bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laser ablation method for the generation of chromium, iron, manganese, nickel, scandium, titanium and vanadium, nanoparticles: control of size and properties
Authors: Simakin Alexander V , Baimler Ilya V , Uvarov Oleg V , Rakov Ignat I , Gudkov Sergey V 
Published: September 2020

Abstract
Using method of laser ablation of massive targets in liquids, nanoparticles (NP) of chromium, iron, manganese, nickel, scandium, titanium and vanadium with controlled characteristics were generated. To generate NP with the desired characteristics, both ablation of macro-sized butt and fragmentation are consumed. Laser fragmentation is the process of melting large NP into small ones using laser radiation. The influence on the distribution of NP by diameter (size) of such key parameters of laser irradiation as the density of energy of beam of laser in the medium and power of the laser is determined. To obtain NP devoid of surface oxide films, organic solvents or water saturated with molecular hydrogen were used as a working fluid. The proposed approaches allow one to obtain NP that meet the following criteria: 1). the type of NP tends to be spherical; 2). 95% of NP have a certain radius; 3). NP consist of a single chemical element, the quantity of impurities is minimal; 4). the crystal lattice of NP is metallic. If necessary, it is possible to generate NP with a surface layer consisting from oxides, as well as fully oxidized NP.
Modeling of the development of the Vuktyl field hydrocarbon system in the depletion mode using a bench installation
Authors: Skibitskaya N.A. , Volkov A.N. , Latishev A.A. , Indrupsky I.M. , Popov A.A. , Bolshakov M.N. , Kuzmin V.A. , Marutyan O.O. 
Published: September 2020

Abstract
The work substantiates the location of liquid hydrocarbons (LH – oil and retrograde condensate) in the dynamic, filtering part of the capacitive volumes of gas-saturated productive deposits of gas condensate and oil and gas condensate fields (GCF and OGCF). The necessity of the development and bench modeling of the production of LH from gas-saturated deposits of GCF and OGCF in the late stages of field development is shown due to the high geological reserves of LH in them and the need to develop them with the aim of component recovery increasing and extending the life of the fields. The experience of bench modeling on the experimental installation of the life cycle of the oil and gas condensate system of the Vuktyl OGCF for the period of its development on the “depletion” mode is described. On the basis of a highly permeable core model, a simulation of the initial fluid saturation was successfully held which fits the initial state of the reservoir system of the Vuktyl OGCF, including the LC (reservoir oil), and also the current thermobaric state and fluid saturation of the reservoir system were simulated. The total mass of LH (reservoir oil and retrograde condensate) in the reservoir model is determined which can be taken as a basis for calculating the LH extraction rate while carrying out further research on bench modeling of LH production technologies in the late stages of Vuktil field development on the core model created. As a result of the works described above, an oil and gas condensate system was created in a highly permeable bench core model which is the model of depleted to maximum condensation pressure reservoir of Vuktyl OGCF.
Chemical stability of modern jet fuels
Authors: Vlasenkova L A , Shatalov K V , Likhterova N M 
Published: September 2020

Abstract
The article shows the need to study the chemical stability of jet engine fuels containing components of deep oil refining and offers a method for studying the chemical stability of jet engine fuels. Based on this method, research was conducted on jet engine fuels of various production technologies and the influence of the hydrocarbon composition on the chemical stability of a mixture of individual hydrocarbons was studied. The inhibitory effect of aromatic hydrocarbons in a mixture with different content of naphthenic hydrocarbons has been studied. Using artificial aging of jet engine fuels, a low level of chemical stability of jet engine fuels based on hydrocracking of vacuum oil strips is shown.
Purification of hydrocarbon-contaminated soils by silicon-rich substances
Authors: Wei X , Matichenkov V V , Bocharnikova E A , Sevostianov S M 
Published: September 2020

