Heterotic M-Theory Cosmology in Four and Five Dimensions

We study rolling radii solutions in the context of the four- and five-dimensional effective actions of heterotic M-theory. For the standard four-dimensional solutions with varying dilaton and T-modulus, we find approximate five-dimensional counterparts. These are new, generically non-separating solutions corresponding to a pair of five-dimensional domain walls evolving in time. Loop corrections in the four-dimensional theory are described by certain excitations of fields in the fifth dimension. We point out that the two exact separable solutions previously discovered are precisely the special cases for which the loop corrections are time-independent. Generically, loop corrections vary with time. Moreover, for a subset of solutions they increase in time, evolving into complicated, non-separating solutions. In this paper we compute these solutions to leading, non-trivial order. Using the equations for the induced brane metric, we present a general argument showing that the accelerating backgrounds of this type cannot evolve smoothly into decelerating backgrounds.Comment: 15 pages, Latex, 1 eps figur

Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP

BACKGROUND: Confocal laser scanning microscopy (CLSM) is the method of choice to study interfacial biofilms and acquires time-resolved three-dimensional data of the biofilm structure. CLSM can be used in a multi-channel modus where the different channels map individual biofilm components. This communication presents a novel image quantification tool, PHLIP, for the quantitative analysis of large amounts of multichannel CLSM data in an automated way. PHLIP can be freely downloaded from RESULTS: PHLIP is an open source public license Matlab toolbox that includes functions for CLSM imaging data handling and ten image analysis operations describing various aspects of biofilm morphology. The use of PHLIP is here demonstrated by a study of the development of a natural marine phototrophic biofilm. It is shown how the examination of the individual biofilm components using the multi-channel capability of PHLIP allowed the description of the dynamic spatial and temporal separation of diatoms, bacteria and organic and inorganic matter during the shift from a bacteria-dominated to a diatom-dominated phototrophic biofilm. Reflection images and weight measurements complementing the PHLIP analyses suggest that a large part of the biofilm mass consisted of inorganic mineral material. CONCLUSION: The presented case study reveals new insight into the temporal development of a phototrophic biofilm where multi-channel imaging allowed to parallel monitor the dynamics of the individual biofilm components over time. This application of PHLIP presents the power of biofilm image analysis by multi-channel CLSM software and demonstrates the importance of PHLIP for the scientific community as a flexible and extendable image analysis platform for automated image processing

Cosmological Solutions in String Theories

We obtain a large class of cosmological solutions in the toroidally-compactified low energy limits of string theories in $D$ dimensions. We consider solutions where a $p$-dimensional subset of the spatial coordinates, parameterising a flat space, a sphere, or an hyperboloid, describes the spatial sections of the physically-observed universe. The equations of motion reduce to Liouville or $SL(N+1,R)$ Toda equations, which are exactly solvable. We study some of the cases in detail, and find that under suitable conditions they can describe four-dimensional expanding universes. We discuss also how the solutions in $D$ dimensions behave upon oxidation back to the $D=10$ string theory or $D=11$ M-theory.Comment: Latex, 21 pages, a reference adjuste

