Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays

Background Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2% of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log2 units ( 6% of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells

Spectral quantification of nonlinear behaviour of the nearshore seabed and correlations with potential forcings at Duck, N.C., U.S.A

Local bathymetric quasi-periodic patterns of oscillation are identified from monthly profile surveys taken at two shore-perpendicular transects at the USACE field research facility in Duck, North Carolina, USA, spanning 24.5 years and covering the swash and surf zones. The chosen transects are the two furthest (north and south) from the pier located at the study site. Research at Duck has traditionally focused on one or more of these transects as the effects of the pier are least at these locations. The patterns are identified using singular spectrum analysis (SSA). Possible correlations with potential forcing mechanisms are discussed by 1) doing an SSA with same parameter settings to independently identify the quasi-periodic cycles embedded within three potentially linked sequences: monthly wave heights (MWH), monthly mean water levels (MWL) and the large scale atmospheric index known as the North Atlantic Oscillation (NAO) and 2) comparing the patterns within MWH, MWL and NAO to the local bathymetric patterns. The results agree well with previous patterns identified using wavelets and confirm the highly nonstationary behaviour of beach levels at Duck; the discussion of potential correlations with hydrodynamic and atmospheric phenomena is a new contribution. The study is then extended to all measured bathymetric profiles, covering an area of 1100m (alongshore) by 440m (cross-shore), to 1) analyse linear correlations between the bathymetry and the potential forcings using multivariate empirical orthogonal functions (MEOF) and linear correlation analysis and 2) identify which collective quasi-periodic bathymetric patterns are correlated with those within MWH, MWL or NAO, based on a (nonlinear) multichannel singular spectrum analysis (MSSA). (...continued in submitted paper)Comment: 50 pages, 3 tables, 8 figure

Applying human factors methods to explore ‘Work as Imagined’ and ‘Work as Done’ in the Emergency Department’s response to chemical, biological, radiological, and nuclear events

The Emergency Department (ED) is a complex, hectic, and high-pressured environment. Chemical, Biological, Radiological, and Nuclear (CBRN) events are multi-faceted emergencies and present numerous challenges to ED staff (first receivers) with large scale trauma, consequently requiring a combination of complex responses. Human Factors and Ergonomics (HF/E) methods such as Hierarchical Task Analysis (HTA) have been used in healthcare research. However, HF/E methods and theory have not been combined to understand how the ED responds to CBRN events. This study aimed to compare Work as Imagined (WAI) and Work as Done (WAD) in the ED CBRN response in a UK based hospital. WAI was established by carrying out document analyses on a CBRN plan and WAD by exploring first receivers response to CBRN scenario cards. The responses were converted to HTAs and compared. The WAI HTAs showed 4-8 phases of general organizational responsibilities during a CBRN event. WAD HTAs placed emphasis on diagnosing and treating presenting conditions. A comparison of WAI and WAD HTAs highlighted common actions and tasks. This study has identified three key differences between WAI and WAD in the ED CBRN response: 1) documentation of the CBRN event 2) treating the patient and 3) diagnosing the presenting complaint. Findings from this study provide an evidence base which can be used to inform future clinical policy and practice in providing safe and high quality care during CBRN events in the ED

First Evidence for Adoption in California Sea Lions

Demographic parameters such as birth and death rates determine the persistence of populations. Understanding the mechanisms that influence these rates is essential to developing effective management strategies. Alloparental behavior, or the care of non-filial young, has been documented in many species and has been shown to influence offspring survival. However, the role of alloparental behavior in maintaining population viability has not been previously studied. Here, we provide the first evidence for adoption in California sea lions and show that adoption potentially works to maintain a high survival rate of young and may ultimately contribute to population persistence. Alloparental behavior should have a positive effect on the population growth rate when the sum of the effects on fitness for the alloparent and beneficiary is positive

