bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Al and Cr alloying by arc cladding on the high-temperature oxidation resistance of MoSi2 materials
Authors: Wang Bin , Sun ShunPing , Wang HongJin , Li XiaoPing , Lei WeiNing 
Published: August 2021

Abstract
Different proportions of Al and Cr alloying MoSi2 were prepared by arc cladding with different mass fractions of MoSi2, Al, and Cr as raw materials. The work studied the effects about of Al and Cr on the phase, high-temperature oxidation morphology, products, and high-temperature oxidation property of MoSi2. The results confirmed that the volume expansion coefficient of Al2O3 generated by material oxidation was low which could reduce the degree of mismatch and the cracks in the oxide film. Cr element had a poor effect on enhancing the continuity and compactness of the oxide film, however, it could improve the stability of t-MoSi2 formation after arc cladding. MoO3 was not formed in the MoSi2 material added with Al and Cr show the surface oxidation. A dense and continuous Al2O3–SiO2 oxide film was formed, and no cracks holes were found in the oxide film. After oxidation at 800 °C–1200 °C for 120 h, the sample still maintained good oxidation protection. According to the calculation of oxidation kinetics, the MoSi2 material added with Al and Cr had good oxidation resistance. 3% Al + 9% Cr + 88% MoSi2 had the optimal high-temperature oxidation resistance about four times than pure MoSi2.
Analysis of inverse synthetic aperture radar imaging in the presence of time-varying plasma sheath
Authors: XIE Yaocong , LI Xiaoping , SHEN Fangfang , BAI Bowen , LIU Yanming , CHEN Xuyang , SHI Lei 
Published: August 2021

Abstract
The plasma sheath can induce radar signal modulation, causing not only ineffective target detection, but also defocusing in inverse synthetic aperture radar (ISAR) imaging. In this paper, through establishing radar echo models of the reentry object enveloped with time-varying plasma sheath, we simulated the defocusing of ISAR images in typical environment. Simulation results suggested that the ISAR defocusing is caused by false scatterings, upon which the false scatterings’ formation mechanism and distribution property are analyzed and studied. The range of false scattering correlates with the electron density fluctuation frequency. The combined value of the electron density fluctuation and the pulse repetition frequency jointly determines the Doppler of false scattering. Two measurement metrics including peak signal-to-noise ratio and structural similarity are used to evaluate the influence of ISAR imaging.
Geographic variation in dispersal of western burrowing owl (Athene cunicularia hypugaea) populations across North America
Authors: Macías-Duarte Alberto , Conway Courtney J 
Published: August 2021

AbstractDispersal is one of the key elements of species’ metapopulation dynamics and, hence, influences global conservation status. Furthermore, determining the geographic variation in magnitude and direction of dispersal throughout a species’ distribution may expand our understanding of the causes of population declines in species of conservation concern. For instance, western burrowing owl (Athene cunicularia hypugaea) populations have declined at the northern and eastern edge of their breeding distribution during the 20th century. In the same period, large areas of thornscrub that did not support breeding owls were converted to irrigated agriculture in the southern edge of the subspecies’ breeding distribution in northwestern Mexico. These farmlands now support some of the highest breeding densities of owls. We tested the hypothesis that owls that colonized this recently created habitat originated from declining migratory populations from the northern portion of the subspecies’ range. We used stable isotopes 2H, 13C, and 15N in owl feathers to infer breeding dispersal patterns throughout the subspecies’ breeding range. Populations near the northern edge of the subspecies’ breeding range had immigrants that dispersed over larger distances than immigrants at low and mid latitude populations. However, agricultural populations in northwestern Mexico disrupted this latitudinal pattern, attracting owls from more distant locations. We also found immigrants originated from further distances in declining populations than increasing populations. Stable isotopes provided no evidence of contemporaneous breeding dispersal from Canadian populations to northwestern Mexico but suggest that agricultural areas in the southern edge of the subspecies’ distribution have altered the continental dispersal pattern.
Resolving complex structures at oncovirus integration loci with conjugate graph
Authors: Jia Wenlong , Xu Chang , Li Shuai Cheng 
Published: August 2021

