Molybdenum Disulfide Nanoribbons with Enhanced Edge Nonlinear Response and Photoresponsivity.

MoS2 nanoribbons have attracted increased interest due to their properties, which can be tailored by tuning their dimensions. Herein, the growth of MoS2 nanoribbons and triangular crystals formed by the reaction between films of MoOx (2

Hunting for mpox (monkeypox) mimickers: Use of the Biofire meningitis/encephalitis panel on lesion swabs to support alternative viral diagnoses.

BACKGROUND: Mpox (formerly monkeypox) is an emerging zoonotic disease of public health concern that presents as a rash mimicking other common viral exanthems. Unlike traditional testing algorithms relying on several assays, the BioFire FilmArray meningitis/encephalitis (ME) panel simultaneously detects common viruses causing rashes; however, Biofire ME is only licensed for testing on cerebral spinal fluid. OBJECTIVES: This study evaluated use of the Biofire ME panel for detection and discrimination of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), varicella zoster virus (VZV), human herpesviruses type 6 (HHV-6), enteroviruses (EVs), and human paraechoviruses (HPeVs) from a dermal or mucocutaneous swabs collected in universal transport media (UTM). STUDY DESIGN: Results of the BioFire ME panel were compared against methods used during clinical testing. Ten-fold serial dilutions in UTM of cultured viruses were used to compare analytical sensitivity, and analytical specificity was assessed using panels of microorganisms in UTM. Clinical sensitivity and specificity were assessed using 20 positive specimens each for HHV-1, HHV-2, HHV-6, VZV, EVs, and HPeV, as well as 35 known negative specimens that included 15 mpox-positive specimens. RESULTS: Biofire ME was as sensitive as comparator methods, and correctly discriminated all HSV-1, HSV-2, VZV, HHV-6, EVs, and HPeVs from mpox and mpox-mimickers. Cross-reaction between EV and rhinoviruses A, B, and C were noted in the specificity panel. CONCLUSIONS: Swabs in UTM collected for mpox testing are suitable for use on the Biofire ME panel, allowing more streamlined diagnostic testing for viral exanthems in patients under investigation for mpox infection.

Pseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007.

Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus Pseudoxanthomonas but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most Pseudoxanthomonas species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4 % similarity to each other but only 97.73-98.29 % to their closest relatives, Pseudoxanthomonas spadix or Pseudoxanthomonas helianthi. Bacteria were studied by whole genome sequencing using average nucleotide identity by Blastn, digital DNA-DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name Pseudoxanthomonas winnipegensis sp. nov. for this cluster. Pseudoxanthomonas spadix DSM 18855T, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Pseudoxanthomonas spadix Young et al. 2007 to document that observation.

Congenital nasal pyriform aperture stenosis: Analysis of twenty cases at a single institution.

OBJECTIVES: Congenital nasal pyriform aperture stenosis (CNPAS) is a rare cause of neonatal respiratory distress that is difficult to treat. The primary objective of this study was to identify factors that predict the need for initial and revision surgery for CNAPS. The secondary objective is to identify risk factors in maternal history associated with the development of CNPAS. METHODS: Infants with CNPAS between 2010 and 2017 were identified by ICD- 9 and 10 codes. Demographics, maternal history, anatomic features on imaging and medical and/or surgical management were reviewed. Frequencies, means and standard deviations were calculated. A p-value <.05 was considered significant. RESULTS: Twenty infants were included. All underwent flexible nasal endoscopy with inability to pass the scope in either nostril in 65% of infants. Nineteen had a CT scan and 13 had a MRI with midline defects in 76.3% and 53.8%, respectively. Solitary central mega-incisor was present in 65%. Half underwent surgical intervention at a mean age of 74.8 days, with 90% requiring revision surgery. There was no difference in pyriform aperture distance in the surgical and non-surgical patient subgroups (5.4 mm and 5.2 mm, p = .6 respectively). No specific variables were predictive of need for initial or revision surgery. Maternal diabetes mellitus (MDM) was found in 55% of mothers of infants with CNPAS. CONCLUSION: Pyriform aperture distance was not a predictor of surgical intervention. MRI should be considered in all infants with CNPAS as the rate of intracranial complications is high. MDM may be a risk factor for CNPAS.