Abstract
Hydrocarbon (HC) contamination of soil occurs during oil extraction, transportation and treatment. To enhance the efficacy of HC-polluted soil restoration is an important challenge. In greenhouse and field experiments, two silicon (Si)-rich substances were tested for reduction of HC content in diesel + used motor oil contaminated soil. Over 3 months the HC content decreased from 3 to 2.8; 1.1 and 0.8% in control, calcium silicate slag- and amorphous Si dioxide-treated soils, respectively. Silicon-rich substances remarkably increased the catalase and dehydrogenase activities in the contaminated soil. Several mechanisms underlying the Si-mediated purification of HC-contaminated soil are suggested: a) changing soil physical properties; b) capsulation of HC molecules by polysilicic acid; c) adsorption of monosilicic acid by HCs leading to enhanced hydrophilicity; d) direct effect on soil microbial activity. Many types of Si-rich materials are cheap and available in large volumes (industrial by-products) that potentially could be used for the purification of HC-polluted environment after ecological expertise of the absence of inorganic pollutants.
PbO2decorated ZnO-TiO2core-shell nanoflower structures by zinc anodising for photo- and anodic degradation of Reactive Black-5 dye
Authors: Harito Christian , Zaidi Syed Z.J. , Bavykin Dmitry V. , Martins Alysson S. , Yuliarto Brian , Walsh Frank C. , de León Carlos Ponce 
Published: September 2020

AbstractThis work shows that metallic zinc can be used as a low-cost substrate or electrode for photocatalyst and electrocatalyst use by anodising in mild bicarbonate solution. Electrochemical anodising was used to produce ZnO nanowires by controlling operational conditions and dip-coating the anodised surface with TiO2to produce a core-shell coating with photocatalytic properties. The PbO2,which is known as good electrocatalyst, was electrodeposited over the ZnO-TiO2core-shell structure to alter its surface for electrocatalytic degradation of dye. The electrochemical and photocatalytic behaviours of the coatings were analysed for the removal of RB-5 dye as model pollutant. For the ZnO-TiO2core-shell, the photocatalytic removal mechanism was driven by the heterojunction photocatalytic effect of photocatalytically active anatase TiO2and wurtzite ZnO. Photocatalysis was switched to electrocatalytic behaviour after incorporation of PbO2.Although the UV light might be blocked by PbO2, the electrochemical degradation was enhanced due to the creation of·OH free radicals over the PbO2particles decorating a ZnO-TiO2core-shell composite coating.
Pulse shape discrimination and exploration of scintillation signals using convolutional neural networks
Authors: Griffiths J , Kleinegesse S , Saunders D , Taylor R , Vacheret A 
Published: September 2020

Abstract
We demonstrate the use of a convolutional neural network to perform neutron-gamma pulse shape discrimination, where the only inputs to the network are the raw digitised silicon photomultiplier signals from a dual scintillator detector element made of 6Li F:ZnS(Ag) scintillator and PVT plastic. A realistic labelled dataset was created to train the network by exposing the detector to an AmBe source, and a data-driven method utilising a separate photomultiplier tube was used to assign labels to the recorded signals. This approach is compared to the charge integration and continuous wavelet transform methods and a simpler artificial neural net. It is found to provide superior levels of discrimination, achieving an area under the curve of 0.996 ± 0.003. We find that the neural network is capable of extracting interpretable features directly from the raw data. In addition, by visualising the high-dimensional representations of the network with the t-SNE algorithm, we discover that not only is this method robust to minor mislabeling of the training dataset but that it is possible to identify an underlying substructure within the signals that goes beyond the original labelling. This technique could be utilised to explore and cluster complex, raw detector data in a novel way that may reveal more insights than standard analysis methods.
The political economy of Biafra separatism and post-war Igbo nationalism in Nigeria
Authors: Nwangwu Chikodiri , Onuoha Freedom C , Nwosu Bernard U , Ezeibe Christian 
Published: September 2020

