bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating Molecular Mechanism and Chemical Space of Chalcones through Knowledge Graph and Machine Learning: A Combined Bio-Cheminformatic Pipeline
Authors: Manaithiya Ajay , Bhowmik Ratul , Acharjee Satarupa , Sharma Sameer , Kumar Sunil , Imran Mohd. , Mathew Bijo , Parkkila Seppo , Aspatwar Ashok 
Published: May 2024

AbstractWe developed a bio-cheminformatics method, exploring disease inhibition mechanisms using machine learning-enhanced quantitative structure-activity relationship (ML-QSAR) models and knowledge-driven neural networks. ML-QSAR models were developed using molecular fingerprint descriptors and the Random Forest algorithm to explore the chemical spaces of Chalcones inhibitors against diverse disease properties, including antifungal, anti-inflammatory, anticancer, antimicrobial, and antiviral effects. We generated and validated robust machine learning-based bioactivity prediction models ((https://ashspred.streamlit.app/) for the top genes. These models underwent ROC and applicability domain analysis, followed by molecular docking studies to elucidate the molecular mechanisms of the molecules. Through comprehensive neural network analysis, crucial genes such as AKT1, HSP90A1, SRC, and STAT3 were identified. The PubChem fingerprint-based model revealed key descriptors: PubchemFP521 for AKT1, PubchemFP180 for SRC, PubchemFP633 for HSP90, and PubchemFP145 and PubchemFP338 for STAT3, consistently contributing to bioactivity across targets. Notably, chalcone derivatives demonstrated significant bioactivity against target genes, with compound RA1 displaying a predictive pIC50value of 5.76 against HSP90A and strong binding affinities across other targets. Compounds RA5 to RA7 also exhibited high binding affinity scores comparable to or exceeding existing drugs. These findings emphasize the importance of knowledge-based neural network-based research for developing effective drugs against diverse disease properties. These interactions warrant furtherin vitroandin vivoinvestigations to elucidate their potential in rational drug design. The presented models provide valuable insights for inhibitor design and hold promise for drug development. Future research will prioritize investigating these molecules formycobacterium tuberculosis, enhancing the comprehension of effectiveness in addressing infectious diseases.
Genomic epidemiology of ESBL-producingEscherichia colifrom humans and an Aotearoa New Zealand river
Authors: Gray Holly A , Biggs Patrick J , Midwinter Anne C , Rogers Lynn E , Fayaz Ahmed , Akhter Rukhshana N , Burgess Sara A 
Published: May 2024

AbstractIn Aotearoa New Zealand, urinary tract infections in humans are commonly caused by extended-spectrum beta-lactamase (ESBL)-producingEscherichia coli. This group of antimicrobial resistant bacteria are often multidrug resistant. However, there is limited information on ESBL-producingE. colifound in the environment and their link with human clinical isolates. In this study, we examined the genetic relationship of environmental and human clinical ESBL-producingE. coliand isolates collected in parallel within the same area over 14 months. Environmental samples were collected from treated effluent, stormwater and multiple locations along an Aotearoa New Zealand river. Treated effluent, stormwater and river water sourced downstream of the treated outflow point were the main sources of ESBL-producingE. coli(7/14 samples, 50.0%; 3/6 samples, 50%; and 15/28 samples, 54% respectively). Whole genome sequence comparison was carried out on 307 human clinical and 45 environmental ESBL-producingE. coliisolates. Sequence type 131 was dominant for both clinical (147/307, 47.9%) and environmental isolates (11/45, 24.4%). The most prevalent ESBL genes were bothblaCTX-M-27andblaCTX-M-15for the clinical isolates (134/307, 43.6%) andblaCTX-M-15for the environmental isolates (28/45, 62.2%). A core single nucleotide polymorphism analysis of these isolates suggested that some strains were shared between humans and the local river. These results highlight the importance of understanding different transmission pathways for the spread of ESBL-producingE. coli.2. Impact statementExtended spectrum beta lactamase (ESBL)-producingE. colifrequently cause urinary tract infections that exhibit multidrug resistance. Surveillance studies have identified the predominant strains and resistance genes associated with urinary tract infections. However, there is limited information on the extent of spread beyond the patient. We describe the genetic relatedness of ESBL-producing environmental and clinicalE. coliisolated during the same temporal-spatial period in Aotearoa New Zealand. Comparative genomic analyses of these bacteria provide evidence of clonal spread between humans and the environment, highlighting the need to integrate environmental surveillance into antimicrobial resistance monitoring.3. Data summaryAll Illumina sequence reads for this study have been deposited in GenBank under BioProject PRJNA1032159, except for strain SB0283h1, whose data can be found under BioProject PRJNA715472. The sequence read accessions for each genome are provided in the supplementary material.The code used for the genomic and statistical analyses is available from the GitHub repositoryhttps://github.com/sburgess1/Manawat-_ESBL.The authors confirm all supporting data and protocols have been provided within the article or through supplementary data files.
O-glycosylation of intrinsically disordered regions regulates homeostasis of membrane proteins in streptococci
Authors: Rahman Mohammad M. , Zamakhaeva Svetlana , Rush Jeffrey S. , Chaton Catherine T. , Kenner Cameron W. , Hla Yin Mon , Tsui Ho-Ching Tiffany , Uversky Vladimir N. , Winkler Malcolm E. , Korotkov Konstantin V. , Korotkova Natalia 
Published: May 2024

