bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of short chain fatty acids (SCFAs) on antimicrobial activity of new β-lactam/β-lactamase inhibitor combinations and on virulence of Escherichia coli isolates
Authors: Kadry Ashraf A. , El-Antrawy May A. , El-Ganiny Amira M. 
Published: February 2023

Abstract
In a healthy gut microbiota, short chain fatty acids (SCFAs) are produced. The antibacterial action of SCFAs against intestinal pathogens makes them useful for ensuring the safety of food and human health. In this study, we aimed to assess the in vitro inhibitory activity of SCFAs, and to report, for the first time, their impact on the activity of new β-lactam/β-lactamase inhibitor combinations. The minimum inhibitory concentrations of acetic, propionic, and butyric acids were determined against E. coli clinical isolates recovered from gastrointestinal infections. Cefoperazone/sulbactam, ceftazidime/avibactam and cefepime/enmetazobactam are new β-lactam/β-lactamase inhibitor combinations that were studied for their combined therapeutic effects. Also, the effects of pH and concentration of SCFAs were evaluated on in vitro bacterial growth and expression of genes encoding for motility, adhesion, invasion, and biofilm formation. SCFAs were tested at concentrations of 12 mM at pH 7.4 (ileum-conditions), in addition to 60 mM and 123 mM, at pH 6.5 (colon-conditions). The tested SCFAs showed the same MIC (3750 μg ml−1 ≃ 60 mM) against all isolates. Furthermore, the addition of SCFAs to the tested β-lactam/β-lactamase inhibitor combinations greatly restored the susceptibility of the isolates. SCFAs had significant effect on bacterial growth and virulence in a pH and concentration-dependent manner; low ileal concentration potentiated E. coli growth, while higher colonic concentration significantly suppressed growth and down-regulated the expression of virulence genes (fliC, ipaH, FimH, BssS). Therefore, the significant inhibitory effect of colonic SCFAs on β-lactam/β-lactamase inhibitor combinations might lead to the development of promising treatment strategies.
Population structure and hybridisation in a population of Hawaiian feral chickens
Authors: Martin Cerezo Maria Luisa , López Saioa , van Dorp Lucy , Hellenthal Garrett , Johnsson Martin , Gering Eben , Henriksen Rie , Wright Dominic 
Published: February 2023

AbstractChickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976–1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke’e State Park and the Alaka’i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.
Lipid-induced transcriptomic changes in blood link to lipid metabolism and allergic response
Authors: Dekkers Koen F. , Slieker Roderick C. , Ioan-Facsinay Andreea , van Iterson Maarten ,   BIOS consortium, Ikram M. Arfan , van Greevenbroek Marleen M. J. , Veldink Jan H. , Franke Lude , Boomsma Dorret I. , Slagboom P. Eline , Jukema J. Wouter , Heijmans Bastiaan T. 
Published: February 2023

AbstractImmune cell function can be altered by lipids in circulation, a process potentially relevant to lipid-associated inflammatory diseases including atherosclerosis and rheumatoid arthritis. To gain further insight in the molecular changes involved, we here perform a transcriptome-wide association analysis of blood triglycerides, HDL cholesterol, and LDL cholesterol in 3229 individuals, followed by a systematic bidirectional Mendelian randomization analysis to assess the direction of effects and control for pleiotropy. Triglycerides are found to induce transcriptional changes in 55 genes and HDL cholesterol in 5 genes. The function and cell-specific expression pattern of these genes implies that triglycerides downregulate both cellular lipid metabolism and, unexpectedly, allergic response. Indeed, a Mendelian randomization approach based on GWAS summary statistics indicates that several of these genes, including interleukin-4 (IL4) and IgE receptors (FCER1A,MS4A2), affect the incidence of allergic diseases. Our findings highlight the interplay between triglycerides and immune cells in allergic disease.
Generalized extinction of fear memory depends on co-allocation of synaptic plasticity in dendrites
Authors: Xu Zhiwei , Geron Erez , Pérez-Cuesta Luis M. , Bai Yang , Gan Wen-Biao 
Published: February 2023

