Faster K-Means Cluster Estimation

There has been considerable work on improving popular clustering algorithm `K-means' in terms of mean squared error (MSE) and speed, both. However, most of the k-means variants tend to compute distance of each data point to each cluster centroid for every iteration. We propose a fast heuristic to overcome this bottleneck with only marginal increase in MSE. We observe that across all iterations of K-means, a data point changes its membership only among a small subset of clusters. Our heuristic predicts such clusters for each data point by looking at nearby clusters after the first iteration of k-means. We augment well known variants of k-means with our heuristic to demonstrate effectiveness of our heuristic. For various synthetic and real-world datasets, our heuristic achieves speed-up of up-to 3 times when compared to efficient variants of k-means.Comment: 6 pages, Accepted at ECIR 201

Quasi-phase-matched high-order harmonic generation using tunable pulse trains

A simple technique for generating trains of ultrafast pulses is demonstrated in which the linear separation between pulses can be varied continuously over a wide range. These pulse trains are used to achieve tunable quasi-phase-matching of high harmonic generation over a range of harmonic orders up to the harmonic cut-off, resulting in enhancements of the harmonic intensity in excess of an order of magnitude. The peak enhancement depends on the separation between pulses, as well as the number of pulses in the train, representing an easily tunable source of quasi-phase-matched high harmonic generation

Infant cortex responds to other humans from shortly after birth

A significant feature of the adult human brain is its ability to selectively process information about conspecifics. Much debate has centred on whether this specialization is primarily a result of phylogenetic adaptation, or whether the brain acquires expertise in processing social stimuli as a result of its being born into an intensely social environment. Here we study the haemodynamic response in cortical areas of newborns (1–5 days old) while they passively viewed dynamic human or mechanical action videos. We observed activation selective to a dynamic face stimulus over bilateral posterior temporal cortex, but no activation in response to a moving human arm. This selective activation to the social stimulus correlated with age in hours over the first few days post partum. Thus, even very limited experience of face-to-face interaction with other humans may be sufficient to elicit social stimulus activation of relevant cortical regions

Optimised XUV holography using spatially shaped high harmonic beams

A phase-only spatial light modulator is used to generate multiple infrared foci, the positions and intensities of which can be controlled programmably, allowing the generation and control of multiple high harmonic beams. Using two such high harmonic beams Fourier transform holography is performed with separate illumination of the object and reference pinhole, making optimal use of the available photon flux. This technique provides new opportunities for imaging at extreme ultraviolet wavelengths

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

A Copine family member, Cpne8, is a candidate quantitative trait gene for prion disease incubation time in mouse

Prion disease incubation time in mice is determined by many factors including genetic background. The prion gene itself plays a major role in incubation time; however, other genes are also known to be important. Whilst quantitative trait loci (QTL) studies have identified multiple loci across the genome, these regions are often large, and with the exception of Hectd2 on Mmu19, no quantitative trait genes or nucleotides for prion disease incubation time have been demonstrated. In this study, we use the Northport heterogeneous stock of mice to reduce the size of a previously identified QTL on Mmu15 from approximately 25 to 1.2 cM. We further characterised the genes in this region and identify Cpne8, a member of the copine family, as the most promising candidate gene. We also show that Cpne8 mRNA is upregulated at the terminal stage of disease, supporting a role in prion disease. Applying these techniques to other loci will facilitate the identification of key pathways in prion disease pathogenesis

Shadoo (Sprn) and prion disease incubation time in mice

Prion diseases are transmissible neurodegenerative disorders of mammalian species and include scrapie, bovine spongiform encephalopathy (BSE), and variant Creutzfeldt-Jakob disease (vCJD). The prion protein (PrP) plays a key role in the disease, with coding polymorphism in both human and mouse influencing disease susceptibility and incubation time, respectively. Other genes are also thought to be important and a plausible candidate is Sprn, which encodes the PrP-like protein Shadoo (Sho). Sho is expressed in the adult central nervous system and exhibits neuroprotective activity reminiscent of PrP in an in vitro assay. To investigate the role of Sprn in prion disease incubation time we sequenced the open reading frame (ORF) in a diverse panel of mice and saw little variation except in strains derived from wild-trapped mice. Sequencing the untranslated regions revealed polymorphisms that allowed us to carry out an association study of incubation period in the Northport heterogeneous stock of mice inoculated with Chandler/RML prions. We also examined the expression level of Sprn mRNA in the brains of normal and prion-infected mice and saw no correlation with either genotype or incubation time. We therefore conclude that Sprn does not play a major role in prion disease incubation time in these strains of mice

The incidence of scarring on the dorsum of the hand

When undertaking image comparison of the hand between accused and perpetrator, it is not unusual for scars to be identified on the back of the hand. To investigate the occurrence of scarring in a discreet sample, a database of 238 individuals was examined, and the dorsum of the right and left hands was gridded for each individual. The position, size and type of scar were recorded within each grid. It was found that, in general, males exhibited a higher incidence of scarring than females. However, males were more likely to show scarring on their left hand whereas females were more likely to exhibit scarring on their right hand. Contrary to the literature, scarring was not most prevalent along the borders of the hand but occurred more frequently in association with the index and middle finger corridor regions. Surgical scars were rare as were large scars whereas linear scars smaller than 6 mm were the most frequently identified. Close to half of the sample did not exhibit scarring on one hand. The importance of understanding the pattern of scarring on the back of the hand is discussed in the light of forensic image comparison analysis

Spatially resolved common-path high-order harmonic interferometry

In this letter we report on interference between high harmonic emission from two longitudinally separated sources driven by the same laser pulse. Compared with previous implementations of in-line interferometry we demonstrate that by analysing the spatially-resolved harmonic signal as a function of longitudinal separation quantum trajectory-dependent interference can be identified. The inline geometry demonstrated here offers a high degree of stability, since both harmonic sources are generated from the same driving pulse, as opposed to pulse replicas, which has typically been the case in other interferometric schemes. The inherent synchronization and high timing stability afforded by this approach offers a new route for the measurement and timing of ultrafast processes

Dynamics of multi-stage infections on networks

This paper investigates the dynamics of infectious diseases with a nonexponentially distributed infectious period. This is achieved by considering a multistage infection model on networks. Using pairwise approximation with a standard closure, a number of important characteristics of disease dynamics are derived analytically, including the final size of an epidemic and a threshold for epidemic outbreaks, and it is shown how these quantities depend on disease characteristics, as well as the number of disease stages. Stochastic simulations of dynamics on networks are performed and compared to output of pairwise models for several realistic examples of infectious diseases to illustrate the role played by the number of stages in the disease dynamics. These results show that a higher number of disease stages results in faster epidemic outbreaks with a higher peak prevalence and a larger final size of the epidemic. The agreement between the pairwise and simulation models is excellent in the cases we consider