RNA-RNA interaction prediction based on multiple sequence alignments

Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both thermodynamic stability and sequence covariation. We present the \emph{a priori} folding algorithm \texttt{ripalign}, whose input consists of two (given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) the partition function, (2) base-pairing probabilities, (3) hybrid probabilities and (4) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm \texttt{rip}, \texttt{ripalign} requires negligible additional memory resource. Furthermore, we incorporate possible structure constraints as input parameters into our algorithm. The algorithm described here is implemented in C as part of the \texttt{rip} package. The supplemental material, source code and input/output files can freely be downloaded from \url{http://www.combinatorics.cn/cbpc/ripalign.html}. \section{Contact} Christian Reidys \texttt{[email protected]}Comment: 8 pages, 9 figure

Analytic solutions to determine critical magnetic fields for thermoelectric magnetohydrodynamics in alloy solidification

During alloy solidification, it has been observed that the morphology of microstructures can be altered by applying an external DC magnetic field. This structural change can be attributed to solutal convective transport introduced by thermoelectric magnetohydrodynamics (TEMHD) which drives fluid motion within the inter-dendritic region. Complex numerical models with grid resolutions on the microscopic scale have been constructed to solve the equations governing TEMHD. To complement these computationally intensive numerical models, analytic solutions were sought. Specifically, the analytic solutions presented herein are asymptotic solutions derived for TEMHD under low and high magnetic field intensities. Combination of these asymptotic solutions leads to simple formulae for estimating critical magnetic fields which can be readily evaluated in terms of characteristic lengths of materials that have been identified in experiments as key parameters of critical fields. Indeed, the critical magnetic fields predicted with the asymptotic solutions exhibit magnitudes consistent with those applied in current ongoing experiments where significant changes in microstructure have been observed. The capability to predict accurate results indicates that the analytic solutions described herein are valuable precursors not only for detailed numerical simulations but also for experimental design to study critical magnetic fields in alloy solidification

Robotic Surgery for Non-Small Cell Lung Cancer

Pulmonary resection has been a cornerstone in the management of patients with non-small cell lung cancer (NSCLC) for decades. In recent years, the popularity of minimally-invasive techniques as the primary method to manage NSCLC has grown significantly. With smaller incisions and a lower incidence of peri-operative complications, minimally-invasive lung resection, accomplished through keyhole incisions with miniaturized cameras and similarly small instruments that work through surgical ports, has been shown to retain equivalent oncologic outcomes to the traditional gold standard open thoracotomy. This technique allows for the safe performance of anatomic lung resection with complete lymphadenectomy and has been a part of thoracic surgery practice for three decades. Robotic-assisted thoracoscopic surgery (RATS) represents another major advancement for lung resection, broadening the opportunity for patients to undergo minimally invasive surgery for NSCLC, and therefore allowing a greater percentage of the lung cancer population to benefit from many of the advantages previously demonstrated from video assisted thoracoscopic surgery (VATS) techniques. RATS surgery is also associated with several technical advantages to the surgeon. For a surgeon who performs open procedures and is looking to adopt a minimally invasive approach, RATS ergonomics are a natural transition compared to VATS, particularly given the multiple degrees of freedom associated with robotic articulating instruments. As a result, this platform has been adopted as a primary approach in numerous institutions across the United States. In this chapter, we will explore the advantages and disadvantages of robotic-assisted surgery for NSCLC and discuss the implications for increased adoption of minimally invasive surgery in the future of lung cancer treatment

Broadband Dispersion-Free Optical Cavities Based on Zero Group Delay Dispersion Mirror Sets

A broadband dispersion-free optical cavity using a zero group delay dispersion (zero-GDD) mirror set is demonstrated. In general zero-GDD mirror sets consist of two or more mirrors with opposite group delay dispersion (GDD), that when used together, form an optical cavity with vanishing dispersion over an enhanced bandwidth in comparison with traditional low GDD mirrors. More specifically, in this paper, we show a realization of such a two-mirror cavity, where the mirrors show opposite GDD and simultaneously a mirror reflectivity of 99.2% over 100 nm bandwidth (480 nm - 580 nm).Physic

