Disordered, stretched, and semiflexible biopolymers in two dimensions

We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system is equivalent to a system with a well-defined intrinsic curvature and a proper renormalized persistence length. We find the exact expression for the distribution function of the equivalent system. However, we show that such an equivalent system does not always exist for the polymer subjected to an external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions, such as the boundary conditions. Furthermore, a short to moderate length biopolymer may be much softer or has a smaller apparent persistent length than what would be expected from the "equivalent system". Moreover, under a strong stretching force and for a long biopolymer, the sequence-disorder is immaterial for elasticity. Finally, the effect of sequence-disorder may depend upon the quantity considered

Transport in bacteriophage P22-infected Salmonella typhimurium

There was rapid efflux of L-leucine, L-phenylalanine, and α-methyl-D-glucoside after infection of Salmonella typhimurium with the clear plaque mutant C1 of phage P22. The efflux was similar to that observed with cyanide or arsenate treatment except that there was partial recovery in the case of phage infection and almost complete recovery under the condition of lysogeny. There was no efflux after infection with the temperature-sensitive mutant ts16C1 at nonpermissive temperature. Superinfection of superinfection exclusion negative lysogen (sie A - sie B-) with C1 led to efflux, whereas the efflux was much less on superinfection of sie A+ Sie B+ lysogen. These results indicate that an effective injection process is enough to cause depression in the cellular transport processes

Decrease in hyperosmotic stress-induced corneal epithelial cell apoptosis by L-carnitine

Purpose: To characterize the osmoprotective properties of L-carnitine on human corneal epithelial cell volume and apoptosis during hyperosmotic stress. Methods: Human corneal limbal epithelial (HCLE) cells were exposed to culture medium at 300 mOsm (isotonic) or 500 mOsm (hyperosmotic) with or without L-carnitine (10 mM). Induction of apoptosis was detected by quantifying the proteolytic activity of caspase-8, caspase-9, and caspase-3/7 using caspase activity assays, the expression of tumor necrosis factor (TNF)-α with enzyme-linked immunosorbent assay, and annexin V/propidium iodide staining of HCLE cells evaluated with confocal microscopy and flow cytometry. Cell volume changes in response to hyperosmotic stress were analyzed using flow cytometry. Results: After the HCLE cells were exposed to hyperosmotic medium (500 mOsm), the percentage of shrunken cells and damaged/dead cells (stained positively for annexin V and/or propidium iodide) was six- and three-fold, respectively, higher than that under isotonic conditions (300 mOsm). This was paralleled by an increase in TNF-α concentration in media and caspase-8, -9, and -3/7 activities (six-, four-, ten-, and twelve-fold, respectively; all showing p\u3c0.001). Addi­tion of L-carnitine during hyperosmotic stress partly restored cell volume and significantly reduced the concentration of TNF-α released (p=0.005) and caspase-9 activity (p=0.0125). Addition of L-carnitine reduced the percentage of hyperosmolarity-induced damaged/dead cells to levels observed under isotonic conditions

Thresholded Covering Algorithms for Robust and Max-Min Optimization

The general problem of robust optimization is this: one of several possible scenarios will appear tomorrow, but things are more expensive tomorrow than they are today. What should you anticipatorily buy today, so that the worst-case cost (summed over both days) is minimized? Feige et al. and Khandekar et al. considered the k-robust model where the possible outcomes tomorrow are given by all demand-subsets of size k, and gave algorithms for the set cover problem, and the Steiner tree and facility location problems in this model, respectively. In this paper, we give the following simple and intuitive template for k-robust problems: "having built some anticipatory solution, if there exists a single demand whose augmentation cost is larger than some threshold, augment the anticipatory solution to cover this demand as well, and repeat". In this paper we show that this template gives us improved approximation algorithms for k-robust Steiner tree and set cover, and the first approximation algorithms for k-robust Steiner forest, minimum-cut and multicut. All our approximation ratios (except for multicut) are almost best possible. As a by-product of our techniques, we also get algorithms for max-min problems of the form: "given a covering problem instance, which k of the elements are costliest to cover?".Comment: 24 page

Test of Quantum Action for Inverse Square Potential

We present a numerical study of the quantum action previously introduced as a parametrisation of Q.M. transition amplitudes. We address the questions: Is the quantum action possibly an exact parametrisation in the whole range of transition times ($0 < T < \infty$)? Is the presence of potential terms beyond those occuring in the classical potential required? What is the error of the parametrisation estimated from the numerical fit? How about convergence and stability of the fitting method (dependence on grid points, resolution, initial conditions, internal precision etc.)? Further we compare two methods of numerical determination of the quantum action: (i) global fit of the Q.M. transition amplitudes and (ii) flow equation. As model we consider the inverse square potential, for which the Q.M. transition amplitudes are analytically known. We find that the relative error of the parametrisation starts from zero at T=0 increases to about $10^{-3}$ at $T=1/E_{gr}$ and then decreases to zero when $T \to \infty$. Second, we observe stability of the quantum action under variation of the control parameters. Finally, the flow equation method works well in the regime of large $T$ giving stable results under variation of initial data and consistent with the global fit method.Comment: Text (LaTeX), Figures(ps

