bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gradient design of imprinted anode for stable Zn-ion batteries
Authors: Cao Qinghe , Gao Yong , Pu Jie , Zhao Xin , Wang Yuxuan , Chen Jipeng , Guan Cao 
Published: February 2023

AbstractAchieving long-term stable zinc anodes at high currents/capacities remains a great challenge for practical rechargeable zinc-ion batteries. Herein, we report an imprinted gradient zinc electrode that integrates gradient conductivity and hydrophilicity for long-term dendrite-free zinc-ion batteries. The gradient design not only effectively prohibits side reactions between the electrolyte and the zinc anode, but also synergistically optimizes electric field distribution, zinc ion flux and local current density, which induces preferentially deposited zinc in the bottom of the microchannels and suppresses dendrite growth even under high current densities/capacities. As a result, the imprinted gradient zinc anode can be stably cycled for 200 h at a high current density/capacity of 10 mA cm−2/10 mAh cm−2, with a high cumulative capacity of 1000 mAh cm−2, which outperforms the none-gradient counterparts and bare zinc. The imprinted gradient design can be easily scaled up, and a high-performance large-area pouch cell (4*5 cm2) is also demonstrated.
Molecular hydrogen in seawater supports growth of diverse marine bacteria
Authors: Lappan Rachael , Shelley Guy , Islam Zahra F. , Leung Pok Man , Lockwood Scott , Nauer Philipp A. , Jirapanjawat Thanavit , Ni Gaofeng , Chen Ya-Jou , Kessler Adam J. , Williams Timothy J. , Cavicchioli Ricardo , Baltar Federico , Cook Perran L. M. , Morales Sergio E. , Greening Chris 
Published: February 2023

AbstractMolecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2oxidation increases with depth and decreases with oxygen concentration, suggesting that H2is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
Magnetic bentonite decorated with Pd nanoparticles and cross-linked polyvinyl pyridine as an efficient nanocatalyst for Suzuki coupling and 4-Nitrophenol reduction reactions
Authors: Daneshafruz Haniyeh , Mohammadi Pourya , Barani Hossein , Sheibani Hassan 
Published: February 2023

AbstractThis study reports the preparation of a novel type of support based on magnetically recyclable bentonite functionalized with divinylbenzene-polyvinyl pyridine (PVP-DVB) for Pd (II) nanocatalyst by a simple cost-effective method. Firstly, the conventional co-precipitation method synthesized Fe3O4nanoparticles (NPs) onto bentonite sheets. Then the prepared magnetic support surface was functionalized by divinylbenzene-polyvinyl pyridine (PVP-DVB) to create a cross-linked polymer with a high coordination ability with palladium. Repeated nitrogen units in the PVP-DVB polymer chain increase the number of Pd bonds and thus lead to higher performance of the nanocatalyst. Finally, the palladium NPs were simultaneously synthesized and immobilized under mild conditions. The synthesized nanocatalyst was characterized by several methods such as scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, vibrating sample magnetometer, inductively coupled plasma mass spectrometry and thermogravimetric analysis. The efficiency of synthesized heterogeneous nanocatalyst was investigated in Suzuki–Miyaura cross-coupling reactions between a range of aryl halides (X = Cl, Br, I) with phenylboronic acid and in the reduction of 4-nitrophenol (4-NP). Moreover, the synthesized nanocatalyst could be easily recovered and reused several times with an efficiency greater than 90%.
Local IL-10 delivery modulates the immune response and enhances repair of volumetric muscle loss muscle injury
Authors: Huynh Tai , Reed Cassandra , Blackwell Zain , Phelps Payton , Herrera Luis C. Pinzon , Almodovar Jorge , Zaharoff David A. , Wolchok Jeffrey 
Published: February 2023

