cudaMap: a GPU accelerated program for gene expression connectivity mapping

Background: Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take >2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping.

Results: cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance.

Conclusion: Emerging 'omics' technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap.

Lighting Strike Protection Systems

refers to composites that are specifically made/modified to provide more than one functionality. Typically, composites' main functionality is structural

Human dental pulp fibroblasts express the "cold-sensing" transient receptor potential channels TRPA1 and TRPM8.

Abstract
INTRODUCTION:
Transient receptor potential (TRP) channels comprise a group of nonselective calcium-permeable cationic channels, which are polymodal sensors of environmental stimuli such as thermal changes and chemicals. TRPM8 and TRPA1 are cold-sensing TRP channels activated by moderate cooling and noxious cold temperatures, respectively. Both receptors have been identified in trigeminal ganglion neurones, and their expression in nonneuronal cells is now the focus of much interest. The aim of this study was to investigate the molecular and functional expression of TRPA1 and TRPM8 in dental pulp fibroblasts.
METHODS:
Human dental pulp fibroblasts were derived from healthy molar teeth. Gene and protein expression was determined by polymerase chain reaction and Western blotting. Cellular localization was investigated by immunohistochemistry, and TRP functionality was determined by Ca(2+) microfluorimetry.
RESULTS:
Polymerase chain reaction and Western blotting showed gene and protein expression of both TRPA1 and TRPM8 in fibroblast cells in culture. Immunohistochemistry studies showed that TRPA1 and TRPM8 immunoreactivity co-localized with the human fibroblast surface protein. In Ca(2+) microfluorimetry studies designed to determine the functionality of TRPA1 and TRPM8 in pulp fibroblasts, we showed increased intracellular calcium ([Ca(2+)](i)) in response to the TRPM8 agonist menthol, the TRPA1 agonist cinnamaldehyde, and to cool and noxious cold stimuli, respectively. The responses to agonists and thermal stimuli were blocked in the presence of specific TRPA1 and TRPM8 antagonists.
CONCLUSIONS:
Human dental pulp fibroblasts express TRPA1 and TRPM8 at the molecular, protein, and functional levels, indicating a possible role for fibroblasts in mediating cold responses in human teeth.

Hard coatings on elastomers for reduced permeability and increased wear resistance

In this study, three different elastomers, namely hydrogenated nitrile butadiene rubber, fluoroelastomer and silicone, have been subjected to two different hard metallised coatings by ion implantation process. The three different elastomers are commonly used in various seal applications, where reduced wear and gas permeability are essential in maintaining seal performance and functionality. Samples of these rubbers have been coated with chromium coating in one set of tests. In the second set of tests, samples of elastomers have been coated with tungsten carbide coating being deposited on all the three different elastomers. Wear, gas permeability and mechanical behaviour of the coated samples were compared with each other and with the control uncoated elastomers. All the coated samples showed good reduction in gas permeability. With the use of metallised coatings, there has been improved resistance to wear in all the coated samples. Adhesion strength and effect of coating on the elastomer have been investigated by mechanical testing. Mechanical tests revealed good adhesion of metal coatings on all the rubber samples, and there was no detrimental effect on the mechanical properties after coating. © 2012 Institute of Materials, Minerals and Mining.

Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription

Antisense transcription is widespread in many genomes; however, how much is functional is hotly debated. We are investigating functionality of a set of long noncoding antisense transcripts, collectively called COOLAIR, produced at Arabidopsis FLOWERING LOCUS C (FLC). COOLAIR initiates just downstream of the major sense transcript poly(A) site and terminates either early or extends into the FLC promoter region. We now show that splicing of COOLAIR is functionally important. This was revealed through analysis of a hypomorphic mutation in the core spliceosome component PRP8. The prp8 mutation perturbs a cotranscriptional feedback mechanism linking COOLAIR processing to FLC gene body histone demethylation and reduced FLC transcription. The importance of COOLAIR splicing in this repression mechanism was confirmed by disrupting COOLAIR production and mutating the COOLAIR proximal splice acceptor site. Our findings suggest that altered splicing of a long noncoding transcript can quantitatively modulate gene expression through cotranscriptional coupling mechanisms.

