bluuebunny/crossref_metadata_2025_split huggingface dataset:
High intraspecies allelic diversity inArabidopsisNLR immune receptors is associated with distinct genomic and epigenomic features
Authors: Sutherland Chandler A. , Prigozhin Daniil M. , Monroe J. Grey , Krasileva Ksenia V. 
Published: January 2023

AbstractPlants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs inArabidopsisCol-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
VAP-mediated membrane tethering mechanisms implicate ER-PM contact function in pH homeostasis
Authors: Hoh Kar Ling , Mu Baicong , See Tingyi , Ng Amanda Yunn Ee , Ng Annabel Qi En , Zhang Dan 
Published: January 2023

AbstractVAMP-associated proteins (VAPs) are highly conserved endoplasmic reticulum (ER) resident proteins that establish ER contacts with multiple membrane compartments in many eukaryotes. However, VAP-mediated membrane tethering mechanisms remain ambiguous. Here, focusing on fission yeast ER-plasma membrane (PM) contact formation, using systematic interactome analyses and quantitative microscopy, we predict a non-VAP-protein direct binding-based tethering mechanism of VAPs. We further demonstrate that VAP-anionic phospholipids interactions underlie ER-PM association and define the pH-responsive nature of VAP-tethered membrane contacts. Importantly, such conserved interactions with anionic phospholipids are generally defective in amyotrophic lateral sclerosis (ALS)-associated human VAPB mutant. Moreover, we identify a conserved FFAT-like motif locating at the autoinhibitory hotspot of the essential PM proton pump Pma1. This modulatory VAP-Pma1 interaction is crucial for pH homeostasis. We thus propose an ingenious strategy for maintaining intracellular pH by coupling Pma1 modulation with pH-sensory ER-PM contacts via VAP-mediated interactions.
Profiles of the composite biomarker specific for β-amyloid accumulation in the brain relevant to age and sex
Authors: Satoh Kouji , Sato-Ueshima Maremi , Kagami-Katsuyama Hiroyo , Nakamura Masakazu , Ogata Akihiko , Maeda-Yamamoto Mari , Nishihira Jun 
Published: January 2023

AbstractAccumulation of β-amyloid (Aβ) in the brain occurs in the early phase of Alzheimer’s disease (AD), without symptoms of cognitive decline. Therefore, early detection of the accumulation phase is essential to prevent or delay AD. In this study, we investigated the effects of age, sex, apoprotein-E (ApoE) genotype and cognitive dysfunction on the ratio of Aβ1-42, Aβ1-40, and amyloid β precursor protein (APP)669-711(composite biomarker: CM) in plasma using a sensitive Time of flight mass spectrometry (TOF-MS). In healthy subjects, the average CM value of males aged 30– 59 years was significantly higher than that of females, but no difference was observed between those aged 60 and 79 years. CM values increased considerably after 50 years of age, especially in females. The effect of the ApoE4 genotype on CM was greater in females than in males. The CM value of patients with AD was higher than that of healthy subjects and that of patients with Parkinson’s disease (PD). The CM value of patients with PD complicated by AD was higher than that of patients with PD. These results suggest that the CM value is influenced by age, sex, ApoE4 genotype, and central nervous system disorder. In addition, the CM value could be a reliable biomarker to distinguish not only patients with AD and healthy subjects but also AD and patients with PD. Since the measurement of CM is less invasive to the subjects, the method is helpful for the early detection of accumulation of Aβ before the appearance of AD symptoms. Moreover, this practical method can be used for differential diagnosis among a variety of patients with dementia.
Assessing racial bias in type 2 diabetes risk prediction algorithms
Authors: Cronjé Héléne T. , Katsiferis Alexandros , Elsenburg Leonie K. , Andersen Thea O. , Rod Naja H. , Nguyen Tri-Long , Varga Tibor V. 
Published: January 2023

AbstractRisk prediction models for type 2 diabetes can be useful for the early detection of individuals at high risk. However, models may also bias clinical decision-making processes, for instance by differential risk miscalibration across racial groups. We investigated whether the Prediabetes Risk Test (PRT) issued by the National Diabetes Prevention Program, and two prognostic models, the Framingham Offspring Risk Score, and the ARIC Model, demonstrate racial bias between non-Hispanic Whites and non-Hispanic Blacks. We used National Health and Nutrition Examination Survey (NHANES) data, sampled in six independent two-year batches between 1999 and 2010. A total of 9,987 adults without a prior diagnosis of diabetes and with fasting blood samples available were included. We calculated race- and year-specific average predicted risks of type 2 diabetes according to the risk models. We compared the predicted risks with observed ones extracted from the US Diabetes Surveillance System across racial groups (summary calibration). All investigated models were found to be miscalibrated with regards to race, consistently across the survey years. The Framingham Offspring Risk Score overestimated type 2 diabetes risk for non-Hispanic Whites and underestimated risk for non-Hispanic Blacks. The PRT and the ARIC models overestimated risk for both races, but more so for non-Hispanic Whites. The risk of type 2 diabetes extracted from these landmark models were more severely overestimated for non-Hispanic Whites compared to non-Hispanic Blacks, potentially resulting in a larger fraction of non-Hispanic Whites being prioritized for a preventive intervention, but also more likely to be overdiagnosed and overtreated, with a larger fraction of non-Hispanic Blacks being potentially underprioritized and undertreated.
Rice Yellow Mottle Virusresistance by genome editing of theOryza sativaL. ssp. japonica nucleoporin geneOsCPR5.1but notOsCPR5.2
Authors: Arra Yugander , Auguy Florence , Stiebner Melissa , Chéron Sophie , Wudick Michael M. , Miras Manuel , Schepler-Luu Van , Cunnac Sébastien , Frommer Wolf B. , Albar Laurence 
Published: January 2023

SummaryRice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locusrymv2(OsCPR5.1) had been identified in African rice (O. glaberrima), however, introgression intoO. sativa ssp. japonicaandindicaremains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogsOsCPR5.1(RYMV2) andOsCPR5.2can be used to introduce RYMV resistance into thejaponicavariety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsisatcpr5mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1loss-of-function mutants were fully resistant, while loss-of-functionoscpr5.2mutants remained susceptible, intimating thatOsCPR5.1plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) ofOsCPR5.1were hypersusceptible to RYMV. In contrast to mutations in the single ArabidopsisAtCPR5gene, which caused severely dwarfed plants,oscpr5.1andoscpr5.2singleknockoutmutants show neither substantial growth defects nor symptoms indicative of programmed cell death, possibly reflecting functional redundancy of the isoforms regarding other important functions. The specific editing ofOsCPR5.1, while maintainingOsCPR5.2activity, provides a promising strategy for generating RYMV-resistance in eliteOryza sativalines as well as for effective stacking with other RYMV resistance genes or other traits.
Equivalence of charge imbalance and external electric fields during free energy calculations of membrane electroporation
Authors: Kasparyan Gari , Hub Jochen S. 
Published: January 2023

AbstractElectric fields across lipid membranes play important roles in physiology, medicine, and biotechnology, rationalizing the wide interest in modeling transmembrane potentials in molecular dynamics simulations. Transmembrane potentials have been implemented with external electric fields or by imposing charge imbalance between the two water compartments of a stacked double-membrane system. We compare the two methods in the context of membrane electroporation, which involves a large change of membrane structure and capacitance. We show that, given that Ewald electrostatics are defined with tinfoil boundary conditions, the two methods lead to (i) identical potentials of means force (PMFs) of pore formation and expansion at various potentials, demonstrating that the two methods impose equivalent driving forces for large-scale transitions at membranes and (ii) to identical polarization of water within thin water wires or open pores, suggesting that the two methods furthermore impose equivalent local electric fields. Without tinfoil boundary conditions, effects from external fields on pore formation are spuriously suppressed or even removed. Together, our study shows that both methods, external fields and charge imbalance, are well suitable for studying large-scale transitions of lipid membranes that involve changes of membrane capacitance. However, using charge imbalance is technically more challenging for maintaining a constant transmembrane potential since it requires updating of the charges as the capacitance of the membrane changes.
Biochemical characterization of a GDP-mannose transporter fromChaetomium thermophilum
Authors: Premageetha Gowtham Thambra Rajan , Dhanabalan KanagaVijayan , Bose Sucharita , Manjunath Lavanyaa , Joseph Deepthi , Paz Aviv , Grandfield Samuel , Nayak Vinod , Bredeston Luis M. , Abramson Jeff , Subramanian Ramaswamy 
Published: January 2023

AbstractNucleotide Sugar Transporters (NSTs) belong to the SLC35 family (human solute carrier) of membrane transport proteins and are crucial components of the glycosylation machinery. NSTs are localized in the ER and Golgi apparatus membranes, where they accumulate nucleotide sugars from the cytosol for subsequent polysaccharide biosynthesis. Loss of NST function impacts the glycosylation of cell surface molecules. Mutations in NSTs cause several developmental disorders, immune disorders, and increased susceptibility to infection. Atomic resolution structures of three NSTs have provided a blueprint for a detailed molecular interpretation of their biochemical properties. In this work, we have identified, cloned, and expressed 18 members of the SLC35 family from various eukaryotic organisms inSaccharomyces cerevisiae.Out of 18 clones, we determined Vrg4 fromChaetomium thermophilum(CtVrg4) is a GDP-mannose transporter with an enhanced melting point temperature (Tm) of 56.9 °C, which increases with the addition of substrates, GMP and GDP-mannose. In addition, we report—for the first time—that the CtVrg4 shows an affinity to bind to phosphatidylinositol lipids.
Designing an internal audit effectiveness model for public sector: qualitative and quantitative evidence from a developing country
Authors: Shuwaili Ahmed Mohammed Jasim , Hesarzadeh Reza , Bagherpour Velashani Mohammad Ali 
Published: January 2023

Purpose
In recent decades, managerial desire to use internal audit services to promote well-controlled organizational processes has significantly increased in the public sector. Yet, there is rare information on how internal audits may effectively be implemented in the public sector. The present research aims to design a comprehensive internal audit effectiveness model for the public sector.

Design/methodology/approach
This research is an applied mixed-methods (qualitative–quantitative) and descriptive survey study. The research population in both qualitative and quantitative sections included all internal and external audit managers and staff of Iraqi public organizations. The study sample of the qualitative section included 28 audit managers and staff selected using purposive sampling, and the study sample of the quantitative section included 399 individuals selected using convenience sampling. The data collection instruments in the qualitative and quantitative sections included semi-structured interviews and questionnaires, respectively. Data analysis was carried out using thematic analysis in Atlas.ti software in the qualitative section. Quantitative analysis and model validation were also performed using path analysis and structural equation modeling in Smart-PLS software in the quantitative section.

Findings
The results of the qualitative section led to the identification of 38 effectiveness factors among seven main categories, which were finally presented in the form of a comprehensive model. The main categories included the communication between internal and external auditors, granting independence and authority to internal auditors, providing specialized human resources, providing technological resources, developing management support, strengthening organizational culture and developing audit plans. In the qualitative section, the model was validated and confirmed. Quantitative results further showed that the compilation of audit plans and the development of management support were the most important factors.

Originality/value
The present study contributes to the literature by providing a comprehensive framework on internal audit with an emphasis on resource-based theory and reducing the research gap in the field of agents influencing internal audit efficacy in the public sector of developing countries. Further, the study provides insights into an under-studied developing country, Iraq.
The role of the organizational and operational dimensions in the open collaboration performance: a strategic alignment perspective
Authors: Kissimoto Kumiko Oshio , Mattos Cláudia Aparecida , Laurindo Fernando José 
Published: January 2023

Purpose
The purpose of this paper is to investigate how the business model and the strategic intent to adopt an open collaboration initiative influence the perceived quality of collaboration outcomes.

Design/methodology/approach
This paper presents a framework to analyze the role of the strategic dimension and the operational dimension in open collaboration initiatives through multiple case studies in three companies to understand how the open collaboration initiative was deployed and how was the level of the alignment between these two dimensions.

Findings
The studied cases revealed that when an open collaboration initiative starts in the strategic dimension and there is an alignment between the organizational dimension and operational dimension, the collaboration outcomes are clearer and more traceable.

Research limitations/implications
The study highlights the need to consider the involvement and the internal alignment between strategic and operational dimensions when deploying an open collaboration activity if they want to achieve all the benefits.

Practical implications
The presented framework can help managers to evaluate and understand how open collaboration activities are deployed within the company.

Social implications
The study shows that when an open collaboration initiative is planned, its results and benefits can be extended to local communities by developing them.

Originality/value
This study aims to analyze the open collaboration initiative’s contribution to the overall organizational performance through the alignment between the organizational dimension and operational dimension perspective.
Project-based learning for proactive skills development of postgraduate students in solar energy building design digitalisation
Authors: Gunarathna Chathuri , Yang Rebecca , Wijeratne Mudiyanselage Pabasara , Amarasinghe Gayashan , Samarasinghalage Tharushi , Weerasinghe R.P. Nilmini , Zhao Hongying , Zhang Chaoxiang , Liu Chengyang , Wang Kaige , Dev Sureshkumar Jayakumari Sujan 
Published: January 2023

PurposeProject-based learning is one of the most effective methods of transferring academic knowledge and skills to real-world situations in higher education. However, its effectiveness is not much investigated focusing on the students' narrative. This study aims at evaluating the students' experience and perspective on adopting project-based learning in master by research and doctoral programmes for proactive skills development.Design/methodology/approachThis study evaluates the self-reflection of 10 postgraduate students and their supervisor who have participated in developing a software tool for solar photovoltaics (PV) integrated building envelope design, management and the related education.FindingsFindings reveal that the students have effectively improved their knowledge on the subject via collaborating with the industry, self-learning/observation, peer learning, problem-solving and teamwork. Dividing the project into student-led tasks has improved the decision-making and leadership skills, risks identification, planning and time management skills. The overall experience has (1) built up confidence in students, (2) enhanced their creativity and critical thinking and (3) improved their proactive skills and context knowledge.Originality/valueA clear research gap can be seen in exploring the effectiveness of project-based learning for master by research and doctoral programmes, which mainly focus on extensive research. These programmes do not necessarily focus on developing students' proactive skills, which is the main requirement if they intend to work in the construction industry. This paper addresses the above research gap by demonstrating the effectiveness of project-based learning for developing the proactive skills in a research-intensive learning environment.
Senolytic drugs, dasatinib and quercetin, attenuate adipose tissue inflammation, and ameliorate metabolic function in old age
Authors: Islam Md Torikul , Tuday Eric , Allen Shanena , Kim John , Trott Daniel W. , Holland William L. , Donato Anthony J. , Lesniewski Lisa A. 
Published: January 2023

AbstractAging results in an elevated burden of senescent cells, senescence‐associated secretory phenotype (SASP), and tissue infiltration of immune cells contributing to chronic low‐grade inflammation and a host of age‐related diseases. Recent evidence suggests that the clearance of senescent cells alleviates chronic inflammation and its associated dysfunction and diseases. However, the effect of this intervention on metabolic function in old age remains poorly understood. Here, we demonstrate that dasatinib and quercetin (D&Q) have senolytic effects, reducing age‐related increase in senescence‐associated β‐galactosidase, expression of p16 and p21 gene and P16 protein in perigonadal white adipose tissue (pgWAT; all p ≤ 0.04). This treatment also suppressed age‐related increase in the expression of a subset of pro‐inflammatory SASP genes (mcp1, tnf‐α, il‐1α, il‐1β, il‐6, cxcl2, and cxcl10), crown‐like structures, abundance of T cells and macrophages in pgWAT (all p ≤ 0.04). In the liver and skeletal muscle, we did not find a robust effect of D&Q on senescence and inflammatory SASP markers. Although we did not observe an age‐related difference in glucose tolerance, D&Q treatment improved fasting blood glucose (p = 0.001) and glucose tolerance (p = 0.007) in old mice that was concomitant with lower hepatic gluconeogenesis. Additionally, D&Q improved insulin‐stimulated suppression of plasma NEFAs (p = 0.01), reduced fed and fasted plasma triglycerides (both p ≤ 0.04), and improved systemic lipid tolerance (p = 0.006). Collectively, results from this study suggest that D&Q attenuates adipose tissue inflammation and improves systemic metabolic function in old age. These findings have implications for the development of therapeutic agents to combat metabolic dysfunction and diseases in old age.
Increase in size and shrub cover improves bird functional diversity in Neotropical urban green spaces
Authors: Melo Marcos Antônio , Piratelli Augusto João 
Published: January 2023

AbstractLatin American cityscapes are growing fast, posing risks to many bird communities and ecosystem services (e.g. seed dispersal and arthropod population control), but few studies have addressed how bird functional diversity respond to urbanization in Neotropical cities. In this study, we tested which biotic (i.e. vegetation characteristics and human and pet disturbances) and abiotic variables (i.e. area size, number of vehicles, and glass panes) influence functional diversity indices of insectivores, frugivores‐nectarivores, migrants, residents, and total bird community at urban green spaces in São Paulo megacity, southeastern Brazil. A rich avian community (235 species) from 25 studied sites was recorded. Generalized linear models (GLM) analyses showed that large‐sized areas of urban green spaces and shrub cover are the main characteristics that drive high bird functional diversity. Small‐sized sites were less favourable for preserving bird functional diversity. We showed that these areas were related to some negative impacts for bird species (e.g. absence of shrub layer, heavy traffic and massive presence of glass panes, and domestic animals), thus causing declines in avian functional diversity. Off‐leash and homeless dogs and cats may cause declines in bird ecological functions (e.g. insect control, seed dispersal and pollination), which are essential to sustain biodiversity. Therefore, as management actions to improve bird diversity and better provisioning of ecosystem functions, we recommend that urban planners and managers should prioritize large‐sized areas with high shrub cover. Additionally, we highlight the need to mitigate the negative impact on birds caused by glass panes, traffic of vehicles, and off‐leash and homeless dogs and cats.