AbstractMemories can be modified by new experience in a specific or generalized manner. Changes in synaptic connections are crucial for memory storage, but it remains unknown how synaptic changes associated with different memories are distributed within neuronal circuits and how such distributions affect specific or generalized modification by novel experience. Here we show that fear conditioning with two different auditory stimuli (CS) and footshocks (US) induces dendritic spine elimination mainly on different dendritic branches of layer 5 pyramidal neurons in the mouse motor cortex. Subsequent fear extinction causes CS-specific spine formation and extinction of freezing behavior. In contrast, spine elimination induced by fear conditioning with >2 different CS-USs often co-exists on the same dendritic branches. Fear extinction induces CS-nonspecific spine formation and generalized fear extinction. Moreover, activation of somatostatin-expressing interneurons increases the occurrence of spine elimination induced by different CS-USs on the same dendritic branches and facilitates the generalization of fear extinction. These findings suggest that specific or generalized modification of existing memories by new experience depends on whether synaptic changes induced by previous experiences are segregated or co-exist at the level of individual dendritic branches.
Proteogenomics of diffuse gliomas reveal molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms
Authors: Wang Yunzhi , Luo Rongkui , Zhang Xuan , Xiang Hang , Yang Bing , Feng Jinwen , Deng Mengjie , Ran Peng , Sujie Akesu , Zhang Fan , Zhu Jiajun , Tan Subei , Xie Tao , Chen Pin , Yu Zixiang , Li Yan , Jiang Dongxian , Zhang Xiaobiao , Zhao Jian-Yuan , Hou Yingyong , Ding Chen 
Published: February 2023

AbstractDiffuse gliomas are devastating brain tumors. Here, we perform a proteogenomic profiling of 213 retrospectively collected glioma tumors. Proteogenomic analysis reveals the downstream biological events leading by EGFR-, IDH1-, TP53-mutations. The comparative analysis illustrates the distinctive features of GBMs and LGGs, indicating CDK2 inhibitor might serve as a promising drug target for GBMs. Further proteogenomic integrative analysis combined with functional experiments highlight the cis-effect of EGFR alterations might lead to glioma tumor cell proliferation through ERK5 medicates nucleotide synthesis process. Proteome-based stratification of gliomas defines 3 proteomic subgroups (S-Ne, S-Pf, S-Im), which could serve as a complement to WHO subtypes, and would provide the essential framework for the utilization of specific targeted therapies for particular glioma subtypes. Immune clustering identifies three immune subtypes with distinctive immune cell types. Further analysis reveals higher EGFR alteration frequencies accounts for elevation of immune check point protein: PD-L1 and CD70 in T-cell infiltrated tumors.
Monometallic interphasic synergy via nano-hetero-interfacing for hydrogen evolution in alkaline electrolytes
Authors: Dastafkan Kamran , Shen Xiangjian , Hocking Rosalie K. , Meyer Quentin , Zhao Chuan 
Published: February 2023

AbstractElectrocatalytic synergy is a functional yet underrated concept in electrocatalysis. Often, it materializes as intermetallic interaction between different metals. We demonstrate interphasic synergy in monometallic structures is as much effective. An interphasic synergy between Ni(OH)2 and Ni-N/Ni-C phases is reported for alkaline hydrogen evolution reaction that lowers the energy barriers for hydrogen adsorption-desorption and facilitates that of hydroxyl intermediates. This makes ready-to-serve Ni active sites and allocates a large amount of Ni d-states at Fermi level to promote charge redistribution from Ni(OH)2 to Ni-N/Ni-C and the co-adsorption of Hads and OHads intermediates on Ni-N/Ni-C moieties. As a result, a Ni(OH)2@Ni-N/Ni-C hetero-hierarchical nanostructure is developed, lowering the overpotentials to deliver −10 and −100 mA cm−2 in alkaline media by 102 and 113 mV, respectively, compared to monophasic Ni(OH)2 catalyst. This study unveils the interphasic synergy as an effective strategy to design monometallic electrocatalysts for water splitting and other energy applications.
Conjugated dual size effect of core-shell particles synergizes bimetallic catalysis
Authors: Zhang Xiaohui , Sun Zhihu , Jin Rui , Zhu Chuwei , Zhao Chuanlin , Lin Yue , Guan Qiaoqiao , Cao Lina , Wang Hengwei , Li Shang , Yu Hancheng , Liu Xinyu , Wang Leilei , Wei Shiqiang , Li Wei-Xue , Lu Junling 
Published: February 2023

