bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced single‐base mutation diversity by the combination of cytidine deaminase with DNA‐repairing enzymes in yeast
Authors: Huang Zi‐Rui , Chen Xiang‐Rong , Liu Dan‐Feng , Cui You‐Zhi , Li Bing‐Zhi , Yuan Ying‐Jin 
Published: August 2023

AbstractThe occurrence of random mutations can increase the diversity of the genome and promote the evolutionary process of organisms. High efficiency mutagenesis techniques significantly accelerate the evolutionary process. In this work, we describe a targeted mutagenesis system named MutaT7trans to significantly increase mutation rate and generate mutations across all four nucleotides in yeast. We constructed different DNA‐repairing enzyme‐PmCDA1‐T7 RNA polymerase (T7 RNAP) fusion proteins, achieved targeted mutagenesis by flanking the target gene with T7 promoters, and tuned the mutation spectra by introducing different DNA‐repairing enzymes. With this mutagenesis tool, the proportion of non‐C → T mutations was 10–11‐fold higher than the cytidine deaminase‐based evolutionary tools, and the transversion mutation frequency was also elevated. The mutation rate of the target gene was significantly increased to 5.25 × 10−3 substitutions per base (s. p. b.). We also demonstrated that MutaT7trans could be used to evolve the CrtE, CrtI, and CrtYB gene in the β‐carotene biosynthesis process and generate different types of mutations.
Machine learning chained neural network analysis of oxygen transport amplifies the physiological relevance of vascularized microphysiological systems
Authors: Tronolone James J. , Mathur Tanmay , Chaftari Christopher P. , Sun Yuxiang , Jain Abhishek 
Published: August 2023

AbstractSince every biological system requires capillaries to support its oxygenation, design of engineered preclinical models of such systems, for example, vascularized microphysiological systems (vMPS) have gained attention enhancing the physiological relevance of human biology and therapies. But the physiology and function of formed vessels in the vMPS is currently assessed by non‐standardized, user‐dependent, and simple morphological metrics that poorly relate to the fundamental function of oxygenation of organs. Here, a chained neural network is engineered and trained using morphological metrics derived from a diverse set of vMPS representing random combinations of factors that influence the vascular network architecture of a tissue. This machine‐learned algorithm outputs a singular measure, termed as vascular network quality index (VNQI). Cross‐correlation of morphological metrics and VNQI against measured oxygen levels within vMPS revealed that VNQI correlated the most with oxygen measurements. VNQI is sensitive to the determinants of vascular networks and it consistently correlates better to the measured oxygen than morphological metrics alone. Finally, the VNQI is positively associated with the functional outcomes of cell transplantation therapies, shown in the vascularized islet‐chip challenged with hypoxia. Therefore, adoption of this tool will amplify the predictions and enable standardization of organ‐chips, transplant models, and other cell biosystems.
Efficient optimization of time‐varying inputs in a fed‐batch cell culture process using design of dynamic experiments
Authors: Luo Yu , Stanton Duane A. , Sharp Rachel C. , Parrillo Alexis J. , Morgan Kelsey T. , Ritz Diana B. , Talwar Sameer 
Published: August 2023

