Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

Isolation basin records of late Quaternary sea-level change, central mainland British Columbia, Canada.

Isolation basin records from the Seymour-Belize Inlet Complex, a remote area of central mainland British Columbia, Canada are used to constrain post-glacial sea-level changes and provide a preliminary basis for testing geophysical model predictions of relative sea-level (RSL) change. Sedimentological and diatom data from three low-lying (<4 m elevation) basins record falling RSLs in late-glacial times and isolation from the sea by ~11,800–11,200 14C BP. A subsequent RSL rise during the early Holocene (~8000 14C BP) breached the 2.13 m sill of the lowest basin (Woods Lake), but the two more elevated basins (sill elevations of ~3.6 m) remained isolated. At ~2400 14C BP, RSL stood at 1.49 ± 0.34 m above present MTL. Falling RSLs in the late Holocene led to the final emergence of the Woods Lake basin by 1604 ± 36 14C BP. Model predictions generated using the ICE-5G model partnered with a small number of different Earth viscosity models generally show poor agreement with the observational data, indicating that the ice model and/or Earth models considered can be improved upon. The best data-model fits were achieved with relatively low values of upper mantle viscosity (5 × 1019 Pa s), which is consistent with previous modelling results from the region. The RSL data align more closely with observational records from the southeast of the region (eastern Vancouver Island, central Strait of Georgia), than the immediate north (Bella Bella–Bella Coola and Prince Rupert-Kitimat) and areas to the north-west (Queen Charlotte Sound, Hecate Strait), underlining the complexity of the regional response to glacio-isostatic recovery.

Has habitat heterogeneity promoted phenotypic and ecological sub-structuring among a Coregonus lavaretus population in a large Scottish lake?

Differences in stable-isotope values, morphology and ecology in whitefish Coregonus lavaretus were investigated between the three basins of Loch Lomond. The results are discussed with reference to a genetic investigation to elucidate any substructuring or spawning site fidelity. Foraging fidelity between basins of Loch Lomond was indicated by delta 13C and delta 15N values of C. lavaretus muscle tissue. There was, however, no evidence of the existence of sympatric morphs in the C. lavaretus population. A previous report of two C. lavaretus 'species' in Loch Lomond probably reflects natural variation between individuals within a single mixed population.

Dynamics of the Indonesian seas circulation. Part I – The influence of bottom topography on temperature and salinity distributions

The influence of bottom topography on the distribution of temperature and salinity in the Indonesian seas region has been studied with a high-resolution model based on the Princeton Ocean Model. One of the distinctive properties of the model is an adequate reproduction of all major topographic features in the region by the model bottom relief. The three major routes of flow of Pacific water through the region have been identified. The western route follows the flow of North Pacific Water through the Sulawesi Sea, Makassar Strait, Flores Sea, and Banda Sea. This is the main branch of the Indonesian Throughflow. The eastern routes follow the flow of South Pacific water through the eastern Indonesian seas. This water enters the region either through the Halmahera Sea or by flowing to the north around Halmahera Island into the Morotai Basin and then into the Maluku Sea. A deep southward flow of South Pacific Water fills the Seram Sea below 1200 m through the Lifamatola Passage. As it enters the Seram Sea, this overflow turns eastward at depths greater than 2000 m, then upwells in the eastern part of the Seram Sea before returning westward at ~1500-2000 m. The flow continues westward across the Seram Sea, spreading to greater depths before entering the Banda Sea at the Buru-Mangole passage. It is this water that shapes the temperature and salinity of the deep Banda Sea. Topographic elevations break the Indonesian seas region down into separate basins. The difference in the distributions of potential temperature, ?, and salinity, S, in adjacent basins is primarily due to specific properties of advection of ? and S across a topographic rise. By and large, the topographic rise blocks deep flow between basins whereas water shallower than the depth of the rise is free to flow between basins. To understand this process, the structure of simulated fields of temperature and salinity has been analyzed. To identify a range of advected ? or S, special sections over the sills with isotherms or isohalines and isotachs of normal velocity have been considered. Following this approach the impact of various topographic rises on the distribution of ? and S has been identified. There are no substantial structural changes of potential temperature and salinity distributions between seasons, though values of some parameters of temperature and salinity distributions, e.g., magnitudes of maxima and minima, can change. It is shown that the main structure of the observed distributions of temperature and salinity is satisfactorily reproduced by the model throughout the entire domain.

