bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self‐contacting Cys, Ser, and Thr residues in high‐resolution protein crystal structures: Tertiary constraints or hydrogen bonds?
Authors: Singh Prathvi , Ramanathan Venkatnarayanan , Sankararamakrishnan Ramasubbu 
Published: November 2024

AbstractFunctional groups in the side‐chains of at least 10 amino acids are mainly involved in tertiary interactions. However, structural and functional significance of intra‐residue interactions has not been fully recognized. In this study, we have analyzed ~5800 non‐redundant high‐resolution protein structures and identified 1166 self‐contacts between the side‐chain S‐H/O‐H and backbone C=O groups in Cys, Ser, and Thr residues that satisfied the geometric criteria to form hydrogen bonds. Quantum chemical calculations using model compounds were used to evaluate single point energy for 45 representative examples from different allowed regions of Ramachandran map. Relative energy profiles obtained by varying the side‐chain dihedral angle χ1 revealed that the energy difference between the crystal structure and the minimum energy conformations is between 0 and 3 kcal/mol. Natural bond orbital analysis (NBO) of self‐contacting Cys residues revealed no charge transfer between Cys side‐chain S‐H and the backbone C=O groups. However, side‐chain hydroxyl and the backbone C=O groups of 90%–95% of all self‐contacting Ser and Thr residues are involved in charge transfer and the second order perturbation energy of majority of them is above 1 kcal/mol. Interaction energies calculated for model compounds along with NBO and NCIPLOT analyses demonstrate that the self‐contacts observed in Ser and Thr residues can be described as hydrogen bonds. These interactions may provide stability to the loop/coil conformations. Self‐contacting Cys residues are buried and the self‐contacts appear to be mostly due to tertiary constraints. Dispersion between the self‐contacting groups is one way to explain the close approach in Cys residues. Mutation studies will further validate and reveal the structural and functional significance of these self‐contacting residues.
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Authors: Liu Zhuoyi , Grigas Alex T. , Sumner Jacob , Knab Edward , Davis Caitlin M. , O'Hern Corey S. 
Published: November 2024

AbstractProteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non‐physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo. Inter‐residue distances measured in vivo can be incorporated as restraints in molecular dynamics (MD) simulations to model protein structural dynamics in vivo. Since most FRET studies only obtain inter‐residue separations for a small number of amino acid pairs, it is important to determine the minimum number of restraints in the MD simulations that are required to achieve a given root‐mean‐square deviation (RMSD) from the experimental structural ensemble. Further, what is the optimal method for selecting these inter‐residue restraints? Here, we implement several methods for selecting the most important FRET pairs and determine the number of pairs that are needed to induce conformational changes in proteins between two experimentally determined structures. We find that enforcing only a small fraction of restraints, , where is the number of amino acids, can induce the conformational changes. These results establish the efficacy of FRET‐assisted MD simulations for atomic scale structural modeling of proteins in vivo.
Characterization of DsrD and its interaction with the DsrAB dissimilatory sulfite reductase
Authors: Barbosa Ana C. C. , Venceslau Sofia S. , Ferreira Delfim , Neukirchen Sinje , Sousa Filipa L. , Melo Manuel N. , Pereira Inês A. C. 
Published: November 2024

AbstractMicrobial dissimilatory sulfate reduction is a key process in the global sulfur and carbon cycles in anoxic ecosystems. In this anaerobic respiration, sulfate is phosphorylated and reduced to sulfite, which is further reduced to a DsrC‐trisulfide by the dissimilatory sulfite reductase DsrAB. DsrD is a small protein that acts as an allosteric activator of DsrAB, increasing the efficiency of sulfite reduction. Here, we report a detailed study of DsrD and its interaction with DsrAB. Sequence similarity analyses show that there are three groups of DsrD in organisms with a reductive‐type DsrAB. The protein regions involved in the DsrD–DsrAB interaction and activity‐promoting effect were investigated through in vitro and in silico studies, including mutations of conserved DsrD residues. The results reveal that the conserved β‐loop of DsrD is involved in the interaction, contributing to a better understanding of its mechanism of action.
Unraveling the Structural Basis of Biased Agonism in the β2‐Adrenergic Receptor Through Molecular Dynamics Simulations
Authors: Plazinski Wojciech , Archala Aneta , Jozwiak Krzysztof , Plazinska Anita 
Published: November 2024

