Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

The determination of a protein''s folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. In this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain Brownian dynamics simulations. The resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, which we call the consensus nucleus, occupy conserved positions along the protein sequence. These residues'' side chains form a tight interaction network within the protein''s core, thus making our consensus nuclei potential folding nuclei. A review of experimental and theoretical literature shows that most (above 80%) of these residues were indeed identified as folding nucleus member in earlier studies.     

Sort vs. hash revisited

Efficient algorithms for processing large volumes of data are very important both for relational and new object-oriented database systems. Many query-processing operations can be implemented using sort- or hash-based algorithms, e.g. intersections, joins, and duplicate elimination. In the early relational database systems, only sort-based algorithms were employed. In the last decade, hash-based algorithms have gained acceptance and popularity, and are often considered generally superior to sort-based algorithms such as merge-join. In this article, we compare the concepts behind sort- and hash-based query-processing algorithms and conclude that (1) many dualities exist between the two types of algorithms, (2) their costs differ mostly by percentages rather than by factors, (3) several special cases exist that favor one or the other choice, and (4) there is a strong reason why both hash- and sort-based algorithms should be available in a query-processing system. Our conclusions are supported by experiments performed using the Volcano query execution engine     

Volcano-an extensible and parallel query evaluation system

To investigate the interactions of extensibility and parallelism in database query processing, we have developed a new dataflow query execution system called Volcano. The Volcano effort provides a rich environment for research and education in database systems design, heuristics for query optimization, parallel query execution, and resource allocation. Volcano uses a standard interface between algebra operators, allowing easy addition of new operators and operator implementations. Operations on individual items, e.g., predicates, are imported into the query processing operators using support functions. The semantics of support functions is not prescribed; any data type including complex objects and any operation can be realized. Thus, Volcano is extensible with new operators, algorithms, data types, and type-specific methods. Volcano includes two novel meta-operators. The choose-plan meta-operator supports dynamic query evaluation plans that allow delaying selected optimization decisions until run-time, e.g., for embedded queries with free variables. The exchange meta-operator supports intra-operator parallelism on partitioned datasets and both vertical and horizontal inter-operator parallelism, translating between demand-driven dataflow within processes and data-driven dataflow between processes. All operators, with the exception of the exchange operator, have been designed and implemented in a single-process environment, and parallelized using the exchange operator. Even operators not yet designed can be parallelized using this new operator if they use and provide the interator interface. Thus, the issues of data manipulation and parallelism have become orthogonal, making Volcano the first implemented query execution engine that effectively combines extensibility and parallelism     

Transgenerational effects of the holocaust: Externalization of aggression in second generation of holocaust survivors.

Examined the psychological characteristics of the children of holocaust survivors. 38 males and females in their late 20's were interviewed; the parents of 19 Ss were holocaust survivors, and the parents of the other 19 Ss were in Israel during World War II and did not suffer directly. It was hypothesized that reactions of the children of the holocaust survivors would include guilt rather than external aggression and a tendency not to externalize aggressive impulses in reaction to frustrating events. The Ss' reactions to a projective test were analyzed, and the responses provide support for the major hypothesis. Results show that sons and daughters of holocaust survivors were less likely to externalize aggression than were those in a control group. This finding is supported by the content analysis of the structured interview conducted with the Ss in both groups. (20 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Water absorption properties of phosphate glass fiber‐reinforced poly‐ϵ‐caprolactone composites for craniofacial bone repair

The moisture uptake of polymers and composites has increasing significance where these materials are specified for invasive, long‐term medical applications. Here we analyze mass gain and the ensuing degradation mechanisms in phosphate glass fiber reinforced poly‐?‐caprolactone laminates. Specimens were manufactured using in situ polymerization of ?‐caprolactone around a bed of phosphate glass fibers. The latter were sized with 3‐aminopropyltriethoxysilane to control the rate of modulus degradation. Fiber content was the main variable in the study, and it was found that the moisture diffusion coefficient increased significantly with increasing fiber volume fraction. Diffusion, plasticization, and leaching of constituents appear to be the dominant aspects of the process over these short‐term tests. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2008     

Refining Genotypes and Phenotypes in KCNA2-Related Neurological Disorders

Pathogenic variants in KCNA2, encoding for the voltage-gated potassium channel K_v1.2, have been identified as the cause for an evolving spectrum of neurological disorders. Affected individuals show early-onset developmental and epileptic encephalopathy, intellectual disability, and movement disorders resulting from cerebellar dysfunction. In addition, individuals with a milder course of epilepsy, complicated hereditary spastic paraplegia, and episodic ataxia have been reported. By analyzing phenotypic, functional, and genetic data from published reports and novel cases, we refine and further delineate phenotypic as well as functional subgroups of KCNA2-associated disorders. Carriers of variants, leading to complex and mixed channel dysfunction that are associated with a gain- and loss-of-potassium conductance, more often show early developmental abnormalities and an earlier onset of epilepsy compared to individuals with variants resulting in loss- or gain-of-function. We describe seven additional individuals harboring three known and the novel KCNA2 variants p.(Pro407Ala) and p.(Tyr417Cys). The location of variants reported here highlights the importance of the proline(405)–valine(406)–proline(407) (PVP) motif in transmembrane domain S6 as a mutational hotspot. A novel case of self-limited infantile seizures suggests a continuous clinical spectrum of KCNA2-related disorders. Our study provides further insights into the clinical spectrum, genotype–phenotype correlation, variability, and predicted functional impact of KCNA2 variants.     

Infiltration and Top Seed Growth-Textured YBCO Bulks With Multiple Holes

The recently reported hole-patterned YBa₂Cu₃O _y (Y123) bulks with improved superconducting properties are highly interesting from material quality and application variety points of view. It is well known that the core of plain bulk superconductors needs to be fully oxygenated and some defects like cracks, pores, and voids must be suppressed in order that the material can trap a high magnetic field or carry a high current density. To minimize the above defects, we have used a combination of standard superconducting ceramic processing and an infiltration technique to prepare regularly perforated YBa₂Cu₃O _y (Y123) bulk superconductors. This process leads to negligible shrinkage upon annealing and a uniform distribution of Y211 inclusions. Texture was evidenced by neutron pole figure measurements. Flux mapping was used to verify the superconducting homogeneity of the samples and to investigate the field-trapping ability. In addition, the textured drilled samples were reinforced using resin or metal impregnation and the influence of the different processing steps on the hardness of the materials has been investigated.