Clarification of rubber mill wastewater by a plant based biopolymer- comparison with common inorganic coagulants

Background: In this study, the efficiency of Guar gum as a biopolymer has been compared with two other widely used inorganic coagulants, ferric chloride (FeCl3) and aluminum chloride (AlCl3), for the treatment of effluent collected from the rubber-washing tanks of a rubber concentrate factory. Settling velocity distribution curves were plotted to demonstrate the flocculating effect of FeCl3, AlCl3 and Guar gum. FeCl3 and AlCl3 displayed better turbidity removal than Guar gum at all settling velocities.

Result: FeCl3, AlCl3 and Guar gum removed 92.8%, 88.2% and 88.1% turbidity, respectively, of raw wastewater at a settling velocity of 0.1 cm min-1, respectively. Scanning electron microscopic (SEM) study conducted on the flocs revealed that Guar gum and FeCl3produced strong intercoiled honeycomb patterned floc structure capable of entrapping suspended particulate matter. Statistical experimental design Response Surface Methodology (RSM) was used to design all experiments, where the type and dosage of flocculant, pH and mixing speed were taken as control factors and, an optimum operational setting was proposed.

Conclusion: Due to biodegradability issues, the use of Guar gum as a flocculating agent for wastewater treatment in industry is highly recommended.

Improvements Relating to Water Treatment

A process for the treatment of water comprising at least the steps of : (a) providing the water in laminar flow; and (b) providing bubblefree aeration to the water. The present invention introduces aerobic treatment into wastewater settlement without any hindrance to the settlement process. The present invention is useable for any settlement step or stage, without limitation, the commonest being primary settlement or final settling.

Later Pleistocene evolution of the Exe valley: A chronstratigraphic model of terrace formation and its implications for Palaeolithic archaeology

This paper presents the ?rst systematic chronostratigraphic study of the river terraces of the Exe catchment in South West England and a new conceptual model for terrace formation in unglaciated basins with applicability to terrace staircase sequences elsewhere. The Exe catchment lay beyond the maximum extent of Pleistocene ice sheets and the drainage pattern evolved from the Tertiary to the Middle Pleistocene, by which time the major valley systems were in place and downcutting began to create a staircase of strath terraces. The higher terraces (8-6) typically exhibit altitudinal overlap or appear to be draped over the landscape, whilst the middle terraces show greater altitudinal separation and the lowest terraces are of a cut and ?ll form. The terrace deposits investigated in this study were deposited in cold phases of the glacial-interglacial Milankovitch climatic cycles with the lowest four being deposited in the Devensian Marine Isotope Stages (MIS) 4-2. A new cascade process-response model is proposed of basin terrace evolution in the Exe valley, which emphasises the role of lateral erosion in the creation of strath terraces and the reworking of inherited resistant lithological components down through the staircase. The resultant emergent valley topography and the reworking of artefacts along with gravel clasts, have important implications for the dating of hominin presence and the local landscapes they inhabited. Whilst the terrace chronology suggested here is still not as detailed as that for the Thames or the Solent System it does indicate a Middle Palaeolithic hominin presence in the region, probably prior to the late Wolstonian Complex or MIS 6. This supports existing data from cave sites in South West England.

