bluuebunny/crossref_metadata_2025_split huggingface dataset:
DEPOT: graph learning delineates the roles of cancers in the progression trajectories of chronic kidney disease using electronic medical records
Authors: Song Qianqian , Liu Xiang , Li Zuotian , Zhang Pengyue , Eadon Michael , Su Jing 
Published: August 2023

AbstractChronic kidney disease (CKD) is a common, complex, and heterogeneous disease impacting aging populations. Determining the landscape of disease progression trajectories from midlife to senior age in a real-world context allows us to better understand the progression of CKD, the heterogeneity of progression patterns among the risk population, and the interactions with other clinical conditions like cancers. In this study, we use electronic health records (EHRs) to outline the CKD progression trajectory roadmap for the Wake Forest Baptist Medical Center (WFBMC) patient population. We establish an EHR cohort (n = 79,434) with patients’ health status identified by 18 Essential Clinical Indices across 508,732 clinical encounters. We develop the DisEase PrOgression Trajectory (DEPOT) approach to model CKD progression trajectories and individualize clinical decision support. The DEPOT is an evidence-driven, graph-based clinical informatics approach that addresses the unique challenges in longitudinal EHR data by systematically using the graph artificial intelligence (graph-AI) model for representation learning and reverse graph embedding for trajectory reconstruction. Moreover, DEPOT includes a prediction model to assign new patients along the progression trajectory. We successfully establish the EHR-based CKD progression trajectories with DEPOT in the WFUBMC cohort. We annotate the trajectories with clinical features, including kidney function, age, and other indices, including cancer. This CKD progression trajectory roadmap reveals diverse kidney failure pathways associated with different clinical conditions. Specifically, we have identified one high-risk trajectory and two low-risk trajectories. Switching pathways from low-risk trajectories to the high-risk one is associated with accelerated decline in kidney function. On this roadmap, high-risk patients are enriched in the skin and GU cancers, which differs from low-risk patients, suggesting fundamentally different disease progression mechanisms. Overall, the CKD progression trajectory roadmap reveals novel diverse renal failure pathways in type 2 diabetes mellitus and highlights disease progression patterns associated with cancer phenotypes.
Modulations in high-density EEG during the suppression of phantom-limb pain with neurostimulation in upper-limb amputees
Authors: Kleeva Daria , Soghoyan Gurgen , Biktimirov Artur , Piliugin Nikita , Matvienko Yury , Sintsov Mikhail , Lebedev Mikhail 
Published: August 2023

AbstractPhantom limb pain (PLP) is a distressing and persistent sensation that occurs after the amputation of a limb. While medication-based treatments have limitations and adverse effects, neurostimulation is a promising alternative approach whose mechanism of action needs research, including electroencephalographic (EEG) recordings for the assessment of cortical manifestation of PLP relieving effects. Here we collected and analyzed high-density EEG data in three patients (P01, P02, and P03). Peripheral nerve stimulation (PNS) suppressed PLP in P01 but was ineffective in P02. By contrast, transcutaneous electrical nerve stimulation (TENS) was effective in P02. In P03, spinal cord stimulation (SCS) was used to suppress PLP. Changes in EEG oscillatory components were analyzed using spectral analysis and Petrosian fractal dimension (FD). With these methods, changes in EEG spatio-spectral components were found in the theta, alpha, and beta bands in all patients, with these effects being specific to each individual. The changes in the EEG patterns were found for both the periods when PLP level was stationary and the periods when PLP was gradually changing after neurostimulation was turned on or off. Overall, our findings align with the proposed roles of brain rhythms in thalamocortical dysrhythmia or disrubtion of excitation and inhibition which has been linked to neuropathic pain. The individual differences in the observed effects could be related to the specifics of each patient’s treatment and the unique spectral characteristics in each of them. These findings pave the way to the closed-loop systems for PLP management where neurostimulation parameters are adjusted based on EEG-derived markers.
Tissue Transglutaminase 2 has higher affinity for relaxed than for stretched fibronectin fibers
Authors: Selcuk Kateryna , Leitner Alexander , Braun Lukas , Le Blanc Fanny , Pacak Paulina , Pot Simon , Vogel Viola 
Published: August 2023