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

BACKGROUND: All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no computationally efficient bioinformatics tool that allows visualizing and exploring these large-scale mutational events. RESULTS: Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment. CONCLUSIONS: The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/

Path integral solution for an angle-dependent anharmonic oscillator

We have given a straightforward method to solve the problem of noncentral anharmonic oscillator in three dimensions. The relative propagator is presented by means of path integrals in spherical coordinates. By making an adequate change of time we were able to separate the angular motion from the radial one. The relative propagator is then exactly calculated. The energy spectrum and the corresponding wave functions are obtained.Comment: Corrected typos and mistakes, To appear in Communications in Theoretical Physic

Comparison of the efficacy of lotrafilcon B and comfilcon A silicone hydrogel bandage contact lenses after transepithelial photorefractive keratectomy

Background: At completion of transepithelial photorefractive keratectomy (t-PRK) surgery, the eye is usually fitted with a bandage contact lens to reduce discomfort and promote epithelial healing. This study aimed to compare the outcomes of eyes fitted with lotrafilcon B versus comfilcon A, silicone hydrogel bandage contact lenses after t-PRK for the correction of low to moderate myopia, with or without astigmatism. Methods: In this comparative, prospective study, patients with myopia &lt; -6 D with or without astigmatism (&lt; 1.75 D), who underwent t-PRK between January and June 2018, were randomly allocated to the lotrafilcon B and comfilcon A groups. Preoperative characteristics, including age, sex, eye treated, uncorrected visual acuity (UCVA), best-corrected visual acuity, mesopic pupil size, central corneal thickness, and refractive error were recorded. Postoperatively, pain score, UCVA, and corneal epithelial defect size on days 1, 4, and 7 were compared between the two groups. Results: Twenty-nine eyes were included in each group. Demographic characteristics and preoperative measurements were similar between the two groups. UCVA was significantly improved on day 7 as compared to day 1 in the comfilcon A group (P = 0.03), but remained the same in the lotrafilcon B group (P = 0.70) as on day 1 postoperatively. There was no significant difference in UCVA between the two groups at any follow-up visits (all P &gt; 0.05). The pain score on the first postoperative day was significantly higher in the lotrafilcon B-fitted eyes than in the comfilcon A group (P &lt; 0.001), but was significantly reduced in both groups compared to day 1 (both P &lt; 0.001). The epithelial defect in the comfilcon A group was significantly greater than in the lotrafilcon B group (P &lt; 0.001) at day 1 postoperatively, with significant improvement in both groups (both P &lt; 0.001). Conclusions: Healing responses were better with lotrafilcon B than with comfilcon A bandage contact lenses. The patients had a greater mean pain score with lotrafilcon B than with comfilcon A lenses on the first postoperative day, yet the final outcome was comparable between the two groups. We did not encounter any postoperative complications related to contact lens wear

Attitudes of Saudi Arabian Undergraduate Medical Students towards Health Research

Objectives: This study aimed to evaluate attitudes, perceptions and perceived barriers towards health research among Saudi Arabian undergraduate medical students. Methods: This cross-sectional study took place between August and October 2014 and included 520 students from five medical schools across Saudi Arabia. An anonymous online survey with 21 close-ended questions was designed to assess students’ attitudes towards research, contribution to research-related activities, awareness of the importance of research, perception of available resources/opportunities for research, appreciation of medical students’ research contributions and perceived barriers to research. Responses were scored on a 5-point Likert scale. Results: A total of 401 students participated in the study (response rate: 77.1%). Of these, 278 (69.3%) were female. A positive attitude towards research was reported by 43.9% of the students. No statistically significant differences were observed between genders with regards to attitudes towards and available resources for research (P = 0.500 and 0.200, respectively). Clinical students had a significantly more positive attitude towards research compared to preclinical students (P = 0.007). Only 26.4% of the respondents believed that they had adequate resources/opportunities for research. According to the students, perceived barriers to undertaking research included time constraints (n = 200; 49.9%), lack of research mentors (n = 95; 23.7%), lack of formal research methodology training (n = 170; 42.4%) and difficulties in conducting literature searches (n = 145; 36.2%). Conclusion:Less than half of the surveyed Saudi Arabian medical students had a positive attitude towards health research. Medical education policies should aim to counteract the barriers identified in this study

Brownian Motion and Polymer Statistics on Certain Curved Manifolds

We have calculated the probability distribution function G(R,L|R',0) of the end-to-end vector R-R' and the mean-square end-to-end distance (R-R')^2 of a Gaussian polymer chain embedded on a sphere S^(D-1) in D dimensions and on a cylinder, a cone and a curved torus in 3-D. We showed that: surface curvature induces a geometrical localization area; at short length the polymer is locally "flat" and (R-R')^2 = L l in all cases; at large scales, (R-R')^2 is constant for the sphere, it is linear in L for the cylinder and reaches different constant values for the torus. The cone vertex induces (function of opening angle and R') contraction of the chain for all lengths. Explicit crossover formulas are derived.Comment: 9 pages, 4 figures, RevTex, uses amssymb.sty and multicol.sty, to appear in Phys. Rev