AbstractProteins harboring intrinsically disordered regions (IDRs) lacking stable secondary or tertiary structures are abundant across the three domains of life. These regions have not been systematically studied in prokaryotes. Our genome-wide analysis identifies extracytoplasmic serine/threonine-rich IDRs in several biologically important membrane proteins in streptococci. We demonstrate that these IDRs areO-glycosylated with glucose by glycosyltransferases GtrB and PgtC2 inStreptococcus pyogenesandStreptococcus pneumoniae, and with N-acetylgalactosamine by a Pgf-dependent mechanism inStreptococcus mutans. Absence of glycosylation leads to a defect in biofilm formation under ethanol-stressed conditions inS. mutans. We link this phenotype to the C-terminal IDR of a post-translocation secretion chaperone PrsA.O-glycosylation of the IDR protects this region from proteolytic degradation. The IDR length attenuates the efficiency of glycosylation and, consequently, the expression level of PrsA. Taken together, our data reveal thatO-glycosylation of IDRs functions as a dynamic switch of protein homeostasis in streptococci.
Structural basis for Rab6 activation by the Ric1-Rgp1 complex
Authors: Feathers J. Ryan , Vignogna Ryan C. , Fromme J. Christopher 
Published: May 2024

ABSTRACTRab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. This structure reveals the overall architecture of the complex and enabled us to identify interactions critical for proper recognition and activation of Rab6 on the Golgi membrane surface. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a novel RabGEF domain by identifying residues required for Rab6 nucleotide exchange. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common specificity mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
Transverse emittance growth due to rf noise in crab cavities: Theory, measurements, cure, and high luminosity LHC estimates
Authors: Baudrenghien P. , Mastoridis T. 
Published: May 2024

The High-Luminosity LHC (HL-LHC) upgrade with planned operation from 2029 onward has a goal of achieving a tenfold increase in the integrated number of recorded collisions thanks to a doubling of the intensity per bunch (2.2×1011 protons) and a reduction of β* (the β value in the two high luminosity detectors, namely ATLAS and CMS) to 15 cm. Such an increase in recorded collisions would significantly expedite new discoveries and exploration. Crab cavities are an important component of the HL-LHC upgrade and will contribute strongly to achieving an increase in the number of recorded collisions. However, noise injected through the crab cavity radio frequency (rf) system could cause significant transverse emittance growth and limit luminosity lifetime. We presented a theoretical formalism relating transverse emittance growth to rf noise in an earlier work. In this follow-up paper, we summarize measurements in the super-proton synchrotron (SPS) at CERN that validate the theory, we present estimates of the emittance growth rates using state-of-the-art rf and low-level rf (LLRF) technologies, and we set the rf noise specifications to achieve acceptable performance. A novel dedicated feedback system acting through the crab cavities to mitigate emittance growth will be required. In this work, we develop a theoretical formalism to evaluate the performance of such a feedback system in any collider, identify limiting components, present simulation results to validate these studies, and derive key design parameters for an HL-LHC implementation of such a feedback system.

Published by the American Physical Society
2024
Enhancing peer instruction in physics: Understanding cognitive processes and refining rules
Authors: Gjerde Vegard , Hagane Sivert 
Published: May 2024

