Non-Negative Local Sparse Coding for Subspace Clustering

Subspace sparse coding (SSC) algorithms have proven to be beneficial to clustering problems. They provide an alternative data representation in which the underlying structure of the clusters can be better captured. However, most of the research in this area is mainly focused on enhancing the sparse coding part of the problem. In contrast, we introduce a novel objective term in our proposed SSC framework which focuses on the separability of data points in the coding space. We also provide mathematical insights into how this local-separability term improves the clustering result of the SSC framework. Our proposed non-linear local SSC algorithm (NLSSC) also benefits from the efficient choice of its sparsity terms and constraints. The NLSSC algorithm is also formulated in the kernel-based framework (NLKSSC) which can represent the nonlinear structure of data. In addition, we address the possibility of having redundancies in sparse coding results and its negative effect on graph-based clustering problems. We introduce the link-restore post-processing step to improve the representation graph of non-negative SSC algorithms such as ours. Empirical evaluations on well-known clustering benchmarks show that our proposed NLSSC framework results in better clusterings compared to the state-of-the-art baselines and demonstrate the effectiveness of the link-restore post-processing in improving the clustering accuracy via correcting the broken links of the representation graph.Comment: 15 pages, IDA 2018 conferenc

Migration of Apicomplexa Across Biological Barriers: The Toxoplasma and Plasmodium Rides

The invasive stages of Apicomplexa parasites, called zoites, have been largely studied in in vitro systems, with a special emphasis on their unique gliding and host cell invasive capacities. In contrast, the means by which these parasites reach their destination in their hosts are still poorly understood. We summarize here our current understanding of the cellular basis of in vivo parasitism by two well-studied Apicomplexa zoites, the Toxoplasma tachyzoite and the Plasmodium sporozoite. Despite being close relatives, these two zoites use different strategies to reach their goal and establish infection

Relationship between FEV1 change and patient-reported outcomes in randomised trials of inhaled bronchodilators for stable COPD: a systematic review.

BACKGROUND: Interactions between spirometry and patient-reported outcomes in COPD are not well understood. This systematic review and study-level analysis investigated the relationship between changes in FEV1 and changes in health status with bronchodilator therapy. METHODS: Six databases (to October 2009) were searched to identify studies with long-acting bronchodilator therapy reporting FEV1 and health status, dyspnoea or exacerbations. Mean and standard deviations of treatment effects were extracted for each arm of each study. Relationships between changes in trough FEV1 and outcomes were assessed using correlations and random-effects regression modelling. The primary outcome was St George's Respiratory Questionnaire (SGRQ) total score. RESULTS: Thirty-six studies (≥ 3 months) were included. Twenty-two studies (23,654 patients) with 49 treatment arms each contributing one data point provided SGRQ data. Change in trough FEV1 and change in SGRQ total score were negatively correlated (r = -0.46, p < 0.001); greater increases in FEV1 were associated with greater reductions (improvements) in SGRQ. The correlation strengthened with increasing study duration from 3 to 12 months. Regression modelling indicated that 100 mL increase in FEV1 (change at which patients are more likely to report improvement) was associated with a statistically significant reduction in SGRQ of 2.5 (95% CI 1.9, 3.1), while a clinically relevant SGRQ change (4.0) was associated with 160.6 (95% CI 129.0, 211.6) mL increase in FEV1. The association between change in FEV1 and other patient-reported outcomes was generally weak. CONCLUSIONS: Our analyses indicate, at a study level, that improvement in mean trough FEV1 is associated with proportional improvements in health status

An Approach to Evaluation of the Effect of Bioremediation on Biological Activity of Environmental Contaminants: Dechlorination of Polychlorinated Biphenyls

The effectiveness of bioremediation efforts is assessed traditionally from the loss of the chemical of interest. In some cases, analytical techniques are coupled with evaluation of toxicity to organisms representative of those found in the affected environment or surrogate organisms. Little is known, however, about the effect of remediation of environmental chemicals on potential toxicity to mammalian organisms. We discuss both an approach that employs mammalian cell system bioassays and the criteria for selection of the assays. This approach has been used to evaluate the biological response to mixtures of polychlorinated biphenyls (PCBs) before and after remediation by reductive dechlorination. The dechlorination process used results in accumulation of congeners substituted in only the ortho and para positions and containing fewer chlorines than the starting mixtures. Evaluation of the dechlorinated mixture reveals a loss of biological activity that could be ascribed to coplanar PCBs not containing chlorine in the ortho positions. Conversely, biological activity associated with ortho-substituted PCB congeners is unaffected or increased by remediation. Thus, the results of the bioassays are consistent with the remediation-induced change in the profile of PCB congeners and the known mechanisms of action of PCBs. The results emphasize a need for evaluation of the products of remediation for biological activity in mammalian systems. Furthermore, the approach outlined demonstrates the potential to assess the impact of remediation on a range of biological activities in mammalian cells and thus to estimate positive and negative effects of remediation strategies on toxicity. Future needs in this area of research include assays to evaluate biological effects under conditions of exposure that mimic those found in the environment and models to extrapolate effects to assess risk to people and wildlife