Intracranial complications of acute sinusitis in children: The role of endoscopic sinus surgery.

OBJECTIVE: To study the role of endoscopic sinus surgery (ESS) in the management of intracranial complications of children with acute rhinosinusitis METHODS: Retrospective chart review at a tertiary care pediatric hospital MAIN OUTCOMES: Demographics, intracranial complications, length of hospital stay (LOS), neurological sequelae, ESS, neurosurgical procedures RESULTS: Twenty-four children with a mean age (SD) of 12.9 years (+/-3.2) with an intracranial complication(s) of acute rhinosinusitis were identified between 2005-2016. A total of 22 were included and 15 (68%) of these were males. The most common complications were: subdural abscess (n=10), epidural abscess (n=10), meningitis (n=5), intraparenchymal abscess (n=5), and cavernous sinus thrombosis (n= 2). Neurologic symptoms included headache (n=12), hemiparesis (n=5) and aphasia (n=3). Average length of stay was 16 (+/- 9.2) days. Average follow up was 7 (+/-5.6) months. One patient had residual seizures and 1 had recurrent rhinosinusitis. Aphasia and hemiparesis resolved in all patients within 1 year. Nineteen (86%) patients had ESS within 4 days of admission. Fourteen patients (63%) had a neurosurgical procedure, 6 (27%) required more than 1 neurosurgical procedure. Six patients (27%) had concurrent neurosurgical drainage and ESS. Four patients (17%) had neurosurgical procedure followed by ESS and 3 patients (13%) were treated only by a neurosurgical procedure. Patients who underwent ESS prior to a neurosurgical procedure had significantly less risk of needing a neurosurgical intervention (OR = .02, p < .01). There was a significantly higher proportion of neurosurgical patients with positive Strep anginosus cultures compared to the ESS only group (85.7% vs 37.5%, p = .02). Studies with larger patient populations are needed to determine the role of ESS in the management of intracranial complications of children with acute rhinosinusitis. DISCUSSION: Early ESS may be associated with less need for neurosurgical procedures.

Outbreak of Norovirus GII.P17-GII.17 in the Canadian Province of Nova Scotia.

Background. Norovirus is the leading cause of viral gastroenteritis, with GII.4 being the most common circulating genotype. Recently, outbreaks in China revealed that norovirus GII.17 GII.P17 had become predominant. Objective. This study aimed to characterize the distribution of norovirus genotypes circulating in Nova Scotia. Methods. Stool specimens were collected from gastrointestinal outbreaks in Nova Scotia between Jan 2014 and June 2015 and subjected to real-time RT-PCR. Norovirus-positive specimens were referred to the National Microbiology Laboratory for sequence-based genotyping. Results. The first norovirus GII.P17-GII.17 outbreak in Canada was identified, but no widespread activity was observed in Nova Scotia. Discussion. It is unknown whether GII.P17-GII.17 is more widespread in Canada since contributions to Canadian surveillance are too sparse to effectively monitor the epidemiology of emerging norovirus genotypes. Conclusions. Presence of norovirus GII.17:P17 in Canada highlights the need for more systematic surveillance to ensure that molecular targets used for laboratory detection are effective and help understand norovirus evolution, epidemiology, and pathogenesis.

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Epidemiology of Enterovirus D68 in Ontario.

