bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenging Reverse Screening: A Benchmark Study for Comprehensive Evaluation
Authors: Li Mingna , Hu Jianxing , Wang Yanxing , Li Yibo , Zhang Liangren , Liu Zhenming 
Published: November 2021

AbstractAs an efficient way of computational target prediction, reverse docking can find not only potential targets but also binding modes for a query ligand. Though the number of available docking tools keeps expanding, there is still not a comprehensive evaluation study which can uncover the advantages and limitations of these strategies in the research field of computational target‐fishing. In this study, we propose a brand‐new evaluation dataset tailor‐made for reverse docking, which is composed of a true positive set (the core set) and two negative sets (the similar decoy set and the dissimilar decoy set). The proposed evaluation dataset can assess the prediction performance of docking tools as various values affected by varying degrees of inter‐target ranking bias. The performance of four classical docking programs (AutoDock, AutoDock Vina, Glide and GOLD) was evaluated utilizing our dataset, and a biased prediction performance was observed regarding binding site properties. The results demonstrated that Glide (SP) and Glide(XP) had the best capacity to find true targets whether there was inter‐target ranking bias or not.
Oxidized Pork Induces Hepatic Steatosis by Impairing Thyroid Hormone Function in Mice
Authors: Ge Yueting , Yang Yuhui , Jiang Yuge , Feng Chuanxing , Li Bowen , Sun Jin , Tang Xue , Shi Yonghui , Le Guowei 
Published: November 2021

ScopeRecent studies have linked high consumption of red and processed meats to an increased risk of non‐alcoholic fatty liver disease, and cooking‐induced oxidation of proteins and amino acids might be contributing factors. Herein, this study investigates the influence of oxidized pork and the protein oxidation biomarker dityrosine (Dityr) on hepatic steatosis in mice.Methods and ResultsLow‐ and high‐oxidative injury pork (LOP and HOP) are freeze‐dried to prepare mouse diets. Mice are fed a diet of either the control, LOP, HOP, LOP+Dityr, or Dityr for 12 weeks. HOP and Dityr intake induced oxidative stress and inflammation that impaired thyroid function and peripheral metabolism (reduced type 1 deiodinase activity) of thyroid hormones (THs). These lead to a decrease in the circulating as well as liver THs and induced hepatic steatosis. This process might be regulated through reduced TH levels and altered TH target genes and proteins related to hepatic lipid metabolism that ultimately inhibited hepatic energy metabolism, as indicated by increased hepatic lipid synthesis, decreased hepatic lipid catabolism, and fatty acid oxidation.ConclusionHOP intake could induce hepatic steatosis by impairing TH function. Dityr plays an important role in the HOP‐induced harmful effects.
A γ‐conical position error representation method considering high‐order position relevance of array elements
Authors: Guo Fang , Liu Zhenyu , Sa Guodong , Tan Jianrong 
Published: November 2021

AbstractThe position errors of array elements, which include systematic and random errors, are inevitable and could lead to the degradation of the radiation performance. For an array antenna, the systematic errors come from the continuous deformation of the reflector while the random errors come from the manufacturing and assembly of array elements. The accurate representation of position errors is important to evaluate the effects of position errors on performance in the design of an array antenna. In previous studies, many methods have been proposed to represent the systematic and random errors. However, few studies have considered the high‐order position relevance of array elements resulting from the systematic errors, which could lead to the inaccurate representation of position errors. Here, a γ‐conical representation method is proposed to consider the γ‐order position relevance of successive array elements. The existing conical representation method and the proposed γ‐conical representation method are used as comparisons to generate simulation data of position errors. The corresponding electrical performance of position errors is calculated with antenna theories and Feko. Prediction models are built based on a linear programming support vector regression algorithm to evaluate the ability of different representation methods. Finally, experiments are conducted on a platform with 8 × 8 array elements to demonstrate the superiority of the γ‐conical representation method.
Accelerating Monte Carlo simulation of light propagation in tissue mimicking turbid medium based on generative adversarial networks
Authors: Wang Shiyuan , Chen Jiaming , Zhang Fengdi , Zhao Mingyang , Cui Xiaoyu , Chen Shuo 
Published: November 2021