AbstractThis study was designed to test the hypothesis that in addition to repairing the architectural and cellular cues via regenerative medicine, the delivery of immune cues (immunotherapy) may be needed to enhance regeneration following volumetric muscle loss (VML) injury. We identified IL-10 signaling as a promising immunotherapeutic target. To explore the impact of targeting IL-10 signaling, tibialis anterior (TA) VML injuries were created and then treated in rats using autologous minced muscle (MM). Animals received either recombinant rat IL-10 or phosphate buffered saline (PBS) controls injections at the site of VML repair beginning 7 days post injury (DPI) and continuing every other day (4 injections total) until 14 DPI. At 56 DPI (study endpoint), significant improvements to TA contractile torque (82% of uninjured values & 170% of PBS values), TA mass, and myofiber size in response to IL-10 treatment were detected. Whole transcriptome analysis at 14 DPI revealed activation of IL-10 signaling, muscle hypertrophy, and lymphocytes signaling pathways. Expression of ST2, a regulatory T (Treg) cell receptor, was dramatically increased at the VML repair site in response to IL-10 treatment when compared to PBS controls. The findings suggest that the positive effect of delayed IL-10 delivery might be due to immuno-suppressive Treg cell recruitment.
Spatio-temporal numerical modeling of stochastic predator-prey model
Authors: Yasin Muhammad W. , Ahmed Nauman , Iqbal Muhammad S. , Raza Ali , Rafiq Muhammad , eldin Elsayed Mohamed Tag , Khan Ilyas 
Published: February 2023

AbstractIn this article, the ratio-dependent prey-predator system perturbed with time noise is numerically investigated. It relates to the population densities of the prey and predator in an ecological system. The initial prey-predator models only depend on the time and a couple of the differential equations. We are considering a model where the prey-predator interaction is influenced by both space and time and the need for a coupled nonlinear partial differential equation with the effect of the random behavior of the environment. The existence of the solutions is guaranteed by using Schauder’s fixed point theorem. The computation of the underlying model is carried out by two schemes. The proposed stochastic forward Euler scheme is conditionally stable and consistent with the system of the equations. The proposed stochastic non-standard finite difference scheme is unconditionally stable and consistent with the system of the equations. The graphical behavior of a test problem for different values of the parameters is shown which depicts the efficacy of the schemes. Our numerical results will help the researchers to consider the effect of the noise on the prey-predator model.
Hydrogen migration in inner-shell ionized halogenated cyclic hydrocarbons
Authors: Abid Abdul Rahman , Bhattacharyya Surjendu , Venkatachalam Anbu Selvam , Pathak Shashank , Chen Keyu , Lam Huynh Van Sa , Borne Kurtis , Mishra Debadarshini , Bilodeau René C. , Dumitriu Ileana , Berrah Nora , Patanen Minna , Rolles Daniel 
Published: February 2023

AbstractWe have studied the fragmentation of the brominated cyclic hydrocarbons bromocyclo-propane, bromocyclo-butane, and bromocyclo-pentane upon Br(3d) and C(1s) inner-shell ionization using coincidence ion momentum imaging. We observe a substantial yield of CH3+ fragments, whose formation requires intramolecular hydrogen (or proton) migration, that increases with molecular size, which contrasts with prior observations of hydrogen migration in linear hydrocarbon molecules. Furthermore, by inspecting the fragment ion momentum correlations of three-body fragmentation channels, we conclude that CHx+ fragments (with x = 0, …, 3) with an increasing number of hydrogens are more likely to be produced via sequential fragmentation pathways. Overall trends in the molecular-size-dependence of the experimentally observed kinetic energy releases and fragment kinetic energies are explained with the help of classical Coulomb explosion simulations.
Solving large-scale discrete time–cost trade-off problem using hybrid multi-verse optimizer model
Authors: Son Pham Vu Hong , Nguyen Dang Nghiep Trinh 
Published: February 2023

