bluuebunny/crossref_metadata_2025_split huggingface dataset:
DomainFit: Identification of Protein Domains in cryo-EM maps at Intermediate Resolution using AlphaFold2-predicted Models
Authors: Gao Jerry , Tong Max , Lee Chinkyu , Gaertig Jacek , Legal Thibault , Bui Khanh Huy 
Published: November 2023

AbstractCryo-electron microscopy (cryo-EM) has revolutionized our understanding of macromolecular complexes, enabling high-resolution structure determination. With the paradigm shift toin situstructural biology recently driven by the ground-breaking development of cryo-focused ion beam milling and cryo-electron tomography, there are an increasing number of structures at sub-nanometer resolution of complexes solved directly within their cellular environment. These cellular complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because the side chains cannot be visualized reliably. Here, we present DomainFit, a program for automated domain-level protein identification from cryo-EM maps at resolutions lower than 4 Å. By fitting domains from artificial intelligence-predicted models such as AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the proteins forming the density. Using DomainFit, we identified two microtubule inner proteins, one of them, a CCDC81 domain-containing protein, is exclusively localized in the proximal region of the doublet microtubule from the ciliateTetrahymena thermophila. The flexibility and capability of DomainFit makes it a valuable tool for analyzingin situstructures.
A simple methods for obtaining a multivalent protein with a variable number of binding sites and estimating its binding parameters
Authors: Mikhaylina Alisa , Lekontseva Natalia , Khairetdinova Albina , Ilyina Nelly , Balobanov Vitalii 
Published: November 2023

AbstractThe study of natural and the design of artificial multivalent proteins is a promising field of molecular biology. Working with such proteins is much more difficult than with their monovalent analogues. In this paper, we show how using a ring of heptameric Sm-like protein as a scaffold, it is possible to create a multivalent protein with a different number of binding sites. This is an urgent task for the study of multivalent and multicenter protein-protein interactions. The method of analysis used in the work allows us to evaluate the stoichiometry and the dissociation constant of complexes of artificial chaperone with a non-native protein. It is shown that for reliable binding of non-native αLA, its interaction with several apical domains of GroEL is necessary. At the same time, the dissociation constant of such a complex does not significantly change with an increase in the number of binding domains in the oligomer. Up to 4 αLA molecules can be attached to the complete heptameric ring of apical domains. The proposed methods have a good cost-to-result ratio and can be applied to the study and design of other new proteins.
Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m6A detection efficiency and calling bias correcting pipeline
Authors: Dennis Allison F. , Xu Zhuwei , Clark David J. 
Published: November 2023

AbstractRecent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Theoretically, nucleosome footprints and nucleosome-depleted regions can be identified using M.EcoGII, which methylates adenines in any sequence context, providing a high-resolution map of accessible regions in each DNA molecule. Here we report PacBio long-read sequence data for budding yeast nuclei treated with M.EcoGII and a bioinformatic pipeline which corrects for three key challenges undermining this promising method. First, detection of m6A in individual DNA molecules by the PacBio software is inefficient, resulting in false footprints predicted by random gaps of seemingly unmethylated adenines. Second, there is a strong bias against m6A base calling as AT content increases. Third, occasional methylation occurs within nucleosomes, breaking up their footprints. After correcting for these issues, our pipeline calculates a correlation coefficient-based score indicating the extent of chromatin heterogeneity within the cell population for every gene. Although the population average is consistent with that derived using other techniques, we observe a wide range of heterogeneity in nucleosome positions at the single-molecule level, probably reflecting cellular chromatin dynamics.
Bioorthogonal metabolic labeling of the virulence factor phenolic glycolipid in mycobacteria
Authors: Guzmán Lindsay E. , Cambier C. J. , Cheng Tan-Yun , Naqvi Kubra F. , Shiloh Michael U. , Moody D. Branch , Bertozzi Carolyn R. 
Published: November 2023