ABSTRACTBiased agonism in G protein‐coupled receptors is a phenomenon resulting in the selective activation of distinct intracellular signaling pathways by different agonists, which may exhibit bias toward either Gs, Gi, or arrestin‐mediated pathways. This study investigates the structural basis of ligand‐induced biased agonism within the context of the β2‐adrenergic receptor (β2‐AR). Atomistic molecular dynamics simulations were conducted for β2‐AR complexes with two stereoisomers of methoxynaphtyl fenoterol (MNFen), that is, compounds eliciting qualitatively different cellular responses. The simulations reveal distinct interaction patterns within the binding cavity, dependent on the stereoisomer. These changes propagate to the intracellular parts of the receptor, triggering various structural responses: the dynamic structure of the intracellular regions of the (R,R)‐MNFen complex more closely resembles the “Gs‐compatible” and “β‐arrestin‐compatible” conformation of β2‐AR, while both stereoisomers maintain structural responses equidistant from the inactive conformation. These findings are confirmed by independent coarse‐grained simulations. In the context of deciphered molecular mechanisms, Trp313 plays a pivotal role, altering its orientation upon interactions with (R,R)‐MNFen, along with the Lys305‐Asp192 ionic bridge. This effect, accompanied by ligand interactions with residues on TM2, increases the strength of interactions within the extracellular region and the binding cavity, resulting in a slightly more open conformation and a minor (by ca. 0.2 nm) increase in the distance between the TM5–TM7, TM1–TM6, TM6–TM7, and TM1–TM5 pairs. On the other hand, an even slighter decrease in the distance between the TM1–TM4 and TM2–TM4 pairs is observed.
Active plasmonic nanodevices: From basic principles to emerging applications
Authors: Zhang Chi , Ding Tao 
Published: November 2024

AbstractTunable plasmonics has shown a wide range of applications in (bio)chemical sensing, displays, actuators, photonic chips, biomedicine, etc. in the last 2 decades. This review focuses on their recent development from the device perspective, which involves the understanding of fundamental principles and specific applications with desired functionality and compatibility. We classify these active plasmonic devices based on the nature of their structures and working environment as colloidal‐based, chip‐based, and colloidal chip‐based to further elaborate their performance and functions. We also highlight recent progress on tunable surface‐enhanced Raman spectroscopy, metasurfaces, and chiroptics to show the emerging applications of tunable plasmonic systems. We conclude this review with a general perception of the research trend in this field and challenges for their practical applications.
Enhancing environmental, social, and governance, performance and reporting through integration of life cycle sustainability assessment framework
Authors: Padilla‐Rivera Alejandro , Hannouf Marwa , Assefa Getachew , Gates Ian 
Published: November 2024

AbstractWe introduce an innovative framework integrating Life Cycle Sustainability Assessment (LCSA) impact categories with Environmental, Social, and Governance (ESG) factors, offering a unified approach for ESG assessment and reporting. It covers sustainable development's key aspects, enabling a detailed evaluation of environmental, economic, and social performance across product and system life cycles, in line with the Sustainable Development Goals (SDGs). Incorporating the UN's 10 principles, the framework fosters a synergy to improve ESG reporting, adaptable across industries. To demonstrate its practicality, a theoretical application in Canada's oil and gas sector highlights how this framework can provide actionable insights for SDG‐aligned performance improvements. This example illustrates how the framework can identify and address sustainability issues, thereby improving ESG performance. Beyond its theoretical contributions, the framework serves as a valuable tool for practitioners and investors, promoting informed and comprehensive ESG reporting. Ultimately, it aims to enhance organizations' contributions towards achieving the SDGs and advancing global sustainability.
Single‐Entity Electrochemistry of N‐Doped Graphene Oxide Nanostructures for Improved Kinetics of Vanadyl Oxidation
Authors: de Oliveira Maida Aysla Costa , Brunet Cabré Marc , Schröder Christian , Nolan Hugo , Pota Filippo , Behan James A. , Barrière Frédéric , McKelvey Kim , Colavita Paula E. 
Published: November 2024

AbstractN‐doped graphene oxides (GO) are nanomaterials of interest as building blocks for 3D electrode architectures for vanadium redox flow battery applications. N‐ and O‐functionalities have been reported to increase charge transfer rates for vanadium redox couples. However, GO synthesis typically yields heterogeneous nanomaterials, making it challenging to understand whether the electrochemical activity of conventional GO electrodes results from a sub‐population of GO entities or sub‐domains. Herein, single‐entity voltammetry studies of vanadyl oxidation at N‐doped GO using scanning electrochemical cell microscopy (SECCM) are reported. The electrochemical response is mapped at sub‐domains within isolated flakes and found to display significant heterogeneity: small active sites are interspersed between relatively large inert sub‐domains. Correlative Raman‐SECCM analysis suggests that defect densities are not useful predictors of activity, while the specific chemical nature of defects might be a more important factor for understanding oxidation rates. Finite element simulations of the electrochemical response suggest that active sub‐domains/sites are smaller than the mean inter‐defect distance estimated from Raman spectra but can display very fast heterogeneous rate constants >1 cm s−1. These results indicate that N‐doped GO electrodes can deliver on intrinsic activity requirements set out for the viable performance of vanadium redox flow battery devices.
3D Printing Hierarchical Porous Nanofibrous Scaffold for Bone Regeneration
Authors: Hu Zhiai , Lin Hengyi , Wang Zhenming , Yi Yating , Zou Shujuan , Liu Hao , Han Xianglong , Rong Xin 
Published: November 2024

AbstractCurrent limitations in 3D printing pose significant challenges for the fabrication of hierarchical 3D scaffolds with nanofibrous structures that simulate the natural bone extracellular matrix (ECM) for enhanced bone regeneration. This study presents an innovative approach to 3D printing customized hierarchical porous scaffolds with nanofiber structures using biodegradable nanofibrous microspheres as the bio‐ink. In vitro investigations demonstrate that the hierarchical porous architecture substantially enhances cell infiltration and proliferation rates, while the nanofiber topology provides physical cues to guide osteogenic differentiation and ECM deposition. When serving as a cell carrier, the 3D‐printed nanofibrous scaffold promotes bone tissue regeneration and integration in vivo. Additionally, the facile and versatile chemical modification facilitates the precise tailoring of the scaffold's functionality. Using nanofibrous microspheres with highly biomimetic and versatile modification properties as the foundational constituent in this universal 3D printing methodology enables comprehensive manipulation of scaffolding biological properties, spanning from macroscopic external morphology to molecular‐scale biochemical kinetics, thereby addressing a diverse spectrum of clinical requisites.
Polymerization Improvement of Graphitic Carbon Nitride Films Derived from Melamine and Thiourea
Authors: Oo May Thawda , Zhao Yanling , Baqi Sabah , Zhou Jiasheng , Phoo May Thawda , Zhang Rui‐Qin 
Published: November 2024

AbstractDeposition of low‐cost, efficient, and environmentally friendly graphitic carbon nitride (g‐CN) films as photoanodes is a crucial step for constructing photoelectrochemical (PEC) cells and exploring their PEC performance. Currently, the improvement of the photocurrent density of g‐CN films is badly needed for their practical applications in PEC water splitting. Enhancing the g‐CN crystallinity by optimizing their synthesis conditions only through screening appropriate reactant precursors is insufficient for this purpose. Herein, using melamine and thiourea precursors with mass ratio 5:1, the degree of polymerization of g‐CN thin films is successfully improved by a thermal vapor condensation method. The obtained pure g‐CN exhibits a remarkably enhanced photocurrent density of 404.4 µA cm−2 at 1.23 V versus reversible hydrogen electrodes. Theoretical calculations reveal that the continuous attachment of small carbodiimide (HN═C═NH) mainly generated by thiourea to the melamine matrix facilitates the formation of large‐area conjugated structure, which fundamentally determines better charge carrier separation and transfer thereby enhancing the PEC performance. This work realizes the synthesis of well‐polymerized g‐CN films with improved PEC activity and offers a computational understanding for the nucleation and growth mechanism of the polycrystalline g‐CN.
Building Robust Manganese Hexacyanoferrate Cathode for Long‐Cycle‐Life Sodium‐Ion Batteries
Authors: Shang Yang , Ren Bo , Wu Ruixue , Lin Jie , Li Xiaoxia , Shen Jixue , Yan Dong , Yang Hui Ying 
Published: November 2024

AbstractManganese Hexacyanoferrate (Mn─HCF) is a preferred cathode material for sodium‐ion batteries used in large‐scale energy storage. However, the inherent vacancies and the presence of H2O within the imperfect crystal structure of Mn─HCF lead to material failure and interface failure when used as a cathode. Addressing the challenge of constructing a stable cathode is an urgent scientific problem that needs to be solved to enhance the performance and lifespan of these batteries. In this review, the crystal structure of Mn─HCF is first introduced, explaining the formation mechanism of vacancies and exploring the various ways in which H2O molecules can be present within the crystal structure. Then comprehensively summarize the mechanisms of material and interfacial failure in Mn─HCF, highlighting the key factors contributing to these issues. Additionally, eight modification strategies designed to address these failure mechanisms are encapsulated, including vacancy regulation, transition metal substitution, high entropy, the pillar effect, interstitial H2O removal, surface coating, surface vacancy repair, and cathode electrolyte interphase reinforcement. This comprehensive review of the current research advances on Mn─HCF aims to provide valuable guidance and direction for addressing the existing challenges in their application within SIBs.
Triphenylamine‐Based Y‐Shaped Self‐Assembled Monolayers for Efficient Tin Perovskite Solar Cells
Authors: Afraj Shakil N. , Kuan Chun‐Hsiao , Cheng Hsu‐Lung , Wang Yun‐Xin , Liu Cheng‐Liang , Shih Yun‐Sheng , Lin Jhih‐Min , Tsai Yi‐Wei , Chen Ming‐Chou , Diau Eric Wei‐Guang 
Published: November 2024

AbstractTriphenylamine‐based Y‐shaped organic sensitizers, specifically TPA‐MN (1), TPA‐CA (2), TPAT‐MN (3), and TPAT‐CA (4), are synthesized and utilized as p‐type self‐assembled monolayers (SAMs) for tin‐based perovskite solar cells (TPSCs). These SAMs are developed using low‐cost starting materials, primarily from triphenylamine (TPA) components. An extensive analysis is conducted to examine the crystalline, morphological, thermal, optical, electrochemical, and optoelectronic characteristics of SAMs 1–4, and the results are compared. A two‐step method is employed to successfully develop tin perovskite layers on all four SAM surfaces. The resulting devices demonstrates PCE in the following order: TPAT‐CA (8.1%) > TPAT‐MN (6.1%) > TPA‐MN (5.0%) > TPA‐CA (4.2%). The TPAT‐CA molecule, which contains a thiophene spacer, performed better than the other three SAMs in terms of rapid hole extraction rate, high hole mobility, and retarded charge recombination. Consequently, SAM TPAT‐CA exhibited the highest device performance with excellent stability over time, retaining ≈90% from the beginning values after storage for 3000 h. The innovative Y‐shaped SAMs describe in this study, characterized by their simple and efficient design, have the potential to contribute significantly to the advancement of perovskite photovoltaics, particularly in the development of cost‐effective TPSC technology.
Being Understood: Epistemic Injustice Towards Young People Seeking Support for Their Mental Health
Authors: Larkin Michael , McCabe Rose , Bortolotti Lisa , Broome Matthew , Craythorne Shioma-Lei , Temple Rachel , Lim Michele , Fadashe Catherine , Sims Chris , Sharples Oscar , Cottrell Josh ,   as part of the Agency in Practice team
Published: November 2024

