Coarse-graining protein energetics in sequence variables

We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties such as energy can be unambiguously expanded in the amino-acid sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of designing proteins, or predicting the compatibility of a sequence with a given structure, by many orders of magnitude. The CE is physically transparent, and can be evaluated through linear regression on the energies of training sequences. We show, as example, that good prediction accuracy is obtained with up to pairwise interactions for a coiled-coil backbone, and that triplet interactions are important in the energetics of a more globular zinc-finger backbone.Comment: 10 pages, 3 figure

Ultra-Fast Evaluation of Protein Energies Directly from Sequence

The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7) compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1–4.7 kcal/mol, R(2) = 0.7–1.0). Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets—a coiled coil, a zinc finger, and a WW domain—as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages, CE is likely to find many uses in computational structural modeling

Discovery of Novel Materials with Broad Resistance to Bacterial Attachment Using Combinatorial Polymer Microarrays

A new class of bacteria-attachment-resistant materials is discovered using a multi-generation polymer microarray methodology that reduces bacterial attachment by up to 99.3% compared with a leading commercially available silver hydrogel anti-bacterial material. The coverage of three bacterial species, Pseudomonas aeruginosa, Staphylococcus aureus, and uropathogenic Escherichia coli is assessed.National Institutes of Health (U.S.) (Grant R01 DE016516

Lean participative process improvement : outcomes and obstacles in trauma orthopaedics

To examine the effectiveness of a “systems” approach using Lean methodology to improve surgical care, as part of a programme of studies investigating possible synergy between improvement approaches. Setting A controlled before-after study using the orthopaedic trauma theatre of a UK Trust hospital as the active site and an elective orthopaedic theatre in the same Trust as control. Participants All staff involved in surgical procedures in both theatres. Interventions A one-day “lean” training course delivered by an experienced specialist team was followed by support and assistance in developing a 6 month improvement project. Clinical staff selected the subjects for improvement and designed the improvements. Outcome Measures We compared technical and non-technical team performance in theatre using WHO checklist compliance evaluation, “glitch count” and Oxford NOTECHS II in a sample of directly observed operations, and patient outcome (length of stay, complications and readmissions) for all patients. We collected observational data for 3 months and clinical data for 6 months before and after the intervention period. We compared changes in measures using 2-way analysis of variance. Results We studied 576 cases before and 465 after intervention, observing the operation in 38 and 41 cases respectively. We found no significant changes in team performance or patient outcome measures. The intervention theatre staff focused their efforts on improving first patient arrival time, which improved by 20 minutes after intervention. Conclusions This version of “lean” system improvement did not improve measured safety processes or outcomes. The study highlighted an important tension between promoting staff ownership and providing direction, which needs to be managed in “lean” projects. Space and time for staff to conduct improvement activities are important for success

Eradication of multidrug-resistant Acinetobacter baumannii in a female patient with total hip arthroplasty, with debridement and retention: a case report

<p>Abstract</p> <p>Introduction</p> <p>Multidrug-resistant <it>Acinetobacter baumannii </it>has become a significant cause of healthcare-associated infections, but few reports have addressed <it>Acinetobacter baumannii </it>infections associated with orthopedic devices. The current recommended treatment for complicated infections due to orthopedic devices, including resistant gram-negative rods, consists of antimicrobial therapy with debridement and removal of implants.</p> <p>Case presentation</p> <p>The patient, a 47-year-old woman, had previously had a prior total hip arthroplasty at 16 years of age for a complex femoral neck fracture, and multiple subsequent revisions. This time, she underwent a fifth revision secondary to pain. Surgery was complicated by hypotension resulting in transfer to the intensive care unit and prolonged respiratory failure. She received peri-operative cefazolin but postoperatively developed surgical wound drainage requiring debridement of a hematoma. Cultures of this grew ampicillin-sensitive <it>Enterococcus </it>and <it>Acinetobacter baumannii </it>(sensitive only to amikacin and imipenem). The patient was started on imipenem. Removal of the total hip arthroplasty was not recommended because of the recent surgical complications, and the patient was eventually discharged home. She was seen weekly for laboratory tests and examinations and, after 4 months of therapy, the imipenem was discontinued. She did well clinically for 7 months before recurrent pain led to removal of the total hip arthroplasty. Intra-operative cultures grew ampicillin-sensitive <it>Enterococcus </it>and coagulase-negative <it>Staphylococcus </it>but no multidrug-resistant <it>Acinetobacter baumannii</it>. The patient received ampicillin for 8 weeks and had not had recurrent infection at the time of writing, 37 months after discontinuing imipenem.</p> <p>Conclusion</p> <p>We describe the successful treatment of an acute infection from multidrug-resistant <it>Acinetobacter baumannii </it>with debridement and retention of the total hip arthroplasty, using monotherapy with imipenem. This case challenges the general assumption that all orthopedic-device infections due to multidrug-resistant gram-negative organisms will require hardware removal. Further studies are needed to determine if organisms such as multidrug-resistant <it>Acinetobacter baumannii </it>are amenable to treatment with hardware retention.</p

Eradication of multidrug-resistant Acinetobacter baumannii in a female patient with total hip arthroplasty, with debridement and retention: a case report