AbstractCore-shell bimetallic nanocatalysts have attracted long-standing attention in heterogeneous catalysis. Tailoring both the core size and shell thickness to the dedicated geometrical and electronic properties for high catalytic reactivity is important but challenging. Here, taking Au@Pd core-shell catalysts as an example, we disclose by theory that a large size of Au core with a two monolayer of Pd shell is vital to eliminate undesired lattice contractions and ligand destabilizations for optimum benzyl alcohol adsorption. A set of Au@Pd/SiO2 catalysts with various core sizes and shell thicknesses are precisely fabricated. In the benzyl alcohol oxidation reaction, we find that the activity increases monotonically with the core size but varies nonmontonically with the shell thickness, where a record-high activity is achieved on a Au@Pd catalyst with a large core size of 6.8 nm and a shell thickness of ~2–3 monolayers. These findings highlight the conjugated dual particle size effect in bimetallic catalysis.
Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat root growth
Authors: Gabay Gilad , Wang Hanchao , Zhang Junli , Moriconi Jorge I. , Burguener German F. , Gualano Leonardo D. , Howell Tyson , Lukaszewski Adam , Staskawicz Brian , Cho Myeong-Je , Tanaka Jaclyn , Fahima Tzion , Ke Haiyan , Dehesh Katayoon , Zhang Guo-Liang , Gou Jin-Ying , Hamberg Mats , Santa-María Guillermo E. , Dubcovsky Jorge 
Published: February 2023

AbstractWheat, an essential crop for global food security, is well adapted to a wide variety of soils. However, the gene networks shaping different root architectures remain poorly understood. We report here that dosage differences in a cluster of monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) modulate key differences in wheat root architecture, which are associated with grain yield under water-limited conditions. Wheat plants with loss-of-function mutations in OPRIII show longer seminal roots, whereas increased OPRIII dosage or transgenic over-expression result in reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA and JA-Ile). Pharmacological inhibition of JA-biosynthesis abolishes root length differences, consistent with a JA-mediated mechanism. Transcriptome analyses of transgenic and wild-type lines show significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways, which parallel changes in ROS distribution. OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals.
Highly-scaled and fully-integrated 3-dimensional ferroelectric transistor array for hardware implementation of neural networks
Authors: Kim Ik-Jyae , Kim Min-Kyu , Lee Jang-Sik 
Published: February 2023

AbstractHardware-based neural networks (NNs) can provide a significant breakthrough in artificial intelligence applications due to their ability to extract features from unstructured data and learn from them. However, realizing complex NN models remains challenging because different tasks, such as feature extraction and classification, should be performed at different memory elements and arrays. This further increases the required number of memory arrays and chip size. Here, we propose a three-dimensional ferroelectric NAND (3D FeNAND) array for the area-efficient hardware implementation of NNs. Vector-matrix multiplication is successfully demonstrated using the integrated 3D FeNAND arrays, and excellent pattern classification is achieved. By allocating each array of vertical layers in 3D FeNAND as the hidden layer of NN, each layer can be used to perform different tasks, and the classification of color-mixed patterns is achieved. This work provides a practical strategy to realize high-performance and highly efficient NN systems by stacking computation components vertically.
Identification of key immune-related genes in dilated cardiomyopathy using bioinformatics analysis
Authors: Li Feng , Du Tong-Yue , Wu Li-Da , Zhang Lei , Liu Huan-Huan , Zhang Zhen-Ye , Zhang Jie , Zhang Zhi-Yuan , Qian Ling-Ling , Wang Ru-Xing , Hao Jian-Feng 
Published: February 2023

