3D printed ultrasound phantoms for clinical training

Ultrasound is a ubiquitous, portable structural imaging technique which is used to provide visual feedback for a range of diagnostic and surgical techniques. Training for these techniques demands a range of teaching models tailored for each application. Existing anatomical models are often overly simple or prohibitively expensive, causing difficulties in obtaining patient or procedure specific models. In this study we present ultrasonic rib phantoms for clinical teaching and training purposes, fabricated by three-dimensional (3D) printing technologies. Models were produced using freely available software and data, and their effectiveness as teaching phantoms evaluated using clinical ultrasound scans of the phantoms

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules.

Background The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. Results A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. Conclusions Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments

Operators on the Fréchet sequence space ces(p+), 1≤p<∞1 \leq p < \infty

[EN] The Fréchet sequence spaces ces(p+) are very different to the Fréchet sequence spaces ¿p+,1¿pp}\ell ^q$$ ℓ p + = ∩ q > p ℓ q . Math. Nachr. 147, 7–12 (1990)Pérez Carreras, P., Bonet, J.: Barrelled Locally Convex Spaces. North Holland, Amsterdam (1987)Pitt, H.R.: A note on bilinear forms. J. Lond. Math. Soc. 11, 171–174 (1936)Ricker, W.J.: A spectral mapping theorem for scalar-type spectral operators in locally convex spaces. Integral Equ. Oper. Theory 8, 276–288 (1985)Robertson, A.P., Robertson, W.: Topological Vector Spaces. Cambridge University Press, Cambridge (1973)Waelbroeck, L.: Topological vector spaces and algebras. Lecture Notes in Mathematics, vol. 230. Springer, Berlin (1971

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

Effects of beta-alanine supplementation on brain homocarnosine/carnosine signal and cognitive function: an exploratory study

Objectives: Two independent studies were conducted to examine the effects of 28 d of beta-alanine supplementation at 6.4 g d-1 on brain homocarnosine/carnosine signal in omnivores and vegetarians (Study 1) and on cognitive function before and after exercise in trained cyclists (Study 2). Methods: In Study 1, seven healthy vegetarians (3 women and 4 men) and seven age- and sex-matched omnivores undertook a brain 1H-MRS exam at baseline and after beta-alanine supplementation. In study 2, nineteen trained male cyclists completed four 20-Km cycling time trials (two pre supplementation and two post supplementation), with a battery of cognitive function tests (Stroop test, Sternberg paradigm, Rapid Visual Information Processing task) being performed before and after exercise on each occasion. Results: In Study 1, there were no within-group effects of beta-alanine supplementation on brain homocarnosine/carnosine signal in either vegetarians (p = 0.99) or omnivores (p = 0.27); nor was there any effect when data from both groups were pooled (p = 0.19). Similarly, there was no group by time interaction for brain homocarnosine/carnosine signal (p = 0.27). In study 2, exercise improved cognitive function across all tests (P0.05) of beta-alanine supplementation on response times or accuracy for the Stroop test, Sternberg paradigm or RVIP task at rest or after exercise. Conclusion: 28 d of beta-alanine supplementation at 6.4g d-1 appeared not to influence brain homocarnosine/ carnosine signal in either omnivores or vegetarians; nor did it influence cognitive function before or after exercise in trained cyclists

A join-based hybrid parameter for constraint satisfaction

We propose joinwidth, a new complexity parameter for the Constraint Satisfaction Problem (CSP). The definition of joinwidth is based on the arrangement of basic operations on relations (joins, projections, and pruning), which inherently reflects the steps required to solve the instance. We use joinwidth to obtain polynomial-time algorithms (if a corresponding decomposition is provided in the input) as well as fixed-parameter algorithms (if no such decomposition is provided) for solving the CSP. Joinwidth is a hybrid parameter, as it takes both the graphical structure as well as the constraint relations that appear in the instance into account. It has, therefore, the potential to capture larger classes of tractable instances than purely structural parameters like hypertree width and the more general fractional hypertree width (fhtw). Indeed, we show that any class of instances of bounded fhtw also has bounded joinwidth, and that there exist classes of instances of bounded joinwidth and unbounded fhtw, so bounded joinwidth properly generalizes bounded fhtw. We further show that bounded joinwidth also properly generalizes several other known hybrid restrictions, such as fhtw with degree constraints and functional dependencies. In this sense, bounded joinwidth can be seen as a unifying principle that explains the tractability of several seemingly unrelated classes of CSP instances

