Dynamically searching for a domain for protein function prediction

The availability of large amounts of protein-protein interaction (PPI) data makes it feasible to use computational approaches to predict protein functions. The base of existing computational approaches is to exploit the known function information of annotated proteins in the PPI data to predict functions of un-annotated proteins. However, these approaches consider the prediction domain (i.e. the set of proteins from which the functions are predicted) as unchangeable during the prediction procedure. This may lead to valuable information being overwhelmed by the unavoidable noise information in the PPI data when predicting protein functions, and in turn, the prediction results will be distorted. In this paper, we propose a novel method to dynamically predict protein functions from the PPI data. Our method regards the function prediction as a dynamic process of finding a suitable prediction domain, from which representative functions of the domain are selected to predict functions of un-annotated proteins. Our method exploits the topological structural information of a PPI network and the semantic relationship between protein functions to measure the relationship between proteins, dynamically select a suitable prediction domain and predict functions. The evaluation on real PPI datasets demonstrated the effectiveness of our proposed method, and generated better prediction results.

Influence of surface mechanical attrition treatment attrition media on the surface contamination and corrosion of magnesium

Surface mechanical attrition treatment (SMAT) is a mechanical peening process used to generate ultrafine grain surfaces on a metal. SMAT was carried out on pure magnesium using different attrition media (zirconia [ZiO2], alumina [Al2O3], and steel balls) to observe the effect on microstructure, surface residual stress, surface composition, and corrosion. Surface contamination from SMAT was characterized using glow discharge optical emission spectroscopy (GDOES). The SMAT process produced a refined grain structure on the surface of Mg but resulted in a region of elemental contamination extending ~10 μm into the substrate, regardless of the media used. Consequently, SMAT-treated surfaces showed an increased corrosion rate compared to untreated Mg, primarily through increased cathodic kinetics. This study highlights the issue of contamination resulting from the SMAT process, which is a penalty that accompanies the significant grain refinement of the surface produced by SMAT. This must be considered if attempting to exploit grain refinement for improving corrosion resistance.

Common ravens raid arctic fox food caches

Cache recovery is critical for evolution of hoarding behaviour, because the energy invested in caching may be lost if consumers other than the hoarders benefit from the cached food. By raiding food caches, animals may exploit the caching habits of others, that should respond by actively defending their caches. The arctic fox (Alopex lagopus) is the main predator of lemmings and goose eggs in the Canadian High Arctic and stores much of its prey in the ground. Common ravens (Corvus corax) are not as successful as foxes in taking eggs from goose nests. This generalist avian predator regularly uses innovation and opportunism to survive in many environments. Here, we provide the first report that ravens can successfully raid food cached by foxes, and that foxes may defend their caches from ravens.

Fur seal mammary gland evasion of involution and cell-matrix interactions

This thesis aimed to exploit the Cape fur seal as an alternative model to study mammary gland development and especially the switch from lactation to involution, as well as better understand cell-matrix interactions in vitro, essential to understanding tissue homeostasis and pathogenesis.

Miley Cyrus, Sinéad O’Connor and the future of feminism

Since her tongue-poking and “twerk”-filled performance at the American Video Music Awards, Miley Cyrus has been the subject of intense media discussion. This has only magnified in the past week, after Irish singer Sinéad O’Connor wrote an open letter to Cyrus, imploring her to “refuse to exploit your body or your sexuality in order for men to make money from you". Cyrus did not react well to being chided by one of her idols and her tweets in response have provoked two further open letters by O’Connor.

Environmental context explains Lévy and Brownian movement patterns of marine predators

An optimal search theory, the so-called Lévy-flight foraging hypothesis1, predicts that predators should adopt search strategies known as Lévy flights where prey is sparse and distributed unpredictably, but that Brownian movement is sufficiently efficient for locating abundant prey2, 3, 4. Empirical studies have generated controversy because the accuracy of statistical methods that have been used to identify Lévy behaviour has recently been questioned5, 6. Consequently, whether foragers exhibit Lévy flights in the wild remains unclear. Crucially, moreover, it has not been tested whether observed movement patterns across natural landscapes having different expected resource distributions conform to the theory’s central predictions. Here we use maximum-likelihood methods to test for Lévy patterns in relation to environmental gradients in the largest animal movement data set assembled for this purpose. Strong support was found for Lévy search patterns across 14 species of open-ocean predatory fish (sharks, tuna, billfish and ocean sunfish), with some individuals switching between Lévy and Brownian movement as they traversed different habitat types. We tested the spatial occurrence of these two principal patterns and found Lévy behaviour to be associated with less productive waters (sparser prey) and Brownian movements to be associated with productive shelf or convergence-front habitats (abundant prey). These results are consistent with the Lévy-flight foraging hypothesis1, 7, supporting the contention8, 9 that organism search strategies naturally evolved in such a way that they exploit optimal Lévy patterns.

