A Solvable Model of Secondary Structure Formation in Random Hetero-Polymers

We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and infinite range interactions (representing polarity forces). We solve our model using a combination of mean field and random field techniques, leading to phase diagrams exhibiting second-order transitions between folded, partially folded and unfolded states, including regions where folding depends on initial conditions. Our theoretical results, which are in excellent agreement with numerical simulations, lead to an appealing physical picture of the folding process: the polarity forces drive the transition to a collapsed state, the steric forces introduce monomer specificity, and the hydrogen bonds stabilise the conformation by damping the frustration-induced multiplicity of states.Comment: 24 pages, 14 figure

Survey propagation for the cascading Sourlas code

We investigate how insights from statistical physics, namely survey propagation, can improve decoding of a particular class of sparse error correcting codes. We show that a recently proposed algorithm, time averaged belief propagation, is in fact intimately linked to a specific survey propagation for which Parisi's replica symmetry breaking parameter is set to zero, and that the latter is always superior to belief propagation in the high connectivity limit. We briefly look at further improvements available by going to the second level of replica symmetry breaking.Comment: 14 pages, 5 figure

Внутригодовые (сезонные) изменения общего содержания биогенных элементов и кислорода в различных районах Севастопольской бухты

Для каждого месяца в период май 1998 г. – май 1999 г. рассчитано абсолютное содержание биогенных элементов и кислорода в пяти различных районах Севастопольской бухты и для всей бухты в целом. Показано, что наиболее чистый (возле входа в бухту) и наиболее грязный (Южная бухта) районы отличаются по динамике накопления и расходования биогенных элементов. Максимальный запас неорганических форм азота, фосфора, и кремнекислоты во всех районах Севастопольской бухты, за исключением района Инкерманской бухты, приходится на январь.Total content of biogenic elements and oxygen in five different areas of the Sevastopol Bay and for the whole bay in general is estimated for each month starting from May, 1998 up to May, 1999. It is shown that the purest (near the bay entrance) and the dirtiest (the Southern Bay) areas are distinguished for dynamics of biogenic elements accumulation and expense. Maximum storage of inorganic forms of nitrogen, phosphorus and silicic acid in all the areas of the Sevastopol Bay, excepting the Inkerman Bay area, falls on January

Random Graph Coloring - a Statistical Physics Approach

The problem of vertex coloring in random graphs is studied using methods of statistical physics and probability. Our analytical results are compared to those obtained by exact enumeration and Monte-Carlo simulations. We critically discuss the merits and shortcomings of the various methods, and interpret the results obtained. We present an exact analytical expression for the 2-coloring problem as well as general replica symmetric approximated solutions for the thermodynamics of the graph coloring problem with p colors and K-body edges.Comment: 17 pages, 9 figure

Identifying Optimal Models to Represent Biochemical Systems

Biochemical systems involving a high number of components with intricate interactions often lead to complex models containing a large number of parameters. Although a large model could describe in detail the mechanisms that underlie the system, its very large size may hinder us in understanding the key elements of the system. Also in terms of parameter identification, large models are often problematic. Therefore, a reduced model may be preferred to represent the system. Yet, in order to efficaciously replace the large model, the reduced model should have the same ability as the large model to produce reliable predictions for a broad set of testable experimental conditions. We present a novel method to extract an “optimal” reduced model from a large model to represent biochemical systems by combining a reduction method and a model discrimination method. The former assures that the reduced model contains only those components that are important to produce the dynamics observed in given experiments, whereas the latter ensures that the reduced model gives a good prediction for any feasible experimental conditions that are relevant to answer questions at hand. These two techniques are applied iteratively. The method reveals the biological core of a model mathematically, indicating the processes that are likely to be responsible for certain behavior. We demonstrate the algorithm on two realistic model examples. We show that in both cases the core is substantially smaller than the full model

Sweet potato development and delivery in sub-Saharan Africa

n sub-Saharan Africa, more than 40% of children under five years of age suffer from vitamin A deficiency. Among several interventions in place to address vitamin A deficiency is biofortification, breeding vitamin A into key staple crops. Staple crops biofortified with beta-carotene, the precursor to vitamin A, are orange in color. Given the natural occurrence of high levels of beta-carotene in many sweet potato varieties, breeding progress for biofortified orange sweet potato (OSP) has been much faster than for the other vitamin A enhanced staples. Nearly 3 million households have been reached with OSP. This paper reviews key factors influencing the uptake of OSP, the breeding investment, five key delivery approaches that have been tested in the region and efforts to broaden government and other stakeholder engagement