AbstractTissue transglutaminase 2 (TG2) plays a vital role in stabilizing extracellular matrix (ECM) proteins through enzymatic crosslinking during tissue growth, repair, and inflammation. TG2 also binds non-covalently to fibronectin (FN), an essential component of the ECM, facilitating cell adhesion, migration, proliferation, and survival. However, the interaction between TG2 and fibrillar FN remains poorly understood, as most studies have focused on soluble or surface-adsorbed FN or FN fragments, which differ in their conformations from insoluble FN fibers. Using a well-establishedin vitroFN-fiber stretch assay, we discovered that the binding of a crosslinking enzyme to ECM fibers is mechano-regulated. TG2 binding to FN is tuned by the mechanical tension of FN fibers, whereby TG2 predominantly co-localizes to low-tension FN fibers, while fiber stretching reduces their affinity for TG2. This mechano-regulated binding relies on the proximity between the N-terminal β-sandwich and C-terminal β-barrels of TG2. Crosslinking mass spectrometry (XL-MS) revealed a novel TG2-FN synergy site within TG2’s C-terminal β-barrels that interacts with FN regions outside of the canonical gelatin binding domain, specifically FNI2and FNIII14-15. Combining XL-MS distance restraints with molecular docking reveals the mechano-regulated binding mechanism between TG2 and modules FNI7-9by which mechanical forces regulate TG2-FN interactions. This highlights a previously unrecognized role of TG2 as a tension sensor for FN fibers. This novel interaction mechanism has significant implications in physiology and mechanobiology, including how force regulate ECM deposition and maturation, and how TG2 mediates cell-ECM adhesion in health and in various pathophysiological processes. Data are available via ProteomeXchange with identifier PXD043976.
Single-cell analysis reveals diversity of tumor-associated macrophages and their interactions with T lymphocytes in glioblastoma
Authors: Batchu Sai , Hanafy Khalid A. , Redjal Navid , Godil Saniya , Thomas Ajith J 
Published: August 2023

AbstractGlioblastoma (GBM) is an aggressive primary CNS malignancy and clinical outcomes have remained stagnant despite introduction of new treatments. Understanding the tumor microenvironment (TME) in which tumor associated macrophages (TAMs) interact with T cells has been of great interest. Although previous studies examining TAMs in GBM have shown that certain TAMs are associated with specific clinical and/or pathologic features, these studies used an outdated M1/M2 paradigm of macrophage polarization and failed to include the continuum of TAM states in GBM. Perhaps most significantly, the interactions of TAMs with T cells have yet to be fully explored. Our study uses single-cell RNA sequencing data from adult IDH-wildtype glioblastoma, with the primary aim of deciphering the cellular interactions of the 7 TAM subtypes with T cells in the GBM TME. Furthermore, the interactions discovered herein are compared to IDH-mutant astrocytoma, allowing for focus on the cellular ecosystem unique to GBM. The resulting ligand-receptor interactions, signaling sources, and global communication patterns discovered provide a framework for future studies to explore methods of leveraging the immune system for treating GBM.
Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex
Authors: Guo Qian , Chen Kai-en , Gimenez-Andres Manuel , Jellett Adam P. , Gao Ya , Simonetti Boris , Liu Meihan , Danson Chris M. , Heesom Kate J. , Cullen Peter J. , Collins Brett M. 
Published: August 2023

