bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sperm DNA methylation mediates the association of male age on reproductive outcomes among couples undergoing infertility treatment
Authors: Oluwayiose Oladele A. , Wu Haotian , Saddiki Hachem , Whitcomb Brian W. , Balzer Laura B. , Brandon Nicole , Suvorov Alexander , Tayyab Rahil , Sites Cynthia K. , Hill Lisa , Marcho Chelsea , Pilsner J. Richard 
Published: February 2021

AbstractParental age at time of offspring conception is increasing in developed countries. Advanced male age is associated with decreased reproductive success and increased risk of adverse neurodevelopmental outcomes in offspring. Mechanisms for these male age effects remain unclear, but changes in sperm DNA methylation over time is one potential explanation. We assessed genome-wide methylation of sperm DNA from 47 semen samples collected from male participants of couples seeking infertility treatment. We report that higher male age was associated with lower likelihood of fertilization and live birth, and poor embryo development (p < 0.05). Furthermore, our multivariable linear models showed male age was associated with alterations in sperm methylation at 1698 CpGs and 1146 regions (q < 0.05), which were associated with > 750 genes enriched in embryonic development, behavior and neurodevelopment among others. High dimensional mediation analyses identified four genes (DEFB126, TPI1P3, PLCH2 and DLGAP2) with age-related sperm differential methylation that accounted for 64% (95% CI 0.42–0.86%; p < 0.05) of the effect of male age on lower fertilization rate. Our findings from this modest IVF population provide evidence for sperm methylation as a mechanism of age-induced poor reproductive outcomes and identifies possible candidate genes for mediating these effects.
Photoneutron spectrometry by novel multi-directional spherical neutron spectrometry system
Authors: Sohrabi Mehdi , Hakimi Amir 
Published: February 2021

AbstractNeutron spectrometry in science and technology applications in general and accurate exotic photoneutron (PN) dosimetry of cancer patients undergoing high-dose high-energy X-rays therapy in medical accelerators in particular is of vital need. In this study, a novel passive multi-directional multi-detector neutron spectrometry system was developed and home-made using 6 polycarbonate/10B detectors on 6 sides of polyethylene (PE) cubes used bare and also embedded at center of PE spheres of 8 different diameters. The system provided well-resolved unfolded directional PN spectra showing thermal and fast PN peaks of 6 sides and mean spectrum in 5 field sizes at isocenter and other locations in 18 MV Siemens ONCOR medical linear accelerator bunker. The neutron spectrometry system developed has unique characteristics such as being simple, efficient, low cost, practical, and insensitive to low-LET radiation with well-resolved directional and mean spectra easily applicable in medicine, health, environment, science and technology in developing and developed laboratories.
Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients
Authors: Jimenez-Solem Espen , Petersen Tonny S. , Hansen Casper , Hansen Christian , Lioma Christina , Igel Christian , Boomsma Wouter , Krause Oswin , Lorenzen Stephan , Selvan Raghavendra , Petersen Janne , Nyeland Martin Erik , Ankarfeldt Mikkel Zöllner , Virenfeldt Gert Mehl , Winther-Jensen Matilde , Linneberg Allan , Ghazi Mostafa Mehdipour , Detlefsen Nicki , Lauritzen Andreas David , Smith Abraham George , de Bruijne Marleen , Ibragimov Bulat , Petersen Jens , Lillholm Martin , Middleton Jon , Mogensen Stine Hasling , Thorsen-Meyer Hans-Christian , Perner Anders , Helleberg Marie , Kaas-Hansen Benjamin Skov , Bonde Mikkel , Bonde Alexander , Pai Akshay , Nielsen Mads , Sillesen Martin 
Published: February 2021