ABSTRACTSurface lipids on pathogenic mycobacteria modulate infection outcomes by regulating host immune responses. Phenolic glycolipid (PGL) is a host-modulating surface lipid that varies among clinicalMycobacterium tuberculosisstrains. PGL is also found inMycobacterium marinumwhere it promotes infection of zebrafish through effects on the innate immune system. Given the important role this lipid plays in the host-pathogen relationship, tools for profiling its abundance, spatial distribution, and dynamics are needed. Here we report a strategy for imaging PGL in live mycobacteria using bioorthogonal metabolic labeling. We functionalized the PGL precursorp-hydroxybenzoic acid (pHB) with an azide group (3-azidopHB). When fed to mycobacteria, 3-azidopHB was incorporated into the cell surface, which could then be visualized via bioorthogonal conjugation of a fluorescent probe. We confirmed that 3-azidopHB incorporates into PGL using mass spectrometry methods and demonstrated selectivity for PGL-producingMycobacterium marinumandMycobacterium tuberculosisstrains. Finally, we applied this metabolic labeling strategy to study the dynamics of PGL within the mycobacterial membrane. This new tool enables visualization of PGL which may facilitate studies of mycobacterial pathogenesis.
DualNetGO: A Dual Network Model for Protein Function Prediction via Effective Feature Selection
Authors: Chen Zhuoyang , Luo Qiong 
Published: November 2023

AbstractMotivationProtein-protein Interaction (PPI) networks are crucial for automatically annotating protein functions. As multiple PPI networks exist for the same set of proteins that capture properties from different aspects, it is a challenging task to effectively utilize these heterogeneous networks. Recently, several deep learning models have combined PPI networks from all evidence, or concatenated all graph embeddings for protein function prediction. However, the lack of a judicious selection procedure prevents the effective harness of information from different PPI networks, as these networks vary in densities, structures, and noise levels. Consequently, combining protein features indiscriminately could increase the noise level, leading to decreased model performance.ResultsWe develop DualNetGO, a dual network model comprised of a classifier and a selector, to predict protein functions by effectively selecting features from different sources including graph embeddings of PPI networks, protein domain and subcellular location information. Evaluation of DualNetGO on human and mouse datasets in comparison with other network-based models show at least 4.5%, 6.2% and 14.2% improvement on Fmax in BP, MF and CC Gene Ontology categories respectively for human, and 3.3%, 10.6% and 7.7% improvement on Fmax for mouse. We demonstrate the generalization capability of our model by training and testing on the CAFA3 data, and show its versatility by incorporating Esm2 embeddings. We further show that our model is insensitive to the choice of graph embedding method and is time- and memory-saving. These results demonstrate that combining a subset of features including PPI networks and protein attributes selected by our model is more effective in utilizing PPI network information than only using one kind of or concatenating graph embeddings from all kinds of PPI networks.Availability and implementationThe source code of DualNetGO and some of the experiment data are available at:https://github.com/georgedashen/DualNetGO.Contactluo@ust.hk,zchen190@connect.hkust-gz.edu.cnSupplementary InformationSupplementary data are available atBioinformaticsonline.
Entrepreneurship and self-service technologies as a driver of customer loyalty to the retailer during the COVID-19 pandemic
Authors: Alves Filipa Freitas , Veloso Cláudia Miranda , Gomes Santana Félix Elisabete , Sousa Bruno Barbosa , Valeri Marco 
Published: November 2023

Purpose This research aims (i) to assess the level of customer satisfaction and loyalty to self-service technologies and Auchan Retail Portugal, (ii) to identify the determinants of customer satisfaction and loyalty to these technologies and also, (iii) to identify their influence on customer loyalty to this modern distribution retailer operating in Portugal.Design/methodology/approach A conceptual model was defined to meet the research objectives and to carry out the quantitative analysis applied to the random sample (n = 483) of customers. The data used where gathered via an online questionnaire survey, which covered all dimensions of the conceptual model, applied in 2021 in Portugal. To validate the hypotheses, Cronbach’s alpha and multiple linear regression models were used.Findings The results reveal that customer satisfaction with self-service technologies has a direct and positive effect on customer loyalty to Auchan Retail Portugal. Furthermore, results reveal that the technology utility factors significantly influence the customer technology experience which has an impact on perceived service quality and perceived risk. The findings of this research provide data on how to improve customer adoption and satisfaction with self-service technology and highlight that these technologies should be part of firm’s competitive strategy.Originality/value This study presents itself as a novelty for science, while granting important contributions to the retailer. It presents an innovative conceptual model that delivers to Auchan the basis for it to move toward smart retail technologies, aiming at the market trend of personalization. For future research, this study can be used as an instrument to evaluate the customer experience with self-service technology and to examine the determinants and effects of self-service technology separately.
Study on life distribution and prediction method of flexible graphite composite reinforced gasket
Authors: Zhang Yunhao , Shao Chunlei , Kong Jing , Zhou Junwei , Zhou Jianfeng 
Published: November 2023

Purpose
This paper aims to prevent gasket sealing failure in engineering, accurately predict gasket life, extend system life and improve sealing reliability. The accelerated life test method of flexible graphite composite–reinforced gaskets is established, the life distribution law of flexible graphite composite–reinforced gaskets is revealed, and the life prediction method of flexible graphite composite–reinforced gaskets with different allowable leakage rates is proposed, which can provide a reference for the life prediction of other types of gaskets.

