bluuebunny/crossref_metadata_2025_split huggingface dataset:
Medical control of a pulse wave fiber optic sensors
Authors: Gerashchenko M , Badeeva E , Murashkina T , Gerashchenko S 
Published: December 2019

Abstract
The modern level of development of systems of measurement, processing and data transmission promote creation of optical multiple parameter medical diagnostic systems. One of intensively developed directions is creation of fiber-optical diagnostic systems on the basis of fiber optic sensors. Fiber optic sensors are characterized by high sensitivity to mechanical oscillations of a surface of a body of the patient under power influence of a blood flow. This property creates premises for design miniature, steady against noises, safe sensors of micromovements. Their fixing on a body of the patient allows to reveal a number of the vital parameters characterizing normal and critical condition of the patient. Results of a research of fiber optic sensors of pressure on the basis of standard single-mode optical SMF-28 fiber are presented in article. The principle of operation of sensors consists in use of physical properties of the fiber - the impact which had in some pressure point on throughput characteristic. The purpose of the real work is the research of a possibility of use of fiber optic sensors of the tunnel, flexural and microflexural types on Bragg’s grid for control of a pulse wave providing more exact determination of parameters of a pulse wave. The offered monitoring systems of a status of patients on the basis of fiber optic sensors in medicine are very perspective.
Optical methods for droplets evaporation on graphene nanocomposite surfaces
Authors: Babenko D D , Dmitriev A S 
Published: December 2019

Abstract
We study the evaporation of water droplets on the surface of graphene nanocomposites of different compositions. Methods for manufacturing samples of nanocomposites, optical methods for studying contact angles and evaporation dynamics are described. New experimental data are presented on the behavior of contact angles and evaporation rates at various temperatures for samples of nanocomposites in both the constant contact line mode and the constant contact angle mode. The features of evaporation for nanocomposites with inclusions of boron nitride and aluminum nitride nanoparticles inside graphene samples are noted.
The combination of PIV and heat flux measurement in study of flow and heat transfer near a circular finned cylinder
Authors: Sapozhnikov S Z , Mityakov V Yu , Seroshtanov V V , Gusakov A A 
Published: December 2019

Abstract
The flow and heat transfer of the finned cylinder are investigated by the methods of PIV, gradient heat flux measurement and thermometry. On the hollow model of a circular cylinder heated by saturated water vapor at atmospheric pressure, five annular fins of 20 mm high and of 10 mm thick are mounted. For the first model, the “acting” fin was hollow, for the second, it was solid and made of titanium alloy VT22. The remaining four fins simulated flow blockage. To visualize the flow in the intercostal space, the fin simulators were made of Perspex. Battery gradient heat flux sensors (GHFSs) with volt-watt sensitivity of 10 mV/W, were installed on the “acting” fin at different distances from the surface of the carrier cylinder. The cylinder rotated around its axis at an angle of φ = 0…180°, which made it possible to obtain the distribution of heat flux over the surface of the fin. By combining PIV diagnostics and gradient heat flux measurement, it was possible to obtain a complex 3D structure of the flow in the intercostal space and the distribution of heat flux on the surface of the fin. The values of the local heat transfer coefficients (HTCs) were also obtained. The dependence of HTC on flow mode and intercostal space is revealed. Comparison of the obtained characteristics for models with hollow and solid fins allowed us to determine in experiment fin efficiency for different intercostal spaces and free-stream velocities. The combination of all three technologies opens up new possibilities in study of flow and convective heat transfer.
Immersion laser-induced ultrasound imaging of solids with complex macroscopic geometry of surface
Authors: Zarubin V , Bychkov A , Simonova V , Cherepetskaya E , Karabutov A 
Published: December 2019

Abstract
In this paper a real-time experimental system and algorithms for immersion two-dimensional laser ultrasonic imaging of solids with complex geometry of surface are presented. Wideband probe ultrasonic pulse is generated photoacoustically in an opaque plate, which absorbs pulsed laser radiation. The back-scattered acoustic field is recorded by a multi-element piezoelectric array. The signals are used to reconstruct refraction-corrected ultrasonic images, which are post-processed to determine positions of the external and internal boundaries of the object. The numerical simulations are carried out to verify the developed algorithms. The proposed approach allowed measuring the positions of the boundaries of the polymethyl methacrylate (PMMA) sample with accuracy of ∼0.1 mm in the direction of the probe beam propagation, and ~0.2-0.3 mm in the perpendicular direction.
Acoustic properties of LNM crystal
Authors: Velikovskii D Yu , Kokshaiskii A I , Milkov M G , Sukharev V A 
Published: December 2019