Meta-analysis of movements in Atlantic leatherback turtles during the nesting season : conservation implications

Despite decades of conservation efforts on the nesting beaches, the critical status of leatherback turtles shows that their survival predominantly depends on our ability to reduce at-sea mortality. Although areas where leatherbacks meet fisheries have been identified during the long distance movements between 2 consecutive nesting seasons, hot-spots of lethal interactions are still poorly defined within the nesting season, when individuals concentrate close to land. Here we report movements of satellite-tracked gravid leatherback turtles during the nesting season in Western Central Africa, South America and the Caribbean Sea, which account for about 70% of the world population. We show that during and at the end of the nesting season, leatherback turtles have the propensity to remain over the continental shelf, yet sometimes perform extended movements and may even nest in neighbouring countries. Leatherbacks exploit coastal commercial fishing grounds and face substantial accidental capture by regional coastal fisheries (e.g. at least 10% in French Guiana). This emphasises the need for regional conservation strategies to be developed at the ocean scale—both at sea and on land—to ensure the survival of the last leatherback turtles.

Satellite tracking reveals unusual diving characteristics for a marine reptile, the olive ridley turtle : Lepidochelys olivacea

The movements, diving behaviour and thermal environment occupied by 4 adult female olive ridley turtles Lepidochelys olivacea in northern Australia were determined through satellite telemetry. Patterns of behaviour recorded were rather unusual compared to other sea turtles in that dives were mainly deep, largely benthic and exceptionally long (>2 h) in some cases, characteristics typical of over-wintering turtles in colder environments. One individual occupied shallow coastal foraging zones, while the others foraged far from land (probably on the seabed) in relatively deep water (>100 m). Individuals performed long dives (frequently >100 min), but from the short post-dive intervals we suggest that these dives were mainly aerobic. Maximum dive depth recorded was 200 ± 20 m (mean maximum depths ranged from 20.1 to 46.7 m across individuals; n = 17328 dives in total; depths ≥3 m were considered ‘dives’) and the maximum duration was 200 ± 20 min (mean durations ranged from 24.5 to 48.0 min across individuals). Temperature profiles indicate that turtles experienced temperatures ranging from 23 to 29°C at the surface, with the lowest temperature recorded (18.7°C) at a depth of 98 m. Only 6.9% of the dives were in water <20°C. From time-allocation at depth (TAD) scores, we demonstrated that many dives reaching the known or inferred sea bottom were U-shaped, but there was no apparent diel signal in dive depth. This suggests that many benthic dives were not associated exclusively with resting behaviour and likely had a foraging component as well. The ability to perform long benthic dives allows this species to exploit deeper benthic environments in addition to the shallow coastal areas more generally occupied by adult hard-shelled sea turtles (e.g. green and hawksbill turtles). Deep benthic dives also occur in certain marine mammals (e.g. narwhals) and sea birds (e.g. rockhopper penguins) and therefore seem to be a general foraging strategy exploited by animals that can perform long dives.

Blind extraction using fractional lower-order statistics

In traditional method to blindly extract interesting source signals sequentially, the second-order or higher-order statistics of signals are often utilized. However, for impulsive sources, both of the second-order and higher-order statistics may degenerate. Therefore, it is necessary to exploit new method for the blind extraction of impulsive sources. Based on the best compression-reconstruction principle, a novel model is proposed in this work, together with the corresponding algorithm. The proposed method can be used for blind extraction of sources which are distributed from alpha stable process. Simulations are given to illustrate availability and robustness of our algorithm.

Bioinspired strategy to reinforce PVA with improved toughness and thermal properties via hydrogen-bond self-assembly

Despite the high strength and stiffness of polymer nanocomposites, they usually display lower deformability and toughness relative to their matrices. Spider silk features exceptionally high stiffness and toughness via the hierarchical architecture based on hydrogen-bond (H-bond) assembly. Inspired by this intriguing phenomenon, we here exploit melamine (MA) to reinforce poly(vinyl alcohol) (PVA) via H-bond self-assembly at a molecular level. Our results have shown that due to the formation of physical cross-link network based on H-bond assembly between MA and PVA, yield strength, Young’s modulus, extensibility, and toughness of PVA are improved by 22, 25, 144, and 200% with 1.0 wt % MA, respectively. Moreover, presence of MA can enhance the thermal stability of PVA to a great extent, even exceeding some nanofillers (e.g., graphene). This work provides a facile method to improve the mechanical properties of polymers via H-bond self-assembly.

