bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new lysine biosynthetic enzyme from a bacterial endosymbiont shaped by genetic drift and genome reduction
Authors: Gilkes Jenna M. , Frampton Rebekah A. , Board Amanda J. , Hudson André O. , Price Thomas G. , Morris Vanessa K. , Crittenden Deborah L. , Muscroft‐Taylor Andrew C. , Sheen Campbell R. , Smith Grant R. , Dobson Renwick C. J. 
Published: June 2024

AbstractThe effect of population bottlenecks and genome reduction on enzyme function is poorly understood. Candidatus Liberibacter solanacearum is a bacterium with a reduced genome that is transmitted vertically to the egg of an infected psyllid—a population bottleneck that imposes genetic drift and is predicted to affect protein structure and function. Here, we define the function of Ca. L. solanacearum dihydrodipicolinate synthase (CLsoDHDPS), which catalyzes the committed branchpoint reaction in diaminopimelate and lysine biosynthesis. We demonstrate that CLsoDHDPS is expressed in Ca. L. solanacearum and expression is increased ~2‐fold in the insect host compared to in planta. CLsoDHDPS has decreased thermal stability and increased aggregation propensity, implying mutations have destabilized the enzyme but are compensated for through elevated chaperone expression and a stabilized oligomeric state. CLsoDHDPS uses a ternary‐complex kinetic mechanism, which is to date unique among DHDPS enzymes, has unusually low catalytic ability, but an unusually high substrate affinity. Structural studies demonstrate that the active site is more open, and the structure of CLsoDHDPS with both pyruvate and the substrate analogue succinic‐semialdehyde reveals that the product is both structurally and energetically different and therefore evolution has in this case fashioned a new enzyme. Our study suggests the effects of genome reduction and genetic drift on the function of essential enzymes and provides insights on bacteria‐host co‐evolutionary associations. We propose that bacteria with endosymbiotic lifestyles present a rich vein of interesting enzymes useful for understanding enzyme function and/or informing protein engineering efforts.
Thermostability and binding properties of single‐chained Fv fragments derived from therapeutic antibodies
Authors: Tadokoro Takashi , Tsuboi Harumi , Nakamura Kota , Hayakawa Tetsushi , Ohmura Reo , Kato Izumi , Inoue Masaki , Tsunoda Shin‐ichi , Niizuma Sayaka , Okada Yukari , Otsuguro Satoko , Maenaka Katsumi 
Published: June 2024

AbstractSmall antibody fragments have recently been used as alternatives to full‐length monoclonal antibodies in therapeutic applications. One of the most popular fragment antibodies is single‐chain fragment variables (scFvs), consisting of variable heavy (VH) and variable light (VL) domains linked by a flexible peptide linker. scFvs have small molecular sizes, which enables good tissue penetration and low immunogenicity. Despite these advantages, the use of scFvs, especially for therapeutic purpose, is still limited because of the difficulty to regulate the binding activity and conformational stability. In this study, we constructed and analyzed 10 scFv fragments derived from 10 representatives of FDA‐approved mAbs to evaluate their physicochemical properties. Differential scanning calorimetry analysis showed that scFvs exhibited relatively high but varied thermostability, from 50 to 70°C of melting temperatures, and different unfolding cooperativity. Surface plasmon resonance analysis revealed that scFvs fragments that exhibit high stability and cooperative unfolding likely tend to maintain antigen binding. This study demonstrated the comprehensive physicochemical properties of scFvs derived from FDA‐approved antibodies, providing insights into antibody design and development.
Characterization of βB2‐crystallin tryptophan mutants reveals two different folding states in solution
Authors: Sun Jiayue , Morishima Ken , Inoue Rintaro , Sugiyama Masaaki , Takata Takumi 
Published: June 2024

