HEAT: a New Tool for Gene Set Enrichment Analysis Using Comprehensive Annotation of Human Genes in H-InvDB

H-InvDB Enrichment Analysis Tool (HEAT) is a new data-mining tool for gene set enrichment analysis based on comprehensive annotations of human genes in H-InvDB. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. The advantage of HEAT is the wide variety of annotation items used for its analysis: chromosomal bands, InterPro functional domains, Gene Ontology terms, KEGG pathways, H-InvDB gene families/groups, SCOP structural domains, subcellular localization predicted by using the Wolf-PSORT program, tissue-specific gene expression as defined in the H-ANGEL database, and transcription factor binding sites in promoter regions based on JASPAR. HEAT accepts lists of human gene identifiers (IDs) including HUGO gene symbols, accession numbers of INSD (DDBJ/EMBL/GenBank), UniProt accession numbers, Gene IDs, Ensembl Gene IDs, H-InvDB Transcript IDs (HIT) and Locus IDs (HIX), etc. Then, HEAT converts the accepted IDs into HIX using the ID Converter System ("http://biodb.jp/":http://biodb.jp/), collects various annotations of H-InvDB representative transcripts, and conducts statistical tests by using Fisher's exact probability. The output of HEAT is a simple report of annotations commonly found among the query genes, which is very useful to grasp the property of a particular gene set. HEAT is freely available at "http://hinv.jp/HEAT/":http://hinv.jp/HEAT/

ABJM with Flavors and FQHE

We add fundamental matters to the N=6 Chern-Simons theory (ABJM theory), and show that D6-branes wrapped over AdS_4 x S^3/Z_2 in type IIA superstring theory on AdS_4 x CP^3 give its dual description with N=3 supersymmetry. We confirm this by the arguments based on R-symmetry, supersymmetry, and brane configuration of ABJM theory. We also analyze the fluctuations of the D6-brane and compute the conformal dimensions of dual operators. In the presence of fractional branes, the ABJM theory can model the fractional quantum Hall effect (FQHE), with RR-fields regarded as the external electric-magnetic field. We show that an addition of the flavor D6-brane describes a class of fractional quantum Hall plateau transition.Comment: 23 pages, Latex, no figures; (v2) references added, typos correcte

On the Connection between N=2 Minimal String and (1,n) Bosonic Minimal String

We study the scattering amplitudes in the N=2 minimal string or equivalently in the N=4 topological string on ALE spaces. We find an interesting connection between the tree level amplitudes of the N=2 minimal string and those of the (1,n) minimal bosonic string. In particular we show that the four and five-point functions of the N=2 string can be directly rewritten in terms of those of the latter theory. This relation offers a map of physical states between these two string theories. Finally we propose a possible matrix model dual for the N=2 minimal string in the light of this connection.Comment: 40 pages, one figure, harvmac, minor corrections, references adde

Fast algorithm for calculating two-photon absorption spectra

We report a numerical calculation of the two-photon absorption coefficient of electrons in a binding potential using the real-time real-space higher-order difference method. By introducing random vector averaging for the intermediate state, the task of evaluating the two-dimensional time integral is reduced to calculating two one-dimensional integrals. This allows the reduction of the computation load down to the same order as that for the linear response function. The relative advantage of the method compared to the straightforward multi-dimensional time integration is greater for the calculation of non-linear response functions of higher order at higher energy resolution.Comment: 4 pages, 2 figures. It will be published in Phys. Rev. E on 1, March, 199

Fractional Quantum Hall Effect via Holography: Chern-Simons, Edge States, and Hierarchy

We present three holographic constructions of fractional quantum Hall effect (FQHE) via string theory. The first model studies edge states in FQHE using supersymmetric domain walls in N=6 Chern-Simons theory. We show that D4-branes wrapped on CP^1 or D8-branes wrapped on CP^3 create edge states that shift the rank or the level of the gauge group, respectively. These holographic edge states correctly reproduce the Hall conductivity. The second model presents a holographic dual to the pure U(N)_k (Yang-Mills-)Chern-Simons theory based on a D3-D7 system. Its holography is equivalent to the level-rank duality, which enables us to compute the Hall conductivity and the topological entanglement entropy. The third model introduces the first string theory embedding of hierarchical FQHEs, using IIA string on C^2/Z_n.Comment: 36 pages, 6 figures; v2: with an improved derivation of Hall conductivity in section 3.2, typo corrections, and additional references; v3: explanations and comments adde