Abstract
The past two decades that coincide with the return of civil rule in most African countries have witnessed the reinforcement of ethnic nationalism and separatist agitations. While scholarly attention has focused on ethnicity to explain the revival of ethnic nationalism, how ethnic and class discourses conflate in the pursuit of ethnic nationalism remains understudied. Using a qualitative-dominant approach, this article interrogates how the Igbo petty bourgeoisie use ethnicity to mask the underlying differences in their material conditions in relation to the alienated masses. It also examines how these differences shape post-war Igbo nationalism. In the main, this article argues that the intersection of ethnic and class discourses is underpinned by unequal distribution of rights and powers accruing from productive resources. This unequal distribution of rights and powers results in differential material well-being and gives rise to conflicts between the dominant and subordinate classes. This explains the divergent approaches of the different factions of Igbo petty bourgeoisie to Igbo nationalism in Nigeria. The article concludes that understanding the political economy of the intersection of ethnic and class discourses is relevant for resolving the nationality question and the Biafra secessionist agitations in Nigeria and others across Africa.
Adversarial deconfounding autoencoder for learning robust gene expression embeddings
Authors: Dincer Ayse B , Janizek Joseph D , Lee Su-In 
Published: September 2020

Abstract

Motivation
Increasing number of gene expression profiles has enabled the use of complex models, such as deep unsupervised neural networks, to extract a latent space from these profiles. However, expression profiles, especially when collected in large numbers, inherently contain variations introduced by technical artifacts (e.g. batch effects) and uninteresting biological variables (e.g. age) in addition to the true signals of interest. These sources of variations, called confounders, produce embeddings that fail to transfer to different domains, i.e. an embedding learned from one dataset with a specific confounder distribution does not generalize to different distributions. To remedy this problem, we attempt to disentangle confounders from true signals to generate biologically informative embeddings.

Results
In this article, we introduce the Adversarial Deconfounding AutoEncoder (AD-AE) approach to deconfounding gene expression latent spaces. The AD-AE model consists of two neural networks: (i) an autoencoder to generate an embedding that can reconstruct original measurements, and (ii) an adversary trained to predict the confounder from that embedding. We jointly train the networks to generate embeddings that can encode as much information as possible without encoding any confounding signal. By applying AD-AE to two distinct gene expression datasets, we show that our model can (i) generate embeddings that do not encode confounder information, (ii) conserve the biological signals present in the original space and (iii) generalize successfully across different confounder domains. We demonstrate that AD-AE outperforms standard autoencoder and other deconfounding approaches.

Availability and implementation
Our code and data are available at https://gitlab.cs.washington.edu/abdincer/ad-ae.

Contact

Supplementary information
Supplementary data are available at Bioinformatics online.
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores
Authors: Ono Yukiteru , Asai Kiyoshi , Hamada Michiaki 
Published: September 2020

Abstract

Motivation
Recent advances in high-throughput long-read sequencers, such as PacBio and Oxford Nanopore sequencers, produce longer reads with more errors than short-read sequencers. In addition to the high error rates of reads, non-uniformity of errors leads to difficulties in various downstream analyses using long reads. Many useful simulators, which characterize long-read error patterns and simulate them, have been developed. However, there is still room for improvement in the simulation of the non-uniformity of errors.

Results
To capture characteristics of errors in reads for long-read sequencers, here, we introduce a generative model for quality scores, in which a hidden Markov Model with a latest model selection method, called factorized information criteria, is utilized. We evaluated our developed simulator from various points, indicating that our simulator successfully simulates reads that are consistent with real reads.

Availability and implementation
The source codes of PBSIM2 are freely available from https://github.com/yukiteruono/pbsim2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mortality and Prognostic Factors of Nontuberculous Mycobacterial Infection in Korea: A Population-based Comparative Study
Authors: Lee Hyewon , Myung Woojae , Lee Eun-Mi , Kim Hyekyeong , Jhun Byung Woo 
Published: September 2020

Abstract

Background
Population-based studies on the mortality burden of nontuberculous mycobacteria (NTM) infection are lacking. We compared the long-term mortality of NTM-infected patients with tuberculosis (TB)-patients and the general population, and investigated mortality-associated factors.

Methods
We analyzed nationwide-data from the Korean National Health Insurance and Korea-Statistical Office between 2002 and 2017. NTM infection was identified using the International Classification of Disease, Tenth Revision code, with one-to-one matching to TB patients and general population controls.

