Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.National Institutes of Health (U.S.) (Grant # 7R01GM74712-5)United States. Defense Advanced Research Projects Agency (contract HR0011-10-C-0168)National Science Foundation (U.S.) (NSF CAREER award 0968682)BBN Technologie

Composition of the pericellular matrix modulates the deformation behaviour of chondrocytes in articular cartilage under static loading

The aim was to assess the role of the composition changes in the pericellular matrix (PCM) for the chondrocyte deformation. For that, a three-dimensional finite element model with depth-dependent collagen density, fluid fraction, fixed charge density and collagen architecture, including parallel planes representing the split-lines, was created to model the extracellular matrix (ECM). The PCM was constructed similarly as the ECM, but the collagen fibrils were oriented parallel to the chondrocyte surfaces. The chondrocytes were modelled as poroelastic with swelling properties. Deformation behaviour of the cells was studied under 15% static compression. Due to the depth-dependent structure and composition of cartilage, axial cell strains were highly depth-dependent. An increase in the collagen content and fluid fraction in the PCMs increased the lateral cell strains, while an increase in the fixed charge density induced an inverse behaviour. Axial cell strains were only slightly affected by the changes in PCM composition. We conclude that the PCM composition plays a significant role in the deformation behaviour of chondrocytes, possibly modulating cartilage development, adaptation and degeneration. The development of cartilage repair materials could benefit from this information

Breastfeeding and weaning practices among Hong Kong mothers: a prospective study

<p>Abstract</p> <p>Background</p> <p>Breastfeeding provides optimal and complete nutrition for newborn babies. Although new mothers in Hong Kong are increasingly choosing to breastfeed their babies, rates of exclusive breastfeeding are low and duration remains short. The purpose of this study was to describe the breastfeeding and weaning practices of Hong Kong mothers over the infant's first year of life to determine the factors associated with early cessation.</p> <p>Methods</p> <p>A cohort of 1417 mother-infant pairs was recruited from the obstetric units of four public hospitals in Hong Kong in the immediate post-partum period and followed prospectively for 12 months or until weaned. We used descriptive statistics to describe breastfeeding and weaning practices and multiple logistic regression to investigate the relationship between maternal characteristics and breastfeeding cessation.</p> <p>Results</p> <p>At 1 month, 3 months, 6 months and 12 months only 63%, 37.3%, 26.9%, and 12.5% of the infants respectively, were still receiving any breast milk; approximately one-half of breastfeeding mothers were exclusively breastfeeding. Younger mothers, those with a longer duration of residence in Hong Kong, and those returning to work postpartum were more likely to wean before 1 month. Mothers with higher education, previous breastfeeding experience, who were breastfed themselves and those who were planning to exclusively breastfeed and whose husbands preferred breastfeeding were more likely to continue breastfeeding beyond 1 month. The introduction of infant formula before 1 month and returning to work postpartum were predictive of weaning before 3 months.</p> <p>Conclusions</p> <p>Breastfeeding promotion programs have been successful in achieving high rates of breastfeeding initiation but the focus must now shift to helping new mothers exclusively breastfeed and sustain breastfeeding for longer.</p

Joint action aesthetics

Synchronized movement is a ubiquitous feature of dance and music performance. Much research into the evolutionary origins of these cultural practices has focused on why humans perform rather than watch or listen to dance and music. In this study, we show that movement synchrony among a group of performers predicts the aesthetic appreciation of live dance performances. We developed a choreography that continuously manipulated group synchronization using a defined movement vocabulary based on arm swinging, walking and running. The choreography was performed live to four audiences, as we continuously tracked the performers’ movements, and the spectators’ affective responses. We computed dynamic synchrony among performers using cross recurrence analysis of data from wrist accelerometers, and implicit measures of arousal from spectators’ heart rates. Additionally, a subset of spectators provided continuous ratings of enjoyment and perceived synchrony using tablet computers. Granger causality analyses demonstrate predictive relationships between synchrony, enjoyment ratings and spectator arousal, if audiences form a collectively consistent positive or negative aesthetic evaluation. Controlling for the influence of overall movement acceleration and visual change, we show that dance communicates group coordination via coupled movement dynamics among a group of performers. Our findings are in line with an evolutionary function of dance–and perhaps all performing arts–in transmitting social signals between groups of people. Human movement is the common denominator of dance, music and theatre. Acknowledging the time-sensitive and immediate nature of the performer-spectator relationship, our study makes a significant step towards an aesthetics of joint actions in the performing arts