Palette-colouring: a belief-propagation approach

We consider a variation of the prototype combinatorial-optimisation problem known as graph-colouring. Our optimisation goal is to colour the vertices of a graph with a fixed number of colours, in a way to maximise the number of different colours present in the set of nearest neighbours of each given vertex. This problem, which we pictorially call "palette-colouring", has been recently addressed as a basic example of problem arising in the context of distributed data storage. Even though it has not been proved to be NP complete, random search algorithms find the problem hard to solve. Heuristics based on a naive belief propagation algorithm are observed to work quite well in certain conditions. In this paper, we build upon the mentioned result, working out the correct belief propagation algorithm, which needs to take into account the many-body nature of the constraints present in this problem. This method improves the naive belief propagation approach, at the cost of increased computational effort. We also investigate the emergence of a satisfiable to unsatisfiable "phase transition" as a function of the vertex mean degree, for different ensembles of sparse random graphs in the large size ("thermodynamic") limit.Comment: 22 pages, 7 figure

Survey propagation at finite temperature: application to a Sourlas code as a toy model

In this paper we investigate a finite temperature generalization of survey propagation, by applying it to the problem of finite temperature decoding of a biased finite connectivity Sourlas code for temperatures lower than the Nishimori temperature. We observe that the result is a shift of the location of the dynamical critical channel noise to larger values than the corresponding dynamical transition for belief propagation, as suggested recently by Migliorini and Saad for LDPC codes. We show how the finite temperature 1-RSB SP gives accurate results in the regime where competing approaches fail to converge or fail to recover the retrieval state

Video-Assisted Thoracoscopic Surgery in Patients With Clinically Resectable Lung Tumors

To investigate the feasibility of thoracoscopic resection, a pilot study was performed in patients with clinically resectable lung tumors. In 40 patients, Video-assisted thoracic surgery (VATS) was performed because of suspicion of malignancy. There were 29 men and 11 women with a median age of 54.8 years (range 18 to 78). Preoperative indications were suspected lung cancer and tumor in 27 patients, assessment of tumor resectability in 7 patients, and probability of metastatic tumors in 6 patients. The final diagnoses in the 27 patients with suspected lung cancer were 12 primary lung cancers, 6 lung metastases, and 9 benign lesions. The success rates for VATS (no conversion to thoracotomy) were 1 of 12 (8.3%) for resectable stage I lung cancer, 8 of 12 (66.7%) for metastatic tumors, and 9 of 9 (100%) for benign tumors. With VATS, 6 of 7 patients (85.7%), possible stage III non-small cell lung cancer, an explorative thoracotomy with was avoided, significantly reducing morbidity. The reasons for conversion to thoracotomy were 1) oncological (N2 lymph node dissection and prevention of tumor spillage) and 2) technical (inability to locate the nodule, central localization, no anatomical fissure, or poor lung function requiring full lung ventilation). The ultimate diagnoses were 19 lung cancers, 12 metastatic lung tumors, and 9 benign lung tumors. Our data show the limitations of VATS for malignant tumors in general use. These findings, together with the fact that experience in performing thoracoscopic procedures demonstrates a learning curve, may limit the use of thoracoscopic resection as a routine surgical procedure, especially when strict oncological rules are respected

Gender responsive communication tools and approaches for scaling the Triple S Technology in Ethiopia and Ghana

The RTB Triple S Scaling project (3S+) is a 27-month project funded by the CGIAR Research Program on Roots, Tubers and Bananas (RTB) and was operational in Ghana and Ethiopia. The aim of the project was to scale out the Triple S technology – a root-based vine production technology suitable for arid and semi-arid areas. Amongst the scaling strategies developed and implemented, was an outreach strategy based on three types of treatment: Core communities, informed communities, spillover communities. Subsequently, various communication tools and approaches were used for the three types of communities. Following use of these strategies, there was a need to assess their effectiveness in aiding technology dissemination, uptake and scaling. A study was designed to assess which communication methods were best suited to the needs of women and men in transmission and delivery of the Triple S innovation scaling package