bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex
Authors: Kayastha Kanwal , Katsyv Alexander , Himmrichs Christina , Welsch Sonja , Schuller Jan M. , Ermler Ulrich , Müller Volker 
Published: February 2022

AbstractLactate oxidation with NAD+ as electron acceptor is a highly endergonic reaction and some anaerobic bacteria overcome the energetic hurdle by flavin-based electron bifurcation/confurcation (FBEB/FBEC) using a lactate dehydrogenase (Ldh) in concert with the electron transferring proteins EtfA and EtfB. The electron cryo-microscopically (cryo-EM) characterized (Ldh-EtfAB)2 complex of Acetobacterium woodii at 2.43 Å resolution consists of a mobile EtfAB shuttle located between the rigid central Ldh and the peripheral EtfAB base units. The FADs of Ldh and the EtfAB shuttle contact each other thereby forming the D (dehydrogenase conducting) state. The intermediary Asp37 and Asp139 may harmonize the redox potentials between the FADs and the pyruvate/lactate pair crucial for FBEC. A plausible novel B (bifurcation conducting) state with the EtfAB base and shuttle FADs in a productive electron transfer distance was derived by integrating Alphafold2 calculations. Kinetic analysis of enzyme variants shed light on the connection between NAD binding/release and D-to-B state transition. The FBEC inactivity when truncating the ferredoxin domain of EtfA substantiates its role as redox relay. Lactate oxidation in Ldh is based on the catalytic base His423 and a metal center. On this basis, a comprehensive catalytic mechanism of the FBEC process was outlined.
Cooperativity and folding kinetics in a multi-domain protein with interwoven chain topology
Authors: Liu Zhenxing , Thirumalai D. 
Published: February 2022

AbstractAlthough a large percentage of eukaryotic proteomes consist of proteins with multiple domains, not much is known about their assembly mechanism, especially those with complicated native state architectures. Some have complex topology in which the structural elements along the sequence are interwoven in such a manner that the domains cannot be separated by cutting at any location along the sequence. We refer to such proteins as Multiply connected Multidomain Proteins (MMPs). The phoshotransferase enzyme Adenylate Kinase (ADK) with three domains (NMP, LID, and CORE), the subject of this study, is an example of MMP. We devised a coarse-grained model to simulate ADK folding initiated by changing either the temperature or guanidinium chloride (GdmCl) concentration. The simulations reproduce the experimentally measured melting temperatures that are associated with two equilibrium transitions, FRET efficiency as a function of GdmCl concentration, and the global folding times nearly quantitatively. Although the NMP domain orders independently, cooperative interactions between the LID and the CORE domains are required for complete assembly of the enzyme. The kinetic simulations show that on the collapse time scale, but less than the global folding time, multiple interconnected metastable states are populated, attesting to the folding heterogeneity. The network connectivity between distinct states shows that the CORE domain folds only after the NMP and LID domains are formed, reflecting the interwoven nature of the chain topology. We propose that the rules for MMP folding must also hold for the folding of RNA enzymes.
Class II UvrA protein Ecm16 requires ATPase activity to render resistance against echinomycin
Authors: Erlandson Amanda , Gade Priyanka , Kim Chu-Young , Mera Paola 
Published: February 2022

II.SummaryBacteria use various strategies to become antibiotic resistant. The molecular details of these strategies are not fully understood. We can increase our understanding by investigating the same strategies found in antibiotic-producing bacteria. In this work, we characterize the self-resistance protein Ecm16 encoded by echinomycin-producing bacteria. Ecm16 is a structural homolog of the Nucleotide Excision Repair (NER) protein UvrA. Expression ofecm16in the heterologous systemEscherichia coliwas sufficient to render resistance against echinomycin. Ecm16 preferentially binds double-stranded DNA over single-stranded DNA and is likely to primarily interact with the backbone of DNA using a nucleotide-independent binding mode. Ecm16’s binding affinity for DNA increased significantly when the DNA is intercalated with echinomycin. Ecm16 can repair echinomycin-induced DNA damage independently of NER. Like UvrA, Ecm16 has ATPase activity and this activity is essential for Ecm16’s ability to render echinomycin resistance. Notably, UvrA and Ecm16 were unable to complement each other’s function. Increasing the cellular levels of UvrA inE. coliwas insufficient to render echinomycin resistance. Similarly, Ecm16 was unable to repair DNA damage that is specific to UvrA. Together, our findings identify new mechanistic details of how a refurbished DNA repair protein Ecm16 can specifically render resistance to the DNA intercalator echinomycin. Our results, together with past observations, suggest a model where Ecm16 recognizes double helix distortions caused by echinomycin and repairs the problem independently of NER.
Synthetic genetic circuits enable reprogramming of plant roots
Authors: Brophy Jennifer A. N. , Magallon Katie J. , Kniazev Kiril , Dinneny José R. 
Published: February 2022

