Dynamic load balancing in parallel KD-tree k-means

One among the most influential and popular data mining methods is the k-Means algorithm for cluster analysis. Techniques for improving the efficiency of k-Means have been largely explored in two main directions. The amount of computation can be significantly reduced by adopting geometrical constraints and an efficient data structure, notably a multidimensional binary search tree (KD-Tree). These techniques allow to reduce the number of distance computations the algorithm performs at each iteration. A second direction is parallel processing, where data and computation loads are distributed over many processing nodes. However, little work has been done to provide a parallel formulation of the efficient sequential techniques based on KD-Trees. Such approaches are expected to have an irregular distribution of computation load and can suffer from load imbalance. This issue has so far limited the adoption of these efficient k-Means variants in parallel computing environments. In this work, we provide a parallel formulation of the KD-Tree based k-Means algorithm for distributed memory systems and address its load balancing issue. Three solutions have been developed and tested. Two approaches are based on a static partitioning of the data set and a third solution incorporates a dynamic load balancing policy.

Reductions in insecticide use from adoption of Bt cotton in South Africa: impacts on economic performance and toxic load to the environment

The study reported presents the findings relating to commercial growing of genetically-modified Bt cotton in South Africa by a large sample of smallholder farmers over three seasons (1998/99, 1999/2000, 2000/01) following adoption. The analysis presents constructs and compares groupwise differences for key variables in Bt v. non-Bt technology and uses regressions to further analyse the production and profit impacts of Bt adoption. Analysis of the distribution of benefits between farmers due to the technology is also presented. In parallel with these socio-economic measures, the toxic loads being presented to the environment following the introduction of Bt cotton are monitored in terms of insecticide active ingredient (ai) and the Biocide Index. The latter adjusts ai to allow for differing persistence and toxicity of insecticides. Results show substantial and significant financial benefits to smallholder cotton growers of adopting Bt cotton over three seasons in terms of increased yields, lower insecticide spray costs and higher gross margins. This includes one particularly wet, poor growing season. In addition, those with the smaller holdings appeared to benefit proportionately more from the technology (in terms of higher gross margins) than those with larger holdings. Analysis using the Gini-coefficient suggests that the Bt technology has helped to reduce inequality amongst smallholder cotton growers in Makhathini compared to what may have been the position if they had grown conventional cotton. However, while Bt growers applied lower amounts of insecticide and had lower Biocide Indices (per ha) than growers of non-Bt cotton, some of this advantage was due to a reduction in non-bollworm insecticide. Indeed, the Biocide Index for all farmers in the population actually increased with the introduction of Bt cotton. The results indicate the complexity of such studies on the socio-economic and environmental impacts of GM varieties in the developing world.

Mutational meltdown in primary endosymbionts: selection limits Muller's ratchet

Background Primary bacterial endosymbionts of insects (p-endosymbionts) are thought to be undergoing the process of Muller's ratchet where they accrue slightly deleterious mutations due to genetic drift in small populations with negligible recombination rates. If this process were to go unchecked over time, theory predicts mutational meltdown and eventual extinction. Although genome degradation is common among p-endosymbionts, we do not observe widespread p-endosymbiont extinction, suggesting that Muller's ratchet may be slowed or even stopped over time. For example, selection may act to slow the effects of Muller's ratchet by removing slightly deleterious mutations before they go to fixation thereby causing a decrease in nucleotide substitutions rates in older p-endosymbiont lineages. Methodology/Principal Findings To determine whether selection is slowing the effects of Muller's ratchet, we determined the age of the Candidatus Riesia/sucking louse assemblage and analyzed the nucleotide substitution rates of several p-endosymbiont lineages that differ in the length of time that they have been associated with their insect hosts. We find that Riesia is the youngest p-endosymbiont known to date, and has been associated with its louse hosts for only 13–25 My. Further, it is the fastest evolving p-endosymbiont with substitution rates of 19–34% per 50 My. When comparing Riesia to other insect p-endosymbionts, we find that nucleotide substitution rates decrease dramatically as the age of endosymbiosis increases. Conclusions/Significance A decrease in nucleotide substitution rates over time suggests that selection may be limiting the effects of Muller's ratchet by removing individuals with the highest mutational loads and decreasing the rate at which new mutations become fixed. This countering effect of selection could slow the overall rate of endosymbiont extinction.

