Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells.

BACKGROUND: Phenotypically identical cells demonstrate predictable, robust behaviours. However, there is uncertainty as to whether phenotypically identical cells are equally similar at the underlying transcriptional level or if cellular systems are inherently noisy. To answer this question, it is essential to distinguish between technical noise and true variation in transcript levels. A critical issue is the contribution of sampling effects, introduced by the requirement to globally amplify the single cell mRNA population, to observed measurements of relative transcript abundance. RESULTS: We used single cell microarray data to develop simple mathematical models, ran Monte Carlo simulations of the impact of technical and sampling effects on single cell expression data, and compared these with experimental microarray data generated from single embryonic neural stem cells in vivo. We show that the actual distribution of measured gene expression ratios for pairs of neural stem cells is much broader than that predicted from our sampling effect model. CONCLUSION: Our results confirm that significant differences in gene expression levels exist between phenotypically identical cells in vivo, and that these differences exceed any noise contribution from global mRNA amplification.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Volunteerism among hospitalists and non-hospitalists at academic and community medical centers in North Carolina

Volunteerism is common in the United States, though less is known about volunteerism among medical professionals. We aimed to record and compare volunteer activities among hospitalists and non-hospitalists in academic and community centers.Includes bibliographical reference

A practical scheme for quantum computation with any two-qubit entangling gate

Which gates are universal for quantum computation? Although it is well known that certain gates on two-level quantum systems (qubits), such as the controlled-not (CNOT), are universal when assisted by arbitrary one-qubit gates, it has only recently become clear precisely what class of two-qubit gates is universal in this sense. Here we present an elementary proof that any entangling two-qubit gate is universal for quantum computation, when assisted by one-qubit gates. A proof of this important result for systems of arbitrary finite dimension has been provided by J. L. and R. Brylinski [arXiv:quant-ph/0108062, 2001]; however, their proof relies upon a long argument using advanced mathematics. In contrast, our proof provides a simple constructive procedure which is close to optimal and experimentally practical [C. M. Dawson and A. Gilchrist, online implementation of the procedure described herein (2002), http://www.physics.uq.edu.au/gqc/].Comment: 3 pages, online implementation of procedure described can be found at http://www.physics.uq.edu.au/gqc

Measuring Entangled Qutrits and Their Use for Quantum Bit Commitment

We produce and holographically measure entangled qudits encoded in transverse spatial modes of single photons. With the novel use of a quantum state tomography method that only requires two-state superpositions, we achieve the most complete characterisation of entangled qutrits to date. Ideally, entangled qutrits provide better security than qubits in quantum bit-commitment: we model the sensitivity of this to mixture and show experimentally and theoretically that qutrits with even a small amount of decoherence cannot offer increased security over qubits.Comment: Paper updated to match published version; 5 pages, 4 figures, images have been included at slightly lower quality for the archiv

EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The mitochondria are involved in many basic functions in cells of vertebrates, and can be considered the power generator of the cell. Though the mitochondria have been extensively studied there appear to be only few expression studies of mitochondrial genes involving a large number of tissues and developmental stages. Here, we conduct an analysis using the PigEST resource 1 which contains expression information from 35 tissues distributed on one normalized and 97 non-normalized cDNA libraries of which 24 are from developmental stages. The mitochondrial PigEST resource contains 41,499 mitochondrial sequences. Results The mitochondrial EST (Expressed Sequence Tag) sequences were assembled into contigs which covers more than 94 percent of the porcine mitochondrial genome, with an average of 976 EST sequences per nucleotide. This data was converted into expression values for the individual genes in each cDNA library revealing differential expression between genes expressed in cDNA libraries from developmental and adult stages. For the 13 protein coding genes (and several RNA genes), we find one set of six genes, containing all cytochrome oxidases, that are upregulated in developmental tissues, whereas the remaining set of seven genes, containing all ATPases, that are upregulated in adult muscle and brain tissues. Further, the COX I (Cytochrome oxidase subunit one) expression profile differs from that of the remaining genes, which could be explained by a tissue specific cleavage event or degradation pattern, and is especially pronounced in developmental tissues. Finally, as expected cDNA libraries from muscle tissues contain by far the largest amount (up to 20%) of expressed mitochondrial genes. Conclusion Our results present novel insight into differences in mitochondrial gene expression, emphasizing differences between adult and developmental tissues. Our work indicates that there are presently unknown mechanisms which work to customize mitochondrial processes to the specific needs of the cell, illustrated by the different patterns between adult and developmental tissues. Furthermore, our results also provide novel insight into how in-depth sequencing can provide significant information about expression patterns.Published versio

EFFECT OF IMPACT SURFACE ON EQUESTRIAN FALLS

This study examines the effect of impact surface on head kinematic response and maximum principal strain (MPS) for equestrian falls. A helmeted Hybrid Ill headform was dropped unrestrained onto three impact surfaces (steel, turf and sand) and three locations. Peak resultant linear acceleration, rotational acceleration and duration of the impact events were measured. A finite element brain model was used to calculate MPS. The results revealed that drops onto steel produced higher peak linear acceleration, rotational acceleration and MPS but lower impact durations than drops to turf and sand. However, despite lower MPS values, turf and sand impacts compared to steel impacts still represented a risk of concussion. This suggests that equestrian helmets standards do not properly account for the loading conditions experienced in equestrian accidents

Measuring Controlled-NOT and two-qubit gate operation

Accurate characterisation of two-qubit gates will be critical for any realisation of quantum computation. We discuss a range of measurements aimed at characterising a two-qubit gate, specifically the CNOT gate. These measurements are architecture-independent, and range from simple truth table measurements, to single figure measures such as the fringe visibility, parity, fidelity, and entanglement witnesses, through to whole-state and whole-gate measures achieved respectively via quantum state and process tomography. In doing so, we examine critical differences between classical and quantum gate operation.Comment: 10 pages (two-column). 1 figur

Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Non-sequence gene data (images, literature, etc.) can be found in many different public databases. Access to these data is mostly by text based methods using gene names; however, gene annotation is neither complete, nor fully systematic between organisms, and is also not generally stable over time. This provides some challenges for text based access, especially for cross-species searches. We propose a method for non-sequence data retrieval based on sequence similarity, which removes dependence on annotation and text searches. This work was motivated by the need to provide better access to large numbers of in situ images, and the observation that such image data were usually associated with a specific gene sequence. Sequence similarity searches are found in existing gene oriented databases, but mostly give indirect access to non-sequence data via navigational links. RESULTS: Three applications were built to explore the proposed method: accessing image data, literature and gene names. Searches are initiated with the sequence of the user's gene of interest, which is searched against a database of sequences associated with the target data. The matching (non-sequence) target data are returned directly to the user's browser, organised by sequence similarity. The method worked well for the intended application in image data management. Comparison with text based searches of the image data set showed the accuracy of the method. Applied to literature searches it facilitated retrieval of mostly high relevance references. Applied to gene name data it provided a useful analysis of name variation of related genes within and between species. CONCLUSION: This method makes a powerful and useful addition to existing methods for searching gene data based on text retrieval or curated gene lists. In particular the method facilitates cross-species comparisons, and enables the handling of novel or otherwise un-annotated genes. Applications using the method are quick and easy to build, and the data require little maintenance. This approach largely circumvents the need for annotation, which can be a major obstacle to the development of genomic scale data resources