Rapid Sequence Identification of Potential Pathogens Using Techniques from Sparse Linear Algebra

The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck. Here we present D$^{4}$RAGenS, a genetic sequence identification algorithm that exhibits the Big Data handling and computational power of the Dynamic Distributed Dimensional Data Model (D4M). The method leverages linear algebra and statistical properties to increase computational performance while retaining accuracy by subsampling the data. Two run modes, Fast and Wise, yield speed and precision tradeoffs, with applications in biodefense and medical diagnostics. The D$^{4}$RAGenS analysis algorithm is tested over several datasets, including three utilized for the Defense Threat Reduction Agency (DTRA) metagenomic algorithm contest

Ferromagnetic Quantum Critical Point in CePd2_2P2_2 with Pd →\rightarrow Ni Substitution

An investigation of the structural, thermodynamic, and electronic transport properties of the isoelectronic chemical substitution series Ce(Pd$_{1-x}$Ni$_x$)$_2$P$_2$ is reported, where a possible ferromagnetic quantum critical point is uncovered in the temperature - concentration ($T-x$) phase diagram. This behavior results from the simultaneous contraction of the unit cell volume, which tunes the relative strengths of the Kondo and RKKY interactions, and the introduction of disorder through alloying. Near the critical region at $x_{\rm{cr}}$ $\approx$ 0.7, the rate of contraction of the unit cell volume strengthens, indicating that the cerium $f$-valence crosses over from trivalent to a non-integer value. Consistent with this picture, x-ray absorption spectroscopy measurements reveal that while CePd$_2$P$_2$ has a purely trivalent cerium $f$-state, CeNi$_2$P$_2$ has a small ($<$ 10 \%) tetravalent contribution. In a broad region around $x_{\rm{cr}}$, there is a breakdown of Fermi liquid temperature dependences, signaling the influence of quantum critical fluctuations and disorder effects. Measurements of clean CePd$_2$P$_2$ furthermore show that applied pressure has a similar initial effect to alloying on the ferromagnetic order. From these results, CePd$_2$P$_2$ emerges as a keystone system to test theories such as the Belitz-Kirkpatrick-Vojta model for ferromagnetic quantum criticality, where distinct behaviors are expected in the dirty and clean limits.Comment: 9 pages, 8 figure

Förster Resonance Energy Transfer (FRET) Correlates of Altered Subunit Stoichiometry in Cys-Loop Receptors, Exemplified by Nicotinic α4β2

We provide a theory for employing Förster resonance energy transfer (FRET) measurements to determine altered heteropentameric ion channel stoichiometries in intracellular compartments of living cells. We simulate FRET within nicotinic receptors (nAChRs) whose α4 and β2 subunits contain acceptor and donor fluorescent protein moieties, respectively, within the cytoplasmic loops. We predict FRET and normalized FRET (NFRET) for the two predominant stoichiometries, (α4)3(β2)2 vs. (α4)2(β2)3. Studying the ratio between FRET or NFRET for the two stoichiometries, minimizes distortions due to various photophysical uncertainties. Within a range of assumptions concerning the distance between fluorophores, deviations from plane pentameric geometry, and other asymmetries, the predicted FRET and NFRET for (α4)3(β2)2 exceeds that of (α4)2(β2)3. The simulations account for published data on transfected Neuro2a cells in which α4β2 stoichiometries were manipulated by varying fluorescent subunit cDNA ratios: NFRET decreased monotonically from (α4)3(β2)2 stoichiometry to mostly (α4)2(β2)3. The simulations also account for previous macroscopic and single-channel observations that pharmacological chaperoning by nicotine and cytisine increase the (α4)2(β2)3 and (α4)3(β2)2 populations, respectively. We also analyze sources of variability. NFRET-based monitoring of changes in subunit stoichiometry can contribute usefully to studies on Cys-loop receptors

Generation Gap and the Impact of the Web on Goods Quality Perceptions

This study explores how age and general online shopping experience affect consumer perceptions on product quality uncertainty. Using the survey data collected from 549 consumers, we investigated how they perceive the uncertainty of product quality on six search, experience and credence goods. The ANOVA results show that age and the Web shopping experience of consumers are significant factors. A generation gap is indeed seen for all but one experience good. Web shopping experience is not a significant factor for search goods but is for experience and credence goods. There is an interaction effect between age and Web shopping experience for one credence good. Implications of these results are discussed