Abstract
We report linear acoustic and acousto-optical properties of LiNa5Mo9O30 (LNM) single crystal. This relatively new crystal, known for its complex crystallographic structure, is optically biaxial with high birefringence of 0.2545 at 450.2 nm, and crystals that consist of molybdates are widely used in different applications, from cintillators, double β-decay detectors, “dark matter” sensors to electro optics. The lowest measured propagation velocity of shear wave was 1200 m/s, and for the longitudinal mode it was 4100 m/s, which are a relatively low value for crystalline media. The maximum attenuation of the longitudinal wave at a frequency of 180 MHz was moderate and equal 20 dB/cm·GHz2. The values of the acousto-optic figure of merit for light diffraction on a longitudinal acoustic wave were also determined, the maximum value of the coefficient was 13 c.u., which exceeds the efficiency of the one used in AO devices material α-SiO2. Thus, the set of measured acoustic and elastic-optical properties shows a new promising optically biaxial material for acousto-optics, which needs for further researching.
Selective scheme of gas concentration measurement based on acousto-optic spectral filters with multi-frequency control signal
Authors: Pisarevsky Yu V , Kolesnikov S A , Lomonov V A , Vinogradov A V 
Published: December 2019

Abstract
A scheme for measuring the concentration of components of gas mixtures improving the selectivity of conventional optical absorption spectroscopy is proposed. The scheme is based on the use of acousto-optic spectral filter as a dispersion element which is fed simultaneously several control signals with frequencies corresponding to the maxima and minima of absorption in the optical spectrum of the measured gas. The scheme is implemented on the basis of the acousto-optic filter based on paratellurite TeO2 crystal, providing the high resolution achieved by reducing the absorption of ultrasound due to the special technology of the growth of high quality crystals and the use of absorption anisotropy of ultrasound in paratellurite. Experimental verification of this approach with measuring the concentration of nitrogen dioxide has confirmed the effectiveness of the proposed scheme.
Estimation of the image quality correction efficiency in optical measurement systems under Scheimpflug condition
Authors: Pechinskaya O V 
Published: December 2019

Abstract
A criterion for evaluating the image quality correction efficiency in optical systems under Scheimpflug conditions is proposed. The limits of applicability of the geometric optics approximation are clarified for the sensor tilt angle calculating. The results of a simulation optical stereoscopic system arm for three cases: normal, oblique system not under the Scheimpflug condition and oblique system under the Scheimpflug condition are presented. The quantitative estimation of the image quality correction efficiency is performed. The ranges of object distances and viewing angles, providing the maximum image quality correction without loss of accuracy due to perspective distortion are defined.
UDSMProt: universal deep sequence models for protein classification
Authors: Strodthoff Nils , Wagner Patrick , Wenzel Markus , Samek Wojciech 
Published: January 2020

Abstract

Motivation
Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step.

Results
We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies.

Availability and implementation
Source code is available under https://github.com/nstrodt/UDSMProt.

Supplementary information
Supplementary data are available at Bioinformatics online.
A U-statistics for integrative analysis of multilayer omics data
Authors: Wang Xiaqiong , Wen Yalu 
Published: January 2020

Abstract

Motivation
The emerging multilayer omics data provide unprecedented opportunities for detecting biomarkers that are associated with complex diseases at various molecular levels. However, the high-dimensionality of multiomics data and the complex disease etiologies have brought tremendous analytical challenges.

Results
We developed a U-statistics-based non-parametric framework for the association analysis of multilayer omics data, where consensus and permutation-based weighting schemes are developed to account for various types of disease models. Our proposed method is flexible for analyzing different types of outcomes as it makes no assumptions about their distributions. Moreover, it explicitly accounts for various types of underlying disease models through weighting schemes and thus provides robust performance against them. Through extensive simulations and the application to dataset obtained from the Alzheimer’s Disease Neuroimaging Initiatives, we demonstrated that our method outperformed the commonly used kernel regression-based methods.

Availability and implementation
The R-package is available at https://github.com/YaluWen/Uomic.

Supplementary information
Supplementary data are available at Bioinformatics online.
A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics
Authors: Zhang Haoyu , Zhao Ni , Ahearn Thomas U , Wheeler William , García-Closas Montserrat , Chatterjee Nilanjan 
Published: January 2020

SummaryCancers are routinely classified into subtypes according to various features, including histopathological characteristics and molecular markers. Previous genome-wide association studies have reported heterogeneous associations between loci and cancer subtypes. However, it is not evident what is the optimal modeling strategy for handling correlated tumor features, missing data, and increased degrees-of-freedom in the underlying tests of associations. We propose to test for genetic associations using a mixed-effect two-stage polytomous model score test (MTOP). In the first stage, a standard polytomous model is used to specify all possible subtypes defined by the cross-classification of the tumor characteristics. In the second stage, the subtype-specific case–control odds ratios are specified using a more parsimonious model based on the case–control odds ratio for a baseline subtype, and the case–case parameters associated with tumor markers. Further, to reduce the degrees-of-freedom, we specify case–case parameters for additional exploratory markers using a random-effect model. We use the Expectation–Maximization algorithm to account for missing data on tumor markers. Through simulations across a range of realistic scenarios and data from the Polish Breast Cancer Study (PBCS), we show MTOP outperforms alternative methods for identifying heterogeneous associations between risk loci and tumor subtypes. The proposed methods have been implemented in a user-friendly and high-speed R statistical package called TOP (https://github.com/andrewhaoyu/TOP)
The Practice of States on Air Defense Identification Zones: Geographical Scope, Object of Identification, and Identification Measures
Authors: Su Jinyuan 
Published: January 2020

