Stochastic protein folding simulation in the three-dimensional HP-model

We present results from three-dimensional protein folding simulations in the HP-model on ten benchmark problems. The simulations are executed by a simulated annealing-based algorithm with a time-dependent cooling schedule. The neighbourhood relation is determined by the pull-move set. The results provide experimental evidence that the maximum depth D of local minima of the underlying energy landscape can be upper bounded by D < n(2/3). The local search procedure employs the stopping criterion (In/delta)(D/gamma) where m is an estimation of the average number of neighbouring conformations, gamma relates to the mean of non-zero differences of the objective function for neighbouring conformations, and 1-delta is the confidence that a minimum conformation has been found. The bound complies with the results obtained for the ten benchmark problems. (c) 2008 Elsevier Ltd. All rights reserved.

Phasic modulation of corticomotor excitability during passive movement of the upper limb: effects of movement frequency and muscle specificity

Modulations in the excitability of spinal reflex pathways during passive rhythmic movements of the lower limb have been demonstrated by a number of previous studies [4]. Less emphasis has been placed on the role of supraspinal pathways during passive movement, and on tasks involving the upper limb. In the present study, transcranial magnetic stimulation (TMS) was delivered to subjects while undergoing passive flexion-extension movements of the contralateral wrist. Motor evoked potentials (MEPs) of flexor carpi radialis (FCR) and abductor pollicus brevis (APB) muscles were recorded. Stimuli were delivered in eight phases of the movement cycle during three different frequencies of movement. Evidence of marked modulations in pathway excitability was found in the MEP amplitudes of the FCR muscle, with responses inhibited and facilitated from static values in the extension and flexion phases, respectively. The results indicated that at higher frequencies of movement there was greater modulation in pathway excitability. Paired-pulse TMS (sub-threshold conditioning) at short interstimulus intervals revealed modulations in the extent of inhibition in MEP amplitude at high movement frequencies. In the APE muscle, there was some evidence of phasic modulations of response amplitude, although the effects were less marked than those observed in FCR. It is speculated that these modulatory effects are mediated via Ia afferent pathways and arise as a consequence of the induced forearm muscle shortening and lengthening. Although the level at which this input influences the corticomotoneuronal pathway is difficult to discern, a contribution from cortical regions is suggested. (C) 2001 Published by Elsevier Science B.V.

Ten Year Performance Evaluation of a Field-Scale Zero-Valent Iron Permeable Reactive Barrier Installed to Remediate Trichloroethene Contaminated Groundwater

The Monkstown Fe0 PRB, Europe’s oldest commercially installed PRB, had been treating trichloroethene (TCE) contaminated groundwater for about 10 years on the Nortel Network site in Northern Ireland when cores were collected in December, 2006. Groundwater data from 2001-2006 indicated that TCE is being remediated to below detection limits as the contaminated groundwater flows through the PRB, Ca and Fe carbonates, crystalline and amorphous FeS, and Fe (oxy)hydroxides precipitates are present in the Fe0 filing material within the PRB. A greater variety of minerals are associated with a 1 cm thick slightly cemented crust at the entrance of the Fe0 section of the reactive vessel and the discontinuous cemented Fe0 material directly below it. Also, a greater presence of microbial communities occurred in the upper portion of the PRB compared to the lower section which might be due to less favourable conditions (i.e. high pH, low oxygen) for microbial growth in the lower section of the PRB. Visual estimation suggests that the Fe0 filings in the effluent section of the PRB have life-span of 10+ years compared to the Fe0 filings in the thin influent section of the PRB which may have a life span of only ~2-5 more years. Multi-tracer tests indicated that preferential pathways have formed in this PRB over the 10 years of operation.

Solid-bound, proton-driven, fluorescent ‘off–on–off’ switches based on PET (photoinduced electron transfer)

Anthracene-based, H+-driven, ‘off–on–off’ fluorescent PET (photoinduced electron transfer) switches are immobilized on organic and inorganic polymeric solids in the form of Tentagel® and silica, respectively. The environment of the organic bead displaces apparent switching thresholds towards lower pH values whereas the Si–O- groups of silica electrostatically cause the opposite effect. These switches are ternary logic gate tags, one of which can be particularly useful in strengthening molecular computational identification (MCID) of small solid objects.

Channel characterization for single- and multiple-antenna wearable systems used for indoor body-to-body communications

In this paper, an analysis of radio channel characteristics for single- and multiple-antenna bodyworn systems for use in body-to-body communications is presented. The work was based on an extensive measurement campaign conducted at 2.45 GHz representative of an indoor sweep and search scenario for fire and rescue personnel. Using maximum-likelihood estimation in conjunction with the Akaike information criterion (AIC), five candidate probability distributions were investigated and from these the kappa - mu distribution was found to best describe small-scale fading observed in the body-to-body channels. Additional channel parameters such as autocorrelation and the cross-correlation coefficient between fading signal envelopes were also analyzed. Low cross correlation and small differences in mean signal levels between potential dual-branch diversity receivers suggested that the prospect of successfully implementing diversity in this type application is extremely good. Moreover, using selection combination, maximal ratio, and equal gain combining, up to 8.69-dB diversity gain can be made available when four spatially separated antennas are used at the receiver. Additional improvements in the combined envelopes through lower level crossing rates and fade durations at low signal levels were also observed.