Testing the efficacy of the glacial buzzsaw: insights from the Sredinny Mountains, Kamchatka

Peak altitudes, hypsometry, geology, and former equilibrium-line altitudes (ELAs) are analyzed across the Sredinny Mountains (Kamchatka). Overall, evidence is found to suggest that the glacial buzzsaw has operated to shape the topography of this mountain range, but the strength of this signature is not spatially uniform. In the southern sector of the mountains, we see evidence that an efficient glacial buzzsaw has acted to impose constraints upon topography, limiting peak altitudes, and concentrating land-surface area (hypsometric maxima) close to palaeo-ELAs. By contrast, in the northern sector of the mountains, a number of peaks rise high above the surrounding topography, and land-surface area is concentrated well below palaeo-ELAs. This deviation from a classic ‘buzzsaw signature’, in the northern sector of the mountains, is considered to reflect volcanic construction during the Quaternary, resulting in a series of high altitude peaks, combined with the action of dynamic glaciers, acting to skew basin topography toward low altitudes, well below palaeo-ELAs. These glaciers are considered to have been particularly dynamic because of their off-shore termination, their proximity to moisture-bearing air masses from the North Pacific, and because accumulation was supplemented by snow and ice avalanching from local high altitude peaks. Overall, the data suggest that the buzzsaw remains a valid mechanism to generally explain landscape evolution in mountain regions, but its signature is significantly weakened in mountain basins that experience both volcanic construction and climatic conditions favouring dynamic glaciation.

The superluminous supernova PS1-11ap: bridging the gap between low and high redshift

We present optical photometric and spectroscopic coverage of the superluminous supernova (SLSN) PS1-11ap, discovered with the Pan-STARRS1 Medium Deep Survey at z = 0.524. This intrinsically blue transient rose slowly to reach a peak magnitude of Mu = −21.4 mag and bolometric luminosity of 8 × 1043 erg s−1 before settling on to a relatively shallow gradient of decline. The observed decline is significantly slower than those of the SLSNe-Ic which have been the focus of much recent attention. Spectroscopic similarities with the lower redshift SN2007bi and a decline rate similar to 56Co decay time-scale initially indicated that this transient could be a candidate for a pair instability supernova (PISN) explosion. Overall the transient appears quite similar to SN2007bi and the lower redshift object PTF12dam. The extensive data set, from 30 d before peak to 230 d after, allows a detailed and quantitative comparison with published models of PISN explosions. We find that the PS1-11ap data do not match these model explosion parameters well, supporting the recent claim that these SNe are not pair instability explosions. We show that PS1-11ap has many features in common with the faster declining SLSNe-Ic, and the light-curve evolution can also be quantitatively explained by the magnetar spin-down model. At a redshift of z = 0.524, the observer-frame optical coverage provides comprehensive rest-frame UV data and allows us to compare it with the SLSNe recently found at high redshifts between z = 2 and 4. While these high-z explosions are still plausible PISN candidates, they match the photometric evolution of PS1-11ap and hence could be counterparts to this lower redshift transient.

A comparative study of biopolymers and alum in the separation and recovery of pulp fibres from paper mill effluent by flocculation

Recovery of cellulose fibres from paper mill effluent has been studied using common polysaccharides or biopolymers such as Guar gum, Xanthan gum and Locust bean gum as flocculent. Guar gum is commonly used in sizing paper and routinely used in paper making. The results have been compared with the performance of alum, which is a common coagulant and a key ingredient of the paper industry. Guar gum recovered about 3.86 mg/L of fibre and was most effective among the biopolymers. Settling velocity distribution curves demonstrated that Guar gum was able to settle the fibres faster than the other biopolymers; however, alum displayed the highest particle removal rate than all the biopolymers at any of the settling velocities. Alum, Guar gum, Xanthan gum and Locust bean gum removed 97.46%, 94.68%, 92.39% and 92.46% turbidity of raw effluent at a settling velocity of 0.5 cm/min, respectively. The conditions for obtaining the lowest sludge volume index such as pH, dose and mixing speed were optimised for guar gum which was the most effective among the biopolymers. Response surface methodology was used to design all experiments, and an optimum operational setting was proposed. The test results indicate similar performance of alum and Guar gum in terms of floc settling velocities and sludge volume index. Since Guar gum is a plant derived natural substance, it is environmentally benign and offers a green treatment option to the paper mills for pulp recycling.

