bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on changing the dielectric constant and radar reflection of foamed polyurethane by adding graphite
Authors: Wang Bin , Liu Yangyong , Dong Maogan , Zuo Guolong 
Published: July 2021

Abstract
Polyurethane is often used for filling and plugging in engineering. However, it is difficult to detect the restoration effect by GPR. For the convenience of detection, graphite was added into polyurethane to change its dielectric constant. Five ratios were designed to measure the dielectric constant under dry and wet conditions. The dielectric constant of polyurethane under dry and wet conditions and the relationship between graphite dosage and detection frequency were obtained. The reflection coefficient of polyurethane -air interface to electromagnetic wave is calculated. The reflection coefficient is increased due to the addition of graphite. According to the results of GPR forward modeling, the filling body can be imaged, and the filling effect can be distinguished obviously.
Experimental Research and Numerical Analysis of the Attenuation Law of Ultrasound Propagating in Shale
Authors: Li Xin , Zhang Jie , Zheng Yundong , Li Cuinan , Li Zhilin , Liu Xu , Zhao Zaipeng , Wang Yao , Li Rongxin , Qi Qi , Du Xiaoxiao 
Published: July 2021

Abstract
To study ultrasound’s attenuation law propagating in shale, we first tested the attenuation rate of ultrasound in air and shale by assembling an experimental device by ourselves. The experimentally measured ultrasonic attenuation coefficient in the air is close to the value obtained from most kinds of literature, so our self-assembled practical device is very reliable. By fitting the experimental data, we found that the average attenuation coefficient of ultrasound in the air is 0.0258 dB/m. The average attenuation coefficient in shale is 0.0657 dB/m. As the ultrasonic power increases, the attenuation coefficient of ultrasound gradually increases. Through calculation and analysis using the ultrasonic intensity formula, we found that the effective propagation distance of ultrasound in shale is about 1.2 m.
Molecular dynamics simulation of the effects of temperature on the microscopic deformation of single crystal magnesium containing a void and a crack
Authors: Chen Zhijun , Yao Junping 
Published: July 2021

Abstract
Mechanical properties of a material are intensively influenced by the presence of flaws. While temperature is the significant factor of the deformation. An embedded atomic potential function is used to simulate the micro-defect deformation behavior under different temperatures loading in HCP Mg with various defects. Defects consisting of a fixed distribution of void and an edge crack. the results of the simulation were analyzed by the stress-strain curve and atomic trajectory diagram. The results show that the tensile deformation behavior of single crystal magnesium with defects changes obviously with temperature. Increases in temperature lead to decreased peak stress and ascending crack propagation speeds, and toughening the material to fracture ultimately. But the increase of crack-propagating speed is not obvious when the temperature is above 600K. The time that the crack extends to the void and in combination with it at low temperature is delayed as compared to that at high temperature.
Transfer-free, scalable photodetectors based on MOCVD-grown 2D-heterostructures
Authors: Hutten Ulrike , Daniel Leon , Grundmann Annika , Stracke Nicole , Abdelbaky Mohamed , Beckmann Yannick , Heuken Michael , Mertin Wolfgang , Kalisch Holger , Vescan Andrei , Bacher Gerd , Kümmell Tilmar 
Published: July 2021

Abstract
2D semiconductors based on transition metal dichalcogenides are highly promising for ultrathin photodetectors due to their thickness in the nanometer range and their exceptional light absorption properties. To enable efficient separation of optically generated electron–hole pairs heterostructures have to be implemented, which are usually prepared by poorly controlled mechanical steps such as exfoliation, transfer and stacking processes that prevent industrial upscaling. Here, semitransparent photodetectors in the mm2 range based on MoS2/WS2 heterostructures are presented that are realized without any transfer step by a scalable metal-organic chemical vapor deposition process on a sapphire substrate in a continuous growth run. The heterostructure device exhibits a responsivity, which is enhanced by about 5–6 orders of magnitude with respect to reference devices based on either MoS2 or WS2 monolayers only. The large gain enhancement is attributed to efficient charge carrier separation at the MoS2/WS2 heterointerface combined with hole trapping, leading to an improved electron transport in the heterostructure under illumination.
Graphene-hexagonal boron nitride van der Waals heterostructures: an examination of the effects of different van der Waals corrections
Authors: Sevilla John Radly M , Putungan Darwin B 
Published: July 2021