AbstractConserved tryptophan residues are critical for the structure and the stability of β/γ‐crystallin in the lenses of vertebrates. During aging, in which the lenses are continuously exposed to ultraviolet irradiation and other environmental stresses, oxidation of tryptophan residues in β/γ‐crystallin is triggered and impacts the lens proteins to varying degrees. Kynurenine derivatives, formed by oxidation of tryptophan, accumulate, resulting in destabilization and insolubilization of β/γ‐crystallin, which correlates with age‐related cataract formation. To understand the contribution of tryptophan modification on the structure and stability of human βB2‐crystallin, five tryptophan residues were mutated to phenylalanine considering its similarity in structure and hydrophilicity to kynurenine. Among all mutants, W59F and W151F altered the stability and homo‐oligomerization of βB2‐crystallin—W59F promoted tetramerization whereas W151F blocked oligomerization. Most W59F dimers transformed into tetramer in a month, and the separated dimer and tetramer of W59F demonstrated different structures and hydrophobicity, implying that the biochemical properties of βB2‐crystallin vary over time. By using SAXS, we found that the dimer of βB2‐crystallin in solution resembled the lattice βB1‐crystallin dimer (face‐en‐face), whereas the tetramer of βB2‐crystallin in solution resembled its lattice tetramer (domain‐swapped). Our results suggest that homo‐oligomerization of βB2‐crystallin includes potential inter‐subunit reactions, such as dissociation, unfolding, and re‐formation of the dimers into a tetramer in solution. The W>F mutants are useful in studying different folding states of βB2‐crystallin in lens.
Sublethal and transgenerational effects of broflanilide on the citrus red mite, Panonychus citri
Authors: Li Ke , Ren Yiting , Liu Xun‐Yan , Pan Deng , Dou Wei , Wang Jin‐Jun , Yuan Guorui 
Published: June 2024

AbstractBACKGROUNDThe citrus red mite, Panonychus citri is a serious pest of the citrus industry and has developed resistance to many acaricides. Broflanilide is a novel meta‐diamide insecticide that binds to a new site on the γ ‐aminobutyric acid receptor with high potency against pests. However, little information has been reported about its effect on the citrus red mite.RESULTSBroflanilide exhibited higher toxicity to female adults and eggs of a laboratory strain of P. citri The median lethal concentration (LC50), 9.769 mg/L and 4.576 mg/L, respectively) than other commonly used acaricides and was also toxic to two P. citri field strains. Broflanilide treatment with LC10, LC20, and LC30 significantly decreased the fecundity and longevity of female adults of F0 P. citri compared with the control. The duration of larva, protonymph, deutonymph and adult, and total life span in the F1 generation were significantly reduced after treatment of F0 with broflanilide. Population parameters, including the intrinsic rate of increase (r) and finite rate of increase (λ), were significantly increased, and the mean generation time (T) of F1 progeny was significantly reduced in the LC20 treatment. The predicted population size of F1 increased when parental female adults were treated with sublethal concentrations.CONCLUSIONBroflanilide had high acaricidal activity toward P. citri, and exposure to a sublethal concentration significantly inhibited the population growth of F0. The transgenerational hormesis effect is likely to cause population expansion of F1. More attention should be paid when broflanilide is applied to control P. citri in citrus orchards. © 2024 Society of Chemical Industry.
T3 + 3: 3 + 3 Design With Delayed Outcomes
Authors: Guo Jiaying , Lu Mengyi , Wan Isabella , Wang Yumin , Han Leng , Zang Yong 
Published: June 2024

ABSTRACTDelayed outcome is common in phase I oncology clinical trials. It causes logistic difficulty, wastes resources, and prolongs the trial duration. This article investigates this issue and proposes the time‐to‐event 3 + 3 (T3 + 3) design, which utilizes the actual follow‐up time for at‐risk patients with pending toxicity outcomes. The T3 + 3 design allows continuous accrual without unnecessary trial suspension and is costless and implementable with pretabulated dose decision rules. Besides, the T3 + 3 design uses the isotonic regression to estimate the toxicity rates across dose levels and therefore can accommodate for any targeted toxicity rate for maximum tolerated dose (MTD). It dramatically facilitates the trial preparation and conduct without intensive computation and statistical consultation. The extension to other algorithm‐based phase I dose‐finding designs (e.g., i3 + 3 design) is also studied. Comprehensive computer simulation studies are conducted to investigate the performance of the T3 + 3 design under various dose‐toxicity scenarios. The results confirm that the T3 + 3 design substantially shortens the trial duration compared with the conventional 3 + 3 design and yields much higher accuracy in MTD identification than the rolling six design. In summary, the T3 + 3 design addresses the delayed outcome issue while keeping the desirable features of the 3 + 3 design, such as simplicity, transparency, and costless implementation. It has great potential to accelerate early‐phase drug development.
Exosomes, and the potential for exosome‐based interventions against COVID‐19
Authors: Rahmani Abolfazl , Soleymani Ali , Almukhtar Mustafa , Behzad Moghadam Kimia , Vaziri Zahra , Hosein Tabar Kashi Ali , Adabi Firoozjah Reza , Jafari Tadi Mehrdad , Zolfaghari Dehkharghani Maryam , Valadi Hadi , Moghadamnia Ali Akbar , Gasser Robin B. , Rostami Ali 
Published: June 2024