AbstractThe shape of a plant’s root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. Here, we construct synthetic genetic circuits to control gene expression with high spatial precision across root tissues. These circuits produce specific patterns of gene expression by combining the activity of multiple native promoters using logical operations. We then use the circuits to predictably alter root structure. This work demonstrates the ability of synthetic genetic circuits to control gene expression across tissues and offers an exciting means to reprogram plant growth.
Requirement of cholesterol for calcium-dependent vesicle fusion by stabilizing synaptotagmin-1-induced membrane bending
Authors: Ali Moussa Houda Yasmine , Shin Kyung Chul , Ponraj Janarthanan , Kim Soo Jin , Ryu Je-Kyung , Mansour Said , Park Yongsoo 
Published: February 2022

ABSTRACTCholesterol is essential for neuronal activity and function. Cholesterol depletion in the plasma membrane impairs synaptic transmission. However, the molecular mechanisms by which cholesterol deficiency leads to defects in vesicle fusion remain poorly understood. Here we show that cholesterol is required for Ca2+-dependent native vesicle fusion using the in-vitro reconstitution of fusion and amperometry to monitor exocytosis in chromaffin cells. Purified native vesicles were crucial for the reconstitution of physiological Ca2+-dependent fusion, whereas vesicle-mimicking liposomes failed to reproduce the cholesterol effect. Intriguingly, cholesterol had no effect on membrane binding of synaptotagmin-1, a Ca2+ sensor for ultrafast fusion. Cholesterol stabilizes local membrane bending induced by synaptotagmin-1, thereby lowering the energy barrier for Ca2+-dependent fusion to occur. Our data provide evidence that cholesterol depletion abolishes Ca2+-dependent vesicle fusion by disrupting synaptotagmin-1-induced membrane bending, and suggests that cholesterol is an important lipid regulator for Ca2+-dependent fusion.
Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
Authors: Kiani Karun , Sanford Eric M. , Goyal Yogesh , Raj Arjun 
Published: February 2022

AbstractA major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor binding events. In concert with RNA-sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short duration treatments with specific perturbations. Here, we used tandem, bulk ATAC-seq and RNA-seq measurements from MCF-7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF-β. We found two classes of genes whose expression showed a significant change: those that showed some change in accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had a lower baseline accessibility prior to exposure to signal. Focusing the analysis specifically on peaks with motifs for transcription factors associated with retinoic acid and TGF-β signaling did not reduce the lack of correspondence. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than drive altered transcriptional status. Together, these results show many gene expression changes can happen independent of changes in accessibility of local chromatin in the context of a single-factor perturbation and suggest that some changes to accessibility changes may occur after changes to expression, rather than before.
Control of Craniofacial Development by the Collagen Receptor, Discoidin Domain Receptor 2
Authors: Mohamed Fatma F. , Ge Chunxi , Cowling Randy T. , Ono Noriaki , Binrayes Abdul-Aziz , Greenberg Barry , Kaartinen Vesa M. , Franceschi Renny T. 
Published: February 2022

AbstractDevelopment of the craniofacial skeleton requires interactions between progenitor cells and the collagen-rich extracellular matrix (ECM). The mediators of these interactions are not well-defined. Mutations in discoidin domain receptor 2 (DDR2), a non-integrin collagen receptor, are associated with craniofacial abnormalities, such as midface hypoplasia and open fontanels. However, the exact role of DDR2 in craniofacial morphogenesis is not known. As will be shown,Ddr2-deficient mice exhibit defects in craniofacial bones including impaired calvarial growth and frontal suture formation, cranial base hypoplasia due to aberrant chondrogenesis and delayed ossification at growth plate synchondroses. As established by localization and lineage tracing studies,Ddr2is expressed in progenitor cell-enriched craniofacial regions including sutures and synchondrosis resting zone cartilage, overlapping with Gli1+ cells, and contributing to chondrogenic and osteogenic lineages during skull growth. Tissue-specific knockouts further established the requirement forDdr2in Gli1+ skeletal progenitors and chondrocytes and suggest important functions in chondrocyte proliferation and orientation as well as ECM organization. These studies establish a cellular basis for regulation of craniofacial morphogenesis by this understudied collagen receptor.
Methodological Insights Accounting talk: developing conversation analysis in accounting research
Authors: Baker Max , Andrew Jane , Roberts John 
Published: February 2022

