bluuebunny/crossref_metadata_2025_split huggingface dataset:
VCF1 is an unconventional p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates
Authors: Mirsanaye Ann Schirin , Hoffmann Saskia , Weisser Melanie , Mund Andreas , Mendez Blanca Lopez , Typas Dimitris , van den Boom Johannes , Benedict Bente , Hendriks Ivo A. , Nielsen Michael Lund , Meyer Hemmo , Duxin Julien P. , Montoya Guillermo , Mailand Niels 
Published: July 2023

SummaryThe hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discovered that FAM104A, a protein of unknown function that we named VCF1 (VCP/p97 Cofactor FAM104 1), acts as a novel p97 cofactor in human cells. Detailed structure-function studies revealed that VCF1 directly binds p97 via a conserved novel α-helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.
Occurrence ofAmaranthus palmeriin Israeli agriculture: status of spread and response to glyphosate and trifloxysulfuron
Authors: Abu-Nassar Jackline , Wallach Amit , Winkler Eilon , Eizenberg Hanan , Matzrafi Maor 
Published: July 2023

AbstractAmaranthus palmeriS. Watson is a dioecious annual weed species, originating from the Southern USA, spreading rapidly beyond its original range into Europe and the Mediterranean region. In Israel,A. palmeridistribution has expanded quickly in recent years, with farmers reporting on weed control failure using acetolactate synthase (ALS) inhibitors. Furthermore, recent studies have documented glyphosate-resistant cases from other countries in the region, such as Spain, Greece, and Turkey. We conducted a survey in order to understandA. palmeridistribution and study the occurrence of herbicide resistance to both glyphosate and trifloxysulfuron in different fields across the country. According to our data,A. palmeripopulation locations are aligned with the major agricultural areas for summer field crops, including the Hula Valley, Jezreel Valley, and the Southern Coastal Plain. Regarding herbicide responses, while several populations showed a reduced response to glyphosate, dose-response assays did not show resistance to the recommended labeled field rate. For the ALS inhibitor trifloxysulfuron, the proportion of resistant individuals was very high, especially in the southern coastline region, with an R-value of 0.77. Four populations used for dose-response studies were highly resistant, surviving at four times the recommended labeled field rate of trifloxysulfuron (30 g a.i. ha-1). Sequencing of the ALS gene, Trp574 to Leu alteration in resistant populations was recorded. The high level of resistance observed in this study, alongside the target-site mutation found in populations ofA. palmeri, endangers the future use of ALS inhibitors in corn, cotton, and other summer crops grown in Israel.
FAM104 proteins promote the nuclear localization of p97/VCP
Authors: Körner Maria , Meyer Susanne , Marincola Gabriella , Kern Maximilian , Grimm Clemens , Schülein-Völk Christina , Fischer Utz , Hofmann Kay , Buchberger Alexander 
Published: July 2023

AbstractThe ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis and DNA damage repair, and its de-regulation is linked to neuro-muscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97–cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. FAM104 proteins bind p97 directlyviaa novel, alpha-helical motif and associate with the p97- UFD1-NPL4 complex in cells. FAM104 proteins localize to the nucleus and promote both the nuclear import and chromatin binding of p97. Loss of FAM104 proteins results in slow growth and hypersensitivity to p97 inhibition in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.
Shared Structural Features of Miro Binding Control Mitochondrial Homeostasis
Authors: Covill-Cooke Christian , Kwizera Brian , López-Doménech Guillermo , Thompson Caleb O.D. , Cheung Ngaam J. , Cerezo Ema , Peterka Martin , Kittler Josef T. , Kornmann Benoît 
Published: July 2023

AbstractMiro proteins are universally conserved mitochondrial calcium-binding GTPases that regulate a multitude of mitochondrial processes, including transport, clearance and lipid trafficking. Miro binds a variety of client proteins involved in these functions. How this binding is operated at the molecular level and whether and how it is important for mitochondrial health, however, remains unknown. Here, we show that known Miro clients all use a similar short motif to bind the same structural element: a highly conserved hydrophobic pocket in the calcium-binding domain of Miro. Using these Miro-binding motifs, we identified direct interactorsde novo, including yeast Mdm34, and mammalian MTFR1/2/1L, VPS13D and Parkin. Given the shared binding mechanism and conservation across eukaryotes, we propose that Miro is a universal mitochondrial adaptor coordinating mitochondrial health.One-Sentence SummaryFunctionally diverse mitochondrial proteins interact with a conserved hydrophobic pocket on the calcium-binding Miro-GTPases.
Variation in the Microbiomes of the Basidiomycete FungiScleroderma citrinum(Pers.) andPisolithus arhizus(Pers.): a tale of two saprotrophs
Authors: Cullings Ken , Bhardwaj Shilpa R. , Spector Michael 
Published: July 2023