Effect of viral load on the outcome of herpes zoster

Varicella-zoster virus (VZV) is a member of the Herpesviridae family, primary infection with which causes varicella, more commonly known as chicken pox. Characteristic of members of the alphaherpesvirus subfamily, VZV is neurotropic and establishes latency in sensory neurons. Reactivation of VZV causes herpes zoster, also known as shingles. The most frequent complication following zoster is chronic and often debilitating pain called postherpetic neuralgia (PHN), which can last for months after the disappearance of a rash. During episodes of acute zoster, VZV viremia occurs in some, but not all, patients; however, the effect of the viral load on the disease outcome is not known. Here we describe the development of a highly specific, sensitive, and reproducible real-time PCR assay to investigate the factors that may contribute to the presence and levels of baseline viremia in patients with zoster and to determine the relationship between viremia and the development and persistence of PHN. VZV DNA was detected in the peripheral blood mononuclear cells (PBMCs) of 78% of patients with acute zoster and in 9% of healthy asymptomatic blood donors. The presence of VZV in the PBMCs of patients with acute zoster was independently associated with age and being on antivirals but not with gender, immune status, extent of rash, the age of the rash at the time of blood sampling, having a history of prodromal pain, or the extent of acute pain. Prodromal pain was significantly associated with higher baseline viral loads. Viral load levels were not associated with the development or persistence of PHN at 6, 12, or 26 weeks.

A naked ape would have fewer parasites

Unusually among the mammals, humans lack an outer layer of protective fur or hair. We propose the hypothesis that humans evolved hairlessness to reduce parasite loads, especially ectoparasites that may carry disease. We suggest that hairlessness is maintained by these naturally selected benefits and by sexual selection operating on both sexes. Hairlessness is made possible in humans owing to their unique abilities to regulate their environment via fire, shelter and clothing. Clothes and shelters allow a more flexible response to the external environment than a permanent layer of fur and can be changed or cleaned if infested with parasites. Naked mole-rats, another hairless and non-aquatic mammal species, also inhabit environments in which ectoparasite transmission is expected to be high, but in which temperatures are closely regulated. Our hypothesis explains features of human hairlessness-such as the marked sex difference in body hair, and its retention in the pubic regions-that are not explained by other theories.

Finite element aided design evolution of composite leaf spring

This paper shows the process of the virtual production development of the mechanical connection between the top leaf of a dual composite leaf spring system to a shackle using finite element methods. The commercial FEA package MSC/MARC has been used for the analysis. In the original design the joint was based on a closed eye-end. Full scale testing results showed that this configuration achieved the vertical proof load of 150 kN and 1 million cycles of fatigue load. However, a problem with delamination occurred at the interface between the fibres going around the eye and the main leaf body. To overcome this problem, a second design was tried using transverse bandages of woven glass fibre reinforced tape to wrap the section that is prone to delaminate. In this case, the maximum interlaminar shear stress was reduced by a certain amount but it was still higher than the material’s shear strength. Based on the fact that, even with delamination, the top leaf spring still sustained the maximum static and fatigue loads required, the third design was proposed with an open eye-end, eliminating altogether the interface where the maximum shear stress occurs. The maximum shear stress predicted by FEA is reduced significantly and a safety factor of around 2 has been obtained. Thus, a successful and safe design has been achieved.

Quantification of mitochondrial DNA mutation load

Mitochondrial DNA (mtDNA) mutations are an important cause of genetic disease and have been proposed to play a role in the ageing process. Quantification of total mtDNA mutation load in ageing tissues is difficult as mutational events are rare in a background of wild-type molecules, and detection of individual mutated molecules is beyond the sensitivity of most sequencing based techniques. The methods currently most commonly used to document the incidence of mtDNA point mutations in ageing include post-PCR cloning, single-molecule PCR and the random mutation capture assay. The mtDNA mutation load obtained by these different techniques varies by orders of magnitude, but direct comparison of the three techniques on the same ageing human tissue has not been performed. We assess the procedures and practicalities involved in each of these three assays and discuss the results obtained by investigation of mutation loads in colonic mucosal biopsies from ten human subjects.

