Temporal patterns of gene expression via nonmetric multidimensional scaling analysis

Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS) analysis for very large data sets as a maximally unsupervised data mining device. We wish to demonstrate its usefulness in the context of bioinformatics. In our motivation is also an aim to demonstrate that intrinsically nonlinear methods are generally advantageous in data mining. Results: The Pearson correlation distance measure is used to indicate the dissimilarity of the gene activities in transcriptional response of cell cycle-synchronized human fibroblasts to serum [Iyer et al., Science vol. 283, p83 (1999)]. These dissimilarity data have been analyzed with our nMDS algorithm to produce an almost circular arrangement of the genes. The temporal expression patterns of the genes rotate along this circular arrangement. If an appropriate preparation procedure may be applied to the original data set, linear methods such as the principal component analysis (PCA) could achieve reasonable results, but without data preprocessing linear methods such as PCA cannot achieve a useful picture. Furthermore, even with an appropriate data preprocessing, the outcomes of linear procedures are not as clearcut as those by nMDS without preprocessing.Comment: 11 pages, 6 figures + online only 2 color figures, submitted to Bioinformatic

Quantum Chromodynamics with Many Flavors

We investigate the phase structure of lattice QCD for general number of flavors $N_F$. Based on numerical data combined with the results of the perturbation theory we propose the following picture: When $N_F \ge 17$, there is only one IR fixed point at vanishing gauge coupling, i.e., the theory in the continuum limit is trivial. On the other hand, when $16 \ge N_F \ge 7$, there is a non-trivial fixed point. Therefore, the theory is non-trivial with anomalous dimensions, however, without quark confinement. Theories which satisfy both quark confinement and spontaneous chiral symmetry breaking in the continuum limit exist only for $N_F \le 6$.Comment: Talk presented by K. Kanaya at the 1997 Yukawa International Seminar (YKIS'97) on ``Non-Perturbative QCD --- Structure of the QCD Vacuum ---'', YITP, Kyoto, Japan, 2--12 Dec. 1997. To be published in the proceedings [Prog. Theor. Phys. Suppl.

Equation of state in 2+1 flavor QCD with improved Wilson quarks by the fixed scale approach

We study the equation of state in 2+1 flavor QCD with nonperturbatively improved Wilson quarks coupled with the RG-improved Iwasaki glue. We apply the $T$-integration method to nonperturbatively calculate the equation of state by the fixed-scale approach. With the fixed-scale approach, we can purely vary the temperature on a line of constant physics without changing the system size and renormalization constants. Unlike the conventional fixed-$N_t$ approach, it is easy to keep scaling violations small at low temperature in the fixed scale approach. We study 2+1 flavor QCD at light quark mass corresponding to $m_\pi/m_\rho \simeq 0.63$, while the strange quark mass is chosen around the physical point. Although the light quark masses are heavier than the physical values yet, our equation of state is roughly consistent with recent results with highly improved staggered quarks at large $N_t$.Comment: 14 pages, 12 figures, v2: Table I and Figure 3 are corrected, reference updated. Main discussions and conclusions are unchanged, v3: version to appear in PRD, v4: reference adde

Phase structure of QCD for general number of flavors

We investigate and elucidate the phase structure of QCD for general number of flavors $N_F$ with Wilson quarks, varying $N_F$ from 2 up to 300. Based on numerical results combined with the result of the perturbation theory we propose the following picture: When $N_F \ge 17$, there is only a trivial fixed point and therefore the theory in the continuum limit is trivial. On the other hand, when $16 \ge N_F \ge 7$, there is a non-trivial fixed point and therefore the theory is non-trivial with anomalous dimensions, however, without quark confinement. Theories which satisfy both quark confinement and spontaneous chiral symmetry breaking in the continuum limit exist only for $N_F \le 6$. We also discuss the structure of the deconfining phase at finite temperatures for the small number of flavors such as $N_F=2$ and 3, through a systematic study of it for general number of flavors.Comment: LaTeX, 7 pages, 10 PS figures, Talk presented at LATTICE96(poster) and LATTICE96(finite temperature

Preliminary evidence supports circulating microRNAs as prognostic biomarkers for type 2 diabetes.

Background:Circulating microRNAs are emerging as potential prognostic biomarkers for the development of type 2 diabetes. However, microRNAs are also associated with complications from impaired glucose metabolism (e.g. endothelial cell function). Prior studies have not evaluated for associations between trajectories of circulating microRNAs with trajectories of fasting blood glucose over time and the responses to behavioral interventions to reduce risk. This study performed longitudinal assessment of microRNAs and fasting blood glucose and identified relationships between microRNAs and behavioral risk reduction interventions. Methods:MicroRNAs (n = 353) were measured in subsets (n = 10, n = 8) of participants from previously completed clinical trials that studied behavioral risk reduction interventions. Fasting blood glucose trajectories were associated with changes in 45 microRNAs over 12 months. Results:Following a 3-month physical activity and dietary intervention compared with baseline, 13 microRNAs were differentially expressed. Seven microRNAs (i.e. miR-106b, miR-20b, miR-363, miR-486, miR-532, miR-92a and miR-93) were commonly identified between the two analyses. Conclusions:Further studies are needed to determine which microRNAs are prognostic biomarkers of risk for type 2 diabetes versus consequences of impaired glucose metabolism. Additional future directions of this research are to differentiate whether microRNAs are prognostic and/or diagnostic biomarkers for risk for type 2 diabetes and predictive biomarkers of responses to risk reduction interventions

Finite Temperature QCD with Wilson Quarks: A Study with a Renormalization Group Improved Gauge Action

Finite temperature transition in lattice QCD with degenerate Wilson quarks is investigated on an $N_t=4$ lattice, using a renormalization group improved gauge action. We find the following for the $N_F=2$ case: 1) The transition is smooth for a wide range of the quark mass. 2) The chiral transition is continuous. 3) The chiral condensation well satisfies a scaling relation with the critical exponents of the 3 dimensional $O(4)$ spin model. For $N_F=3$, we find that the chiral transition is of first order.Comment: 4 pages (6 figures), Postscript file, Contribution to Lattice 95 proceeding