bluuebunny/crossref_metadata_2025 huggingface dataset:
Cu-based high-entropy two-dimensional oxide as stable and active photothermal catalyst
Authors: Li Yaguang , Bai Xianhua , Yuan Dachao , Yu Chenyang , San Xingyuan , Guo Yunna , Zhang Liqiang , Ye Jinhua
Published: June 2023

Cu-based nanocatalysts are the cornerstone of various industrial catalytic processes. Synergistically strengthening the catalytic stability and activity of Cu-based nanocatalysts is an ongoing challenge. Herein, the high-entropy principle is applied to modify the structure of Cu-based nanocatalysts, and a PVP templated method is invented for generally synthesizing six-eleven dissimilar elements as high-entropy two-dimensional (2D) materials. Taking 2D Cu2Zn1Al0.5Ce5Zr0.5Ox as an example, the high-entropy structure not only enhances the sintering resistance from 400 °C to 800 °C but also improves its CO2 hydrogenation activity to a pure CO production rate of 417.2 mmol g−1 h−1 at 500 °C, 4 times higher than that of reported advanced catalysts. When 2D Cu2Zn1Al0.5Ce5Zr0.5Ox are applied to the photothermal CO2 hydrogenation, it exhibits a record photochemical energy conversion efficiency of 36.2%, with a CO generation rate of 248.5 mmol g−1 h−1 and 571 L of CO yield under ambient sunlight irradiation. The high-entropy 2D materials provide a new route to simultaneously achieve catalytic stability and activity, greatly expanding the application boundaries of photothermal catalysis.
Rio1 downregulates centromeric RNA levels to promote the timely assembly of structurally fit kinetochores
Authors: Smurova Ksenia , Damizia Michela , Irene Carmela , Stancari Stefania , Berto Giovanna , Perticari Giulia , Iacovella Maria Giuseppina , D’Ambrosio Ilaria , Giubettini Maria , Philippe Réginald , Baggio Chiara , Callegaro Elisabetta , Casagranda Andrea , Corsini Alessandro , Polese Vincenzo Gentile , Ricci Anna , Dassi Erik , De Wulf Peter
Published: June 2023

Kinetochores assemble on centromeres via histone H3 variant CENP-A and low levels of centromere transcripts (cenRNAs). The latter are ensured by the downregulation of RNA polymerase II (RNAPII) activity, and cenRNA turnover by the nuclear exosome. Using S. cerevisiae, we now add protein kinase Rio1 to this scheme. Yeast cenRNAs are produced either as short (median lengths of 231 nt) or long (4458 nt) transcripts, in a 1:1 ratio. Rio1 limits their production by reducing RNAPII accessibility and promotes cenRNA degradation by the 5’−3’exoribonuclease Rat1. Rio1 similarly curtails the concentrations of noncoding pericenRNAs. These exist as short transcripts (225 nt) at levels that are minimally two orders of magnitude higher than the cenRNAs. In yeast depleted of Rio1, cen- and pericenRNAs accumulate, CEN nucleosomes and kinetochores misform, causing chromosome instability. The latter phenotypes are also observed with human cells lacking orthologue RioK1, suggesting that CEN regulation by Rio1/RioK1 is evolutionary conserved.
Detecting lithium plating dynamics in a solid-state battery with operando X-ray computed tomography using machine learning
Authors: Huang Ying , Perlmutter David , Fei-Huei Su Andrea , Quenum Jerome , Shevchenko Pavel , Parkinson Dilworth Y. , Zenyuk Iryna V. , Ushizima Daniela
Published: June 2023