AbstractIn cell culture process development, we rely largely on an iterative, one‐factor‐at‐a‐time procedure based on experiments that explore a limited process space. Design of experiments (DoE) addresses this issue by allowing us to analyze the effects of process inputs on process responses systematically and efficiently. However, DoE cannot be applied directly to study time‐varying process inputs unless an impractically large number of bioreactors is used. Here, we adopt the methodology of design of dynamic experiments (DoDE) and incorporate dynamic feeding profiles efficiently in late‐stage process development of the manufacture of therapeutic monoclonal antibodies. We found that, for the specific cell line used in this article, (1) not only can we estimate the effect of nutrient feed amount on various product attributes, but we can also estimate the effect, develop a statistical model, and use the model to optimize the slope of time‐trended feed rates; (2) in addition to the slope, higher‐order dynamic characteristics of time‐trended feed rates can be incorporated in the design but do not have any significant effect on the responses we measured. Based on the DoDE data, we developed a statistical model and used the model to optimize several process conditions. Our effort resulted in a tangible improvement in productivity—compared with the baseline process without dynamic feeding, this optimized process in a 200‐L batch achieved a 27% increase in titer and > 92% viability. We anticipate our application of DoDE to be a starting point for more efficient workflows to optimize dynamic process conditions in process development.
Chemical Composition, Mosquito Larvicidal and Antimicrobial Activities, and Molecular Docking Study of Essential Oils of Cinnamomum melastomaceum, Neolitsea buisanensis and Uvaria microcarpa from Vietnam
Authors: Pham Ty Viet , Ha Nguyen Xuan , Luyen Nguyen Dinh , Xuan Thao Hoang , Le Quoc Thang , Hung Nguyen Huy , The Son Ninh 
Published: August 2023

AbstractThe leaf oil compositions of two Lauraceae and one Annonaceae plants cultivated in Vietnam were analysed by GC/MS (gas chromatography‐mass spectrometry) analysis. The leaf oil of the first Lauraceae plant Cinnamomum melastomaceum contained 34 identified compounds, in which benzyl benzoate (38.5 %), linalool (19.9 %), (E)‐caryophyllene (10.5 %), and α‐terpineol (6.9 %) were the major compounds. The leaves of the second Lauraceae plant Neolitsea buisanensis gave an oil with the main compounds (E)‐β‐ocimene (24.0 %), benzyl benzoate (15.8 %), bicyclogermacrene (14.9 %), and (E)‐caryophyllene (6.3 %). The leaf oil of the Annonaceae plant Uvaria microcarpa consisted of the principal compounds (E)‐caryophyllene (18.0 %), bicyclogermacrene (8.1 %), and δ‐elemene (6.1 %). Two Lauraceae oil samples exhibited strong mosquito larvicidal activity against Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus with LC50 and LD90 values of less than 50 μg/mL. The Annonaceae oil sample showed strong antimicrobial activity against the fungus Aspergillus niger ATCC 1015 with the MIC (minimum inhibitory concentration) value of 32 μg/mL. In the docking approach, the major compounds (E)‐caryophyllene, bicyclogermacrene, and benzyl benzoate interacted with the mosquito odorant‐binding protein 3OGN, whereas (E)‐caryophyllene, bicyclogermacrene, and δ‐elemene also potentially interacted with the 4ZA5 protein of fungus A. niger.
Theoretical, in Vitro Antiproliferative, and in Silico Molecular Docking and Pharmacokinetics Studies of Heteroleptic Nickel(II) and Copper(II) Complexes of Thiosemicarbazone‐Based Ligands and Pefloxacin
Authors: Ahmed Sumeer , Mahendiran Dharmasivam , Bhat Ajmal Rashid , Rahiman Aziz Kalilur 
Published: August 2023

AbstractTwelve new heteroleptic nickel(II) and copper(II) complexes of the type [M(L1–6)(Pfx)2] (1–12), where L1–6=2‐benzylidenehydrazinecarbothioamide (L1), 2‐benzylidene‐N‐methylhydrazinecarbothioamide (L2), 2‐benzylidene‐N‐phenylhydrazinecarbothioamide (L3), 2‐(4‐methylbenzylidene)hydrazinecarbothioamide (L4), 2‐(4‐methylbenzylidene)‐N‐methylhydrazinecarbothioamide (L5) and 2‐(4‐methylbenzylidene)‐N‐phenylhydrazinecarbothioamide (L6), Pfx=pefloxacin and M=Ni(II) or Cu(II) have been synthesised, and their structures were confirmed by different spectral techniques. The spectral data and density functional theory (DFT) calculations supported the bonding of pefloxacin drug molecule via one of the carboxylate oxygen atoms and the pyridone oxygen atom, and the thiosemicarbazone ligand via the imine nitrogen and the thione sulfur atoms with the metal(II) ion, forming distorted octahedral geometry. In vitro antiproliferative activity of the synthesized complexes was evaluated against three human breast cancer (T47D, estrogen negative (MDA‐MB‐231) and estrogen positive (MCF‐7)) as well as non‐tumorigenic human breast epithelial (MCF‐10a) cell lines, which showed the higher activity for the copper(II) complexes. The interaction of the synthesized complexes with an oncogenic protein H‐ras (121 p) was explored by in silico molecular docking studies. Further, in silico pharmacokinetics and ADMET parameters were also analysed to predict the drug‐likeness as well as non‐toxic and non‐carcinogenic behavior, and safe oral administration of the complexes.
Tuning the Solution Self‐Assembly of a Peptide‐PEG (Polyethylene Glycol) Conjugate with α‐Cyclodextrin
Authors: Castelletto Valeria , Kowalczyk Radoslaw M. , Seitsonen Jani , Hamley Ian W 
Published: August 2023

