Time-resolved spectroscopy of macromolecules: Effect of helical structure on the torsional dynamics of DNA and RNA

The torsional rigidity of DNA and RNA is measured via the fluorescence depolarization technique

Study of volatile contaminants in reclaimed water

Different methods were evaluated for reducing the volatile contaminants found in water recovered from urine by distillation. The use of activated carbon, addition of potassium permanganate, and the use of oxidation catalyst are described along with laboratory tests. It is concluded that catalytic decomposition appears to be feasible, and further investigation is recommended

Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Subnanosecond time‐resolved fluorescence depolarization has been used to monitor the reorientation of ethidium bromide intercalated in native DNA, synthetic polynucleotide complexes, and in supercoiled plasmid DNA. The fluorescence polarization anisotropy was successfully analyzed with an elastic model of DNA dynamics, including both torsion and bending, which yielded an accurate value for the torsional rigidity of the different DNA samples. The dependence of the torsional rigidity on the base sequence, helical structure, and tertiary structure was experimentally observed. The magnitude of the polyelectrolyte contribution to the torsional rigidity of DNA was measured over a wide range of ionic strength, and compared with polyelectrolyte theories for the persistence length. We also observed a rapid initial reorientation of the intercalated ethidium which had a much smaller amplitude in RNA than in DNA

A Study of Optical Observing Techniques for Extra-Galactic Supernova Remnants: Case of NGC 300

We present the results of a study of observational and identification techniques used for surveys and spectroscopy of candidate supernova remnants (SNRs) in the Sculptor Group galaxy NGC 300. The goal of this study was to investigate the reliability of using [Sii]/Halpha > 0.4 in optical SNR surveys and spectra as an identifying feature of extra-galactic SNRs (egSNRs) and also to investigate the effectiveness of the observing techniques (which are hampered by seeing conditions and telescope pointing errors) using this criterion in egSNR surveys and spectrographs. This study is based on original observations of these objects and archival data obtained from the Hubble Space Telescope which contained images of some of the candidate SNRs in NGC 300. We found that the reliability of spectral techniques may be questionable and very high-resolution images may be needed to confirm a valid identification of some egSNRs.Comment: 27 Figures, 10 table

Factor VIIa administration in traumatic brain injury: an AAST-MITC propensity score analysis.

Background:Recombinant factor VIIa (rFVIIa) has been used off-label as an adjunct in the reversal of warfarin therapy and management of hemorrhage after trauma. Only a handful of these reports are rigorous studies, from which results regarding safety and effectiveness have been mixed. There remains no clear consensus as to the role of rFVIIa in traumatic brain injury (TBI). Methods:Eleven level 1 trauma centers provided clinical data and head CT scans of patients with a Glasgow Coma Scale (GCS) score of ≤13 and radiographic evidence of TBI. A propensity score (PS) to receive rFVIIa in those surviving ≥2 days was calculated for each patient based on patient demographics, comorbidities, physiology, Injury Severity Score, admission GCS score, and treatment center. Patients receiving rFVIIa within 24 hours of admission were matched to patients who did not receive rFVIIa for outcomes assessment. Subgroup analysis evaluated patients with primary head injury with PS matching. Results:There were 4284 patient observations; 129 received rFVIIa. Groups were comparable after matching. No differences in mortality or morbidity were found. Improvement in GCS score from admission to discharge was less among those receiving rFVIIa (5.5 vs. 2.4; P value 0.001); however, there was no difference in average GCS score at discharge. No significant differences in outcomes were identified in patients with isolated TBI receiving rFVIIa. Discussion:rFVIIa in early management of TBI is not associated with a decreased risk of mortality or morbidity, and may negatively impact recovery and functional status at discharge in the severely injured patient with polytrauma. Level of evidence:Level III. Study type:Therapeutic/care management

Parameter inference in mechanistic models of cellular regulation and signalling pathways using gradient matching

A challenging problem in systems biology is parameter inference in mechanistic models of signalling pathways. In the present article, we investigate an approach based on gradient matching and nonparametric Bayesian modelling with Gaussian processes. We evaluate the method on two biological systems, related to the regulation of PIF4/5 in Arabidopsis thaliana, and the JAK/STAT signal transduction pathway

Towards a grid-enabled simulation framework for nano-CMOS electronics

The electronics design industry is facing major challenges as transistors continue to decrease in size. The next generation of devices will be so small that the position of individual atoms will affect their behaviour. This will cause the transistors on a chip to have highly variable characteristics, which in turn will impact circuit and system design tools. The EPSRC project "Meeting the Design Challenges of Nano-CMOS Electronics" (Nana-CMOS) has been funded to explore this area. In this paper, we describe the distributed data-management and computing framework under development within Nano-CMOS. A key aspect of this framework is the need for robust and reliable security mechanisms that support distributed electronics design groups who wish to collaborate by sharing designs, simulations, workflows, datasets and computation resources. This paper presents the system design, and an early prototype of the project which has been useful in helping us to understand the benefits of such a grid infrastructure. In particular, we also present two typical use cases: user authentication, and execution of large-scale device simulations

The envirome and the connectome: exploring the structural noise in the human brain associated with socioeconomic deprivation

Complex cognitive functions are widely recognized to be the result of a number of brain regions working together as large-scale networks. Recently, complex network analysis has been used to characterize various structural properties of the large scale network organization of the brain. For example, the human brain has been found to have a modular architecture i.e. regions within the network form communities (modules) with more connections between regions within the community compared to regions outside it. The aim of this study was to examine the modular and overlapping modular architecture of the brain networks using complex network analysis. We also examined the association between neighborhood level deprivation and brain network structure – modularity and grey nodes. We compared network structure derived from anatomical MRI scans of 42 middle-aged neurologically healthy men from the least (LD) and the most deprived (MD) neighborhoods of Glasgow with their corresponding random networks. Cortical morphological covariance networks were constructed from the cortical thickness derived from the MRI scans of the brain. For a given modularity threshold, networks derived from the MD group showed similar number of modules compared to their corresponding random networks, while networks derived from the LD group had more modules compared to their corresponding random networks. The MD group also had fewer grey nodes – a measure of overlapping modular structure. These results suggest that apparent structural difference in brain networks may be driven by differences in cortical thicknesses between groups. This demonstrates a structural organization that is consistent with a system that is less robust and less efficient in information processing. These findings provide some evidence of the relationship between socioeconomic deprivation and brain network topology

Supporting security-oriented, collaborative nanoCMOS electronics research

Grid technologies support collaborative e-Research typified by multiple institutions and resources seamlessly shared to tackle common research problems. The rules for collaboration and resource sharing are commonly achieved through establishment and management of virtual organizations (VOs) where policies on access and usage of resources by collaborators are defined and enforced by sites involved in the collaboration. The expression and enforcement of these rules is made through access control systems where roles/privileges are defined and associated with individuals as digitally signed attribute certificates which collaborating sites then use to authorize access to resources. Key to this approach is that the roles are assigned to the right individuals in the VO; the attribute certificates are only presented to the appropriate resources in the VO; it is transparent to the end user researchers, and finally that it is manageable for resource providers and administrators in the collaboration. In this paper, we present a security model and implementation improving the overall usability and security of resources used in Grid-based e-Research collaborations through exploitation of the Internet2 Shibboleth technology. This is explored in the context of a major new security focused project at the National e-Science Centre (NeSC) at the University of Glasgow in the nanoCMOS electronics domain