AbstractThe analysis of the relationship between time and cost is a crucial aspect of construction project management. Various optimization techniques have been developed to solve time–cost trade-off problems. A hybrid multi-verse optimizer model (hDMVO) is introduced in this study, which combines the multi-verse optimizer (MVO) and the sine cosine algorithm (SCA) to address the discrete time–cost trade-off problem (DTCTP). The algorithm's optimality is evaluated by using 23 well-known benchmark test functions. The results demonstrate that hDMVO is competitive with MVO, SCA, the dragonfly algorithm and ant lion optimization. The performance of hDMVO is evaluated using four benchmark test problems of DTCTP, including two medium-scale instances (63 activities) and two large-scale instances (630 activities). The results indicate that hDMVO can provide superior solutions in the time–cost optimization of large-scale and complex projects compared to previous algorithms.
Allolobophora caliginosa coelomic fluid and extract alleviate glucocorticoid-induced osteoporosis in mice by suppressing oxidative stress and regulating osteoblastic/osteoclastic-related markers
Authors: Abdelfattah Marwa Ahmed , Mohamed Ayman Saber , Ibrahim Sherif Abdelaziz , Fahmy Sohair R. 
Published: February 2023

AbstractAllolobophora calignosa (Ac) is a folk medicine for millennia, as it possesses many biological activities. This study aimed to investigate the chemo-preventive activity of A.calignosa coelomic fluid (AcCF) and A.calignosa extract (AcE) on glucocorticoid-induced osteoporosis (GIOP) in mice. Characterization and in vitro biological activity of AcE and AcCF has been assessed. Male CD-1 mice were subcutaneously received dexamethasone (DEX) (1 mg/kg, 5 times/week) and concurrently intraperitoneally treated with either AcCF (20 mg/kg) or AcE (45 mg/kg) every other day for 28 days. Serum and bone homogenates were subjected for qPCR and biochemical analysis. AcE and AcCF treatment significantly increased bone mineral density (BMD), bone mineral content (BMC), calcium (Ca), phosphorus (P), and calcitonin levels, whereas activity of serum alkaline phosphatase (ALP), bone alkaline phosphatase (BALP), serum acidic phosphatase (ACP), bone acidic phosphatase (BACP) and parathyroid hormone (PTH) levels were significantly reduced compare with untreated GIOP mice. Treatment with AcE and AcCF modulates oxidative stress and downregulated Rank and Mmp9 expression, as well as increased glycosaminoglycan content in the organic bone matrix, resulting in osteoclastogenesis inhibition. Overall, AcCF and AcE show a chemo-preventive activity against GIOP by inhibiting oxidative stress and regulating expression and/or activity of osteoblast/osteoclast-related markers.
De novo transcriptome assembly from the nodal root growth zone of hydrated and water-deficit stressed maize inbred line FR697
Authors: Sen Sidharth , King Shannon K. , McCubbin Tyler , Greeley Laura A. , Mertz Rachel A. , Becker Cheyenne , Niehues Nicole , Zeng Shuai , Stemmle Jonathan T. , Peck Scott C. , Oliver Melvin J. , Fritschi Felix B. , Braun David M. , Sharp Robert E. , Joshi Trupti 
Published: February 2023

AbstractCertain cultivars of maize show increased tolerance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaptation, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated from various FR697 plant tissue samples. The Necklace pipeline was used to combine a Trinity de novo assembly along with a reference guided assembly and the Viridiplantae proteome to generate an annotated consensus “SuperTranscriptome” assembly of 47,915 transcripts with a N50 of 3152 bp in length. The results were compared by Blastn to maize reference genes, a Benchmarking Universal Single-Copy Orthologs (BUSCO) genome completeness report and compared with three maize reference genomes. The resultant ‘SuperTranscriptome’ was demonstrated to be of high-quality and will serve as an important reference for analysis of the maize nodal root transcriptomic response to environmental perturbations.
Consolidation of metabolomic, proteomic, and GWAS data in connective model of schizophrenia
Authors: Kopylov Arthur T. , Stepanov Alexander A. , Butkova Tatiana V. , Malsagova Kristina A. , Zakharova Natalia V. , Kostyuk Georgy P. , Elmuratov Artem U. , Kaysheva Anna L. 
Published: February 2023