Abstract
The structural and electronic properties of graphene on hexagonal boron nitride (hBN) as 2D van der Waals heterostructure were calculated using density functional theory method with van der Waals corrections. Four van der Waals corrections, along with conventional PBE-DFT, were utilized: the inter-atomic potentials-based DFT-D2, DFT-D3, Tkatchenko-Sheffler (TS), and the ab-initio, non-local correlation terms-based vdW-DF2-B86R. Results show that the structural properties of the 2D heterostructure, especially the inter-monolayer spacing, are consistent with previous theoretical works. In terms of energetics, the conventional PBE-DFT functional resulted to no binding between graphene and hBN, while utilizing the TS correction resulted to graphene-hBN adhesion energy value that is consistent with previous theoretical and experimental works. Electronic structure wise, the conventional PBE-DFT essentially predicted a zero-gap graphene on hBN, while all calculations involving van der Waals corrections resulted to band gaps that are consistent with previous studies. However, with the exception of TS, all van der Waals corrections predicted a Dirac cone that is shifted upward in energy from the Fermi level, making graphene artificially p-doped. As such, TS is recommended as one of the most appropriate van der Waals corrections for graphene-hBN 2D heterostructure. This work demonstrated the variations in graphene-hBN electronic properties as a result of the different implementations of the van der Waals corrections, but could be as useful as the more expensive theoretical methods such as GW.
A mini-review on proton conduction of BaZrO3-based perovskite electrolytes
Authors: Regalado Vera Clarita Y , Ding Hanping , Peterson David , Gibbons William T , Zhou Meng , Ding Dong 
Published: July 2021

Abstract
Proton conducting ceramics show promise in fuel cells, electrolyzers, permeation membranes, sensor applications, and membrane reactors. Among several types of materials that exhibit proton conduction, perovskite oxides show high proton conductivity at intermediate temperatures, presenting potential benefits for long-term use and lower costs for energy applications. Doped barium zirconate, BaZrO3, is a material that has shown high proton conductivity with encouraging chemical stability. Therefore, it is considered a promising material especially for proton-conducting solid oxide electrochemical cells. Although the proton conduction of doped BaZrO3 has been extensively characterized, the specific phenomena behind its proton conduction are not fully understood. Only recently have specialized techniques and computational tools begun to elucidate the phenomena that determine the conduction properties of the material. In this mini review, an evaluation of the factors affecting the proton conductivity of doped BaZrO3 perovskites and the phenomena governing variations in proton concentration and mobility are presented. Special attention is given to proton interactions with dopants and their resulting effect on hydration and transport properties. Technical strategies are provided to give some guidance on the development of protonic ceramics in energy conversion applications.
Mirage: estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families
Authors: Fukunaga Tsukasa , Iwasaki Wataru 
Published: July 2021

AbstractMotivationReconstruction of gene copy number evolution is an essential approach for understanding how complex biological systems have been organized. Although various models have been proposed for gene copy number evolution, existing evolutionary models have not appropriately addressed the fact that different gene families can have very different gene gain/loss rates.ResultsIn this study, we developed Mirage (MIxtuRe model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates. Mirage can use three models for formulating heterogeneous evolution among gene families: the discretized Γ model, probability distribution-free model and pattern mixture (PM) model. Simulation analysis showed that Mirage can accurately estimate heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that the PM model fits genome data from various taxonomic groups better than the other heterogeneous models. Using Mirage, we revealed that metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated.Availability and implementationThe source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
An astonishing wealth of new proteasome homologs
Authors: Fuchs Adrian C D , Alva Vikram , Lupas Andrei N 
Published: July 2021

Abstract

Motivation
The proteasome is the main proteolytic machine for targeted protein degradation in archaea and eukaryotes. While some bacteria also possess the proteasome, most of them contain a simpler and more specialized homolog, the heat shock locus V protease. In recent years, three further homologs of the proteasome core subunits have been characterized in prokaryotes: Anbu, BPH and connectase. With the inclusion of these members, the family of proteasome-like proteins now exhibits a range of architectural and functional forms, from the canonical proteasome, a barrel-shaped protease without pronounced intrinsic substrate specificity, to the monomeric connectase, a highly specific protein ligase.