Operando X-ray micro-computed tomography (µCT) provides an opportunity to observe the evolution of Li structures inside pouch cells. Segmentation is an essential step to quantitatively analyzing µCT datasets but is challenging to achieve on operando Li-metal battery datasets due to the low X-ray attenuation of the Li metal and the sheer size of the datasets. Herein, we report a computational approach, batteryNET, to train an Iterative Residual U-Net-based network to detect Li structures. The resulting semantic segmentation shows singular Li-related component changes, addressing diverse morphologies in the dataset. In addition, visualizations of the dead Li are provided, including calculations about the volume and effective thickness of electrodes, deposited Li, and redeposited Li. We also report discoveries about the spatial relationships between these components. The approach focuses on a method for analyzing battery performance, which brings insight that significantly benefits future Li-metal battery design and a semantic segmentation transferrable to other datasets.
Lipid droplet-associated lncRNA LIPTER preserves cardiac lipid metabolism
Authors: Han Lei , Huang Dayang , Wu Shiyong , Liu Sheng , Wang Cheng , Sheng Yi , Lu Xiongbin , Broxmeyer Hal E. , Wan Jun , Yang Lei
Published: June 2023

Lipid droplets (LDs) are cellular organelles critical for lipid homeostasis, with intramyocyte LD accumulation implicated in metabolic disorder-associated heart diseases. Here we identify a human long non-coding RNA, Lipid-Droplet Transporter (LIPTER), essential for LD transport in human cardiomyocytes. LIPTER binds phosphatidic acid and phosphatidylinositol 4-phosphate on LD surface membranes and the MYH10 protein, connecting LDs to the MYH10-ACTIN cytoskeleton and facilitating LD transport. LIPTER and MYH10 deficiencies impair LD trafficking, mitochondrial function and survival of human induced pluripotent stem cell-derived cardiomyocytes. Conditional Myh10 deletion in mouse cardiomyocytes leads to LD accumulation, reduced fatty acid oxidation and compromised cardiac function. We identify NKX2.5 as the primary regulator of cardiomyocyte-specific LIPTER transcription. Notably, LIPTER transgenic expression mitigates cardiac lipotoxicity, preserves cardiac function and alleviates cardiomyopathies in high-fat-diet-fed and Leprdb/db mice. Our findings unveil a molecular connector role of LIPTER in intramyocyte LD transport, crucial for lipid metabolism of the human heart, and hold significant clinical implications for treating metabolic syndrome-associated heart diseases.
Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-α-amino acids in vitro and in vivo
Authors: Fricke Riley , Swenson Cameron V. , Roe Leah Tang , Hamlish Noah Xue , Shah Bhavana , Zhang Zhongqi , Ficaretta Elise , Ad Omer , Smaga Sarah , Gee Christine L. , Chatterjee Abhishek , Schepartz Alanna
Published: June 2023

The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-l-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-l-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.
Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes
Authors: Zehnle Hanna , Laso-Pérez Rafael , Lipp Julius , Riedel Dietmar , Benito Merino David , Teske Andreas , Wegener Gunter
Published: June 2023

Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.
Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems
Authors: Lombard Fabien , Bourdin Guillaume , Pesant Stéphane , Agostini Sylvain , Baudena Alberto , Boissin Emilie , Cassar Nicolas , Clampitt Megan , Conan Pascal , Da Silva Ophélie , Dimier Céline , Douville Eric , Elineau Amanda , Fin Jonathan , Flores J. Michel , Ghiglione Jean-François , Hume Benjamin C. C. , Jalabert Laetitia , John Seth G. , Kelly Rachel L. , Koren Ilan , Lin Yajuan , Marie Dominique , McMinds Ryan , Mériguet Zoé , Metzl Nicolas , Paz-García David A. , Pedrotti Maria Luiza , Poulain Julie , Pujo-Pay Mireille , Ras Joséphine , Reverdin Gilles , Romac Sarah , Rouan Alice , Röttinger Eric , Vardi Assaf , Voolstra Christian R. , Moulin Clémentine , Iwankow Guillaume , Banaigs Bernard , Bowler Chris , de Vargas Colomban , Forcioli Didier , Furla Paola , Galand Pierre E. , Gilson Eric , Reynaud Stéphanie , Sunagawa Shinichi , Sullivan Matthew B. , Thomas Olivier P. , Troublé Romain , Thurber Rebecca Vega , Wincker Patrick , Zoccola Didier , Allemand Denis , Planes Serge , Boss Emmanuel , Gorsky Gaby
Published: June 2023