Therapies for neonatal encephalopathy: Targeting the latent, secondary and tertiary phases of evolving brain injury

In term and near-term neonates with neonatal encephalopathy, therapeutic hypothermia protocols are well established. The current focus is on how to improve outcomes further and the challenge is to find safe and complementary therapies that confer additional protection, regeneration or repair in addition to cooling. Following hypoxia-ischemia, brain injury evolves over three main phases (latent, secondary and tertiary), each with a different brain energy, perfusion, neurochemical and inflammatory milieu. While therapeutic hypothermia has targeted the latent and secondary phase, we now need therapies that cover the continuum of brain injury that spans hours, days, weeks and months after the initial event. Most agents have several therapeutic actions but can be broadly classified under a predominant action (e.g., free radical scavenging, anti-apoptotic, anti-inflammatory, neuroregeneration, and vascular effects). Promising early/secondary phase therapies include Allopurinol, Azithromycin, Exendin-4, Magnesium, Melatonin, Noble gases and Sildenafil. Tertiary phase agents include Erythropoietin, Stem cells and others. We review a selection of promising therapeutic agents on the translational pipeline and suggest a framework for neuroprotection and neurorestoration that targets the evolving injury

"I am your mother and your father!": In vitro derived gametes and the ethics of solo reproduction

In this paper, we will discuss the prospect of human reproduction achieved with gametes originating from only one person. According to statements by a minority of scientists working on the generation of gametes in vitro, it may become possible to create eggs from men’s non-reproductive cells and sperm from women’s. This would enable, at least in principle, the creation of an embryo from cells obtained from only one individual: ‘solo reproduction’. We will consider what might motivate people to reproduce in this way, and the implications that solo reproduction might have for ethics and policy. We suggest that such an innovation is unlikely to revolutionise reproduction and parenting. Indeed, in some respects it is less revolutionary than in vitro fertilisation as a whole. Furthermore, we show that solo reproduction with in vitro created gametes is not necessarily any more ethically problematic than gamete donation—and probably less so. Where appropriate, we draw parallels with the debate surrounding reproductive cloning. We note that solo reproduction may serve to perpetuate reductive geneticised accounts of reproduction, and that this may indeed be ethically questionable. However, in this it is not unique among other technologies of assisted reproduction, many of which focus on genetic transmission. It is for this reason that a ban on solo reproduction might be inconsistent with continuing to permit other kinds of reproduction that also bear the potential to strengthen attachment to a geneticised account of reproduction. Our claim is that there are at least as good reasons to pursue research towards enabling solo reproduction, and eventually to introduce solo reproduction as an option for fertility treatment, as there are to do so for other infertility related purposes

Observation of the thermal Casimir force

Quantum theory predicts the existence of the Casimir force between macroscopic bodies, due to the zero-point energy of electromagnetic field modes around them. This quantum fluctuation-induced force has been experimentally observed for metallic and semiconducting bodies, although the measurements to date have been unable to clearly settle the question of the correct low-frequency form of the dielectric constant dispersion (the Drude model or the plasma model) to be used for calculating the Casimir forces. At finite temperature a thermal Casimir force, due to thermal, rather than quantum, fluctuations of the electromagnetic field, has been theoretically predicted long ago. Here we report the experimental observation of the thermal Casimir force between two gold plates. We measured the attractive force between a flat and a spherical plate for separations between 0.7 $\mu$m and 7 $\mu$m. An electrostatic force caused by potential patches on the plates' surfaces is included in the analysis. The experimental results are in excellent agreement (reduced $\chi^2$ of 1.04) with the Casimir force calculated using the Drude model, including the T=300 K thermal force, which dominates over the quantum fluctuation-induced force at separations greater than 3 $\mu$m. The plasma model result is excluded in the measured separation range.Comment: 6 page

The Caenorhabditis chemoreceptor gene families

Background: Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Results: Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Conclusion: Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.JHT was supported by NIH grant RO1GM48700 and HMR by R01AI56081