Identification of a collagen type I adhesin of Bacteroides fragilis

Bacteroides fragilis is an opportunistic pathogen which can cause life threatening infections in humans and animals. The ability to adhere to components of the extracellular matrix, including collagen, is related to bacterial host colonisation. Collagen Far Western analysis of the B. fragilis outer membrane protein (OMP) fraction revealed the presence two collagen adhesin bands of ∼31 and ∼34 kDa. The collagen adhesins in the OMP fraction were separated and isolated by two-dimensional SDS-PAGE and also purified by collagen affinity chromatography. The collagen binding proteins isolated by both these independent methods were subjected to tandem mass spectroscopy for peptide identification and matched to a single hypothetical protein encoded by B. fragilis NCTC 9343 (BF0586), conserved in YCH46 (BF0662) and 638R (BF0633) and which is designated in this study as cbp1 (collagen binding protein). Functionality of the protein was confirmed by targeted insertional mutagenesis of the cbp1 gene in B. fragilis GSH18 which resulted in the specific loss of both the ∼31 kDa and the ∼34 kDa adhesin bands. Purified his-tagged Cbp1, expressed in a B. fragilis wild-type and a glycosylation deficient mutant, confirmed that the cbp1 gene encoded the observed collagen adhesin, and showed that the 34 kDa band represents a glycosylated version of the ∼31 kDa protein. Glycosylation did not appear to be required for binding collagen. This study is the first to report the presence of collagen type I adhesin proteins in B. fragilis and to functionally identify a gene encoding a collagen binding protein. © 2014 Galvão et al.

Optical and magneto-optical properties of gold core cobalt shell magnetoplasmonic nanowire arrays

In this work we present core–shell nanowire arrays of gold coated with a nanometric layer of cobalt. Despite the extremely small Co volume, these core–shell nanowires display large magneto-optical activity and plasmonic resonance determined by the geometry of the structure. Therefore, we are able to tune both the plasmonic and magneto-optical response in the visible range. Through optical and ellipsometric measurements in transmission, and applying a magnetic field to the sample, it is possible to modulate the value of the phase angle (Del {Δ}) between the S and P polarised components. It was found that the core–shell sample produced an order of magnitude larger variation in Del with changing magnetic field direction, compared with hollow cobalt tubes. The enhancement of magneto optical properties through the plasmonic nature of the gold core is complemented with the ability to induce magnetic influence over optical properties via an externally applied field. Moreover, we demonstrate for the first time the ability to use the remanent magnetisation of the Co, in conjunction with the optical properties defined by the Au, to observe remanent optical states in this uniquely designed structure. This new class of magnetoplasmonic metamaterial has great potential in a wide range of applications, from bio-sensing to data storage due to the tuneable nature of multiple resonance modes and dual functionality.

Langerhans cells promote early germinal center formation in response to Leishmania-derived cutaneous antigens

Efficient formation of early GCs depends on the close interaction between GC B cells and antigen-primed CD4+ follicular helper T cells (TFH). A tight and stable formation of TFH/B cell conjugates is required for cytokine-driven immunoglobulin class switching and somatic hypermutation of GC B cells. Recently, it has been shown that the formation of TFH/B cell conjugates is crucial for B-cell differentiation and class switch following infection with Leishmania major parasites. However, the subtype of DCs responsible for TFH-cell priming against dermal antigens is thus far unknown. Utilizing a transgenic C57BL/6 mouse model designed to trigger the ablation of Langerin+ DC subsets in vivo, we show that the functionality of TFH/B cell conjugates is disturbed after depletion of Langerhans cells (LCs): LC-depleted mice show a reduction in somatic hypermutation in B cells isolated from TFH/B cell conjugates and markedly reduced GC reactions within skin-draining lymph nodes. In conclusion, this study reveals an indispensable role for LCs in promoting GC B-cell differentiation following cutaneous infection with Leishmania major parasites. We propose that LCs are key regulators of GC formation and therefore have broader implications for the development of allergies and autoimmunity as well as for future vaccination strategies.