The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.
Discovery of the allosteric inhibitor from actinomyces metabolites to target EGFRCSTMLR mutant protein: molecular modeling and free energy approach
Authors: Saini Ravi , Kumari Sonali , Bhatnagar Aditi , Singh Amit , Mishra Abha
Published: June 2023

EGFR (epidermal growth factor receptor), a surface protein on the cell, belongs to the tyrosine kinase family, responsible for cell growth and proliferation. Overexpression or mutation in the EGFR gene leads to various types of cancer, i.e., non-small cell lung cancer, breast, and pancreatic cancer. Bioactive molecules identified in this genre were also an essential source of encouragement for researchers who accomplished the design and synthesis of novel compounds with anticancer properties. World Health Organization (WHO) report states that antibiotic resistance is one of the most severe risks to global well-being, food safety, and development. The world needs to take steps to lessen this danger, such as developing new antibiotics and regulating their use. In this study, 6524 compounds derived from Streptomyces sp. were subjected to drug-likeness filters, molecular docking, and molecular dynamic simulation for 1000 ns to find new triple mutant EGFRCSTMLR (EGFR-L858R/T790M/C797S) inhibitors. Docking outcomes revealed that five compounds showed better binding affinity (− 9.074 to − 9.3 kcal/mol) than both reference drug CH7233163 (− 6.11 kcal/mol) and co-crystallized ligand Osimertinib (− 8.07 kcal/mol). Further, molecular dynamic simulation confirmed that ligand C_42 exhibited the best interaction at the active site of EGFR protein and comprised a better average radius of gyration (3.87 Å) and average SASA (Solvent Accessible Surface Area) (82.91 Å2) value than co-crystallized ligand (4.49 Å, 222.38 Å2). Additionally, its average RMSD (Root Mean Square Deviation) (3.25 Å) and RMSF (Root Mean Square Fluctuation) (1.54 Å) values were highly similar to co-crystallized ligand (3.07 Å, 1.54 Å). Compared to the reference ligand, it also demonstrated conserved H-bond interactions with the residues MET_793 and GLN_791 with strong interaction probability. In conclusion, we have found a potential drug with no violation of the rule of three, Lipinski's rule of five, and 26 other vital parameters having great potential in medicinal and pharmaceutical industries applications and can overcome synthetic drug issues.
Genomic and molecular landscape of homologous recombination deficiency across multiple cancer types
Authors: Shi Zhiwen , Chen Bolin , Han Xiao , Gu Weiyue , Liang Shuzhi , Wu Lin
Published: June 2023

Homologous recombination deficiency (HRD) causes faulty double-strand break repair and is a prevalent cause of tumorigenesis. However, the incidence of HRD and its clinical significance in pan-cancer patients remain unknown. Using computational analysis of Single-nucleotide polymorphism array data from 10,619 cancer patients, we demonstrate that HRD frequently occurs across multiple cancer types. Analysis of the pan-cancer cohort revealed that HRD is not only a biomarker for ovarian cancer and triple-negative breast cancer, but also has clinical prognostic value in numerous cancer types, including adrenocortical cancer and thymoma. We discovered that homologous recombination–related genes have a high mutation or deletion frequency. Pathway analysis shows HRD is positively correlated with the DNA damage response and the immune-related signaling pathways. Single cell RNA sequencing of tumor-infiltrating lymphocytes reveals a significantly higher proportion of exhausted T cells in HRD patients, indicating pre-existing immunity. Finally, HRD could be utilized to predict pan-cancer patients’ responses to Programmed cell death protein 1 immunotherapy. In summary, our work establishes a comprehensive map of HRD in pan-cancer. The findings have significant implications for expanding the scope of Poly ADP-ribose polymerase inhibitor therapy and, possibly, immunotherapy.
Physical and chemical characterization of smokeless tobacco products in India
Authors: Sharma Priyamvada , Cheah Nuan Ping , Kaur Jagdish , Sathiya Kumar Sandhya , Rao Vijayashree , Morsed Faridatul Akmam , Choo Michelle Yong Bing , Murthy Pratima
Published: June 2023