Some No-go Theorems for String Duals of Non-relativistic Lifshitz-like Theories

We study possibilities of string theory embeddings of the gravity duals for non-relativistic Lifshitz-like theories with anisotropic scale invariance. We search classical solutions in type IIA and eleven-dimensional supergravities which are expected to be dual to (2+1)-dimensional Lifshitz-like theories. Under reasonable ansaetze, we prove that such gravity duals in the supergravities are not possible. We also discuss a possible physical reason behind this.Comment: 18 pages, Latex, flux conditions clarified (v2), brief summary of results added (v3

Comments on 2D Type IIA String and Matrix Model

We consider a type IIA-like string theory with RR-flux in two dimension and propose its matrix model dual. This string theory describes a Majorana fermion in the two dimensional spacetime. We also discuss its scattering amplitudes both in the world-sheet theory and in the matrix model.Comment: 21 pages, Harvmac, to appear in JHEP, relation to 2d superstring constructed by D. Kutasov hep-th/9110041 is clarifie

Fructosamine and glycated hemoglobin as biomarkers of glycemic control in people with type 2 diabetes mellitus and cancer (GlicoOnco study)

Introduction: Glycemic control is important to avoid diabetes complications in individuals with cancer. There is no evidence for HbA1c and fructosamine as reliable biomarkers in these conditions. There are particularities in caring for patients with diabetes and cancer that can alter these biomarkers. Objective: The aim of this study was to evaluate HbA1c and fructosamine as glycemic biomarkers in people with type 2 diabetes and cancer, undergoing clinical or surgical oncological treatment. Methods: The authors conducted a single-center, retrospective analysis with people who have cancer and diabetes. Comparison of glycemic biomarkers (HbA1c, fructosamine, and Self-Monitoring of Blood Glucose [SMBG]) was performed including evaluation in individuals undergoing chemotherapy, using glucocorticoids, with anemia, hypoproteinemia or with reduced estimated Glomerular Filtration Rate (eGFR). Results: There was a strong positive correlation between fructosamine and HbA1c (n = 318, r = 0.66, p < 0.001) in people with diabetes and cancer even in those under chemotherapy (n = 101, r = 0.61, p < 0.001) or using glucocorticoids (n = 96, r = 0.67, p<0.001). There was a strong correlation between HbA1c and fructosamine in subjects with anemia (n = 111, r = 0.66, p < 0.001), hypoproteinemia (n = 54, r = 0.67, p < 0.001), or with eGFR ≥ 60 mL/min/1.73 m2 (n = 189, r = 0.70, p < 0.001), and moderate correlation with hypoalbuminemia (n = 21, r = 0.54, p = 0.001) and with reduced eGFR (n = 67, r = 0.57, p < 0.001). The correlations between fructosamine and HbA1c with SMBG were moderate (n = 164, r = 0.49, p < 0.001; n = 111, r = 0.55, p < 0.001, respectively), strong in subjects undergoing chemotherapy, with hypoalbuminemia or hypoproteinemia, and at least moderate, if eGFR < 60 mL/min/1.73 m2 or with anemia. Conclusions: Fructosamine and HbA1c can be used as glycemic biomarkers in people with diabetes and cancer, even in those with anemia, hypoproteinemia, or undergoing chemotherapy

Flux Backgrounds in 2D String Theory

We study RR flux backgrounds in two dimensional type 0 string theories. In particular, we study the relation between the 0A matrix model and the extremal black hole in two dimensions. Using T-duality we find a dual flux background in type 0B theory and propose its matrix model description. When the Fermi level is set to zero this system remains weakly coupled and exhibits a larger symmetry related to the structure of flux vacua. Finally, we construct a two dimensional type IIB background as an orbifold of the 0B background.Comment: Harvmac, 40 pages, 6 figs, minor changes, references adde

AdS Bubbles, Entropy and Closed String Tachyons

We study the conjectured connection between AdS bubbles (AdS solitons) and closed string tachyon condensations. We confirm that the entanglement entropy, which measures the degree of freedom, decreases under the tachyon condensation. The entropies in supergravity and free Yang-Mills agree with each other remarkably. Next we consider the tachyon condensation on the AdS twisted circle and argue that its endpoint is given by the twisted AdS bubble, defined by the double Wick rotation of rotating black 3-brane solutions. We calculated the Casimir energy and entropy and checked the agreements between the gauge and gravity results. Finally we show an infinite boost of a null linear dilaton theory with a tachyon wall (or bubble), leads to a solvable time-dependent background with a bulk tachyon condensation. This is the simplest example of spacetimes with null boundaries in string theory.Comment: 45 pages, 6 figures, harvmac, eq.(2.16) corrected, references adde