AbstractCyclodextrins are saccharide ring molecules which act as host cavities that can encapsulate small guest molecules or thread polymer chains. We investigate the influence of alpha‐cyclodextrin (αCD) on the aqueous solution self‐assembly of a peptide‐polymer conjugate YYKLVFF‐PEG3K previously studied by our group [Castelletto et al., Polym. Chem., 2010, 1, 453–459]. This conjugate comprises a designed amyloid‐forming peptide YYKLVFF that contains the KLVFF sequence from Amyloid β peptide, Aβ16‐20, along with two aromatic tyrosine residues to enhance hydrophobicity, as well as polyethylene glycol PEG with molar mass 3 kg mol−1. The conjugate self‐assembles into β‐sheet fibrils in aqueous solution. Here we show that complexation with αCD instead generates free‐floating nanosheets in aqueous solution (with a β‐sheet structure). The nanosheets comprise a bilayer with a hydrophobic peptide core and highly swollen PEG outer layers. The transition from fibrils to nanosheets is driven by an increase in the number of αCD molecules threaded on the PEG chains, as determined by 1H NMR spectroscopy. These findings point to the use of cyclodextrin additives as a powerful means to tune the solution self‐assembly in peptide‐polymer conjugates and potentially other polymer/biomolecular hybrids.
Effect of biochar application on corn and soybean yield in Michigan and Ohio
Authors: Silva‐Pumarada Gabriela , Shrestha Raj K. , Chiavegato Marília , Mercer Kristin , Agyei Benjamin K. , Singh Maninder P. , Lindsey Laura E. 
Published: August 2023

Core Ideas
Biochar was applied to three field locations in Fall 2020 to test impact on corn and soybean yield.
In 2021, corn yield was unaffected by biochar application compared to the non‐treated control.
In 2022, soybean yield increased with biochar application at one out of three locations.
Highly Soluble Ambipolar anti‐Perylene‐3,4 : 9,10‐bis(benzimidazole)s Stabilize a Room‐Temperature Columnar Hexagonal Phase
Authors: Behera Paresh Kumar , Yadav Kajal , Patra Alakananda , Gupta Ravindra Kumar , Rao D. S. Shankar , Kumar Sandeep , Pandey Upendra Kumar , Achalkumar Ammathnadu Sudhakar 
Published: August 2023

AbstractA new series of highly soluble perylene anti‐bis(4,5‐dialkoxybenzimidazole)s bearing branched flexible chains stabilizing room temperature columnar hexagonal phase and with balanced ambipolar charge carrier mobility is reported for the first time. Only the anti isomer was successfully separated and characterized. These compounds have a high extinction coefficient, small optical band gap and wide absorption range, thus making them a promising class of ambipolar organic semiconductors capable of self‐organizing.
The effect of nitrogen and water management on the yield and endogenous hormone levels of drip‐irrigated rice
Authors: Zhao Lei , Wang Guodong , Luo Honghai , Tang Qingyun , Song Zhiwen , Li Yuxiang 
Published: August 2023