AbstractDilated cardiomyopathy (DCM) is characterized by the left ventricular dilatation and impaired myocardial systolic dysfunction with high mortality and morbidity. However, the underlying mechanisms remain elusive. We first identified the differentially expressed genes (DEGs) between the DCM and control group using two expression profiles from GSE3585 and GSE84796. Enrichment analysis was conducted to explore the potential mechanisms underlying DCM. A total of four algorithms, including key module of MCODE, degree, maximum neighborhood component (MNC), and maximal clique centrality (MCC), were used to identify the hub genes within Cytoscape. The correlation between hub genes and infiltrated immune cells was evaluated to determine potential immune-related genes. The expression analysis and diagnosis value analysis of potential immune-related genes were performed. Finally, the expression analysis with GSE57338 and relationship analysis with the comparative toxicogenomics database (CTD) were performed to identify the key immune-related genes in DCM. A total of 80 DEGs were screened for DCM. Enrichment analysis revealed that DEGs were involved in the immune-related pathological process. Immune infiltration analysis indicated a potentially abnormal immune response in DCM. Four up-regulated genes (COL1A2, COL3A1, CD53, and POSTN) were identified as potential immune-related genes. Finally, three genes (COL1A2, COL3A1, and POSTN) were determined as the key immune-related genes in DCM via expression analysis with a validation set (GSE57338) and relationship analysis with CTD. Our study suggested that the upregulated COL1A2, COL3A1, and POSTN might be the key immune-related genes for DCM. Further studies are needed to validate the underlying mechanisms.
Appropriate screening mammography method for patients with breast implants
Authors: Park Jihee , Ko Eun Young , Han Boo-Kyung , Ko Eun Sook , Choi Ji Soo , Kim Haejung 
Published: February 2023

AbstractIn this study, we aimed to evaluate the benefits and losses of mammography with and without implant displacement (ID) and propose an appropriate imaging protocol for the screening of breasts with implants. We evaluated mammograms of 162 breasts in 96 patients including 71 breasts with biopsy-proven cancers. Mammography of each breast included standard MLO and ID MLO images. We reviewed the mammograms using clinical image quality criteria, which consist of parameters that evaluate the proper positioning of the breast and the image resolution. Standard MLO images showed significantly higher scores for proper positioning but showed significantly lower scores for image resolution than the ID MLO images. Moreover, standard MLO images showed significantly higher kVp, mAs, and compressed breast thickness than the ID MLO images. The organ dose was also higher in the standard MLO images than in the ID MLO images, but the difference was not statistically significant. In mammography with proven cancer, ID MLO images showed significantly higher degree of cancer visibility than standard MLO images. For screening mammography in patients with breast implants, ID MLO view alone is sufficient for MLO projection with reducing the patient’s radiation dose without compromising the breast cancer detection capability, especially in dense breasts with subpectoral implants.
Genetic algorithm optimization of broadband operation in a noise-like pulse fiber laser
Authors: Lapre Coraline , Meng Fanchao , Hary Mathilde , Finot Christophe , Genty Goëry , Dudley John M. 
Published: February 2023