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics

BACKGROUND: Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools is now available for both isotopically labeled and label-free liquid chromatography mass spectrometry (LC-MS) based quantitative proteomics. However, they are generally not comparable to each other in terms of functionality, user interfaces, information input/output, and do not readily facilitate appropriate statistical data analysis. These limitations, along with the array of choices, present a daunting prospect for biologists, and other researchers not trained in bioinformatics, who wish to use LC-MS-based quantitative proteomics. RESULTS: We have developed Corra, a computational framework and tools for discovery-based LC-MS proteomics. Corra extends and adapts existing algorithms used for LC-MS-based proteomics, and statistical algorithms, originally developed for microarray data analyses, appropriate for LC-MS data analysis. Corra also adapts software engineering technologies (e.g. Google Web Toolkit, distributed processing) so that computationally intense data processing and statistical analyses can run on a remote server, while the user controls and manages the process from their own computer via a simple web interface. Corra also allows the user to output significantly differentially abundant LC-MS-detected peptide features in a form compatible with subsequent sequence identification via tandem mass spectrometry (MS/MS). We present two case studies to illustrate the application of Corra to commonly performed LC-MS-based biological workflows: a pilot biomarker discovery study of glycoproteins isolated from human plasma samples relevant to type 2 diabetes, and a study in yeast to identify in vivo targets of the protein kinase Ark1 via phosphopeptide profiling. CONCLUSION: The Corra computational framework leverages computational innovation to enable biologists or other researchers to process, analyze and visualize LC-MS data with what would otherwise be a complex and not user-friendly suite of tools. Corra enables appropriate statistical analyses, with controlled false-discovery rates, ultimately to inform subsequent targeted identification of differentially abundant peptides by MS/MS. For the user not trained in bioinformatics, Corra represents a complete, customizable, free and open source computational platform enabling LC-MS-based proteomic workflows, and as such, addresses an unmet need in the LC-MS proteomics field

PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

The ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000 unique high-confidence phosphorylation sites mapping to nearly 3500 gene models and 4600 distinct phosphoproteins of the Drosophila melanogaster Kc167 cell line. This constitutes the most comprehensive phosphorylation map of any single source to date. To enhance the utility of PhosphoPep, we also provide an array of software tools that allow users to browse through phosphorylation sites on single proteins or pathways, to easily integrate the data with other, external data types such as protein–protein interactions and to search the database via spectral matching. Finally, all data can be readily exported, for example, for targeted proteomics approaches and the data thus generated can be again validated using PhosphoPep, supporting iterative cycles of experimentation and analysis that are typical for systems biology research

Singularities In Scalar-Tensor Cosmologies

In this article, we examine the possibility that there exist special scalar-tensor theories of gravity with completely nonsingular FRW solutions. Our investigation in fact shows that while most probes living in such a Universe never see the singularity, gravity waves always do. This is because they couple to both the metric and the scalar field, in a way which effectively forces them to move along null geodesics of the Einstein conformal frame. Since the metric of the Einstein conformal frame is always singular for configurations where matter satisfies the energy conditions, the gravity wave world lines are past inextendable beyond the Einstein frame singularity, and hence the geometry is still incomplete, and thus singular. We conclude that the singularity cannot be entirely removed, but only be made invisible to most, but not all, probes in the theory.Comment: 23 pages, latex, no figure

The Worldvolume Action of Kink Solitons in AdS Spacetime

A formalism is presented for computing the higher-order corrections to the worldvolume action of co-dimension one solitons. By modifying its potential, an explicit "kink" solution of a real scalar field in AdS spacetime is found. The formalism is then applied to explicitly compute the kink worldvolume action to quadratic order in two expansion parameters--associated with the hypersurface fluctuation length and the radius of AdS spacetime respectively. Two alternative methods are given for doing this. The results are expressed in terms of the trace of the extrinsic curvature and the intrinsic scalar curvature. In addition to conformal Galileon interactions, we find a non-Galileon term which is never sub-dominant. This method can be extended to any conformally flat bulk spacetime.Comment: 32 pages, 3 figures, typos corrected and additional comments adde

The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency

Supergravity Brane Cosmologies

Solitonic brane cosmologies are found where the world-volume is curved due to the evolution of the dilaton field on the brane. In many cases, these may be related to the solitonic Dp- and M5-branes of string and M-theory. An eleven-dimensional interpretation of the D8-brane cosmology of the massive type IIA theory is discussed in terms of compactification on a torus bundle. Braneworlds are also found in Horava-Witten theory compactified on a Calabi-Yau three-fold. The possibility of dilaton-driven inflation on the brane is discussed.Comment: 7 pages, In press, Physical Review

DNA methylation-based classification of central nervous system tumours.

Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology