Visual direction finding by fishes

The use of visual orientation, in the absence of landmarks, for underwater direction finding exercises by fishes is reviewed. Celestial directional clues observed directly near the water surface or indirectly at an asymptatic depth are suggested as possible orientation aids

Similarity-Detection and Localization

The detection of similarities between long DNA and protein sequences is studied using concepts of statistical physics. It is shown that mutual similarities can be detected by sequence alignment methods only if their amount exceeds a threshold value. The onset of detection is a continuous phase transition which can be viewed as a localization-delocalization transition. The ``fidelity'' of the alignment is the order parameter of that transition; it leads to criteria for the selection of optimal alignment parameters.Comment: 4 pages including 4 figures (308kb post-script file

Genetic Correlations in Mutation Processes

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a critical rate, the underlying tree morphology is almost irrelevant, while mutation rates higher than this critical rate lead to strong tree-dependent correlations. We show analytically that identical critical behavior underlies all multiple point correlations. This behavior generally characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig

The Fall and Rise of US Inequities in Premature Mortality: 1960–2002

Nancy Krieger and colleagues found evidence of decreasing, and then increasing or stagnating, socioeconomic and racial inequities in US premature mortality and infant death from 1960 to 2002

Counting, generating and sampling tree alignments

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis.In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees $S$ and $T$. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal RNA secondary structures alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 201

Thermodynamics of protein folding: a random matrix formulation

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows however that the evolution of the statistical measures e.g Gibbs free energy, heat capacity, entropy is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies.Comment: 21 Pages, no figure

Polarized light field under dynamic ocean surfaces: Numerical modeling compared with measurements

As part of the Radiance in a Dynamic Ocean (RaDyO) program, we have developed a numerical model for efficiently simulating the polarized light field under highly dynamic ocean surfaces. Combining the advantages of the three-dimensional Monte Carlo and matrix operator methods, this hybrid model has proven to be computationally effective for simulations involving a dynamic air-sea interface. Given water optical properties and ocean surface wave slopes obtained from RaDyO field measurements, model-simulated radiance and polarization fields under a dynamic surface are found to be qualitatively comparable to their counterparts from field measurements and should be quantitatively comparable if the light field measurement and the wave slope/water optical property measurements are appropriately collocated and synchronized. This model serves as a bridge to connect field measurements of water optical properties, wave slopes and polarized light fields. It can also be used as a powerful yet convenient tool to predict the temporal underwater polarized radiance in a real-world situation. When appropriate surface measurements are available, model simulation is shown to reveal more dynamic features in the underwater light field than direct measurements

Addition-Deletion Networks

We study structural properties of growing networks where both addition and deletion of nodes are possible. Our model network evolves via two independent processes. With rate r, a node is added to the system and this node links to a randomly selected existing node. With rate 1, a randomly selected node is deleted, and its parent node inherits the links of its immediate descendants. We show that the in-component size distribution decays algebraically, c_k ~ k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with the addition rate r. Structural properties of the network including the height distribution, the diameter of the network, the average distance between two nodes, and the fraction of dangling nodes are also obtained analytically. Interestingly, the deletion process leads to a giant hub, a single node with a macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure

Narrow safety range of intraoperative rectal irradiation exposure volume for avoiding bleeding after seed implant brachytherapy

<p>Abstract</p> <p>Background & Purpose</p> <p>Rectal toxicity is less common after ¹²⁵I seed implant brachytherapy for prostate cancer, and intraoperative rectal dose-volume constraints (the constraint) is still undetermined in pioneering studies. As our constraint failed to prevent grade 2 or 3 rectal bleeding (bled-pts) in 5.1% of patients, we retrospectively explored another constraint for the prevention of rectal bleeding.</p> <p>Materials and methods</p> <p>The study population consisted of 197 patients treated with the brachytherapy as monotherapy using real-time intraoperative transrectal ultrasound (US)-guided treatment at a prescribed dose of 145 Gy. Post-implant dosimetry was performed on Day 1 and Day 30 after implantation using computed tomography (CT) imaging. Rectal bleeding toxicity was classified by CTC-AE ver. 3.0 during a mean 29-month (range, 12-48 months) period after implantation. The differences in rV100s were compared among intraoperative, Day 1 and Day 30 dosimetry, and between that of patients with grade 2 or 3 rectal bleeding (the bled-pts) and of the others (the spared-pts). All patients were divided into groups based on provisional rV100s that were increased stepwise in 0.1-cc increments from 0 to 1.0 cc. The difference in the ratios of the bled-pts to the spared-pts was tested by chi-square tests, and their odds ratios were calculated (bled-OR). All statistical analyses were performed by <it>t</it>-tests.</p> <p>Results</p> <p>The mean values of rV100us, rV100CT_1, and rV100CT_30 were 0.31 ± 0.43, 0.22 ± 0.36, and 0.59 ± 0.68 cc, respectively. These values temporarily decreased (p = 0.020) on Day 1 and increased (p = 0.000) on Day 30. There was no significant difference in rV100s between the bled-pts and spared-pts at any time of dosimetry. The maximum bled-OR was identified among patients with an rV100us value above 0.1 cc (p = 0.025; OR = 7.8; 95% CI, 1.4-145.8); an rV100CT_1 value above 0.3 cc (p = 0.014; OR = 16.2; 95% CI, 3.9-110.7), and an rV100CT_30 value above 0.5 cc (p = 0.019; OR = 6.3; 95% CI, 1.5-42.3).</p> <p>Conclusion</p> <p>By retrospective analysis exploring rV100 as intraoperative rectal dose-volume thresholds in ¹²⁵I seed implant brachytherapy for prostate cancer, it is proved that rV100 should be less than 0.1 cc for preventing rectal bleeding.</p

Detailed analysis of the ANO-2 turbine trip test

A RELAP5/MOD1 (Cycle 18) computer code simulation of the ANO-2 turbine trip test from 98% power level was performed for use in vendor code qualification studies. Results focused on potential improvements to simulation capabilities and plant data acquisition systems to provide meaningful comparisons between the calculations and the test data. The turbine trip test was selected because it resulted in an unplanned sequence of events that broadly affected the plant process systems and their controls. The pressurizer spray valve stuck open at an undetermined flow area, and an atmospheric dump valve remained stuck fully open while several atmospheric dump and secondary side safety valves were unavailable throughout. Thus, although the plant remained always in a safe condition, this transient potentially provided an unusual set of data against which the fidelity of a NSSS simulation by RELAP5/MOD1 along with certain vendor analysis codes might be judged