bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitting high-resolution electron density maps from atomic models to solution scattering data
Authors: Chamberlain Sarah R. , Moore Stephen , Grant Thomas D. 
Published: June 2023

AbstractSolution scattering techniques, such as small and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for a free fitting parameter commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated which uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization results in a significant improvement of the calculated scattering profiles compared to the leading software. The algorithm is computationally efficient, showing more than tenfold reduction in execution time compared to the leading software. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package (https://github.com/tdgrant1/denss). In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms utilizing SWAXS data while decreasing the risk of overfitting.Statement of SignificanceAccurate calculation of small and wide-angle scattering (SWAXS) profiles from atomic models is useful for studying the solution state and conformational dynamics of biological macromolecules in solution. Here we present a new approach to calculating SWAXS profiles from atomic models using high resolution real space density maps. This approach includes novel calculations of solvent contributions that remove a significant fitting parameter. The algorithm is tested on multiple high quality experimental SWAXS datasets, showing improved accuracy compared to leading software. The algorithm is computationally efficient and robust to overfitting, paving the way for increasing the accuracy and resolution of modeling algorithms utilizing experimental SWAXS data.
Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states
Authors: Lin David Yin-wei , Kueffer Lauren E. , Juneja Puneet , Wales Thomas , Engen John R. , Andreotti Amy H. 
Published: June 2023

AbstractFull-length BTK has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology (PHTH) domain and proline-rich regions (PRR) contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveals only the SH3-SH2-kinase core with no electron density visible for the PHTH-PRR segment. CryoEM data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. On the way to activation, disassembly of the SH3-SH2-kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with PIP3. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.
High-resolution structure of mouse radial spoke and its in-situ structure in ependymal cilia revealed by cryo-EM and cryo-ET
Authors: Meng Xueming , Xu Cong , Li Jiawei , Qiu Benhua , Luo Jiajun , Hong Qin , Tong Yujie , Fang Chuyu , Feng Yanyan , Ma Rui , Shi Xiangyi , Lin Cheng , Pan Chen , Zhu Xueliang , Yan Xiumin , Cong Yao 
Published: June 2023

AbstractRadial spokes (RS) transmit mechanochemical signals between the central pair (CP) and axonemal dynein arms to coordinate ciliary motility. However, the high-resolution structure of mammalian RS remains missing. Here, we present the high-resolution cryo-EM structure of mouse RS head-neck complex in both monomer and dimer forms and reveal the intrinsic dynamics of the dimer. We also map the genetic mutations related to primary ciliary dyskinesia and asthenospermia on the head-neck complex. Moreover, we present the unprecedented cryo-ET and sub-tomogram averaging map of mouse ependymal cilia, whose beating creates unidirectional cerebrospinal fluid flow, and build the models for RS1-3, IDAs, and N-DRC. Strikingly, our cryo-ET map reveals the lack of IDA-b/c/e and the absence of tektin filaments within the A-tubule of doublet microtubules in ependymal cilia compared with mammalian respiratory cilia and sperm flagella. This tissue-specific feature may represent an evolutionary choice driven by the functional requirements on ependymal cilia. Our findings reveal the RS head-neck assembly mechanism, shed light on the coordinated rigid and elastic RS-CP interaction modes beneficial for the regulation of asymmetric ciliary beating, and also facilitate understandings on the etiology of ciliary dyskinesia-related ciliopathies.
Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex
Authors: Gao Yu , Dong Qiping , Arachchilage Kalpana Hanthanan , Risgaard Ryan D. , Syed Moosa , Sheng Jie , Schmidt Danielle K. , Jin Ting , Liu Shuang , Knaack Sara , Doherty Dan , Glass Ian , Levine Jon E. , Wang Daifeng , Chang Qiang , Zhao Xinyu , Sousa André M. M. 
Published: June 2023

SUMMARYThe prefrontal cortex (PFC) is critical for myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, using Patch-seq and single-nucleus multiomic analyses, we identified genes and regulatory networks governing the maturation of distinct neuronal populations in the PFC of rhesus macaque. We discovered that specific electrophysiological properties exhibited distinct maturational kinetics and identified key genes underlying these properties. We unveiled that RAPGEF4 is important for the maturation of resting membrane potential and inward sodium current in both macaque and human. We demonstrated that knockdown ofCHD8, a high-confidence autism risk gene, in human and macaque organotypic slices led to impaired maturation, via downregulation of key genes, includingRAPGEF4. Restoring the expression ofRAPGEF4rescued the proper electrophysiological maturation of CHD8-deficient neurons. Our study revealed regulators of neuronal maturation during a critical period of PFC development in primates and implicated such regulators in molecular processes underlying autism.
Electrophysiological correlates of (mis)judging social information
Authors: Wischnewski Miles , Hörberg Michael O.Y. , Schutter Dennis J.L.G. 
Published: June 2023

