Polarized light propagation through scattering media: time-resolved Monte Carlo simulations and experiments

A study of polarized light transmitted through randomly scattering media of a polystyrene-microsphere solution is described. Temporal profiles of the Stokes vectors and the degree of polarization are measured experimentally and calculated theoretically based on a Monte Carlo technique. The experimental results match the theoretical results well, which demonstrates that the time-resolved Monte Carlo technique is a powerful tool that can contribute to the understanding of polarization propagation in biological tissue. Analysis based on the Stokes-Mueller formalism and the Mie theory shows that the first scattering event determines the major spatial patterns of the transmitted Stokes vectors. When an area detected at the output surface of a turbid medium is circularly symmetrical about the incident beam, the temporal profile of the transmitted light is independent of the incident polarization state. A linear relationship between the average order of the scatters and the light propagation time can be used to explain the exponential decay of the degree of polarization of transmitted light

Data Compression Strategies for Use in Advanced Metering Infrastructure Networks

Internet of Things technology has advanced rapidly. For example, numerous sensors can be deployed in a city to collect a variety of data, and such data can be used to monitor the city’s situation. A possible application of such data is smart metering implemented by power suppliers for their consumers; smart metering involves installing a multiplicity of smart meters that, in conjunction with data centers, form a smart grid. Because a smart gird must collect and send data automatically, the establishment of advanced metering infrastructure (AMI) constitutes the primary step to establishing a smart grid. However, problems remain in smart metering: data traffic from smart meters flows rapidly at a huge volume, resulting in bandwidth bottlenecks. Thus, this chapter proposes some data compression technologies as well as a novel scheme for reducing the communication data load in AMI architectures

Templated fabrication of large area subwavelength antireflection gratings on silicon

We report a cheap and scalable bottom-up technique for fabricating wafer-scale, subwavelength-structured antireflection coatings on single-crystalline silicon substrates. Spin-coated monolayer colloidal crystals are utilized as shadow masks to generate metallic nanohole arrays. Inverted pyramid arrays in silicon can then be templated against nanoholes by anisotropic wet etching. The resulting subwavelength gratings greatly suppress specular reflection at normal incidence. The reflection spectra for flat silicon and the templated gratings at long wavelengths agree well with the simulated results using a rigorous coupled wave analysis model. These subwavelength gratings are of great technological importance in crystalline silicon solar cells

BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale

Capturing the semantics of related biological concepts, such as genes and mutations, is of significant importance to many research tasks in computational biology such as protein-protein interaction detection, gene-drug association prediction, and biomedical literature-based discovery. Here, we propose to leverage state-of-the-art text mining tools and machine learning models to learn the semantics via vector representations (aka. embeddings) of over 400,000 biological concepts mentioned in the entire PubMed abstracts. Our learned embeddings, namely BioConceptVec, can capture related concepts based on their surrounding contextual information in the literature, which is beyond exact term match or co-occurrence-based methods. BioConceptVec has been thoroughly evaluated in multiple bioinformatics tasks consisting of over 25 million instances from nine different biological datasets. The evaluation results demonstrate that BioConceptVec has better performance than existing methods in all tasks. Finally, BioConceptVec is made freely available to the research community and general public via https://github.com/ncbi-nlp/BioConceptVec.Comment: 33 pages, 6 figures, 7 tables, accepted by PLOS Computational Biolog

Association analysis of monoamine oxidase A gene and bipolar affective disorder in Han Chinese

<p>Abstract</p> <p>Background</p> <p>Monoamine oxidase A (MAOA) is a mitochondrial enzyme involved in degrading several different biological amines, including serotonin. Although several pieces of evidence suggested that MAOA is important in the etiology of bipolar affective disorder (BPD), associations for markers of the MAOA gene with BPD were not conclusive and the association has not been investigated in Taiwanese population. This study was designed to illustrate the role of MAOA in the etiology of BPD in Han Chinese.</p> <p>Methods</p> <p>Two markers, a dinucleotide polymorphism in exon 2 and a functional uVNTR on the promoter of the <it>MAOA </it>gene, were used to study the genetic association in 108 unrelated patients with BPD and 103 healthy controls. Allelic distributions of two polymorphisms were analyzed and, caused the MAOA located at X chromosome, haplotype association was performed using haplotype unambiguously assigned in male participants.</p> <p>Results</p> <p>While no difference in allelic distributions of two MAOA polymorphisms was found, the risk haplotype 114S was associated with BPD in male patients (<it>P </it>= 0.03). The significance, however, was not found in female patients with 114S haplotype.</p> <p>Conclusion</p> <p>Results from this study suggest that MAOA may have a gender-specific and small effect on the etiology of BPD in Taiwan. Due to the limited sample size, results from this study need to be confirmed in replicates.</p