Flawed Premises and Unexpected Consequences: Support of Regional Languages in Europe:Support of Regional Languages in Europe

This article discusses the relationship between three language communities in Europe with variant levels of official recognition, namely Kashub, Sorb, and Silesian, and the institutions of their host states as regards their respective use, promotion, and revital-ization. Most language communities across the world campaign for recognition within a geographic/political region, or on the basis of a historic/group identity to ensure their language's use and status. The examples discussed here illustrate that language recognition and policies resulting therefrom and promoting official monolin-gualism strengthen the symbolic status of the language but contribute little to the functionality of language communities outside the area. As this article illustrates, in increasingly multilingual societies, language policies cut off its speakers from the political, economic, and social opportunities accessible through the medium of languages that lack official recognition locally. © 2014 Taylor & Francis Group, LLC.

On-off based charging strategies for EVs connected to a Low Voltage distributon network

The development of appropriate Electric Vehicle (EV) charging strategies has been identified as an effective way to accommodate an increasing number of EVs on Low Voltage (LV) distribution networks. Most research studies to date assume that future charging facilities will be capable of regulating charge rates continuously, while very few papers consider the more realistic situation of EV chargers that support only on-off charging functionality. In this work, a distributed charging algorithm applicable to on-off based charging systems is presented. Then, a modified version of the algorithm is proposed to incorporate real power system constraints. Both algorithms are compared with uncontrolled and centralized charging strategies from the perspective of both utilities and customers. © 2013 IEEE.

Web adoption by Irish credit unions: Performance implications

The purpose of this paper is to examine website adoption and its resultant effects on credit union performance in Ireland over the period 2002 to 2010. While there has been a steady increase in web adoption over the period a sizeable proportion (53%) of credit unions did not have a web-based facility in 2010. To gauge web functionality the researchers accessed all websites in 2010/2011 and it transpired that most sites were classified as informational with limited transactional options. Panel data techniques are then used to capture the dynamic nature of website diffusion and to investigate the effect of website adoption on cost and performance. The empirical analysis reveals that credit unions that have web-based functionality have a reduced spread between the loan and pay-out rate with this primarily caused by reduced loan rates. This reduced spread, although small, is found to both persist and increase over time.

A Functional Variant of Elafin With Improved Anti-inflammatory Activity for Pulmonary Inflammation

Elafin is a serine protease inhibitor produced by epithelial and immune cells with anti-inflammatory properties. Research has shown that dysregulated protease activity may elicit proteolytic cleavage of elafin, thereby impairing the innate immune function of the protein. The aim of this study was to generate variants of elafin (GG- and QQ-elafin) that exhibit increased protease resistance while retaining the biological properties of wild-type (WT) elafin. Similar to WT-elafin, GG- and QQ-elafin variants retained antiprotease activity and susceptibility to transglutaminase-mediated fibronectin cross-linking. However, in contrast to WT-elafin, GG- and QQ-elafin displayed significantly enhanced resistance to degradation when incubated with bronchoalveolar lavage fluid from patients with cystic fibrosis. Intriguingly, both variants, particularly GG-elafin, demonstrated improved lipopolysaccharide (LPS) neutralization properties in vitro. In addition, GG-elafin showed improved anti-inflammatory activity in a mouse model of LPS-induced acute lung inflammation. Inflammatory cell infiltration into the lung was reduced in lungs of mice treated with GG-elafin, predominantly neutrophilic infiltration. A reduction in MCP-1 levels in GG-elafin treated mice compared to the LPS alone treatment group was also demonstrated. GG-elafin showed increased functionality when compared to WT-elafin and may be of future therapeutic relevance in the treatment of lung diseases characterized by a protease burden.