AbstractPatients with severe COVID-19 have overwhelmed healthcare systems worldwide. We hypothesized that machine learning (ML) models could be used to predict risks at different stages of management and thereby provide insights into drivers and prognostic markers of disease progression and death. From a cohort of approx. 2.6 million citizens in Denmark, SARS-CoV-2 PCR tests were performed on subjects suspected for COVID-19 disease; 3944 cases had at least one positive test and were subjected to further analysis. SARS-CoV-2 positive cases from the United Kingdom Biobank was used for external validation. The ML models predicted the risk of death (Receiver Operation Characteristics—Area Under the Curve, ROC-AUC) of 0.906 at diagnosis, 0.818, at hospital admission and 0.721 at Intensive Care Unit (ICU) admission. Similar metrics were achieved for predicted risks of hospital and ICU admission and use of mechanical ventilation. Common risk factors, included age, body mass index and hypertension, although the top risk features shifted towards markers of shock and organ dysfunction in ICU patients. The external validation indicated fair predictive performance for mortality prediction, but suboptimal performance for predicting ICU admission. ML may be used to identify drivers of progression to more severe disease and for prognostication patients in patients with COVID-19. We provide access to an online risk calculator based on these findings.
Reduction of visual stimulus artifacts using a spherical tank for small, aquatic animals
Authors: Wang Kun , Arrenberg Burkhard , Hinz Julian , Arrenberg Aristides B. 
Published: February 2021

AbstractDelivering appropriate stimuli remains a challenge in vision research, particularly for aquatic animals such as zebrafish. Due to the shape of the water tank and the associated optical paths of light rays, the stimulus can be subject to unwanted refraction or reflection artifacts, which may spoil the experiment and result in wrong conclusions. Here, we employ computer graphics simulations and calcium imaging in the zebrafish optic tectum to show, how a spherical glass container optically outperforms many previously used water containers, including Petri dish lids. We demonstrate that aquatic vision experiments suffering from total internal reflection artifacts at the water surface or at the flat container bottom may result in the erroneous detection of visual neurons with bipartite receptive fields and in the apparent absence of neurons selective for vertical motion. Our results and demonstrations will help aquatic vision neuroscientists on optimizing their stimulation setups.
A two dimensional semi-continuum model to explain wetting front instability in porous media
Authors: Kmec Jakub , Fürst Tomáš , Vodák Rostislav , Šír Miloslav 
Published: February 2021

AbstractModelling fluid flow in an unsaturated porous medium is a complex problem with many practical applications. There is enough experimental and theoretical evidence that the standard continuum mechanics based modelling approach is unable to capture many important features of porous media flow. In this paper, a two-dimensional semi-continuum model is presented that combines ideas from continuum mechanics with invasion percolation models. The medium is divided into blocks of finite size that retain the nature of a porous medium. Each block is characterized by its porosity, permeability, and a retention curve. The saturation and pressure of the fluids are assumed to be uniform throughout each block. It is demonstrated that the resulting semi-continuum model is able to reproduce (1) gravity induced preferential flow with a spatially rich system of rivulets (fingers) characterized by saturation overshoot, (2) diffusion-like flow with a monotonic saturation profile, (3) the transition between the two. The model helps to explain the formation of the preferential pathways and their persistence and structure (the core and fringe of the fingers), the effect of the initial saturation of the matrix, and the saturation overshoot phenomenon.
Ab initio predictions of structure and physical properties of the Zr2GaC and Hf2GaC MAX phases under pressure
Authors: Qureshi Muhammad Waqas , Ma Xinxin , Tang Guangze , Paudel Ramesh 
Published: February 2021

AbstractThe electronic structure, structural stability, mechanical, phonon, and optical properties of Zr2GaC and Hf2GaC MAX phases have been investigated under high pressure using first-principles calculations. Formation enthalpy of competing phases, elastic constants, and phonon calculations revealed that both compounds are thermodynamically, mechanically, and dynamically stable under pressure. The compressibility of Zr2GaC is higher than that of Hf2GaC along the c-axis, and pressure enhanced the resistance to deformation. The electronic structure calculations reveal that M2GaC is metallic in nature, and the metallicity of Zr2GaC increased more than that of Hf2GaC at higher pressure. The mechanical properties, including elastic constants, elastic moduli, Vickers hardness, Poisson’s ratio anisotropy index, and Debye temperature, are reported with fundamental insights. The elastic constants C11 and C33 increase rapidly compared with other elastic constants with an increase in pressure, and the elastic anisotropy of Hf2GaC is higher than that of the Zr2GaC. The optical properties revealed that Zr2GaC and Hf2GaC MAX phases are suitable for optoelectronic devices in the visible and UV regions and can also be used as a coating material for reducing solar heating at higher pressure up to 50 GPa.
Novel semi-analytical optoelectronic modeling based on homogenization theory for realistic plasmonic polymer solar cells
Authors: Arefinia Zahra , Samajdar Dip Prakash 
Published: February 2021