Estimation of in situ stresses using anisotropic elasticity and suction measurements

Sampling and specimen preparation produce changes in mean effective stresses and pore water pressures, even with ‘perfect sampling’. The paper takes an existing simplified three-parameter cross-anisotropic elastic model and uses it to model these changes. The required ratio of cross-anisotropic parameters J/3G* can be obtained from standard CIU triaxial tests. If measurements are also made of suctions in unloaded specimens in the laboratory, then a combination of J/3G*, the measured suction, and the effective overburden pressure permits an estimation of the horizontal effective pressure and the K 0 ‘at rest’ coefficient. This can be helpful in numerical modelling that needs to start from in situ conditions, and in planning pressure levels for reconsolidation of clay specimens in the laboratory. Tests were done on Belfast Upper Boulder Clay from a depth of 28 m. Values of horizontal in situ effective stress estimated from these measurements compare favorably with conventional estimates of the ‘at rest’ coefficient K 0 and the overconsolidation ratio. Estimates of horizontal stress in London Clay were made using published data and the results compared with actual measurements. Again reasonable agreement was obtained.

Epidemiology of Adolescent Rugby Injuries: A Systematic Review

OBJECTIVE: Despite recent increases in the volume of research in professional rugby union, there is little consensus on the epidemiology of injury in adolescent players. We undertook a systematic review to determine the incidence, severity, and nature of injury in adolescent rugby union players.

DATA SOURCES: In April 2009, we performed a computerized literature search on PubMed, Embase, and Cochrane Controlled Trials Register (via Ovid). Population-specific and patient-specific search terms were combined in the form of MEDLINE subject headings and key words (wound$ and injur$, rugby, adolescent$). These were supplemented with related-citation searches on PubMed and bibliographic tracking of primary and review articles.

STUDY SELECTION: Prospective epidemiologic studies in adolescent rugby union players.

DATA SYNTHESIS: A total of 15 studies were included, and the data were analyzed descriptively. Two independent reviewers extracted key study characteristics regarding the incidence, severity, and nature of injuries and the methodologic design.

CONCLUSIONS: Wide variations existed in the injury definitions and data collection procedures. The incidence of injury necessitating medical attention varied with the definition, from 27.5 to 129.8 injuries per 1000 match hours. The incidence of time-loss injury (>7 days) ranged from 0.96 to 1.6 per 1000 playing hours and from 11.4/1000 match hours (>1 day) to 12-22/1000 match hours (missed games). The highest incidence of concussion was 3.3/1000 playing hours. No catastrophic injuries were reported. The head and neck, upper limb, and lower limb were all common sites of injury, and trends were noted toward greater time loss due to upper limb fractures or dislocations and knee ligament injuries. Increasing age, the early part of the playing season, and the tackle situation were most closely associated with injury. Future injury-surveillance studies in rugby union must follow consensus guidelines to facilitate interstudy comparisons and provide further clarification as to where injury-prevention strategies should be focused.

Propagating Wave Phenomena Detected in Observations and Simulations of the Lower Solar Atmosphere

We present high-cadence observations and simulations of the solar photosphere, obtained using the Rapid Oscillations in the Solar Atmosphere imaging system and the MuRAM magnetohydrodynamic (MHD) code, respectively. Each data set demonstrates a wealth of magnetoacoustic oscillatory behavior, visible as periodic intensity fluctuations with periods in the range 110–600 s. Almost no propagating waves with periods less than 140 s and 110 s are detected in the observational and simulated data sets, respectively. High concentrations of power are found in highly magnetized regions, such as magnetic bright points and intergranular lanes. Radiative diagnostics of the photospheric simulations replicate our observational results, confirming that the current breed of MHD simulations are able to accurately represent the lower solar atmosphere. All observed oscillations are generated as a result of naturally occurring magnetoconvective processes, with no specific input driver present. Using contribution functions extracted from our numerical simulations, we estimate minimum G-band and 4170 Å continuum formation heights of 100 km and 25 km, respectively. Detected magnetoacoustic oscillations exhibit a dominant phase delay of −8◦ between the G-band and 4170 Å continuum observations, suggesting the presence of upwardly propagating waves.More than 73% of MBPs (73% from observations and 96% from simulations) display upwardly propagating wave phenomena, suggesting the abundant nature of oscillatory behavior detected higher in the solar atmosphere may be traced back to magnetoconvective processes occurring in the upper layers of the Sun’s convection zone.