PurposeThis paper proposes a research method for analysing talk about accounting concepts, systems and numbers. The authors argue that studying accounting talk in situ is a fruitful way to understand both the role accounting plays in the framing of relationships between individuals and the associated emotional content of these exchanges. As such, the authors argue that conversation analysis (CA) is a useful complement to interviews in qualitative research.Design/methodology/approachThe authors introduce a specific approach to CA called positioning theory, which captures the linguistic and emotional subtleties embedded within interpersonal interactions, and the way accounting impacts and mediates these relations through measuring, assessment and control. The authors draw on one particularly animated conversation about accounting in a manufacturing company. The conversation was a largely emotional and animated exchange between individuals where talk about accounting was imbued with metaphors, violence, sex and humour.FindingsWhile participants in conversations may appear to draw on similar forms of language and expression, CA allows researchers to see that the meaning of these shared expressions change based on who is saying them, whom they are saying them to and how they are saying them. Dissecting conversations as they unfold, offers a more nuanced and multifaceted understanding of accounting as central to the social fabric of organisational life.Originality/valueAs opposed to interviews, which often suffer from the rationality of hindsight (referred to as retrospective rationality), CA captures the unfolding nature of accounting talk in real-time–not upon reflection.
Energy-aware multipath routing in WSN using improved invasive weed elephant herd optimization
Authors: Vishal Sharad Hingmire , Desai Santosh R. , Krishnrao Kanse Yuvraj 
Published: February 2022

Purpose
In a wireless sensor network (WSN), the sensor nodes are distributed in the network, and in general, they are linked through wireless intermediate to assemble physical data. The nodes drop their energy after a specific duration because they are battery-powered, which also reduces network lifetime. In addition, the routing process and cluster head (CH) selection process is the most significant one in WSN. Enhancing network lifetime through balancing path reliability is more challenging in WSN. This paper aims to devise a multihop routing technique with developed IIWEHO technique.

Design/methodology/approach
In this method, WSN nodes are simulated originally, and it is fed to the clustering process. Meanwhile, the CH is selected with low energy-based adaptive clustering model with hierarchy (LEACH) model. After CH selection, multipath routing is performed by developed improved invasive weed-based elephant herd optimization (IIWEHO) algorithm. In addition, the multipath routing is selected based on certain fitness functions like delay, energy, link quality and distance. However, the developed IIWEHO technique is the combination of IIWO method and EHO algorithm.

Findings
The performance of developed optimization method is estimated with different metrics, like distance, energy, delay and throughput and achieved improved performance for the proposed method.

Originality/value
This paper presents an effectual multihop routing method, named IIWEHO technique in WSN. The developed IIWEHO algorithm is newly devised by incorporating EHO and IIWO approaches. The fitness measures, which include intra- and inter-distance, delay, link quality, delay and consumption of energy, are considered in this model. The proposed model simulates the WSN nodes, and CH selection is done by the LEACH protocol. The suitable CH is chosen for transmitting data through base station from the source to destination. Here, the routing system is devised by a developed optimization technique. The selection of multipath routing is carried out using the developed IIWEHO technique. The developed optimization approach selects the multipath depending on various multi-objective functions.
Implementing social sustainability through market pressures: an inter-organizational network analysis in the Pakistani apparel supply chain
Authors: Fontana Enrico , Atif Muhammad , Heuer Mark 
Published: February 2022

PurposeThis article encourages novel approaches in the SSCM literature to create transformative change for workers in developing countries' apparel supply chains. It examines how suppliers' implementation of social sustainability is moderated by buyers' pressures (through dyadic ties) and by similar suppliers' pressures (through extended ties).Design/methodology/approachThe article adopts a qualitative method design based on fieldwork and 21 face-to-face interviews with suppliers' senior managers. The data were collected between 2017 and 2020 in the factory premises of suppliers in Pakistan.FindingsThis article distinguishes the pressures that moderate suppliers' implementation of social sustainability positively (top-down encouragement, informal exchange and competitive convergence) and negatively (unrewarded commitment) through social ties. Hence, it shows how suppliers experience constrained proactivity as a state of tension.Originality/valueThe article primarily contributes to the SSCM literature by informing how similar suppliers' pressures in the business community constitute important processes of social governance and are key to create transformative change upstream in apparel supply chains. Against this backdrop, it cautions about buyers' opposite pressures and misuse of their negotiation power, which indirectly holds back and dilutes transformative change.
Fear appeal, coping appeal and mobile health technology persuasion: a two-stage scenario-based survey of the elderly
Authors: Sun Yongqiang , Feng Yafei , Shen Xiao-Liang , Guo Xitong 
Published: February 2022