Development tools for opportunistic pervasive computing

The goal of the POBICOS project is a platform that facilitates the development and deployment of pervasive computing applications destined for networked, cooperating objects. POBICOS object communities are heterogeneous in terms of the sensing, actuating, and computing resources contributed by each object. Moreover, it is assumed that an object community is formed without any master plan; for example, it may emerge as a by-product of acquiring everyday, POBICOS-enabled objects by a household. As a result, the target object community is, at least partially, unknown to the application programmer, and so a POBICOS application should be able to deliver its functionality on top of diverse object communities (we call this opportunistic computing). The POBICOS platform includes a middleware offering a programming model for opportunistic computing, as well as development and monitoring tools. This paper briefly describes the tools produced in the first phase of the project. Also, the stakeholders using these tools are identified, and a development process for both the middleware and applications is presented. © 2009 IEEE.

Middleware mechanisms for agent mobility in wireless sensor and actuator networks

This paper describes middleware-level support for agent mobility, targeted at hierarchically structured wireless sensor and actuator network applications. Agent mobility enables a dynamic deployment and adaptation of the application on top of the wireless network at runtime, while allowing the middleware to optimize the placement of agents, e.g., to reduce wireless network traffic, transparently to the application programmer. The paper presents the design of the mechanisms and protocols employed to instantiate agents on nodes and to move agents between nodes. It also gives an evaluation of a middleware prototype running on Imote2 nodes that communicate over ZigBee. The results show that our implementation is reasonably efficient and fast enough to support the envisioned functionality on top of a commodity multi-hop wireless technology. Our work is to a large extent platform-neutral, thus it can inform the design of other systems that adopt a hierarchical structuring of mobile components. © 2012 ICST Institute for Computer Science, Social Informatics and Telecommunications Engineering.

Long-term health-related quality of life of prostate cancer survivors varies by primary treatment. Results from the PiCTure (Prostate Cancer Treatment, your experience) study

PURPOSE: Men are living longer with prostate cancer. In a two-country study, we investigated the health-related quality of life (HRQoL) of prostate cancer survivors up to 18 years post-diagnosis.

METHODS: Postal questionnaires were administered in 2012 to 6559 prostate cancer (ICD10 C61) survivors 2-18 years post-diagnosis, identified through population-based cancer registries in Ireland. HRQoL was measured using QLQ-C30 and QLQ-PR25. HRQoL, functional and symptom scores were compared by primary treatment(s) using multiple linear regression.

RESULTS: Fifty-four percent responded (n = 3348). After controlling for socio-demographic and clinical factors, global HRQoL varied significantly by primary treatment (p < 0.001); compared to radical prostatectomy (RP), survivors who received androgen deprivation therapy alone (ADT; p < 0.001) or external beam radiotherapy (EBRT) without concurrent ADT (p = 0.001) had significantly lower global HRQoL. The global HRQoL of men who received brachytherapy (p = 0.157), EBRT with concurrent ADT (p = 0.940) or active surveillance/watchful waiting (p = 0.388) was not significantly different from men treated with RP. There were statistically and clinically significant differences in general (fatigue, pain, dyspnoea, appetite loss, constipation, diarrhoea, financial difficulties) and disease-specific symptoms (sexual, urinary, bowel, ADT) by primary treatment. Fatigue and insomnia scores were high for survivors in all treatment groups.

CONCLUSIONS: Prostate cancer survivors' long-term HRQoL varied with primary treatment.

IMPLICATIONS OF CANCER SURVIVORS: Population-based information regarding statistically and clinically significant treatment effects on long-term global HRQoL, symptom burden and functionality should be provided during treatment decision-making. Screening for symptoms and utilising interventions during long-term follow-up may improve survivors' HRQoL.