Heteropolymers in a Solvent at an Interface

Exact bounds are obtained for the quenched free energy of a polymer with random hydrophobicities in the presence of an interface separating a polar from a non polar solvent. The polymer may be ideal or have steric self-interactions. The bounds allow to prove that a ``neutral'' random polymer is localized near the interface at any temperature, whereas a ``non-neutral'' chain is shown to undergo a delocalization transition at a finite temperature. These results are valid for a quite general a priori probability distribution for both independent and correlated hydrophobic charges. As a particular case we consider random AB-copolymers and confirm recent numerical studies.Comment: 4 pages, no figure

Melting behavior and different bound states in three-stranded DNA models

Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and Scheraga models). Within this framework, the existence of a three strand DNA bound state in conditions where a duplex DNA would be in the denaturated state was recently predicted from a study of three directed polymer models on simplified hierarchical lattices ($d>2$) and in $1+1$ dimensions. Such phenomenon which is similar to the Efimov effect in nuclear physics was named Efimov-DNA. In this paper we study the melting of the three-stranded DNA on a Sierpinski gasket of dimensions $d<2$ by assigning extra weight factors to fork openings and closings, to induce a two-strand DNA melting. In such a context we can find again the existence of the Efimov-DNA-like state but quite surprisingly we discover also the presence of a different phase, to be called a mixed state, where the strands are pair-wise bound but without three chain contacts. Whereas the Efimov DNA turns out to be a crossover near melting, the mixed phase is a thermodynamic phase.Comment: corrected file uploade

Invariant mass distribution of jet pairs produced in association with a W boson at CDF

We present a study of the invariant mass spectra of jets produced in association with a W boson decaying into a lepton and a neutrino. Events of this signature are critical to studies of vector boson pair production, top-quark physics, Higgs boson physics, and searches for beyond the standard model particles. We present a search for high-mass resonances decaying into jets, and find no significant excess above the standard model background prediction

Sustainable medical research by effective and comprehensive medical skills: overcoming the frontiers by predictive, preventive and personalized medicine

BACKGROUND: Clinical research and practice require affordable objectives, sustainable tools, rewarding training strategies and meaningful collaboration. METHOD: Our unit delivers courses on project design and management promoting ideas, useful skills, teaching and exploring implementation of networks and existing collaborations. We investigated the effectiveness of a sustainable approach of comprehensive diagnosis and care and its usefulness within concrete models of research project teaching methodology. RESULTS: The model of predictive, preventive and personalized medicine (PPPM) of adolescent hypertension, developed since 1976 and still active, was displayed. This is a paradigm of comprehensive PPPM aimed at the management of a recognized, but actually neglected, societal and clinical problem. The second model was addressed to the analysis of performance of an outpatient diagnostic and therapy unit and its relationship with the emergency department. Part of the patients, 4,057 cancer patients presenting at the emergency care, were addressed to the outpatient diagnostic and therapy unit for further assessment, treatment and follow-up. The stay in DH was 6.3 ± 2.1 non-consecutive days, with shortage of costs, vs. in-hospital stays. Research planning courses, based on these models, ensued in an increase of competitive project submission and successful funding. DISCUSSION: Active promotion of interdisciplinary knowledge and skills is warranted. Misleading messages and information are detrimental not only to healthy and sick people but, equally, to all health professionals: efforts for basing on evidence by research any statement are needed. The actual pre-requisite of personalized medicine is the coherent and articulated promotion of the professional quality of staff. Health professionals should and can be skilled in sustainable non-invasive diagnostic procedures, in non-pharmacological intervention, in translational research (from epidemiology to personalized therapy) and in timely dissemination of the information. CONCLUSION: Recommendations are provided according to PPPM: proposed models are based on financial sustainability and patient's satisfaction criteria and are addressed to research projects and dissemination also by e-learning. The guidelines of the EU calls in personalized medicine are able to provide a critical added value by accurate planning, transparency of assessment and unbiased reports, dissemination and exploitation

Simplicity is the ultimate sophistication. PR electrocardiographic intervals for smart forecasting of decline in renal function

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Regular coffee: a magic bullet or a naked gun? Regular coffee but not espresso drinking is protective against fibrosis in NAFLD.

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Statistics and quantum maximum entropy principle

By using the reduced Wigner formalism we consider a kinetic theory for a quantum gas. We introduce a set of generalized kinetic fields and obtain a hierarchy of Quantum Hydrodynamic (QHD) equations for the corresponding macroscopic variables. To close the QHD system a maximum entropy principle is asserted, and to explicitly incorporate particles indistinguishability a proper quantum entropy is analyzed in terms of the reduced density matrix. This approach implies a quantum generalization of the corresponding Lagrange multipliers. Quantum contributions are expressed in powers of ¯h2

Key interaction patterns in proteins revealed by cluster expansion of the partition function

The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence design. To achieve this goal, we employed a cluster expansion of the partition function in the space of sequences and evaluated numerically the statistical importance of each cluster. An important feature of this procedure is that it is applied to a dense, finite system. We found that patterns that contribute most to the partition function are cycles with even numbers of nodes, while cliques are typically detrimental. Each cluster also gives a contribute to the sequence entropy, which is a measure of the evolutionary designability of a fold. We compared the entropies associated with different interaction patterns to their abundances in the native structures of real proteins

When a DNA Triple helix melts: An analog of the Efimov state

The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix but by forming a triple helix. It is predicted here that such a three chain system exhibits the unusual behaviour of the existence of a three chain bound state in the absence of any two being bound. This phenomenon is analogous to the Efimov state in three particle quantum mechanics. A scaling theory is used to justify the Efimov connection. Real space renormalization group (RG), and exact numerical calculations are used to validate the prediction of a biological Efimov effect.Comment: Replaced by the (almost) published version, except the word "curiouser

Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence of specific patterns adopted by protein sequences and structures to deal with backbone self-entanglement. A large scale analysis of the Protein Data Bank shows that loops significantly intertwined with another chain portion are typically closed by weakly bound amino acids. Why is this energetic frustration maintained? A possible picture is that entangled loops are formed only toward the end of the folding process to avoid kinetic traps. Consistently, these loops are more frequently found to be wrapped around a portion of the chain on their N-terminal side, the one translated earlier at the ribosome. Finally, these motifs are less abundant in natural native states than in simulated protein-like structures, yet they appear in 32% of proteins, which in some cases display an amazingly complex intertwining