The Geometry of Nonlinear Embeddings in Kernel Discriminant Analysis

Fisher's linear discriminant analysis is a classical method for classification, yet it is limited to capturing linear features only. Kernel discriminant analysis as an extension is known to successfully alleviate the limitation through a nonlinear feature mapping. We study the geometry of nonlinear embeddings in discriminant analysis with polynomial kernels and Gaussian kernel by identifying the population-level discriminant function that depends on the data distribution and the kernel. In order to obtain the discriminant function, we solve a generalized eigenvalue problem with between-class and within-class covariance operators. The polynomial discriminants are shown to capture the class difference through the population moments explicitly. For approximation of the Gaussian discriminant, we use a particular representation of the Gaussian kernel by utilizing the exponential generating function for Hermite polynomials. We also show that the Gaussian discriminant can be approximated using randomized projections of the data. Our results illuminate how the data distribution and the kernel interact in determination of the nonlinear embedding for discrimination, and provide a guideline for choice of the kernel and its parameters

Interactions between topsoil properties and ecophysiological responses of mangroves (Avicennia marina) along the tidal gradient in an arid region in Qatar

This study investigated the interactions between topsoil properties and ecophysiological responses of Avicennia marina along the tidal gradient in an arid region in Qatar. In February 2017, three plots were established, each at a distance of 0 m (D0), 50 m (D50), and 100 m (D100) from the inland boundary of a mangrove forest. Soil samples were collected at 0–10-cm depth in each plot to determine the chemical properties, and the density of seedlings, saplings, and trees was measured. Moreover, above- (AGB) and below-ground biomass (BGB) were calculated using an allometric equation for A. marina with the measured diameter at breast height in February 2017. As an indicator of salt stress, chlorophyll fluorescence parameters were measured in October 2017. Salinity (45.60 ppt) and exchangeable sodium percentage (ESP; 29.02%) at D100 were significantly highest. AGB was higher at D100 (41.44 Mg ha–1) than at D0 (0 Mg ha–1) and D50 (7.33 Mg ha–1), and BGB was higher at D100 (44.91 Mg ha–1) than only at D0 (0 Mg ha–1). There was no significant difference in the density of seedlings, saplings, or trees or the chlorophyll fluorescence parameters among the plots. Salt stress was not induced despite the hypersalinity at this site, since A. marina growing in an arid climate can endure strong salinity. Soil pH was highest at D0, followed by at D50 and D100. Organic matter, total nitrogen, available phosphorus, and cation exchange capacity were significantly higher at D100 than at D0 and D50. Higher concentrations of nutrients on the seaward side might result from the tidal gradient and a large input of organic matter and low soil alkalinity.Qatar University Grant (QUUG-CAS-DBES-15/16-5); the Biodiversity Conservation Fund of Kazakhstan (Q1727701); the Korean Ministry of Environment (2014001310008

Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library

<p>Abstract</p> <p>Background</p> <p>The primary regulator of spermatogenesis, a highly ordered and tightly regulated developmental process, is an intrinsic genetic program involving male germ cell-specific genes.</p> <p>Results</p> <p>We analyzed the mouse spermatocyte UniGene library containing 2155 gene-oriented transcript clusters. We predict that 11% of these genes are testis-specific and systematically identified 24 authentic genes specifically and abundantly expressed in the testis via in <it>silico </it>and <it>in vitro </it>approaches. Northern blot analysis disclosed various transcript characteristics, such as expression level, size and the presence of isoform. Expression analysis revealed developmentally regulated and stage-specific expression patterns in all of the genes. We further analyzed the genes at the protein and cellular levels. Transfection assays performed using GC-2 cells provided information on the cellular characteristics of the gene products. In addition, antibodies were generated against proteins encoded by some of the genes to facilitate their identification and characterization in spermatogenic cells and sperm. Our data suggest that a number of the gene products are implicated in transcriptional regulation, nuclear integrity, sperm structure and motility, and fertilization. In particular, we found for the first time that Mm.333010, predicted to contain a trypsin-like serine protease domain, is a sperm acrosomal protein.</p> <p>Conclusion</p> <p>We identify 24 authentic genes with spermatogenic cell-specific expression, and provide comprehensive information about the genes. Our findings establish a new basis for future investigation into molecular mechanisms underlying male reproduction.</p