Abstract
Oncovirus integrations cause copy number variations and complex structural variations (SVs) on host genomes. However, the understanding of how inserted viral DNA impacts the local genome remains limited. The linear structure of the oncovirus integrated local genomic map (LGM) will lay the foundations to understand how oncovirus integrations emerge and compromise the host genome’s functioning. We propose a conjugate graph model to reconstruct the rearranged LGM at integrated loci. Simulation tests prove the reliability and credibility of the algorithm. Applications of the algorithm to whole-genome sequencing data of human papillomavirus (HPV) and hepatitis B virus (HBV)-infected cancer samples gained biological insights on oncovirus integrations. We observed four affection patterns of oncovirus integrations from the HPV and HBV-integrated cancer samples, including the coding-frame truncation, hyper-amplification of tumor gene, the viral cis-regulation inserted at the single intron and at the intergenic region. We found that the focal duplicates and host SVs are frequent in the HPV-integrated LGMs, while the focal deletions are prevalent in HBV-integrated LGMs. Furthermore, with the results yields from our method, we found the enhanced microhomology-mediated end joining might lead to both HPV and HBV integrations and conjectured that the HPV integrations might mainly occur during the DNA replication process. The conjugate graph algorithm code and LGM construction pipeline, available at https://github.com/deepomicslab/FuseSV.
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics
Authors: Kim Mirae , Hong Soonwoo , Yankeelov Thomas E , Yeh Hsin-Chih , Liu Yen-Liang 
Published: August 2021

Abstract

Motivation
Motions of transmembrane receptors on cancer cell surfaces can reveal biophysical features of the cancer cells, thus providing a method for characterizing cancer cell phenotypes. While conventional analysis of receptor motions in the cell membrane mostly relies on the mean-squared displacement plots, much information is lost when producing these plots from the trajectories. Here we employ deep learning to classify breast cancer cell types based on the trajectories of epidermal growth factor receptor (EGFR). Our model is an artificial neural network trained on the EGFR motions acquired from six breast cancer cell lines of varying invasiveness and receptor status: MCF7 (hormone receptor positive), BT474 (HER2-positive), SKBR3 (HER2-positive), MDA-MB-468 (triple negative, TN), MDA-MB-231 (TN) and BT549 (TN).

Results
The model successfully classified the trajectories within individual cell lines with 83% accuracy and predicted receptor status with 85% accuracy. To further validate the method, epithelial–mesenchymal transition (EMT) was induced in benign MCF10A cells, noninvasive MCF7 cancer cells and highly invasive MDA-MB-231 cancer cells, and EGFR trajectories from these cells were tested. As expected, after EMT induction, both MCF10A and MCF7 cells showed higher rates of classification as TN cells, but not the MDA-MB-231 cells. Whereas deep learning-based cancer cell classifications are primarily based on the optical transmission images of cell morphology and the fluorescence images of cell organelles or cytoskeletal structures, here we demonstrated an alternative way to classify cancer cells using a dynamic, biophysical feature that is readily accessible.

Availability and implementation
A python implementation of deep learning-based classification can be found at https://github.com/soonwoohong/Deep-learning-for-EGFR-trajectory-classification.

Supplementary information
Supplementary data are available at Bioinformatics online.
Unipept Visualizations: an interactive visualization library for biological data
Authors: Verschaffelt Pieter , Collier James , Botzki Alexander , Martens Lennart , Dawyndt Peter , Mesuere Bart 
Published: August 2021

Abstract

Summary
The Unipept Visualizations library is a JavaScript package to generate interactive visualizations of both hierarchical and non-hierarchical quantitative data. It provides four different visualizations: a sunburst, a treemap, a treeview and a heatmap. Every visualization is fully configurable, supports TypeScript and uses the excellent D3.js library.

