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

On Irrelevance and Algorithmic Equality in Predicative Type Theory

Dependently typed programs contain an excessive amount of static terms which are necessary to please the type checker but irrelevant for computation. To separate static and dynamic code, several static analyses and type systems have been put forward. We consider Pfenning's type theory with irrelevant quantification which is compatible with a type-based notion of equality that respects eta-laws. We extend Pfenning's theory to universes and large eliminations and develop its meta-theory. Subject reduction, normalization and consistency are obtained by a Kripke model over the typed equality judgement. Finally, a type-directed equality algorithm is described whose completeness is proven by a second Kripke model.Comment: 36 pages, superseds the FoSSaCS 2011 paper of the first author, titled "Irrelevance in Type Theory with a Heterogeneous Equality Judgement

Serpentinization as a reactive transport process: The brucite silicification reaction

Serpentinization plays a fundamental role in the biogeochemical and tectonic evolution of the Earth and perhaps many other rocky planetary bodies. Yet, geochemical models still fail to produce accurate predictions of the various modes of serpentinization, which limits our ability to predict a variety of related geological phenomena over many spatial and temporal scales. Here, we utilize kinetic and reactive transport experiments to parameterize the brucite silicification reaction and provide fundamental constraints on SiO2 transport during serpentinization. We show that, at temperatures characteristic of the sub-seafloor at the serpentinite-hosted Lost City Hydrothermal Field (150°C), the assembly of Si tetrahedra onto MgOH2 (i.e., brucite) surfaces is a rate-limiting elementary reaction in the production of serpentine and/or talc from olivine. Moreover, this reaction is exponentially dependent on the activity of aqueous silica [see manuscript], such that it can be calculated according to the rate law: [see manuscript]. Calculations performed with this rate law demonstrate that both brucite and Si are surprisingly persistent in serpentinizing environments, leading to elevated Si concentrations in fluids that can be transported over comparatively large distances without equilibrating with brucite. Moreover, applying this rate law to an open-system reactive transport experiment indicates that advection, preferential flow pathways, and reactive surface area armoring can diminish the net rate of Si uptake resulting from this reaction even further. Because brucite silicification is a fundamentally rate-limiting elementary reaction for the production of both serpentine and talc from forsterite, our new constraints are applicable across the many environments where serpentinization occurs. The unexpected but highly consequential behavior of this simple reaction emphasizes the need for considering serpentinization and many other hydrothermal processes in a reactive transport framework whereby fluid, solute, and heat transport are intimately coupled to kinetically-controlled reactions

Molecular and cellular mechanisms underlying the evolution of form and function in the amniote jaw.

The amniote jaw complex is a remarkable amalgamation of derivatives from distinct embryonic cell lineages. During development, the cells in these lineages experience concerted movements, migrations, and signaling interactions that take them from their initial origins to their final destinations and imbue their derivatives with aspects of form including their axial orientation, anatomical identity, size, and shape. Perturbations along the way can produce defects and disease, but also generate the variation necessary for jaw evolution and adaptation. We focus on molecular and cellular mechanisms that regulate form in the amniote jaw complex, and that enable structural and functional integration. Special emphasis is placed on the role of cranial neural crest mesenchyme (NCM) during the species-specific patterning of bone, cartilage, tendon, muscle, and other jaw tissues. We also address the effects of biomechanical forces during jaw development and discuss ways in which certain molecular and cellular responses add adaptive and evolutionary plasticity to jaw morphology. Overall, we highlight how variation in molecular and cellular programs can promote the phenomenal diversity and functional morphology achieved during amniote jaw evolution or lead to the range of jaw defects and disease that affect the human condition

Permeability, porosity, and mineral surface area changes in basalt cores induced by reactive transport of CO2-rich brine