AbstractDespite of multiple systematic studies of schizophrenia based on proteomics, metabolomics, and genome-wide significant loci, reconstruction of underlying mechanism is still a challenging task. Combination of the advanced data for quantitative proteomics, metabolomics, and genome-wide association study (GWAS) can enhance the current fundamental knowledge about molecular pathogenesis of schizophrenia. In this study, we utilized quantitative proteomic and metabolomic assay, and high throughput genotyping for the GWAS study. We identified 20 differently expressed proteins that were validated on an independent cohort of patients with schizophrenia, including ALS, A1AG1, PEDF, VTDB, CERU, APOB, APOH, FASN, GPX3, etc. and almost half of them are new for schizophrenia. The metabolomic survey revealed 18 group-specific compounds, most of which were the part of transformation of tyrosine and steroids with the prevalence to androgens (androsterone sulfate, thyroliberin, thyroxine, dihydrotestosterone, androstenedione, cholesterol sulfate, metanephrine, dopaquinone, etc.). The GWAS assay mostly failed to reveal significantly associated loci therefore 52 loci with the smoothened p < 10−5 were fractionally integrated into proteome-metabolome data. We integrated three omics layers and powered them by the quantitative analysis to propose a map of molecular events associated with schizophrenia psychopathology. The resulting interplay between different molecular layers emphasizes a strict implication of lipids transport, oxidative stress, imbalance in steroidogenesis and associated impartments of thyroid hormones as key interconnected nodes essential for understanding of how the regulation of distinct metabolic axis is achieved and what happens in the conditioned proteome and metabolome to produce a schizophrenia-specific pattern.
Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose
Authors: Soares Rodrigues Carla Inês , den Ridder Maxime , Pabst Martin , Gombert Andreas K. , Wahl Sebastian Aljoscha 
Published: February 2023

AbstractBoth the identity and the amount of a carbon source present in laboratory or industrial cultivation media have major impacts on the growth and physiology of a microbial species. In the case of the yeast Saccharomyces cerevisiae, sucrose is arguably the most important sugar used in industrial biotechnology, whereas glucose is the most common carbon and energy source used in research, with many well-known and described regulatory effects, e.g. glucose repression. Here we compared the label-free proteomes of exponentially growing S. cerevisiae cells in a defined medium containing either sucrose or glucose as the sole carbon source. For this purpose, bioreactor cultivations were employed, and three different strains were investigated, namely: CEN.PK113-7D (a common laboratory strain), UFMG-CM-Y259 (a wild isolate), and JP1 (an industrial bioethanol strain). These strains present different physiologies during growth on sucrose; some of them reach higher specific growth rates on this carbon source, when compared to growth on glucose, whereas others display the opposite behavior. It was not possible to identify proteins that commonly presented either higher or lower levels during growth on sucrose, when compared to growth on glucose, considering the three strains investigated here, except for one protein, named Mnp1—a mitochondrial ribosomal protein of the large subunit, which had higher levels on sucrose than on glucose, for all three strains. Interestingly, following a Gene Ontology overrepresentation and KEGG pathway enrichment analyses, an inverse pattern of enriched biological functions and pathways was observed for the strains CEN.PK113-7D and UFMG-CM-Y259, which is in line with the fact that whereas the CEN.PK113-7D strain grows faster on glucose than on sucrose, the opposite is observed for the UFMG-CM-Y259 strain.
Differential gene expression analysis using RNA-seq in the blood of goats exposed to transportation stress
Authors: Naldurtiker Aditya , Batchu Phaneendra , Kouakou Brou , Terrill Thomas H. , McCommon George W. , Kannan Govind 
Published: February 2023

AbstractTransportation stress causes significant changes in physiological responses in goats; however, studies exploring the transcriptome of stress are very limited. The objective of this study was to determine the differential gene expressions and related pathways in the blood samples using RNA-seq procedure in Spanish goats subjected to different durations of transportation stress. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (1) transported for 180 min, (2) transported for 30 min, or (3) held in pens (control). Blood samples were collected before and after treatment for stress hormone, metabolite, and transcriptomic analysis. RNA-seq technology was used to obtain the transcriptome profiles of blood. Analysis of physiological data using SAS showed that plasma cortisol concentrations were higher(P < 0.01) in 180 min and 30 min groups compared to the control group. Enrichment analysis of DEGs related to transportation stress through Gene Ontology and KEGG databases revealed that the differentially expressed genes related to inflammatory pathways, caspases, and apoptosis such asIL1R2, CASP14, CD14, TLR4, andMAPK14were highly enriched in the transported group of goats compared to non-transported goats. Stress in goats leads to a sequence of events at cellular and molecular levels that causes inflammation and apoptosis.
Estimation of dye concentration by using Kubelka–Munk and Allen–Goldfinger reflective models: comparing the performance
Authors: Safi Mahdi , Amirshahi Seyed Hossein 
Published: February 2023