AbstractImproving the management of water and fertilizers is an effective method for enhancing the seed‐setting performance of rice. This study aimed to explore the regulation of optimized water and nitrogen management on the root–leaf hormone balance and seed‐setting performance of drip‐irrigated rice. In a 2‐year field experiment, T‐43 (a drought‐resistant cultivar) and LX‐3 (a drought‐sensitive cultivar) were cultivated under two drip irrigation treatments (W1, limited, and W2, deficit) and three nitrogen fertilization treatments (N1, seedling:tillering:panicle:grain‐filling, 30%:50%:13%:7%; N2, 20%:40%:30%:10%; and N3, 10%:30%:40%:20%). Compared with other treatments, the W1N2 treatment increased the seed‐setting rate and grain biomass accumulation (2.7%–9.2% and 4.5%–69.8%) of the two cultivars on the basis of producing a higher effective panicle number, and T‐43 had a much higher seed‐setting rate and yield than LX‐3 (6.8%–14.6%). Increased fertilizer applications at the panicle and grain‐filling stages (N2) enhanced the root oxidation activity (ROA) and the zeatin+zeatin riboside (Z + ZR) and gibberellic acid (GA3) contents in the roots in the 0–10 cm layer and in the leaves from the heading stage to 20 days after heading. The grain biomass accumulation of T‐43 was significantly positively correlated with abscisic acid (ABA) and Z + ZR in the roots and leaves, while the grain biomass accumulation of LX‐3 was significantly positively correlated with auxin, ABA, Z + ZR/ABA, and GA3/ABA in the roots in the 10–20 cm layer. Overall, W1N2 promoted grain biomass accumulation by modulating the Z + ZR and ABA balance in roots and leaves, improved the root–shoot ratio, and enhanced ROA, thereby improving the seed‐setting performance of drip‐irrigated T‐43 rice.
Compact and low phase noise LC‐VCO design using novel V‐shaped inductor in 0.18‐μm CMOS technology for Ku‐band applications
Authors: Ahmed Taha Mohamed , Mansour Islam , Allam Ahmed , El Dessouky Mohamed , Pokharel Ramesh K. , Abdel‐Rahman Adel B. 
Published: August 2023

SummaryAn innovative, high‐quality factor, and small‐area V‐shaped inductor is presented in this article to improve the performance of voltage‐controlled oscillators (VCOs). The differential inductance of the suggested V‐shaped inductor in the resonator and the buffer is 280 pH and 630 pH, respectively. The inductor area is compacted by 42% and 76% compared to the conventional inductor with the same inductance value. Using 0.18‐ CMOS technology, the proposed V‐shaped inductor is employed to design a compact VCO operating at Ku‐band. The proposed VCO has a simulated phase noise range of −114 to −114.6 dBc/Hz, which is relatively constant. Also, its simulated frequency tuning range (FTR) is 5.6 % from 14.03 to 14.74 GHz. The power consumption is 2.2 mW. The simulated figure of merit (FoM) ranges from −193.5 to −194.2 dBc/Hz, which is enhanced by 6%. The designed VCO core area is 0.034 mm2, which is compacted by 35% compared to using a conventional spiral inductor. The achieved area‐included figure of merit ( ) is −208.7 dBc/Hz. The VCO has an output power of −6.8 dBm and a good harmonic suppression of 29.4 dB between the fundamental and the second harmonic.
Inverse relationship between Fusobacterium nucleatum amount and tumor CD274 (PD‐L1) expression in colorectal carcinoma
Authors: Ugai Tomotaka , Shimizu Takashi , Kawamura Hidetaka , Ugai Satoko , Takashima Yasutoshi , Usui Genki , Väyrynen Juha P , Okadome Kazuo , Haruki Koichiro , Akimoto Naohiko , Masugi Yohei , da Silva Annacarolina , Mima Kosuke , Zhang Xuehong , Chan Andrew T , Wang Molin , Garrett Wendy S , Freeman Gordon J , Meyerhardt Jeffrey A , Nowak Jonathan A , Song Mingyang , Giannakis Marios , Ogino Shuji 
Published: August 2023

