VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing.

Detection and analysis of viral genomes with Nanopore sequencing has shown great promise in the surveillance of pathogen outbreaks. However, the number of virus detection pipelines supporting Nanopore sequencing is very limited. Here, we present VirPipe, a new pipeline for the detection of viral genomes from Nanopore or Illumina sequencing input featuring streamlined installation and customization. AVAILABILITY AND IMPLEMENTATION: VirPipe source code and documentation are freely available for download at https://github.com/KijinKims/VirPipe, implemented in Python and Nextflow.

Delayed Influenza Treatment in Children With False-Negative Rapid Antigen Test: A Retrospective Single-Center Study in Korea 2016-2019.

BACKGROUND: We aimed to examine the delay in antiviral initiation in rapid antigen test (RAT) false-negative children with influenza virus infection and to explore the clinical outcomes. We additionally conducted a medical cost-benefit analysis. METHODS: This single-center, retrospective study included children (aged < 10 years) with influenza-like illness (ILI), hospitalized after presenting to the emergency department during three influenza seasons (2016-2019). RAT-false-negativity was defined as RAT-negative and polymerase chain reaction-positive cases. The turnaround time to antiviral treatment (TAT) was from the time when RAT was prescribed to the time when the antiviral was administered. The medical cost analysis by scenarios was also performed. RESULTS: A total of 1,430 patients were included, 7.5% were RAT-positive (n = 107) and 2.4% were RAT-false-negative (n = 20). The median TAT of RAT-false-negative patients was 52.8 hours, significantly longer than that of 4 hours in RAT-positive patients (19.2-100.1, P < 0.001). In the multivariable analysis, TAT of ≥ 24 hours was associated with a risk of severe influenza infection and the need for mechanical ventilation (odds ratio [OR], 6.8, P = 0.009 and OR, 16.2, P = 0.033, respectively). The medical cost varied from $11.7-187.3/ILI patient. CONCLUSION: Antiviral initiation was delayed in RAT-false-negative patients. Our findings support the guideline that children with influenza, suspected of having severe or progressive infection, should be treated immediately.

The Epidemiology and Etiology of Cholangitis After Kasai Portoenterostomy in Patients With Biliary Atresia.

OBJECTIVES: We investigated the incidence and characteristics of cholangitis after Kasai portoenterostomy (KPE) in patients with biliary atresia. We also examined the distribution and antimicrobial susceptibility patterns of the causative pathogens, which were isolated in sterile specimens, such as blood and ascites. METHODS: A retrospective chart review was performed in patients with biliary atresia who underwent KPE at Severance Children's Hospital in Korea from 2006 to 2015. The Kaplan-Meier method was used to assess the cumulative incidence of cholangitis. RESULTS: Among the 160 included patients, there were 494 episodes of cholangitis in 126 patients (78.8%) during the study period. The cumulative incidence of cholangitis at 1 and 5 years after KPE was 75.5% and 84.2%, respectively, and cholangitis recurred in most cases (76.2%). The cumulative incidence of culture-proven cholangitis at 1 and 5 years after KPE was 22.1% and 23.9%, respectively. Enterococcus faecium (27.7%) was the most prevalent pathogen, followed by Escherichia coli (14.9%), Enterobacter cloacae (10.6%), and Klebsiella pneumoniae (8.5%). Gram-positive isolates (n = 19) showed low susceptibility to ampicillin (42.1%) and gentamicin (66.7%), and only 38.1% of Gram-negative isolates (n = 21) were susceptible to cefotaxime. CONCLUSIONS: The present study is the largest to show the high incidence and characteristics of cholangitis after KPE in patients with biliary atresia. Enterococcus is a common pathogen of cholangitis after KPE and should be considered when choosing empiric antimicrobial therapy.

Cerebellar infarction after posterior direct reduction and fixation to treat an unstable Jefferson fracture: a case report.

A 42-year-old man had an unstable Jefferson type IV atlas fracture with unilateral vertebral artery occlusion after a diving accident. We performed C1-ring reconstruction with a crosslink rod and C2 fixation to directly reduce the fracture fissure. Within 6 h, cerebellar hemisphere infarction developed. After decompressive craniectomy, duroplasty, and release of the vertebral artery occlusion caused by the transfixing rod, a postoperative computed tomography angiogram showed that blood flow in the right vertebral artery improved. We suggest cautiously inserting screws into the fractured C1 lateral mass and gently tightening the crosslink rod to prevent distal migration of a thrombus.

Electrothermal MEMS parallel plate rotation for single-imager stereoscopic endoscopes.

This work reports electrothermal MEMS parallel plate-rotation (PPR) for a single-imager based stereoscopic endoscope. A thin optical plate was directly connected to an electrothermal MEMS microactuator with bimorph structures of thin silicon and aluminum layers. The fabricated MEMS PPR device precisely rotates an transparent optical plate up to 37° prior to an endoscopic camera and creates the binocular disparities, comparable to those from binocular cameras with a baseline distance over 100 µm. The anaglyph 3D images and disparity maps were successfully achieved by extracting the local binocular disparities from two optical images captured at the relative positions. The physical volume of MEMS PPR is well fit in 3.4 mm x 3.3 mm x 1 mm. This method provides a new direction for compact stereoscopic 3D endoscopic imaging systems.

Neural étendue expander for ultra-wide-angle high-fidelity holographic display.