AbstractAcross many domains, it is important for us to feel that we are understood by others. This is crucial when we are disclosing a vulnerability or seeking help for a problem. When these disclosures or help-seeking requests relate to mental health difficulties, our interactions with others can carry many threats, including stigmatisation; inappropriate moral or character judgements; overly stringent threshold evaluations; and assumptions about our personal circumstances and social resources. In this chapter, we summarise some of the core findings from empirical and qualitative studies which examine what happens when young people meet with health professionals to disclose or to seek help for their experiences with poor mental health. We then draw out some key implications for improving relational and communicative practices amongst mental health professionals. We focus on those implications which are highlighted by those members of our team who are young adults with experiences of accessing mental health services and reflect on these implications in the light of insights from the literature on epistemic injustice.
Not All Psychiatric Diagnoses are Created Equal: Comparing Depression and Borderline Personality Disorders
Authors: Watts Jay 
Published: November 2024

AbstractThe validity of psychiatric diagnoses has been at the heart of enduring and divisive debates in mental health discourse for over fifty years, often reaching a stalemate. Whilst some consider a diagnosis essential for validation and support, others view it as an obstacle to personal meaning-making. This chapter proposes that considering epistemic injustice may offer a valuable approach to overcome this impasse. By examining four facets of epistemic injustice—objectification, moral agency, trivialization, and narrative agency—it juxtaposes patient perspectives on borderline personality disorder and depression, arguably the least and most popular diagnoses with patients in psychiatry. Leveraging these four facets, it delves into the experiences of two representative patients, Cara and John, showing how epistemic injustice operates differently across diagnoses. This analysis suggests the importance of epistemic injustice as a tool in critically evaluating the usefulness of specific psychiatric diagnoses, enriching traditional metrics of reliability and validity in nosology. Moreover, it encourages a shift in clinical training to embrace reflective practices and restructure power dynamics in clinical encounters, promoting greater epistemic participation.
Ameliorating Epistemic Injustice with Digital Health Technologies
Authors: Lalumera Elisabetta 
Published: November 2024

AbstractThis chapter discusses the potential of digital phenotyping to ameliorate epistemic injustice in mental health. Digital phenotyping, which analyses behavioural patterns from user data or smart devices, shows promise in improving mental health care. Whilst concerns exist that it may exacerbate epistemic injustice by overshadowing individual experiences, the chapter presents a different viewpoint. Through a fictional case study, digital phenotyping is portrayed as aiding individuals seeking help by offering more accurate evidence and supporting shared decision-making. The objection that digital technology overrides personal claims is countered by arguing against absolute epistemic priority for any diagnostic tool in medicine. The chapter acknowledges the need for technological advancements and ethical considerations but maintains a positive outlook on the future of digital phenotyping in mental healthcare.
The Discursive Tactics of the Menstrual Movement: Destigmatisation, Intersectionality and Collective Identity
Authors: Tomlinson Maria Kathryn 
Published: November 2024

AbstractDrawing on interviews with 32 menstrual activists, this chapter analyses the discursive tactics that are used by the menstrual movement in Great Britain. It explores how this movement seeks to transform the mediation of menstruation as well as how menstrual activists advocate for social change via traditional and social media. The chapter explores various discursive strategies used by the 32 participants to alter the mediation of menstruation and, as a result, improve the lives of women and other people who menstruate. Tactics include using non-stigmatising language, speaking openly about menstruation, highlighting the intersectional nature of menstrual experience and promoting the inclusion of menstruating people of all genders and ethnicities. The chapter argues that, for menstrual activists, transforming the mediation of menstruation both on social media and in news media is a vital step towards destigmatising menstruation and reducing social inequalities in Great Britain. Furthermore, the chapter explores the influence of neoliberalism on menstrual activism as well as various points of disagreement and tension within the menstrual movement. This includes a lack of consensus about which discourses are the most effective for engendering social change.