AbstractObjectivesThe CD274 (programmed cell death 1 ligand 1, PD‐L1)/PDCD1 (programmed cell death 1, PD‐1) immune checkpoint axis is known to regulate the antitumor immune response. Evidence also supports an immunosuppressive effect of Fusobacterium nucleatum. We hypothesised that tumor CD274 overexpression might be inversely associated with abundance of F. nucleatum in colorectal carcinoma.MethodsWe assessed tumor CD274 expression by immunohistochemistry and F. nucleatum DNA within tumor tissue by quantitative PCR in 812 cases among 4465 incident rectal and colon cancer cases that had occurred in two prospective cohort studies. Multivariable logistic regression analyses with inverse probability weighting were used to adjust for selection bias because of tissue data availability and potential confounders including microsatellite instability status, CpG island methylator phenotype, LINE‐1 methylation level and KRAS, BRAF and PIK3CA mutations.ResultsFusobacterium nucleatum DNA was detected in tumor tissue in 109 (13%) cases. Tumor CD274 expression level was inversely associated with the amount of F. nucleatum in colorectal cancer tissue (P = 0.0077). For one category‐unit increase in three ordinal F. nucleatum categories (negative vs. low vs. high), multivariable‐adjusted odds ratios (with 95% confidence interval) of the low, intermediate and high CD274 categories (vs. negative) were 0.78 (0.41–1.51), 0.64 (0.32–1.28) and 0.50 (0.25–0.99), respectively (Ptrend = 0.032).ConclusionsTumor CD274 expression level was inversely associated with the amount of F. nucleatum in colorectal cancer tissue, suggesting that different immunosuppressive mechanisms (i.e. PDCD1 immune checkpoint activation and tumor F. nucleatum enrichment) tend to be used by different tumor subgroups.
Impact of age on characteristics, performance measures and outcomes of inpatients for heart failure in Beijing, China
Authors: Yuan Cong , He Liu , Du Xin , Jiang Chao , Xia Shi‐Jun , Zhao Xin , Li Song‐Nan , Sang Cai‐Hua , Long De‐Yong , Dong Jian‐Zeng , Ma Chang‐Sheng 
Published: August 2023

AbstractAimsThis study aims to provide representative information on heart failure (HF) patients in China, especially older adults aged ≥75 years. We aim to clarify the age‐related discrepancies in performance measures and the modifying effect of age on the impact of HF patients' characteristics on clinical outcomes.Methods and resultsAll HF patients admitted into five tertiary and four secondary hospitals of the Capital Medical University were divided into two groups according to age: 1419 (53.3%) were <75 years, and 1244 (46.7%) were ≥75 years. Older HF patients were more likely to be women, with higher left ventricular ejection fraction, with co‐morbidities including chronic obstructive pulmonary disease/asthma, anaemia, chronic kidney disease, stroke/transient ischemic attack (TIA), atrial fibrillation/atrial flutter, hypertension, and coronary artery disease, while obesity, diabetes mellitus, hypercholesterolaemia and valvular heart disease were more prevalent among younger HF patients. Left ventricular ejection fraction assessment was performed in a similar proportion of patients in the younger and older groups (81.7% vs. 80.5%, P = 0.426), while B‐type natriuretic peptide/N terminal pro brain natriuretic peptide was tested in a lower proportion in the younger group (84.8% vs. 89%, P = 0.001). At discharge, HF with reduced ejection fraction patients were less likely to receive beta‐blockers, angiotensin‐converting enzyme inhibitors/angiotensin II receptor blockers, or combined beta‐blockers and angiotensin‐converting enzyme inhibitors/angiotensin II receptor blockers therapy in the older group (49.74% vs. 63.2%, P = 0.002; 52.9% vs. 64.7%, P = 0.006; and 28.57% vs. 45.5%, P < 0.001, respectively) but were equally likely to receive mineralocorticoid receptor antagonists in the two age groups (80.8% vs. 84.1%, P = 0.322). Older patients with HF had higher risk of in‐hospital and 1 year mortality (2.7% vs. 1.3%, P = 0.011; 21.7% vs. 12.5%; P < 0.001, respectively). Higher body mass index was associated with better outcomes in both age groups. New York Heart Association functional class IV and estimated glomerular filtration rate < 60 mL/min/1.73 m2 were independent predictors of 1 year mortality. The associations between patients' characteristics and risk of mortality were not modified by age.ConclusionsHF patients aged ≥75 years had distinct clinical profiles, received worse in‐hospital therapies and experienced higher in‐hospital and 1 year mortality.
Bio‐inspired Design of Bidirectional Oxygen Reduction and Oxygen Evolution Reaction Molecular Electrocatalysts
Authors: Awasthi Mahendra K. , Saini Abhishek , Das Chandan , Banerjee Anwesha , Shah Naseer Ahmad , Lahiri Goutam Kumar , Dutta Arnab 
Published: August 2023

