bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design Principles for Inflammasome Inhibition by Pyrin-Only-Proteins
Authors: Mazanek Zachary , Wu Shuai , Belotte Gretchen , Zhou Jeffery J. , Stallings Christina M. , Garg Archit , Lueck Jacob , Sohn Jungsan 
Published: August 2022

AbstractInflammasomes are filamentous signaling platforms essential for host defense against various intracellular calamities such as pathogen invasion and genotoxic stresses. However, dysregulated inflammasomes cause an array of human diseases including autoinflammatory disorders and cancer. It was recently identified that endogenous pyrin-only-proteins (POPs) regulate inflammasomes by directly inhibiting their filament assembly. Here, by combining Rosetta in silico, in vitro, and in cellulo methods, we investigate the target specificity and inhibition mechanisms of POPs. In contrast to a previous report, we find that POP1 is a poor inhibitor of the central inflammasome adaptor ASC. Instead, POP1 inhibits the assembly of upstream receptor PYD filaments such as those of AIM2, IFI16, NLRP3, and NLRP6. Moreover, not only does POP2 directly suppress the nucleation of ASC, but it can also inhibit the elongation of receptor filaments. In addition to inhibiting the elongation of AIM2 and NLRP6 filaments, POP3 potently suppresses the nucleation of ASC. Our Rosetta analyses and biochemical experiments consistently suggest that a combination of favorable and unfavorable interactions between POPs and PYDs is necessary for effective recognition and inhibition. Together, we reveal the intrinsic target redundancy of POPs and their inhibitory mechanisms.
Association of mortality and aspirin use for COVID-19 residents at VA Community Living Center Nursing Homes
Authors: Abul Yasin , Devone Frank , Bayer Thomas A , Halladay Christopher , McConeghy Kevin , Mujahid Nadia , Singh Mriganka , Leeder Ciera , Gravenstein Stefan , Rudolph James L. 
Published: August 2022

AbstractBackground/ObjectivesCoronavirus disease 2019 (COVID-19) is associated with a hypercoagulable state and increased thrombotic risk in infected individuals. Several complex and varied coagulation abnormalities were proposed for this association1. Acetylsalicylic acid(ASA, aspirin) is known to have inflammatory, antithrombotic properties and its use was reported as having potency to reduce RNA synthesis and replication of some types of coronaviruses including human coronavirus-299E (CoV-229E) and Middle East Respiratory Syndrome (MERS)-CoV 2,3. We hypothesized that chronic low dose aspirin use may decrease COVID-19 mortality relative to ASA non-users.MethodsThis is a retrospective, observational cohort analysis of residents residing at Veterans Affairs Community Living Centers from December 13, 2020, to September 18, 2021, with a positive SARS-CoV-2 PCR test. Low dose aspirin users had low dose (81mg) therapy (10 of 14 days) prior to the positive COVID date and were compared to aspirin non-users (no ASA in prior 14 days). The primary outcome was mortality at 30 and 56 days post positive test and hospitalization.ResultsWe identified 1.823 residents who had SARS-CoV-2 infection and 1,687 residents were eligible for the study. Aspirin use was independently associated with a reduced risk of 30 days of mortality (adjusted HR, 0.60, 95% CI, 0.40-0.90) and 56 days of mortality (adjusted HR, 0.67, 95% CI, 0.47-0.95)ConclusionChronic low dose aspirin use for primary or secondary prevention of cardiovascular events is associated with lower COVID-19 mortality. Although additional randomized controlled trials are required to understand these associations and the potential implications more fully for improving care, aspirin remains a medication with known side effects and clinical practice should not change based on these findings.
Trait Stacking Simultaneously Enhances Provitamin A Carotenoid and Mineral Bioaccessibility in Biofortified Sorghum bicolor
Authors: Dzakovich Michael P. , Debelo Hawi , Albertsen Marc C. , Che Ping , Jones Todd J. , Simon Marissa K. , Zhao Zuo-Yu , Glassman Kimberly , Ferruzzi Mario G. 
Published: August 2022

AbstractVitamin A, iron, and zinc deficiencies are major nutritional inadequacies in sub-Saharan Africa and disproportionately affect women and children. Biotechnology strategies have been tested to individually improve provitamin A carotenoid or mineral content and/or bioaccessibility in staple crops including sorghum (Sorghum bicolor). However, concurrent carotenoid and mineral enhancement has not been thoroughly assessed and antagonism between these chemical classes has been reported. This work evaluated two genetically engineered constructs containing a suite of heterologous genes to increase carotenoid stability and pathway flux, as well as phytase to catabolize phytate and increase mineral bioaccessibility. Kernels from transformed sorghum events were processed into model porridges and evaluated for carotenoid and mineral content as well as bioaccessibility. Transgenic events produced markedly higher amounts of carotenoids (26.4 µg/g) compared to null segregants (4.2 µg/g) and wild-type control (Tx430; 3.7 µg/g). A 200 g serving of porridge made with these transgenic events represents a projected 53.7% of a 4– 8-year-old child’s vitamin A estimated average requirement. Phytase activation by pre-steeping flour resulted in significant phytate reduction (9.4 to 4.2 mg/g), altered the profile of inositol phosphate metabolites, and reduced molar ratios of phytate to iron (16.0 to 4.1); and zinc (19.0 to 4.9) in engineered material; suggesting improved mineral bioaccessibility. Improved phytate:mineral ratios did not significantly affect micellarization and bioaccessible provitamin A carotenoids were over 2300% greater in transgenic events compared to corresponding null segregants and wild-type controls. These data suggest that combinatorial approaches to enhance micronutrient content and bioaccessibility are feasible and warrant further assessment in human studies.
Call patterns encode and transmit emotion in marmoset monkeys
Authors: Huang Junfeng , Liu Hailin , Wang Chen , Ma He , Sun Yongkang , Chang Liangtang , Gong Neng 
Published: August 2022

AbstractMarmoset monkeys have attracted much attention as a non-human primate model for studying vocal communication, but the call pattern and its meaning in marmoset communication are largely unknown. Here, we analyze sounds produced by hundreds of marmosets either in isolation or in pairs and reveal distinct call patterns in marmoset communication. The most prominent phee calls could be categorized into multiple grades based on the number of comprising phee syllables. Call transitions exhibited non-random patterns, favoring transition to the same or adjacent grade, with long sequences limited within two adjacent grades. The interval, composition, and temporal distribution of calls were significantly different between isolated and paired marmosets. Notably, different patterns of phee calls correlated with the heart rates and emotional states of marmoset, with the higher call grade reflecting a more agitated state. Antiphonal calling also exhibited distinct patterns and phee calls directly affected the heart rate of the listener in a manner depending on the grade of phee calls. Thus, phee call patterns in marmosets could encode emotional states and transmit emotion between turn-taking marmosets. How emotional expression in animals evolves into semantic communication in humans remains a mystery. Such complex call patterns in marmoset vocalization could represent the evolutionary prelude to semantic communication in primates.
Ocular findings, surgery details and outcomes in proliferative diabetic retinopathy patients with chronic kidney disease
Authors: Li Jipeng , Chandra Aman , Liu Lin , Zhang Lin , Xu Jun , Zhao Meng 
Published: August 2022