Results
A total of 530 401 individuals were analyzed, including 183 267 with NTM infections; 166 666 with TB; and 180 468 controls. The overall 6-, 10-, and 14-year cumulative survival probabilities in the NTM group were 86.3%, 80.8%, and 77.1%, respectively, which were significantly lower than those of the TB or control groups (log-rank P &lt; .0001). In cases of NTM and TB coinfection, the overall 6-, 10-, and 14-year cumulative survival probabilities were 75.1%, 65.4%, and 57.0%, respectively. Multivariable analysis indicated that old age, male gender, province, and various respiratory or nonrespiratory comorbidities were significantly associated with mortality of NTM infection. The use of a macrolide (more than 1 year) negatively correlated with mortality of NTM infection (adjusted hazard ratio [aHR] 0.61, 95% confidence interval [CI] .53–.71), regardless of azithromycin (aHR 0.60, 95% CI .43–.85) or clarithromycin use (aHR 0.63, 95% CI .53–.75).

Conclusions
NTM-infected patients had poor prognosis when compared to TB patients or the general population, especially for NTM and TB coinfection. NTM mortality was associated with certain demographic characteristics, but long-term use of macrolides may provide survival benefits.
Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Avidity Maturation and Association with Disease Severity
Authors: Luo Yiqi Ruben , Chakraborty Indrani , Yun Cassandra , Wu Alan H B , Lynch Kara L 
Published: September 2020

Abstract
The kinetics of IgG avidity maturation during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was studied. The IgG avidity assay, using a novel label-free immunoassay technology, revealed a strong correlation between IgG avidity and days since symptom onset. Peak readings were significantly higher in severe than mild disease cases.
An aortic root abscess in a patient with a bicuspid aortic valve: a case report
Authors: Balzan Elyse , Borg Alexander 
Published: September 2020

Abstract

Background
Infective endocarditis is a serious infection associated with high mortality and severe complications, such as heart failure, uncontrolled infection, and embolic events. Certain populations, including individuals with a prosthetic valve and those with native valve disease, such as bicuspid aortic valve, are considered to be more at risk of developing infective endocarditis.

Case summary
A 51-year-old previously healthy male presented with a 2-week history of persistent fever, malaise, and night sweats despite taking a long course of oral antibiotics. Examination was unremarkable; however, blood tests showed elevated inflammatory markers. Three sets of blood cultures revealed coagulase-negative gram-positive cocci (later identified as Staphylococcus lugdunensis), and the patient was subsequently started on IV antibiotics. His echocardiography showed a bicuspid aortic valve with severe regurgitation, and an aortic root abscess surrounding a dilated aortic root. In view of the presence of locally uncontrolled infection, the patient was referred for urgent debridement of the abscess and replacement of the aortic valve with tissue prosthesis. Fortunately, after a total of 6 weeks of IV antibiotics and successful operative management, our patient made a complete recovery.

Discussion
The development of an aortic root abscess occurs in 10–40% of cases of aortic valve endocarditis. Clinically, this should be suspected in any patient with endocarditis who fails to improve despite appropriate antibiotic therapy. This case demonstrates that severe infective endocarditis can develop in apparently healthy individuals due to underlying cardiac abnormalities.
Nonesterified Fatty Acids and Hospitalizations Among Older Adults: The Cardiovascular Health Study
Authors: Ahiawodzi Peter D , Buzkova Petra , Djousse Luc , Ix Joachim H , Kizer Jorge R , Mukamal Kenneth J 
Published: September 2020

Abstract

Background
We sought to determine associations between total serum concentrations of nonesterified fatty acids (NEFAs) and incident total and cause-specific hospitalizations in a community-living cohort of older adults.

Methods
We included 4715 participants in the Cardiovascular Health Study who had fasting total serum NEFA measured at the 1992/1993 clinic visit and were followed for a median of 12 years. We identified all inpatient admissions requiring at least an overnight hospitalization and used primary diagnostic codes to categorize cause-specific hospitalizations. We used Cox proportional hazards regression models to determine associations with time-to-first hospitalization and Poisson regression for the rate ratios (RRs) of hospitalizations and days hospitalized.

