Untargeted metagenomics protocol for the diagnosis of infection from CSF and tissue from sterile sites

Metagenomic next-generation sequencing (mNGS) is an untargeted technique capable of detecting all microbial nucleic acid within a sample. This protocol outlines our wet laboratory method for mNGS of cerebrospinal fluid (CSF) specimens and tissues from sterile sites. We use this method routinely in our clinical service, processing 178 specimens over the past 2.5 years in a laboratory that adheres to ISO:15189 standards. We have successfully used this protocol to diagnose multiple cases of encephalitis and hepatitis

TEF, Vol. 1 No. 1

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Mapping the Circumstellar Environment of T Tauri with Fluorescent H_2 Emission

We have obtained three long-slit, far UV spectra of the pre-main sequence system T Tauri. These HST/STIS spectra show a strong and variable on-source spectrum composed of both fluoresced H_2 and stellar chromospheric lines. Extended H_2 emission is seen up to 10" from the T Tau system. The on-source and extended H_2 are both pumped by H I Lyman alpha. The on-source H_2 is pumped by the red wing of a broad, self-absorbed Ly-alpha line, while the progressions seen in the extended gas are pumped from near line center. This suggests that the extended H_2 is pumped locally, and not by the stellar Ly-alpha line. The H_2 to the north and west coincides with the evacuated cavity bounded by the optical reflection nebulosity; to the south the extended H_2 coincides with the HH 255 outflow from the embedded infrared companion T Tau S. The spatial profile of the extended gas shows a prominent dip coincident with the position of T Tau S. This may be absorption by a disk associated with T Tau S. There is no evidence for absorption by a disk surrounding T Tau N large enough to obscure T Tau S.Comment: 46 pages, including 12 figures and 5 tables. To appear in the Astronomical Journal, December 200

The Effects of Sodium Phosphate Supplementation on Physiological Responses to Submaximal Exercise and 20 km Cycling Time-Trial Performance

The aim of this study was to examine the effects of sodium phosphate (SP) supplementation on 26 physiological responses to submaximal exercise and 20 km cycling time-trial performance. Using a 27 randomised, double-blind, crossover design, 20 endurance-trained male cyclists (age: 31 ± 6 years; 28 height: 1.82 ± 0.07 m; body mass: 76.3 ± 7.0 kg; maximal oxygen uptake [V̇O2max]: 57.9 ± 5.5 mL·kg-29 1·min-1) completed two supplementation trials separated by a 14-day washout period. The trials 30 consisted of 10 minutes of cycling at 65% V̇O2max followed by a 20 km time-trial. Expired air was 31 monitored throughout each trial for the evaluation of V̇O2, minute ventilation (V̇E), and respiratory 32 exchange ratio (RER). Heart rate was monitored during each trial along with ratings of perceived 33 exertion (RPE) and blood lactate concentration. For four days before each trial, participants ingested 50 34 mg∙kg fat-free-mass-1·day-1 of either SP or placebo. There were no effects (p ≥ 0.05) of supplementation 35 on physiological responses during cycling at 65% V̇O2max. There were also no effects of 36 supplementation on time-trial performance (placebo: 32.8 ± 2.2 mins; SP: 32.8 ± 2.3 mins). 37 Nevertheless, relative to placebo, SP increased V̇E (mean difference: 3.81 L·min-1; 95% likely range: 38 0.16-7.46 L·min-1), RER (mean difference: 0.020; 95% likely range: 0.004-0.036), and RPE (mean 39 difference: 0.39; 95% likely range: 0.04-0.73) during time-trials; as well as post time-trial blood lactate 40 concentration (mean difference: 1.06 mmol·L-1; 95% likely range: 0.31-1.80 mmol·L-1). In conclusion, 41 SP supplementation has no significant effects on submaximal physiological responses or 20 km time-42 trial performance

