bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atlas-based finite element analyses with simpler constitutive models predict personalized progression of knee osteoarthritis: data from the osteoarthritis initiative
Authors: Mononen Mika E. , Paz Alexander , Liukkonen Mimmi K. , Turunen Mikael J. 
Published: June 2023

AbstractNew technologies are required to support a radical shift towards preventive healthcare. Here we focus on evaluating the possibility of finite element (FE) analysis-aided prevention of knee osteoarthritis (OA), a disease that affects 100 million citizens in the US and EU and this number is estimated to increase drastically. Current clinical methods to diagnose or predict joint health status relies on symptoms and tissue failures obtained from clinical imaging. In a joint with no detectable injuries, the diagnosis of the future health of the knee can be assumed to be very subjective. Quantitative approaches are therefore needed to assess the personalized risk for the onset and development of knee OA. FE analysis utilizing an atlas-based modeling approach has shown a preliminary capability for simulating subject-specific cartilage mechanical responses. However, it has been verified with a very limited subject number. Thus, the aim of this study is to verify the real capability of the atlas-based approach to simulate cartilage degeneration utilizing different material descriptions for cartilage. A fibril reinforced poroviscoelastic (FRPVE) material formulation was considered as state-of-the-art material behavior, since it has been preliminary validated against real clinical follow-up data. Simulated mechanical tissue responses and predicted cartilage degenerations within knee joint with FRPVE material were compared against simpler constitutive models for cartilage. The capability of the atlas-based modeling to offer a feasible approach with quantitative evaluation for the risk for the OA development (healthy vs osteoarthritic knee, p < 0.01, AUC ~ 0.7) was verified with 214 knees. Furthermore, the results suggest that accuracy for simulation of cartilage degeneration with simpler material models is similar to models using FPRVE materials if the material parameters are chosen properly.
The efficacy of biosynthesized silver nanoparticles against Pseudomonas aeruginosa isolates from cystic fibrosis patients
Authors: Al-Momani Hafez , Almasri Muna , Al Balawi Dua’A. , Hamed Saja , Albiss Borhan Aldeen , Aldabaibeh Nour , Ibrahim Lugain , Albalawi Hadeel , Al Haj Mahmoud Sameer , Khasawneh Ashraf I. , Kilani Muna , Aldhafeeri Muneef , Bani-Hani Muayyad , Wilcox Matthew , Pearson Jeffrey , Ward Christopher 
Published: June 2023

AbstractThe high antibiotic resistance of Pseudomonas aeruginosa (PA) makes it critical to develop alternative antimicrobial agents that are effective and affordable. One of the many applications of silver nanoparticles (Ag NPs) is their use as an antimicrobial agent against bacteria resistant to common antibiotics. The key purpose of this research was to assess the antibacterial and antibiofilm effectiveness of biosynthesized Ag NPs against six biofilm-forming clinically isolated strains of PA and one reference strain (ATCC 27853). Ag NPs were biosynthesized using a seed extract of Peganum harmala as a reducing agent. Ag NPs were characterized by Ultraviolet–visible (UV–Vis) spectroscopy and scanning transmission electron microscopy (STEM). The effect of Ag NPs on biofilm formation and eradication was examined through micro-titer plate assays, and the minimal inhibitory (MIC) and minimum bactericidal (MBC) concentrations determined. In addition, real-time polymerase chain reactions (RT-PCR) were performed to examine the effects of Ag NPs on the expression of seven PA biofilm-encoding genes (LasR, LasI, LssB, rhIR, rhII, pqsA and pqsR). The biosynthesized Ag NPs were spherically-shaped with a mean diameter of 11 nm. The MIC for each PA strain was 15.6 µg/ml, while the MBC was 31.25 µg/ml. All PA strains exposed to Ag NPs at sub-inhibitory concentrations (0.22–7.5 µg/ml) showed significant inhibitory effects on growth and biofilm formation. Biomass and biofilm metabolism were reduced dependent on Ag NP concentration. The expression of the quorum-sensing genes of all strains were significantly reduced at an Ag NP concentration of 7.5 µg/ml. The results demonstrate the extensive in-vitro antibacterial and antibiofilm performance of Ag NPs and their potential in the treatment of PA infection. It is recommended that future studies examine the possible synergy between Ag NPs and antibiotics.
First-principles density functional theoretical study on the structures, reactivity and spectroscopic properties of (NH) and (OH) Tautomer's of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one
Authors: Halim Shimaa Abdel , Abdel-Rahman Mohamed A. 
Published: June 2023

AbstractThe tautomerizations mechanism of 4-(methylsulfanyl)-3[(1Z)-1-(2-phenylhydrazinylidene) ethyl] quinoline-2(1H)-one were inspected in the gas phase and ethanol using density function theory (DFT) M06-2X and B3LYP methods. Thermo-kinetic features of different conversion processes were estimated in temperature range 273–333 K using the Transition state theory (TST) accompanied with one dimensional Eckert tunneling correction (1D-Eck). Acidity and basicity were computed as well, and the computational results were compared against the experimental ones. Additionally, NMR, global descriptors, Fukui functions, NBO charges, and electrostatic potential (ESP) were discussed. From thermodynamics analysis, the keto form of 4-(methylsulfanyl)-3-[(1Z)-1-(2 phenylhydrazinylidene) quinoline-2(1H)-one is the most stable form in the gas phase and ethanol and the barrier heights required for tautomerization process were found to be high in the gas phase and ethanol ~ 38.80 and 37.35 kcal/mol, respectively. DFT methods were used for UV–Vis electronic spectra simulation and the time-dependent density functional theory solvation model (TDDFT-SMD) in acetonitrile compounds.
Heterogeneity of voltage gated sodium current density between neurons decorrelates spiking and suppresses network synchronization in Scn1b null mouse models
Authors: Hull Jacob M. , Denomme Nicholas , Yuan Yukun , Booth Victoria , Isom Lori L. 
Published: June 2023

AbstractVoltage gated sodium channels (VGSCs) are required for action potential initiation and propagation in mammalian neurons. As with other ion channel families, VGSC density varies between neurons. Importantly, sodium current (INa) density variability is reduced in pyramidal neurons of Scn1b null mice. Scn1b encodes the VGSC β1/ β1B subunits, which regulate channel expression, trafficking, and voltage dependent properties. Here, we investigate how variable INa density in cortical layer 6 and subicular pyramidal neurons affects spike patterning and network synchronization. Constitutive or inducible Scn1b deletion enhances spike timing correlations between pyramidal neurons in response to fluctuating stimuli and impairs spike-triggered average current pattern diversity while preserving spike reliability. Inhibiting INa with a low concentration of tetrodotoxin similarly alters patterning without impairing reliability, with modest effects on firing rate. Computational modeling shows that broad INa density ranges confer a similarly broad spectrum of spike patterning in response to fluctuating synaptic conductances. Network coupling of neurons with high INa density variability displaces the coupling requirements for synchronization and broadens the dynamic range of activity when varying synaptic strength and network topology. Our results show that INa heterogeneity between neurons potently regulates spike pattern diversity and network synchronization, expanding VGSC roles in the nervous system.
Cardiac phase detection in echocardiography using convolutional neural networks
Authors: Farhad Moomal , Masud Mohammad Mehedy , Beg Azam , Ahmad Amir , Ahmed Luai A. , Memon Sehar 
Published: June 2023