The rapid proliferation of smokeless tobacco (SLT) in India has occurred without adequate information on the possible dangers and toxicity of these products. Tobacco flavors as well as nicotine (both protonated and un-protonated) are responsible for health dangers and addiction. The study aimed to offer information on the physical characteristics of commonly used smokeless tobacco products (including microscopic analysis), along with nicotine content (both total and un-protonated), pH, moisture, and flavors. The Standard Operating Procedures (SOPs) validated by the World Health Organization (WHO) recognized Tobacco Testing Laboratory TobLabNet) were applied for the analysis of various constituents of the SLTs. The microscopic analysis indicated that some of the SLT products like khaini were finely processed and available in filter pouches for users’ convenience and prolonged use leading to prolonged retention and addiction potential. Nicotine absorption and availability (both protonated and un-protonated) are affected by moisture and pH. Essences provide a pleasant aroma and flavor, with an increased risk of misuse and other health problems. Few chewing tobacco and Zarda had the lowest levels of un-protonated nicotine (0.10–0.52% and 0.15–0.21%, respectively), whereas Gul, Gudhaku, and Khaini had the highest levels, ranging from 95.33 to 99.12%. Moisture and pH ranged from 4.54 to 50.19% and 5.25–10.07 respectively. Menthol (630.74–9681.42 µg/g) was the most popular flavour, followed by Eucalyptol (118.16–247.77 µg/g) and camphor (148.67 and 219.317 µg/g). SLT’s health concerns and addiction dangers are exacerbated by the high proportion of bioavailable nicotine coupled with flavors. The findings of this study have important implications for the regulation and use of SLT in countries where use of SLT is prevalent.
Evaluation of epigenetic methylation biomarkers for the detection of colorectal cancer using droplet digital PCR
Authors: Petit J. , Carroll G. , Zhao J. , Roper E. , Pockney P. , Scott R. J.
Published: June 2023

Colorectal cancer (CRC) is the third most common cancer worldwide. Screening programs allow early diagnosis and have improved the clinical management of this disease. Aberrant DNA methylation is increasingly being explored as potential biomarkers for many types of cancers. In this study we investigate the methylation of ten target genes in 105 CRC and paired normal adjacent colonic tissue samples using a MethylLight droplet digital PCR (ML-ddPCR) assay. Receiver operator characteristic (ROC) curves were used to determine the diagnostic performance of all target genes individually and in combination. All 515 different combinations of genes showed significantly higher levels of methylation in CRC tissue. The combination of multiple target genes into a single test generally resulted in greater diagnostic accuracy when compared to single target genes. Our data confirms that ML-ddPCR is able to reliably detect significant differences in DNA methylation between CRC tissue and normal adjacent colonic tissue in a specific selection of target genes.
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

New 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

The 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

The 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

Voltage 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

Echocardiography 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

The 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

Floods 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

Endogenous 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

Neutralizing 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

The 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

Areas 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.
Fetuin A functionalisation of biodegradable PLLA-co-PEG nonwovens towards enhanced biomineralisation and osteoblastic growth behaviour
Authors: Oschatz Stefan , Teske Michael , Burmeister Ulrike , Illner Sabine , Senz Volkmar , Lang Hermann , Grabow Niels , Markhoff Jana
Published: June 2023

Fetuin A functionalisation of biodegradable PLLA-co-PEG nonwovens lead to enhanced biomineralisation and improved cell morphology and spreading in vitro.
Principles of nucleic acid toehold mediated strand displacement (TMSD) reaction model and its applications in cell environment
Authors: Tang Linlin , Luo Tao , Fan Sisi , Liu Yan , Song Jie
Published: June 2023

We summarize the principles of nucleic acid TMSD reaction and highlight the successful development of the application of nucleic acid TMSD reaction in the cell environment.
Correction: Systematic shape evolution of Co3O4 nanocrystals from octahedra to spheres under the influence of C2O42− and PVP
Authors: Kang Min , Zhou Hai , Wu Dong , Lv Baoliang
Published: June 2023

