Construction and Control of Genetic Regulatory Networks: A Multivariate Markov Chain Approach

In the post-genomic era, the construction and control of genetic regulatory networks using gene expression data is a hot research topic. Boolean networks (BNs) and its extension Probabilistic Boolean Networks (PBNs) have been served as an effective tool for this purpose. However, PBNs are difficult to be used in practice when the number of genes is large because of the huge computational cost. In this paper, we propose a simplified multivariate Markov model for approximating a PBN The new model can preserve the strength of PBNs, the ability to capture the inter-dependence of the genes in the network, qnd at the same time reduce the complexity of the network and therefore the computational cost. We then present an optimal control model with hard constraints for the purpose of control/intervention of a genetic regulatory network. Numerical experimental examples based on the yeast data are given to demonstrate the effectiveness of our proposed model and control policy.published_or_final_versio

Electrical Impedance Tomography for Biomedical Applications: Circuits and Systems Review

There has been considerable interest in electrical impedance tomography (EIT) to provide low-cost, radiation-free, real-time and wearable means for physiological status monitoring. To be competitive with other well-established imaging modalities, it is important to understand the requirements of the specific application and determine a suitable system design. This paper presents an overview of EIT circuits and systems including architectures, current drivers, analog front-end and demodulation circuits, with emphasis on integrated circuit implementations. Commonly used circuit topologies are detailed, and tradeoffs are discussed to aid in choosing an appropriate design based on the application and system priorities. The paper also describes a number of integrated EIT systems for biomedical applications, as well as discussing current challenges and possible future directions

Comparative Stress Levels among Residents in Three Chinese Provincial Capitals, 2001 and 2008

Objectives To compare stress levels among residents in large Chinese cities between 2001 and 2008. Methods Survey data were collected in three mainland Chinese capital cities in two waves, in 2001 and 2008, respectively. Participants were recruited through a multi-stage stratified sampling process. Stress was assessed using the Perceived Stress Scale, Chinese version (CPSS). Descriptive methods were used to estimate mean stress levels and associated 95% confidence intervals. Estimates were adjusted by post-stratification weights. Results Indicating stable stress levels, respective adjusted mean stress scores for the combined samples of study participants were 23.90 (95%CI: 23.68–24.12) in 2001 and 23.69 (95%CI: 23.38–24.01) in 2008. A lower stress level in 2008 than in 2001 manifested among residents who were under 25 years of age; female; with a college or higher level education; divorced, widowed, or separated; members of the managerial and clerical group; students or army personnel; or with an annual income of at least 30,000 RMB. Conclusion The overall stress level did not change among the combined sample of residents in the three Chinese study cities between 2001 and 2008. However, levels remained high and varied across social strata, and may have reflected a national trend among urban residents. Findings indicate a need for a new health policy, and call for the design and implementation of evidence-based interventions that target the highest-risk groups

Population structured by witchcraft beliefs

Anthropologists have long argued that fear of victimization through witchcraft accusations promotes cooperation in small-scale societies1. Others have argued that witchcraft beliefs undermine trust and therefore reduce social cohesion2. However, there are very few, if any, quantified empirical examples demonstrating how witchcraft labels can structure cooperation in real human communities. Here we show a case from a farming community in China where people labelled zhu were thought capable of supernatural activity, particularly poisoning food. The label was usually applied to adult women heads of household and often inherited down the female line. We found that those in zhu households were less likely to give or receive gifts or farm help to or from non-zhu households; nor did they have sexual partnerships or children with those in non-zhu households. However, those in zhu households did preferentially help and reproduce with each other. Although the tag is common knowledge to other villagers and used in cooperative and reproductive partner choice, we found no evidence that this assortment was based on cooperativeness or quality. We favour the explanation that stigmatization originally arose as a mechanism to harm female competitors. Once established, fear that the trait is transmissible may help explain the persistence of this deep-rooted cultural belief