AbstractNumerical-based simulations of plasmonic polymer solar cells (PSCs) incorporating a disordered array of non-uniform sized plasmonic nanoparticles (NPs) impose a prohibitively long-time and complex computational demand. To surmount this limitation, we present a novel semi-analytical modeling, which dramatically reduces computational time and resource consumption and yet is acceptably accurate. For this purpose, the optical modeling of active layer-incorporated plasmonic metal NPs, which is described by a homogenization theory based on a modified Maxwell–Garnett-Mie theory, is inputted in the electrical modeling based on the coupled equations of Poisson, continuity, and drift–diffusion. Besides, our modeling considers the effects of absorption in the non-active layers, interference induced by electrodes, and scattered light escaping from the PSC. The modeling results satisfactorily reproduce a series of experimental data for photovoltaic parameters of plasmonic PSCs, demonstrating the validity of our modeling approach. According to this, we implement the semi-analytical modeling to propose a new high-efficiency plasmonic PSC based on the PM6:Y6 PSC, having the highest reported power conversion efficiency (PCE) to date. The results show that the incorporation of plasmonic NPs into PM6:Y6 active layer leads to the PCE over 18%.
GATA4 blocks squamous epithelial cell gene expression in human esophageal squamous cells
Authors: Stavniichuk Roman , DeLaForest Ann , Thompson Cayla A. , Miller James , Souza Rhonda F. , Battle Michele A. 
Published: February 2021

AbstractGATA4 promotes columnar epithelial cell fate during gastric development. When ectopically expressed in the developing mouse forestomach, the tissue emerges as columnar-like rather than stratified squamous with gene expression changes that parallel those observed in the pre-malignant squamous to columnar metaplasia known as Barrett’s esophagus (BE). GATA4 mRNA up-regulation and gene amplification occur in BE and its associated cancer, esophageal adenocarcinoma (EAC), and GATA4 gene amplification correlates with poor patient outcomes. Here, we explored the effect of ectopic expression of GATA4 in mature human esophageal squamous epithelial cells. We found that GATA4 expression in esophageal squamous epithelial cells compromised squamous cell marker gene expression and up-regulated expression of the canonical columnar cell cytokeratin KRT8. We observed GATA4 occupancy in the p63, KRT5, and KRT15 promoters, suggesting that GATA4 directly represses expression of squamous epithelial cell marker genes. Finally, we verified GATA4 protein expression in BE and EAC and found that exposure of esophageal squamous epithelial cells to acid and bile, known BE risk factors, induced GATA4 mRNA expression. We conclude that GATA4 suppresses expression of genes marking the stratified squamous epithelial cell lineage and that this repressive action by GATA4 may have implications in BE and EAC.
Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes
Authors: Armbrecht L. , Hallegraeff G. , Bolch C. J. S. , Woodward C. , Cooper A. 
Published: February 2021

AbstractMarine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticatesedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryotesedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate thesedaDNA component, establishing a new proxy to assesssedaDNA authenticity, “% eukaryotesedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophoreEmiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.
Homeostatic plasticity and burst activity are mediated by hyperpolarization-activated cation currents and T-type calcium channels in neuronal cultures
Authors: Rátkai Anikó , Tárnok Krisztián , Aouad Hajar El , Micska Brigitta , Schlett Katalin , Szücs Attila 
Published: February 2021