Results
We employed systematic sequence searches to show that we have only seen the tip of the iceberg so far and that beyond the hitherto known proteasome homologs lies a wealth of distantly related, uncharacterized homologs. We describe a total of 22 novel proteasome homologs in bacteria and archaea. Using sequence and structure analysis, we analyze their evolutionary history and assess structural differences that may modulate their function. With this initial description, we aim to stimulate the experimental investigation of these novel proteasome-like family members.

Availability and implementation
The protein sequences in this study are searchable in the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) with ProtBLAST/PSI-BLAST and with HHpred (database ‘proteasome_homologs’). The following data are available at https://data.mendeley.com/datasets/t48yhff7hs/3: (i) sequence alignments for each proteasome-like homolog, (ii) the coordinates for their structural models and (iii) a cluster-map file, which can be navigated interactively in CLANS and gives direct access to all the sequences in this study.

Supplementary information
Supplementary data are available at Bioinformatics online.
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)
Authors: Seneviratne Akila J , Peters Sean , Clarke David , Dausmann Michael , Hecker Michael , Tully Brett , Hains Peter G , Zhong Qing 
Published: July 2021

Abstract

Motivation
The output of electrospray ionization–liquid chromatography mass spectrometry (ESI-LC-MS) is influenced by multiple sources of noise and major contributors can be broadly categorized as baseline, random and chemical noise. Noise has a negative impact on the identification and quantification of peptides, which influences the reliability and reproducibility of MS-based proteomics data. Most attempts at denoising have been made on either spectra or chromatograms independently, thus, important 2D information is lost because the mass-to-charge ratio and retention time dimensions are not considered jointly.

Results
This article presents a novel technique for denoising raw ESI-LC-MS data via 2D undecimated wavelet transform, which is applied to proteomics data acquired by data-independent acquisition MS (DIA-MS). We demonstrate that denoising DIA-MS data results in the improvement of peptide identification and quantification in complex biological samples.

Availability and implementation
The software is available on Github (https://github.com/CMRI-ProCan/CRANE). The datasets were obtained from ProteomeXchange (Identifiers—PXD002952 and PXD008651). Preliminary data and intermediate files are available via ProteomeXchange (Identifiers—PXD020529 and PXD025103).

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimation for the bivariate quantile varying coefficient model with application to diffusion tensor imaging data analysis
Authors: Pietrosanu Matthew , Shu Haoxu , Jiang Bei , Kong Linglong , Heo Giseon , He Qianchuan , Gilmore John , Zhu Hongtu 
Published: July 2021

SummaryDespite interest in the joint modeling of multiple functional responses such as diffusion properties in neuroimaging, robust statistical methods appropriate for this task are lacking. To address this need, we propose a varying coefficient quantile regression model able to handle bivariate functional responses. Our work supports innovative insights into biomedical data by modeling the joint distribution of functional variables over their domains and across clinical covariates. We propose an estimation procedure based on the alternating direction method of multipliers and propagation separation algorithms to estimate varying coefficients using a B-spline basis and an $L_2$ smoothness penalty that encourages interpretability. A simulation study and an application to a real-world neurodevelopmental data set demonstrates the performance of our model and the insights provided by modeling functional fractional anisotropy and mean diffusivity jointly and their association with gestational age and sex.
Recombinant erythropoietin does not augment hypothermic white matter protection after global cerebral ischaemia in near-term fetal sheep
Authors: Wassink Guido , Davidson Joanne O , Crisostomo Alyssa , Zhou Kelly Q , Galinsky Robert , Dhillon Simerdeep K , Lear Christopher A , Bennet Laura , Gunn Alistair J 
Published: July 2021