AbstractPurposeMonte Carlo (MC) simulation is the most frequently used method to numerically model the light propagation in biological tissues because of its high flexibility and precision. Although MC simulation is assumed to be capable of achieving any desired precision, larger number of photons are always necessary for more precise simulation, leading to its major limitation of intensive computation. In this work, the authors present a way to adapt generative adversarial networks (GAN) to accelerate MC simulation.MethodsThe pix2pix network, a variant of GAN, was investigated to reconstruct precise MC simulation results from the results roughly modeled by small amount of photons, thus the computation time was expected to be significantly saved. The proposed method was tested on single‐layer embedded tumor models to derive the absorption distribution maps.ResultsThe results demonstrate that the absorption distribution maps reconstructed from the simulation of only 10 000 photons were very similar to those modeled by using 1 000 000 photons, based on the criterion of peak signal to noise ratio (PSNR) and percentage difference of power coupling efficiencies, and the simulation process was proved to be accelerated by approximately 102 times.ConclusionsFor the first time, GAN was adapted to save computation time of MC simulation of light propagation. By achieving MC simulation with acceptable quality, the proposed method can speed up the computation by hundreds of times.
Fundamentals of turbulent flow spectrum imaging
Authors: Dillinger Hannes , McGrath Charles , Guenthner Christian , Kozerke Sebastian 
Published: November 2021

PurposeTo introduce a mathematical framework and in‐silico validation of turbulent flow spectrum imaging (TFSI) of stenotic flow using phase‐contrast MRI, evaluate systematic errors in quantitative turbulence parameter estimation, and propose a novel method for probing the Lagrangian velocity spectra of turbulent flows.Theory and MethodsThe spectral response of velocity‐encoding gradients is derived theoretically and linked to turbulence parameter estimation including the velocity autocorrelation function spectrum. Using a phase‐contrast MRI simulation framework, the encoding properties of bipolar gradient waveforms with identical first gradient moments but different duration are investigated on turbulent flow data of defined characteristics as derived from computational fluid dynamics. Based on theoretical insights, an approach using velocity‐compensated gradient waveforms is proposed to specifically probe desired ranges of the velocity autocorrelation function spectrum with increased accuracy.ResultsPractical velocity‐encoding gradients exhibit limited encoding power of typical turbulent flow spectra, resulting in up to 50% systematic underestimation of intravoxel SD values. Depending on the turbulence level in fluids, the error due to a single encoding gradient spectral response can vary by 20%. When using tailored velocity‐compensated gradients, improved quantification of the Lagrangian velocity spectrum on a voxel‐by‐voxel basis is achieved and used for quantitative correction of intravoxel SD values estimated with velocity‐encoding gradients.ConclusionTo address systematic underestimation of turbulence parameters using bipolar velocity‐encoding gradients in phase‐contrast MRI of stenotic flows with short correlation times, tailored velocity‐compensated gradients are proposed to improve quantitative mapping of turbulent blood flow characteristics.
Pediatric pneumonia (PedPne) lung ultrasound score and inflammatory markers: A pilot study
Authors: Ciuca Ioana M. , Dediu Mihaela , Pop Liviu L. 
Published: November 2021