Availability and implementation
The Unipept Visualizations library is available for download on NPM: https://npmjs.com/unipept-visualizations. All source code is freely available from GitHub under the MIT license: https://github.com/unipept/unipept-visualizations
Excess Invasive Meningococcal Disease Associated With Seasonal Influenza, South Africa, 2003–2018
Authors: Meiring Susan , Tempia Stefano , Dominic Emanuel M , de Gouveia Linda , McAnerney Jo , von Gottberg Anne , Cohen Cheryl 
Published: August 2021

Abstract

Background
Invasive meningococcal disease (IMD) is a devastating illness with high mortality rates. Like influenza, endemic IMD is seasonal, peaking in winter. Studies suggest that circulation of influenza virus may influence the timing and magnitude of IMD winter peaks.

Methods
This ecological study used weekly data from 2 nationwide surveillance programs: Viral Watch (proportion of outpatient influenza-positive cases from throat or nasal swab samples) and GERMS-SA (laboratory-confirmed cases of IMD), occurring across South Africa from 2003 through 2018 in all age bands. A bivariate time series analysis using wavelet transform was conducted to determine cocirculation of the diseases and the time lag between the peak seasons. We modeled excess meningococcal disease cases attributable to influenza cocirculation, using univariate regression spline models. Stata and R statistical software packages were used for the analysis.

Results
A total of 5256 laboratory-confirmed IMD cases were reported, with an average annual incidence of 0.23 episodes per 100 000 population and a mean seasonal peak during week 32 (±3 weeks). Forty-two percent of swab samples (10 421 of 24 741) were positive for influenza during the study period. The mean peak for all influenza occurred at week 26 (±4 weeks). There was an average lag time of 5 weeks between annual influenza and IMD seasons. Overall, 5% (1%–9%) of IMD cases can be attributable to influenza cocirculation, with, on average, 17 excess IMD cases per year attributable to influenza.

Conclusions
A quantifiable proportion of IMD in South Africa is associated with influenza cocirculation; therefore, seasonal influenza vaccination may have an effect on preventing a small portion of IMD in addition to preventing influenza.
Simulated heatwave and fishing stressors alter corticosteroid and energy balance in neonate blacktip reef sharks, Carcharhinus melanopterus.
Authors: Schoen Alexandra N , Bouyoucos Ian A , Anderson W Gary , Wheaton Catharine J , Planes Serge , Mylniczenko Natalie D , Rummer Jodie L 
Published: August 2021

Abstract
The increasing frequency and duration of marine heatwaves attributed to climate change threatens coastal elasmobranchs and may exacerbate existing anthropogenic stressors. While the elasmobranch stress response has been well studied, the role of the unique corticosteroid—1α-hydroxycorticosterone (1α-OHB)—in energy balance is not understood. Therefore, 1α-OHB’s utility as a stress biomarker in elasmobranch conservation physiology is equivocal. Here, we analyse the roles of corticosteroids, 1α-OHB and corticosterone, and metabolites, glucose and 3-hydroxybutyrate (3-HB), in response to stress in a protected tropical shark species, the blacktip reef shark (Carcharhinus melanopterus). Wild-caught neonates were exposed to ambient (27°C) or heatwave conditions (29°C) and subsequently a simulated fishing stressor (1 min air exposure). Blood samples were taken prior to temperature exposure, prior to air exposure, and 30 min, 1 h, 24 h, and 48 h post-air exposure at treatment temperatures. Plasma 1α-OHB was elevated for 48 h in 27°C-exposed sharks but declined over time in 29°C-exposed sharks. Plasma 1α-OHB was not correlated with either metabolite. Plasma glucose was higher and plasma 3-HB was lower in 29°C-exposed sharks. In a separate experiment, blood samples were collected from both neonate and adult sharks immediately following capture and again 5 min later, and analysed for corticosteroids and metabolites. Plasma 1α-OHB increased in neonates within 5 min, but neonates displayed lower plasma 1α-OHB and higher glucose concentrations than adults. We conclude that 1α-OHB does not serve as a classic glucocorticoid role in C. melanopterus under these stressors. Furthermore, we show for the first time, ontogenetic differences in plasma 1α-OHB. Ultimately, our findings provide insights into hormonal control of energy mobilization during stress in C. melanopterus, particularly during simulated heatwave conditions, which seem to alter both endocrine and energy mobilization. Further work is needed to determine the utility of 1α-OHB as a biomarker for the mobilization of energy during a stress event in elasmobranchs.
Telomerase therapy reverses vascular senescence and extends lifespan in progeria mice
Authors: Mojiri Anahita , Walther Brandon K , Jiang Chongming , Matrone Gianfranco , Holgate Rhonda , Xu Qiu , Morales Elisa , Wang Guangyu , Gu Jianhua , Wang Rongfu , Cooke John P 
Published: August 2021

