Foundations of Dissipative Particle Dynamics

We derive a mesoscopic modeling and simulation technique that is very close to the technique known as dissipative particle dynamics. The model is derived from molecular dynamics by means of a systematic coarse-graining procedure. Thus the rules governing our new form of dissipative particle dynamics reflect the underlying molecular dynamics; in particular all the underlying conservation laws carry over from the microscopic to the mesoscopic descriptions. Whereas previously the dissipative particles were spheres of fixed size and mass, now they are defined as cells on a Voronoi lattice with variable masses and sizes. This Voronoi lattice arises naturally from the coarse-graining procedure which may be applied iteratively and thus represents a form of renormalisation-group mapping. It enables us to select any desired local scale for the mesoscopic description of a given problem. Indeed, the method may be used to deal with situations in which several different length scales are simultaneously present. Simulations carried out with the present scheme show good agreement with theoretical predictions for the equilibrium behavior.Comment: 18 pages, 7 figure

Inflammation decreases keratin level in ulcerative colitis; inadequate restoration associates with increased risk of colitis-associated cancer

Background Keratins are intermediate filament (IF) proteins, which form part of the epithelial cytoskeleton and which have been implicated pathology of inflammatory bowel diseases (IBD). Methods In this study biopsies were obtained from IBD patients grouped by disease duration and subtype into eight categories based on cancer risk and inflammatory status: quiescent recent onset (<5 years) UC (ROUC); UC with primary sclerosing cholangitis; quiescent long-standing pancolitis (20–40 years) (LSPC); active colitis and non-inflamed proximal colonic mucosa; pancolitis with dysplasia-both dysplastic lesions (DT) and distal rectal mucosa (DR); control group without pathology. Alterations in IF protein composition across the groups were determined by quantitative proteomics. Key protein changes were validated by western immunoblotting and immunohistochemical analysis. Result Acute inflammation resulted in reduced K8, K18, K19 and VIM (all p<0.05) compared to controls and non inflamed mucosa; reduced levels of if– associated proteins were also seen in DT and DR. Increased levels of keratins in LSPC was noted relative to controls or ROUC (K8, K18, K19 and VIM, p<0.05). Multiple K8 forms were noted on immunoblotting, with K8 phosphorylation reduced in progressive disease along with an increase in VIM:K8 ratio. K8 levels and phosphorylation are reduced in acute inflammation but appear restored or elevated in subjects with clinical and endoscopic remission (LSPC) but not apparent in subjects with elevated risk of cancer. Conclusions These data suggest that keratin regulation in remission may influence subsequent cancer risk

Non-linear numerical simulations of magneto-acoustic wave propagation in small-scale flux tubes

We present results of non-linear, 2D, numerical simulations of magneto-acoustic wave propagation in the photosphere and chromosphere of small-scale flux tubes with internal structure. Waves with realistic periods of three to five minutes are studied, after applying horizontal and vertical oscillatory perturbations to the equilibrium model. Spurious reflections of shock waves from the upper boundary are minimized thanks to a special boundary condition. This has allowed us to increase the duration of the simulations and to make it long enough to perform a statistical analysis of oscillations. The simulations show that deep horizontal motions of the flux tube generate a slow (magnetic) mode and a surface mode. These modes are efficiently transformed into a slow (acoustic) mode in the vA < cS atmosphere. The slow (acoustic) mode propagates vertically along the field lines, forms shocks and remains always within the flux tube. It might deposit effectively the energy of the driver into the chromosphere. When the driver oscillates with a high frequency, above the cut-off, non-linear wave propagation occurs with the same dominant driver period at all heights. At low frequencies, below the cut-off, the dominant period of oscillations changes with height from that of the driver in the photosphere to its first harmonic (half period) in the chromosphere. Depending on the period and on the type of the driver, different shock patterns are observed.Comment: 22 pages 6 color figures, submitted to Solar Physics, proceeding of SOHO 19/ GONG 2007 meeting, Melbourne, Australi

Disordered macrophage cytokine secretion underlies impaired acute inflammation and bacterial clearance in Crohn's disease

The cause of Crohn's disease (CD) remains poorly understood. Counterintuitively, these patients possess an impaired acute inflammatory response, which could result in delayed clearance of bacteria penetrating the lining of the bowel and predispose to granuloma formation and chronicity. We tested this hypothesis in human subjects by monitoring responses to killed Escherichia coli injected subcutaneously into the forearm. Accumulation of 111In-labeled neutrophils at these sites and clearance of 32P-labeled bacteria from them were markedly impaired in CD. Locally increased blood flow and bacterial clearance were dependent on the numbers of bacteria injected. Secretion of proinflammatory cytokines by CD macrophages was grossly impaired in response to E. coli or specific Toll-like receptor agonists. Despite normal levels and stability of cytokine messenger RNA, intracellular levels of tumor necrosis factor (TNF) were abnormally low in CD macrophages. Coupled with reduced secretion, these findings indicate accelerated intracellular breakdown. Differential transcription profiles identified disease-specific genes, notably including those encoding proteins involved in vesicle trafficking. Intracellular destruction of TNF was decreased by inhibitors of lysosomal function. Together, our findings suggest that in CD macrophages, an abnormal proportion of cytokines are routed to lysosomes and degraded rather than being released through the normal secretory pathway

The remarkable outburst of the highly-evolved post period-minimum dwarf nova SSS J122221.7−311525