Catalyst Interface Engineering for Improved 2D Film Lift-Off and Transfer

The mechanisms by which chemical vapor deposited (CVD) graphene and hexagonal boron nitride (h-BN) films can be released from a growth catalyst, such as widely used copper (Cu) foil, are systematically explored as a basis for an improved lift-off transfer. We show how intercalation processes allow the local Cu oxidation at the interface followed by selective oxide dissolution, which gently releases the 2D material (2DM) film. Interfacial composition change and selective dissolution can thereby be achieved in a single step or split into two individual process steps. We demonstrate that this method is not only highly versatile but also yields graphene and h-BN films of high quality regarding surface contamination, layer coherence, defects, and electronic properties, without requiring additional post-transfer annealing. We highlight how such transfers rely on targeted corrosion at the catalyst interface and discuss this in context of the wider CVD growth and 2DM transfer literature, thereby fostering an improved general understanding of widely used transfer processes, which is essential to numerous other applications.We acknowledge funding from the ERC (InsituNANO, grant 279342). R.W. acknowledges an EPSRC Doctoral Training Award (EP/M506485/1). During this work, S.T. was supported in parts by a DFG research fellowship under grant TA 1122/1-1:1. J.A.A.-W. acknowledges a Research Fellowship from Churchill College, Cambridge. Z.A.V.V. acknowledges funding from ESPRC grant EP/L016087/1. P.B. and B.S.J. thank the Danish National Research Foundation Centre for Nanostructured graphene, DNRF103, and EU Horizon 2020 “Graphene Flagship” 696656. T.J.B. and P.R.W. acknowledge financial support from EU FP7-6040007 “GLADIATOR” and Innovation Fund Denmark Da-Gate 0603-005668B. P.R.K. acknowledges a Lindemann Trust Fellowship

Advanced EFL learners' beliefs about language learning and teaching: a comparison between grammar, pronunciation, and vocabulary

This paper reports on the results of a study exploring learners’ beliefs on the learning and teaching of English grammar, pronunciation and vocabulary at tertiary level. While the importance of learners’ beliefs on the acquisition process is generally recognized, few studies have focussed on and compared learners’ views on different components of the language system. A questionnaire containing semantic scale and Likert scale items probing learners’ views on grammar, pronunciation and vocabulary was designed and completed by 117 native speakers of Dutch in Flanders, who were studying English at university. The analysis of the responses revealed that (i) vocabulary was considered to be different from grammar and pronunciation, both in the extent to which an incorrect use could lead to communication breakdown and with respect to the learners’ language learning strategies, (ii) learners believed in the feasibility of achieving a native-like proficiency in all three components, and (iii) in-class grammar, pronunciation and vocabulary exercises were considered to be useful, even at tertiary level. The results are discussed in light of pedagogical approaches to language teaching

N95 Respirator Reuse, Decontamination Methods, and Microbial Burden: a Randomized Controlled Trial

PURPOSE: to evaluate the effectiveness and ease of N95 respirator decontamination methods in a clinic setting and to identify the extent of microbial colonization on respirators associated with reuse. METHODS: In a prospective fashion, N95 respirators (n = 15) were randomized to a decontamination process (time, dry heat, or ultraviolet C light [UVC]) in outpatient clinics. Each respirator was re-used up to 5 separate clinic sessions. Swabs on each respirator for SARS-CoV-2, bacteria, and fungi were obtained before clinic, after clinic and post-treatment. Mask integrity was checked after each treatment (n = 68). Statistical analyses were performed to determine factors for positive samples. RESULTS: All three decontamination processes reduced bacteria counts similarly. On multivariate mixed model analysis, there were an additional 8.1 colonies of bacteria (95% CI 5.7 to 10.5; p \u3c 0.01) on the inside compared to the outside surface of the respirators. Treatment resulted in a decrease of bacterial load by 8.6 colonies (95% CI -11.6 to -5.5; p \u3c 0.01). Although no decontamination treatment affected the respirator filtration efficiency, heat treatments were associated with the breakdown of thermoplastic elastomer straps. Contamination with fungal and SARS-CoV-2 viral particles were minimal to non-existent. CONCLUSIONS: Time, heat and UVC all reduced bacterial load on reused N95 respirators. Fungal contamination was minimal. Heat could permanently damage some elastic straps making the respirators nonfunctional. Given its effectiveness against microbes, lack of damage to re-treated respirators and logistical ease, UVC represents an optimal decontamination method for individual N95 respirators when reuse is necessary

