Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

Phase Locked Loop and Modulo Games, The Dogma Loops; and “Finding Ibrida”

This dissertation consists of two independent musical compositions and an article detailing the process of the design and assembly of an electric guitar with particular emphasis on the carefully curated suite of embedded effects.

The first piece, 'Phase Locked Loop and Modulo Games' is scored for electric guitar and a single echo of equal volume less than a beat away. One could think of the piece as a 15 minute canon at the unison at the dotted eighth note (or at times the quarter or triplet-quarter), however the compositional motivation is more about weaving a composite texture between the guitar and its echo that is, while in theory extremely contrapuntal, in actuality is simply a single [superhuman] melodic line.

The second piece, 'The Dogma Loops' picks up a few compositional threads left by ‘Phase Locked Loop’ and weaves them into an entirely new tapestry. 'Phase Locked Loop' is motivated by the creation of a complex musical composite that is for the most part electronically transparent. 'The Dogma Loops' questions that same notion of composite electronic complexity by essentially asking a question: "what are the inputs to an interactive electronic system that create the most complex outputs via the simplest musical means possible?"

'The Dogma Loops' is scored for Electric Guitar (doubling on Ukulele), Violin and Violoncello. All of the principal instruments require an electronic pickup (except the Uke). The work is in three sections played attacca; [Automation Games], [Point of Origin] and [Cloning Vectors].

The third and final component of the document is the article 'Finding Ibrida.' This article details the process of the design and assembly of an electric guitar with integrated effects, while also providing the deeper context (conceptual and technical) which motivated the efforts and informed the challenges to hybridize the various technologies (tubes, transistors, digital effects and a microcontroller subsystem). The project was motivated by a desire for rigorous technical and hands-on engagement with analog signal processing as applied to the electric guitar. ‘Finding Ibrida’ explores sound, some myths and lore of guitar tech and the history of electric guitar distortion and its culture of sonic exploration.

Membrane binding of plasmid DNA and endocytic pathways are involved in electrotransfection of mammalian cells.

Electric field mediated gene delivery or electrotransfection is a widely used method in various studies ranging from basic cell biology research to clinical gene therapy. Yet, mechanisms of electrotransfection are still controversial. To this end, we investigated the dependence of electrotransfection efficiency (eTE) on binding of plasmid DNA (pDNA) to plasma membrane and how treatment of cells with three endocytic inhibitors (chlorpromazine, genistein, dynasore) or silencing of dynamin expression with specific, small interfering RNA (siRNA) would affect the eTE. Our data demonstrated that the presence of divalent cations (Ca(2+) and Mg(2+)) in electrotransfection buffer enhanced pDNA adsorption to cell membrane and consequently, this enhanced adsorption led to an increase in eTE, up to a certain threshold concentration for each cation. Trypsin treatment of cells at 10 min post electrotransfection stripped off membrane-bound pDNA and resulted in a significant reduction in eTE, indicating that the time period for complete cellular uptake of pDNA (between 10 and 40 min) far exceeded the lifetime of electric field-induced transient pores (∼10 msec) in the cell membrane. Furthermore, treatment of cells with the siRNA and all three pharmacological inhibitors yielded substantial and statistically significant reductions in the eTE. These findings suggest that electrotransfection depends on two mechanisms: (i) binding of pDNA to cell membrane and (ii) endocytosis of membrane-bound pDNA.

Construction of invisibility cloaks of arbitrary shape and size using planar layers of metamaterials

Transformation optics (TO) is a powerful tool for the design of electromagnetic and optical devices with novel functionality derived from the unusual properties of the transformation media. In general, the fabrication of TO media is challenging, requiring spatially varying material properties with both anisotropic electric and magnetic responses. Though metamaterials have been proposed as a path for achieving such complex media, the required properties arising from the most general transformations remain elusive, and cannot implemented by state-of-the-art fabrication techniques. Here, we propose faceted approximations of TO media of arbitrary shape in which the volume of the TO device is divided into flat metamaterial layers. These layers can be readily implemented by standard fabrication and stacking techniques. We illustrate our approximation approach for the specific example of a two-dimensional, omnidirectional "invisibility cloak", and quantify its performance using the total scattering cross section as a practical figure of merit. © 2012 American Institute of Physics.

Gold mining in the Peruvian Amazon: global prices, deforestation, and mercury imports.

Many factors such as poverty, ineffective institutions and environmental regulations may prevent developing countries from managing how natural resources are extracted to meet a strong market demand. Extraction for some resources has reached such proportions that evidence is measurable from space. We present recent evidence of the global demand for a single commodity and the ecosystem destruction resulting from commodity extraction, recorded by satellites for one of the most biodiverse areas of the world. We find that since 2003, recent mining deforestation in Madre de Dios, Peru is increasing nonlinearly alongside a constant annual rate of increase in international gold price (∼18%/yr). We detect that the new pattern of mining deforestation (1915 ha/year, 2006-2009) is outpacing that of nearby settlement deforestation. We show that gold price is linked with exponential increases in Peruvian national mercury imports over time (R(2) = 0.93, p = 0.04, 2003-2009). Given the past rates of increase we predict that mercury imports may more than double for 2011 (∼500 t/year). Virtually all of Peru's mercury imports are used in artisanal gold mining. Much of the mining increase is unregulated/artisanal in nature, lacking environmental impact analysis or miner education. As a result, large quantities of mercury are being released into the atmosphere, sediments and waterways. Other developing countries endowed with gold deposits are likely experiencing similar environmental destruction in response to recent record high gold prices. The increasing availability of satellite imagery ought to evoke further studies linking economic variables with land use and cover changes on the ground.

Colchicine effectiveness in symptom and inflammation modification in knee osteoarthritis (COLKOA): study protocol for a randomized controlled trial.

BACKGROUND: Despite the high prevalence and global impact of knee osteoarthritis (KOA), current treatments are palliative. No disease modifying anti-osteoarthritic drug (DMOAD) has been approved. We recently demonstrated significant involvement of uric acid and activation of the innate immune response in osteoarthritis (OA) pathology and progression, suggesting that traditional gout therapy may be beneficial for OA. We therefore assess colchicine, an existing commercially available agent for gout, for a new therapeutic application in KOA. METHODS/DESIGN: COLKOA is a double-blind, placebo-controlled, randomized trial comparing a 16-week treatment with standard daily dose oral colchicine to placebo for KOA. A total of 120 participants with symptomatic KOA will be recruited from a single center in Singapore. The primary end point is 30% improvement in total Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score at week 16. Secondary end points include improvement in pain, physical function, and quality of life and change in serum, urine and synovial fluid biomarkers of cartilage metabolism and inflammation. A magnetic resonance imaging (MRI) substudy will be conducted in 20 participants to evaluate change in synovitis. Logistic regression will be used to compare changes between groups in an intention-to-treat analysis. DISCUSSION: The COLKOA trial is designed to evaluate whether commercially available colchicine is effective for improving signs and symptoms of KOA, and reducing synovial fluid, serum and urine inflammatory and biochemical joint degradation biomarkers. These biomarkers should provide insights into the underlying mechanism of therapeutic response. This trial will potentially provide data to support a new treatment option for KOA. TRIAL REGISTRATION: The trial has been registered at clinicaltrials.gov as NCT02176460 . Date of registration: 26 June 2014.