Clustering with instance and attribute level side information

Selecting a suitable proximity measure is one of the fundamental tasks in clustering. How to effectively utilize all available side information, including the instance level information in the form of pair-wise constraints, and the attribute level information in the form of attribute order preferences, is an essential problem in metric learning. In this paper, we propose a learning framework in which both the pair-wise constraints and the attribute order preferences can be incorporated simultaneously. The theory behind it and the related parameter adjusting technique have been described in details. Experimental results on benchmark data sets demonstrate the effectiveness of proposed method

Legume Green Manuring Improves Soil Fertility and Plant Growth of Eucalyptus Plantation in South Subtropical China

Legume green manure is extensively planted to improve soil fertility in crop field. However, the application of legume in Eucalyptus plantation is still limited and depends on site specific and species. Therefore, the objective of this study was to determine the effects of green manure interplantation on soil fertility and plant growth of Eucalyptus plantation in a short term. A field experiment of one year was established to investigate the green manure growth, forest soil nutrients and Eucalyptus plant growth inter-planted with two legume species (Tephrosia candida, TC and Sesbania cannabina, SC) at south subtropical China. Legumes were inter-planted in linear among the tree space of Eucalyptus stand. Result showed that the green manure inter-plantation increased soil organic matter by 9.66% of TC and 18.44% of SC. Soil available nitrogen, phosphorus and potassium were improved significantly by the legume treatments as well. The increment of height and diameter at breast height of Eucalyptus during the experiment was significant in legume treatments. Thus, the timber volume increment was improved significantly by 46.81% of TC and 35.47% of SC compared with the control treatment. Therefore, the inter-plantation of legume green manure under the Eucalyptus plantation is effective to improve soil fertility and tree growth. Such a measure is potential and referenced for the sustainable forest management

Comparative miRNA Expression Profiles in Individuals with Latent and Active Tuberculosis

The mechanism of latent tuberculosis (TB) infection remains elusive. Several host factors that are involved in this complex process were previously identified. Micro RNAs (miRNAs) are endogenous ∼22 nt RNAs that play important regulatory roles in a wide range of biological processes. Several studies demonstrated the clinical usefulness of miRNAs as diagnostic or prognostic biomarkers in various malignancies and in a few nonmalignant diseases. To study the role of miRNAs in the transition from latent to active TB and to discover candidate biomarkers of this transition, we used human miRNA microarrays to probe the transcriptome of peripheral blood mononuclear cells (PBMCs) in patients with active TB, latent TB infection (LTBI), and healthy controls. Using the software package BRB Array Tools for data analyses, 17 miRNAs were differentially expressed between the three groups (P<0.01). Hierarchical clustering of the 17 miRNAs expression profiles showed that individuals with active TB clustered independently of individuals with LTBI or from healthy controls. Using the predicted target genes and previously published genome-wide transcriptional profiles, we constructed the regulatory networks of miRNAs that were differentially expressed between active TB and LTBI. The regulatory network revealed that several miRNAs, with previously established functions in hematopoietic cell differentiation and their target genes may be involved in the transition from latent to active TB. These results increase the understanding of the molecular basis of LTBI and confirm that some miRNAs may control gene expression of pathways that are important for the pathogenesis of this infectious disease

Case Report: Mycobacterium kansasii causing infective endocarditis explored by metagenomic next-generation sequencing

In this report, we describe the first case of infective endocarditis caused by Mycobacterium kansasii in a 45-year-old male patient who presented with a 10-day fever and decompensated cirrhosis. Despite negative results in blood culture and pathology, we employed metagenomic next-generation sequencing (mNGS) to analyze the genome sequences of both the host and microbe. The copy number variation (CNV) indicated a high risk of liver disease in the patient, which correlated with biochemical examination findings. Notably, M. kansasii sequences were detected in peripheral blood samples and confirmed through Sanger sequencing. Unfortunately, the patient’s condition deteriorated, leading to his demise prior to heart surgery. Nevertheless, we propose that mNGS could be a novel approach for diagnosing M. kansasii infection, particularly in cases where blood culture and pathology results are unavailable. It is important to consider M. kansasii infection as a potential cause of endocarditis and initiate appropriate anti-infection treatment

Stress-Activated Kinase MKK7 Governs Epigenetics of Cardiac Repolarization for Arrhythmia Prevention

