Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots

<p>Abstract</p> <p>Background</p> <p>An important and yet rather neglected question related to bioinformatics predictions is the estimation of the amount of data that is needed to allow reliable predictions. Bioinformatics predictions are usually validated through a series of figures of merit, like for example sensitivity and precision, and little attention is paid to the fact that their performance may depend on the amount of data used to make the predictions themselves.</p> <p>Results</p> <p>Here I describe a tool, named Fragmented Prediction Performance Plot (FPPP), which monitors the relationship between the prediction reliability and the amount of information underling the prediction themselves. Three examples of FPPPs are presented to illustrate their principal features. In one example, the reliability becomes independent, over a certain threshold, of the amount of data used to predict protein features and the intrinsic reliability of the predictor can be estimated. In the other two cases, on the contrary, the reliability strongly depends on the amount of data used to make the predictions and, thus, the intrinsic reliability of the two predictors cannot be determined. Only in the first example it is thus possible to fully quantify the prediction performance.</p> <p>Conclusion</p> <p>It is thus highly advisable to use FPPPs to determine the performance of any new bioinformatics prediction protocol, in order to fully quantify its prediction power and to allow comparisons between two or more predictors based on different types of data.</p

A critical assessment of the pairing symmetry in NaxCoO2.yH2O

We examine each of the symmetry-allowed pairing states of NaxCoO2.yH2O and compare their properties to what is experimentally and theoretically established about the compound. In this way, we can eliminate the vast majority of states that are technically allowed and narrow the field to two, both of f-wave type states. We discuss the expected features of these states and suggest experiments that can distinguish between them. We also discuss odd-frequency gap pairing and how it relates to available experimental evidence

Suboccipital craniotomy in the surgical treatment of Chiari I malformation

The object of this study was to present craniotomy for Chiari type I patients. Six patients with Chiari type I underwent suboccipital craniotomy. All patients showed clinical improvement, and none had any complications. Two patients had syringomyelia; it disappeared in entirety. We describe the procedure for posterior fossa decompression. Three-dimensional volumetric analysis using Vitrea workstation for postoperative posterior fossa volumes was calculated and was seen to have been increased on an average, from pre-operative (168 cc) to postoperative volume (192 cc). We thus conclude that suboccipital craniotomy results in resolution of the Chiari symptoms yet achieves effective expansion of posterior fossa

A molecular insight into algal-oomycete warfare : cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii

Peer reviewedPublisher PD

A computationally efficient method for hand–eye calibration

Purpose: Surgical robots with cooperative control and semiautonomous features have shown increasing clinical potential, particularly for repetitive tasks under imaging and vision guidance. Effective performance of an autonomous task requires accurate hand–eye calibration so that the transformation between the robot coordinate frame and the camera coordinates is well defined. In practice, due to changes in surgical instruments, online hand–eye calibration must be performed regularly. In order to ensure seamless execution of the surgical procedure without affecting the normal surgical workflow, it is important to derive fast and efficient hand–eye calibration methods. Methods: We present a computationally efficient iterative method for hand–eye calibration. In this method, dual quaternion is introduced to represent the rigid transformation, and a two-step iterative method is proposed to recover the real and dual parts of the dual quaternion simultaneously, and thus the estimation of rotation and translation of the transformation. Results: The proposed method was applied to determine the rigid transformation between the stereo laparoscope and the robot manipulator. Promising experimental and simulation results have shown significant convergence speed improvement to 3 iterations from larger than 30 with regard to standard optimization method, which illustrates the effectiveness and efficiency of the proposed method

A Common Origin for Neutrino Anarchy and Charged Hierarchies

The generation of exponential flavor hierarchies from extra-dimensional wavefunction overlaps is re-examined. We find, surprisingly, that coexistence of anarchic fermion mass matrices with such hierarchies is intrinsic and natural to this setting. The salient features of charged fermion and neutrino masses and mixings can thereby be captured within a single framework. Both Dirac and Majorana neutrinos can be realized. The minimal phenomenological consequences are discussed, including the need for a fundamental scale far above the weak scale to adequately suppress flavor-changing neutral currents. Two broad scenarios for stabilizing this electroweak hierarchy are studied, warped compactification and supersymmetry. In warped compactifications and "Flavorful Supersymmetry," where non-trivial flavor structure appears in the new TeV physics, Dirac neutrinos are strongly favored over Majorana by lepton flavor violation tests. We argue that this is part of a more general result for flavor-sensitive TeV-scale physics. Our scenario strongly suggests that the supersymmetric flavor problem is not solved locally in the extra dimension, but rather at or below the compactification scale. In the supersymmetric Dirac case, we discuss how the appearance of light right-handed sneutrinos considerably alters the physics of dark matter.Comment: Comparison with the Froggatt-Nielsen mechanism omitted. Some clarifications added. This is the version accepted by PRL with a longer abstract

