bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reaction mechanism of acetonitrile, olefins, and amines catalyzed by Ag2CO3: A DFT investigation
Authors: Chen Bin , Zhou Da‐Gang , Yang Li‐Jun 
Published: December 2023

AbstractThe mechanism of Ag2CO3‐catalyzed reactions of acetonitrile, olefins, and amines was investigated by using the M06‐L‐D3/6‐311 + G(d,p) method and level, and solvation model based on solute electron density (SMD) model was applied to simulate the solvent effect. Calculations show that the Ag2CO3 could achieve the Csp3‐H activation by coordinating with the terminal nitrogen atom of CH3CN; then, the addition reaction happened between the obtained Ag‐complex intermediate and olefin via the coordination of Ag and benzene ring; finally, the obtained radical intermediate continues to go through one single electron transfer (SET) process, addition reaction, and H‐shift reaction to yield the final product. The computational results reveal that Fe3+ cation would have assisted the SET process successfully and the path of direct addition with the amine is the optimal. Fukui function and dual descriptor can be used to predict the reactive sites, and electron spin density isosurface graphs can analyze the structures and reveal the substances.
Flexible protein–protein docking with a multitrack iterative transformer
Authors: Chu Lee‐Shin , Ruffolo Jeffrey A. , Harmalkar Ameya , Gray Jeffrey J. 
Published: December 2023

AbstractConventional protein–protein docking algorithms usually rely on heavy candidate sampling and reranking, but these steps are time‐consuming and hinder applications that require high‐throughput complex structure prediction, for example, structure‐based virtual screening. Existing deep learning methods for protein–protein docking, despite being much faster, suffer from low docking success rates. In addition, they simplify the problem to assume no conformational changes within any protein upon binding (rigid docking). This assumption precludes applications when binding‐induced conformational changes play a role, such as allosteric inhibition or docking from uncertain unbound model structures. To address these limitations, we present GeoDock, a multitrack iterative transformer network to predict a docked structure from separate docking partners. Unlike deep learning models for protein structure prediction that input multiple sequence alignments, GeoDock inputs just the sequences and structures of the docking partners, which suits the tasks when the individual structures are given. GeoDock is flexible at the protein residue level, allowing the prediction of conformational changes upon binding. On the Database of Interacting Protein Structures (DIPS) test set, GeoDock achieves a 43% top‐1 success rate, outperforming all other tested methods. However, in the standard DIPS train/test splits, we discovered contamination of close homologs in the training set. After decontaminating the training set, the success rate is 31%. On the DB5.5 test set and a benchmark dataset of antibody–antigen complexes, GeoDock outperforms the deep learning models trained using the same dataset but falls behind most of the conventional methods and AlphaFold‐Multimer. GeoDock attains an average inference speed of under 1 s on a single GPU, enabling its application in large‐scale structure screening. Although binding‐induced conformational changes are still a challenge owing to limited training and evaluation data, our architecture sets up the foundation to capture this backbone flexibility. Code and a demonstration Jupyter notebook are available athttps://github.com/Graylab/GeoDock.
Cover crops terminated with roller‐crimper to manage Cynodon dactylon and other weeds in vineyards
Authors: Cabrera‐Pérez Carlos , Royo‐Esnal Aritz , Català Bruna , Baraibar Bàrbara , Recasens Jordi 
Published: December 2023

BACKGROUNDUsing cover crops in organic vineyards can provide many advantages, including weed suppression. However, their effectiveness may depend on the weed community, the cover crop species and the termination method. The most common practice for cover crop termination is shredding, but rapid residue decomposition can allow noxious species like Cynodon dactylon to proliferate during summer and compete with the vines. The use of roller‐crimpers as an alternative method can be effective in some cropping systems, but no studies have focused on their use in the inter‐row of vineyards. The objective of this study was to evaluate the effectiveness of seven cover crops (spontaneous, Avena strigosa, Hordeum vulgare, Lolium multiflorum, Phacelia tanacetifolia, Sinapis alba and X Triticosecale) and two termination methods (shredding or roller‐crimper) in managing C. dactylon during summer.RESULTSIn 2020, rolled A. strigosa, P. tanacetifolia and the spontaneous flora limited the coverage of C. dactylon more than shredding (increases of 3% and 18% in C. dactylon cover from July to September in rolled and shredded cover crops, respectively), while in 2021, rolling was better than shredding for all cover crop species in September (5% and 18% increases, respectively).CONCLUSIONRoller‐crimping cover crops was an effective method to control C. dactylon in vineyard inter‐rows but it did not consistently work for all cover crops in both years. Our study is one of the first to test the efficacy of roller‐crimpers to manage summer weeds in vineyards. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Estimating the impact of carbon inefficiency and overuse of energy on the economics of water companies: A case study for England and Wales
Authors: Maziotis Alexandros , Sala‐Garrido Ramon , Mocholi‐Arce Manuel , Molinos‐Senante Maria 
Published: December 2023