Multicamera sport player tracking with Bayesian estimation of measurements

We propose a complete application capable of tracking multiple objects in an environment monitored by multiple cameras. The system has been specially developed to be applied to sport games, and it has been evaluated in a real association-football stadium. Each target is tracked using a local importance-sampling particle filter in each camera, but the final estimation is made by combining information from the other cameras using a modified unscented Kalman filter algorithm. Multicamera integration enables us to compensate for bad measurements or occlusions in some cameras thanks to the other views it offers. The final algorithm results in a more accurate system with a lower failure rate. (C) 2009 Society of Photo-Optical Instrumentation Engineers. [DOI: 10.1117/1.3114605]

An audit of hospital admissions for acute upper gastrointestinal haemorrhage

A retrospective survey was made of all 189 patients admitted with acute upper gastrointestinal haemorrhage to the Belfast City Hospital in one year. The commonest single reason for admission was peptic ulcer disease, but this was lower than in other published series from the United Kingdom. Overall mortality was 4.8%. The majority of patients did not require either blood transfusion or surgery. There may be potential benefits of endoscopic haemostatic techniques to deal with this condition.

A longitudinal analysis of estimation, counting skills, and mathematical ability across the first school year

In response to claims that the quality (and in particular linearity) of children's mental representation of number acts as a constraint on number development, we carried out a longitudinal assessment of the relationships between number line estimation, counting, and mathematical abilities. Ninety-nine 5-year-olds were tested on 4 occasions at 3 monthly intervals. Correlations between the 3 types of ability were evident, but while the quality of children's estimations changed over time and performance on the mathematical tasks improved over the same period, changes in one were not associated with changes in the other. In contrast to the earlier claims that the linearity of number representation is potentially a unique contributor to children's mathematical development, the data suggest that this variable is not significantly privileged in its impact over and above simple procedural number skills. We propose that both early arithmetic success and estimating skill are bound closely to developments in counting ability.

Combined studies of DFT atomistic modelling and in situ FTIR spectroscopy on surface oxidants and CO oxidation at Ru electrodes

We report the combined studies of density functional theory (DFT) calculations and electrochemical in situ FTIR spectroscopy on surface oxidants and mechanisms of CO oxidation at the Ru(0001) electrodes. It is shown that CO can co-adsorb with both O and OH species at lower potential region where a low coverage of the (2 x 2)-O/OH adlayer formed; the oxidation of CO adsorbates takes place at higher potentials where a high coverage of the (1 x 1)-O/OH adlayer formed. Surface O species are not the active oxidants under all coverages studied, due to the high reaction barriers between CO and O (>1 eV). However, surface OH species with higher coverage are identified as the active oxidants, and CO oxidation takes place via a two-steps' mechanism of CO + 3OH -> COOH + 2OH -> CO2 + H2O + OH, in which three nearby OH species are involved in the CO2 formation: CO reacts with OH, forming COOH; COOH then transfers the H to a nearby OH to form H2O and CO2, at the same time, another H in the H2O transfers to a nearby OH to form a weak adsorbed H2O and a new OH. The reaction barrier of these processes is reduced significantly to around 0.50 eV. These new results not only provide an insight into surface active oxidants on Ru, which is directly relevant to fuel cell catalysis, but also reveals the extra complexity of catalytic reactions taking place at solid/liquid electrochemical interface in comparison to the relatively simpler ones at solid/gas phase. 

On the Complexity of Universal Leader Election

Electing a leader is a fundamental task in distributed computing. In its implicit version, only the leader must know who is the elected leader. This paper focuses on studying the message and time complexity of randomized implicit leader election in synchronous distributed networks. Surprisingly, the most "obvious" complexity bounds have not been proven for randomized algorithms. The "obvious" lower bounds of O(m) messages (m is the number of edges in the network) and O(D) time (D is the network diameter) are non-trivial to show for randomized (Monte Carlo) algorithms. (Recent results that show that even O(n) (n is the number of nodes in the network) is not a lower bound on the messages in complete networks, make the above bounds somewhat less obvious). To the best of our knowledge, these basic lower bounds have not been established even for deterministic algorithms (except for the limited case of comparison algorithms, where it was also required that some nodes may not wake up spontaneously, and that D and n were not known).

We establish these fundamental lower bounds in this paper for the general case, even for randomized Monte Carlo algorithms. Our lower bounds are universal in the sense that they hold for all universal algorithms (such algorithms should work for all graphs), apply to every D, m, and n, and hold even if D, m, and n are known, all the nodes wake up simultaneously, and the algorithms can make anyuse of node's identities. To show that these bounds are tight, we present an O(m) messages algorithm. An O(D) time algorithm is known. A slight adaptation of our lower bound technique gives rise to an O(m) message lower bound for randomized broadcast algorithms.

An interesting fundamental problem is whether both upper bounds (messages and time) can be reached simultaneously in the randomized setting for all graphs. (The answer is known to be negative in the deterministic setting). We answer this problem partially by presenting a randomized algorithm that matches both complexities in some cases. This already separates (for some cases) randomized algorithms from deterministic ones. As first steps towards the general case, we present several universal leader election algorithms with bounds that trade-off messages versus time. We view our results as a step towards understanding the complexity of universal leader election in distributed networks.