The prognostic impact of EGFR, ErbB2 and MET gene amplification in human gastric carcinomas as measured by quantitative Real-Time PCR

Purpose: Identification of critical genes which play pivotal roles in controlling tumor growth and survival will establish the basis for developing therapeutic targets. In this study, we focused on frequencies of EGFR, ErbB2 and MET gene amplification in gastric cancer patients to develop personalized medicine to improve the treatment. Method: EGFR, ErbB2 and MET gene amplification, and mRNA expression were analyzed by the quantitative Real-Time PCR in paraffin-embedded samples from 115 patients with gastric cancer. Results: EGFR, ErbB2 and MET genes were amplified in 11.3 % (13/115), 6.1 % (7/115) and 19.1 % (22/115) of cancerous specimens, respectively. The correlation coefficient test clearly indicated that gene amplification in these three genes was positively correlated with mRNA transcription (EGFR: R = 0.631, p = 0.009; ErbB2: R = 0.652, p = 0.023; MET: R = 0.715, p < 0.001). EGFR and MET gene amplification was significantly associated with Ki-67 MI (p = 0.022 and p = 0.015). MET amplification was also significantly associated with age of ≥60 years (p = 0.021) and tumor size of ≥5 cm (p = 0.032). MET amplification, but not EGFR and ErbB2, was a significant prognostic factor in poor survival among patients with gastric cancer. Conclusions: EGFR, ErbB2 and MET genes are frequently amplified in gastric carcinoma. EGFR, ErbB2 and MET gene amplification is positively correlated with mRNA transcription. MET gene amplification correlates with a poor prognosis and poor survival in gastric carcinomas. © 2015, Springer-Verlag Berlin Heidelberg

Lasso formulation of the shortest path problem

The shortest path problem is formulated as an $l_1$-regularized regression problem, known as lasso. Based on this formulation, a connection is established between Dijkstra's shortest path algorithm and the least angle regression (LARS) for the lasso problem. Specifically, the solution path of the lasso problem, obtained by varying the regularization parameter from infinity to zero (the regularization path), corresponds to shortest path trees that appear in the bi-directional Dijkstra algorithm. Although Dijkstra's algorithm and the LARS formulation provide exact solutions, they become impractical when the size of the graph is exceedingly large. To overcome this issue, the alternating direction method of multipliers (ADMM) is proposed to solve the lasso formulation. The resulting algorithm produces good and fast approximations of the shortest path by sacrificing exactness that may not be absolutely essential in many applications. Numerical experiments are provided to illustrate the performance of the proposed approach.Comment: 17 page

Stochastic thermodynamic engines under time-varying temperature profile

In the present paper, we study the power output and efficiency of overdamped stochastic thermodynamic engines that are in contact with a heat bath having a temperature that varies periodically with time. This is in contrast to most of the existing literature that considers the Carnot paradigm of alternating contact with heat baths having different fixed temperatures, hot and cold. Specifically, we consider a periodic and bounded but otherwise arbitrary temperature profile and derive explicit bounds on the power and efficiency achievable by a suitable controlling potential that couples the thermodynamic engine to the external world. Standing assumptions in our analysis are bounds on the norm of the gradient of effective potentials -- in the absence of any such constraint, the physically questionable conclusion of arbitrarily large power can be drawn.Comment: 14 page

On the relation between information and power in stochastic thermodynamic engines

The common saying, that information is power, takes a rigorous form in stochastic thermodynamics, where a quantitative equivalence between the two helps explain the paradox of Maxwell's demon in its ability to reduce entropy. In the present paper, we build on earlier work on the interplay between the relative cost and benefits of information in producing work in cyclic operation of thermodynamic engines (by Sandberg etal. 2014). Specifically, we study the general case of overdamped particles in a time-varying potential (control action) in feedback that utilizes continuous measurements (nonlinear filtering) of a thermodynamic ensemble, to produce suitable adaptations of the second law of thermodynamics that involve information

Inertialess Gyrating Engines

A typical model for a gyrating engine consists of an inertial wheel powered by an energy source that generates an angle-dependent torque. Examples of such engines include a pendulum with an externally applied torque, Stirling engines, and the Brownian gyrating engine. Variations in the torque are averaged out by the inertia of the system to produce limit cycle oscillations. While torque generating mechanisms are also ubiquitous in the biological world, where they typically feed on chemical gradients, inertia is not a property that one naturally associates with such processes. In the present work, seeking ways to dispense of the need for inertial effects, we study an inertia-less concept where the combined effect of coupled torque-producing components averages out variations in the ambient potential and helps overcome dissipative forces to allow sustained operation for vanishingly small inertia. We exemplify this inertia-less concept through analysis of two of the aforementioned engines, the Stirling engine and the Brownian gyrating engine. An analogous principle may be sought in biomolecular processes as well as in modern-day technological engines, where for the latter, the coupled torque-producing components reduce vibrations that stem from the variability of the generated torque.Comment: 9 pages, 7 figure