Four reactive flow-through laboratory experiments (two each at 0.1 ml/min and 0.01 ml/min flow rates) at 150°C and 150 bar (15 MPa) are conducted on intact basalt cores to assess changes in porosity, permeability, and surface area caused by CO2-rich fluid-rock interaction. Permeability decreases slightly during the lower flow rate experiments and increases during the higher flow rate experiments. At the higher flow rate, core permeability increases by more than one order of magnitude in one experiment and less than a factor of two in the other due to differences in preexisting flow path structure. X-ray computed tomography (XRCT) scans of pre- and post-experiment cores identify both mineral dissolution and secondary mineralization, with a net decrease in XRCT porosity of ∼0.7% – 0.8% for all four cores. (Ultra) small-angle neutron scattering ((U)SANS) datasets indicate an increase in both (U)SANS porosity and specific surface area (SSA) over the ∼ 1 nm- to 10 µm-scale range in post-experiment basalt samples, with differences due to flow rate and reaction time. Net porosity increases from summing XRCT and (U)SANS analyses are consistent with core mass decreases. (U)SANS data suggest an overall preservation of the pore structure with no change in mineral surface roughness from reaction, and the pore structure is unique in comparison to previously published basalt analyses. Together, these datasets illustrate changes in physical parameters that arise due to fluid-basalt interaction in relatively low pH environments with elevated CO2 concentration, with significant implications for flow, transport, and reaction through geologic formations

Severe malaria in children leads to a significant impairment of transitory otoacoustic emissions--a prospective multicenter cohort study.

BACKGROUND: Severe malaria may influence inner ear function, although this possibility has not been examined prospectively. In a retrospective analysis, hearing impairment was found in 9 of 23 patients with cerebral malaria. An objective method to quickly evaluate the function of the inner ear are the otoacoustic emissions. Negative transient otoacoustic emissions are associated with a threshold shift of 20 dB and above. METHODS: This prospective multicenter study analyses otoacoustic emissions in patients with severe malaria up to the age of 10 years. In three study sites (Ghana, Gabon, Kenya) 144 patients with severe malaria and 108 control children were included. All malaria patients were treated with parental artesunate. RESULTS: In the control group, 92.6 % (n = 108, 95 % confidence interval 86.19-6.2 %) passed otoacoustic emission screening. In malaria patients, 58.5 % (n = 94, malaria vs controls p < 0.001, 95 % confidence interval 48.4-67.9 %) passed otoacoustic emission screening at the baseline measurement. The value increased to 65.2 % (n = 66, p < 0.001, 95 % confidence interval 53.1-75.5 %) at follow up 14-28 days after diagnosis of malaria. The study population was divided into severe non-cerebral malaria and severe malaria with neurological symptoms (cerebral malaria). Whereas otoacoustic emissions in severe malaria improved to a passing percentage of 72.9 % (n = 48, 95 % confidence interval 59-83.4 %) at follow-up, the patients with cerebral malaria showed a drop in the passing percentage to 33 % (n = 18) 3-7 days after diagnosis. This shows a significant impairment in the cerebral malaria group (p = 0.012 at days 3-7, 95 % confidence interval 16.3-56.3 %; p = 0.031 at day 14-28, 95 % confidence interval 24.5-66.3 %). CONCLUSION: The presented data show that 40 % of children have involvement of the inner ear early in severe malaria. In children, audiological screening after severe malaria infection is not currently recommended, but is worth investigating in larger studies

Systemic AAV vectors for widespread and targeted gene delivery in rodents

We recently developed adeno-associated virus (AAV) capsids to facilitate efficient and noninvasive gene transfer to the central and peripheral nervous systems. However, a detailed protocol for generating and systemically delivering novel AAV variants was not previously available. In this protocol, we describe how to produce and intravenously administer AAVs to adult mice to specifically label and/or genetically manipulate cells in the nervous system and organs, including the heart. The procedure comprises three separate stages: AAV production, intravenous delivery, and evaluation of transgene expression. The protocol spans 8 d, excluding the time required to assess gene expression, and can be readily adopted by researchers with basic molecular biology, cell culture, and animal work experience. We provide guidelines for experimental design and choice of the capsid, cargo, and viral dose appropriate for the experimental aims. The procedures outlined here are adaptable to diverse biomedical applications, from anatomical and functional mapping to gene expression, silencing, and editing