Secondary Sex Ratio among Women Exposed to Diethylstilbestrol in Utero

BACKGROUND. Diethylstilbestrol (DES), a synthetic estrogen widely prescribed to pregnant women during the mid-1900s, is a potent endocrine disruptor. Previous studies have suggested an association between endocrine-disrupting compounds and secondary sex ratio. METHODS. Data were provided by women participating in the National Cancer Institute (NCI) DES Combined Cohort Study. We used generalized estimating equations to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the relation of in utero DES exposure to sex ratio (proportion of male births). Models were adjusted for maternal age, child's birth year, parity, and cohort, and accounted for clustering among women with multiple pregnancies. RESULTS. The OR for having a male birth comparing DES-exposed to unexposed women was 1.05 (95% CI, 0.95-1.17). For exposed women with complete data on cumulative DES dose and timing (33%), those first exposed to DES earlier in gestation and to higher doses had the highest odds of having a male birth. The ORs were 0.91 (95% C, 0.65-1.27) for first exposure at ≥ 13 weeks gestation to < 5 g DES; 0.95 (95% CI, 0.71-1.27) for first exposure at ≥ 13 weeks to ≥ 5 g; 1.16 (95% CI, 0.96-1.41) for first exposure at < 13 weeks to < 5 g; and 1.24 (95% CI, 1.04-1.48) for first exposure at < 13 weeks to ≥ 5 g compared with no exposure. Results did not vary appreciably by maternal age, parity, cohort, or infertility history. CONCLUSIONS. Overall, no association was observed between in utero DES exposure and secondary sex ratio, but a significant increase in the proportion of male births was found among women first exposed to DES earlier in gestation and to a higher cumulative dose.National Cancer Institute (N01-CP-21168, N01-CP-51017, N01-CP-01289

The spectral variability of FSRQs

The optical variability of 29 flat spectrum radio quasars in SDSS Stripe 82 region are investigated by using DR7 released multi-epoch data. All FSRQs show variations with overall amplitude ranging from 0.24 mag to 3.46 mag in different sources. About half of FSRQs show a bluer-when-brighter trend, which is commonly observed for blazars. However, only one source shows a redder-when-brighter trend, which implies it is rare in FSRQs. In this source, the thermal emission may likely be responsible for the spectral behavior.Comment: 4 pages, 1 figure, to be published in Journal of Astrophysics and Astronomy, as a proceeding paper of the conference "Multiwavelength Variability of Blazars", Guangzhou, China, September 22-24, 201

Evaluating semi-supervision methods for medical image segmentation: applications in cardiac magnetic resonance imaging

PURPOSE: Purpose Neural networks have potential to automate medical image segmentation but require expensive labeling efforts. While methods have been proposed to reduce the labeling burden, most have not been thoroughly evaluated on large, clinical datasets or clinical tasks. We propose a method to train segmentation networks with limited labeled data and focus on thorough network evaluation. APPROACH: We propose a semi-supervised method that leverages data augmentation, consistency regularization, and pseudolabeling and train four cardiac magnetic resonance (MR) segmentation networks. We evaluate the models on multiinstitutional, multiscanner, multidisease cardiac MR datasets using five cardiac functional biomarkers, which are compared to an expert’s measurements using Lin’s concordance correlation coefficient (CCC), the within-subject coefficient of variation (CV), and the Dice coefficient. RESULTS: The semi-supervised networks achieve strong agreement using Lin’s CCC (>0.8), CV similar to an expert, and strong generalization performance. We compare the error modes of the semi-supervised networks against fully supervised networks. We evaluate semi-supervised model performance as a function of labeled training data and with different types of model supervision, showing that a model trained with 100 labeled image slices can achieve a Dice coefficient within 1.10% of a network trained with 16,000+ labeled image slices. CONCLUSION: We evaluate semi-supervision for medical image segmentation using heterogeneous datasets and clinical metrics. As methods for training models with little labeled data become more common, knowledge about how they perform on clinical tasks, how they fail, and how they perform with different amounts of labeled data is useful to model developers and users

