Divergences in maximal supersymmetric Yang-Mills theories in diverse dimensions

The main aim of this paper is to study the scattering amplitudes in gauge field theories with maximal supersymmetry in dimensions D=6,8 and 10. We perform a systematic study of the leading ultraviolet divergences using the spinor helicity and on-shell momentum superspace framework. In D=6 the first divergences start at 3 loops and we calculate them up to 5 loops, in D=8,10 the first divergences start at 1 loop and we calculate them up to 4 loops. The leading divergences in a given order are the polynomials of Mandelstam variables. To be on the safe side, we check our analytical calculations by numerical ones applying the alpha-representation and the dedicated routines. Then we derive an analog of the RG equations for the leading pole that allows us to get the recursive relations and construct the generating procedure to obtain the polynomials at any order of (perturbation theory) PT. At last, we make an attempt to sum the PT series and derive the differential equation for the infinite sum. This equation possesses a fixed point which might be stable or unstable depending on the kinematics. Some consequences of these fixed points are discussed.Comment: 43 pages, 13 figures, pdf LaTex, v2 minor changes and references adde

Construction of Infrared Finite Observables in N=4 Super Yang-Mills Theory

In this paper we give all the details of the calculation that we presented in our previous paper ArXiv:0908.0387 where the infrared structure of the MHV gluon amplitudes in the planar limit for ${\cal N}=4$ super Yang-Mills theory was considered in the next-to-leading order of perturbation theory. Explicit cancellation of the infrared divergencies in properly defined inclusive cross-sections is demonstrated first in a toy model example of "conformal QED" and then in the real ${\cal N}=4$ SYM theory. We give the full-length details both for the calculation of the real emission and for the diagrams with splitting in initial and final states. The finite parts for some inclusive differential cross-sections are presented in an analytical form. In general, contrary to the virtual corrections, they do not reveal any simple structure. An example of the finite part containing just the log functions is presented. The dependence of inclusive cross-section on the external scale related to the definition of asymptotic states is discussed.Comment: 49 pages, LATEX, 6 eps figures; Minor changes, Refs adde

CART - a chemical annotation retrieval toolkit

MOTIVATION: Data on bioactivities of drug-like chemicals is rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases. RESULTS: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling

Drug-induced gene-expression profiles that invert disease profiles have recently been illustrated to be a starting point for drug repositioning. In this study, we validate this approach and focus on prediction of novel drugs for colorectal cancer, for which there is a pressing need to find novel antimetastatic compounds. We computationally predicted three novel and still unknown compounds against colorectal cancer: citalopram (an antidepressant), troglitazone (an antidiabetic), and enilconazole (a fungicide). We verified the compounds by in vitro assays of clonogenic survival, proliferation, and migration and in a subcutaneous mouse model. We found evidence that the mode of action of these compounds may be through inhibition of TGF{beta} signaling. Furthermore, one compound, citalopram, reduced tumor size as well as the number of circulating tumor cells and metastases in an orthotopic mouse model of colorectal cancer. This study proposes citalopram as a potential therapeutic option for patients with colorectal cancer, illustrating the potential of systems pharmacology

dc readout experiment at the Caltech 40m prototype interferometer

The Laser Interferometer Gravitational Wave Observatory (LIGO) operates a 40m prototype interferometer on the Caltech campus. The primary mission of the prototype is to serve as an experimental testbed for upgrades to the LIGO interferometers and for gaining experience with advanced interferometric techniques, including detuned resonant sideband extraction (i.e. signal recycling) and dc readout (optical homodyne detection). The former technique will be employed in Advanced LIGO, and the latter in both Enhanced and Advanced LIGO. Using dc readout for gravitational wave signal extraction has several technical advantages, including reduced laser and oscillator noise couplings as well as reduced shot noise, when compared to the traditional rf readout technique (optical heterodyne detection) currently in use in large-scale ground-based interferometric gravitational wave detectors. The Caltech 40m laboratory is currently prototyping a dc readout system for a fully suspended interferometric gravitational wave detector. The system includes an optical filter cavity at the interferometer's output port, and the associated controls and optics to ensure that the filter cavity is optimally coupled to the interferometer. We present the results of measurements to characterize noise couplings in rf and dc readout using this system

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR

Stimulation of cells with epidermal growth factor (EGF) induces internalization and partial degradation of the EGF receptor (EGFR) by the endo-lysosomal pathway. For continuous cell functioning, EGFR plasma membrane levels are maintained by transporting newly synthesized EGFRs to the cell surface. The regulation of this process is largely unknown. In this study, we find that EGF stimulation specifically increases the transport efficiency of newly synthesized EGFRs from the endoplasmic reticulum to the plasma membrane. This coincides with an up-regulation of the inner coat protein complex II (COPII) components SEC23B, SEC24B, and SEC24D, which we show to be specifically required for EGFR transport. Up-regulation of these COPII components requires the transcriptional regulator RNF11, which localizes to early endosomes and appears additionally in the cell nucleus upon continuous EGF stimulation. Collectively, our work identifies a new regulatory mechanism that integrates the degradation and transport of EGFR in order to maintain its physiological levels at the plasma membrane

High-resolution transcription atlas of the mitotic cell cycle in budding yeast.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Extensive transcription of non-coding RNAs has been detected in eukaryotic genomes and is thought to constitute an additional layer in the regulation of gene expression. Despite this role, their transcription through the cell cycle has not been studied; genome-wide approaches have only focused on protein-coding genes. To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome. RESULTS: We discovered 523 antisense transcripts, of which 80 cycle or are located opposite periodically expressed mRNAs, 135 unannotated intergenic non-coding RNAs, of which 11 cycle, and 109 cell-cycle-regulated protein-coding genes that had not previously been shown to cycle. We detected periodic expression coupling of sense and antisense transcript pairs, including antisense transcripts opposite of key cell-cycle regulators, like FAR1 and TAF2. CONCLUSIONS: Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle. It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time. This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs