A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

<p>Abstract</p> <p>Background</p> <p>The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters.</p> <p>Methods</p> <p>In this work, we propose <it>e</it>-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters.</p> <p>Results</p> <p>We present results in real data showing the effectiveness of <it>e</it>-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in <it>Saccharomyces cerevisiae </it>in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series.</p> <p>Discussion</p> <p>The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to efficiently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms.</p> <p>Availability</p> <p>A prototype implementation of the algorithm coded in Java together with the dataset and examples used in the paper is available in <url>http://kdbio.inesc-id.pt/software/e-ccc-biclustering</url>.</p

Adoption of cloud computing as innovation in the organization

Over the years, there has been a heavy reliance on cloud computing as IT has innovated through time. In recent times cloud computing has grown monumentally. Many organizations rely on this technology to perform their business as usual and use it as a backbone of their companies' IT infrastructure. This paper investigates the organizational adaptation for cloud computing technology - reviewing case studies from various institutions and companies worldwide to provide a detailed analysis of innovative techniques with cloud computing. We investigate the features and delivery approaches cloud computing offers and the potential challenges and constraints we face when adopting cloud computing into the business setting. We also explore the cybersecurity elements associated with cloud computing, focusing on intrusion detection and prevention and understanding how that can be applied in the cloud. Finally, we investigate the future research directions for cloud computing and expand this paper into further articles with experiments and results

DNA replication stress restricts ribosomal DNA copy number

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number

Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms

<p>Abstract</p> <p>Background</p> <p>Biclustering is an important analysis procedure to understand the biological mechanisms from microarray gene expression data. Several algorithms have been proposed to identify biclusters, but very little effort was made to compare the performance of different algorithms on real datasets and combine the resultant biclusters into one unified ranking.</p> <p>Results</p> <p>In this paper we propose differential co-expression framework and a differential co-expression scoring function to objectively quantify quality or goodness of a bicluster of genes based on the observation that genes in a bicluster are co-expressed in the conditions belonged to the bicluster and not co-expressed in the other conditions. Furthermore, we propose a scoring function to stratify biclusters into three types of co-expression. We used the proposed scoring functions to understand the performance and behavior of the four well established biclustering algorithms on six real datasets from different domains by combining their output into one unified ranking.</p> <p>Conclusions</p> <p>Differential co-expression framework is useful to provide quantitative and objective assessment of the goodness of biclusters of co-expressed genes and performance of biclustering algorithms in identifying co-expression biclusters. It also helps to combine the biclusters output by different algorithms into one unified ranking i.e. meta-biclustering.</p

Evidence for the existence of powder sub-populations in micronized materials : Aerodynamic size-fractions of aerosolized powders possess distinct physicochemical properties

This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.Purpose: To investigate the agglomeration behaviour of the fine ( 12.8 µm) particle fractions of salmeterol xinafoate (SX) and fluticasone propionate (FP) by isolating aerodynamic size fractions and characterising their physicochemical and re-dispersal properties. Methods: Aerodynamic fractionation was conducted using the Next Generation Impactor (NGI). Re-crystallized control particles, unfractionated and fractionated materials were characterized for particle size, morphology, crystallinity and surface energy. Re-dispersal of the particles was assessed using dry dispersion laser diffraction and NGI analysis. Results: Aerosolized SX and FP particles deposited in the NGI as agglomerates of consistent particle/agglomerate morphology. SX particles depositing on Stages 3 and 5 had higher total surface energy than unfractionated SX, with Stage 5 particles showing the greatest surface energy heterogeneity. FP fractions had comparable surface energy distributions and bulk crystallinity but differences in surface chemistry. SX fractions demonstrated higher bulk disorder than unfractionated and re-crystallized particles. Upon aerosolization, the fractions differed in their intrinsic emission and dispersion into a fine particle fraction (< 5.0 µm). Conclusions: Micronized powders consisted of sub-populations of particles displaying distinct physicochemical and powder dispersal properties compared to the unfractionated bulk material. This may have implications for the efficiency of inhaled drug deliveryPeer reviewe

Neuroprotective Effect of Transplanted Human Embryonic Stem Cell-Derived Neural Precursors in an Animal Model of Multiple Sclerosis

BACKGROUND: Multiple sclerosis (MS) is an immune mediated demyelinating disease of the central nervous system (CNS). A potential new therapeutic approach for MS is cell transplantation which may promote remyelination and suppress the inflammatory process. METHODS: We transplanted human embryonic stem cells (hESC)-derived early multipotent neural precursors (NPs) into the brain ventricles of mice induced with experimental autoimmune encephalomyelitis (EAE), the animal model of MS. We studied the effect of the transplanted NPs on the functional and pathological manifestations of the disease. RESULTS: Transplanted hESC-derived NPs significantly reduced the clinical signs of EAE. Histological examination showed migration of the transplanted NPs to the host white matter, however, differentiation to mature oligodendrocytes and remyelination were negligible. Time course analysis of the evolution and progression of CNS inflammation and tissue injury showed an attenuation of the inflammatory process in transplanted animals, which was correlated with the reduction of both axonal damage and demyelination. Co-culture experiments showed that hESC-derived NPs inhibited the activation and proliferation of lymph node-derived T cells in response to nonspecific polyclonal stimuli. CONCLUSIONS: The therapeutic effect of transplantation was not related to graft or host remyelination but was mediated by an immunosuppressive neuroprotective mechanism. The attenuation of EAE by hESC-derived NPs, demonstrated here, may serve as the first step towards further developments of hESC for cell therapy in MS

Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis

Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of “barcoded" DNA-tag reporters, “Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics

You Name It – How Memory and Delay Govern First Name Dynamics

The adoption and abandonment of first names through time is a fascinating phenomenon that may shed light on social dynamics and the forces that determine cultural taste in general. Here we show that baby name dynamics is governed almost solely by deterministic forces, even though the emerging abundance statistics resembles the one obtained from a pure drift model. Exogenous events are shown to affect the name dynamics very rarely, and most of the year-to-year fluctuations around the deterministic trend may be attributed solely to demographic noise. We suggest that the rise and fall of a name reflect an “infection” process with delay and memory. The symmetry between adoption and abandonment speed emerges from our model without further assumptions

‘Working with the media taught us a lot’: Understanding The Guardian’s Katine initiative

One of the more important ventures in the world of media and development over the past decade has been The Guardian newspaper’s ‘Katine’ project in Uganda. The newspaper, with funding from its readers and Barclays Bank, put more than 2.5 million pounds into a Ugandan sub-county over the course of 4 years. The project was profiled on a dedicated Guardian microsite, with regular updates in the printed edition of the newspaper. In this article, I look at the relationship that developed between journalists and the non-governmental organisation and show that the experience was both disorienting and reorienting for the development project that was being implemented. The scrutiny of the project that appeared on the microsite disoriented the non-governmental organisation, making its work the subject of public criticism. The particular issues explored by journalists also reoriented what the non-governmental organisation did on the ground. I also point to the ways the relationship grew more settled as the project moved along, suggesting the amount of work that sometimes goes into what is often characterised as the relatively uncritical relationship between journalists and non-governmental organisations