Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

RO PUF Design in FPGAs with new comparison strategies

A Physical Unclonable Function (PUF) can be used to provide authentication of devices by producing die-unique responses. In PUFs based on ring oscillators (ROs), the responses are derived from the oscillation frequencies of the ROs. However, RO PUFs can be vulnerable to attack due to the frequency distribution characteristics of the RO arrays. In this paper, in order to improve the design of RO PUFs for FPGA devices, the frequencies of RO arrays implemented on a large number of FPGA chips are statistically analyzed. Three RO frequency distribution (ROFD) characteristics are observed and discussed. Based on these ROFD characteristics, two RO comparison strategies are proposed that can be used to improve the design of RO PUFs. It is found that the symmetrical RO comparison strategy has the highest entropy density.

Improving RO PUF design using frequency distribution characteristics

A Physical Unclonable Function (PUF) can be used to provide authentication of devices by producing die-unique responses. In PUFs based on ring oscillators (ROs) the responses are derived from the oscillation frequencies of the ROs. However, RO PUFs can be vulnerable to attack due to the frequency distribution characteristics of the RO arrays. In this letter, in order to improve the design of RO PUFs for FPGA devices, the frequencies of RO arrays implemented on a large number of FPGA chips are statistically analyzed. Three RO frequency distribution (ROFD) characteristics, which can be used to improve the design of RO PUFs are observed and discussed.

Comparison of two suspension control strategies for multi-axle heavy truck

Two simple and effective control strategies for a multi-axle heavy truck, modified skyhook damping (MSD) control and proportional-integration-derivative (PID) control, were implemented into functional virtual prototype (FVP) model and compared in terms of road friendliness and ride comfort. A four-axle heavy truck-road coupling system model was established using FVP technology and validated through a ride comfort test. Then appropriate passive air suspensions were chosen to replace the rear tandem suspensions of the original truck model for preliminary optimization. The mechanical properties and time lag of dampers were taken into account in simulations of MSD and PID semi-active dampers implemented using MATLAB/Simulink. Through co-simulations with Adams and MATLAB, the effects of semi-active MSD and PID control were analyzed and compared, and control parameters which afforded the best comprehensive performance for each control strategy were chosen. Simulation results indicate that compared with the passive air suspension truck, semi-active MSD control improves both ride comfort and road-friendliness markedly, with optimization ratios of RMS vertical acceleration and RMS tyre force ranging from 10.1% to 44.8%. However, semi-active PID control only reduces vertical vibration of the driver’s seat by 11.1%, 11.1% and 10.9% on A, B and C level roads respectively. Both strategies are robust to the variation of road level.

Control strategies to prevent total hip replacement-related infections : a systematic review and mixed treatment comparison

OBJECTIVE: To synthesise the available evidence and estimate the comparative efficacy of control strategies to prevent total hip replacement (THR)-related surgical site infections (SSIs) using a mixed treatment comparison. DESIGN: Systematic review and mixed treatment comparison. SETTING: Hospital and other healthcare settings. PARTICIPANTS: Patients undergoing THR. PRIMARY AND SECONDARY OUTCOME MEASURES: The number of THR-related SSIs occurring following the surgical operation. RESULTS: 12 studies involving 123 788 THRs and 9 infection control strategies were identified. The strategy of 'systemic antibiotics+antibiotic-impregnated cement+conventional ventilation' significantly reduced the risk of THR-related SSI compared with the referent strategy (no systemic antibiotics+plain cement+conventional ventilation), OR 0.13 (95% credible interval (CrI) 0.03-0.35), and had the highest probability (47-64%) and highest median rank of being the most effective strategy. There was some evidence to suggest that 'systemic antibiotics+antibiotic-impregnated cement+laminar airflow' could potentially increase infection risk compared with 'systemic antibiotics+antibiotic-impregnated cement+conventional ventilation', 1.96 (95% CrI 0.52-5.37). There was no high-quality evidence that antibiotic-impregnated cement without systemic antibiotic prophylaxis was effective in reducing infection compared with plain cement with systemic antibiotics, 1.28 (95% CrI 0.38-3.38). CONCLUSIONS: We found no convincing evidence in favour of the use of laminar airflow over conventional ventilation for prevention of THR-related SSIs, yet laminar airflow is costly and widely used. Antibiotic-impregnated cement without systemic antibiotics may not be effective in reducing THR-related SSIs. The combination with the highest confidence for reducing SSIs was 'systemic antibiotics+antibiotic-impregnated cement+conventional ventilation'. Our evidence synthesis underscores the need to review current guidelines based on the available evidence, and to conduct further high-quality double-blind randomised controlled trials to better inform the current clinical guidelines and practice for prevention of THR-related SSIs.