Correction for ‘Systematic shape evolution of Co3O4 nanocrystals from octahedra to spheres under the influence of C2O42− and PVP’ by Min Kang et al., CrystEngComm, 2016, 18, 9299–9306, https://doi.org/10.1039/C6CE02106A.
Leveraging machine learning engineering to uncover insights into heterogeneous catalyst design for oxidative coupling of methane
Authors: Nishimura Shun , Li Xinyue , Ohyama Junya , Takahashi Keisuke
Published: June 2023

Unveiling current issues in the investigation of highly-active heterogeneous catalysts using machine learning engineering techniques was discussed in the case of oxidative coupling of methane with support vector regression and Bayesian optimization.
Biocatalytic formal regio- and enantioselective Markovnikov hydroamination of aryl alkenes to chiral amines
Authors: Jin Qi , Zhang Jingqi , Huang Shuangping , Gao Lili , Chang Honghong , Zhang Jiandong
Published: June 2023

A novel fully biocatalytic system for regio- and enantioselective hydroamination of 4-hydroxystyrenes to useful and valuable chiral amines in good yields and excellent ee.
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.
Ordered growth of metal oxides in patterned multi-angle microstructures
Authors: Ji Zhenkai , Sun Min , Chen Tiantian , Shen Xinyi , Xu Xiuzhen , Zhong Yan , Wang Dadong , Ma Jiwei , Chen Bo , Yi Zhiguo , Xu Xiaobin
Published: June 2023

Pre-crystallization seeding and hydrothermal growth of TiO2nanorod arrays.
Magnetic polyborate nanoparticles as a green and efficient catalyst for one-pot four-component synthesis of highly substituted imidazole derivatives
Authors: Malihishoja Alireza , Dekamin Mohammad G. , Eslami Mohammad
Published: June 2023

Magnetic polybiorate nanoparticles were prepared from H3BO3via a simple ball-milling procedure and explored as a green and highly efficient catalyst for the synthesis of tetra-substituted imidazoles from cascade cyclocondensation as well as in situ air oxidation.
Austalide derivative from marine-derived Aspergillus sp. and evaluation of its cytotoxic and ADME/TOPKAT properties
Authors: Elnaggar Mohamed S. , Elissawy Ahmed M. , Youssef Fadia S. , Kicsák Máté , Kurtán Tibor , Singab Abdel Nasser B. , Kalscheuer Rainer
Published: June 2023

New meroterpenoid derivative (austalide Z) isolated from the marine-derived fungal endophyte Aspergillus sp. with 9 known compounds. Cytotoxic evaluation of the isolated compounds against Caco-2 cell lines reveal weak to moderate activities.
A new melilite-type rare-earth borate CdTbGaB2O7 and multicolor tunable emission in the CdTb1−xSmxGaB2O7 (0 ≤ x ≤ 0.2) phosphors
Authors: Chen Xuean , Zhang Jinyuan , Xiao Weiqiang , Song Xiaoyan
Published: June 2023

A new borate CdTbGaB2O7 was synthesized and characterized and luminescence properties of CdTb1−xSmxGaB2O7 (0 ≤ x ≤ 0.2) were investigated.
Process intensification of continuous-flow seATRP by a sonicated multi-reactor setup
Authors: Zhang Suqi , Junkers Tanja , Kuhn Simon
Published: June 2023

A sonicated electrochemical multi-reactor setup is demonstrated for continuous-flow seATRP.
Bidirectional photoswitchability in an iron(iii) spin crossover complex: symmetry-breaking and solvent effects
Authors: Díaz-Torres Raúl , Chastanet Guillaume , Collet Eric , Trzop Elzbieta , Harding Phimphaka , Harding David J.
Published: June 2023

Two solvates, one showing symmetry-breaking spin crossover and bidirectional photoswitchability from a [HS-LS] state, are reported.
Chemiluminescent duplex analysis using phenoxy-1,2-dioxetane luminophores with color modulation
Authors: Gutkin Sara , Tannous Rozan , Jaber Qais , Fridman Micha , Shabat Doron
Published: June 2023

Chemiluminescence phenoxy-1,2-dioxetane luminophores for multiplex analysis of enzymes and bioanalytes.
Light-driven room temperature methane gas sensor based on Ag modified flower-like ZnO microsphere
Authors: Li Mengwei , Sun Xueya , Wang Yihui , Qin Cong , Cao Jianliang , Wang Yan
Published: June 2023