Exploiting high quality PEDOT:PSS–SWNT composite formulations for wet-spinning multifunctional fibers

In order to exploit the inherent properties of carbon nanotubes (CNT) in any polymer composite, systematic control of carbon nanotube loading and protocols that mitigate against CNT bundling are required. If such composites are to be rendered in fiber form via wet-spinning, then CNT bundling during the coagulation process must also be avoided. Here we have achieved this by utilizing highly exfoliated single walled carbon nanotubes (SWNT) and poly(3,4-ethylenedioxythiophene):poly(styrenesulfonicacid) (PEDOT:PSS) to obtain wet-spinnable composite formulations at various nanotube volume fractions (Vf). The addition of only 0.02 Vf of aggregate-free and individually dispersed SWNT resulted in a significant enhancement of modulus, tensile strength, electrical conductivity and two cell electrode specific capacitance of PEDOT:PSS–SWNT composite fibers to 5.2 GPa, 200 MPa, 450 S cm−1 and 59 F g−1 by the rate of dY/dVf = 89 GPa, dσ/dVf = 3.2 GPa, dS/dVf = 13 300 S cm−1 and 6 folds, respectively.

Investigating retention characteristics of a mixed-mode stationary phase and the enhancement of monolith selectivity for high-performance liquid chromatography

The synthesis and chromatographic behavior of an analytical size mixed-mode bonded silica monolith was investigated. The monolith was functionalized by an in situ modification process of a bare silica rod with chloro(3-cyanopropyl)dimethyl silane and chlorodimethyl propyl phenyl silane solutions. These ligands were selected in order to combine both resonance and nonresonance π-type bonding within a single separation environment. Selectivity studies were undertaken using n-alkyl benzenes and polycyclic aromatic hydrocarbons in aqueous methanol and acetonitrile mobile phases to assess the methylene and aromatic selectivities of the column. The results fit with the linear solvent strength theory suggesting excellent selectivity of the column was achieved. Comparison studies were performed on monolithic columns that were functionalized separately with cyano and phenyl ligands, suggesting highly conjugated molecules were able to successfully exploit both of the π-type selectivities afforded by the two different ligands on the mixed-mode column.

How well do predators adjust to climate-mediated shifts in prey distribution? A study on Australian water pythons

Climate change can move the spatial location of resources critical for population viability, and a species' resilience to such changes will depend upon its ability to flexibly shift its activities away from no-longer-suitable sites to exploit new opportunities. Intuition suggests that vagile predators should be able to track spatial shifts in prey availability, but our data on water pythons (Liasis fuscus) in tropical Australia suggest a less encouraging scenario. These pythons undergo regular long-range (to >10 km) seasonal migrations to follow flooding-induced migrations by their prey (native dusky rats, Rattus colletti). However, when an extreme flooding event virtually eliminated rats for a three-year period, the local pythons did not disperse despite the presence of abundant rats only 8 km away; instead, many pythons starved to death. This inflexibility suggests that some vagile species that track seasonally migrating prey may do so by responding to habitat attributes that have consistently predicted prey availability over evolutionary time, rather than reacting to proximate cues that signal the presence of prey per se. A species' vulnerability to climate change will be increased by an inability to shift its activities away from historical sites toward newly favorable areas.

Programmed function of the tammar mammary gland; the role of milk proteins in gut development

 This thesis aimed to exploit the unique reproductive strategy of marsupials such as the tammar wallaby to prove that milk may regulate postnatal growth and development of organs such as the stomach.

Designing a responsive material system with physical computing

This paper focuses on an investigation to explore architectural design potentials with a responsive material system and physical computing. Contemporary architects and designers are seeking to integrate physical computing in responsive architectural designs; however, they have largely borrowed from engineering technology's mechanical devices and components. There is the opportunity to investigate an unexplored design approach to exploit the responsive capacity of material properties as alternatives to the current focus on mechanical components and discrete sensing devices. This opportunity creates a different design paradigm for responsive architecture that investigates the potential to integrate physical computing with responsive materials as one integrated material system. Instead of adopting highly intricate and expensive materials, this approach is explored through accessible and off-the-shelf materials to form a responsive material system, called Lumina. Lumina is implemented as an architectural installation called Cloud that serves as a morphing architectural skin. Cloud is a proof of concept to embody a responsive material system with physical computing to create a reciprocal and luminous architectural intervention for a selected dark corridor. It represents a different design paradigm for responsive architecture through alternative exploitation of contemporary materials and parametric design tools. © 2014, The Association for Computer-Aided Architectural Design Research in Asia (CAADRIA), Hong Kong.