AbstractIntroductionPneumonia is the principal cause of death among children worldwide. Lung ultrasound (LUS) is a reliable tool for the diagnosis and assessment of community‐acquired pneumonia in children. Furthermore, objective parameters, including the pneumonia LUS score, might be useful for pneumonia monitoring. Thus, our aim was to present a newly developed LUS score for pediatric pneumonia (PedPne) and evaluate its relationship with commonly assessed inflammatory markers.MethodsChildren referred to the Pediatric Pneumology Clinic between September 2017 and February 2018 with suspected pneumonia were screened for eligibility for inclusion in the study and informed consent was obtained. In addition to clinical assessment, LUS was performed during consultation, and inflammatory biomarkers, including C‐reactive protein level, erythrocyte sedimentation rate (ESR), and leukocyte count, were measured in all inpatients. An LUS score for pneumonia and pleurisy in children (pediatric pneumonia lung ultrasound score [PedPne LUS]) was subsequently developed. Chest radiography (CXR) was also performed according to local guidelines for pneumonia diagnosis. Spearman's correlation test was used to evaluate the correlation between the PedPne score and inflammatory markers.ResultsA total of 217 patients were screened, of which 64 patients diagnosed with consolidated pneumonia were included in this study. The median PedPne LUS score of the included patients was 8.02, which was consistent with the consolidations detected on LUS and confirmed by CXR. A very strong positive correlation was found between the LUS PedPne score and C‐reactive protein and ESR, and a good correlation was found with the leukocyte count.ConclusionThe LUS pneumonia score is a reliable parameter for the evaluation of pneumonia, and shows a strong correlation with inflammatory biomarkers. The PedPne LUS score is a potential noninvasive surrogate parameter of inflammation in pediatric pneumonia.
Patient specific Polymethyl methacrylate customised cranioplasty using 3D printed silicone moulds: Technical note
Authors: Scerrati Alba , Travaglini Francesco , Gelmi Clarissa Ann Elisabeth , Lombardo Andrea , De Bonis Pasquale , Cavallo Michele Alessandro , Zamboni Paolo 
Published: November 2021

AbstractIntroductionCranioplasty after decompressive craniectomy can be performed with several techniques and materials. With the common use of 3D printing, custom cranioplasty can be produced at affordable cost. Aim of this technical note is to describe our technique for producing patient specific Polymethyl methacrylate (PMMA) cranioplasty using 3D printed silicone moulds.Materials and MethodsWe enrolled seven patients from January 2020 to June 2021 who required surgery for cranioplasty. The 3D printing was used to produce silicone moulds for defining the exact shape of the PMMA cranioplasty, according to the CT scan of the patient.ResultsWe performed seven procedures. The mean time of the surgery was 80 min. All cranioplasties perfectly matched the patient specific anatomy. No complications occurred.ConclusionsUsing 3D printed patient specific silicone moulds and PMMA resulted to be effective, with affordable costs and ensuring a good cosmetic result.
Physical characterization of glacial rock flours from fjord deposits in South Greenland–Toward soil amendment
Authors: Pesch Charles , Weber Peter Lystbæk , Moldrup Per , de Jonge Lis Wollesen , Arthur Emmanuel , Greve Mogens Humlekrog 
Published: November 2021

AbstractGreenlandic fjords contain vast amounts of glacially derived mineral material (glacial rock flour [GRF]), which may be used to amend structureless, low‐clay, and water‐repellent agricultural soils in South Greenland and elsewhere. In this study, we investigate key physical amendment properties of GRF from 16 different deposits in South Greenland. The clay‐sized fraction varied largely (range, 0.11–0.57 kg kg−1), and the particles were mostly angular. The specific surface area (SSA) determined by either ethylene glycol monomethyl ether (EGME, polar liquid) (range, 13.32–88.06 m2 g−1) or water‐vapor adsorption (range, 10.62–63.82 m2 g−1) agreed well (r = .90) and were comparable to kaolinitic‐clay dominated cultivated soils (KA‐soils) with clay content similar to the GRFs. The cation exchange capacities (CECs) (range, 4.25–21.91 cmol kg−1) were similar to or higher than those of the KA‐soils. The water content at the permanent wilting point (PWP) for the GRFs were considerably lower than those of the KA‐soils. The addition of 5% GRF to a sandy soil from Greenland showed a tendency (although not statistically significant) to increase plant available water (PAW). However, very high GRF addition (10 and 15%) significantly decreased the PAW. The specific surface charge (CEC/SSA) of the GRFs were higher than for comparable KA‐soils, suggesting a good soil amendment potential. The results from this study are valuable toward designing sustainable GRF amendment strategies, matching a given cultivated soil with the right amount and type of GRF.
A ketogenic supplement improves white matter energy supply and processing speed in mild cognitive impairment
Authors: Roy Maggie , Fortier Mélanie , Rheault François , Edde Manon , Croteau Etienne , Castellano Christian‐Alexandre , Langlois Francis , St‐Pierre Valérie , Cuenoud Bernard , Bocti Christian , Fulop Tamas , Descoteaux Maxime , Cunnane Stephen C. 
Published: November 2021