ZnO microspheres loaded with Ag nanoparticles were synthesized and exhibited good light-driven CH4 sensing performance.
Template-free hydrothermal synthesis of nickel sulfide nanocrystals on MWCNTs: efficient and stable bifunctional electroactive material for oxygen electrocatalysis
Authors: Yadav Mamta , Singh Devesh Kumar , Ganesan Vellaichamy
Published: June 2023

Efficient and low-cost bifunctional electrocatalyst for oxygen electrocatalysis is developed using nickel sulfide and multi-walled carbon nanotubes.
Highly reversible, dendrite-free and low-polarization Zn metal anodes enabled by a thin SnO2layer for aqueous Zn-ion batteries
Authors: Zhang Yuejuan , Chen Penghui , Li Mingming , Li Shaoqing , Yue Ying , Wang Yanchun , Xie Sishen , Zhou Weiya
Published: June 2023

Dendrite-free Zn anodes protected by a zincophilic, hydrophilic and thin (∼100 nm) SnO2layer exhibited an outstanding electrochemical performance over a wide range of cycling, especially for Zn plating/stripping with large current and high capacity.
Electrolyte ions-matching hierarchically porous biochar electrodes with an extended potential window for next-generation supercapacitors
Authors: Rama Raju Ganji Seeta , Kondrat Svyatoslav , Chodankar Nilesh R. , Hwang Seung-Kyu , Lee Jeong Han , Long Teng , Pavitra Eluri , Patil Swati J. , Ranjith Kugalur Shanmugam , Rao M. V. Basaveswara , Wu Peng , Roh Kwang Chul , Huh Yun Suk , Han Young-Kyu
Published: June 2023

A balanced hierarchical pore ratio enhances the energy storage of biomass-derived activated carbon electrodes while a hybrid electrolyte extends the potential window, facilitating the fabrication of high-energy density next-generation symmetric supercapacitors.
Unveiling the role of cobalt doping in optimizing ammonia electrosynthesis on iron–cobalt oxyhydroxide hollow nanocages
Authors: Han Xinxin , Liu Cheng , Tang Yuan , Meng Qiangguo , Zhou Weizhen , Chen Shixia , Deng Shuguang , Wang Jun
Published: June 2023

A series of FeCoOOH HNCs were constructed via controlled Co doping; the right amount of Co doping can lower the energy barrier of *N2 → *NNH → *NNHH, induced by the preferential proton adsorption on Co sites to drive NH3 electrosynthesis.
Folate targeting self-limiting hyperthermic nanoparticles for controlled photothermal therapy
Authors: George Sharon , Srinivasan Asha , Tulimilli SubbaRao V. , Madhunapantula SubbaRao V. , Palantavida Shajesh
Published: June 2023

A new temperature reporting, fluorescent photothermal agent with cancer targeting ability based on gold nanorods.
3,5-Dicyanopyridine motifs for electron-transporting semiconductors: from design and synthesis to efficient organic light-emitting diodes
Authors: Leitonas Karolis , Vigante Brigita , Volyniuk Dmytro , Bucinskas Audrius , Keruckiene Rasa , Dimitrijevs Pavels , Chiu Tien-Lung , Grazulevicius Juozas Vidas , Arsenyan Pavel
Published: June 2023

Proposing 3,5-dicyanopyridine motifs for the design of electroactive materials for optoelectronic devices, three electron-transporting semiconductors are synthesised. The best performance was observed for OLED containing FPDD as a host (EQE = 21.9%).
Multifunctional pseudohalide-based ionic liquid doping promotes efficient and stable perovskite solar cells
Authors: Guo Xing , Lin Zhenhua , Cao Wenying , Xu Yumeng , Wang Qingrui , Zhang Boyao , Hao Yue , Chang Jingjing
Published: June 2023

The introduction of TEAPF6, a multifunctional pseudohalide-based ionic liquid, into a perovskite film could increase the film crystal quality and reduce charge recombination, resulting in an improvement in the efficiency and stability of PSCs.
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

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.