bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of the effective diameters of porous media to the non-Darcy flow analyses
Authors: Shin Chang-Hoon 
Published: March 2022

AbstractNon-Darcy flows are a vital event leading to the inaccuracy in flow performance evaluation, particularly in the fractured wells in shale gas and tight oil deposits. The internal flow commonly indicates high flow rates at the early period of production, owing to the large geometric size of hydraulic fracture and high porosity in proppant packs. After that, the production flow rate decays steeply until the Darcy flow regime is attained. Therefore, accurate porous flow analyses from the Darcy to Forchheimer and then turbulent flow regimes are essential for optimal facility designs and economic productions in the unconventional deposits. The Comiti capillary model is recognised as the leading non-Darcy flow correlation for simple packed beds comprising mono-size grains. However, in actual hydraulic fractures, various types of proppants are used simultaneously and generally combined with numerous soil grains of different sizes and shapes. In this study, the Comiti model is modified by incorporating the effective diameters of the porous media and then examined for mixed complex multi-size packs. Subsequently, a novel type of non-Darcy flow equation is presented according to the logarithmic turbulent friction factor based on the physical variables determined only in the Darcy flow regime. The new equation presents accurate results for all the types of proppant packs under wide porosity and permeability ranges. The generalised non-Darcy flow correlation, which can be extensively employed from the Darcy to non-Darcy flow analyses, particularly beyond the Forchheimer regime, is presented for the accurate flow evaluation of the fractured reservoirs.
In silico analysis of SARS-CoV-2 proteins as targets for clinically available drugs
Authors: Chan Wallace K. B. , Olson Keith M. , Wotring Jesse W. , Sexton Jonathan Z. , Carlson Heather A. , Traynor John R. 
Published: March 2022

AbstractThe ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires treatments with rapid clinical translatability. Here we develop a multi-target and multi-ligand virtual screening method to identify FDA-approved drugs with potential activity against SARS-CoV-2 at traditional and understudied viral targets. 1,268 FDA-approved small molecule drugs were docked to 47 putative binding sites across 23 SARS-CoV-2 proteins. We compared drugs between binding sites and filtered out compounds that had no reported activity in an in vitro screen against SARS-CoV-2 infection of human liver (Huh-7) cells. This identified 17 “high-confidence”, and 97 “medium-confidence” drug-site pairs. The “high-confidence” group was subjected to molecular dynamics simulations to yield six compounds with stable binding poses at their optimal target proteins. Three drugs—amprenavir, levomefolic acid, and calcipotriol—were predicted to bind to 3 different sites on the spike protein, domperidone to the Mac1 domain of the non-structural protein (Nsp) 3, avanafil to Nsp15, and nintedanib to the nucleocapsid protein involved in packaging the viral RNA. Our “two-way” virtual docking screen also provides a framework to prioritize drugs for testing in future emergencies requiring rapidly available clinical drugs and/or treating diseases where a moderate number of targets are known.
Genome wide association study of frost tolerance in wheat
Authors: Soleimani Behnaz , Lehnert Heike , Babben Steve , Keilwagen Jens , Koch Michael , Arana-Ceballos Fernando Alberto , Chesnokov Yuriy , Pshenichnikova Tatyana , Schondelmaier Jörg , Ordon Frank , Börner Andreas , Perovic Dragan 
Published: March 2022

AbstractWinter wheat growing areas in the Northern hemisphere are regularly exposed to heavy frost. Due to the negative impact on yield, the identification of genetic factors controlling frost tolerance (FroT) and development of tools for breeding is of prime importance. Here, we detected QTL associated with FroT by genome wide association studies (GWAS) using a diverse panel of 276 winter wheat genotypes that was phenotyped at five locations in Germany and Russia in three years. The panel was genotyped using the 90 K iSelect array and SNPs in FroT candidate genes. In total, 17,566 SNPs were used for GWAS resulting in the identification of 53 markers significantly associated (LOD ≥ 4) to FroT, corresponding to 23 QTL regions located on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B and 7D). The strongest QTL effect confirmed the importance of chromosome 5A for FroT. In addition, to our best knowledge, eight FroT QTLs were discovered for the first time in this study comprising one QTL on chromosomes 3A, 3D, 4A, 7D and two on chromosomes 1B and 2D. Identification of novel FroT candidate genes will help to better understand the FroT mechanism in wheat and to develop more effective combating strategies.
Pharmacological differences between beta-blockers and postoperative mortality following colon cancer surgery
Authors: Ekestubbe Lovisa , Bass Gary Alan , Forssten Maximilian Peter , Sjölin Gabriel , Cao Yang , Matthiessen Peter , Ahl Hulme Rebecka , Mohseni Shahin 
Published: March 2022