Photonic quantum technologies

The first quantum technology, which harnesses uniquely quantum mechanical effects for its core operation, has arrived in the form of commercially available quantum key distribution systems that achieve enhanced security by encoding information in photons such that information gained by an eavesdropper can be detected. Anticipated future quantum technologies include large-scale secure networks, enhanced measurement and lithography, and quantum information processors, promising exponentially greater computation power for particular tasks. Photonics is destined for a central role in such technologies owing to the need for high-speed transmission and the outstanding low-noise properties of photons. These technologies may use single photons or quantum states of bright laser beams, or both, and will undoubtably apply and drive state-of-the-art developments in photonics

Some Aspects of Multifractal analysis

The aim of this survey is to present some aspects of multifractal analysis around the recently developed subject of multiple ergodic averages. Related topics include dimensions of measures, oriented walks, Riesz products etc

Factors affecting the disclosure of diabetes by ethnic minority patients: a qualitative study among Surinamese in the Netherlands

<p>Abstract</p> <p>Background</p> <p>Diabetes and related complications are common among ethnic minority groups. Community-based social support interventions are considered promising for improving diabetes self-management. To access such interventions, patients need to disclose their diabetes to others. Research on the disclosure of diabetes in ethnic minority groups is limited. The aim of our study was to explore why diabetes patients from ethnic minority populations either share or do not share their condition with people in their wider social networks.</p> <p>Methods</p> <p>We conducted a qualitative study using semi-structured interviews with 32 Surinamese patients who were being treated for type 2 diabetes by general practitioners in Amsterdam, the Netherlands.</p> <p>Results</p> <p>Most patients disclosed their diabetes only to very close family members. The main factor inhibiting disclosure to people outside this group was the Surinamese cultural custom that talking about disease is taboo, as it may lead to shame, gossip, and social disgrace for the patient and their family. Nevertheless, some patients disclosed their diabetes to people outside their close family circles. Factors motivating this decision were mostly related to a need for facilities or support for diabetes self-management.</p> <p>Conclusions</p> <p>Cultural customs inhibited Surinamese patients in disclosing their diabetes to people outside their very close family circles. This may influence their readiness to participate in community-based diabetes self-management programmes that involve other groups. What these findings highlight is that public health researchers and initiatives must identify and work with factors that influence the disclosure of diabetes if they are to develop community-based diabetes self-management interventions for ethnic minority populations.</p

Structural and Mutational Analysis of Functional Differentiation between Synaptotagmins-1 and -7

Synaptotagmins are known to mediate diverse forms of Ca2+-triggered exocytosis through their C2 domains, but the principles underlying functional differentiation among them are unclear. Synaptotagmin-1 functions as a Ca2+ sensor in neurotransmitter release at central nervous system synapses, but synaptotagmin-7 does not, and yet both isoforms act as Ca2+ sensors in chromaffin cells. To shed light into this apparent paradox, we have performed rescue experiments in neurons from synaptotagmin-1 knockout mice using a chimera that contains the synaptotagmin-1 sequence with its C2B domain replaced by the synaptotagmin-7 C2B domain (Syt1/7). Rescue was not achieved either with the WT Syt1/7 chimera or with nine mutants where residues that are distinct in synaptotagmin-7 were restored to those present in synaptotagmin-1. To investigate whether these results arise because of unique conformational features of the synaptotagmin-7 C2B domain, we determined its crystal structure at 1.44 Å resolution. The synaptotagmin-7 C2B domain structure is very similar to that of the synaptotagmin-1 C2B domain and contains three Ca2+-binding sites. Two of the Ca2+-binding sites of the synaptotagmin-7 C2B domain are also present in the synaptotagmin-1 C2B domain and have analogous ligands to those determined for the latter by NMR spectroscopy, suggesting that a discrepancy observed in a crystal structure of the synaptotagmin-1 C2B domain arose from crystal contacts. Overall, our results suggest that functional differentiation in synaptotagmins arises in part from subtle sequence changes that yield dramatic functional differences