AbstractIn the face of climate change, it becomes crucial to motivate action and policies within water companies towards achieving carbon neutrality. Estimating the economic consequences of inaction can be a compelling catalyst for change. In this study, the carbon inefficiency and overuse of energy among a selection of English and Welsh water companies were assessed, along with their impact on the operational costs of producing and delivering drinking water over the period from 2010 to 2019. In doing so, a stochastic frontier analysis primal system was employed. The findings revealed that, on average, water companies exhibited a carbon inefficiency of 0.699. The overuse of energy relative to other inputs was estimated to be 71.4%. Consequently, water companies incurred a production cost increase of 0.089 £/m3. This research demonstrates that transitioning towards a low‐carbon urban water cycle is not merely an environmental beneficial endeavor; it also involves significant economic advantages.
Biomimetic Transparent Layered Tough Aerogels for Thermal Superinsulation and Triboelectric Nanogenerator
Authors: Hu Zhenyu , Zhang Xiaoyu , Sun Qi , Gu Puzhong , Liang Xing , Yang Xiao , Liu Muxiang , Huang Jia , Wu Guangming , Zu Guoqing 
Published: December 2023

AbstractTransparent aerogels are ideal candidates for thermally insulating windows, solar thermal receivers, electronics, etc. However, they are usually prepared via energy‐consuming supercritical drying and show brittleness and low tensile strength, significantly restricting their practical applications. It remains a great challenge to prepare transparent aerogels with high tensile strength and toughness. Herein, biomimetic transparent tough cellulose nanofiber‐based nanocomposite aerogels with a layered nanofibrous structure are achieved by vacuum‐assisted self‐assembly combined with ambient pressure drying. The nacre‐like layered homogeneous nanoporous structures can reduce light scattering and effectively transfer stress and prevent stress concentration under external forces. The aerogels exhibit an attractive combination of excellent transparency and hydrophobicity, high compressive and tensile strengths, high toughness, excellent machinability, thermal superinsulation, and wide working temperature range (−196 to 230 °C). It is demonstrated that they can be used for superinsulating windows of buildings and high‐efficient thermal management for electronics and human bodies. In addition, a prototype of transparent flexible aerogel‐based triboelectric nanogenerator is developed. This work provides a promising pathway toward transparent tough porous materials for energy saving/harvesting, thermal management, electronics, sensors, etc.
Adenosine Triphosphate‐Activated Cascade Reactor for On‐Demand Antibacterial Treatment Through Controlled Hydroxyl Radical Generation
Authors: Chen Huihong , Fu Shanshan , Chen Xiaoqian , Chen Ruyi , Tan Hongliang 
Published: December 2023

AbstractNanozymes have shown promise for antibacterial applications, but their effectiveness is often hindered by low catalytic performances in physiological conditions and uncontrolled production of hydroxyl radicals (·OH). To address these limitations, a comprehensive approach is presented through the development of an adenosine triphosphate (ATP)‐activated cascade reactor (GGPcs). The GGPcs reactor synergistically combines the distinct properties of zeolitic imidazolate framework‐8 (ZIF‐8) and chitosan‐integrated hydrogel microsphere. The ZIF‐8 allows for the encapsulation of G‐quadruplex/hemin DNAzyme to achieve ATP‐responsive ·OH generation at neutral pH, while the hydrogel microsphere creates a confinement environment that facilitates glucose oxidation and provides a sufficient supply of H2O2. Importantly, the integrated chitosan in the hydrogel microsphere shields ZIF‐8 from undesired disruption caused by gluconic acid, ensuring the responsive specificity of ZIF‐8 toward ATP. By activating GGPcs with ATP secreted by bacteria, its effectiveness as an antibacterial agent is demonstrated for the on‐demand treatment of bacterial infection with minimal side effects. This comprehensive approach has the potential to facilitate the design of advanced nanozyme systems and broaden their biological applications.
A Tumor‐Specific Cascade‐Activating Smart Prodrug System for Enhanced Targeted Therapy
Authors: Wang Qiwei , Jin Duo , Liu Chengbin , Shi Lili , Li Tao 
Published: December 2023