Systematic identification and integrative analysis of novel genes expressed specifically or predominantly in mouse epididymis

BACKGROUND: Maturation of spermatozoa, including development of motility and the ability to fertilize the oocyte, occurs during transit through the microenvironment of the epididymis. Comprehensive understanding of sperm maturation requires identification and characterization of unique genes expressed in the epididymis. RESULTS: We systematically identified 32 novel genes with epididymis-specific or -predominant expression in the mouse epididymis UniGene library, containing 1505 gene-oriented transcript clusters, by in silico and in vitro analyses. The Northern blot analysis revealed various characteristics of the genes at the transcript level, such as expression level, size and the presence of isoform. We found that expression of the half of the genes is regulated by androgens. Further expression analyses demonstrated that the novel genes are region-specific and developmentally regulated. Computational analysis showed that 15 of the genes lack human orthologues, suggesting their implication in male reproduction unique to the mouse. A number of the novel genes are putative epididymal protease inhibitors or β-defensins. We also found that six of the genes have secretory activity, indicating that they may interact with sperm and have functional roles in sperm maturation. CONCLUSION: We identified and characterized 32 novel epididymis-specific or -predominant genes by an integrative approach. Our study is unique in the aspect of systematic identification of novel epididymal genes and should be a firm basis for future investigation into molecular mechanisms underlying sperm maturation in the epididymis

Cost-benefit analysis of water source improvements through borehole drilling or rehabilitation: an empirical study based on a cluster randomized controlled trial in the Volta Region, Ghana.

BACKGROUND: Despite remarkable progress in water coverage improvements, diseases associated with poor water remain a considerable public health problem in many developing countries. OBJECTIVE: We aimed to estimate the costs and benefits of drilling or rehabilitating boreholes with handpumps in resource-poor settings and hard-to-reach areas. METHODS: Diarrheal reduction in the population was predicted on the basis of the empirical findings from a cluster randomized controlled trial. The full investment and estimated annual running costs were used to calculate the intervention costs. Direct economic benefits of avoiding child diarrheal disease, indirect economic benefits related to health improvements, and non-health benefits related to water improvement were estimated. One-way and multi-way sensitivity analyses were performed to determine the robustness of the findings. RESULTS: Our analysis found that the return on a US$1 investment was US$ 9.4 for borehole drilling and US$ 14.1 for borehole rehabilitation. Time savings were the main contributor, accounting for 68% of the benefits, followed by the economic benefits of averted child deaths, which contributed to 15% of the benefits. The sensitivity analyses suggested that improving water sources yields high returns under all circumstances, and that borehole rehabilitation is more efficient than borehole drilling. CONCLUSION: This study explicitly justifies increased investment in water improvement in rural areas and demonstrates the high returns of rehabilitating boreholes. We hope that this study will be used as evidence for informing the policy decisions of governments or international agencies regarding further investments in improved water coverage in rural areas and the selection of appropriately designed interventions

Developing indicators of pattern identification in patients with stroke using traditional Korean medicine

Abstract Background The traditional Korean medical diagnoses employ pattern identification (PI), a diagnostic system that entails the comprehensive analysis of symptoms and signs. The PI needs to be standardized due to its ambiguity. Therefore, this study was performed to establish standard indicators of the PI for stroke through the traditional Korean medical literature, expert consensus and a clinical field test. Methods We sorted out stroke patterns with an expert committee organized by the Korean Institute of Oriental Medicine. The expert committee composed a document for a standardized pattern of identification for stroke based on the traditional Korean medical literature, and we evaluated the clinical significance of the document through a field test. Results We established five stroke patterns from the traditional Korean medical literature and extracted 117 indicators required for diagnosis. The indicators were evaluated by a field test and verified by the expert committee. Conclusions This study sought to develop indicators of PI based on the traditional Korean medical literature. This process contributed to the standardization of traditional Korean medical diagnoses.</p