AbstractSince late 2019, the world has been devastated by the coronavirus disease 2019 (COVID‐19) induced by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), with more than 760 million people affected and ∼seven million deaths reported. Although effective treatments for COVID‐19 are currently limited, there has been a strong focus on developing new therapeutic approaches to address the morbidity and mortality linked to this disease. An approach that is currently being investigated is the use of exosome‐based therapies. Exosomes are small, extracellular vesicles that play a role in many clinical diseases, including viral infections, infected cells release exosomes that can transmit viral components, such as miRNAs and proteins, and can also include receptors for viruses that facilitate viral entry into recipient cells. SARS‐CoV‐2 has the ability to impact the formation, secretion, and release of exosomes, thereby potentially facilitating or intensifying the transmission of the virus among cells, tissues and individuals. Therefore, designing synthetic exosomes that carry immunomodulatory cargo and antiviral compounds are proposed to be a promising strategy for the treatment of COVID‐19 and other viral diseases. Moreover, exosomes generated from mesenchymal stem cells (MSC) might be employed as cell‐free therapeutic agents, as MSC‐derived exosomes can diminish the cytokine storm and reverse the suppression of host anti‐viral defences associated with COVID‐19, and boost the repair of lung damage linked to mitochondrial activity. The present article discusses the significance and roles of exosomes in COVID‐19, and explores potential future applications of exosomes in combating this disease. Despite the challenges posed by COVID‐19, exosome‐based therapies could represent a promising avenue for improving patient outcomes and reducing the impact of this disease.
Liver involvement in dengue: A systematic review
Authors: Campana Valentine , Inizan Catherine , Pommier Jean‐David , Menudier Luce Yemadje , Vincent Muriel , Lecuit Marc , Lamballerie Xavier De , Dupont‐Rouzeyrol Myrielle , Murgue Bernadette , Cabié André 
Published: June 2024

AbstractLiver involvement is an unusual yet frequently overlooked dengue complication. Pivotal for an efficient clinical management, the early diagnosis of dengue‐associated liver involvement relies on an accurate description of its clinical and biological characteristics, its prognosis factors, its association with severe dengue and its clinical management. We conducted a systematic review by searching PubMed and Web of Science databases for original case reports, cohort and cross‐sectional studies reporting the clinical and/or biological features of dengue‐associated liver involvement. The study was registered in PROSPERO (CRD42021262657). Of the 2552 articles identified, 167 were included. Dengue‐associated liver involvement was characterised by clinical features including abdominal pain, hepatomegaly, jaundice, nausea/vomiting, and an echogenic liver exhibiting hepatocellular necrosis and minimal inflammation. Elevated Aspartate Aminotransferase and Alanine Aminotransferase but also elevated bilirubin, Alkaline Phosphatase, gamma‐glutamyl transferase, increased International Normalised Ratio, creatinine and creatine kinase, lower albumin and prolonged prothrombin and activated partial thromboplastin time were prevalent in dengue‐associated liver involvement. Cardiovascular and haematological systems were frequently affected, translating in a strong association with severe dengue. Liver involvement was more common in males and older adults. It was associated with dengue virus serotype‐2 and secondary infections. Early paracetamol intake increased the risk of liver involvement, which clinical management was mostly conservative. In conclusion, this systematic review demonstrates that early monitoring of transaminases, clinical assessment, and ultrasound examination allow an efficient diagnosis of dengue‐associated liver involvement, enabling the early identification and management of severe dengue.
An enhanced and expanded Toolbox for River Velocimetry using Images from Aircraft (TRiVIA)
Authors: Legleiter Carl J. , Kinzel Paul J. 
Published: June 2024

