Bidirectional Transformation "bx" (Dagstuhl Seminar 11031)

Bidirectional transformations bx are a mechanism for maintaining the consistency of two (or more) related sources of information. Researchers from many different areas of computer science including databases (DB), graph transformations (GT), software engineering (SE), and programming languages (PL) are actively investigating the use of bx to solve a diverse set of problems. Although researchers have been actively working on bidirectional transformations in the above mentioned communities for many years already, there has been very little cross-discipline interaction and cooperation so far. The purpose of a first International Meeting on Bidirectional Transformations (GRACE-BX), held in December 2008 near Tokyo, was therefore to bring together international elites, promising young researchers, and leading practitioners to share problems, discuss solutions, and open a dialogue towards understanding the common underpinnings of bx in all these areas. While the GRACE-BX meeting provided a starting point for exchanging ideas in different communities and confirmed our believe that there is a considerable overlap of studied problems and developed solutions in the identified communities, the Dagstuhl Seminar 11031 on ``Bidirectional Transformations\u27\u27 also aimed at providing a place for working together to define a common vocabulary of terms and desirable properties of bidirectional transformations, develop a suite of benchmarks, solve some challenging problems, and launch joint efforts to form a living bx community of cooperating experts across the identified subdisciplines. This report documents the program and the outcomes of Dagstuhl Seminar 11031 with abstracts of tutorials, working groups, and presentations on specific research topics

Surgical and Medical Applications of Drones: A Comprehensive Review

Drones have the ability to gather real time data cost effectively, to deliver payloads and have initiated the rapid evolution of many industrial, commercial, and recreational applications. Unfortunately, there has been a slower expansion in the field of medicine. This article provides a comprehensive review of current and future drone applications in medicine, in hopes of empowering and inspiring more aggressive investigation

Evaluation of sUAS Education and Training Tools

The wide distribution and demographic composition of students seeking small unmanned aircraft system (sUAS) education presents a need to fully understand the capabilities, limitations, and dependencies of effective training tools. Concepts, practices, and technologies associated with modeling and simulation, immersive gaming, augmented and mixed-reality, and remote operation have demonstrated efficacy to support engaged student learning and objective satisfaction. Identification and comparison of key attributes critical to an aviation educational framework, such as competency-based training, enables educational designers to identify those tools with the highest potential to support successful learning. A series of factors, such as system performance, regulatory compliance, environmental conditions, technological familiarity, and personal experience, require consideration in the selection, optimization, and application of such tools. Embry-Riddle and the Sinclair College National UAS Training and Certification Center have overseen the development, launch, and sustainment of respective sUAS education programs. Effectiveness of these programs is dependent on continuous evaluation of tools, specific to educational settings. A relevant example was the assessment of popular multirotor sUAS conducted by ERAU-W, which led to publication of the “Small Unmanned Aircraft System Consumer Guide” and selection of the Parrot BeBop 2 platform to support sUAS operations curricula. The intent of this work is to present critical considerations, including influencing factors and dependencies, associated with the selection and adoption of technological tools best supporting sUAS education. Background details; emerging approaches, models, and technologies; and examples of past tool evaluation, inclusive of assessment criteria and observations, are discussed. Finally, a series of reflective remarks, including recommendations, relating to evaluation, adaptation, and incorporation of future tools supporting sUAS education are presented

Rapid chain tracing of polypeptide backbones in electron-density maps

A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented

Rapid model building of β-sheets in electron-density maps

A method for rapid model building of β-sheets at moderate resolution is presented

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.

We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases

Subfamily-Specific Adaptations in the Structures of Two Penicillin-Binding Proteins from Mycobacterium tuberculosis

Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis

An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein

Campylobacter jejuni is a Gram-negative food-borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain Barre syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two-domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a K-d of similar to 10(-7) M consistent with a role as a receptor for a high- affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC-type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni