RAMPS: reconfigurable architecture for minimal perfect sequencing using the Convey hybrid core computer

The alignment of many short sequences of DNA, called reads, to a long reference genome is a common task in molecular biology. When the problem is expanded to handle typical workloads of billions of reads, execution time becomes critical. While existing solutions attempt to align a high percentage of the reads using a small memory footprint, RAMPS (Reconfigurable Architecture for Minimal Perfect Sequencing) focuses on perform fast exact matching. Using the human genome as a reference, RAMPS aligns short reads on the order of hundreds of thousands of times faster than current software implementations such as SOAP2 or Bowtie, and about 1000 times faster than GPU implementations such as SOAP3. Whereas other aligners require hours to preprocess reference genomes, RAMPS can preprocess the human genome in a few minutes, opening doors via the ability to use arbitrary reference sources for alignment to increase the amount of data that exactly aligns with the reference

Smaller family sizes and ageing populations may reduce long-run savings rates

As developing countries embark on demographic transitions, the phenomenon of declining birth rates and family size becomes an increasingly important policy dilemma. Demography has implications for a country’s labour supply, savings rates, and capital formation, all of which shape and influence its economic growth. In today’s blog, the authors argue that increases in aggregate savings from declining family sizes may be transitory, and as populations begin ageing, a declining ratio of working-aged to retired workers may reduce long-run savings rates

Material for surface-enhanced Raman spectroscopy, and SER sensors and method for preparing same

Metal-doped sol-gel materials, suitable for use as sensors for surface-enhanced Raman spectroscopic analysis for trace chemical detection, are produced by effecting gelation and solvent removal of a doped sol-gel under mild temperature conditions. At least in certain instances reaction and drying will desirably be effected in an oxygen-starved environment. The metal of the sol-gel material functions, when irradiated, to produce a plasmon field for interaction with molecules of an analyte in contact therewith, increasing by orders of magnitude Raman photons that are generate by excitation radiation, and the method allows matching of the metal and metal particle size to a wavelength of light (or incident radiation, e.g., laser radiation) to generate surface plasmons. The porosity of the sol-gel material dramatically increases the surface area, and thereby the amount of metal exposed for analyte interaction. The sensors provided may be in the form of glass vials, fiber optics, multi-well micro-sample plates, etc., having surface coatings of the doped sol-gel material, to provide sampling systems for use in a Raman instrument

New Material for Surface-Enhanced Raman Spectroscopy

A chemical method of synthesis and application of coating materials that are especially suitable for surface-enhanced Raman spectroscopy (SERS) has been developed. The purpose of this development is to facilitate the utilization of the inherently high sensitivity of SERS to detect chemicals of interest (analytes) in trace amounts, without need for lengthy sample preparation. Up to now, the use of SERS has not become routine because the methods available have not been able to reproduce sampling conditions and provide quantitative measurements. In contrast, the coating materials of the present method enable analysis with minimum preparation of samples, and SERS measurements made using these materials are reproducible and reversible. Moreover, unlike in methods investigated in prior efforts to implement SERS, sampling is not restricted to such specific environments as electrolytes or specific solvents. The coating materials of this method are porous glasses, formed in sol-gel processes, that contain small particles of gold or silver metal. Materials of this type can be applied to the sample-contact surfaces of a variety of sampling and sensing devices, including glass slides, glass vials, fiber-optic probes, and glass tubes. Glass vials with their insides coated according to this method are particularly convenient for SERS to detect trace chemicals in solutions: One simply puts a sample solution containing the analyte(s) into a vial, then puts the vial into a Raman spectrometer for analysis. The chemical ingredients and the physical conditions of the sol-gel process have been selected so that the porous glass formed incorporates particles of the desired metal with size(s) to match the wavelength(s) of the SERS excitation laser in order to optimize the generation of surface plasmons. The ingredients and processing conditions have further been chosen to tailor the porosity and polarity of the glass to optimize the sample flow and the interaction between the analyte(s) and the plasmon field that generates Raman photons. The porous silica network of a sol-gel glass creates a unique environment for stabilizing SERS-active metal particles. Relative to other material structures that could be considered for SERS, the porous silica network offers higher specific surface area and thus greater interaction between analyte molecules and metal particles. Efforts to perform SERS measurements with the help of sampling devices coated by this method have been successful. In tests, numerous organic and inorganic chemicals were analyzed in several solvents, including water. The results of the tests indicate that the SERS measurements were reproducible within 10 percent and linear over five orders of magnitude. One measure of the limits of detectability of chemicals in these tests was found to be a concentration of 300 parts per billion. Further development may eventually make it possible to realize the full potential sensitivity of SERS for detecting some analytes in quantities as small as a single molecule