Computational Optimal Transport and Filtering on Riemannian manifolds

In this paper we extend recent developments in computational optimal transport to the setting of Riemannian manifolds. In particular, we show how to learn optimal transport maps from samples that relate probability distributions defined on manifolds. Specializing these maps for sampling conditional probability distributions provides an ensemble approach for solving nonlinear filtering problems defined on such geometries. The proposed computational methodology is illustrated with examples of transport and nonlinear filtering on Lie groups, including the circle $S^1$, the special Euclidean group $SE(2)$, and the special orthogonal group $SO(3)$.Comment: 6 pages, 7 figure

Comparison of quadruple and triple Furazolidone containing regimens on eradication of helicobacter pylori

Background: The effectiveness of classic standard triple therapy regimen of helicobacter pylori (H. pylori) eradication has decreased to unacceptably low levels, largely related to development of resistance to metronidazole and clarithromycin. Thus successful eradication of H. pylori infections remains challenging. Therefore alternative treatments with superior effectiveness and safety should be designed and appropriately tested in all areas depending on the native resistance patterns. Furazolidone has been used successfully in eradication regimens previously and regimens containing furazolidone may be an ideal regimen. Methods: H. pylori infected patients with proven gastric or duodenal ulcers and /or gastric or duodenal erosions at Imam Khomeini Hospital in Sari/Northern Iran, were randomly allocated into three groups: group A (OABF) with furazolidone (F) (200 mg bid.), group B (OABM-F) metronidazole (M) (500 mg bid.) for the first five days, followed by furazolidone (F) (200 mg bid.) for the second five days and group C (OAF) with furazolidone (F) (200 mg tid.). Omeprazole (O) (20 mg bid.) and amoxicillin (A) (1000 mg bid.) were given in all groups; bismuth (B) (240 mg bid.) was prescribed in groups A&B. Duration of all eradication regimens were ten days. Eight weeks after treatment, a 14C-urea breath test was performed for evaluation of H. pylori eradication. Results: A total of 372 patients were enrolled in three groups randomly (124 patients in each group); 120 (97) patients in group A (OABF), 120 (97) in group B (OABM-F) and 116 (93) in group C (OAF) completed the study. The intention-to-treat eradication rates were 83.7 (95 CI= 77.3-90.4), 79.8 (95 CI= 72.6-87), and 84.6 (95 CI= 78.2-91.1) and per-protocol eradication rates were 86.6 (95 CI= 80.5-92.8), 82.5 (95 CI= 75.6-89.4), and 90.5 (95 CI= 85.1-95.9) for groups OABF, OABM-F, and OAF, respectively. No statistical significant differences were found in case of severe drug adverse effects between the above mentioned three groups (p> 0.05). The most common side effects, namely nausea and fever, occurred in all groups, but more frequently in group C (OAF) (p< 0.05). Conclusion: In developing countries such as Iran, furazolidone-based regimens can substitute clarithromycinbased regimens for H. pylori eradication because of a very low level of resistance, low cost and high effectiveness. Considering per-protocol eradication rate of ten days OAF regimen, and the acceptable limit of ninety percent, we recommend this regimen in developing countries such as Iran to be substituted of classic standard triple therapy. In order to minimize rare serious adverse effects, one week high dose OAF regimen should be taken into consideration in other studies

ISMRM Open Science Initiative for Perfusion Imaging (OSIPI): ASL pipeline inventory

Purpose: To create an inventory of image processing pipelines of arterial spin labeling (ASL) and list their main features, and to evaluate the capability, flexibility, and ease of use of publicly available pipelines to guide novice ASL users in selecting their optimal pipeline. Methods: Developers self-assessed their pipelines using a questionnaire developed by the Task Force 1.1 of the ISMRM Open Science Initiative for Perfusion Imaging. Additionally, each publicly available pipeline was evaluated by two independent testers with basic ASL experience using a scoring system created for this purpose. Results: The developers of 21 pipelines filled the questionnaire. Most pipelines are free for noncommercial use (n = 18) and work with the standard NIfTI (Neuroimaging Informatics Technology Initiative) data format (n = 15). All pipelines can process standard 3D single postlabeling delay pseudo-continuous ASL images and primarily differ in their support of advanced sequences and features. The publicly available pipelines (n = 9) were included in the independent testing, all of them being free for noncommercial use. The pipelines, in general, provided a trade-off between ease of use and flexibility for configuring advanced processing options. Conclusion: Although most ASL pipelines can process the common ASL data types, only some (namely, ASLPrep, ASLtbx, BASIL/Quantiphyse, ExploreASL, and MRICloud) are well-documented, publicly available, support multiple ASL types, have a user-friendly interface, and can provide a useful starting point for ASL processing. The choice of an optimal pipeline should be driven by specific data to be processed and user experience, and can be guided by the information provided in this ASL inventory