<p>Abstract</p> <p>Introduction</p> <p>Multidrug-resistant <it>Acinetobacter baumannii </it>has become a significant cause of healthcare-associated infections, but few reports have addressed <it>Acinetobacter baumannii </it>infections associated with orthopedic devices. The current recommended treatment for complicated infections due to orthopedic devices, including resistant gram-negative rods, consists of antimicrobial therapy with debridement and removal of implants.</p> <p>Case presentation</p> <p>The patient, a 47-year-old woman, had previously had a prior total hip arthroplasty at 16 years of age for a complex femoral neck fracture, and multiple subsequent revisions. This time, she underwent a fifth revision secondary to pain. Surgery was complicated by hypotension resulting in transfer to the intensive care unit and prolonged respiratory failure. She received peri-operative cefazolin but postoperatively developed surgical wound drainage requiring debridement of a hematoma. Cultures of this grew ampicillin-sensitive <it>Enterococcus </it>and <it>Acinetobacter baumannii </it>(sensitive only to amikacin and imipenem). The patient was started on imipenem. Removal of the total hip arthroplasty was not recommended because of the recent surgical complications, and the patient was eventually discharged home. She was seen weekly for laboratory tests and examinations and, after 4 months of therapy, the imipenem was discontinued. She did well clinically for 7 months before recurrent pain led to removal of the total hip arthroplasty. Intra-operative cultures grew ampicillin-sensitive <it>Enterococcus </it>and coagulase-negative <it>Staphylococcus </it>but no multidrug-resistant <it>Acinetobacter baumannii</it>. The patient received ampicillin for 8 weeks and had not had recurrent infection at the time of writing, 37 months after discontinuing imipenem.</p> <p>Conclusion</p> <p>We describe the successful treatment of an acute infection from multidrug-resistant <it>Acinetobacter baumannii </it>with debridement and retention of the total hip arthroplasty, using monotherapy with imipenem. This case challenges the general assumption that all orthopedic-device infections due to multidrug-resistant gram-negative organisms will require hardware removal. Further studies are needed to determine if organisms such as multidrug-resistant <it>Acinetobacter baumannii </it>are amenable to treatment with hardware retention.</p

Perspicuity and Granularity in Refinement

This paper reconsiders refinements which introduce actions on the concrete level which were not present at the abstract level. It draws a distinction between concrete actions which are "perspicuous" at the abstract level, and changes of granularity of actions between different levels of abstraction. The main contribution of this paper is in exploring the relation between these different methods of "action refinement", and the basic refinement relation that is used. In particular, it shows how the "refining skip" method is incompatible with failures-based refinement relations, and consequently some decisions in designing Event-B refinement are entangled.Comment: In Proceedings Refine 2011, arXiv:1106.348

Cerca i gestió de la informació : les principals fonts d'informació en ciència i tecnologia

Background Standard operating procedures (SOPs) should improve safety in the operating theatre, but controlled studies evaluating the effect of staff-led implementation are needed. Methods In a controlled interrupted time series, we evaluated three team process measures (compliance with WHO surgical safety checklist, non-technical skills and technical performance) and three clinical outcome measures (length of hospital stay, complications and readmissions) before and after a 3-month staff-led development of SOPs. Process measures were evaluated by direct observation, using Oxford Non-Technical Skills II for non-technical skills and the ‘glitch count’ for technical performance. All staff in two orthopaedic operating theatres were trained in the principles of SOPs and then assisted to develop standardised procedures. Staff in a control operating theatre underwent the same observations but received no training. The change in difference between active and control groups was compared before and after the intervention using repeated measures analysis of variance. Results We observed 50 operations before and 55 after the intervention and analysed clinical data on 1022 and 861 operations, respectively. The staff chose to structure their efforts around revising the ‘whiteboard’ which documented and prompted tasks, rather than directly addressing specific task problems. Although staff preferred and sustained the new system, we found no significant differences in process or outcome measures before/after intervention in the active versus the control group. There was a secular trend towards worse outcomes in the postintervention period, seen in both active and control theatres. Conclusions SOPs when developed and introduced by frontline staff do not necessarily improve operative processes or outcomes. The inherent tension in improvement work between giving staff ownership of improvement and maintaining control of direction needs to be managed, to ensure staff are engaged but invest energy in appropriate change

Measuring Servitization Progress and Outcome:The Case of ‘Advanced Services’

The purpose of this paper is to establish a framework for assessing the progress and outcome of a manufacturer’s transformation towards becoming a provider of ‘advanced services’ – a complex bundling of products and services, whereby manufacturers offer capabilities and outcomes instead of products alone. ‘Advanced services’ represent the most complex offering in the current servitization trend among manufacturers. However, current performance measures lack the breadth and focus to assess progress or outcomes, and so support research and practice of organisational transformation efforts required. To address this gap the paper investigates how a manufacturer’s efforts to become an ‘advanced services’ provider can be comprehensively measured, and develops a framework for assessing the transformation journey towards becoming an ‘advanced services’ provider. The research method is based on (1) a systematic literature review process to create a comprehensive set of service-related performance measures that are available to assess a manufacturer’s servitization efforts, followed by (2) an engagement with an expert panel to synthesise the identified measures and create a set of ‘advanced services’ performance measures. The proposed framework is presented as a scorecard that can be used in practice to assess the progress and outcome of a manufacturer’s transformation towards becoming a provider of ‘advanced services’