Comparison of the impact of six heat-load management strategies on thermal responses and milk production of feed-pad and pasture fed dairy cows in a subtropical environment

Exposure to hot environments affects milk yield (MY) and milk composition of pasture and feed-pad fed dairy cows in subtropical regions. This study was undertaken during summer to compare MY and physiology of cows exposed to six heat-load management treatments. Seventy-eight Holstein-Friesian cows were blocked by season of calving, parity, milk yield, BW, and milk protein (%) and milk fat (%) measured in 2 weeks prior to the start of the study. Within blocks, cows were randomly allocated to one of the following treatments: open-sided iron roofed day pen adjacent to dairy (CID) + sprinklers (SP); CID only; non-shaded pen adjacent to dairy + SP (NSD + SP); open-sided shade cloth roofed day pen adjacent to dairy (SCD); NSD + sprinkler (sprinkler on for 45 min at 1100 h if mean respiration rate >80 breaths per minute (NSD + WSP)); open-sided shade cloth roofed structure over feed bunk in paddock + 1 km walk to and from the dairy (SCP + WLK). Sprinklers for CID + SP and NSD + SP cycled 2 min on, 12 min off when ambient temperature >26°C. The highest milk yields were in the CID + SP and CID treatments (23.9 L cow−1 day−1), intermediate for NSD + SP, SCD and SCP + WLK (22.4 L cow−1 day−1), and lowest for NSD + WSP (21.3 L cow−1 day−1) (P < 0.05). The highest (P < 0.05) feed intakes occurred in the CID + SP and CID treatments while intake was lowest (P < 0.05) for NSD + WSP and SCP + WLK. Weather data were collected on site at 10-min intervals, and from these, THI was calculated. Nonlinear regression modelling of MY × THI and heat-load management treatment demonstrated that cows in CID + SP showed no decline in MY out to a THI break point value of 83.2, whereas the pooled MY of the other treatments declined when THI >80.7. A combination of iron roof shade plus water sprinkling throughout the day provided the most effective control of heat load.

Prevalence and Forms of Bullying among Business Professionals: A Comparison of Two Different Strategies for Measuring Bullying

The aim of this study was to analyse the prevalence and forms of workplace bullying among business professionals holding predominantly managerial or expert positions. A cross-sectional survey study was conducted among Finnish professionals with a university degree in business studies. In the study two different strategies for measuring bullying were used and compared. When provided a definition of bullying, 8.8% of the respondents reported that they had at least occasionally been bullied during the past 12 months. However, when using a slightly modified version of the Negative Acts Questionnaire (Einarsen & Hoel 2001), containing a list of 32 predefined negative and potentially harassing acts, as many as 24.1% of the respondents reported that they had been subjected to at least one of the negative acts on a weekly basis. The respondents had experienced predominantly work-related negative acts, e.g. that their opinions and views were ignored, that they were given unreasonable deadlines or that information was withheld. Although the prevalence rates reported with the two strategies varied considerably, there was still consistency between the two strategies in the sense that those who had classified themselves as bullied also reported higher exposure rates to almost all of the negative acts included.