Mantle flow, volatiles, slab-surface temperatures and melting dynamics in the north Tonga arc-Lau back-arc basin

The Fonualei Spreading Center affords an excellent opportunity to evaluate geochemical changes with increasing depth to the slab in the Lau back-arc basin. We present H2O and CO2 concentrations and Sr, Nd, Pb, Hf and U-Th-Ra isotope data for selected glasses as well as new Hf isotope data from boninites and seamounts to the north of the Tonga arc. The Pb and Hf isotope data are used to show that mantle flow is oriented to the southwest and that the tear in the northern end of the slab may not extend east as far as the boninite locality. Along the Fonualei Spreading Center, key geochemical parameters change smoothly with increasing distance from the arc front and increasing slab surface temperatures. The latter may range from 720 to 866 degrees C, based on decreasing H2O/Ce ratios. Consistent with experimental data, the geochemical trends are interpreted to reflect changes in the amount and composition of wet pelite melts or super-critical fluids and aqueous fluids derived from the slab. With one exception, all of the lavas preserve both U-238 excesses and Ra-226 excesses. We suggest that lavas from the Fonualei Spreading Center and Valu Fa Ridge are dominated by fluid-fluxed melting whereas those from the East and Central Lau Spreading Centers, where slab surface temperatures exceed similar to 850-900 degrees C, are largely derived through decompression. A similar observation is found for the Manus and East Scotia back-arc basins and may reflect the expiry of a key phase such as lawsonite in the subducted basaltic crust.

Validation of a regional Indonesian seas model based on a comparison between model and INSTANT transports

The International Nusantara Stratification and Transport (INSTANT) program measured currents through multiple Indonesian Seas passages simultaneously over a three-year period (from January 2004 to December 2006). The Indonesian Seas region has presented numerous challenges for numerical modelers - the Indonesian Throughflow (ITF) must pass over shallow sills, into deep basins, and through narrow constrictions on its way from the Pacific to the Indian Ocean. As an important region in the global climate puzzle, a number of models have been used to try and best simulate this throughflow. In an attempt to validate our model, we present a comparison between the transports calculated from our model and those calculated from the INSTANT in situ measurements at five passages within the Indonesian Seas (Labani Channel, Lifamatola Passage, Lombok Strait, Ornbai Strait, and Timor Passage). Our Princeton Ocean Model (POM) based regional Indonesian Seas model was originally developed to analyze the influence of bottom topography on the temperature and salinity distributions in the Indonesian seas region, to disclose the path of the South Pacific Water from the continuation of the New Guinea Coastal Current entering the region of interest up to the Lifamatola Passage, and to assess the role of the pressure head in driving the ITF and in determining its total transport. Previous studies found that this model reasonably represents the general long-term flow (seasons) through this region. The INSTANT transports were compared to the results of this regional model over multiple timescales. Overall trends are somewhat represented but changes on timescales shorter than seasonal (three months) and longer than annual were not considered in our model. Normal velocities through each passage during every season are plotted. Daily volume transports and transport-weighted temperature and salinity are plotted and seasonal averages are tabulated.

Modelling the fate of persistent organic pollutants (POPs) in the North Sea system

The environmental fate of selected persistent organic pollutants (POPs) in the North Sea system is modelled with a high resolution Fate and Transport Ocean Model (FANTOM) that uses hydrodynamic model output from the Hamburg Shelf Ocean Model (HAMSOM). Large amounts of POPs enter the North Sea from the surrounding highly populated, industrialised and agricultural countries. Major pathways to the North Sea are atmospheric deposition and river inputs, with additional contributions coming from bottom sediments and adjacent seas. The model domain covers the entire North Sea region, extending northward as far as the Shetland Islands, and includes adjacent basins such as the Skagerrak, Kattegat, and the westernmost part of the Baltic Sea. Model resolution (for both models) is 1.5’ latitude x 2.5’ longitude (approximately 3 km horizontal resolution) with 30 vertical levels. The POP model also has 20 sediment layers. Important model processes controlling the fate of POPs in the North Sea system are discussed. Results focus on Lindane gamma- HCH or gamma-hexachlorocyclohexane) and PCB 153.