Improvement in survival among HIV-infected individuals in the Republic of Korea: Need for an early HIV diagnosis

<p>Abstract</p> <p>Background</p> <p>There is little information describing survival in HIV-infected patients after primary diagnosis in Korea, and changes in survival over time. This study investigated survival times, survival characteristics, and changes in survival after initial HIV diagnosis. Survival was characterized by evaluation of the immune status at primary HIV diagnosis nationwide.</p> <p>Methods</p> <p>A total of 5,323 HIV-infected individuals were registered with the government and followed until the end of 2007. Survival following HIV diagnosis was estimated based on epidemiological characteristics. We examined 3,369 individuals with available initial CD4+ T-cell counts within 6 months of HIV diagnosis to estimate survival based on immune status at diagnosis. The association between epidemiological variables and survival times was analyzed with univariate and multivariate Cox's proportional hazards model.</p> <p>Results</p> <p>Individuals died during the study period (n = 980), and 45% of the individuals died within 6 months of HIV diagnosis. The median survival following HIV diagnosis was 16.7 years. Survival were longer in women, in younger persons, in individuals diagnosed at blood centers, and in individuals diagnosed later in the study period. Survival were shortest in individuals with CD4+ T-cell counts <200 cells/mm³at HIV diagnosis. These results suggest that early HIV diagnosis in Korea is imperative to increase survival and to promote the quality of life for HIV-infected individuals with governmental support.</p> <p>Conclusion</p> <p>The median survival time of HIV-infected individuals following HIV diagnosis was 16.7 years in Korea. The survival was significantly lower in individuals with CD4+ T-cell counts <200 cells/mm³at HIV diagnosis and higher by introduction of drugs and development of therapy.</p

Complementary and Alternative Medicine for Idiopathic Parkinson’s Disease: An Evidence-Based Clinical Practice Guideline

Patients with idiopathic Parkinson’s disease (IPD) require long-term care and are reported to use complementary and alternative medicine (CAM) interventions frequently. This CAM-specific clinical practice guideline (CPG) makes recommendations for the use of CAM, including herbal medicines, acupuncture, moxibustion, pharmaco-acupuncture, and qigong (with Tai chi) in patients with IPD. This guideline was developed using an evidence-based approach with randomized controlled trials currently available. Even though this CPG had some limitations, mainly originating from the bias inherent in the research on which it is based, it would be helpful when assessing the value of the CAM interventions frequently used in patients with IPD

Michel electrons analysis in the fine-grained detectors for T2K

Over the decades, neutrino physics has advanced remarkably. Confirmation of neutrino oscillation is one of the important results. It indicates that neutrinos have non-zero mass and flavor mixing. T2K is an experiment designed to observe neutrino oscillations. It is an accelerator-based experiment with a baseline of 295 km across Japan from Tokai to Kamioka. The accelerator and the near detector are at Tokai and the far detector is at Kamioka. The near detector characterizes neutrino interactions in the absence of oscillation effects. Fine-Grained Detectors (FGDs) are a part of the near detector, which provide target mass and track particles emerging from neutrino interactions occurring in the detector. The primary neutrino interaction channel mode of interest is the charged-current quasi-elastic (CCQE) interaction. In CCQE interactions, a charged-lepton and a proton are in the final state. The neutrino energy is reconstructed and its flavor is identified by the charged lepton. Other, non-CCQE neutrino interactions have another particles in the final state such as pions. The pions may stop in an FGD and decay to produce muons, which in turn stop and decay to produce electrons. The electrons from muon decay at rest are called Michel electrons. Michel electrons are a powerful tool to distinguish CCQE and non-CCQE interactions. This thesis describes the studies of Michel electron activity in the near detector using cosmic rays.Science, Faculty ofPhysics and Astronomy, Department ofGraduat