Intussusception trends in Hong Kong children

OBJECTIVES: To assess trends in intussusception and to validate the coding in Hong Kong's computerised discharge information system. DESIGN: Case notes were reviewed for all children under the age of 5 years who had a discharge diagnosis indicating intussusception or a procedure indicating reduction of intussusception during the 6-year period 1 July 1997 through 30 June 2003. RESULTS: Intussusception rates for infants under 1 year of age (108/100,000) and under 5 years of age (38/100,000) were slightly higher than previous estimates (78-100/100,000 and 27-32/100,000, respectively) that used passive discharge data alone. CONCLUSIONS: Hong Kong's passive computer data systems could be used to monitor rates of intussusception after the introduction of new rotavirus vaccines, provided readmissions, inter-hospital transfers, and hospital follow-ups for the same episode are taken into account.published_or_final_versio

Chiral Effective Lagrangian and Quark Masses

The status of lattice determinations of quark masses is reviewed (with the exception of m_b). Attempts to extract the low-energy constants in the effective chiral Lagrangian are discussed, with special emphasis on those couplings which are required to test the hypothesis of a massless up-quark. Furthermore, the issue of quenched chiral logarithms is addressed.Comment: Invited talk presented at Lattice2002(plenary), 12 pages, 3 figure

Absence of association between angiotensin converting enzyme polymorphism and development of adult respiratory distress syndrome in patients with severe acute respiratory syndrome: a case control study

BACKGROUND: It has been postulated that genetic predisposition may influence the susceptibility to SARS-coronavirus infection and disease outcomes. A recent study has suggested that the deletion allele (D allele) of the angiotensin converting enzyme (ACE) gene is associated with hypoxemia in SARS patients. Moreover, the ACE D allele has been shown to be more prevalent in patients suffering from adult respiratory distress syndrome (ARDS) in a previous study. Thus, we have investigated the association between ACE insertion/deletion (I/D) polymorphism and the progression to ARDS or requirement of intensive care in SARS patients. METHOD: One hundred and forty genetically unrelated Chinese SARS patients and 326 healthy volunteers were recruited. The ACE I/D genotypes were determined by polymerase chain reaction and agarose gel electrophoresis. RESULTS: There is no significant difference in the genotypic distributions and the allelic frequencies of the ACE I/D polymorphism between the SARS patients and the healthy control subjects. Moreover, there is also no evidence that ACE I/D polymorphism is associated with the progression to ARDS or the requirement of intensive care in the SARS patients. In multivariate logistic analysis, age is the only factor associated with the development of ARDS while age and male sex are independent factors associated with the requirement of intensive care. CONCLUSION: The ACE I/D polymorphism is not directly related to increased susceptibility to SARS-coronavirus infection and is not associated with poor outcomes after SARS-coronavirus infection

Phylogenetic Analysis of West Nile Virus, Nuevo Leon State, Mexico

West Nile virus RNA was detected in brain tissue from a horse that died in June 2003 in Nuevo Leon State, Mexico. Nucleotide sequencing and phylogenetic analysis of the premembrane and envelope genes showed that the virus was most closely related to West Nile virus isolates collected in Texas in 2002

What factors influence training opportunities for older workers? Three factorial surveys exploring the attitudes of HR professionals

The core research questions addressed in this paper are: what factors influence HR professionals in deciding whether to approve training proposals for older workers? What kind of training are they more likely to recommend for older employees and in which organizational contexts? We administered three factorial surveys to 66 HR professionals in Italy. Participants made specific training decisions based on profiles of hypothetical older workers. Multilevel analyses indicated that access to training decreases strongly with age, while highly-skilled older employees with low absenteeism rates are more likely to enjoy training opportunities. In addition, older workers displaying positive performance are more likely to receive training than older workers who perform poorly, suggesting that training late in working life may serve as a reward for good performance rather than as a means of enhancing productivity. The older the HR professional evaluating training proposals, the higher the probability that older workers will be recommended for training. keywords: training; older workers; HR professionals; factorial survey; multilevel model