Abstractβ-blocker therapy has been positively associated with improved survival in patients undergoing oncologic colorectal resection. This study investigates if the type of β-blocker used affects 90-day postoperative mortality following colon cancer surgery. The study was designed as a nationwide retrospective cohort study including all adult (≥ 18 years old) patients with ongoing β-blocker therapy who underwent elective and emergency colon cancer surgery in Sweden between January 1, 2007 and December 31, 2017. Patients were divided into four cohorts: metoprolol, atenolol, bisoprolol, and other beta-blockers. The primary outcome of interest was 90-day postoperative mortality. A Poisson regression model with robust standard errors was used, while adjusting for all clinically relevant variables, to determine the association between different β-blockers and 90-day postoperative mortality. A total of 9254 patients were included in the study. There was no clinically significant difference in crude 90-day postoperative mortality rate [n (%)] when comparing the four beta-blocker cohorts metoprolol, atenolol, bisoprolol and other beta-blockers. [97 (1.8%) vs. 28 (2.0%) vs. 29 (1.7%) vs. 11 (1.2%), p = 0.670]. This remained unchanged when adjusting for relevant covariates in the Poisson regression model. Compared to metoprolol, there was no statistically significant decrease in the risk of 90-day postoperative mortality with atenolol [adj. IRR (95% CI): 1.45 (0.89–2.37), p = 0.132], bisoprolol [adj. IRR (95% CI): 1.45 (0.89–2.37), p = 0.132], or other beta-blockers [adj. IRR (95% CI): 0.92 (0.46–1.85), p = 0.825]. In patients undergoing colon cancer surgery, the risk of 90-day postoperative mortality does not differ between the investigated types of β-adrenergic blocking agents.
Coronary calcification and bone microarchitecture by high-resolution peripheral quantitative computed tomography from the São Paulo Ageing and Health (SPAH) Study
Authors: Guzman Luis Fernando Escobar , Lopes Neuza Helena Moreira , Torres Georgea H. Fernandes , Takayama Liliam , de Sousa Andrade Solange , Lanz-Luces José Ramón , Pereira Rosa Maria R. , Rochitte Carlos Eduardo 
Published: March 2022

AbstractEpidemiological studies reveal a link between osteoporosis and the risk of ischemic cardiovascular disease. We illustrate an association between coronary calcification and bone microarchitecture in older adults based on the SPAH study. This cross-sectional research comprised 256 individuals subjected to cardiac coronary computed tomography angiography (CCTA) for coronary artery calcification (CAC), high-resolution peripheral quantitative computed tomography (HR-pQCT) at the tibia and radius with standardized z score parameters, and dual-energy X-ray absorptiometry (DXA) to evaluate bone status. We used Student’s t test and the Mann–Whitney and Chi-squared tests for comparison of basal measurements. Association analysis was performed using the Poisson regression model with adjustment for CAC and sex. Multivariate analysis revealed different bone variables for predicting CAC in DXA and HR-pQCT scenarios. Although most of the bone parameters are related to vascular calcification, only cortical porosity (Ct.Po) remained uniform by HR-pQCT. Results for were as follows: the tibia—women (exp β = 1.12 (95% CI 1.10–1.13, p < 0.001) and men (exp β = 1.44, 95% CI 1.42–1.46, p < 0.001); the radius—women (exp β = 1.07 (95% CI 1.07–1.08, p < 0.001) and men (exp β = 1.33 (95% CI 1.30–1.37, p < 0.001). These findings suggest an inverse relationship between CAC and cortical bone content, as assessed by HR-pQCT, with higher coronary calcification in individuals older than 65 years.
Benchmarking of quantum protocols
Authors: Liao Chin-Te , Bahrani Sima , da Silva Francisco Ferreira , Kashefi Elham 
Published: March 2022