AbstractPurposeWe investigated the influence of impaired renal function on fundus characteristics, pars-plana vitrectomy (PPV) details, and outcomes in patients with proliferative diabetic retinopathy (PDR).Designa retrospective cohort studyMethodsWe investigated a consecutive series of PDR patients who underwent PPV. The diabetic complications, previous photocoagulation, intravitreal injections before PPV, ocular findings during PPV, surgical details, short-term visual outcome and post-PPV complications were recorded and compared between patients with and without impaired renal function.Results149 patients had normal renal function (67.7%) and 71 (32.3%) patients had impaired renal function, 85.4% of patients were identified with chronic kidney disease (CKD) during the preoperative assessment. Impaired renal function was related to hypertension (3.40[1.58-7.29], p=0.002), incomplete panretinal photocoagulation (PRP) (3.18[1.50-6.72], p=0.002), severe fibrovascular membrane (8.19[3.43-19.54], p<0.001), and extensive retinal vascular closure (3.40[1.54-7.52], p=0.002). There was a more frequent occurrence of severe intraoperative bleeding (56.3%, 32.2%, p=0.001), a higher percentage of intraocular subretinal fluid drainage (45.1%, 22.1%, p=0.008) in patients with impaired renal function. The percentage of patients whose visual acuity (VA) increased was similar between two groups (46.4%, 54.3%, p=0.34).ConclusionsIn PDR patients, screening for CKD was required before PPV. PDR patients with impaired renal function tended to have more severe ischemic retinal conditions. Comparable PPV outcomes could be obtained in patients with and without impaired renal damage.
From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles
Authors: Naudin Elise A. , Albanese Katherine I. , Smith Abigail J. , Mylemans Bram , Baker Emily G. , Weiner Orion D. , Andrews David M. , Tigue Natalie , Savery Nigel J. , Woolfson Derek N. 
Published: August 2022

ABSTRACTThe design of completely synthetic proteins from first principles—de novo protein design—is challenging. This is because, despite recent advances in computational protein-structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles, which, in turn, could be used in chemical and synthetic biology to direct protein-protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg—i.e., the sequence signature of many helical bundles—the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design.
Yeast and Mammalian Epsins Use Different Determinants for Localization and Function: Role of Clathrin/AP2/Ubiquitin Binding Motifs and Poly-Glutamine Stretches
Authors: Madhivanan Kayalvizhi , Subramanian Sneha , Cao Lingyan , Mukherjee Debarati , Sen Arpita , Hsieh Wen-Chieh , Hanna Claudia B. , Wang Beibei , Chen Hong , Staiger Chris J. , Aguilar R. Claudio 
Published: August 2022

ABSTRACTEpsins are endocytic adaptor proteins involved in the internalization of important membrane proteins such as EGFR and Notch ligands. Therefore, this protein family impacts critical signaling pathways and processes such as cell migration and cytokinesis and is ultimately required for embryo development in mammals and cell viability in yeast. Intriguingly, although Epsins are conserved and display similar binding determinants, the process of endocytosis in yeast and mammals exhibit some dramatic mechanistic differences. Therefore, we wondered if the function of Epsins in these organisms are similar and are similarly regulated or they also differ. Since proper and timely localization is needed for function, we determined what elements target Epsins to endocytic sites in yeast vs mammals. Specifically, using a systematic/combinatorial mutagenesis approach we produced a collection of yeast and human Epsin mutated variants that was tested for localization at endocytic sites and for function.Our results showed that the intrinsically disordered carboxy-terminus holds the major determinants (involved in binding of ubiquitin, AP2, clathrin and EH domain-containing proteins) for proper intracellular localization of different Epsin paralogs and homologs in yeast and mammals, while also having a major impact on function. Importantly, we established hierarchies of carboxy-terminal binding determinants for sustaining Epsin localization which turned to be different for human vs. yeast cells; favoring clathrin and AP2 binding in the former and recognition of cargo and EH domain-containing proteins for the latter. Further, we found evidence in both systems that yeast Epsins also use for localization regions of the protein that were until now of unknown functional relevance, i.e., glutamine-rich sequences. Interestingly, some molecular determinants within the Epsin molecule seem to have functional importance beyond its contribution to localization to endocytic sites. Based on these findings, we propose working models for Epsin function and recruitment to membranes/endocytic sites at different maturation stages.
Prediction of Golgi Polarity in Collectively Migrating Epithelial Cells Using Graph Neural Network
Authors: Khuntia Purnati , Das Tamal 
Published: August 2022

