SpeedSeq: ultra-fast personal genome analysis and interpretation.

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers performance competitive with or superior to current methods for detecting germline and somatic single-nucleotide variants, structural variants, insertions and deletions, and it includes novel functionality for streamlined interpretation.

Polymeric Semiconductor in Field-Effect Transistors Utilizing Flexible and High-Surface Area Expanded Poly(tetrafluoroethylene) Membrane Gate Dielectrics.

Organic field-effect transistors (OFETs) were fabricated using three high-surface area and flexible expanded-poly(tetrafluoroethylene) (ePTFE) membranes in gate dielectrics, along with the semiconducting polymer poly[2,5-bis(2-octyldodecyl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione-3,6-diyl)-alt-(2,2':5',2″:5″,2‴-quaterthiophen-5,5‴-diyl)] (PDPP4T). The transistor behavior of these devices was investigated following annealing at 50, 100, 150, and 200 °C, all sustained for 1 h. For annealing temperatures above 50 °C, the OFETs displayed improved transistor behavior and a significant increase in output current while maintaining similar magnitudes of Vth shifts when subjected to static voltage compared to those kept at ambient temperature. We also tested the response to NO2 gas for further characterization and for possible applications. The ePTFE-PDPP4T interface of each membrane was characterized via scanning electron microscopy for all four annealing temperatures to derive a model for the hole mobility of the ePTFE-PDPP4T OFETs that accounts for the microporous structure of the ePTFE and consequently adjusts the channel width of the OFET. Using this model, a maximum hole mobility of 1.8 ± 1.0 cm2/V s was calculated for the polymer in an ePTFE-PDPP4T OFET annealed at 200 °C, whereas a PDPP4T OFET using only the native silicon wafer oxide as a gate dielectric exhibited a hole mobility of just 0.09 ± 0.03 cm2/V s at the same annealing condition. This work demonstrates that responsive semiconducting polymer films can be deposited on nominally nonwetting and extremely bendable membranes, and the charge carrier mobility can be significantly increased compared to their as-prepared state by using thermally durable polymer membranes with unique microstructures as gate dielectrics.

Influence of polystyrenesulfonate on electron transfer quenching of ruthenium trisbipyridine luminescence by viologens: non-covalent assembly and covalent tethering of the ruthenium complex.

A new copolymer (RuB-PSS) of ruthenium(II)bis-(2,2'-bipyridine)(4-vinyl 2,2'-bipyridine) and styrene sulfonate was prepared which tethers the ruthenium chromophore directly to the polymer backbone. The photophysical properties of the copolymer, and its luminescence quenching by viologens, were compared with those of ruthenium(II)tris-bipyridine, [Ru(bpy)(3)](2+), bound non-covalently to polystyrenesulfonate (PSS) via hydrophobic and electrostatic interactions. Enhancement of ruthenium polypyridyl complex luminescence in both systems is due to decreased rates of non-radiative decay when removed from bulk water as well as reduced oxygen quenching. Molecular dynamics simulations show an open PSS chain conformation with induction of local curvature around the ruthenium centres. Hence, the complexes remain exposed to water, albeit less so than in bulk solution, as evidenced by low enhancement of bound [Ru(phen)(2)dppz](2+) emission. Quenching by O(2) is hindered for both systems due to combined polarity, ionic strength, and viscosimetric effects that influence local concentrations and diffusion of reactants. Electron transfer quenching of the Ru centre by zwitterionic propyl viologen sulfonate (PVS(0)) and cationic methyl viologen (MV(2+)) is enhanced for [Ru(bpy)(3)](2+)/PSS, but retarded for RuB-PSS, despite the attraction of the quenchers for PSS. PSS binding hinders separation of the electron transfer products relative to aqueous solution, excepting an increase for RuB-PSS/PVS(0). We conclude that anionic hydrophobic polymers such as PSS can differentially influence forward- and reverse- electron transfer reactions depending on the charge and hydrophobicity of the reactants. In the context of small molecule binding, we find that PSS provides a tenable model for DNA.

Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area.