AbstractQuantum network protocols offer new functionalities such as enhanced security to communication and computational systems. Despite the rapid progress in quantum hardware, it has not yet reached a level of maturity that enables execution of many quantum protocols in practical settings. To develop quantum protocols in real world, it is necessary to examine their performance considering the imperfections in their practical implementation using simulation platforms. In this paper, we consider several quantum protocols that enable promising functionalities and services in near-future quantum networks. The protocols are chosen from both areas of quantum communication and quantum computation as follows: quantum money, W-state based anonymous transmission, verifiable blind quantum computation, and quantum digital signature. We use NetSquid simulation platform to evaluate the effect of various sources of noise on the performance of these protocols, considering different figures of merit. We find that to enable quantum money protocol, the decoherence time constant of the quantum memory must be at least three times the storage time of qubits. Furthermore, our simulation results for the w-state based anonymous transmission protocol show that to achieve an average fidelity above 0.8 in this protocol, the storage time of sender’s and receiver’s particles in the quantum memory must be less than half of the decoherence time constant of the quantum memory. We have also investigated the effect of gate imperfections on the performance of verifiable blind quantum computation. We find that with our chosen parameters, if the depolarizing probability of quantum gates is equal to or greater than 0.05, the security of the protocol cannot be guaranteed. Lastly, our simulation results for quantum digital signature protocol show that channel loss has a significant effect on the probability of repudiation.
Mitochondrial phylogeny of the brittle star genus Ophioderma
Authors: Lessios H. A. , Hendler Gordon 
Published: March 2022

AbstractWe reconstructed the mitochondrial phylogeny of the species of the brittle star genus Ophioderma, using sequences of the Cytochrome Oxidase I gene (COI) to address four questions: (i) Are the species of Ophioderma described on morphological evidence reflected in mitochondrial genealogy? (ii) Which species separated from which? (iii) When did speciation events occur? (iv) What is the rate of COI evolution in ophiuroids? We found that most of the 22 described species we sampled coincide with monophyletic clusters of COI sequences, but there are exceptions, most notably in the eastern Pacific, in which three undescribed species were indicated. The COI phylogeny lacks resolution in the deeper nodes, but it does show that there are four species pairs, the members of which are found on either side of the central American Isthmus. Two pairs with a genetic distance of ~ 4% between Atlantic and Pacific members were probably split during the final stages of Isthmus completion roughly 3 million years ago. The rate of divergence provided by these pairs allowed the calibration of a relaxed molecular clock. Estimated dates of divergence indicate that the lineages leading to extant species coalesce at times much older than congeneric species in other classes of echinoderms, suggesting that low extinction rates may be one of the reasons that ophiuroids are species-rich. The mean rate of COI substitution in Ophioderma is three times slower than that of echinoids. Conclusions of previous mitochondrial DNA studies of ophiuroids that relied on echinoid calibrations to determine divergence times need to be revised.
A new intelligent bearing fault diagnosis model based on triplet network and SVM
Authors: Yang Kaisi , Zhao Lianyu , Wang Chenglin 
Published: March 2022

AbstractSeparating sensitive characteristic signals from original vibration data is an important challenge for rolling bearing fault diagnosis. Because it is difficult to obtain large number of damaged bearings, Rolling bearing fault datasets are often small sample datasets. For the classification of small sample rolling bearing fault datasets, we propose a coupling vibration data classification method based on triplet embedding. The method is divided into two steps: feature extraction and fault identification. First, build a triple embedding based on the CNN model to reduce the original vibration signal, and then train the SVM model for classification. Compared with traditional features and autoencoder, triplet network can learn the differences between samples. Make classification training easier and more accurate. We have evaluated the performance of this method through two bearing experiment examples. The experimental results show that this method is superior to stacked autoencoder, stacked denoising autoencoder and CNN.
Extracellular matrix-derived and low-cost proteins to improve polyurethane-based scaffolds for vascular grafts
Authors: Rodrigues Isabella C. P. , Lopes Éder S. N. , Pereira Karina D. , Huber Stephany C. , Jardini André Luiz , Annichino-Bizzacchi Joyce M. , Luchessi Augusto D. , Gabriel Laís P. 
Published: March 2022