Field-free platform for Majorana-like zero mode in superconductors with a topological surface state

Superconducting materials exhibiting topological properties are emerging as an exciting platform to realize fundamentally new excitations from topological quantum states of matter. In this letter, we explore the possibility of a field-free platform for generating Majorana zero energy excitations by depositing magnetic Fe impurities on the surface of candidate topological superconductors, LiFeAs and PbTaSe2. We use scanning tunneling microscopy to probe localized states induced at the Fe adatoms on the atomic scale and at sub-Kelvin temperatures. We find that each Fe adatom generates a striking zero-energy bound state inside the superconducting gap, which do not split in magnetic fields up to 8 T, underlining a nontrivial topological origin. Our findings point to magnetic Fe adatoms evaporated on bulk superconductors with topological surface states for exploring Majorana zero modes and quantum information science under field-free conditions

Male Choice in the Stream-Anadromous Stickleback Complex

Studies of mating preferences and pre-mating reproductive isolation have often focused on females, but the potential importance of male preferences is increasingly appreciated. We investigated male behavior in the context of reproductive isolation between divergent anadromous and stream-resident populations of threespine stickleback, Gasterosteus aculeatus, using size-manipulated females of both ecotypes. Specifically, we asked if male courtship preferences are present, and if they are based on relative body size, non-size aspects of ecotype, or other traits. Because male behaviors were correlated with each other, we conducted a principal components analysis on the correlations and ran subsequent analyses on the principal components. The two male ecotypes differed in overall behavioral frequencies, with stream-resident males exhibiting consistently more vigorous and positive courtship than anadromous males, and an otherwise aggressive behavior playing a more positive role in anadromous than stream-resident courtship. We observed more vigorous courtship toward smaller females by (relatively small) stream-resident males and the reverse pattern for (relatively large) anadromous males. Thus size-assortative male courtship preferences may contribute to reproductive isolation in this system, although preferences are far from absolute. We found little indication of males responding preferentially to females of their own ecotype independent of body size

Long-Term Mortality of Patients with Septic Ocular or Central Nervous System Complications from Pyogenic Liver Abscess: A Population-Based Study

Background: Taiwan is endemic for pyogenic liver abscess (PLA). Septic ocular or central nervous system (CNS) complications derived from PLA can result in catastrophic disability. We investigated the epidemiology and long-term prognosis of PLA patients with septic ocular or CNS complications over an 8-year period. Methodology/Principal Findings: We extracted 21,307 patients with newly diagnosed PLA from a nationwide health registry in Taiwan between 2000 and 2007. The frequency of and risk factors for PLA with septic ocular or CNS complications were determined. The 2-year survival of these patients was compared between those with and without septic ocular or CNS complications. Septic ocular or CNS complications accounted for 2.1 % of all PLA patients. Age and the Charlson comorbidity index were significantly lower in PLA patients with ocular or CNS complications than those without. Diabetes and age,65 years were independent predictors of septic ocular or CNS complications. The 2-year mortality of patients with septic ocular or CNS complications was similar to those without complications (24.8 % vs. 27.5%, p = 0.502). However, among patients,65 years old and a Charlson index #1, the 2-year mortality was significantly higher in those with than without complications (18.6 % vs. 11.8%, p = 0.001). Conclusions/Significance: Physicians should recognize that catastrophic disability due to ocular or neurologica

Stochastic Gravity: Theory and Applications

Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein-Langevin equation, which has in addition sources due to the noise kernel. In the first part, we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. In the second part, we describe three applications of stochastic gravity theory. First, we consider metric perturbations in a Minkowski spacetime, compute the two-point correlation functions of these perturbations and prove that Minkowski spacetime is a stable solution of semiclassical gravity. Second, we discuss structure formation from the stochastic gravity viewpoint. Third, we discuss the backreaction of Hawking radiation in the gravitational background of a black hole and describe the metric fluctuations near the event horizon of an evaporating black holeComment: 100 pages, no figures; an update of the 2003 review in Living Reviews in Relativity gr-qc/0307032 ; it includes new sections on the Validity of Semiclassical Gravity, the Stability of Minkowski Spacetime, and the Metric Fluctuations of an Evaporating Black Hol