ABSTRACTIn the stationary epithelium, the Golgi apparatus assumes an apical position, above the cell nucleus. However, during wound healing and morphogenesis, as the epithelial cells starts migrating, it relocalizes closer to the basal plane. On this plane, the position of Golgi with respect to the cell nucleus defines the organizational polarity of a migrating epithelial cell, which is crucial for an efficient collective migration. Yet, factors influencing the Golgi polarity remain elusive. Here we constructed a graph neural network-based deep learning model to systematically analyze the dependency of Golgi polarity on multiple geometric and physical factors. In spite of the complexity of a migrating epithelial monolayer, our simple model was able to predict the Golgi polarity with 75% accuracy. Moreover, the model predicted that Golgi polarity predominantly correlates with the orientation of maximum principal stress. Finally, we found that this correlation operates locally since progressive coarsening of the stress field over multiple cell-lengths reduced the stress polarity-Golgi polarity correlation as well as the predictive accuracy of the neural network model. Taken together, our results demonstrated that graph neural networks could be a powerful tool towards understanding how different physical factors influence collective cell migration. They also highlighted a previously unknown role of physical cues in defining the intracellular organization.
Modeling the impact of green supply chain practices on environmental performance: the mediating role of ecocentricity
Authors: Appiah Michael Karikari , Odei Samuel Amponsah , Kumi-Amoah Gifty , Yeboah Samuel Ankomah 
Published: August 2022

PurposeThis study aims to examine the relationship between green supply chain management (Green SCM) practices and environmental performance, and develop an integrated model to explain the mediating role of ecocentricity on the relationship between Green SCM practices and environmental performance in the context of the Ghanaian downstream petroleum industry.Design/methodology/approachTo address the objectives of the study, a survey had been conducted among companies in the Ghanaian downstream value chain. The paper used the structural equation modeling approach and smart partial least squares (Smart-PLS) analytical tool.FindingsThe study revealed that Green SCM practices had a significant and positive relationship with supply chain ecocentricity and environmental performance. The study further revealed that supply chain ecocentricity significantly mediated the relationship between Green SCM practices and environmental performance.Practical implicationsThe study has developed a new integrated model to enhance oil and gas marketing and distribution company's adaptation and implementation of Green SCM practices.Originality/valueThe study had successfully applied the natural resource-based view and the stakeholder theory in the context of Ghana's downstream petroleum industry. Specifically, these theories had been integrated to form a new model to explain the relationship between Green SCM practices, supply chain ecocentricity and environmental performance in the context of Ghana's downstream petroleum industry. The newly developed integrated model has wider predictability as compared to the individual theories.
Developing a feature-centric and affordance-based conceptualization of social media interactions
Authors: Sajtos Laszlo , Cao Joanne T. , Zhang Wen , Peko Gabrielle , Sundaram David 
Published: August 2022

PurposeDespite the significance of online communication and interactions, previous research has not systematically compared all features on a single platform from the users' perspective. This study aims to fill this gap by extensively reviewing the current literature on social media affordances and proposes and tests a feature-centric and affordance-based conceptualization of social media platforms (SMPs) between users, features, the audience and content.Design/methodology/approachThis research surveys users on Facebook, one of the largest SMPs, and asks them to assess 20 features of Facebook on six relational affordances between users, features, audience and content. The data in this study were collected on Amazon Mechanical Turk (MTurk) with participants from the US Correspondence analysis was employed to examine the relationship between affordances and the ties among affordances, features and outcomes.FindingsResults of the study indicate that users perceive features differently, and employing features as the unit of analysis captures users' interactions effectively. The findings support the presence of user-oriented affordances, such as presentation flexibility, association and content association. These three affordances can be summarized in two higher-level ones: self-expression and connection (SEC) and persona-linked content (PLC). Our findings of the two dimensions, SEC and PLC, highlight the importance of targets and their connections in understanding social media interactions' dynamic nature.Practical implicationsBy proposing to shift the focus from platforms to features, this study suggests that companies should focus on understanding the features they use for their users to interact with their brand, rather than merely ensuring that their company is omnipresent on all platforms. This study underlines the need to focus on features that will help managers influence interpersonal and user-brand communications and interactions on social media.Originality/valueThis research is the first to put features at the center of its investigation and quantitatively examine the relationship between social media features and affordances in a social media context. In all, this research provides a new unit of analysis that is more suitable for researchers to build a robust conceptual foundation for affordances. We believe that conceptualizing audience and content as outcomes, distinguishing it from features and creating connections between them as affordances is the unique aspect of our conceptualization.
Is kindness invaluable? The impact of benefit and cost on prosocial behavior intentions
Authors: Jaw Chyi , Chi Kuei-Ju , Li Guan-Jia 
Published: August 2022