AbstractDetailed, accurate information on flow patterns in river channels can improve understanding of habitat conditions, geomorphic processes, and potential hazards to help inform water management. Data describing flow patterns in river channels can be obtained efficiently via image‐based techniques that have become more widely used in recent years as the number of platforms for acquiring images has expanded and the number of algorithms for inferring velocities has grown. Image‐based techniques have been incorporated into various software packages, including the Toolbox for River Velocimetry using Images from Aircraft (TRiVIA). TRiVIA is a freely available, standalone computer program that provides a comprehensive workflow for performing particle image velocimetry (PIV)‐based analyses within a graphical interface. This paper summarizes major enhancements incorporated into the latest release of TRiVIA, version 2.1. For example, a new Tool for Input Parameter Selection (TIPS) provides guidance for specifying key inputs to the PIV algorithm by allowing users to explore relationships between flow velocity, pixel size, output vector spacing, and frame interval. Improved visualization capabilities include the ability to create streamlines and display PIV output on an interactive web map. The program now provides greater flexibility for importing field data in various formats and selecting which observations to use for accuracy assessment. The most substantial additions to TRiVIA 2.1 are the ability to integrate bathymetric information with image‐derived velocity estimates to calculate river discharge and to use images acquired from moving aircraft to efficiently map long segments of large rivers to support habitat assessment, contaminant transport studies, and a range of other applications.
Alternative agrifood systems and the economic sustainability of farmers' cooperatives: The Chinese experience
Authors: Hu Zhanping , Zhang Qian Forrest 
Published: June 2024

AbstractMost registered farmers' cooperatives in China are de facto private enterprises; while many bring economic gains to farmers, they do not function as cooperatives. Among the small minority that started as authentic cooperatives, however, most struggled to provide economic benefits to members, unable to achieve economic sustainability. The failure of true farmers' cooperatives in China has been widely studied; the success of the few that did become economically sustainable, however, remains poorly understood. Using a sample of 70 farmers' cooperatives across the country and comparing three “extreme cases”—cooperatives that are both authentic and economically successful—with the rest, this study argues that participation in alternative agrifood systems is the key to their success. In the Chinese context, smallholders are deeply integrated into the conventional agrifood system and have gained technology and market access through the mediation of private enterprises and public institutions, leaving little space for cooperatives. Only in alternative agrifood systems, which prioritize product quality and authenticity and value closer relationships between producers and consumers, do cooperatives, as a unique governance institution based on trust, have advantages. Our case analysis shows how cooperatives brought smallholders economic gains and achieved economic sustainability through shifting to ecologically sustainable farming and building alternative distributive networks. This finding adds a new dimension to our understanding of the relationship between smallholder cooperatives and sustainable development: in capitalist agrifood systems, ecologically sustainable agrifood alternatives provide the basis for cooperatives' social and economic sustainability.
Linking local and global: Assessing water scarcity risk through nested trade networks
Authors: Wang Chenglong , Shuai Chenyang , Chen Xi , Sun Jingran , Zhao Bu 
Published: June 2024

AbstractAs water scarcity escalates globally, there is a growing focus on assessing its economic impact, both locally and through trade networks, defined as water scarcity risk (WSR). Given China's pivotal role as a top importer and exporter, coupled with significant spatial disparities in water scarcity across its provinces, understanding the spread of water scarcity risks within China and their interplay with global water dynamics is imperative yet relatively unexplored. This study constructs a nested Multi‐Regional Input‐Output (MRIO) model to evaluate water scarcity risk, connecting Chinese provinces with global counterparts. Notably, we integrate the spatial heterogeneity of environmental flow requirement as a vital criterion for long‐term sustainable water management in our assessment. Our findings reveal substantial economic impacts caused by water scarcity, with a global WSR valued at $11.1 trillion, of which $6.2 trillion is attributed to trade. Critical regions, sectors, and region‐sectors are identified, offering valuable insights for targeted interventions. This study presents a unique perspective on global water scarcity risk assessment at a higher resolution scale, laying the groundwork for the formulation of effective water scarcity risk mitigation strategies aligned with sustainable development goals, particularly SDG 6 and 8.
A Cellulose Reinforced Polyacrylamide/Polyvinyl Alcohol Dual Network Hydrogel for Flexible Sensors
Authors: Meng Lingling , Li Weihao , Ding Shijie , Liu En , Liu Da 
Published: June 2024