Maternal therapy with Ad.VEGF-A165 increases fetal weight at term in a guinea pig model of fetal growth restriction

OBJECTIVES: We have demonstrated that transient uterine artery VEGF overexpression improves fetal growth in growth restricted sheep pregnancy. We tested this hypothesis in guinea pig pregnancies, where placental physiology more closely resembles that in humans. METHOD: Virgin guinea pigs were nutrient restricted peri-conceptually to create fetal growth restriction (FGR). At day 29-36 (term=65days) at laparotomy Ad.VEGF-A165 or Ad.LacZ (1x1010vp) were applied externally to the uterine circulation using a thermosensitive gel. Dams were sacrificed after 3-8 days or at term. Pups were weighed and tissues sampled for vector spread, VEGF expression and its downstream effects. RESULTS: Ad.VEGF-A165 significantly increased fetal weight at term (88.01±13.36g, n=26) compared to control Ad.LacZ treatment (85.52±13.00g, n=19, p=0.028). Brain, liver, lung weight and crown rump length were significantly larger 3-8 days post-administration, VEGF expression was demonstrated by ELISA and confirmed by immunohistochemistry in transduced tissues. RT-PCR of term samples confirmed vector transduction in target tissues, but the transgene was undetectable in fetal samples. Tissue histological analysis and blood biochemistry/haematological examination was normal. Uterine arteries from Ad.VEGF-A165-treated dams relaxed more completely than those from Ad.LacZ treated dams. CONCLUSIONS: Maternal uterine artery Ad.VEGF-A165 increases fetal growth velocity and term fetal weight in growth restricted guinea pig pregnancy

Altruism can proliferate through group/kin selection despite high random gene flow

The ways in which natural selection can allow the proliferation of cooperative behavior have long been seen as a central problem in evolutionary biology. Most of the literature has focused on interactions between pairs of individuals and on linear public goods games. This emphasis led to the conclusion that even modest levels of migration would pose a serious problem to the spread of altruism in group structured populations. Here we challenge this conclusion, by analyzing evolution in a framework which allows for complex group interactions and random migration among groups. We conclude that contingent forms of strong altruism can spread when rare under realistic group sizes and levels of migration. Our analysis combines group-centric and gene-centric perspectives, allows for arbitrary strength of selection, and leads to extensions of Hamilton's rule for the spread of altruistic alleles, applicable under broad conditions.Comment: 5 pages, 2 figures. Supplementary material with 50 pages and 26 figure

Measuring measurement

Measurement connects the world of quantum phenomena to the world of classical events. It plays both a passive role, observing quantum systems, and an active one, preparing quantum states and controlling them. Surprisingly - in the light of the central status of measurement in quantum mechanics - there is no general recipe for designing a detector that measures a given observable. Compounding this, the characterization of existing detectors is typically based on partial calibrations or elaborate models. Thus, experimental specification (i.e. tomography) of a detector is of fundamental and practical importance. Here, we present the realization of quantum detector tomography: we identify the optimal positive-operator-valued measure describing the detector, with no ancillary assumptions. This result completes the triad, state, process, and detector tomography, required to fully specify an experiment. We characterize an avalanche photodiode and a photon number resolving detector capable of detecting up to eight photons. This creates a new set of tools for accurately detecting and preparing non-classical light.Comment: 6 pages, 4 figures,see video abstract at http://www.quantiki.org/video_abstracts/0807244

Characteristics of the Early Immune Response Following Transplantation of Mouse ES Cell Derived Insulin-Producing Cell Clusters

Background The fully differentiated progeny of ES cells (ESC) may eventually be used for cell replacement therapy (CRT). However, elements of the innate immune system may contribute to damage or destruction of these tissues when transplanted. Methodology/Principal Findings Herein, we assessed the hitherto ill-defined contribution of the early innate immune response in CRT after transplantation of either ESC derived insulin producing cell clusters (IPCCs) or adult pancreatic islets. Ingress of neutrophil or macrophage cells was noted immediately at the site of IPCC transplantation, but this infiltration was attenuated by day three. Gene profiling identified specific inflammatory cytokines and chemokines that were either absent or sharply reduced by three days after IPCC transplantation. Thus, IPCC transplantation provoked less of an early immune response than pancreatic islet transplantation. Conclusions/Significance Our study offers insights into the characteristics of the immune response of an ESC derived tissue in the incipient stages following transplantation and suggests potential strategies to inhibit cell damage to ensure their long-term perpetuation and functionality in CRT

Multidimensional Homeier's generalized class and its application to planar 1D Bratu problem

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