Peer Instruction gives practice in the abstract language of physics, addresses common misconceptions among students, and is more effective than traditional lecturing. However, it is not clear what makes Peer Instruction effective nor how we might improve the method. An emerging perspective is that what makes Peer Instruction effective is how it stimulates certain cognitive processes. Research also indicates that providing rules for discussion may improve the effect of peer instruction. Hence, we wanted to answer two research questions in this study: (i) What cognitive learning processes occur during peer discussions? (ii) How do students follow discussion rules? To answer our research questions, we recorded and thematically analyzed peer discussions during Peer Instruction in an introductory physics course. The most prevalent cognitive process during peer discussions was decoding the problem. The most prevalent type of explanation was explanations with physics concepts, which usually led the students to an incorrect answer. The next most prevalent type of explanation was explanation with physics models, which usually led the students to the correct answer. The students also explained with reference to their experience or examples—intuitive or analogical explanations—and it usually added little to the conversation, was wrong, or created confusion. Some discussion rules had limited impact, prompting suggestions for rule improvements to optimize Peer Instruction. Our work contributes to the literature on Peer Instruction with a cognitively based description of the learning processes and how we might further improve and ensure the effectiveness of Peer Instruction.

Published by the American Physical Society
2024
Testing the permanent income hypothesis using the Spanish Christmas Lottery
Authors: Cabanillas-Jiménez Guillermo 
Published: May 2024

Purpose
This study aims to investigate the impact of local windfall gains from the Spanish Christmas lottery on household consumption behavior.

Design/methodology/approach
The study applies differences-in-differences to assess permanent income hypothesis (PIH) validity, examining pre- and postlottery consumption effects. Additionally, it also uses an instrumental variable regression, using the lottery shock as an instrument for total expenditures, to estimate the Engel curves.

Findings
The paper finds a PIH violation; households in winning region notably increase consumption on durable and nondurable goods compared to nonwinning ones. Moreover, durable goods consumption is responsive to lottery winnings, while nondurable goods consumption are unit-elastic to expenditure shocks.

Originality/value
To the best of the author’s knowledge, this is the first paper analyzing the effects of winning regions of the Spanish Christmas lottery in all types of consumption goods, testing its consequences in the PIH and estimating its effects in the Engel curves.
Measurement and evaluation methods in corporate communications through the prism of Lasswell’s model
Authors: Oltarzhevskyi Dmytro 
Published: May 2024

PurposeThis study aims to conceptualize, rethink and systematize methods used for measurement and evaluation (M&E) corporate communication.Design/methodology/approachThe reflection is based on 462 key English-language books and papers devoted to M&E in the fields of corporate communication and public relations from the 1970th to 2023. Keywords in the titles and abstracts found the necessary materials. A critical analysis of the central concepts, models and methods described in the literature was conducted. As a result, a new model that unifies and structures the M&E toolkit is proposed for discussion.FindingsDespite the significant contribution to developing a wide range of M&E models, they are still not perfect and universal. In addition, this system of approaches is continuously self-evolving and changing under the influence of digital innovations, so it requires steady rethinking and updating. On the other hand, most previous studies focused on communication management processes, losing focus on communication aspects. This led to the need for an alternative view based on proven theories to fill this gap. The proposed model combines quantitative and qualitative M&E methods for the five main components of corporate communication (communicator, audience, content, channels and result), covering a wide range of tools, from statistical and sociological research to big data analysis and neuro research.Originality/valueThis work contributes to developing the M&E theory of corporate communication, systematizing existing methods and opening new research perspectives. From a practical point of view, companies can use the presented approach for a more accurate and objective internal evaluation of the main components of corporate communication.
Analysis of e-government and digital society indicators over the years: a comparative study of the EU member states
Authors: Lnenicka Martin , Luterek Mariusz , Majo Lorraine Tinashe 
Published: May 2024

Purpose
Benchmarking e-government and digital society developments using relevant indicators provides crucial insights into what aspects to consider while building a resilient digital society in which digital public services are delivered effectively and sustainably. The purpose of this paper is to analyse selected indices and indicators over the years and provide findings and recommendations on what indicators contribute most to the development.

Design/methodology/approach
A mixed research approach was used to conduct the research and collect, analyse and interpret data. A qualitative analysis involving the search, decomposition and comparison approaches to identify e-government and digital society reports, indices, rankings and indicators was followed by a quantitative analysis comprising of regression and cluster analyses.

Findings
The findings revealed that changes in the mix of indicators used by e-government and digital society indices can be attributed to advances in ICT and channels through which people communicate and receive information. The authors found that digital and telecommunication infrastructures and the quality of their parameters such as broadband have the biggest influence on progress of the e-government and digital societies developments and contribute most to clustering of the EU member states into groups.