AbstractIntroductionWhite matter (WM) energy supply is crucial for axonal function and myelin maintenance. An exogenous source of ketones, the brain's alternative fuel to glucose, bypasses the brain's glucose‐specific energy deficit and improves cognitive outcomes in mild cognitive impairment (MCI). How an additional supply of ketones affects glucose or ketone uptake in specific WM fascicles in MCI has not previously been reported.MethodsThis 6‐month interventional study included MCI participants randomized to a placebo (n = 16) or ketogenic medium chain triglyceride (kMCT; n = 17) drink. A neurocognitive battery and brain imaging were performed pre‐ and post‐intervention. WM fascicle uptake of ketone and glucose and structural properties were assessed using positron emission tomography and diffusion imaging, respectively.ResultsKetone uptake was increased in the kMCT group by 2.5‐ to 3.2‐fold in all nine WM fascicles of interest (P < .001), an effect seen both in deep WM and in fascicle cortical endpoints. Improvement in processing speed was positively associated with WM ketone uptake globally and in individual fascicles, most importantly the fornix (r = +0.61; P = .014).DiscussionA 6‐month kMCT supplement improved WM energy supply in MCI by increasing ketone uptake in WM fascicles. The significant positive association with processing speed suggests that ketones may have a role in myelin integrity in MCI.
The weak-gravity bound and the need for spin in asymptotically safe matter-gravity models
Authors: de Brito Gustavo P. , Eichhorn Astrid , dos Santos Rafael Robson Lino 
Published: November 2021

Abstract
We discover a weak-gravity bound in scalar-gravity systems in the asymptotic-safety paradigm. The weak-gravity bound arises in these systems under the approximations we make, when gravitational fluctuations exceed a critical strength. Beyond this critical strength, gravitational fluctuations can generate complex fixed-point values in higher-order scalar interactions. Asymptotic safety can thus only be realized at sufficiently weak gravitational interactions. We find that within truncations of the matter-gravity dynamics, the fixed point lies beyond the critical strength, unless spinning matter, i.e., fermions and vectors, is also included in the model.
Awakening sleeper cells: a narrative review on bacterial magic spot synthetases as potential drug targets to overcome persistence
Authors: Veetilvalappil Vimal Venu , Aranjani Jesil Mathew , Mahammad Fayaz Shaik , Joseph Alex 
Published: November 2021