ABSTRACTEndosomal membrane trafficking is mediated by specific protein coats and formation of actin-rich membrane domains. The Retromer complex coordinates with sorting nexin (SNX) cargo adaptors including SNX27, and the SNX27–Retromer assembly interacts with the WASH complex which nucleates actin filaments establishing the endosomal reycling domain. Crystal structures, modelling, biochemical and cellular validation reveal how the FAM21 subunit of WASH interacts with both Retromer and SNX27. FAM21 binds the FERM domain of SNX27 using acidic-Asp-Leu-Phe (aDLF) motifs similar to those found in the SNX1 and SNX2 subunits of the ESCPE-1 complex. Overlapping FAM21 repeats and a specific Pro-Leu containing motif bind three distinct sites on Retromer involving both the VPS35 and VPS29 subunits. Mutation of the major VPS35-binding site does not prevent cargo recycling, however it partially reduces endosomal WASH association indicating that a network of redundant interactions promote endosomal activity of the WASH complex. These studies establish the molecular basis for how SNX27–Retromer is coupled to the WASH complex via overlapping and multiplexed motif-based interactions required for the dynamic assembly of endosomal membrane recycling domains.Significance StatementCell surface transmembrane proteins are regulated by a constant cycle of internalization and recycling from intracellular endosomal compartments. The Retromer protein complex and the sorting nexin adaptor protein play a critical role in the retrieval of hundreds of proteins responsible for ion transport, glucose metabolism, neurotransmission, and other cell functions. We have defined the mechanism by which both Retromer and SNX27 engage the actin-nucleating complex called WASH through multiple repeated sequences in the subunit FAM21. Dysfunction in WASH, Retromer and SNX27 are implicated in various disorders including Parkinson’s disease, Alzheimer’s disease, hereditary spastic paraplegia, and this work provides important insights into the assembly of these essential endosomal sorting machineries.
Diatoms exhibit dynamic chloroplast calcium signals in response to high light and oxidative stress
Authors: Flori Serena , Dickenson Jack , Gaikwad Trupti , Cole Isobel , Smirnoff Nicholas , Helliwell Katherine , Brownlee Colin , Wheeler Glen 
Published: August 2023

AbstractDiatoms are a group of silicified algae that play a major role in marine and freshwater ecosystems. Diatom chloroplasts were acquired by secondary endosymbiosis and exhibit important structural and functional differences from the primary plastids of land plants and green algae. Many functions of primary plastids, including photoacclimation and inorganic carbon acquisition, are regulated by calcium-dependent signalling processes. Calcium signalling has also been implicated in the photoprotective responses of diatoms, although the nature of calcium elevations in diatom chloroplasts and their wider role in cell signalling remains unknown. Using genetically encoded calcium indicators, we find that the diatomPhaeodactylum tricornutumexhibits dynamic chloroplast calcium elevations that are distinct from those found in land plants. Chloroplast calcium ([Ca2+]chl) acts independently from the cytosol and is not elevated by stimuli that induce large cytosolic calcium ([Ca2+]cyt) elevations. In contrast, high light and exogenous hydrogen peroxide (H2O2) induce large, sustained calcium elevations in the chloroplast stroma that are not replicated in the cytosol. Measurements using the fluorescent H2O2sensor roGFP2-Orp1 indicate that [Ca2+]chlelevations induced by these stimuli correspond to the accumulation of H2O2in the chloroplast. [Ca2+]chlelevations were also induced by the addition of methyl viologen, which acts to generate superoxide within the chloroplast, and by treatments that disrupt non-photochemical quenching (NPQ). The findings indicate that diatoms generate specific calcium elevations in the chloroplast in response to high light and oxidative stress that likely modulate the activity of calcium-sensitive components in photoprotection and other regulatory pathways.
The Auxin Response Factor ARF27 is required for maize root morphogenesis
Authors: Dash Linkan , McReynolds Maxwell R. , Draves Melissa A. , Khangura Rajdeep S. , Muench Rebekah L. , Khor Jasper , Callwood Jodi B. , Cowling Craig L. , Mejia Ludvin , Lang Michelle G. , Dilkes Brian P. , Walley Justin W. , Kelley Dior R. 
Published: August 2023