AbstractDeveloping intelligently targeted drugs with low side effects is urgent for cancer treatment. Toward this goal, a tumor‐specific cascade‐activating smart prodrug system consisting of a G‐quadruplex(G4)‐modulated tumor‐targeted DNA vehicle and a well‐designed cellular stimuli‐responsive ligand‐drug conjugates (LDCs) is proposed. An original “donor–acceptor” binary fluorescent ligand, with ultrahigh affinity, brightness, and photostability, is engineered to tightly bind G4 structures and significantly improve the nuclease resistance of the DNA vehicle, which serves as a bridge contributing to the construction of the prodrug system, named ApG4/LDCs. Sodium nitroprusside and doxorubicin are loaded into ApG4/LDCs in one pot and generate nitric oxide and superoxide anion in response to cancer cellular environments, which in cascade generates peroxynitrite to cause DNA damage while promoting the self‐monitored drug release to achieve enhanced targeted therapy. Such a cascade activation and self‐reinforcement process is executed only when the prodrug system targets the tumor tissue followed by cell uptake, showing significant antitumor efficacy and greatly weakening the damage to normal tissues. Given the unique features, the innovative strategy for prodrug design may open a new door to precision disease treatment.
Advances of Smart Stimulus‐Responsive Microneedles in Cancer Treatment
Authors: Chu Huaqing , Xue Jiangtao , Yang Yuan , Zheng Hui , Luo Dan , Li Zhou 
Published: December 2023

AbstractMicroneedles (MNs) have emerged as a highly promising technology for delivering drugs via the skin. They provide several benefits, including high drug bioavailability, non‐invasiveness, painlessness, and high safety. Traditional strategies for intravenous delivery of anti‐tumor drugs have risks of systemic toxicity and easy development of drug resistance, while MN technology facilitates precise delivery and on‐demand release of drugs in local tissues. In addition, by further combining with stimulus‐responsive materials, the construction of smart stimulus‐responsive MNs can be achieved, which can respond to specific physical/chemical stimuli from the internal or external environment, thereby further improving the accuracy of tumor treatment and reducing toxicity to surrounding tissues/cells. This review systematically summarizes the classification, materials, and reaction mechanisms of stimulus‐responsive MNs, outlines the benefits and challenges of various types of MNs, and details their application and latest progress in cancer treatment. Finally, the development prospects of smart MNs in tumor treatment are also discussed, bringing inspiration for future precision treatment of tumors.
Surface Roughness Effects on Confined Nanoscale Transport of Ions and Biomolecules
Authors: Ma Chaofan , Zheng Fei , Xu Wei , Liu Wei , Xu Changhui , Chen Yunfei , Sha Jingjie 
Published: December 2023

AbstractBiological channels, especially membrane proteins, play a crucial role in metabolism, facilitating the transport of nutrients and other materials across cell membranes in a bio‐electrolyte environment. Artificial nanopores are employed to study ion and biomolecule transport behavior inside. While the non‐specific interaction between the nanopore surface and transport targets has garnered significant attention, the impact of surface roughness is overlooked. In this study, Nanopores with different levels of inner surface roughness is created by adjusting the FIB (Focus Ion Beam) fabrication parameters. Experiments and molecular dynamics (MD) simulations are employed to demonstrate that greater roughness results from larger FIB beam currents and shorter processing times. Lower roughness increases the capture rate of biomolecules, while greater roughness enhances the normalized blockade current (ΔI/I0). The phenomenon of rougher nanopores are attributed to a barrier‐dominated capture mechanism and more likely to induce DNA folding. This transport barrier exists in rough nanopores by utilizing steer molecular dynamics (SMD) simulations to investigate the force profile of a dA10 DNA molecule during translocation is demonstrated. This work illustrates how surface roughness influences the ionic current features and the translocation of biomolecules, paving a new way for tunning the molecule transport in nanopores.
Direct Capturing and Regulating Key Intermediates for High‐Efficiency Oxygen Evolution Reactions
Authors: Qian Zheng‐Xin , Peng Chun‐Kuo , Yue Mu‐Fei , Hsu Liang‐Ching , Zeng Ji‐Shuang , Wei Di‐Ye , Du Zi‐Yu , Xu Ge‐Yang , Zhang Hua , Tian Jing‐Hua , Chen San‐Yuan , Lin Yan‐Gu , Li Jian‐Feng 
Published: December 2023

AbstractDeveloping efficient oxygen evolution reaction (OER) electrocatalysts can greatly advance the commercialization of proton exchange membrane (PEM) water electrolysis. However, the unclear and disputed reaction mechanism and structure‐activity relationship of OER pose significant obstacles. Herein, the active site and intermediate for OER on AuIr nanoalloys are simultaneously identified and correlated with the activity, through the integration of in situ shell‐isolated nanoparticle‐enhanced Raman spectroscopy and X‐ray absorption spectroscopy. The AuIr nanoalloys display excellent OER performance with an overpotential of only 246 mV to achieve 10 mA cm−2 and long‐term stability under strong acidic conditions. Direct spectroscopic evidence demonstrates that *OO adsorbed on IrOx sites is the key intermediate for OER, and it is generated through the O–O coupling of adsorbed oxygen species directly from water, providing clear support for the adsorbate evolution mechanism. Moreover, the Raman information of the *OO intermediate can serve as a universal “in situ descriptor” that can be obtained both experimentally and theoretically to accelerate the catalyst design. It unveils that weakening the interactions of *OO on the catalysts and facilitating its desorption would boost the OER performance. This work deepens the mechanistic understandings on OER and provides insightful guidance for the design of more efficient OER catalysts.
Work‐from‐home impacts on software project: A global study on software development practices and stakeholder perceptions
Authors: Nguyen‐Duc Anh , Khanna Dron , Le Giang Huong , Greer Des , Wang Xiaofeng , Zaina Luciana Martinez , Matturro Gerardo , Melegati Jorge , Guerra Eduardo , Kettunen Petri , Hyrynsalmi Sami , Edison Henry , Sales Afonso , Chanin Rafael , Rutitis Didzis , Kemell Kai‐Kristian , Aldaeej Abdullah , Mikkonen Tommi , Garbajosa Juan , Abrahamsson Pekka 
Published: December 2023

ContextThe COVID‐19 pandemic has had a disruptive impact on how people work and collaborate across all global economic sectors, including software business. While remote working is not new for software engineers, forced WFH situations come with both limitations and opportunities. As the ‘new normal’ for working might be based on the current state of Work‐from‐home (WFH), it is useful to understand what has happened and learn from that.ObjectiveThis study aims to gain insights into how their WFH arrangement impacts project management and software engineering. We are also interested in exploring these impacts in different contexts, such as startups and established companies.MethodWe conducted a global‐scale, cross‐sectional survey during the spring and summer 2021. Our results are based on quantitative and qualitative analysis of 297 valid responses.ResultsWe characterize the profile of WFH in both spatial and temporal aspects, together with a set of common collaborative tools and coordination and control mechanisms. We revealed some areas of project management that are relatively more challenging during WFH situations, such as coordination, communication and project planning. We also revealed a mixed picture of the perceived impact of WFH on different software engineering activities.ConclusionWFH is a situational phenomenon which can have both negative and positive impact on software teams. For practitioners, we suggest a unified approach to consider the context of WFH, collaborative tools, associated coordination and control approaches and a process that resolve those aspects that are sensitive to physical interaction.
Boosting Learners' Confidence in Learning English: Can Self‐Efficacy‐Based Intervention Make a Difference?
Authors: Li Jiajing , Wang Chuang , Zhao Yao , Li Yijie 
Published: December 2023