Abstract

Aims
Hutchinson-Gilford progeria syndrome (HGPS) is an accelerated ageing syndrome associated with premature vascular disease and death due to heart attack and stroke. In HGPS a mutation in lamin A (progerin) alters nuclear morphology and gene expression. Current therapy increases the lifespan of these children only modestly. Thus, greater understanding of the underlying mechanisms of HGPS is required to improve therapy. Endothelial cells (ECs) differentiated from induced pluripotent stem cells (iPSCs) derived from these patients exhibit hallmarks of senescence including replication arrest, increased expression of inflammatory markers, DNA damage, and telomere erosion. We hypothesized that correction of shortened telomeres may reverse these measures of vascular ageing.

Methods and results
We generated ECs from iPSCs belonging to children with HGPS and their unaffected parents. Telomerase mRNA (hTERT) was used to treat HGPS ECs. Endothelial morphology and functions were assessed, as well as proteomic and transcriptional profiles with attention to inflammatory markers, DNA damage, and EC identity genes. In a mouse model of HGPS, we assessed the effects of lentiviral transfection of mTERT on measures of senescence, focusing on the EC phenotype in various organs. hTERT treatment of human HGPS ECs improved replicative capacity; restored endothelial functions such as nitric oxide generation, acetylated low-density lipoprotein uptake and angiogenesis; and reduced the elaboration of inflammatory cytokines. In addition, hTERT treatment improved cellular and nuclear morphology, in association with a normalization of the transcriptional profile, effects that may be mediated in part by a reduction in progerin expression and an increase in sirtuin 1 (SIRT1). Progeria mice treated with mTERT lentivirus manifested similar improvements, with a reduction in inflammatory and DNA damage markers and increased SIRT1 in their vasculature and other organs. Furthermore, mTERT therapy increased the lifespan of HGPS mice.

Conclusion
Vascular rejuvenation using telomerase mRNA is a promising approach for progeria and other age-related diseases.
A Metabolomic Aging Clock Using Human Cerebrospinal Fluid
Authors: Hwangbo Nathan , Zhang Xinyu , Raftery Daniel , Gu Haiwei , Hu Shu-Ching , Montine Thomas J , Quinn Joseph F , Chung Kathryn A , Hiller Amie L , Wang Dongfang , Fei Qiang , Bettcher Lisa , Zabetian Cyrus P , Peskind Elaine , Li Gail , Promislow Daniel E L , Franks Alexander 
Published: August 2021

Abstract
Quantifying the physiology of aging is essential for improving our understanding of age-related disease and the heterogeneity of healthy aging. Recent studies have shown that, in regression models using “-omic” platforms to predict chronological age, residual variation in predicted age is correlated with health outcomes, and suggest that these “omic clocks” provide measures of biological age. This paper presents predictive models for age using metabolomic profiles of cerebrospinal fluid (CSF) from healthy human subjects and finds that metabolite and lipid data are generally able to predict chronological age within 10 years. We use these models to predict the age of a cohort of subjects with Alzheimer’s and Parkinson’s disease and find an increase in prediction error, potentially indicating that the relationship between the metabolome and chronological age differs with these diseases. However, evidence is not found to support the hypothesis that our models will consistently overpredict the age of these subjects. In our analysis of control subjects, we find the carnitine shuttle, sucrose, biopterin, vitamin E metabolism, tryptophan, and tyrosine to be the most associated with age. We showcase the potential usefulness of age prediction models in a small data set (n = 85) and discuss techniques for drift correction, missing data imputation, and regularized regression, which can be used to help mitigate the statistical challenges that commonly arise in this setting. To our knowledge, this work presents the first multivariate predictive metabolomic and lipidomic models for age using mass spectrometry analysis of CSF.
Source models of long-period seismic events at Galeras volcano, Colombia
Authors: Torres Roberto , Kumagai Hiroyuki , Taguchi Kimiko 
Published: August 2021