We report extensive 3-yr multiwavelength observations of the WZ Sge-type dwarf nova SSS J122221.7−311525 during its unusual double superoutburst, the following decline and in quiescence. The second segment of the superoutburst had a long duration of 33 d and a very gentle decline with a rate of 0.02 mag d−1, and it displayed an extended post-outburst decline lasting at least 500 d. Simultaneously with the start of the rapid fading from the superoutburst plateau, the system showed the appearance of a strong near-infrared excess resulting in very red colours, which reached extreme values (B − I ≃ 1.4) about 20 d later. The colours then became bluer again, but it took at least 250 d to acquire a stable level. Superhumps were clearly visible in the light curve from our very first time-resolved observations until at least 420 d after the rapid fading from the superoutburst. The spectroscopic and photometric data revealed an orbital period of 109.80 min and a fractional superhump period excess ≲0.8 per cent, indicating a very low mass ratio q ≲ 0.045. With such a small mass ratio the donor mass should be below the hydrogen-burning minimum mass limit. The observed infrared flux in quiescence is indeed much lower than is expected from a cataclysmic variable with a near-main-sequence donor star. This strongly suggests a brown-dwarf-like nature for the donor and that SSS J122221.7−311525 has already evolved away from the period minimum towards longer periods, with the donor now extremely dim

Oracle-based optimization applied to climate model calibration

In this paper, we show how oracle-based optimization can be effectively used for the calibration of an intermediate complexity climate model. In a fully developed example, we estimate the 12 principal parameters of the C-GOLDSTEIN climate model by using an oracle- based optimization tool, Proximal-ACCPM. The oracle is a procedure that finds, for each query point, a value for the goodness-of-fit function and an evaluation of its gradient. The difficulty in the model calibration problem stems from the need to undertake costly calculations for each simulation and also from the fact that the error function used to assess the goodness-of-fit is not convex. The method converges to a Fbest fit_ estimate over 10 times faster than a comparable test using the ensemble Kalman filter. The approach is simple to implement and potentially useful in calibrating computationally demanding models based on temporal integration (simulation), for which functional derivative information is not readily available

Limit on Tau Neutrino Mass from τ−→π−π+π−π0ντ\tau^{-}\to \pi^{-}\pi^{+}\pi^{-}\pi^{0}\nu_{\tau}

From a data sample of 29058 $\tau^\pm\to\pi^\pm\pi^+\pi^-\pi^0\nu_\tau$ decays observed in the CLEO detector we derive a 95% confidence upper limit on the tau neutrino mass of 28 MeV.Comment: 17 pages postscript, also available through http://w4.lns.cornell.edu/public/CLN

Short-term quality of life after myomectomy for uterine fibroids from the compare-uf fibroid registry

Background Uterine fibroids may decrease quality of life in a significant proportion of affected women. Myomectomy offers a uterine-sparing treatment option for patients with uterine fibroids that can be performed abdominally, laparoscopically (with or without robotic assistance), and hysteroscopically. Quality of life information using validated measures for different myomectomy routes, especially hysteroscopic myomectomy, is limited. Objective To compare women’s perception of their short-term health-related quality of life measures and reported time to return to usual activities and return to work for different routes of myomectomy. Materials and Methods Comparing Options for Management: Patient-centered Results for Uterine Fibroids (COMPARE-UF) is a prospective nationwide fibroid registry that enrolled premenopausal women seeking treatment for uterine fibroids at 8 clinical sites. For this analysis, we included women undergoing hysteroscopic, abdominal, or laparoscopic myomectomy who completed the postprocedure questionnaire scheduled between 6 and 12 weeks after surgery. Health-related quality of life outcomes, such as pain, anxiety, and return to usual activitie, were assessed for each route. The hysteroscopic myomectomy group had large differences in demographics, fibroid number, and uterine size compared to the other groups; thus, a direct comparison of quality of life measures was performed only for abdominal and laparoscopic approaches after propensity weighting. Propensity weighting was done using 24 variables that included demographics, quality of life baseline measures, and fibroid and uterine measurements. Results A total of 1206 women from 8 COMPARE-UF sites underwent myomectomy (338 hysteroscopic, 519 laparoscopic, and 349 abdominal). All women had substantial improvement in short-term health-related quality of life and symptom severity scores, which was not different among groups. Average symptom severity scores decreased about 30 points in each group. Return to usual activities averaged 0 days (interquartile range, 0–14 days) for hysteroscopic myomectomy, 21 days (interquartile range, 14–28 days) for laparoscopic myomectomy, and 28 days (interquartile range, 14–35 days) for abdominal myomectomy. After propensity adjustment, quality of life outcomes in the laparoscopic and abdominal myomectomy groups were similar except for more anxiety in the laparoscopic myomectomy group and slightly more pain in the abdominal myomectomy group. After propensity weighting, return to usual activities favored laparoscopic compared to abdominal procedures; median time was the same at 21 days, but the highest quartile of women in the abdominal group needed an additional week of recovery (interquartile range,14.0–28.0 for laparoscopic versus 14.0–35.0 for abdominal, P < .01). Time to return to work was also longer in the abdominal arm (median, 22 days; interquartile range, 14–40 days, versus median, 42; interquartile range, 27–56). Conclusion Women who underwent myomectomy had substantial improvement in health-related quality of life, regardless of route of myomectomy. After propensity weighting, abdominal myomectomy was associated with a nearly 2-week longer time to return to work than laparoscopic myomectomy