AbstractVascular graft surgeries are often conducted in trauma cases, which has increased the demand for scaffolds with good biocompatibility profiles. Biodegradable scaffolds resembling the extracellular matrix (ECM) of blood vessels are promising vascular graft materials. In the present study, polyurethane (PU) was blended with ECM proteins collagen and elastin (Col-El) and gelatin (Gel) to produce fibrous scaffolds by using the rotary jet spinning (RJS) technique, and their effects on in vitro properties were evaluated. Morphological and structural characterization of the scaffolds was performed using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Micrometric fibers with nanometric rugosity were obtained. Col-El and Gel reduced the mechanical strength and increased the hydrophilicity and degradation rates of PU. No platelet adhesion or activation was observed. The addition of proteins to the PU blend increased the viability, adhesion, and proliferation of human umbilical vein endothelial cells (HUVECs). Therefore, PU-Col-El and PU-Gel scaffolds are promising biomaterials for vascular graft applications.
Aquatic birds have middle ears adapted to amphibious lifestyles
Authors: Zeyl Jeffrey N. , Snelling Edward P. , Connan Maelle , Basille Mathieu , Clay Thomas A. , Joo Rocío , Patrick Samantha C. , Phillips Richard A. , Pistorius Pierre A. , Ryan Peter G. , Snyman Albert , Clusella-Trullas Susana 
Published: March 2022

AbstractBirds exhibit wide variation in their use of aquatic environments, on a spectrum from entirely terrestrial, through amphibious, to highly aquatic. Although there are limited empirical data on hearing sensitivity of birds underwater, mounting evidence indicates that diving birds detect and respond to sound underwater, suggesting that some modifications of the ear may assist foraging or other behaviors below the surface. In air, the tympanic middle ear acts as an impedance matcher that increases sound pressure and decreases sound vibration velocity between the outside air and the inner ear. Underwater, the impedance-matching task is reversed and the ear is exposed to high hydrostatic pressures. Using micro- and nano-CT (computerized tomography) scans of bird ears in 127 species across 26 taxonomic orders, we measured a suite of morphological traits of importance to aerial and aquatic hearing to test predictions relating to impedance-matching in birds with distinct aquatic lifestyles, while accounting for allometry and phylogeny. Birds that engage in underwater pursuit and deep diving showed the greatest differences in ear structure relative to terrestrial species. In these heavily modified ears, the size of the input areas of both the tympanic membrane and the columella footplate of the middle ear were reduced. Underwater pursuit and diving birds also typically had a shorter extrastapedius, a reduced cranial air volume and connectivity and several modifications in line with reversals of low-to-high impedance-matching. The results confirm adaptations of the middle ear to aquatic lifestyles in multiple independent bird lineages, likely facilitating hearing underwater and baroprotection, while potentially constraining the sensitivity of aerial hearing.
DNA barcoding and phylogeography of the Hoplias malabaricus species complex
Authors: Guimarães Karen Larissa Auzier , Lima Marcos Prado , Santana Diego José , de Souza Mendelsohn Fujiie Belém , Barbosa Rômulo Sarmento , Rodrigues Luís Reginaldo Ribeiro 
Published: March 2022

AbstractHoplias malabaricus (Bloch, 1794) is a carnivorous fish species widely distributed from northern to southern South America. This taxon is believed to be a good model for the investigation of biogeographic events that shape the ichthyofauna evolution in the Neotropical freshwater systems. However, many studies have revealed that H. malabaricus hides a species complex that hampers its taxonomic identity and limit its practical value for evolutionary and biogeographic studies. In this paper, we used the mitochondrial gene cytochrome c oxidase subunit I (COI) to delimit cryptic species and explore the phylogeography of H. malabaricus sensu stricto. We found genetic evidence for putative new species in the genus Hoplias and showed that H. malabaricus (Bloch, 1794) is a major clade assigned to barcode index number (BIN) BOLD:ABZ3047. This species is structured in six subpopulations differentiated by high Fst values and restricts gene flow. The subpopulations of the São Francisco/East Atlantic/Eastern Northeast Atlantic/Parnaíba/Itapecuru River basins and Tapajós River Basin were the most differentiated and showed demographic fluctuations. The present distributional pattern is most likely explained through a scenario from the Pleistocene.
Neural spatio-temporal patterns of information processing related to cognitive conflict and correct or false recognitions
Authors: Janik Romuald A. , Podolak Igor T. , Struski Łukasz , Ceglarek Anna , Lewandowska Koryna , Sikora-Wachowicz Barbara , Marek Tadeusz , Fafrowicz Magdalena 
Published: March 2022