AbstractCrop root systems are central to nutrition acquisition and water usage. Root hairs and lateral roots contribute to fine-scale patterning of root systems and can offer many advantages for improving root function without drastically impacting overall system architecture. Key genetic regulators underpinning root hair morphogenesis have been well characterized in the model plant Arabidopsis but are less understood in maize. Here, we identify a novel determinant of root hair morphogenesis and auxin responses in maize, AUXIN RESPONSE FACTOR27 (ARF27), using both reverse and quantitative genetic approaches. ARF27 is enriched in maize primary root tissues at both the transcript and protein level. Loss ofARF27leads to short primary roots and reduced root hair formation, while lateral root density is unaltered. Inarf27roots, auxin-responsive gene expression is dysregulated, which is consistent with the predicted function of this transcription factor. Moreover, a genome wide association study (GWAS) to uncover genetic determinants of auxin-dependent root traits identifiedARF27as a candidate gene. Furthermore, auxin hypersensitive maize genotypes exhibit altered crown root length and surface area in field-grown plants. A gene regulatory network (GRN) was reconstructed and an ARF27 subnetwork was integrated with DAP-seq and GWAS data to identify ARF27 target genes. The ARF27 GRN includes known maize root development genes, such asROOTLESS CONCERNING CROWN ROOTS (RTCS), ROOTHAIRLESS 3 (RTH3)andRTH6. Altogether this work identifies a novel genetic driver of auxin-mediated root morphogenesis in maize that can inform agricultural strategies for improved crop performance.
Impact of faith on food marketing and consumer behaviour: a review
Authors: Santovito Savino , Campo Raffaele , Rosato Pierfelice , Khuc Long Dai 
Published: August 2023

PurposeThe aim of this manuscript is to study the current scientific literature on food marketing and religion, by giving an overview of current knowledge and the possible future research opportunities once found the gaps.Design/methodology/approachThis a classic literature review carried on by considering marketing, consumer behaviour and management journals as well as religion-focused ones.FindingsCurrent literature highlights how faith impacts on food marketing and religious consumers choices (and not only). Most of the papers focus on Islam. Considering the globalised economy, the authors’ findings highlight also the relevance of religious certifications for less/not religious people, because of certified food is considered safe and healthy.Originality/valueThe paper joins and reviews two research fields whose connection is growing, so it is relevant to know the current status of scientific literature, which is updated compared to recent literature.
Theoretical analysis and numerical simulation of axial tensile behavior of pipe joints based on bi-linear cohesive bond-slip model
Authors: Yuan Hong , Han Jun , Lu Huaqiang , Li Junhui , Zeng Lan 
Published: August 2023

PurposeDue to its inexpensive production costs, low stress concentration and maintenance-friendliness, the adhesive bonded pipe joint is frequently utilized for pipe connection. However, further theoretical analysis is needed to understand the debonding failure mechanism of such bonded pipe joints under axial tension.Design/methodology/approachIn this study, based on the bi-linear cohesive zone model, the integrated closed-form solutions were derived by considering the axial stiffness ratio and failure stage to determine the relative interfacial slip, interfacial shear stress and relationship of tension–displacement in the bonded pipe joint.FindingsAdditionally, solutions for the critical bonded length and the ultimate load capacity were put forth. Besides, the numerical study was conducted to verify the theoretical solutions regarding the load–displacement relationship. The interfacial shear stress distribution at different failure stages was presented to understand the interfacial shear stress transmission and debonding process. The effect of bonded length on the ultimate load and ductility of pipe joints was also discussed.Originality/valueThe findings in this study can give a reference for the design of bonded pipe joints in their actual engineering applications.
Health professions’ perspective on emergency remote education
Authors: Ribeiro Cleide Gisele , Ramos Plinio dos Santos , Bechara Raimundo Nonato , de Oliveira Juliano Machado , de Almeida Erika Bicalho , Miguel Soraida Sozzi , Ricardo Djalma Rabelo , de Oliveira Rodrigo Guerra 
Published: August 2023