Results
We identified 21 339 hospitalizations during follow-up. In fully adjusted models, higher total NEFAs were significantly associated with higher risk of incident hospitalization (hazard ratio [HR] per SD [0.2 mEq/L] = 1.07, 95% confidence interval [CI] = 1.03–1.10, p &lt; .001), number of hospitalizations (RR per SD = 1.04, 95% CI = 1.01–1.07, p = .01), and total number of days hospitalized (RR per SD = 1.06, 95% CI = 1.01–1.10, p = .01). Among hospitalization subtypes, higher NEFA was associated with higher likelihood of mental, neurologic, respiratory, and musculoskeletal causes of hospitalization. Among specific causes of hospitalization, higher NEFA was associated with diabetes, pneumonia, and gastrointestinal hemorrhage.

Conclusions
Higher fasting total serum NEFAs are associated with a broad array of causes of hospitalization among older adults. While some of these were expected, our results illustrate a possible utility of NEFAs as biomarkers for risk of hospitalization, and total days hospitalized, in older adults. Further research is needed to determine whether interventions based on NEFAs might be feasible.
Demographic and Socioeconomic Disparities in Life Expectancy With Hearing Impairment in the United States
Authors: West Jessica S , Lynch Scott M 
Published: September 2020

AbstractObjectivesHearing impairment is one of the most common disabilities among older people, and its prevalence will increase as the U.S. population ages. However, little is known about social disparities in onset or transitions into and out of hearing impairment, nor how these transitions impact years of life to be spent impaired.MethodWe investigate the number of years an “average” person can expect to live with and without hearing impairment after age 50; sex, race, educational, and regional differences in these expectancies; and the implication of hearing impairment for remaining life expectancy. Bayesian multistate life table methods are applied to 9 waves of data from the Health and Retirement Study (1998–2014) to investigate social disparities in life expectancy with hearing impairment (n = 20,200) for the general population, people hearing impaired at age 50, and people hearing unimpaired at age 50.ResultsMen, Hispanics, persons with less educational attainment, and those born in the south can expect to live a larger proportion of their remaining lives hearing impaired. Although transitions from hearing impaired to unimpaired occur, those with some hearing impairment at age 50 can expect to live more years with hearing impairment, and hearing impairment does not shorten remaining life expectancy.DiscussionSignificant sociodemographic disparities in hearing impaired life expectancy exist. In contrast to past research, we find that hearing impairment does not affect total life expectancy. Future research should consider the consequences of hearing impairment for years to be lived with other age-related and potentially downstream health outcomes.
Debt Stress and Debt Illusion: The Role of Consumer Credit, Reverse and Standard Mortgages
Authors: Haurin Donald R , Moulton Stephanie , Loibl Cäzilia , Brown Julia K 
Published: September 2020

Abstract

Objectives
This study examines the relationship of debt stress and reverse mortgage borrowing and compares it to stress from standard mortgages and consumer debt. Debt stress is measured as a self-reported response to the amount of debt.

Methods
Using a unique national data set of 1,026 homeowners who chose whether to obtain a reverse mortgage in 2010, we estimate the relationship of 2014 levels of debt stress with various types of debt, assets, and income. Using an ordered probit model, we address the endogeneity of our measures of mortgage and consumer debt using an instrumental variables regression model.

Results
We found that consumer debt causes more stress per dollar of debt compared to mortgage debt. Reverse mortgages cause a relatively low level of stress per dollar of debt compared with standard mortgage debt. The average treatment effect of originating a reverse mortgage indicates statistically significantly higher probability of reporting no and not very much debt stress.

Discussion
Reverse mortgage debt causes a complex stress response. Stress per dollar of debt is lower for reverse than standard mortgages 4 years after origination. However, reverse mortgages’ loan balance grows over time causing total stress to increase, while stress from a standard mortgage decreases as it is repaid. If an older adult uses reverse mortgage funds to repay consumer debt then total stress is reduced.