AbstractMagic spot synthetases are emerging targets to overcome persistence caused by stringent response. The ‘stringent response’ is a bacterial stress survival mechanism, which results in the accumulation of alarmones (also called Magic spots) leading to the formation of dormant persister cells. These ‘sleeper cells’ evade antibiotic treatment and could result in relapse of infection. This review broadly investigates the phenomenon of stringent response and persistence, and specifically discusses the distribution, classification, and nomenclature of proteins such as Rel/SpoT homologs (RSH), responsible for alarmone synthesis. The authors further explain the relevance of RSH as potential drug targets to break the dormancy of persister cells commonly seen in biofilms. One of the significant factors that initiate alarmone synthesis is nutrient deficiency. In a starved condition, ribosome-associated RSH detects deacylated tRNA and initiates alarmone synthesis. Accumulation of alarmones has a considerable effect on bacterial physiology, virulence, biofilm formation, and persister cell formation. Preventing alarmone synthesis by inhibiting RSH responsible for alarmone synthesis will prevent or reduce persister cells’ formation. Magic spot synthetases are thus potential targets that could be explored to overcome persistence seen in biofilms.
Activation of bimetallic PtFe nanoparticles with zeolite-type cesium salts of vanadium-substituted polyoxometallates toward electroreduction of oxygen at low Pt loadings for fuel cells
Authors: Renzi Marco , Nobili Francesco , Miecznikowski Krzysztof , Kostuch Aldona , Wadas Anna , Rutkowska Iwona A. , Kulesza Pawel J. 
Published: November 2021

AbstractThe catalytic activity of commercial carbon-supported PtFe (PtFe/C) nanoparticles admixed with mesoporous polyoxometalate Cs3H3PMo9V3O40, (POM3-3–9), has been evaluated towards oxygen reduction reaction (ORR) in acid medium. The polyoxometalate cesium salt co-catalyst/co-support has been prepared by titration using the aqueous solution of phosphovanadomolibdic acid. The synthesized material has been characterized by transmission electron microscopy (TEM) and X-ray diffraction (XRD). The results confirm formation of the polyoxometalate salt with the characteristic Keggin-type structure. The composite catalyst has been prepared by mixing the POM3-3–9 sample with the commercial PtFe/C by sonication. The diagnostic rotating ring-disk voltammetric studies are consistent with good performance of the system with low Pt loading during ORR. The fuel cell membrane electrode assembly (MEA) utilizing the PtFe/POM-based cathode has exhibited comparable or better performance (at relative humidity on the level of 100, 62, and 17%), in comparison to the commercial MEA with higher Pt loading at the cathode. Furthermore, based on the cell potential and power density polarization curves, noticeable improvements in the fuel cell behavior have been observed at the low relative humidity (17%). Finally, the accelerated stress test, which uses the potential square wave between 0.4 V and 0.8 V, has been performed to evaluate MEA stability for at least 100 h. It has been demonstrated that, after initial losses, the proposed catalytic system seems to retain stable performance and good morphological rigidity.
How is COVID-19 altering the manufacturing landscape? A literature review of imminent challenges and management interventions
Authors: Kapoor Kawaljeet , Bigdeli Ali Ziaee , Dwivedi Yogesh K. , Raman Ramakrishnan 
Published: November 2021

AbstractDisruption from the COVID-19 pandemic has caused major upheavals for manufacturing, and has severe implications for production networks, and the demand and supply chains underpinning manufacturing operations. This paper is the first of its kind to pull together research on both—the pandemic-related challenges and the management interventions in a manufacturing context. This systematic literature review reveals the frailty of supply chains and production networks in withstanding the pressures of lockdowns and other safety protocols, including product and workforce shortages. These, altogether, have led to closed facilities, reduced capacities, increased costs, and severe economic uncertainty for manufacturing businesses. In managing these challenges and stabilising their operations, manufacturers are urgently intervening by—investing in digital technologies, undertaking resource redistribution and repurposing, regionalizing and localizing, servitizing, and targeting policies that can help them survive in this altered economy. Based on holistic analysis of these challenges and interventions, this review proposes an extensive research agenda for future studies to pursue.
Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins
Authors: Guo Weijian , Sun Di , Cao Yang , Xiao Linlin , Huang Xin , Ren Wenhua , Xu Shixia , Yang Guang 
Published: November 2021

AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the generaTursiopsandStenellaare monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis ofTursiopsandStenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status ofTursiopsandStenellabecause the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxonD-statistic (ABBA-BABA) test, five-taxonDFOILtest, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers.This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.