A Novel Family of Cyst Proteins with Epidermal Growth Factor Repeats in Giardia lamblia

The biological goal of Giardia lamblia life cycle is differentiation into a cyst form (encystation) that can survive in the environment and infect a new host. Since cystic stages are key to transmission of parasites, this differentiation may be a target for interruption of the life cycle. Synthesis and assembly of the extracellular cyst wall are the major hallmarks of this important differentiation. During encystation, cyst wall structural proteins are coordinately synthesized and are mainly targeted to the cyst wall. However, only a few such proteins have been identified to date. In this study, we used a combination of bioinformatics and molecular approaches to identify new cyst structural proteins from G. lamblia and found a group of Epidermal Growth Factor (EGF)-like Repeats containing Cyst Proteins (EGFCPs). Interestingly, the levels of EGFCPs proteins increased significantly during encystation, which matches the characteristics of the Giardia cyst wall protein. Further characterization and localization studies suggest that EGFCPs may function like cyst wall proteins, involved in differentiation of G. lamblia trophozoites into cysts. Our results provide valuable information regarding the function of a new group of cyst proteins in parasite differentiation into cysts and help develop ways to interrupt the parasite life cycle

Integrin-mediated membrane blebbing is dependent on the NHE1 and NCX1 activities.

Integrin-mediated signal transduction and membrane blebbing have been well studied to modulate cell adhesion, spreading and migration^1-6^. However, the relationship between membrane blebbing and integrin signaling has not been explored. Here we show that integrin-ligand interaction induces membrane blebbing and membrane permeability change. We found that sodium-proton exchanger 1 (NHE1) and sodium-calcium exchanger 1 (NCX1) are located in the membrane blebbing sites and inhibition of NHE1 disrupts membrane blebbing and decreases membrane permeability change. However, inhibition of NCX1 enhances cell blebbing to cause cell swelling which is correlated with an intracellular sodium accumulation induced by NHE17. These data suggest that sodium influx induced by NHE1 is a driving force for membrane blebbing growth, while sodium efflux induced by NCX1 in a reverse mode causes membrane blebbing retraction. Together, these data reveal a novel function of NHE1 and NCX1 in membrane permeability change and blebbing and provide the link for integrin signaling and membrane blebbing

Polarized light propagation through scattering media: time-resolved Monte Carlo simulations and experiments

A study of polarized light transmitted through randomly scattering media of a polystyrene-microsphere solution is described. Temporal profiles of the Stokes vectors and the degree of polarization are measured experimentally and calculated theoretically based on a Monte Carlo technique. The experimental results match the theoretical results well, which demonstrates that the time-resolved Monte Carlo technique is a powerful tool that can contribute to the understanding of polarization propagation in biological tissue. Analysis based on the Stokes-Mueller formalism and the Mie theory shows that the first scattering event determines the major spatial patterns of the transmitted Stokes vectors. When an area detected at the output surface of a turbid medium is circularly symmetrical about the incident beam, the temporal profile of the transmitted light is independent of the incident polarization state. A linear relationship between the average order of the scatters and the light propagation time can be used to explain the exponential decay of the degree of polarization of transmitted light

Control of Kaposi's Sarcoma-Associated Herpesvirus Reactivation Induced by Multiple Signals

The ability to control cellular functions can bring about many developments in basic biological research and its applications. The presence of multiple signals, internal as well as externally imposed, introduces several challenges for controlling cellular functions. Additionally the lack of clear understanding of the cellular signaling network limits our ability to infer the responses to a number of signals. This work investigates the control of Kaposi's sarcoma-associated herpesvirus reactivation upon treatment with a combination of multiple signals. We utilize mathematical model-based as well as experiment-based approaches to achieve the desired goals of maximizing virus reactivation. The results show that appropriately selected control signals can induce virus lytic gene expression about ten folds higher than a single drug; these results were validated by comparing the results of the two approaches, and experimentally using multiple assays. Additionally, we have quantitatively analyzed potential interactions between the used combinations of drugs. Some of these interactions were consistent with existing literature, and new interactions emerged and warrant further studies. The work presents a general method that can be used to quantitatively and systematically study multi-signal induced responses. It enables optimization of combinations to achieve desired responses. It also allows identifying critical nodes mediating the multi-signal induced responses. The concept and the approach used in this work will be directly applicable to other diseases such as AIDS and cancer