Design/methodology/approach
In this study, flexible graphite composite–reinforced gaskets were tested for long-term high-temperature sealing performance on a multi-sample gasket accelerated life test rig. The data were also analyzed using the least squares method and the K-S hypothesis calibration method. A gasket time-dependent leakage model and an accelerated life model were also developed. Constant stress-accelerated life tests were conducted on flexible graphite composite–reinforced gaskets. On this basis, a gasket life prediction method at different allowable leakage rates was proposed.

Findings
The life distribution law of flexible graphite composite–reinforced gaskets is revealed. The results show that the life of the gasket obeys the Weibull distribution. The time-correlated leakage model and accelerated life model of the gasket were established. And the accelerated life test method of the flexible graphite composite–reinforced gasket was established. The life distribution parameters, accelerated life model parameters and life estimates of gaskets were obtained through tests. On this basis, a gasket life prediction method under different leakage rates was proposed, which can be used as a reference for other types of gaskets.

Practical implications
The research in this paper can better provide guidance for the use and replacement of gaskets in the project, which is also very meaningful for predicting the leakage condition of gaskets in the bolted flange connection system and taking corresponding control measures to reduce energy waste and pollution and ensure the safe operation of industrial equipment.

Originality/value
A multi-specimen gasket-accelerated life test device has been developed, and the design parameters of the device have reached the international advanced level. The life distribution law of the flexible graphite composite–reinforced gasket was revealed. The accelerated life test method for the flexible graphite composite–reinforced gasket was established. The life prediction method of the flexible graphite composite–reinforced gasket under different allowable leakage rates was proposed.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-08-2023-0254/
Entrepreneurs' visibility, media attention and corporate climate risk disclosure – based on Chinese listed companies
Authors: Li Xiaoyi 
Published: November 2023

PurposeAs China's economy begins to transform into a high-quality development, and under the national “carbon peak and carbon neutral” target, all sectors of society and industries need to transform to green development to varying degrees, coupled with the catalyst of epidemics and other factors, new development requirements are put forward for enterprises to better fulfill their climate risk disclosure behaviors. Thus, it is clear that improving corporate climate risk disclosure is of far-reaching significance to both countries and enterprises.Design/methodology/approachThis study incorporates management science, psychology and other related knowledge fields, based on stakeholder theory and media dependency theory, and aims to improve the level of corporate compliance with climate risk disclosure, suggesting the influence of entrepreneurs' visibility on corporate climate risk disclosure; on this basis, the role of entrepreneurs' visibility and media attention on corporate climate risk disclosure is verified through an empirical model; finally, targeted and effective response strategies are proposed to improve corporate climate risk disclosure, set reasonable media attention and increase the effectiveness of entrepreneurs' visibility.FindingsThis paper establishes a multiple regression model using A-share listed companies in China from 2016 to 2022 as the research sample, verifies the intrinsic association between entrepreneurial visibility and corporate climate risk climate disclosure through empirical analysis, and further examines the mediating role of media attention in the relationship between the two. The results show that entrepreneurs' visibility is positively related to the level of corporate climate risk disclosure, with media attention playing a part in mediating the relationship between the two. Increasing entrepreneurs' visibility is conducive to increasing the level of corporate climate risk disclosure. Therefore, it contributes to the dual incentive effect of reputation and compensation.Originality/valueThis study incorporates management science, psychology and other related knowledge fields, based on stakeholder theory and media dependency theory, and aims to improve the level of corporate compliance with climate risk disclosure, suggesting the influence of entrepreneurs' visibility on corporate climate risk disclosure; on this basis, the role of entrepreneurs' visibility and media attention on corporate climate risk disclosure is verified through an empirical model; finally, targeted and effective response strategies are proposed to improve corporate climate risk disclosure, set reasonable media attention and increase the effectiveness of entrepreneurs' visibility.
Caring for environment sustainability: how human capital, natural resources and economic growth interact with ecological footprint in Morocco?
Authors: Neifar Malika , Ghorbel Amira , Bouaziz Kawthar 
Published: November 2023