Comparison of the miscibility strategies in poly(benzyl methacrylate)-polystyrene blends

Exothermic interactions like hydrogen bonding, ionic and charge transfer, etc., and ''copolymer effect'' are commonly used to induce miscibility in immiscible blends. The efficacy of these methods in promoting miscibility in poly(benzyl methacrylate) (PBMA)-polystyrene (PS) immiscible blends has been studied by suitably modifying the structure of the component polymers. It has been found that hydrogen bonding approach is most advantageous among these approaches as it involves the need for minimum interacting sites. It has also been shown that these results can be extended to the blends of poly(acrylate)s or poly(methacrylate)s with PS. (C) 1996 John Wiley & Sons, Inc.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

Comparison of Experimental Strategies to Control Torpedograss

Studies were conducted to evaluate whether the herbicide imazapyr or a combination of imazapyr and fluridone could be used effectively to control torpedograss ( Panicum repens L.), an exotic perennial plant that has replaced more than 6,000 ha of native vegetation and degraded quality wildlife habitat in Lake Okeechobee, Florida. Torpedograss was controlled for more than one year in some areas following a single aerial treatment using 0.56, 0.84, or 1.12 kg acid equivalents (ae) imazapyr/ha. Combining imazapyr and fluridone did not increase the level of torpedograss control. In areas where plant biomass was reduced by fire prior to being treated with 0.84 or 1.12 kg ae imazapyr/ha, torpedograss was controlled for more than two years and native plant species, including duck potato ( Sagittaria lancifolia L.) and pickerelweed ( Pontederia cordata L.) became the dominant vegetation in less than one year. Although torpedograss was controlled in some areas, little or no long-term control was observed at 16 of the 26 treatment locations. To reduce the uncertainty associated with predicting long-term treatment affects, additional studies are needed to determine whether environmental factors such as periphyton mats, plant thatch, hydroperiod and water depth affect treatment efficacy. , he

Knowledge, attitudes and perceptions of management strategies and regulations of the Florida Keys National Marine Sanctuary by commercial fishers, dive operators, and environmental group members: A baseline characterization and 10-year comparison

This research is part of the Socioeconomic Research & Monitoring Program for the Florida Keys National Marine Sanctuary (FKNMS), which was initiated in 1998. In 1995-96, a baseline study on the knowledge, attitudes and perceptions of proposed FKNMS management strategies and regulations of commercial fishers, dive operators and on selected environmental group members was conducted by researchers at the University of Florida and the University of Miami’s Rosenstiel School of Atmospheric and Marine Science (RSMAS). The baseline study was funded by the U.S. Man and the Biosphere Program, and components of the study were published by Florida Sea Grant and in several peer reviewed journals. The study was accepted into the Socioeconomic Research & Monitoring Program at a workshop to design the program in 1998, and workshop participants recommended that the study be replicated every ten years. The 10-year replication was conducted in 2004-05 (commercial fishers) 2006 (dive operators) and 2007 (environmental group members) by the same researchers at RSMAS, while the University of Florida researchers were replaced by Thomas J. Murray & Associates, Inc., which conducted the commercial fishing panels in the FKNMS. The 10-year replication study was funded by NOAA’s Coral Reef Conservation Program. The study not only makes 10-year comparisons in the knowledge, attitudes and perceptions of FKNMS management strategies and regulations, but it also establishes new baselines for future monitoring efforts. Things change, and following the principles of “adaptive management”, management has responded with changes in the management plan strategies and regulations. Some of the management strategies and regulations that were being proposed at the time of the baseline 1995-96 study were changed before the management plan and regulations went into effect in July 1997. This was especially true for the main focus of the study which was the various types of marine zones in the draft and final zoning action plan. Some of the zones proposed were changed significantly and subsequently new zones have been created. This study includes 10-year comparisons of socioeconomic/demographic profiles of each user group; sources and usefulness of information; knowledge of purposes of FKNMS zones; perceived beneficiaries of the FKNMS zones; views on FKNMS processes to develop management strategies and regulations; views on FKNMS zone outcomes; views on FKNMS performance; and general support for FKNMS. In addition to new baseline information on FKNMS zones, new baseline information was developed for spatial use, investment and costs-and-earnings for commercial fishers and dive operators, and views on resource conditions for all three user groups. Statistical tests were done to detect significant changes in both the distribution of responses to questions and changes in mean scores for items replicated over the 10-year period. (PDF has 143 pages.)