Transmission characteristics of EM wave in a finite thickness plasma

One of the key factors for solving the problems of re-entry communication interruption is electromagnetic (EM) wave transmission characteristics in a plasma. Theoretical and experimental studies were carried out on specific transmission characteristics for different plasma sheath characteristic under thin sheath condition in re-entry state. The paper presents systematic studies on the variations of wave attenuation characteristics versus plasma sheath thickness L, collision frequency &nu;, electron density ne and wave working frequency f in a &phi; 800mm high temperature shock tube. In experiments, L is set to 4 cm and 38 cm. &nu; is 2 GHz and 15 GHz. ne is from 1&times;10^10 cm&minus;3 to 1&times;10^13 cm&minus;3, and f is set to 2, 5, 10, 14.6 GHz, respectively. Meanwhile, Wentzel&ndash;Kramers&ndash;Brillouin (WKB) and finite-difference time-domain (FDTD) methods are adopted to carry out theoretical simulation for comparison with experimental results. It is found that when L is much larger than EM wavelength &lambda; (thick sheath) and &nu; is large, the theoretical result is in good agreement with experimental one, when sheath thickness L is much larger than &lambda;, while &nu; is relatively small, two theoretical results are obviously different from the experimental ones. It means that the existing theoretical model can not fully describe the contribution of &nu;. Furthermore, when L and &lambda; are of the same order of magnitude (thin sheath), the experimental result is much smaller than the theoretical values, which indicates that the current model can not properly describe the thin sheath effect on EM attenuation characteristics

Controlled synthesis of SPION@SiO₂ nanoparticles using design of experiments

The synthesis of single-core superparamagnetic iron oxide nanoparticles (SPIONs) coated with a silica shell of controlled thickness remains a challenge, due to the dependence on a multitude of experimental variables. Herein, we utilise design of experiment (DoE) to study the formation of SPION@SiO2 nanoparticles (NPs) via reverse microemulsion. Using a 33 full factorial design, the influence of reactant concentration of tetraethyl orthosilicate (TEOS) and ammonium hydroxide (NH4OH), as well as the number of fractionated additions of TEOS on the silica shell was investigated with the aim of minimising polydispersity and increasing the population of SPION@SiO2 NPs formed. This investigation facilitated a reproducible and controlled approach for the high yield synthesis of SPION@SiO2 NPs with uniform silica shell thickness. Application of a multiple linear regression analysis established a relationship between the applied experimental variables and the resulting silica shell thickness. These experimental variables were similarly found to dictate the monodispersity of the SPION@SiO2 NPs formed. The overall population of single-core@shell particles was dependent on the interaction between the number of moles of TEOS and NH4OH, with no influence from the number of fractionated additions of TEOS. This work demonstrates the complexity of the preparative method and produces an accessible and flexible synthetic model to achieve monodisperse SPION@SiO2 NPs with controllable shell thickness

Tuneable Singlet Exciton Fission and Triplet-Triplet Annihilation in an Orthogonal Pentacene Dimer

We report fast and highly efficient intramolecular singlet exciton fission in a pentacene dimer, consisting of two covalently attached, nearly orthogonal pentacene units. Fission to triplet excitons from this ground state geometry occurs within 1 ps in isolated molecules in solution and dispersed solid matrices. The process exhibits a sensitivity to environmental polarity and competes with geometric relaxation in the singlet state, while subsequent triplet decay is strongly dependent on conformational freedom. The near orthogonal arrangement of the pentacene units is unlike any structure currently proposed for efficient singlet exciton fission and may lead to new molecular design rules.JW acknowledges financial support from Singapore MOE Tier 3 grant (MOE2014-T3-1-004). SL thanks AGS Scholarship support from the A*STAR Singapore. The work was supported by the EPSRC (grant number EP/G060738/1). We acknowledge the use of the Darwin Supercomputer of the University of Cambridge High 18 Performance Computing Service (http://www.hpc.cam.ac.uk/) and the EPSRC UK National Service for Computational Chemistry Software (NSCCS) at Imperial College London in carrying out this work.This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/adfm.20150153