•Sequencing results and cost were compared for three library kits and benchtop sequencers.•Breadth of coverage at genome termini was influenced by library preparation.•The Ion Torrent S5 generates ...more high-quality reads at lower cost than the PGM.•Indels in homopolymer regions were observed in Ion Torrent S5 consensus genomes.•Illumina MiSeq was the least expensive platform for low-throughput runs.
Next-generation sequencing is a powerful tool for virological surveillance. While Illumina® and Ion Torrent® sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. The Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms were evaluated using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The Ion Torrent S5 510 chip runs produced more reads at a lower cost per sample than the highest output Ion Torrent PGM 318 chip run, and generated the highest proportion of reads for enterovirus D68 samples. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., Ion Torrent 510 and Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 and Illumina MiSeq V2) there is less of a difference in the cost per sample between the two sequencing platforms ($5.47-$10.25 more per sample for an Ion Torrent 530 chip run when multiplexing 24 samples). These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs.
Objective
Quantitative data on visual outcomes after trans-sphenoidal surgery is lacking in the literature. This study aims to address this by quantitatively assessing visual field outcomes after ...endoscopic trans-sphenoidal pituitary adenectomy using the capabilities of modern semi-automated kinetic perimetry.
Methods
Visual field area (deg
2
) calculated on perimetry performed before and after surgery was statistically analysed. Functional improvement was assessed against UK driving standards.
Results
Sixty-four patients (128 eyes) were analysed (May 2016–Nov 2019). I4e and I3e isopter area significantly increased after surgery (
p
< 0.0001). Of eyes with pre-operative deficits: 80.7% improved and 7.9% worsened; the median amount of improvement was 60% (IQR 6–246%). Median increase in I4e isopter was 2213deg
2
(IQR 595–4271deg
2
) and in I3e isopter 1034 deg
2
(IQR 180–2001 deg
2
). Thirteen out of fifteen (87%) patients with III4e data regained driving eligibility after surgery. Age and extent of resection (EOR) did not correlate with visual improvement. Better pre-operative visual field area correlated with a better post-operative area (
p
< 0.0001). However, the rate of improvement in the visual field area increased with poorer pre-operative vision (
p
< 0.0001).
Conclusions
A median visual field improvement of 60% may be expected in over 80% of patients. Functionally, a significant proportion of patients can expect to regain driving eligibility. EOR did not impact on visual recovery. When the primary goal of surgery is alleviating visual impairment, optic apparatus decompression without the aim for gross total resection appears a valid strategy. Patients with the worst pre-operative visual field often experience the greatest improvement, and therefore, poor pre-operative vision alone should not preclude surgical intervention.
Background
The object of this study was to assess whether increasing operative experience results in greater endoscopic trans-sphenoidal resection of pituitary macroadenomas and lower complications.
...Methods
A retrospective single institution cohort study was performed. Subjects underwent endoscopic trans-sphenoidal resection of pituitary macroadenoma between July 2009 and July 2016 by three neurosurgeons. Following data collection, statistical analysis compared percentage of tumor resection and length of hospital stay (LOS) with experience. Complications including CSF leak are reported.
Results
In total, 142 patients (87 male, 55 female) mean age 55.1 were included. Surgeon 1 performed 106 cases; surgeon 2 performed 23 cases; and surgeon 3 performed 13 cases. Mean pre-operative tumor volumes were 8.18 cm
3
, 6.52 cm
3
, and 3.47 cm
3
and post-operative volumes were 2.21, 1.74, and 1.93 cm
3
for surgeons 1, 2, and 3, respectively. Respective percentage resections were 74.3, 77.2, and 52.1%. Analysis demonstrated no difference in tumor resection with increasing experience for all three surgeons (
p
= 0.11,
p
= 0.17, and
p
= 0.26). Tumor consistency and cavernous sinus involvement did not appear to affect tumor resection. Mean LOS was 5 days, 4 days, and 3 days, respectively, with no significant correlation with experience for all three surgeons. Intraoperative CSF leak incidence was 19/106 (18%) for surgeon 1, 6/23(26%) for surgeon 2, and 2/13(15%) for surgeon 3. Primary closure rate was 96.3% and only three other complications occurred.