A review of topographic controls on moraine distribution

Ice-marginal moraines are often used to reconstruct the dimensions of former ice masses, which are then used as proxies for palaeoclimate. This approach relies on the assumption that the distribution of moraines in the modern landscape is an accurate reflection of former ice margin positions during climatically controlled periods of ice margin stability. However, the validity of this assumption is open to question, as a number of additional, nonclimatic factors are known to influence moraine distribution. This review considers the role played by topography in this process, with specific focus on moraine formation, preservation, and ease of identification (topoclimatic controls are not considered). Published literature indicates that the importance of topography in regulating moraine distribution varies spatially, temporally, and as a function of the ice mass type responsible for moraine deposition. In particular, in the case of ice sheets and ice caps ( > 1000 km2), one potentially important topographic control on where in a landscape moraines are deposited is erosional feedback, whereby subglacial erosion causes ice masses to become less extensive over successive glacial cycles. For the marine-terminating outlets of such ice masses, fjord geometry also exerts a strong control on where moraines are deposited, promoting their deposition in proximity to valley narrowings, bends, bifurcations, where basins are shallow, and/or in the vicinity of topographic bumps. Moraines formed at the margins of ice sheets and ice caps are likely to be large and readily identifiable in the modern landscape. In the case of icefields and valley glaciers (10–1000 km2), erosional feedback may well play some role in regulating where moraines are deposited, but other factors, including variations in accumulation area topography and the propensity for moraines to form at topographic pinning points, are also likely to be important. This is particularly relevant where land-terminating glaciers extend into piedmont zones (unconfined plains, adjacent to mountain ranges) where large and readily identifiable moraines can be deposited. In the case of cirque glaciers (< 10 km2), erosional feedback is less important, but factors such as topographic controls on the accumulation of redistributed snow and ice and the availability of surface debris, regulate glacier dimensions and thereby determine where moraines are deposited. In such cases, moraines are likely to be small and particularly susceptible to post-depositional modification, sometimes making them difficult to identify in the modern landscape. Based on this review, we suggest that, despite often being difficult to identify, quantify, and mitigate, topographic controls on moraine distribution should be explicitly considered when reconstructing the dimensions of palaeoglaciers and that moraines should be judiciously chosen before being used as indirect proxies for palaeoclimate (i.e., palaeoclimatic inferences should only be drawn from moraines when topographic controls on moraine distribution are considered insignificant).

Viability of Pseudomonas aeruginosa in cough aerosols generated by persons with cystic fibrosis

Background Person-to-person transmission of respiratory pathogens, including Pseudomonas aeruginosa, is a challenge facing many cystic fibrosis (CF) centres. Viable P aeruginosa are contained in aerosols produced during coughing, raising the possibility of airborne transmission.

Methods Using purpose-built equipment, we measured viable P aeruginosa in cough aerosols at 1, 2 and 4 m from the subject (distance) and after allowing aerosols to age for 5, 15 and 45 min in a slowly rotating drum to minimise gravitational settling and inertial impaction (duration). Aerosol particles were captured and sized employing an Anderson Impactor and cultured using conventional microbiology. Sputum was also cultured and lung function and respiratory muscle strength measured.

Results Nineteen patients with CF, mean age 25.8 (SD 9.2) years, chronically infected with P aeruginosa, and 10 healthy controls, 26.5 (8.7) years, participated. Viable P aeruginosa were detected in cough aerosols from all patients with CF, but not from controls; travelling 4 m in 17/18 (94%) and persisting for 45 min in 14/18 (78%) of the CF group. Marked inter-subject heterogeneity of P aeruginosa aerosol colony counts was seen and correlated strongly (r=0.73-0.90) with sputum bacterial loads. Modelling decay of viable P aeruginosa in a clinic room suggested that at the recommended ventilation rate of two air changes per hour almost 50 min were required for 90% to be removed after an infected patient left the room.

Conclusions: Viable P aeruginosa in cough aerosols travel further and last longer than recognised previously, providing additional evidence of airborne transmission between patients with CF.