AbstractThe proper utilization of renewable energy sources has emerged as a major challenge in our pursuit of a sustainable and carbon‐neutral energy landscape. Small molecule activation is a key component for proper utilization of renewable energy resources, where O2/H2O redox couple is reckoned to be a potential game changer. In this regard, electrocatalytic oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) have become the prime interest of catalyst designers. Typically, these ORR and OER electrocatalysts are developed distinctly; however, very soon, the requirement of a bidirectional ORR/OER electrocatalyst becomes obvious for practical applicability and rapid energy transduction purposes. A bidirectional catalyst is defined as a catalyst capable of driving a redox reaction in opposing directions. This review has portrayed the development of enzyme structure‐inspired design of molecular bidirectional ORR/OER catalysts. The strategic incorporation of secondary and outer coordination sphere features has significantly enhanced the performance of these catalysts, which can be monitored via the key catalytic parameters. These bifunctional OER/ORR catalysts are vital for metal‐air battery and fuel cell applications and appropriately poised to lay the foundation for an efficient, economical, and eco‐friendly pathway for sustainable energy usage with the rational assembly of energy converting and storage devices.
Potassium Persulfate‐Glucose Mediated Synthesis of (3)‐S‐Arylthioindoles from Indole and Thiophenols in Water
Authors: Kumar Nitin , Venkatesh Rapelly , Singh Sundaram , Kandasamy Jeyakumar 
Published: August 2023

AbstractAn efficient and eco‐friendly method has been developed for the preparation of functionalized 3‐(S)‐arylthioindoles in good to excellent yields from indoles and aryl thiols in water. The coupling reaction was prompted by K2S2O8 in the presence of glucose at room temperature. Broad substrate scope, functional group tolerance, room temperature reactions and metal‐free conditions are the salient features of the developed methodology.
Impact of micro graphite particles addition on the mechanical behavior of Al2011 alloy metal composites
Authors: Raksha M. S. , Basavalingappa Adaveesh , Nagaral Madeva , Anjinappa Chandrashekar , Omprakash B. , Razak Abdul , Hasan Nasim 
Published: August 2023

AbstractMicron‐sized graphite particles additions to Al2011 alloy were investigated to know their impact on mechanical properties. The stir cast method was used to manufacture the Al2011 alloy with 2 and 4 wt% of graphite particles reinforced composites. The microstructural analysis and mechanical properties of the synthesized composites were tested. Scanning electron microscope (SEM) and energy dispersive spectroscopy (EDS) spectrums were used to characterize the microstructure of the samples that were obtained from the casting. SEM micrographs indicated the homogeneous distribution of particles and the EDS patterns confirmed the presence of graphite particles. Al2011 alloy hardness was decreased with the addition of graphite particles. Further, with the addition of 2 and 4 wt% of graphite particles in the Al2011 alloy, the ultimate tensile and yield strengths of composites were increased with increase in elongation. SEM micrographs of tensile fractured surfaces were used to study the various fractured behaviors in the Al2011 alloy‐graphite composites.