AbstractThe noise-like pulse regime of optical fiber lasers is highly complex, and associated with multiscale emission of random sub-picosecond pulses underneath a much longer envelope. With the addition of highly nonlinear fiber in the cavity, noise-like pulse lasers can also exhibit supercontinuum broadening and the generation of output spectra spanning 100’s of nm. Achieving these broadest bandwidths, however, requires careful optimization of the nonlinear polarization rotation based saturable absorber, which involves a very large potential parameter space. Here we study the spectral characteristics of a broadband noise-like pulse laser by scanning the laser operation over a random sample of 50,000 polarization settings, and we quantify that these broadest bandwidths are generated in only $$\sim$$
∼
0.5% of cases. We also show that a genetic algorithm can replace trial and error optimization to align the cavity for these broadband operating states.
Synthesis of new diphenyl urea-clubbed imine analogs and its Implications in diabetic management through in vitro and in silico approaches
Authors: Pasha Anam Rubbab , Khan Ajmal , Ullah Saeed , Halim Sobia Ahsan , Hussain Javid , Khalid Muhammad , Naseer Muhammad Moazzam , El-kott Attalla F. , Negm Sally , Al-Harrasi Ahmed , Shafiq Zahid 
Published: February 2023

AbstractType II diabetes mellitus (T2DM) is a global health issue with high rate of prevalence. The inhibition of α-glucosidase enzyme has prime importance in the management of T2DM. This study was established to synthesize Schiff bases of 1,3-dipheny urea (3a–y) and to investigate their in vitro anti-diabetic capability via inhibiting α-glucosidase, a key player in the catabolism of carbohydrates. The structures of all compounds were confirmed through various techniques including, Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR) and mass-spectrometry (MS) methods. Interestingly all these compounds displayed potent inhibition IC50 values in range of 2.14–115 µM as compared to acarbose used as control. Additionally, all the compounds were docked at the active site of α-glucosidase to predict their mode of binding. The docking results indicates that Glu277 and Asn350 play important role in the stabilization of these compounds in the active site of enzyme. These molecules showed excellent predicted pharmacokinetics, physicochemical and drug-likeness profile. The anti-diabetic potential of these molecules signifies their medical importance and provide insights into prospective therapeutic options for the treatment of T2DM.
Zeolite A powder and beads from sugarcane bagasse fly ash modified with iron(III) oxide-hydroxide for lead adsorption
Authors: Praipipat Pornsawai , Ngamsurach Pimploy , Roopkhan Naritsara 
Published: February 2023

AbstractThe discharging of lead-contaminated wastewater is a concern because of its toxicity to living organisms and water quality resulting in dangerous water consumption, so it is highly recommended to remove lead from wastewater to be below water quality standards for a safe environment. Zeolite A sugarcane bagasse fly ash powder (ZB), zeolite A sugarcane bagasse fly ash powder mixed iron(III) oxide-hydroxide (ZBF), zeolite A sugarcane bagasse fly ash beads (ZBB), zeolite A sugarcane bagasse fly ash powder mixed iron(III) oxide-hydroxide beads (ZBFB), and zeolite A sugarcane bagasse fly ash beads coated iron(III) oxide-hydroxide (ZBBF) were synthesized and characterized in various techniques. Their lead removal efficiencies were investigated by batch experiments, adsorption isotherms, and kinetics. The specific surface area, pore volume, and pore size of ZB were close values to zeolite A standard (STD), and ZBF had the highest specific surface area and the smallest pore size than others. ZB and ZBF demonstrated crystalline phases whereas ZBB, ZBFB, and ZBBF were amorphous phases. The surface morphology of ZB was a cubic shape similar to STD. ZBF demonstrated an agglomerated formation of ZB and iron(III) oxide-hydroxide whereas ZBFB and ZBBF had sphere shapes with coarse surfaces. Si, Al, O, Fe, Na, Ca, O–H, (Si, Al)–O, H2O, and D4R were detected in all materials. The surface charges of all zeolite A materials had negatively charged at all pH values, and their surfaces increased more negatively charged with increasing pH value which pH 5 illustrated as the highest negatively charged in all materials. Their lead removal efficiencies were higher than 82%. Langmuir isotherm and pseudo-second-order kinetic models were well explained for their adsorption patterns and mechanisms. Finally, ZBBF is a good offer for applying in industrial wastewater treatment systems because of its easy operation and saving costs than ZBF.