A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing error rates of modern sequencers present many new computational challenges in data interpretation. These challenges have led to the development of new classes of mapping tools and {\em de novo} assemblers. These algorithms are challenged by the continued improvement in sequencing throughput. We here describe digital normalization, a single-pass computational algorithm that systematizes coverage in shotgun sequencing data sets, thereby decreasing sampling variation, discarding redundant data, and removing the majority of errors. Digital normalization substantially reduces the size of shotgun data sets and decreases the memory and time requirements for {\em de novo} sequence assembly, all without significantly impacting content of the generated contigs. We apply digital normalization to the assembly of microbial genomic data, amplified single-cell genomic data, and transcriptomic data. Our implementation is freely available for use and modification

Detection of an Extrasolar Planet Atmosphere

We report high precision spectrophotometric observations of four planetary transits of HD 209458, in the region of the sodium resonance doublet at 589.3 nm. We find that the photometric dimming during transit in a bandpass centered on the sodium feature is deeper by (2.32 +/- 0.57) x 10^{-4} relative to simultaneous observations of the transit in adjacent bands. We interpret this additional dimming as absorption from sodium in the planetary atmosphere, as recently predicted from several theoretical modeling efforts. Our model for a cloudless planetary atmosphere with a solar abundance of sodium in atomic form predicts more sodium absorption than we observe. There are several possibilities that may account for this reduced amplitude, including reaction of atomic sodium into molecular gases and/or condensates, photoionization of sodium by the stellar flux, a low primordial abundance of sodium, or the presence of clouds high in the atmosphere.Comment: 26 pages, 8 figures, accepted by ApJ 2001 November 1

Effects of Anxiety on Attentional Allocation and Task Performance: An Information Processing Analysis

An information processing signal detection methodology was employed to examine attentional allocation and its correlates in both normal comparison (NC) and generalized anxiety disorder (GAD) participants. In particular, the impact of neutral distractor and negative feedback cues on performance of an attention vigilance task was investigated. Individuals with GAD (N = 15) evidenced impaired performance on an attention vigilance task relative to NC participants (N = 15) when neutral distractor cues were presented. Contrary to prediction, no group differences in performance were detected under conditions in which participants were presented negative feedback cues they were told were relevant to their performance. Instead, GAD participants exhibited improvement during the experimental task such that their performance was equivalent to NC participants. Across trials, the clinically anxious group endorsed significantly higher levels of worry and negative affectivity; however, they failed to respond with concomitant physical arousal (e.g. increased muscle tension). These data are discussed within the context of Eysenck and Calvo\u27s processing efficiency theory. Additionally, the results of this investigation provide support for Barlow\u27s conceptualization of anxiety as requiring the interaction of cognitive schema and physiological arousal

Low-Dose Continuous 5-Fluorouracil Combined with Leucovorin, nab-Paclitaxel, Oxaliplatin, and Bevacizumab for Patients with Advanced Pancreatic Cancer: A Retrospective Analysis.

BackgroundContinuous-infusion 5-fluorouracil (5FU) and calcium leucovorin plus nab-paclitaxel and oxaliplatin have been shown to be active in patients with pancreatic cancer. As a protracted low-dose infusion, 5FU is antiangiogenic, and has synergy with bevacizumab. As shown in the treatment of breast cancer, bevacizumab and nab-paclitaxel are also synergetic.ObjectiveIn this paper we retrospectively analyze the survival of 65 patients with advanced pancreatic cancer who were treated with low-dose continuous (metronomic) chemotherapy given in conjunction with conventional anti-VEGF therapy.Patients and methodsSince July of 2008, we have treated 65 patients with 5FU (180 mg/m2/day × 14 days) via an ambulatory pump. Calcium leucovorin (20 mg/m2 IV), nab-paclitaxel (60 mg/m2) IV as a 30-min infusion, and oxaliplatin (50 mg/m2) IV as a 60-min infusion were given on days 1, 8, and 15. Bevacizumab (5 mg/kg) IV over 30 min was administered on days 1 and 15. Cycles were repeated every 28-35 days. There were 42 women and 23 men, and the median age was 59 years. Forty-six patients had stage IV disease.ResultsThe median survival was 19 months, with 82% of patients surviving 12 months or longer. The overall response rate was 49%. There were 28 patients who had received prior treatment, 15 of whom responded to therapy. Fifty-two patients had elevated CA 19-9 prior to treatment. Of these, 21 patients had 90% or greater reduction in CA 19-9 levels. This cohort had an objective response rate of 71% and a median survival of 27 months. Thirty patients stopped treatment due to disease progression, and an additional 22 stopped because of toxicity. One patient died while on therapy.ConclusionsThis non-gemcitabine-based regimen resulted in higher response rates and better survival than what is commonly observed with therapy given at conventional dosing schedules. Low-dose continuous (metronomic therapy) cytotoxic chemotherapy combined with antiangiogenic therapy is safe and effective