PurposeThe COVID-19 pandemic has created a significant disruption in the educational systems worldwide. Some institutions opted for emergency remote education due to the need to cancel in-person activities. The aims of this paper were to evaluate the use of asynchronous methodology in health sciences education, determine whether asynchronous methodology was sacrificing overall student satisfaction, and investigate whether satisfaction improved as the program develops.Design/methodology/approachInitially, there was phase 1 that corresponded to four weeks of activities. Each professor produced a video lesson, and after each video lesson, a weekly educational activity was made available. Next, phase 2 was implemented using the same methodology, however lasting six weeks. Three questionnaires were developed, and a Likert scale was administered to verify the students’ level of satisfaction. Data were analyzed using frequency distributions, mean values, standard deviation and confidence interval. The normality of the sum data (total of the questionnaires) was tested using the Kolmogorov–Smirnov test.FindingsAlthough the students pointed out that the asynchronous methodology facilitated access to the content and considered this methodology satisfactory, they expressed a reduced level of satisfaction regarding emergency remote education in general when data from the first weeks were compared to those of the previous weeks. It is clear that students became increasingly discouraged and tired over time, which motivated the institution to shift into a combination of synchronous and asynchronous methodology to improve student learning.Originality/valueTeaching in the field of health care encompasses difficult competencies that sometimes are impossible to be learned remotely, so there is a need to examine and evaluate properly the remote education in this area. With careful planning, educational institutions can evaluate their experiences during the pandemic, allowing those involved to highlight strengths and identify weaknesses to better prepare for future needs to improve remote education.
Transgenerational control intention and employment practices of family firms in China
Authors: Chen Jiawen , Li Pengfei , Liu Linlin 
Published: August 2023

PurposeThis study aims to examine the employment practices of family firms in emerging markets. Drawing from the social exchange theory, the authors propose that transgenerational control intention enhances the motivation for family owners to engage in favorable employment practices as inducement for future contribution of employees.Design/methodology/approachMultilevel regression models were applied to test the hypotheses with a sample of 3033 Chinese private family firms.FindingsThe results show that the employment practices of family firms are positively associated with transgenerational control intention, and the effect of transgenerational control intention is contingent on regional social trust.Originality/valueThis study highlights the role of transgenerational control intention of family owners in motivating favorable employment in family firms. The study adds nuance to the variances in employment behaviors of family firms as well as the family owner-employee exchange relationship in emerging markets.
Wine international market structure and competitiveness
Authors: Thomé Karim Marini , Paiva Vitoria Angie Leal , Gois Tafarel Carvalho de 
Published: August 2023

Purpose
This paper aims to analyse the wine market in relation to international competitiveness and international market structure.

Design/methodology/approach
To describe the international market structure, this paper uses Herfindahl–Hirschman Index and Net Export Index to measure export competitiveness revealed symmetric comparative advantage (RSCA). Finally, survival function analyses were developed using the Kaplan–Meier product-limit estimator to characterise the stability and duration of the competitiveness in the international wine market of each country and after they were grouped into Old and New World wine-exporting countries, and Wilcoxon and the Log-rank tests were used to compare the survivor functions.

Findings
The findings have revealed that the import market structure has remained unconcentrated, whereas the export market structure is moderately concentrated. Concerning trade characteristics, France, Italy, Spain, Australia, Chile, New Zealand, Portugal, Argentina, South Africa and Georgia are exporters. Austria is a trader (re-exporter), and the USA, Germany, the UK and the Netherlands are importers with strong domestic consumption. Regarding the RSCA, the New and Old World wine-exporting countries have high scores, specifically France, Italy, Spain, Australia, Chile, New Zealand, Portugal, Argentina, South Africa and Georgia. However, the advantages have weakened for most of the countries analysed. Only a few Old World wine-exporting counties (France, Italy, Spain, Portugal and Georgia) have demonstrated stable comparative advantages over time. However, when grouped into Old World and New World, their survivor functions present little statistical differentiation during the period.

Originality/value
The originality of the paper is that it applies the industrial organisation and comparative advantage approaches to the wine international market, highlighting the top global players. The paper also makes valuable contributions to the wine literature by analysing the duration and stability of comparative advantage in the worldwide wine trade at a country level and comparing them grouped into Old and New World wine-exporting countries.