Conclusions
This study demonstrates that in our institution there is no statistically significant learning curve for the endoscopic resection of pituitary macroadenoma. However, there is a trend of improvement in tumor resection with experience for one surgeon. These findings suggest that the surgeons in our institution were capable of performing this procedure effectively with a low complication rate since adoption of the endoscopic technique in 2009.
In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and ...the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.
Mechanical stress in interconnections is a problem of growing importance in VLSI devices. The origins of this stress are discussed, and a measurement technique based on the determination of wafer ...curvature with a laser scanning device is described. The changes in stress observed during thermal cycles are interpreted quantitatively in terms of a simple model of elastic and plastic strain in the metal. The effects of changes in deposition conditions, film composition, and film structure are discussed.
The politicization of climate change and the difficulty of achieving multi-level or sectoral stakeholder coordination are common institutional barriers to effective climate change adaptation ...governance outcomes. In the U.S., quasi-government organizations (QGOs) were designed to overcome such barriers, albeit traditionally for non-climatic purposes. This study’s objective is to illustrate how the design characteristics of QGOs may be useful for overcoming the above climate adaptation barriers. Methodologically, this paper analyzes six case studies, selected to illustrate the major characteristics of QGOs, of climate-focused and non climate-focused QGOs at the sub-national level in the U.S. Non climate-focused examples are included for comparison with, and to supplement, the limited number of QGOs currently working on climate efforts. For each case, this study focuses on eight design characteristics: seven that represent measures of political and financial independence, and one focused on board composition, to illustrate the extent to which QGOs enable multi-level and multi-sectoral stakeholder coordination. This study finds that among the assortment of existing QGO designs some are particularly well suited to overcoming either the politicization of climate adaptation policy or obstacles to enhancing policy coordination, while some reduce both, albeit to a lesser extent. Broadly, this paper concludes that QGOs can strengthen effective action by depoliticizing informational sources and fostering cross scale coordination of planning and implementation.
Face masks and personal respirators are used to curb the transmission of SARS-CoV-2 in respiratory droplets; filters embedded in some personal protective equipment could be used as a non-invasive ...sample source for applications, including at-home testing, but information is needed about whether filters are suited to capture viral particles for SARS-CoV-2 detection. In this study, we generated inactivated virus-laden aerosols of 0.3-2 microns in diameter (0.9 µm mean diameter by mass) and dispersed the aerosolized viral particles onto electrostatic face mask filters. The limit of detection for inactivated coronaviruses SARS-CoV-2 and HCoV-NL63 extracted from filters was between 10 to 100 copies/filter for both viruses. Testing for SARS-CoV-2, using face mask filters and nasopharyngeal swabs collected from hospitalized COVID-19-patients, showed that filter samples offered reduced sensitivity (8.5% compared to nasopharyngeal swabs). The low concordance of SARS-CoV-2 detection between filters and nasopharyngeal swabs indicated that number of viral particles collected on the face mask filter was below the limit of detection for all patients but those with the highest viral loads. This indicated face masks are unsuitable to replace diagnostic nasopharyngeal swabs in COVID-19 diagnosis. The ability to detect nucleic acids on face mask filters may, however, find other uses worth future investigation.
Carotid artery invasion by squamous cell carcinoma of the upper aerodigestive tract is a poor prognostic indicator and a relative indicator of tumour inoperability. A number of imaging modalities are ...available for detecting such invasion, but, because of its availability, computerised tomography (CT) is the usual modality. We have analysed the CT scans of 196 patients referred to the department with an upper aerodigestive tract squamous cell carcinoma. Comparing the scans with the operative findings indicates that CT scans significantly overestimate carotid artery invasion.
SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor ...binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
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•The receptor-binding motif (RBM) is a highly variable region of SARS-CoV-2 spike•RBM mutation N439K has emerged independently in multiple lineages•N439K increases spike affinity for hACE2; viral fitness and disease are unchanged•N439K confers resistance to several mAbs and escapes some polyclonal responses
Epidemiological, clinical, molecular, and structural characterization of the N439K mutation in the SARS-CoV-2 spike receptor binding motif demonstrates that it results in similar viral fitness compared to wild-type while conferring resistance against some neutralizing monoclonal antibodies and reducing the activity of some polyclonal antibody responses.
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