NetEvo: A computational framework for the evolution of dynamical complex networks

NetEvo is a computational framework designed to help understand the evolution of dynamical complex networks. It provides flexible tools for the simulation of dynamical processes on networks and methods for the evolution of underlying topological structures. The concept of a supervisor is used to bring together both these aspects in a coherent way. It is the job of the supervisor to rewire the network topology and alter model parameters such that a user specified performance measure is minimised. This performance measure can make use of current topological information and simulated dynamical output from the system. Such an abstraction provides a suitable basis in which to study many outstanding questions related to complex system design and evolution

Size Dependence of Nanoscale Wear of Silicon Carbide

Nanoscale, single-asperity wear of single-crystal silicon carbide (sc-SiC) and nanocrystalline silicon carbide (nc-SiC) is investigated using single-crystal diamond nanoindenter tips and nanocrystalline diamond atomic force microscopy (AFM) tips under dry conditions, and the wear behavior is compared to that of single-crystal silicon with both thin and thick native oxide layers. We discovered a transition in the relative wear resistance of the SiC samples compared to that of Si as a function of contact size. With larger nanoindenter tips (tip radius around 370 nm), the wear resistances of both sc-SiC and nc-SiC are higher than that of Si. This result is expected from the Archard's equation because SiC is harder than Si. However, with the smaller AFM tips (tip radius around 20 nm), the wear resistances of sc-SiC and nc-SiC are lower than that of Si, despite the fact that the contact pressures are comparable to those applied with the nanoindenter tips, and the plastic zones are well-developed in both sets of wear experiments. We attribute the decrease in the relative wear resistance of SiC compared to that of Si to a transition from a wear regime dominated by the materials' resistance to plastic deformation (i.e., hardness) to a regime dominated by the materials' resistance to interfacial shear. This conclusion is supported by our AFM studies of wearless friction, which reveal that the interfacial shear strength of SiC is higher than that of Si. The contributions of surface roughness and surface chemistry to differences in interfacial shear strength are also discussed

Languaging the local in the global: Across the Pacific and beneath southern skies

Abstract not availabl

Towards an engineering theory of evolution

Effective biological engineering requires the acknowledgement of evolution and its consideration during the design process. In this perspective, the authors present the concept of the evotype to reason about and shape the evolutionary potential of natural and engineered biosystems

From colonies to TEQSA: Vortices and thermals of legislative change

This paper situates, through Constitutional law, the reach of Commonwealth powers into fields of State governance in Australia. Particular attention is given to the changing ambit of the corporations power with the 2011 enactment of the Tertiary Education Quality and Standards Agency Act (TEQSA). The Australian constitutional system was founded on the principle of federalism, a legal-political system whereby power is shared between Commonwealth and State governments. The passing of the TEQSA Act has established an Australia-wide, standards-based, regulatory framework for national consistency in higher education. This Act was passed under the authority of the constitutional corporations power. Due attention is given to High Court of Australia determinations showing how the corporations power has reached further and further into State governance, including that of education, thus affecting public policy. By this legal narrative, I propose that the law is acting as a sword, while casting the favours of a regulatory shield, and potentially impinging on academic rights as corporate citizens, as education is caught in the vortices and thermals of legislative change

Chemotaxonomic responses of autotrophic periphyton communities to nutrient additions in pools of an intermittent stream

1. The algal groups present in periphyton communities form an important base of autochthonous food webs in freshwater streams. Nitrogen (N) and phosphorus (P) are key macronutrients in aquatic systems. Excess nutrients benefit some algal groups over others. 2. We paired a nutrient-diffusing substrata limitation experiment with high performance liquid chromatography to (a) identify which nutrient(s) limit periphyton production, and (b) how the periphyton biomass and community structure changes between isolated pools of differing hydrological characteristics along an intermittent dryland stream. 3. Unique peaks for 21 pigments were identified and matched with published values. We then produced a PERMANOVA model using pigment ratios and CHEMTAX analysis to explore changes in community structure resulting from nutrient addition. 4. Periphyton communities in these pools were co-limited by N and P. Nitrogen additions caused the periphyton to shift from diatom- to chlorophyte-dominated community structure and benefited cyanophyta growth. Phosphorus additions reduced the relative proportion of diatoms and also resulted in an increase in pheophoribide-a, a pigment indicative of cell lysis, demonstrating a detrimental impact of P additions. 5. Outcomes of this study show that when adding nutrient to a system there may be subtle shifts in community composition which can be telescoped up the food web regardless of the system's nutrient status

Phosphorus sorption characteristics and interactions with leaf litter‑derived dissolved organic matter leachate in iron‑rich sediments of a sub‑tropical ephemeral stream

This study investigated the infuence of dissolved organic matter (DOM) additions on phosphate sorption kinetics of iron-rich sediments (39–50% hematite and goethite) from an ephemeral stream in the arid Pilbara region of sub-tropical northwest Australia. While phosphate sorption in stream sediments is known to be strongly infuenced by sediment mineralogy as well as interactions with DOM, the mechanisms and signifcance of DOM on P-release from sediments with high sorption capacities, are largely undescribed. We assessed phosphorus (P) sorption behaviours by adding a range of solutions of known inorganic P concentrations that were amended with variable loadings of DOM derived from leachates of leaf litter to sediments from stream pools during the non-fowing phase. We compared the sorption capacity of the sediments and concurrent changes in DOM composition measured using fuorescence spectroscopy. We show that the low-dose DOM addition (~ 4 mg L−1 DOC) had the efect of reducing sediment P adsorption capacity, while for the high-dose DOM addition (~ 45 mg L−1 DOC), it was increased. The high-dose DOM was similar to pore water DOC and likely saturated sediment surface adsorption sites and produced P–OM–Fe complexes. This resulted in increased removal of P from solution. Sediment P sorption characteristics were well ftted to both Freundlich and Langmuir isotherm models regardless of DOC concentration. Langmuir P sorption maxima ranged from 0.106 to 0.152 mg g−1. General P sorption characteristics of these iron-rich sediments did not difer among pools of contrasting hydrological connectivity. Our results show how humic-rich DOM can modulate the sediment P availability in dryland streams. Unravelling the complexities of P availability is of particular significance to further our understanding of biogeochemical processes in aquatic ecosystems where P often acts as a limiting nutrient

