ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application

Abstract Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository

Band gap opening by two-dimensional manifestation of Peierls instability in graphene

Using first-principles calculations of graphene having high-symmetry distortion or defects, we investigate band gap opening by chiral symmetry breaking, or intervalley mixing, in graphene and show an intuitive picture of understanding the gap opening in terms of local bonding and antibonding hybridizations. We identify that the gap opening by chiral symmetry breaking in honeycomb lattices is an ideal two-dimensional (2D) extension of the Peierls metal-insulator transition in 1D linear lattices. We show that the spontaneous Kekule distortion, a 2D version of the Peierls distortion, takes place in biaxially strained graphene, leading to structural failure. We also show that the gap opening in graphene antidots and armchair nanoribbons, which has been attributed usually to quantum confinement effects, can be understood with the chiral symmetry breaking

Semiconductor-less vertical transistor with I-ON/I-OFF of 10(6)

Semiconductors have long been perceived as a prerequisite for solid-state transistors. Although switching principles for nanometer-scale devices have emerged based on the deployment of two-dimensional (2D) van der Waals heterostructures, tunneling and ballistic currents through short channels are difficult to control, and semiconducting channel materials remain indispensable for practical switching. In this study, we report a semiconductor-less solid-state electronic device that exhibits an industry-applicable switching of the ballistic current. This device modulates the field emission barrier height across the graphene-hexagonal boron nitride interface with ION/IOFF of 106 obtained from the transfer curves and adjustable intrinsic gain up to 4, and exhibits unprecedented current stability in temperature range of 15–400 K. The vertical device operation can be optimized with the capacitive coupling in the device geometry. The semiconductor-less switching resolves the long-standing issue of temperature-dependent device performance, thereby extending the potential of 2D van der Waals devices to applications in extreme environments. © 2021, The Author(s).1

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Component model synthesis using model updating with neural networks

A component model synthesis (CMS) has been explored by carrying out model updating with neural networks. Structural system identification was achieved by applying the degree of freedom (DOF)-based reduction method and the inverse perturbation method. Experimental vibration data were restored to a full finite element model to update the numerical model. The experimental data were obtained using the specific sensor location selection method. The system identification was improved using the system equivalent reduction-expansion process by carrying out proper orthogonal decomposition. The proposed CMS was applied for a tank bracket model by simplifying the bolt assembly. Top and bottom parts of the tank bracket were each constructed to have a modally equivalent model. The convolutional neural network was adopted by training the density, Young's modulus and contact properties to improve the computational efficiency.N

The Right to Urban Streams: Quantitative Comparisons of Stakeholder Perceptions in Defining Adaptive Stream Restoration

Assuring healthy streams in the urban environment is a major goal for restoration scientists, urban planners, and city practitioners around the globe. In South Korea, many urban stream restoration efforts are designed to provide safe water to society and enhance ecological functions. We examined the extent to which the individual interests and different values of multiple stakeholders were considered in previous decision-making in two urban stream restoration projects. The relevant data on stream restoration were collected through the nominal group technique (NGT) and the analytic hierarchy process (AHP) for the two stream cases of a populated inland area and a coastal region in South Korea. The AHP results provide information about the comparative weights of the values of ecological restoration (priority score: 0.487), social restoration (priority score: 0.231), and landscape revitalization (priority score: 0.279) of the Ahn-Yang stream and ecological restoration (priority score: 0.527), social restoration (priority score: 0.182), and landscape revitalization (priority score: 0.290) of the Sahn-Jee stream. The stakeholders of the populated metropolitan area had a relatively high awareness of their role in environmental restoration, thus it was natural for them to place a high value on social restoration

Structural and quantum-state phase transition in van der Waals layered materials

Van der Waals layered transition metal dichalcogenides can exist in many different atomic and electronic phases. Such diverse polymorphisms not only provide a route for investigating novel topological states, such as quantum spin Hall insulators, superconductors and Weyl semimetals, but may also have applications in fields ranging from electronic and optical/quantum devices to electrochemical catalysis. And the methods for triggering robust phase transitions between polymorphs are evolving and diversifying - several growth processes, high-pressure/strain methods, and optical, electronic and chemical treatments have been developed. Here, we discuss recent progress on phase transitions and the related physics in layered materials, and demonstrate unique features compared with conventional solid-state materials. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved182