bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure, physicochemical properties, and biological activities of protein hydrolysates from Zanthoxylum seed
Authors: Dong Si‐Yu , Li Ying‐Qiu , Sun Xin , Sun Gui‐Jin , Wang Chen‐Ying , Liang Yan , Hua Dong‐Liang , Chen Lei , Mo Hai‐Zhen
Published: December 2023

BACKGROUND

Zanthoxylum seed, as a low‐cost and easily accessible plant protein resource, has good potential in the food industry. But protein and its hydrolysates from Zanthoxylum seed are underutilized due to the dearth of studies on them. This study aimed to investigate the structure and physicochemical and biological activities of Zanthoxylum seed protein (ZSP) hydrolysates prepared using Protamex®, Alcalase®, Neutrase®, trypsin, or pepsin.

RESULTS

Hydrolysis using each of the five enzymes diminished average particle size and molecular weight of ZSP but increased random coil content. ZSP hydrolysate prepared using pepsin had the highest degree of hydrolysis (24.07%) and the smallest molecular weight (<13 kDa) and average particle size (129.80 nm) with the highest solubility (98.9%). In contrast, ZSP hydrolysate prepared using Alcalase had the highest surface hydrophobicity and foaming capacity (88.89%), as well as the lowest foam stability (45.00%). Moreover, ZSP hydrolysate prepared using Alcalase exhibited the best hydroxyl‐radical scavenging (half maximal inhibitory concentration (IC50) 1.94 mg mL−1) and ferrous‐ion chelating (IC50 0.61 mg mL−1) activities. Additionally, ZSP hydrolysate prepared using pepsin displayed the highest angiotensin‐converting enzyme inhibition activity (IC50 0.54 mg mL−1).

CONCLUSION

These data showed that enzyme hydrolysis improved the physicochemical properties of ZSP, and enzymatic hydrolysates of ZSP exhibited significant biological activity. These results provided validation for application of ZSP enzymatic hydrolysates as antioxidants and antihypertensive agents in the food or medicinal industries. © 2023 Society of Chemical Industry.
Characteristics of microplastics in dryland soils after long‐term film mulching and the effect of cropping type in western Liaoning Province, China
Authors: Luo Qing , Zhang Xinyu , Wang Congcong , Yang Ning , Sun Zhanxiang , Feng Liangshan
Published: December 2023

Microplastic (MP) pollution poses a significant environmental challenge on a global scale. In the semi‐arid region of western Liaoning, China, agricultural films have been widely utilized to enhance crop production over an extended period. However, there is a scarcity of research on the presence of MPs in the soil of farmlands in this area. Consequently, a total of 25 dryland soil samples from western Liaoning that had been mulched for more than 10 years and had been used to grow a variety of crops were gathered for the current study. The abundance, particle size, shape, and potential sources of MPs were examined, and the impact of different crop varieties on MPs characteristics was investigated. MPs abundance ranged from 6960 ± 1939 to 34,710 ± 9974 n kg−1, with the average and median of 14,305 ± 7015 and 12,270 ± 1621 n kg−1. MPs with sizes of less than 0.05, 0.05–0.1, and 0.1–0.4 mm were found in 42.7%, 33.8%, and 18.8% of cases, respectively. The most common shapes were fragments, microbeads, and films, with percentages of 47.1%, 22.3%, and 17.9%, respectively. A total of three polymers were found: polyethylene, polypropylene, and polystyrene in a proportion of 44.8%, 43.7%, and 11.5%, respectively. Based on the shape of the MPs, principal component analysis and cluster analysis revealed that the primary sources for MPs may be agricultural mulch, irrigation water, and the weathering of hard plastics like agricultural packaging. Compared to other crop types, soils growing sweet potato and peanut had significantly higher MP abundances. Moreover, soils growing sweet potato had significantly higher percentages of MPs with 0.05–0.1 mm particle size. Regardless of the crop type grown, fragments are the most common shape, while the proportion of other shapes varies depending on the crop type. The aforementioned findings suggest that MP pollution in farmland soil in western Liaoning is more severe and that the kind of crop cultivation affects the characteristics of MPs in the soil.
Novel insights into HBV‐hepatocellular carcinoma at single‐cell sequencing
Authors: Yin Dandan , Zhou Tao , Xia Xuyang , Han Chang , Liu Zhaoqian , Li Qiu , Shu Yang , Xu Heng
Published: December 2023

A significant proportion of hepatocellular carcinoma (HCC) is pathologically associated with hepatitis B virus (HBV) infection, followed by unsatisfied clinical outcomes. The increasing unmet need for HBV‐associated hepatocellular carcinoma (HBV‐HCC) treatment drives to deeper understand the role of the intricate immune microenvironment, tumor cell plasticity and dynamics of tumor evolution in HBV‐associated hepatic carcinogenesis. Thus, a comprehensive understanding of cross‐talk between HBV, host cells, and tumor microenvironment is of fundamental importance for identifying immune imbalance and heterogeneity in HBV‐HCC. Over the past 5 years, the application of single‐cell RNA sequencing (scRNA‐seq) in the understanding of heterogeneity and dynamics of immune cells, clonal evolution, and cancer stem cell (CSC) subsets of tumor cells has established a landscape for HBV‐HCC tumor ecosystem. Novel insights into anatomizing immune escape mechanisms and tumor drug resistance have remarkably facilitated the revolution of HBV‐HCC clinical treatment. Here, we provided a summary of HCC at single‐cell resolution and details on the basic workflow, limitations, and improvements of scRNA‐seq. The review highlights novel insights derived from scRNA‐seq on advances in the immune microenvironment and tumor heterogeneity of HBV‐HCC.
Mechanical response of concrete pipe rehabilitated by liner under external load: Analytical solution
Authors: Zhai Kejie , Fang Hongyuan , Wang Niannian , Li Bin , Dong Jiaxiu , Xue Binghan
Published: December 2023

Using pipe lines to rehabilitate concrete drainage pipes is a popular trenchless technique. In this paper, the concrete pipe and liner are equivalent to a symmetrical structural mechanics problem, and the mechanical solution of the composite structure is obtained using the force method. Subsequently, the analytical solutions are compared with the test and finite element results. The distribution law of axial force, bending moment, and shear force of the composite structure are obtained, and the circumferential strain law of the inner and outer surfaces of the host pipe is analyzed. Lastly, the influence of pipe diameter and liner thickness on the bearing capacity of the host pipe is examined. The results indicate that the axial and shear force distribution of the composite structure remains the same for different pipe diameters, as the distribution diagrams of shear and axial force along the circumferential direction coincide. While the elastic modulus and thickness of the liner have no effect on the internal force distribution of the composite structure, they do directly affect the stress state of the host pipe. Additionally, the bottom support causes abrupt changes in the bending moments and strains of the host pipe.
Museum experience and its impact on visitor reactions
Authors: Addis Michela , Copat Valentina , Martorana Cecilia
Published: December 2023

Designing engaging visitor experiences has become a paramount concern for museums; however, a comprehensive understanding of the impact of museum experiences on visitors' reactions remains incomplete. Our paper aims to assist museums in implementing more effective strategies. By examining three distinct characteristics of museum experiences—subjectivity, multidimensionality, and co‐creation—we formulate four hypotheses to assess the influence of visitor journeys on their reactions. We concentrate on the journey at the Capitoline Museums, employing qualitative and quantitative methods (in‐depth interviews, subjective personal introspection, non‐participant observation, and questionnaires) involving 110 participants. Our findings indicate that (a) Visitor attitudinal and behavioral reactions exhibit consistency for the overall experience but not when analyzed for specific areas; (b) Visitor satisfaction is correlated with the number of companions but not with the number of visited areas in the museum experience; (c) Visitor's apparent dominance over visitor satisfaction is not linked to visitor satisfaction. We develop a managerial decision‐making framework that empowers museums to create captivating experiences for their visitors.
Control‐oriented models of the shallow water equations using energy‐conserving discretization schemes
Authors: Mayer Luca , Wurm Jens , Woittennek Frank
Published: December 2023

In this study, we introduce higher‐order approximation schemes for a 1D shallow‐water model with a moving boundary and arbitrary cross‐section. The model equations are formulated using Lagrange coordinates to handle the time‐varying spatial domain. By discretizing the action functional on a material‐fixed grid and applying an appropriate quadrature scheme, we derive a finite‐dimensional model. This model, taking mass conservation into account as an auxiliary condition, results in a system of semi‐explicit differential‐algebraic equations (DAE). Unlike previous work, we employ higher‐order quadrature formulae to enhance numerical accuracy, albeit at the cost of more complex nonlinear DAE. In order to compare the performance of the resulting models obtained from using different quadrature schemes, a comprehensive simulation study is conducted.
Soybean oil‐based nanocomposites for dye adsorption: AESO‐chitosan‐graphene oxide synergy in water treatment
Authors: Dare Masoud Tavakoli , Bazmi Maryam , Khosravi Amirhosein , Monem Mohammad , Jafari Aliakbar , Khonakdar Hossein Ali
Published: December 2023

This study presents the synthesis and characterization of a bio‐adsorbent (A‐C2‐G3) based on the acrylated epoxidized soybean oil (AESO) for the efficient removal of methylene blue (MB) dye from aqueous solutions. The adsorbent was synthesized by incorporating chitosan and nano graphene oxide into the AESO matrix, followed by crosslinking through the UV curing process. The effects of various parameters, including pH, contact time, initial dye concentration, adsorbent dosage, and ionic strength, on the adsorption performance were systematically investigated. The experimental data were best fitted by the Langmuir isotherm model, suggesting a monolayer adsorption process, with a maximum adsorption capacity of 263.87 mg g−1. The adsorption kinetics followed the pseudo‐second‐order model, indicating the significance of electron exchange between the adsorbate and adsorbent during the process. Three primary interaction mechanisms at the interface between MB and A‐C2‐G3 and the A‐C2‐G3 bio‐adsorbent were identified: electrostatic interactions, hydrogen bond formation, and π–π stacking. The reusability of the synthesized adsorbent was evaluated through a series of adsorption–desorption cycles, maintaining high adsorption capacities for up to three cycles. These findings highlight the potential of the AESO‐based bio‐adsorbent for effective MB dye removal from wastewater.
Assessing computational tools for predicting protein stability changes upon missense mutations using a new dataset
Authors: Zheng Feifan , Liu Yang , Yang Yan , Wen Yuhao , Li Minghui
Published: December 2023

Insight into how mutations affect protein stability is crucial for protein engineering, understanding genetic diseases, and exploring protein evolution. Numerous computational methods have been developed to predict the impact of amino acid substitutions on protein stability. Nevertheless, comparing these methods poses challenges due to variations in their training data. Moreover, it is observed that they tend to perform better at predicting destabilizing mutations than stabilizing ones. Here, we meticulously compiled a new dataset from three recently published databases: ThermoMutDB, FireProtDB, and ProThermDB. This dataset, which does not overlap with the well‐established S2648 dataset, consists of 4038 single‐point mutations, including over 1000 stabilizing mutations. We assessed these mutations using 27 computational methods, including the latest ones utilizing mega‐scale stability datasets and transfer learning. We excluded entries with overlap or similarity to training datasets to ensure fairness. Pearson correlation coefficients for the tested tools ranged from 0.20 to 0.53 on unseen data, and none of the methods could accurately predict stabilizing mutations, even those performing well in anti‐symmetric property analysis. While most methods present consistent trends for predicting destabilizing mutations across various properties such as solvent exposure and secondary conformation, stabilizing mutations do not exhibit a clear pattern. Our study also suggests that solely addressing training dataset bias may not significantly enhance accuracy of predicting stabilizing mutations. These findings emphasize the importance of developing precise predictive methods for stabilizing mutations.
Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data
Authors: Ravichandran Ashwin , Araque Juan C. , Lawson John W.
Published: December 2023

Protein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure–function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient‐weighted Class Activation Mapping for graphs (Graph Grad‐CAM) to automatically identify structurally important residues and residue‐residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad‐CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well‐known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad‐CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub‐classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high‐throughput identification of protein structure–function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
Metameric influences on conformational selectivity for zwitterionic pyridinium cyclopentadienide and its aza analogues. Quantum mechanical studies on linear and nonlinear optoelectronic properties
Authors: Sitha Sanyasi
Published: December 2023

This contribution reports the structure–property correlations for few already synthesized bi‐aryl types of zwitterionic molecules. Quantum mechanical methodologies like, HF, MP2, B3LYP, CAM‐B3LYP, LC‐ωPBE, M06‐2X, and ωB97xD were used to investigate the optoelectronic properties of some interesting metameric pairs, where the molecules were bonded either through Reichardt's or Brooker's modes. Different bonding modes and inter‐ring attractive forces are assigned to investigate three distinct cases (i) metameric enforcements & preferential resonance stabilizations, (ii) inter‐ring hydrogen bonded stabilizations through hetero‐atoms in the ring, and (iii) an amalgamation of these two forces. Computations indicate unusual structural preferences (planar vs. twisted) by the metameric pairs, and thus direct reflections of these behaviors on some of the important tensorial properties like, dipole moments, polarizabilities, hyperpolarizabilities, and so forth were observed. The metameric manipulation on structure–property correlations shown by these molecules can be utilized as useful strategies for efficient chromophore design, not only in the field of nonlinear optics, but also in other areas of research connecting to advanced functional materials for technological applications.
A fast, accurate and uncalibrated robotic puncture method
Authors: Li ShangHong , Wang Qiwan , Yan Biao , Yang Rongqian , Zhan Yinwei
Published: December 2023

Background

Robotic puncture system (RPS) consists of an optical tracking system (OTS) and a robotic arm gripping the puncture needle. Typically, the RPS requires hand‐eye calibration before the surgery in order to obtain the relative position between the OTS and the robotic arm. However, if there is any displacement or angular deviation in either the robotic arm or the OTS, the calibration results become invalid, necessitating recalibration.

Methods

We propose an uncalibrated robotic puncture method that does not rely on the hand‐eye relationship of the RPS. By constructing angle and position graph jacobian matrices respectively, and employing Square Root Cubature Kalman Filter for online estimation. This enables obtaining control variables for the robot to perform puncture operations.

Results

In simulation experiments, our method achieves an average error of 1.3495 mm and an average time consumption of 39.331 s.

Conclusions

Experimental results indicate that our method possesses high accuracy, low time consumption, and strong robustness.
The changing epidemiology of preterm labour and delivery: A systematic literature review
Authors: Li Tina , Rochon Hannah , Szabo Shelagh M. , Kourmaeva Emilia , Manuel Megan , Patel Vanessa Perez
Published: December 2023

Objective

To identify and synthesize epidemiologic data for preterm labour (PTL) and preterm birth (PTB).

Methods

A systematic search, with protocol registered in PROSPERO, was implemented in MEDLINE and EMBASE and supplemented by web‐based and grey literature searches. Observational, population‐based studies in the United States, Canada, United Kingdom, France, Germany, Spain, and Italy, published in English between 2012 and 2022 were considered for inclusion. Estimates by country were reported and stratified by gestational age, birth plurality, and race/ethnicity, data permitting.

Results

Ten publications and nine grey literature reports were included. Epidemiologic estimates of PTL were reported for the United Kingdom and France: PTL was diagnosed in 2.2% of pregnancies and preceded 50% of PTBs. PTB rates were reported for the United States, Canada, United Kingdom, France, and Spain. Among live births in these countries, annual PTB incidence ranged from 5.9% (Spain, 2020) to 10.2% (United States, 2019). Most countries reported the PTB incidence by gestational age; reports by birth plurality or race/ethnicity were scarce. PTB rates for Germany or Italy were not identified.

Conclusions

While PTBs were well‐reported overall and by gestational age, how rates varied by plurality, race/ethnicity and etiology is unclear. Epidemiologic estimates for PTL, a leading cause of PTB, were rarely reported in the literature. Population‐based research is needed to understand the burden of PTL and for decision making regarding the management of this condition.
Revealing cation and metal gradients in and underneath passive films of the stainless steel 1.4652 in acidic and alkaline electrolytes with angular resolved dual energy X‐ray photo‐electron spectroscopy
Authors: Olsson Claes‐Olof A. , Hauert Roland , Neus Igual‐Muñoz Anna , Mischler Stefano , Schmutz Patrik
Published: December 2023

Passive films on the superaustenitic stainless steel 1.4652 were studied using angular resolved hard X‐ray photo‐electron spectroscopy (HAXPES), which provides an increased information depth compared to conventional X‐ray photo‐electron spectroscopy (XPS). Elemental depth profiles in the oxide as well as gradients in the underlying metal were established using a dedicated algorithm. The utility was exemplified for three different conditions of film formation: (i) as polished and as polarized to the high passive end in (ii) 1 M H2SO4 and (iii) 1 M NaOH. The use of a superaustenitic material ascertained that metal signals from the main contributors to film formation: Fe, Cr, Ni, and Mo remained above the detection limit throughout the data set. With the dual‐source technique (XPS, HAXPES), it was possible to investigate metal gradients underneath the passive film. For polarizations in an acidic environment, a metallic nickel enrichment of the order of 5 Å was found. For a corresponding polarization in an alkaline environment, the metal region closest to the oxide/metal interface was enriched in iron, followed by concentration gradients down to about 50 Å into the metal.
Multiply robust estimation of natural indirect effects with multiple ordered mediators
Authors: Tai An‐Shun , Lin Sheng‐Hsuan
Published: December 2023

Multiple mediation analysis is a powerful methodology to assess causal effects in the presence of multiple mediators. Several methodologies, such as G‐computation and inverse‐probability‐weighting, have been widely used to draw inferences about natural indirect effects (NIEs). However, a limitation of these methods is their potential for model misspecification. Although powerful semiparametric methods with high robustness and consistency have been developed for inferring average causal effects and for analyzing the effects of a single mediator, a comparably robust method for multiple mediation analysis is still lacking. Therefore, this theoretical study proposes a method of using multiply robust estimators of NIEs in the presence of multiple ordered mediators. We show that the proposed estimators not only enjoy the multiply robustness to model misspecification, they are also consistent and asymptotically normal under regular conditions. We also performed simulations for empirical comparisons of the finite‐sample properties between our multiply robust estimators and existing methods. In an illustrative example, a dataset for liver disease patients in Taiwan is used to examine the mediating roles of liver damage and liver cancer in the pathway from hepatitis B/C virus infection to mortality. The model is implemented in the open‐source R package “MedMR.”
Interface‐Guided Computational Protein Design Reveals Bebtelovimab‐Resistance Mutations in SARS‐CoV‐2 RBD: Correlation with Global Viral Genomes and Bebtelovimab‐Escape Mutations
Authors: Maurya Shweata , Kumar Shivank , Padhi Aditya K.
Published: December 2023

The emergence of novel mutations in the SARS‐CoV‐2 spike protein challenges monoclonal antibody (mAb) effectiveness. Comprehending resistance mutations and pinpointing vulnerable spike protein residues is vital for enhanced antibody design. To address this issue, we employed an interface‐guided computational protein design (CPD) approach to decode bebtelovimab‐resistance mutations and uncover susceptible residues within the receptor‐binding domain (RBD). Utilizing structural‐modeling and high‐throughput techniques, we mapped the bebtelovimab‐RBD interface, identifying critical resistance mutations through analysis of binding energetics and residue interactions. Our design protocol integrated stability predictions, side‐chain conformational sampling, and binding affinity calculations to prioritize substitutions that restore antibody recognition and neutralization. Previously unexplored susceptible RBD residues were also discovered, offering new therapeutic avenues. Comparative analysis with COVID‐19 patient data validated the predicted resistance mutations (69 %–100 % correlation, based on different MinProp cut‐offs). Precision and recall values, calculated by comparing our predictions with experimentally reported bebtelovimab‐escape mutants, demonstrated the performance and accuracy of our predictions. Investigation of intermolecular interactions highlighted the importance of van der Waals forces, hydrogen bond energy, and electrostatic contributions in bebtelovimab‐RBD binding affinity. This computational design empowers the decoding of resistance mutations and the development of next‐generation antibodies against viral variants, strengthening our response to SARS‐CoV‐2 and related coronaviruses.
Divergent Strategy for the Synthesis of Indolopyrazines Fused to Benzopyrimidinones and Benzimidazoles: Identification of Antiproliferative Molecules
Authors: Alkubaisi Bilal O. , Sebastian Anusha , Bauer Maximilian , Sultan Shaista , El‐Awady Raafat , Wehbe Ayeh , Yassin Mariam , Vunnam Srinivasulu , El‐Gamal Mohammed I. , Al‐Tel Taleb H.
Published: December 2023

Despite the continued efforts and advancements in anti‐cancer drug discovery, cancer is still considered as one of the leading causes of mortality globally. Hence, the discovery of novel chemotherapeutic agents that displayed a prominent effect against cancer is a pressing need. In this study, an expeditious cascade was used to access a pilot library of indolopyrazine fused to imidazole and pyrimidinone heterocyclic scaffolds. The synthetic strategy utilized a cascade reaction that combined Mannich with aza‐Michael addition reactions followed by coupling with a variety of amines. Phenotypic screening of the developed library against HCT116 colon and MCF‐7 breast cancer cell lines identified chemotypes that formed the basis for hit‐to‐lead development of anti‐cancer agents. The intriguing architecture and scope of functional variability of these types of pentacyclic molecules made them appropriate motifs for the development of lead drug candidates.
Effective Photocatalytic Ethanol Reforming into High‐Value‐Added Multicarbon Compound Coupled with H2 Production Over Pt‐S3 Sites at PtSA–ZnIn2S4 Interface
Authors: Wu Shiting , Li Xiaohui , Liu Jiaqi , Wu Hanfeng , Xu Hanshuai , Bai Wangfeng , Mao Liang , Shi Xiaowei
Published: December 2023

Selective photocatalytic production of high‐value acetaldehyde concurrently with H2 from bioethanol is an appealing approach to meet the urgent environment and energy issues. However, the difficult ethanol dehydrogenation and insufficient active sites for proton reduction within the catalysts, and the long spatial distance between these two sites always restrict their catalytic activity. Here, guided by the strong metal‐substrate interaction effect, an atomic‐level catalyst design strategy to construct Pt‐S3 single atom on ZnIn2S4 nanosheets (PtSA‐ZIS) is demonstrated. As active center with optimized H adsorption energy to facilitate H2 evolution reaction, the unique Pt single atom also donates electrons to its neighboring S atoms with electron‐enriched sites formed to activate the O─H bond in *CH3CHOH and promote the desorption of *CH3CHO. Thus, the synergy between Pt single atom and ZIS together will reduce the energy barrier for the ethanol oxidization to acetaldehyde, and also narrow the spatial distance for proton mass transfer. These features enable PtSA‐ZIS photocatalyst to produce acetaldehyde with a selectivity of ≈100%, which will spontaneously transform into 1,1‐diethoxyethane via acetalization to avoid volatilization. Meanwhile, a remarkable H2 evolution rate (184.4 µmol h−1) is achieved with a high apparent quantum efficiency of 10.50% at 400 nm.
Smart DNA sensors‐based molecular identification for cancer subtyping
Authors: Gao Yingying , Xiong Mengyi , Gong Chaonan , Wang Bo , Bai Longwei , Zhang Xiao‐Bing
Published: December 2023

Molecular subtyping of cancer can greatly help to understand the development of disease and predict tumor behavior. Exploring detection methods for precise subtyping is appealing to prognosis and personalized therapy. During the past decades, DNA‐based biosensors have exhibited great potential in cancer diagnosis due to their structural programmability and functional diversity. Despite the encouraging progress that has been made, there remains an issue in improving the accuracy and sensitivity of cancer subtyping due to the complex process of disease, especially in preclinical or clinical applications. To accelerate the development of DNA sensors in the identification of cancer subtypes, in this review, we summarized their advances in molecular subtyping by analyzing the heterogeneity in categories and levels of biomarkers between cancer subtypes. The strategies toward genomic and proteomic heterogeneity in cells or on the cell surface, as well as the cancer excretions including extracellular vesicles (EVs) and microRNA (miRNAs) in serum, are summarized. Current challenges and the opportunities of DNA‐based sensors in this field are also discussed.
A Comprehensive Review on Non‐Trivalent Bismuth‐Based Materials: Structure, Synthesis, and Strategies for Improving Photocatalytic Performance
Authors: Han Qiaofeng , Ding Huiwei , Wang Zhihao
Published: December 2023

Bi‐based semiconducting materials have received tremendous attention due to their availability, non/low toxicity, ecological friendship, rich chemical forms, and good visible‐light‐driven photocatalytic performance. As compared to the commonly investigated trivalent bismuth (Bi(III))‐based photocatalysts, non‐trivalent bismuth‐based materials (NTBBMs), such as BiO2−x, Bi2O4−x, Bi4O7, NaBiO3, and so on, exhibit excellent visible‐light‐ and even full‐spectrum‐driven photocatalytic activity as they hold narrow bandgap, suitable positions of conduction band and valence band, and relatively redox‐sensitive structures. In this review, it is attempted to summarize the recent progress in the preparation, microstructures, and modification strategies of various NTBBMs‐based photocatalysts. At the end, the advantages and disadvantages of NTBBMs‐based photocatalysts and future perspectives are presented.
FLight: A lightweight federated learning framework in edge and fog computing
Authors: Zhu Wuji , Goudarzi Mohammad , Buyya Rajkumar
Published: December 2023

The number of Internet of Things (IoT) applications, especially latency‐sensitive ones, have been significantly increased. So, cloud computing, as one of the main enablers of the IoT that offers centralized services, cannot solely satisfy the requirements of IoT applications. Edge/fog computing, as a distributed computing paradigm, processes, and stores IoT data at the edge of the network, offering low latency, reduced network traffic, and higher bandwidth. The edge/fog resources are often less powerful compared to cloud, and IoT data is dispersed among many geo‐distributed servers. Hence, Federated Learning (FL), which is a machine learning approach that enables multiple distributed servers to collaborate on building models without exchanging the raw data, is well‐suited to edge/fog computing environments, where data privacy is of paramount importance. Besides, to manage different FL tasks on edge/fog computing environments, a lightweight resource management framework is required to manage different incoming FL tasks while does not incur significant overhead on the system. Accordingly, in this article, we propose a lightweight FL framework, called FLight, to be deployed on a diverse range of devices, ranging from resource‐limited edge/fog devices to powerful cloud servers. FLight is implemented based on the FogBus2 framework, which is a containerized distributed resource management framework. Moreover, FLight integrates both synchronous and asynchronous models of FL. Besides, we propose a lightweight heuristic‐based worker selection algorithm to select a suitable set of available workers to participate in the training step to obtain higher training time efficiency. The obtained results demonstrate the efficiency of the FLight. The worker selection technique reduces the training time of reaching 80% accuracy by 34% compared to sequential training, while asynchronous one helps to improve synchronous FL training time by 64%.
Designing access control security protocol for Industry 4.0 using Blockchain‐as‐a‐Service
Authors: Vangala Anusha , Das Ashok Kumar , Kumar Neeraj , Vijayakumar Pandi , Karuppiah Marimuthu , Park Youngho
Published: December 2023

Industry 4.0 is a revolution of the operations in the industrial manufacturing for increased productivity, trade and commerce. It is heavily reliant on the automation of the processes and equipment along with complex interconnectivity and insightful analysis using machine learning. The interconnectivity of the manufacturing devices from various industrial sites brings with it several security issues related to communication. This article focuses on solving the security issue of access control between such devices and enable seamless secure communication for the proper functioning of the industry. An access control scheme has been proposed that achieves the necessary security features of anonymity, traceability, and forward secrecy. It is also shown that the proposed scheme takes less communication and computational costs, and is strongly resilient against various attacks such as impersonation attack, replay attack, and denial‐of‐service attack as compared to other relevant schemes.
Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed
Authors: Singer William M. , Lee Yi‐Chen , Shea Zachary , Vieira Caio Canella , Lee Dongho , Li Xiaoying , Cunicelli Mia , Kadam Shaila S. , Khan Mohammad Aamir Waseem , Shannon Grover , Mian M. A. Rouf , Nguyen Henry T. , Zhang Bo
Published: December 2023

Soybean [Glycine max (L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end‐uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and amino acids, oil and fatty acids, carbohydrates, and specific food‐grade considerations; discusses the application of advanced breeding technology such as CRISPR/Cas9 in creating seed composition variations; and provides future directions and breeding recommendations regarding soybean seed composition traits.
The value of soil temperature data versus soil moisture data for state, parameter, and flux estimation in unsaturated flow model
Authors: Kandala Rajsekhar , Franssen Harrie‐Jan Hendricks , Chaudhuri Abhijit , Sekhar M.
Published: December 2023

This synthetic study explores the value of near‐surface soil moisture and soil temperature measurements for the estimation of soil moisture and soil temperature profiles, soil hydraulic and thermal parameters, and latent heat and sensible heat fluxes using data assimilation (ensemble Kalman filter) in combination with unsaturated zone flow modeling (HYDRUS‐1D), for 12 United States Department of Agriculture soil textures in a homogeneous and bare soil scenario. The soil moisture profile is estimated with a root mean square error (RMSE) of 0.04 cm3/cm3 for univariate soil temperature assimilation and 0.01 cm3/cm3 for univariate soil moisture assimilation. Soil temperature assimilation performs better for soils with higher clay content compared to soils with higher sand content. The latent and sensible heat fluxes are estimated with smaller RMSE for univariate soil temperature assimilation compared to univariate soil moisture assimilation for 8 out of 12 soil types. As the climate condition changes from hot semi‐arid to sub‐humid climate, the soil moisture assimilation performs better for high permeable soil but worse for low permeable soil. In summary, the findings suggest that for most soil texture classes, assimilating soil temperature in vadose zone models is skillful to improve latent heat flux, soil moisture profile, and soil hydraulic parameters. Joint assimilation with soil moisture can further enhance the accuracy of the model outputs for all range of soil texture and climate conditions.
Creolizing Science in Mayra Montero’s Palm of Darkness
Authors: Mardorossian Carine M. , Wong Angela Veronica
Published: December 2023

Through a discussion of Mayra Montero’s In the Palm of Darkness, this chapter examines and challenges what Caribbean novelist Wilson Harris identified as “the break which occurred between science and art, science and an imaginative psychological, even magical apprehension of the universe” (41). The novel reveals that it is in the violent subjugation of women that the costs of such a break are most visibly articulated. Montero’s narrative represents an Afro-Caribbean cosmology that is more open to enfolding other realities and knowledges (including a scientific one) in contrast to a Western and hierarchical worldview that defines itself through its dismissal of otherness and alternative epistemologies. At the same time, both approaches are taken to task for the triangulating structures through which they may seek to project their own authority via an erasure of femininity. As such, the novel schematizes a form of “creolizing science” that recognizes usually opposed dimensions of human existence as compatible, creolized forms of knowledge and identity that do not undo difference so much as “enfold the spirit of those who ignore your glory” (In the Palm of Darkness 181).
Monstrous Genealogies: Indo-Caribbean Feminist Reckonings with the Violent Past
Authors: Outar Lisa
Published: December 2023

This chapter explores the ways in which three contemporary Indo-Caribbean women writers trouble traditional understandings of teleology, genealogy, and the divide between the “natural” and “unnatural,” revealing the hauntings of characters by intergenerational trauma and secrets and by specters of gendered violence that rupture conventional temporalities. I examine Ingrid Persaud’s 2020 novel Love After Love, Vashti Bowlah’s 2015 short story “The Churile of Sugarcane Valley,” and Krystal M. Ramroop’s 2020 short story “Midnight’s Mischievous Mistress” to show how these writers redirect images of monstrous femininity contained both within patriarchal understandings of gender roles and within Caribbean folklore. I trace Persaud’s engagement with alternate models of powerful femininity to be found in kali mai worship and her offering of examples of cleansing violence via both ritual practices of creolized Indo-Caribbean religion and the erotic application of pain in a dominatrix/submissive relationship. And, following the work of scholars such as Giselle Anatol who explore how that which is repressed and denigrated about womanhood emerges in Caribbean folkloric figures, I examine the reclaiming of such monstrous figures as the churile and the diablesse by Bowlah and Ramroop for their own imaginings of violence’s role in the furthering of feminist visions of justice.
Ukrainian Prison Officers and Their Power
Authors: Symkovych Anton
Published: December 2023

Finding research on prison officers that does not emphasise their importance—even centrality—to prisons’ daily operation and to the implementation of prison ambition more generally proves almost impossible. Even so, depending on jurisdiction, uniformed prison staff’s portrayals range from ‘czars and gods’ to disempowered and hectored conductors of penal power that merely flows through them. Power lies at the heart of prison—prisonis about power. In the current chapter, drawing on the case of Ukrainian prison officers, I discuss how officers in the same prison can understand and deploy their power differently. I underscore the limitation of presenting them as a dichotomy of a ‘powerful/powerless’ homogeneous group and explain how cultural legacies, legal and organisational ramifications of the anomic society in transition, and officers’ personal views, priorities, and considerations of legitimacy frame officers’ use of power. I highlight that even in a country where prisoners enjoy limited rights and the state grants staff enormous power, prison officers must inhabit their power carefully and maintain prisoners’ alignment to preserve workable order.
Introduction
Authors: Schauer Gila A.
Published: December 2023

In this chapter, I address why it is important and necessary to conduct research on the relationship between intercultural competence and pragmatics. I then provide information on the data collection instrument, the participants and the research questions of this study. This is followed by an overview of the content of the individual chapters in this book.
Methodology
Authors: Schauer Gila A.
Published: December 2023

In this chapter, I first provide background information on the modern foreign language teachers who completed the questionnaire on which the present study about intercultural competence and pragmatics is based. This includes details about their ages, gender identities, native languages, higher education background and L2 teaching experiences, as well as the modern foreign language(s) they were teaching and their teaching contexts. I then provide information on the online survey and its individual items. This is followed by information on the research procedure. The questionnaire that was used in the present study can be found in the Appendix of this chapter.
Results: Components of Intercultural Competence
Authors: Schauer Gila A.
Published: December 2023

In this chapter, I analyse and discuss the answers that the language teachers gave in questions 2 and 3 of the survey about intercultural competence and pragmatics; these two questions focus on the components of intercultural competence. Question 2 is a multiple-choice question featuring 24 potential components of intercultural competence ranging from ability to produce situationally appropriatelanguage to tolerance, and thus presented a variety of options—representing abilities, knowledge, skills and attitudes or characteristics—from which the teachers could choose. Question 3 is a yes/no question (that also included a don’t know option) and concentrates on the linguistic components of intercultural competence. It included 12 items ranging from acronyms and abbreviations to swear wordsand taboo language.
The Metabolic Theory of Ecology as a Mechanistic Approach
Authors: Martins Gonçalo
Published: December 2023

Philosophy of science has recently given a great deal of attention to the concept of mechanism. However, unlike the biological mechanisms identified in other fields of the life sciences, ecological mechanisms have not been exhaustively examined. The aim of this chapter is to critically analyze the Metabolic Theory of Ecology. This theory is supposed to provide a unification of population, community and ecosystem approaches rooted in the ecophysiology of individual organisms. In this context, metabolism plays a fundamental role as the unifying concept between levels. According to its authors, this is a mechanistic approach to ecology involving decomposability into parts that structure the different levels of ecological organization and into mechanisms that can be characterized by identifying a phenomenon, parts, causing, and organization. I shall first argue that its mechanistic nature needs clarification. I shall then suggest that the theory can explain some phenomena at various levels of ecological organization and can describe some patterns or tendencies in nature, although it is not able to completely elucidate their mechanistic basis, i.e., to explain the mechanisms that produce these patterns.
Causing and Composing Evolution: Lessons from Evo-Devo Mechanisms
Authors: Villegas Cristina
Published: December 2023

Evolutionary developmental biology (evo-devo) is often vindicated by theoreticians of the field as a mechanistic science that brings a mechanistic perspective into evolutionary biology. Usually, it is also portrayed as stressing the causal role that development plays in the evolutionary process. However, mechanistic studies in evo-devo typically refer to lineage-specific transformations and lack the generality that evolutionary explanations usually aim for. After reviewing the prospects and limits of a mechanistic view of evo-devo and their studies of homology and novelty, in this chapter I propose a way to combine the mechanistic view of evo-devo with the population-level inclination of more classical approaches to evolution. Such a proposal provides a philosophical framework for understanding the causal role of development in evolution both as mechanistic and as generalizable, population-level.
Organisms Need Mechanisms; Mechanisms Need Organisms
Authors: Bechtel William , Bich Leonardo
Published: December 2023

According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little to say about how mechanisms relate to the organism in which they reside. A key feature of organisms, emphasized by the autonomy tradition, is that organisms maintain themselves. To do this, they rely on mechanisms. But mechanisms must be controlled so that they produce the phenomena for which they are responsible when and in the manner needed by the organism. To account for how they are controlled, we characterize mechanisms as sets of constraints on the flow of free energy. Some constraints are flexible and can be acted on by other mechanisms, control mechanisms, that utilize information procured from the organism and its environment to alter the flexible constraints in other mechanisms so that they produce phenomena appropriate to the circumstances. We further show that control mechanisms in living organisms are organized heterarchically—control is carried out primarily by local controllers that integrate information they acquire as well as that which they procure from other control mechanisms. The result is not a hierarchy of control but an integrated network of control mechanisms that has been crafted over the course of evolution.
Searching for Protein Folding Mechanisms: On the Insoluble Contrast Between Thermodynamic and Kinetic Explanatory Approaches
Authors: Vallejos-Baccelliere Gabriel , Vecchi Davide
Published: December 2023

The protein folding problem is one of the foundational problems of biochemistry and it is still considered unsolved. It basically consists of two main questions: what are the factors determining the stability of the protein’s native structure and how does the protein acquire it starting from an unfolded state. Since its first formulation, two main explanatory approaches have dominated the field of protein folding research: a thermodynamic approach focused on energetic features and a kinetic approach focused on the temporal development of protein chains and structural considerations. Although these two approaches are tightly intertwined in biochemical practice and largely agree on which are the parts and activities in which the phenomenon under study should be decomposed to, there nevertheless exist important contrasts that have had repercussions on the development of the field and still engender vigorous debate. We shall analyse the historical development of the field and crucial aspects of current scientific debates. On this basis, we argue that the main sources of disagreement centre on the causal interpretation of thermodynamic and kinetic explanations, on the explanatory relevance assigned to different features of the phenomena under study and on the status of the ontological assumptions concerning the entities under study.