Abstract
Therapeutic hypothermia for hypoxic-ischaemic encephalopathy provides partial white matter protection. Recombinant erythropoietin reduces demyelination after hypoxia-ischaemia, but it is unclear whether adjunct erythropoietin treatment can further improve outcomes after therapeutic hypothermia. Term-equivalent fetal sheep received sham-ischaemia (n = 9) or cerebral ischaemia for 30 min (ischaemia-vehicle, n = 8), followed by intravenous infusion of recombinant erythropoietin (ischaemia-Epo, n = 8; 5000 IU/kg bolus dose, then 833.3 IU/kg/h), cerebral hypothermia (ischaemia-hypothermia, n = 8), or recombinant erythropoietin plus hypothermia (ischaemia-Epo-hypothermia, n = 8), from 3 to 72 h post-ischaemia. Foetal brains were harvested at 7 days after cerebral ischaemia. Ischaemia was associated with marked loss of total Olig2-positive oligodendrocytes with reduced density of myelin and linearity of the white matter tracts (P &lt; 0.01), and microglial induction and increased caspase-3-positive apoptosis. Cerebral hypothermia improved the total number of oligodendrocytes and restored myelin basic protein (P &lt; 0.01), whereas recombinant erythropoietin partially improved myelin basic protein density and tract linearity. Both interventions suppressed microgliosis and caspase-3 (P &lt; 0.05). Co-treatment improved 2′,3′-cyclic-nucleotide 3′-phosphodiesterase-myelin density compared to hypothermia, but had no other additive effect. These findings suggest that although hypothermia and recombinant erythropoietin independently protect white matter after severe hypoxia-ischaemia, they have partially overlapping anti-inflammatory and anti-apoptotic effects, with little additive benefit of combination therapy.
Vaccine Effectiveness Against Acute Respiratory Illness Hospitalizations for Influenza-Associated Pneumonia During the 2015–2016 to 2017–2018 Seasons: US Hospitalized Adult Influenza Vaccine Effectiveness Network (HAIVEN)
Authors: Ghamande Shekhar , Shaver Courtney , Murthy Kempapura , Raiyani Chandni , White Heath D , Lat Tasnim , Arroliga Alejandro C , Wyatt Dayna , Talbot H Keipp , Martin Emily T , Monto Arnold S , Zimmerman Richard K , Middleton Donald B , Silveira Fernanda P , Ferdinands Jill M , Patel Manish M , Gaglani Manjusha 
Published: July 2021

AbstractBackgroundEvidence for vaccine effectiveness (VE) against influenza-associated pneumonia has varied by season, location, and strain. We estimate VE against hospitalization for radiographically identified influenza-associated pneumonia during 2015–2016 to 2017–2018 seasons in the US Hospitalized Adult Influenza Vaccine Effectiveness Network (HAIVEN).MethodsAmong adults aged ≥18 years admitted to 10 US hospitals for acute respiratory illness (ARI), clinician-investigators used keywords from reports of chest imaging performed during 3 days around hospital admission to assign a diagnosis of “definite/probable pneumonia.” We used a test-negative design to estimate VE against hospitalization for radiographically identified laboratory-confirmed influenza-associated pneumonia, comparing reverse transcriptase–polymerase chain reaction–confirmed influenza cases with test-negative subjects. Influenza vaccination status was documented in immunization records or self-reported, including date and location. Multivariable logistic regression models were used to adjust for age, site, season, calendar-time, and other factors.ResultsOf 4843 adults hospitalized with ARI included in the primary analysis, 266 (5.5%) had “definite/probable pneumonia” and confirmed influenza. Adjusted VE against hospitalization for any radiographically confirmed influenza-associated pneumonia was 38% (95% confidence interval [CI], 17–53%); by type/subtype, it was 74% (95% CI, 52–87%) influenza A (H1N1)pdm09, 25% (95% CI, −15% to 50%) A (H3N2), and 23% (95% CI, −32% to 54%) influenza B. Adjusted VE against intensive care for any influenza was 57% (95% CI, 19–77%).ConclusionsInfluenza vaccination was modestly effective among adults in preventing hospitalizations and the need for intensive care associated with influenza pneumonia. VE was significantly higher against A (H1N1)pdm09 and was low against A (H3N2) and B.
Resistin deletion protects against heart failure injury by targeting DNA damage response
Authors: Zhao Baoyin , Bouchareb Rihab , Lebeche Djamel 
Published: July 2021

