Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Philadelphia-Negative Classical Myeloproliferative Neoplasms: Critical Concepts and Management Recommendations From European LeukemiaNet

We present a review of critical concepts and produce recommendations on the management of Philadelphia-negative classical myeloproliferative neoplasms, including monitoring, response definition, first-and second-line therapy, and therapy for special issues. Key questions were selected according the criterion of clinical relevance. Statements were produced using a Delphi process, and two consensus conferences involving a panel of 21 experts appointed by the European LeukemiaNet (ELN) were convened. Patients with polycythemia vera (PV) and essential thrombocythemia (ET) should be defined as high risk if age is greater than 60 years or there is a history of previous thrombosis. Risk stratification in primary myelofibrosis (PMF) should start with the International Prognostic Scoring System (IPSS) for newly diagnosed patients and dynamic IPSS for patients being seen during their disease course, with the addition of cytogenetics evaluation and transfusion status. High-risk patients with PV should be managed with phlebotomy, low-dose aspirin, and cytoreduction, with either hydroxyurea or interferon at any age. High-risk patients with ET should be managed with cytoreduction, using hydroxyurea at any age. Monitoring response in PV and ET should use the ELN clinicohematologic criteria. Corticosteroids, androgens, erythropoiesis-stimulating agents, and immunomodulators are recommended to treat anemia of PMF, whereas hydroxyurea is the first-line treatment of PMF-associated splenomegaly. Indications for splenectomy include symptomatic portal hypertension, drug-refractory painful splenomegaly, and frequent RBC transfusions. The risk of allogeneic stem-cell transplantation-related complications is justified in transplantation-eligible patients whose median survival time is expected to be less than 5 years.

Non Classical Design in MOSFETs for Improving OTA gain-bandwidth trade off

In this paper, gain-bandwidth (GB) trade-off associated with analog device/circuit design due to conflicting requirements for enhancing gain and cutoff frequency is examined. It is demonstrated that the use of a nonclassical source/drain (S/D) profile (also known as underlap channel) can alleviate the GB trade-off associated with analog design. Operational transconductance amplifier (OTA) with 60 nm underlap S/D MOSFETs achieve 15 dB higher open loop voltage gain along with three times higher cutoff frequency as compared to OTA with classical nonunderlap S/D regions. Underlap design provides a methodology for scaling analog devices into the sub-100 nm regime and is advantageous for high temperature applications with OTA, preserving functionality up to 540 K. Advantages of underlap architecture over graded channel (GC) or laterally asymmetric channel (LAC) design in terms of GB behavior are demonstrated. Impact of transistor structural parameters on the performance of OTA is also analyzed. Results show that underlap OTAs designed with spacer-to-straggle ratio of 3.2 and operated below a bias current of 80 microamps demonstrate optimum performance. The present work provides new opportunities for realizing future ultra wide band OTA design with underlap DG MOSFETs in silicon-on-insulator (SOI) technology. Index Terms—Analog/RF, double gate, gain-bandwidth product, .

Berry phase for a spin 1/2 particle in a classical fluctuating field

The effect of fluctuations in the classical control parameters on the Berry phase of a spin 1/2 interacting with an adiabatically cyclically varying magnetic field is analyzed. It is explicitly shown that in the adiabatic limit dephasing is due to fluctuations of the dynamical phase.

Connections between Classical and Parametric Network Entropies

This paper explores relationships between classical and parametric measures of graph (or network) complexity. Classical measures are based on vertex decompositions induced by equivalence relations. Parametric measures, on the other hand, are constructed by using information functions to assign probabilities to the vertices. The inequalities established in this paper relating classical and parametric measures lay a foundation for systematic classification of entropy-based measures of graph complexity.

Classical novae from the POINT-AGAPE microlensing survey of M31 - II. Rate and statistical characteristics of the nova population

The POINT-AGAPE (Pixel-lensing Observations with the Isaac Newton Telescope-Andromeda Galaxy Amplified Pixels Experiment) survey is an optical search for gravitational microlensing events towards the Andromeda galaxy (M31). As well as microlensing, the survey is sensitive to many different classes of variable stars and transients. In our first paper of this series, we reported the detection of 20 classical novae (CNe) observed in Sloan r' and i' passbands.