AbstractSelf‐efficacy is theorized as a malleable construct that can be influenced by teachers' instructions; however, limited effort has been devoted to evaluating the effectiveness of self‐efficacy interventions. This study leverages a mixed methods design to evaluate the effectiveness of a self‐efficacy intervention over 16 weeks among Chinese English as a foreign language learners. Data were collected from 102 secondary school students (52 and 50 students in the intervention and comparison groups, respectively). We also interviewed nine students from the intervention class. Repeated measures mixed analyses of variance were employed to check the changes in self‐efficacy, intrinsic motivation, engagement, and academic achievement over time as well as to detect the differences in these aspects between the comparison and the intervention groups. Moreover, thematic analysis was adopted to handle the qualitative data. Results of the quantitative phase showed that the explicit self‐efficacy supports worked effectively in promoting self‐efficacy, intrinsic motivation, and language proficiency. Results of the qualitative phase triangulated the findings from the quantitative phase, illuminating the broad‐spectrum effect of self‐efficacy support. Implications and directions for future research are discussed.
Caffeic acid attenuates tissue damage and inflammatory response in Klebsiella pneumonia by modulating AhR‐Src‐STAT3‐IL‐10 signaling pathway
Authors: Chen Mei‐ling , Jiang Hui‐yu , Zeng Jun , Huang Ling , Lv Chuan‐zhu 
Published: December 2023

AbstractCA is a plant derivative with antibacterial and antiviral pharmacological effects, however, the therapeutic effect of CA on Klebsiella pneumonia and its mechanism study is still unclear. A rat KP model was established in vitro, a pneumonia cell model was established in vivo, the histopathological changes in the lungs were observed by HE staining after CA treatment, the expression of relevant inflammatory factors was detected by ELISA, the changes in the expression of proteins related to the AhR‐Src‐STAT3‐IL‐10 signaling pathway were detected by Western blot and immunofluorescence in the lungs, and the interactions between the proteins were verified by COIP relationship. The results showed that CA was able to attenuate the injury and inflammatory response of lung tissues, and molecular docking showed that there were binding sites between CA and AhR, and COIP demonstrated that AhR interacted with both STAT3 and Ser. In addition, CA was able to up‐regulate the expression levels of pathway‐related proteins of AhR, IL‐10, p‐Src, and p‐STAT3, and AhR knockdown was able to reduce LPS‐induced inflammatory responses and up‐regulate pathway‐related proteins, whereas CA treatment of AhR‐knockdown‐treated A549 cells did not show any statistically significant difference compared with the AhR knockdown group, demonstrating that CA exerts its pharmacological effects. These findings elucidated the mechanism of CA in the treatment of KP and demonstrated that CA is a potential therapeutic agent for KP.
Repeated intratracheal instillation of whole‐cigarette smoke condensate to assess lung damage in a rat model
Authors: Kim Jinhee , Cho Yoon , Oh Gi‐Jun , Park Hae‐Bin , Yang Mi Jin , Park Chul‐Min , Kim Yong‐Hyun , Choi Kyung‐Chul , Go Ryeo‐Eun , Kim Min‐Seok 
Published: December 2023

AbstractCigarette smoke induces an inflammatory response in the lungs by recruiting inflammatory cells, leading to lung diseases such as lung cancer, chronic obstructive pulmonary disease, and pulmonary fibrosis. Existing inhalation exposure methods for assessing the adverse effects of cigarette smoke require expensive equipment and are labor‐intensive. Therefore, we attempted to develop a novel method to assess these adverse effects using intratracheal instillation (ITI) of whole cigarette smoke condensate (WCSC). The WCSC (0, 5, 10, or 20 mg/mL) was administered by ITI once daily for 6 or 12 days using an automatic video instillator. Repeated WCSC ITI increased the lung weight, and monocyte chemoattractant protein‐1 (MCP‐1), neutrophil, and lymphocyte levels within bronchoalveolar lavage fluid compared to the control. In the histopathological analysis of the lung tissue, a mild inflammatory response was observed in the 6 and 12 days 20 mg/mL WCSC exposure groups. The genome‐wide RNA‐seq expression patterns revealed that inflammatory and immune response‐related genes, such as the chemokine signaling pathway, Th1/Th2 cell differentiation, and cytokine‐cytokine receptor interaction, were employed following WCSC exposure. In addition, MCP‐1 was time‐dependent and increased in the 10 mg/mL exposure group compared to the control group. These results suggested that the WCSC might induce the potential pulmonary inflammatory response. Furthermore, we proposed that ITI may be a rapid and effective method of evaluating the adverse effects of WCSC within a short exposure period (less than 2 weeks), and it can be used to evaluate cigarette inhalation toxicity studies as an alternative method.