AbstractEchocardiography is a commonly used and cost-effective test to assess heart conditions. During the test, cardiologists and technicians observe two cardiac phases—end-systolic (ES) and end-diastolic (ED)—which are critical for calculating heart chamber size and ejection fraction. However, non-essential frames called Non-ESED frames may appear between these phases. Currently, technicians or cardiologists manually detect these phases, which is time-consuming and prone to errors. To address this, an automated and efficient technique is needed to accurately detect cardiac phases and minimize diagnostic errors. In this paper, we propose a deep learning model called DeepPhase to assist cardiology personnel. Our convolutional neural network (CNN) learns from echocardiography images to identify the ES, ED, and Non-ESED phases without the need for left ventricle segmentation or electrocardiograms. We evaluate our model on three echocardiography image datasets, including the CAMUS dataset, the EchoNet Dynamic dataset, and a new dataset we collected from a cardiac hospital (CardiacPhase). Our model outperforms existing techniques, achieving 0.96 and 0.82 area under the curve (AUC) on the CAMUS and CardiacPhase datasets, respectively. We also propose a novel cropping technique to enhance the model’s performance and ensure its relevance to real-world scenarios for ES, ED, and Non ES-ED classification.
Electropolymerized polypyrrole-MOF composite as a coating material for SPME fiber for extraction VOCs liberated by bacteria
Authors: Mametov Radik , Sagandykova Gulyaim , Monedeiro-Milanowski Maciej , Gabryś Dorota , Pomastowski Paweł 
Published: June 2023

AbstractThe synthesis of efficient and low-cost coatings for solid-phase microextraction attracted much attention. Conductive polymers are excellent candidates for this purpose due to the possibility of electropolymerization, which results in the reproducible synthesis of films. A plethora of studies reported in the literature concluded that modification of conductive polymers with innovative materials could lead to an increase in sensitivity toward specific analytes. In this work, the metal–organic framework-polypyrrole composite was electrodeposited in one step directly onto a stainless-steel substrate. The effect of synthesis parameters on extraction efficiency was investigated. The obtained PPy@ZIF-8 coating was subjected to physical–chemical characterization using electron microscopy and Fourier-transform IR spectroscopy. The main finding of the study was that the values of the limit of detection and intra- and inter-day reproducibility for analytes with different chemical structures were found to be lower as compared to pure polypyrrole coating. Furthermore, the obtained polypyrrole-MOF coating was applied for the collection of profiles of volatile organic compounds liberated by bacteria. Hence, the polypyrrole@ZIF-8 coating synthesized using a low-cost and facile approach presented in this study can be useful for the profiling of VOCs liberated by bacteria.
GIS-based hydrodynamic modeling for urban flood mitigation in fast-growing regions: a case study of Erbil, Kurdistan Region of Iraq
Authors: Mustafa Andam , Szydłowski Michał , Veysipanah Mozafar , Hameed Hasan Mohammed 
Published: June 2023

AbstractFloods threaten urban infrastructure, especially in residential neighborhoods and fast-growing regions. Flood hydrodynamic modeling helps identify flood-prone locations and improve mitigation plans' resilience. Urban floods pose special issues due to changing land cover and a lack of raw data. Using a GIS-based modeling interface, input files for the hydrodynamic model were developed. The physical basin's properties were identified using soil map data, Land Use Land Cover (LULC) maps, and a Digital Elevation Model (DEM). So, the HEC-RAS 2-D hydrodynamic model was developed to estimate flood susceptibility and vulnerability in Erbil, Iraq. The case study examines the quality of flood modeling results using different DEM precisions. Faced with the difficulty, this study examines two building representation techniques: Building Block (BB) and Building Resistance (BR). The work presented here reveals that it is possible to apply the BR technique within the HEC-RAS 2-D to create urban flood models for regions that have a lack of data or poor data quality. Indeed, the findings confirmed that the inundated areas or areas where water accumulated in past rainfall events in Erbil are the same as those identified in the numerical simulations. The study's results indicate that the Erbil city is susceptible to flood hazards, especially in areas with low-lying topography and substantial precipitation. The study's conclusions can be utilized to plan and develop flood control structures, since it identified flood-prone areas of the city.
Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
Authors: Veglia Alex J. , Bistolas Kalia S. I. , Voolstra Christian R. , Hume Benjamin C. C. , Ruscheweyh Hans-Joachim , Planes Serge , Allemand Denis , Boissin Emilie , Wincker Patrick , Poulain Julie , Moulin Clémentine , Bourdin Guillaume , Iwankow Guillaume , Romac Sarah , Agostini Sylvain , Banaigs Bernard , Boss Emmanuel , Bowler Chris , de Vargas Colomban , Douville Eric , Flores Michel , Forcioli Didier , Furla Paola , Galand Pierre E. , Gilson Eric , Lombard Fabien , Pesant Stéphane , Reynaud Stéphanie , Sunagawa Shinichi , Thomas Olivier P. , Troublé Romain , Zoccola Didier , Correa Adrienne M. S. , Vega Thurber Rebecca L. 
Published: June 2023

AbstractEndogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
A spike-targeting bispecific T cell engager strategy provides dual layer protection against SARS-CoV-2 infection in vivo
Authors: Li Fanlin , Xu Wei , Zhang Xiaoqing , Wang Wanting , Su Shan , Han Ping , Wang Haiyong , Xu Yanqin , Li Min , Fan Lilv , Zhang Huihui , Dai Qiang , Lin Hao , Qi Xinyue , Liang Jie , Wang Xin , Jiang Shibo , Xie Youhua , Lu Lu , Yang Xuanming 
Published: June 2023

AbstractNeutralizing antibodies exert a potent inhibitory effect on viral entry; however, they are less effective in therapeutic models than in prophylactic models, presumably because of their limited efficacy in eliminating virus-producing cells via Fc-mediated cytotoxicity. Herein, we present a SARS-CoV-2 spike-targeting bispecific T-cell engager (S-BiTE) strategy for controlling SARS-CoV-2 infection. This approach blocks the entry of free virus into permissive cells by competing with membrane receptors and eliminates virus-infected cells via powerful T cell-mediated cytotoxicity. S-BiTE is effective against both the original and Delta variant of SARS-CoV2 with similar efficacy, suggesting its potential application against immune-escaping variants. In addition, in humanized mouse model with live SARS-COV-2 infection, S-BiTE treated mice showed significantly less viral load than neutralization only treated group. The S-BiTE strategy may have broad applications in combating other coronavirus infections.
Crystal structure of adenosine A2A receptor in complex with clinical candidate Etrumadenant reveals unprecedented antagonist interaction
Authors: Claff Tobias , Schlegel Jonathan G. , Voss Jan H. , Vaaßen Victoria J. , Weiße Renato H. , Cheng Robert K. Y. , Markovic-Mueller Sandra , Bucher Denis , Sträter Norbert , Müller Christa E. 
Published: June 2023

AbstractThe Gs protein-coupled adenosine A2A receptor (A2AAR) represents an emerging drug target for cancer immunotherapy. The clinical candidate Etrumadenant was developed as an A2AAR antagonist with ancillary blockade of the A2BAR subtype. It constitutes a unique chemotype featuring a poly-substituted 2-amino-4-phenyl-6-triazolylpyrimidine core structure. Herein, we report two crystal structures of the A2AAR in complex with Etrumadenant, obtained with differently thermostabilized A2AAR constructs. This led to the discovery of an unprecedented interaction, a hydrogen bond of T883.36 with the cyano group of Etrumadenant. T883.36 is mutated in most A2AAR constructs used for crystallization, which has prevented the discovery of its interactions. In-vitro characterization of Etrumadenant indicated low selectivity versus the A1AR subtype, which can be rationalized by the structural data. These results will facilitate the future design of AR antagonists with desired selectivity. Moreover, they highlight the advantages of the employed A2AAR crystallization construct that is devoid of ligand binding site mutations.
Hydrothermal ferromanganese oxides around a petit-spot volcano on old and cold oceanic crust
Authors: Azami Keishiro , Machida Shiki , Hirano Naoto , Nakamura Kentaro , Yasukawa Kazutaka , Kogiso Tetsu , Nakanishi Masao , Kato Yasuhiro 
Published: June 2023