AbstractHomeostatic plasticity stabilizes neuronal networks by adjusting the responsiveness of neurons according to their global activity and the intensity of the synaptic inputs. We investigated the homeostatic regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) and T-type calcium (CaV3) channels in dissociated and organotypic slice cultures. After 48 h blocking of neuronal activity by tetrodotoxin (TTX), our patch-clamp experiments revealed an increase in the depolarizing voltage sag and post-inhibitory rebound mediated by HCN and CaV3 channels, respectively. All HCN subunits (HCN1 to 4) and T-type Ca-channel subunits (CaV3.1, 3.2 and 3.3) were expressed in both control and activity-deprived hippocampal cultures. Elevated expression levels of CaV3.1 mRNA and a selective increase in the expression of TRIP8b exon 4 isoforms, known to regulate HCN channel localization, were also detected in TTX-treated cultured hippocampal neurons. Immunohistochemical staining in TTX-treated organotypic slices verified a more proximal translocation of HCN1 channels in CA1 pyramidal neurons. Computational modeling also implied that HCN and T-type calcium channels have important role in the regulation of synchronized bursting evoked by previous activity-deprivation. Thus, our findings indicate that HCN and T-type Ca-channels contribute to the homeostatic regulation of excitability and integrative properties of hippocampal neurons.
Room-temperature synthesis of earth-abundant semiconductor ZnSiN2 on amorphous carbon
Authors: Coelho-Júnior Horácio , Silva Bruno G. , Labre Cilene , Loreto Renan P. , Sommer Rubem L. 
Published: February 2021

AbstractThis manuscript reports room-temperature one-step synthesis of earth-abundant semiconductor ZnSiN2 on amorphous carbon substrates using radio frequency reactive magnetron co-sputtering. Transmission Electron Microscopy and Rutherford Backscattering Spectrometry analysis demonstrated that the synthesis has occurred as ZnSiN2 nanocrystals in the orthorhombic phase, uniformly distributed on amorphous carbon. The technique of large-area deposition on an amorphous substrate can be interesting for flexible electronics technologies. Our results open possibilities for environmentally friendly semiconductor devices, leading to the development of greener technologies.
Immunoglobulin G responses to variant forms of Plasmodium vivax merozoite surface protein 9 upon natural infection in Thailand
Authors: Songsaigath Sunisa , Makiuchi Takashi , Putaporntip Chaturong , Pattanawong Urassaya , Kuamsab Napaporn , Tachibana Hiroshi , Jongwutiwes Somchai 
Published: February 2021

AbstractMerozoite surface protein 9 (MSP9) constitutes a ligand complex involved in erythrocyte invasion by malarial merozoites and is a promising vaccine target. Plasmodium vivax MSP9 (PvMSP9) is immunogenic upon natural malaria exposure. To address whether sequence diversity in PvMSP9 among field isolates could affect natural antibody responses, the recombinant proteins representing two variants each for the N- and the C-terminal domains of PvMSP-9 were used as antigens to assess antibody reactivity among 246 P. vivax-infected patients’ sera from Tak and Ubon Ratchathani Provinces in Thailand. Results revealed that the seropositivity rates of IgG antibodies to the N-terminal antigens were higher than those to the C-terminal antigens (87.80% vs. 67.48%). Most seropositive sera were reactive to both variants, suggesting the presence of common epitopes. Variant-specific antibodies to the N- and the C-terminal antigens were detected in 15.85% and 16.70% of serum samples, respectively. These seropositivity rates were not significant difference between provinces. The seropositivity rates, levels and avidity of anti-PvMSP9 antibodies exhibited positive trends towards increasing malaria episodes. The IgG isotype responses to the N- and the C-terminal antigens were mainly IgG1 and IgG3. The profile of IgG responses may have implications for development of PvMSP9-based vaccine.
Computation offloading game in multiple unmanned aerial vehicle‐enabled mobile edge computing networks
Authors: Ren Yanling , Xie Zhibin , Ding Zhenfeng , Sun Xiyuan , Xia Jie , Tian Yubo 
Published: February 2021