PurposeThis study attempts to come in help for Morocco by investigating rigorously the linkage between environmental degradation, measured by ecological footprint (EF), and the gross domestic product growth (EG), the human capital (HC) index and the natural resources (NR) depletion over the period of 1980:Q1 to 2021:Q1. The paper examines the validity of environmental Kuznets curve (EKC) hypothesis in the Moroccan context.Design/methodology/approachUnlike previous studies, which are based only on the autoregressif dynamic linear (ARDL) model, this paper investigates two recent models: the novel DYNARDL simulation approach and the Kernel-based regularized least squares (KRLS) technics and uses in addition the frequency domain causality (FDC) test.FindingsModels output say a significant and negative association between HC and the EF and a significant and positive interplay between economic growth and environmental quality in the long term. In the short term, findings reveal a significant and negative association between NR and the EF. Based on the FDC test, results conclude about a unidirectional causality from NR to the EF in short-, medium-, and long-term. Moreover, results validate the EKC hypothesis for the Moroccan environment sustainability.Originality/valueIn this study, the researchers use the “ecological footprint” as dependent variable to obtain more accurate and comprehensive assessment of environmental deterioration. Based on time series data investigations, this study is the first paper, which validates the EKC hypothesis and develops important policy implications for Morocco context to achieve sustainable development targets.
Unlocking circular economy potential: evaluating production processes through circular value stream mapping in real case studies
Authors: Kalemkerian Florencia , Pozzi Rossella , Tanco Martin , Creazza Alessandro , Santos Javier 
Published: November 2023

PurposeThe purpose of this study is to propose a new mapping tool called Circular Value Stream Mapping (C-VSM) that combines Circular Economy principles with Lean tools to enhance sustainability performance in operations.Design/methodology/approachTo develop the C-VSM tool, the researchers conducted a literature review and a focus group. The tool was then applied to two real case studies in the agri-food sector, specifically analyzing an artichoke and olive oil producer, to assess its validity and effectiveness.FindingsThe study introduces the Circular Resource Box (CRB) as a key innovation in the C-VSM tool. This visual representation effectively captures resource circularity and how resources and wastes are managed, making it easy to identify circularity in the production process. By combining qualitative and quantitative information with this visual representation, companies can identify improvement opportunities aligned with the CE.Research limitations/implicationsThe research is limited in scope as it focuses on the application of the C-VSM tool in the agri-food sector. Further research could explore its applicability in other industries and settings to understand its broader impact.Practical implicationsThe C-VSM tool provides practical benefits to companies seeking to transition from linear to circular production processes. It enables practitioners to identify opportunities to reduce environmental impacts and optimize production operations in line with CE.Originality/valueThe introduction of the C-VSM tool is a novel approach that bridges the gap between Lean Manufacturing and CE concepts, advancing the understanding of how CE thinking can be effectively implemented in operations.
Implementing universal design for learning in the library and across campus to promote more inclusive pedagogy
Authors: Kirsch Breanne A. 
Published: November 2023

PurposeThe purpose of this case study is to determine the effectiveness of the UDL academy in terms of the number of UDL techniques used by faculty after participating in the academy and surveys to explore faculty perceptions of UDL.Design/methodology/approachThis quantitative case study utilized faculty surveys about the UDL academy, class observations and review of course syllabi to determine the effectiveness of the UDL academy and explore the experience of implementing UDL.FindingsThe UDL initiative has been a positive and effective experience. Broadly, faculty have had positive perceptions of UDL implementations based on faculty surveys. The effectiveness of the UDL academy was demonstrated by the number of UDL techniques used by faculty increased significantly for faculty that participated in the UDL academy. The control group of faculty members did not increase the number of UDL techniques used based on class observations and a review of course syllabi.Research limitations/implicationsThis research is from one librarian's perspective since the librarian led the UDL initiative and is the sole librarian with faculty status currently at the institution. As a proponent of UDL, the librarian's perspective may be biased. Librarians can implement UDL to reduce educational barriers and support student success. Additionally, librarians can offer support to faculty in learning about UDL by offering a similar UDL academy.Practical implicationsMost faculty were able to incorporate UDL elements into their courses and responded positively to the concept of integrating UDL in the classroom, feeling that it helped improve their teaching. These results demonstrate that faculty can integrate UDL into higher education to use effective teaching strategies after participating in a UDL academy.Originality/valueThis paper is an original work describing a campus UDL initiative from a librarian's perspective.