Circadian rhythmicity in emerging mood disorders: state or trait marker?

Background: Circadian rhythm disturbances overlap with the symptoms of mood episodes and may trigger or prolong mood symptoms. There is limited research on the role of circadian disturbances in mood disorders in young people and/or first episode cases of unipolar and bipolar disorders. Methods: Actigraphy was undertaken for about 14 days in 63 post-pubertal individuals aged 13–25 years with a recent onset of a mood disorder meeting recognised diagnostic criteria. We examined associations between three easily interpretable markers of circadian rhythm activity (amplitude, acrophase and rhythmicity index) and demography and clinical characteristics. Then, circadian markers were compared between diagnostic groups, controlling for potential confounders. Results: Longer duration of illness was correlated with reduced circadian rhythmicity and lower levels of activity over 24 h. A delay in the timing of maximum activity was associated with the level of manic but not depressive symptoms. The circadian rhythmicity index differentiated unipolar from bipolar cases, and in bipolar but not unipolar disorder, the rhythmicity was less robust in those with more severe manic or depressive symptoms. Conclusions: Less robust circadian rhythmicity, especially associated with increasing symptom severity, may represent a more specific or a trait marker of young people with mood disorders who are at higher risk of a bipolar course of illness

Altered patterns of senescence and ripening in gf, a stay-green mutant of tomato (Lycopersicon esculentum Mill.)

The gf tomato mutant, which retains chlorophyll during ripening, has been found to be affected in leaf senescence. The leaves of the gf mutant show an absolute stay-green phenotype. As leaf senescence and fruit ripening proceed, there is a marked difference in chlorophyll content between wild-type and gf. In both attached and detached leaf studies, or after treatment with ethylene, the leaves withered and abscised in gf with only slight loss of chlorophyll and carotenoids. Total protein content declined and free amino acids increased during leaf senescence in wild-type and gf, but Western analysis showed that LHCII polypeptides were retained at higher levels in gf. Expression of senescence-related mRNAs increased normally in gf whereas those for cab, rbcS and rbcL declined in both mutant and wild-type. The mutant possesses enzyme activity for chlorophyllase, the formation of phaeophorbide a by the action of Mg-dechelatase and the oxygenolytic opening of the porphyrin macrocycle. Analysis of chlorophyll breakdown products in fruit indicated that gf, like other stay-green mutants, accumulates chlorophyllides a and b, but phaeophorbide a does not accumulate in vivo. This may indicate that, in the mutant, in vivo the action of phaeophorbide a-oxygenase is somehow prevented, either by altered accessibility or transport of components required for thylakoid disassembly or the absence of another facto

Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS)

Background: Amyotrophic lateral sclerosis (ALS), a common late-onset neurodegenerative disease, is associated with fronto-temporal dementia (FTD) in 3-10% of patients. A mutation in CHMP2B was recently identified in a Danish pedigree with autosomal dominant FTD. Subsequently, two unrelated patients with familial ALS, one of whom also showed features of FTD, were shown to carry missense mutations in CHMP2B. The initial aim of this study was to determine whether mutations in CHMP2B contribute more broadly to ALS pathogenesis. Methodology/Principal Findings: Sequencing of CHMP2B in 433 ALS cases from the North of England identified 4 cases carrying 3 missense mutations, including one novel mutation, p. Thr104Asn, none of which were present in 500 neurologically normal controls. Analysis of clinical and neuropathological data of these 4 cases showed a phenotype consistent with the lower motor neuron predominant (progressive muscular atrophy (PMA)) variant of ALS. Only one had a recognised family history of ALS and none had clinically apparent dementia. Microarray analysis of motor neurons from CHMP2B cases, compared to controls, showed a distinct gene expression signature with significant differential expression predicting disassembly of cell structure; increased calcium concentration in the ER lumen; decrease in the availability of ATP; down-regulation of the classical and p38 MAPK signalling pathways, reduction in autophagy initiation and a global repression of translation. Transfection of mutant CHMP2B into HEK-293 and COS-7 cells resulted in the formation of large cytoplasmic vacuoles, aberrant lysosomal localisation demonstrated by CD63 staining and impairment of autophagy indicated by increased levels of LC3-II protein. These changes were absent in control cells transfected with wild-type CHMP2B. Conclusions/Significance: We conclude that in a population drawn from North of England pathogenic CHMP2B mutations are found in approximately 1% of cases of ALS and 10% of those with lower motor neuron predominant ALS. We provide a body of evidence indicating the likely pathogenicity of the reported gene alterations. However, absolute confirmation of pathogenicity requires further evidence, including documentation of familial transmission in ALS pedigrees which might be most fruitfully explored in cases with a LMN predominant phenotype