Chemical Sensing Using Fiber Cavity Ring-Down Spectroscopy

Waveguide-based cavity ring-down spectroscopy (CRD) can be used for quantitative measurements of chemical concentrations in small amounts of liquid, in gases or in films. The change in ring-down time can be correlated to analyte concentration when using fiber optic sensing elements that change their attenuation in dependence of either sample absorption or refractive index. Two types of fiber cavities, i.e., fiber loops and fiber strands containing reflective elements, are distinguished. Both types of cavities were coupled to a variety of chemical sensor elements, which are discussed and compared

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Effect of Bamlanivimab vs Placebo on Incidence of COVID-19 Among Residents and Staff of Skilled Nursing and Assisted Living Facilities: A Randomized Clinical Trial

IMPORTANCE Preventive interventions are needed to protect residents and staff of skilled nursing and assisted living facilities from COVID-19 during outbreaks in their facilities. Bamlanivimab, a neutralizing monoclonal antibody against SARS-CoV-2, may confer rapid protection from SARS-CoV-2 infection and COVID-19. OBJECTIVE To determine the effect of bamlanivimab on the incidence of COVID-19 among residents and staff of skilled nursing and assisted living facilities. DESIGN, SETTING, AND PARTICIPANTS Randomized, double-blind, single-dose, phase 3 trial that enrolled residents and staff of 74 skilled nursing and assisted living facilities in the United States with at least 1 confirmed SARS-CoV-2 index case. A total of 1175 participants enrolled in the study from August 2 to November 20, 2020. Database lock was triggered on January 13, 2021, when all participants reached study day 57. INTERVENTIONS Participants were randomized to receive a single intravenous infusion of bamlanivimab, 4200mg (n = 588), or placebo (n = 587). MAIN OUTCOMES AND MEASURES The primary outcomewas incidence of COVID-19, defined as the detection of SARS-CoV-2 by reverse transcriptase–polymerase chain reaction and mild or worse disease severity within 21 days of detection, within 8 weeks of randomization. Key secondary outcomes included incidence of moderate or worse COVID-19 severity and incidence of SARS-CoV-2 infection. RESULTS The prevention population comprised a total of 966 participants (666 staff and 300 residents) who were negative at baseline for SARS-CoV-2 infection and serology (mean age, 53.0 [range, 18-104] years; 722 [74.7%] women). Bamlanivimab significantly reduced the incidence of COVID-19 in the prevention population compared with placebo (8.5%vs 15.2%; odds ratio, 0.43 [95%CI, 0.28-0.68]; P < .001; absolute risk difference, −6.6 [95%CI, −10.7 to −2.6] percentage points). Five deaths attributed to COVID-19 were reported by day 57; all occurred in the placebo group. Among 1175 participants who received study product (safety population), the rate of participants with adverse events was 20.1% in the bamlanivimab group and 18.9% in the placebo group. The most common adverse events were urinary tract infection (reported by 12 participants [2%] who received bamlanivimab and 14 [2.4%] who received placebo) and hypertension (reported by 7 participants [1.2%] who received bamlanivimab and 10 [1.7%] who received placebo). CONCLUSIONS AND RELEVANCE Among residents and staff in skilled nursing and assisted living facilities, treatment during August-November 2020 with bamlanivimab monotherapy reduced the incidence of COVID-19 infection. Further research is needed to assess preventive efficacy with current patterns of viral strains with combination monoclonal antibody therapy