In August 2014, children's hospitals in Kansas City, Missouri and Chicago, Illinois notified the Centers for Disease Control and Prevention (CDC) about increased numbers of pediatric patients hospitalized with severe respiratory illness (SRI). In response to CDC reports, Public Health Ontario Laboratories (PHOL) launched an investigation of patients being tested for enterovirus D-68 (EV-D68) in Ontario, Canada. The purpose of this investigation was to enhance our understanding of EV-D68 epidemiology and clinical features. Data for this study included specimens submitted for EV-D68 testing at PHOL from September 1, 2014 to October 31, 2014. Comparisons were made between patients who tested positive for the virus (cases) and those testing negative (controls). EV-D68 was identified in 153/907 (16.8%) of patients tested. In the logistic regression model adjusting for age, sex, setting and time to specimen collection, individuals younger than 20 years of age were more likely to be diagnosed with EV-D68 compared to those 20 and over, with peak positivity at ages 5-9 years. Cases were not more likely to be hospitalized than controls. Cases were more likely to be identified in September than October (OR 8.07; 95% CI 5.15 to 12.64). Routine viral culture and multiplex PCR were inadequate methods to identify EV-D68 due to poor sensitivity and inability to differentiate EV-D68 from other enterovirus serotypes or rhinovirus. Testing for EV-D68 in Ontario from July to December, 2014 detected the presence of EV-D68 virus among young children during September-October, 2014, with most cases detected in September. There was no difference in hospitalization status between cases and controls. In order to better understand the epidemiology of this virus, surveillance for EV-D68 should include testing of symptomatic individuals from all treatment settings and patient age groups, with collection and analysis of comprehensive clinical and epidemiological data.

Detection of enterovirus D68 in Canadian laboratories.

The recent emergence of a severe respiratory disease caused by enterovirus D68 prompted investigation into whether Canadian hospital and provincial laboratories can detect this virus using commercial and laboratory-developed assays. This study demonstrated analytical sensitivity differences between commercial and laboratory-developed assays for the detection of enterovirus D68.

A mobile biosafety microanalysis system for infectious agents.

Biological threats posed by pathogens such as Ebola virus must be quickly diagnosed, while protecting the safety of personnel. Scanning electron microscopy and microanalysis requires minimal specimen preparation and can help to identify hazardous agents or substances. Here we report a compact biosafety system for rapid imaging and elemental analysis of specimens, including powders, viruses and bacteria, which is easily transportable to the site of an incident.

Unforeseen high temperature and humidity stability of FeCl3 intercalated few layer graphene.

We present the first systematic study of the stability of the structure and electrical properties of FeCl3 intercalated few-layer graphene to high levels of humidity and high temperature. Complementary experimental techniques such as electrical transport, high resolution transmission electron microscopy and Raman spectroscopy conclusively demonstrate the unforseen stability of this transparent conductor to a relative humidity up to 100% at room temperature for 25 days, to a temperature up to 150°C in atmosphere and to a temperature as high as 620°C in vacuum, that is more than twice higher than the temperature at which the intercalation is conducted. The stability of FeCl3 intercalated few-layer graphene together with its unique values of low square resistance and high optical transparency, makes this material an attractive transparent conductor in future flexible electronic applications.

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform.

Studying fungal biodiversity using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables.Here, we introduce PIPITS, an open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.We provide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.

A filtration based technique for simultaneous SEM and TEM sample preparation for the rapid detection of pathogens.

Diagnostic electron microscopy for infectious diseases has the advantage that "everything" in the specimen can be observed, without a priori knowledge of the likely identity of the microorganisms present in the sample. The classical specimen preparation method used employs a droplet of sample, which allows particles to adsorb to a support film, and is subsequently negative stained. This "grid on drop" procedure has a sensitivity range of approximately 106 viruses per mL if no enrichment procedures are used. In the current investigation we present a novel use of filtration that allows us to detect viruses at concentrations as low as 102 viruses per mL. We present here methods based on filtration, in which total virus, and not virus concentration, is the limiting factor for detection. We show that filtration is more sensitive than conventional negative staining and can detect as few as 5 × 103 particles per sample.

Detection of circulating norovirus genotypes: hitting a moving target.