AbstractIn this paper, polyacrylamide (PAM) was used as the main matrix material to form the first layer network structure, and polyvinyl alcohol (PVA) was used as the secondary matrix material to form the second layer network structure. The hydrogels were prepared by free radical in‐situ polymerization and physical cross‐linking. This hydrogel was characterized not only by its semi‐interpenetrating network structure, in which cellulose nanocrystals (CNC) penetrate through the polyacrylamide network but also by the physically and chemically cross‐linked hybrid PAM/PVA double network. The structure and appearance of the hydrogels were characterized by scanning electron microscope and Fourier transform infrared spectrometer, and a series of tests were carried out to detect their mechanical properties, electrical properties and sensing properties. The results show that the hydrogel has good mechanical properties (the elongation at break can reach 600 % and the stress at break can reach 0.16 MPa), and the hydrogel also has good sensing and electrical properties. The addition of organic solvents makes the hydrogels have excellent antifreeze and water retention properties and also have excellent swelling properties. Therefore, the PAM/PVA/CNC dual network interpenetrating composite hydrogel has potential application value in the field of flexible sensors.
Emerging Trends in Nano‐Functionalized Scaffolds for Chronic Wound Healing
Authors: Koolabadi Zeinab , Taghipour Niloofar , Rouhani Maryam , Heidari Keshel Saeed , Soleimani Masoud 
Published: June 2024

AbstractThis review discusses recent studies on the combination of nanoparticles (NPs) and biomaterials for the treatment of chronic wounds, especially diabetic foot ulcers (DFUs). This article provides a concise overview of several types of NPs. We will discuss how these NPs possess inherent characteristics that enhance the bioactivity, mechanical strength, tissue adhesion, and antibacterial properties of wound repairing scaffolds. Additionally, we explore their capacity to carry active substances and genes to the wound site. In this context, a comprehensive elucidation of various notable complexities associated with wound repair is provided, alongside corresponding strategies to mitigate them. So that, the adoption of NPs within wound dressings is advocated as a proficient technological approach to address each of these challenges. Furthermore, this article examines several physical and chemical techniques employed by researchers for the incorporation of NPs into scaffolds.
Conducting Carbon Black Nano‐Filler Doped Polymer Electrolyte for Electrochemical Application
Authors: Singh Negi Shubham , Rawat Suneyana , Singh Pramod K. , Savilov Serguei V. , Yadav Tarun , Yahya M. Z. A. , Chandra Singh Ram 
Published: June 2024

AbstractThis study provides a development of polymer electrolytes with an emphasis on their use in electrochemical devices. In present study we develop a new conducting carbon black (CB) powder dispersed into polyethylene oxide (PEO) polymer electrolyte using solution cast method. Various characterization techniques such as Impedance spectroscopy technique (EIS), Fourier transform infrared spectroscopy (FTIR), and Window stability (LSV) Linear sweep voltammetry has been studied in detail. The maximum ionic conductivity polymer electrolyte was at 0.05 wt%. of CB with σ value 1.20×10−5 S/cm. Finally the prepared CB dispersed polymer electrolyte using maximum conductivity sample is sandwiched between electrodes to fabricate an Electric double layer capacitor and Dye‐sensitized solar cell which show highest electrical capacity value of 68.5 F/gm at 5 mV/s respectively and 2.97 % efficiency shown by solar cell at 1 sun condition.
Tungsten Doping of Two‐Dimensional VO2 Nanoribbons for Rapid Zinc Ion Storage Channels
Authors: Fan Hong , Wang Kefan , Xu Zewen 
Published: June 2024

AbstractVanadium‐based oxides are promising candidates for use in aqueous zinc‐ion batteries owing to their open framework structure that facilitates rapid Zn2+ deintercalation. To improve the kinetics, a two‐dimensional nanoribbon‐shaped W‐VO2 cathode material was developed by pre‐embedding tungsten atoms into VO2(B) using a one‐step hydrothermal method. The large interlayer spacing in the W‐VO2 nanosheets aided in the deintercalation of hydrated Zn2+ ions. The 1 % W‐doped electrode exhibited stable cycling, reaching a high capacity of 365.8 mAh g−1 at 0.3 A g−1, with a 92.6 % capacity retention (338.8 mAh g−1) after 200 cycles. Impressively, 84.3 % of the capacity is retained after 1200 cycles at 1 A g−1. The zinc storage mechanism of W‐VO2 was elucidated through in situ X‐ray diffraction and X‐ray photoelectron spectroscopy, highlighting the benefits of tungsten doping on tunnel structure stability and Zn2+ deintercalation reversibility in VO2 electrodes.