Size and Scope of Iron County Agriculture 2019

Iron County is located in the southwestern portion of the state and is bordered by Nevada on the west. Other surrounding Utah counties include Beaver, Garfield, Kane, and Washington. As of 2017, the population was estimated at 51,001. The county seat is Parowan, while the largest city is Cedar City. This fact sheet details the land ownership, growing season, crop and livestock production, and farm income of Iron County agriculture

Action Ball: An Analysis of Energy Expenditure and Subjective Experiences of Participants

Energy expenditure and subjective experiences of college students participating in action ball were examined through two studies. In Study 1, six students participated in action ball while using a portable metabolic analyzer. Energy expenditure data from these students were compared to American College of Sports Medicine (ASCM) daily activity recommendations. Participating in forty minutes of action ball exceeded the ACSM recommendation of 3.0-5.9 metabolic equivalent of tasks (METs). Participation in action ball did not, however, exceed the ACSM kilocalories (kcal) standard. In Study 2, hypotheses about differences between action ball and the other two sports were tested. Data from 109 students in five physical education classes were analyzed. Three of the classes (n=72 students) participated in action ball, one class participated in basketball (n=14), and one class participated in ultimate Frisbee (n=23 students). Heart rate (HR), kcal, and four indicators of subjective experience quality were measured during and immediately after participation. Action ball produced greater kcal expenditure than basketball. Action ball yielded significantly greater deep structured experience prevalence than basketball (Week 12). Action ball also yielded significantly less deep structured experience frequency than ultimate Frisbee (Week 12) and basketball (Week 12). Collectively, results suggest that action ball provides similar energy expenditure and experience quality to other similar sports

A method of encoding generalized link diagrams

We describe a method of encoding various types of link diagrams, including those with classical, flat, rigid, welded, and virtual crossings. We show that this method may be used to encode link diagrams, up to equivalence, in a notation whose length is a cubic function of the number of 'riser marks'. For classical knots, the minimal number of such marks is twice the bridge index, and a classical knot diagram in minimal bridge form with bridge index $b$ may be encoded in space $\mathcal{O}(b^2)$. A set of moves on the notation is defined. As a demonstration of the utility of the notation we give another proof that the Kishino virtual knot is non-classical.Comment: 17 pages, 13 figures; to appear in the Journal of Knot Theory & Its Ramification

Predictors of appropriate therapy in patients with implantable cardioverter-defibrillator for primary prevention of sudden cardiac death

The purpose of this study was to evaluate predictors of appropriate therapy in patients with implantable cardioverter-defibrillators (ICD) for primary prevention of sudden cardiac death. A retrospective cohort of 321 patients with systolic heart failure undergoing ICD placement for primary prevention of sudden cardiac death was queried with a mean follow-up period of 2.6 years. Appropriate ICD therapy was defined as therapy delivered for termination of a ventricular tachyarrhythmia. Appropriate ICD therapy was delivered in 142 (44%) of the patients. In a multivariate model, body mass index ≥28.8 kg/m2, chronic kidney disease, left ventricular ejection fraction ≤20% and metabolic syndrome were found to be independent predictors of appropriate ICD therapy. Appropriate ICD therapy was associated with higher cardiovascular mortality. These findings show the importance of identification of risk factors, especially metabolic syndrome, in patients following ICD implantation as aggressive treatment of these co-morbidities may decrease appropriate ICD therapy and cardiovascular mortality

AtomSim: web-deployed atomistic dynamics simulator

AtomSim, a collection of interfaces for computational crystallography simulations, has been developed. It uses forcefield-based dynamics through physics engines such as the General Utility Lattice Program, and can be integrated into larger computational frameworks such as the Virtual Neutron Facility for processing its dynamics into scattering functions, dynamical functions etc. It is also available as a Google App Engine-hosted web-deployed interface. Examples of a quartz molecular dynamics run and a hafnium dioxide phonon calculation are presented