Resource Allocation in MIMO setup

In a multi-input multi-output (MIMO) setup, where one side of the link comprises a linear antenna array, data can be transmitted over the direction of incident rays. Channel capacity for this setup is studied in this paper. We define two different setups; one when the energy is constant and equal over all rays, and one when available energy is evenly distributed over rays. For the latter, we show that there is an upper bound for channel capacity, regardless of the number of rays and antennas. Also, we have compared this setup with the legacy single-input single-output (SISO) AWGN channel

Viral Infections and Interferons in the Development of Obesity

Obesity is now a prevalent disease worldwide and has a multi-factorial etiology. Several viruses or virus-like agents including members of adenoviridae, herpesviridae, slow virus (prion), and hepatitides, have been associated with obesity; meanwhile obese patients are shown to be more susceptible to viral infections such as during influenza and dengue epidemics. We examined the co-factorial role of viral infections, particularly of the persistent cases, in synergy with high-fat diet in induction of obesity. Antiviral interferons (IFNs), as key immune regulators against viral infections and in autoimmunity, emerge to be a pivotal player in the regulation of adipogenesis. In this review, we examine the recent evidence indicating that gut microbiota uphold intrinsic IFN signaling, which is extensively involved in the regulation of lipid metabolism. However, the prolonged IFN responses during persistent viral infections and obesogenesis comprise reciprocal causality between virus susceptibility and obesity. Furthermore, some IFN subtypes have shown therapeutic potency in their anti-inflammation and anti-obesity activity

Xenopus Interferon Complex: Inscribing the Amphibiotic Adaption and Species-Specific Pathogenic Pressure in Vertebrate Evolution?

Several recent studies have revealed previously unknown complexity of the amphibian interferon (IFN) system. Being unique in vertebrate animals, amphibians not only conserve and multiply the fish-like intron-containing IFN genes, but also rapidly evolve amniote-like intronless IFN genes in each tested species. We postulate that the amphibian IFN system confers an essential model to study vertebrate immune evolution in molecular and functional diversity to cope with unprecedented pathophysiological requirement during terrestrial adaption. Studies so far have ascribed a potential role of these IFNs in immune regulation against intracellular pathogens, particularly viruses; however, many knowledge gaps remain elusive. Based on recent reports about IFN’s multifunctional properties in regulation of animal physiological and defense responses, we interpret that amphibian IFNs may evolve novel function pertinent to their superior molecular diversity. Such new function revealed by the emerging studies about antifungal and developmental regulation of amphibian IFNs will certainly promote our understanding of immune evolution in vertebrates to address current pathogenic threats causing amphibian decline

West Nile Virus and Pattern Recognition Receptors

West Nile Virus (WNV), RNA virus is a member of the flaviviridae family that causes flu like symptoms in infected individuals, however in 1-2% cases, it causes severe neurological diseases such as encephalitis. There is no antiviral or vaccine approved so far to prevent WNV disease, therefore research to understand immune pathology is very important. Pattern Recognition Receptors (PRR) are proteins that are expressed by cells to detect virus infection and play an important role in the innate immune system. When a PRR such as Toll-Like Receptors (TLR) and Nod-Like Receptors (NLR) detects a replicating virus, signals are sent out to warn the body and other neighboring cells that there is a foreign presence within the body. These signals include production of antiviral cytokines and interferons (IFN) that recruit the leukocytes to help fight off the infection. However, it has been discovered that different viruses produce unique cell signals that may act as either a positive and/or negative regulator of the cytokine production and the effectiveness of the immune system. My lab works on understanding the function of two novel innate immune molecules, NLRC5 (a member of NLR family) and TREM-1 (amplifier of inflammation). Therefore, this project will involve WNV infection of mouse immune cells from wild-type mouse and mouse deficient with NLRC5 and TREM-1 and compare specific innate immune markers using real-time RT-PCRs. At the end of my training, I will gain understanding of the research conducted in infectious disease area and will also learn several important techniques

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu

Generation of Polyclonal Rabbit Antisera Specific to the Zika Virus Capsid Protein

Zika virus (ZIKV), a mosquito-borne flavivirus, is an emerging zoonotic pathogen closely related to Japanese encephalitis virus, West Nile virus, dengue virus, and yellow fever virus. Although ZIKV infection generally produces only mild symptoms in some infected individuals, it has recently been associated with a growing number of neurological diseases, including Guillain-Barré syndrome in ZIKV-infected adults and microcephaly in infants born to ZIKV-infected women. Like all flaviviruses, ZIKV has a plus-strand RNA genome encoding ten functional proteins (designated C, prM, E, NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Of these ten, the C (capsid) protein is an essential structural protein required for the formation of infectious viral particles. In order to produce the antiserum specifically recognizing the ZIKV C protein in this study, we expressed and purified the ZIKV C protein as a glutathione-S-transferase (GST) fusion protein in E. coli. The ZIKV C protein-coding region was PCR-amplified using the genomic RNA of ZIKV PRVABC-59, and the amplicons were cloned into the pGEX-4T-1 E. coli expression vector. GST-C fusion proteins were purified using a glutathione sepharose column. Subsequently, the GST-C fusion proteins were used for immunization with rabbits. Western blot analysis using the ZIKV-infected Vero cell lysates were performed to examine the reactivity of the antisera to the ZIKV C protein. Thus, this study provides a useful reagent for the diagnosis and understanding of the viral morphogenesis in the ZIKV-infected cells