PurposeIn the modern increasingly competitive milieu of cause marketing activities, both profit and nonprofit organizations expect their advocation of prosocial programs to gain the support of target customers. Previous research shows the effect from adding participant's personal attributes or social influence factors. This study considers the effects of benefit incentives and cost/reward influences to enhance prosocial behaviors.Design/methodology/approachThree between-subject experiments were conducted and SPSS Statistics ANOVA was employed to analyze the experimental results.FindingsRewarding time delays and prosocial efforts have no significant impact on the relationship between other-benefit incentives and willingness to engage in prosocial behaviors, but do significantly impact the self-benefit incentives condition. However, the negative effect of self-benefit condition can be mitigated by high rewards.Research limitations/implicationsSince prosocial campaigns proposed by organizations in this study include both profit and nonprofit organizations, perhaps two category organization types should be attentively classified to evaluate the effects.Practical implicationsUnder social marketing campaigns with self-benefit incentives conditions, the empirical findings of this study show that profit and nonprofit organizations can provide higher reward values to mitigate the adverse effects of high participating costs.Social implicationsSocial marketing campaigns with other-benefit incentives are less affected by high participating costs and highlight the value of altruism.Originality/valueThis study provides valuable suggestions for both profit and nonprofit organizations to use self-benefit/other-benefit incentives under cost related factors influence to encourage customers' prosocial behaviors.
Digital supply chain research trends: a systematic review and a maturity model for adoption
Authors: Weerabahu W.M. Samanthi Kumari , Samaranayake Premaratne , Nakandala Dilupa , Hurriyet Hilal 
Published: August 2022

PurposeThis study investigates the enablers and challenges of digital supply chains (DSCs) adoption and develops a digital supply chain maturity (DSCM) model as a basis for developing guidelines for DSC adoption in the digital transformation journey.Design/methodology/approachThe research involves a systematic literature review (SLR) of Industry 4.0 (I4) adoption in supply chain (SC) practices to identify key enablers and associated maturity levels. The literature search of published articles during the 1997–2020 period and subsequent screening resulted in 64 articles. A DSCM model was developed using the categorization of important enablers and associated levels transitioning from the traditional SC to the DSC ecosystem.FindingsFour broader categories of DSC enablers and challenges were identified from the content analysis of SLR. Digital strategy alongside I4 technologies and human capital were prominent in DSC adoption as I4 technologies and human capital depend on other enablers such as dynamic capabilities (DCs). Lack of infrastructure and financial constraints to implementing I4 were significant challenges in the DSC adoption.Research limitations/implicationsThe proposed DSCM model provides a holistic view of enablers and maturity levels from traditional SC to DSC adoption. However, the DSCM model needs to be empirically validated and streamlined further using inputs from practitioners.Practical implicationsThe proposed DSCM model can be used as a framework to guide practitioners in assessing maturity and developing implementation plans for successful DSC adoption.Originality/valueThis research introduces a novel DSC maturity model through a holistic view of enablers and maturity levels from traditional SC to DSC adoption.