Generalized Tests for Eight GRB Luminosity Relations

Long duration Gamma-Ray Bursts (GRBs) have eight luminosity relations where observable burst properties can yield the burst luminosity and hence distance. This turns GRBs into useful tools of cosmology. Recently, two tests have been proposed (by Nakar & Piran and by Li) for which one of the eight relations is claimed to have significant problems. In this paper, we generalize these tests and apply them to all eight GRB luminosity relations. (a) All eight relations pass the Nakar & Piran test after accounting for the uncertainties on the data and the dispersions of the correlations. (b) All eight relations are good when the GRB redshifts are known, for example for calibration of the relations and for GRB Hubble diagram purposes. (c) We confirm the earlier results that the E_gamma,iso - E_peak Amati relation must produce very large error bars whenever an unknown redshift being sought is >1.4. (d) The E_gamma - E_peak relation of Ghirlanda et al. must produce very large error bars whenever an unknown redshift being sought is >3.4. (e) The other six relations have no problem at all from the ambiguity test of Li.Comment: Ap.J. Letters in press, 11 page

Cell density and actomyosin contractility control the organization of migrating collectives within an epithelium

The mechanisms underlying collective migration are important for understanding development, wound healing, and tumor invasion. Here we focus on cell density to determine its role in collective migration. Our findings show that increasing cell density, as might be seen in cancer, transforms groups from broad collectives to small, narrow streams. Conversely, diminishing cell density, as might occur at a wound front, leads to large, broad collectives with a distinct leader–follower structure. Simulations identify force-sensitive contractility as a mediator of how density affects collectives, and guided by this prediction, we find that the baseline state of contractility can enhance or reduce organization. Finally, we test predictions from these data in an in vivo epithelium by using genetic manipulations to drive collective motion between predicted migratory phases. This work demonstrates how commonly altered cellular properties can prime groups of cells to adopt migration patterns that may be harnessed in health or exploited in disease

Kaon differential flow in relativistic heavy-ion collisions

Using a relativistic transport model, we study the azimuthal momentum asymmetry of kaons with fixed transverse momentum, i.e., the differential flow, in heavy-ion collisions at beam momentum of 6 GeV/c per nucleon, available from the Alternating Gradient Synchrotron (AGS) at the Brookhaven National Laboratory (BNL). We find that in the absence of kaon potential the kaon differential flow is positive and increases with transverse momentum as that of nucleons. The repulsive kaon potential as predicted by theoretical models, however, reduces the kaon differetnial flow, changing it to negative for kaons with low momenta. Cancellation between the negative differential flow at low mementa and the positive one at high momenta is then responsible for the experimentally observed nearly vanishing in-plane transverse flow of kaons in heavy ion experiments.Comment: Phys. Rev. C in pres

Predictors of chronic fatigue syndrome and mood disturbance after acute infection

Prospective cohort studies following individuals from acute infections have documented a prevalent post-infective fatigue state meeting diagnostic criteria for chronic fatigue syndrome (CFS) – that is, a post-infective fatigue syndrome (PIFS). The Dubbo Infection Outcomes Study (DIOS) was a prospective cohort following individuals from acute infection with Epstein-Barr virus (EBV), Ross River virus (RRV), or Q fever through to assessment of caseness for CFS designated by physician and psychiatrist assessments at 6 months. Previous studies in DIOS have revealed that functional genetic polymorphisms in both immunological (pro- and anti-inflammatory cytokines) and neurological (the purinergic receptor, P2X7) genes are associated with both the severity of the acute infection and subsequent prolonged illness. Principal components analysis was applied to self-report data from DIOS to describe the severity and course of both the overall illness and concurrent mood disturbance. Associations between demographics and acute infection characteristics, with prolonged illness course as well as the PIFS outcome were examined using multivariable statistics. Genetic haplotype-driven functional variations in the neuropeptide Y (NPY) gene previously shown to be associated with brain responses to stress, and to trait anxiety were also examined as predictors. The sample included 484 subjects (51% female, median age 32, IQR 19–44), of whom 90 (19%) met diagnostic criteria for CFS at 6 months. Participants with greater overall illness severity and concurrent mood disturbance in the acute illness had a more prolonged illness severity (HR = 0.39, 95% CI: 0.34–0.46, p 0.05). Severe acute infective illnesses predicted prolonged illness, prolonged mood disturbance and PIFS. These factors may facilitate early intervention to manage both PIFS and mood disturbances