A Search for CO Absorption in the Transmission Spectrum of HD 209458b

We observed one transit of the extrasolar planet HD 209458b with the NIRSPEC spectrograph on the Keck II telescope. Using time series of low-noise observations in the wavelength range 2.0 micron to 2.5 micron, we searched for extra absorption from the 1st overtone rotation-vibration band of CO near 2.3 micron. This was not detected, with a detection limit that fails to test simple models of the planetary atmosphere by a factor of about 3. Great improvements in the detectability of the CO spectrum features could be realized by observing a transit that is centered near stellar meridian passage, and in better weather. Since it appears that similar observations taken under better circumstances might succeed, we describe our analysis procedures in detail.Comment: 22 pages, 2 figure

Linear angular momentum multiplexing-conceptualization and experimental evaluation with antenna arrays

Linear Angular Momentum Multiplexing is a new method for providing highly spectrally efficient short range communication between a transmitter and receiver, where one may move at speed transverse to the propagation. Such applications include rail, vehicle and hyperloop transport systems communicating with fixed infrastructure on the ground. This paper describes how the scientific concept of linear angular momentum multiplexing evolves from orbital angular momentum multiplexing. The essential parameters for implementing this concept are: a long array at least at one of the ends of the link; antenna element radiation characteristics; and the array element spacing relative to the propagation distance. These parameters are also backed by short range measurements carried out at 2.4GHz used to model the Rice fading channel and determine resilience to multipath fading

Modeling and Development of a Magnetic Bearing Controller for a High Speed Flywheel System

This paper describes a modeling effort used to develop an improved type of magnetic bearing controller, called a modal controller, for use on high speed flywheel systems. The controller design is based on models of the flywheel system, is designed to directly control the natural dynamics of the spinning rotor, and is generic enough to be readily adapted to future flywheel systems. Modeling and development are described for two key controller subsystems: the modal controller subsystem, which allows direct control over the rotor rigid body modes, and the bending mode compensation subsystem, which tracks, and prevents interference from, the rotor bending modes during flywheel operation. Integration of modeling results into the final controller is described and data taken on the NASA Glenn D1 flywheel module during high speed operation are presented and discussed. The improved modal controller described in this paper has been successfully developed and implemented and has been used for regular hands-free operation of the D1 flywheel module up to its maximum operating speed of 60,000 RPM

Impact of Outpatient vs Inpatient ABSSSI Treatment on Outcomes: A Retrospective Observational Analysis of Medical Charts Across US Emergency Departments

Background The objective of this study was to characterize treatment of patients with acute bacterial skin and skin structure infections (ABSSSIs) and describe the association between hospital admission and emergency department (ED) visits or readmissions within 30 days after initial episode of care (IEC). Methods This was a retrospective, observational, cohort study of adults with ABSSSI who presented to an ED between July 1, 2012, and June 30, 2013. Patient, health care facility, and treatment characteristics, including unplanned ED visits or readmissions, were obtained through manual chart review and abstraction. Adjusted logistic regression analysis examined likelihood of all-cause unplanned ED visits or readmissions between admitted and nonadmitted patients. Results Records from 1527 ED visits for ABSSSI from 40 centers were reviewed (admitted, n = 578 [38%]; nonadmitted, n = 949 [62%]). Admitted patients were typically older (mean age, 52.2 years vs 43.0 years), more likely to be morbidly obese (body mass index \u3e 40 kg/m2; 17.3% vs 9.1%), and had more comorbidities (Charlson Comorbidity Index ≥ 4; 24.4% vs 6.8%) compared with those not admitted. In the primary analysis, adjusted logistic regression, controlling for comorbidities and severity of illness, demonstrated that there was a similar likelihood of all-cause unplanned ED visits or readmissions between admitted and nonadmitted patients (odds ratio, 1.03; 95% confidence interval, 0.74–1.43; P = .87). Conclusions ABSSSI treatment pathways leveraging outpatient treatment vs hospital admission support similar likelihood of unplanned 30-day ED visits or readmissions, an important clinical outcome and quality metric at US hospitals. Further research regarding the decision criteria around hospital admission to avoid potentially unnecessary hospitalizations is warranted