Holographic displays can generate light fields by dynamically modulating the wavefront of a coherent beam of light using a spatial light modulator, promising rich virtual and augmented reality applications. However, the limited spatial resolution of existing dynamic spatial light modulators imposes a tight bound on the diffraction angle. As a result, modern holographic displays possess low étendue, which is the product of the display area and the maximum solid angle of diffracted light. The low étendue forces a sacrifice of either the field-of-view (FOV) or the display size. In this work, we lift this limitation by presenting neural étendue expanders. This new breed of optical elements, which is learned from a natural image dataset, enables higher diffraction angles for ultra-wide FOV while maintaining both a compact form factor and the fidelity of displayed contents to human viewers. With neural étendue expanders, we experimentally achieve 64 × étendue expansion of natural images in full color, expanding the FOV by an order of magnitude horizontally and vertically, with high-fidelity reconstruction quality (measured in PSNR) over 29 dB on retinal-resolution images.

Management of Neonatal Hepatic Hemangiomas: A Single-Center Experience Focused on Challenging Cases.

Background: Management of hepatic hemangioma (HH) in infancy ranges from close monitoring to surgical resection. We analyzed the clinical characteristics and outcomes of HH according to its treatment options, with particular focus on challenging cases. Methods: Data of patients diagnosed with HHs in their first year of life and followed up for at least 1 year were retrospectively reviewed and divided into treatment and observation groups. Serial imaging results, serum alpha-fetoprotein (AFP) levels, medications, and clinical outcomes were compared. The detailed clinical progress in the treatment group was reviewed separately. Results: A total of 87 patients (75 in the observation group and 12 in the treatment group) were included. The median HH size at the initial diagnosis and the maximum size were significantly larger in the treatment group than the observation group (2.2 [0.5-10.3] cm vs. 1.0 [0.4-4.0] cm and 2.1 [0.7-13.2] vs. 1.1 [0.4-4.0], respectively; all p < 0.05]. The median initial and last serum AFP levels were significantly higher in the treatment group than in the observation group (76,818.7 vs. 627.2 and 98.4 vs. 8.7, respectively; all p < 0.05). Serum AFP levels in both groups rapidly declined during the first 3 months of life and were almost undetectable after 6 months. Among the challenging cases, a large (14 × 10 × 6.5 cm sized) focal HH was successfully treated using stepwise medical-to-surgical treatment. Conclusions: Patients with large HH and mild symptoms can be treated using stepwise pharmacotherapy. More aggressive surgical treatment of tumors unresponsive to initial pharmacotherapy may help shorten the treatment period and improve outcomes.

Placement of a Subclavian Tunneled Hemodialysis Catheter with the Patient's Arm Raised May Reduce the Risk of Complications: Two Cases Report.

The subclavian vein is an uncommon route for tunneled hemodialysis catheter (tHDC) placement because of its potency for future dialysis access. However, when favored access routes have been exhausted because of repeated catheterization or limited life expectancy, the subclavian vein can be used for urgent hemodialysis. A subclavian catheterization has a technical problem. The subclavian vein often forms a right angle with the vena cava, and advancing stiff peel-away sheath can cause a vascular injury. However, raising the patient's arm can alter the position of the guidewire and, therefore, change the angle of the vein favorable for tHDC placement. Herein, we report two patients who underwent subclavian catheterization; one experienced an injury to the superior vena cava after undergoing the conventional procedure, whereas the other patient with raised arm during the catheterization procedure had safe catheter placement.

Factors associated with the response to postnatal dexamethasone use in very low birthweight infants: a nationwide cohort study.

BACKGROUND: Dexamethasone is widely used as a systemic corticosteroid to treat and prevent bronchopulmonary dysplasia (BPD) in preterm infants. We evaluated the current epidemiology of dexamethasone use to prevent BPD and analyse the factors associated with the response to dexamethasone in very low birthweight infants using a nationwide database. METHODS: We included very low birthweight infants born between January 2013 and December 2020 with a gestational age of 23-31 weeks using data from the Korean Neonatal Network registry. Patients were grouped based on their dexamethasone use into 'Dex' or 'No Dex' groups. Clinical variables and data were collected, and the annual trends of dexamethasone use and the proportion of patients who received dexamethasone according to gestational age were analysed. Respiratory outcomes were compared between the groups. Univariate and multivariate analyses were performed to analyse factors associated with the response to dexamethasone in BPD. RESULTS: Of 11 261 eligible infants, 2313 (20.5%) received dexamethasone, and 1714 (74.1%) of them were diagnosed with moderate-to-severe BPD. The 8-year annual prevalence of dexamethasone use was 17.7-22.3%. The 'Dex' group had more moderate-to-severe BPD, more frequent invasive ventilation use at a postmenstrual age of 36 weeks and longer ventilator duration. Birth weight, 5-minute APGAR score, pulmonary hypertension within the first 28 days, surgical treatment of patent ductus arteriosus, medical treatment of patent ductus arteriosus, pathological chorioamnionitis, hydrocortisone or budesonide use, surgical management of necrotising enterocolitis and fungal sepsis were associated with BPD after dexamethasone use. CONCLUSIONS: Approximately 20.5% of preterm infants received dexamethasone, and the frequency increased as gestational age decreased. Poor response to dexamethasone was associated with antenatal and postnatal inflammation, low birth weight and early pulmonary hypertension.

Neural nano-optics for high-quality thin lens imaging.

Nano-optic imagers that modulate light at sub-wavelength scales could enable new applications in diverse domains ranging from robotics to medicine. Although metasurface optics offer a path to such ultra-small imagers, existing methods have achieved image quality far worse than bulky refractive alternatives, fundamentally limited by aberrations at large apertures and low f-numbers. In this work, we close this performance gap by introducing a neural nano-optics imager. We devise a fully differentiable learning framework that learns a metasurface physical structure in conjunction with a neural feature-based image reconstruction algorithm. Experimentally validating the proposed method, we achieve an order of magnitude lower reconstruction error than existing approaches. As such, we present a high-quality, nano-optic imager that combines the widest field-of-view for full-color metasurface operation while simultaneously achieving the largest demonstrated aperture of 0.5 mm at an f-number of 2.