Unsupervised Adaptation for High-Dimensional with Limited-Sample Data Classification Using Variational Autoencoder

High-dimensional with limited-sample size (HDLSS) datasets exhibit two critical problems: (1) Due to the insufficiently small-sample size, there is a lack of enough samples to build classification models. Classification models with a limited-sample may lead to overfitting and produce erroneous or meaningless results. (2) The 'curse of dimensionality' phenomena is often an obstacle to the use of many methods for solving the high-dimensional with limited-sample size problem and reduces classification accuracy. This study proposes an unsupervised framework for high-dimensional limited-sample size data classification using dimension reduction based on variational autoencoder (VAE). First, the deep learning method variational autoencoder is applied to project high-dimensional data onto lower-dimensional space. Then, clustering is applied to the obtained latent-space of VAE to find the data groups and classify input data. The method is validated by comparing the clustering results with actual labels using purity, rand index, and normalized mutual information. Moreover, to evaluate the proposed model strength, we analyzed 14 datasets from the Arizona State University Digital Repository. Also, an empirical comparison of dimensionality reduction techniques shown to conclude their applicability in the high-dimensional with limited-sample size data settings. Experimental results demonstrate that variational autoencoder can achieve more accuracy than traditional dimensionality reduction techniques in high-dimensional with limited-sample-size data analysis

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer

Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploited the normal allele-specific differential methylation of the M6P/IGF2R intron 2 CpG island to rapidly evaluate potential LOH in ovarian cancers, since every normal individual is informative. To this end, we developed a method for bisulfite modification of genomic DNA in 96-well format that allows for rapid methylation profiling. We identified ovarian cancers with M6P/IGF2R LOH, but unexpectedly also found frequent abnormal acquisition of methylation on the paternally inherited allele at intron 2. These results demonstrate the utility of our high-throughput method of bisulfite modification for analysis of large sample numbers. They further show that the methylation status of the intron 2 CpG island may be a useful indicator of LOH and biomarker of disease

A new global river network database for macroscale hydrologic modeling

Coarse-resolution (upscaled) river networks are critical inputs for runoff routing in macroscale hydrologic models. Recently, Wu et al. (2011) developed a hierarchical dominant river tracing (DRT) algorithm for automated extraction and spatial upscaling of river networks using fine-scale hydrography inputs. We applied the DRT algorithms using combined HydroSHEDS and HYDRO1k global fine-scale hydrography inputs and produced a new series of upscaled global river network data at multiple (1/16° to 2°) spatial resolutions. The new upscaled results are internally consistent and congruent with the baseline fine-scale inputs and should facilitate improved regional to global scale hydrologic simulations

Spatial Confinement Affects the Heterogeneity and Interactions Between Shoaling Fish

Living objects are able to consume chemical energy and process information independently from others. However, living objects can coordinate to form ordered groups such as schools of fish. This work considers these complex groups as living materials and presents imaging-based experiments of laboratory schools of fish to understand how this non-equilibrium activity affects the mechanical properties of a group. We use spatial confinement to control the motion and structure of fish within quasi-2D shoals of fish. Using image analysis techniques, we make quantitative observations of the structures, their spatial heterogeneity, and their temporal fluctuations. Furthermore, we utilize Monte Carlo simulations to replicate the experimentally observed area distribution patterns which provide insight into the effective interactions between fish and confirm the presence of a confinement-based behavioral preference transition. In addition, unlike in short-range interacting systems, here structural heterogeneity and dynamic activities are positively correlated as a result of complex interplay between spatial arrangement and behavioral dynamics in fish collectives.Comment: 18 pages, 7 Figure

Mucin binding reduces colistin antimicrobial activity

Colistin has found increasing use in treating drug-resistant bacterial lung infections, but potential interactions with pulmonary biomolecules have not been investigated. We postulated that colistin, like aminoglycoside antibiotics, may bind to secretory mucin in sputum or epithelial mucin that lines airways, reducing free drug levels. To test this hypothesis, we measured binding of colistin and other antibiotics to porcine mucin, a family of densely glycosylated proteins used as a surrogate for human sputum and airway mucin. Antibiotics were incubated in dialysis tubing with or without mucin, and concentrations of unbound antibiotics able to penetrate the dialysis tubing were measured over time using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The percentage of antibiotic measured in the dialysate after 4 h in the presence of mucin, relative to the amount without mucin, was 15% for colistin, 16% for polymyxin B, 19% for tobramycin, 52% for ciprofloxacin, and 78% for daptomycin. Antibiotics with the strongest mucin binding had an overall polybasic positive charge, whereas those with comparatively little binding were less basic. When comparing MICs measured with or without added mucin, colistin and polymyxin B showed >100-fold increases in MICs for multiple Gram-negative bacteria. Preclinical evaluation of mucin binding should become a standard procedure when considering the potential pulmonary use of new or existing antibiotics, particularly those with a polybasic overall charge. In the airways, mucin binding may reduce the antibacterial efficacy of inhaled or intravenously administered colistin, and the presence of sub-MIC effective antibiotic concentrations could result in the development of antibiotic resistance