AbstractIf the relationship between the reflectance function (K/S) and dye concentration (C) is known, the color of the dyed textile (R∞) and C could be predicted from each other. In the present work, the concentration value estimated from the reflectance data using two reflective models, i.e. the Kubelka–Munk and the Allen–Goldfinger is compared. First, the Allen–Goldfinger model was run by using the absorption coefficient of dyes in fiber, i.e. the unit k/s values instead of that in the solution. The results showed that the replacement of the unit k/s for the Beer–Lambert absorption coefficient in the Allen–Goldfinger model causes lower error in the prediction of the spectral reflectance factor as well as the dye concentration. However, this model did not lead to better results. Then, an inverse form was used to estimate the concentration of dyes from the corresponding spectral reflectance. Consequently, it was observed that the Kubelka–Munk model is still a more reliable method while benefiting from more simplicity than the Allen–Goldfinger model. The analysis of errors showed that the results deeply depend on different factors such as the applied concentration range as well as the dye spectral adsorption behavior.
Ferroptosis-associated lncRNA prognostic signature predicts prognosis and immune response in clear cell renal cell carcinoma
Authors: Lai Jiayi , Miao Shiqi , Ran Longke 
Published: February 2023

AbstractClear cell Renal Cell Carcinoma (ccRCC), the most deadly and life-threatening tumor in the urinary system, has a dismal prognosis and a high risk of metastasizing. Regulation of ferroptosis is a prospective therapeutic target to eradicate malignant cells. Our objective was to seek ferroptosis-associated long non-coding RNAs (FALs) and developed a prediction signature for ccRCC. We extracted transcriptome data and clinical information from The Cancer Genome Atlas (TCGA) databases. Ferroptosis-associated genes (FAGs) were obtained from FerrDb database. A ferroptosis-associated lncRNA prognostic signature (FLPS) of ccRCC was generated utilizing univariate Cox regression, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression, sequentially, based on 8 lncRNAs (LINC00460, AC124854.1, AC084876.1, IGFL2-AS1, LINC00551, AC083967.1, AC073487.1, and LINC02446). The signature's independent predictive value for ccRCC was demonstrated using univariate and multivariate regression analysis (P < 0.05). Subsequently, by combining independent predictive factors, a prognostic nomogram was established. Immunity analysis proclaimed a striking difference in terms of cells, function, checkpoints, and ESTIMATE scores between low- and high-risk groups. Overall, the innovative signature of ferroptosis-associated signatures may have a considerable effect on the immune response and prognosis for ccRCC.
Afforesting arid land with renewable electricity and desalination to mitigate climate change
Authors: Caldera Upeksha , Breyer Christian 
Published: February 2023

AbstractAfforestation is one of the most practised carbon dioxide removal methods but is constrained by the availability of suitable land and sufficient water resources. In this research, existing concepts of low-cost renewable electricity (RE) and seawater desalination are built upon to identify the global CO2 sequestration potential if RE-powered desalination plants were used to irrigate forests on arid land over the period 2030–2100. Results indicate a cumulative CO2 sequestration potential of 730 GtCO2 during the period. Global average cost is estimated to be €457 per tCO2 in 2030 but decrease to €100 per tCO2 by 2100, driven by the decreasing cost of RE and increasing CO2 sequestration rates of the forests. Regions closer to the coast with abundant solar resources and cooler climate experience the least costs, with costs as low as €50 per tCO2 by 2070. The results suggest a key role for afforestation projects irrigated with RE-based desalination within the climate change mitigation portfolio, which is currently based on bioenergy carbon capture and storage, and direct air carbon capture and storage plants.