Abstract
This note provides a survey of the practice of States on ADIZs. It is found that while some ADIZs are entirely within territorial airspace, most extend beyond the outer limit into the airspace above the EEZs and even the high seas; and in the part beyond territorial airspace, transiting aircraft are prevalently subject to identification. Transiting military aircraft, which most of the time refuse to identify themselves voluntarily by submitting a flight plan or reporting their positions, may nevertheless be identified passively through radar detection, radio communication or close visual check. As most ADIZs are within the claiming State’s FIRs, transiting civil aircraft can be identified “unconsciously” through civil air traffic control. Where an ADIZ extends beyond the claiming State’s FIRs, most transiting civil aircraft comply with voluntary identification measures, presumably due to the light extra burden incurred. The non-compliant are easy to identify through passive means such as radar detection and radio communication, with the use of close visual check highly unnecessary.
Influenza Vaccine Effectiveness Against Influenza-Related Mortality in Australian Hospitalized Patients: A Propensity Score Analysis
Authors: Nation Monica L , Moss Robert , Spittal Matthew J , Kotsimbos Tom , Kelly Paul M , Cheng Allen C 
Published: January 2020

Abstract

Background
Data on influenza vaccine effectiveness (IVE) against mortality are limited, with no Australian data to guide vaccine uptake. We aimed to assess IVE against influenza-related mortality in Australian hospitalized patients, assess residual confounding in the association between influenza vaccination and mortality, and assess whether influenza vaccination reduces the severity of influenza illness.

Methods
Data were collected between 2010 and 2017 from a national Australian hospital-based sentinel surveillance system using a case-control design. Adults and children admitted to the 17 study hospitals with acute respiratory symptoms were tested for influenza using nucleic acid testing; all eligible test-positive cases, and a subset of test-negative controls, were included. Propensity score analysis and multivariable logistic regression were used to determine the adjusted odds ratio (aOR) of vaccination, with IVE = 1 – aOR × 100%. Residual confounding was assessed by examining mortality in controls.

Results
Over 8 seasons, 14038 patients were admitted with laboratory-confirmed influenza. The primary analysis included 9298 cases and 6451 controls, with 194 cases and 136 controls dying during hospitalization. Vaccination was associated with a 31% (95% confidence interval [CI], 3%–51%; P = .033) reduction in influenza-related mortality, with similar estimates in the National Immunisation Program target group. Residual confounding was identified in patients ≥65 years old (aOR, 1.92 [95% CI, 1.06–3.46]; P = .031). There was no evidence that vaccination reduced the severity of influenza illness (aOR, 1.07 [95% CI, .76–1.50]; P = .713).

Conclusions
Influenza vaccination is associated with a moderate reduction in influenza-related mortality. This finding reinforces the utility of the Australian vaccination program in protecting those most at risk of influenza-related deaths.
Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics
Authors: Whittles Lilith K , White Peter J , Didelot Xavier 
Published: January 2020

Abstract

Background
Gonorrhea incidence is increasing rapidly in many countries, while antibiotic resistance is making treatment more difficult. Combined with evidence that two meningococcal vaccines are likely partially protective against gonorrhea, this has renewed interest in a gonococcal vaccine, and several candidates are in development. Key questions are how protective and long-lasting a vaccine needs to be, and how to target it. We assessed vaccination’s potential impact and the feasibility of achieving the World Health Organization’s (WHO) target of reducing gonorrhea incidence by 90% during 2018–2030, by comparing realistic vaccination strategies under a range of scenarios of vaccine efficacy and duration of protection, and emergence of extensively-resistant gonorrhea.

Methods
We developed a stochastic transmission-dynamic model, incorporating asymptomatic and symptomatic infection and heterogeneous sexual behavior in men who have sex with men (MSM). We used data from England, which has a comprehensive, consistent nationwide surveillance system. Using particle Markov chain Monte Carlo methods, we fitted to gonorrhea incidence in 2008–2017, then used Bayesian forecasting to examine an extensive range of scenarios.