BACKGROUND: Ventricular arrhythmia is a leading cause of cardiac mortality. Most antiarrhythmics present paradoxical proarrhythmic side effects, culminating in a greater risk of sudden death. METHODS: We describe a new regulatory mechanism linking mitogen-activated kinase kinase-7 deficiency with increased arrhythmia vulnerability in hypertrophied and failing hearts using mouse models harboring mitogen-activated kinase kinase-7 knockout or overexpression. The human relevance of this arrhythmogenic mechanism is evaluated in human-induced pluripotent stem cell-derived cardiomyocytes. Therapeutic potentials by targeting this mechanism are explored in the mouse models and human-induced pluripotent stem cell-derived cardiomyocytes. RESULTS: Mechanistically, hypertrophic stress dampens expression and phosphorylation of mitogen-activated kinase kinase-7. Such mitogen-activated kinase kinase-7 deficiency leaves histone deacetylase-2 unphosphorylated and filamin-A accumulated in the nucleus to form a complex with Kruppel-like factor-4. This complex leads to Kruppel-like factor-4 disassociation from the promoter regions of multiple key potassium channel genes (Kv4.2, KChIP2, Kv1.5, ERG1, and Kir6.2) and reduction of their transcript levels. Consequent repolarization delays result in ventricular arrhythmias. Therapeutically, targeting the repressive function of the Kruppel-like factor-4/histone deacetylase-2/filamin-A complex with the histone deacetylase-2 inhibitor valproic acid restores K+ channel expression and alleviates ventricular arrhythmias in pathologically remodeled hearts. CONCLUSIONS: Our findings unveil this new gene regulatory avenue as a new antiarrhythmic target where repurposing of the antiepileptic drug valproic acid as an antiarrhythmic is supported.British Heart Foundation [PG/09/052/27833, PG/14/71/31063, PG/12/76/29852, FS/15/16/31477]; Medical Research Council [G1002082, MC_PC_13070]; American Heart Association National Scientist Development Grants [12SDG12070077]; National Basic Research Program of China [2012CB518000]SCI(E)ARTICLE7683-69913

Association of Genetic Variants of Melatonin Receptor 1B with Gestational Plasma Glucose Level and Risk of Glucose Intolerance in Pregnant Chinese Women

BACKGROUND: This study aimed to explore the association of MTNR1B genetic variants with gestational plasma glucose homeostasis in pregnant Chinese women. METHODS: A total of 1,985 pregnant Han Chinese women were recruited and evaluated for gestational glucose tolerance status with a two-step approach. The four MTNR1B variants rs10830963, rs1387153, rs1447352, and rs2166706 which had been reported to associate with glucose levels in general non-pregnant populations, were genotyped in these women. Using an additive model adjusted for age and body mass index (BMI), association of these variants with gestational fasting and postprandial plasma glucose (FPG and PPG) levels were analyzed by multiple linear regression; relative risk of developing gestational glucose intolerance was calculated by logistic regression. Hardy-Weinberg Equilibrium was tested by Chi-square and linkage disequilibrium (LD) between these variants was estimated by measures of D' and r(2). RESULTS: In the pregnant Chinese women, the MTNR1B variant rs10830963, rs1387153, rs2166706 and rs1447352 were shown to be associated with the increased 1 hour PPG level (p=8.04 × 10(-10), 5.49 × 10(-6), 1.89 × 10(-5) and 0.02, respectively). The alleles were also shown to be associated with gestational glucose intolerance with odds ratios (OR) of 1.64 (p=8.03 × 10(-11)), 1.43 (p=1.94 × 10(-6)), 1.38 (p=1.63 × 10(-5)) and 1.24 (p=0.007), respectively. MTNR1B rs1387153, rs2166706 were shown to be associated with gestational FPG levels (p=0.04). Our data also suggested that, the LD pattern of these variants in the studied women conformed to that in the general populations: rs1387153 and rs2166706 were in high LD, they linked moderately with rs10830963, but might not linked with rs1447352;rs10830963 might not link with rs1447352, either. In addition, the MTNR1B variants were not found to be associated with any other traits tested. CONCLUSIONS: The MTNR1B is likely to be involved in the regulation of glucose homeostasis during pregnancy

Reactive Intermediates in Secondary Organic Aerosol and Oxidative Potential

Secondary organic aerosol (SOA) contributes a significant fraction of particulate matter (PM), which has important impacts on climate change and public health. Reactive intermediates in SOA are compounds with relatively high reactivities, whose environmental fate can significantly influence the physicochemical properties of aerosol. The present thesis characterizes the reactive intermediates in OA by evaluating their potential role in atmospheric chemistry and human health. Organic peroxides are highly reactive components detected in a variety of organic aerosol systems. The current work investigates the reactivity of organic peroxides towards SO2 through laboratory measurements of bulk-phase and heterogeneous reaction kinetics. Results indicate that this interaction is important for particulate sulfate formation and other aerosol characteristics. Furthermore, organic peroxides can serve as a significant source of reactive oxygen species (ROS) and exhibit high oxidative potential (OP) as observed in OA from cooking emissions. Among OA from various emission sources, the OP of polycyclic aromatic hydrocarbons derived SOA is the highest while the evolution in the atmosphere remains obscure. Using naphthalene SOA (NSOA) as a model system, secondary ozonolysis and oligomerization was found to enhance the OP of NSOA while chelation with transition metal (Cu2+) reduces the OP. Photochemical aging can initially enhance and then decrease the cytotoxicity of NSOA. Post-translational level results from proteome-wide analysis show that quinones and other unsaturated carbonyls are responsible for the toxicity of NSOA during atmospheric aging. This work contributes to our understanding of the dynamic evolution and potential health impacts from organic aerosol in the atmosphere.Ph.D