CONTEXT: Severe acute respiratory syndrome (SARS) is an emerging infectious disease that first manifested in humans in China in November 2002 and has subsequently spread worldwide. OBJECTIVES: To describe the clinical characteristics and short-term outcomes of SARS in the first large group of patients in North America; to describe how these patients were treated and the variables associated with poor outcome. DESIGN, SETTING, AND PATIENTS: Retrospective case series involving 144 adult patients admitted to 10 academic and community hospitals in the greater Toronto, Ontario, area between March 7 and April 10, 2003, with a diagnosis of suspected or probable SARS. Patients were included if they had fever, a known exposure to SARS, and respiratory symptoms or infiltrates observed on chest radiograph. Patients were excluded if an alternative diagnosis was determined. MAIN OUTCOME MEASURES: Location of exposure to SARS; features of the history, physical examination, and laboratory tests at admission to the hospital; and 21-day outcomes such as death or intensive care unit (ICU) admission with or without mechanical ventilation. RESULTS: Of the 144 patients, 111 (77%) were exposed to SARS in the hospital setting. Features of the clinical examination most commonly found in these patients at admission were self-reported fever (99%), documented elevated temperature (85%), nonproductive cough (69%), myalgia (49%), and dyspnea (42%). Common laboratory features included elevated lactate dehydrogenase (87%), hypocalcemia (60%), and lymphopenia (54%). Only 2% of patients had rhinorrhea. A total of 126 patients (88%) were treated with ribavirin, although its use was associated with significant toxicity, including hemolysis (in 76%) and decrease in hemoglobin of 2 g/dL (in 49%). Twenty-nine patients (20%) were admitted to the ICU with or without mechanical ventilation, and 8 patients died (21-day mortality, 6.5%; 95% confidence interval [CI], 1.9%-11.8%). Multivariable analysis showed that the presence of diabetes (relative risk [RR], 3.1; 95% CI, 1.4-7.2; P =.01) or other comorbid conditions (RR, 2.5; 95% CI, 1.1-5.8; P =.03) were independently associated with poor outcome (death, ICU admission, or mechanical ventilation). CONCLUSIONS: The majority of cases in the SARS outbreak in the greater Toronto area were related to hospital exposure. In the event that contact history becomes unreliable, several features of the clinical presentation will be useful in raising the suspicion of SARS. Although SARS is associated with significant morbidity and mortality, especially in patients with diabetes or other comorbid conditions, the vast majority (93.5%) of patients in our cohort survived.

Interpretation of diagnostic laboratory tests for severe acute respiratory syndrome: the Toronto experience.

BACKGROUND: An outbreak of severe acute respiratory syndrome (SARS) began in Canada in February 2003. The initial diagnosis of SARS was based on clinical and epidemiological criteria. During the outbreak, molecular and serologic tests for the SARS-associated coronavirus (SARS-CoV) became available. However, without a "gold standard," it was impossible to determine the usefulness of these tests. We describe how these tests were used during the first phase of the SARS outbreak in Toronto and offer some recommendations that may be useful if SARS returns. METHODS: We examined the results of all diagnostic laboratory tests used in 117 patients admitted to hospitals in Toronto who met the Health Canada criteria for suspect or probable SARS. Focusing on tests for SARS-CoV, we attempted to determine the optimal specimen types and timing of specimen collection. RESULTS: Diagnostic test results for SARS-CoV were available for 110 of the 117 patients. SARS-CoV was detected by means of reverse-transcriptase polymerase chain reaction (RT-PCR) in at least one specimen in 59 (54.1%) of 109 patients. Serologic test results of convalescent samples were positive in 50 (96.2%) of 52 patients for whom paired serum samples were collected during the acute and convalescent phases of the illness. Of the 110 patients, 78 (70.9%) had specimens that tested positive by means of RT-PCR, serologic testing or both methods. The proportion of RT-PCR test results that were positive was similar between patients who met the criteria for suspect SARS (50.8%, 95% confidence interval [CI] 38.4%-63.2%) and those who met the criteria for probable SARS (58.0%, 95% CI 44.2%-70.7%). SARS-CoV was detected in nasopharyngeal swabs in 33 (32.4%) of 102 patients, in stool specimens in 19 (63.3%) of 30 patients, and in specimens from the lower respiratory tract in 10 (58.8%) of 17 patients. INTERPRETATION: These findings suggest that the rapid diagnostic tests in use at the time of the initial outbreak lack sufficient sensitivity to be used clinically to rule out SARS. As tests for SARS-CoV continue to be optimized, evaluation of the clinical presentation and elucidation of a contact history must remain the cornerstone of SARS diagnosis. In patients with SARS, specimens taken from the lower respiratory tract and stool samples test positive by means of RT-PCR more often than do samples taken from other areas.