PurposePrior researches on the adoption of mobile health services (MHS) concentrate on the subjective cognitive appraisals resulting in technology adoption, while ignoring how to shape those cognitive appraisals by the objective message design strategies which are easier to operate in practice. Based on protection motivation theory (PMT), the current research aims to explore the antecedents of cognitive appraisals by focusing on message design strategies of fear appeal and coping appeal.Design/methodology/approachA two-stage scenario-based survey of 204 participants was conducted to collect data. The authors chose SPSS and covariance-based structural equation modeling (CB-SEM) approach with the software LISREL 8.8 to test our model.FindingsThe results show that the relationship between fear appeal and fear arousal is inverted U-shaped such that the degree of fear arousal is the greatest when the fear appeal is at a moderate level. Perceived usefulness for the message with negative framing is higher than that with positive framing. Furthermore, fear appeal and coping appeal have a significant interaction on the adoption of MHS at different stages.Research limitations/implicationsThe sample data of this study come from a special health service of a special group in China, which limits the universality of our research results for other groups or health care services. Therefore, future researchers can validate the model in other research scenarios and sample populations.Originality/valueThis study shows how fear appeal and coping appeal work together to influence individuals' adoption intention. The authors’ findings expand the theoretical depth of PMT and fear theory, enriching the theoretical connotation of framing effect in mobile health technology adoption context, which add new insights to design more persuasive messages through fear appeal and coping appeal for researchers and MHS providers in mobile health communication or propaganda.
Supply chain sustainability risk decision support model using integrated Preference Selection Index (PSI) method and prospect theory
Authors: Sutrisno Agung , Kumar Vikas 
Published: February 2022

PurposeThe purpose of this paper is to introduce the integrated model of the Preference Selection Index (PSI) and the prospect theory as new means to appraise the impact of supply chain sustainability risks based on five pillars of sustainability. Research has shown that sustainability risk assessment has a strong positive impact on improving the performance of enterprises.Design/methodology/approachThis study adopts a new decision support model for assessing supply chain sustainability risk based on additional failure mode and effect analysis parameters and its integration with PSI methodology and prospect theory. A case example of the supply chain small and medium enterprise (SME) producing fashion have been used in this study.FindingsThe result of this study reveals some critical supply chain sustainability risks affecting the sustainability of enterprises under study.Research limitations/implicationsThe use of a limited sample is often associated as a limitation in the research studies and this study is based on findings from SMEs in the fashion retail supply chain. This preliminary study provides academics and practitioners an exemplar of supply chain sustainability risk assessment using integration of the PSI method and prospect theory.Practical implicationsThe result of this study is beneficial for practitioners, particularly owner–managers of SMEs who can use this study as guidance on how to consider risk behavior to identify and select the critical sustainability risks and plan mitigating strategies accordingly.Originality/valueScientific studies on using the PSI and its integration with prospect theory as means to assess the criticality of supply chain sustainability risks is very rare. To the best of the authors’ knowledge, this is the first paper that presents the integrated model of the PSI and prospect theory to rank supply chain sustainability risks based on five pillars of sustainability.
Additive manufacturing with fibre-reinforcement – design guidelines and investigation into the influence of infill patterns
Authors: Plocher Janos , Wioland Jean-Baptiste , Panesar Ajit Singh 
Published: February 2022

Purpose
Fibre-reinforced additive manufacturing (FRAM) with short and continuous fibres yields light and stiff parts and thus increasing industry acceptance. High material anisotropy and specific manufacturing constraints shift the focus towards design for AM (DfAM), particularly on toolpath strategies. Assessing the design-property-processing relations of infill patterns is fundamental to establishing design guidelines for FRAM.

Design/methodology/approach
Subject to the DfAM factors performance, economy and manufacturability, the efficacy of two conventional infill patterns (grid and concentric) was compared with two custom strategies derived from the medial axis transformation (MAT) and guided by the principal stresses (MPS). The recorded stiffness and strength, the required CPU and print time, and the degree of path undulation and effective fibre utilisation (minimum printable fibre length) associated with each pattern, served as assessment indices for different case studies. Moreover, the influence of material anisotropy was examined, and a stiffness-alignment index was introduced to predict a pattern’s performance.

Findings
The highest stiffnesses and strengths were recorded for the MPS infill, emphasising the need for tailoring print paths rather than using fixed patterns. In contrast to the grid infill, the concentric infill offered short print times and reasonable utilisation of continuous fibres. The MAT-based infill yielded an excellent compromise between the three DfAM factors and experimentally resulted in the best performance.

Originality/value
This constitutes the first comprehensive investigation into infill patterns under DfAM consideration for FRAM, facilitating design and processing choices.