AbstractIn this study we used high throughput DNA sequencing and ICP-MS to compare the microbiome of the common earthball fungus,Scleroderma citrinum(Pers.) to that of its sister taxon in the Sclerodermataceae,Pisolithus arhizus(Scop.). ICP-MS analysis demonstrates thatS. citrinumis enriched in silica, sulfur and zinc relative toP. arhizus, whileP. arhizusis enriched in arsenic, calcium, cadmium, cobalt, copper, lithium, magnesium, molybdenum, nickel, potassium and vanadium. Statistical analysis of molecular data indicates that the microbiome ofP. arhizusis both richer and more diverse than that ofS. citrinum, and that the microbiomes are significantly different with that ofS. citrinumbeing enriched in Cyanobacteria represented by the chloroplast of a photosynthetic, cryptoendolithic red alga, Saccharibacteria (TM-7), and Planctomycetes, while that ofP. arhizusis enriched in Gemmatimonadetes, Latescibacteria, Elusomicrobia, and Tectomicrobia. Further, theP. arhizusmicrobiome is enriched in anaerobes relatives to that ofS. citrinum, probably reflecting anaerobic zones previously measured inP. arhizus. Together, the data indicate diverse microbiomes comprised of aromatic hydrocarbon-degrading, metal- and radiotolerant bacteria, indicating that these fungi may provide a rich source of novel microbes suitable for bioremediation strategies.
CRUX, a platform for visualising, exploring and analysing cancer genome cohort data
Authors: El-Kamand Sam , Quinn Julian M.W. , Sareen Heena , Becker Therese M. , Wong-Erasmus Marie , Cowley Mark J. 
Published: July 2023

ABSTRACTTo better understand how tumours develop, identify prognostic biomarkers, and find new treatments, researchers have generated vast catalogues of cancer genome data. However, these datasets are complex so interpreting their important features requires specialized computational skills and analytical tools, which presents a significant technical challenge. To address this, we developed CRUX, a platform for exploring genomic data from cancer cohorts. CRUX enables researchers to perform common analyses including cohort comparisons, biomarker discovery, survival analysis, and create visualisations including oncoplots and lollipop charts. CRUX simplifies cancer genome analysis in several ways: (1) it has an easy-to-use graphical interface; (2) it enables users to create custom cohorts, as well as analyse precompiled public and private user-created datasets; (3) it allows analyses to be run locally to address data privacy concerns (though an online version is also available); and (4) it makes it easy to use additional specialized tools by exporting data in the correct formats. We showcase CRUX’s capabilities with case studies employing different types of cancer genome analysis, demonstrating how it can be used flexibly to generate valuable insights into cancer biology. CRUX is freely available athttps://github.com/CCICB/CRUXandhttps://ccicb.shinyapps.io/crux(DOI: 10.5281/zenodo.8015714).
Regulation of late-acting operons by three transcription factors and a CRISPR-Cas component duringMyxococcus xanthusdevelopment
Authors: Saha Shreya , Kroos Lee 
Published: July 2023

SummaryUpon starvation rod-shapedMyxococcus xanthusbacteria form mounds and then differentiate into round stress-resistant spores. Little is known about the regulation of late-acting operons important for spore formation. C-signaling has been proposed to activate FruA, which binds DNA cooperatively with MrpC to increase transcription of many genes. We report that this model can explain regulation of thefadIJoperon involved in spore metabolism, but not that of the spore coat biogenesis operonsexoA-I,exoL-P, andnfsA-H. Rather, a mutation infruAincreased the transcript levels from these operons early in development, suggesting negative regulation by FruA initially, and a mutation inmrpCaffected transcript levels from each operon differently. FruA bound to all four promoter regionsin vitro, but strikingly each promoter region was unique in terms of whether or not MrpC and the DNA-binding domain of Nla6 bound, and in terms of cooperative binding. Furthermore, the DevI component of a CRISPR-Cas system is a negative regulator of all four operons, based on transcript measurements. Our results demonstrate complex regulation of sporulation genes by three transcription factors and a CRISPR-Cas component, which we propose thwarts viral intrusion while making spores suited to withstand starvation and environmental insults.
Consumer perceptions of sustainability labels for alternative food networks
Authors: Teufer Birgit , Waiguny Martin K.J. , Grabner-Kräuter Sonja 
Published: July 2023

