, 84 (7) years; 582 (59.1%) men; mean Society of Thoracic Surgeons (STS) score, 11.4% (4.0%); and mean LVSVI, 27.6 (5.0) mL/m2. The discharge LVSVI values by group were SLF, 23.1 (3.5) mL/m2; MLF, 31.7 (2.2) mL/m2; and NF, 43.1 (7.0). All-cause mortality at 1 year was SLF, 26.5%; MLF, 20.1%; and NF, 19.6% (P¿=¿.045). Mean LVSVI normalized by 6 months in the MLF (35.9 [9.3] mL/m2) and NF (38.8 [11.1] mL/m2) groups, but remained low in the SLF group at 6 months and 1 year (31.4 [8.4] and 33.0 [8.3] mL/m2], respectively) (P¿<¿.001 for all groups). Reported as multivariate hazard ratio, mortality at 1 year was higher in the SLF group compared with the other groups (1.61; 95% CI, 1.17-2.23; P¿=¿.004). In addition to SLF, sex (1.59; 95% CI, 1.18-2.13; P¿=¿.002), presence of atrial fibrillation (1.41; 95% CI, 1.06-1.87; P¿=¿.02), STS score (1.03; 95% CI, 1.01-1.06; P¿=¿.02), presence of moderate or severe mitral regurgitation at discharge (1.65; 95% CI, 1.21-2.26; P¿=¿.001), pre-TAVR mean transvalvular gradient (0.98; 95% CI, 0.97-0.99; P¿=¿.004), and effective orifice area index (1.87; 95% CI, 1.09-3.19; P¿=¿.02) were independent predictors of 1-year mortality.CONCLUSIONS AND RELEVANCE: Severe LF at discharge is associated with an increased risk of mortality following TAVR in patients with severe AS and preexisting LF. The identification of remedial causes of persistent LF after TAVR may represent an opportunity to improve the outcome of these patients

Human neutrophil clearance of bacterial pathogens triggers anti-microbial gamma delta T cell responses in early infection

Human blood Vc9/Vd2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vc9/Vd2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vc9/Vd2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-c and tumor necrosis factor (TNF)-a. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vc9/Vd2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-a dependent proliferation of Vc9/Vd2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting cd T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vc9/Vd2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The cd T celldriven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of cd T cells and TNF-a and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive cd T cells in early infection and suggest novel diagnostic and therapeutic approaches.Martin S. Davey, Chan-Yu Lin, Gareth W. Roberts, Sinéad Heuston, Amanda C. Brown, James A. Chess, Mark A. Toleman, Cormac G.M. Gahan, Colin Hill, Tanya Parish, John D. Williams, Simon J. Davies, David W. Johnson, Nicholas Topley, Bernhard Moser and Matthias Eber

Protein Pattern Formation

Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole oscillations of Min proteins in \textit{E. coli} whose biological function is to ensure precise cell division. Cell polarization, a prerequisite for processes such as stem cell differentiation and cell polarity in yeast, is also mediated by a diffusion-reaction process. More generally, these functional modules of cells serve as model systems for self-organization, one of the core principles of life. Under which conditions spatio-temporal patterns emerge, and how these patterns are regulated by biochemical and geometrical factors are major aspects of current research. Here we review recent theoretical and experimental advances in the field of intracellular pattern formation, focusing on general design principles and fundamental physical mechanisms.Comment: 17 pages, 14 figures, review articl

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/