AbstractUsing a visual short-term memory task and employing a new methodological approach, we analyzed neural responses from the perspective of the conflict level and correctness/erroneous over a longer time window. Sixty-five participants performed the short-term memory task in the fMRI scanner. We explore neural spatio-temporal patterns of information processing in the context of correct or erroneous response and high or low level of cognitive conflict using classical fMRI analysis, surface-based cortical data, temporal analysis of interpolated mean activations, and machine learning classifiers. Our results provide evidence that information processing dynamics during the retrieval process vary depending on the correct or false recognition—for stimuli inducing a high level of cognitive conflict and erroneous response, information processing is prolonged. The observed phenomenon may be interpreted as the manifestation of the brain’s preparation for future goal-directed action.
Highly efficient heat-dissipation power driven by ferromagnetic resonance in MFe2O4 (M = Fe, Mn, Ni) ferrite nanoparticles
Authors: Lee Jae-Hyeok , Kim Yongsub , Kim Sang-Koog 
Published: March 2022

AbstractWe experimentally demonstrated that heat-dissipation power driven by ferromagnetic resonance (FMR) in superparamagnetic nanoparticles of ferrimagnetic MFe2O4 (M = Fe, Mn, Ni) gives rise to highly localized incrementation of targeted temperatures. The power generated thereby is extremely high: two orders of magnitude higher than that of the conventional Néel-Brownian model. From micromagnetic simulation and analytical derivation, we found robust correlations between the temperature increment and the intrinsic material parameters of the damping constant as well as the saturation magnetizations of the nanoparticles’ constituent materials. Furthermore, the magnetization–dissipation-driven temperature increments were reliably manipulated by extremely low strengths of applied AC magnetic fields under resonance field conditions. Our experimental results and theoretical formulations provide for a better understanding of the effect of FMR on the efficiency of heat generation as well as straightforward guidance for the design of advanced materials for control of highly localized incrementation of targeted temperatures using magnetic particles in, for example, magnetic hyperthermia bio-applications.
A plasmon modulator by directly controlling the couple of photon and electron
Authors: Hu Xue-fang , Zhao Xiang-yue , Gu Yin-wei , Jin Shu-ping , Cui Yi-ping , Lu Chang-gui 
Published: March 2022

AbstractThe manipulation of surface plasmon polaritons plays a pivotal role in plasmonic science and technology, however, the modulation efficiency of the traditional method suffers from the weak light-matter interaction. Herein, we propose a new method to overcome this obstacle by directly controlling the couple of photon and electron. In this paper, a hybrid graphene-dielectric- interdigital electrode structure is numerically and experimentally investigated. The plasmon is excited due to the confined carrier which is regulated by the potential wells. The frequency of plasmon can be tuned over a range of ~ 33 cm−1, and the obtained maximum extinction ratio is 8% via changing the confined area and the density of carrier. These findings may open up a new path to design the high efficiency all-optical modulator because the electrons can also be driven optically.
Theoretical studies on quantum imaging with time-integrated single-photon detection under realistic experimental conditions
Authors: Go Byeong-Yoon , Lee Changhyoup , Lee Kwang-Geol 
Published: March 2022

AbstractWe study a quantum-enhanced differential measurement scheme that uses quantum probes and single-photon detectors to measure a minute defect in the absorption parameter of an analyte under investigation. For the purpose, we consider two typical non-classical states of light as a probe, a twin-Fock state and a two-mode squeezed vacuum state. Their signal-to-noise ratios (SNRs) that quantifies the capability of detecting the defect are compared with a corresponding classical imaging scheme that employs a coherent state input. A quantitative comparison is made in terms of typical system imperfections such as photon loss and background noise that are common in practice. It is shown that a quantum enhancement in SNR can be described generally by the Mandel Q-parameter and the noise-reduction-factor, which characterize an input state that is incident to the analyte. We thereby identify the conditions under which the quantum enhancement remains and can be further increased. We expect our study to provide a guideline for improving the SNR in quantum imaging experiments employing a differential measurement scheme with time-integrated single-photon detectors.