Analysis of HSP90-related folds with MED-SuMo classification approach

Three-dimensional structural information is critical for understanding functional protein properties and the precise mechanisms of protein functions implicated in physiological and pathological processes. Comparison and detection of protein binding sites are key steps for annotating structures with functional predictions and are extremely valuable steps in a drug design process. In this research area, MED-SuMo is a powerful technology to detect and characterize similar local regions on protein surfaces. Each amino acid residue’s potential chemical interactions are represented by specific surface chemical features (SCFs). The MED-SuMo heuristic is based on the representation of binding sites by a graph structure suitable for exploration by an efficient comparison algorithm. We use this approach to analyze one particular SCOP superfamily which includes HSP90 chaperone, MutL/DNA topoisomerase, histidine kinases, and α-ketoacid dehydrogenase kinase C (BCK). They share a common fold and a common region for ATP-binding. To analyze both similar and differing features of this fold, we use a novel classification method, the MED-SuMo multi approach (MED-SMA). We highlight common and distinct features of these proteins. The different clusters created by MED-SMA yield interesting observations. For instance, one cluster gathers three types of proteins (HSP90, topoisomerase VI, and BCK) which all bind the drug radicicol

Justifying the Special Theory of Relativity with Unconceived Methods

Many realists argue that present scientific theories will not follow the fate of past scientific theories because the former are more successful than the latter. Critics object that realists need to show that present theories have reached the level of success that warrants their truth. I reply that the special theory of relativity has been repeatedly reinforced by unconceived scientific methods, so it will be reinforced by infinitely many unconceived scientific methods. This argument for the special theory of relativity overcomes the critics’ objection, and has advantages over the no-miracle argument and the selective induction for it

River Restoration in the Twenty-First Century: Data and Experiential Knowledge to Inform Future Efforts

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71999/1/j.1526-100X.2007.00243.x.pd

Refutations of the Two Pessimistic Inductions

Both the pessimistic inductions over scientific theories and over scientists are built upon what I call proportional pessimism: as theories are discarded, the inductive rationale for concluding that the next theories will be discarded grows stronger. I argue that proportional pessimism clashes with the fact that present theories are more successful than past theories, and with the implications of the assumptions that there are finitely and infinitely many unconceived alternatives. Therefore, the two pessimistic inductions collapse along with proportional pessimism

Computational fragment-based drug design to explore the hydrophobic subpocket of the mitotic kinesin Eg5 allosteric binding site

International audienceEg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix alpha2 (L5/alpha2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would fill simultaneously both pockets. Some of the latter having original scaffolds and substituents in the hydrophobic pocket are identified in libraries of synthetically accessible molecules by the MED-Search software

Self-assembled monolayer of designed and synthesized triazinedithiolsilane molecule as interfacial adhesion enhancer for integrated circuit

Self-assembled monolayer (SAM) with tunable surface chemistry and smooth surface provides an approach to adhesion improvement and suppressing deleterious chemical interactions. Here, we demonstrate the SAM comprising of designed and synthesized 6-(3-triethoxysilylpropyl)amino-1,3,5-triazine-2,4-dithiol molecule, which can enhance interfacial adhesion to inhibit copper diffusion used in device metallization. The formation of the triazinedithiolsilane SAM is confirmed by X-ray photoelectron spectroscopy. The adhesion strength between SAM-coated substrate and electroless deposition copper film was up to 13.8 MPa. The design strategy of triazinedithiolsilane molecule is expected to open up the possibilities for replacing traditional organosilane to be applied in microelectronic industry

Comparing two intramedullary devices for treating trochanteric fractures: A prospective study

<p>Abstract</p> <p>Background</p> <p>Intertrochanteric fractures are surgically treated by using different methods and implants. The optional type of surgical stabilization is still under debate. However, between devices with the same philosophy, different design characteristics may substantially influence fracture healing. This is a prospective study comparing the complication and final functional outcome of two intramedullary devices, the intramedullary hip screw (IMHS) and the ENDOVIS nail.</p> <p>Materials and methods</p> <p>Two hundred fifteen patients were randomized on admission in two treatment groups. Epidemiology features and functional status was similar between two treatment groups. Fracture stability was assessed according to the Evan's classification. One hundred ten patients were treated with IMHS and 105 with ENDOVIS nail.</p> <p>Results</p> <p>There were no significant statistical differences between the two groups regarding blood loss, transfusion requirements and mortality rate. In contrast, the number of total complications was significantly higher in the ENDOVIS nail group. Moreover, the overall functional and walking competence was superior in the patients treated with the IMHS nail.</p> <p>Conclusions</p> <p>These results indicate that the choice of the proper implant plays probably an important role in the final outcome of surgical treatment of intertrochanteric fractures. IMHS nail allows for accurate surgical technique, for both static and dynamic compression and high rotational stability. IMHS nail proved more reliable in our study regarding nail insertion and overall uncomplicated outcome.</p

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools

An ontology for strongly sustainable business models: Defining an enterprise framework compatible with natural and social science

Business is increasingly employing sustainability practices, aiming to improve environmental and social responsibility while maintaining and improving profitability. For many organizations, profit-oriented business models are a major constraint impeding progress in sustainability. A formally defined ontology, a model definition, for profit-oriented business models has been employed globally for several years. However, no equivalent ontology is available in research or practice that enables the description of strongly sustainable business models, as validated by ecological economics and derived from natural, social, and system sciences. We present a framework of strongly sustainable business model propositions and principles as findings from a transdisciplinary review of the literature. A comparative analysis was performed between the framework and the Osterwalder profit-oriented ontology for business models. We introduce an ontology that enables the description of successful strongly sustainable business models that resolves weaknesses and includes functionally necessary relationships

Participatory instructional redesign by students and teachers in secondary education: effects on perceptions of instruction

Könings, K. D., Brand-Gruwel, S., & Van Merriënboer, J. J. G. (2011). Participatory instructional redesign by students and teachers in secondary education: effects on perceptions of instruction. Instructional Science, 39(5), 737–762.Students’ perceptions of instruction are important because they direct the learning of students. The fact that teachers have only limited knowledge of these perceptions is likely to threaten the effectiveness of learning, because congruence between interpretations of an instructional intervention is necesarry for its optimal use. This study examines participatory design as a strategy for taking student perceptions into account in instructional re/design. Participatory design meetings of groups of teachers and seven co-designing students in a secondary education setting identified changes to improve the regular education process. The results on changes in student perceptions, perceived-desired discrepancy, and teacher-student disagreement showed some improvement for the co-designers but, unexpectedly, limited or even negative effects for the non-co-designing students. Possible causes are discussed. Participatory design seems to have potential for improving education, but further research is needed