SUMMARY
Long-period (LP) seismic events have occurred repeatedly at Galeras volcano, Colombia, during the transition from effusive dome formation to explosive Vulcanian eruptions. Since 1989, two types of LP events have been observed there: one characterized by long-lasting, decaying harmonic oscillations (NLP events) and the other by non-harmonic oscillatory features (BLP events). NLP events are attributed to resonances of a dusty gas-filled crack in the magma plugging the eruptive conduit. Sixteen episodes of NLP events occurred at Galeras during 1992–2010, each characterized by systematic temporal variations in the frequencies and quality factors of NLP events. Our and previous estimates of crack model parameters during three of those NLP episodes indicate that the similar temporal variations in crack geometry and fluid properties can be explained by an increase in the ash content within the crack and a decrease in crack volume. We found that NLP events, associated with low SO2 fluxes, are anticorrelated with BLP events, which are accompanied by high SO2 emissions. From our observations and analytical results, we inferred that BLP events are generated by resonances of open cracks in the uppermost magma plug, corresponding to tuffisite veins, that efficiently transfer volcanic gases. After sufficient degassing and densification, the magma plug effectively seals the conduit. The growing overpressure in the deeper magma is then released through a shear fracture along the conduit margin. The intrusion of deeper, vesiculated magma into the shear fracture depressurizes and fragments the magma, producing a dusty gas and triggering the crack resonances that generate NLP events. Our results thus indicate that the evolution of the properties of the magma plug controls the occurrences of BLP and NLP events at Galeras. Although NLP events do not always precede explosive eruptions, they indicate that an important overpressure is building in the shallow conduit.
Left ventricular unloading during extracorporeal life support for myocardial infarction with cardiogenic shock: surgical venting versus Impella device
Authors: Radakovic Darko , Zittermann Armin , Knezevic Alen , Razumov Artyom , Opacic Dragan , Wienrautner Nicole , Flottmann Christian , Rojas Sebastian V , Fox Henrik , Schramm René , Morshuis Michiel , Rudolph Volker , Gummert Jan , Deutsch Marcus-André 
Published: August 2021

Abstract

OBJECTIVES
Patients in cardiogenic shock supported with venoarterial extracorporeal membrane oxygenation (VA-ECMO) may experience severe complications from reduced left ventricular (LV) unloading and increased cardiac afterload. These effects are usually modified by adding a percutaneous direct Impella vent or surgical LV vent on top of VA-ECMO in selected patients. However, direct comparisons between 2 LV unloading strategies in patients with cardiogenic shock due to myocardial infarction are lacking. Therefore, we sought to investigate the impact of these 2 different approaches.

METHODS
We enrolled 112 patients treated with an Impella or surgical LV vent during VA-ECMO support between January 2014 and February 2020. The primary endpoint was 30-day mortality. Secondary endpoints included rates of myocardial recovery or transition to durable mechanical circulatory support. Additionally, we assessed adverse events such as peripheral ischaemic complications requiring intervention, sepsis and ischaemic stroke.

RESULTS
At 30 days, 38 patients in the Impella group (54%) and 26 patients in the surgical LV vent group (63%) had died (relative risk with Impella 0.78, 95% confidence interval 0.47–1.30; P = 0.35). Impella group and the surgical LV vent group differed significantly with respect to the secondary end points including rates of myocardial recovery (24% and 7%, respectively; P = 0.022) and rates of durable mechanical circulatory support (17% and 42%, P = 0.012). Complication rates were not statistically different between the 2 groups.

CONCLUSIONS
The use of Impella device as therapeutic unloading therapy during VA-ECMO did not significantly reduce 30-day mortality compared to surgical LV vent in patients with cardiogenic shock due to acute myocardial infarction.