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  • Oxford University Press (OUP)  (4)
  • 1
    In: Clinical Chemistry, Oxford University Press (OUP), Vol. 68, No. 1 ( 2021-12-30), p. 143-152
    Abstract: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT–qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. Methods We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT–qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. Results After optimization, SwabExpress has a low limit of detection at 2–4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT–qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. Conclusion SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
    Type of Medium: Online Resource
    ISSN: 0009-9147 , 1530-8561
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 2
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2018
    In:  Monthly Notices of the Royal Astronomical Society Vol. 477, No. 2 ( 2018-06-21), p. 1903-1912
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 477, No. 2 ( 2018-06-21), p. 1903-1912
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2016084-7
    SSG: 16,12
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  • 3
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Inflammatory Bowel Diseases Vol. 27, No. Supplement_1 ( 2021-01-21), p. S15-S16
    In: Inflammatory Bowel Diseases, Oxford University Press (OUP), Vol. 27, No. Supplement_1 ( 2021-01-21), p. S15-S16
    Abstract: Although ileal pouch-anal anastomosis (IPAA) is the surgical procedure of choice of many patients with ulcerative colitis and other conditions, some patients may require pouch excision (PE). We aimed to describe our experience with pouch excisions and associated outcomes with an emphasis on late medical, endoscopic, and surgical interventions for IBD. Methods We performed a retrospective review of a prospective colorectal surgery database. All PEs performed at our quaternary pouch center from 2006 – 2019 were included; pelvic exenteration, PE with neo-IPAA or Kock-pouch were excluded. Early complications occurred & lt;30 days, late complications & gt;30 days. Medications taken prior to PE were included if taken within 12 weeks of pouch excision. Data are reported in frequency (proportion) or median (interquartile range). Results A total of 197 cases met inclusion criteria, and were performed by 23 surgeons, median 6 excision (IQR 2 - 14) cases over a 14-year period: of these, 105 had their index pouch created at our quaternary pouch referral center (overall PE rate 2.7%). Indications for PE are shown in Table 1. Median time to PE was 7 years and 94 (48%) patients had re-diversion prior to PE. Medications prior to PE: 34 (17%) steroids, 27 (14%) biologics, and 22 (11%) immune-modulators. The median duration of surgery was 4 hours (3.2–5). The median estimated blood loss was 263 ml (150–500) with 24 patients (12%) requiring at least one unit of packed red blood cells intra-operatively. Most pouch excisions were done through laparotomy; 2 cases (1%) were started robotically and 11 cases (10%) laparoscopically with a 26% conversion rate. Intersphincteric dissection was used in 172 cases (87%) while 26 cases (13%) required abdomino-perineal resection, of which 58% had a neoplastic indication. Intra-operative, early and late complications are shown in Table 2; 40 patients (20%) had perineal wound complications in less than 30 days, while 26 patients (13%) had long-term perineal wound complications, of which 15 patients required return to the operating room. After PE, 23 patients (12%) required continuation of IBD medications, 6 patients (3.1%) required surgery, and 4 patients (2%) required endoscopic intervention for their IBD. Conclusions In this large series of ileoanal pouch excisions, we found that perineal wound complications are common, but infrequently require operative intervention. For most IBD patients in this series, pouch excision did appear to be a destination therapy for IBD with a small minority requiring ongoing medical therapy for IBD.
    Type of Medium: Online Resource
    ISSN: 1078-0998 , 1536-4844
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2022
    In:  Monthly Notices of the Royal Astronomical Society Vol. 510, No. 2 ( 2022-01-05), p. 2657-2670
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 510, No. 2 ( 2022-01-05), p. 2657-2670
    Abstract: Modelling star formation and resolving individual stars in numerical simulations of molecular clouds and galaxies is highly challenging. Simulations on very small scales can be sufficiently well resolved to consistently follow the formation of individual stars, whilst on larger scales sinks that have masses sufficient to fully sample the IMF can be converted into realistic stellar populations. However, as yet, these methods do not work for intermediate scale resolutions whereby sinks are more massive compared to individual stars but do not fully sample the IMF. In this paper, we introduce the grouped star formation prescription, whereby sinks are first grouped according to their positions, velocities, and ages, then stars are formed by sampling the IMF using the mass of the groups. We test our grouped star formation method in simulations of various physical scales, from sub-parsec to kilo-parsec, and from static isolated clouds to colliding clouds. With suitable grouping parameters, this star formation prescription can form stars that follow the IMF and approximately mimic the original stellar distribution and velocity dispersion. Each group has properties that are consistent with a star-forming region. We show that our grouped star formation prescription is robust and can be adapted in simulations with varying physical scales and resolution. Such methods are likely to become more important as galactic or even cosmological scale simulations begin to probe sub-parsec scales.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2016084-7
    SSG: 16,12
    Location Call Number Limitation Availability
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