AbstractSocial information can be used to optimize decision making. However, the simultaneous presentation of multiple sources of advice can lead to a distinction bias in judging the validity of the information. While involvement of event-related potential (ERP) components in social information processing has been studied, how they are modulated by (mis)judging advisor’s information validity remains unknown. In two experiments participants performed a decision making task with highly accurate or inaccurate cues. Each experiment consisted of a initial, learning and test phase. During the learning phase three advice cues were simultaneously presented and the validity of them had to be assessed. The effect of different cue constellations on ERPs was investigated. In the subsequent test phase, the willingness to follow or oppose an advice cue was tested. Results demonstrated the distinction bias with participants over or underestimating the accuracy of the most uncertain cues. The P2 amplitude was significantly increased during cue presentation when advisors were in disagreement as compared to when all were in agreement, regardless of cue validity. Further, a larger P3 amplitude during outcome presentation was found when advisors were in disagreement and increased with more informative cues. As such, most uncertain cues were related to the smallest P3 amplitude. Findings suggest that misjudgment of social information is related to P3 amplitude subserving evaluation information and learning. This study provides novel insights into the role of P2 and P3 components during judgement of social information validity.
Dendritic excitations govern back-propagation via a spike-rate accelerometer
Authors: Park Pojeong , Wong-Campos David , Itkis Daniel G. , Lee Byung Hun , Qi Yitong , Davis Hunter , Antin Benjamin , Pasarkar Amol , Grimm Jonathan B. , Plutkis Sarah E. , Holland Katie L. , Paninski Liam , Lavis Luke D. , Cohen Adam E. 
Published: June 2023

SummaryDendrites on neurons support nonlinear electrical excitations, but the computational significance of these events is not well understood. We developed molecular, optical, and analytical tools to map sub-millisecond voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons under diverse optogenetic and synaptic stimulus patterns, in acute brain slices. We observed history-dependent spike back-propagation in distal dendrites, driven by locally generated Na+spikes (dSpikes). Dendritic depolarization created a transient window for dSpike propagation, opened by A-type KVchannel inactivation, and closed by slow NaVinactivation. Collisions of dSpikes with synaptic inputs triggered calcium channel and N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials, with accompanying complex spikes at the soma. This hierarchical ion channel network acts as a spike-rate accelerometer, providing an intuitive picture of how dendritic excitations shape associative plasticity rules.
Revisiting the use of dioxane as a reference compound for determination of the hydrodynamic radius of proteins by pulsed field gradient NMR spectroscopy
Authors: Tranchant Emil E. , Pesce Francesco , Jacobsen Nina L. , Fernandes Catarina B. , Kragelund Birthe B. , Lindorff-Larsen Kresten 
Published: June 2023

ABSTRACTMeasuring the compaction of a protein or complex is key to understand the interactions within and between biomolecules. Experimentally, protein compaction is often probed either by estimating the radius of gyration (Rg) obtained from small-angle X-ray scattering (SAXS) experiments or the hydrodynamic radius (Rh) obtained for example by pulsed field gradient nuclear magnetic resonance (PFG NMR) spectroscopy. PFG NMR experiments generally report on the translational diffusion coefficient, which in turn can be used to estimateRhusing an internal standard. Here, we examine the use of 1,4-dioxane as an internal NMR standard to account for sample viscosity and uncertainty about the gradient strength. Specifically, we revisit the basis for the commonly used reference value for theRhof dioxane (2.12 Å) that is used to convert measured diffusion coefficients into a hydrodynamic radius. We follow the same approach that was used to establish the current reference value for theRhby measuring SAXS and PFG NMR data for a set of seven different proteins and using these as standards. Our analysis shows that the currentRhreference value for 1,4-dioxaneRh(2.12 Å) is underestimated, and we instead suggest a new value of 2.27 Å ± 0.04 Å. Using this updated reference value results in a ∼7% increase inRhvalues for proteins whose hydrodynamic radius have been measured by PFG NMR. We discuss the implications for ensemble descriptions of intrinsically disordered proteins and evaluation of effect resulting from for example ligand binding, posttranslational modifications, or changes to the environment.
The usage of sourdough powder as the natural preservative and glycemic index lowering agent in salty muffins
Authors: Çetin Babaoğlu Hümeyra , Arslan Tontul Sultan , Karaduman Lokman , Üzgü Yakup 
Published: June 2023

