GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

<p>Abstract</p> <p>Background</p> <p>Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website <url>http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/</url> or from the author LHH.</p> <p>Findings</p> <p>The Nutritious Rice for the World Project (NRW) on World Community Grid predicted <it>de novo</it>, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used.</p> <p>Conclusions</p> <p>GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale.</p

PROTINFO: new algorithms for enhanced protein structure predictions

We describe new algorithms and modules for protein structure prediction available as part of the PROTINFO web server. The modules, comparative and de novo modelling, have significantly improved back-end algorithms that were rigorously evaluated at the sixth meeting on the Critical Assessment of Protein Structure Prediction methods. We were one of four server groups invited to make an oral presentation (only the best performing groups are asked to do so). These two modules allow a user to submit a protein sequence and return atomic coordinates representing the tertiary structure of that protein. The PROTINFO server is available at

Modeling multi-valued biological interaction networks using Fuzzy Answer Set Programming

Fuzzy Answer Set Programming (FASP) is an extension of the popular Answer Set Programming (ASP) paradigm that allows for modeling and solving combinatorial search problems in continuous domains. The recent development of practical solvers for FASP has enabled its applicability to real-world problems. In this paper, we investigate the application of FASP in modeling the dynamics of Gene Regulatory Networks (GRNs). A commonly used simplifying assumption to model the dynamics of GRNs is to assume only Boolean levels of activation of each node. Our work extends this Boolean network formalism by allowing multi-valued activation levels. We show how FASP can be used to model the dynamics of such networks. We experimentally assess the efficiency of our method using real biological networks found in the literature, as well as on randomly-generated synthetic networks. The experiments demonstrate the applicability and usefulness of our proposed method to find network attractors

Resilience-enhancing solution to mitigate risk for sustainable supply chain-an empirical study of elevator manufacturing

As the complexity of supply chains increases, the enhancement of resilience for mitigating sustainable disruption risks in supply chains is an important issue. Quality function deployment (QFD) has been successfully applied in many domains to solve multicriteria decision-making (MCDM) problems. However, research on developing two houses of quality to connect sustainable supply chain disruption risks, resilience capacities, and resilience-enhancing features in elevator manufacturing supply chains by using the MCDM approach is lacking. This study aims to develop a framework for exploring useful decision-making by integrating the MCDM approach and QFD. By applying the framework, supply chain resilience can be improved by identifying the major sustainable risks and the key resilience to mitigate these risks. Important managerial insights and practical implications are obtained from the framework implementation in a case study of the elevator manufacturing industry. To strengthen resilience and thus mitigate key risks, the most urgent tasks are to connect the working site and the backstage to enhance product development and design and to share real-time job information. When these features are strengthened, agility, capacity, and visibility can be improved. Finally, unexpected events lead to changes in supplier delivery dates, and factors such as typhoon and lack of critical capacities/skilled employees with the greatest impact can be alleviated. This framework will provide an effective and pragmatic approach for constructing sustainable supply chain risk resilience in the elevator manufacturing industry.</p

Detection of subtle neurological alterations by the Catwalk XT gait analysis system

BACKGROUND: A new version of the CatWalk XT system was evaluated as a tool for detecting very subtle alteration in gait based on higher speed sample rate; the system could also demonstrate minor changes in neurological function. In this study, we evaluated the neurological outcome of sciatic nerve injury intervened by local injection of hyaluronic acid. Using the CatWalk XT system, we looked for differences between treated and untreated groups and differences within the same group as a function of time so as to assess the power of the Catwalk XT system for detecting subtle neurological change. METHODS: Peripheral nerve injury was induced in 36 Sprague–Dawley rats by crushing the left sciatic nerve using a vessel clamp. The animals were randomized into one of two groups: Group I: crush injury as the control; Group II: crush injury and local application with hyaluronic acid. These animals were subjected to neurobehavior assessment, histomorphology evaluation, and electrophysiology study periodically. These data were retrieved for statistical analysis. RESULTS: The density of neurofilament and S-100 over the distal end of crushed nerve showed significant differences either in inter-group comparison at various time points or intra-group comparison from 7 to 28 days. Neuronal structure architecture, axon counts, intensity of myelination, electrophysiology, and collagen deposition demonstrate significant differences between the two groups. There was significant difference of SFI and angle of ankle in inter- group analysis from 7 to 28 days, but there were no significant differences in SFI and angle of ankle at time points of 7 and 14 days. In the Cat Walk XT analysis, the intensity, print area, stance duration, and swing duration all showed detectable differences at 7, 14, 21, and 28 days, whereas there were no significant difference at 7 and 14 days with CatWalk 7 testing. In addition, there were no significant differences of step sequence or regularity index between the two versions. CONCLUSION: Hyaluronic acid augmented nerve regeneration as early as 7 days after crush injury. This subtle neurological alteration could be detected through the CatWalk XT gait analysis but not the SFI, angle of ankle, or CatWalk 7 methods

A review on architectural and urban design approaches to reducing the urban heat island effect

With the ongoing rapid urbanisation, humans enjoy the comfort of living with the use of advanced technology and infrastructure, without consideration towards the pollution produced daily, such as waste, heat, and exhaust gas emissions. Human-induced climate change has resulted in extreme weather and climate events, causing a consequential increase in the urban heat island effect. A large amount of radiant heat is focused in the city area, threatening the threshold of comfort in urban living, affecting our future generations to come. Therefore, this paper discusses how this phenomenon could be mitigated through a few design approaches. The existence of green roofs helps reduce the direct absorption of heat in buildings while water bodies help lower the surrounding temperature of a place. Additionally, using high reflectivity and spectral emissivity materials in buildings can also lower heat absorption into a building. Also, the design of urban wind corridors increases airflow into an area, hence cooling the surrounding temperature. When these steps are strategically incorporated into a design, the amount of heat could be significantly reduced, hence extenuating the urban heat island effect. However, more in-depth research is needed to ensure that it could successfully palliate the urban heat island effect in a city. It is hoped that this study could be a comprehensive guide to designers and engineers, or any individuals in the field of architecture and urban design in tackling the problem, hence achieving their target in eliminating the urban heat island effect in future works

Switch activation of PI-PLC downstream signals in activated macrophages with wortmannin

AbstractPhosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2) has been known to serve as a substrate for phosphatidylinositol 3-kinase (PI3K) and phosphoinositide-specific phospholipase C (PI-PLC), which can produce PtdIns(3,4,5)P3 and inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) and diacylglycerol (DAG), respectively. In this study, we elucidated the role of PI-PLC during the LPS-activated mouse macrophages RAW264.7 treated with PI3K inhibitor wortmannin. First, wortmannin treatment enhanced Ins(1,4,5)P3 production and iNOS expression in LPS-activated macrophages. Inhibition of PI3K by p85 siRNA also showed an enhancement of iNOS expression. On the other hand, overexpression of PI3K by ras-p110 expression plasmid significantly decreased iNOS expression in LPS-activated macrophages. In addition, overexpression of wild-type or dominant-negative Akt expression plasmid did not affect the iNOS expression in LPS-activated macrophages. Second, treatment of PI-PLC inhibitor U73122 reversed the enhancement of iNOS expression, the increase of phosphorylation level of ERK, JNK and p38, and the increase of AP-1-dependent gene expression in wortmannin-treated and LPS-activated macrophages. However, NF-κB activity determined by EMSA assay and reporter plasmid assay did not change during LPS-activated macrophages with or without wortmannin. We propose that the inhibition of PI3K by wortmannin in mouse macrophages enhances the PI-PLC downstream signals, and subsequently increases the LPS induction of iNOS expression independently of Akt pathway