Linking carbon and sulphur cycling during simulated drought cycles in peat from six sites across the UK

Water table draw-down is thought to increase peat decomposition and, therefore, DOC release. However, several studies have shown lower DOC concentrations during droughts relative to ‘normal’ periods with high water table. We carried out controlled incubation experiments at 10°C on 10x10 cm peat soil cores collected from six UK sites across a sulphur deposition gradient. Our aim was to quantify the balance between microbial consumption and chemical precipitation of DOC due to episodic acidification driven by sulphur redox reactions by comparing changes in soil water chemistry to microbial activity (i.e. soil respiration and trace gas fluxes). During dry periods, all sites showed a concurrent increase in SO4 and soil respiration and a decline in DOC. However, the magnitude of change in both DOC and SO4 varied considerably between sites according to historical sulphur deposition loads and the variation in acid/base chemistry.

Speech perception and phonological short-term memory capacity in language impairment: preliminary evidence from adolescents with specific language impairment (SLI) and autism spectrum disorders (ASD)

Background: The cognitive bases of language impairment in specific language impairment (SLI) and autism spectrum disorders (ASD) were investigated in a novel non-word comparison task which manipulated phonological short-term memory (PSTM) and speech perception, both implicated in poor non-word repetition. Aims: This study aimed to investigate the contributions of PSTM and speech perception in non-word processing and whether individuals with SLI and ASD plus language impairment (ALI) show similar or different patterns of deficit in these cognitive processes. Method & Procedures: Three groups of adolescents (aged 14–17 years), 14 with SLI, 16 with ALI, and 17 age and non-verbal IQ matched typically developing (TD) controls, made speeded discriminations between non-word pairs. Stimuli varied in PSTM load (two- or four-syllables) and speech perception load (mismatches on a word-initial or word-medial segment). Outcomes & Results: Reaction times showed effects of both non-word length and mismatch position and these factors interacted: four-syllable and word-initial mismatch stimuli resulted in the slowest decisions. Individuals with language impairment showed the same pattern of performance as those with typical development in the reaction time data. A marginal interaction between group and item length was driven by the SLI and ALI groups being less accurate with long items than short ones, a difference not found in the TD group. Conclusions & Implications: Non-word discrimination suggests that there are similarities and differences between adolescents with SLI and ALI and their TD peers. Reaction times appear to be affected by increasing PSTM and speech perception loads in a similar way. However, there was some, albeit weaker, evidence that adolescents with SLI and ALI are less accurate than TD individuals, with both showing an effect of PSTM load. This may indicate, at some level, the processing substrate supporting both PSTM and speech perception is intact in adolescents with SLI and ALI, but also in both there may be impaired access to PSTM resources.

Selective biodegradation of keratin matrix in feather rachis reveals classic bioengineering

Flight necessitates that the feather rachis is extremely tough and light. Yet, the crucial filamentous hierarchy of the rachis is unknown—study hindered by the tight chemical bonding between the filaments and matrix. We used novel microbial biodegradation to delineate the fibres of the rachidial cortex in situ. It revealed the thickest keratin filaments known to date (factor >10), approximately 6 µm thick, extending predominantly axially but with a small outer circumferential component. Near-periodic thickened nodes of the fibres are staggered with those in adjacent fibres in two- and three-dimensional planes, creating a fibre–matrix texture with high attributes for crack stopping and resistance to transverse cutting. Close association of the fibre layer with the underlying ‘spongy’ medulloid pith indicates the potential for higher buckling loads and greater elastic recoil. Strikingly, the fibres are similar in dimensions and form to the free filaments of the feather vane and plumulaceous and embryonic down, the syncitial barbules, but, identified for the first time in 140+ years of study in a new location—as a major structural component of the rachis. Early in feather evolution, syncitial barbules were consolidated in a robust central rachis, definitively characterizing the avian lineage of keratin.