AbstractAreas of old and cold oceanic plate lack conventional volcanism and have been assumed to be devoid of submarine hydrothermal activity. However, petit-spot volcanoes are common in areas of flexure of such oceanic plates. Here, we report hydrothermal ferromanganese oxides dredged from the vicinity of a petit-spot volcano at 5.7 km water depth in an area of oceanic plate flexure east of the Japan Trench. The bulk chemical, lead isotopic and mineralogical compositions of the samples indicate their formation by low-temperature hydrothermal activity, which can be interpreted as being caused by fluid–rock interactions at <200 °C. We propose that interaction of local marine sediments with volatile-rich petit-spot magmas may produce hydrothermal fluids containing not only iron and manganese but also enough amounts of carbon dioxide and methane to have implications for the global carbon cycle. However, contemporary hydrothermal activities at petit-spot volcanoes have not been confirmed yet.
Machine-learning-accelerated screening of single metal atoms anchored on MnPS3 monolayers as promising bifunctional oxygen electrocatalysts
Authors: Li Xinyi , Lin Shiru , Yan Tingyu , Wang Zhongxu , Cai Qinghai , Zhao Jingxiang 
Published: June 2023

By carefully tuning the kinds of the SACs anchored on MnPS3 monolayer, Rh and Ni atoms can be utilized bifunctional catalysts for ORR/OER.
Improvement in bilirubin influence on cholesterol efflux capacity evaluation using the immobilized liposome-bound gel beads method
Authors: Miyakoshi Tsunehiro , Mutsuda Yume , Horiuchi Yuna , Kameda Takahiro , Tozuka Minoru , Ohkawa Ryunosuke 
Published: June 2023

Abstract
Introduction: High-density lipoprotein (HDL) has a cholesterol efflux capacity (CEC) that protects against atherosclerosis. Recently, we developed an assay for CEC evaluation, named the immobilized liposome-bound gel beads (ILG) method, which is a highly accurate, simple, and safe method for CEC evaluation because it uses liposomes and BODIPY-labeled cholesterol instead of cultured cells and radioactive substances, respectively. Although the ILG method can be implemented in clinical settings, our previous study revealed that bilirubin causes a positive error in the CEC value. Therefore, in the present study, we attempted to improve the influence of bilirubin levels on the ILG method.
Methods: To investigate why bilirubin caused a positive error in CEC values when using the ILG method, 3D fluorescence spectra of BODIPY-labeled cholesterol and bilirubin were measured. To avoid the fluorescence emitted by bilirubin, CEC was measured using the ILG method with shifting of excitation wavelength for BODIPY-labeled cholesterol quantification. In addition, we used bilirubin oxidase to oxidize bilirubin during the incubation time of the ILG method to weaken bilirubin fluorescence.
Results: We found that bilirubin emitted fluorescence at the measurement setting of the ILG method. By shifting the excitation wavelength, the positive error caused by bilirubin was improved by approximately 70%. Furthermore, by utilizing bilirubin oxidase, the false-high values of CEC were improved by approximately 80%.
Conclusions: Bilirubin interferes with CEC assay using BODIPY-cholesterol, but we successfully improved the influence of bilirubin on CEC evaluation using the ILG method. These improvements will promote the clinical application of the ILG method.
Investigation on baicalin‐loaded chitosan film crosslinked by graphene oxide and its biocompatibility
Authors: Zhu Yu , Zhang Lu , Zhou Lei , Li Xin , Zhao Yuancong , Wang Jin 
Published: June 2023

AbstractChitosan has good biocompatibility, in vivo biodegradability and certain physiological activity, which can be used as a drug carrier to stabilise and protect drug components, causing the promotion of drug absorption and controlling drug release. Using graphene oxide (GO) as a cross‐linking agent, the functional groups in its lamellar structure can interact effectively with the functional groups in chitosan molecules, leading to enhanced mechanical properties and optimize the controlled drug‐release behaviour. GO/chitosan composite films were prepared by the solution mixing method with various GO content and exhibit many hydrogen bonds between the GO and chitosan. There were no obviously agglomerated GO particles in the surface of composite films, and the lamellar structure can be observed in the cross section of the composite films. Differential thermal analysis (DTA) indicated that the addition of GO increased the stability of the chitosan film. The baicalin‐loaded GO/Chitosan also exhibited pH dependent release behaviour, with an increasing release amount and rate at lower pH medium. In addition, the result of biological evaluations showed that the GO/Chitosan films had good cytocompatibility in vitro and histocompatibility at appropriate GO concentrations. This investigation offered a new pH‐dependent drug carrier potentially applied for tumour and atherosclerosis treatment.