PurposeSustainability labels play a crucial role in providing consumers with quick and easily accessible information to assess the environmental, social and economic impacts of products. This research examines how different sustainability labels influence consumer perceptions and assessments of alternative food networks (AFNs).Design/methodology/approachThe authors conducted three cross-sectional studies to explore consumer perceptions of sustainability labels for AFNs. The authors tested labels representing the three sustainability dimensions, labels of different graphical quality and different awarding bodies.FindingsConsumers did not differentiate between sustainability dimensions but assessed labels in a holistic manner. The overall rating of a label positively influenced perceived sustainability. Self-designed and professionally designed labels had a positive effect on the intention to buy from an AFN. Professionally designed labels also enhanced the perceived authenticity of the networks. Notably, the source of the label, whether self-awarded or awarded by an official body, did not significantly impact consumer perceptions. However, interaction effects revealed professionally designed labels had a stronger positive effect on purchase intention when they were self-awarded.Practical implicationsAFNs can derive benefits from using labels. Self-organized, non-profit AFNs are well advised to have labels professionally designed.Originality/valueThis research contributes to the understanding of the effects of sustainability labels for community-based AFNs, diverging from the traditional focus on individual products.
Critical risk factors for construction supply chain in China: a fuzzy synthetic evaluation analysis
Authors: Deng Binchao , Lv Xindong , Du Yaling , Li Xiaoyu , Yin Yilin 
Published: July 2023

PurposeInefficiency dilemmas in project governance are caused by various risks arising from the characteristic of construction supply chain projects, such as poor project performance, conflicts between stakeholders and cost overrun. This research aims to establish a fuzzy synthetic evaluation (FSE) model to analyze construction supply chain risk factors. Corresponding risk mitigation strategies are provided to facilitate the improvement performance of ongoing construction supply chain projects.Design/methodology/approachA literature review is utilized to reveal the deficiencies of construction supply chain risk management. Thus, a total of five hundred (500) questionnaires are distributed to construction professionals, and four hundred and thirty-five (435) questionnaires are recovered to obtain the evaluation data of construction professionals on critical risk factors. Additionally, the FSE is used to analyze and rank the significance of critical risk factors. Finally, this research discusses nine critical risk factors with high weight in the model, and explains the reason for the significance of critical risk factors in the construction supply chain.FindingsThe questionnaire results show that the thirty-one (31) identified critical risk factors are verified by related practitioners (government departments, universities and research institutions, owners, construction units, financial institutions, design units, consulting firms). Thirty-one (31) identified critical risk factors are divided into common risks, risks from contractors and risks from owners. The most significant factors in the three categories, respectively, are “political risks,” “owner's unprofessional” approach and “cash flow.” Managing these risks can facilitate the development of the construction supply chain.Originality/valueThis paper expands the research perspective of construction supply chain risk management and complements the risks in the construction supply chain. For practitioners, the research result provides some corresponding measures to deal with these risks. For researchers, the research result provides the direction of construction supply chain risk treatment.
Developing a framework for higher education institution building maintenance via soft system methodology
Authors: Ebekozien Andrew , Aigbavboa Clinton , Samsurijan Mohamad Shaharudin , Rohayati Mohd Isa , Malek Nor Malina 
Published: July 2023

PurposeInadequate strategic planning and maintenance budget may undermine the maintenance of the Higher Education Institution Building (HEIB). Studies have shown that a customised maintenance concept such as Soft System Methodology (SSM) can improve public building maintenance operations. There is a paucity of studies regarding public HEIB maintenance in Nigeria via an SSM approach. Therefore, the research investigated the state of public HEIB and developed a framework to improve public HEIB maintenance practices in Nigeria.Design/methodology/approachThe research adopted SSM to understand Nigeria’s public HEIB maintenance practices. The SSM permitted a substitute approach to improve public HEIB maintenance practices via a developed framework. Data were collated via virtual interviews with experts, and findings were presented in line with the SSM seven steps.FindingsFindings show that besides the shoddy state of public HEIB maintenance, there is no public digitalised HEIB framework to improve maintenance practices across Nigeria’s higher education institutions. The study developed a digitalised framework with the support of Computerised Maintenance Management System from the findings. It would reposition the public HEIB and stir up various agencies/departments/units managing maintenance for better service delivery via integrated delivery, practical, methodological and managerial aspects.Originality/valueThe research investigated Nigeria’s public HEIB maintenance practices via SSM to identify the required document and propose a feasible framework to improve Nigeria’s HEIB maintenance practices. Besides the developed conceptual framework, Nigeria’s HEIB maintenance practitioners and higher institution chief executives can use the recommended framework as guidelines to improve HEIB maintenance practices.
What does “sustainable supply chain management” really mean? A contribution to bridging the gap between research, education and practice
Authors: Fritz Morgane M.C. , Ruel Salomée 
Published: July 2023

PurposeThis study explores practitioners' perspectives on and definitions of sustainable supply chain management (SSCM), which are then compared to academic definitions to identify new implications for researchers, educators and practitioners.Design/methodology/approachAn abductive, explorative and qualitative approach was followed in the form of a review and classification of 31 academic definitions of SSCM as well as 30 interviews with supply chain (SC) practitioners.FindingsThe practitioners' answers show a lack of awareness of upstream and downstream challenges as the practitioners' focus on practices within the practitioners' firms, where the economic and environmental dimensions prevail. However, the practitioners highlighted understudied topics in SSCM: human resources policies, leadership for sustainability and ethics.Research limitations/implicationsThis research stimulates discussion on how to teach an SSCM course and which directions to follow to ensure that research has an impact on practices. Practitioners' focus on the practitioners' everyday practices confirms that practice-based theories, amongst others, are relevant in the field and that more interdisciplinary research is needed to highlight the contributions of human resource management (HRM) and business ethics to SSCM.Practical implicationsThe proposed framework clearly defines the scope of the practices and research (upstream or downstream of the SC or within the firm), which will allow practitioners to contribute to SSCM more holistically.Social implicationsEducators and researchers have a crucial role to play in clarifying the meaning of SSCM for students who are future practitioners and consumers. Interacting more with practitioners could help.Originality/valueThis research is targeted not only to researchers and practitioners but also educators.
Investor’s behaviour to COVID-19 vaccine: an event study on health and pharmaceutical sector in India
Authors: Gupta Himani , Gupta Ayushi 
Published: July 2023

Purpose
The devastating acute COVID-19 epidemic crippled the global economy in 2020. Within a month of the COVID-19 epidemic, every industry saw its stock prices plummet the most. Ending the COVID-19 pandemic will need equitable access to safe and effective vaccinations. This study aims to look at the link between COVID-19 vaccination and the stock markets for health and pharmaceutical sector.

Design/methodology/approach
The researchers used a mean-adjusted return model and event research approach to figure out how the first dose of the COVID-19 vaccine affects health and pharmaceutical sector stock market returns.

Findings
The evidence-based outcome indicates that immunisation announcement affects health and pharmaceutical company returns. Furthermore, the study concludes that the health and pharmaceutical industry is inefficient for a short period of time, but after 41 days, the sector absorbs the noisy information.

Originality/value
Since the outbreak, the development of COVID-19 vaccines has been a key focus of shareholders and investors. This study is unique in that it investigates the effect of the first dosage of SARS-CoV-2 vaccination on equity returns in the health and pharmaceutical industries, and it is likely to make a substantial contribution to the capital market literature on event methodology.
Effect of the sliding-rolling ratio on the force chain properties of granular flow lubrication interfaces
Authors: Cheng Pengfei 
Published: July 2023

Purpose
To further understand the granular flow lubrication mechanism in metal contact pairs, the effect of sliding-rolling ratio on the force chain properties was investigated.

Design/methodology/approach
The parallel inter-plate model of the granular flow lubrication was established with discrete element method. Then, the correlation law between sliding-rolling ratio and force chain evolution properties was calculated and analyzed with PFC2D software platform.

Findings
Numerical calculation results show that the dynamic fluctuation property of force chain is existed, and the shock frequency of it is increased with the increase of sliding-rolling ratio. The same evolution law is also occurred for the bearing rate of strong force chain in the initial expansion and final compression phases, and the opposite phenomena is obtained for the overall expansion phase. Moreover, the directivity of strong force chain is changed by the sliding-rolling ratio. With the increase of sliding-rolling ratio, the directivity of strong force chain is first tended to y-axis, and then inclined to the x-axis in the whole phases. The basic reason is that a clamping up and downward movement impact for the neighbor particles are the essence of the above phenomenon.

Originality/value
The main contribution of this work is to lay a theory foundation of interfacial lubrication mechanism with granular flow.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-05-2023-0133/
Impacts of inbound logistics capabilities on supply chain resilience: insight from Vietnamese textile industry
Authors: Nguyen Thi Binh , Nguyen Do Khanh Linh , Ha Minh Hang , Do Thi Thuy Linh , Ngo Tien Dat 
Published: July 2023

Purpose
This study aims to examine the impact of inbound logistics on dynamic supply chain capabilities and, subsequently, on supply chain resilience in the Vietnamese textile industry.

Design/methodology/approach
A conceptual framework based on a resource-based view was empirically tested using partial least squares structural equation modeling and data collected from 215 Vietnamese textile enterprises from December 2021 to March 2022.

Findings
The research shows that inbound logistics capability positively affects dynamic supply chain capabilities. In particular, the study has ratified reengineering as the chief factor that textile firms should consider when building a resilient supply chain.

Originality/value
This study considers the Vietnamese textile industry to assess the indirect effect of inbound logistics on supply chain resilience through dynamic supply chain capabilities in a theoretical sense while assisting managers in comprehending the functions of supply chain collaboration, agility and reengineering as the foundation for supply chain resilience in a managerial sense.