BACKGROUND: Although national surveillance programs are in place to monitor norovirus epidemiology, the emergence of new strains and the genetic diversity among genotypes can be challenging for clinical laboratories. This study evaluated the analytical and clinical performance characteristics of one real-time RT-PCR and two end-point RT-PCRs commonly used in microbiology laboratories. METHODS: Lower limit of detection (LoD) was determined using 10-fold dilutions of noroviruses belonging to different genotypes. The clinical performance of the real-time and end-point RT-PCRs was assessed in parallel using nucleic acids extracted from 186 stool specimens. RESULTS: The real-time RT-PCR was highly sensitive and specific for the detection of norovirus genotypes that are currently circulating in Canada. In contrast, the two end-point RT-PCRs displayed poor analytical sensitivity or complete failure to detect certain norovirus genotypes, which was correlated to sequence mismatches in the primer-binding sites. In an attempt to improve norovirus detection with the end-point RT-PCRs, both assays were processed concurrently and detection from either assay was considered a positive result. Concurrent testing resulted in only a modest increase in clinical sensitivity (75.0%) compared to each assay alone (62.5% and 71.9%). However, the false positivity rate increased from 1.98% and 3.36% for the assays alone to 5.47% with concurrent testing. CONCLUSIONS: This study emphasizes the benefits of a real-time method and provides support for routine surveillance to monitor norovirus epidemiology and ongoing proficiency testing to ensure detection of circulating norovirus genotypes.

How do filovirus filaments bend without breaking?

Viruses of the Mononegavirales have helical nucleocapsids containing a single-stranded negative-sense RNA genome complexed with the nucleoprotein and several other virus-encoded proteins. This RNA-protein complex acts as the template for replication and transcription during infection. Recent structural data has advanced our understanding of how these functions are achieved in filoviruses, which include dangerous pathogens such as Ebola virus. Polyploid filoviruses package multiple genome copies within strikingly long filamentous viral envelopes, which must be flexible to avoid breakage of the 19kb non-segmented genomic RNA. We review how the structure of filoviruses and paramyxoviruses permits this morphological flexibility in comparison to rhabdoviruses that have short, bullet-shaped virions with relatively rigid envelopes.

MS-H: a novel proteomic approach to isolate and type the E. coli H antigen using membrane filtration and liquid chromatography-tandem mass spectrometry (LC-MS/MS).

Serotyping is the long-standing gold standard method to determine E. coli H antigens; however, this method requires a panel of H-antigen specific antibodies and often culture-based induction of the H-antigen flagellar motility. In this study, a rapid and accurate method to isolate and identify the Escherichia coli (E. coli) H flagellar antigen was developed using membrane filtration and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Flagella were isolated from pure culture, digested with trypsin, and then subjected to LC-MS/MS using one of two systems (Agilent-nano-LC-QSTAR XL or Proxeon-nano-LC-LTQ-Orbitrap XL). The resulting peptide sequence data were searched against a custom E. coli flagella/H antigen database. This approach was evaluated using flagella isolated from reference E. coli strains representing all 53 known H antigen types and 41 clinical E. coli strains. The resulting LC-MS/MS classifications of H antigen types (MS-H) were concordant with the known H serogroup for all 53 reference types, and of 41 clinical isolates tested, 38 (92.7%) were concordant with the known H serogroup. MS-H clearly also identified two clinical isolates (4.9%) that were untypeable by serotyping. Notably, successful detection and classification of flagellar antigens with MS-H did not generally require induction of motility, establishing this proteomic approach as more rapid and cost-effective than traditional methods, while providing equitable specificity for typing E. coli H antigens.

Higher-order mode fiber enables high energy chirped-pulse amplification.

Energy scaling of femtosecond fiber lasers has been constrained by nonlinear impairments and optical fiber damage. Reducing the optical irradiance inside the fiber by increasing mode size lowers these effects. Using an erbium-doped higher-order mode fiber with 6000 µm(2) effective area and output fundamental mode re-conversion, we show a breakthrough in pulse energy from a monolithic fiber chirped pulse amplification system using higher-order mode propagation generating 300 µJ pulses with duration <500 fs (FWHM) and peak power >600 MW at 1.55 µm. The erbium-doped HOM fiber has both a record large effective mode area and excellent mode stability, even when coiled to reasonable diameter. This demonstration proves efficacy of a new path for high energy monolithic fiber-optic femtosecond laser systems.