Functional diversification of Argonautes in nematodes:an expanding universe

In the last decade, many diverse RNAi (RNA interference) pathways have been discovered that mediate gene silencing at epigenetic, transcriptional and post-transcriptional levels. The diversity of RNAi pathways is inherently linked to the evolution of Ago (Argonaute) proteins, the central protein component of RISCs (RNA-induced silencing complexes). An increasing number of diverse Agos have been identified in different species. The functions of most of these proteins are not yet known, but they are generally assumed to play roles in development, genome stability and/or protection against viruses. Recent research in the nematode Caenorhabditis elegans has expanded the breadth of RNAi functions to include transgenerational epigenetic memory and, possibly, environmental sensing. These functions are inherently linked to the production of secondary siRNAs (small interfering RNAs) that bind to members of a clade of WAGOs (worm-specific Agos). In the present article, we review briefly what is known about the evolution and function of Ago proteins in eukaryotes, including the expansion of WAGOs in nematodes. We postulate that the rapid evolution of WAGOs enables the exceptional functional plasticity of nematodes, including their capacity for parasitism

Adiponectin Prevents Diabetic Premature Senescence of Endothelial Progenitor Cells and Promotes Endothelial Repair by Suppressing the p38 MAP Kinase/p16INK4A Signaling Pathway

OBJECTIVE - A reduced number of circulating endothelial progenitor cells (EPCs) are casually associated with the cardiovascular complication of diabetes. Adiponectin exerts multiple protective effects against cardiovascular disease, independent of its insulin-sensitizing activity. The objective of this study was to investigate whether adiponectin plays a role in modulating the bioavailability of circulating EPCs and endothelial repair. RESEARCH DESIGN AND METHODS - Adiponectin knockout mice were crossed with db+/- mice to produce db/db diabetic mice without adiponectin. Circulating number of EPCs were analyzed by flow cytometry. Reendothelialization was evaluated by staining with Evans blue after wire-induced carotid injury. RESULTS - In adiponectin knockout mice, the number of circulating EPCs decreased in an age-dependent manner compared with the wild-type controls, and this difference was reversed by the chronic infusion of recombinant adiponectin. In db/db diabetic mice, the lack of adiponectin aggravated the hyperglycemia-induced decrease in circulating EPCs and also diminished the stimulatory effects of the PPARγ agonist rosiglitazone on EPC production and reendothelialization. In EPCs isolated from both human peripheral blood and mouse bone marrow, treatment with adiponectin prevented high glucose-induced premature senescence. At the molecular level, adiponectin decreased high glucose-induced accumulation of intracellular reactive oxygen species and consequently suppressed activation of p38 MAP kinase (MAPK) and expression of the senescence marker p16INK4A. CONCLUSIONS - Adiponectin prevents EPC senescence by inhibiting the ROS/p38 MAPK/p16 INK4A signaling cascade. The protective effects of adiponectin against diabetes vascular complications are attributed in part to its ability to counteract hyperglycemia-mediated decrease in the number of circulating EPCs. © 2010 by the American Diabetes Association.published_or_final_versio

Inhibition of carcinogen induced c-Ha-ras and c-fos proto-oncogenes expression by dietary curcumin

BACKGROUND: We investigated the chemopreventive action of dietary curcumin on 7,12-dimethylbenz(a)anthracene (DMBA)-initiated and 12,0-tetradecanoylphorbol-13-acetate (TPA)-promoted skin tumor formation in Swiss albino mice. Curcumin, a yellow coloring matter isolated from roots of Curcuma longa Linn, is a phenolic compound possessing antioxidant, free radical scavenger, and antiinflammatory properties. It has been shown by previously reported work that TPA-induced skin tumors were inhibited by topical application of curcumin, and curcumin has been shown to inhibit a variety of biological activities of TPA. Topical application of curcumin was reported to inhibit TPA-induced c-fos, c-jun and c-myc gene expression in mouse skin. This paper reports the effects of orally administered curcumin, which was consumed as a dietary component at concentrations of 0.2 % or 1 %, in ad libitum feeding. RESULTS: Animals in which tumors had been initiated with DMBA and promoted with TPA experienced significantly fewer tumors and less tumor volume if they ingested either 0.2% or 1% curcumin diets. Also, the dietary consumption of curcumin resulted in a significantly decreased expression of ras and fos proto-oncogenes in the tumorous skin, as measured by enhanced chemiluminesence Western blotting detection system (Amersham). CONCLUSIONS: Whereas earlier work demonstrated that topical application of curcumin to mouse skin inhibited TPA-induced expression of c-fos, c-jun and c-myc oncogenes, our results are the first to show that orally consumed curcumin significantly inhibited DMBA- and TPA-induced ras and fos gene expression in mouse skin