AbstractBecause of extreme sensitivity to time and energy consumption, many computation‐ and data‐intensive tasks are difficult to implement on mobile terminals and cannot meet the needs of the rapid development of mobile networks. To solve this problem, mobile edge computing (MEC) appears to be a promising solution. In this study, we propose two offloading schemes in the multiple unmanned aerial vehicles (UAVs) enabled MEC network. Their optimisation goals are to minimise the global computing time and energy consumption of all UAVs, respectively. Different from previous research, the UAV can perform tasks locally or offload an appropriate percentage to the desired MEC server in the two proposed schemes. In order to get the minimum global computing time, we prove the existence condition and obtain the optimal offloading proportion. In addition, in order to minimise global energy consumption, we also obtain the optimal offloading proportion and present the optimal transmission power through solving Karush–Kuhn–Tucker conditions. Finally, because UAVs are selfish, we adopt the game theory to get optimal solutions of the proposed offloading strategies. Numerical results verify that the proposed schemes can effectively decrease the global computing time and energy consumption, especially for a large number of UAVs.
Impact of connected vehicle environment on driving performance: A case of an extra‐long tunnel scenario
Authors: Chang Xin , Rong Jian , Li Haijian , Wu Yiping , Zhao Xiaohua 
Published: February 2021

AbstractIn view of the benefits and a promising prospect of the emerging connected vehicles (CV), more and more vehicles will be equipped with the in‐vehicle human‐machine interface (HMI). This study aims to assess the comprehensive impacts of HMIs on individual driving performance, traffic safety, and eco‐driving behaviour based on a driving simulator. In order to explore how a driver responds to warnings when approaching a tunnel, this study divided the experimental road into five zones according to warning positions. A comparative analysis was conducted to examine the changes in driving comfort, speeding behaviour, the standard deviation of speed, time headway (THW), fuel consumption, and emissions. Results showed that the HMI could be beneficial to speed adjustment before entering a tunnel. Meanwhile, HMI may affect the THW of vehicles. Drivers were usually more cautious when the HMI was on. However, no significant effects of the HMI for driving comfort and eco‐driving behaviour can be observed. It is expected that more efficient technology and different warning strategies can be developed to enhance eco‐safe driving for different zones because they have different effects. The findings of this study are also helpful for active safety management and for evaluating the effectiveness of CV systems.
Temporal evolution of small-scale internetwork magnetic fields in the solar photosphere
Authors: Campbell R. J. , Mathioudakis M. , Collados M. , Keys P. H. , Asensio Ramos A. , Nelson C. J. , Kuridze D. , Reid A. 
Published: February 2021

Context. While the longitudinal field that dominates in photospheric network regions has been studied extensively, small-scale transverse fields have recently been found to be ubiquitous in the quiet internetwork photosphere and this merits further study. Furthermore, few observations have been able to capture how this field evolves.
Aims. We aim to statistically characterize the magnetic vector in a quiet Sun internetwork region and observe the temporal evolution of specific small-scale magnetic features.
Methods. We present two high spatio-temporal resolution observations that reveal the dynamics of two disk-centre internetwork regions taken by the new GREGOR Infrared Spectrograph Integral Field Unit with the highly magnetically sensitive photospheric Fe I line pair at 15648.52 Å and 15652.87 Å. We record the full Stokes vector and apply inversions with the Stokes inversions based on response functions code to retrieve the parameters characterizing the atmosphere. We consider two inversion schemes: scheme 1 (S1), where a magnetic atmosphere is embedded in a field free medium, and scheme 2 (S2), with two magnetic models and a fixed 30% stray light component.
Results. The magnetic properties produced from S1 inversions returned a median magnetic field strength of 200 and 240 G for the two datasets, respectively. We consider the median transverse (horizontal) component, among pixels with Stokes Q or U, and the median unsigned longitudinal (vertical) component, among pixels with Stokes V, above a noise threshold. We determined the former to be 263 G and 267 G, and the latter to be 131 G and 145 G, for the two datasets, respectively. Finally, we present three regions of interest, tracking the dynamics of small-scale magnetic features. We apply S1 and S2 inversions to specific profiles of interest and find that the latter produces better approximations when there is evidence of mixed polarities. We find patches of linear polarization with magnetic flux density of the order of 130−150 G and find that linear polarization appears preferentially at granule-intergranular lane boundaries. The weak magnetic field appears to be organized in terms of complex ‘loop-like’ structures, with transverse fields often flanked by opposite polarity longitudinal fields.