Ordering theories: typologies and conceptual frameworks for sociotechnical change

What theories or concepts are most useful at explaining socio technical change? How can – or cannot – these be integrated? To provide an answer, this study presents the results from 35 semi-structured research interviews with social science experts who also shared more than two hundred articles, reports and books on the topic of the acceptance, adoption, use, or diffusion of technology. This material led to the identification of 96 theories and conceptual approaches spanning 22 identified disciplines. The article begins by explaining its research terms and methods before honing in on a combination of fourteen theories deemed most relevant and useful by the material. These are: Sociotechnical Transitions, Social Practice Theory, Discourse Theory, Domestication Theory, Large Technical Systems, Social Construction of Technology, Sociotechnical Imaginaries, Actor-Network Theory, Social Justice Theory, Sociology of Expectations, Sustainable Development, Values Beliefs Norms Theory, Lifestyle Theory, and the Unified Theory of Acceptance and Use of Technology. It then positions these theories in terms of two distinct typologies. Theories can be placed into five general categories of being centered on agency, structure, meaning, relations or norms. They can also be classified based on their assumptions and goals rooted in functionalism, interpretivism, humanism or conflict. The article lays out tips for research methodology before concluding with insights about technology itself, analytical processes associated with technology, and the framing and communication of results. An interdisciplinary theoretical and conceptual inventory has much to offer students, analysts and scholars wanting to study technological change and society

Combined Tevatron upper limit on gg->H->W+W- and constraints on the Higgs boson mass in fourth-generation fermion models

Report number: FERMILAB-PUB-10-125-EWe combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg->H->W+W- in p=pbar collisions at the Fermilab Tevatron Collider at sqrt{s}=1.96 TeV. With 4.8 fb-1 of integrated luminosity analyzed at CDF and 5.4 fb-1 at D0, the 95% Confidence Level upper limit on \sigma(gg->H) x B(H->W+W-) is 1.75 pb at m_H=120 GeV, 0.38 pb at m_H=165 GeV, and 0.83 pb at m_H=200 GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% Confidence Level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.We combine results from searches by the CDF and D0 collaborations for a standard model Higgs boson (H) in the process gg→H→W+W- in pp̅ collisions at the Fermilab Tevatron Collider at √s=1.96  TeV. With 4.8  fb-1 of integrated luminosity analyzed at CDF and 5.4  fb-1 at D0, the 95% confidence level upper limit on σ(gg→H)×B(H→W+W-) is 1.75 pb at mH=120  GeV, 0.38 pb at mH=165  GeV, and 0.83 pb at mH=200  GeV. Assuming the presence of a fourth sequential generation of fermions with large masses, we exclude at the 95% confidence level a standard-model-like Higgs boson with a mass between 131 and 204 GeV.Peer reviewe

Initial experience with off-pump left ventricular assist device implantation in single center: retrospective analysis

<p>Abstract</p> <p>Background</p> <p>We hypothesize that implantation of left ventricular assist device through off-pump technique is feasible and has a comparable result to implantation on cardiopulmonary bypass and could improve one-year survival.</p> <p>Methods</p> <p>This retrospective, observational, single-center study was conducted on 29 consecutive patients at our institution who underwent off-pump left ventricular assist device implantation by a single surgeon.</p> <p>Results</p> <p>Twenty-seven procedures were performed successfully using the off-pump technique. The survival rate was 92% at 30 days, 76% at 90 days, and 67% at one year. We compared the one-year survival of different implantation periods, and divided our study into three time intervals (2004-2005, 2006, and 2007). There was a trend in reduction in number of deaths over one year that demonstrated a decrease in death rate from 50% to 17%, as well as improvement in our experience over time. However, this trend is not statistically significant (p = 0.08) due to limited sample size.</p> <p>Conclusions</p> <p>Based upon our findings, off-pump left ventricular assist device implantation is a feasible surgical technique, and combining this technique with improved device technology in the future may provide even greater improvement in patient outcomes.</p