The spatial distribution of carbon dioxide in an environmental test chamber

The spatial distribution of CO2 level in a classroom carried out in previous field work research has demonstrated that there is some evidence of variations in CO2 concentration in a classroom space. Significant fluctuations in CO2 concentration were found at different sampling points depending on the ventilation strategies and environmental conditions prevailing in individual classrooms. However, how these variations are affected by the emitting sources and the room air movement remains unknown. Hence, it was concluded that detailed investigation of the CO2 distribution need to be performed on a smaller scale. As a result, it was decided to use an environmental chamber with various methods and rates of ventilation, for the same internal temperature and heat loads, to study the effect of ventilation strategy and air movement on the distribution of CO2 concentration in a room. The role of human exhalation and its interaction with the plume induced by the body's convective flow and room air movement due to different ventilation strategies were studied in a chamber at the University of Reading. These phenomena are considered to be important in understanding and predicting the flow patterns in a space and how these impact on the distribution of contaminants. This paper attempts to study the CO2 dispersion and distribution at the exhalation zone of two people sitting in a chamber as well as throughout the occupied zone of the chamber. The horizontal and vertical distributions of CO2 were sampled at locations with a probability that CO2 variation is considered high. Although the room size, source location, ventilation rate and location of air supply and extract devices all can have influence on the CO2 distribution, this article gives general guidelines on the optimum positioning of CO2 sensor in a room.

Persistence of varicella-zoster virus viraemia in patients with herpes zoster.

BACKGROUND: Herpes zoster is caused by the reactivation of varicella-zoster virus from sensory neurons. The commonest complication following zoster is chronic pain termed post herpetic neuralgia. OBJECTIVES: To investigate the dynamics of VZV viraemia and viral load following the resolution of zoster and its relationship to PHN development. STUDY DESIGN: Blood samples were collected at baseline, 1 month, 3 months and 6 month from a prospective study of 63 patients with active zoster. Quantification of VZV DNA in whole blood was performed using a real-time PCR assay. RESULTS: During acute zoster, all patients had detectable VZV DNA in their blood. VZV DNA remained detectable in the blood of 91% of patients at 6 months although levels declined significantly (p<0.0001). A history of prodromal symptoms (p=0.005) and severity of pain at baseline (p=0.038) as well as taking antivirals (p=0.046) and being immunocompromised (p=0.043) were associated, with longer time to recovery from PHN. Viral DNA loads were consistently higher in patients with risk factors for PHN and higher viral DNA loads over time were associated with longer time to recovery (p=0.058 overall and 0.038 in immunocompetent). CONCLUSIONS: Based on these observations we hypothesise that VZV replication persists following acute shingles and that higher viral DNA loads contribute to the risk factors for PHN.

The elasticity of demand is about occupancy, not prices: building European demand curves based on occupancy elasticity

The peak congestion of the European grid may create significant impacts on system costs because of the need for higher marginal cost generation, higher cost system balancing and increasing grid reinforcement investment. The use of time of use rates, incentives, real time pricing and other programmes, usually defined as Demand Side Management (DSM), could bring about significant reductions in prices, limit carbon emissions from dirty power plants, and improve the integration of renewable sources of energy. Unlike previous studies on elasticity of residential electricity demand under flat tariffs, the aim of this study is not to investigate the known relatively inelastic relationship between demand and prices. Rather, the aim is to assess how occupancy levels vary in different European countries. This reflects the reality of demand loads, which are predominantly determined by the timing of human activities (e.g. travelling to work, taking children to school) rather than prices. To this end, two types of occupancy elasticity are estimated: baseline occupancy elasticity and peak occupancy elasticity. These represent the intrinsic elasticity associated with human activities of single residential end-users in 15 European countries. This study makes use of occupancy time-series data from the Harmonised European Time Use Survey database to build European occupancy curves; identify peak occupancy periods; draw time use demand curves for video and TV watching activity; and estimate national occupancy elasticity levels of single-occupant households. Findings on occupancy elasticities provide an indication of possible DSM strategies based on occupancy levels and not prices.