Originality/value
The paper provides insights into how the structures of related indices changed over the years and how different indicators contribute to benchmarking of e-government and digital society developments by means of their weights. It provides governments with recommendations on which indicators to focus most.
Believing in the power of belief: a study on the formation mechanism of innovative behavior from the perspectives of intrinsic and extrinsic spiritual inspiration
Authors: Liu Yuanyuan , Zhang Fan , Li Bin , Liu Pingqing , Liu Shuzhen , Sun Qiong 
Published: May 2024

PurposeThis study reveals the trigger of innovative behavior from the perspective of intrinsic and extrinsic spiritual inspiration and provides a new research idea for the formation mechanism of innovative behavior. The purpose of this study is to provide certain guidance and implications for enterprises to cultivate and enhance employees’ innovative behavior.Design/methodology/approachWe conducted three studies, collected multi-source data (N = 1,175) from different countries longitudinally, as well as used hierarchical regression analysis and fuzzy-set quantitative comparative analysis to verify the theoretical model.FindingsAccording to the findings, both spiritual leadership and career calling have a positive impact on employees’ innovative behavior through the mediating effect of autonomous motivation and the moderating effect of person-vocation fit.Originality/valueInnovative behavior is the positive professional pursuit of employees, which is difficult to form without the motivation of spiritual factors. Spirituality is a complex concept that contains intrinsic and extrinsic spiritual factors, both of which could stimulate employees’ innovative behavior. Although many discussions have been held on this topic in recent years, little attention has been paid simultaneously to the motivating effects of the two perspectives. Drawn from self-determination theory, this study explores the mechanisms of two spiritual motivation paths (i.e. the intrinsic and extrinsic spiritual motivation paths) in the improvement of employees’ innovative behavior.
Examining the impact of pharmacist professionalism and celebrity endorsers on dietary supplement purchase intention: the moderating role of product knowledge
Authors: Chou Shihyu , Chen Chi-Wen , Shen Zi-Ling 
Published: May 2024

Purpose
This study aims to explore how consumers’ purchase intentions concerning dietary supplements are affected by two pivotal factors: pharmacist professionalism and celebrity endorser attractiveness. In addition, this study investigates the moderating role of consumers’ awareness of product knowledge about dietary supplements in the relationship between brand trust and purchase intention.

Design/methodology/approach
The research data was collected through online questionnaires from a convenience sample of 340 individuals residing in Taiwan. The research model, consisting of four hypotheses, was formulated based on a literature review. The partial least squares structural equation modeling technique was used for data analysis.

Findings
The findings indicate positive effects of both pharmacist professionalism and celebrity endorser attractiveness on dietary supplement brand trust. The results also suggest a significant impact of brand trust on purchase intention. Finally, product knowledge significantly moderates the relationship between brand trust and purchase intention.

Practical implications
The findings from this study provide valuable insights for marketers, pharmacists and practitioners about the drivers of consumers’ dietary supplement purchase behavior. It will enable marketers to develop better strategies for the dietary supplement market segment.

Originality/value
This paper has made a significant contribution to the understanding of consumer buying intentions toward dietary supplements, addressing a gap in the literature. First, unlike previous research, this study considers both pharmacist professionalism and celebrity endorser attractiveness in the research model, effectively bridging this gap. Furthermore, this study identifies the pivotal role of brand trust as a critical factor in enhancing consumers’ purchase intentions toward dietary supplements, offering valuable insights for dietary supplement companies regarding consumer purchase decision-making.
Formation of structural holes in R&D context: the effect of inventors’ knowledge abilities and patenting output
Authors: Wang Yalan , Wang Chengjun , Wang Wei , Sun Xiaoming 
Published: May 2024

Purpose
This study aims to investigate the influence of inventors’ abilities to acquire external knowledge, provide broad and professional knowledge and patenting output (i.e. different types of inventors) on the formation of structural holes.

Design/methodology/approach
The authors collected 59,798 patents applied for and granted in the USA by 33 of the largest firms worldwide in the pharmaceutical industry between 1975 and 2014. A random-effects tobit model was used to test the hypotheses.

Findings
The inventors’ ability to acquire external knowledge contributes to the formation of structural holes. While inventors’ ability to provide broad knowledge positively affects the formation of structural holes, their ability to provide professional knowledge works otherwise. In addition, key inventors and industrious inventors are more likely to form structural holes than talents.

Originality/value
The results identify individual factors that affect the formation of structural holes and improve the understanding of structural hole theory. This study is unique in that most scholars have studied the consequences of structural hole formation rather than their antecedents. Studies on the origin of structural holes neglect the effect of inventors’ knowledge abilities and patenting output. By addressing this gap, this study contributes to a more comprehensive theoretical understanding of structural holes. The results can guide managers in managing structural holes in accordance with inventors’ knowledge abilities and patenting outputs, which optimize the allocation of network resources.