Results
Even in the worst-case scenario of untreatable infection emerging, the WHO target is achievable if all MSM attending sexual health clinics receive a vaccine offering ≥ 52% protection for ≥ 6 years. A vaccine conferring 31% protection (as estimated for MeNZB) for 2–4 years could reduce incidence in 2030 by 45% in the worst-case scenario, and by 75% if &gt; 70% of resistant gonorrhea remains treatable.

Conclusions
Even a partially-protective vaccine, delivered through a realistic targeting strategy, could substantially reduce gonorrhea incidence, despite antibiotic resistance.
Effects of Influenza Vaccination in the United States During the 2018–2019 Influenza Season
Authors: Chung Jessie R , Rolfes Melissa A , Flannery Brendan , Prasad Pragati , O’Halloran Alissa , Garg Shikha , Fry Alicia M , Singleton James A , Patel Manish , Reed Carrie ,   US Influenza Vaccine Effectiveness Network, the Influenza Hospitalization Surveillance Network, and the Assessment Branch, Immunization Services Division, Centers for Disease Control and Prevention, Kim Sara S , Martin Emily T , Monto Arnold S , Jackson Michael L , Jackson Lisa A , McLean Huong Q , Belongia Edward A , King Jennifer P , Zimmerman Richard K , Nowalk Mary Patricia , Balasubramani G K , Bear Todd M , Hickey Robert , Raviotta Jonathan M , Suyama Joe , Weissman Alexandra J , Williams John V , Gaglani Manjusha , Raiyani Chandni , Smith Michael , Murthy Kempapura , Clipper Lydia , Reis Michael , Rao Arundhati , Walker Kimberly , Volz Marcus , Mutnal Manohar , Cummings Charisse N , Yousey-Hindes Kimberly , McMullen Chelsea , Chai Shua J , Anderson Evan J , Monroe Maya L , Risk Ilene , Herlihy Rachel , Kim Sue , Spina Nancy , Billing Laurie , Schaffner William , Keipp Talbot H , Thomas Ann , McMahon Melissa 
Published: January 2020

Abstract

Background
Multivalent influenza vaccine products provide protection against influenza A(H1N1)pdm09, A(H3N2), and B lineage viruses. The 2018–2019 influenza season in the United States included prolonged circulation of A(H1N1)pdm09 viruses well-matched to the vaccine strain and A(H3N2) viruses, the majority of which were mismatched to the vaccine. We estimated the number of vaccine-prevented influenza-associated illnesses, medical visits, hospitalizations, and deaths for the season.

Methods
We used a mathematical model and Monte Carlo algorithm to estimate numbers and 95% uncertainty intervals (UIs) of influenza-associated outcomes prevented by vaccination in the United States. The model incorporated age-specific estimates of national 2018–2019 influenza vaccine coverage, influenza virus–specific vaccine effectiveness from the US Influenza Vaccine Effectiveness Network, and disease burden estimated from population-based rates of influenza-associated hospitalizations through the Influenza Hospitalization Surveillance Network.

Results
Influenza vaccination prevented an estimated 4.4 million (95%UI, 3.4 million–7.1 million) illnesses, 2.3 million (95%UI, 1.8 million–3.8 million) medical visits, 58 000 (95%UI, 30 000–156 000) hospitalizations, and 3500 (95%UI, 1000–13 000) deaths due to influenza viruses during the US 2018–2019 influenza season. Vaccination prevented 14% of projected hospitalizations associated with A(H1N1)pdm09 overall and 43% among children aged 6 months–4 years.

Conclusions
Influenza vaccination averted substantial influenza-associated disease including hospitalizations and deaths in the United States, primarily due to effectiveness against A(H1N1)pdm09. Our findings underscore the value of influenza vaccination, highlighting that vaccines measurably decrease illness and associated healthcare utilization even in a season in which a vaccine component does not match to a circulating virus.
Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study
Authors: Kerkhoff Andrew D , Rutishauser Rachel L , Miller Steve , Babik Jennifer M 
Published: January 2020

Abstract
We assessed the real-world utility of universal broad-range polymerase chain reaction sequencing for pathogen detection. Among 1062 clinical samples, 107/1062 (10.1%) had a clinically significant, positive result, with substantial variation by specimen type. Clinical management was changed in 44/1062 (4.1%). These data can help maximize utility of this emerging diagnostic.
Calciphylaxis or vascular oxalosis?
Authors: El-Saygeh Skye , Roese Douglas , Moe Sharon M 
Published: January 2020

AbstractWe report the case of a 31-year-old female with primary hyperoxaluria type 1 with end-stage kidney disease who developed severe peripheral vascular disease leading to limb amputation initially thought to be secondary to calciphylaxis. However, polarized review of the pathologic specimen revealed calcium oxalate deposition in the lumen of blood vessels. This unusual presentation of systemic oxalosis demonstrates the adverse consequences of elevations of serum oxalate in patients with hyperoxaluria and that levels can acutely worsen with abrupt onset of kidney failure.