Abstract

Aims
Increased resistin (Retn) levels are associated with development of cardiovascular diseases. However, the role of Retn in heart failure (HF) is still unclear. Here we probed the functional and molecular mechanism underlying the beneficial effect of Retn deletion in HF.

Methods and results
Wild-type (WT) and adipose tissue-specific Retn-knockout (RKO) mice were subjected to transverse aortic constriction (TAC)-induced HF. Cardiac function and haemodynamic changes were measured by echocardiography and left ventricular catheterization. Adipose tissue Retn deletion attenuated while Retn cardiac-selective overexpression, via a recombinant adeno-associated virus-9 vector, exacerbated TAC-induced hypertrophy, cardiac dysfunction, and myocardial fibrosis in WT and RKO mice. Mechanistically, we showed that Gadd45α was significantly increased in RKO HF mice while cardiac overexpression of Retn led to its downregulation. miR148b-3p directly targets Gadd45α and inhibits its expression. Retn overexpression upregulated miR148b-3p expression and triggered DNA damage response (DDR) in RKO-HF mice. Inhibition of miR148b-3p in vivo normalized Gadd45α expression, decreased DDR, and reversed cardiac dysfunction and fibrosis. In vitro Retn overexpression in adult mouse cardiomyocytes activated miR148b-3p and reduced Gadd45α expression. Gadd45α overexpression in H9C2-cardiomyoblasts protected against hydrogen peroxide- and Retn-induced DDR.

Conclusion
These findings reveal that diminution in circulating Retn reduced myocardial fibrosis and apoptosis, and improved heart function in a mouse model of HF, at least in part, through attenuation of miR148b-3p and DDR. The results of this study indicate that controlling Retn levels may provide a potential therapeutic approach for treating pressure overload-induced HF.
Long-term outcomes after aortic valve replacement using a 19-mm bioprosthesis
Authors: Okamura Homare , Kusadokoro Sho , Mieno Makiko , Kimura Naoyuki , Yamaguchi Atsushi 
Published: July 2021

Abstract

OBJECTIVES
Transcatheter aortic valve replacement is known to be associated with improved haemodynamics in patients with aortic stenosis and a small aortic annulus. However, limited benchmark data are available regarding the long-term outcomes in patients treated with surgical aortic valve replacement (SAVR). We investigated the long-term outcomes of SAVR using a 19-mm bioprosthesis.

METHODS
This study included consecutive patients who underwent SAVR using a 19-mm bioprosthesis at our hospital between 2008 and 2012.

RESULTS
In a total of 132 patients, moderate and severe prosthesis–patient mismatch occurred in 36 (27.3%) and 7 patients (5.3%), respectively. The median follow-up period was 7.7 years. The overall 5- and 10-year survival rates were 79.4% and 52.9%, respectively. The 5- and 10-year freedom from major adverse valve-related events rates were 89.6% and 74.2%, respectively. Neither moderate nor severe prosthesis–patient mismatch was associated with late mortality, major adverse valve-related events or heart failure. Follow-up echocardiographic data were obtained at a median interval of 4.8 years in 80% of patients who survived ≥6 months postoperatively. Follow-up echocardiographic data showed a significantly increased left ventricular ejection fraction, decreased mean transvalvular/transprosthetic pressure gradients and a decreased mean left ventricular mass. At follow-up, we observed moderate or severe haemodynamic structural valve deterioration in 17 patients; however, structural valve deterioration did not affect late survival or freedom from major adverse valve-related events rates, or heart failure.

CONCLUSIONS
SAVR using the 19-mm bioprosthesis was associated with satisfactory long-term clinical and haemodynamic outcomes.