PurposeThe article aimed to use sourdough powder as a natural preservative against mould growth and a glycemic index reducer agent.Design/methodology/approachIn this study, muffin production was carried out with sourdough powder addition at the rate of 0, 15 and 30%. To obtain the sourdough powder, sourdough was fermented by using Lactobacillus fermentum, Lactococcus lactis (previously isolated from spontaneous sourdough) and Saccharomyces cerevisiae.FindingsThe specific volume, number of crumb pores and total pore area were not adversely affected by the addition of 15% or 30% sourdough powder (p > 0.05). The sourdough addition reduced the L* values of the muffin crust, while the b* value of the muffin crumb with 30% sourdough powder decreased compared to the control (p < 0.05). The addition of sourdough powder decreased eGI and RDS values and increased SDS content of samples (p < 0.05). In storage, the mould growth was observed in the control group and samples containing 15% sourdough powder on the 5th day, while the samples containing 30% sourdough powder were moulded on the 7th day. The sourdough powder increased the hardness and chewiness values of samples (p < 0.05), while it had no significant effect on springiness, cohesiveness and resilience (p > 0.05).Originality/valueThe sourdough powder provides a lower glycemic index and longer microbial shelf life that makes the product advantageous in consumer demand. This is the first time sourdough powder has been used to achieve this purpose.
In what ways does human capital influence the relationship between financial development and economic growth?
Authors: Saroj Shekhar , Shastri Rajesh Kumar , Singh Priyanka , Tripathi Mano Ashish , Dutta Sanjukta , Chaubey Akriti 
Published: June 2023

PurposeHuman capital is a portfolio of rich skills that the labour possesses. Human capital has attracted significant attention from scholars. Nevertheless, empirical findings on the utility of human capital have often been divided. To address the research gap in the literature, the authors attempt to understand how human capital plays a significant role in financial development and economic growth nexus.Design/methodology/approachThe authors rely on secondary data published by the World Bank. The authors use econometric tools such as the autoregressive distributive lag (ARDL) model and related statistical tests to study the relationship between human capital, India's financial growth and gross domestic product (GDP) growth.FindingsStudy findings suggest that human capital and financial development contribute significantly to economic growth. Further, the authors found that human capital has a positive and significant moderating effect on the path of joining financial development and economic growth.Practical implicationsThe study contributes to the human capital debate. Despite the rich body of literature, the study based on World Bank data confirms the previous findings that investment in human capital is always useful for the financial and economic growth of the nation.Originality/valueThis paper reveals some unique findings regarding effect of financial development and economic growth nexus which opens the window of new dimension to think about their nexus. It also provides a different pathway to foster the economic growth by using human capital and financial development as together, especially in India.
Trait gratitude and subjective career success: the mediating roles of growth mindset and network breadth
Authors: Zhang Shilei , Zhao Teng , Liu Xinyi , Wei Chunhao , Liu Sijun 
Published: June 2023

PurposeBuilding on the broaden-and-build theory and incorporating a self-regulatory perspective, this study examines the relationship between trait gratitude and subjective career success and investigates the mediating roles of growth mindset of work and career network breadth.Design/methodology/approachTime-lagged data were collected in three waves from a sample of 314 employees in China. Hypotheses were tested using structural equation modeling.FindingsThe findings demonstrate that trait gratitude is positively related to SCS, mediated by growth mindset of work as an indicator of psychological resources and career network breadth as an indicator of social resources. Trait gratitude is more strongly associated with network breadth (i.e., social resources) than with growth mindset (i.e., psychological resources).Practical implicationsOrganizations may find trait gratitude an applicable addition to the selection criteria during the recruitment process.Originality/valueBy identifying trait gratitude as an antecedent of SCS and revealing its underlying mechanisms, the current study points to a new perspective on the study of career success.
The effect of R & D laboratories on MNE subsidiary performance: a primary survey in a European Mediterranean country
Authors: Georgopoulos Antonios , Aggelopoulos Eleftherios , Paraschi Elen Paraskevi , Kalogera Maria 
Published: June 2023

PurposeThis paper aims to examine the effect of R&D laboratories on the perceived performance of MNE subsidiaries during recession.Design/methodology/approachEmploying resource-based view and knowledge-based theory, the authors investigate a unique sample of 171 technologically heterogenous foreign MNE subsidiaries located in Greece over the period of recession 2009–2016. The sample subsidiaries operate different types of R&D laboratories.FindingsThe authors find that MNE subsidiaries with advanced R&D laboratories such as locally integrated laboratories (LILs) and internationally interdependent laboratories (IILs) perform better in recession than subsidiaries with support laboratories (SLs) or subsidiaries without R&D laboratories. Overall, the authors find an asymmetric performance contribution of R&D laboratories at subsidiary level.Originality/valueThe study provides useful insights into the environmentally derived “knowledge-based - performance” context, so filling an important research gap, since little is known about the performance impact of the input-side of technological activity at MNE subsidiary level, especially as regards R&D facilities/infrastructure. Based on the findings the authors identify important managerial implications.
Dialogic research mentoring in pre-service teacher education
Authors: Tuyan Seden Eraldemir 
Published: June 2023

PurposeThis paper presents the results of my learning using my expertise in teacher-research mentoring to address the needs of pre-service teachers and the requirements of the action research course in English language teaching. It reflects on the different procedures of my mentoring model, enriched by the dialogic research mentoring strategies informed by Freire's dialogic pedagogy.Design/methodology/approachThrough this first-person action research, the author aims to improve her teacher-research mentoring practice. As an inquiry into her own actions, the author examines her experiences, her understanding of them, and the potential meaning for her work as a teacher-research mentor during the two years she tutored the action research course. The author explores the procedures of the mentoring model she developed and the effectiveness of dialogic research mentoring in promoting critical consciousness and taking positive action in pre-service English language teachers.FindingsEffective actualization of the teacher-research mentoring process facilitates mentors' refinement and understanding of their roles during teacher-research mentoring. Perceived barriers can be overcome by adopting nine relevant strategies, which can be grouped into three themes: community-building, nurturing competencies, and fostering growth. Accordingly, the research mentoring model incorporates these strategies.Originality/valueThe insights enriched the existing knowledge of the dynamics of mentoring in general and of teacher-research in particular. Additionally, the study offers strategies developed based on my informed actions as the researcher to attain more effective outcomes during the research mentoring process.
Adopting retail technology in crises: integrating TAM and prospect theory perspectives
Authors: Burgess Brigitte , Yaoyuneyong Gallayanee , Pollitte Wesley A. , Sullivan Pauline 
Published: June 2023

PurposeThis paper combines prospect theory (PT) and the technology acceptance model (TAM) proposing that technology anxiety (TA), risk averseness (RA), concern and resistance to use inhibit technology acceptance, while trust, social influence (SI) and compatibility are enablers to technology acceptance, particularly in the context of consumer adoption of retail technologies during crises.Design/methodology/approachA review of PT and TAM literature was conducted to develop a model which considers the impact of inhibitors and enablers on retail technology acceptance.FindingsThis investigation establishes a theoretical model of mid-crisis retail technology adoption behavior that can be tested quantitatively. Several propositions regarding relationships between proposed inhibitors, enablers and TAM are presented, as well as implications for future research.Originality/valueThis investigation further integrates PT and TAM, proposing that PT is an appropriate framework to investigate inhibitors and enablers of retail technology acceptance during crises.
Antecedents and mediators of experiential retailing consumer behavior
Authors: Meng Hu , Sun Yangyang , Liu Xinxin , Li Yujia , Yang Yingjie 
Published: June 2023

PurposeAn experiential retailing strategy is considered cardiotonic for consumers and brands. When such a stimulus is used, what cognition and behaviors are generated is an issue worthy of study. Therefore, the purpose of this study is to explore the factors and mechanisms that affect consumer response and relationship quality through empirical research.Design/methodology/approachBased on theoretical deduction, this paper proposes a conceptual model that includes four antecedents: experiential scene atmosphere (ESA), highlight design, interaction approach and value fit. These affect consumer–brand relationship quality (CRQ) through consumer identification (CI), brand identity (BI) and experiential immersion degree. In two rounds of predictive tests, 624 and 481 valid data were collected, respectively, and the feasibility of the scale was verified scrupulously. Furthermore, 427 participants reported the participants' tendencies in a formal empirical study.FindingsThe results show that the direct effects of antecedents, mediators and dependent variables are significant. Although the mediating effect of BI in experiential highlighting design on CRQ is not supported, other consumer response variables have a full or partial mediating effect.Originality/valueThis study not only functions as an innovation of research perspective enriching the theoretical framework of the influence mechanism of experiential retailing, but also strengthens the discussion on the role of value fit, especially emotional value fit, in experiential retailing.